title: CFU-G/M U2AF1 S34F 2

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

description:
mye-s34f-2
processed data file:
A3SS JunctionCountOnly1:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt

data_processing:
Sequencing: Samples were sequenced on Illumina HiSeq 2500
Base calling: Basecalls was performed using Illumina bclToFastq v1.8.4
Alignment: Stampy v1.0.23 after pre-mapping with bwa v0.7.0
genome build: Genome was hs37d5 from the 1000 genomes project
pre-mRNA splicing analysis: Aberrant splicing events were analysed by rMATS

source_name: granulomonocytic progenitor cells_U2AF1 S34F

growth_protocol: Colony-forming cell assays were performed using MethoCult H4434 and H4534 methylcellulose (StemCell Technologies) according to the manufacturer's instructions.

extract_protocol:
Total RNA was extracted using Trizol reagent, DNase treated (Invitrogen) and purified using XP beads (Beckman Coulter).
Purified DNAse treated total RNA (100ng) was processed using NEBNext DNA Library Prep Kit (NEB) as per manufacturer’s protocol for Illumina with two alterations: custom indexes were designed in house to barcode sequences for multiplexing and an additional purification step was performed using XP beads (Beckman Coulter) rather than size selection.

tag: cell lineage

value: granulomonocytic

tag: transduction

value: U2AF1 S34F

tag: colony type

value: CFU-G


title: miR873Mut_Con_2

status: Public on Apr 25 2017

type: SRA

city: Brisbane

first: Sarah

middle: Marguerite

last: Williams

state: QLD

address: QBI Building 79, University of Queensland, St Lucia

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description: Mutant miR-873-5p transfection rep 2 control transcriptome

library_source: transcriptomic

data_processing:
Illumina adaptor sequences were removed and reads quality trimmed with Trimmomatic.
Sequences were aligned to the human GRCh38 Ensembl release 83 transcriptome with TopHat2
Gene-level counts were generated from paired reads in HTseq-count (Parameters: -s reverse -m union).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of sequence fragments aligned to each gene.

molecule: total RNA

organism: Homo sapiens

source_name: SH-SY5Y cell line

extract_protocol:
RNA was purified with RNAeasy columns (QiAGEN).
Sequencing libraries prepared from 100 ng input RNA with Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Control 'Con' samples are whole transcriptome. Pulldown 'PD' samples are matched sample subjected to tagged-microRNA mRNA capture.

tag: microrna

tag: replicate

tag: treatment

value: Con - control transcriptome


title: CFU-G/M U2AF1 S34F 3

description:
mye-s34f-3
processed data file:
A3SS JunctionCountOnly1:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: miR873Mut_Con_1

description: Mutant miR-873-5p transfection rep 1 control transcriptome


title: miR873Mut_Con_4

description: Mutant miR-873-5p transfection rep 4 control transcriptome


title: CFU-G/M U2AF1 wild-type 2

description:
mye-wt-2
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt

source_name: granulomonocytic progenitor cells_U2AF1 wild-type

value: U2AF1 wild-type


title: miR873WT_Con_4

description: Wild-type miR-873-5p transfection rep 4 control transcriptome


title: CFU-G/M U2AF1 S34F 1

description:
mye-s34f-1
processed data file:
A3SS JunctionCountOnly1:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt

value: CFU-M


title: miR873WT_Con_2

description: Wild-type miR-873-5p transfection rep 2 control transcriptome


title: miR873WT_Con_1

description: Wild-type miR-873-5p transfection rep 1 control transcriptome


title: miR873Mut_PD_4

description: Mutant miR-873-5p transfection rep 4 pulldown

value: PD - pulldown


title: CFU-G/M U2AF1 wild-type 1

description:
mye-wt-1
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: CFU-G/M empty vector 2

description:
mye-empty-2
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt

source_name: granulomonocytic progenitor cells_empty vector

value: empty vector


title: BJ Young MYOD WT DM Rep1

city: Cambridge

first: Alessandra

last: Dall'Agnese

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

data_processing:
BJ: Reads were mapped using TopHat2.1.1 with option -p 8 -g 1 -segment-length 12 -library-type fr-unstranded to homo sapiens hg19 genome, HTSeq-0.6.1p1 with option "stranded=no" was used to assign mapped reads ro H. sapiens GRCh37.75 genes. Differential gene expression analysis was performed using DESEq2.
Genome_build: hg19
Supplementary_files_format_and_content: Differential gene expression

source_name: BJ

growth_protocol: BJ cells were cultured in DMEM supplemented with 10% FBS, nonessential amino acids

extract_protocol:
For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction.
BJ: Illumina kits.

treatment_protocol: BJ cells were infected with Adeno Track or Adenovirus containing MYOD WT or MYOD Y30F, cells were induced to differentiate in DMEM supplemented with 2% horse serum (DM)

tag: cell type

value: Skin fibroblasts

tag: ectopic gene expression

value: MYOD WT

tag: passage from isolation

value: passage Low 12


title: miR873Mut_PD_1

description: Mutant miR-873-5p transfection rep 1 pulldown


title: miR873Mut_PD_2

description: Mutant miR-873-5p transfection rep 2 pulldown


title: miR873WT_PD_2

description: Wild-type miR-873-5p transfection rep 2 pulldown


title: miR873Mut_PD_3

description: Mutant miR-873-5p transfection rep 3 pulldown


title: miR873WT_PD_4

description: Wild-type miR-873-5p transfection rep 4 pulldown


title: miR873WT_Con_3

description: Wild-type miR-873-5p transfection rep 3 control transcriptome


title: miR873WT_PD_3

description: Wild-type miR-873-5p transfection rep 3 pulldown


title: BFU-E U2AF1 S34F 1

description:
ery-s34f-1
processed data file:
A3SS JunctionCountOnly1:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt

source_name: erythroid progenitor cells_U2AF1 S34F

value: erythroid

value: BFU-E


title: BFU-E U2AF1 S34F 2

description:
ery-s34f-2
processed data file:
A3SS JunctionCountOnly1:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: BFU-E U2AF1 S34F 3

description:
ery-s34f-3
processed data file:
A3SS JunctionCountOnly1:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: CFU-G/M empty vector 1

description:
mye-empty-1
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: miR873WT_PD_1

description: Wild-type miR-873-5p transfection rep 1 pulldown


title: BFU-E U2AF1 wild-type 3

description:
ery-wt-3
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt

source_name: erythroid progenitor cells_U2AF1 wild-type


title: BFU-E empty vector 3

description:
ery-empty-3
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt

source_name: erythroid progenitor cells_empty vector


title: SW480_72h_R_crizo_2uM_3

city: Vienna

first: Giulio

last: Superti-Furga

state: Wien

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM

data_processing:
Data acquisition performed with HiSeq Control Software (HCS)  2.0.12.0
Basecalling performed with Illumina Real-Time Analysis (RTA) software 1.17.21.3
BCL to BAM file conversion and demultiplexing was performed with Illumina2bam tools 1.17 (https://github.com/wtsi-npg/illumina2bam)
Transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.0.10, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e73, September 2013) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.1.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was used to assemble transcripts from spliced read alignments, using the Ensembl e73 transcriptome as the reference as well as de novo assembly of transcript models. Differential expression was assessed with Cuffdiff v2.1.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) and biomaRt (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) were used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCh37 (UCSC hg19)
Supplementary_files_format_and_content: Output is comparison of gene expression from DMSO treatment to crizotinib treatment

molecule: polyA RNA

growth_protocol: SW480 cells were seeded in complete medium (DMEM plus 10% FCS containing penicillin and streptomycin) in 6-well plates for 24 h

extract_protocol:
medium was aspirated and cells washed with PBS. Total RNA was isolated using the RNeasy kit (Qiagen) and RNA amount was measured using Qubit 2.0 Fluorometric Quantitation system (Life Technologies). RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad).
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 2000 using 50 bp single-read chemistry.

treatment_protocol: (R)-crizotinib was added to a final concentration of 2 µM. incubation at 37 °C for 72 h

tag: cell line

tag: agent

value: (R)-crizotinib


title: BFU-E empty vector 2

description:
ery-empty-2
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: BFU-E empty vector 1

description:
ery-empty-1
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: SW480_72h_R_crizo_2uM_1


title: SW480_72h_DMSO_3

value: control


title: CFU-G/M U2AF1 wild-type 3

description:
mye-wt-3
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: CFU-G/M empty vector 3

description:
mye-empty-3
processed data file:
A3SS JunctionCountOnly1:
mye empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
mye S34F vs empty A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
mye empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
mye S34F vs empty A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
mye empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
mye empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
mye S34F vs empty SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
mye empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
mye S34F vs empty MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
mye empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
mye empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
mye S34F vs empty RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
mye empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
mye S34F vs empty RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: SW480_72h_DMSO_2


title: SW480_72h_DMSO_1


title: BFU-E U2AF1 wild-type 2

description:
ery-wt-2
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: BFU-E U2AF1 wild-type 1

description:
ery-wt-1
processed data file:
A3SS JunctionCountOnly1:
ery empty vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS JunctionCountOnly 2:
ery S34F vs WT A3SS.MATS.JunctionCountOnly.txt
A3SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A3SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS JunctionCountOnly1:
ery empty vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS JunctionCountOnly 2:
ery S34F vs WT A5SS.MATS.JunctionCountOnly.txt
A5SS ReadsOnTargetAndJunctionCounts1:
ery empty vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
SE JunctionCountOnly1:
ery empty vs WT SE.MATS.JunctionCountOnly.txt
SE JunctionCountOnly 2:
ery S34F vs WT SE.MATS.JunctionCountOnly.txt
SE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
SE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT SE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE JunctionCountOnly1:
ery empty vs WT MXE.MATS.JunctionCountOnly.txt
MXE JunctionCountOnly 2:
ery S34F vs WT MXE.MATS.JunctionCountOnly.txt
MXE ReadsOnTargetAndJunctionCounts1:
ery empty vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI JunctionCountOnly1:
ery empty vs WT RI.MATS.JunctionCountOnly.txt
RI JunctionCountOnly 2:
ery S34F vs WT RI.MATS.JunctionCountOnly.txt
RI ReadsOnTargetAndJunctionCounts1:
ery empty vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt
RI ReadsOnTargetAndJunctionCounts 2:
ery S34F vs WT RI.MATS.ReadsOnTargetAndJunctionCounts.txt


title: SW480_72h_R_crizo_2uM_2


title: KO-3 (7 weeks)

city: La Jolla

first: Min

last: Zong

state: California

address: 9500 Giman Dr.

institute: UCSD

description: β-catenin KO in hepatocytes

data_processing:
Sequenced reads were de-multiplexed and trimmed for adaptor sequence
Sequenced reads were mapped to GRCm38 genome using STAR with parameters --runThreadN 16 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Mapped SAM files were then compressed and sorted using samtools view, sort and index
Find significant changes in gene expression using Cuffdiff
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample as well as fold changes and q value between two groups.

organism: Mus musculus

source_name: Liver

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

treatment_protocol: Total plasmids encoding the Sleeping Beauty transposase and transposons with MET/CAT (10 µg pT3-EF1α-c-MET (human)+10 µg pT3-EF1α -ΔN90-β-catenin (human)+0.8 µg HSB2), were injected hydrodynamically into 2 month-old  mice, Mice were sacrificed at 2-month-old without injection (0 day), 3 days or 7 weeks after MET/CAT injection.

tag: strain

tag: tissue

value: Liver

tag: genotype

value: beta-catenin KO in hepatocytes


title: KO Gonadal CL [KO G 6]

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

description: KO G 6

data_processing:
RNA-sequencing was performed by the UT Southwestern McDermott Sequencing Core on an Illumina HiSeq 2500 v3 Sequencing System.  Data was processed by the UT Southwestern McDermott Center Bioinformatics Core.
Stranded, single-end 50-base-pair reads were generated. Reads were aligned using TopHat2 and Bowtie2.
Raw counts were generated using Cufflinks and featureCounts. Cuffdiff and edgeR were used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data is supplied as a matrix table of normalized abudance measurements

source_name: KO Gonadal CL

growth_protocol: Mice were maintained on a 12 hr light/dark cycle in a temperature-controlled environment (room temperature, 22°C; thermoneutrality, 30°C). Mice were given free access to food and water, and maintained on a standard chow diet.

extract_protocol:
RNA was extracted with Trizol and purified through ethanol precipitation.
The library was constructed by the UT Southwestern McDermott Sequencing Core using the Illumina TruSeq Stranded mRNA Sample Preparation protocol.

treatment_protocol: Control and Vis-KO mice were housed at room temperature (22°C) until 6 weeks of age then transferred to thermoneutral housing conditions (30°C) for 2 weeks.  After 2 weeks at thermoneutrality, mice were treated with PBS (vehicle) or CL316,243 (1 mg/kg, intraperitoneal) daily for 3 days. On the 4th day, tissues were harvested for analysis.

tag: strain background

tag: genotype/variation

tag: treated with

value: Gonadal adipose tissue


title: KO-2 (7 weeks)

description: β-catenin KO in hepatocytes


title: PC-3M-luc cells RNAi Control, biological replicate 1

city: Freiburg

first: Anett

last: Ketscher

state: BW

address: Breisacher Str. 66

department: Urology

country: Germany

institute: University Freiburg

description: RNAi Control-Rpl1

data_processing:
We aligned these reads to the hg19 build of the human genome using TopHat version 2
The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR and DESeq version 1.8.3.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the overall read count for a specific transcript (indicated by the NM accession number)

source_name: PC-3M-luc_RNAi control

growth_protocol: Human PC-3M-luc prostate cancer cells were maintained in Eagle's minimal essential medium (EMEM) supplemented with 10 % FBS and glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

treatment_protocol: Knockdown was performed using Dharmafect 2 according to the manufaturer's instructions. Cells were harvested 72 h post transfection

value: human prostate carcinoma cell line

value: RNAi Control

tag: passages


title: PC-3M-luc cells RNAi Control, biological replicate 2

description: RNAi Control-Rpl2


title: WT-2 (7 weeks)

description: WT

value: WT


title: KO Gonadal CL [KO G 5]

description: KO G 5

value: CL316,243 (1 mg/kg, intraperitoneal) daily for 3 days


title: PC-3M-luc cells RNAi LSD1, biological replicate 2

description: RNAi LSD1 Rpl2

source_name: PC-3M-luc_RNAi LSD1

value: RNAi LSD1


title: 26EA3

first: Irina

last: Mohorianu

department: Medical Sciences Division

institute: University of Oxford

description: Sample 29

data_processing:
we kept for further analysis, only the reads which did not contain Ns (99% of the reads)
the reads were mapped to the D. melanogaster genome (v5.46), using PatMaN (Prueffer et al 2008), full length, no mis-matches allowed.
for comparison purposes, the reads in every sample were resampled to a fixed total (the method is called bootstrapping normalization and is presented in the accompanying manuscript)
the expression levels were obtained as indicated in Mortazavi et al 2008
the differential expression was first determined between tissues (HT vs A) and next between the treatments (with vs without rivals)
Genome_build: D. melanogaster v 5.46, www.flybase.org
Supplementary_files_format_and_content: csv files which contain the gene expression levels.

organism: Drosophila melanogaster

source_name: 26h_without rivals_abdomen

growth_protocol: Dahomey wild type males were raised at a density of 100 larvae per vial on SY medium (100g brewer’s yeast powder, 100g sugar, 20g agar, 30ml Nipagin (10% solution) and 3ml propionic acid per litre of medium). Upon eclosion, males were stored 10 per vial and then at 1d old placed in individual vials for 5days.

extract_protocol:
Focal males were then snap frozen in liquid nitrogen. Prior to RNA extraction, males were separated into abdomen and Head+Thorax body parts. RNA was extracted (MiRVana kit) from pools of n = 40 male body parts and sent for RNA sequencing (Illumina HiSeq, 50 cycles, non directional, 4 samples per lane). Differential expression of transcripts was validated by using qRT-PCR onall three replicates of the same biological samples.
Baseclear provider, mRNA-Seq Library preparation using standard TruSeq library protocol. RNA sequencing = 50 cycles, single-read 4 samples per lane.

treatment_protocol: Rival wild type males were then introduced to the focal males for 2, 26 or 50h.

value: Dahomey

value: wild type

tag: Sex

value: male

tag: sample group

value: without rivals

tag: time point

value: abdomen tissue


title: 02RA3

description: Sample 27

source_name: 2h_with rivals_abdomen

value: with rivals


title: 26EH3

description: Sample 30

source_name: 26h_without rivals_head+thorax

value: head+thorax tissue


title: 26RA3

description: Sample 31

source_name: 26h_with rivals_abdomen


title: 02RH3

description: Sample 28

source_name: 2h_with rivals_head+thorax


title: LSD1, ChIPseq, PC-3M-luc cells, biological replicate 1

library_source: genomic

data_processing:
peak finding algorithm MACS 1.41
All peaks with FDR greater than 1 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are wiggle (wig) and bed files. The wig files include the read data mapped to the hg19 genome. The bed files contain the peaks that were obtained when normalizing the reads of the LSD1 ChIP-Seq to the Input.

molecule: genomic DNA

source_name: PC-3M-luc cells

extract_protocol:
PMID: 18066052
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2
PMID:19261174

value: Control

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: KO Gonadal CL [KO G 4]

description: KO G 4


title: 50RH3

description: Sample 36

source_name: 50h_with rivals_head+thorax


title: 26RH3

description: Sample 32

source_name: 26h_with rivals_head+thorax


title: KO-1 (7 weeks)

description: β-catenin KO in hepatocytes

value: Liver


title: Input, PC-3M-luc cells, biological replicate 1

tag: cell type


title: WT-3 (7 weeks)

description: WT


title: 02EH3

description: Sample 26

source_name: 2h_without rivals_head+thorax


title: 50RA3

description: Sample 35

source_name: 50h_with rivals_abdomen


title: WT-1 (7 weeks)

description: WT


title: 50EH3

description: Sample 34

source_name: 50h_without rivals_head+thorax


title: PC-3M-luc cells RNAi LSD1, biological replicate 1

description: RNAi LSD1 Rpl1


title: 50EA3

description: Sample 33

source_name: 50h_without rivals_abdomen


title: KO-3 (3 days)

description: β-catenin KO in hepatocytes

value: beta-catenin KO in hepatocytes


title: KO-2 (3 days)

description: β-catenin KO in hepatocytes


title: KO Gonadal Vehicle [KO G 3]

description: KO G 3

source_name: KO Gonadal Vehicle

value: PBS (vehicle) daily for 3 days

value: Gonadal adipose tissue


title: KO-1 (3 days)

description: β-catenin KO in hepatocytes

source_name: Liver


title: KO Gonadal Vehicle [KO G 2]

description: KO G 2


title: WT-3 (3 days)

description: WT


title: KO Gonadal Vehicle [KO G 1]

description: KO G 1


title: WT-2 (3 days)

description: WT


title: KO-3 (0 day)

description: β-catenin KO in hepatocytes


title: WT Gonadal CL [WT G 5]

description: WT G 5

source_name: WT Gonadal CL

value: Control; Cre negative


title: WT-1 (3 days)

description: WT

value: WT


title: WT Gonadal CL [WT G 4]

description: WT G 4

value: CL316,243 (1 mg/kg, intraperitoneal) daily for 3 days


title: WT-3 (0 day)

description: WT


title: WT-2 (0 day)

description: WT


title: 50EH2

description: Sample 22


title: WT Gonadal Vehicle [WT G 3]

description: WT G 3

source_name: WT Gonadal Vehicle


title: 26RA2

description: Sample 19


title: 02EA3

description: Sample 25

source_name: 2h_without rivals_abdomen


title: WT-1 (0 day)

description: WT


title: 26EH2

description: Sample 18


title: 02RH2

description: Sample 16


title: KO-1 (0 day)

description: β-catenin KO in hepatocytes


title: WT Gonadal Vehicle [WT G 2]

description: WT G 2


title: 26RH2

description: Sample 20


title: 50RH2

description: Sample 24


title: WT Inguinal CL [WT I 6]

description: WT I 6

source_name: WT Inguinal CL

value: Inguinal adipose tissue


title: 26EA2

description: Sample 17

source_name: 26h_without rivals_abdomen

value: Dahomey


title: 02RA2

description: Sample 15

source_name: 2h_with rivals_abdomen

value: wild type


title: WT Gonadal Vehicle [WT G 1]

description: WT G 1


title: WT Inguinal CL [WT I 5]

description: WT I 5


title: 50RA2

description: Sample 23

value: male


title: KO-2 (0 day)

description: β-catenin KO in hepatocytes


title: WT Gonadal CL [WT G 6]

description: WT G 6


title: 50EA2

description: Sample 21

value: without rivals


title: YO1849_YSEQ167

city: Seattle

first: Aimee

last: Dudley

state: Washington

address: 720 Broadway

institute: PNDRI

data_processing:
Read-pair alignment was carried out using Bowtie2 (version 2.1.0) with the parameters [-N 1 -I 50 -X 450 -p 6 --reorder -x -S] and allowing 1 mismatch per read
For each strain, read alignments were converted to gene counts using featureCounts (version 1.4.0) in the Subread package, with the parameters [-a -o -t gene –g ID –s 2 -T 1 -p -P -d 50 -D 450]
Genome_build: S288c (R64-1-1)  with the FASTA and GFF files extended to include non-coding RNAs (ncRNAs) and genes present in F45
Supplementary_files_format_and_content: counts per gene in tab delimited format

organism: Saccharomyces cerevisiae

source_name: Four day old colonies of strain F45 overexpressing HEK2

growth_protocol: Colonies were grown on YPD (2 % glucose plus G418 to maintain plasmid selection) plates at 30° C for 4 days, after which whole colonies were harvested by scraping off the surface of the agar plate.

extract_protocol:
Hot acid phenol extraction
5 µg of total RNA for each sample was  processed using the Tru-Seq stranded mRNA kit (Illumina) following manufacturer instructions

value: overexpressing HEK2


title: WT Inguinal Vehicle [WT I 3]

description: WT I 3

source_name: WT Inguinal Vehicle


title: WT Inguinal CL [WT I 4]

description: WT I 4


title: 02EH2

description: Sample 14


title: 02EA2

description: Sample 13

value: abdomen tissue


title: 50RH1

description: Sample 12

value: with rivals

value: head+thorax tissue


title: WT Inguinal Vehicle [WT I 1]

description: WT I 1


title: YO1849_YSEQ164


title: 50RA1

description: Sample 11


title: WT Inguinal Vehicle [WT I 2]

description: WT I 2


title: YO1849_YSEQ166


title: WT BAT CL [WT B 6]

description: WT B 6

source_name: WT BAT CL

value: Brown adipose tissue


title: YO1845_YSEQ167

source_name: Four day old colonies of strain F45 overexpressing SFL1

value: overexpressing SFL1


title: YO1845_YSEQ166


title: 50EA1

description: Sample 9


title: 50EH1

description: Sample 10


title: WT BAT CL [WT B 5]

description: WT B 5


title: 26RH1

description: Sample 8

source_name: 26h_with rivals_head+thorax


title: YO1845_YSEQ165


title: YO1845_YSEQ164


title: YO1849_YSEQ165


title: 26RA1

description: Sample 7

source_name: 26h_with rivals_abdomen


title: WT BAT CL [WT B 4]

description: WT B 4


title: WT BAT Vehicle [WT B 3]

description: WT B 3

source_name: WT BAT Vehicle


title: 26EH1

description: Sample 6

source_name: 26h_without rivals_head+thorax


title: YO1835_YSEQ167

source_name: Four day old colonies of strain F45 overexpressing ROF1

value: overexpressing ROF1


title: WT BAT Vehicle [WT B 2]

description: WT B 2

value: PBS (vehicle) daily for 3 days


title: YO1835_YSEQ166


title: 26EA1

description: Sample 5


title: WT BAT Vehicle [WT B 1]

description: WT B 1


title: YO1835_YSEQ165


title: 02RH1

description: Sample 4

source_name: 2h_with rivals_head+thorax


title: YO1835_YSEQ164


title: 02EH1

description: Sample 2

source_name: 2h_without rivals_head+thorax


title: 02RA1

description: Sample 3


title: 02EA1

description: Sample 1


title: YO1832_YSEQ165

source_name: Four day old colonies of strain F45 overexpressing TOS8

value: overexpressing TOS8


title: YO1832_YSEQ166


title: FLAG ChIP-seq negative control

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Genome_build: mm10
Supplementary_files_format_and_content: 5hmc peaks in bed file, ChIP-seq peaks in bed file

source_name: MEL-FLAG Control Cells

extract_protocol:
DNA was extracted by phenol/choloroform method.
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method (Song et al, Nature Biotechnology, 2011). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25-50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol [PMID: 21151123].
Enriched DNA from MeDIP were subjected to library construction using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according the manufacturer’s protocol.

value: MEL cells


title: FAIRE-seq in WT

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
The reads were mapped onto the TAIR10 genome build using Bowtie
To identify regions that were significantly enriched, we used MACS and SICER with parameters of W:200 (Window length), G:600 (Gap size) for  for H3K27me3 and FDR <1E-2. Enriched regions were detected against the islands of background control with the same parameter.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0

growth_protocol: Plants were grown in chambers at 20°C on sterile half-strength MS medium and 0.8% agar under long-days (16h of light at 20°C, 8h of darkness at 18°C).

extract_protocol:
The genomic DNA extraction protocol was not provided.
ChIP-seq assays were performed on 14-day-old  seedlings using anti-GFP (Clontech 632592), anti-H3K27me3 (Millipore), anti-H3K9Ac (Millipore), anti-H3K9me2 (Millipore). ATAC-seq, Mnase-seq and FAIRE-seq were performed on wildtype seedlings.

treatment_protocol: Seeds were surface-sterilized by treatment with bayrochlore for 20 min, washed, and imbibed in sterile-water for 2–4 days at 4 °C to obtain homogeneous germination.

tag: ecotype

tag: developmental stage

value: seedlings

tag: age

value: 14 days


title: YO1832_YSEQ164

tag: strain


title: ATACseq in WT

data_processing:
Library strategy: ATAC-seq
The reads were mapped onto the TAIR10 genome build using Bowtie
To identify regions that were significantly enriched, we used MACS and SICER with parameters of W:200 (Window length), G:600 (Gap size) for  for H3K27me3 and FDR <1E-2. Enriched regions were detected against the islands of background control with the same parameter.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS


title: YO1829_YSEQ167

source_name: Four day old colonies of strain F45 overexpressing SAN1

value: overexpressing SAN1


title: H3K9me2 in WT

value: anti-H3K9me2 (Millipore 07-449)


title: H3K27me3 in WT

value: anti-H3K27me3 (Millipore 07-449)


title: Mnase in WT


title: H3K9Ac in WT

value: anti-H3K9Ac (Millipore 07-449)


title: H3K9Ac ChIPseq Input

value: none (Input for Histone ChIP-seq)


title: YO1829_YSEQ166


title: Tet2-FLAG_ChIP-seq

description:
Tet2 ChIP-seq
Illumina Genome Analyzer

source_name: MEL-FLAG-Tet2 cells


title: 5hmC-WT-1 #2

description:
5hmC Profiling (hMe-Seal)
Illumina Genome Analyzer

source_name: LK Cells

tag: seq

value: LK Cells


title: -N1Q

city: Hermosillo

first: Miguel

middle: Angel

last: Hernandez

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas No. 46

department: Coordinación de Tecnología de Alimentos de Origen Vegetal

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo

description: Sequencing by Illumina in paired-end mode 2X100

data_processing:
RNA-Seq reads were quality checked using FastQC v0.11.2
The reads were aligned to U. maydis genome using BWA software with the default parameters
The quantification of reads per gene was performed with HTSeq using default parameters, only reads that mapped correctly in paired-end and with unique hit were considered for further analysis.
Then the reads per gene were normalized to counts per million (cpm). The genes with minimum 2 cpm in at least one sample were considered as transcriptionally active and used for subsequent analyses.
Differential expression was estimated with the software package edgeR (R version: 3.0.1, edgeR version: 3.2.4); using statistical methods based on pair wise comparisons. The common dispersion used was 0.1. Genes that exhibited an FDR ≤0.05 and a log2 Fold Change >1 (log2FC) were considered to have significant differential expression.
Genome_build: NCBI GenBank the project accession number AACP00000000 (Kämper et al., 2006. Nature)
Supplementary_files_format_and_content: tab-delimited text Ot6735 file includes the raw counts of reads for each predicted gene in the U. maydis genome
Supplementary_files_format_and_content: tab-delimited text Ot6736 file includes the raw counts of reads for each predicted gene in the U. maydis genome

organism: Mycosarcoma maydis

source_name: Cells

growth_protocol: U. maydis cells were maintained in 50% glycerol at -70 ºC, recovered in complete medium, and subsequently grown in liquid minimum medium pH7 at 28 ºC 24h.

extract_protocol:
Cells were recovered from the above describe media by centrifugation, and total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions, and purified with QIAGEN columns (Cat. 28104). The isolated RNA was checked for yield and quality by measuring the absorbance ratio at A260/280 and A260/230 using a Nanodrop (Thermo Fisher Scientific, Wilmington, DE, USA), and its integrity was evaluated by formaldehyde-agarose gel electrophoresis.
The RNA-Seq libraries were sequenced by Illumina-HiSeq system (Illumina Inc. San Diego, CA, USA) with the paired-end mode and read length of 100nt.

treatment_protocol: U. maydis cells were inoculated to an initial concentration of 106 cells/ml in 500 ml of MM pH 7 with (NH4)NO3 as nitrogen source, and in the same basal medium without (NH4)NO3 and incubated under shaking conditions (250 rpm) at 28 ºC for 24 h.

value: yeast cells

tag: growth condition

value: without (NH4)NO3


title: BAF60 ChIPseq

value: BAF60:GFP anti-GFP  (Clontech 632592)


title: 5hmC-Tet2KO-2 #2


title: YO1832_YSEQ167


title: +N1Q

value: with 0.3% (NH4)NO3


title: YO1829_YSEQ164


title: 5hmC-Tet2KO-1 #2


title: BG2 Young 2

status: Public on Apr 24 2017

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Candida_glabrata reference build Ensemble_R31 (ASM254v2.31) with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.  All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR  and TMM normalized to adjust for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Candida_glabrata reference build Ensemble_R31 (ASM254v2.31)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each or all samples.

organism: Nakaseomyces glabratus

source_name: BG2_young_whole cell

growth_protocol: Comparable number of young or old yeast cells (background strain BG2) were grown in yeast extract peptone with 2% for 16 hours at 37degCelsius with agitation at 150rpm

extract_protocol:
Total RNA was extracted using a QIAGEN RNeasy kit (mechanical disruption) per manufacturer's instructions
The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”).  A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample.  In pooling of multiple libraries for running on 2 lanes of 50bp single reads, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 24 RNA libraries.  Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.

value: 0-2 generation-old cell grown in 2% YPD

value: CGTCGCT


title: YO1829_YSEQ165


title: H3.3KD_H3K4me3_#1

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Reads were mapped to the TAIR10 genome by allowing up to 2 mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed in to one read.
Genome_build: TAIR10
Supplementary_files_format_and_content: Column 1 is chromosome. Column 2 is the genomic strand(+/-) the read mapped to. Column 3 is the genomic coordinate the read mapped to.

source_name: 10 day seedlings

growth_protocol: Sterilized seeds were grown on 1 x MS medium with glucose at long day conditions in a Percival incubator for 10 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: Columbia

value: H3K4me3 (Abcam, ab8580)


title: H3.3KD_H3K36me3_#1

value: H3K36me3 (Abcam, ab9050)


title: BAF60 ChIPseq Input

value: seedlings

value: none (Input for BAF60 ChIP-seq)


title: H3.3KD_H3K36me3_#2


title: H3.3KD_H1_#2

value: H1 (Agrisera, AS11 1801)


title: H3.3KD_H1_#1


title: H3.3KD_H2A.Z_#1

value: H2A.Z (inhouse synthesized)


title: 5hmC-WT-2 #2


title: H3.3KD_H3_#2

value: H3 (Abcam, ab1791)


title: WT_H3K36me3_#1


title: WT_H3K4me3_#1


title: WT_H1_#1


title: WT_H3K36me3_#2


title: H3.3KD_H3_#1


title: WT_H2A.Z_#1


title: WT_H3_#2


title: WT_H3_#1


title: D152V_Rescue_rep2

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
fastq reads were aligned to the human genome build hg19 using bwa mem v0.7.13 with default parameters
reads with mapq<20 and improperly aligned reads were filtered using SAMtools v0.1.19
peak calling was performed MACS2 v2.1.1 with '-m 5 50 --bw 150 --fix-bimodal --extsize 100   call summits -q 0.01' as parameters
resulting peaks were refined using the bdgcmp function of MACS2 v2.1.1 with the 'ppois' method
bedGraph files containing refined peaks were converted to bigWig format using the tool, bedGraphToBigWig v4 and visualized in the UCSC genome browser
Genome_build: hg19
Supplementary_files_format_and_content: tracks (peaks) in bigWig file format

source_name: human erythroleukemic cell line

growth_protocol: K-562 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin Streptamycin. For selection of stable cell lines, 200 µg/ml G418 was added to the cells

extract_protocol: Illumina Nextera Library prep kit (FC-121-1030)

treatment_protocol: No treatment

tag: tissue

value: human erythroleukemic cell line

tag: cell line

tag: stably expressing

tag: sirna


title: D152V_Rescue_rep1


title: MYB-WT_Rescue_rep3


title: Day 17 hPSC derived V2a Interneuron cultures

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

data_processing:
demultiplexing performed with "bcl2fastq" - 10xGenomics Cellranger v 1.2
alignment to hg19 - 10xGenomics Cellranger v 1.2
Annotated using Ensembl version 70
Filtered reads - 10xGenomics Cellranger v 1.2
Further filtering - Seurat (version 1.4 )
Clustering - Seurat (version)
Genome_build: hg19
Supplementary_files_format_and_content: matrix.mtx.gz contains the counts for a 62069x4492 matrix stored in the Matrix Market interchange format (matrix.tsv_dense.gz is a dense version of matrix.mtx.gz)

source_name: H7 human embryonic stem cells

growth_protocol: Novel differentiation protocol published in Butts et al., PNAS 2017

extract_protocol:
V1 Chromium Single Cell 3' Solution (10x Genomics)
V1 Chromium Single Cell 3' Solution (10x Genomics)

tag: culture

value: V2a Interneuron cultures


title: MYB-WT_Rescue_rep2


title: D152V_Rescue_rep3


title: MYB-WT_Rescue_rep1


title: MYB_KnockDown_rep3


title: MYB_KnockDown_rep1


title: siRNA_Control_rep3

value: siGENOME non-targeting siRNA


title: siRNA_Control_rep2


title: MYB_KnockDown_rep2


title: siRNA_Control_rep1


title: WT_H1_#2


title: DeltaCRISPR01+02_CasE-Flag _CoIP_ -PNK

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description: Sample 13

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl (vi READemption)
Coverage calculation and normalization (via READemption)
Genome_build: ASM21085v1 (GCF_000210855.1)
Supplementary_files_format_and_content: wiggle

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacterial cells

extract_protocol:
Frozen cell pellets from liquid cultures were lysed, and total RNA was extracted from the lysates using the hot-phenol method described previously (Blomberg et al., 1990). For enrichement of CRISPR transcripts, total RNA was freed of residual genomic DNA by DNase I treatment, and equal amounts of Salmonella RNA were incubated with Polynucleotidekinase (PNK) (Fermentas) or in buffer alone as previously described (Nickel et al., 2013).
Libraries for Illumina sequencing (HiSeq) of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis.

tag: treatment

value: no T4-PNK

tag: ncbi refseq

tag: genotype/variation

tag: rip antibody

value: Monoclonal ANTI-FLAG M2 (SIGMA,F1804-5MG,SLBG5673V)


title: wt_CasE-Flag_ control CoIP_+PNK

description: Sample 12

value: wt, CasE-Flag


title: DeltaCRISPR01+02_CasE-Flag_control CoIP_-PNK

description: Sample 15


title: DeltaCRISPR01+02_CasD-Flag_CoIP_+PNK

description: Sample 6

value: [delta]CRISPR01+02, CasD-Flag


title: wt_CasE-Flag_ CoIP_+PNK

description: Sample 10


title: wt_CasD-Flag_ control CoIP_-PNK

description: Sample 3

value: wt, CasD-Flag


title: DeltaCRISPR01+02_CasD-Flag_control CoIP_-PNK

description: Sample 7


title: DeltaCRISPR01+02_CasE-Flag_control CoIP_+PNK

description: Sample 16


title: wt_CasE-Flag _CoIP_-PNK

description: Sample 9


title: wt_CasD-Flag_ CoIP_ +PNK

description: Sample 2


title: wt_CasD-Flag _CoIP_ -PNK

description: Sample 1


title: TSPAN8_Low_Input

city: San Antonio

first: Brian

middle: P.

last: Hermann

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
For RRBS, Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline implemented in Python (using the mm10 genome annotation). Residual cytosines (Cs) in each read were first converted to thymines (Ts), with each such conversion noted for subsequent analysis. A reference sequence database was constructed from the 50-bp ends of each computationally predicted MspI-TaqI fragment in the 40–350 bp size range. All Cs in each fragment end were then converted to Ts; the converted reads were aligned to the converted reference by Bowtie. The number of mismatches in the induced alignment was then counted between the unconverted read and reference, ignoring cases in which a T in the unconverted read is matched to a C in the unconverted reference. For a given read, the best alignment was kept. If there was more than one best alignment, the read was discarded as non-unique. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. Fisher’s exact test or t-test was performed for each CpG site which has at least 5 reads covered. Also, promoter, gene body and CpG island annotations were added for each CpG. Genome positions were converted to mm9 for data presentation and final processing by liftover from mm10 to mm9.
For ChIP-seq,  reads from each sample were aligned to mouse genome (mm9) using ELAND (Illumina), sequence aligns (75 bases) were then 3’ extended in silico to a length of 200bp and assigned to 32bp bins along the genome, normalized to the same number of unique reads (~16M) and peaks were called using the SICER algorithm (Zang et al., Bioinformatics 25, 1952-1958, 2009) at a cutoff of FDR≤1E-10 and a Gap parameter of 600 bp (which merges peaks located within 600 bp of each other into a single “island”).
Genome_build: mm10 (RRBS) or mm9 (ChIP-seq)
Supplementary_files_format_and_content: RRBS results are shown in CpG_result_table.txt.gz, which is a matrix table listing all detected CpG dinucleotides and methylation status (%) in both samples and significance calls.
Supplementary_files_format_and_content: ChIP-seq results are found in TSPAN8_ChIP_Intervals.xlsx, which is an excel spreadsheet with three matrix tables (three tabs), each listing all of the intervals (peaks) found in each sample type. Each tab/table lists results from one histone modification (H3K4me3, H3K27Ac and H3K27me3, respectively).

source_name: P6 ID4-EGFP+ spermatogonia from mouse testes

growth_protocol: LT-11B6 (Id4-eGfp transgenic mice on C57BL/6 background) from Jon Oatley (Washington State University; Chan et al., 2014 Genes & Development 28: 1351-1362) were bred to produce pup male mice. Testes from postnatal day 6 (P6)  pups were used to produce testis cell suspensions that were stained with antibodies against TSPAN8 and subsequently used for FACS. For the "high" subpopulations of ID4-EGFP+ spermatogonia (based on TSPAN8 antibody labeling), the top 1/3 most robustly stained cells were sorted, while for the low subpopulations, the bottom 1/3 most weak positive stained cells were selected.

extract_protocol:
Sorted P6 ID4-EGFP+ spermatogonia and subpopulations defined by antibody labeling for TSPAN8 were used for Reduced-representation bisulfite sequencing (RRBS) analysis of methylome or ChIP-seq analysis of post-translational modifications of histones (H3K4me3, H3K27me3 and H3K27Ac). For RRBS, snap-frozen cell pellets from five independent sorts of TSPAN8-High and TSPAN8-Low ID4-EGFP+ spermatogonia were used for genomic DNA isolation and RRBS was performed using the Methyl-MidiSeq service by Zymo Research (Irvine, CA).  For ChIP-seq, snap-frozen cell pellets from eight independent sorts of the TSPAN8-High and TSPAN8-Low subpopulations were subjected to low-input ChIP-seq service by Active Motif (Carlsbad, CA) using proprietary approaches. Briefly, native (unfixed) chromatin was isolated, quantified, and 9000 (H3K4me3) to 34000 (H3K27me3 and H3K27Ac) cell equivalents of chromatin (6.6pg/cell) were used for each ChIP reaction using antibodies against H3K4me3 (Active Motif 39159), H3K27Ac (Active Motif 39133) or H3K27me3 (Millipore, 07-449). ChIP'd genomic DNA or genomic DNA from residual chromatin were subsequently used for sequencing.
For RRBS, libraries were prepared from 300 ng of genomic DNA digested with the BfaI, MseI, and MspI restriction enzymes and the fragments produced were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine. Adapter-ligated fragments were filled in and 3’-terminal-A extended, then purified using the Zymo Research (ZR) DNA Clean & Concentrator – 5 kit (Cat#: D4003). Bisulfite treatment of the fragments was done using the EZ DNA Methylation – Lightning kit (ZR, Cat#: D5030). PCR was performed and the size and concentration of the fragments were confirmed on the Agilent 2200 TapeStation, then sequenced on the Illumina Hiseq 2500 with PE50 parameters. For ChIP-seq, ChIP and input samples were prepared for amplification by converting overhangs into phosphorylated blunt ends, 3’ adenylation, ligation of Illumina adaptors and library size selection (175-225 bp) on an agarose gel. Adaptor-ligated libraries were then amplified for 18 cycles and resulting DNAs were purified, quantified, and tested by qPCR to assess quality of amplification reactions. Amplified DNA libraries subjected to Illumina sequencing with HiSeq2000 instrument (SE50).

tag: cell population

value: TSPAN8-low subpopulation of P6 ID4-EGFP+


title: TSPAN8_Low_H3K27Ac_ChIP-seq


title: TSPAN8_High_Input

value: TSPAN8-high subpopulation of P6 ID4-EGFP+


title: TSPAN8_Low_H3K4me3_ChIP-seq


title: TSPAN8_High_H3K27me3_ChIP-seq


title: TSPAN8_High_H3K27Ac_ChIP-seq


title: TSPAN8_High_H3K4me3_ChIP-seq


title: wt_CasE-Flag_ control CoIP_-PNK

description: Sample 11


title: Brn3aKOP3RGC2

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Basecalls and quality scores performed using SCS v2.10 for RGC samples and RTA 1.18.61 for brain samples and Fastq files generated from reads passing chastity filtering.
The reference assembly GRCm38.p3 with transcript annotation Ensembl v78 was used for alignment and quantitation. Reads were first trimmed of 3' Illumina adapter using Trimmomatic v0.32. Transcript quantitation was accomplished by streaming read alignment from Bowtie2 v2.2.1 (Langmead and Salzberg, 2012) to eXpress v1.3.1 (Roberts and Pachter, 2013; Roberts et al., 2013).  Bowtie2 alignment settings were used as previously described (Roberts et al., 2013) and eXpress setting –r-stranded was used for directional transcript analysis.  Bias corrected effective counts were used for downstream normalization and differential expression analysis.
Genome_build: GRCm38.p3 with Ensembl 78
Supplementary_files_format_and_content: Comma separated value file containing the eXpress output of effective count values.

source_name: RGCs from Brn3aAP/KO at post-natal day 3 replicate 2

growth_protocol: RGCs were separated from the cellular suspension by immunomagnetic purification, using Anti-  Mouse IgG coated Dynal beads (Invitrogen, Carlsbad, CA, USA) coupled to an anti-AP mouse monoclonal  antibody (VIB, Ghent, Belgium). Pre-coating of the Dynal beads with anti-AP (0.3 μg/10 μl Dynabead  suspension) was performed for 40 min at room temperature, followed by two PBS washes. Approximately 2  *10^6 pre-coated Dynabeads were incubated with 10^7 dissociated retinal cells for 40 min at RT with gentle  rotation. The unbound retinal supernatant was separated from the bead-coupled AP-positive RGCs using a  magnetic separator (Magna-Sep, Invitrogen). After two additional washes with PBS (0.1% BSA), the Dynal  bead coupled AP positive cells were resuspended in 50 μL RLT lysis buffer (RNeasy, Qiagen, Venelo,  Netherlands) and stored at -80C. The remaining cellular suspension was centrifuged at 1200 rpm 5 min,  resuspended in 350 μL RLT and stored at -80C. For visualizing retinal recipient areas of the brain, C57B/6 P0.5 pups were anesthetized on ice, eyes  were injected with 1 ul Alexa Flour 488-conjugated cholera toxin B (right eye) and 594-conjugated cholera  toxin B (left eye) (Molecular Probes). Brains were collected at P3.5 and vibratome sectioned at 150-200μm  in chilled ACSF (126 mM NaCl, 3 mM KCl, 26 mM NaHCO3, 1 mM NaH2PO3, 1 mM CaCl2, 8 mM  MgSO4, 10 mM Dextrose, pH = 7.4) Retinorecipient areas of the brain including lateral geniculate nucleus  (LGN), superior colliculus (SC), and pretectal area (PA) were identified and dissected under a fluorescent  stereomicroscope in ice cold ACSF. Remaining brain sections were pooled and used as control. Samples  were immediately placed in RLT lysis buffer (RNAeasy, Qiagen) and stored at -80C.

extract_protocol:
Total RNA was extracted by RNeasy (Qiagen).
Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each RGC library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases, whereas brain samples were sequenced with paired-end 125 bases on HiSeq2500.  Fastq files were generated from reads passing chastity filter.
Stranded mRNA-seq (dUTP method)

tag: genotype

value: retina

tag: cell type

value: AP positive RGC

tag: age (days post-natal)


title: TSPAN8_Low_H3K27me3_ChIP-seq


title: Brn3bHETE15SN2

source_name: retinal supernatent control from Brn3aAP/WT at post-natal day 3 replicate 3

value: retinal supernatent control


title: Brn3bKOE15RGC1

source_name: RGCs from Brn3aAP/KO at post-natal day 3 replicate 1


title: Brn3bKOE15SN1

source_name: retinal supernatent control from Brn3aAP/KO at post-natal day 3 replicate 1


title: DeltaCRISPR01+02_CasE-Flag_CoIP_ +PNK

description: Sample 14

value: [delta]CRISPR01+02, CasE-Flag


title: Brn3bKOE15RGC2


title: Brn3bHETE15RGC2

source_name: RGCs from Brn3aAP/WT at post-natal day 3 replicate 2


title: DeltaCRISPR01+02_CasD-Flag _CoIP_-PNK

description: Sample 5


title: wt_CasD-Flag_ control CoIP_ +PNK

description: Sample 4


title: DeltaCRISPR01+02_CasD-Flag_control CoIP_+PNK

description: Sample 8


title: Brn3bHETP3SN1

source_name: retinal supernatent control from Brn3aAP/WT at post-natal day 3 replicate 1


title: Brn3bHETE15RGC1

source_name: RGCs from Brn3aAP/WT at post-natal day 3 replicate 1


title: Brn3aHETP3RGC2


title: Brn3aHETP3SN1


title: Brn3bHETP3RGC1


title: Brn3bKOP3RGC1


title: Brn3bKOP3SN1


title: Brn3aHETP3RGC1


title: Brn3bHETP3RGC2


title: M1Brain

source_name: whole brain replicate 1

value: wild type

value: whole brain

value: tissue


title: PTA

source_name: pretectal area  replicate 1

value: pretectal area


title: M1SC

source_name: superior colliculus replicate 1

value: superior colliculus


title: M2SC

source_name: superior colliculus  replicate 2


title: M1LGN

source_name: lateral geniculate nuclease replicate 1

value: lateral geniculate nuclease


title: Brn3aKOP3RGC1


title: Brn3bKOP3RGC2


title: M2LGN

source_name: lateral geniculate nuclease replicate 2


title: Brn3aKOP3SN1


title: TBI_3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
WT Balb/c mouse: isolation of small intestine 12h after irradiation
ResDESeq_t_12h_TBI_vs_t_12h_TBI_3pRNA
ResDESeq_t_12h_TBI_vs_t_12h_TBI_3pRNA_aIFNAR

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner that maps reads genomically and resolves reads across splice junctions.  We used the 2 pass mapping method in which the reads are mapped twice. The first mapping pass used a list of known annotated junctions from Ensemble.
Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done. After mapping we computed the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases.
The raw count matrix generated by HTSeq was then processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which was used to both normalize the full dataset and analyze differential expression between sample groups.
A heatmap was generated using the heatmap.2 function from the gplots R package. The data plot was the mean centered normalized log2 expression of the top 100 significant genes. For simple hierarchical clustering the correlation metric was used (Dij = 1 - cor(Xi,Xj)) with the Pearson correlation on the normalized log2 expression values.
The heatmap depicted in shows all genes listed in the interferome database (Rusinova, I., Forster, S., Yu, S., Kannan, A., Masse, M., Cumming, H., Chapman, R., and Hertzog, P. J. (2013) Nucleic Acids Res 41, D1040-1046) that show significantly changed gene expression of 3pRNA pretreated and irradiated mice compared to both the other groups simultaneously
Genome_build: mm9
Supplementary_files_format_and_content: xls files, expression count matrix from the mapped reads

source_name: small intestine (Balb/c)

extract_protocol:
Small sections of mouse small intestine were homogenized in Trizol and processed according to instructions with reagent.
RNA samples were used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Balb/c mice were either solely irradiated (9Gy) (n=3), pretreated with Rig-I agonist 3pRNA prior (d-1) to irradiation (n=3) or pre-treated with 3pRNA (d-1) + α-IFNaR1 blocking antibody (d-2) prior to irradiation (n=3)

value: Balb/c

tag: protocol


title: M3LGN

source_name: lateral geniculate nuclease replicate 3

tag: strain


title: TBI_3pRNA_d-1_1

description:
WT Balb/c mouse: i.v. injection of 3pRNA 24h prior to irradiation, isolation of small intestine 12h after irradiation
ResDESeq_t_12h_TBI_vs_t_12h_TBI_3pRNA
ResDESeq_t_12h_TBI_3pRNA_vs_t_12h_TBI_3pRNA_aIFNAR


title: TBI_3pRNA_d-1_aIFNAR1_d-2_1

description:
WT Balb/c mouse:i.v. injection of a-IFNAR1 blocking antibody 48h prior to irradiation, i.v. injection of 3pRNA 24h prior to irradiation, isolation of small intestine 12h after irradiation
ResDESeq_t_12h_TBI_vs_t_12h_TBI_3pRNA_aIFNAR
ResDESeq_t_12h_TBI_3pRNA_vs_t_12h_TBI_3pRNA_aIFNAR


title: TBI_3pRNA_d-1_2

value: i.v. injection of 3pRNA 24h prior to irradiation, isolation of small intestine 12h after irradiation


title: TBI_3pRNA_d-1_aIFNAR1_d-2_3

value: i.v. injection of a-IFNAR1 blocking antibody 48h prior to irradiation, i.v. injection of 3pRNA 24h prior to irradiation, isolation of small intestine 12h after irradiation


title: TBI_2

value: isolation of small intestine 12h after irradiation


title: TBI_3pRNA_d-1_3


title: M3SC

source_name: superior colliculus replicate 3


title: TBI_1


title: TSPAN8-high-Me

source_name: P6 ID4-EGFP+ spermatogonia from mouse testes


title: TSPAN8-low-Me


title: Pmel-shPTEN-H4K91AC

city: Houston

first: Kadir

middle: Caner

last: Akdemir

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: processed data file: Pmel-shPTEN_45_dense.bed

data_processing:
ChIP-Seq reads were aligned using Bowtie (version 1.0.0) to human genome assembly NCBI Build 37 (UCSC hg19) with the following parameters: -n 1 -m 1 --best –strata (uniquely mapped reads with one mismatch were retained).
We used the ChromHMM method with default parameters to derive genome-wide chromatin state maps for all cell types. Sequencing reads that map to the same genomic location and strand were counted once in the input data in order to avoid biases due to PCR artifacts. This number of states was chosen, because it was the minimum number required to separate bivalent and poised states from active states. The 45 state model was learned jointly on all chromatin marks from H and Hmp. The chromatin state segmentation of Hmel-shGFP, Hmel-shPTEN, Pmel-shGFP and Pmel-shPTEN was produced subsequently by applying this model to the chromatin data from these cell types. Prior to that, we normalized each chromatin mark in Pmel-shGFP and Pmel-shPTEN to have the same number of binary calls across these two cell types in the binarization procedure of ChromHMM.
Genome_build: hg19
Supplementary_files_format_and_content: Gnome segmentation files generated for each cell type by ChromHMM.
Supplementary_files_format_and_content: *18_dense.bed files contain 18 state chromatin model data based on ChIP-Seq dataset for each individual cell line.

source_name: Pmel-shPTEN

growth_protocol: Cells were maintained in standard tissue culture conditions (5% CO2 , 37oC) in DMEM medium supplemented with 10%FBS and Pen-Strep.

extract_protocol:
Cells (5 million per antibody) were crosslinked using 1% paraformaldehyde for 10mins at 37 degrees. Reaction was quenched by 0.125M glycine for 5mins, cells washed with PBS and stored at -80oC. Next day cells were thawed on ice and lysed with RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton x-100, 0.2%SDS, 0.1% DOC) for 10min on ice. Sonication was performed using Branson Sonifier 250 to achieve shear length of 200-500bp. Antibodies were bound to dynabeads for 1 hr at 4oC. Extracts were then incubated overnight with antibody-dynabead mixture Immunecomplexes were then washed 5 times with RIPA buffer, once with RIPA-500 (RIPA with 500mM NaCl) and once with LiCl wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and decrosslinking was performed in direct elution buffer (10mM Tris-Cl pH 8.0, 5mM EDTA, 300mM NaCl, 0.5% SDS) by incubating immunecomplxes at 65oC for 4-16hrs. Proteinase K (20mg/ml) and RNaseA treatment was performed and DNA cleaned up using SPRI beads (Beckman-Coulter).
Libraries were prepared using NEB reagents as described earlier (Garber et al 2012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300-500 bp (insert plus adaptor and PCR primer sequences) were size selected by SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were infected with mko-shGFP or mko-shPTEN lentiviruses. Two hundred million cells were harvested for ChIP.

tag: partially transformed melanocytic line

value: PMEL

tag: clone subtype

value: Pmel-shPTEN

tag: cell phentype

value: tumorigenic variant

tag: chip antibody

tag: chip antibody vendor-cat.#


title: TBI_3pRNA_d-1_aIFNAR1_d-2_2


title: Pmel-shPTEN-IgG

value: IgG

value: Rabbit IgG (Millipore)


title: Pmel-shPTEN-H4TETRAAC

value: Active Motif-39179


title: Pmel-shPTEN-H4K5AC


title: Pmel-shPTEN-H4K20ME2

value: Active Motif-39173


title: Pmel-shPTEN-H4K20ME3


title: Pmel-shPTEN-H4K8AC


title: Pmel-shPTEN-H4K20ME1


title: Pmel-shPTEN-H4


title: Pmel-shPTEN-H4K12AC

value: Active Motif-39165


title: Pmel-shPTEN-H3K79ME2


title: Pmel-shPTEN-H3K79ME1


title: Pmel-shPTEN-H3K79ME3


title: Pmel-shPTEN-H3K4ME2


title: Pmel-shPTEN-H3K9ME3


title: Pmel-shPTEN-H3K27ME3


title: Pmel-shPTEN-H3K36ME2


title: Pmel-shPTEN-H3K36ME1


title: Pmel-shPTEN-H3K9ME1


title: Pmel-shPTEN-H3K4ME3


title: Pmel-shPTEN-H3K4ME1


title: Pmel-shPTEN-H3K9AC


title: Pmel-shPTEN-H3K36ME3


title: Pmel-shPTEN-H3K36AC

value: Active Motif-39379


title: Pmel-shPTEN-H3K4AC


title: Pmel-shPTEN-H3K27AC


title: Pmel-shPTEN-H3K27ME1


title: Pmel-shPTEN-H4K16AC


title: Pmel-shPTEN-H3K23AC


title: Pmel-shPTEN-H3K18AC


title: Pmel-shPTEN-H3K14AC


title: Pmel-shPTEN-H2BK5AC

value: Active Motif-39123


title: Pmel-shPTEN-H2BK15AC


title: Pmel-shPTEN-H2BK120AC

value: Active Motif-39119


title: Pmel-shGFP-IgG

description: processed data file: Pmel-shGFP_45_dense.bed

source_name: Pmel-shGFP

value: Pmel-shGFP

value: non-tumorigenic variant


title: M2Brain

source_name: whole brain replicate 2

value: wild type

tag: tissue

value: whole brain

value: tissue


title: Pmel-shPTEN-H2AK5AC


title: Pmel-shGFP-H4K91AC


title: Pmel-shGFP-H4TETRAAC


title: Pmel-shGFP-H4K20ME3


title: PP MRC4

city: Stanford

first: Kazuki

last: Nagashima

address: 290 Jane Stanford Way, Room W117 Fischbach Lab

department: Bioengineering

institute: Stanford University

data_processing:
Data were acquired on an Ion Proton (Thermo Fisher)
The software used for the analysis was CLC Genomics Workbench ver. 9 (CLC).
The reads acquired were aligned to the GRCm38.84 genome assembly.
Filtering parameters were as follows; Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8 and Similarity fraction, 0.8.
RPKM value was calculated and regarded as gene expression.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Xls files include RPKM values for each Sample.

source_name: Mesenchymal cells sorted from Peyer's patches

extract_protocol:
Total RNA was extracted using Rneasy plus micro kit (Qiagen).
cDNA was synthesized and amplified using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories).

value: Peyer's patches

tag: cell surface marker


title: Pmel-shGFP-H4K20ME1

value: PMEL


title: PP MRC1


title: Pmel-shGFP-H4K5AC


title: Pmel-shGFP-H4K16AC


title: PP MRC5


title: Pmel-shGFP-H4K20ME2


title: PP MRC3


title: Pmel-shGFP-H3K9ME3


title: Pmel-shGFP-H4K12AC


title: Pmel-shGFP-H4K8AC


title: Pmel-shGFP-H4


title: PP MCi4


title: PP MCi5


title: PP MRC2


title: Pmel-shPTEN-H3

value: Pmel-shPTEN


title: PP MCi3


title: Pmel-shGFP-H3K9ME1


title: PP MCi2


title: Pmel-shGFP-H3K9AC


title: Pmel-shGFP-H3K79ME3


title: PP control3

source_name: Epithelial cells isolated from Peyer's patches

value: RANK flox/delta


title: PP control4


title: PP MCi1


title: Pmel-shGFP-H3K79ME1


title: Pmel-shGFP-H3K4ME2


title: Pmel-shGFP-H3K79ME2


title: Pmel-shGFP-H3K4ME3


title: PP cKO4

value: Vil1-Cre RANK flox/delta


title: Pmel-shGFP-H3K4AC


title: Pmel-shGFP-H3K36ME3


title: PP control1


title: PP control2


title: Pmel-shGFP-H3K4ME1


title: Pmel-shGFP-H3K36ME2


title: PP cKO1


title: PP cKO2


title: Pmel-shGFP-H3K36AC


title: RNA sequencing of set25 mutant worms biological replicate 3

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

description:
set25
RNA sequencing of set25 mutant worms grown at a reference temperature of 20 degrees
SL33_16183_GTGGCC

data_processing:
Sequence mapping to the transcriptome using tophat v2.1.0 --no-coverage-search -i 10 -I 40000 -g 20
Assigning reads to genes using featureCounts v1.5.1 -s 2 -B -p -M --fraction -t exon -g gene_name -O
Count normalization was done using DESeq2 v1.8.1.
Genome_build: C. elegans genome assembly WS215 from WormBase and annotation from Ensembl release 70
Supplementary_files_format_and_content: Matrix of raw number of reads mapping to each gene

organism: Caenorhabditis elegans

source_name: whole multiple worms_20C_set25

growth_protocol: To prepare samples for sequencing worms were grown continuously ( > 20 generations) at 20 °C. Synchronized gravid adult worms were collected and RNA extracted. To obtain synchronized gravid animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 72 - 76 hours at 20 °C. We used 3 plates for each replicate and three replicates for each condition. We monitored the cultures to ensure that they did no starve at any point. Animals were collected in M9 and RNA extracted using TRIzol® extraction protocol.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
Libraries for RNA-seq were prepared from 400 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (ref. RS-122-2201, Illumina) using the included RiboZero reagents to deplete ribosomal RNAs according to manufacturer's instructions. The poly(A)-mRNA selection step was not carried out. Samples were sequenced with 2x50 bp paired-end reads using Illumina HiSeq v4 sequencing chemistry.

tag: strain background

tag: developmental stage

value: gravid adult


title: RNA sequencing of set25 mutant worms biological replicate 2

description:
set25
RNA sequencing of set25 mutant worms grown at a reference temperature of 20 degrees
SL32_16182_TAGCTT


title: PP cKO3


title: RNA sequencing of Low Worms biological replicate 3

description:
control
Worms grown continuously at 20C
WL33_12382_GTGAAA

source_name: whole multiple worms_20C_control

growth_protocol: To prepare samples for sequencing N2 worms grown continuously ( > 20 generations) at 20 °C were shifted to 25 °C as L4 larvae and grown at that temperature for five generations. At the fifth generation, synchronized gravid adult worms were collected and RNA extracted. To obtain synchronized gravid F0 animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 54 - 56 hours at 25 °C.  These constituted the F0 ancestral population. Before reaching adulthood, at L4 stage, a fraction of these animals were transferred to 20 °C and propagated for 3 more generation at that temperature. To obtain synchronized gravid F3 animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 72 - 76 hours at 20 °C. A control population was processed in parallel, starting from L4 animals grown continuously at 20 °C. We used 3 plates for each replicate and three replicates for each condition. We monitored the cultures to ensure that they did no starve at any point. Animals were collected in M9 and RNA extracted using TRIzol® extraction protocol.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
Libraries for RNA-seq were prepared from 400 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (ref. RS-122-2201, Illumina) using the included RiboZero reagents to deplete ribosomal RNAs according to manufacturer's instructions. The poly(A)-mRNA selection step was not carried out. Samples were sequenced with 2x50 bp paired-end reads using Illumina HiSeq v4 sequencing chemistry.
paired-end mRNA-Seq

value: wild-type


title: Pmel-shGFP-H3K27AC


title: Pmel-shGFP-H3K23AC


title: RNA sequencing of Low Worms biological replicate 2

description:
control
Worms grown continuously at 20C
WL32_12381_GAGTGG


title: RNA sequencing of Low Worms biological replicate 1

description:
control
Worms grown continuously at 20C
WL31_12380_GTCCGC


title: Pmel-shGFP-H3K18AC


title: RNA sequencing of High Worms F3 biological replicate 2

description:
F3
Worms grown at 25C and then transferred to 20C for three generations
WH32_12378_GATCAG

source_name: whole multiple worms_transferred to 20C_F3


title: RNA sequencing of High Worms biological replicate 3

description:
F0
Worms grown continuously at 25C
WH03_12376_TGACCA

source_name: whole multiple worms_25C_F0


title: Pmel-shGFP-H3K14AC


title: Pmel-shGFP-H2BK5AC


title: Pmel-shGFP-H3


title: Pmel-shGFP-H2BK15AC