title: U87PS4B-94

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
U87PS4B.cts.txt
U87PS4B_R2

data_processing:
PLATE-Seq data are comprised of sets of two paired-end reads. The first read contains an 8-base barcode sequence that identifies the well from which a given sample originates. The second read contains a sequence that typically maps strand-specifically to the 3’-end of an mRNA transcript. We first record the barcode sequence associated with each read. The barcode sequences are designed so that a single error can be corrected, and so we allow an edit distance of one from the actual barcode sequences. Next, we use the bwa-mem aligner to map the set of second reads to a pre-assembled human transcriptome (hg19, UCSC known genes). We then demultiplex the resulting alignments and count the number of uniquely mapped reads associated with each gene. We define a read as uniquely mapped if the maximum alignment score among alignments that map to the correct strand is associated with a single gene.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are formatted as tab-delimited text and contain the number of uniquely mapped reads for each gene in each sample.

source_name: U87 cell line

growth_protocol: BT20 cells: BT20 epithelial breast carcinoma cells were cultured in white 96-well tissue culture-treated plates (Greiner 655083) at a starting density of 8,000 cells per well in 100 uL of Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. U87 cells: Cells were maintained in EMEM medium (Corning cat no. 10-009) containing 10% fetal bovine serum, 100 u/ml Penicillin Streptomycin (Thermo Fisher Scientific cat no. 15140122), in 37℃ incubator with 5% CO2 and 95% humidity control.  LnCAP cells: LnCAP cells were grown in RPMI1640 with 10% FBS at 37C, 5% CO2, and 95% humidity.

extract_protocol:
PLATE-Seq: Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 uL of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 uL of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295xg for 1 minute to eliminate air bubbles followed by incubation for 90 minutes at room temperature with shaking at 200 rpm. Lystate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 uL of Elution Buffer (nuclease-free water supplemented with 0.4 U/uL SUPERaseIN (ThermoFisher)), incubation at 65°C for five minutes, and incubation at room temperature for 5 minutes. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 uL tips on the Hamilton STAR.
To anneal primers for reverse transcription, 3 uL of 100 uM adapter-linked oligo(dT) primers are added to each well along with 10 uL of 5x ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 uL channel pipetting system. The plate is then heated to 94°C for two minutes and placed immediately on ice for 5 minutes. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 uL per well. The plate is then centrifuged at 295xg for 1 minute and incubated at 42°C for 2 hours. At this point, the samples can optionally be frozen at -80°C.
To remove excess primer, 1 uL of a four-fold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25°C for one hour. To hydrolyze the RNA, we add 20 uL of a 1:1 mixture of 1M sodium hydroxide and 0.5M EDTA to each well and incubate at 65°C for 15 minutes. The wells are then pooled together into a single tube to which 80 uL of 12 M hydrochloric acid are added to neutralize the sample.  At this point, the pooled sample can optionally be frozen at -80°C.
The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer?s instructions, and pooled cDNA is eluted in 15 uL of nuclease-free water. For second-strand synthesis, 1 uL of 10 mM dNTP mixture and 1 uL of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70°C for two minutes and immediately placed on ice for five minutes. Next, 2 uL of NEB Buffer 2 (New England BioLabs) and 1 uL of Klenow Large Fragment DNA Polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 minutes. The reaction is then stopped by addition of EDTA to a final concentration of 50 uM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs) with 0.5 uM Illumina RP1 primer and Illumina RPIx primer (where x is a number indicating the Illumina index). The thermocycling protocol begins with 98°C for 30 seconds followed by 10-12 cycles of 98°C for 15 seconds, 62°C for 15 seconds, and 72°C for 60 seconds followed by a seven-minute incubation at 72°C.
TruSeq: To compare PLATE-Seq and conventional RNA-Seq, we conducted a small-scale screen in a single 96-well plate.  We treated each well containing cultured BT20 cells with one of seven compounds or DMSO (vehicle) including mitoxantrone, crizotinib, albendazole, idarubicin, aprepitant, gemcitabine, and bortezomib with 12 replicate wells for each condition.  Half of the material in each well was allocated to PLATE-Seq, and 96 libraries were constructed using the automated, pooled procedure described above.  For the other half, we pooled two sets of six wells for each condition to generate 16 samples in total (two replicates for each condition). We then extracted total RNA from each pool using an RNeasy column (Qiagen) and subjected the total RNA to Illumina TruSeq poly(A)+ RNA-Seq library construction according to the manufacturer?s instructions.
RNA-Seq using PLATE-Seq or Illumina TruSeq

treatment_protocol: BT20 and U87 cells: After 24 hours of incubation, the plates were treated with drugs. Each drug was dosed at the concentration at which the cells were 80% viable after 48 hours of treatment. After 6 hours of treatment (BT20) or 24 hours of treatment (U87), the medium was replaced with 100 mL of FBS supplemented with 10% DMSO and the plates were frozen at -80C prior to PLATE-Seq. After thawing for PLATE-Seq, cells were washed twice with phosphate-buffered saline (PBS) prior to lysis.

tag: drug

value: Lylamine hydrochloride

tag: concentration (um)

tag: library construction

value: PLATE-Seq


title: U87PS4B-92

status: Public on Apr 07 2017

type: SRA

state: NY

country: USA

description:
U87PS4B.cts.txt
U87PS4B_R2

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

value: PLUMBAGIN


title: U87PS4B-95

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-90

description:
U87PS4B.cts.txt
U87PS4B_R2

value: AMINACRINE


title: U87PS4B-91

description:
U87PS4B.cts.txt
U87PS4B_R2

value: DIHYDROCELASTROL


title: U87PS4B-93

description:
U87PS4B.cts.txt
U87PS4B_R2

value: (R)-(-)-Niguldipine hydrochloride


title: ChlamyBabeni1-2

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description:
Sample name: C5_Site1
Sample 5_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using BWA v.0.7.10 to a de novo Elodea nuttalii transcriptome.
The reads were mapped with TopHat v.2.0.11 on the Chlamydomonas renhardtii 236 genome.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis were performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2.
Genome_build: de novo transcriptome Elodea nuttallii (Nicole Regier, Rebecca Beauvais-Flück, Vera I. Slaveykova, Claudia Cosio. Mercury exposure under enhanced ultraviolet radiation in Elodea nuttallii: effects on bioaccumulation, transcriptome, pigment content and oxidative stress endpoints. Aquatic toxicology under review.)
Genome_build: Chlamydomonas reinhardtii 236 (Phytozome v.9.1)
Supplementary_files_format_and_content: normalized*: Excel file with normalized counts in cpm (count per million) for each Sample.
Supplementary_files_format_and_content: DEG*: Excel file with significantly differentially expressed genes with a fold change 2 threshold and FRD 5% correction.
Supplementary_files_format_and_content: Elodea_muttallii.fasta: FASTA file of the de novo Elodea nuttallii transcriptome assembly.

molecule: total RNA

organism: Chlamydomonas reinhardtii

source_name: ChlamyBabeni1-2 whole cells

growth_protocol: Up to middle exponential phase (~1x10^6 cells·ml-1) in a (4x) diluted tris-acetate-phosphate (TAP) medium.

extract_protocol:
TRI-Reagent
The libraries were prepared with 300 ng of total RNA as starting material and processed with the Illumina TruSeq mRNA stranded kit according to the manufacturer instructions.

treatment_protocol: 2h in situ exposure in the River Olt.

tag: tissue

value: whole cell


title: U87PS4B-89

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-87

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-88

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tasquinimod


title: U87PS4B-86

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-85

description:
U87PS4B.cts.txt
U87PS4B_R2

value: PX 12


title: U87PS4B-83

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Nebivolol hydrochloride


title: Sox10_RNASeq_Ribo_16ss_2

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: Sox10 BAC driving biotin ligase.

data_processing:
ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes.
RNA-seq reads were mapped using STAR (v.2.4.2a).
BAM files incorporating reads belonging to either DNA strand were generated using custom python script.
Genome_build: danRer7 (Zv9)
Supplementary_files_format_and_content: bigWig files

organism: Danio rerio

extract_protocol:
Nuclei isolation using biotin-tagged outer nuclear envelope, adapted from INTACT procedure. Polyribosome isolation using biotin-tagged Rpl10 protein, adapted from TRAP procedure. FACS procedure using cell-specific fluorescent marker, following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al., 2013, adapted for FACS-sorted embryonic cells.
RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non-directional sequencing libraries after polyA-selection of RNA transcripts (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB) were built using NEBnext Ultra RNA library kit for Illumina (NEB). Following ribodepletion using Ribo-ZeroTM Magnetic Kit (Epicentre), directional RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (KAPABiosystems).

tag: strain/background

value: AB/TU

value: neural crest and otic

tag: assay

value: RNA-seq stranded

value: polyribosome-associated

tag: ribodepleted

value: ribodepleted

value: InVivoBiotinylatedPolysomes

tag: strand

value: reverse


title: U87PS4B-84

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Picoplatin


title: U87PS4B-79

description:
U87PS4B.cts.txt
U87PS4B_R2

value: TETRACHLOROISOPHTHALONITRILE

value: PLATE-Seq


title: U87PS4B-81

description:
U87PS4B.cts.txt
U87PS4B_R2

value: WIN 64338 hydrochloride


title: U87PS4B-80

description:
U87PS4B.cts.txt
U87PS4B_R2

value: KINETIN RIBOSIDE


title: U87PS4B-77

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Triciribine


title: U87PS4B-78

description:
U87PS4B.cts.txt
U87PS4B_R2

value: SULCONAZOLE NITRATE


title: U87PS4B-74

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Rocilinostat (ACY-1215)


title: U87PS4B-70

description:
U87PS4B.cts.txt
U87PS4B_R2

value: IKK 16


title: U87PS4B-71

description:
U87PS4B.cts.txt
U87PS4B_R2

value: CGP 71683 hydrochloride


title: U87PS4B-72

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-75

description:
U87PS4B.cts.txt
U87PS4B_R2

value: TAK-700 (Orteronel)


title: U87PS4B-82

description:
U87PS4B.cts.txt
U87PS4B_R2

value: 2,3-DCPE hydrochloride


title: U87PS4B-69

description:
U87PS4B.cts.txt
U87PS4B_R2

value: RS 17053 hydrochloride


title: U87PS4B-73

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Propranolol HCl


title: U87PS4B-63

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Sofrastaurin


title: U87PS4B-62

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-64

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tariquidar


title: U87PS4B-61

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Prinomastat hydrochloride


title: U87PS4B-67

description:
U87PS4B.cts.txt
U87PS4B_R2

value: 4 -METHOXYCHALCONE


title: U87PS4B-65

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Triapine


title: U87PS4B-76

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tasisulam

value: PLATE-Seq


title: U87PS4B-56

description:
U87PS4B.cts.txt
U87PS4B_R2

value: TOTAROL


title: U87PS4B-58

description:
U87PS4B.cts.txt
U87PS4B_R2

value: NNC 05-2090 hydrochloride


title: U87PS4B-57

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-59

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Ryuvidine


title: U87PS4B-55

description:
U87PS4B.cts.txt
U87PS4B_R2

value: PRISTIMERIN


title: U87PS4B-68

description:
U87PS4B.cts.txt
U87PS4B_R2

value: THYMOQUINONE


title: U87PS4B-54

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-46

description:
U87PS4B.cts.txt
U87PS4B_R2

value: ER 27319 maleate


title: U87PS4B-47

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-52

description:
U87PS4B.cts.txt
U87PS4B_R2

value: UNTREATED


title: U87PS4B-53

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-48

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-50

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Resminostat


title: U87PS4B-44

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-51

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Selinexor (KPT-330)


title: U87PS4B-66

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Zibotentan (ZD4054)


title: U87PS4B-40

description:
U87PS4B.cts.txt
U87PS4B_R2

value: DMSO


title: U87PS4B-49

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Pracinostat (SB939)


title: U87PS4B-43

description:
U87PS4B.cts.txt
U87PS4B_R2

value: HOMIDIUM BROMIDE


title: U87PS4B-45

description:
U87PS4B.cts.txt
U87PS4B_R2

value: A-7 hydrochloride


title: U87PS4B-41

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-60

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Perifosine (KRX-0401)


title: U87PS4B-39

description:
U87PS4B.cts.txt
U87PS4B_R2

value: SCIO 469 hydrochloride


title: U87PS4B-32

description:
U87PS4B.cts.txt
U87PS4B_R2

value: SAPPANONE A DIMETHYL ETHER

value: PLATE-Seq


title: U87PS4B-33

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Methyl 2,5-dihydroxycinnamate


title: U87PS4B-35

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Bax channel blocker


title: U87PS4B-34

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-37

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Plinabulin (NPI-2358)


title: U87PS4B-38

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Refametinib (RDEA119, Bay 86-9766)


title: U87PS4B-36

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Pacritinib (SB1518)


title: U87PS4B-31

description:
U87PS4B.cts.txt
U87PS4B_R2

value: CELASTROL


title: U87PS4B-27

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Savolitinib (Volitinib; AZD6094; HMPL-504)


title: U87PS4B-30

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Volasertib (BI 6727)


title: U87PS4B-42

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Voreloxin (SNS-595)


title: U87PS4B-28

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tandutinib (MLN518)


title: U87PS4B-26

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Raltitrexed


title: U87PS4B-29

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tivozanib (AV-951)


title: U87PS4B-25

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Pixantrone (BBR-2778), dimaleate salt


title: U87PS4B-22

description:
U87PS4B.cts.txt
U87PS4B_R2

value: SDM25N hydrochloride


title: KI_CRZ1__37C_rep3

city: Durham

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

data_processing:
Illumina CASAVA v.1.8.2 was used for base calling. A one-base mismatch was allowed in barcodes during demultiplexing.
Quality filtering was performed using fastq-mcf to remove sequencing adapters and trim low quality bases
Tophat2 was used to map the processed reads; parameters used were "--transcriptome-max-hits 1 --max-multihits 1 --max-intron-length 4000 --library-type fr-unstranded --no-coverage-search"
htseq-count was used to determine read counts per gene; parameters used were "--stranded=no --type=exon --idattr=gene_id"
Genome_build: H99 genome version 2, downloaded from the Broad Institute
Supplementary_files_format_and_content: .tab files were generated using htseq-count, for each row, column 1 is gene name, and column 2 is the raw (not normalized) read count for that gene

organism: Cryptococcus neoformans H99

source_name: liquid culture

growth_protocol:
grown at 37C
Strains were grown overnight at 24°C with shaking, until an OD600 = 0.5 was reached. Cell cultures were divided in two. One half was incubated at 24°C while the other half was transferred to 37°C, for a further 2 hours

extract_protocol:
Cells were collected by centrifugation, frozen at -80°C, and then lyophilized overnight. Total RNA was isolated from lyophilized cells using Trizol solution (Invitrogen Life Technologies, Carlsbad, CA) and the Qiagen RNeasy® Mini kit (Qiagen, Valencia, CA).
cDNA libraries were prepared for sequencing using the Illumina RNA TruSeq kit, following the manufacturer's protocol

tag: growth temperature

tag: genotype

tag: replicate


title: U87PS4B-19

description:
U87PS4B.cts.txt
U87PS4B_R2

value: ACRIFLAVINIUM HYDROCHLORIDE


title: U87PS4B-18

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Vindesine sulphate


title: U87PS4B-16

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Talazoparib (BMN673)

value: PLATE-Seq


title: U87PS4B-23

description:
U87PS4B.cts.txt
U87PS4B_R2


title: KI_CNA1__37C_rep3


title: WT__37C_rep3

value: WT


title: U87PS4B-21

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tetrindole mesylate


title: U87PS4B-17

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Tirapazamine


title: U87PS4B-15

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Satraplatin (JM216)


title: KI_CNA1__24C_rep3

growth_protocol:
grown at 24C
Strains were grown overnight at 24°C with shaking, until an OD600 = 0.5 was reached. Cell cultures were divided in two. One half was incubated at 24°C while the other half was transferred to 37°C, for a further 2 hours


title: WT__24C_rep3


title: U87PS4B-24

description:
U87PS4B.cts.txt
U87PS4B_R2


title: KO_crz1__24C_rep3


title: KO_crz1__37C_rep2


title: U87PS4B-12

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-11

description:
U87PS4B.cts.txt
U87PS4B_R2

value: 10-DEBC hydrochloride


title: KI_CRZ1__37C_rep2


title: KO_cna1__37C_rep2


title: KI_CNA1__37C_rep2


title: U87PS4B-13

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Pirarubicin


title: U87PS4B-10

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-9

description:
U87PS4B.cts.txt
U87PS4B_R2

value: IPAG


title: KO_crz1__37C_rep3


title: U87PS4B-8

description:
U87PS4B.cts.txt
U87PS4B_R2


title: KI_CNA1__24C_rep2


title: U87PS4B-7

description:
U87PS4B.cts.txt
U87PS4B_R2

value: BENZALKONIUM CHLORIDE


title: KO_cna1__24C_rep2


title: U87PS4B-6

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Varlitinib


title: KI_CRZ1__24C_rep2


title: U87PS4B-4

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Talampanel


title: KO_crz1__24C_rep2


title: WT__24C_rep2


title: U87PS4B-3

description:
U87PS4B.cts.txt
U87PS4B_R2


title: U87PS4B-20

description:
U87PS4B.cts.txt
U87PS4B_R2

value: DIALLYL TRISULFIDE


title: KI_CNA1__37C_rep1


title: U87PS4B-14

description:
U87PS4B.cts.txt
U87PS4B_R2


title: KI_CRZ1__24C_rep3


title: WT__37C_rep2


title: KO_cna1__37C_rep1


title: KO_crz1__37C_rep1


title: U87PS4B-1

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Pimasertib (AS-703026)


title: WT__37C_rep1


title: U87PS4B-0

description:
U87PS4B.cts.txt
U87PS4B_R2

value: OSI-906 (Linsitinib)


title: U87PS4A-95

description:
U87PS4A.cts.txt
U87PS4A_R2


title: KO_cna1__24C_rep1


title: U87PS4A-94

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Lylamine hydrochloride


title: U87PS4B-5

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Telatinib


title: U87PS4A-93

description:
U87PS4A.cts.txt
U87PS4A_R2

value: (R)-(-)-Niguldipine hydrochloride


title: U87PS4A-91

description:
U87PS4A.cts.txt
U87PS4A_R2

value: DIHYDROCELASTROL

value: PLATE-Seq


title: U87PS4A-92

description:
U87PS4A.cts.txt
U87PS4A_R2

value: PLUMBAGIN


title: U87PS4B-2

description:
U87PS4B.cts.txt
U87PS4B_R2

value: Quizartinib (AC220)


title: U87PS4A-89

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-90

description:
U87PS4A.cts.txt
U87PS4A_R2

value: AMINACRINE


title: Sox10_ATACSeq_16ss_2

description: Sox10 BAC driving mCherry expression for FACS.

library_source: genomic

molecule: genomic DNA

value: AB/TU

value: neural crest

value: ATAC-seq

value: whole cell

value: FACS


title: Sox10_ATACSeq_16ss_1

value: neural crest and otic


title: KI_CNA1__24C_rep1


title: U87PS4A-86

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-84

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Picoplatin


title: U87PS4A-85

description:
U87PS4A.cts.txt
U87PS4A_R2

value: PX 12


title: KI_CRZ1__37C_rep1


title: U87PS4A-87

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-83

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Nebivolol hydrochloride


title: KI_CRZ1__24C_rep1


title: TCMF3

city: Guangzhou

first: Liu

last: Yihua

address: Wushan street, Tianhe

country: China

institute: South China Agricultural University

data_processing:
Data were analyzed using a t-test procedure with an independent samples test with SPSS 19.0 (SPSS Inc., Chicago, IL, USA). P<0.05 was considered as a significant difference between the means of the two groups. The results are presented as the means ± standard errors (SE). The correlation between the two methods, deep sequencing and qPCR, was analyzed by Pearson’s correlation coefficients.   Sequencing data processing was according to the following procedures: briefly, the raw reads were subjected to an Illumina pipeline filter (Solexa 0.3) and then the dataset was further processed with ACGT1-miR (LC Sciences, Houston, TX, USA) to remove unmappable reads. The unique sequences were mapped to specific species in miRBase 20.0 by BLAST search or to genomes to obtain pre-miRNA (mir) and mature miRNA (miR) sequences.
The alignment software, bowtie 0.12.8, was used to map the reads back to the transcriptome. Then, the number of mapped clean reads for each unigene was counted and normalized into a RPKM value (Reads Per kb per Million reads), which is widely used to calculate the unigene expression (Mortazavi et al., 2008). To detect differentially expressed genes, statistical analyses among libraries were performed following the formula as described (Shen et al., 2012), where FDR (false discovery rate) were used to determine the threshold the P value in multiple tests and analyses using the q-value package (Benjamini et al., 2001). In our work, the differentially expressed unigenes between two samples were screened with the threshold of FDR ≤ 0.001 and the absolute value of log2Ratio ≥ 1. Furthermore, the GO classifications and the KEGG pathway enrichments were compared between up-regulated and down-regulated  unigenes.
Genome_build: scrofa.Sscrofa10.2
Supplementary_files_format_and_content: expression data of miRNA and differential analysis reuslts and .xlsx

organism: Sus scrofa

source_name: TCMF

growth_protocol: The experimental animals were purchased from the experimental animal center of Guangdong Wen’s Foodstuffs Group Co., Ltd. (Yunfu, China). A total of 60 146-day-old castrated Pietrain×Duroc×Landrace×Yorkshire finishing swine with an average initial body weight of 84.05 ± 0.86 kg were divided randomly into two dietary treatment groups as follows: controls (CON, basal diet, 14.49% crude protein, 13.73 MJ/kg digestible energy, 0.86% available lysine) and TCMF (basal diet+2.5 g/kg TCMF). The animals were subjected to five replications per treatment with six pigs per pen (3.5 m × 4 m). The pigs were provided free access to feed and water and were housed in a controlled environment. The experiment lasted for 35 days following a 7-day adaptation to the new diet.

extract_protocol:
Total RNA was extracted from the longissimus dorsi muscle of the pigs using Total RNA Kit Ι reagent (Omega Bio-Tek, Norcross, GAUSA) according to the manufacturer protocol. DNase (Promega, Madison, WI, USA) was used to eliminate trace genomic DNA contamination. RNA purity was identified by determining the absorbance of the RNA at 260 nm and 280 nm [31]. The quality of the extracted RNA was examined using the 28S, 18S, and 5S rRNA bands on ethidium bromide-stained agarose gels.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: basal diet+2.5 g/kg TCMF

tag: harvest stage

value: weight of 84.05 ± 0.86 kg

value: muscle fibers in skeletal muscle


title: Control3

source_name: control

value: basal diet, 14.49% crude protein, 13.73 MJ/kg digestible energy, 0.86% available lysine


title: U87PS4A-82

description:
U87PS4A.cts.txt
U87PS4A_R2

value: 2,3-DCPE hydrochloride

value: PLATE-Seq


title: U87PS4A-81

description:
U87PS4A.cts.txt
U87PS4A_R2

value: WIN 64338 hydrochloride


title: KO_crz1__24C_rep1


title: Control1


title: Control2


title: U87PS4A-80

description:
U87PS4A.cts.txt
U87PS4A_R2

value: KINETIN RIBOSIDE


title: TCMF1


title: U87PS4A-79

description:
U87PS4A.cts.txt
U87PS4A_R2

value: TETRACHLOROISOPHTHALONITRILE


title: U87PS4A-88

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tasquinimod


title: U87PS4A-78

description:
U87PS4A.cts.txt
U87PS4A_R2

value: SULCONAZOLE NITRATE


title: U87PS4A-76

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tasisulam


title: U87PS4A-77

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Triciribine


title: U87PS4A-75

description:
U87PS4A.cts.txt
U87PS4A_R2

value: TAK-700 (Orteronel)


title: U87PS4A-74

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Rocilinostat (ACY-1215)


title: U87PS4A-71

description:
U87PS4A.cts.txt
U87PS4A_R2

value: CGP 71683 hydrochloride


title: U87PS4A-73

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Propranolol HCl


title: U87PS4A-72

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-70

description:
U87PS4A.cts.txt
U87PS4A_R2

value: IKK 16


title: PE098-A2-95

description:
PE098-A2.cts.txt
PE098-A2_R2

source_name: LnCAP cell line

value: untreated


title: PE098-A2-94

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-68

description:
U87PS4A.cts.txt
U87PS4A_R2

value: THYMOQUINONE


title: U87PS4A-65

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Triapine


title: U87PS4A-67

description:
U87PS4A.cts.txt
U87PS4A_R2

value: 4 -METHOXYCHALCONE


title: U87PS4A-66

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Zibotentan (ZD4054)

value: PLATE-Seq


title: PE098-A2-93

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-92

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-64

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tariquidar


title: PE098-A2-91

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-88

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-90

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-61

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Prinomastat hydrochloride


title: U87PS4A-63

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Sofrastaurin


title: PE098-A2-89

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-87

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-60

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Perifosine (KRX-0401)


title: PE098-A2-85

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-86

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-62

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-59

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Ryuvidine


title: U87PS4A-69

description:
U87PS4A.cts.txt
U87PS4A_R2

value: RS 17053 hydrochloride


title: U87PS4A-58

description:
U87PS4A.cts.txt
U87PS4A_R2

value: NNC 05-2090 hydrochloride


title: PE098-A2-84

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-83

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-57

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-82

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-55

description:
U87PS4A.cts.txt
U87PS4A_R2

value: PRISTIMERIN


title: U87PS4A-54

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-81

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-78

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-79

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-80

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-51

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Selinexor (KPT-330)


title: WT__24C_rep1

value: WT


title: PE098-A2-77

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-50

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Resminostat


title: PE098-A2-75

description:
PE098-A2.cts.txt
PE098-A2_R2

value: untreated


title: PE098-A2-74

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-49

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Pracinostat (SB939)


title: PE098-A2-73

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-47

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-56

description:
U87PS4A.cts.txt
U87PS4A_R2

value: TOTAROL


title: U87PS4A-46

description:
U87PS4A.cts.txt
U87PS4A_R2

value: ER 27319 maleate


title: PE098-A2-72

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-44

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-43

description:
U87PS4A.cts.txt
U87PS4A_R2

value: HOMIDIUM BROMIDE


title: U87PS4A-42

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Voreloxin (SNS-595)

value: PLATE-Seq


title: PE098-A2-70

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-71

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-52

description:
U87PS4A.cts.txt
U87PS4A_R2

value: UNTREATED


title: U87PS4A-53

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-40

description:
U87PS4A.cts.txt
U87PS4A_R2

value: DMSO


title: PE098-A2-68

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-39

description:
U87PS4A.cts.txt
U87PS4A_R2

value: SCIO 469 hydrochloride


title: PE098-A2-76

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-66

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-67

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-45

description:
U87PS4A.cts.txt
U87PS4A_R2

value: A-7 hydrochloride


title: PE098-A2-65

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-38

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Refametinib (RDEA119, Bay 86-9766)


title: U87PS4A-36

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Pacritinib (SB1518)


title: U87PS4A-37

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Plinabulin (NPI-2358)


title: U87PS4A-48

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-63

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-64

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-60

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-34

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-61

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-69

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-32

description:
U87PS4A.cts.txt
U87PS4A_R2

value: SAPPANONE A DIMETHYL ETHER


title: PE098-A2-62

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-41

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-31

description:
U87PS4A.cts.txt
U87PS4A_R2

value: CELASTROL


title: PE098-A2-57

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-58

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-33

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Methyl 2,5-dihydroxycinnamate


title: PE098-A2-56

description:
PE098-A2.cts.txt
PE098-A2_R2

value: untreated


title: U87PS4A-30

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Volasertib (BI 6727)


title: PE098-A2-55

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-29

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tivozanib (AV-951)


title: U87PS4A-35

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Bax channel blocker


title: PE098-A2-54

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-26

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Raltitrexed


title: U87PS4A-27

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Savolitinib (Volitinib; AZD6094; HMPL-504)


title: PE098-A2-53

description:
PE098-A2.cts.txt
PE098-A2_R2

value: PLATE-Seq


title: U87PS4A-28

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tandutinib (MLN518)


title: PE098-A2-52

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-25

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Pixantrone (BBR-2778), dimaleate salt


title: U87PS4A-24

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-23

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-51

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-50

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-59

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-49

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-21

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tetrindole mesylate


title: U87PS4A-20

description:
U87PS4A.cts.txt
U87PS4A_R2

value: DIALLYL TRISULFIDE


title: PE098-A2-47

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-46

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-19

description:
U87PS4A.cts.txt
U87PS4A_R2

value: ACRIFLAVINIUM HYDROCHLORIDE


title: PE098-A2-48

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-18

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Vindesine sulphate


title: PE098-A2-45

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-17

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Tirapazamine


title: PE098-A2-43

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-15

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Satraplatin (JM216)


title: PE098-A2-42

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-40

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-39

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-14

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-12

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-11

description:
U87PS4A.cts.txt
U87PS4A_R2

value: 10-DEBC hydrochloride


title: PE098-A2-38

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-22

description:
U87PS4A.cts.txt
U87PS4A_R2

value: SDM25N hydrochloride


title: PE098-A2-37

description:
PE098-A2.cts.txt
PE098-A2_R2

value: untreated


title: U87PS4A-10

description:
U87PS4A.cts.txt
U87PS4A_R2


title: U87PS4A-9

description:
U87PS4A.cts.txt
U87PS4A_R2

value: IPAG


title: U87PS4A-8

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-36

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-35

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-7

description:
U87PS4A.cts.txt
U87PS4A_R2

value: BENZALKONIUM CHLORIDE


title: PE098-A2-34

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-33

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-5

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Telatinib


title: U87PS4A-6

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Varlitinib


title: PE098-A2-44

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-41

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-32

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-4

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Talampanel


title: U87PS4A-16

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Talazoparib (BMN673)

value: PLATE-Seq


title: U87PS4A-3

description:
U87PS4A.cts.txt
U87PS4A_R2


title: PE098-A2-31

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-30

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-2

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Quizartinib (AC220)


title: U87PS4A-13

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Pirarubicin


title: PE098-A2-29

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-28

description:
PE098-A2.cts.txt
PE098-A2_R2


title: TCMF2

value: basal diet+2.5 g/kg TCMF

value: weight of 84.05 ± 0.86 kg

value: muscle fibers in skeletal muscle


title: U87PS4A-1

description:
U87PS4A.cts.txt
U87PS4A_R2

value: Pimasertib (AS-703026)


title: PE098-A2-27

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS4A-0

description:
U87PS4A.cts.txt
U87PS4A_R2

value: OSI-906 (Linsitinib)


title: U87PS1B-95

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Pazopanib


title: U87PS1B-94

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Sonidegib / Erismodegib


title: PE098-A2-25

description:
PE098-A2.cts.txt
PE098-A2_R2

value: untreated


title: PE098-A2-26

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-93

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Fludarabine


title: PE098-A2-23

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-91

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cytarabine


title: U87PS1B-92

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Osimertinib (AZD9291)


title: PE098-A2-22

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-24

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-21

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-88

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Gemcitabine


title: U87PS1B-90

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Toremifene


title: U87PS1B-89

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Daunorubicin hydrochloride


title: PE098-A2-19

description:
PE098-A2.cts.txt
PE098-A2_R2

value: PLATE-Seq


title: PE098-A2-20

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-18

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-87

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vinorelbine


title: PE098-A2-17

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-85

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Bosutinib


title: U87PS1B-86

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Octreotide in Water


title: U87PS1B-84

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Trametinib (GSK1120212)


title: PE098-A2-15

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-83

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mitotane


title: PE098-A2-14

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-82

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cisplatin


title: U87PS1B-81

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Folinic acid calcium salt


title: PE098-A2-13

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-11

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-12

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-79

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Imatinib


title: PE098-A2-10

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-9

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-8

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-77

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Palbociclib (PD-0332991) HCl


title: PE098-A2-7

description:
PE098-A2.cts.txt
PE098-A2_R2

value: untreated


title: U87PS1B-75

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cladribine


title: U87PS1B-76

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Romidepsin


title: U87PS1B-73

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Busulfan


title: PE098-A2-6

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-4

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-74

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Axitinib


title: PE098-A2-3

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-5

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-16

description:
PE098-A2.cts.txt
PE098-A2_R2


title: PE098-A2-2

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-72

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mithramycin A


title: U87PS1B-70

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vemurafenib (PLX4032)


title: U87PS1B-69

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Oxaliplatin

value: PLATE-Seq


title: PE098-A2-0

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-80

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Nilotinib (AMN-107)


title: PE098-A1-95

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-67

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Tamoxifen


title: U87PS1B-66

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Leuprolide (Leuprorelin; Lupron)


title: PE098-A2-1

description:
PE098-A2.cts.txt
PE098-A2_R2


title: U87PS1B-65

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Teniposide


title: PE098-A1-94

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-92

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-78

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Omacetaxine / Homoharringtonine


title: U87PS1B-68

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mechlorethamine


title: PE098-A1-93

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-91

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-63

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Clofarabine


title: PE098-A1-90

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-62

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Tofacitinib citrate (CP-690550 citrate)


title: PE098-A1-89

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated


title: U87PS1B-71

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vismodegib (GDC-0449)


title: PE098-A1-88

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-60

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Topotecan hydrochloride


title: PE098-A1-86

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-59

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Lapatinib Ditosylate (Tykerb)


title: PE098-A1-87

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-58

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Dabrafenib (GSK2118436)


title: U87PS1B-57

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Carmustine


title: PE098-A1-84

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-55

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mitomycin C


title: PE098-A1-82

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-64

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vinblastine


title: PE098-A1-81

description:
PE098-A1.cts.txt
PE098-A1_R2

value: PLATE-Seq


title: PE098-A1-79

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-85

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-78

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-54

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cabazitaxel (Jevtana)


title: U87PS1B-56

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vandetanib (ZD6474)


title: PE098-A1-77

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-61

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Dactinomycin


title: PE098-A1-76

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-75

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-50

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Bleomycin sulfate


title: U87PS1B-52

description:
U87PS1B.cts.txt
U87PS1B_R2

value: UNTREATED


title: PE098-A1-74

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-72

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-48

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Ibrutinib


title: U87PS1B-49

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Dasatinib


title: PE098-A1-83

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-51

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Gefitinib


title: U87PS1B-44

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Olaparib (AZD2281)


title: U87PS1B-45

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Vorinostat


title: U87PS1B-46

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Irinotecan


title: U87PS1B-47

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Hydroxyurea


title: PE098-A1-80

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated


title: PE098-A1-71

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-43

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Exemestane


title: U87PS1B-53

description:
U87PS1B.cts.txt
U87PS1B_R2


title: PE098-A1-70

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-41

description:
U87PS1B.cts.txt
U87PS1B_R2

value: DMSO


title: PE098-A1-69

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-42

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Temsirolimus


title: U87PS1B-40

description:
U87PS1B.cts.txt
U87PS1B_R2

value: PLATE-Seq


title: PE098-A1-68

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-67

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-66

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-65

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-39

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Crizotinib


title: U87PS1B-38

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Ponatinib (AP24534)


title: U87PS1B-33

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Erlotinib


title: U87PS1B-36

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Raloxifene


title: U87PS1B-35

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Alectinib (CH5424802)x


title: U87PS1B-34

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Letrozole


title: U87PS1B-32

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Tretinoin


title: U87PS1B-30

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Decitabine


title: PE098-A1-63

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-60

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-31

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Bexarotene


title: PE098-A1-73

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-64

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-62

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-58

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-59

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-29

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Ceritinib (LDK378)


title: U87PS1B-28

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Doxorubicin


title: PE098-A1-56

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-26

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Epirubicin Hydrochloride


title: U87PS1B-37

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Sunitinib Malate


title: U87PS1B-27

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Afatinib


title: PE098-A1-54

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated


title: PE098-A1-55

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-53

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-23

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Pentostatin


title: U87PS1B-24

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mitoxanthrone dihydrochloride

value: PLATE-Seq


title: PE098-A1-52

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-61

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-51

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-21

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Amsacrine


title: PE098-A1-49

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-48

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-22

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Regorafenib (BAY 73-4506)


title: PE098-A1-44

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-19

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Etoposide


title: U87PS1B-18

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Pomalidomide


title: PE098-A1-46

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-57

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-42

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-20

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Docetaxel


title: PE098-A1-50

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-17

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Lenvatinib (E7080)


title: PE098-A1-43

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-41

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-15

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Paclitaxel


title: PE098-A1-40

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-13

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Panobinostat (LBH589)


title: U87PS1B-14

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Arsenic trioxide


title: U87PS1B-25

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Carfilzomib (PR-171)


title: PE098-A1-38

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-12

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Fulvestrant


title: U87PS1B-11

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cabozantinib - XL 184


title: PE098-A1-39

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-9

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Melphalan


title: U87PS1B-10

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Lenalidomide


title: PE098-A1-37

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated


title: PE098-A1-35

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-36

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-34

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-8

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Sorafenib


title: PE098-A1-32

description:
PE098-A1.cts.txt
PE098-A1_R2

value: PLATE-Seq


title: PE098-A1-33

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-6

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Idarubicin


title: U87PS1B-7

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Belinostat


title: U87PS1B-3

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Ixabepilone


title: PE098-A1-31

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-4

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Cobimetinib (GDC-0973, RG7420)


title: PE098-A1-28

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-29

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-30

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1B-1

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Ixazomib (MLN2238)


title: U87PS1B-2

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Azacitidine


title: U87PS1B-0

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Bortezomib


title: U87PS1A-95

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Pazopanib


title: PE098-A1-25

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-27

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-26

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-94

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Sonidegib / Erismodegib


title: PE098-A1-24

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-23

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-92

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Osimertinib (AZD9291)


title: U87PS1B-5

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Thioguanine


title: U87PS1A-90

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Toremifene


title: PE098-A1-22

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-21

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-91

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cytarabine


title: PE098-A1-20

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-89

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Daunorubicin hydrochloride


title: U87PS1A-88

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Gemcitabine


title: U87PS1B-16

description:
U87PS1B.cts.txt
U87PS1B_R2

value: Mercaptopurine


title: PE098-A1-45

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated

value: PLATE-Seq


title: PE098-A1-18

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-86

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Octreotide in Water


title: U87PS1A-87

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vinorelbine


title: PE098-A1-19

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-85

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Bosutinib


title: U87PS1A-93

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Fludarabine


title: PE098-A1-16

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-47

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-84

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Trametinib (GSK1120212)


title: U87PS1A-82

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cisplatin


title: U87PS1A-83

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mitotane


title: U87PS1A-81

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Folinic acid calcium salt


title: PE098-A1-15

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-14

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-12

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-11

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-79

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Imatinib


title: PE098-A1-10

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-78

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Omacetaxine / Homoharringtonine


title: PE098-A1-17

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-8

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PE098-A1-6

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-77

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Palbociclib (PD-0332991) HCl


title: U87PS1A-75

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cladribine


title: U87PS1A-76

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Romidepsin


title: PE098-A1-7

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-73

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Busulfan


title: PE098-A1-13

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-74

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Axitinib


title: PE098-A1-3

description:
PE098-A1.cts.txt
PE098-A1_R2

value: untreated


title: U87PS1A-71

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vismodegib (GDC-0449)

value: PLATE-Seq


title: U87PS1A-80

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Nilotinib (AMN-107)


title: PE098-A1-1

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-72

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mithramycin A


title: U87PS1A-70

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vemurafenib (PLX4032)


title: PE098-A1-0

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-68

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mechlorethamine


title: PF003-94

description:
PF003.cts.txt
PF003_R2

source_name: BT20 cell line

value: Bortezomib (Velcade)


title: PF003-95

description:
PF003.cts.txt
PF003_R2

value: DMSO


title: U87PS1A-66

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Leuprolide (Leuprorelin; Lupron)


title: PF003-93

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: U87PS1A-67

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Tamoxifen


title: PE098-A1-9

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-65

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Teniposide


title: PE098-A1-4

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PF003-92

description:
PF003.cts.txt
PF003_R2

value: Aprepitant (MK - 0869)


title: PE098-A1-5

description:
PE098-A1.cts.txt
PE098-A1_R2


title: U87PS1A-64

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vinblastine


title: PE098-A1-2

description:
PE098-A1.cts.txt
PE098-A1_R2


title: PF003-90

description:
PF003.cts.txt
PF003_R2

value: Albendazole (Albenza)


title: U87PS1A-61

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Dactinomycin


title: PF003-89

description:
PF003.cts.txt
PF003_R2

value: Crizotinib


title: PF003-91

description:
PF003.cts.txt
PF003_R2

value: Idarubicin HCl


title: U87PS1A-69

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Oxaliplatin

value: PLATE-Seq


title: PF003-88

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride


title: U87PS1A-59

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Lapatinib Ditosylate (Tykerb)


title: U87PS1A-60

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Topotecan hydrochloride


title: U87PS1A-58

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Dabrafenib (GSK2118436)


title: U87PS1A-62

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Tofacitinib citrate (CP-690550 citrate)


title: PF003-87

description:
PF003.cts.txt
PF003_R2

value: DMSO


title: PF003-86

description:
PF003.cts.txt
PF003_R2

value: Bortezomib (Velcade)


title: PF003-85

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: PF003-84

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-56

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vandetanib (ZD6474)


title: PF003-83

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-54

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cabazitaxel (Jevtana)


title: PF003-81

description:
PF003.cts.txt
PF003_R2


title: PF003-82

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-53

description:
U87PS1A.cts.txt
U87PS1A_R2

value: UNTREATED


title: PF003-80

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-63

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Clofarabine


title: U87PS1A-52

description:
U87PS1A.cts.txt
U87PS1A_R2


title: PF003-79

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-51

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Gefitinib


title: PF003-78

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-57

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Carmustine


title: U87PS1A-50

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Bleomycin sulfate


title: PF003-77

description:
PF003.cts.txt
PF003_R2


title: PF003-76

description:
PF003.cts.txt
PF003_R2

value: Aprepitant (MK - 0869)


title: U87PS1A-48

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Ibrutinib

value: PLATE-Seq


title: PF003-75

description:
PF003.cts.txt
PF003_R2

value: Idarubicin HCl


title: U87PS1A-55

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mitomycin C


title: U87PS1A-47

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Hydroxyurea


title: PF003-73

description:
PF003.cts.txt
PF003_R2

value: Crizotinib


title: U87PS1A-46

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Irinotecan


title: U87PS1A-44

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Olaparib (AZD2281)


title: PF003-72

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride


title: U87PS1A-45

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Vorinostat


title: U87PS1A-42

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Temsirolimus


title: U87PS1A-43

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Exemestane


title: PF003-69

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: PF003-71

description:
PF003.cts.txt
PF003_R2

value: DMSO


title: PF003-74

description:
PF003.cts.txt
PF003_R2

value: Albendazole (Albenza)


title: U87PS1A-41

description:
U87PS1A.cts.txt
U87PS1A_R2


title: PF003-67

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-39

description:
U87PS1A.cts.txt
U87PS1A_R2


title: PF003-66

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-49

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Dasatinib


title: U87PS1A-38

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Ponatinib (AP24534)


title: U87PS1A-37

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Sunitinib Malate


title: PF003-65

description:
PF003.cts.txt
PF003_R2

value: PLATE-Seq


title: U87PS1A-36

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Raloxifene


title: PF003-64

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-35

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Alectinib (CH5424802)x


title: PF003-63

description:
PF003.cts.txt
PF003_R2


title: PF003-70

description:
PF003.cts.txt
PF003_R2

value: Bortezomib (Velcade)


title: PF003-62

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-34

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Letrozole


title: U87PS1A-33

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Erlotinib


title: PF003-61

description:
PF003.cts.txt
PF003_R2


title: PF003-60

description:
PF003.cts.txt
PF003_R2

value: Aprepitant (MK - 0869)


title: U87PS1A-40

description:
U87PS1A.cts.txt
U87PS1A_R2


title: PF003-68

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-32

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Tretinoin


title: U87PS1A-31

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Bexarotene


title: PF003-58

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-27

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Afatinib


title: PF003-56

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride


title: PF003-57

description:
PF003.cts.txt
PF003_R2

value: Crizotinib


title: PF003-59

description:
PF003.cts.txt
PF003_R2

value: Idarubicin HCl


title: U87PS1A-28

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Doxorubicin


title: U87PS1A-29

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Ceritinib (LDK378)


title: U87PS1A-26

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Epirubicin Hydrochloride


title: U87PS1A-25

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Carfilzomib (PR-171)


title: PF003-55

description:
PF003.cts.txt
PF003_R2

value: DMSO

value: PLATE-Seq


title: U87PS1A-30

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Decitabine


title: PF003-54

description:
PF003.cts.txt
PF003_R2

value: Bortezomib (Velcade)


title: PF003-53

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: PF003-52

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-24

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mitoxanthrone dihydrochloride


title: PF003-51

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-23

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Pentostatin


title: PF003-50

description:
PF003.cts.txt
PF003_R2

value: Albendazole (Albenza)


title: U87PS1A-22

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Regorafenib (BAY 73-4506)


title: PF003-49

description:
PF003.cts.txt
PF003_R2


title: PF003-48

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-21

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Amsacrine


title: PF003-47

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-20

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Docetaxel


title: U87PS1A-17

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Lenvatinib (E7080)


title: U87PS1A-16

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Mercaptopurine


title: U87PS1A-18

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Pomalidomide


title: PF003-44

description:
PF003.cts.txt
PF003_R2

value: Aprepitant (MK - 0869)


title: PF003-45

description:
PF003.cts.txt
PF003_R2


title: PF003-43

description:
PF003.cts.txt
PF003_R2

value: Idarubicin HCl


title: U87PS1A-15

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Paclitaxel


title: PF003-42

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-12

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Fulvestrant


title: U87PS1A-11

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cabozantinib - XL 184

value: PLATE-Seq


title: PF003-40

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride


title: U87PS1A-10

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Lenalidomide


title: PF003-41

description:
PF003.cts.txt
PF003_R2

value: Crizotinib


title: PF003-39

description:
PF003.cts.txt
PF003_R2

value: DMSO


title: U87PS1A-14

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Arsenic trioxide


title: PF003-38

description:
PF003.cts.txt
PF003_R2

value: Bortezomib (Velcade)


title: PF003-37

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: PF003-36

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-19

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Etoposide


title: U87PS1A-8

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Sorafenib


title: PF003-35

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-7

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Belinostat


title: PF003-34

description:
PF003.cts.txt
PF003_R2

value: Albendazole (Albenza)


title: U87PS1A-5

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Thioguanine


title: U87PS1A-4

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Cobimetinib (GDC-0973, RG7420)


title: PF003-33

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-6

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Idarubicin


title: U87PS1A-2

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Azacitidine


title: U87PS1A-13

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Panobinostat (LBH589)


title: U87PS1A-3

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Ixabepilone

value: PLATE-Seq


title: PF003-32

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride


title: PF003-30

description:
PF003.cts.txt
PF003_R2


title: PF003-29

description:
PF003.cts.txt
PF003_R2


title: PF003-46

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-9

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Melphalan


title: U87PS1A-0

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Bortezomib


title: PF003-27

description:
PF003.cts.txt
PF003_R2

value: Idarubicin HCl


title: PF003-25

description:
PF003.cts.txt
PF003_R2

value: Crizotinib


title: PF003-26

description:
PF003.cts.txt
PF003_R2


title: PF003-24

description:
PF003.cts.txt
PF003_R2


title: PF003-22

description:
PF003.cts.txt
PF003_R2

value: Bortezomib (Velcade)


title: PF003-23

description:
PF003.cts.txt
PF003_R2

value: DMSO


title: PF003-19

description:
PF003.cts.txt
PF003_R2


title: PF003-20

description:
PF003.cts.txt
PF003_R2

value: Aprepitant (MK - 0869)


title: PF003-21

description:
PF003.cts.txt
PF003_R2

value: Gemcitabine HCl (Gemzar)


title: PF003-18

description:
PF003.cts.txt
PF003_R2

value: Albendazole (Albenza)


title: PF003-17

description:
PF003.cts.txt
PF003_R2


title: PF003-16

description:
PF003.cts.txt
PF003_R2


title: PF003-31

description:
PF003.cts.txt
PF003_R2


title: PF003-15

description:
PF003.cts.txt
PF003_R2


title: PF003-14

description:
PF003.cts.txt
PF003_R2


title: PF003-28

description:
PF003.cts.txt
PF003_R2


title: PF003-12

description:
PF003.cts.txt
PF003_R2


title: PF003-11

description:
PF003.cts.txt
PF003_R2


title: PF003-10

description:
PF003.cts.txt
PF003_R2


title: U87PS1A-1

description:
U87PS1A.cts.txt
U87PS1A_R2

value: Ixazomib (MLN2238)


title: PF003-13

description:
PF003.cts.txt
PF003_R2


title: PF003-7

description:
PF003.cts.txt
PF003_R2


title: PF003-8

description:
PF003.cts.txt
PF003_R2


title: PF003-5

description:
PF003.cts.txt
PF003_R2


title: PF003-6

description:
PF003.cts.txt
PF003_R2


title: PF003-9

description:
PF003.cts.txt
PF003_R2


title: PF003-4

description:
PF003.cts.txt
PF003_R2


title: PF003-3

description:
PF003.cts.txt
PF003_R2


title: PF003-2

description:
PF003.cts.txt
PF003_R2


title: PF003-1

description:
PF003.cts.txt
PF003_R2


title: NK_Ezh2cKO_rep1

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

description:
EN2
SpNK.edgeR.txt

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with Tophat v 2.1.0.
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements provided as edgeR output files

organism: Mus musculus

source_name: NK

extract_protocol:
Total RNA was isolated using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations.
Libraries were constructed using Nugen’s Ovation Ultralow Library systems and were subsequently subjected to 76 cycles of NextSeq500 sequencing.

treatment_protocol: CLPs (Lin-CD117intCD135+CD127+), pro-B (CD19+B220+CD43+), DN3 (Lin-CD25+CD117-), NK (Lin-DX5+NK1.1+), ILC2P (Lin-Sca1hiCD127+) were sorted from Ezh2fl/fl Il7racre/+ mice and Il7racre/+ controls into RLT buffer.  Two to three independent samples per genotype were assessed.

tag: strain

value: Spleen

tag: cell type

value: NK

value: Ezh2-fl/fl Il7ra-cre/+


title: NK_Ezh2cKO_rep2

description:
EN3
SpNK.edgeR.txt


title: NK_Cntrl_rep3

description:
CN3
SpNK.edgeR.txt


title: NK_Cntrl_rep2

description:
CN2
SpNK.edgeR.txt


title: ILC2P_Cntrl_rep3

description:
CI3
ILC2.edgeR.txt

value: Bone Marrow


title: ILC2P_Ezh2cKO_rep2

description:
EI2
ILC2.edgeR.txt


title: ILC2P_Ezh2cKO_rep3

description:
EI3
ILC2.edgeR.txt


title: ILC2P_Cntrl_rep2

description:
CI2
ILC2.edgeR.txt


title: ILC2P_Cntrl_rep1

description:
CI1
ILC2.edgeR.txt


title: CLP_Cntrl_rep3

description:
CC3
CLP.edgeR.txt

source_name: CLP

value: CLP


title: WT paraquat rep3_root_RNA-seq

city: Adelaide

first: Alice

middle: Louise

last: Burgess

state: SA

address: Frome road

department: Genetics and Evolution

country: Australia

institute: University of Adelaide

description: rRNA depleted RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq data was adaptor-trimmed using "Trimmomatic"
Trimmed reads were mapped to the Arabidopsis TAIR10 reference genome using "TopHat"
Diferentially expressed genes were detected using "Limma"
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel file with differential expressed genes from all comparisons from "Limma". File is available on series (GSE80053) record.

organism: Arabidopsis thaliana

source_name: 6 days after germination seedling roots grown on 1/2 MS media plates

growth_protocol: Roots were harvested from seedlings grown on 1/2 MS media plates

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH). Ribosomal RNA was depleted using Epicentre Ribo-Zero rRNA removal kits (Plant Seed/Root) prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants were either grown on media without paraquat, or with 0.01 uM paraquat

tag: cultivar

value: wild type

value: root

tag: treatment

value: oxidative stress (0.01 uM paraquat)


title: trm4b paraquat rep3_root_RNA-seq

description: rRNA depleted RNA


title: WT paraquat rep1_root_RNA-seq

description: rRNA depleted RNA


title: trm4b paraquat rep2_root_RNA-seq

description: rRNA depleted RNA


title: WT paraquat rep2_root_RNA-seq

description: rRNA depleted RNA


title: trm4b paraquat rep1_root_RNA-seq

description: rRNA depleted RNA


title: CLP_Ezh2cKO_rep2

description:
EC2
CLP.edgeR.txt


title: CLP_Cntrl_rep1

description:
CC1
CLP.edgeR.txt


title: DN3_Ezh2cKO_rep2

description:
ET2
DN3.edgeR.txt

value: Thymus


title: trm4b rep3_root_RNA-seq

description: rRNA depleted RNA

value: control conditions


title: DN3_Ezh2cKO_rep3

description:
ET3
DN3.edgeR.txt


title: CLP_Ezh2cKO_rep1

description:
EC1
CLP.edgeR.txt


title: PF003-0

description:
PF003.cts.txt
PF003_R2

value: Mitoxantrone Hydrochloride

value: PLATE-Seq


title: WT rep3_root_RNA-seq

description: rRNA depleted RNA


title: CLP_Cntrl_rep2

description:
CC2
CLP.edgeR.txt


title: NK_Cntrl_rep1

description:
CN1
SpNK.edgeR.txt


title: DN3_Ezh2cKO_rep1

description:
ET1
DN3.edgeR.txt


title: WT rep1_root_RNA-seq

description: rRNA depleted RNA


title: DN3_Cntrl_rep3

description:
CT3
DN3.edgeR.txt


title: WT rep2_root_RNA-seq

description: rRNA depleted RNA


title: DN3_Cntrl_rep1

description:
CT1
DN3.edgeR.txt


title: trm4b rep2_roots

description:
rRNA depleted RNA
RNA Bisulfite-seq
Processed data files: Supplementary_Table_2.xlsx and Supplementary_Table_3.xlsx

data_processing:
Library strategy: RNA Bisulfite-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, and filtered for low-quality reads using "Trimmomatic"
Trimmed reads were then globally mapped to in silico bisulfite converted Arabidopsis TAIR 10 reference genome using "TopHat"
Differential methylation and overall methylation calls were called using FDR 0.3 and methylation percentage greater than or equal to 1%
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel file containing overall methylation calls (Supplementary_Table_2) and excel file containing wild type versus trm4b-1 differential methylation calls (Supplementary_Table_3). Processed data files are available on the SuperSeries (GSE80054) record.

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH). Ribosomal RNA was depleted using Epicentre Ribo-Zero rRNA removal kits (Plant Seed/Root) and then bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.


title: proB_Ezh2cKO_rep2

description:
EB2
proB.edgeR.txt

source_name: pro-B

value: pro-B


title: trm4b rep3_roots


title: trm4b rep2_root_RNA-seq

description: rRNA depleted RNA


title: trm4b rep1_roots


title: ILC2P_Ezh2cKO_rep1

description:
EI1
ILC2.edgeR.txt


title: proB_Ezh2cKO_rep1

description:
EB1
proB.edgeR.txt


title: trm4b rep1_root_RNA-seq

description: rRNA depleted RNA


title: proB_Cntrl_rep1

description:
CB1
proB.edgeR.txt


title: proB_Cntrl_rep2

description:
CB2
proB.edgeR.txt


title: WT rep2_roots


title: proB_Cntrl_rep3

description:
CB3
proB.edgeR.txt


title: WT rep2_shoots

description:
rRNA depleted RNA
RNA Bisulfite-seq
Processed data files: Supplementary_Table_2.xlsx, Supplementary_Table_3.xlsx and Supplementary_Table_5.xlsx.xls

data_processing:
Library strategy: RNA Bisulfite-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, and filtered for low-quality reads using "Trimmomatic"
Trimmed reads were then globally mapped to in silico bisulfite converted Arabidopsis TAIR 10 reference genome using "TopHat"
Differential methylation and overall methylation calls were called using FDR 0.3 and methylation percentage greater than or equal to 1%
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel files contain differential methylation for pair-wise comparisons (Supplementary_Table_3 [wildtype vs trm4b-1], Supplementary_Table_5 [wildtype vs trdmt1-1]) and overall methylation calls (Supplementary_Table_2). Processed data files are available on the SuperSeries (GSE80054) record.

source_name: 10 days after germination seedling shoots grown on 1/2 MS media plates

growth_protocol: Seedlings were grown on 1/2 MS media plates

extract_protocol:
RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH). Ribosomal RNA was depleted using Epicentre Ribo-Zero rRNA removal kits (Plant leaf) and then bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.

value: shoots


title: trm4b rep2_siliques

description:
RNA Bisulfite-seq
rRNA depleted RNA
Processed data file: Supplementary_Table_2.xlsx  and Supplementary_Table_3.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, and filtered for low-quality reads using "Trimmomatic"
Trimmed reads were then globally mapped to in silico bisulfite converted Arabidopsis TAIR 10 reference genome using "TopHat"
Differential methylation and overall methylation calls were called using FDR 0.3 and methylation percentage greater than or equal to 1%
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel files contain differential methylation for pair-wise comparisons (Supplementary_Table_3) and overall methylation calls (Supplementary_Table_2). Processed data files are available on the SuperSeries (GSE80054) record.

source_name: 1 day after pollination siliques

growth_protocol: Plants were grown on soil

value: silique


title: WT rep3_roots


title: trdmt1 rep2_shoots

description:
rRNA depleted RNA
RNA Bisulfite-seq
Processed data files: Supplementary_Table_2.xlsx, Supplementary_Table_5.xlsx.xls


title: trm4b rep3_siliques


title: trdmt1 rep1_shoots


title: trm4b rep1_shoots

description:
rRNA depleted RNA
RNA Bisulfite-seq
Processed data files: Supplementary_Table_2.xlsx, Supplementary_Table_3.xlsx


title: trm4b rep2_shoots


title: WT rep1_shoots


title: trm4b rep1_siliques


title: DN3_Cntrl_rep2

description:
CT2
DN3.edgeR.txt


title: WT rep1_siliques


title: WT rep2_siliques


title: PHAX_1

city: Montpellier

first: Edouard

last: Bertrand

address: 1919 Route de Mendes

department: SERANAD

country: France

institute: CNRS

data_processing:
Filtering reads: Reads were trimmed to remove the 3’-linker sequence and quality filtered using flexbar (options -q 20 -as AGATCGGAAGAGCGGTTCAGC -ao 4 -u 3 -m 17 -n 4)
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Reads alignment: Reads were aligned to the hg19 Homo sapiens genome sequence by Tophat version 2.0.10, using a transcript annotation file (--GTF option) from Illumina iGenomes.
Collapsing reads: To remove PCR duplicates, reads mapped to the same start position in the genome and sharing the same 3-nucleotide random barcode sequence were collapsed.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files showing the normalized read density per position along the genome.

growth_protocol: The indicated cells were stably transfected with constructs containing the cDNA of the gene of interest, under the control of its respective endogenous gene promoter, with an localization and affinity purification (LAP)-tag with an N- or C-terminal GFP moiety, or a C-terminal 3xFLAG-tag

extract_protocol:
RNA-protein complexes were isolated by affinity purification using protein tags
The iCLIP library was constructed as described in Konig et al. (2011) with the additional modifications of Lubas et al. (2015), which include differences in sonication and washing buffers.

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

tag: cell line

value: HeLa

tag: transfected with

value: PHAX

tag: tag


title: ZC3H18_1

source_name: 3x FLAG-tag

value: HEK293 Flp-In T-Rex

value: 3x FLAG-tag


title: ARS2_2

source_name: localization and affinity purification (LAP)-tag


title: PHAX_2

value: localization and affinity purification (LAP)-tag


title: ZC3H18_2


title: ARS2_1


title: CBP20_2


title: WT rep1_roots


title: ElodeaBabeni2-2

description:
Sample name: EB2_2
Sample 8_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

organism: Elodea nuttallii

source_name: ElodeaBabeni2-2 shoots

growth_protocol: Collected in situ in clean site.

tag: section

value: 10cm of top with apex


title: ElodeaBabeni2-1

description:
Sample name: EB2_1
Sample 7_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

source_name: ElodeaBabeni2-1 shoots

tag: tissue


title: ElodeaBabeni1-3

description:
Sample name: EB1_4
Sample 6_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EV_FC2_FDR5.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

source_name: ElodeaBabeni1-3 shoots


title: CBP20_1


title: ElodeaBabeni2-3

description:
Sample name: EB2_5
Sample 9_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

source_name: ElodeaBabeni2-3 shoots


title: ElodeaValcea3

description:
Sample name: EV4
Sample 3_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB2_vs_EV_FC2_FDR5.xlsx

source_name: ElodeaValcea3 shoots


title: ElodeaValcea2

description:
Sample name: EV2
Sample 2_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB2_vs_EV_FC2_FDR5.xlsx

source_name: ElodeaValcea2 shoots


title: ElodeaBabeni1-2

description:
Sample name: EB1_3
Sample 5_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EV_FC2_FDR5.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

source_name: ElodeaBabeni1-2 shoots


title: xzl.gga.WL.testis.wt.adult.rep1.RNAseq

city: Rochester

first: Xin

last: Li

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

data_processing:
Analyses were performed using piPipes v1.4 (Han et al., 2014). All data from the ribosome profiling and RNA-seq were analyzed using the latest chicken genome release galGal5 (GCA_000002315.3).
The pair-end total RNA-seq reads were aligned to the genome using TopHat 2.0.12 (Trapnell et al., 2009). Reads were mapped using the ‘-g 100’ flag. The direct transcriptome mapping results were quantified using eXpress (Roberts and Pachter, 2013).
Ribosome protected fragments (RPFs) 26–32 nt long were selected for further analysis. The RPF abundance per TE or per piRNA cluster was quantified by eXpress, and reported as reads per kilobase pair per million reads mapped to the genome (rpkm) using a pseudo count of 0.01.
Genome_build: gg5
Supplementary_files_format_and_content: summary table

organism: Gallus gallus

source_name: testes

extract_protocol: Ribosome profiling Illumina-compatible sequencing libraries were prepared as the following.  The RPFs were then resolved on a 15% acrylamide (19:1), 8 M urea denaturing gel for 1 h 30 min at 35 W and fragments ranging from 26 nt to 35 nt size-selected from the gel. Size-selected RNAs were extracted from the gel slice by electro elution using GeBAflex tube, and the rRNAs were removed by Ribo-Zero Gold. The 3´ ends of recovered RNAs are dephosphorylated by PNK (New England BioLabs) in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol and 300 mM NaCl) at 37 °C for 3 h and then by Alkaline Phosphatase at 37 °C for 1 h. Dephosphorylated RNA footprints were then follow our small RNA library construction protocol except adding the step of 5´ end phosphorylation by PNK (New England BioLabs) using the PNK buffer with 1mM ATP at 37 °C for 1 h before 5´ ligation. Adaptor sequence: TGGAATTCTC. Strand-specific RNA-seq libraries were constructed following the TruSeq RNA sample preparation protocol as previously described (Li et al., 2013). rRNAs were depleted from total RNAs by Ribo-Zero Gold (Epicentre Biotechnologies, Madison, WI, USA). The library was sequenced using the paired-end 2 x 50 nt platform on a HiSeq 2000.

tag: developmental stage

value: adult

value: White Leghorn

value: wild-type


title: ElodeaBabeni1-1

description:
Sample name: EB1_2
Sample 4_En
Processed data file: normalized_counts_edgeR_cpm_Ellodea.xlsx
Processed data file: DEG_EB1_vs_EV_FC2_FDR5.xlsx
Processed data file: DEG_EB1_vs_EB2_FC2_FDR5.xlsx

source_name: ElodeaBabeni1-1 shoots


title: Myotubes Day7, Biological Reaplicate 2

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Myotubes_Day7_Interaction_Matrix_Corr_500kb.txt

data_processing:
We used HiCUP (hicup_v0.5.3) (http://www.bioinformatics.babraham.ac.uk/projects/hicup/) pipeline to analyse the HiC libraries. The pipeline was fed with the forward and the reverse reads generated from the sequencing for each of the six libraries. Sequencing reads were mapped to the reference genome (Mus_musculus_GRCh38) using bowtie aligner to generate BAM files. BAM files obtained this way have the corresponding forward and reverse reads of a sequenced DNA fragment mapped to the reference genome as a pair (di-tag). The choice to use HiCUP software for HiC data mapping was motivated by the ability of the pipeline to execute a variety of filtering steps.
We employed the HOMER HiC software pipeline (http://biowhat.ucsd.edu/homer/)(Heinz et al., 2011) to generate interaction matrices, to perform identification of A and B compartments and to determine significant interactions. Briefly, paired-end (i.e. di-tags) reads outputted from HiCUP were checked for GC content (“-checkGC”) and reads originating from regions with unusually high tag density “5 fold higher” (‘‘-removeSpikes 10000 5’’) were removed. Next, only read pairs where both ends mapped near restriction sites for HindIII “AAGCTT” (e.g. maximum distance from restriction site is 1.5x of the insert fragment size) were retained specifying (‘‘-both’’) option. Further, normalized interaction matrices for each biological replicate were generated using 500kb bin size resolution. Normalization is based on the generation of a background model using the entire genome which calculates the number of expected reads between any two loci accounting both for linear distance and sequencing depth. Generally, the normalized interaction matrices output the ratio of observed to expected interactions. When the normalized matrices were generated the “-corr” function was specified which replaces the number of interactions with a Pearson Correlation Coefficient representing how each region interacts with  any other region.
Genome_build: mm10
Supplementary_files_format_and_content: Intreaction matrices generated at 500kb resolution using the information from two Biological replicates for each condition

source_name: myotubes differentiated in vitro from myoblasts cultured from the thigh muscle of C3H mice after a crush injury

growth_protocol: Myoblasts from the skeletal muscle-derived C2C12 cell line were obtained from American Type Culture Collection (ATCC® CRL1772™). C2C12 myoblasts were propagated at 37 ˚C, 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) (high glucose, +pyruvate, +phenol red, +L-Glutamine) (Gibco® 11995-073) supplemented with 10% fetal bovine serum (FBS; Gibco®) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco®). All experiments were performed using cells at passage 3. Myoblasts were plated at a low cellular density of 5 × 103/cm2 (to achieve sub-confluent myoblast cultures) or a high cellular density of 2.5 × 104/cm2 (to allow cell crowding and myogenic differentiation to occur). Cells from the same source culture were plated in parallel at the appropriate cell density into T-75 tissue culture flasks (Greiner bio-one, 658175) (75 cm2 growth surface, 20 mL media volume, (for HiC extraction) and 12W Multiwell Plates (Greiner bio-one, 665180)  (3.9 cm2/well growth surface, 1 mL/well media volume) (for RNA extraction and cellular fixation). Six replicate T75 culture flasks were plated for each experimental condition in order to achieve estimated cell numbers required for analysis. Following 72 hours proliferation, cells which were plated at the low density were harvested as sub-confluent myoblast cultures (Myoblasts). At the same time (D0), high density cultures were switched to differentiation media (DMEM (Gibco® 11995-073) supplemented with 2% horse serum (HS, Gibco®  16050-122)) and antibiotics (penicillin 100 U/ml, streptomycin 100 μg/ml) (Gibco® 15140-122)) to induce myotube formation. Following 3 days of differentiation myotube cultures were either harvested (Myotubes(Day3)), or switched to differentiation media supplemented with 10 µg/mL Cytosine β-D-arabinofuranoside (AraC, Sigma, C1768) in order to kill/eliminate remaining myoblasts and obtain more purified myotube cultures. On day 5, AraC media was replenished and AraC purified myotube cultures were harvested on day 7 (Myotubes(Day7+AraC)). The experimental procedure was repeated on an independent occasion using a second stock C2C12 source vial.

extract_protocol: HiC libraries were prepared as described previously (Lieberman-Aiden et al. 2009), with minor modifications. Cells were cross-linked with formaldehyde and lysed in lysis buffer before the chromatin was digested with HindIII. Following digestion the restriction sites were filled in and marked by incorporating biotinylated dCTP. The ligation of the filled in blunt DNA ends was performed in dilute condition to promote ligation between DNA fragments residing within the same cross-links. Cross-links were then reversed and DNA purified. After the removal of the biotin from unligated ends using the action of T4 DNA polymerase, the DNA libraries were sheared by sonication and the DNA ends were repaired using the combined action of T4 DNA polymerase, T4 polynucleotide kinase and Klenow DNA polymerase. An 'A' was added to the 3' ends of the end repaired blunt DNA fragments using Klenow (exo-) to prevent the ends from ligating to one another during adapter ligation. Further the DNA was electrophoresed on 1.5% agarose gel and DNA between 300 and 650 base pairs was excised and purified. Paired-end adapters for sequencing (Truseq nano DNA LT kit ) were attached to the HiC libraries. For the amplification of the HiC libraries, 2 PCR reactions for all replicates and samples were used with the exception of Myoblasts Replicate 2 and Myotubes(Day7+AraC) Replicate 1 where 4 PCR reactions were used with total volume of 50 μl (22.5 μl template [2.5 μl Streptavidin beads and 20 μl 1XNEBbuffer] + 22.5 μl Enhanced PCR mix + 5 μl Primer cocktail), were performed to amplify sufficient PCR products (~ 1 μg) for sequencing. The temperature profile was 95°C (3 min) followed by 15 cycles ( 98°C, 20 s; 60°C, 15 s; 72°C, 30 s) and a final extension (72°C, 5 min). The PCR products from each HiC library were purified by mixing with 1x volume Ampure beads (Truseq nano DNA LT kit; Illumina).

value: treated with AraC between Day 3 and Day 7 in DM

tag: protocol

value: "diluted" HiC


title: xzl.gga.WL.testis.wt.adult.rep1+rept2+rept3.RPF

description: RPF

data_processing:
Library strategy: Ribo-seq
Analyses were performed using piPipes v1.4 (Han et al., 2014). All data from the ribosome profiling and RNA-seq were analyzed using the latest chicken genome release galGal5 (GCA_000002315.3).
The pair-end total RNA-seq reads were aligned to the genome using TopHat 2.0.12 (Trapnell et al., 2009). Reads were mapped using the ‘-g 100’ flag. The direct transcriptome mapping results were quantified using eXpress (Roberts and Pachter, 2013).
Ribosome protected fragments (RPFs) 26–32 nt long were selected for further analysis. The RPF abundance per TE or per piRNA cluster was quantified by eXpress, and reported as reads per kilobase pair per million reads mapped to the genome (rpkm) using a pseudo count of 0.01.
Genome_build: gg5
Supplementary_files_format_and_content: summary table


title: Myotubes Day3, Biological Replicate 2

description: Myotubes_Day3_Interaction_Matrix_Corr_500kb.txt

value: not treated with AraC