title: CC from tonsil 4

tag: cell type

value: Centrocyte

value: Healthy donor

value: Tonsil


title: S14

status: Public on Aug 23 2019

type: SRA

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

library_source: transcriptomic

data_processing:
RNA-Seq reads were mapped to the mouse genome (mm10, Genome Reference Consortium GRCm38)  in the strand-specific mode using HISAT2.
Number of uniquely aligned reads (q > 10) to the exonic region of each gene were counted using HTSeq based on the GenCode annotation version M16 (Ensembl v91)
Genes that achieved at least one read count per million reads (cpm) in at least four samples (i.e., number of samples per group) were kept. Conditional quantile normalisation (cqn) was then performed accounting for gene length and GC content, and a log2 transformed RPKM expression matrix was subsequently generated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Ang + Low dose Cil

growth_protocol: Primary mouse cardiomyocyte cells were isolated from the whole hearts of 1-3-day old C57/BL6 wild-type mice.Following 5 days incubation at 37°C, 5% CO2, primary mouse cardiomyocytes were serum starved for 24 hours in a 0.5% FBS-DMEM media. Cells were then washed and recoated with complete cardiomyocyte growth media. For cardiomyocyte hypertrophy assessment 1uM angiotensin II (Alfa Aesar) was added to cardiomyocyte growth media post serum starvation (i.e. day 6 post-culture), and this was repeated the next day. In tandem to angiotensin II treatment, cells were either treated with vehicle or low dose Cilengitide (20nM) (Bachem). After 8-day culture and treatment, cardiomyocytes were either lysed for RNA analysis.

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Bart's and the London Genome Centre for processing. Library preps were made using PolyA-capture.

value: cardiomyocytes

tag: treatment

value: Ang II (1uM) + Low dose Cil (20nM)

tag: strain

tag: genotype/variation

value: wild-type


title: CC from tonsil 3

type: RNA

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

description: CD19posCD38hiCD10posIgDnegCXCR4neg cells

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2.0 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by the GC-RMA algorithm. Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations

label: biotin

organism: Homo sapiens

source_name: Centrocyte purified from human non tumorla tonsil

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

extract_protocol: RNA extraction was performed using Qiazol (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were purified by FACSARIA sorting strategy from non tumoral tonsils using following phenotypes : CD19posCD38hiCD10posIgDnegCXCR4pos for CB or CXCR4neg for CC

tag: disease

tag: tissue


title: ESS 69

city: Stockholm

first: Joseph

middle: Woodward

last: Carlson

address: P1:02 Radiumhemmet

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description: Thermo Fisher Scientific Human Gene 2.1 ST Array

hyb_protocol: GeneTitan™ Instrument User Guide for Expression  ArrayPlates, P/N 702933

scan_protocol: standard Affymetrix protocol

data_processing: The data were normalized with the default settings on Thermo Fishers Expression Console 1.4.1.46 Software.

label: biotiin

source_name: Sarcomas

label_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit, P/N 703089

extract_protocol: none provided by submitter

value: Undifferentiated Uterine Sarcomas

tag: mitotic index group

value: Low

tag: hormone receptor expression

value: Positive

tag: rna group

value: Proliferative

tag: nuclear atypia

value: Uniform

tag: cnv group

value: High

tag: cell density

value: no info

tag: time to last follow up (months)

tag: status at last follow up

value: Dead


title: ESS 68

value: LMS-like

value: No Data


title: S16


title: CC from tonsil 1


title: ESS 66

value: Negative


title: ESS 67

value: Pleomorphic


title: ESS 70

value: Developmental


title: S13


title: CB from tonsil 5

description: CD19posCD38hiCD10posIgDnegCXCR4pos cells

source_name: Centroblast purified from human non tumorla tonsil

value: Centroblast

value: Healthy donor

value: Tonsil


title: S12

source_name: Low dose Cil

value: cardiomyocytes

value: Low dose Cilengitide (20nM)

value: wild-type


title: CB from tonsil 6


title: S11


title: ESS 65

value: Undifferentiated Uterine Sarcomas

value: Low

value: Positive

value: Alive


title: S10


title: CB from tonsil 3


title: CB from tonsil 4


title: S9


title: S8

source_name: Angiotensin II

value: Angiotensin II (1uM)


title: ESS 63

value: High

value: Dead


title: ESS 64

value: No Data

value: LMS-like


title: ESS 58

value: Negative

value: Pleomorphic


title: S7


title: ESS 59

value: Developmental


title: ESS 61

value: Proliferative


title: ESS 62


title: ESS 55

value: Uniform


title: S6

value: cardiomyocytes


title: ESS 49


title: CB from tonsil 6 non stimulated

source_name: Centroblast purified from human non tumoral tonsil and cultured 3 hours without stimulation

growth_protocol: Centroblasts were purified from non tumoral tonsils by FACSARIA sorting strategy using following phenotypes : CD19posCD38hiCD10posIgDnegCXCR4pos . Cells were immediately put in cultured with ou without CD40L and IL21

value: Healthy donor

value: Tonsil


title: ESS 54

value: Undifferentiated Uterine Sarcomas


title: CB from tonsil 1

value: Centroblast


title: ESS 51

value: Low

value: Positive


title: CB from tonsil 6 CD40L-IL21 stimulated

source_name: Centroblast purified from human non tumoral tonsil and cultured 3 hours with CD40L - IL21 stimulation


title: CB from tonsil 2


title: ESS 52


title: CB from tonsil 5 CD40L-IL21 stimulated


title: ESS 46

value: ECM


title: ESS 53

value: High


title: S5

value: Angiotensin II (1uM)

value: wild-type


title: ESS 47

value: No Data

value: Dead


title: ESS 45

value: Pleomorphic


title: ESS 41

value: Negative


title: ESS 43

value: LMS-like


title: S3

source_name: Control

value: Saline


title: CB from tonsil 4 CD40L-IL21 stimulated


title: ESS 39

value: Uniform

value: Alive


title: CB from tonsil 5 non stimulated

value: Healthy donor

value: Tonsil


title: S2

value: cardiomyocytes


title: ESS 40

value: Undifferentiated Uterine Sarcomas

value: Low


title: S1


title: Tyrosol_3

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome and generate BAM files
DESeq algorithm was used to obtain normalized gene expression values (StrandNGS software)
Gene expression differences between treated and control groups were compared by moderated T-test; Benjamini-Hochberg False Discovery Rate was used for multiple testing correction.
Genome_build: C. parapsilosis CDC317 (candida genome database; Genome: C_parapsilosis_CDC317_version_s01-m03-r27_features_with_chromosome_sequences.gff.gz; http://www.candidagenome.org/download/gff/C_parapsilosis_CDC317/archive/)
Supplementary_files_format_and_content: Exel file includes RPKM and fold change values

organism: Candida parapsilosis

source_name: fungal cells_tyrosol

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 30ºC with 3.7 Hz shaking frequency for 18 hours then diluted to OD640 0.2 value in 20 mL of YPD and incubated at 37ºC with 2.3 Hz shaking frequency.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent (Chomczynski BioTechniques. 1993; 15:536–7.) and glass beads. RNA concentration and purity were determined using NanoDrop (ThermoFisher Scientific, Waltham, MA USA) and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using TruSeq RNA Sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94°C. First strand cDNA was generated by random priming reverse transcription; double stranded cDNA was generated in a second strand synthesis step. After repairing ends, A-tailing and adapter ligation steps, adapter-ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp-long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSpace.

treatment_protocol: Following 4 hours incubation time YPD medium was supplemented with a final concentration of 15 mM tyrosol and fungal cells were collected 2 hours following tyrosol exposure by centrifugation (5 min, RCF=4000g, 4°C). The cells were washed three times with phosphate-buffered saline and stored at -70°C until use.

value: CLIB 214

tag: genotype

value: wild type

value: 15 mM tyrosol


title: Control_3

source_name: fungal cells_control

value: none (control)


title: Tyrosol_2


title: Tyrosol_1


title: CB from tonsil 4 non stimulated


title: CB from tonsil 3 CD40L-IL21 stimulated


title: NH4+_plus_1

city: guangzhou

first: guangxin

last: liu

address: 501 Zhongkai Road, Haizhu District, Guangzhou

country: China

institute: zhongkai university of agriculture and engineering

data_processing:
The quality of the raw sequence data were first assessed by FastQC and the sequences were then filtered and trimmed by Trimmomatic
The remaining reads were used to map to the reference genome of B. velezensis FZB42 (NC_009725.1) by Bowtie2
Alignments reported from Bowtie2 were further processed by the BEDTools software
Differential expression of all of transcripts was quantified through DEGseq software
Differential expressed genes were simply defined as at least 2-fold change with Q value <0.05.
Genome_build: B. velezensis FZB42 (NC_009725.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Bacillus velezensis

growth_protocol: Bacteia were growth in minimal medium with initial OD600=0.02

extract_protocol:
Bacteria were lysed by constantly grinding in the presence of liquid nitrogen with the total RNA extracted using TRIzol reagent (Invitrogen), and finally dissolved in 50 μL RNase-free water.
The total RNA quality was evaluated after ribosomal RNAs were removed. The RNA was then fragmented and used as a template for a randomly primed PCR. Strand-specific cDNA libraries were prepared by standard techniques for subsequent Illumina sequencing (Illumina HiSeq 2000)

tag: culture condition

value: minimal medium containing 10 mmol/L NH4+-N

tag: time point

value: late log phase (0.4 - 0.7 OD)


title: NH4+_plus_3


title: ESS 42

value: No Data

value: ECM

value: Pleomorphic

value: Dead


title: P14-9

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Data quality was assessed with htseq-qa
Reads were aligned to the Aspergillus niger NRRL3 genome (https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Aspni_NRRL3_1) using TMAP 3.0.1 (https://github.com/iontorrent/TS/tree/master/Analysis/TMAP) , the ION Torrent aligner designed for ION data, with the –g parameter set to 0 (soft clip right and left ends of each read) and the –a parameter set to 1 (return only best alignment, random choice in case of ties).
BAM file outputs were then mapped to genes using htseq-count (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287950/ ) using default settings.
Differential expression analysis  was conducted using the R package DESeq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8).
Genome_build: NRRL3
Supplementary_files_format_and_content: .txt files are 2 columns: gene ID and raw counts; Gene IDs correspond to the gene annotation available at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Aspni_NRRL3_1

organism: Aspergillus niger

source_name: mycelia

growth_protocol: A newly developed culturing system called the pie-plate was used that is a variation on the previously described ring-plate (Levin, A.M., de Vries, R.P. & Wosten, H.A. Localization of protein secretion in fungal colonies using a novel culturing technique; the ring-plate system. Journal of microbiological methods 69, 399-401 (2007). The pie-plate with liquid medium (no agar) was covered by a perforated polycarbonate membrane that allows the transfer of proteins and metabolites, but not of fungal hyphae. The fungus was inoculated at the center of the plate and grew radially. The carbon source present in the compartments influenced the radial growth, resulting in a non-symmetrical colony. The compartments were physically separated and therefore influence of one compartment to the other has to be mediated by the fungal mycelium. To evaluate influence of one compartment on the other, the same carbon source was used in three neighboring compartments. This means that one compartment was surrounded by compartments with the same carbon source, while the other two had a different carbon source on one side.

extract_protocol:
The mycelia growing on each of the compartments was sampled by cutting through the polycarbonate (PC) membrane along the boundary of the compartment with a scalpel blade and then the PC membrane was peeled away before transferring the mycelia to a 2 mL tube and flash freezing in liquid nitrogen; these samples were used for RNA isolation as described previously (PMID:26314379).
The SMARTerR UltraTM Low RNA kit (catalog number 634851) was used to generate full length cDNA template library according to the instruction manual, followed by Ion Plus fragment library kit (Thermo Fisher Scientific, cat# 4471252) to fragment cDNA and barcode adapter ligation for template prep.  Template library was quantified using the Ion Library TaqMan™ Quantitation Kit (Thermo Fisher Scientific, cat# 4468802). The emulsion clonal bead amplification to generate bead templates for Ion Torrent platform using the Ion PI™ Hi-Q™ Chef Kit (Thermo Fisher Scientific, A27198) with Ion PI™ Chip Kit v3 (Thermo Fisher Scientific, cat#A26771) on the Ion Chef System (Thermo Fisher Scientific). Sequencing was performed using the Ion PI™ Hi-Q™ Sequencing 200 Kit (Thermo Fisher Scientific, cat# A26772) on Ion Proton sequencer.

tag: cell type

value: mycelia

tag: substrate

value: wheat bran (WB)

tag: plate

value: C

tag: compartment


title: Control_2

tag: strain

tag: treatment


title: Control_1


title: CB from tonsil 2 non stimulated

tag: disease

value: Healthy donor

tag: tissue

value: Tonsil


title: CB from tonsil 2 CD40L-IL21 stimulated


title: Glu_3

value: minimal medium containing Gln-N (as control)


title: ESS 37

value: Undifferentiated Uterine Sarcomas

tag: mitotic index group

value: High

tag: hormone receptor expression

tag: rna group

value: Developmental

value: Uniform


title: CB from tonsil 3 non stimulated


title: ESS 35

value: Low

value: Positive

tag: nuclear atypia

tag: cnv group

tag: cell density


title: ESS 34

value: Negative

tag: time to last follow up (months)

tag: status at last follow up

value: Alive


title: P14-8


title: ESS 38

value: LMS-like


title: ESS 33


title: ESS 31

value: No Data


title: Glu_2

tag: culture condition

tag: time point

value: late log phase (0.4 - 0.7 OD)


title: Myo1A-Gal4 x MPC RNAi 3

city: Salt Lake City

first: Carl

last: Thummel

state: UT

address: 15 North 2030 East, Room 5200

department: Human Genetics

country: USA

institute: University of Utah

data_processing:
base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v4
RNA-seq reads were aligned to the dm3 genome build with Ensembl transcript splice alignments using novoalign
Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection    Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM and equal volumes were pooled in preparation for Illumina sequence analysis.   Additional details of the library preparation process are described below:  Library construction is performed using the Illumina TruSeq Stranded mRNA Library Preparation Kit (cat# RS-122-2101, RS-122-2102) as described below.  Briefly, total RNA (100 ng to 4 ug) is poly-A selected using poly-T  oligo-attached magnetic beads.  Poly-A RNA eluted from the magnetic beads is fragmented and primed with random hexamers in preparation for cDNA synthesis.  First strand reverse transcription is accomplished using Superscript II Reverse Transcriptase (Invitrogen cat#18064-014).  Second strand cDNA synthesis is accomplished using DNA polymerase I and Rnase H under conditions in which dUTP is substituted for dTTP, yielding blunt-ended cDNA fragments in which the second strand with dUTP.  An A-base is added to the blunt ends as a means to prepare the cDNA fragments for adapter ligation and block concatamer formation during the ligation step.  Adapters containing a T-base overhang  are ligated to the A-tailed DNA fragments.  Ligated fragments are PCR-amplified (12-15 cycles) under conditions in which the pcr reaction enables amplification of the first strand cDNA product, whereas attempted amplifciation of the second strand product stalls at dUTP bases and therefore is not represented in the amplified library.  The PCR-amplified library is purified using Agencourt AMPure XP beads (Beckman Coulter Genomics cat#A63881).  Following amplification, the library is purified by bead based methodologies.  The concentration of the amplified library is measured with a NanoDrop spectrophotometer and an aliquot of the library is resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size distribution of the sequencing library.  Libraries are adjusted to a concentration of approximately 10 nM and quantitative PCR is performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter ligated library molecules.  The concentration is further adjusted following qPCR to prepare the library for Illumina sequence analysis.
HiSeq 50 Cycle Single-Read Sequencing version 4  Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).
Genome_build: dm3
Supplementary_files_format_and_content: xlsx file containing analyzed output from DESeq.

organism: Drosophila melanogaster

source_name: intestine

extract_protocol:
Intestines were removed, flash frozen in trizol, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestine

tag: age

value: RNAi was activated for 7 days in 4-5 days old adults

tag: genotype

value: MPC RNAi


title: NH4+_plus_2

value: minimal medium containing 10 mmol/L NH4+-N


title: P14-7

tag: cell type

value: mycelia

tag: substrate

value: wheat bran (WB)

tag: plate

value: C

tag: compartment


title: P14-6

value: sugar beet pulp (SBP)


title: CB from tonsil 1 non stimulated

tag: disease

value: Healthy donor

tag: tissue

value: Tonsil


title: P14-5


title: CB from tonsil 1 CD40L-IL21 stimulated


title: Myo1A-Gal4 x MPC RNAi 2

tag: strain


title: P14-4


title: P14-3

value: glucose


title: Myo1A-Gal4  x MPC RNAi 1

value: MPC RNAI


title: P14-2


title: P11-9

value: B


title: Myo1A-Gal4  x mCherry RNAi 2

value: control RNAi


title: P11-7


title: Myo1A-Gal4  x mCherry RNAi 3


title: P11-6


title: P11-8


title: Myo1A-Gal4 x mCherry RNAi 1


title: P11-5


title: Glu_1

value: minimal medium containing Gln-N (as control)


title: A3MK503

city: Shanghai

first: Haifang

last: Wang

address: NO 320, Yue Yang Road

institute: Institute of Neuroscience

data_processing:
Sequence images were transformed to per read base call files (fastq files) with Illumina software BaseCaller and CASAVA v1.8.2.
We first check the quality of the data via fastqc (v.0.10.0, Babraham Bioinformatics). Raw sequence reads were aligned to Macaca mulatta genome (ensembl 73) by Tophat program (V2.0.8 custom parameters: --no-coverage-search) (Trapnell et al. 2009, Bioinformatics). The gene annotation was downloaded from RhesusBase v2.0 (http://www.rhesusbase.org/), which use all published Macaque RNA-seq data to refine ensembl Macaque gene annotation. The reads number mapped to each gene were calculated use bedtools (v2.16.2 default parameters) (Aaron et al. 2010, Bioinformatics).
Genome_build: Macaca mulatta (ensembl 73)
Supplementary_files_format_and_content: text file of read counts for each gene

organism: Macaca fuscata

extract_protocol:
RNA were extracted at the TAL using Phenol Chloroform extraction.
1 μg of total RNA were converted into Illumina sequencing libraries using the TruSeq RNA Sample Preparation Kit (Illumina, RS-122-2002) as per manufacturer’s protocol.

treatment_protocol: Global ischemia was induced by clipping the subclavian artery for 18 minutes, while controls received similar operations (Tonchev et al, 2003) without clipping of artery to remove any controversy of gene expression changes due to operation apart from the clipping of the artery.

tag: treatment

value: postischemic

value: SVZa


title: A3MK508

value: control


title: Trans het mutant 3

value: intestine

value: 7-10 days old adults

value: MPC Mutant


title: A3MK507


title: P11-4

value: mycelia


title: P11-3


title: A3MK504


title: P14-1


title: A3MK501


title: Trans het mutant 2


title: A3MK506


title: Trans het mutant 1


title: NBTII Cell line treated with HGF at 48 hour, replicate 2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Rat 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0002 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
RaGene-1_0-st-v1.r4.pgf
RaGene-1_0-st-v1.r4.mps

organism: Rattus norvegicus

source_name: Cell Line

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

growth_protocol: Cells were grown in DMEM 10% FBS and 100 units/ml penicillin-streptomycin,  37°C in 5% CO2

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated in media with 5ng/ml HGF added

tag: cell line

value: NBTII


title: A2MK507


title: ESS 32

value: Undifferentiated Uterine Sarcomas

tag: mitotic index group

value: High

tag: hormone receptor expression

value: Negative

tag: rna group

value: Developmental

tag: nuclear atypia

value: Uniform

tag: cnv group

value: Dead


title: P11-2

value: glucose

value: B


title: P11-1


title: NBTII Cell line treated with HGF at 24 hour, replicate2


title: Precise excision control 2

value: wild type


title: Precise excision control 3


title: A2MK506

value: postischemic


title: A2MK504

value: SVZa


title: Precise excision control 1


title: A2MK508

value: control


title: A2MK503


title: P7-7

value: wheat bran (WB)

value: A


title: P7-8


title: P7-6

value: sugar beet pulp (SBP)


title: A2MK501


title: A1MK508


title: NBTII Cell line treated with HGF at 9 hour, replicate 2


title: NBTII Cell line treated with HGF at 4 hour, replicate 2


title: A1MK506


title: P7-9

value: mycelia


title: NBTII Cell line treated with HGF at 24 hour, replicate 1

value: NBTII


title: NBTII Cell line treated with HGF at 2 hour, replicate 2


title: NBTII Cell line at 0 hour, replicate 2

description: NBTII Cell line at 0 hour


title: P7-4


title: P7-5


title: P7-3


title: A1MK507


title: P7-2


title: A1MK504


title: A1MK503


title: P7-1


title: A1MK501


title: CS_seedlings_H3K27me3_ChIP_seq

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

library_source: genomic

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq and DNaseI-seq  data,  HISAT2 2.1.020 for RNA-seq data ,  Bismark_v0.19.0 for bisulfite-seq data , all with default settings.
For ChIP-seq  and DNaseI-seq data, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–50 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In RNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided;In DNaseI-seq , peak files were provided ; In Bisulfite-seq ,BigWig files with position and  methylation ratio were provided.

molecule: genomic DNA

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Chromatin or RNA was extracted from 12-days-old seedlingss, using standard protocols. , 2 μg mRNA ,2μg total RNA (rRNA depleted) were used to prepare mRNA-seq and lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq，DnaseI-seq and Bisulfite-seq
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions  (Illumina) to produce 150bp paired-end reads.

treatment_protocol: No treatment applied.

value: 12-days-old seedlings

tag: cultivar

value: Chinses Spring

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: RAW49

status: Public on Aug 22 2019

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

country: Germany

institute: University Medicine Halle (Saale)

description: AA supplemented/LPS stimulated

data_processing:
Basecalls and Demultiplexing was performed using CASAVA version 1.4
Raw reads were adapter trimmed with cutadapt version 1.9.1. Only adapter trimmed reads between 15 and 27 bp lengthwere considered processed miRNAs and selected for alignment.
small RNA seq reads were aligned to the GRCm38/GRCh38 genome assembly using Bowtie2 version 2.2.7 allowing 1 mismatch and alignment to multiple targets
Reads were annotated by intersecting genome coordinates of known miRNAs from miRBase version 21  using Bedtools version 2.25.0
Reads were counted using the R/Bioconductor programming environment by application of the ShortRead library and the table function together with the miRNA name in the annotation
Count normalisation was done using the R/Bioconductor packages DESeq2 and EdgeR
Genome_build: GRCm38 (RAW264.7 samples) or GRCh38 (TIME samples)
Supplementary_files_format_and_content: Processed data files contain raw counts, DESeq and EdgeR normalised counts as labelled

growth_protocol: Cells were cultured according to ATCC recommendations

extract_protocol:
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Prep kit v2. Size restriction (140-165bp), purification, and quantification of barcoded libraries were performed using the Library quantification kit - Illumina/Universal. For cluster generation up to 10 libraries per were factored using an Illumina cBot.

treatment_protocol: The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling either 72 h (RAW264.7) or 144 h (TIME). Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of either LPS (1 µg/mL; from E. coli serotype 0111:B4) for cell line RAW264.7 or the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml for cell line TIME.

tag: cell type

value: macrophage

value: AA supplemented/LPS stimulated


title: RAW57

description: DHA supplemented/LPS stimulated

value: DHA supplemented/LPS stimulated


title: RAW142

description: unsupplemented/LPS stimulated

value: unsupplemented/LPS stimulated


title: NBTII Cell line treated with HGF at 9 hour, replicate 1


title: OVCAR3-siBHLHE41 #A

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from OVCAR3 cells treated with siRNA targeting BHLHE41 (siBHLHE41 #A)

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Clario S Assay, human). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: OVCAR3 cells treated with siBHLHE41 #A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human ovarian cancer RMG1 and OVCAR3 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) and Roswell Park Memorial Institute (RPMI) 1640 medium, respectively.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: RMG1 cells were transfected with CPNE8-targeting siRNAs or control siRNA, and OVCAR3 cells were transfected with BHLHE41-targeting siRNAs or control siRNA.

value: ovarian cancer cell line

tag: genotype/variation


title: RAW51

description: AA supplemented/LPS stimulated


title: RAW55

description: DHA supplemented/LPS stimulated


title: RAW78

description: unsupplemented/LPS stimulated


title: RAW79

description: unsupplemented/LPS stimulated


title: SLAMF9-/- replica 3

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description: DEoutput.xlsx

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using option alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESeq2 output

source_name: bone marrow

extract_protocol:
A total of 100,000 pDCs (CD19-, CD11B-, CD11C inter+, B220+, PDCA+) were collected in triplicates from the bone marrow of WT and SLAMF9 deficient mice.
Inhouse poly A based RNA seq

value: BM pDCs

tag: genomic background

value: SLAMF9 knockout


title: OVCAR3-siBHLHE41 #B

description: Gene expression data from OVCAR3 cells treated with siRNA targeting BHLHE41 (siBHLHE41 #B)

source_name: OVCAR3 cells treated with siBHLHE41 #B


title: SLAMF9-/- replica 2

description: DEoutput.xlsx


title: RMG1-siCPNE8 #B

description: Gene expression data from RMG1 cells treated with siRNA targeting CPNE8 (siCPNB8 #B)

source_name: RMG1 cells treated with siCPNE8 #B


title: OVCAR3-siControl

description: Gene expression data from OVCAR3 cells treated with control siRNA

source_name: OVCAR3 cells treated with siControl

value: siControl


title: RAWi

description: AA supplemented/unstimulated

value: AA supplemented/unstimulated


title: RAW47

description: AA supplemented/LPS stimulated


title: RAW28

description: DHA supplemented/unstimulated

value: DHA supplemented/unstimulated


title: RAWh

description: AA supplemented/unstimulated


title: ESS 60

source_name: Sarcomas

value: Undifferentiated Uterine Sarcomas

value: High

value: Negative

value: ECM

value: Pleomorphic

tag: cell density

tag: time to last follow up (months)

tag: status at last follow up

value: Dead


title: RAWg

description: AA supplemented/unstimulated

tag: treatment


title: NBTII Cell line treated with HGF at 4 hour, replicate 1

tag: cell line

value: NBTII


title: NBTII Cell line treated with HGF at 2 hour, replicate 1


title: NBTII Cell line treated with HGF at 6 hour, replicate 2


title: RMG1-siControl

description: Gene expression data from RMG1 cells treated with control siRNA

source_name: RMG1 cells treated with siControl


title: RAW56

description: DHA supplemented/LPS stimulated

value: macrophage


title: NBTII Cell line treated with HGF at 48 hour, replicate 1


title: NBTII Cell line at 0 hour, replicate 1

description: NBTII Cell line at 0 hour


title: RMG1-siCPNE8 #A

description: Gene expression data from RMG1 cells treated with siRNA targeting CPNE8 (siCPNB8 #A)

source_name: RMG1 cells treated with siCPNE8 #A


title: NBTII Cell line treated with HGF at 6 hour, replicate 1


title: Wild type replica3

description: DEoutput.xlsx

tag: strain

value: Wild type


title: RAW26

description: DHA supplemented/unstimulated


title: Wild type replica1

description: DEoutput.xlsx


title: SLAMF9-/- replica 1

description: DEoutput.xlsx


title: RAWb

description: unsupplemented/unstimulated

value: unsupplemented/unstimulated


title: Wild type replica2

description: DEoutput.xlsx


title: RAWa

description: unsupplemented/unstimulated


title: RAW18

description: unsupplemented/unstimulated


title: RAW24

description: DHA supplemented/unstimulated


title: Striatum, R6/2 + PLX3397 3

city: Irvine

first: Kim

last: Green

state: CA

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: Comma delimited file includes RPKM values for all Samples.

extract_protocol:
Brains were removed, microdissected and flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Plus Universal Mini Kit (73404, Qiagen) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

tag: genotype

tag: tissue

value: brain (striatum)


title: Striatum, Wild-type + PLX3397 3

value: Wild-type


title: Striatum, Wild-type + PLX3397 2


title: Striatum, Wild-type 2

value: Vehicle


title: Striatum, Wild-type 1


title: Striatum, R6/2 + PLX3397 2


title: Striatum, R6/2 2


title: Striatum, Wild-type 3


title: Striatum, R6/2 3


title: Striatum, R6/2 1


title: Pten/p53 - F2

first: Sebastian

last: Brandner

state: State...

address: Queen square house, UCL Institute of Neurology

department: Institute of Neurology

institute: University College London

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 mm10 whole genome using Tophat2
PCR duplicates were filtered out with picard 1.72 then HTSeq to count transcripts and DESeq to normalise and analyse in R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Subventricular zone

growth_protocol: Cells were cultured in DMEM/F12 supplemented with B27, EGF, and FGF.

extract_protocol:
Total RNA were extracted with miRCURY RNA isolation kit (Exiqon, #300110) according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: a mix of C57BL/6 and FVB

value: Brain

tag: developmental stage

value: adult mice


title: Striatum, Wild-type + PLX3397 1


title: 110spc4 anoxic 1 (NnrR control)

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description:
wt
B. diazoefficiens wild type grown anoxically in completely filled bottles

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2.2 µg of labeled cDNA  were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com).

organism: Bradyrhizobium diazoefficiens

source_name: B. diazoefficiens wild type grown in anoxic conditions

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: B. diazoefficiens cells were cultured in YEM medium (Daniel and Appleby, 1972) with 10 mM nitrate. Cells were first grown oxically in PSY medium, washed and further grown anoxically in YEM medium to an optical density at 600 (OD600) of about 0.2. Anoxic conditions were obtained by incubation in completely filled bottles.

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: No treatment was applied

tag: growth condition

value: anoxic

tag: medium

value: YEM


title: 8678 anoxic 2

description:
NnrR
B. diazoefficiens nnrR mutant grown anoxically in completely filled bottles

source_name: B. diazoefficiens nnrR mutant grown in anoxic conditions


title: 110spc4 anoxic 3 (NnrR control)


title: 110spc4 anoxic 2 (NnrR control)


title: Vector_TILs

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

description: 10x single cell RNA-seq (3' polyA capture), CD8+ TILs harvested from E0771-mCherry-OVA tumors in Rag-/- mice previously adoptively transferred with CD8 T+ cells infected with Vector

data_processing:
Raw sequencing output was first preprocessed by Cell Ranger 1.3 (10x Genomics) (Zheng et al., 2017b) using cellranger mkfastq, count, and aggr (no normalization mode). *I1*.fastq.gz = sample index, *R1*fastq.gz = cell barcode + UMI, *R2*.fastq.gz = transcript
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix. Cell barcodes ending in "-1" correspond to sgDhx37 cells, while "-2" barcodes correspond to Vector cells

molecule: polyA RNA

source_name: Tumor-infiltrating CD8 T cells, transduced with lenti-Vector

extract_protocol: 10x Genomics Chromium Single-cell 3' RNA-seq  (v2)

value: C57BL/6J, OT-1; Cas9

value: CD8 T cells

value: Vector


title: 8678 anoxic 3


title: sgDhx37_TILs

description: 10x single cell RNA-seq (3' polyA capture), CD8+ TILs harvested from E0771-mCherry-OVA tumors in Rag-/- mice previously adoptively transferred with CD8 T+ cells infected with sgDhx37

source_name: Tumor-infiltrating CD8 T cells, transduced with lenti-sgDhx37


title: KO_12h_Rep2

city: Beijing

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15).
The Fastq files were aligned to the reference genome (mm10 and VSV) using Hisat2 (v2.1.0).
Reads mapped to tRNA and rRNA are removed and each sample obtained ~ 30 million useful reads for the following analysis.
Stringtie (v1.3.3b) was used to calculate the FPKM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Genome_build: mm10 and VSV
Supplementary_files_format_and_content: FPKM

source_name: Peritoneal macrophages

growth_protocol: Mouse primary peritoneal macrophages were harvested from mice 3 days after intraperitoneal injection of thioglycolate and cultured in endotoxin-free DMEM medium with 10% (v/v) fetal bovine serum (FBS, Gibco).

extract_protocol:
Total RNA was isolated from peritoneal macrophages with TRIzol reagent (Invitrogen) and performed using Ribo-Zero Gold rRNA Removal Kit (Illumina).
The RNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: Cells were uninfected or infected with VSV (MOI=1) for 8 or 12 hours.

value: Mouse primary peritoneal macrophages

value: VSV infection for 12h


title: Idh1/Pten/p53 - A1

city: London


title: Striatum, R6/2 + PLX3397 1


title: Pten/p53 - S4

data_processing:
Illumina Casava1.7 software used for basecalling.
Filtering: CHASTITY
Normalization: EdgeR
Genome_build: miRBase 20
Supplementary_files_format_and_content: tab-delimited text files include tags per million (TPM) value

extract_protocol:
Total RNA were extracted with miRCURY RNA isolation kit (Exiqon, #300110) according to manufacturer's protocol
A total of 500ng total RNA was converted into microRNA NGS libraries using  NEBNEXT library generation kit (New England Biolabs Inc.) according to the  manufacturer’s instructions. Each individual RNA sample had adaptors ligated to its  3’ and 5’ ends and converted into cDNA. Then the cDNA was pre-amplified with  specific primers containing sample specific indexes. After 15 cycle pre-PCR the  libraries were purified on QiaQuick columns and the insert efficiency evaluated by  Bioanalyzer 2100 instrument on high sensitivity DNA chip (Agilent Inc.). The  microRNA cDNA libraries were size fractionated on a LabChip XT (Caliper Inc.) and  a band representing adaptors and 15-40 bp insert excised using the manufacturer’s  instructions. Samples were then quantified using qPCR and concentration standards.  Based on quality of the inserts and the concentration measurements the libraries  were pooled in equimolar concentrations (all concentrations of libraries to be pooled  are of the same concentration). The library pool(s) were finally quantified again with  qPCR and optimal concentration of the library pool used to generate the clusters on  the surface of a flowcell before sequencing using v3 sequencing methodology  according to the manufacturer instructions (Illumina Inc.)


title: Idh1/Pten/p53 - A2


title: Pten/p53 - F1


title: CTR (negative control siRNA)

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: The cells were treated with negative control siRNA followed by culturing at 37°C for 2 days

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: RMA performed with GeneChip Analysis Suite

source_name: Normal human epidermal keratinocytes

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Normal human epidermal keratinocytes (KK-4009; Lot, #05298; Kurabo Industries Ltd., Osaka, Japan) were cultured in Humedia-KG2 (Kurabo Industries Ltd, Osaka, Japan) supplemented with 20% FBS in a humidified atmosphere with 5% CO2. All experiments were carried out on cells at the third passage.

extract_protocol: Total RNA was prepared from normal human epidermal keratinocytes (KK-4009; Lot, #05298; Kurabo Industries Ltd., Osaka, Japan) using a method previously described [Makino et al., J Biol Chem. 2001 Dec 14;276(50):47445-52.] and was pretreated with DNase I (Roche Diagnostics, Basel, Schweiz). RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: The cells were transfected with siRNA duplexes (ambion, silencer select, Thermo Fisher Scientific K.K., Tokyo, Japan) by a reverse transfection method using Lipofectoamine RNAiMAX (Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer’s instructions. Two or three days after the transfection, the cells were used for the experiments.

tag: Sex

value: male

tag: race

value: Caucasian

tag: age

value: newborn

value: skin

tag: life span

value: third passage

tag: morphology

value: cobblestone appearance

tag: knockdown

value: negative control siRNA


title: KD (siRNA for TCHHL1)

description: The cells were treated with siRNA for TCHHL1 followed by culturing at 37°C for 2 days

value: TCHHL1 siRNA


title: 8678 anoxic 1

source_name: B. diazoefficiensnnrR mutant grown in anoxic conditions


title: KO_8h_Rep2

tag: cell type

value: VSV infection for 8h


title: Pten/p53 - S3

value: a mix of C57BL/6 and FVB

value: Brain

value: adult mice


title: WT_12h_Rep2

value: wild type


title: Idh1/Pten/p53 - S6


title: KO_12h_Rep1


title: KO_8h_Rep1


title: KO_0h_Rep1

value: No treatment


title: Idh1/Pten/p53 - S12


title: WT_8h_Rep2


title: Idh1/Pten/p53 - S5


title: 9B

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads obtained from PFC were mapped to mm10 using HISAT2 (Kim et al., 2015).
Counts of reads mapped to genes were obtained using HTSeq-count (Anders et al., 2015) against Ensembl v90 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using HTSeq-count

source_name: Prefrontal cortex neurons

growth_protocol: C57BL/6J mice were euthanized 24 hours after final behavior via cervical dislocation. In order to acquire only infected tissue within prefrontal cortex (PFC), microdissection was performed under a fluorescent microscope. Brain slices containing PFC were either visualized on blade and punched directly or suspended in cold phosphate buffered saline (PBS) prior to tissue dissection. PFC was collected as either a single midline 12- gauge punch or bilateral 14-gauge punches, which varied according to virus spread. However, only PFC was included in dissections. Mice were excluded from analysis when the PFC was not correctly targeted. Dissected tissue was immediately frozen on dry ice.

extract_protocol:
Total RNA was isolated from frozen dissected PFC tissue using QIAzol lysis reagent and purified using the miRNAeasy mini kit (Qiagen). For RNA being utilized for RNA-seq, RNA integrity (RIN) was assayed using an Aligent 2100 Bioanalyzer (Aligent, Santa Clara CA).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA). Briefly, mRNA was polyA selected from the total RNA pool. mRNA was then fragmented and converted to cDNA with reverse transcriptase followed by cDNA size selection and purification with AMPure XP beads (Beckman Coulter, Brea CA). To identify eachsample, strand-specific adapters were ligated to adenylated 3’ ends and an additional size selection step was performed. The cDNA library was then amplified using polymerase chain reaction. During this step, barcodes of six base pairs were added to the adaptors. Library quality and concentration was measured by the Bioanalyzer before sequencing.

tag: sgrna

value: CRE-motif

tag: over-expression

value: Defeat


title: 9C

value: non-targeted


title: WT_8h_Rep1

value: Mouse primary peritoneal macrophages

tag: treatment


title: 9A


title: WT_12h_Rep1

value: VSV infection for 12h


title: 7H


title: KO_0h_Rep2


title: 7E


title: 5E

value: Control


title: KO_0h_IP_Rep2

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15)
The Fastq files were aligned to the reference genome (mm10 and VSV) using Hisat2 (v2.1.0)
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Genome_build: mm10 and VSV
Supplementary_files_format_and_content: bed

extract_protocol:
Total RNA was isolated from peritoneal macrophages with TRIzol reagent (Invitrogen) then subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit (61006, Invitrogen) following the manufacturer’s instructions. For m6A-immunoprecipitation (IP) samples, RNA fragmentation and immunoprecipitated of m6A-containing RNA fragments via anti-m6A antibody (202003, Synaptic System) were performed.
The input mRNA sample (input) and purified mRNA sample (m6A-IP) were used for library construction by TruSeq Stranded mRNA Library Preparation kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were uninfected or infected with VSV (MOI=1) for 6 hours.

tag: merip antibody


title: WT_6h_IP_Rep2

tag: strain

value: VSV infection for 6h

value: anti-m6A antibody (202003, Synaptic System)


title: 5D

tag: genotype


title: KO_6h_IP_Rep2


title: WT_0h_IP_Rep2


title: KO_6h_Input_Rep2


title: WT_0h_Rep2


title: 5B


title: KO_0h_Input_Rep2


title: 5A


title: WT_0h_Input_Rep2


title: WT_6h_Input_Rep2


title: 3H


title: 3C


title: 3D


title: KO_6h_IP_Rep1


title: WT_6h_IP_Rep1


title: 3G


title: WT_0h_IP_Rep1


title: 5C


title: KO_6h_Input_Rep1


title: WT_0h_Rep1


title: 7A


title: 1G


title: 5G


title: 3A


title: 3B


title: KO_0h_IP_Rep1


title: KO_0h_Input_Rep1


title: WT_0h_Input_Rep1


title: 1E


title: 1C


title: 1A


title: 13F_Ibu3_18

city: Montpellier

first: Brigitte

last: Boizet Bonhoure

address: 141 rue de la Cardonille

department: Human Genetic Institute

institute: CNRS UMR9002

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 with bowtie v2.1.0.
Quantification : Gene expression was quantified using HTSeq v0.6.1 (intersection-nonempty mode) and Ensembl release 86 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: ovary

extract_protocol:
13.5 dpc ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Sample Preparation kit according to Illumina user guide (PN 15031047) with the following modifications: 2 minutes mRNA fragmentation and 12 cycles library PCR amplification.

treatment_protocol: 30mg/kg/day APAP+ 15mg/kg/day IBU or ethanol (control) were alternately administrated every 3 hours (4 times, 150ml by gavage) to wild type CD1 pregnant females between 10.5 and 13.5dpc.

value: 13.5 days post coitum (dpc)

tag: exposure

value: APAP+IBU

tag: tissue

value: 13.5 dpc ovary


title: 13F_Ibu2_17

tag: developmental stage


title: 13F_ctl3_15

value: control


title: 13F_ctl1_13


title: MeCP2_ChIPRx_DKO1_rep1

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

data_processing:
The sequences were separately aligned to either human genome(hg19) using Bowtie 2 with the options --sensitive --score-min L,-1.5,-0.3. PCR duplicate are removed for further analysis.
PCR duplicate are removed using samtools rmdup for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Input normalized bigwig files were generated using bamCompare of deepTools package with the options –normalizeUsing CPM –extendReads 200.

source_name: colon cancer cell line

growth_protocol: HCT116 cell line and DNMT1 (Δexons3-5/Δexons3-5); DNMT3B (-/-) of HCT116 (horizon, HD R02-079), named as DKO1, were maintained in RPMI 1640 (Sigma, R8758), supplemented with 10% FBS (Welgene, S001-01) and Penicillin/Streptomycin (Lonza, 17-602E) at 5% CO2 in 37°C. Drosophila S2 cells (ATCC, CRL-1963) were cultured in Schneider’s Drosophila Medium(Gibco, 21720024) supplemented with 10% fetal bovine serum (Welgene, S001-01) in 25°C.

extract_protocol:
HCT116 or DKO1 cells (density of 0.5~0.6 x 106 cells/ml) were washed with 10 ml of PBS and cross-linked with 1% formaldehyde for 5 min. The crosslinking reactions were quenched with 10x Glycine stop solution. The cross-linked HCT116 or DKO1 cells were lysed in lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% IGEPAL CA-630, pH 8.0) using a dounce homogenizer (Kimble-Kontes. 885300-0002) to aid in nuclei release. The released nuclei was pelleted by centrifugation (10 min, 5000 rpm at 4C) and stored at -80°C. As a reference exogenous genome, Drosophila S2 cells were cross-linked with 1% formaldehyde for 5 min and were quenched with 10x Glycine stop solution. The Drosophila S2 cells were then washed 3 times with ice cold PBS. Washed cell pellets were flash frozen and stored at -80°C. For each ChIP-Rx experiment, HCT116 or DKO1 cells and drosophila S2 cells were combined with ratio of 3:1 and sonicated for 15 min with 30 sec intervals to shear genomic DNA using Bioruptor XL (Diagenode). The sheared genomic DNA was evaluated by electrophoresis for their size ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was incubated with H3K27me3 (Diagenode, pAb-069-050) or MeCP2 (Diagenode, pAb-052-050). After pull down, genomic DNA in the complex was reverse cross-linked by DNase-free Proteinase K and purified.
For ChIP-seq experiments, H3K27me3 or MeCP2 ChIPed, or input DNA were used to prepare ChIP-seq libraries as described (NEXTflex ChIP-seq kit, Bio Scientific, NOVA 5143-01 and NEXTflex ChIP-seq Barcodes-6, NOVA 514120) followed by high throughput sequencing with Illumina NextSeq500.

value: colon cancer cell line

tag: cell line

tag: spike-in reference

value: Drosophila melanogaster

value: 3 to1

tag: chip antibody

value: MeCP2 (Diagenode, pAb-052-050)


title: MeCP2_ChIPRx_DKO1_rep2

description: DNMT1 (Δexons3-5/Δexons3-5); DNMT3B (-/-) of HCT116


title: 13F_ctl2_14


title: MeCP2_ChIPRx_HCT116_rep1


title: H3K27me3_ChIPRx_DKO1_rep2

value: H3K27me3 (Diagenode, pAb-069-050)


title: H3K27me3_ChIPRx_DKO1_rep1


title: H3K27me3_ChIPRx_HCT116_rep2


title: H3K27me3_ChIPRx_HCT116_rep1


title: Input_ChIPRx_DKO1_rep2


title: WT_6h_Input_Rep1

value: wild type


title: Input_ChIPRx_DKO1_rep1


title: 1B

value: CRE-motif

value: Defeat


title: Input_ChIPRx_HCT116_rep2


title: A375-CTX-72hr-2

city: Parkville

first: Karen

last: Sheppard

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Center

data_processing:
Illumina CASAVA 1.8.2 was used for base calling and quality control was performed using RNA-SeQC v1.1.7
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg38 ) using HISAT2
featureCounts v1.6.2 was used to count the number of reads per gene
Limma-Voom method was applied for data normalisation and differential gene expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: csv file includes normalized counts for each sample

growth_protocol: A375 cells were cultured in fully supplemented RPMI medium

extract_protocol:
Total RNA was extracted RNeasy Mini Kit as per manufacturer's instructions, Ribo-RNA depletion was performed
RNA libraries were prepared for sequencing according to standard Illumina protocols (TruSeq RNA Sample Preparation Guide v2 Guide)

treatment_protocol: A375 cells were treated with either 1 μΜ Palbociclib (CDK4i) or 500 nM GSK3326595 (PRMT5i) for 72 hr. Control groups were grown in 0.01% DMSO.

tag: tissue source

value: Melanoma

tag: replicate

value: Replicate 2


title: control1

city: Shenyang‘

first: Zheng

last: Zhang

address: 155N Nanjing Road, Heping district

department: Dermatology

institute: No.1 Hospital of China Medical University

data_processing:
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Supplementary_files_format_and_content: excel format with Number of raw junction read

source_name: exosome

extract_protocol:
Total RNA was isolated from the exosomes using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and quantified using the NanoDrop ND-1000.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: blood plasma

tag: diagnosis

value: healthy

tag: rna fraction

value: exosome


title: control2


title: 13F_Ibu1_16

value: 13.5 days post coitum (dpc)


title: MeCP2_ChIPRx_HCT116_rep2


title: MondoA_KD_ChIP-seq

city: Philadelphia

first: Byungyong

last: Ahn

state: Pennsylvania

address: 3400 Civic Center Blvd Bldg 421

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
reads alignment by STAR 2.5.0c with parameters "--runMode alignReads --runThreadN 4 --genomeDir %s --readFilesIn %s --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outReadsUnmapped None --alignIntronMax 1 --genomeLoad LoadAndKeep --readFilesCommand zcat --limitBAMsortRAM 10000000000 --outFileNamePrefix %s" with "--genomeDir" for your reference genome, "--readFilesIn" for your input raw data and "--outFileNamePrefix" for the output prefix
tag directory made by Homer 5.10 for each Sample and only unique mapped reads were used
Peak calling by the "findPeaks" command in Homer 5.10 using the default setting
Bigwig files were generated by Homer and bedGraphToBigWig command
motif analysis by the "findMotifsGenome" command in Homer 5.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig

source_name: Primary skeletal myotube

growth_protocol: Primary human skeletal myoblasts are cultured in low glucose DMEM supplemented with 10% fetal bovine serum. When the cells reach 80-90% confluency, the cells are switched to differentiation media composed of alpha-MEM with 2% fetal bovine serum. This media is replaced every other day.

extract_protocol:
Lysates were clarified from sonicated nuclei and MondoA or Histione-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, Catalog # 0344)

treatment_protocol: siRNA against MondoA or control was transfected on day 6 following differentiaiton. The cells were harvested 3days after transfection.

tag: cell type

value: Primary human myocytes

value: MondoA KD

tag: passages

value: MondoA (ProteinTech, catalog # 13614-1-AP, lot # 00042515)


title: Input_ChIPRx_HCT116_rep1

value: colon cancer cell line


title: treat1

value: cutaneous squamous cell carcinoma


title: A375-CTX-72hr-1

value: Replicate 1


title: H3K27ac_Control_ChIP-seq

value: control

value: H3K27ac (Abcam, catalog # ab4729, lot no. GR3211959-1)


title: A375-PD991-72hr-2

value: Palbociclib (PD991) - 72hr


title: A375-PD991-72hr-1


title: MondoA_Control_ChIP-seq


title: control3


title: A375-DMSO-72hr-1

value: Vehicle (DMSO) - 72 hr


title: A375-DMSO-72hr-2


title: H9_substate 2

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human embryonic stem cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and 480 ng cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software GX14.9.1 (Agilent) using default parameters.

source_name: H9, passage 50, substate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: H9 cells were maintained on Matrigel (BD Biosciences) in TeSR-E8 (STEMCELL Technologies). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared by using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: human embryonic stem cell


title: H9_substate 1

source_name: H9, passage 35, substate 1


title: treat3


title: treat2


title: Cell_451

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-61_S353_L006_R1_001.fastq.gz

data_processing:
The raw fastq files were trimmed using TrimGalore! In pair-end mode with default parameters.
The trimmed fastq data were aligned to human reference genome Hg38 using STAR in pair-end mode with default parameters.
The alignment results were inputted to featureCounts to compute the number of reads mapped back to each gene in each sample.
Genome_build: hg38
Supplementary_files_format_and_content: Read count table for each gene in each sample generated by featureCounts software.

source_name: single cell isolated from hESC derived 3D-retinal ordanoid

growth_protocol: H9 hESCs were maintained in Essential-8 (E8) medium (Invitrogen) on Vitronectin (VTN-N)-coated plates and passaged twice weekly. Medium was changed every day.

extract_protocol: Retinal organoids were dissociated in Accutase (StemPro) for 30 min to create a single-cell suspension. Cells were collected by centrifugation at 300 × g for 5 min and resuspended in 500 μL RDM. we used a mouth pipette to immediately transfer single cells into prepared lysis buffer. scRNA-seq library was constructed following modified Smart-seq2 protocol[6]. In detail, samples were incubated at 72°C for 3 min. The first-strand cDNA was reverse-synthesized using oligo(dT) and template-switching oligonucleotides (TSO). The synthesized first-strand cDNAs were amplified by 18 cycles. After purification, 0.1 ng cDNA were used for Nextera tagmentation (illumina) and library construction. Sequencing was performed on Illumina HiSeq 4000.

treatment_protocol: hESC were enzymatically lifted with dispase (2 mg/mL) and grown as aggregates in suspension. Medium was switched from E8 to neural induction medium (NIM: DMEM/F12 1:1, 1% N2 supplement, MEM nonessential amino acids, penicillin-streptomycin and 2 µg/ml heparin sulfate) gradually over the course of four days. On D7, cell aggregates were attached to the plate with 10% fetal bovine serum (FBS) to facilitate attachment. On D16 cultures were switched to retinal differentiation medium (RDM: DMEM/F12 (3:1), 2% B27 supplement, MEM nonessential amino acids and penicillin-streptomycin). On D18, neural retina structures were manually dissected from the plate and allowed to form free-floating organoids in RDM. From D30, RDM was supplemented with 10% FBS, 100 µM Taurine, 2mM GlutaMAX and 0.5 µM retinoic acid for long-term differentiation.

value: cell from hESC derived 3D-retinal ordanoid


title: Cell_450

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-57_S247_L005_R1_001.fastq.gz


title: Cell_447

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-98_S390_L006_R1_001.fastq.gz


title: Cell_449

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-9_S301_L006_R1_001.fastq.gz


title: RRBS: PCOS-31

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) Reads were trimmed using  trim_galore v0.4.3 with the --rrbs flag (using cutadapt v1.4.2).
2) Trimmed reads were mapped to hg38 and methylation levels estimated using Bismark v0.18.1 and Bowtie2 on default settings
3) Differential methylation analysis was performed with RnBeads v1.10.7 with human annotation RnBeads.hg38 v1.10.0. Threshold for minimal acceptable coverage was set to 10.
Genome_build: hg38
Supplementary_files_format_and_content: Coverage (cov) files contain the coverage per sample data processing step 2.

source_name: Peripheral Blood

extract_protocol:
DNA extracted using the Qiagen all prep DNA/RNA/miRNA universal kit (#80224, Germany)
RRBS was performed using Diagenode Premium RRBS Kit (#C02030033, U.S.A)

treatment_protocol: PBMCs were isolated by ficoll gradient and stored in LN2. Cryopreserved PBMCs were thawed then stained PBMCs before being sorted in using the FACS-Aria (BD, U.S.A).

value: T helper cells

tag: group

value: PCOS


title: RRBS: CONT-29

value: CONT


title: Cell_448

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-99_S391_L006_R1_001.fastq.gz


title: RRBS: CONT-30


title: RRBS: PCOS-28


title: Cell_446

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-97_S389_L006_R1_001.fastq.gz


title: Cell_445

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-96_S388_L006_R1_001.fastq.gz


title: RRBS: PCOS-26


title: RRBS: PCOS-25


title: Cell_443

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-94_S386_L006_R1_001.fastq.gz


title: RRBS: PCOS-27


title: Cell_442

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-93_S385_L006_R1_001.fastq.gz


title: Cell_444

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-95_S387_L006_R1_001.fastq.gz


title: RRBS: CONT-24


title: RRBS: CONT-23


title: RRBS: CONT-22


title: Cell_438

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-8_S300_L006_R1_001.fastq.gz


title: RRBS: CONT-21


title: Cell_439

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-90_S382_L006_R1_001.fastq.gz


title: Cell_437

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-89_S381_L006_R1_001.fastq.gz


title: Cell_436

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-88_S380_L006_R1_001.fastq.gz


title: RRBS: PCOS-20


title: Cell_435

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-87_S379_L006_R1_001.fastq.gz


title: RRBS: PCOS-15


title: RRBS: PCOS-12


title: RRBS: CONT-14


title: Cell_431

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-83_S375_L006_R1_001.fastq.gz


title: Cell_441

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-92_S384_L006_R1_001.fastq.gz


title: Cell_434

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-86_S378_L006_R1_001.fastq.gz


title: Cell_433

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-85_S377_L006_R1_001.fastq.gz


title: RRBS: PCOS-13


title: Cell_430

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-82_S374_L006_R1_001.fastq.gz


title: RRBS: PCOS-11


title: RRBS: PCOS-18


title: Cell_427

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-7_S299_L006_R1_001.fastq.gz


title: Cell_429

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-81_S373_L006_R1_001.fastq.gz


title: RRBS: PCOS-9


title: Cell_440

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-91_S383_L006_R1_001.fastq.gz


title: Cell_432

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-84_S376_L006_R1_001.fastq.gz


title: Cell_428

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-80_S372_L006_R1_001.fastq.gz


title: Cell_426

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-79_S371_L006_R1_001.fastq.gz


title: RRBS: PCOS-7


title: Cell_425

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-78_S370_L006_R1_001.fastq.gz


title: RRBS: CONT-5


title: RRBS: CONT-6


title: RRBS: CONT-16


title: RRBS: CONT-10


title: RRBS: PCOS-4


title: Cell_422

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-75_S367_L006_R1_001.fastq.gz


title: RRBS: CONT-19


title: Cell_421

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-74_S366_L006_R1_001.fastq.gz


title: Cell_419

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-72_S364_L006_R1_001.fastq.gz


title: RRBS: PCOS-8


title: Cell_418

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-71_S363_L006_R1_001.fastq.gz


title: Cell_424

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-77_S369_L006_R1_001.fastq.gz


title: RNAseq: PCOS-29

data_processing:
1) RNAseq raw reads were aligned to human genome (hg38) using STAR v2.5.3a.
2) Gene read coverages were computed with featureCounts and Gencode (release 26) GTF file (rRNA annotation were excluded).
3) Differential expression analysis was performed using DESeq2 v3.6.
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of normalized read counts (generated by DESeq2).

extract_protocol:
RNA  extracted using the Qiagen all prep DNA/RNA/miRNA universal kit (#80224, Germany)
RNA sequencing was performed according to Illumina TruSeq Stranded Total RNA with Ribo-Zero   Gold protocol.


title: RNAseq: CONT-28


title: Cell_417

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-70_S362_L006_R1_001.fastq.gz


title: RRBS: CONT-1


title: RNAseq: PCOS-25


title: RNAseq: CONT-22


title: Cell_415

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-69_S361_L006_R1_001.fastq.gz


title: RRBS: CONT-3


title: Cell_414

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-68_S360_L006_R1_001.fastq.gz


title: RNAseq: CONT-21


title: Cell_416

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-6_S298_L006_R1_001.fastq.gz


title: RNAseq: PCOS-26


title: Cell_413

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-67_S359_L006_R1_001.fastq.gz


title: Cell_411

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-65_S357_L006_R1_001.fastq.gz


title: Cell_412

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-66_S358_L006_R1_001.fastq.gz


title: RNAseq: CONT-20


title: RNAseq: CONT-17


title: RNAseq: PCOS-19


title: Cell_410

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-64_S356_L006_R1_001.fastq.gz


title: RNAseq: CONT-15


title: RRBS: CONT-2


title: Cell_420

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-73_S365_L006_R1_001.fastq.gz


title: RNAseq: CONT-1


title: Cell_409

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-63_S355_L006_R1_001.fastq.gz


title: Cell_408

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-62_S354_L006_R1_001.fastq.gz


title: Cell_407

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-60_S352_L006_R1_001.fastq.gz


title: S159_EGSFA_NBP2-57757

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
20190201_SUM159_EGS-FA_NBP2-57757_GP6614_S12
ChIP-seq for EN1 in SUM159 cells

data_processing:
ChIP-Seq: QC, alignment and peak calling was performed using ChiLin pipeline 2.0.0 (https://www.ncbi.nlm.nih.gov/m/pubmed/27716038/?i=6&from=chilin). Briefly, reads were aligned to GRCh37/hg19 using BWA, and peak calling was performed using MACS2, in chilin.
RNA-Seq: Datasets were aligned to the human reference GRCh37/hg19 genome and to the mouse reference GRCm38/mm10 genome, both using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic. Samples were filtered to remove contamination (mouse contamination). Reads uniquely mapped only to the target genome were kept, along with uniquely mapped reads that had significantly better alignment scores in the target genome compared to the contamination genome.
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: bed file (BED6+4) of factor peaks from MACS2 peakcaller.

growth_protocol: Xenograft RNA-seq: Animal experiments were performed following protocol 11-023 approved by DFCI ACUC. SUM149 or SUM159 cells (1 x 106) expressing TET-inducible Luciferase or EN1-targeting shRNAs were resuspended in 50% Matrigel (BD Biosciences) and injected orthotopically into the mammary fat pads of 6-week old female NOG mice (Taconic).

extract_protocol:
ChIP-seq: cell monolayers were fixed with 1% formaldehyde for 10 min, at room temperature for H3K27ac and FOXA1 ChIP-seq, or 37C for V5-EN1 and TLE3 ChIP-seq. Cells were fixet with 1.5mM EGS during 30 min and adding 1% paraformaldehyde during the last 10 min for b-catenin ChIP-seq. All cell fixations were wuenched by adding 125mM glycine during 5 min. After 2 ice-cold PBS washes, cells were scrapped off in PBS, pelleted and snap-frozen. RNA-seq: cells were washed 3 times with ice-cold PBS, scrapped off the plates, pelleted and snap frozen into liquid nitrogen. For RNA-extraction, the RNeasy Mini Kit (Qiagen, #74106) was used, with in-column DNA digestion.
ChIP-seq: the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) was used following manufacturer's instructions. RNA-seq: libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: Xenograft RNA-seq: When the tumors became palpable, shRNAs were induced in the treatment group by administering a doxycycline diet (625ppm). Animals were euthanized and tumors were harvested when tumors in the control group reached ~ 1.5 cm size


title: S149_37FA_NBP2-57757

description:
20190201_SUM149_FA_NBP2-57757_GP6614_S9
ChIP-seq for EN1 in SUM149 cells


title: Cell_406

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-5_S297_L006_R1_001.fastq.gz


title: Cell_405

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-59_S351_L006_R1_001.fastq.gz


title: Cell_404

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-58_S350_L006_R1_001.fastq.gz


title: Cell_403

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-57_S349_L006_R1_001.fastq.gz


title: SUM149_shEN1-2_Doxy_0R

description:
20190207_SUM149_shEN1-2_Doxy_0R_GP6615_S19
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-2 with doxycycline
SUM149_shEN1-2_Doxy_0R.Aligned.sortedByCoord.out.hg19.mm10-filtered

tag: hairpin

tag: treatment

value: Dox


title: SUM159_shEN1-2_NoDoxy_0L

description:
20190207_SUM159_shEN1-2_NoDoxy_0L_GP6615_S5
RNA-seq of SUM159 PDX cells with TET-inducible shEN1-2 without doxycycline
SUM159_shEN1-2_NoDoxy_0L.Aligned.sortedByCoord.out.hg19.mm10-filtered

value: No Dox


title: SUM159_shluc_NoDoxy_4L

description:
20190207_SUM159_shluc_NoDoxy_4L_GP6615_S2
RNA-seq of SUM149 PDX cells with TET-inducible shLuc without doxycycline
SUM159_shluc_NoDoxy_4L.Aligned.sortedByCoord.out.hg19.mm10-filtered

value: shluc


title: Cell_402

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-56_S348_L006_R1_001.fastq.gz


title: SUM149_shluc_Doxy_1R

description:
20190207_SUM149_shluc_Doxy_1R_GP6615_S12
RNA-seq of SUM159 PDX cells with TET-inducible shLuc with doxycycline
SUM149_shluc_Doxy_1R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_401

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-55_S347_L006_R1_001.fastq.gz


title: Cell_400

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-54_S346_L006_R1_001.fastq.gz


title: SUM159_shluc_NoDoxy_1L

description:
20190207_SUM159_shluc_NoDoxy_1L_GP6615_S1
RNA-seq of SUM159 PDX cells with TET-inducible shLuc without doxycycline
SUM159_shluc_NoDoxy_1L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_399

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-53_S345_L006_R1_001.fastq.gz


title: SUM159_shEN1-2_Doxy_3R

description:
20190207_SUM159_shEN1-2_Doxy_3R_GP6615_S8
RNA-seq of SUM159 PDX cells with TET-inducible shEN1-2 with doxycycline
SUM159_shEN1-2_Doxy_3R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_398

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-52_S344_L006_R1_001.fastq.gz


title: SUM149_shEN1-1_NoDoxy_4L

description:
20190207_SUM149_shEN1-1_NoDoxy_4L_GP6615_S14
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-1 without doxycycline
SUM149_shEN1-1_NoDoxy_4L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM159_shluc_Doxy_3L

description:
20190207_SUM159_shluc_Doxy_3L_GP6615_S4
RNA-seq of SUM159 PDX cells with TET-inducible shLuc with doxycycline
SUM159_shluc_Doxy_3L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_397

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-51_S343_L006_R1_001.fastq.gz


title: Cell_396

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-50_S342_L006_R1_001.fastq.gz


title: SUM159_shEN1-2_Doxy_0R

description:
20190207_SUM159_shEN1-2_Doxy_0R_GP6615_S7
RNA-seq of SUM159 PDX cells with TET-inducible shEN1-2 with doxycycline
SUM159_shEN1-2_Doxy_0R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_394

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-49_S341_L006_R1_001.fastq.gz


title: Cell_395

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-4_S296_L006_R1_001.fastq.gz


title: MCF7_EN1_EN1ab

description:
20151218-MCF7-EN1-EN1-GP2598_S9
ChIP-seq for EN1 in MCF7 cells with EN1 overexpression


title: SUM149_shEN1-2_NoDoxy_2R

description:
20190207_SUM149_shEN1-2_NoDoxy_2R_GP6615_S18
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-2 without doxycycline
SUM149_shEN1-2_NoDoxy_2R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM149_shEN1-1_NoDoxy_1L

description:
20190207_SUM149_shEN1-1_NoDoxy_1L_GP6615_S13
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-1 without doxycycline
SUM149_shEN1-1_NoDoxy_1L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM149_shluc_NoDoxy_1R

description:
20190207_SUM149_shluc_NoDoxy_1R_GP6615_S10
RNA-seq of SUM149 PDX cells with TET-inducible shLuc without doxycycline
SUM149_shluc_NoDoxy_1R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM159_shluc_Doxy_1R

description:
20190207_SUM159_shluc_Doxy_1R_GP6615_S3
RNA-seq of SUM159 PDX cells with TET-inducible shLuc with doxycycline
SUM159_shluc_Doxy_1R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_393

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-48_S340_L006_R1_001.fastq.gz


title: Cell_423

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-76_S368_L006_R1_001.fastq.gz


title: Cell_391

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-46_S338_L006_R1_001.fastq.gz


title: Cell_388

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-43_S335_L006_R1_001.fastq.gz


title: Cell_392

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-47_S339_L006_R1_001.fastq.gz


title: SUM159_shEN1-2_NoDoxy_2L

description:
20190207_SUM159_shEN1-2_NoDoxy_2L_GP6615_S6
RNA-seq of SUM159 PDX cells with TET-inducible shEN1-2 without doxycycline
SUM159_shEN1-2_NoDoxy_2L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM149_shluc_NoDoxy_0R

description:
20190207_SUM149_shluc_NoDoxy_0R_GP6615_S9
RNA-seq of SUM149 PDX cells with TET-inducible shLuc without doxycycline
SUM149_shluc_NoDoxy_0R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: SUM149_shEN1-2_NoDoxy_0R

description:
20190207_SUM149_shEN1-2_NoDoxy_0R_GP6615_S17
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-2 without doxycycline
SUM149_shEN1-2_NoDoxy_0R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_390

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-45_S337_L006_R1_001.fastq.gz


title: SUM149_shEN1-1_Doxy_4L

description:
20190207_SUM149_shEN1-1_Doxy_4L_GP6615_S16
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-1 with doxycycline
SUM149_shEN1-1_Doxy_4L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_389

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-44_S336_L006_R1_001.fastq.gz


title: SUM149_shEN1-2_Doxy_3R

description:
20190207_SUM149_shEN1-2_Doxy_3R_GP6615_S20
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-2 with doxycycline
SUM149_shEN1-2_Doxy_3R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_385

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-40_S332_L006_R1_001.fastq.gz


title: SUM149_shluc_Doxy_0L

description:
20190207_SUM149_shluc_Doxy_0L_GP6615_S11
RNA-seq of SUM149 PDX cells with TET-inducible shLuc with doxycycline
SUM149_shluc_Doxy_0L.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_387

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-42_S334_L006_R1_001.fastq.gz


title: Cell_386

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-41_S333_L006_R1_001.fastq.gz


title: SUM159_BRD4_DMSO_Input_R1

description: input for sample SUM159_H3K27ac

data_processing:
RNA-Seq, ChIP-Seq: Illumina Casava1.7 software used for basecalling.
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
RNA-Seq: Datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19 refGene annotation file available at the UCSC Genome Browser.
ChIP-Seq: QC, alignment and peak calling was performed using ChiLin pipeline 2.0.0 (https://www.ncbi.nlm.nih.gov/m/pubmed/27716038/?i=6&from=chilin). Briefly, reads were aligned to GRCh37/hg19 using BWA, and peak calling was performed using MACS2, in chilin.
Genome_build: RNA-Seq and ChIP-Seq: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: bed file (BED6+4) of factor peaks from MACS2 peakcaller.

growth_protocol: SUM149 and SUM159: DMEM/F12, 5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin, 50 U/mL penicillin and 50 μg/ml streptomycin. MCF7: 4.5mg/l glucose DMEM, 10% FBS, 10 μg/ml insulin, 50 U/mL penicillin and 50 μg/ml streptomycin

treatment_protocol: SUM149 and SUM159: 5x10exp5 cells were seeded in 150mm tissue culture plates, allowed to attach and grow for 24h and then treated or not with 0.1ug/mL doxycycline hyclate for 5 days, with one media change at day 3. MCF7: 2x10exp6 cells were seeded in 150mm tissue culture plate. After 24h, media were change and allow to grow for 5 days, with one media change at day 3.

value: input


title: Cell_384

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-3_S295_L006_R1_001.fastq.gz


title: SUM149_shEN1-1_Doxy_2R

description:
20190207_SUM149_shEN1-1_Doxy_2R_GP6615_S15
RNA-seq of SUM149 PDX cells with TET-inducible shEN1-1 with doxycycline
SUM149_shEN1-1_Doxy_2R.Aligned.sortedByCoord.out.hg19.mm10-filtered


title: Cell_383

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-39_S331_L006_R1_001.fastq.gz


title: SUM149_RT_Input

description: input for sample SUM149_shEN1_Control_TLE3_P, sample SUM149_shEN1_Doxy_TLE3_P, sample SUM149_shEN1_Control_H3K27ac, and sample SUM149_shEN1_Dox_H3K27ac


title: SUM159_RT_Input

description: input for sample  SUM159_Control_TLE3_P and sample SUM159_Doxy_TLE3_P


title: Cell_381

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-37_S329_L006_R1_001.fastq.gz


title: Cell_382

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-38_S330_L006_R1_001.fastq.gz


title: MCF7_EN1_RT_Input

description: input for sample MCF7_EN1_TLE3_P and sample MCF7_EN1overexpession_FOXA1ab. Input of MCF7 cells in EN1 over-expressing condition.


title: Cell_380

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-36_S328_L006_R1_001.fastq.gz


title: SUM149_Doxy_Input_EGS

description: input for sample S149_shEN1_D_bcat_R. Input of SUM149 cells in EN1 knockdown condition.


title: MCF7_EN1_Input_EGS

description: input for sample MCF7_EN1_bcat_R. Input of MCF7 cells in EN1 over-expression condition


title: MCF7_lacZ_Input_EGS

description: input for sample MCF7_LacZ_bcat_R. Input of MCF7 cell in LacZ condition.


title: Cell_377

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-33_S325_L006_R1_001.fastq.gz


title: Cell_376

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-32_S324_L006_R1_001.fastq.gz


title: SUM159_Input

description: input for sample SUM159_V5EN_37


title: MCF7_Input_37

description: input for sample MCF7_37_V5EN1


title: Cell_374

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-30_S322_L006_R1_001.fastq.gz


title: Cell_373

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-2_S294_L006_R1_001.fastq.gz


title: Cell_371

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-28_S320_L006_R1_001.fastq.gz


title: SUM149_shEN1_Dox_H3K27ac

description: ChIP-seq for H3K27ac in SUM149 cells after EN1 knockdown


title: SUM149_shEN1_Control_H3K27ac

description: ChIP-seq for H3K27ac in SUM149 cells (control)


title: SUM149_Input_37

description: input for sample SUM149_37_V5EN1


title: Cell_372

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-29_S321_L006_R1_001.fastq.gz


title: MCF7_lacZ_FOXA1ab

description: ChIP-seq for FOXA1 in MCF7 cells (LacZ control)

value: LacZ control


title: MCF7_lacZ_RT_Input

description: input for sample MCF7_Z_TLE3_P and sample MCF7_lacZ_FOXA1ab. Input of MCF7 cells in LacZ condition.


title: Cell_369

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-26_S318_L006_R1_001.fastq.gz


title: SUM159_Doxy_TLE3_P

description: ChIP-seq for TLE3 in SUM159 cells after EN1 knockdown


title: Cell_367

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-24_S316_L006_R1_001.fastq.gz


title: SUM159_Control_TLE3_P

description: ChIP-seq for TLE3 in SUM159 cells (control)


title: Cell_366

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-23_S315_L006_R1_001.fastq.gz


title: MCF7_EN1overexpession_FOXA1ab

description: ChIP-seq for FOXA1 in MCF7 cells after EN1 over expression

value: EN1 over-expression


title: Cell_379

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-35_S327_L006_R1_001.fastq.gz


title: SUM149_shEN1_Doxy_TLE3_P

description: ChIP-seq for TLE3 in SUM149 cells after EN1 knockdown


title: Cell_365

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-22_S314_L006_R1_001.fastq.gz


title: Cell_375

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-31_S323_L006_R1_001.fastq.gz


title: Cell_363

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-20_S312_L006_R1_001.fastq.gz


title: Cell_364

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-21_S313_L006_R1_001.fastq.gz


title: SUM159_H3K27ac

description: ChIP-seq for H3K27ac in SUM159 cells


title: Cell_370

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-27_S319_L006_R1_001.fastq.gz


title: Cell_362

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-1_S293_L006_R1_001.fastq.gz


title: Cell_361

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-19_S311_L006_R1_001.fastq.gz


title: MCF7_Z_TLE3_P

description: ChIP-seq for TLE3 in MCF7 cells (LacZ control)


title: S149_shEN1_D_bcat_R

description: ChIP-seq for Beta-catenin in SUM149 cells after EN1 knockdown

value: Beta-catenin


title: S149_shEN1_C_bcat_R

description: ChIP-seq for Beta-catenin in SUM149 cells (control)


title: MCF7_EN1_TLE3_P

description: ChIP-seq for TLE3 in MCF7 cells after EN1 over expression


title: Cell_360

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-18_S310_L006_R1_001.fastq.gz


title: Cell_359

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-17_S309_L006_R1_001.fastq.gz


title: Cell_368

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-25_S317_L006_R1_001.fastq.gz


title: Cell_358

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-16_S308_L006_R1_001.fastq.gz


title: MCF7_LacZ_bcat_R

description: ChIP-seq for Beta-catenin in MCF7 cells (LacZ control)


title: MCF7_EN1_bcat_R

description: ChIP-seq for Beta-catenin in MCF7 cells after EN1 over expression


title: SUM159_V5EN_37

description: ChIP-seq for exogenously expressed V5-tagged EN1 in SUM159 cells

value: exogenously expressed V5-tagged EN1 expression


title: Cell_357

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-15_S307_L006_R1_001.fastq.gz


title: Cell_356

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-14_S306_L006_R1_001.fastq.gz


title: Cell_355

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-13_S305_L006_R1_001.fastq.gz


title: Cell_354

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-12_S304_L006_R1_001.fastq.gz


title: MCF7_37_V5EN1

description: ChIP-seq for exogenously expressed V5-tagged EN1 in MCF7 cells


title: MCF7_LACZ_1

description: RNA-seq of MCF7 cells with LacZ (control)


title: SUM149_37_V5EN1

description: ChIP-seq for exogenously expressed V5-tagged EN1 in SUM149 cells


title: Cell_353

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-11_S303_L006_R1_001.fastq.gz


title: SUM149_shEN1_Control_TLE3_P

description: ChIP-seq for TLE3 in SUM149 cells (control)


title: MCF7_EN1_2

description: RNA-seq of MCF7 cells following EN1 over expression


title: MCF7_EN1_1


title: SUM159PT_shEN1-2_Day-5_Dox-plus_2

description: RNA-seq of SUM159 cells after 5 days with TET-inducible shEN1 with doxycycline

tag: days


title: Cell_352

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-10_S302_L006_R1_001.fastq.gz


title: Cell_351

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-102_S394_L006_R1_001.fastq.gz


title: SUM159PT_shEN1-2_Day-5_Dox-plus_1


title: SUM159PT_shEN1-2_Day-5_Dox-minus_2

description: RNA-seq of SUM159 cells after 5 days with TET-inducible shEN1 without doxycycline (control)


title: Cell_350

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-4-101_S393_L006_R1_001.fastq.gz


title: Cell_347

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-99_S289_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-2_Day-5_Dox-minus_1


title: Cell_348

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-9_S199_L005_R1_001.fastq.gz


title: Cell_346

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-98_S288_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-1_Day-5_Dox-plus_1


title: Cell_345

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-97_S287_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-1_Day-5_Dox-plus_2


title: MCF7_LACZ_2


title: SUM159PT_shEN1-1_Day-5_Dox-minus_1


title: Cell_344

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-96_S286_L005_R1_001.fastq.gz


title: Cell_342

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-94_S284_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-2_Day-3_Dox-plus_2

description: RNA-seq of SUM159 cells after 3 days with TET-inducible shEN1 with doxycycline


title: Cell_341

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-93_S283_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-2_Day-3_Dox-minus_2

description: RNA-seq of SUM159 cells after 3 days with TET-inducible shEN1 without doxycycline (control)


title: SUM159PT_shEN1-2_Day-3_Dox-plus_1


title: Cell_340

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-92_S282_L005_R1_001.fastq.gz


title: Cell_343

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
18B-3-95_S285_L005_R1_001.fastq.gz


title: SUM159PT_shEN1-2_Day-3_Dox-minus_1


title: Cell_339

description:
READ_COUNT_UCSC_table_Xiying_retinal_organoid.txt
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