title: WT_C10_sRNAs-rep2 [small RNA-seq]

data_processing:
All sRNA-seq data were mapped to the Tetrahymena thermophila 2016 genome using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For sRNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files (read length is selected by 'minlength=27 and maxlength=31') by using “bamCoverage” from deepTools with parameters “--outFileFormat bigwig --normalizeUsingRPKM  --binSize 1”.
Genome_build: Tetrahymena thermophila micronuclear genome 2016 (http://159.226.67.237/sun/TetBLAST/blast/db/T_thermophila_Mic_Supercontig_id.fa)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Total RNA was extracted from Tetrahymena cells using the RNeasy Protect Cell Mini Kit (Qiagen), as described (TetraFGD: http://tfgd.ihb.ac.cn/index/smphelp). Small RNA was enriched by mirVana™ miRNA Isolation Kit (Ambion).
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep Kit (RS-200-0012).
Small RNA library with RNA 3’ Adapter (RA3) 5’ TGGAATTCTCGGGTGCCAAGG

value: Tetrahymena wildtype strains CU427 and CU459


title: EZL1KO_C3-rep1

status: Public on Feb 28 2019

type: SRA

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
All RNA-seq data were mapped to theTetrahymena thermophila 2016 genome using Tophat2 (2.1.1), which was shown to be accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Then, duplicated reads for pair-end data were removed, but not single-end data by SAMtools (v1.5).
For RNA-seq, the bigwig files for visualization in Integrative Genomics Viewer (IGV) were generated from BAM files by using “bamCoverage” from deepTools with parameters “--ignoreDuplicates --normalizeUsingRPKM --skipNonCoveredRegions --binSize 50”.
Genome_build: Tetrahymena thermophila micronuclear genome 2016 (http://159.226.67.237/sun/TetBLAST/blast/db/T_thermophila_Mic_Supercontig_id.fa)
Supplementary_files_format_and_content: bigwig

molecule: total RNA

organism: Tetrahymena thermophila

growth_protocol: Tetrahymena cells were grown at 30 oC in SPP medium (Sweet and Allis 1998).

extract_protocol:
Total RNA was extracted from Tetrahymena cells using the RNeasy Protect Cell Mini Kit (Qiagen), as described (TetraFGD: http://tfgd.ihb.ac.cn/index/smphelp). Polyadenylated transcripts were enriched using the Sera‐Mag magnetic oligo (dT) beads (GE).
First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101).

treatment_protocol: To initiate conjugation, log-phase growing cells (~2×105 /ml) of two different mating types were washed, starved, and mixed in 10 mM Tris (pH 7.4) or Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

tag: strain background

value: Tetrahymena wildtype strains CU427 and CU428

tag: genotype/variation

tag: cell type

value: C3 (3 hours post-mixing)


title: DCL1KO_C3-rep1


title: WT_C10_sRNAs-rep1 [small RNA-seq]

value: wild type

value: C10 (10 hours post-mixing)


title: PDD1KO_C10_sRNAs-rep1 [small RNA-seq]


title: PDD1KO_C10_sRNAs-rep2 [small RNA-seq]


title: EZL1KO_C10_sRNAs-rep1 [small RNA-seq]


title: EZL1KO_C10_sRNAs-rep2 [small RNA-seq]


title: DCL1KO_C10_sRNAs-rep2 [small RNA-seq]


title: DCL1KO_C10_sRNAs-rep1 [small RNA-seq]


title: p65-TNF-0h

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

library_source: genomic

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension of average fragments size.
Supplementary_files_format_and_content: RPKM values were calculated by Cuffdiff and stored as tab separated texts.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
ChIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). P65 antibody (Cat# sc-372) was purchased from Santa Cruz.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.

value: Human embryonic kidney

tag: cell line

value: HEK 293 transfected with reporter construct

value: somatic cell

value: non-treated

tag: tissue

value: embryonic kidney

tag: developmental stage

value: embryos

tag: library strategy

value: ChIP

tag: antibody

value: sc-372, Santa Cruz


title: TetTKO-B21-RNAseq-rep1

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantitified by Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM values were calculated by Cuffdiff and stored as tab separated texts.

tag: tissue source

value: somatic cells

value: non-treated, Tet1/2/3 triple-KO


title: TetTKO-B21-RNAseq-rep2


title: p65-TNF-12h


title: ctrl-B21-RNAseq-rep1


title: ctrl-RNAseq-rep2

value: mRNA-seq


title: ctrl-RNAseq-rep1


title: EZL1KO_C3-rep2


title: RNA-Seq of Mus musculus: P6 Lhx4-null retina biological replicate 3

status: Public on Feb 23 2019

city: Rochester

first: Xuhui

last: Dong

state: NY

address: 601 ELMWOOD AVE

institute: University of Rochester

description:
Mutant  biological replicate 3
M3

data_processing:
alignment: Tophat 2
differentially expressed gene identification: Cufflinks
Genome_build: GRCm38
Supplementary_files_format_and_content: RPKM, Gene expression profile in  the Lhx4-null retina at P6

organism: Mus musculus

source_name: retina

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: C57BL/6J; 129S6 mixed background

value: Postnatal day 6

tag: genotype


title: 5Aza-dC-treat-RNAseq-rep2 dataset 2

value: 5Aza-dC treated


title: RNA-Seq of Mus musculus: P6 Lhx4-null retina biological replicate 2

description:
Mutant  biological replicate 2
M2


title: 5Aza-dC-treat-RNAseq-rep1 dataset 2


title: input-TNF-12h

value: input


title: RNA-Seq of Mus musculus: P6 control retina biological replicate 2

description:
Control biological replicate 2
C2

value: control


title: input-TNF-0h


title: ctrl-B21-RNAseq-rep2


title: RNA-Seq of Mus musculus: P6 control retina biological replicate 3

description:
Control biological replicate 3
C3


title: RNA-Seq of Mus musculus: P6 control retina biological replicate 1

description:
Control biological replicate 1
C1


title: 10876X33_2011_old_Female_pre_high

status: Public on Feb 18 2019

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

description:
counts.txt
10876X33

data_processing:
Reads were aligned to the human genome from Ensembl release 87 using STAR v 2.5.2b.
Reads mapping uniquely to features in the Ensembl human GTF were assigned using featureCounts v 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 v 1.16.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCount output files were combined into a single tab-delimited matrix reporting raw counts.

source_name: vastus lateralis muscle

extract_protocol:
10-15mg of tissue was placed in Tri reagent LS (Molecular Research Center, Cincinnati, OH, USA) and disrupted via hand-held homogenizer (Bio-Gen PRO200; Pro Scientific, Oxford, CT, USA).  Chloroform was added to separate the RNA into an aqueous phase that was then precipitated using isopropanol.   Extracted RNA was then washed with ethanol and suspended in nuclease-free water with EDTA.  RNA integrity and quantity was determined using the EPOCH (Take3; BioTek) spectrophotometer.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2301 and RS-122-2302).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

treatment_protocol: The samples used for this study are from muscle biopsies obtained from the vastus laterails using the Bergstrom needle technique with manual suction after anesthetizing with 1% lidocaine.  Biopsies from young (18-28 years) and old (60-79 years) subjects that underwent identical procedural treatments were obtained before bed rest (Day 1), after bed rest (Day 5).  Briefly, both male and female subjects were recruited within the Salt Lake City area and screened to ensure the absence of preexisting medical conditions.  After screening, participants were subjected to 5 days of supervised bed rest.  During bed rest, caloric intake for each subject was evenly distributed across meals and days predetermined by a research dietician. Bathroom and hygiene activities were performed in a wheel chair while the remainder of time was spent in a bed. Nursing staff was available 24 hours a day during the duration of bed rest.  Bed rest took place at the University of Utah Center for Clinical and Translational Science (CCTS).

tag: subject

tag: time

value: pre bed rest

tag: age

value: old

tag: Sex

value: Female

value: vastus lateralis muscle

tag: susceptibility

value: high


title: 10876X30_2007_old_Female_post

description:
counts.txt
10876X30

value: post bed rest

value: Not used in Susceptibility Study


title: 10876X31_2009_old_Female_pre_high

description:
counts.txt
10876X31


title: 10876X34_2011_old_Female_post_high

description:
counts.txt
10876X34


title: 10876X27_2006_old_Female_pre_low

description:
counts.txt
10876X27

value: low


title: 10876X36_2012_old_Female_post

description:
counts.txt
10876X36


title: 10876X32_2009_old_Female_post_high

description:
counts.txt
10876X32


title: 10876X29_2007_old_Female_pre

description:
counts.txt
10876X29


title: RNA-Seq of Mus musculus: P6 Lhx4-null retina  biological replicate 1

description:
Mutant  biological replicate 1
M1


title: 10876X24_2004_old_Female_post_high

description:
counts.txt
10876X24


title: 10876X23_2004_old_Female_pre_high

description:
counts.txt
10876X23


title: 10876X21_2003_old_M_pre_low

description:
counts.txt
10876X21

value: Male


title: 10876X28_2006_old_Female_post_low

description:
counts.txt
10876X28


title: 10876X35_2012_old_Female_pre

description:
counts.txt
10876X35


title: 10876X16_1016_young_Female_post_high

description:
counts.txt
10876X16

value: young


title: 10876X18_1017_young_Female_post_high

description:
counts.txt
10876X18


title: 10876X25_2005_old_M_pre_high

description:
counts.txt
10876X25


title: 10876X14_1013_young_M_post_low

description:
counts.txt
10876X14


title: 10876X19_2002_old_Female_pre_low

description:
counts.txt
10876X19


title: 10876X22_2003_old_M_post_low

description:
counts.txt
10876X22


title: 10876X17_1017_young_Female_pre_high

description:
counts.txt
10876X17


title: 10876X11_1012_young_Female_pre_high

description:
counts.txt
10876X11


title: 10876X12_1012_young_Female_post_high

description:
counts.txt
10876X12


title: 10876X10_1011_young_Female_post_high

description:
counts.txt
10876X10


title: 10876X13_1013_young_M_pre_low

description:
counts.txt
10876X13


title: 10876X15_1016_young_Female_pre_high

description:
counts.txt
10876X15


title: 10876X7_1010_young_Female_pre_low

description:
counts.txt
10876X7


title: 10876X6_1009_young_Female_post_low

description:
counts.txt
10876X6


title: 10876X9_1011_young_Female_pre_high

description:
counts.txt
10876X9


title: 10876X5_1009_young_Female_pre_low

description:
counts.txt
10876X5


title: 10876X4_1007_young_Female_post_low

description:
counts.txt
10876X4


title: 10876X2_1003_young_M_post_low

description:
counts.txt
10876X2


title: 10876X3_1007_young_Female_pre_low

description:
counts.txt
10876X3


title: 10876X20_2002_old_Female_post_low

description:
counts.txt
10876X20


title: 14406X20_3029_old_M_post_high

description:
counts.txt
14406X20


title: 14406X19_3029_old_M_pre_high

description:
counts.txt
14406X19


title: 10876X1_1003_young_M_pre_low

description:
counts.txt
10876X1


title: 14406X17_3026_old_M_pre_high

description:
counts.txt
14406X17


title: 14406X15_3025_old_M_pre_high

description:
counts.txt
14406X15


title: 14406X14_3024_old_M_post_low

description:
counts.txt
14406X14


title: 14406X16_3025_old_M_post_high

description:
counts.txt
14406X16


title: 14406X12_3021_old_Female_post_low

description:
counts.txt
14406X12


title: 10876X8_1010_young_Female_post_low

description:
counts.txt
10876X8


title: 14406X9_3012_old_M_pre_low

description:
counts.txt
14406X9


title: 14406X11_3021_old_Female_pre_low

description:
counts.txt
14406X11


title: 14406X5_3010_old_M_pre_high

description:
counts.txt
14406X5


title: 14406X8_3013_old_M_post_low

description:
counts.txt
14406X8


title: 14406X2_3005_old_M_post_low

description:
counts.txt
14406X2


title: 14406X10_3012_old_M_post_low

description:
counts.txt
14406X10


title: 14406X6_3010_old_M_post_high

description:
counts.txt
14406X6


title: 14406X13_3024_old_M_pre_low

description:
counts.txt
14406X13


title: 14406X4_3008_old_M_post_low

description:
counts.txt
14406X4


title: 14406X1_3005_old_M_pre_low

description:
counts.txt
14406X1


title: 14406X18_3026_old_M_post_high

description:
counts.txt
14406X18


title: 14406X3_3008_old_M_pre_low

description:
counts.txt
14406X3


title: 14406X7_3013_old_M_pre_low

description:
counts.txt
14406X7


title: SORT1 saturation mutagenesis library

status: Public on Feb 15 2019

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

description: Amplified from Promega pGL4.23c vector backbone without reporter gene

data_processing:
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis software. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those identified in the library assigment were considered.
Only barcodes observed in RNA and DNA of the same sample were considered.
Genome_build: GRCh37, GRCh38
Supplementary_files_format_and_content: Non-FASTA data files are in gzip-compressed text file formats. Files with the sufix variants.txt.gz contain an assignment of barcodes to sequence variants. Variant locations are described in a coordinate system that starts 20 bases up- und and downstream of the targeted region. FASTA files contain the wild-type sequence. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts in tab-separated text format.

molecule: other

source_name: Cloned human PCR product

growth_protocol: HepG2, HEK293T, HeLa, HaCaT, Min6, Neuro-2a, LNCap, SK-MEL-28 were obtained from American Type Culture Collection, and primary gliobastoma (GBM) cell line SF7996 was obtained from UCSF (Dr. Costello’s lab). 2.0x10^5 cells were cultured in 96-well plates overnight using standard protocols. LNCaP was grown in media with 100nM DHT.

extract_protocol:
After cells were harvested, genomic DNA and total RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen 80204). Total RNA was subjected to mRNA selection (Oligotex, Qiagen 72022) and treated with Turbo DNase (Thermo Fisher Scientific AM2238) to remove contaminating DNA.
For each replicate, RNA was reverse transcribed with Superscript II (Invitrogen 18064-014) using a primer downstream of the tag, which contained a sample index and a P7 Illumina adaptor sequence. The resulting cDNA was first pooled and then split into multiple reactions to reduce PCR jackpotting effects. Amplification was performed with Kapa Robust polymerase (Roche KK5024) for three cycles, incorporating unique molecular identifiers (UMIs) 10 bp in length. PCR products were cleaned up with AMPure XP beads (Beckman Coulter A63880) to remove the primers and concentrate the products. These products underwent a second round of amplification in eight reactions per replicate for 15 cycles, with a reverse primer containing only P7. All reactions were pooled, run on an agarose gel for size-selection, and then sequenced.

treatment_protocol: For each experiment, about 5 million cells were plated in 15-cm plates and incubated for 24 hours before transfection. Each of three independent cultures (replicates) were transfected with 15 μg of the constructed MPRA libraries using X-tremeGENE HP (Roche 06366236001) for 24 hours (except for PKLR additionally transfected for 48 hours and MYC rs6983267 transfected for 32 hours, with 20nM LiCl being added after 24 hours). The ZRS library was co-transfected with HOXD13 as well as HOXD13 and HAND2 in two separate experiments.

value: Saturation mutagenesis MPRA library

value: 10-beta Electrocompetent E. coli (NEB C3020K)


title: SORT1-flip saturation mutagenesis library


title: SORT1.2 saturation mutagenesis library


title: PKLR saturation mutagenesis library

description: Amplified from Promega pGL4.11c vector backbone without reporter gene


title: TERT saturation mutagenesis library

description: Amplified from Promega pGL4.11b vector backbone without reporter gene


title: TCF7L2 saturation mutagenesis library

description: Amplified from Promega pGL4.23d vector backbone without reporter gene


title: GP1BB saturation mutagenesis library


title: UC88 saturation mutagenesis library


title: HBG1 saturation mutagenesis library


title: HBB saturation mutagenesis library


title: LDLR.2 saturation mutagenesis library


title: IRF6 saturation mutagenesis library


title: TERT-GBM-SiScramble-RNA-3: TERT-GBM-SiScramble transfection RNA replicate 3

description: Targeted barcode amplification incl. UMIs

molecule: polyA RNA

source_name: cell line

value: Primary gliobastoma cell line obtained from UCSF Costello lab


title: TERT-GBM-SiScramble-DNA-2: TERT-GBM-SiScramble transfection DNA replicate 2


title: TERT-GBM-SiScramble-RNA-1: TERT-GBM-SiScramble transfection RNA replicate 1


title: FOXE1 saturation mutagenesis library


title: ZRS saturation mutagenesis library

description: Amplified from Promega pGL4Zc vector backbone without reporter gene


title: TERT-GBM-SiScramble-DNA-3: TERT-GBM-SiScramble transfection DNA replicate 3


title: TERT-GBM-SiGABPA-RNA-3: TERT-GBM-SiGABPA transfection RNA replicate 3


title: TERT-GBM-SiScramble-DNA-1: TERT-GBM-SiScramble transfection DNA replicate 1


title: HNF4A saturation mutagenesis library


title: LDLR saturation mutagenesis library


title: MYCrs6983267 saturation mutagenesis library


title: RET saturation mutagenesis library

description: Amplified from Promega pGL3c vector backbone without reporter gene


title: F9 saturation mutagenesis library


title: TERT-GBM-SiGABPA-RNA-1: TERT-GBM-SiGABPA transfection RNA replicate 1


title: TERT-GBM-SiScramble-RNA-2: TERT-GBM-SiScramble transfection RNA replicate 2


title: MSMB saturation mutagenesis library


title: TERT-GBM-SiGABPA-DNA-1: TERT-GBM-SiGABPA transfection DNA replicate 1


title: TERT-GBM-SiGABPA-DNA-3: TERT-GBM-SiGABPA transfection DNA replicate 3


title: TERT-GBM-RNA-1: TERT-GBM transfection RNA replicate 1


title: SORT1-RNA-3: SORT1 transfection RNA replicate 3

value: Human epithelial liver cancer cell line


title: TERT-GBM-RNA-3: TERT-GBM transfection RNA replicate 3


title: SORT1-flip-RNA-1: SORT1-flip transfection RNA replicate 1


title: TERT-GBM-SiGABPA-DNA-2: TERT-GBM-SiGABPA transfection DNA replicate 2


title: SORT1-flip-RNA-2: SORT1-flip transfection RNA replicate 2


title: SORT1-RNA-1: SORT1 transfection RNA replicate 1


title: TERT-GBM-DNA-3: TERT-GBM transfection DNA replicate 3


title: SORT1.2-RNA-1: SORT1.2 transfection RNA replicate 1


title: TERT-GBM-DNA-1: TERT-GBM transfection DNA replicate 1


title: SORT1-RNA-2: SORT1 transfection RNA replicate 2


title: TERT-GBM-DNA-2: TERT-GBM transfection DNA replicate 2


title: SORT1.2-RNA-2: SORT1.2 transfection RNA replicate 2


title: SORT1.2-DNA-3: SORT1.2 transfection DNA replicate 3


title: SORT1-DNA-1: SORT1 transfection DNA replicate 1


title: SORT1.2-RNA-3: SORT1.2 transfection RNA replicate 3


title: SORT1.2-DNA-2: SORT1.2 transfection DNA replicate 2


title: SORT1-DNA-3: SORT1 transfection DNA replicate 3


title: SORT1-flip-DNA-2: SORT1-flip transfection DNA replicate 2


title: SORT1.2-DNA-1: SORT1.2 transfection DNA replicate 1


title: SORT1-flip-DNA-3: SORT1-flip transfection DNA replicate 3


title: SORT1-flip-RNA-3: SORT1-flip transfection RNA replicate 3


title: SORT1-flip-DNA-1: SORT1-flip transfection DNA replicate 1


title: SORT1-DNA-2: SORT1 transfection DNA replicate 2


title: 10876X26_2005_old_M_post_high

description:
counts.txt
10876X26


title: TERT-GBM-RNA-2: TERT-GBM transfection RNA replicate 2


title: RET-RNA-2: RET transfection RNA replicate 2

value: Mouse neuroblastoma cell line


title: PKLR_48h-RNA-1: PKLR_48h transfection RNA replicate 1

value: Human chronic myelogenous leukemia cell line


title: RET-DNA-1: RET transfection DNA replicate 1


title: RET-RNA-1: RET transfection RNA replicate 1


title: RET-DNA-2: RET transfection DNA replicate 2


title: PKLR_48h-RNA-2: PKLR_48h transfection RNA replicate 2


title: PKLR_48h-RNA-3: PKLR_48h transfection RNA replicate 3


title: PKLR_24h-RNA-2: PKLR_24h transfection RNA replicate 2


title: PKLR_24h-RNA-3: PKLR_24h transfection RNA replicate 3


title: PKLR_48h-DNA-1: PKLR_48h transfection DNA replicate 1


title: PKLR_48h-DNA-3: PKLR_48h transfection DNA replicate 3


title: TERT-GBM-SiGABPA-RNA-2: TERT-GBM-SiGABPA transfection RNA replicate 2


title: PKLR_48h-DNA-2: PKLR_48h transfection DNA replicate 2


title: MYCrs6983267-RNA-2: MYCrs6983267 transfection RNA replicate 2

value: Human embryonic kidney 293T cell line


title: PKLR_24h-DNA-3: PKLR_24h transfection DNA replicate 3


title: PKLR_24h-DNA-2: PKLR_24h transfection DNA replicate 2


title: PKLR_24h-RNA-1: PKLR_24h transfection RNA replicate 1


title: MYCrs6983267-RNA-3: MYCrs6983267 transfection RNA replicate 3


title: PKLR_24h-DNA-1: PKLR_24h transfection DNA replicate 1


title: RET-DNA-3: RET transfection DNA replicate 3


title: MYCrs6983267-RNA-1: MYCrs6983267 transfection RNA replicate 1


title: MYCrs11986220-RNA-2: MYCrs11986220 transfection RNA replicate 2

value: LNCaP

value: Human lymph node carcinoma of the prostate cell line


title: MYCrs6983267-DNA-1: MYCrs6983267 transfection DNA replicate 1


title: MYCrs11986220-RNA-3: MYCrs11986220 transfection RNA replicate 3


title: MYCrs6983267-DNA-3: MYCrs6983267 transfection DNA replicate 3


title: MYCrs11986220-DNA-3: MYCrs11986220 transfection DNA replicate 3


title: MYCrs6983267-DNA-2: MYCrs6983267 transfection DNA replicate 2


title: MYCrs11986220-RNA-1: MYCrs11986220 transfection RNA replicate 1


title: MSMB-RNA-3: MSMB transfection RNA replicate 3


title: MSMB-RNA-1: MSMB transfection RNA replicate 1


title: MSMB-DNA-3: MSMB transfection DNA replicate 3


title: MYCrs11986220-DNA-2: MYCrs11986220 transfection DNA replicate 2


title: MYCrs11986220-DNA-1: MYCrs11986220 transfection DNA replicate 1


title: RET-RNA-3: RET transfection RNA replicate 3


title: MSMB-RNA-2: MSMB transfection RNA replicate 2


title: MSMB-DNA-1: MSMB transfection DNA replicate 1


title: LDLR-DNA-3: LDLR transfection DNA replicate 3


title: LDLR-RNA-2: LDLR transfection RNA replicate 2


title: MSMB-DNA-2: MSMB transfection DNA replicate 2


title: LDLR-DNA-2: LDLR transfection DNA replicate 2


title: LDLR.2-RNA-3: LDLR.2 transfection RNA replicate 3


title: LDLR-RNA-1: LDLR transfection RNA replicate 1


title: LDLR.2-DNA-2: LDLR.2 transfection DNA replicate 2


title: LDLR.2-DNA-3: LDLR.2 transfection DNA replicate 3


title: LDLR.2-RNA-1: LDLR.2 transfection RNA replicate 1


title: IRF6-RNA-3: IRF6 transfection RNA replicate 3

value: HaCaT

value: Human immortalized keratinocyte line


title: LDLR.2-DNA-1: LDLR.2 transfection DNA replicate 1


title: LDLR-DNA-1: LDLR transfection DNA replicate 1


title: LDLR.2-RNA-2: LDLR.2 transfection RNA replicate 2


title: LDLR-RNA-3: LDLR transfection RNA replicate 3


title: IRF6-RNA-1: IRF6 transfection RNA replicate 1


title: IRF6-RNA-2: IRF6 transfection RNA replicate 2


title: IRF6-DNA-1: IRF6 transfection DNA replicate 1


title: IRF4-RNA-2: IRF4 transfection RNA replicate 2

value: Human cutaneous melanoma cell line


title: IRF4-RNA-1: IRF4 transfection RNA replicate 1


title: IRF4-DNA-2: IRF4 transfection DNA replicate 2


title: HNF4A-RNA-2: HNF4A transfection RNA replicate 2


title: HNF4A-RNA-3: HNF4A transfection RNA replicate 3


title: IRF4-DNA-1: IRF4 transfection DNA replicate 1


title: IRF4-DNA-3: IRF4 transfection DNA replicate 3


title: IRF6-DNA-2: IRF6 transfection DNA replicate 2


title: HBG1-RNA-3: HBG1 transfection RNA replicate 3

value: Human erythroblast cancer cell line


title: HNF4A-RNA-1: HNF4A transfection RNA replicate 1


title: HNF4A-DNA-3: HNF4A transfection DNA replicate 3


title: HBG1-DNA-2: HBG1 transfection DNA replicate 2


title: HBG1-RNA-1: HBG1 transfection RNA replicate 1


title: HBG1-DNA-3: HBG1 transfection DNA replicate 3


title: HNF4A-DNA-1: HNF4A transfection DNA replicate 1


title: HBB-RNA-3: HBB transfection RNA replicate 3


title: HBB-RNA-1: HBB transfection RNA replicate 1


title: IRF4-RNA-3: IRF4 transfection RNA replicate 3


title: HBB-DNA-2: HBB transfection DNA replicate 2


title: HBB-DNA-1: HBB transfection DNA replicate 1


title: HBG1-RNA-2: HBG1 transfection RNA replicate 2


title: HBG1-DNA-1: HBG1 transfection DNA replicate 1


title: GP1BB-RNA-2: GP1BB transfection RNA replicate 2


title: GP1BB-RNA-3: GP1BB transfection RNA replicate 3


title: HBB-RNA-2: HBB transfection RNA replicate 2


title: GP1BB-DNA-2: GP1BB transfection DNA replicate 2


title: HBB-DNA-3: HBB transfection DNA replicate 3


title: GP1BB-DNA-3: GP1BB transfection DNA replicate 3


title: GP1BB-DNA-1: GP1BB transfection DNA replicate 1


title: HNF4A-DNA-2: HNF4A transfection DNA replicate 2


title: FOXE1-RNA-2: FOXE1 transfection RNA replicate 2

value: HeLa

value: Human endocervical adenocarcinoma cell line


title: FOXE1-RNA-1: FOXE1 transfection RNA replicate 1


title: IRF6-DNA-3: IRF6 transfection DNA replicate 3


title: F9-DNA-1: F9 transfection DNA replicate 1


title: F9-RNA-1: F9 transfection RNA replicate 1


title: GP1BB-RNA-1: GP1BB transfection RNA replicate 1


title: F9-RNA-3: F9 transfection RNA replicate 3


title: BCL11A-RNA-3: BCL11A transfection RNA replicate 3


title: FOXE1-DNA-1: FOXE1 transfection DNA replicate 1


title: BCL11A-DNA-3: BCL11A transfection DNA replicate 3


title: F9-RNA-2: F9 transfection RNA replicate 2


title: BCL11A-RNA-1: BCL11A transfection RNA replicate 1


title: FOXE1-DNA-3: FOXE1 transfection DNA replicate 3


title: BCL11A-DNA-2: BCL11A transfection DNA replicate 2


title: BCL11A-RNA-2: BCL11A transfection RNA replicate 2


title: ZRS-h13-RNA-2: ZRS-h13 transfection RNA replicate 2

value: Mouse embryonic fibroblast cell line


title: BCL11A-DNA-1: BCL11A transfection DNA replicate 1


title: ZRS-h13-RNA-3: ZRS-h13 transfection RNA replicate 3


title: ZRS-h13-RNA-1: ZRS-h13 transfection RNA replicate 1


title: F9-DNA-2: F9 transfection DNA replicate 2


title: ZRS-h13h2-RNA-2: ZRS-h13h2 transfection RNA replicate 2


title: BCL11A saturation mutagenesis library


title: ZRS-h13h2-RNA-1: ZRS-h13h2 transfection RNA replicate 1


title: F9-DNA-3: F9 transfection DNA replicate 3


title: FOXE1-DNA-2: FOXE1 transfection DNA replicate 2


title: MYCrs11986220 saturation mutagenesis library


title: ZRS-h13h2-DNA-1: ZRS-h13h2 transfection DNA replicate 1


title: FOXE1-RNA-3: FOXE1 transfection RNA replicate 3


title: ZRS-h13h2-DNA-2: ZRS-h13h2 transfection DNA replicate 2


title: ZRS-h13-DNA-2: ZRS-h13 transfection DNA replicate 2


title: ZRS-h13h2-DNA-3: ZRS-h13h2 transfection DNA replicate 3


title: ZFAND3-RNA-3: ZFAND3 transfection RNA replicate 3

value: Mouse INsulinoma 6, pancreatic beta cell line


title: ZRS-h13-DNA-1: ZRS-h13 transfection DNA replicate 1


title: ZFAND3-RNA-1: ZFAND3 transfection RNA replicate 1


title: ZFAND3 saturation mutagenesis library

value: Saturation mutagenesis MPRA library


title: ZFAND3-DNA-2: ZFAND3 transfection DNA replicate 2


title: ZRS-h13-DNA-3: ZRS-h13 transfection DNA replicate 3


title: ZFAND3-DNA-3: ZFAND3 transfection DNA replicate 3


title: ZRS-h13h2-RNA-3: ZRS-h13h2 transfection RNA replicate 3


title: UC88-RNA-1: UC88 transfection RNA replicate 1


title: IRF4 saturation mutagenesis library

value: 10-beta Electrocompetent E. coli (NEB C3020K)


title: UC88-DNA-3: UC88 transfection DNA replicate 3


title: UC88-DNA-1: UC88 transfection DNA replicate 1


title: UC88-DNA-2: UC88 transfection DNA replicate 2


title: TERT-HEK-RNA-3: TERT-HEK transfection RNA replicate 3


title: TERT-HEK-RNA-1: TERT-HEK transfection RNA replicate 1


title: TERT-HEK-DNA-3: TERT-HEK transfection DNA replicate 3


title: TERT-HEK-DNA-2: TERT-HEK transfection DNA replicate 2


title: TERT-HEK-DNA-1: TERT-HEK transfection DNA replicate 1


title: TCF7L2-RNA-2: TCF7L2 transfection RNA replicate 2


title: TCF7L2-RNA-3: TCF7L2 transfection RNA replicate 3


title: ZFAND3-DNA-1: ZFAND3 transfection DNA replicate 1


title: TCF7L2-DNA-3: TCF7L2 transfection DNA replicate 3


title: UC88-RNA-3: UC88 transfection RNA replicate 3


title: ZFAND3-RNA-2: ZFAND3 transfection RNA replicate 2


title: S76.F1

status: Public on Feb 07 2019

city: Santa Cruz

first: Christopher

last: Villarreal

state: CA

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

description:
PrimaryOrganoidAndPublishedCPM.txt
Raw data available at dbGaP under accession: phs000989.v3.p1

data_processing:
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
Human GRCh38.79.gtf
The listed genes in the processed data file are human genes mapped to each respective species using the comparative annotation toolkit (PMID: 29884752). Reads are mapped to each species' native genome and quantified based transcript models from comparative annotation toolkit.
The file GSE124299-metadata on processed samples.xlsx  includes the metadata for all samples in this study-- both the new samples listed in this Series and the re-analyzed samples, including accession IDs, when available.
Genome_build: Human: GRCh38.p2; NCBI:GCA_000001405.17
Genome_build: Chimpanzee: Clint_PTRv2 / UCSC: panTro6
Genome_build: Macaque: RheMac8
Supplementary_files_format_and_content: log(CPM+1)

source_name: iPS-derived cerebral organoid

growth_protocol: Cerebral organoids using Kadoshima et al., 2013 from Sasai lab

extract_protocol:
Fluidigm C1 small IFC (100-5759; 100-6201);  SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

tag: datecaptured

value: Female

tag: organoidid

tag: protocol

value: Kadoshima

tag: captureplate

tag: capturechamber


title: S75.E12

tag: tissue


title: S76.A2


title: S76.A3


title: TCF7L2-DNA-2: TCF7L2 transfection DNA replicate 2

tag: cell line

tag: cell type


title: S75.C11


title: S75.D11


title: S76.C1


title: TCF7L2-DNA-1: TCF7L2 transfection DNA replicate 1


title: UC88-RNA-2: UC88 transfection RNA replicate 2

value: Mouse neuroblastoma cell line


title: S75.B9


title: S75.A12


title: S218.G1

description: PrimaryOrganoidAndPublishedCPM.txt

organism: Macaca mulatta

source_name: Primary

value: Primary


title: S218.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S218.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S120.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S218.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: TCF7L2-RNA-1: TCF7L2 transfection RNA replicate 1


title: S120.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: Balb_c_4T1_5_35

status: Public on Feb 06 2019

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
Mapping using STAR (v 2.5.2a; parameters:  --runMode alignReads --genomeLoad LoadAndExit) to a combined human (GRCh38) and mouse (GRCm38) genome reference
The gene-level expression counts computed with featureCounts (v1.5.1) using the gene annotations obtained from RefSeq (release 70).
To normalize gene counts for cell-specific biases, we used size factors computed utilizing the deconvolution strategy developed by Lun et al. (2016) implemented in the scran (v1.6.5) package available on R/Bioconductor
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing the gene counts as obtained from featureCounts; processed_normalized_matrix_hs.txt.gz and processed_normalized_matrix_mm.txt.gz contain normalized counts for human and mouse,  respectively, using the method implemented in scran R/bioconductor package; sce_hs.rds.gz and sce_mm.rds.gz are R Data Format files containing a SingleCellExperiment class object for human and mouse, respectively.

source_name: CTC

extract_protocol:
Individual cells from CTC-WBC-clusters were mechanically separated with gentle micromanipulation (CellCelector, ALS). AF488/FITC-positive (or GFP-positive) and BV605-negative CTCs or AF488/FITC-negative and BV605-positive WBCs were immediately transferred into individual tubes (#321-032-501, Axygen) containing 2.5 μl RLT Plus lysis buffer (#1053393, Qiagen) and 1U/μl SUPERase In RNase Inhibitor (#AM2694, Invitrogen). Samples were immediately frozen on dry ice and kept at -80°C until further processing
Libraries were prepared with Smart -Seq2 protocol

tag: origin

value: mouse

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

value: CTC-single

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor

value: Balb


title: TERT-HEK-RNA-2: TERT-HEK transfection RNA replicate 2

value: Human embryonic kidney 293T cell line


title: S218.F1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid

tag: age (weeks)


title: Balb_c_4T1_5_33

source_name: WBC

value: CTC-single-WBC

value: WBC


title: Balb_c_4T1_Gra

source_name: Granulocytes

value: Granulocytes


title: Balb_c_4T1_plts

source_name: Platelets

value: Platelets


title: Balb_c_4T1_19


title: Balb_c_4T1_B_cell

source_name: B cells

value: B cells


title: Balb_c_4T1_Tcell

source_name: T cells

value: T cells


title: S218.D1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: captureplate

tag: capturechamber


title: Balb_c_4T1_17

value: CTC-cluster-WBC


title: Balb_c_4T1_13


title: Balb_c_4T1_9


title: Balb_c_4T1_15


title: Balb_c_4T1_18


title: Balb_c_4T1_5


title: Balb_c_4T1_16


title: Balb_c_4T1_6


title: Balb_c_4T1_7


title: Balb_c_4T1_12

source_name: CTC-WBC

value: CTC-WBC


title: Balb_c_4T1_10


title: Balb_c_4T1_14


title: Balb_c_4T1_1


title: PyMT_CTC_B9

value: transgenic

value: CTC-cluster

value: PyMT


title: Balb_c_4T1_2


title: PyMT_CTC_B5


title: Balb_c_4T1_3


title: Balb_c_4T1_Mono

source_name: Monocytes

value: Monocytes


title: PyMT_CTC_B8


title: PyMT_CTC_B4


title: Balb_c_4T1_11

value: mouse


title: PyMT_CTC_B6


title: PyMT_CTC_B3


title: Balb_c_4T1_8


title: Balb_c_4T1_NK

source_name: NK cells

value: NK cells


title: PyMT_CTC_B2

value: CTC


title: PyMT_CTC_B15


title: Balb_c_4T1_4

value: Balb


title: PyMT_CTC_B1


title: PyMT_CTC_A19


title: PyMT_CTC_B13


title: PyMT_CTC_A16


title: PyMT_CTC_A15


title: PyMT_CTC_B14


title: PyMT_CTC_A12


title: PyMT_CTC_A20


title: PyMT_CTC_A17


title: PyMT_CTC_A11


title: NSG_4T1_CTC_62

value: xenograft

value: NSG


title: NSG_4T1_CTC_56


title: NSG_4T1_CTC_61

value: WBC


title: NSG_4T1_CTC_45


title: NSG_4T1_CTC_44


title: NSG_4T1_CTC_37


title: NSG_4T1_CTC_43


title: NSG_4T1_CTC_35

value: CTC-single


title: NSG_4T1_CTC_25


title: NSG_4T1_CTC_17


title: NSG_4T1_CTC_36


title: NSG_4T1_CTC_55


title: NSG_4T1_CTC_129

value: CTC-single-WBC


title: PyMT_CTC_B7


title: NSG_4T1_CTC_14


title: NSG_4T1_CTC_127


title: NSG_4T1_CTC_16


title: NSG_4T1_CTC_116


title: Balb_c_4T1_5_20


title: NSG_4T1_CTC_128


title: LM2_CTC_G20


title: Balb_c_4T1_CTC_H13


title: Balb_c_4T1_CTC_37


title: Balb_c_4T1_CTC_H15


title: NSG_4T1_CTC_50


title: Balb_c_4T1_CTC_36


title: Balb_c_4T1_CTC_H14


title: Balb_c_4T1_CTC_32


title: Balb_c_4T1_CTC_28


title: Balb_c_4T1_CTC_27


title: Balb_c_4T1_CTC_31


title: Balb_c_4T1_CTC_30


title: Balb_c_4T1_CTC_29


title: Balb_c_4T1_CTC_25


title: NSG_4T1_CTC_117


title: Balb_c_4T1_CTC_21


title: NSG_4T1_CTC_126


title: Balb_c_4T1_CTC_23


title: Balb_c_plt

value: Platelets


title: Br16_NSG_Mono


title: Balb_c_Tcells

value: T cells


title: Br16_NSG_Gra

value: Granulocytes


title: Balb_c_4T1_CTC_22

value: CTC-cluster-WBC


title: NSG_Gra


title: Balb_c_NK


title: PLT_NSG

value: PLT


title: Balb_c_Bcells

value: B cells


title: Br16_C16


title: Balb_c_4T1_CTC_H12


title: Balb_c_Gra


title: Br16_B47


title: Br16_B27


title: PyMT_Gra

value: PyMT


title: NSG_NK


title: PyMT_Bcell


title: Br16_AC36


title: PyMT_NK


title: Br16_C14


title: Br16_B21


title: Br46_5_49

value: patient


title: Br16_6

value: CTC-cluster


title: Br46_6_Br30_2


title: Br16_5


title: Br16_4


title: Br16_B13

value: mouse


title: PLT_PYMT


title: Br7_5_WBC


title: Br46_1_45

value: CTC


title: NSG_Mono

value: Monocytes


title: PyMT_Tcell


title: Br16_8


title: Br16_7


title: Br7_4_WBC


title: Br46_4_48


title: Br16_2


title: Br7_1_BS

value: CTC-WBC


title: Br16_1


title: LM2_CTC_G32

value: xenograft


title: Br7_2


title: Brx50_NSG_CTC_A7


title: Brx50_NSG_CTC_A5


title: Brx50_NSG_CTC_A4


title: Balb_c_4T1_CTC_26

value: Balb


title: Br16_3


title: Br7_6


title: Br7_5

value: CTC-single


title: Br61_Mono


title: Brx50_NSG_CTC_A2


title: Br61_GRA


title: Br7_7_12


title: Br61_Tcells


title: Br61_CTC___6


title: Br61_CTC___50

value: WBC


title: LM2_CTC_G19


title: LM2_CTC_G33


title: Br7_1_SG


title: LM2_CTC_G34


title: Br61_CTC___48


title: Br61_CTC___47


title: Br61_CTC___49


title: Brx50_NSG_CTC_A6


title: Br61_CTC___42


title: Br61_CTC___43

value: CTC-single-WBC


title: Br61_CTC___39


title: Br61_NK

value: NK cells


title: Brx50_NSG_CTC_A3


title: Br61_CTC___34


title: Br61_CTC___35


title: Br61_CTC___25


title: Br61_PLTS

value: Platelets


title: Br61_CTC___15

value: CTC-cluster-WBC


title: Br61_CTC___44


title: Br61_CTC___4


title: Br61_CTC___38


title: Br61_CTC___36


title: Br57_CTC__8


title: Br57_CTC__5


title: Br61_Bcells


title: Br61_CTC___10


title: Br57_CTC__9


title: Br61_CTC___27


title: Br61_CTC___23


title: Br57_CTC__20


title: Br61_CTC___20


title: Br61_CTC___31


title: Br57_CTC__4


title: Br61_CTC___41


title: Br61_CTC___16


title: Br61_CTC___22


title: Br61_CTC___24


title: Br61_CTC___14


title: Br61_CTC___18


title: Br57_CTC__14


title: Br57_CTC__7


title: Br57_CTC__11


title: Br57_CTC__12


title: Br61_CTC___13


title: Br57_CTC__1


title: Br57_CTC__3


title: Br57_CTC__17


title: Br45_CTC_5


title: Br45_plt


title: Br45_Tcells

value: T cells


title: Br57_CTC__2


title: Br11_9


title: Br45_B_cells

value: B cells


title: Br45_CTC_3


title: Br57_CTC__13


title: Br57_CTC__15


title: Br57_CTC__16


title: Br11_7


title: Br61_CTC___45


title: Br11_6


title: Br53_CTC_4


title: Br11_3


title: Br57_CTC__10


title: Br53_CTC_1


title: Br11_19


title: Br11_18


title: Br53_CTC_3


title: Br45_Mono


title: Br11_15


title: Br45_CTC_6


title: Br11_13


title: Br45_NK


title: Br11_17


title: Br45_CTC_2


title: Br11_11


title: Br11_8


title: Br53_CTC_2


title: Br11_4


title: Br39_15


title: Br30_plts


title: HV1_plts


title: Br38_12


title: Hv3_plts


title: Hv2_plts


title: Br38_Mono


title: Br38_Bcell


title: Br38_NK


title: Br44_8


title: Br11_10


title: Br44_7


title: Br44_3


title: Br11_14


title: Br39_23


title: Br39_16


title: Br11_1


title: Br44_6


title: Br11_2


title: Br39_28


title: Br23_23


title: Br39_1


title: Br38_Tcell


title: Br23_24


title: Br23_15


title: Br23_12


title: Br38_6


title: Br23_29


title: Br38_5


title: Br38_Gra

value: Granulocytes


title: Br23_27

value: patient


title: Br23_30


title: Br30_12


title: Br44_1


title: Br37_1


title: Br23_20

value: CTC-cluster


title: Br23_14


title: Br23_25


title: HV3_Gra


title: Br30_Gra


title: Br37_2


title: HV3_Mono


title: Br23_28


title: Br23_13


title: Br30_11


title: Br38_plts


title: HV2_Bcell


title: HV2_Tcell


title: Br26_6


title: HV1_Gra


title: CD_LM2_45

value: CD


title: Br41_Bcells


title: HV3_NK


title: HV3_Tcell


title: HV2_NK


title: HV2_Gra


title: CD_LM2_41

value: CTC


title: HV3_Bcell


title: CD_LM2_37


title: CD_LM2_39


title: CD_LM2_34


title: Br30_Bcell


title: Br30_Tcell


title: CD_LM2_33


title: Br30_Mono

value: Monocytes


title: Br41_Mono


title: Br30_NK


title: CD_LM2_31


title: HV2_Mono


title: PLT_Br41

value: PLT


title: Br41_Tcells


title: CD_LM2_29

value: xenograft


title: Br23_26


title: Br41_NK


title: CD_LM2_38


title: CD_LM2_43


title: CD_LM2_44


title: CD_LM2_40


title: CD_LM2_27


title: CD_Br16_62


title: 6_HV1_Tcell


title: CD_LM2_32


title: CD_LM2_36


title: 7_HV1_Bcells


title: 8_HV1_Mono


title: CD_LM2_35


title: 5_HV1_NK


title: CD_Br16_65


title: CD_Br16_64


title: CD_Br16_52


title: CD_LM2_30


title: CD_Br16_60


title: CD_Br16_58


title: CD_Br16_56


title: CD_Br16_48


title: Br16_C17


title: CD_Br16_61


title: CD_Br16_59


title: Br16_C15


title: CD_Br16_55


title: CD_Br16_54


title: Br16_C11


title: CD_Br16_53


title: CD_LM2_28


title: Br16_C8


title: Br16_C34


title: Br16_C6


title: CD_Br16_51


title: CD_Br16_49


title: CD_Br16_50


title: Br16_C1


title: CD_Br16_57


title: CD_Br16_46


title: Br16_C33


title: Br16_B55


title: Br16_C13


title: CD_Br16_63


title: Br16_B52


title: CD_Br16_47


title: Br16_C12


title: Br16_B50


title: Br16_C4


title: CD_LM2_42


title: Br16_C10


title: Br16_B48


title: Br16_C7


title: Br16_C5


title: Br16_B34


title: Br16_B58


title: Br16_B30


title: Br16_B29


title: Br16_C3


title: Br16_B56


title: Br16_C2


title: Br16_B57


title: Br16_B60


title: Br16_B59


title: Br16_B26


title: Br16_B25


title: Br16_B49


title: Br16_B46


title: Br16_B22


title: Br16_B61


title: Br16_B19


title: Br16_B24


title: Br16_B53


title: Br16_B14


title: Br16_B10


title: Br16_B11


title: Br16_B51


title: Br16_B12


title: Br16_B6


title: Br16_B8


title: Br16_B32


title: Br16_B45


title: Br16_B20


title: Br16_B28


title: Br16_B2


title: Br16_B16


title: Br16_AC39


title: Br16_B33


title: Br16_AC35


title: Br16_B17


title: Br16_AC33


title: Br16_B7


title: Br16_AC20


title: Br16_AC18


title: Br16_AC16


title: Br16_AC15


title: Br16_B23


title: Br16_B5


title: Br16_B3


title: Br16_AC13


title: Br16_AC40


title: Br16_AC12


title: Br16_AC38


title: Br16_AC7


title: Br16_B31


title: Br16_AC6


title: LM2_G15


title: Br16_AC19


title: Br16_AC14


title: Br16_AC4


title: LM2_G10


title: LM2_G9


title: Br16_AC17


title: LM2_G5


title: LM2_G2


title: LM2_E7


title: LM2_E5


title: Br16_AC9


title: Br16_AC37


title: Br16_AC5


title: LM2_G13


title: Br16_AC34


title: LM2_E2


title: Br16_AC3


title: Br16_AC1


title: LM2_G6


title: LM2_G14


title: Br16_AC10


title: Br16_B4


title: LM2_G4


title: LM2_G11


title: LM2_G12


title: LM2_A89


title: LM2_A86


title: LM2_A90


title: Br16_AC8


title: LM2_A83


title: LM2_E4


title: LM2_G8

organism:
Homo sapiens
Mus musculus

value: CTC-WBC


title: LM2_G1


title: DamWT-Tcf7l2

status: Public on Jan 23 2019

city: Darlinghurst

first: Tomasz

last: Szczesnik

state: NSW

address: 405 Liverpool St

country: Australia

institute: Victor Chang Cardiac Research Institute

data_processing:
Library strategy: DamID-seq
Genomic alignment: bwa mem (version 0.7.15)
Remove reads not originating from a possible methylation site (GATC).
Sum all reads to give a count per GATC.
Genome_build: mm10
Supplementary_files_format_and_content: .bedgraph contains the read count at each GATC.

source_name: embryonic stem cell culture

growth_protocol: Mouse embryonic stem cells cultured in the usual way: gelatinised plates, mES + 2I (XV, UO126), split every 3 days.

extract_protocol:
Purlink genomic DNA extraction kit (Invitrogen #K182001).
DamID-seq. Overnight DpnI digestion produces blunt ends, onto with an illumina PE1 sequencing adapter is ligated overnight with T4 ligase. This is followed by Nextera library construction with the following differences: only the i7 adapter is used, 4 extra cycles are used for amplification, and a higher AMPure bead concentration (1.6x) is used.

treatment_protocol: Treated with doxycycline for the specified number of hours immediately prior to DNA extraction.

tag: tissue

value: embryonic stem cell culture

tag: strain

tag: dox treatment (hours)

tag: measure

value: adenine (GATC) methylation


title: LM2_A93

tag: origin

tag: number of cells

tag: number of ctc

tag: cell type


title: LM2_E6

tag: number of wbc attached

tag: sample type

value: CTC-single

tag: ctc-cluster size

tag: ctc-cluster id


title: Uninduced


title: LM2_E3

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor


title: MCF10A-scramble shRNA-TGFβ1-1.5hr rep2

status: Public on Jan 18 2019

city: Iowa City

first: Hank

last: Qi

state: IA

address: 1-632 Bowen Science Building

institute: University of Iowa

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then pseudo-aligned using the kallisto method
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files including lengths, counts and transcripts per million (TPM) for mRNA transcripts

growth_protocol: MCF10A cells were cultured in DMEM-F12 supplemented with 20 ng/ml Epidermal Growth Factor (EGF) (Sigma), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma), 500 ng/ml hydrocortisone (Sigma), and 5% horse serum. Cells were maintained in the specified medium supplemented with 1× Penicillin–Streptomycin (Gibco) and incubated in 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from MCF10A/control cells using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. The efficiency of PHF8 overexpression was determined by immunoblotting and qRT-PCR. RNA-seq libraries were made using the TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero™ Human/Mouse/Rat, RS-122-2201) and multiplexed with Illumina barcodes. Two biological duplicates of MCF10A/control samples treated with TGF-β1 for 1.5 hours were submitted for sequencing on a HiSeq2500 instrument following protocols supplied by Illumina (San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols. 50-bp paired-end reads were generated. More than 20 Mb reads were produced for each library.

treatment_protocol: TGF-β1 (Calbiochem) was added into the medium directly at 5 ng/ml.

value: Mammary Epithelial Cells

tag: cell line

tag: treatment

value: scramble shRNA TGF[beta]1


title: LM2_A94


title: genomic DNA from sample184

status: Public on Jan 16 2019

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples, resultng in 249874 data rows out of a possible 485577 (provided in the matrix_normalized.txt)

label: Cy5 and Cy3

source_name: case_whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: age

tag: Sex

value: M

tag: tissue

value: whole blood

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample36

description: whole blood case sample

value: F


title: LM2_A81

tag: origin

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

tag: cell type


title: LM2_E1

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor


title: MCF10A-scramble shRNA-TGFβ1-1.5hr rep1

tag: cell line

tag: treatment


title: genomic DNA from sample500

description: whole blood control sample

source_name: control_whole blood

tag: diagnosis

value: control

tag: age

tag: Sex

tag: tissue

tag: cellcount-nk

tag: cellcount-bcell


title: genomic DNA from sample537

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: DamR95A

tag: strain

tag: dox treatment (hours)

tag: measure


title: MCF10A-scramble shRNA rep2

tag: origin

value: scramble shRNA


title: genomic DNA from sample261

description: whole blood control sample


title: genomic DNA from sample489

description: whole blood case sample


title: genomic DNA from sample451

description: whole blood control sample


title: genomic DNA from sample242

description: whole blood control sample


title: genomic DNA from sample341

description: whole blood case sample


title: DamN126A-Tcf7l2


title: genomic DNA from sample322

description: whole blood case sample


title: genomic DNA from sample10

description: whole blood case sample


title: genomic DNA from sample533

description: whole blood case sample


title: genomic DNA from sample218

description: whole blood case sample


title: DamWT


title: genomic DNA from sample281

description: whole blood control sample


title: DamR95A-Tcf7l2


title: LM2_A85

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

tag: cell type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat


title: genomic DNA from sample491

description: whole blood case sample

tag: diagnosis

tag: age

tag: Sex

tag: tissue

tag: cellcount-nk


title: genomic DNA from sample147

description: whole blood case sample

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample33

description: whole blood case sample


title: genomic DNA from sample279

description: whole blood control sample


title: genomic DNA from sample331

description: whole blood case sample


title: genomic DNA from sample61

description: whole blood case sample


title: genomic DNA from sample132

description: whole blood case sample


title: genomic DNA from sample31

description: whole blood case sample


title: MCF10A-scramble shRNA rep1

tag: origin

tag: cell line

tag: treatment


title: genomic DNA from sample409

description: whole blood case sample


title: genomic DNA from sample149

description: whole blood control sample


title: genomic DNA from sample21

description: whole blood case sample


title: genomic DNA from sample527

description: whole blood control sample


title: genomic DNA from sample502

description: whole blood control sample


title: genomic DNA from sample99

description: whole blood case sample


title: genomic DNA from sample81

description: whole blood case sample


title: genomic DNA from sample87

description: whole blood case sample


title: genomic DNA from sample436

description: whole blood case sample


title: genomic DNA from sample186

description: whole blood control sample


title: genomic DNA from sample301

description: whole blood case sample


title: genomic DNA from sample372

description: whole blood control sample


title: genomic DNA from sample179

description: whole blood control sample


title: genomic DNA from sample522

description: whole blood case sample


title: genomic DNA from sample287

description: whole blood case sample


title: genomic DNA from sample92

description: whole blood case sample


title: genomic DNA from sample278

description: whole blood control sample


title: genomic DNA from sample156

description: whole blood control sample


title: genomic DNA from sample208

description: whole blood case sample


title: genomic DNA from sample263

description: whole blood control sample


title: genomic DNA from sample534

description: whole blood case sample


title: genomic DNA from sample139

description: whole blood case sample


title: genomic DNA from sample359

description: whole blood control sample


title: genomic DNA from sample46

description: whole blood case sample


title: genomic DNA from sample492

description: whole blood case sample


title: genomic DNA from sample244

description: whole blood control sample


title: genomic DNA from sample205

description: whole blood control sample


title: genomic DNA from sample45

description: whole blood case sample


title: genomic DNA from sample225

description: whole blood control sample


title: genomic DNA from sample297

description: whole blood case sample


title: genomic DNA from sample145

description: whole blood case sample


title: genomic DNA from sample142

description: whole blood case sample


title: genomic DNA from sample455

description: whole blood case sample


title: genomic DNA from sample220

description: whole blood control sample


title: DamN126A

tag: strain

tag: dox treatment (hours)

tag: measure


title: genomic DNA from sample472

description: whole blood control sample


title: genomic DNA from sample257

description: whole blood control sample


title: genomic DNA from sample201

description: whole blood control sample


title: genomic DNA from sample64

description: whole blood case sample


title: genomic DNA from sample232

description: whole blood case sample


title: genomic DNA from sample388

description: whole blood case sample


title: genomic DNA from sample206

description: whole blood control sample


title: genomic DNA from sample166

description: whole blood control sample


title: genomic DNA from sample386

description: whole blood control sample


title: genomic DNA from sample412

description: whole blood case sample


title: genomic DNA from sample532

description: whole blood case sample


title: genomic DNA from sample488

description: whole blood case sample


title: genomic DNA from sample168

description: whole blood control sample


title: genomic DNA from sample481

description: whole blood case sample


title: genomic DNA from sample47

description: whole blood case sample


title: genomic DNA from sample393

description: whole blood case sample


title: genomic DNA from sample421

description: whole blood case sample


title: genomic DNA from sample517

description: whole blood case sample


title: genomic DNA from sample501

description: whole blood case sample


title: genomic DNA from sample69

description: whole blood case sample


title: genomic DNA from sample358

description: whole blood control sample


title: genomic DNA from sample43

description: whole blood case sample


title: genomic DNA from sample124

description: whole blood case sample


title: genomic DNA from sample237

description: whole blood case sample


title: genomic DNA from sample423

description: whole blood case sample


title: genomic DNA from sample529

description: whole blood case sample


title: genomic DNA from sample438

description: whole blood case sample


title: genomic DNA from sample498

description: whole blood case sample


title: genomic DNA from sample445

description: whole blood case sample


title: genomic DNA from sample307

description: whole blood case sample


title: genomic DNA from sample26

description: whole blood case sample


title: genomic DNA from sample130

description: whole blood case sample


title: genomic DNA from sample518

description: whole blood case sample


title: genomic DNA from sample449

description: whole blood case sample


title: genomic DNA from sample512

description: whole blood control sample


title: genomic DNA from sample383

description: whole blood control sample


title: genomic DNA from sample355

description: whole blood control sample


title: genomic DNA from sample75

description: whole blood case sample


title: genomic DNA from sample374

description: whole blood case sample


title: genomic DNA from sample14

description: whole blood case sample


title: genomic DNA from sample325

description: whole blood case sample


title: genomic DNA from sample140

description: whole blood case sample


title: genomic DNA from sample101

description: whole blood case sample


title: genomic DNA from sample442

description: whole blood control sample


title: genomic DNA from sample125

description: whole blood case sample


title: genomic DNA from sample369

description: whole blood case sample


title: genomic DNA from sample196

description: whole blood control sample


title: genomic DNA from sample507

description: whole blood control sample


title: genomic DNA from sample348

description: whole blood case sample


title: genomic DNA from sample411

description: whole blood case sample


title: genomic DNA from sample525

description: whole blood case sample


title: genomic DNA from sample4

description: whole blood case sample


title: genomic DNA from sample119

description: whole blood case sample


title: genomic DNA from sample439

description: whole blood case sample


title: genomic DNA from sample499

description: whole blood control sample


title: genomic DNA from sample305

description: whole blood case sample


title: genomic DNA from sample15

description: whole blood case sample


title: genomic DNA from sample123

description: whole blood case sample


title: genomic DNA from sample406

description: whole blood case sample


title: genomic DNA from sample70

description: whole blood case sample


title: genomic DNA from sample536

description: whole blood case sample


title: genomic DNA from sample285

description: whole blood control sample


title: genomic DNA from sample59

description: whole blood case sample


title: genomic DNA from sample241

description: whole blood case sample


title: genomic DNA from sample351

description: whole blood control sample


title: genomic DNA from sample277

description: whole blood control sample


title: genomic DNA from sample181

description: whole blood control sample


title: genomic DNA from sample82

description: whole blood case sample


title: genomic DNA from sample394

description: whole blood case sample


title: genomic DNA from sample42

description: whole blood case sample


title: genomic DNA from sample44

description: whole blood case sample


title: genomic DNA from sample284

description: whole blood case sample


title: genomic DNA from sample290

description: whole blood case sample


title: genomic DNA from sample95

description: whole blood case sample


title: genomic DNA from sample306

description: whole blood case sample


title: genomic DNA from sample167

description: whole blood control sample


title: genomic DNA from sample153

description: whole blood control sample


title: genomic DNA from sample154

description: whole blood control sample


title: genomic DNA from sample229

description: whole blood control sample


title: genomic DNA from sample195

description: whole blood control sample


title: genomic DNA from sample250

description: whole blood control sample


title: genomic DNA from sample508

description: whole blood control sample


title: genomic DNA from sample253

description: whole blood control sample


title: genomic DNA from sample187

description: whole blood control sample


title: genomic DNA from sample27

description: whole blood case sample


title: genomic DNA from sample312

description: whole blood control sample


title: genomic DNA from sample407

description: whole blood case sample


title: genomic DNA from sample178

description: whole blood control sample


title: genomic DNA from sample448

description: whole blood control sample


title: genomic DNA from sample516

description: whole blood case sample


title: genomic DNA from sample248

description: whole blood control sample


title: genomic DNA from sample219

description: whole blood control sample


title: genomic DNA from sample313

description: whole blood case sample


title: genomic DNA from sample256

description: whole blood control sample


title: genomic DNA from sample476

description: whole blood case sample


title: genomic DNA from sample114

description: whole blood case sample


title: genomic DNA from sample329

description: whole blood case sample


title: genomic DNA from sample368

description: whole blood case sample


title: genomic DNA from sample324

description: whole blood control sample


title: genomic DNA from sample88

description: whole blood case sample


title: genomic DNA from sample336

description: whole blood control sample


title: genomic DNA from sample223

description: whole blood control sample


title: genomic DNA from sample73

description: whole blood case sample


title: genomic DNA from sample126

description: whole blood case sample


title: genomic DNA from sample276

description: whole blood control sample


title: genomic DNA from sample226

description: whole blood control sample


title: genomic DNA from sample48

description: whole blood case sample


title: genomic DNA from sample338

description: whole blood case sample


title: genomic DNA from sample417

description: whole blood case sample


title: genomic DNA from sample111

description: whole blood case sample


title: genomic DNA from sample430

description: whole blood control sample


title: genomic DNA from sample93

description: whole blood case sample


title: genomic DNA from sample367

description: whole blood control sample


title: genomic DNA from sample486

description: whole blood control sample


title: genomic DNA from sample343

description: whole blood control sample


title: genomic DNA from sample22

description: whole blood case sample


title: genomic DNA from sample454

description: whole blood case sample


title: genomic DNA from sample67

description: whole blood case sample


title: genomic DNA from sample150

description: whole blood control sample


title: genomic DNA from sample120

description: whole blood case sample


title: genomic DNA from sample190

description: whole blood control sample


title: genomic DNA from sample373

description: whole blood case sample


title: genomic DNA from sample354

description: whole blood control sample


title: genomic DNA from sample262

description: whole blood case sample


title: genomic DNA from sample357

description: whole blood control sample


title: genomic DNA from sample249

description: whole blood case sample


title: genomic DNA from sample135

description: whole blood case sample


title: genomic DNA from sample521

description: whole blood case sample


title: genomic DNA from sample339

description: whole blood case sample


title: genomic DNA from sample66

description: whole blood case sample


title: genomic DNA from sample89

description: whole blood case sample


title: genomic DNA from sample121

description: whole blood case sample


title: genomic DNA from sample105

description: whole blood case sample


title: genomic DNA from sample415

description: whole blood control sample


title: genomic DNA from sample234

description: whole blood control sample


title: genomic DNA from sample160

description: whole blood case sample


title: genomic DNA from sample462

description: whole blood case sample


title: genomic DNA from sample337

description: whole blood case sample


title: genomic DNA from sample505

description: whole blood case sample


title: genomic DNA from sample280

description: whole blood case sample


title: genomic DNA from sample376

description: whole blood control sample


title: genomic DNA from sample444

description: whole blood case sample


title: genomic DNA from sample71

description: whole blood case sample


title: genomic DNA from sample212

description: whole blood control sample


title: genomic DNA from sample334

description: whole blood case sample


title: genomic DNA from sample222

description: whole blood case sample


title: genomic DNA from sample35

description: whole blood case sample


title: genomic DNA from sample136

description: whole blood case sample


title: genomic DNA from sample418

description: whole blood case sample


title: genomic DNA from sample303

description: whole blood control sample


title: genomic DNA from sample266

description: whole blood control sample


title: genomic DNA from sample346

description: whole blood control sample


title: genomic DNA from sample360

description: whole blood control sample


title: genomic DNA from sample362

description: whole blood case sample


title: genomic DNA from sample211

description: whole blood case sample


title: genomic DNA from sample453

description: whole blood case sample


title: genomic DNA from sample32

description: whole blood case sample


title: genomic DNA from sample173

description: whole blood control sample


title: genomic DNA from sample400

description: whole blood case sample


title: genomic DNA from sample410

description: whole blood control sample


title: genomic DNA from sample420

description: whole blood case sample


title: genomic DNA from sample530

description: whole blood case sample


title: genomic DNA from sample224

description: whole blood control sample


title: genomic DNA from sample98

description: whole blood case sample


title: genomic DNA from sample129

description: whole blood case sample


title: genomic DNA from sample180

description: whole blood control sample


title: genomic DNA from sample340

description: whole blood control sample


title: genomic DNA from sample247

description: whole blood case sample


title: genomic DNA from sample233

description: whole blood control sample


title: genomic DNA from sample366

description: whole blood case sample


title: genomic DNA from sample483

description: whole blood case sample


title: genomic DNA from sample264

description: whole blood case sample


title: genomic DNA from sample29

description: whole blood case sample


title: genomic DNA from sample214

description: whole blood control sample


title: genomic DNA from sample473

description: whole blood control sample


title: genomic DNA from sample5

description: whole blood case sample


title: genomic DNA from sample510

description: whole blood control sample


title: genomic DNA from sample91

description: whole blood case sample


title: genomic DNA from sample117

description: whole blood case sample


title: genomic DNA from sample435

description: whole blood case sample


title: genomic DNA from sample151

description: whole blood control sample


title: genomic DNA from sample457

description: whole blood case sample


title: genomic DNA from sample304

description: whole blood case sample


title: genomic DNA from sample192

description: whole blood case sample


title: genomic DNA from sample165

description: whole blood control sample


title: genomic DNA from sample395

description: whole blood control sample


title: genomic DNA from sample416

description: whole blood case sample


title: genomic DNA from sample456

description: whole blood case sample


title: genomic DNA from sample402

description: whole blood case sample


title: genomic DNA from sample310

description: whole blood case sample


title: genomic DNA from sample3

description: whole blood case sample


title: genomic DNA from sample215

description: whole blood control sample


title: genomic DNA from sample432

description: whole blood case sample


title: genomic DNA from sample523

description: whole blood case sample


title: genomic DNA from sample464

description: whole blood case sample


title: genomic DNA from sample54

description: whole blood case sample


title: genomic DNA from sample389

description: whole blood case sample


title: genomic DNA from sample496

description: whole blood control sample


title: genomic DNA from sample493

description: whole blood case sample


title: genomic DNA from sample300

description: whole blood case sample


title: genomic DNA from sample302

description: whole blood case sample


title: genomic DNA from sample371

description: whole blood case sample


title: genomic DNA from sample246

description: whole blood control sample


title: genomic DNA from sample437

description: whole blood case sample


title: genomic DNA from sample399

description: whole blood case sample


title: genomic DNA from sample474

description: whole blood case sample


title: genomic DNA from sample209

description: whole blood control sample


title: genomic DNA from sample327

description: whole blood control sample


title: genomic DNA from sample106

description: whole blood case sample


title: genomic DNA from sample202

description: whole blood case sample


title: genomic DNA from sample141

description: whole blood case sample


title: genomic DNA from sample159

description: whole blood control sample


title: genomic DNA from sample294

description: whole blood case sample


title: genomic DNA from sample320

description: whole blood control sample


title: genomic DNA from sample528

description: whole blood case sample


title: genomic DNA from sample384

description: whole blood control sample


title: genomic DNA from sample85

description: whole blood case sample


title: genomic DNA from sample230

description: whole blood control sample


title: genomic DNA from sample443

description: whole blood case sample


title: genomic DNA from sample199

description: whole blood control sample


title: genomic DNA from sample188

description: whole blood control sample


title: genomic DNA from sample475

description: whole blood case sample


title: genomic DNA from sample2

description: whole blood case sample


title: genomic DNA from sample382

description: whole blood case sample


title: genomic DNA from sample193

description: whole blood control sample


title: genomic DNA from sample333

description: whole blood case sample


title: genomic DNA from sample326

description: whole blood case sample


title: genomic DNA from sample252

description: whole blood control sample


title: genomic DNA from sample127

description: whole blood case sample


title: genomic DNA from sample243

description: whole blood case sample


title: genomic DNA from sample148

description: whole blood control sample


title: genomic DNA from sample286

description: whole blood control sample


title: genomic DNA from sample110

description: whole blood case sample


title: genomic DNA from sample96

description: whole blood case sample


title: genomic DNA from sample503

description: whole blood control sample


title: genomic DNA from sample398

description: whole blood case sample


title: genomic DNA from sample49

description: whole blood case sample


title: genomic DNA from sample236

description: whole blood control sample


title: genomic DNA from sample377

description: whole blood case sample


title: genomic DNA from sample231

description: whole blood case sample


title: genomic DNA from sample424

description: whole blood case sample


title: genomic DNA from sample157

description: whole blood control sample


title: genomic DNA from sample404

description: whole blood case sample


title: genomic DNA from sample254

description: whole blood control sample


title: genomic DNA from sample363

description: whole blood case sample


title: genomic DNA from sample216

description: whole blood control sample


title: genomic DNA from sample311

description: whole blood case sample


title: genomic DNA from sample108

description: whole blood case sample


title: genomic DNA from sample163

description: whole blood control sample


title: genomic DNA from sample330

description: whole blood case sample


title: genomic DNA from sample112

description: whole blood case sample


title: genomic DNA from sample479

description: whole blood case sample


title: genomic DNA from sample463

description: whole blood case sample


title: genomic DNA from sample200

description: whole blood control sample


title: genomic DNA from sample60

description: whole blood case sample


title: genomic DNA from sample405

description: whole blood case sample


title: genomic DNA from sample191

description: whole blood case sample


title: genomic DNA from sample396

description: whole blood case sample


title: genomic DNA from sample428

description: whole blood control sample


title: genomic DNA from sample207

description: whole blood control sample


title: genomic DNA from sample490

description: whole blood control sample


title: genomic DNA from sample494

description: whole blood control sample


title: genomic DNA from sample240

description: whole blood control sample


title: genomic DNA from sample447

description: whole blood case sample


title: genomic DNA from sample381

description: whole blood case sample


title: genomic DNA from sample118

description: whole blood case sample


title: genomic DNA from sample446

description: whole blood case sample


title: genomic DNA from sample169

description: whole blood control sample


title: genomic DNA from sample379

description: whole blood case sample


title: genomic DNA from sample482

description: whole blood control sample


title: genomic DNA from sample269

description: whole blood control sample


title: genomic DNA from sample350

description: whole blood case sample


title: genomic DNA from sample484

description: whole blood control sample


title: genomic DNA from sample319

description: whole blood case sample


title: genomic DNA from sample332

description: whole blood case sample


title: genomic DNA from sample429

description: whole blood control sample


title: genomic DNA from sample361

description: whole blood case sample


title: genomic DNA from sample413

description: whole blood case sample


title: genomic DNA from sample378

description: whole blood case sample


title: genomic DNA from sample308

description: whole blood control sample


title: genomic DNA from sample51

description: whole blood case sample


title: genomic DNA from sample17

description: whole blood case sample


title: genomic DNA from sample18

description: whole blood case sample


title: genomic DNA from sample1

description: whole blood case sample


title: genomic DNA from sample273

description: whole blood control sample


title: genomic DNA from sample239

description: whole blood case sample


title: genomic DNA from sample309

description: whole blood case sample


title: genomic DNA from sample137

description: whole blood case sample


title: genomic DNA from sample28

description: whole blood case sample


title: genomic DNA from sample213

description: whole blood case sample


title: genomic DNA from sample235

description: whole blood control sample


title: genomic DNA from sample275

description: whole blood control sample


title: genomic DNA from sample55

description: whole blood case sample


title: genomic DNA from sample238

description: whole blood control sample


title: genomic DNA from sample267

description: whole blood control sample


title: genomic DNA from sample9

description: whole blood case sample


title: genomic DNA from sample138

description: whole blood case sample


title: genomic DNA from sample13

description: whole blood case sample


title: genomic DNA from sample177

description: whole blood case sample


title: genomic DNA from sample12

description: whole blood case sample


title: genomic DNA from sample514

description: whole blood control sample


title: genomic DNA from sample11

description: whole blood case sample


title: genomic DNA from sample519

description: whole blood case sample


title: genomic DNA from sample103

description: whole blood case sample


title: genomic DNA from sample485

description: whole blood case sample


title: genomic DNA from sample57

description: whole blood case sample


title: genomic DNA from sample295

description: whole blood control sample


title: genomic DNA from sample143

description: whole blood case sample


title: genomic DNA from sample347

description: whole blood case sample


title: genomic DNA from sample251

description: whole blood control sample


title: genomic DNA from sample468

description: whole blood case sample


title: genomic DNA from sample170

description: whole blood control sample


title: genomic DNA from sample134

description: whole blood case sample


title: genomic DNA from sample487

description: whole blood control sample


title: genomic DNA from sample431

description: whole blood case sample


title: genomic DNA from sample25

description: whole blood case sample


title: genomic DNA from sample441

description: whole blood control sample


title: genomic DNA from sample109

description: whole blood case sample


title: genomic DNA from sample74

description: whole blood case sample


title: genomic DNA from sample342

description: whole blood control sample


title: genomic DNA from sample515

description: whole blood control sample


title: genomic DNA from sample520

description: whole blood case sample


title: genomic DNA from sample296

description: whole blood case sample


title: genomic DNA from sample321

description: whole blood case sample


title: genomic DNA from sample408

description: whole blood case sample


title: genomic DNA from sample427

description: whole blood control sample


title: genomic DNA from sample227

description: whole blood case sample


title: genomic DNA from sample298

description: whole blood case sample


title: genomic DNA from sample282

description: whole blood control sample


title: genomic DNA from sample122

description: whole blood case sample


title: genomic DNA from sample197

description: whole blood control sample


title: genomic DNA from sample314

description: whole blood case sample


title: genomic DNA from sample155

description: whole blood control sample


title: genomic DNA from sample349

description: whole blood case sample


title: genomic DNA from sample128

description: whole blood case sample


title: genomic DNA from sample495

description: whole blood case sample


title: genomic DNA from sample434

description: whole blood case sample


title: genomic DNA from sample116

description: whole blood case sample


title: genomic DNA from sample56

description: whole blood case sample


title: genomic DNA from sample68

description: whole blood case sample


title: genomic DNA from sample265

description: whole blood case sample


title: genomic DNA from sample175

description: whole blood control sample


title: genomic DNA from sample39

description: whole blood case sample


title: genomic DNA from sample260

description: whole blood control sample


title: genomic DNA from sample478

description: whole blood control sample


title: genomic DNA from sample422

description: whole blood case sample


title: genomic DNA from sample58

description: whole blood case sample


title: genomic DNA from sample344

description: whole blood control sample


title: genomic DNA from sample323

description: whole blood case sample


title: genomic DNA from sample391

description: whole blood case sample


title: genomic DNA from sample77

description: whole blood case sample


title: genomic DNA from sample102

description: whole blood case sample


title: genomic DNA from sample524

description: whole blood case sample


title: genomic DNA from sample182

description: whole blood control sample


title: genomic DNA from sample20

description: whole blood case sample


title: genomic DNA from sample204

description: whole blood control sample


title: genomic DNA from sample426

description: whole blood case sample


title: genomic DNA from sample259

description: whole blood control sample


title: genomic DNA from sample511

description: whole blood case sample


title: genomic DNA from sample345

description: whole blood control sample


title: genomic DNA from sample353

description: whole blood control sample


title: genomic DNA from sample97

description: whole blood case sample


title: genomic DNA from sample268

description: whole blood control sample


title: genomic DNA from sample104

description: whole blood case sample


title: genomic DNA from sample401

description: whole blood case sample


title: genomic DNA from sample62

description: whole blood case sample


title: genomic DNA from sample185

description: whole blood control sample


title: genomic DNA from sample131

description: whole blood case sample


title: genomic DNA from sample470

description: whole blood case sample


title: genomic DNA from sample217

description: whole blood case sample


title: genomic DNA from sample52

description: whole blood case sample


title: genomic DNA from sample72

description: whole blood case sample


title: genomic DNA from sample63

description: whole blood case sample


title: genomic DNA from sample50

description: whole blood case sample


title: genomic DNA from sample258

description: whole blood control sample


title: genomic DNA from sample158

description: whole blood control sample


title: genomic DNA from sample8

description: whole blood case sample


title: genomic DNA from sample513

description: whole blood control sample


title: genomic DNA from sample113

description: whole blood case sample


title: genomic DNA from sample203

description: whole blood control sample


title: genomic DNA from sample41

description: whole blood case sample


title: genomic DNA from sample299

description: whole blood case sample


title: genomic DNA from sample174

description: whole blood control sample


title: genomic DNA from sample526

description: whole blood case sample


title: genomic DNA from sample356

description: whole blood control sample


title: genomic DNA from sample23

description: whole blood case sample


title: genomic DNA from sample65

description: whole blood case sample


title: genomic DNA from sample19

description: whole blood case sample


title: genomic DNA from sample504

description: whole blood control sample


title: genomic DNA from sample403

description: whole blood control sample


title: genomic DNA from sample471

description: whole blood case sample


title: genomic DNA from sample80

description: whole blood case sample


title: genomic DNA from sample531

description: whole blood case sample


title: genomic DNA from sample467

description: whole blood control sample


title: genomic DNA from sample293

description: whole blood control sample


title: genomic DNA from sample115

description: whole blood case sample


title: genomic DNA from sample90

description: whole blood case sample


title: genomic DNA from sample86

description: whole blood case sample


title: genomic DNA from sample210

description: whole blood control sample


title: genomic DNA from sample30

description: whole blood case sample


title: genomic DNA from sample450

description: whole blood case sample


title: genomic DNA from sample94

description: whole blood case sample


title: genomic DNA from sample171

description: whole blood control sample


title: genomic DNA from sample460

description: whole blood case sample


title: genomic DNA from sample144

description: whole blood case sample


title: genomic DNA from sample535

description: whole blood control sample


title: genomic DNA from sample328

description: whole blood case sample


title: genomic DNA from sample316

description: whole blood case sample


title: genomic DNA from sample452

description: whole blood case sample


title: genomic DNA from sample16

description: whole blood case sample


title: genomic DNA from sample466

description: whole blood case sample


title: genomic DNA from sample40

description: whole blood case sample


title: genomic DNA from sample392

description: whole blood case sample


title: genomic DNA from sample221

description: whole blood control sample


title: genomic DNA from sample255

description: whole blood control sample


title: genomic DNA from sample387

description: whole blood case sample


title: genomic DNA from sample315

description: whole blood case sample


title: genomic DNA from sample469

description: whole blood case sample


title: genomic DNA from sample152

description: whole blood control sample


title: genomic DNA from sample283

description: whole blood case sample


title: genomic DNA from sample24

description: whole blood case sample


title: genomic DNA from sample100

description: whole blood case sample


title: genomic DNA from sample364

description: whole blood case sample


title: genomic DNA from sample245

description: whole blood case sample


title: genomic DNA from sample419

description: whole blood case sample


title: genomic DNA from sample458

description: whole blood case sample


title: genomic DNA from sample83

description: whole blood case sample


title: genomic DNA from sample414

description: whole blood case sample


title: genomic DNA from sample425

description: whole blood control sample


title: genomic DNA from sample198

description: whole blood control sample


title: genomic DNA from sample385

description: whole blood case sample


title: genomic DNA from sample318

description: whole blood case sample


title: genomic DNA from sample84

description: whole blood case sample


title: genomic DNA from sample164

description: whole blood control sample


title: genomic DNA from sample189

description: whole blood control sample


title: genomic DNA from sample53

description: whole blood case sample


title: genomic DNA from sample397

description: whole blood case sample


title: genomic DNA from sample477

description: whole blood control sample


title: genomic DNA from sample288

description: whole blood control sample


title: genomic DNA from sample183

description: whole blood case sample


title: genomic DNA from sample272

description: whole blood control sample


title: genomic DNA from sample506

description: whole blood case sample


title: genomic DNA from sample271

description: whole blood control sample


title: genomic DNA from sample7

description: whole blood case sample


title: genomic DNA from sample497

description: whole blood control sample


title: genomic DNA from sample317

description: whole blood case sample


title: genomic DNA from sample465

description: whole blood case sample


title: genomic DNA from sample335

description: whole blood case sample


title: genomic DNA from sample172

description: whole blood control sample


title: genomic DNA from sample228

description: whole blood control sample


title: genomic DNA from sample461

description: whole blood case sample


title: genomic DNA from sample365

description: whole blood case sample


title: genomic DNA from sample370

description: whole blood case sample


title: genomic DNA from sample78

description: whole blood case sample


title: genomic DNA from sample133

description: whole blood case sample


title: genomic DNA from sample37

description: whole blood case sample


title: genomic DNA from sample480

description: whole blood control sample


title: genomic DNA from sample274

description: whole blood control sample


title: genomic DNA from sample38

description: whole blood case sample


title: genomic DNA from sample194

description: whole blood case sample


title: genomic DNA from sample76

description: whole blood case sample


title: genomic DNA from sample440

description: whole blood control sample


title: genomic DNA from sample146

description: whole blood control sample


title: genomic DNA from sample390

description: whole blood case sample


title: genomic DNA from sample380

description: whole blood control sample


title: genomic DNA from sample289

description: whole blood case sample


title: genomic DNA from sample79

description: whole blood case sample


title: genomic DNA from sample292

description: whole blood case sample


title: genomic DNA from sample162

description: whole blood control sample


title: genomic DNA from sample509

description: whole blood case sample


title: genomic DNA from sample161

description: whole blood control sample


title: genomic DNA from sample270

description: whole blood control sample


title: genomic DNA from sample433

description: whole blood control sample


title: genomic DNA from sample34

description: whole blood case sample


title: genomic DNA from sample107

description: whole blood case sample


title: genomic DNA from sample291

description: whole blood control sample


title: genomic DNA from sample352

description: whole blood case sample


title: genomic DNA from sample375

description: whole blood case sample


title: ChIP-seq siSpt6 gH2AX R2

status: Public on Nov 21 2018

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
Nascent RNAs were purified from Pol II IP products of solublilized chromatin. DNA were purified from chromatin IP products.
Libraries were prepared according to the protocols of NEBNext small RNA library preparation kit (NEB) for mNET-seq; NEBNext Ultra II Directional RNA Library preparation kit (NEB) for Chromatin, Nucleoplasmic, Cytoplasmic and Nuclear poly(A)+ RNA-seq and RDIP-seq; QuantSeq 3' mRNA-Seq library preparation kit REV for Illumina (Lexogen) for 3'RNA-seq; NEBNext Ultra II DNA Library preparation kit (NEB) for mNucD-seq and ChIP-seq

treatment_protocol: siRNAs were transfected for 55-60 hours according to RNAiMAX reagent protocol.

value: HeLa

tag: antibody

value: 05-636:Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301. Merck Millipore

tag: knockdown


title: genomic DNA from sample176

description: whole blood control sample


title: ChIP-seq siSpt6 INTS3 R2

value: 16620-1-AP:INTS3 antibody, Rabbit Polyclonal. Proteintech


title: genomic DNA from sample6

description: whole blood case sample


title: genomic DNA from sample459

description: whole blood case sample


title: ChIP-seq siSpt6 INTS3 R1


title: ChIP-seq siSpt6 Input R3


title: ChIP-seq siSpt6 Input R2


title: ChIP-seq siSpt6 gH2AX R1


title: ChIP-seq siLuc gH2AX R2

value: siLuc


title: ChIP-seq siLuc Input R2


title: ChIP-seq siSpt6 Input R1


title: ChIP-seq siLuc INTS3 R2


title: ChIP-seq siLuc Input R3


title: ChIP-seq siLuc INTS3 R1


title: mNucD-seq siSpt6 H3K36me3 R2

data_processing:
Library strategy: mNucD-seq
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

value: MABIO333:Anti-trimethyl Histone H3 (Lys36) mAb. MBL International Corporation


title: ChIP-seq siLuc Input R1


title: mNucD-seq siSpt6 H3 R1

value: MABIO301:Anti-Histone H3 mAb. MBL International Corporation


title: mNucD-seq siSpt6 H3K36me3 R1


title: mNucD-seq siLuc H3K36me3 R2

value: MABIO333:Anti-trimethyl Histone H3 (Lys36) mAb. MBL International Corporation.


title: ChIP-seq siLuc gH2AX R1


title: mNucD-seq siLuc Input R1


title: mNucD-seq siSpt6 Input R2


title: mNucD-seq H3K36me3 R1


title: mNucD-seq siSpt6 H3 R2


title: mNucD-seq siSpt6 Input R1


title: mNucD-seq siLuc H3 R1


title: mNucD-seq H3K4me1 R2

value: MABI0302:Anti-monomethyl Histone H3 (Lys4) mAb. MBL International Corporation


title: mNucD-seq H3K4me3 R2

value: MABIO304:Anti-trimethyl Histone H3 (Lys4) mAb. MBL International Corporation


title: 3' RNA-seq siSpt6 R3


title: mNucD-seq siLuc H3K36me3 R1


title: 3' RNA-seq siSpt6 R2


title: 3' RNA-seq siSpt6 R1


title: mNucD-seq H3K4me1 R1


title: mNucD-seq siLuc Input R2


title: mNucD-seq H3K36me3 R2


title: 3' RNA-seq siLuc R2


title: mNucD-seq Input R1


title: mNucD-seq H3K27me3 R2

value: MABIO323:Anti-trimethyl Histone H3 (Lys27) mAb. MBL International Corporation


title: mNucD-seq H3K27me3 R1


title: mNucD-seq H3K4me3 R1


title: genomic DNA from neuroblastoma 172

status: Public on Dec 19 2018

city: Heidelberg

first: Kai-Oliver

last: Henrich

address: INF 280

institute: German Cancer Research Center DKFZ

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Raw data files generated from the array usage were preprocessed using the minfi Bioconductor package (preprocessIllumina function).

source_name: neuroblastoma 172

extract_protocol: Genomic DNA was extracted from snap-frozen neuroblastoma tissue using standard procedures.

tag: tert status

value: TERT non-rearranged

tag: alt status

value: ALT negative

tag: mycn status

value: MYCN-amplified

tag: atrx status

value: ATRX non-mutated

value: TERT expression low

value: neuroblastoma


title: 3' RNA-seq siLuc R3


title: Nuclear poly(A)+ RNA-seq siSpt6 R1


title: Cytoplasmic RNA-seq siSpt6 R2


title: mNucD-seq Input R2


title: Cytoplasmic RNA-seq siLuc R2


title: Cytoplasmic RNA-seq siSpt6 R1


title: 3' RNA-seq siLuc R1


title: Nucleoplasmic RNA-seq siSpt6 R3


title: Nuclear poly(A)+ RNA-seq siSpt6 R2


title: Nuclear poly(A)+ RNA-seq siLuc R2


title: Nuclear poly(A)+ RNA-seq siLuc R1


title: Nucleoplasmic RNA-seq siLuc R2


title: Cytoplasmic RNA-seq siLuc R1


title: Nucleoplasmic RNA-seq siSpt6 R2


title: Nucleoplasmic RNA-seq siLuc R3


title: Nucleoplasmic RNA-seq siSpt6 R1


title: Chromatin RNA-seq siLuc R4


title: Total mNET-seq siSpt6 R2

data_processing:
Library strategy: mNET-seq
Adapters were trimmed with BBduk (3' RNA-seq) or with Cutadapt v1.9.1 (mNET-seq, others RNA-seq, ChIP-seq and mNucD-seq)
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq and RNA-seq) or with Bowtie2 v2.2.5 (ChIP-seq, mNucD-seq, 3' RNA-seq and RDIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq and mNucD-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
RNA-seq differential expression was performed with HTseq and DESeq2.
Bigwig files were generated with the bedGraphToBigWig script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

value: MABIO601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation


title: Nucleoplasmic RNA-seq siLuc R1

value: HeLa