title: ChIP-Seq Apicidin H3K4me3 rep1


title: AM_D14_Rep1

status: Public on Apr 03 2017

type: SRA

city: denver

first: steve

middle: C

last: pugliese

state: CO

address: 12700 East 19th Avenue

department: Medicine

country: USA

institute: University of Colorado

library_source: transcriptomic

data_processing:
Derived sequences were analyzed by applying a custom computational pipeline consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and ascertainment of differential gene expression (CITES). In short, reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks, and differential expression analyzed with ANOVA in R.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing average FKPM data (3 samples) for control sea level macrophage and hypoxic macrophage counterpart (IM D4 or D14, AM D4 or D14).  Fold change, P value, q value and individual FKPM values for each sample also listed

molecule: total RNA

organism: Mus musculus

source_name: Alveolar macrophage hypoxia day 14

extract_protocol:
Mice lung was digested, macrophages were facs sorted and RNA was isolated using trizol extraction and qiagen Rneasy MinElute kit
RNA libraries were prepared for sequencing using standard Illumina protocols with Nugen ovation amplication kit

treatment_protocol: mice remained at sea level or were exposed to simulated altitude of 18,000 feet

tag: strain

tag: tissue

value: lung

tag: tissue compartment

value: alveolus

tag: cell type

value: macrophage


title: AM_D4_Rep3

source_name: Alveolar macrophage hypoxia day 4


title: AM_D14_Rep3


title: ChIP-Seq DMSO H3K4me3 rep2

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

library_source: genomic

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
After preprocessing, the RNA sequenced reads were mapped to T.vaginalis genome using RSEM with bowtie2 v2.0.0-beta7.
ChIP sequence reads were mapped to T.vaginalis genome using bowtie2 v2.0.0-beta7.
FPKM (fragments per kilobase of exon per million fragments mapped) for RNA-Seq were calculated using RSEM.
ChIP-Seq read counts were calculated for each gene using HTSeq v0.6.1 and were converted log2 CPM (count per million) values using Bioconductor package edgeR v3.6.8
Peaks for ChIP-seq data were called using HOMER with the options: -gsize 176000000 -F 2, -fdr 0.05 -size 150 -minDist 150.
Genome_build: ASM282v1
Supplementary_files_format_and_content: RNA-Seq bigwig files were generated using RSEM and ChIP-Seq bigwig files were generated using Galaxy tools.

molecule: genomic DNA

organism: Trichomonas vaginalis

source_name: Trichomonas vaginalis_ChIP-Seq DMSO H3K4me3

growth_protocol: The T016 strain of Trichomonas vaginalis was axenically subcultivated at 37°C in Diamond’s trypticase–yeast extract–maltose (TYM) medium with 10% heat-inactivated horse serum and 0.5% penicillin/streptomycin.

extract_protocol:
Genomic DNA extraction protocol not provided.
ChIP-seq library construction protocol not provided.

treatment_protocol: HDAC inhibitor, apicidin (70nM) and TSA (1μM) were treated for 4hrs.

tag: treatment

value: DMSO

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: AM_D4_Rep2


title: oRG_OSVZ_sc123

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

country: China

institute: China Medical University

description: single cell sequencing

data_processing:
Adaptor contamination and low-quality reads were removed from the raw data
TopHat (version 2.0.10) was used for sequence alignment, and FPKM values were generated by Cufflinks (version 2.1.1)
Remove genes with average FPKM<1

molecule: polyA RNA

organism: Homo sapiens

source_name: human embroynic outer radial glial cell (oRG)

extract_protocol:
The single cells were lysed. The released mRNAs were reverse translated into cDNAs and were amplified. The amplified cDNAs were fragmented to about 200bp, and were constructed into the cDNA library.
manual of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370L)
cDNA libraries were sequenced on Illumina HiSeq 2500 instruments

tag: developmental stage

value: embryo

tag: Stage

value: prenatal human brain

tag: cell subtype

tag: sequence type

value: single cell sequencing


title: 07_R102_DRG

city: Glostrup

first: Lisette

last: Kogelman

address: Nordre Ringvej 67

department: Danish Headache Centre

country: Denmark

institute: Rigshospital Glostrup

description: PolyA RNA

data_processing:
Filtering using NGSQC toolkit, default settings.
Alignment using STAR.
Quantification of reads using HTSeq.
Genome_build: Rattus norvegicus 6.0.83 (Rnor_6.0)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count data (output from HTSeq).

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Reversed night/day conditions, food and water ad lib.

extract_protocol:
TG and DRG were dissected and frozen in isopentane on dry ice.
RNA extracted using NucleoSpin RNA kit in combination with QIAzol. mRNA isolated using poly(A) selection.
Sequencing on Illumina HiSeq 2500 platform.

treatment_protocol: Anaesthetized with intraperitoneal injection of pentobarbital with lidocaine, perfused with cold saline to remove blood from tissue.

tag: strain/background

value: Wistar Han

value: Dorsal root ganglia

tag: age

value: 10 weeks

tag: Sex

value: male

tag: rat identifier


title: AM_D4_Rep1


title: RNA-Seq TSA

source_name: Trichomonas vaginalis_RNA-Seq TSA

extract_protocol:
Total RNA from purified cells was isolated with the GeneAll Biotechnology Hybrid-R Total RNA kit.
Libraries were prepared according to Illumina's Truseq Stranded mRNA kit.

value: TSA


title: IM_D4_Rep2

source_name: interstitial macrophage hypoxia day 4

value: interstitial


title: AM_SL_Rep2

source_name: Aleolar macrophage sea level


title: RNA-Seq Apicidin rep2

source_name: Trichomonas vaginalis_RNA-Seq Apicidin

value: Apicidin


title: WT_2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description:
RNA later treated
W2

data_processing:
Each transcriptome was loaded to occupy 1/4 of the lane capacity in a flow cell. C-Bot (TruSeq PE Cluster Kit v3, Illumina) was used for cluster generation and Illumina HiSeq2000 platform (TruSeq SBS Kit v3 reagent kit) for paired end sequencing
100M reads obtained for wild type and control respectively
100bp paired-end reads were then quality trimmed to a length of 93bp
For differential gene expression, sequences were aligned against the TAIR10 genome using TopHat (v2.0.8b) with the options --bowtie1 and --no-discordant in two runs and a mean inner distance between mate pairs of 112 to 133 (std dev 50). Transcript counts werecalculated with HTSeq with features marked in the Ensembl v72 TAIR10 Gene Transfer Format annotation. Differential gene expression was assessed with the DEseq package.
For splicing analysis, quality filtered reads in FASTQ format were trimmed to 80 nucleotide using the rMATS trimFastq python script. The trimmed reads were then aligned to the TAIR10 genome build using STAR.
Supplementary_files_format_and_content: DEseq_DifferentialGeneExpression.txt: differential gene expression in tab delimited text file
Supplementary_files_format_and_content: rMATs_A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative 5' splicing in tab delimited text format
Supplementary_files_format_and_content: rMATs_MXE.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, mutually exclusive exons in tab delimited text format
Supplementary_files_format_and_content: rMATs_RI.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, retained introns in tab delimited text format
Supplementary_files_format_and_content: rMATs_SE.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative splicing, skipped exons in tab delimited text format
Supplementary_files_format_and_content: rMATs_A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt: Alternative 3' splicing in tab delimited text format

organism: Arabidopsis thaliana

source_name: root tips

growth_protocol: 5-days old seedlings

extract_protocol:
seedlings treated with RNA later, RNA extracted with Ambion RNA kit (AM1919)
The poly(A)+ RNA was reverse transcribed to cDNA (SuperScript Double-Stranded cDNA Synthesis Kit, Life Technologies). Random hexamers (New England BioLabs) were used for priming the first strand synthesis reaction and SPRI beads (Agencourt AMPure XP, Beckman Coulter) for purification of cDNA. Illumina compatible Nextera Technology (Illumina) was used for preparation of RNA-seq libraries, employing DNA fragmentation and tagging by in vitro cut-and-paste transposition. 60 ng of cDNA was used instead of DNA. After the tagmentation reaction, the fragmented cDNA was purified with SPRI beads. In order to add the Illumina specific bridge PCR compatible sites and enrich the library, limited-cycle PCR (5 cycles) was performed according to the instructions for the Nextera system with minor modifications. For bar coded libraries, 50 X Nextera Adaptor 2 was replaced with a bar coded Illumina-compatible Adaptors from the Nextera Bar Codes kit (Illumina) in PCR setup. SPRI beads were used for purification of the PCR-products and the library QC was evaluated by Agilent Bioanalyzer (Agilent).

treatment_protocol: MS medium

tag: genotype/variation

value: WT

tag: ecotype

tag: tissue source

value: 2mm root tips


title: RNA-Seq Apicidin rep1

tag: strain


title: IM_SL_Rep3

source_name: interstitial macrophage sea level

tag: tissue

value: lung


title: AM_SL_Rep1

tag: tissue compartment

value: alveolus


title: RNA-Seq DMSO rep3

source_name: Trichomonas vaginalis_RNA-Seq DMSO


title: Veh3

city: Cleveland

first: Aleksander

last: Tworak

state: Ohio

address: 2109 Adelbert Rd

department: SOM Pharmacology

institute: Case Western Reserve University

description: unchallenged

data_processing:
Base-calling and alignment were performed using the Illumina pipeline software ELAND v1.7. Reads from two lanes for each sample were combined in one raw file.
Raw reads were processed and aligned with the University of California–Santa Cruz (UCSC; Santa Cruz, CA, USA) mouse genome assembly and transcript annotation (mm10) using the Genomic Short-read Nucleotide Alignment Program (GSNAP).
The Rsubread package  was used for reads quantification.
Genes with less than 0.5 counts per million mapped reads in at least three libraries were removed from the subsequent analysis. In addition, datasets were corrected against potential photoreceptor contamination by removing a set of genes exhibiting very high expression in mouse photoreceptors, as compared to the RPE.
Data normalization and differential expression analysis were performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes annotation data, differential expression analysis (Trt vs Veh), and normalized raw read counts.

source_name: Retinal pigment epithelium_unchallenged

growth_protocol: The RPE was isolated from 10- to 12-day-old C57BL/6J mice as described previously (Diemer et al., Adv Exp Med Biol. 2008). Disrupted RPE cells were seeded onto 24-well, 0.4-μm transwell permeable supports (Corning Inc., Corning, NY) with the RPE from ∼1 eye/well to allow polarization of cells. Cells were grown for 5–6 d at 37°C in 5% CO2 before their use in phagocytosis assays.

extract_protocol:
POS-challenged (Trt) and control (Veh) RPE cells (n=3) were used for RNA isolation with Trizol (ThermoFisher Scientific), followed by poly(A) RNA fraction isolation with an Oligotex kit (Qiagen), according to the manufacturer's directions. Six cDNA libraries were generated (one for each biological replicate under each condition) and run separately, each on two lanes of the Genome Analyzer IIx (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultured RPE cells were challenged with mouse POS membranes for 1.5 h at a density of ~10 POS/RPE cell at 37 oC in 5% CO2. Cells were subsequently washed three times with DPBS, suspended in 100 uL of DPBS/well and transferred to a 1.5 mL centrifuge tube. Cells then were pelleted at 1500g at 4oC for 15 min. The supernatant was discarded and cell pellets were suspended in RNAlater stabilization reagent (Qiagen, Valencia, CA).

tag: cell type

value: Retinal pigment epithelium

tag: culture method

value: Primary culture


title: ChIP-Seq TSA H3K4me3

source_name: Trichomonas vaginalis_ChIP-Seq TSA H3K4me3

tag: treatment

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: Veh2

description: unchallenged


title: RNA-Seq DMSO rep1

value: DMSO


title: Trt3

description: challenged with POS

source_name: Retinal pigment epithelium_challenged with POS


title: AM_D14_Rep2

value: macrophage


title: Veh1

description: unchallenged


title: RNA-Seq DMSO rep2


title: TSA Input

source_name: Trichomonas vaginalis_TSA Input


title: Trt2

description: challenged with POS


title: Trt1

description: challenged with POS


title: Apicidin input

source_name: Trichomonas vaginalis_Apicidin input


title: DMSO Input

source_name: Trichomonas vaginalis_DMSO Input


title: Wild-type (1hr)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Sequence fragments were aligned on TAIR10 genome using bowtie program (version 1.1.2).
Only pairs whose distance was less than 1kb were counted using our in-house program and peaks were identified using MACS2 program (version 2.1.1).
Genome_build: tair10
Supplementary_files_format_and_content: wiggle

source_name: whole plant

growth_protocol: Wild-type arabidopsis taliana (Col-0) were grown on soil for 14days.

extract_protocol:
Please see Kim et al. (2014) Methods in Mol.Biol.;1062:405-26. doi: 10.1007/978-1-62703-580-4_22. ChIP assay  was used  Histon H4 ac antibody (Millipore 06-866).
Bar-code sequencing by SOLiD 5500 standard protocol  (Thermo Fisher Scientific)
Used SOLiD 5500 standard protocol for ChIP-seq.

treatment_protocol: Treated with 10mM acetici acid solution or water for 9days. Solutions were added to soil.

tag: time

value: not treated

tag: antibody

value: Histone H4 ac antibody (Millipore 06-866)


title: ChIP-Seq TSA H3K27Ac

source_name: Trichomonas vaginalis_ChIP-Seq TSA H3K27Ac

value: H3K27Ac (Abcam, ab4729)


title: RNA-Seq Apicidin rep3


title: ChIP-Seq DMSO H3K27Ac rep2

source_name: Trichomonas vaginalis_ChIP-Seq DMSO H3K27Ac


title: Treated with acetic acid (9hr)

value: acetic acid


title: Treated with acetic acid (1hr)


title: Wild-type (9hr)


title: Input

value: control


title: Wild-type without treatment (0hr)


title: ChIP-Seq DMSO H3K27Ac rep1


title: ChIP-Seq Apicidin H3K27Ac rep2

source_name: Trichomonas vaginalis_ChIP-Seq Apicidin H3K27Ac


title: Clone_8_Kappa-VJ-seq

status: Public on Apr 01 2017

city: Jerusalem

first: Yehudit

last: Bergman

address: Hebrew University Medical School, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Library strategy: Kappa-VJ-seq
ATAC-seq: Basecalls were derived from the standard illumina Nextseq 500 software. Adapter sequences and low quality bases were removed from reads using trim_galore. Processed reads were mapped using bowtie2 to the mm10 mouse genome, where nucleotides located on SNPs from the castaneous genome were masked (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR-duplicate reads were removed with Picard. Peaks of open chromatin were called from all of the mapped reads using Homer software43. Allelic reads within peaks were counted using HTseq-count.
Nuclear RNA-seq - Basecalls were derived from the standard Illumina Nextseq 500 software or HiSeq1000 RTA software. Adapter sequences and low quality bases were removed from reads using trim_galore. Reads were mapped to the mm10 mouse genome using bowtie2, after masking nucleotides located on SNPs from the cast genome (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR duplicates removed using Picard (Broad institute). Read coverage tracks were made using bedtools. Reads over ENSEMBL genes were counted with HTseq-count.
Kappa-VJ-seq - Basecalls were derived from the standard illumina Miseq software. sequences were quality trimmed (trim_galore) and aligned to a hybrid B6/Cast genome assembly using bowtie2, with Cast polymorphic sites substituted based on the Sanger Mouse Genome Project database (release 1505). Reads over each Vκ segment were counted (HTseq-count) and normalized to the total mapped rearranged fragment number to allow comparison of the Vκ repertoire contribution between different libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Total and allelically sorted alignments from ATAC-seq and RNA-seq - bedgraph format. Mapped allelic Vkappa rearrangement read counts from Igk-VJ-seq - txt format

source_name: Bone marrow derived pre-B cell

growth_protocol: Cells isolated from the bone marrow of B6/Cast mice were grown in RPMI 1640 + 10% FBS, penicillin-streptomycin (Gibco), L-glutamine (Gibco) and 50 μM of β-Mercaptoethanol (Gibco) on irradiated ST2 feeder cells. IL-7 was added to conditioned medium collected from J558L-IL7 secreting cells (as provided by A. Rolink) in order to select for pre-B cell populations.

extract_protocol: ATAC-seq - Nuclei from ~50,000 cells were isolated using NP-40-containing buffer. Extracted nuclei were treated with transposed with Nextera (illumina) Tn5 transposase for 30 minutes. Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes. Libraries were then sequenced using Illumina NextSeq 500 with 2x75 bp or 2x35 reads. Nuclear RNA-seq - Nuclei were obtained from 16 million cells per sample by incubation in 4 ml 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40, 5 min on ice, followed by a wash with the same solution without NP40. RNA was isolated with RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion). RNA was depleted of Ribosomal RNA with RiboZero-gold (Illumina). Stranded RNA-seq libraries were prepared following standard second-strand dU incorperating protocols (Parkhomchuk et al., 2009). Kappa-VJ-seq - RNA was extracted from cells with Highpure RNA isolation kit (Roche). RNA was poly-A enriched using poly-dT beads (Life technologies) in two selection cycles and RT then performed using AffinityScript QPCR cDNA Synthesis Kit (Agilent) with an RT primer specific for the Cκ region 5’-ATGCTGTAGGTGCTGTCTTT-3’. The residual RNA was degraded with 0.1N NaOH, neutralized with 0.1M acetic acid and the single strand cDNA then purified using Silane beads (Life technologies). A 3TR3 adapter ('5-/Phos/ AGATCGGAAGAGCACACGTCTG/3SpC3/-3') was ligated to the 3’ end by overnight incubation with T4 RNA ligase (NEB) at 22°C, and the cDNA then purified from excess adapter with Silane beads and PCR amplified for 12 cycles using the reverse complement of the 3RT3 adapter as the forward primer and the upstream Cκ region as the reverse primer with the partial Truseq illumina adapter added to the beginning (5’-TACACGACGCTCTTCCGATCT-ACTGGATGGTGGGAAGATGGAT-3’). The PCR product was cleaned with 0.7x ampure XT beads, amplified with indexed universal Illumina adapter primers for an additional 7 cycles to obtain ~550 bp libraries.

tag: ex-vivo vs cell culture

value: Cell Culture


title: Clone_B52_Kappa-VJ-seq


title: Clone_E93_Kappa-VJ-seq


title: Clone_4_Kappa-VJ-seq


title: Clone_B52_RNA_rep1

data_processing:
ATAC-seq: Basecalls were derived from the standard illumina Nextseq 500 software. Adapter sequences and low quality bases were removed from reads using trim_galore. Processed reads were mapped using bowtie2 to the mm10 mouse genome, where nucleotides located on SNPs from the castaneous genome were masked (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR-duplicate reads were removed with Picard. Peaks of open chromatin were called from all of the mapped reads using Homer software43. Allelic reads within peaks were counted using HTseq-count.
Nuclear RNA-seq - Basecalls were derived from the standard Illumina Nextseq 500 software or HiSeq1000 RTA software. Adapter sequences and low quality bases were removed from reads using trim_galore. Reads were mapped to the mm10 mouse genome using bowtie2, after masking nucleotides located on SNPs from the cast genome (Sanger mouse genome project - release 1505). Reads falling on SNPs were then sorted to genome of origin using SNPsplit (Babraham institute) and PCR duplicates removed using Picard (Broad institute). Read coverage tracks were made using bedtools. Reads over ENSEMBL genes were counted with HTseq-count.
Kappa-VJ-seq - Basecalls were derived from the standard illumina Miseq software. sequences were quality trimmed (trim_galore) and aligned to a hybrid B6/Cast genome assembly using bowtie2, with Cast polymorphic sites substituted based on the Sanger Mouse Genome Project database (release 1505). Reads over each Vκ segment were counted (HTseq-count) and normalized to the total mapped rearranged fragment number to allow comparison of the Vκ repertoire contribution between different libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Total and allelically sorted alignments from ATAC-seq and RNA-seq - bedgraph format. Mapped allelic Vkappa rearrangement read counts from Igk-VJ-seq - txt format


title: Clone_B52_RNA_rep2


title: ChIP-Seq Apicidin H3K27Ac rep1


title: Clone_8_RNA_rep1


title: Clone_8_RNA_rep2


title: pre-B_pool_Kappa-VJ-seq


title: Clone_4_36hr_Kappa-VJ-seq


title: Clone_4_12hr_Kappa-VJ-seq


title: RNA-Seq Control

status: Public on Apr 02 2017

first: Sun Hyun

last: Chang

address: Rm7112 Bd200 Gwanakro1 Gwanak-gu

department: Applied Biology and Chemistry

institute: Seoul National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genomic DNA reference(Tair10) using bowtie aligner.
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using a protocol from TRAPNELL, Cole, et al., Nature protocols, 2012.
Genome_build: arabidopsis genomic DNA reference (Tair10)
Supplementary_files_format_and_content: FPKM data

growth_protocol: Plants were grown in 1/2 MS solid media for 7 days with 16/8=light/dark at 22℃.

extract_protocol:
Total RNA was extracted using RNeasy plant mini-prep kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype background

value: wild type control

value: 7-day old

value: shoot; cotyledon


title: RNA-Seq wn1

value: whitening mutant wn1

tag: age


title: Clone_4_RNA_rep2


title: Clone_4_24hr_Kappa-VJ-seq


title: Clone_4_RNA_rep1


title: KO#1 LCM

city: San Francisco

first: D'juan

middle: T.

last: Farmer

address: 513 Parnassus Ave

institute: UCSF

data_processing:
Reads were mapped to the mouse GRCm38 genome using Tophat v.2.0.9 (Trapnell et al., 2009).
Gene expression was measured from the mapped reads by using HT-seq-count (Anders et al., 2014) in intersection-strict mode, which counts the reads aligning to each annotated gene (gene set, Ensembl.org).
Differentially expressed genes were called using the DESeq2 R package, (Anders and Huber, 2010) considering genes differentially expressed with FDR < 0.1. Only genes with normalized count values above 10 in all samples were evaluated.
One WT samples was removed due to contamination of non-surface ectoderm tissues, as evident by decreased markers of Pax6, Krt5, and others that constant across all other samples
Genome_build: GRCm38 genome
Supplementary_files_format_and_content: Excel (xlsx); DESeq2 analysis of 3 controls (1 omitted for contamination), and four knockouts

source_name: Surface ectoderm from KO E12.5 embryos

extract_protocol:
Embryo collection. E12.5 WT and miR-205 knockout embryos were collected, flash frozen in OCT, and  sectioned using a cryostatLaser capture and RNA isolation. The laser capture staining protocol was adapted from the Laser Capture Molecular Core at Ohio State University. Briefly, E12.5 embryo heads were dissected and flash frozen in OCT for cyrosectioning. Sections were collected at 10 µM onto RNase-Zap treated 1.0 PEN membrane slides from Zeiss and stored at -80°C. Frozen sections were immediately submerged into ice cold RNase free 70% ethanol, stained in Vector® Hematoxylin QS for 30 sec, and then rinsed in RNase water, following by 95% ethanol and 100% ethanol. Slides were then air dried and returned to -80°C before laser capture. The surface ectoderm between the eye and brain was isolated using the Zeiss PALM into 0.5 mL tubes containing Qiagen RLT buffer. Three embryos were pooled together per sample. RNA was isolated using a Qiagen RNeasy Plus Micro kit and assessed on an Agilent 2100 Bioanalyzer using Agilent RNA Pico Chips. All samples had a RIN above 7.0.
cDNA synthesis and library preparation. cDNA was generated using Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing according to manufacturer’s recommendations. Sequencing libraries were prepared with 1 ng of cDNA using the Nextera XT DNA Library Prep Kit according to manufacturer’s recommendations. The final product was then run on a Novex 4-12% TBE gel and DNA between 300-500 nt was selected. Paired end 100 bp sequencing was performed on an llumina HiSeq 2500 (UCSF Institute for Human Genetics Genomics Core).

value: miR-205 knockout

tag: developmental stage

value: Surface Ectoderm


title: KO#2 LCM


title: WT #4 LCM

source_name: Surface ectoderm from WT E12.5 embryos

value: wild type


title: WT #3 LCM


title: KO#3 LCM


title: KO#4 LCM


title: WT #2 LCM


title: Clone_3_Kappa-VJ-seq


title: Th2 72h H3K4Me3 ChIP-seq

city: Cincinnati

first: Yrina

last: Rochman

state: OH

address: 3333 Burnet Avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2860

data_processing:
RNA-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
STAR PARAMS:       --clip3pNbases 0      --seedSearchStartLmax 15   --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1   --outFilterMismatchNmax 5   --clip5pNbases 0
ChIP-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one allowed error in a sequence and no more than one  hit was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2. To visualize the data, it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size from MACS2 output.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv file includes peak information.

source_name: spleen + lymph nodes

growth_protocol: CD4 cells were grown in complete RPMI medium supplemented with 10% FCS

extract_protocol:
RNA was harvested using BioRad total RNA extraction kit with DNaseI treatment. For ChIP cells were fixed with 0.8% formaldehyde for 8 min at RT and DNA was processed and sonicated according to the protocol from Covaris using Covaris S220 sonicator for 4-5 min.
RNA  libraries for pair-end read sequencing were prepared by using standard Illumina protocols. ChIP libraries were prepared by using ThruPLEX DNA kit (Rubicon).

treatment_protocol: aCD3 plate bound (5ug/ml) + aCD28 soluble (2ug/ml), with or w/o IL-4 (20 ng/ml, PeproTech) or TSLP (40 ng/ml, R&D)

tag: mouse strain

value: naive CD4 purified cells

tag: chip antibodies

value: H3K4Me3 (Millipore,17-614)


title: Th_TSLP 72h H3K4Me3 ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2861


title: Th0 72h aIL4/4R H3K4Me3 ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2997


title: Th_TSLP 72h H3K27Ac ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2381

value: H3K27Ac  (Diagenode, C15410196)


title: Clone_4_48hr_Kappa-VJ-seq


title: Th2 72h H3K27Ac ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2380


title: Th0 72h aIL4/4R H3K36Me3 ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2335


title: Th2 72h H3K36Me3 ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2337


title: Th2 48h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1216

data_processing:
RNA-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
STAR PARAMS:       --clip3pNbases 0      --seedSearchStartLmax 15   --alignSJDBoverhangMin 1 --outFilterMultimapNmax 1   --outFilterMismatchNmax 5   --clip5pNbases 0
ChIP-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one allowed error in a sequence and no more than one  hit was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2. To visualize the data, it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size from MACS2 output.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv file includes RPKM values and read numbers for each sample


title: Th0 72h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1375


title: Th0 6h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1208


title: Th2 72h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1377


title: Th0 48h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1214


title: Th_TSLP 6h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1209


title: Th_TSLP 72h H3K36Me3 ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2376


title: Th_TSLP 72h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1376


title: clinic7

city: Boston

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

description: late symptomatic stages

data_processing:
Reads were trimmed to 36 nt and ligation adapters removed using the adrec.jar program from seqBuster suite ( Pantano et al. , 2010 ). Sequences were mapped to the hg19 genome.
miRNAs were quantified with seqbuster and cluster with seqcluster (https://github.com/lpantano/seqcluster).
All scripts used for the figures are: https://github.com/lpantano/small-RNA-analysis
Genome_build: hg19
Supplementary_files_format_and_content: miRNA expression data. Adapter removal and mirna annotation done with seqcluster.

source_name: brain

extract_protocol:
For each sample, 50–60 mg of frozen amygdala was homogenized and then RNA isolated with miRNeasy (Qiagen) following manufacturer's instructions.
Small RNA indexed libraries for sequencing were prepared from 1 μg of total RNA, using the Trueseq kit (Illumina), according to manufacturer specifications

value: brain

tag: brain section

value: amygdala

tag: braak stages

tag: Sex

value: Male

tag: disease state

value: Parkinson's disease


title: Th2 2h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1207


title: Th_TSLP 24h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1212


title: Th2 24h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1213


title: Th2 6h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1210


title: Th0 24h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1211


title: control_clinic7

description: controls

tag: tissue


title: clinic6

description: late symptomatic stages


title: Th_TSLP 2h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1206

tag: cell type


title: clinic5

description: late symptomatic stages


title: Th_TSLP 48h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1215


title: clinic4

description: late symptomatic stages


title: clinic2

description: late symptomatic stages


title: Th0 2h RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1205


title: clinic3

description: late symptomatic stages


title: Th0 72h aIL4/4R H3K27Ac ChIP-seq

description:
ChIP-Seq Illumina platform
BioWardrobe IDs: 2378


title: clinic1

description: late symptomatic stages


title: control_clinic6

description: controls


title: control_clinic5

description: controls


title: control_clinic4

description: controls


title: naïve CD4 RNA-seq

description:
RNA-Seq Illumina platform dUTP
BioWardrobe IDs: 1204


title: control_clinic3

description: controls


title: control_clinic1

description: controls


title: preclinic7

description: early-premotor


title: control_clinic2

description: controls


title: preclinic6

description: early-premotor


title: preclinic1

description: early-premotor


title: preclinic3

description: early-premotor


title: control_preclinic7

description: controls


title: control_preclinic6

description: controls


title: preclinic5

description: early-premotor


title: preclinic4

description: early-premotor


title: MCF7.CPT.ribo.rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

institute: Tel Aviv University

data_processing:
Library strategy: Ribo-seq
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations. Only uniquely mapped reads were used in subsequent analyses. RNA expression and Ribosome-occupancy levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
RPKM levels below 1.0 were set to 1.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

growth_protocol: MCF7 cells were grown on 15-cm tissue culture dishes at normal conditions until were approximately 85% confluent.

extract_protocol:
RNA-seq: Applying Trizol on growing cells
Ribo-seq: Cells were treated with cycloheximide (100 μg/ml) for 5 minutes, washed with ice-cold phosphate-buffered saline (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg/ml cycloheximide, 1X complete protease inhibitor). Lysates were centrifuged at 5,000 rpm and the supernatant was treated with 2 U/μl of RNase I (Ambion) for 45 min at room temperature. Lysates were fractionated on a linear sucrose gradient (7% to 47%) using the SW-41Ti rotor at 36,000 rpm for 2 h. Fractions enriched in monosomes were pooled and treated with proteinase K (Roche) in a 1% SDS solution. Released RNA fragments were purified using TRIsure reagent and precipitated in the presence of glycogen.
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
Ribo-seq: For libraries preparation, RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30 to 33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England BioLabs, Inc.) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England BioLabs, Inc.) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

treatment_protocol: Cells were treated with Campthotecin (6 micromolar final conc.) or DMSO (as control) for 5 hours

tag: cell line

value: CPT


title: preclinic2

description: early-premotor


title: control_preclinic4

description: controls

value: control


title: MCF7.C.ribo.rep2

tag: treatment


title: MCF7.CPT.ribo.rep1


title: control_preclinic5

description: controls


title: control_preclinic3

description: controls


title: control_preclinic2

description: controls


title: control_preclinic1

description: controls


title: MCF7.C.ribo.rep1


title: MCF7.CPT.rna.rep1

data_processing:
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations. Only uniquely mapped reads were used in subsequent analyses. RNA expression and Ribosome-occupancy levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
RPKM levels below 1.0 were set to 1.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.


title: MCF7.C.rna.rep2


title: MCF7.CPT.rna.rep2


title: MCF7.C.rna.rep1


title: 4-KMT2D ChIP-seq BYL719

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Reads were first processed with Trimmomatic to remove the adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to hg19 human genome with the bowtie aligner.
KMT2D peaks were called using MACS2.
Differentially accessible peaks from this atlas were identified with DESeq by counting all read ends overlapping peaks in each condition. DESeq was run with a log2-fold-change threshold of 1, and FDR < 0.1.
The distribution of the peaks around the TSS was calculated using the ChIPpeakAnno package.
Genome_build: hg19 human genome
Supplementary_files_format_and_content: bw files were generated using deeptools.

source_name: Breast Cancer Cell

growth_protocol: T47D cells were maintained in RPMI 1640 with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
Cells were lysed and sonicated leading to a DNA average size of 200bp. Protein G dynabeads were pre-incubated with 5μg of KMT2D antibody (HPA035977, Sigma) with pre cleared chromatin. The complexes were reverse cross-linked and DNA was purified.
Due to low enrichment due to antibody lot issues, ChIP-seq libraries were prepared using the total 5 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: 60 milion T47D cells were treated with DMSO or BYL719 1μM for 4hr.

value: T47D cell

tag: passages

tag: chip antibody

value: Anti-KMT2D, HPA035977, Sigma

value: BYL719 1uM for 4hr


title: 3-T47D-BYL719-Input


title: 2-KMT2D ChIP-seq  DMSO

value: DMSO


title: 1-T47D-DMSO-Input


title: 3565_culture_rep1

first: Tyler

middle: E

last: Miller

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

data_processing:
For gene expression analysis, reads were aligned to the hg19 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et  al., 2009).
The distribution of alignments was analyzed using the CollectRnaSeqMetrics module of Picard v1.89 (http://picard.sourceforge.net/).
FPKM values for known genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option. FPKM values were Quantile Normalized.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM values from Cufflinks

source_name: Primary Patient Derived Tumor Model

growth_protocol: IN528 cells from a primary patient derived GBM tumor model were grown in serum free cell culture conditions

extract_protocol:
Cells were collected and lysed in trizol
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform by Case Western Genomics Core

value: primary patient-derived GBM cells


title: 3565_IC_rep3

growth_protocol: IN528 cells from a primary patient derived GBM tumor model were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.

extract_protocol:
Cells were dissociated from the tumor, depleted of mouse cells twice by Miltenyi mouse depletion kit and MACS magnetic sorting and then lysed in Trizol.
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform by Case Western Genomics Core


title: 3565_IC_rep1


title: 3565_culture_rep2


title: 3565_IC_rep2


title: BT549 input DNA

first: Logan

middle: A

last: Walsh

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq sequencing was performed at the Memorial Sloan Kettering Center for Molecular Oncology (Manhattan, NY, USA) using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA, USA). Raw sequencing data were aligned to the hg37 genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.10 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/). Further indel realignment, base-quality score recalibration and duplicate-read removal were performed using the Genome Analysis Toolkit (GATK) version 3.2.2 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508/) following raw reads alignments guidelines  (http://www.nature.com/ng/journal/v43/n5/pdf/ng.806.pdf). Peaks were called from the resulting bam files by Model-based Analysis of ChIP-seq (MACS2) version 2.1.0  (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868217/) following the manual at https://github.com/taoliu/MACS/.  As a first filtering step, resulting raw peaks were filtered by pval<0.01. Next, for each peak, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated for IP (immuno-precipitated) and INPUT (for ChIP-seq) bam files. Only peaks with RPKM INPUT/RPKM IP ratio greater than 0.5 were reported to final results.
Genome_build: hg37

source_name: breast cancer

growth_protocol: Cells were grown according to ATCC guidelines

extract_protocol:
ChIP was performed using the EZ-Magna ChIP™ G - Chromatin Immunoprecipitation Kit (Millipore) according to manufacturers. instructions.
Libraries were prepared using KAPA HTP library preparation kit (KK8234).

value: breast cancer cell line

tag: subtype

value: triple negative breast cancer


title: BT549_ChIPseq_rep2


title: BT549_ChIPseq_rep1


title: BT549_RIPseq_rep3

data_processing:
RIP-seq sequencing was performed at the Memorial Sloan Kettering Center for Molecular Oncology (Manhattan, NY, USA) using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA, USA). Raw sequencing data were aligned to the hg37 genome build using the Burrows-Wheeler Aligner (BWA) version 0.7.10 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/). Further indel realignment, base-quality score recalibration and duplicate-read removal were performed using the Genome Analysis Toolkit (GATK) version 3.2.2 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508/) following raw reads alignments guidelines  (http://www.nature.com/ng/journal/v43/n5/pdf/ng.806.pdf). Peaks were called from the resulting bam files by Model-based Analysis of ChIP-seq (MACS2) version 2.1.0  (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868217/) following the manual at https://github.com/taoliu/MACS/.  As a first filtering step, resulting raw peaks were filtered by pval<0.01. Next, for each peak, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated for IP (immuno-precipitated) and INPUT (for ChIP-seq) bam files. Only peaks with RPKM INPUT/RPKM IP ratio greater than 0.5 were reported to final results.
Genome_build: hg37

extract_protocol:
RIP was performed using the EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to manufacturers. instructions.
TruSeq® Stranded Total RNA LT kit (illumina).
Ribosomal RNA depletion


title: BT549_RIPseq_rep1


title: MDAMB231_ChIPseq_rep2


title: MCF7-scramble-136

data_processing:
Raw reads in the fastq format were aligned to Human Genome HG19 using the RNA-seq STAR aligner version 2.4.0d (http://www.ncbi.nlm.nih.gov/pubmed/23104886, http://www.ncbi.nlm.nih.gov/pubmed/26334920) as recommended by user manual downloaded along with the software. STAR aligner was chosen for mapping accuracy and speed (http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2722.html).  Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website (http://www.gencodegenes.org/releases/19.html)) using the FeatureCounts read summarization program (http://www.ncbi.nlm.nih.gov/pubmed/?term=24227677) following the user guide (http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf). Individual count files were merged to generate the raw-counts matrix by an in-house R script, normalized to account for differences in library size and the variance was stabilized by fitting the dispersion to a negative-binomial distribution as implemented in the DESeq R package (http://bioconductor.org/packages/release/bioc/html/DESeq.html)(Anders and Huber, 2010).
Genome_build: HG19
Supplementary_files_format_and_content: txt file contains feature count matrix

source_name: breast cancer cell line

extract_protocol:
RNA was extracted from cells using an RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: MCF7 cells

value: breast


title: MDAMB231_RIPseq_rep3


title: MDAMB231_RIPseq_rep2


title: MDAMB231_ChIPseq_rep3


title: MDAMB231_RIPseq_rep1


title: BT549_RIPseq_rep2


title: MCF7-scramble-135


title: BT549_ChIPseq_rep3


title: MCF7-mock-134


title: MDAMB231_ChIPseq_rep1


title: MDAMB231 input DNA


title: White Adipocyte - 4105D

city: Cambridge

first: Curtis

middle: Robert

last: Warren

state: Massachusetts

address: 7 Divinity Ave

department: Stem Cell And Regenerative Biology

institute: Harvard University

data_processing:
Assembly - Bowtie 2 (TopHat2.0.13)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens/Ensembl/GRCh37 whole genome sequence using  TopHat2.0.13 with parameters "tophat -p 16 -g 1 -N 2 -r 50 --mate-std-dev 70 --no-coverage-search -o"
Fragments per kilobase of transcript per million mapped reads  (FPKM) were calculated using cufflinks/2.2.1 with gene/transcript annotation ("Ensembl_GRCh37.v74.gtf") with parameters "-G Homo_sapiens.GRCh37.74.gtf --total-hits-norm --no-update-check --library-type fr-unstranded "
rseqc/v2.6.2 for generating mapping statistics metrics from accepted.bam files
Genome_build: NCBI v37 Homo sapiens Reference Genome (hg19)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Warren et al Cell Stem Cell 2016

extract_protocol:
Warren et al Cell Stem Cell 2016
Warren et al Cell Stem Cell 2016

treatment_protocol: Warren et al Cell Stem Cell 2016

value: Peripheral Blood Mononuclear Cells

value: White Adipocyte

tag: 1p13 genotype

value: Minor/Minor


title: MCF7-mock-133


title: White Adipocyte - 2633D


title: White Adipocyte - 4105B


title: MCF7-NKX6-130


title: White Adipocyte - 2633B


title: White Adipocyte - 25727G


title: White Adipocyte - 25727B


title: MCF7-NKX6-129


title: White Adipocyte - 25642C


title: White Adipocyte - 25642B


title: MCF7-TSHZ3-128


title: MCF7-TSHZ3-127


title: MCF7-ZMAT4-126


title: White Adipocyte - 24472D


title: MCF7-IRX6-123


title: MCF7-PRRX1-122


title: White Adipocyte - 22512D


title: MCF7-IRX6-124


title: MCF7-PRRX1-121


title: MCF7-HOXA11-120


title: MCF7-ZMAT4-125


title: White Adipocyte - 1998E


title: MCF7-HOXA11-119


title: White Adipocyte - 16939B


title: White Adipocyte - 22512A


title: MCF7-CNBP-118


title: MCF7-CNBP-117


title: White Adipocyte - 14685B


title: White Adipocyte - 16126E


title: MCF7-ZNF589-115


title: White Adipocyte - 14685A


title: White Adipocyte - 16126C


title: MCF7-CBFA2T2-114


title: MCF7-CBFA2T2-113


title: MCF7-ZNF142-112


title: White Adipocyte - 24472K


title: White Adipocyte - 14157C


title: White Adipocyte - 13352E


title: White Adipocyte - 1998G


title: White Adipocyte - 16939A


title: White Adipocyte - 13352A


title: MCF7-ZNF142-111


title: White Adipocyte - 12888B


title: MCF7-FOXD4L6-106


title: MCF7-ZNF253-109


title: MCF7-PAX5-108


title: White Adipocyte - 1296C


title: MCF7-ZNF589-116


title: MCF7-FOXD4L6-105


title: White Adipocyte - 1296E


title: White Adipocyte - 1236B


title: MCF7-PAX5-107


title: White Adipocyte - 1236C


title: White Adipocyte - 12022C


title: White Adipocyte - 12022B


title: MCF7-TRIM25-103


title: MCF7-TRIM25-104


title: White Adipocyte - 14157A


title: T47D-scramble-102

value: T47D cells


title: White Adipocyte - 10950C


title: White Adipocyte - 10950A


title: T47D-mock-100


title: T47D-mock-99


title: White Adipocyte - 9462B

value: Major/Major


title: MCF7-ZNF253-110


title: White Adipocyte - 2098A_Fat


title: T47D-NKX6-96


title: White Adipocyte - 12888A


title: White Adipocyte - 9462A


title: White Adipocyte - 921B


title: T47D-NKX6-95


title: T47D-TSHZ3-93


title: T47D-ZMAT4-92


title: White Adipocyte - 921C


title: T47D-ZMAT4-91


title: T47D-scramble-101


title: Lsg1-TAP LSUs with Mnase-rpL35

city: Regensburg

first: Philipp

last: Milkereit

address: Universitätsstr. 31

department: Lehrstuhl für Biochemie III

country: Germany

institute: Universität Regensburg

description: Processed data file: suppTable_S4.xlsx

data_processing:
Before mapping, 7 nucleotide random barcodes on the 5' end of reads 1 were removed and reads 1 and 2 with a “AGATCGG” sequence at a distance of more than 20 nucleotides from their 5’ end were trimmed at this site. Mapping of reads on the S .cerevisiae rDNA region (strain S288c) was done using Bowtie 2 with standard parameters. For each dataset, 300,000 mapped reads with an insert size between 75 and 750 nucleotides and a Bowtie 2 quality score of Q>=40 were selected for further statistical evaluation. Bias introduced during PCR amplification was estimated and corrected as described in Kielpinski and Vinther (Nucleic Acids Res. 2014 Apr;42(8):e70. doi: 10.1093/nar/gku167) making use of the random barcode in the adapter primer. Accordingly, for each experimental condition, reads were grouped based on identical mapped start site and length and in each group the number of observed unique random barcodes was determined. This number was then further corrected by taking into account possible ligation of cDNA fragments of one of the groups with adapters with identical barcodes. The likelihood of these ligation events was estimated based on the amount of different random barcodes encoded in the adapter primer and the observed frequency of adenine, guanine, cytosine or thymine at each barcode position in the mapped reads (see Kielpinski and Vinther, Nucleic Acids Res. 2014 Apr;42(8):e70. doi: 10.1093/nar/gku167). The resulting estimated unique counts for cDNA fragments with defined start and stop positions were used to calculate for each position in LSU pre-rRNA the coverage and the termination to coverage ratio (TCR). Calculated TCR values for each experimental condition are given in the processed data files. To estimate the noise of random stops of primer extension reactions at each pre-rRNA position for each experimental sample, 100 virtual datasets were created in which the pool of observed fragment start sites was randomly combined with the pool of observed fragment lengths. Coordinates of fragments ending at sites with high TCR values (>15%) were kept as observed in the experimental dataset. The averaged coverage distribution of the virtual datasets matched strikingly well the one observed in the experimental dataset (coefficient of determination R2 > 0.98 for all datasets), thus indicating that selectivity in priming sites together with the fragment length distribution are major factors influencing the local noise of termination events. The local noise was then estimated as the maximum TCR within a region of 5 nucleotides of all virtual datasets derived from either Lsg1-TAP or Noc3-TAP particles. All data processing and visualization was done with VBA scripts in the Excel (Microsoft) environment.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: suppTable_S4.xlsx: Excel table with TCR values for each position in the S. cerevisiae 35S rRNA for Lsg1-TAP or Noc3-TAP LSU precursors with no MNase, MNase-rpL5, MNase-rpL27 or MNase rpL35.

organism: Saccharomyces cerevisiae

source_name: Lsg1-TAP LSUs, MNase-rpL35

growth_protocol: Yeast strains were cultivated in YPD to an optical density between 0.8 and 1.2.

extract_protocol:
Cells from 6 liters of culture (Noc3-TAP strains) or from 2 liters of culture (Lsg1-TAP strains) were then harvested by centrifugation at room temperature (3000g) and were washed in 15 ml ice cold buffer AG100 (100 mM potassium chloride, 20 mM Tris pH8, 5 mM magnesium acetate, 5 mM EGTA pH8, 1 mM PMSF, 2 mM Benzamidine). To each gram of wet cell pellet, 1.5 milliliter of cold buffer AG100 with 0.04 Units/microliter RNasin (Promega) was added and the resulting suspension was distributed in portions of 0.8 milliliter to reaction tubes (2 milliliter volume) loaded with 1.4 gram of glass beads (0.75-1 millimeter, Roth). The tubes were rigorously mixed on a vibrax mixer (IKA) at 4°C and maximum speed for three times 8 minutes with cooling on ice in between. The extract was cleared from cell debris and glass beads by two consecutive centrifugation steps for 5 minutes at 13000g and 4°C and transfer of the respective supernatants to new reaction tubes. Protein concentrations of the clarified extracts were determined by Bradford protein assay (Bio-Rad) and a volume containing 300 microgram protein was taken off for RNA analyses (see below, RNA was dissolved in 30 microliter of water). Triton X-100 and Tween 20 were added to final concentrations of 0.5% (w/v) and 0.1% (w/v) , respectively, and the extracts were loaded on 150 microliter IgG sepharose beads (GE Healthcare) equilibrated in buffer AG100+ (AG100 adjusted to 0.5% (w/v) Triton X-100 and 0.1% (w/v) Tween 20 ). After batch incubation at 4°C for 1 hour, the affinity matrix was transferred into 15 milliliter plastic columns (Poly Prep chromatography columns, 0.8 x 4 centimeter, Bio-Rad) and washed twice with 2 milliliter of ice cold AG100+ and once with 10 milliliter of AG100+. The matrix was transferred in 0.5ml of ice cold AG100 into a 1.5 ml reaction tube, 10% of the suspension was taken off for RNA analyses (see below, RNA was dissolved in 10 microliter of water), and after centrifugation for 2 minutes at 2000g at 4°C, the volume was reduced to 200 microliter by removing some of the supernatant. Calcium chloride was added to the suspension to a final concentration of 8mM and after 10 minutes incubation at 16°C, RNA was extracted (see below, RNA was dissolved in 60 microliter of water).
Libraries were prepared as described by Kielpinski and Vinther (Nucleic Acids Res. 2014 Apr;42(8):e70. doi: 10.1093/nar/gku167). Briefly, cDNAs were generated by random primer extension reactions, ligated to an adapter and amplified by PCR. PCR fragments of a size range between 200 and 600 basepairs were selected by gel electrophoresis. The expected size distribution of the amplified sequencing libraries was confirmed using a high sensitive DNA kit on a 2100-Bioanalyzer capillary electrophoresis system (Agilent Technologies). Paired-end sequencing (2x 80 nt) was done on an Illumina MiSeq system (Illumina).

tag: genetic background

tag: tagged protein


title: Noc3-TAP LSUs with Mnase-rpL35

description: Processed data file: suppTable_S4.xlsx

source_name: Noc3-TAP LSUs, MNase-rpL35


title: Lsg1-TAP LSUs with Mnase-rpL27

description: Processed data file: suppTable_S4.xlsx

source_name: Lsg1-TAP LSUs, MNase-rpL27


title: Noc3-TAP LSUs with Mnase-rpL5

description: Processed data file: suppTable_S4.xlsx

source_name: Noc3-TAP LSUs, MNase-rpL5


title: Noc3-TAP LSUs with Mnase-rpL27

description: Processed data file: suppTable_S4.xlsx

source_name: Noc3-TAP LSUs, MNase-rpL27


title: Noc3-TAP LSUs with no Mnase

description: Processed data file: suppTable_S4.xlsx

source_name: Noc3-TAP LSUs, no MNase


title: T47D-IRX6-89


title: Lsg1-TAP LSUs with Mnase-rpL5

description: Processed data file: suppTable_S4.xlsx

source_name: Lsg1-TAP LSUs, MNase-rpL5


title: White Adipocyte - 554D


title: White Adipocyte - 521C


title: T47D-PRRX1-88


title: White Adipocyte - 554A


title: T47D-PRRX1-87


title: White Adipocyte - 4064B


title: T47D-HOXA11-86


title: T47D-TSHZ3-94


title: White Adipocyte - 4064A


title: T47D-HOXA11-85


title: T47D-CNBP-84


title: White Adipocyte - 3726A


title: White Adipocyte - 521E


title: White Adipocyte - 3726B


title: White Adipocyte - 4756A


title: T47D-CNBP-83


title: White Adipocyte - 2945B


title: T47D-ZNF589-82


title: T47D-CBFA2T2-80


title: T47D-IRX6-90


title: White Adipocyte - 2945A


title: T47D-CBFA2T2-79


title: White Adipocyte - 2098A


title: White Adipocyte - 2098B


title: T47D-ZNF589-81


title: White Adipocyte - 4756B


title: White Adipocyte - 18961A


title: White Adipocyte - 18719D


title: Lsg1-TAP LSUs with no Mnase

description: Processed data file: suppTable_S4.xlsx

source_name: Lsg1-TAP LSUs, no MNase


title: T47D-ZNF253-76


title: T47D-ZNF142-77


title: T47D-PAX5-74


title: White Adipocyte - 1673F


title: T47D-ZNF253-75


title: T47D-PAX5-73


title: White Adipocyte - 1673B


title: White Adipocyte - 1660F


title: T47D-FOXD4L6-72


title: T47D-TRIM25-70


title: White Adipocyte - 1660E


title: T47D-FOXD4L6-71


title: White Adipocyte - 1649A


title: White Adipocyte - 18961C


title: T47D-ZNF142-78


title: White Adipocyte - 1441G


title: MDAMB231-scramble-67

value: MDAMB231 cells


title: MDAMB231-scramble-68


title: MDAMB231-mock-66


title: White Adipocyte - 1293A


title: White Adipocyte - 1441F


title: MDAMB231-mock-65


title: MDAMB231-BNC2-62


title: White Adipocyte - 18719B


title: White Adipocyte - 12569B


title: MDAMB231-BNC2-61


title: White Adipocyte - 12569A


title: MDAMB231-TSHZ3-59


title: MDAMB231-TSHZ3-60


title: iPSC - 4105B

value: iPSC


title: iPSC - 2633D


title: iPSC - 2633B


title: MDAMB231-IRX6-58


title: iPSC - 25727G


title: MDAMB231-FOXQ1-55


title: iPSC - 25727B


title: MDAMB231-FOXQ1-56


title: MDAMB231-IRX6-57


title: T47D-TRIM25-69


title: iPSC - 25642C


title: White Adipocyte - 1293B


title: iPSC - 25642B


title: iPSC - 24472K


title: MDAMB231-PRRX1-53


title: MDAMB231-HOXA11-52


title: MDAMB231-PRRX1-54


title: iPSC - 22512D


title: MDAMB231-RPL7-49


title: MDAMB231-RPL7-50


title: MDAMB231-HOXA11-51


title: iPSC - 4105D


title: MDAMB231-YBX1-48


title: iPSC - 1998E


title: iPSC - 16939B


title: MDAMB231-YBX1-47


title: iPSC - 1998G


title: MDAMB231-ZNF581-46


title: iPSC - 16939A


title: iPSC - 16126E


title: MDAMB231-ZNF581-45


title: MDAMB231-CTBP1-43


title: MDAMB231-CTBP1-44


title: iPSC - 16126C


title: iPSC - 14685B


title: MDAMB231-CNBP-42


title: iPSC - 14685A


title: iPSC - 14157C


title: iPSC - 24472D


title: White Adipocyte - 1649B


title: iPSC - 22512A


title: MDAMB231-ZNF589-40


title: iPSC - 13352E


title: MDAMB231-FOXD4L6-38


title: iPSC - 14157A


title: iPSC - 13352A


title: MDAMB231-TRIM25-35


title: iPSC - 1296C


title: MDAMB231-FOXD4L6-37


title: iPSC - 12888B


title: iPSC - 12888A


title: BT549-scramble-33

value: BT549 cells


title: BT549-mock-32


title: iPSC - 1236C


title: iPSC - 1236B


title: TZ+fzSPZ4

city: Stanford

first: Pascale

middle: S

last: Guiton

state: CA

address: Sherman Fairchild Science Building  Stanford School of Medicine 299 campus Drive

department: Microbiology and Immunology

institute: Stanford University

description: Barcode: ACTGAT

data_processing:
Raw reads were uploaded onto the CLC Genomics Workbench 8.0 (Qiagen) platform for independent alignments against the genomes of Rattus norvegicus (Ensembl.org/Rnor.6.0) and Toxoplasma Type II Me49 strain (ToxoDB-24, Me49 genome). All parameters were left at their default values.
Many genes are so highly conserved across evolution that they have sequences that are almost identical between Toxoplasma and rat. This makes it difficult to know exactly which reads in a given sample from infected cells derive from the Toxoplasma vs. rat versions of the gene. Because of this, we needed to identify and exclude such genes from our analysis. To do this, we first searched the uninfected and mock-infected RNASeq data for reads mapping to the Toxoplasma genome; because these samples were uninfected, any such reads would indicate spurious matches. We then compared the number of such reads to the number for the same gene in the infected samples where Toxoplasma infection is present. After normalizing total read numbers to be the same for each sample, any Toxoplasma gene that in the uninfected controls had ≥20% of the number of reads in the TZ or SPZ samples was deemed compromised and so it was excluded from all downstream analyses.  Toxoplasma genes that had an average number of reads in the uninfected samples <20% of the average adjusted reads in the infected sample were left in the analysis but the read numbers from the infected sample were adjusted by subtracting the average number of reads in the uninfected and mock samples, after normalization for total read number. Genes with less than 5 exon reads mapping to the rat genome or to the parasite genome in all samples were excluded from further analysis. The number of total reads mapped to each genome after the adjustments described above was used to determine the RPKM (Reads Per Kilobase of transcript per Million mapped reads), rounded to the nearest one-tenth value, as the relative expression for each rat and Toxoplasma gene in each sample
SAMseq package for the R platform was used to identify genes with significant changes between two samples. To identify genes with statistically different expressions between samples, we set the delta (Δ) value at 10% FDR (False Discovery Rate) with q-value less than 5%.
Only genes with q-value less than 5% and an average of at least 5 exon reads in one of the two conditions being compared were considered for further analysis. Among these genes, only those with RPKM ratios ≥1.5 for the two samples being compared and consistent in the two infections with tachyzoites (“TZ” and “TZ+fzSPZ”) were included in the list of differentially expressed genes.
Genome_build: ToxoDB-24, Me49 genome
Genome_build: Ensembl.org/Rnor.6.0
Supplementary_files_format_and_content: tab delimited text files include gene ID, exon length, total gene reads and total exon reads obtained from CLC genomics for each sample when mapped to either Toxoplasma or Rat genome

source_name: intestinal epithelial cell with tachyzoites and frozen sporozoites

extract_protocol:
Total RNA was extracted from each sample at 8 hour post infection using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols by Stanford University Functional Genomic Facility

tag: host cell line

value: ATCC IEC-18

tag: passage

tag: infection

value: IEC-18 infected with tachyzoites in presence of frozen sporozoites

tag: toxoplasma strain


title: TZ+fzSPZ2

description: Barcode: GGCTAC


title: BT549-BNC2-28


title: iPSC - 12022B


title: BT549-BNC2-27


title: TZ+fzSPZ1

description: Barcode: TAGCTT


title: BT549-TSHZ3-26


title: MDAMB231-TRIM25-36


title: iPSC - 1296E


title: TZ4

description: Barcode: CGTACG

source_name: intestinal epithelial cell with tachyzoites

value: IEC-18 infected with tachyzoites


title: MDAMB231-ZNF589-39


title: TZ3

description: Barcode: GTTTCG


title: iPSC - 10950A


title: BT549-TSHZ3-25


title: BT549-scramble-34


title: iPSC - 9462B


title: BT549-IRX6-24


title: BT549-IRX6-23


title: TZ2

description: Barcode: GATCAG


title: TZ1

description: Barcode: ACTTGA


title: iPSC - 921C


title: BT549-FOXQ1-22


title: iPSC - 9462A


title: iPSC - 12022C


title: SPZ4

description: Barcode: GTGGCC

source_name: intestinal epithelial cell with sporozoites

value: IEC-18 infected with sporozoites


title: iPSC - 921B


title: TZ+fzSPZ3

description: Barcode: GAGTGG


title: MDAMB231-CNBP-41


title: BT549-mock-31


title: iPSC - 10950C


title: iPSC - 554D


title: BT549-PRRX1-20


title: BT549-FOXQ1-21


title: BT549-PRRX1-19


title: iPSC - 554A


title: iPSC - 521E


title: SPZ2

description: Barcode: CAGATC


title: SPZ1

description: Barcode: GCCAAT


title: Mock4

description: Barcode: GTCCGC

source_name: intestinal epithelial cell

value: IEC-18 with uninfected cell lysate


title: SPZ3

description: Barcode: GTGAAA


title: BT549-HOXA11-18


title: iPSC - 521C


title: iPSC - 4756B


title: BT549-RPL7-16


title: Mock3

description: Barcode: CCGTCC


title: Mock2

description: Barcode: ACAGTG


title: iPSC - 4756A


title: BT549-RPL7-15


title: Mock1

description: Barcode: TGACCA


title: iPSC - 4064B


title: BT549-YBX1-14


title: fzSPZ4

description: Barcode: ATGTCA

source_name: Intestinal epithelial cell with frozen sporozoites

value: IEC-18 with frozen sporozoites


title: BT549-YBX1-13


title: iPSC - 4064A


title: fzSPZ3

description: Barcode: AGTTCC


title: iPSC - 3726B


title: fzSPZ2

description: Barcode: TTAGGC


title: BT549-ZNF581-12


title: iPSC - 3726A


title: iPSC - 2945B


title: fzSPZ1

description: Barcode: CGATGT


title: BT549-CTBP1-10


title: UN4

description: Barcode: ATTCCT

source_name: Intestinal epithelial cell

value: Uninfected


title: iPSC - 2945A


title: BT549-HOXA11-17


title: BT549-CNBP-8


title: BT549-CTBP1-9


title: UN3

description: Barcode: AGTCAA


title: iPSC - 2098B


title: iPSC - 2098A


title: UN1

description: Barcode: ATCACG


title: BT549-CNBP-7


title: UN2

description: Barcode: CTTGTA


title: BT549-ZNF589-6


title: iPSC - 18961A


title: BT549-ZNF589-5


title: BT549-FOXD4L6-4


title: iPSC - 18961C


title: BT549-FOXD4L6-3


title: BT549-TRIM25-2


title: BT549-ZNF581-11


title: iPSC - 1673F


title: BT549-TRIM25-1


title: iPSC - 18719D


title: iPSC - 1660F


title: iPSC - 18719B


title: iPSC - 1673B


title: iPSC - 1649B


title: iPSC - 1660E


title: iPSC - 1649A


title: iPSC - 1441G


title: SW48-p53KO_CTL

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNASeq reads were aligned to Human Hg19 reference genome using TopHat2 version 2.0.8
Fusion detection was done using TopHat2 fusion version 2.0.8
fpkm was generated using Cufflink version 2.2.1
Genome_build: Hg19
Supplementary_files_format_and_content: fpkm files are tab delimited text files for each sample. Fusion results are tab delimited text files of each sample.

growth_protocol: all cell lines were cultured in DMEM with 10% FBS, at 37 degrees C, 5% CO2

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
The Illumina Total RNASeq protocol involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go on the sequencer.

treatment_protocol: The cells were untreated or treated with DOXO at 300 nM for 16 hours

value: colorectal cancer

value: untreated


title: iPSC - 1441F

value: Peripheral Blood Mononuclear Cells


title: SW48-p53KO_DOXO

value: Doxorubicin at a final concentration of 300 nM for 16 hours


title: SW48-p53WT_CTL


title: RKO-p53KO_CTL

source_name: RKO


title: SW48-p53WT_DOXO


title: iPSC - 1293A


title: RKO-p53KO_DOXO


title: RKO-p53WT_DOXO


title: RKO-p53WT_CTL


title: iPSC - 1293B


title: iPSC - 12569B


title: HCT116-p53KO_DOXO


title: iPSC - 12569A


title: CD56-L21ER_RNA-Seq

first: Christian

middle: J

last: Berrios

address: 450 Brookline Ave; Mayer 443

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Reads were mapped to a transcriptome index generated from the hg19 human reference genome, using Tophat 2.0.4 and Bowtie1 with default parameters. Human-aligned reads were quantified at the gene level using Cufflinks 1.3.0 to FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Foreskin-derived Merkel cells

growth_protocol: CD56+ cells expressing MCPyV-ER or GFP and MKL-1 cells were seeded in 6 cm dishes for 72 hours in CnT-57 media.

extract_protocol:
Cells were harvested and total RNA was purified using RNeasy Plus Mini Kit (Qiagen) and mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England BioLabs)

value: Foreskin-derived Merkel cells

tag: expression construct

value: Merkel cell poylomavirus (MCCL21) early-region

value: Skin

tag: age

value: Neonatal


title: HCT116-p53WT_DOXO rep2

tag: disease state


title: HCT116-p53KO_CTL


title: HCT116-p53WT_DOXO rep1


title: CD56-GFP_RNA-Seq

tag: cell type

value: GFP

tag: tissue


title: HCT116-p53WT_CTL rep1

tag: cell line

tag: treatment


title: MKL-1_RNA-Seq

source_name: Merkel cell carcinoma cell line

value: Merkel cell carcinoma cell line

value: 26 Years Old


title: HCT116-p53WT_CTL rep2


title: Sample_TP3

city: Houston

first: Jian

last: Chen

state: TX

address: 1515 Holcombe Boulevard - Unit 1466

institute: The University of Texas M. D. Anderson Cancer Center

description: Human hepatocellular cancer  from patient

data_processing:
Whole-transcriptome RNA sequencing of 4 matched human hepatocellular cancer samples/normal liver smapls, and 4  human hepatocellular cancer samples.  The sequencing was carried out on an Illumina HiSeq2000 sequencer.
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI Human  chromosome genome build 37.2 using  the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification was carried using HTSeq
A gene model gtf file corresponding to the NCBI human reference genome build 37.2 was used in the quantification.
DESeq2 was used to identify significant differences in gene expression profiles between the noemal mucosa and colon adenomas.
Genome_build: hg19
Supplementary_files_format_and_content: RPKMs in Excel format

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: tissue type

value: hepatocellular cancer


title: Sample_TP504

source_name: Human hepatocellular cancer  from patient


title: Sample_TP301


title: Sample_TP2


title: IN528culture Rep2

source_name: Primary Patient Derived Tumor Model

extract_protocol:
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform by Beckman-Coulter Genomics.

treatment_protocol: cell characterization: Cells were collected and lysed in trizol

tag: microenvironment

value: in vitro


title: IN528culture Rep1


title: Sample_9195-N

description: Human normal liver from patient

source_name: Human normal liver from patient

value: normal liver


title: 3aub

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

institute: European Molecular Biology Laboratory (EMBL)

description: The sample was generated using GTGG as 4-nt barcode preceding a 5-nt random barcode (UMI); note the first 4-nt of the reads should be the reverse complement of the listed barcode

data_processing:
Basecalls performed using CASAVA version 1.4
Trimming of Illumina 3' adapter (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) and sequencing barcodes (experimental barcode)
Collapsing/deduplication based on UMI barcodes
Alignment to the Drosophila genome using TopHat v 2.0.13
Searched for clusters enriched for iCLIP crosslink sites
Statistical testing and bootstrapping for significance estimation of each crosslink cluster using custom R scripts
Genome_build: Ensembl dm3 v73
Supplementary_files_format_and_content: Bed files containing the location of clusters with increased iCLIP crosslink signal

organism: Drosophila melanogaster

source_name: cultured UASp-GFP-aub/+;bam∆86hs-bam/nos-gal4 bam∆86  GSC

growth_protocol: UASp-GFP-aub/+;bam∆86hs-bam/nos-gal4 bam∆86 GSC lines were established according to the published procedures (Niki et al., 2006)

extract_protocol:
The rest of the iCLIP experiment was carried out according to the published procedures (Huppertz et al., 2013)
RNA libraries were prepared for sequencing using published procedures (Huppertz et al., 2013)
The iCLIP libraries were designed to include 4-nt unique experimental barcodes (identifying the sequencing library), followed by 5-nt random molecular barcodes (UMI) to assist in detecting PCR duplicates.

treatment_protocol: GSCs cultured in 150mm culture dishes were treated by UV irradiation with 150mJ/cm2 at 254nm

tag: drug treatment


title: 2aub

description: The sample was generated using GGTT as 4-nt barcode preceding a 5-nt random barcode (UMI); note the first 4-nt of the reads should be the reverse complement of the listed barcode


title: Sample_9128-T


title: Sample_9128-N

description: Human normal liver from patient


title: Sample_9194-N

description: Human normal liver from patient


title: tSTATcc-460H_4nspacer (unbound)

city: St. Louis

first: Basab

last: Roy

state: MO

address: 4515 Mckinley avenue

department: Department of Genetics

institute: Washington University School of Medicine

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460H_4nspacer.txt

data_processing:
Extracting binding sites sequence from raw reads.
Count read numbers for each variant, classified by bound or unbound in specseq.
The bound/unbound ratio for each variant and the negative logarithm of the retios were caculated.
Each processed file summarizes all these values in five columns. The first column represents a specific sequence in the library. Columns two to five represent numbers of bound reads, numbers of unbound reads, the bound/unbound ratios and the negative logarithms of the ratios, respectively.
Genome_build: N/A
Supplementary_files_format_and_content: Tab delimited text files.

molecule: other

organism: synthetic construct

source_name: Synthesized DNA

extract_protocol:
All EMSA were done with STAT1 and mutants in 1X NEB Cutsmart buffer (50mM Potassium Acetate, 20mM Tris-acetate, 10mM Magnesium Acetate, 100μg/ml BSA, pH 7.9@25°C), supplemented with 10% glycerol with 1mM of dsDNA and were incubated for 30 minutes on ice. Electrophoresis mobility assay (EMSA) were done using native 12% PAGE prepared as Tris/Glycine (25mM Tris pH 8.3; 192mM glycine) mini-gels. These gels were first pre-run using 1X Tris/Glycine buffer (25mM Tris pH 8.3; 192mM glycine) at 200V for 30 minutes, then samples were loaded for an additional run of 60 minutes at 200 V at 4°C. After EMSA, the gels were stained with ethidium bromide and visualized using Biorad gel imager. Each band detected in the EMSA were excised and the DNA in the gel extracted by incubating for 30 mins at 50°C in 50ml acrylamide gel extraction buffer (500mM Ammonium acetate, 10mM Magnesium Acetate, 1mM EDTA, 0.1% SDS). Sample in the extraction buffer were purified with QIAquick Nucleotide Removal Kit (Qiagen) following the manufacturer’s instructions. Each fraction of DNA was barcoded and amplified using HotStart PCR Master Mix (Lambda Biotech). DNA was denatured at 94°C for 30 seconds, annealed at 55°C for 30 seconds and extend at 72°C for 45 seconds per round for 12 to 20 rounds with modified Indexed-Illumina primers.. The PCR product was then purified again using QIAquick Nucleotide Removal Kit.
DNA libraries for EMSA were constructed by either using GAATAGTCTCATTAACACCGGTTCNNNGAAAGATCATCAAGAGCACACGGG and GAATAGTCTCATTAACACCGGNNNCCGGAAAGATCATCAAGAGCACACGGG (for STAT1 and STAT1-N460H mutant) separately or mixing them (Other STAT1 mutants such as K336A, S459A, S459R, N460A, N460R, Q463A, Q463R). GAATAGTCTCATTAACACCGGTTCNNNNGAAAGATCATCAAGAGCACACGGG or GCTGCCACTAGAGTTT TNNNNGGAA AAGATCATCAAGAGCACACGGG were used in combination with either STAT1 or N460H mutant for studying the effect of 4-nt spacer in binding. The effect of CpG methylation was studied by mixing libraries, GACTAGTCTCATTAACACCAGTTCNNNGAAAGATCATCAAGAGCAGACTGG and GACTAGTCTCATTAAGACCAGTTCNNNGAAAGATCATCAAGAGCAGACTGG or GACTAGTCTCATTAACACCAG NNNCCGGAAAGATCATCAAGAGCAGACTGG and GACTAGTCTCATTAAGACCAGNNNCCGGAAAGATCATCAAGAGCAGACTGG. A single nucleotide internal barcode (higlighted and underlined) was used to distinguish the libreries in mixture. To make double-stranded DNA (dsDNA) libraries, 100 pmole single-strand degenerate template sequences were mixed with an equal amount of primer reverse complementary to the 3' flanking region of the binding site (highlighted). In the presence of Taq Polymerase, a brief 10-sec denaturing followed by 10 min of 55 degree annealing/extension is sufficient to make dsDNA libraries. The reaction mixtres were digested by 1 ml NEB Exo I exo- nuclease (New England Biolabs, Beverly, MA) for 30 min to eliminate unextended single-stranded DNAs (ssDNA). All final dsDNA products were purified by QIAGEN (Valencia, CA) PCR purification columns.

tag: library

value: DNA oligos


title: tSTATcc-460H_Respacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460H_re.txt


title: tSTATcc-460H_4nspacer (bound)


title: tSTATcc-Respacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc_re.txt


title: tSTATcc-4nspacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-4nspacer.txt


title: tSTATcc-463R_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-463R_spacer.txt

extract_protocol:
All EMSA were done with STAT1 and mutants in 1X NEB Cutsmart buffer (50mM Potassium Acetate, 20mM Tris-acetate, 10mM Magnesium Acetate, 100μg/ml BSA, pH 7.9@25°C), supplemented with 10% glycerol with 1mM of dsDNA and were incubated for 30 minutes on ice. Electrophoresis mobility assay (EMSA) were done using native 12% PAGE prepared as Tris/Glycine (25mM Tris pH 8.3; 192mM glycine) mini-gels. These gels were first pre-run using 1X Tris/Glycine buffer (25mM Tris pH 8.3; 192mM glycine) at 200V for 30 minutes, then samples were loaded for an additional run of 60 minutes at 200 V at 4°C. After EMSA, the gels were stained with ethidium bromide and visualized using Biorad gel imager. Each band detected in the EMSA were excised and the DNA in the gel extracted by incubating for 30 mins at 50°C in 50ml acrylamide gel extraction buffer (500mM Ammonium acetate, 10mM Magnesium Acetate, 1mM EDTA, 0.1% SDS). Sample in the extraction buffer were purified with QIAquick Nucleotide Removal Kit (Qiagen) following the manufacturer’s instructions. Each fraction of DNA was barcoded and amplified using HotStart PCR Master Mix (Lambda Biotech). DNA was denatured at 94°C for 30 seconds, annealed at 55°C for 30 seconds and extend at 72°C for 45 seconds per round for 12 to 20 rounds with modified Indexed-Illumina primers.. The PCR product was then purified again using QIAquick Nucleotide Removal Kit.
DNA libraries for EMSA were constructed by either using GAATAGTCTCATTAACACCGGTTCNNNGAAAGATCATCAAGAGCACACGGG and GAATAGTCTCATTAACACCGGNNNCCGGAAAGATCATCAAGAGCACACGGG (for STAT1 and STAT1N460H mutant) separately or mixing them (Other STAT1 mutants such as K336A, S459A, S459R, N460A, N460R, Q463A, Q463R). The effect of CpG methylation was studied by mixing libraries, GACTAGTCTCATTAACACCAGTTCNNNGAAAGATCATCAAGAGCAGACTGG and GACTAGTCTCATTAAGACCAGTTCNNNGAAAGATCATCAAGAGCAGACTGG or GACTAGTCTCATTAACACCAG NNNCCGGAAAGATCATCAAGAGCAGACTGG and GACTAGTCTCATTAAGACCAGNNNCCGGAAAGATCATCAAGAGCAGACTGG. A single nucleotide internal barcode (higlighted and underlined) was used to distinguish the libreries in mixture. To make double-stranded DNA (dsDNA) libraries, 100 pmole single-strand degenerate template sequences were mixed with an equal amount of primer reverse complementary to the 3' flanking region of the binding site (highlighted). In the presence of Taq Polymerase, a brief 10-sec denaturing followed by 10 min of 55 degree annealing/extension is sufficient to make dsDNA libraries. The reaction mixtres were digested by 1 ml NEB Exo I exo- nuclease (New England Biolabs, Beverly, MA) for 30 min to eliminate unextended single-stranded DNAs (ssDNA). All final dsDNA products were purified by QIAGEN (Valencia, CA) PCR purification columns.


title: IN528ic Rep2

treatment_protocol: cell characterization: Cells were dissociated from the tumor, depleted of mouse cells twice by Miltenyi mouse depletion kit and MACS magnetic sorting and then lysed in Trizol.

value: in vivo


title: Sample_9401-T


title: tSTATcc-463A_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-463A_spacer.txt


title: IN528ic Rep1


title: tSTATcc-463A_palindrome (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-463A_palindrome.txt


title: Sample_9401-N

description: Human normal liver from patient


title: tSTATcc-460R_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460R_spacer.txt


title: 1aub

description: The sample was generated using GACC as 4-nt barcode preceding a 5-nt random barcode (UMI); note the first 4-nt of the reads should be the reverse complement of the listed barcode


title: Sample_9195-T


title: tSTATcc-460R_spacer (unbound)


title: Sample_9194-T


title: tSTATcc-460H_Respacer (unbound)


title: tSTATcc-459R_spacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-459R_spacer.txt


title: tSTATcc-463R_palindrome (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-463R_palindrome.txt


title: tSTATcc-460A_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460A_palindrome.txt


title: tSTATcc-463R_spacer (unbound)


title: tSTATcc-Respacer (bound)


title: tSTATcc-459R_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-459R_palindrome.txt


title: tSTATcc-4nspacer (bound)


title: tSTATcc-463A_spacer (unbound)


title: tSTATcc-463A_palindrome (bound)


title: tSTATcc-463R_palindrome (bound)


title: tSTATcc-459A_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-459A_palindrome.txt


title: tSTATcc-460R_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460R_palindrome.txt


title: tSTATcc-460R_palindrome (unbound)


title: tSTATcc-460A_spacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460A_spacer.txt


title: tSTATcc-460A_spacer (bound)


title: TALEN-Y537S-c37-E2-TT14-MP2580

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

department: School of Medicine

institute: New York University

data_processing:
ChIP-seq reads were aligned using bowtie
Peaks were called using MACS2 with default parameters, including a q value < 0.001
bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
A binding intensity matrix was generated using bamliquidator
Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
Genome_build: hg19
Supplementary_files_format_and_content: peaks bed files for ER ChIP

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.

extract_protocol: Cell lines before ChIP were then either introduced to White Medium DMEM with or without supplemental E2 or Doxycycline, Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit

tag: cell subtype - mutation

tag: condition

value: White Medium


title: TALEN-Y537S-c37-TT13-MP2580


title: TALEN-P5-TT1-MC2639

value: Parental


title: tSTATcc-459R_palindrome (unbound)


title: tSTATcc-459R_spacer (bound)


title: T47D-Y537S-DOX-TS6-MP2496

data_processing:
ChIP-seq reads were aligned using bowtie
Peaks were called using MACS2 with default parameters, including a q value < 0.001
bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
A binding intensity matrix was generated using bamliquidator
Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ER ChIP
Supplementary_files_format_and_content: Count Matrix Files for two separate experiments, one for MCF7 Parental and Tamoxifen Resistant lines, and anotherr for RUNX2 with and without DOX

extract_protocol: Cell lines before ChIP were then either introduced to White Medium DMEM with or without supplemental E2 or Doxycycline, Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit. All of the ChIP-seq performed was done using a combination of Estrogen Receptor ab-10/Thermo Scientific/# MS315PABX and Estrogen Receptor HC-20/Santa Cruz Biotechnolofy/sc-543.

value: Doxycycline


title: tSTATcc-336A_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-336A_spacer.txt


title: tSTATcc-460A_palindrome (unbound)


title: TALEN-P5-E2-TT2-MC2639


title: tSTATcc-336A_spacer (unbound)


title: tSTATcc-460H_spacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460H_spacer.txt


title: tSTATcc-336A_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-336A_palindrome.txt


title: Y537S-DOXE2-rep2-S2-8-MP2867

value: Doxycycline + E2


title: T47D-Y537S-E2-TS7-MP2496


title: tSTATcc-460H_spacer (bound)


title: tSTATcc-459A_palindrome (unbound)


title: tSTATcc-459A_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-459A_spacer.txt


title: tSTATcc-460H_palindrome (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-460H_palindrome.txt


title: tSTATcc-459A_spacer (unbound)


title: T47D-Y537S-DOXE2-TS8-MP2496


title: Y537S-DOXE2-SSS5-MP2498


title: Y537S-DOX-rep2-S2-4-MP2867


title: tSTATcc_unmet_palindrome (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-unmet_palindrome.txt


title: Y537S-DOX-rep1-S2-3-MP2867


title: Y537S-DOX-SSS3-MP2498


title: Y537S-DOXE2-rep1-S2-7-MP2867


title: tSTATcc_unmet_palindrome (bound)


title: tSTATcc_met_palindrome (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-met_palindrome.txt


title: tSTATcc-336A_palindrome (unbound)


title: Y537N-DOXE2-NN8-MP2497


title: Y537S-E2-rep1-S2-5-MP2867


title: Y537S-E2-SSS4-MP2498


title: Y537S-E2-rep2-S2-6-MP2867


title: Y537N-DOX-NN6-MP2497


title: tSTATcc_unmet_spacer (unbound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-unmet_spacer.txt


title: tSTATcc_met_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-met_spacer.txt


title: tSTATcc_unmet_spacer (bound)


title: Y537N-DOXE2-N5-RJ2274


title: tSTATcc_palindrome (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-palindrome.txt


title: tSTATcc_palindrome (unbound)


title: tSTATcc_spacer (bound)

description:
Contains bound and unbound reads needed to calculate relative binding energies.
tSTATcc-spacer.txt


title: Y537N-DOX-N7-RJ2274


title: Y537N-E2-N6-RJ2274


title: D538G-DOX-GG6-MP2488


title: Y537N-E2-NN7-MP2497


title: IRJ71-MCF7_D538G_WM_E2_DOX_RNAseq

data_processing:
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ER ChIP
Supplementary_files_format_and_content: Count Matrix Files for two separate experiments, one for MCF7 Parental and Tamoxifen Resistant lines, and anotherr for RUNX2 with and without DOX

extract_protocol: Cell lines were extracted using the Rneasy (Qiagen # 74104) kit with the substitution of Trizol instead of Buffer RLT. Preparation for sequaencing is done using the Illumina Truseq RNAseq v2 kit (15025063)


title: IRJ68-MCF7_D538G_WM_E2_RNAseq


title: D538G-DOXE2-GG8-MP2488


title: IRJ65-MCF7_D538G_WM_DOX_RNAseq


title: tSTATcc-460H_palindrome (bound)


title: tSTATcc_met_palindrome (bound)


title: IRJ70-MCF7_D538G_WM_E2_DOX_RNAseq


title: IRJ66-MCF7_D538G_WM_DOX_RNAseq


title: IRJ69-MCF7_D538G_WM_E2_RNAseq


title: IRJ64-MCF7_D538G_WM_DOX_RNAseq


title: IRJ62-MCF7_D538G_WM_RNAseq


title: IRJ61-MCF7_D538G_WM_RNAseq


title: IRJ56-MCF7_D538G_FM_RNAseq

value: Full Medium


title: IRJ57-MCF7_D538G_FM_RNAseq


title: IRJ58-MCF7_D538G_FM_DOX_RNAseq


title: tSTATcc_spacer (unbound)


title: IRJ52-MCF7_Y537N_WM_E2_DOX_RNAseq


title: tSTATcc_met_spacer (unbound)


title: IRJ53-MCF7_Y537N_WM_E2_DOX_RNAseq


title: IRJ59-MCF7_D538G_FM_DOX_RNAseq


title: IRJ72-MCF7_D538G_WM_E2_DOX_RNAseq


title: IRJ51-MCF7_Y537N_WM_E2_RNAseq


title: IRJ55-MCF7_D538G_FM_RNAseq


title: IRJ50-MCF7_Y537N_WM_E2_RNAseq


title: D538G-E2-GG7-MP2488


title: IRJ67-MCF7_D538G_WM_E2_RNAseq


title: IRJ47-MCF7_Y537N_WM_DOX_RNAseq


title: IRJ48-MCF7_Y537N_WM_DOX_RNAseq


title: IRJ63-MCF7_D538G_WM_RNAseq


title: IRJ60-MCF7_D538G_FM_DOX_RNAseq


title: IRJ42-MCF7_Y537N_FM_DOX_RNAseq


title: IRJ44-MCF7_Y537N_WM_RNAseq


title: IRJ40-MCF7_Y537N_FM_DOX_RNAseq


title: IRJ41-MCF7_Y537N_FM_DOX_RNAseq


title: IRJ45-MCF7_Y537N_WM_RNAseq


title: IRJ43-MCF7_Y537N_WM_RNAseq


title: IRJ46-MCF7_Y537N_WM_DOX_RNAseq


title: IRJ39-MCF7_Y537N_FM_RNAseq


title: IRJ37-MCF7_Y537N_FM_RNAseq


title: IRJ38-MCF7_Y537N_FM_RNAseq


title: IRJ34-MCF7_Y537S_WM_E2_DOX_RNAseq


title: IRJ36-MCF7_Y537S_WM_E2_DOX_RNAseq


title: IRJ49-MCF7_Y537N_WM_E2_RNAseq


title: IRJ32-MCF7_Y537S_WM_E2_RNAseq


title: IRJ33-MCF7_Y537S_WM_E2_RNAseq


title: IRJ30-MCF7_Y537S_WM_DOX_RNAseq


title: IRJ31-MCF7_Y537S_WM_E2_RNAseq


title: IRJ29-MCF7_Y537S_WM_DOX_RNAseq


title: IRJ27-MCF7_Y537S_WM_RNAseq


title: IRJ28-MCF7_Y537S_WM_DOX_RNAseq


title: IRJ23-MCF7_Y537S_FM_DOX_RNAseq


title: IRJ24-MCF7_Y537S_FM_DOX_RNAseq


title: IRJ21-MCF7_Y537S_FM_RNAseq


title: IRJ22-MCF7_Y537S_FM_DOX_RNAseq


title: IRJ19-MCF7_Y537S_FM_RNAseq


title: IRJ20-MCF7_Y537S_FM_RNAseq


title: IRJ18-T47D_Y537S_WM_E2_DOX_RNAseq


title: IRJ54-MCF7_Y537N_WM_E2_DOX_RNAseq


title: IRJ17-T47D_Y537S_WM_E2_DOX_RNAseq


title: IRJ15-T47D_Y537S_WM_E2_RNAseq


title: IRJ16-T47D_Y537S_WM_E2_DOX_RNAseq


title: IRJ35-MCF7_Y537S_WM_E2_DOX_RNAseq


title: IRJ14-T47D_Y537S_WM_E2_RNAseq


title: Sample_402_Brd4_rep2

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

source_name: primary T cells

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48-72h and treated with JQ1 and MS402 for 2 hours before harvesting for further analysis.

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using a Nucleospin RNA kit (Clontech).
ChIP-Seq: ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. RNA-Seq: Extracted RNA was subjected to polyA selection and standard Illumina RNA-seq library prep procedures.

tag: strain

value: primary T cells

tag: chip-antibody

value: Brd4 (Bethyl; IHC-00396)


title: Sample_402_input_rep1


title: Sample_402_input_rep2


title: Sample_402_Brd4_rep1


title: Sample_402_Brd2_rep1

value: Brd2 (Bethyl; IHC-00612)


title: IRJ11-T47D_Y537S_WM_DOX_RNAseq


title: IRJ10-T47D_Y537S_WM_DOX_RNAseq


title: RNA_seq_Th17_rep1


title: IRJ26-MCF7_Y537S_WM_RNAseq


title: RNA_seq_Th17_rep2


title: IRJ25-MCF7_Y537S_WM_RNAseq


title: RNA_seq_Th17_MS402_rep2


title: IRJ8-T47D_Y537S_WM_RNAseq


title: IRJ9-T47D_Y537S_WM_RNAseq


title: RNA_seq_Th17_MS402_rep1


title: IRJ7-T47D_Y537S_WM_RNAseq


title: RNA_seq_Th17_JQ1_rep2


title: IRJ6-T47D_Y537S_FM_DOX_RNAseq


title: IRJ5-T47D_Y537S_FM_DOX_RNAseq


title: RNA_seq_Th17_JQ1_rep1


title: IRJ4-T47D_Y537S_FM_DOX_RNAseq


title: IRJ3-T47D_Y537S_FM_RNAseq


title: IRJ12-T47D_Y537S_WM_DOX_RNAseq