title: 005_EP: Granulosa cells_12h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 12 hours after induction of ovulation
005_EP

source_name: Granulosa cells collected 12 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: +5dV3_rep1

status: Public on Mar 01 2020

type: SRA

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

country: Germany

institute: University of Cologne

library_source: transcriptomic

data_processing:
The reads were mapped to the Arabis alpina reference genome (Assembly Version 5) using HISAT2 package with default settings. The SAM files obtained after mapping were converted into BAM files.
Genes were assembled and quantified in each sample using StringTie package. The raw gene count was obtained by feeding the .gtf file to a python script (prepDE.py) obtained from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual.
The raw gene counts table was further analysed with DESeq2 to obtain differentially expressed genes.
Differentially expressed genes within 2 conditions with a fold change of 2 and a p-value significance <0.05 were analysed further.
Genome_build: Arabis alpina ( NCBI ID: 17813)
Supplementary_files_format_and_content: .xlsx file containing raw read counts produced with StringTie, normalized FPKM counts produced with TopHat, calculated log2 fold changes and p-value produced by DESeq2, annotation were downloaded from TAIR

molecule: polyA RNA

organism: Arabis alpina

source_name: lateral buds

growth_protocol: Plants were grown for 8 weeks in long day conditions (16h light at 20°C, 8h dark at 18°C) and vernalized in a growth chamber for 12 weeks (16h light, 8h dark, at 4°C) before transfering them back to long day condition for 5 days

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using the NEBNext Ultra Directional II RNA Library Prep Kit for Illumina (New England Biolabs) at the Cologne Genome Centre and sequencing was carried out using a HiSeq3000 (Illumina) with 1 x 150 bp single reads.

treatment_protocol: Buds of the dormant zone (V2) and buds in the growing zone (V3) were harvested at the end of the vernalization period (+0) and 5 days later (+5d)

tag: arabis alpina ecotype

value: Pajares

tag: time of harvesting

value: 5 days after vernalization (+5d)

tag: zone of the plant


title: 004_OPU: Granulosa cells_36h_rFSH_GNRHa

type: RNA

city: Køge

first: Liv

middle: la Cour

last: Poulsen

address: Lykkebækvej 14

department: Gynaecology and Obstetrics

country: Denmark

institute: Zealand University Hospital

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
004_OPU

hyb_protocol: RNA was processed using Clariom™ D Pico Assay (Applied Biosystems, Thermo Fisher, USA) according to the manufacturer’s protocol, using the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images. Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC, Affymetrix, Thermo Fisher, USA).

data_processing: The 83 raw CEL-files were imported into Transcriptome Analysis Console (TAC 4.0.1, applied Biosystems, Thermo Fisher Scientific, MA, USA) . Normalization and summarization were performed by the SST-RMA (Robust Multichip Analysis) approach.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa

label_protocol: Phycoerytrin conjugated streptavidin

growth_protocol: Granulosa cells were isolated from aspirated follicular fluid with a pipette as blood clots and vessels were avoided. The cells were washed through a 4-well dish containing PBS and 0,1% PVA, transferred to a cryotube with minimal PBS, snap frozen in liquid nitrogen and stored at -80⁰C until RNA extraction.

extract_protocol: The Arcturus PicoPure® RNA isolation kit (Applied Biosystems, CA, USA) was used to isolate total RNA from GC according to the manufacturer’s instructions

treatment_protocol: Patients were treated with individually dosed rFSH (Puregon®, MSD, Denmark) or hMG (Menopur®, Ferring, Denmark) starting on day 2-3 of the menstrual cycle. From stimulation day 5-6 a GnRH antagonist (Ganirelix 0,25 mg (Fyremadel®, SUN pharma, Netherlands)) was administered daily. When at least three follicles reached ≥17 mm in diameter, an ovulation trigger (hCG (6500 IU (Ovitrelle®, Merck Serono, Germany) or GNRHa (buserelin 0,5 mg (Suprefact®, Sanofi-Aventis)) was administered and oocyte pick up was planned for 36 hours later.

tag: tissue

value: granulosa cells isolated from aspirated follicular fluid

tag: ovulation time point

tag: treatment

value: rFSH

tag: ovulation induction

value: GNRHa


title: 106_r2: TF106 Zm00001d020267 ChIP-Seq

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

country: China

institute: CUHK

description: Contain genome coverage bigwig files for each replicates and the peak file generated by IDR

library_source: genomic

data_processing:
For mapping, we aligned the raw reads to the unmasked maize genome (B73 RefGen_v4) using Bowtie 2 (version 2.2.5) under the default parameters with the 3’  100 bp trimming option. Reads with mapping quality >= 10 were kept and PCR duplicates are removed using SAMTools (version 1.3). Deeptools bamcoverage was used to convert the BAM to bigwig files for viewing.
For peak calling, BAM files of biological replicates were used to call peaks with the SPP peak caller using relaxed parameters “-i = <INPUT BAM file>”, “-npeak = 300,000”, with input as control. Peaks in the transformed TF genebody itself are removed. Reproducible peaks were obtained with the IDR (Irreproducible discovery rate) statistical framework (version 2.0.3), as implemented in the PhantomPeakQualTools package, using 1% IDR as the threshold (cut-off).
To identify the high confident target genes of each TF, we used the probabilistic model TIP (Cheng et al., Bioinformatics, 2011, 3221–3227) with FDR 0.05 as cutoff.
Genome_build: B73 RefGen_v4
Supplementary_files_format_and_content: peak and bigwig files
Supplementary_files_format_and_content: TF_target_TIP.txt: High cofident TF target genes called by TIP

molecule: genomic DNA

organism: Zea mays

source_name: Leaf protoplast

growth_protocol: Leaf protoplast from 1-2 weeks old maize seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with streptavidin dynabeads.
Libraries were prepared according to Illumina's instructions using purified HS-Tn5 transposase, Tn5-MEA/B adapter as well as N5xx and N7xx PCR primers.

treatment_protocol: PEG mediated protoplast transformation

tag: cultivar

value: Leaf protoplast

tag: transcription factor


title: HS_1

city: YiWu

first: wang

middle: chuan

last: wen

address: No. 288, Yang Cun road, Chou Jiang Street, Yiwu, Zhejiang

institute: AnnoGene

data_processing:
bcl2fastq2-v2.19.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence, then mapped to GRCh38.91 whole genome using hisat2-2.1.0 with default parameters
Reads count was calculated by htseq-count with  parameters -t exon -f bam -s no -a 10
Genome_build: GRCh38.91
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: human embryonic stem cells

extract_protocol:
Adherent  cells and suspension cells were extracted from the blood of tissue samples ,then add lysate TRNzol-A+ ,after lysis ,centrifugation with chloroform ,RNA was extracted from supernatant
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human embryonic stem cells

tag: cell type

value: hepatic specification

tag: passage


title: 002_OPU: Granulosa cells_36h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
002_OPU


title: 104_r2: TF104 Zm00001d030891 ChIP-Seq


title: +5dV2_rep3


title: +5dV2_rep2


title: B3

city: Qingdao

first: Yuanxiang

last: Li

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of sciences

data_processing:
The library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene function was annotated based on the following databases:
Nr (NCBI non-redundant protein sequences);
Nt (NCBI non-redundant nucleotide sequences);
Pfam (Protein family);
KOG/COG (Clusters of Orthologous Groups of proteins);
Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database);
GO (Gene Ontology).
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Supplementary_files_format_and_content: tab-delimited files include RPKM values for each Sample ...

organism: Dunaliella salina

source_name: algal cells

growth_protocol: Algal cells were cultivated at 22 ± 1°C with 50 ± 5 μmol photons·m−2s−1 provided by cold white fluorescent lamps with 14:10 h light-dark cycles.

extract_protocol:
Algal cells were harvested by centrifugation for 4 min at 2,000 ×g at room temperature, fast frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells in mid-exponential growth phase were harvested by centrifugation for 4 min at 2,000 ×g at room temperature, and inoculated into fresh medium for different wavelength of irradiance.

tag: growth phase

value: mid-exponential phase

tag: light wavelength

value: blue light (450 nm, 50 μmol photons m−2s−1)


title: B2


title: +5dV2_rep1


title: 104_r1: TF104 Zm00001d030891 ChIP-Seq


title: B1


title: 002_EP: Granulosa cells_32h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
002_EP

source_name: Granulosa cells collected 32 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with GNRHa


title: 103_r2: TF103 Zm00001d017176 ChIP-Seq


title: +0V3_rep3

value: end of the vernalization (+0)


title: Hypothalamus [JL203]

city: Davis

first: Simon

middle: Jesse

last: Lopez

state: CA

address: One Shields Ave

department: MMI

country: USA

institute: UC Davis

description:
JL203
processed data file: hypothalamus_counts.txt

data_processing:
WGBS: CpG_me, DMRichR
RNA-seq: htstream, STAR
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: hypothalamus_counts.txt: Gene feature counts output from STAR aligner for each hypothalamus sample.
Supplementary_files_format_and_content: cortex_counts.txt: Gene feature counts output from STAR aligner for each cortex sample.
Supplementary_files_format_and_content: DMRs.xlsx: DMRs for each pair-wise group comparison output from DMRichR.
Supplementary_files_format_and_content: maternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all maternal samples.
Supplementary_files_format_and_content: paternal_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for all paternal samples.
Supplementary_files_format_and_content: control_background_smoothed_methylation.txt: Background region individual smoothed methylation values output by DMRichR for maternal and paternal wild-tpe samples.

organism: Rattus norvegicus

source_name: hypothalamus

extract_protocol:
WGBS: Illumina TruSeq DNA Methylation Kit (Illumina EGMK81312).
RNA-seq: NEB NEBNext rRNA Depletion Kit (NEB E6310L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420S).

tag: parent-of-origin

value: Maternal

tag: time

tag: genotype/variation

value: Deletion

tag: Sex

value: Female

value: Hypothalamus


title: R3

value: red light (660 nm, 50 μmol photons•m−2s−1)


title: 001_OPU: Granulosa cells_36h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 36 hours after induction of ovulation
001_OPU

source_name: Granulosa cells collected 36 hours after induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG

value: rhCG


title: 103_r1: TF103 Zm00001d017176 ChIP-Seq


title: 001_EP: Granulosa cells_0h_rFSH_rhCG

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment before induction of ovulation
001_EP

source_name: Granulosa cells collected before induction of ovulation in a patient treated with rFSH, ovulation induced with rhCG


title: Hypothalamus [JL200]

description:
JL200
processed data file: hypothalamus_counts.txt

value: Wild-type


title: 100_r2: TF100 Zm00001d034417 ChIP-Seq


title: +0V3_rep2

tag: arabis alpina ecotype

value: Pajares


title: R1


title: Smad4 KO-39.5°C

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.01
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

organism: Mus musculus

source_name: Spleen+Lymph nodes

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
The RNA-seq library was constructed with NEXTflex RNA-seq kit (Bioo Scientific)

treatment_protocol: Naïve CD4+ T cells were activated and cultured under IL-6 plus TGF-β1 at 37°C and 39.5°C

value: Th17 cells

tag: strain

value: Spleen+Lymph nodes

tag: age

value: 3 days in vitro

tag: genotype

value: Smad4 KO


title: 100_r1: TF100 Zm00001d034417 ChIP-Seq

tag: tissue

value: Leaf protoplast


title: R2


title: +0V2_rep3

tag: time of harvesting

tag: zone of the plant


title: 004_EP: Granulosa cells_32h_rFSH_GNRHa

description:
Gene Expression data from human granulosa cells, collected from a patient undergoing fertility treatment 32 hours after induction of ovulation
004_EP

value: granulosa cells isolated from aspirated follicular fluid

tag: ovulation time point

tag: treatment

value: rFSH

tag: ovulation induction

value: GNRHa


title: Smad4 KO-37°C

tag: cell type


title: +0V3_rep1

value: end of the vernalization (+0)


title: +0V2_rep2


title: WT-39.5°C

value: wild type


title: W1

tag: growth phase

value: mid-exponential phase

value: cool white light (50 μmol photons•m−2s−1)


title: +0V2_rep1


title: WT-37°C


title: W2

tag: light wavelength


title: ST-C-2_colony_cells

city: Guangzhou

first: dayong

last: liang

state: Guangdong

address: 604, Huangpu Avenue West, Tianhe District

institute: Jinan University

description: replicate 2

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using
TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After
cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and
paired-end reads were generated.The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right  files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the  left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all  other parameters set default.
In the process of sequencing, we use novaseq, the Illumina sequencing platform;When we calculate the readcount and fpkm, we use the rsem software, version: v1.2.15, to make statistics on the results after mapping, and further get the number of readcount of each sample compared to each gene, and carry out fpkm conversion on it, and then analyze the gene expression level

organism: Phaeocystis globosa

source_name: colony stage

extract_protocol:
the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ST

value: Exponential growth period

tag: region

value: Shantou, China


title: 106_r1: TF106 Zm00001d020267 ChIP-Seq

tag: cultivar

tag: transcription factor


title: head, 2d_rw440_sib2

city: Kunigami kun

first: Nishtha

last: Ranawat

state: Okinawa

address: 1919-1 Tancha Onna son

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

data_processing:
Hiseq Control Software HD v3.4.0 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 whole genome using hisat2  with parameters -k 3 -p 36
Raw count data was obtained by featureCounts with parameters -p -T 36  -t exon -g gene_id -a "GRCz11" cut -f 1,7-12
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text file includes raw count data for each sample in one file

organism: Danio rerio

source_name: head

extract_protocol:
Total RNA was extracted from 2dpf zebrafish embryos using Sepazol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Head

value: 2days post fertilization

value: wildtype


title: W3


title: ST-C-1_colony_cells

description: replicate 1


title: head, 2d_rw440_mut3


title: GX-C-3_colony_cells

description: replicate 3

value: GX

value: Beibu Gulf, Guangxi, China


title: GX-C-2_colony_cells

description: replicate 2


title: head, 2d_rw440_mut2


title: ST-C-3_colony_cells

description: replicate 3


title: head, 2d_rw440_sib3


title: GX-C-1_colony_cells

description: replicate 1


title: head, 2d_rw440_mut1


title: G0_YAP1_ChIP-seq

status: Public on Feb 29 2020

city: Houston

first: Deepavali

last: Chakravarti

state: TX

address: 1881East Rd

institute: MD Anderson Cancer Center

description:
YAP ChIP-seq (Novus, NB110-58358
3-G0Ab

data_processing:
Base-calling was performed with NextSeq RTA version 2.4.11.0; bcl2fastq version 2.20.0 was used to convert the bcl files into fastq files
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.2.2 with the following criteria: --best --chunkmbs 320
Peak-calling was performed using MACS version 1.4.2
Bigwig files were generated using deepTools version 2.7.15 by scaling the bam files to reads per kilobase per million (RPKM) using the following criteria: bamCoverage –b–normalizeUsing RPKM–smoothLength 300–binSize 30–extendReads 200 –o
Differential peaks were called using MACS2 with the following criteria: bdgdiff –g 60 –l 120
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Intestinal crypt epithelium

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Intestinal crypt epithelium

tag: disease state

value: Telomere proficient

tag: developmental stage

value: Adult (8-12 weeks)

tag: chip antibody

value: YAP ChIP-seq (Novus, NB110-58358)


title: Liver_2months_rep2

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression in 2-month adult liver

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar). Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNA that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis (resulting in a reduced dataset of 17,307 data rows).

source_name: adult 2-month liver

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Mouse C57BL/6 total RNA was purchased from Zyagen.

tag: strain

tag: age

value: Liver


title: Liver_2months_rep1

description: Gene expression in 2-month adult liver

tag: tissue


title: G3_Input

value: telomere dysfunctional

value: none (input)


title: head, 2d_rw440_sib1

tag: genotype


title: G3_YAP1_ChIP-seq

description:
YAP ChIP-seq (Novus, NB110-58358
4-G3Ab


title: Liver_E18_rep3

description: Gene expression in mouse embryo E18.5 day

source_name: prenatal liver

value: Embryo


title: Liver_2months_rep3

description: Gene expression in 2-month adult liver


title: Liver_E18_rep2


title: Graft2

city: BEAUCOUZE

first: Adrien

last: PERRIN

address: 42 Rue Georges Morel

country: France

institute: INRA - IRHS

hyb_protocol: Hybridizations were performed on a NimbleGen Hybridization System 4 (mix mode B) at 42°C overnight.

scan_protocol: NimbleGen MS 200 v1.2 software was used for microarray scans The Agilent Feature Extraction 11.5 software was used to extract pair-data files from the scanned images

data_processing: We used the dye switch approach for statistical analysis as described in Depuydt et al. (2009). Analyses were performed using the R language (R Development Core Team, 2009); data were normalized with the lowess method, and differential expression analyses were performed using the lmFit function and the Bayes moderated t test using the package LIMMA (Smyth, Michaud, and Scott 2005).

organism: Malus domestica

source_name: Grafted plant

label_protocol: Complemantary DNA (cDNA) were synthesized and hybridized with the Low Input Quick Amp Labeling Kit, two-color (Agilent, Foster City, CA, USA).

growth_protocol: Malus domestica materials were obtained from ‘GDDH13’ (Lespinasse et al. 1999) line (X9273). Grafted plant materials were obtained by grafting budwood of ‘GDDH13’ orchard tree (2001) on the rootstock ‘MM106’. Seedling materials were obtained by self-fertilization of ‘GDDH13’ tree (2007), apple fruit were then harvested to get seed. Seed dormancy was removed by 3 months of cold stratification before sowing. A clone of the original ‘GDDH13’ from orchard, grafted onto an MM106 rootstock in 2007 and growing in the greenhouse since was used as reference mature adult tree.

extract_protocol: The RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel, Hoerdt, France) according the manufacturer’s protocol

tag: leaf age

value: last and completely opened leave

tag: dye swap description

value: T3-2 VS G2


title: Tree3-1

source_name: Adult mature tree


title: 150LmoNAc

city: Austin

first: Rajani

last: Maiya

address: 1601B Trinity St., Stop Z0700 HDB 5.322

department: Neuroscience

institute: The University of Texas at Austin

description: 150LmoNAc abundance

data_processing:
Samples were sequenced on the NextSeq-500 (Illumina) platform with a read depth of approximately 20 million reads (paired end 150bp reads).  Read quality was assessed using MultiQC (Version 1.7).
Sorted BAM files were analyzed using Integrative Genomics Viewer (IGV) (Broad Institute).
Reads were mapped on to a reference genome (UCSC mm9) using HiSat2
Raw counts were quantified using HTSeq (version 0.11.1)
The R package DeSeq2 (2) was used to identify differentially expressed genes between WT and Lmo4gt/+ mice. Statistical significance was estimated using a nominal p-value less than or equal to 0.05.
Genome_build: UCSC MM9
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: Nucleus Accumbens

extract_protocol:
Brains were rapidly extracted and frozen in a dry ice bath containing isopentame. 300 micron thick sections containing the basolateral amygdala (BLA) and Nucleus Accumbens (NAc) was cut on the cryostat and brain regions were punched using a micropunch. RNA was extracted using the Magmax-96 kit from Ambion. DNA contamination was removed by DNAse treatment.
RNAseq libraries were prepared for sequencing using standard illumina protocols using the NextSeq 500/550 High Output kit, Illumina Inc., San Diego, CA
polyA enriched RNAs (MicroPolyA purification kit, Life Technologies, Carlsbad, CA) were used for library construction

value: 8-12 weeks


title: Graft1

value: T2-2 VS G1


title: 159LmoNAc

description: 159LmoNAc abundance


title: 157LmoNAc

description: 157LmoNAc abundance


title: 149LmoNAc

description: 149LmoNAc abundance


title: Tree3-2


title: Tree2-2


title: 147LmoNAc

description: 147LmoNAc abundance


title: Seed1-Seed2

source_name: Seedling plant

value: T2-1 VS S1S2


title: 127LmoNAc

description: 127LmoNAc abundance


title: Tree2-1


title: Seed3-Seed4


title: 160WTNAc

description: 160WTNAc abundance

value: WT


title: G0_Input


title: 122LmoNAc

description: 122LmoNAc abundance


title: 158WTNAc

description: 158WTNAc abundance


title: 138LmoNAc

description: 138LmoNAc abundance


title: 156WTNAc

description: 156WTNAc abundance


title: 148WTNAc

description: 148WTNAc abundance


title: 135WTNAc

description: 135WTNAc abundance


title: 133WTNAc

description: 133WTNAc abundance


title: 134WTNAc

description: 134WTNAc abundance


title: 159LmoBLA

description: 159LmoBLA abundance

source_name: Basolateral Amygdala


title: 136WTNAc

description: 136WTNAc abundance


title: 129WTNAc

description: 129WTNAc abundance


title: Liver_E18_rep1

value: embryo


title: 139WTNAc

description: 139WTNAc abundance


title: 150LmoBLA

description: 150LmoBLA abundance


title: 149LmoBLA

description: 149LmoBLA abundance


title: 157LmoBLA

description: 157LmoBLA abundance


title: 147LmoBLA

description: 147LmoBLA abundance


title: 127LmoBLA

description: 127LmoBLA abundance


title: 122LmoBLA

description: 122LmoBLA abundance


title: 138LmoBLA

description: 138LmoBLA abundance


title: 160WTBLA

description: 160WTBLA abundance


title: 158WTBLA

description: 158WTBLA abundance


title: 128LmoBLA

description: 128LmoBLA abundance


title: 151WTBLA

description: 151WTBLA abundance


title: 156WTBLA

description: 156WTBLA abundance


title: 136WTBLA

description: 136WTBLA abundance


title: 133WTBLA

description: 133WTBLA abundance


title: 134WTBLA

description: 134WTBLA abundance


title: 135WTBLA

description: 135WTBLA abundance


title: 129WTBLA

description: 129WTBLA abundance


title: 148WTBLA

description: 148WTBLA abundance


title: 192CS12_12 days_whole seedling_PIF7::PIF7-MYC (D108)_ZT12_27C

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

data_processing:
Genome_build: Ath-TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. Duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 192CS19 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: _RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: .narrowPeak: ENCODE narrowPeak containing MACS2-called peaks.

organism: Arabidopsis thaliana

source_name: PIF7::PIF7-MYC (D108) seedlings

growth_protocol: Seedlings were grown at 27C in LD for 12 days and harvested at ZT12. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

extract_protocol:
seeds were sterilised and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7  and harvested at the indicated time.
The efficiency of ChIP materials was assessed by qPCR prior to in-house library preparation. Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina  IP-202-1024) and samples sequenced on NextSeq500 machine from Illumina using NextSeq® 500/550 High Output Kit v2 (75 cycles) TG-160-2005. Sequence reads were analysed using in-house pipelines. The libraries were sequenced at the Sainsbury Laboratory Cambridge University Services sequencing facility.

value: PIF7::PIF7-MYC (D108)

value: Columbia

value: whole seedling

tag: photoperiod

value: LD

tag: temperature

tag: replicate

value: single

tag: fragmentation method

value: sonication

value: SIGMA A7470-Anti-c-Myc Agarose Affinity Gel antibody produced in rabbit

tag: growth


title: Growth plate_Proliferative Zone_2

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

hyb_protocol: Agilent Gene Expression Hybridization Kit to  44K whole-genome microarrays  (G4122A, Agilent Technologies, Santa Clara, CA

scan_protocol: Agilent scanner G2505B

data_processing:
Agilent Feature Extraction V8.1.1.1
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.12694
Normalization: Shift to 75 percentile
Baseline Transformation: None

source_name: Growth plate Proliferative Zone

label_protocol: Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ)

extract_protocol: PicoPure RNA isolation kit (Arcturus Bioscience, Mountain View, CA)

value: femoral growth plate cartilage

tag: zone

value: Proliferative Zone

value: Swiss White

value: 14 days-old


title: Growth plate_Prehypertrophic Zone_4

source_name: Growth plate Prehypertrophic Zone

value: Prehypertrophic Zone


title: Growth plate_Proliferative Zone_3


title: Growth plate_Prehypertrophic Zone_1


title: Growth plate_Prehypertrophic Zone_3


title: Growth plate_Proliferative Zone_1


title: Growth plate_Prehypertrophic Zone_2


title: 192CS11_12 days_whole seedling_PIF7::PIF7-MYC (D108)_ZT12_17C

growth_protocol: Seedlings were grown at 17C in LD for 12 days and harvested at ZT12. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

tag: cultivar


title: Growth plate_Hypertrophic Zone_2

source_name: Growth plate Hypertrophic Zone

value: Hypertrophic Zone


title: TEL_AML_03

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from BaF3 cells trasfected with TEL-AML1 fusion transcript (mifepristone-inducible GeneSwitch system, Life Technologies, Carlsbad, CA, USA)

hyb_protocol: Following fragmentation and labelling,12,5 μg of aRNAA were hybridized for 16 hr at 45C on GeneChip Mouse 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: BaF3 cell line

label_protocol: Labeled and Fragmented aRNA were prepared according to the standard GeneChip 3'IVT Plus protocol starting from 100 ng of Total RNA

growth_protocol: All BaF3 clones were cultured in RPMI medium supplemented with 10% FCS, 2% MoIL-3–conditioned medium containing IL-3, 10 μM 2-mercaptoethanol, and 0.2 mg/ml hygromycin B (Invitrogen). In addition TEL_AML1 clones were cultured in the presence of 0.05 mg/ml Zeocin (Invitrogen)

extract_protocol: RNA was isolated from fresh cells using Trizol

treatment_protocol: The expression of TEL-AML1 was induced by adding to the culture medium 0.0125 nM mifepristone (Invitrogen)/3.8 × 105 cells for 3 days

tag: cell line

value: TEL-AML1 BaF3

tag: sample code

value: experiment 1


title: ESC-derived cortical progenitors, day13, CTIP2:GFP-

city: Kyoto

first: Bumpei

last: Samata

address: 53 Kawahara-cho, Shogoin

institute: Kyoto university

description: CTIP2:GFP KI mESCs were generated by homologous recombination in 129SVEV ESC lines.

hyb_protocol: Labeled cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with GeneSpring version 13.0 using default analysis settings and global scaling as normalization method (RMA16).
MoGene-1_0-st-v1.pgf
MoGene-1_0-st-v1.mps

source_name: mES-derived cells (day13 CTIP2:GFP-)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Ambion WT Expression Kit, Affymetrix).

growth_protocol: The ESCs were cultured by SFEBq method before cell sorting.

extract_protocol: Total RNA was extracted by RNeasy micro Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: Sorted cells (at least 80000 cells) were subjected to RNA extraction.

tag: cell type

value: ESC-derived cortical progenitors

tag: sorted cells

tag: time


title: Growth plate_Hypertrophic Zone_3

tag: strain

tag: age


title: TEL_AML_13

description: Gene expression data from BaF3 cells trasfected with empty vector (mifepristone-inducible GeneSwitch system, Life Technologies, Carlsbad, CA, USA)

tag: genotype

value: wt BaF3

value: experiment 4


title: TEL_AML_11

value: experiment 3


title: ESC-derived cortical progenitors, day11, CTIP2:GFP-

source_name: mES-derived cells (day11 CTIP2:GFP-)


title: ESC-derived cortical progenitors, day13, CTIP2:GFP+

source_name: mES-derived cells (day13 CTIP2:GFP+)


title: Growth plate_Hypertrophic Zone_1

tag: tissue


title: Growth plate_Proliferative Zone_4


title: ESC-derived cortical progenitors, day12, CTIP2:GFP+

source_name: mES-derived cells (day12 CTIP2:GFP+)


title: TEL_AML_01


title: 192CS10_12 days_whole seedling_PIF7::PIF7-MYC (D108)_ZT8_27C

growth_protocol: Seedlings were grown at 27C in LD for 12 days and harvested at ZT8. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

value: PIF7::PIF7-MYC (D108)

value: Columbia

value: whole seedling

tag: chip antibody


title: TEL_AML_05

value: experiment 2


title: ESC-derived cortical progenitors, day11, CTIP2:GFP+

source_name: mES-derived cells (day11 CTIP2:GFP+)


title: 192CS9_12 days_whole seedling_PIF7::PIF7-MYC (D108)_ZT8_17C

growth_protocol: Seedlings were grown at 17C in LD for 12 days and harvested at ZT8. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

tag: photoperiod

value: LD

value: single

value: sonication

value: SIGMA A7470-Anti-c-Myc Agarose Affinity Gel antibody produced in rabbit


title: 186CS12_12 days_whole seedling_PIF7::PIF7-MYC (D108)_ZT12_27C

data_processing:
Genome_build: Ath-TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. Duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 186CS23 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: _RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: .narrowPeak: ENCODE narrowPeak containing MACS2-called peaks.

tag: temperature

value: grown at 27C in LD for 12 days and harvested at ZT12.


title: Growth plate_Hypertrophic Zone_4

value: femoral growth plate cartilage

value: Swiss White

value: 14 days-old


title: TEL_AML_09


title: Maj4-6

city: Boston

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

data_processing:
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Genome_build: mm9
Supplementary_files_format_and_content: Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.

source_name: 12MAB CX3CR1+ mononuclear phagocytes from cauda 2

growth_protocol: EGFP+ mononuclear phagocytes were isolated by double cell sorting from the initial segments (IS), caput/corpus and cauda epididymal regions of CX3CR1 EGFP +/- transgenic mice that specifically express EGFP in mononuclear phagocytes.  Each sample  was obtained using 4 epididymides.

extract_protocol:
The RNA was isolated using PicoRNA KIT (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.

value: express EGFP under the control of the CX3CR1 gene

value: epididymis

tag: tissue region

value: cauda

value: CX3CR1+ mononuclear phagocytes

value: 12 weeks


title: ESC-derived cortical progenitors, day12, CTIP2:GFP-

source_name: mES-derived cells (day12 CTIP2:GFP-)

value: ESC-derived cortical progenitors


title: Maj4-5

source_name: 11MAB CX3CR1+mononuclear phagocytes from cauda 1


title: Maj4-4

source_name: 10MAB CX3CR1+ mononuclear phagocytes from caput/corpus 2

value: caput/corpus


title: TEL_AML_07

value: TEL-AML1 BaF3


title: 139WTBLA

description: 139WTBLA abundance

value: WT

value: 8-12 weeks


title: Maj4-1

source_name: 7MAB CX3CR1+ mononuclear phagocytes from IS 1

value: initial segments (IS)


title: Maj4-2

source_name: 8MAB  CX3CR1+ mononuclear phagocytes from IS 2


title: Maj4-3

source_name: 9MAB  CX3CR1+ mononuclear phagocytes from caput/corpus 1


title: Maj3-6

source_name: 6MAB  CX3CR1+ mononuclear phagocytes from cauda 2


title: Maj3-5

source_name: 3MAB  CX3CR1+ mononuclear phagocytes from cauda 1


title: Maj3-2

source_name: 4MAB CX3CR1+ mononuclear phagocytes from IS 2


title: Maj3-4

source_name: 5MAB CX3CR1+mononuclear phagocytes from caput/corpus 2


title: SS2_16_741

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

data_processing:
All reads aligned using STAR, count matrix generated using rpkmforgenes with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, using file with unique positions from MULTo. Gene annotations used were transcripts in RefSeq.
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: SS2_count: SS2 count matrix in tabular format; SS2_ercc_count: SS2 ercc matrix in tabular format; SS2_layout: SS2 cell layout in csv format.

source_name: Kidney (n=3 mice)

extract_protocol:
Enzymatic digestion and FACS
Smart-seq2

value: kidney

tag: disease status

value: 1x Healthy, 1x Day 2 UUO, 1x Day 10 UUO (mixed sample)


title: Maj3-1

source_name: 1MAB CX3CR1+ mononuclear phagocytes from IS 1


title: SS2_16_740


title: SS2_16_733


title: SS2_16_737


title: SS2_16_734


title: SS2_16_735


title: 188CRS9_Week2_seedling_phyC_OX_ZT20_20C

data_processing:
Genome_build: Bd21-v3-1
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. Duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 188CS11 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: _RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: .narrowPeak: ENCODE narrowPeak containing MACS2-called peaks.

organism: Brachypodium distachyon

source_name: phyC_OX seedlings

growth_protocol: Seedlings were grown at 20C in LD for Week2 and harvested at ZT20. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

extract_protocol:
3g seedlings for each set were fixed under vacuum for 20 min in 1xPBS  (10 mM PO43−, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775 SIGMA). The reaction was quenched by adding glycine to a final concentration of 62 mM. Chromatin immunoprecipitation (ChIP) was performed as described (12), with the exception that 100 µl FLAG M2 agarose affinity gel antibody was used (A2220 SIGMA-Aldrich) per sample. Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina  IP-202-1024) and samples sequenced on NextSeq500 machine from Illumina using NextSeq® 500/550 High Output Kit v2 (75 cycles) TG-160-2005. Sequence reads were analysed using in-house pipelines.
The efficiency of ChIP materials was assessed by qPCR prior to in-house library preparation. Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina  IP-202-1024) and samples sequenced on NextSeq500 machine from Illumina using NextSeq® 500/550 High Output Kit v2 (75 cycles) TG-160-2005. Sequence reads were analysed using in-house pipelines. The libraries were sequenced at the Sainsbury Laboratory Cambridge University Services sequencing facility.

value: seedling

value: LD

tag: replicate

value: single

tag: fragmentation method

value: sonication

value: FLAG M2 agarose affinity gel antibody SIGMA A2220


title: [ESI+]_3

city: Stanford

first: Zachary

middle: Hugh

last: Harvey

address: 269 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Raw FASTQs were pseudo-aligned and quantified using Kallisto v0.43.1
Genome_build: 288C build R64
Supplementary_files_format_and_content: Data are provided as a tab-delimited file containing the ORF name, the estimated counts, the effective length of the transcript mapped, and an estimate of error in the quantification.

organism: Saccharomyces cerevisiae

source_name: Cultured cells

growth_protocol: All cells were grown in rich media (YPD) to mid-logarithm (OD600~0.5)

extract_protocol:
Hot acid phenol extraction of total RNA
Dynal Oligo-dT bead enrichment followed by reverse transcription and subsequent cDNA fragmentation using a Covaris E220. Fragment distribution was 200-400 bp, with a peak around 300 bp. Fragmented cDNA was then processed into a sequencing library using the RNA HyperPrep Kit (cat. KK854) and Kapa Biosystems Library Amplification kit (KK2612). Adaptors and barcodes used synthesized as single-stranded oligonucleotides and were Illumina TruSeq-compatible. Library quantification was performed using Kapa Library amplification kit (cat.KK4824), with final QC being performed by Agilent Bioanalyzer. Paired-end sequencing was performed on an Illumina NextSeq 500

tag: genotype/variation

value: [ESI+] diploid

tag: biological replicate


title: [ESI+]_2


title: [ESI+]_1


title: TEL_AML_15

source_name: BaF3 cell line

tag: cell line

tag: sample code

value: experiment 4


title: Naïve_3

value: naive


title: SuperficialTemporaArtery_AdultMoyamoyaDisease#73_rep1

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

institute: Nagoya University Hospital

description: STA MMD 4

hyb_protocol: A Cy3-labeled amplified cDNA sample (2 µg), prepared without the fragmentation reaction, was used for hybridization (24 hours at 65 ℃) to the oligonucleotide spotted microarray slide (Human Whole Genome, SurePrint G3 Human GE v2 8×60K Microarray; Agilent Technologies). Subsequent washing and drying were performed according to the Agilent hybridization protocol.

scan_protocol: The slide was scanned with an Agilent Model G2505A DNA microarray scanner.

data_processing: Signal intensity was quantified from the scanned image using Feature Extraction Software version 11.0.1.1 (Agilent Technologies).

source_name: Superficial Temporal Artery, Adult Moyamoya Disease, Patient Number 73, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 2ug cDNA using the SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions.  Dye incorporation and cDNA yield were checked with the NanoDrop One Spectrophotometer.

extract_protocol: Total RNA was extracted from each MCA and STA specimen with an RNeasy Micro Kit (Qiagen). The purified total RNA was amplified with an Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands)

treatment_protocol: We excised the vessel wall of the MCA following the reported procedure, and also obtained a small piece of the STA. Tissue samples were collected into RNAlater (Qiagen, Hilden, Germany) and stored at -80 °C.

tag: condition

value: Adult Moyamoya Disease

tag: individual

value: Patient Number 73

value: Artery Wall (STA)

tag: gender

value: Female


title: SuperficialTemporaArtery_AdultMoyamoyaDisease#69_rep1

description: STA MMD 3

source_name: Superficial Temporal Artery, Adult Moyamoya Disease, Patient Number 69, replicate 1

value: Patient Number 69

tag: age


title: SuperficialTemporaArtery_InternalCarotidArteryAneurysm#104_rep1

description: STA IA 1

source_name: Superficial Temporal Artery, Internal Carotid Artery Aneurysm, Patient Number 104, replicate 1

value: Internal Carotid Artery Aneurysm

value: Patient Number 104


title: SuperficialTemporaArtery_InternalCarotidArteryAneurysm#115_rep1

description: STA IA 4

source_name: Superficial Temporal Artery, Internal Carotid Artery Aneurysm, Patient Number 115, replicate 1

value: Patient Number 115


title: SuperficialTemporaArtery_InternalCarotidArterylAneurysm#106_rep1

description: STA IA 2

source_name: Superficial Temporal Artery, Internal Carotid Artery Aneurysm, Patient Number 106, replicate 1

value: Patient Number 106


title: 188CRS7_Week2_seedling_ELF3_OX_ZT20_20C

source_name: ELF3_OX seedlings

tag: genotype

tag: cultivar

value: seedling


title: 188CRS8_Week2_seedling_ELF3_OX_ZT20_20C

growth_protocol: Seedlings were grown at 20C in SD for Week2 and harvested at ZT20. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

tag: tissue

value: SD

tag: chip antibody


title: SuperficialTemporaArtery_InternalCarotidArteryAneurysm#114_rep1

description: STA IA 3

source_name: Superficial Temporal Artery, Internal Carotid Artery Aneurysm, Patient Number 114, replicate 1

value: Patient Number 114


title: Naïve_2

tag: strain


title: 188CRS4_Week2_seedling_ELF3_OX_ZT4_20C

growth_protocol: Seedlings were grown at 20C in LD for Week2 and harvested at ZT4. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

tag: photoperiod

value: LD

tag: temperature

value: single

value: sonication


title: 188CRS3_Week2_seedling_ELF3_OX_ZT0_20C

growth_protocol: Seedlings were grown at 20C in LL for Week2 and harvested at ZT0. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

value: LL

tag: replicate

value: FLAG M2 agarose affinity gel antibody SIGMA A2220


title: 188CRS6_Week2_seedling_PRR37_OX_ZT4_20C

source_name: PRR37_OX seedlings

tag: fragmentation method


title: 188CRS5_Week2_seedling_ELF3_OX_ZT4_20C

growth_protocol: Seedlings were grown at 20C in SD for Week2 and harvested at ZT4. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.


title: 188CRS2_Week2_seedling_ELF3_OX_ZT0_20C

growth_protocol: Seedlings were grown at 20C in SD for Week2 and harvested at ZT0. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.


title: 188CRS1_Week2_seedling_ELF3_OX_ZT0_20C

growth_protocol: Seedlings were grown at 20C in LD for Week2 and harvested at ZT0. Seeds were sterilized and sown on ½ X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.


title: SuperficialTemporalArtery_AdultMoyamoyaDisease#63_rep1

description: STA MMD 1

source_name: Superficial Temporal Artery, Adult Moyamoya Disease, Patient Number 63, replicate 1

value: Adult Moyamoya Disease

value: Patient Number 63


title: 188CRS10_Week2_seedling_phyC_OX_ZT20_20C


title: snt1∆ homozygous diploid mRNA-seq, replicate 1

data_processing:
mRNA-seq reads were pseudoaligned, de-duplicated, and quantified using Kallisto quant v 0.44 using default parameters with bootstrapping.
Genome_build: R64
Supplementary_files_format_and_content: est_counts      tpm

source_name: Whole organism

growth_protocol: Cells were grown to mid-logarithmic phase in rich media (YPD).

extract_protocol:
Total RNA was extracted using a standard hot acid phenol Total RNA was extracted from diploid yeast strains grown to mid-exponential phase (OD600 ~0.5) using a standard hot acid phenol protocol followed by chloroform extraction and ethanol precipitation. Afterwards, RNA was resuspended in DEPC-treated water and quantified on a NanoDrop spectrophotometer. Further quality control and ribosomal RNA evaluation was performed by analysis on an Agilent Bioanalyzer 2100 Nano RNA assay at the Protein and Nucleic Acid Facility (Stanford).
For library generation, ERCC spike-in controls (Invitrogen) were added, and total RNA was reverse-transcribed by on-bead polyA-tail priming with Superscript IV (Invitrogen), and then fragmented on a Covaris E220 to a size range of 200–400 bp. Fragmented cDNA was end-repaired and A-tailed, and dual-index sequencing adaptors were ligated using the NEBNext Ultra II DNA Library Prep Kit. Prepared libraries were sequenced on the Illumina HiSeq 4000 platform at the Stanford Functional Genomics Facility using paired-end reads.

tag: genotype/variation

value: snt1delta homozygous diploid


title: snt1∆ homozygous diploid mRNA-seq, replicate 2


title: 128LmoNAc

description: 128LmoNAc abundance

source_name: Nucleus Accumbens

value: 8-12 weeks


title: SuperficialTemporalArtery_AdultMoyamoyaDisease#66_rep1

description: STA MMD 2

source_name: Superficial Temporal Artery, Adult Moyamoya Disease, Patient Number 66, replicate 1

value: Patient Number 66

value: Artery Wall (STA)

value: Male


title: set3∆ homozygous diploid mRNA-seq, replicate 2

value: set3delta homozygous diploid


title: hos2∆ homozygous diploid mRNA-seq, replicate 2

value: hos2delta homozygous diploid


title: hos2∆ homozygous diploid mRNA-seq, replicate 1


title: [ESI+] Diploid mRNA-seq, replicate 2

value: [ESI+] Diploid


title: [ESI+] Diploid mRNA-seq, replicate 1


title: Naïve_1

value: naive

tag: biological replicate


title: Naive Diploid mRNA-seq, replicate 1

value: Naive Diploid


title: SP_36

status: Public on Feb 28 2020

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

data_processing:
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.4.4
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 12.0.3
mapping of fastq files to mus musculus (GRCm38) sequence and calculation of Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed using CLC Genomics Workbench 12.0.3 (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8)
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV sheets of expression values (RPKM, TPM, total reads and unique reads) of murine genes (Name, GeneID, ENSEMBL)

source_name: sections of murine spleen

extract_protocol:
Sections of liver and spleen were preserved in RNAlater Stabilization Solution (Thermo Fisher Scientific) and frozen. Thawed samples were transferred to PBS and homogenized. One-eighth of the homogenate was mixed with TRIzol Reagent (Thermo Fisher Scientific). BMDM were directly lysed in TRIzol Reagent and frozen. Total RNA was isolated according to the manufacturer’s protocol. The quantity and quality of the extracted RNA was assessed using a Thermo Fisher Scientific qubit 2.0 fluorometer with the Qubit RNA BR Assay Kit (Thermo Fisher Scientific, Q10211) and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer RNA Kit (Agilent, DNF-471), respectively.
Sequencing libraries were prepared using an illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, 20020599) in combination with TruSeq RNA UD Indexes (Illumina, 20022371) according to the illumina guidelines. Sequencing libraries were sequenced paired-end (2 x 50 bp) using an illumina NovaSeq 6000 S1 Reagent Kit (100 cycles; Illumina, 20012865) on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: Ly6efl/fl (WT) and Ly6e∆HSC (KO) mice were injected intraperitoneally with 5000 PFU MHV-A59 or PBS for a mock infection control.

value: spleen

value: female

tag: conditional ly6e knock-out

value: ko

tag: inoculation

value: MHV

tag: time

value: 5 d p.i.


title: SP_35


title: SP_33

value: wt


title: set3∆ homozygous diploid mRNA-seq, replicate 1


title: SP_34


title: Naive Diploid mRNA-seq, replicate 2


title: SP_24

value: PBS


title: SP_29

value: 3 d p.i.


title: SP_32


title: SP_27


title: SP_30


title: SP_26


title: SP_28


title: SP_23


title: SP_31


title: SP_25


title: SP_22


title: SP_20


title: SP_21


title: SP_19


title: SP_16

source_name: sections of murine liver

value: liver


title: SP_17


title: SP_15


title: SP_18


title: SP_13


title: SP_07


title: SP_06


title: SP_05


title: SP_11


title: SP_04


title: SP_03


title: SP_09


title: SP_10


title: SP_14


title: SP_01


title: SP_02


title: RNAseq_3B1.3L-d4_s3

city: Urbana

first: Jun

middle: S

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for DNMT3B1, DNMT3L, KanR, and zeoR  (We excluded other DNMTs from the reference to prevent multiple alignment to highly similar DNMT sequences). (See KIsequences.DNMT3B1.fa and KIgenes.DNMT3B1.gff in supplementary folder: DNMTsequences.zip).

data_processing:
Paired-end RNA-seq reads were mapped to the K. phaffii genome using TopHat2 (version 2.1.1) with the options -g 1 --prefilter-multihits --library-type fr-unstranded
Mapped reads were filtered with samtools view (version 1.7) using the options  -h -f  3 -F 3596 -q 13, and read pairs mapping to different chromosomes were removed
Gene expression values, in units of FPKM (fragments per kilobase of transcript per million mapped reads), were calculated from filtered bam/sam files using cuffnorm (version 2.2.1) with the options --library-norm geometric --library-type fr-unstranded
RNA-seq read count tables were generated with HTSeq-count (version 0.9.1) using options -s no -I ID -t gene
Genome_build: ASM170808v1
Supplementary_files_format_and_content: Text file produced by htseq-count. Gene IDs refer to ID attributes in file GCA_001708085.1_ASM170808v1_genomic.gff.gz at https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/708/085/GCA_001708085.1_ASM170808v1. Counts are number of read-pairs associated with each gene

organism: Komagataella phaffii

source_name: Komagataella phaffii

growth_protocol: Cells were grown in YPD for 1 day, then subcultured into BMGY for the next 5 days

extract_protocol:
Spheroblasts were lysed and RNA purified using RNEasy plus mini kit (Qiagen)
Library construction was done by Beijing Genomics Institute (BGI)

value: Strain NRRL Y- 11430, ATCC 76273

tag: transformation

value: AvrII digested DNMT3B13L


title: SP_12

tag: gender


title: SP_08


title: WGBS_3B1.3L-d4_s2

description: doi: 10.1038/ncomms12211 strain Integration site 1

data_processing:
Paired-end reads from each experiment were trimmed using Trim Galore (version 0.4.4) with the command trim_galore --paired --trim 1 --clip_r1 8 --clip_r2 8 --three_prime_clip_r1 8 --three_prime_clip_r2 8
Read duplicates were removed
Reads were aligned to the bisulfite converted K. phaffii genome with bismark  (version 0.18.0) using the command bismark --bowtie2 -N 1 -D 25 -R 5 --score_min L,0,-0.4. --X 2000 --unmapped
We attempted a second alignment of the first-strand reads from unaligned read pairs using the command bismark --bowtie2 -N 1 -D 25 -R 5 --score_min L,0,-0.4
We obtained CpG-context files from paired-end alignments using the command “bismark_methylation_extractor --no_overlap –comprehensive”
We obtained CpG-context files from single-end alignments using the command “bismark_methylatoin_extractor –comprehensive”
We concatentated CpG-context files generated from pair-end and single-end alignments
Genome_build: ASM170808v1
Supplementary_files_format_and_content: Bismark CpG-context file returned by bismark_methylation_extractor.  Tab delimited text file. Columns are seq-ID, methylation state, chromosome, start position (1-based), methylation call

extract_protocol:
Genomic DNA purified using Master Pure Yeast DNA Purifiation Kit (Epicentre)
total DNA was submitted to the Beijing Genome Institute (BGI) for BS-treatment, library construction and sequencing on an Illumina HiSeq X Ten instrument.


title: RNAseq_3B1.3L-d4_s1


title: WGBS_3B1.3L-d4_s1


title: RNAseq_3B1.3L-d3_s3


title: WGBS_3B1.3L-d3_s2


title: RNAseq_3B1.3L-d3_s1


title: WGBS_3B1.3L-d2_s2


title: WGBS_3B1.3L-d3_s1


title: RNAseq_3B1.3L-d4_s2


title: WGBS_3B1.3L-d1_s1


title: RNAseq_3B1.3L-d2_s2


title: RNAseq_3B1.3L-d1_s3


title: RNAseq_3B1.3L-d2_s1


title: WGBS_Control_s2

value: AvrII digested DNMT Control


title: WGBS_3B1.3L-d2_s1


title: RNAseq_3B1.3L-d1_s2


title: RNAseq_3B1.3L-d3_s2


title: WGBS_Control_s1


title: WGBS_3L_s2

value: AvrII digested DNMT3L


title: RNAseq_3B1.3L-d1_s1


title: WGBS_3L_s1


title: RNAseq_Control_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for all DNMTs, KanR, and zeoR. (See KIsequences.all.fa and KIgenes.all.gff in supplementary folder: DNMTsequences.zip).


title: WGBS_3B1_s2

value: AvrII digested DNMT3B1


title: WGBS_3B1_s1


title: RNAseq_Control_s2


title: WGBS_3A2_s2

value: AvrII digested DNMT3A2


title: RNAseq_Control_s1


title: RNAseq_3L_s2


title: WGBS_3A2.3L_s2

value: AvrII digested DNMT3A23L


title: RNAseq_3L_s1


title: WGBS_3A2.3L_s1


title: RNAseq_3B1_s3


title: WGBS_3A1_s2

value: AvrII digested DNMT3A1


title: WGBS_3A1_s1


title: WGBS_3A1.3L_s2

value: AvrII digested DNMT3A13L


title: RNAseq_3B1_s1


title: RNAseq_3A2_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for DNMT3A2, DNMT3L, KanR, and zeoR  (We excluded other DNMTs from the reference to prevent multiple alignment to highly similar DNMT sequences). (See KIsequences.DNMT3A2.fa and KIgenes.DNMT3A2.gff in supplementary folder: DNMTsequences.zip).


title: WGBS_3A1.3L_s1


title: RNAseq_3A2_s2


title: WGBS_1A_s2

value: AvrII digested DNMT1A


title: RNAseq_3B1_s2


title: RNAseq_3A2_s1


title: RNAseq_3A2.3L_s3


title: Kasumi-9_CytoScanHD_array

type: genomic

city: Ibaraki

first: Fumio

last: Kasai

state: Osaka

address: Saito-Asagi 7-6-8

department: JCRB Cell Bank

institute: National Institute of Biomedical Innovation

description: Hybridized to CytoScan™ HD Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The data analysis was performed based on the GRCh37 (hg19) reference using the Chromosome Analysis Suite software, ChAS 4.0.

source_name: leukemia cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cultured cells using the Qiagen AllPrep DNA/RNA Mini Kit. DNA quality and quantity was assessed using the NanoDrop.

tag: cell line

tag: cell type

value: BCP-ALL


title: RNAseq_3A2.3L_s2


title: WGBS_3B1.3L-d1_s2


title: RNAseq_3A2.3L_s1


title: Kasumi-1_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: RNAseq_3A1_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for DNMT3A1, DNMT3L, KanR, and zeoR  (We excluded other DNMTs from the reference to prevent multiple alignment to highly similar DNMT sequences). (See KIsequences.DNMT3A1.fa and KIgenes.DNMT3A1.gff in supplementary folder: DNMTsequences.zip).


title: RNAseq_3A1_s2


title: WGBS_1A.3L_s1

value: AvrII digested DNMT1A3L


title: Kasumi-4_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array

value: CML-BC


title: RNAseq_3A1.3L_s2


title: RNAseq_3A1.3L_s3


title: RNAseq_3A1.3L_s1


title: WGBS_1A_s1


title: WGBS_3A2_s1


title: RNAseq_3A1_s1


title: Kasumi-5_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array

value: T-ALL


title: RNAseq_1A_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for DNMT1A, DNMT3L, KanR, and zeoR  (We excluded other DNMTs from the reference to prevent multiple alignment to highly similar DNMT sequences). (See KIsequences.DNMT1A.fa and KIgenes.DNMT1A.gff in supplementary folder: DNMTsequences.zip).

value: AvrII digested DNMT 1A


title: RNAseq_1A_s2


title: RNAseq_1A_s1


title: RNAseq_1A.3L_s3

value: AvrII digested DNMT 1A3L


title: Kasumi-8_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: RNAseq_1A.3L_s1


title: ChIP-Seq: SMC3 r2

status: Public on Feb 27 2020

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: p-val. threshold 1e-10

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.1
bowtie2 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup.
ChIP-seq: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq readmapping, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
TDF files for IGV and Juicebox browser were generated from wig files using igvtools toTDF
Genome_build: hg19
Supplementary_files_format_and_content: juicer tools pre derived .hic files (Aiden Lab) containing Hi-C matrices for usage with juicebox and juicer tools for Hi-C, and .wig.tdf files for ChIP-Seq data
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S -p 1e-10] and represent genomic distribution of the factors as described in the paper. Further processing to tdf files for IGV and Juicebox usage.

source_name: cervical carcinoma

growth_protocol: HeLa Kyoto cells were synchronized at G1.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

tag: RNAi

tag: genotype


title: ChIP-Seq: SMC3 r1

description: p-val. threshold 1e-10

tag: chip antibody


title: ChIP-Seq: SMC3ac - ESCO1 depleted

description: p-val. threshold 1e-10

value: ESCO1 depleted


title: ChIP-Seq: SMC3ac w.t.

description: p-val. threshold 1e-10


title: Kasumi-10_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: ChIP-Seq: CTCF r2

description: p-val. threshold 1e-10

value: CTCF


title: RNAseq_1A.3L_s2

tag: strain

value: Strain NRRL Y- 11430, ATCC 76273


title: ChIP-Seq: CTCF r1

description: p-val. threshold 1e-10


title: ChIP-Seq: STAG2-GFP r2

description: p-val. threshold 1e-10

value: GFP


title: ChIP-Seq: STAG2-GFP r1

description: p-val. threshold 1e-10


title: Hi-C: STAG2-AID + Auxin

description: MboI digestion

value: STAG2-AID with Auxin


title: Kasumi-6_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: ChIP-Seq: STAG1-GFP r2

description: p-val. threshold 1e-10


title: Hi-C: STAG2-AID

description: MboI digestion

value: STAG2-AID no Auxin


title: Kasumi-7_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: Hi-C: ESCO1 depleted

description: HindIII digestion


title: Hi-C: CTCF and STAG2 depleted

description: HindIII digestion

value: CTCF / STAG2

value: CTCF / STAG2 depleted


title: Hi-C: STAG1-AID + Auxin

description: MboI digestion

value: STAG1-AID with Auxin


title: ChIP-Seq: STAG1-GFP r1

description: p-val. threshold 1e-10


title: Hi-C: STAG2 depleted

description: HindIII digestion

value: STAG2 siRNA depleted


title: Hi-C: STAG1 depleted

description: HindIII digestion

value: STAG1 siRNA depleted


title: Hi-C: STAG2 depleted high resolution

description: MboI digestion


title: Hi-C: CTCF and STAG1 depleted

description: HindIII digestion

value: CTCF / STAG1

value: CTCF / STAG1 depleted


title: Hi-C: STAG1-AID

description: MboI digestion

value: STAG1-AID no Auxin


title: Hi-C: CTCF depleted

description: HindIII digestion

value: CTCF depleted


title: Kasumi-2_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array

value: BCP-ALL


title: Kasumi-3_CytoScanHD_array

description: Hybridized to CytoScan™ HD Array


title: Hi-C: STAG1 depleted high resolution

description: MboI digestion

value: HeLa Kyoto


title: Hi-C: HeLa G1 High Resolution control - MboI

description: MboI digestion

value: w.t. G1


title: WGBS_1A.3L_s2

value: AvrII digested DNMT1A3L


title: Hi-C: CTCF and ESCO1 depleted

description: HindIII digestion

value: ESCO1 / STAG2

value: ESCO1 / STAG2 depleted


title: Tempus xO assay mRNA sequencing [82-SN]

status: Public on Feb 26 2020

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

institute: Northwestern University

description:
82-SN
Skin
Whole transcriptome RNA sequencing

data_processing:
FASTQ files containing raw sequencing data were generated using BCL2FASTQ version 2.17 from Illumina Inc.
NovoAlign version 3.05.00 was used for reference sequence alignment.
RNA expression analysis was conducted with CRISP version 1.4.2.4.
Genome_build: GRCh37, GRCh38, 1000 genomes human reference, HG19, ExAC Database V 0.3.1, Tempus Knowledge database (KDB) V.0.1 COSMIC database version 79 GRCh37
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing RNA counts were generated from FASTQ files using CRISP version 1.4.2.4.

source_name: Spitz Tumor

extract_protocol:
Tumor total nucleic acid was extracted from at least ten 5-micron FFPE tissue sections with tumor cellularity > 20% by a Chemagic360 instrument (PerkinElmer, MA) using a source-specific magnetic bead protocol and digested with proteinase K. Nucleic acid is quantified by a Quant-iT picogreen dsDNA reagent Kit or Quant-iT Ribogreen RNA Kit (Life Technologies, CA). A Covaris ultrasonicator mechanically sheared 100 nanograms of DNA from each tumor and normal sample to an average size of 200 base pairs (bp).
Libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems, MA). One hundred nanograms of RNA per tumor sample was fragmented in the presence of magnesium to an average size of 200 bp. The RNA then underwent first strand cDNA synthesis using random primers, followed by combined second strand synthesis and A-tailing, adapter ligation, bead-based cleanup and library amplification. Samples were then hybridized with the IDT xGEN Exome Research Panel (IDT Inc., CA) and sequenced to obtain > 50 million reads on the Illumina HiSeq 4000 System (Illumina, Inc., San Diego, CA) utilizing patterned flow cell technology.

tag: tissue

value: Spitz Tumor


title: Tempus xO assay mRNA sequencing [84-SN]

description:
84-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [69-SM]

description:
69-SM
Skin
Whole transcriptome RNA sequencing

source_name: Spitzoid Melanoma

value: Spitzoid Melanoma


title: Tempus xO assay mRNA sequencing [71-AST]

description:
71-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [68-SN]

description:
68-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [6-SM]

description:
6-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [79-MWS]

description:
79-MWS
Skin
Whole transcriptome RNA sequencing

source_name: Melanoma with Spitzoid Features

value: Melanoma with Spitzoid Features


title: Tempus xO assay mRNA sequencing [80-SN]

description:
80-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [78-AST]

description:
78-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [8-SM]

description:
8-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [73-SN]

description:
73-SN
Skin
Whole transcriptome RNA sequencing


title: Hi-C: G1 sync. Control - HindIII - 2 reps.

description: HindIII digestion


title: Tempus xO assay mRNA sequencing [74-AST]

description:
74-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [76-AST]

description:
76-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [64-SM]

description:
64-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [83-SN]

description:
83-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [66-AST]

description:
66-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [5-AST]

description:
5-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [67-SM]

description:
67-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [60-AST]

description:
60-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [85-AST]

description:
85-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [59-AST]

description:
59-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [53-AST]

description:
53-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [58-SM]

description:
58-SM
Skin
Whole transcriptome RNA sequencing


title: RNAseq_3L_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for all DNMTs, KanR, and zeoR. (See KIsequences.all.fa and KIgenes.all.gff in supplementary folder: DNMTsequences.zip).

value: Strain NRRL Y- 11430, ATCC 76273

value: AvrII digested DNMT3L


title: Tempus xO assay mRNA sequencing [7-SM]

description:
7-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [4-AST]

description:
4-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [75-ASN]

description:
75-ASN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [62-AST]

description:
62-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [48-AST]

description:
48-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [44-AST]

description:
44-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [27-AST]

description:
27-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [46-AST]

description:
46-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [41-AST]

description:
41-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [30-SN]

description:
30-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [32-SN]

description:
32-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [36-AST]

description:
36-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [2-AST]

description:
2-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [35-AST]

description:
35-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [37-AST]

description:
37-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [47-AST]

description:
47-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [23-AST]

description:
23-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [40-AST]

description:
40-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [42-AST]

description:
42-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [235-SM]

description:
235-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [33-SN]

description:
33-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [24-AST]

description:
24-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [234-SM]

description:
234-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [3-AST]

description:
3-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [26-AST]

description:
26-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [236-SM]

description:
236-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [45-AST]

description:
45-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [38-AST]

description:
38-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [233-SM]

description:
233-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [29-SM]

description:
29-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [22-AST]

description:
22-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [228-SM]

description:
228-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [225-SM]

description:
225-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [223-MWS]

description:
223-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [224-MWS]

description:
224-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [211-MWS]

description:
211-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [217-MWS]

description:
217-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [204-SM]

description:
204-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [212-MWS]

description:
212-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [215-SM]

description:
215-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [220-SM]

description:
220-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [18-AST]

description:
18-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [21-AST]

description:
21-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [1-AST]

description:
1-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [195-AST]

description:
195-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [191-AST]

description:
191-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [193-SN]

description:
193-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [19-AST]

description:
19-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [192-AST]

description:
192-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [194-AST]

description:
194-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [187-SN]

description:
187-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [185-SN]

description:
185-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [188-AST]

description:
188-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [184-SN]

description:
184-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [189-SN]

description:
189-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [183-SN]

description:
183-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [186-SN]

description:
186-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [182-AST]

description:
182-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [181-SN]

description:
181-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [180-AST]

description:
180-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [222-MWS]

description:
222-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [17-AST]

description:
17-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [20-AST]

description:
20-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [179-AST]

description:
179-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [177-SN]

description:
177-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [178-AST]

description:
178-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [171-MWS]

description:
171-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [175-AST]

description:
175-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [176-AST]

description:
176-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [16-AST]

description:
16-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [169-MWS]

description:
169-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [168-AST]

description:
168-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [170-MWS]

description:
170-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [172-SN]

description:
172-SN
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [163-MWS]

description:
163-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [167-MWS]

description:
167-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [166-MWS]

description:
166-MWS
Skin
Whole transcriptome RNA sequencing


title: RNAseq_3B1.3L-d2_s3

description:
doi: 10.1038/ncomms12211 strain Integration site 1
The reference for alignment was composed of the WT K. phaffii geneome as well as sequences for DNMT3B1, DNMT3L, KanR, and zeoR  (We excluded other DNMTs from the reference to prevent multiple alignment to highly similar DNMT sequences). (See KIsequences.DNMT3B1.fa and KIgenes.DNMT3B1.gff in supplementary folder: DNMTsequences.zip).

value: AvrII digested DNMT3B13L


title: Tempus xO assay mRNA sequencing [162-SM]

description:
162-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [165-MWS]

description:
165-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [164-MWS]

description:
164-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [157-SM]

description:
157-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [15-AST]

description:
15-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [151-MWS]

description:
151-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [160-MWS]

description:
160-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [154-SM]

description:
154-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [152-MWS]

description:
152-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [14-AST]

description:
14-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [149-SM]

description:
149-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [150-SM]

description:
150-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [13-AST]

description:
13-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [130-MWS]

description:
130-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [12-AST]

description:
12-AST
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [129-MWS]

description:
129-MWS
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [127-SM]

description:
127-SM
Skin
Whole transcriptome RNA sequencing


title: Tempus xO assay mRNA sequencing [10-AST]

description:
10-AST
Skin
Whole transcriptome RNA sequencing


title: Spsc_37_03

status: Public on Feb 25 2020

city: Messina

first: Orazio

last: Romeo

address: Viale Ferdinando Stagno d'Alcontres, 31

department: Department of Chemical, Biological, Pharmaceutical and Environmental Sciences

institute: University of Messina

description: replicate 3

data_processing:
For each sequenced library, Illumina raw reads were pre-processed with the program Trimmomatic (v.0.39) to remove adapters and sequences with low Phred-scores (minimum Phred-quality score: ≥25; minimum length: 35)
The software STAR (v.2.7.1a) was used to map cleaned reads on the previously published and annotated S. schenckii reference genome (GenBank: GCA_000961545.1). Mapping quality was evaluated using the Qualimap 2 software (v.2.2.1).
For each RNA-seq library, fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated and used to estimate the number of detected transcripts. A FPKM cut-off >1 in at least one of the six libraries was used to establish whether a transcript was expressed by S. schenckii cells from which RNA was extracted. The transcripts whose FPKM value was below the threshold value of 1 were considered not detected by RNA-seq method employed.
The normalization of raw counts was performed using the trimmed means of M-values (TMM) method in the HTSFilter package. Differentially expressed (DE) genes were identified using the edgeR package. The genes whose expression levels showed an absolute log2 fold-change (Log2FC) value ≥ 1 and a false discovery rate (FDR) ≤ 0.05 were considered to be significantly differentially expressed.
Genome_build: GenBank: GCA_000961545.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sporothrix schenckii

source_name: yeast-form culture

growth_protocol: To induce the yeast-like and mold formation, as well as the expression of genes associated with these two different morphologies, six test tubes, each containing 25 mL of YPD broth (1% yeast extract, 2% peptone, and 2% dextrose), were inoculated with 50 µL of a standardized suspension of S. schenckii conidia from a 4-days-old YPD agar culture grown at 28°C. Inoculated YPD broth tubes were incubated in triplicate at 37°C and 25°C respectively, and monitored daily up to 6 days to confirm the expected morphology of the organism (yeast-like cells at 37°C and hyphae at 25°C).

extract_protocol:
Total RNA extraction was performed by using the Ribopure Yeast extraction kit (Thermofisher, Italy) following the manufacturer’s instructions. Purified RNA was quantified spectrophotometrically at 260 nm and 280 nm and the RNA integrity was evaluated with an Agilent 2100 Bioanalyzer instrument using the RNA 6000 Nano kit (Agilent Technologies, Italy). High-quality total RNA (OD260/280 ≥2.0; RIN value ≥8.0) was used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols.
TruSeq stranded mRNA chemistry (Illumina)

tag: growth temperature

value: Yeast


title: Spsc_37_01

description: replicate 1


title: Spsc_25_01

description: replicate 1

source_name: mold-form culture

value: Mold


title: Spsc_25_03

description: replicate 3


title: Spsc_25_02

description: replicate 2


title: Tempus xO assay mRNA sequencing [131-SM]

description:
131-SM
Skin
Whole transcriptome RNA sequencing


title: PC3-RRM2-2

status: Public on Feb 20 2020

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: RRM2 cell_2

data_processing:
Dara processing were performed with Partek Flow according to Manufactures Instruction
Supplementary_files_format_and_content: Excel File contain the gene list

growth_protocol: Cell are cultured in standard condition according to ATCC

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA kit  (Zymo Research, Irvine, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human Prostate cancer Cell

tag: cell  type

value: Transformed  cell

tag: source

value: ATCC


title: Input_ChIP-Seq_AP2-G_GFP_E1_rep1

status: Public on Feb 18 2020

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

description:
Input_ChIP-Seq_AP2-G_GFP_E1_rep1
E1_HP1_1_FE.bigWig

data_processing:
Demultiplexing with bcl2fastq (Illumina) software v2.19.1.403
ChIP-Seq reads aligned to the genome using BWA v0.7.10-r789 with default parameters
Data sorted, indexed and PCR duplicates filteres using samtools v1.3
Peak calling (callpeak option) and calculation of fold enrichment over input (bdgcmp option) performed with MACS2 (v2.1.1.20160309) software using -BAMPE and --SPMR options.
Genome_build: PlasmoDB-29_Pfalciparum3D7
Supplementary_files_format_and_content: BigWig files obtained using bedGraphToBigWig software v4

organism: Plasmodium falciparum

source_name: In vitro cultured blood stage cells

growth_protocol: Blood stage P. falciparum parasites were cultured in human O+ red blood cells in RPMI-1640 medium supplemented with Albumax II (10% v/v), hypoxanthine (200 μM) and gentamycin (50 μg/ml) in 3% CO2 and 5% O2 at 37 °C.

extract_protocol:
ChIP was performed as previously described (Zanghi et al, 2018 Cell. Rep.) with parasites synchronised at 36 hpi. Sonicated chromatin (500 ng DNA content) was immunoprecipitated overnight with 0.5 μg of anti-HP1 polyclonal rabbit antibodies. and incubated after with 25 μl of Dynabeads Protein G (Invitrogen) for two hours. Subsequent washing, cross-link reversion and DNA extraction were carried out as described before.
Sequencing libraries were produced with the immunoprecipitated DNA using the MicroPlex Library Preparation Kit v2 (Diagenode) with the KAPA HiFi polymerase (Kapa Biosystems) for the PCR amplification. For each ChIP sample, a control DNA corresponding to the ChIP input was processed in parallel.


title: Input_ChIP-Seq_AP2-G_GFP_E1_rep2

description:
Input_ChIP-Seq_AP2-G_GFP_E1_rep2
E1_HP1_2_FE.bigWig


title: Input_ChIP-Seq_AP2-G_GFP_H8_rep2

description:
Input_ChIP-Seq_AP2-G_GFP_H8_rep2
H8_HP1_2_FE.bigWig


title: PC3-EV2

description: empty vector Cell_2


title: PC3-EV1

description: empty vector Cell_1


title: Input_ChIP-Seq_AP2-G_GFP_H8_rep1

description:
Input_ChIP-Seq_AP2-G_GFP_H8_rep1
H8_HP1_1_FE.bigWig


title: Input_ChIP-Seq_WT_rep1

description:
Input_ChIP-Seq_WT_rep1
A11_HP1_1_FE.bigWig

value: NF54 A11 parental wildtype


title: Spsc_37_02

description: replicate 2


title: HP1_ChIP-Seq_AP2-G_GFP_E1_rep2

description:
HP1_ChIP-Seq_AP2-G_GFP_E1_rep2
E1_HP1_2_FE.bigWig

value: Rabbit anti-HP1 (Genscript Customized, see Chen et al 2016 Sci. Rep.)


title: wnt4CD24l_11

status: Public on Feb 22 2020

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

description: Wnt-4 fl/fl CD24 Low

hyb_protocol: Fluidics protocol FS450_0007

scan_protocol: GeneChip® Scanner 3000 7G  and Power Tools software package (Affymetrix)

data_processing:
Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA) using the Affymetrix Expression Console Software (version 1.1.2800)
GeneSpring GX 7.3.1

source_name: Mammary glands

label_protocol: Ovation® Pico WTA System V2 and FL-Ovation cDNA Biotin module V2 (Nugen)

growth_protocol: Conditionally Wnt4 deleted (MMTV::Cre+.Wnt4fl/fl.mT/mG) and control (MMTV::Cre+.Wnt4wt/wt.mT/mG) 10 to 14-week-old female mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The concentration and purity of cRNA was verified on the Bioanalyzer

treatment_protocol: At sacrifice, mammary grafts were mechanically and enzymatically digested, and total cell population was labeled with CD24. Subsequently, cells were FACSsorted based on GFP into CD24 high (Luminal) and CD24 low (myoepithelial) cells, which were then lysed, RNA was extracted, and analyzed by microarray analysis.

value: Wnt4 deletion


title: wtCD24h_14

description: Wt CD24 High

value: WT


title: wtCD24l_9

description: Wt CD24 Low


title: wtCD24l_1

description: Wt CD24 Low


title: wtCD24h_10

description: Wt CD24 High


title: PC3-RRM2-1

description: RRM2 cell_1


title: wnt4CD24h_4

description: Wnt-4 fl/fl CD24 High


title: wtCD24h_2

description: Wt CD24 High


title: HP1_ChIP-Seq_WT_rep2

description:
HP1_ChIP-Seq_WT_rep2
A11_HP1_2_FE.bigWig


title: wnt4CD24h_16

description: Wnt-4 fl/fl CD24 High


title: HP1_ChIP-Seq_AP2-G_GFP_H8_rep2

description:
HP1_ChIP-Seq_AP2-G_GFP_H8_rep2
H8_HP1_2_FE.bigWig


title: wnt4CD24h_12

description: Wnt-4 fl/fl CD24 High


title: HP1_ChIP-Seq_AP2-G_GFP_E1_rep1

description:
HP1_ChIP-Seq_AP2-G_GFP_E1_rep1
E1_HP1_1_FE.bigWig


title: HP1_ChIP-Seq_AP2-G_GFP_H8_rep1

description:
HP1_ChIP-Seq_AP2-G_GFP_H8_rep1
H8_HP1_1_FE.bigWig


title: HP1_ChIP-Seq_WT_rep1

description:
HP1_ChIP-Seq_WT_rep1
A11_HP1_1_FE.bigWig


title: wtCD24l_13

description: Wt CD24 Low


title: wnt4CD24l_15

description: Wnt-4 fl/fl CD24 Low


title: TF ChIP-seq from HEK293 (ENCLB650WFT)

status: Public on Feb 12 2020

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR146NLL/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-REPIN1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR146NLL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB650WFT
size range: 450-650

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-REPIN1 fusion protein

tag: antibody

tag: line

value: cell line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-REPIN1 under the control of a CMV promoter.

tag: biosample encode accession

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

tag: health state

value: unknown

tag: age

tag: dev stage

value: embryonic

tag: link

value: ENCBS430QMH at ENCODE; https://www.encodeproject.org/ENCBS430QMH/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: TF ChIP-seq from HEK293 (ENCLB794PLP)

description:
https://www.encodeproject.org/experiments/ENCSR185QFX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF549 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR185QFX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR300VIY, ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2018-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB794PLP
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-ZNF549 originated from HEK293

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS327AYJ at ENCODE; https://www.encodeproject.org/ENCBS327AYJ/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045