title: P7-3-Nano-FFPE

description:
Patient 7 late on-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 5

hyb_protocol: 300ng RNA was hybridised for 18hrs at 65C with custom NanoString capture probeset and detection codeset. Samples were held at 4C prior to purification and mobilisation at high sensitivity in the nCounter Prep Station (NanoString)

scan_protocol: 555 fields of view (Max) were imaged per sample using the nCounter digital analyser (NanoString) and RCC (reporter code count) files exported for analysis

data_processing: Using the nSolver 3.0 software

source_name: Breast cancer tissue.

value: breast cancer

tag: time point

value: late on-treatment biopsy


title: TruSeq_NoPNK

status: Public on May 03 2019

type: SRA

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
TruSeq sRNA adapter and STP oligo sequences were trimmed from reads using cutadapt (v1.91), filtering reads <15 nt.
Trimmed reads were aligned to the sequences of the synthetic RNA pool using the sRNAnalyzer pipeline. A bowtie library containing the sRNAnalyzer sequences was prepared and added to the manifest required as input. sRNAnalyzer was run using default parameters (allowing up to 2 mismatches), sequentially aligning to Univec contaminates and then the sRNA pipeline.
Read counts from sRNAnalyzer ".profile" files were loaded into R for processing
Alignment strand and mismatch information are used to assign sequences to best alignment between Univec contaminates and sRNA pool. The alignment with the fewest mismatches is identified for each read, and kept for analysis only if it matches the + strand of the sRNA pool.
Read counts are combined (sum) for all sequences in the pool, allowing 0-2 mismatches on the + strand. Ambiguous alignments are divided among the respective sequences.
Read counts-per-million (CPM) are calculated using the total number of filtered reads aligned to the synthetic pool.
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited "profile" files contain all alignments to Univec and sRNA synthetic pool sequences reported by sRNAnalyzer. The columns include: 1) Alignment database ID with # mismatched and alignment orientation; 2) Unique sequence id with count (format: ID-count); 3) read sequence; 4) ID of aligned sRNA database subject; 5) Start position of alignment in subject. Relative position and base difference of mismatch, if applicable. (format: alignStart,mmPos:OldBase>NewBase). 6) read count, 7) n/a. Supplementary .txt file contains CPM values calculated from processing and filtering the .profile files.

molecule: total RNA

organism: synthetic construct

source_name: Synthetic sRNA equimolar pool (SynthRNA476v1)

extract_protocol:
10 femtomoles of the synthetic, equimolar pool were taken from previously-frozen aliquots for each library. The aliquots were either directly used in library construction, or pre-treated with T4 PNK. To perform phospho-small RNA-seq, synthetic and plasma RNA samples were pretreated with T4 polynucleotide kinase (NEB, Ipswich, MA, US) using an RNA input of 7 ul in a final volume reaction of 10 ul and following the manufacturer’s instructions. After the enzymatic treatment, biological RNA samples were purified by performing sequential washes in silica columns (Zymo, Irvine, CA, US): (i) 900 ul of buffer RWT (Qiagen, Hilden, Germany); (ii) 900 ul of buffer RPE (Qiagen, Hilden, Germany); (iii) 900 ul of ethanol 200 proof, molecular biology grade (Fisher Scientific, Waltham, MA, US) and; (iv) 900 ul of 80% ethanol.
Standard ligation-based small RNA libraries were prepared using the TruSeq small RNA kit (Illumina, San Diego, CA, US) according to the manufacturer instructions. Size selection was performed using pre-cast 6% acrylamide gels (Invitrogen, Waltham, MA, US) including all products from 140-200 bp plus any additional visible bands of greater size.

treatment_protocol: The synthetic, equimolar pools were synthezised, HPLC purified and quantified spectrophotometrically by IDT (Coralville, IA), ndwere pooled and aliquoted upon receipt in prelabeled DNA-, DNase-, RNase-, and pyrogen-free screw cap tubes with low adhesion surface and stored immediately at −80 C.

tag: treatment


title: OX40JAG Treg

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

library_source: genomic

data_processing:
Raw reads were quality trimmed to minimum Q20 using Trimmomatic (Bolger, et al., 2014) using parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20. Reads were mapped to the reference genome in a bisulfite-conversion-aware manner using Bismark (Krueger and Andrews, 2011). Apparent PCR duplicates were removed using deduplicate_bismark. Methylation status per read was obtained with bismark_methylation_extractor. Percent methylation levels, plus total read count and methylated read count, were then summarized per CpG; CpGs with fewer than 5x coverage were set to 0 counts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files: CpG coordinates (chromosome and position, mm10), total coverage, methylated coverage, and % methylation reported for each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: CD4+CD25hi Treg cells

growth_protocol: 6-week-old NOD mice were treated with PBS or OX40L and Jagged-1 proteins once a week for three weeks. A week after final treatment CD4+CD25- Teff cells and CD4+CD25hi Treg cells were sorted by FACS.

extract_protocol: Libraries were prepared with the Hyper Library construction kit from Kapa Biosystems (Roche) and treated with the Lightning EZ kit from Zymo Research

tag: strain

value: NOD

tag: tissue

value: Spleen

tag: agent

tag: age

value: 10 weeks

tag: cell type

value: CD4+CD25hi Treg cells


title: Aerobic

city: Spokane

first: Jennifer

middle: Niven

last: Shepherd

state: WA

address: 502 E Boone Avenue

department: Department of Chemistry and Biochemistry

institute: Gonzaga University

data_processing:
Ribozero subtraction
Cufflinks' "--frag-bias-correct" option to correct for sequence-specific bias from the random priming
Genome_build: Mapping to R. rubrum ATCC11170 genome
Supplementary_files_format_and_content: txt files with #reads and RPKM of anaerobic and aerobic samples

organism: Rhodospirillum rubrum

source_name: sixth generation aerobic culture

growth_protocol: Anaerobic cultures were grown to stationary phase (OD660 = 4) and aerobic cultures were grown to stationary phase (OD660 = 2) at 30 C in light with no oxygen or dark with aeration, respectively

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and rRNA was removed by Ribominus (Invitrogen)
UW High Throughput Genomics unit performed RNA-Seq library construction using Illumina’s TruSeq kit. Double stranded libraries were generated and sequenced to ~ 20 million tags using 36 bp single ended sequencing. Run type: TRUSEQ V3

treatment_protocol: Anaerobic cultures were grown in screw-capped vials filled to capacity and aerobic cultures were grown in Erlenmeyer flasks 20% full with shaking at 250 rpm

tag: genotype

value: Wild-type


title: P8-1-Nano-FFPE

type: RNA

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
Patient 8 pre-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 6

organism: Homo sapiens

extract_protocol: RNA was extracted from fresh frozen tissue using the Qiagen miRNeasy kit.

value: pre-treatment biopsy


title: Anaerobic

source_name: sixth generation anaerobic culture


title: Sample 12

type: genomic

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: neurons from post-mortem human brain

hyb_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

data_processing: Data generated from the microarrays were preprocessed with Minfi v1.19.12. Normalization was performed with noob, followed by quantile normalization. All samples had sex matching that predicted from the methylome.  Probes that overlapping SNPs (MAF > 5%) on the CpG or single-base extension were excluded (11,812 probes), as were probes known to be cross-reactive (42,558 probes; PMID: 27330998) and those that failed detectability (P>0.01) in >20% samples (1,170 probes). After processing, 812,663 probes were left. Based on principal component analysis (PCA) co-clustering, one sample, despite being labeled NeuN+, clustered with NeuN- samples and was excluded from downstream analyses. Downstream analyses were performed using beta values ; only samples that were also genotyped were used in differential methylation analyses.

label: Cy5 and Cy3

source_name: FACS-sorted neurons from the frontal cortex of the human brain

growth_protocol: DNA was extracted from post-mortem brain samples. No growth protocols were used.

extract_protocol: Genomic DNA from each NeuN+ and NeuN- fraction of each sample was isolated using standard phenol-chloroform extraction methods.

treatment_protocol: Neuronal nuclei were separated using a flow cytometry-based approach, similar to as previously described (PMID: 25369517,PMID: 19078943). Human brain tissue (250 mg) for each sample was minced in 2 mL PBSTA (0.3 M sucrose, 1X phosphate buffered saline (PBS), 0.1% Triton X-100). Samples were then homogenized in PreCellys CKMix tubes with a Minilys (Bertin Instruments) set at 3,000 rpm for three 5 sec intervals, 5 min on ice between intervals. Samples homogenates were filtered through Miracloth (EMD Millipore), followed by a rinse with an additional 2 mL of PBSTA. Samples were then place on a sucrose cushion (1.4 M sucrose) and nuclei were pelleted by centrifugation at 4,000 × g for 30 min 4°C using a swinging bucket rotor. For each sample, the supernatant was removed and the pellet was incubated in 700 μl of 1X PBS on ice for 20 min. The nuclei were then gently resuspended and blocking mix (100 μl of 1X PBS with 0.5% BSA (Thermo Fisher Scientific) and 10% normal goat serum (Gibco) was added to each sample. NeuN-488 (1:500; Abcam) was added and samples were incubated 45 min at 4°C with gentle mixing. Immediately prior to flow cytometry sorting, nuclei were stained with 7-AAD (Thermo Fisher Scientific) and passed through a 30 μM filter (SystemX). Nuclei positive for 7-AAD and either NeuN+ (neuronal) or NeuN- (non-neuronal) were sorted using an Influx (BD Biosciences) at the Faculty of Medicine Flow Cytometry Facility at the University of Toronto (Toronto, ON, Canada). Approximately 1 million NeuN+ nuclei were sorted for each sample. Immediately, after sorting nuclei were placed on ice and then precipitated by raising the volume to 10 mL with 1X PBS and adding 2 mL 1.8 M sucrose, 50 μl 1M CaCl2 and 30 μl Mg(Ace)2 and centrifugation at 1,786 × g for 15 min at 4°C. The supernatant was removed from NeuN+ and NeuN- samples and pellets were stored at -80°C.

value: frontal cortex of the brain

tag: sampleID

tag: Sex

value: Male

tag: race

value: White

value: Schizophrenia

tag: tissuebank

value: Sepulveda

tag: pmi

value: NeuN+


title: 3 Frontal cortex of the human brain

description: Frontal cortex of the human brain

scan_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

data_processing: Genome Studio was used to process raw intensities, following manufacturer's suggestions

label: Cy3 and Cy5

source_name: Frontal cortex of the human brain

extract_protocol: DNA was extracted using standard phenol-chloroform extract methods

treatment_protocol: No treatment was applied to these samples.

tag: index

value: Bipolar


title: OX40JAG Teff

source_name: CD4+CD25-Teff cells

value: CD4+CD25-Teff cells


title: P8-2-Nano-FFPE

description:
Patient 8 early on-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 7

value: early on-treatment biopsy


title: P7-2-Nano-FFPE

description:
Patient 7 early on-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 4

value: breast cancer


title: liver-adlib-untreated-S346

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description:
LIV1_S346
adlib food, no treatment

hyb_protocol: Gene chip hybridization, washing and scanning were carried out according to Affymetrix protocols.

scan_protocol: Scanning was carried out according to Affymetrix protocols

data_processing: Normalization was done via the Robust Multichip Average (RMA) algorithm.

label: biotin

source_name: liver

label_protocol: RNA was further processed for hybridization to Affymetrix HT MG-430 PM Array Plates at the Microarray Department of the University of Amsterdam, the Netherlands. RNA amplication and labeling were carried out according to Affymetrix protocols

growth_protocol: Animals were allowed to acclimatize for one week before the start of the experiments. Standard laboratory conditions were maintained, i.e. temperature 22ºC, humidity 50%, and a 12 h light/12 h dark cycle. All mice had free access to water and food unless mentioned otherwise. The experimental protocol was approved by the Animal Experiments Committee under the Dutch National Experiments on Animals Act, and complied with the 1986 directive 86/609/EC of the Council of Europe.

extract_protocol: The median liver lobe was isolated for array analysis and directly stored in RNAlater Solution and stored at 4ºC until further analysis.  For gene expression analysis, total RNA was extracted from frozen liver tissue using the QIAzol lysis Reagent and miRNAeasy Mini Kit (QIAGEN, Hilden, Germany), as described in the Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program; animal tissues; aqueous phase. RNA was eluted in RNase free water and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Scientific). Subsequently, quality assessment of the RNA was done using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) and RNA kits and reagents belonging to the same manufacturer.

treatment_protocol:
For tumor growth: mice were anaesthetized (isoflurane inhalation, 5% isoflurane inhalation initially and then 2% isoflurane with a 1:1 air:oxygen mixture for maintenance of anesthesia). Both lateral flanks were shaved for precise injection. 2.5 x 10^5 cells of the murine colon carcinoma cell line C26 were injected on both sides in a volume of 100 µL suspension, using a 21G needle. Tumors were allowed to grow for 12 days before start of the experiment.
Fasting: mice were either fasted for 3 days or fed ad libitum (adlib). After the fasting period, mice were fed adlib again.
Chemotherapy: mice were treated with a single weight-adjusted dose of 133 mg/kg of irinotecan intraperitoneally. The control groups received vehicle treatment (sodium chloride 0.9%). Two hours after injection, the fasted groups received a weighed amount of adlib food. Mice were sacrificed 12 hours after injection by exsanguination.

tag: gender

value: male

value: liver

tag: feeding protocol

value: ad libitum food


title: Sample 19

description: neurons from post-mortem human brain

label_protocol: Reagent/array were purchased from Illumina. The experiment was carried out in Sickkids TCAG Microarray facility according to the recommended protocol by Illumina.

value: Harvard HBTRC


title: Sample 18

description: neurons from post-mortem human brain

value: Control


title: 2 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Female


title: Ctrl Treg

value: NOD

value: Spleen

value: PBS

value: 10 weeks

value: CD4+CD25hi Treg cells


title: 1 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Male

value: White

value: Sepulveda


title: Ctrl Teff

value: CD4+CD25-Teff cells


title: P6-4-Nano-FFPE

description:
Patient 6 later on-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 3

value: later on-treatment biopsy


title: P6-3-Nano-FFPE

description:
Patient 6 late on-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 2

value: breast cancer

value: late on-treatment biopsy


title: 8 Frontal cortex of the human brain

description: Frontal cortex of the human brain

value: Bipolar


title: P6-1-Nano-FFPE

description:
Patient 6 pre-treatment biopsy sequenced using Nanostring technology from FFPE.
SAMPLE 1

value: pre-treatment biopsy


title: P1-2-Clar-FF

description:
Patient 1 early on-treatment biopsy sequenced using Affymetrix Clariom S technology from fresh frozen.
SAMPLE 2

hyb_protocol: As per Affymetrix protocol.

scan_protocol: As per standard protocol for Affymetrix Clariom S Pico assay microarrays, using a GCS2500 scanner.

data_processing: All statistical analyses were performed using the R/Bioconductor software (http://www.bioconductor.org/) unless stated otherwise. Preprocessing—the raw CEL files were preprocessed using robust multichip average methodology, which encompasses background correction, normalization, and summarization. Nonspecific filtering—using Affymetrix’ absolute call data, genes with “present” calls in fewer than 80% of arrays were discarded so reducing genes whose expression were largely in the noise range.

label_protocol: As per Affymetrix protocol.

value: early on-treatment biopsy


title: Sample 27_AB343

status: Public on May 02 2019

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: MEF

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility; Cell lines were grown in tissue culture

extract_protocol:
For samples 1-16: Each mouse was euthanized and bone marrow harvested by crushing of the femur, tibia and ilia. Cell suspensions were stained with FACS antibodies and single cells sorted into capture plates
For samples 17-34: Cells were trypsinzed to form a single cell suspension and FACS sorted into capture plates
3' end mRNA libraries were prepared for sequencing using MARS-seq2.0 - improvements to MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation; Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header

tag: cell line

value: MEF

tag: tissue/cell type

value: Cell line

tag: treatment/sample info.

value: low volume

tag: protocol optimization parameter

value: Evaluation of protocol performance, using low volume RT


title: Sample 26_AB342

source_name: ES

tag: strain

value: ES


title: Sample 30_AB416

value: high volume

value: Evaluation of protocol performance, using high volume RT


title: Sample 28_AB345

source_name: ES/MEF

value: ES/MEF

value: mixture ES/MEF 1:1


title: Sample 25_AB341


title: P1-1-Clar-FF

description:
Patient 1 pre-treatment biopsy sequenced using Affymetrix Clariom S technology from fresh frozen.
SAMPLE 1

tag: tissue

tag: time point


title: Sample 29_AB415


title: P1-3-Clar-FF

description:
Patient 1 late on-treatment biopsy sequenced using Affymetrix Clariom S technology from fresh frozen.
SAMPLE 3


title: Sample 24_AB340


title: Sample 9

description: neurons from post-mortem human brain

value: frontal cortex of the brain

tag: age

value: Female

value: White

value: Sepulveda

value: NeuN+


title: Sample 22_AB330


title: Sample 21_AB329


title: Sample 16_AB134

tag: mouse age

value: 8 weeks

value: BM

tag: selection marker

value: Lin- cKit+ Sca1- CD34+ FcgR(low)

value: Invitrogen

value: Optimization of second strand synthesis


title: Sample 14_AB132

value: Invitrogen less DNA pol


title: Sample 13_AB131

value: Invitrogen + more RNaseH


title: Sample 10

description: neurons from post-mortem human brain

tag: sampleID

tag: Sex

value: Schizophrenia


title: Sample 23_AB339

value: ES

value: Cell line

value: low volume

value: Evaluation of protocol performance, using low volume RT


title: Sample 11_AB129

value: NEB 1:4


title: Sample 10_AB128


title: Sample 6_AB124


title: Sample 8_AB126


title: Sample 4_AB122


title: Sample 5_AB123


title: Sample 9_AB127

value: NEB


title: Sample 7

description: neurons from post-mortem human brain

value: frontal cortex of the brain

value: Female

tag: race

value: White

value: Bipolar

tag: tissuebank


title: Sample 3_AB121

value: 8 weeks

value: BM


title: Sample 2_AB120

value: Lin- cKit+ Sca1- CD34+ FcgR(low)

value: Invitrogen


title: B16-F10 CD133- cells

city: Nashville

first: Chris

middle: P

last: Shidal

state: TN

address: 2525 West End Ave 6th Floor

department: Medicine

institute: Vanderbilt University Medical Center

description: miR expression data from CD133- B16-F10 murine melanoma cells

hyb_protocol: Hybridizations were performed at 48C for 16 hours at 60 rpm in a hybridization oven per the manufacturers recommendations.

scan_protocol: Following washing and staining procedures, array microchips  were scanned using a GeneChip Scanner (Affymetrix).

data_processing:
Image data were analyzed using Affymetrix Power Tools and subsequently by Transcriptome Analysis Console (TAC, Affymetrix).
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: B16-F10 skin melanoma from C57BL/6J mouse

label_protocol: Biotin labelling and hybridizations were performed using the FlashTag Biotin HSR RNA labeling kit (Applied Biosystems) according to the manuscfacturers protocol using an input of 500 micrograms of total RNA.

growth_protocol: B16-F10 cells were grown as oncospheres in DMEM/F-12 serum free media containing 1x N-2 supplement (Gibco), 10 ng/mL epidermal growth factor (EGF), and 10 ng/mL basic fibroblast growth factor (bFGF) in low cluster 6 well plates prior to dissociation, labelling, and sorting.

extract_protocol: Triazol extractions were performed using the Qiagen miRNeasy kit and used according to the manufacturers recommendation.

treatment_protocol: Spheres were collected by centrifugation at 300g for 10 minutes. The pellet was briefly dissociated into a single cell suspension using TrypLE (Gibco) enzyme-free dissociation buffer, and cells were subsequently labelled with a PE conjugated anti-CD133 antibody. FACS was performed to collect CD133+ and CD133- samples. Cells were stored in Triazol extraction reagent at -80C until total RNA isolation was performed.

tag: cell type

value: melanotic skin melanoma

tag: cell population

value: CD133- FACS


title: Sample 1_AB119

value: Optimization of second strand synthesis


title: Sample 11

description: neurons from post-mortem human brain

value: Male

value: Schizophrenia

value: Sepulveda

tag: pmi

value: NeuN+


title: 440.PT

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Basecalls performed using Ion Torrent basecaller with parameters: -barcode-filter 0.01 -barcode-filter-minreads 10  -phasing-residual-filter=2.0 -num-unfiltered 1000 -barcode-filter-postpone 1
Reads were aligned to the hg19 genome assembly (hg19 AmpliSeq Transcriptome ERCC v1) with tmap (parameters: mapall stage1 map4)
Transcript abundances were calculated with HTSeq-count, version 0.6.0, target regions: hg19_AmpliSeq_Transcriptome_21K_v1
Transcript abundances were normalized with DESeq 2, version 1.12.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files with abundances calculated with DESeq 2

source_name: primary colon tumor

extract_protocol:
Tissue (~10 mg) was immersed in 2 mL of hypotonic buffer A [10 mM HEPES (pH 7.9), 2 mM MgCl2, and 2 mM KCl] supplemented with protease and phosphatase inhibitors (Thermo, 78441) and 40 U/mL ribonuclease inhibitor (Invitrogen, 10777-019). RNA was extracted with standard Ion Torrent protocol. The RNA concentration was measured using a Nanodrop instrument.
RNA-sequencing library was prepared from 200 ng of total RNA using Ion Total RNA-seq Kit v2 (standard Ion Torrent protocol)

tag: resection location

value: colon


title: 916.N

source_name: normal colon


title: 440.N


title: 916.PT


title: 916.MT

source_name: lymph node metastasis

value: lymph node


title: 244.PT


title: 244.N


title: Sample 5

description: neurons from post-mortem human brain

value: frontal cortex of the brain


title: 244.MT


title: 1379.PT


title: 1459.PT


title: Sample 4

description: neurons from post-mortem human brain


title: 440.MT


title: Sample 6

description: neurons from post-mortem human brain

value: Female


title: 1379.MT


title: 1175.PT


title: 1175.N


title: 1459.MT


title: 1010.PT


title: 1175.MT


title: 1010.MT


title: Sample 8

description: neurons from post-mortem human brain

value: White


title: 1379.N


title: 1319.N


title: Sample 3

description: neurons from post-mortem human brain

value: Harvard HBTRC


title: Sample 15_AB133

value: 8 weeks

tag: tissue/cell type


title: Sample 1

description: neurons from post-mortem human brain

value: Bipolar


title: 1010.N


title: s2lab_Rep2_IP

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic v. 0.3.2 with the following command "trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:205 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 2.3.3 -p 16 –very-sensitive" against the genome of Arabidopsis thaliana (TAIR10).
Filtering step: Mapped reads were sorted with with samtools v. 1.6 with the command "samtools sort -m 6G -@ 4" and the files indexed with "samtools index".
Duplicated reads were removed with sambamba markdup v. 0.6.6 and read density was scored over 10-bp non-overlapping bins and normalized to 1x genome woverage with deepTools v. 3.0.0 with the command "bamCoverage -p 8 --normalizeTo1x 120000000 -bs 10 -of bigwig"
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.

organism: Arabidopsis thaliana

source_name: 6 day-old Seedlings

growth_protocol: Arabidopsis used in this study were in the Columbia-0 (Col) ecotype and grown for 6 days on MS medium 0.9% agar without sugar.

extract_protocol:
Chromatin extraction and immunoprecipitation was carried out as in Bourbousse et al., PLoS Genetics (2012). Chromatin was extracted from Arabidopsis seedlings. 100μg of Arabidopsis chromatin was immunoprecipiated with an anti-H3K4me3 antibody (Millipore, 07-473).
The resulting DNA then was used for library preparation with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) . The ChIP libraries were sequenced in PE2x100bp mode on a HiSeq2500 Illumina machine.

treatment_protocol: Seedlings were grown under a 16h/8h (23/19°C) light/dark photoperiod (100 μmol.m−2.s−1).

tag: genotype/variation

value: s2las2lb mutant

tag: antibodies


title: s2lab_Rep1_IP


title: A2B5+ iOPC(H)_OCT4_Rep2

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Foreskin fibroblasts

growth_protocol: Fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and H9-hESCs were grown in E8 medium

extract_protocol:
H9-hESCs and A2B5+ iOPCs were cross-linked with 1% (wt/vol) formaldehyde fixation buffer, resuspended and lysed using an EZ-ChIP kit (Upstate, Millipore). To shear the cross-linked DNA, the lysates were subjected to 30 cycles of 30 seconds of sonication followed by 30 seconds of rest on ice with a Bioruptor sonicator (Diagenode, UCD-200) and incubated with protein G agarose beads and 3 μg of an anti-OCT4 antibody overnight at 4°C. After chromatin immunoprecipitation, the rest of the experiments were performed according to the manufacturer's protocols
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

value: Foreskin fibroblasts

tag: cell line

value: A2B5+ iOPCs(H)

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody cat. #


title: A2B5+ iOPC(M)_OCT4_Rep2

tag: tissue

value: A2B5+ iOPCs(M)


title: A2B5+ iOPC(M)_input_Rep1


title: s2lb_Rep1_IP

value: s2lb mutant


title: Sample 2

description: neurons from post-mortem human brain

tag: age

value: Control


title: A2B5+ iOPC(M)_input_Rep2


title: A2B5+ iOPC(H)_input_Rep3


title: s2lb_Rep2_IP


title: A2B5+ iOPC(H)_OCT4_Rep3


title: A2B5+ iOPC(M)_OCT4_Rep1


title: s2la_Rep2_IP

value: s2la mutant


title: s2lb_Rep2_input

value: input


title: WT_Rep1_IP

value: wild-type


title: s2lb_Rep1_input


title: s2lab_Rep2_input


title: s2la_Rep2_input


title: s2la_Rep1_input


title: WT_Rep2_input


title: WT_Rep2_IP


title: WT_Rep1_input


title: MORF2OX NF2

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

data_processing:
BRB-SeqTools (https://brb.nci.nih.gov/seqtools/) was used to calculate the raw counts of each gene. In detail, the RNA-seq raw reads were aligned to Arabidopsis reference genome (TAIR10) using TopHat version 2.1.1 with bowtie2-2.3.1 and gene-level raw counts data files were generated using HTSeq version 0.6.1. The raw counts were applied to Bioconductor package edgeR in R language to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) of each gene, and to identify the differentially expressed genes (DEGs).
Genome_build: Arabidopsis reference genome (TAIR10)
Supplementary_files_format_and_content: tab-delimited text files include raw counts of each gene for each sample

source_name: Whole seedling

growth_protocol: Seedling were growing under 24 h light condition with 100 µmol.m-2.s-1 light intensity at 22 °C on 1/2 Linsmaier and Skoog (LS) medium with or without 5 μM norflurazon.

extract_protocol:
Total RNA was isolated from pooled (> 100 individual plants of the same genotype) whole seedlings using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) with dsDNase treated.
500 ng total RNA of each sample was used to prepare the RNA-seq libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). Single-end sequencing was run on Illumina HiSeq 2500 sequencing machine (Illumina).

value: whole seedling

tag: treatment

value: 5 μM norflurazon

tag: treatment time

value: 5 days

tag: background ecotype

tag: genotype


title: MORF2OX(w) NF2


title: MORF2OX(w) NF1


title: Col6-3 NF1

value: wildtype


title: siPCBP2-2

city: Hefei

first: Hao

last: Wang

state: Anhui

address: 81 Meishan Road

country: China

institute: Anhui Medical University

data_processing:
Data Assessment and Quality Control  FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by  Trimmomatic (version 0.36) according to several steps:  (1)Removing adaptor sequence if reads contains;  (2)Removing low quality bases from reads 3’ to 5’ (Q < 20);  (3)Removing low quality bases from reads 5’ to 3’ (Q < 20);  (4)Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp);  (5)Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data  was used for further analysis.
Alignment with Reference Genome  Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
The expression levels are all standardized to FPKM
Functional Analysis of Differentially Expressed Genes  Functional enrichment analyses including Gene Ontology (GO) and KEGG was performed to identify which  DEGs were significantly enriched in GO terms or metabolic pathways. Gene Ontology (GO) is an international standard classification system for gene function. DEGs are mapped to the GO terms (biological functions) in the database, the number of genes in every term is calculated, and a hypergeometric test is performed to identify significantly enriched GO terms in the gene list out of the background of the reference gene list. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database is a public database of pathway data, KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways enriched in DEGs compared to a reference gene background, using the hypergeometric test. GO terms and KEGG pathway with false discovery rate (q-value) < 0.05 were considered as significantly altered.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM

source_name: Breast cancer cell line MDA-MB-231-siPCBP2

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), then the purity and quality of the total RNA were checked using UVmini-1240 (SHIMADZU, Japan). The total RNA was sent to Kangcheng Biotechnology Co. (Shanghai, China) for RNA-Seq analysis.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor was ligated to prepare for library. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were then quantified and pooled. Paired- end sequencing of the library was performed on the HiSeq XTen sequencers (Illumina, San Diego, CA).

tag: cell type

value: breast cancer cells

value: cells were transfected with PCBP2


title: gun1-9 NF1


title: gun1-9 NF2


title: Col6-3 LS1

value: no treatment


title: Col6-3 LS2


title: Col6-3 NF2


title: Con1

source_name: Breast cancer cell line MDA-MB-231, untreated

value: untreated


title: Con2


title: MORF2OX NF1


title: siPCBP2-1


title: s2la_Rep1_IP


title: Sample 19_AB2789H and AB2789M

organism:
Homo sapiens
Mus musculus

source_name: hES(WIBR)/mES

tag: strain

value: WIBR

value: human embryonic stem cells

tag: treatment/sample info.

value: Human/mouse 1:1

tag: protocol optimization parameter

value: Evaluation of doublet number


title: Sample 20_AB2790H and AB2790M

tag: tissue/cell type


title: s2lab_Rep1_input

tag: genotype/variation

value: s2las2lb mutant


title: Sample 18_AB2788H and AB2788M


title: sporadic CRC patient diagnosed over 45 years without Lynch syndrome 2

city: Madrid

first: ELISA

last: CONDE MORENO

address: Carretera de Colmenar KM9.100

department: Pathology

country: Spain

institute: Instituto Ramón y Cajal de Investigación Sanitaria, IRYCIS

description: 750ng of each RNA sample was pooled to prepare the common reference mix

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent  Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007)

source_name: embedded paraffine colon tissue

label_protocol: 750 ng total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer

extract_protocol: Total RNA enriched in miRNAs was extracted with miRNaeasy FFPE kit (Qiagen, 217504), following manufacturer´s indications

value: colon

tag: disease state

tag: tumor stage

value: IIIB

tag: tumor side

value: Left

tag: tumor grade

value: Well differentiated

source_name: embedded paraffine tissue (Pool of all the samples)


title: CRC patient with Lynch syndrome 1

value: CRC patient with Lynch syndrome

value: Moderately differentiated


title: sporadic CRC patient diagnosed under 45 years without Lynch syndrome 2

value: IIA

value: Right


title: sporadic CRC patient diagnosed under 45 years without Lynch syndrome 1


title: Sample 17_AB2787H and AB2787M

tag: cell line


title: CRC patient with Lynch syndrome 2

tag: tissue

value: Transverse


title: CRC patient with Lynch syndrome 3

tag: age


title: 1520.PT

tag: resection location


title: Non tumor colonic mucosae

value: colonic mucosae

value: Non tumor

value: Non applicable


title: 1520.MT

value: lymph node


title: A2B5+ iOPC(H)_input_Rep2

value: Foreskin fibroblasts

value: A2B5+ iOPCs(H)

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: GPS24938

city: Castanet-Tolosan

first: Laurent

last: Cauquil

address: 24 chemin de Borde Rouge

institute: INRA

description: gene expression at 49d with NF treatment

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 6.0 pmol Cy3/μg of cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25× Agilent Fragmentation Buffer and 10× Agilent Blocking Agent, following the manufacturer’s instructions. Subsequently, 25 μl of 2× Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the Rabbit Custom Gene Expression Microarrays (Agilent Technologies, design ID: 042421) for 17 hours at 65°C in a rotating Agilent hybridization oven (Agilent Technologies).

scan_protocol: Immediately after washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies), which used a scan protocol with a resolution of 3 μm and a dynamic range of 20 bits.

data_processing: The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE2_107_Sep09 protocol.

organism: Oryctolagus cuniculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared using 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA, USA) following the recommended protocol. Specific activities and cRNA yields were determined using the NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol: Not provided

value: Ileum

tag: treatment

value: no fecal pellets (NF)

tag: day


title: GPS24930

description: gene expression at 35d with FF treatment

value: fecal pellets from doe (FF)


title: GPS24929


title: GPS24935

description: gene expression at 49d with FFab treatment

value: fecal pellets from doe under antibiotics (FFab)


title: GPS24927

description: gene expression at 35d with FFab treatment


title: GPS24940


title: GPS24931

description: gene expression at 35d with NF treatment


title: Sample 7_AB125

tag: strain

tag: mouse age

value: 8 weeks

value: BM

tag: selection marker

value: Lin- cKit+ Sca1- CD34+ FcgR(low)

tag: treatment/sample info.

value: Invitrogen less DNA pol

value: Optimization of second strand synthesis


title: GPS24937

description: gene expression at 49d with FF treatment


title: GPS24922


title: Sample 12_AB130

tag: tissue/cell type

tag: protocol optimization parameter


title: GPS24926


title: GPS24928


title: GPS24939


title: GPS24919


title: GPS24936


title: GPS24932


title: GPS24925


title: GPS24934


title: GPS24921


title: GPS24918


title: GPS24917


title: GPS24910


title: GPS24913


title: GPS24916


title: GPS24911


title: GPS24920


title: GPS24912


title: GPS24909


title: GPS24908


title: GPS24899


title: GPS24900


title: GPS24903


title: GPS24914


title: GPS24901


title: GPS24895


title: GPS24902


title: GPS24898


title: GPS24892


title: GPS24907


title: GPS24894


title: Eedmz-/- Blastocyst Rep 3

first: Sundeep

last: Kalantry

address: 1241 Catherine Street

department: Human Genetics

description: Zp3:CRE was used to excise floxed exon 7 of Eed in the oocytes of the mother

data_processing:
VCFtools was used to generate in silico 129/S1 and JF1/Ms genomes
Sequencing reads were separately mapped to each of the 129/S1 and JF1/Ms in silico genomes using STAR
For allelic expression analysis, only RNA-seq reads overlapping known SNP sites that differ between the 129/S1 and JF1/Ms genomes were retained. All multi-mapping reads were excluded from the analysis. For each SNP site, reads mapping to the 129/S1 and JF1/Ms X chromosomes were counted and the proportion of reads from each X chromosome identified. Allelic expression was calculated individually for each SNP site; for genes containing multiple SNPs, the paternal-X percentage for all SNPs was averaged to calculate gene-level allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files including X-linked gene names and percent paternal allelic expression

organism: Mus musculus domesticus x M. m. molossinus

source_name: whole embryo

extract_protocol:
mRNA was extracted from individual whole embryos using the Dynabeads mRNA DIRECT Kit
Poly-A purification followed by strand-specific library preparation using Takara SMARTer Seq V4 low input kit

value: whole embryo

value: 129/S1 and JF1/Ms (hybrid)

tag: developmental stage

value: embryonic day 3.5

tag: genotype

value: Eedmz-/-


title: GPS24875


title: Eedmz-/- Blastocyst Rep 1


title: Eedm-/- Blastocyst Rep 5

value: Eedm-/-;z-/fl


title: GPS24893


title: GPS24891


title: sporadic CRC patient diagnosed over 45 years without Lynch syndrome 1

value: colon

tag: disease state

tag: tumor stage

value: IVA

tag: tumor side

value: Left

tag: tumor grade

value: Well differentiated


title: GPS24886

tag: tissue

value: Ileum

value: no fecal pellets (NF)


title: GPS24881

value: fecal pellets from doe under antibiotics (FFab)


title: GPS24884

value: fecal pellets from doe (FF)


title: GPS24877


title: Eedfl/fl Blastocyst Rep 2

value: Eedfl/fl


title: GPS24872


title: GPS24889


title: GPS24883


title: GPS24890


title: GPS24874


title: GPS24882


title: GPS24880


title: GPS24871


title: GPS24876


title: GPS24873


title: GPS24885


title: Eedfl/fl Blastocyst Rep 1


title: HSUR1 m20 replicate 3

city: New Haven

first: Paulina

last: Pawlica

state: CT

address: 295 Congress Avenue, BCMM Room 131

department: MBB

institute: Yale University

data_processing:
The reads were trimmed of adaptors using fastx_clipper (FASTX-Toolkit; http://hannonlab.cshl.edu/fastx_toolkit) and filtered using fastq_quality_filter (FASTX-Toolkit) with parameters -q 20 and -p 80.
Reads shorter than 35 bp were aligned to mature miRNAs sequences from miRbase_v21 using STAR (Dobin et al., 2013) with settings: --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 14 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1.
SAMtools (Dobin et al., 2013) were used to count aligned reads.
Genome_build: miRbase_v21
Supplementary_files_format_and_content: raw counts table

source_name: BJAB_HSUR1 m20

growth_protocol: BJAB cells were grown in RPMI supplemented with 10% fetal bovine serum, 5% L-glutamine and 1% pen/strep.

extract_protocol:
Small RNAs were gel isolated.
NEBNext® Multiplex Small RNA Library Prep for Illumina (NEB) was used according to manufacturer’s guide.

treatment_protocol: Cells were transduced with HSUR1 WT and its mutants using lentiviral vectors.

tag: cell line

value: BJAB cells

tag: genotype/variation

value: HSUR1 m20

tag: molecule subtype

value: small RNA


title: HSUR1 m30 replicate 2

source_name: BJAB_HSUR1 m30

value: HSUR1 m30


title: HSUR1 m30 replicate 3


title: HSUR1 m20 replicate 1


title: HSUR1 m30 replicate 1


title: HSUR1 m4 replicate 2

source_name: BJAB_HSUR1 m4

value: HSUR1 m4


title: HSUR1 m4 replicate 3


title: HSUR1 m20 replicate 2


title: HSUR1 WT replicate 3

source_name: BJAB_HSUR1 WT

value: HSUR1 WT


title: HSUR1 WT replicate 1


title: empty vector replicate 2

source_name: BJAB_empty vector

value: empty vector


title: HSUR1 WT replicate 2


title: HSUR1 m4 replicate 1


title: empty vector replicate 3


title: MB231.3D.Sample.3 (RNA-seq)

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed using systemPipeR bioconductor package,
rsem-calculate-expression --star --star-gzipped-read-file --output-genome-bam -p 48 --paired-end
Genome_build: hg19
Supplementary_files_format_and_content: expected_count, TPM, FPKM

source_name: Breast Cancer Cell Line

growth_protocol: A549 and MDA-MB-231 cells were culture in 2D culture in DMEM+10% FBS and in Matrigels based 3D culture in DMEM+10% FBS.

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent in 2D culture and on day 4 in 3D culture using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: No treatment.

value: Breast Cancer Cell Line MDA-MB-231

value: Breast

tag: growth protocol


title: MB231.3D.Sample.2 (RNA-seq)


title: Eedmz-/- Blastocyst Rep 2

institute: University of Michigan

value: whole embryo

tag: strain

value: 129/S1 and JF1/Ms (hybrid)

value: embryonic day 3.5

value: Eedmz-/-


title: MB231.3D.Sample.1 (RNA-seq)


title: MB231.2D.Sample.3 (RNA-seq)


title: empty vector replicate 1


title: MB231.2D.Sample.2 (RNA-seq)


title: MB231.2D.Sample.1 (RNA-seq)


title: A549.3D.Sample.3 (RNA-seq)

source_name: Lung Cancer Cell Line

value: Lung Cancer Cell Line A549

value: Lung


title: A549.3D.Sample.1 (RNA-seq)


title: A549.3D.Sample.2 (RNA-seq)


title: A549.2D.Sample.3 (RNA-seq)


title: LA-NPC_NM17

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: Gene expression data from LA-NPC which did not develop distant metastasis after treatment

hyb_protocol: Total RNA was hybridized to Affymetrix Human Gene 2.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: Raw data were normalized using 'oligo package' in R language with Robust Multi-array Analysis (RMA). We used Bayes statistics implemented by eBayes in 'limma package' to compute significant differentially expressed probes between metastatic and non-metastatic groups. Since RNA from FFPE samples are highly and randomly fragmented, here we impose Fisher's exact test to verify if a transcript is indeed significant differentially expressed. Differential expressed transcripts were characterized according to the criterion of empirical Fold change >1.5 and empirical Bayes test P-value <0.05.  Transcript-level processed data with Fisher's test are available on the series record in the file transcriptionlevel_fisher_lima_nordata_limma.xlsx.  Probe-set level data are available in the sample table and in the file  nor_data_rma_probelevel.csv which includes statistics.

label_protocol: Total RNA were amplified with the Ovation FFPE WTA System (NuGEN), the Encore Biotin Module (NuGEN) was used for fragmentation and labeling.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Germany).

value: Nasopharyngeal carcinoma

tag: metastasis status

value: no


title: LA-NPC_NM23


title: LA-NPC_NM15


title: LA-NPC_NM19


title: LA-NPC_NM21


title: LA-NPC_NM24


title: LA-NPC_NM16


title: A549.2D.Sample.2 (RNA-seq)


title: LA-NPC_NM9


title: LA-NPC_NM12


title: A549.2D.Sample.1 (RNA-seq)


title: LA-NPC_NM14


title: LA-NPC_NM11


title: LA-NPC_NM13


title: LA-NPC_NM7


title: LA-NPC_NM10


title: MB231.3D.Sample.2 (BS-seq)

description:
Cytosine methylation
MB231.3D.2

data_processing:
trim_galore using standard settings
Bismark with Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: coverage files

growth_protocol: MDA-MB-231 cells were culture in 2D culture in DMEM+10% FBS and in Matrigels based 3D culture in DMEM+10% FBS.

extract_protocol:
Total cell DNA was extracted when cells were ~80% confluent in 2D culture and on day 4 in 3D culture using TRIZOL.
Bisulfite treatment of genomic DNA is performed using the Zymo EZ  DNA Methylation Lightning Kit1. The libraries were prepared using TruSeq Methyl Capture EPIC Library Prep Kit.


title: LA-NPC_NM4


title: LA-NPC_NM20


title: LA-NPC_M23

description: Gene expression data from LA-NPC which developed diatant metastasis after treatment

value: yes


title: LA-NPC_NM18


title: LA-NPC_M24


title: MB231.3D.Sample.1 (BS-seq)

description:
Cytosine methylation
MB231.3D.1


title: LA-NPC_NM22


title: LA-NPC_NM5


title: LA-NPC_NM2


title: MB231.2D.Sample.1 (BS-seq)

description:
Cytosine methylation
MB231.2D.1


title: LA-NPC_NM1


title: LA-NPC_M20


title: LA-NPC_M21


title: LA-NPC_NM6


title: LA-NPC_NM8


title: LA-NPC_M22


title: H9hESCs_input

source_name: Human embryonic stem cells (H9)

value: Human embryonic stem cells

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #


title: LA-NPC_M16


title: A2B5+ iOPC(H)_input_Rep1

value: Foreskin fibroblasts

value: A2B5+ iOPCs(H)


title: LA-NPC_M19


title: Eedm-/- Blastocyst Rep 4

city: Ann Arbor

value: Eedm-/-;z-/fl


title: LA-NPC_M14


title: Eedm-/- Blastocyst Rep 3


title: Eedm-/- Blastocyst Rep 2


title: Eedm-/- Blastocyst Rep 1


title: LA-NPC_NM3


title: CFTRneg_Treated_3

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

description: Generated using CRISPR/Cas9-mediated mutagenesis of CFTR

data_processing:
Trimming and filtering of the reads to remove adaptor sequences and low-quality nucleotides were performed using Trimmomatic (v 0.36). 100bp samples were trimmed to 75bp before continuing with the rest of the analysis.
The filtered reads were aligned to the UCSC human genome hg19 as a reference using Bowtie2 (v 2.3.4.3) and Tophat (v 2.1.1). Assembly of transcriptomes and quantification of their expression was performed using Cufflinks (v 2.2.1).  Expression levels were expressed as fragments per kilobase of exon per million fragments mapped (FPKM).
Statistical significance in differential gene expression between groups was determined with Cuffdiff (v 2.2.1).  Both p and q values were determined and defined as uncorrected p-value of the test statistic and FDR-adjusted p-value of test-statistic, respectively.
Data were further analyzed and visualized using CummeRbund run under the R package (v 3.4.4)
Hierarchical clustering (heat map) of genes with differential expression was generated using Complete Linkage as the clustering method, Euclidian distance as the similarity measure, and Z-Score as normalization with TIBCO Spotfire Software (Palo Alto, CA). Pathway analysis was done using Gene Set Enrichment Analysis (GSEA) (Broad Institute, software.broadinstitute.org/gsea), a computational method that determines statistical significance of a priori defined set of genes between two groups. The Hallmark gene set from the Molecular Signature Database (MSigDB) collection was used to explore overrepresented pathways. It comprises of 50 hallmarks condensed from over 4,000 overlapping gene sets from v4.0 MSigDB collections C1 through C6.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file for each sample including FPKM values and locus

source_name: Caco2 cells

growth_protocol: Caco-2 cells obtained from the American Type Culture Collection (ATCC) were maintained in Eagle’s minimum essential medium with 10% FBS, 1% glutamine, and 1% penicillin-streptomycin. Cells were cultured at 37°C in an atmosphere of 95% O2 - 5% CO2

extract_protocol:
Total RNA was harvested using RNAeasy kit per manufacturer instructions, Qiagen Inc, Valencia, CA)
RNA-Seq libraries were generated using TruSeq stranded Total RNA Ribo-Zero human gold kit (Illumina, San Diego, CA) and the quality of resulting libraries was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). Sequencing was carried out using either an Illumina HiSeq 2500 Rapid Run flowcell – 2x100bp run or an Illumina NextSeq 550 HO - 2x75bp run, as indicated below.

treatment_protocol: Cells were exposed to 100ng/ml TNFa for 2 hours prior to harvesting RNA for RT PCR and RNAseq

value: Colonic adenocarcinoma-derived cell line

value: CFTR null

tag: clone

tag: treatment

value: 100ng/ml TNFa for 2 hours


title: LA-NPC_M18


title: MB231.2D.Sample.2 (BS-seq)

city: Spokane

description:
Cytosine methylation
MB231.2D.2

value: Breast Cancer Cell Line MDA-MB-231

value: Breast


title: LA-NPC_M17


title: LA-NPC_M15


title: Eed-/- Blastocyst Rep 4

value: whole embryo

value: 129/S1 and JF1/Ms (hybrid)

tag: developmental stage

tag: genotype

value: Eed-/-


title: LA-NPC_M9


title: LA-NPC_M13


title: LA-NPC_M8


title: Eed-/- Blastocyst Rep 3

value: embryonic day 3.5


title: Eed-/- Blastocyst Rep 2


title: CFTRneg_Treated_1


title: Eed-/- Blastocyst Rep 1


title: LA-NPC_M2


title: LA-NPC_M10


title: LA-NPC_M12


title: CFTRneg_Nontreated_3


title: Eedfl/- Blastocyst Rep 4

value: Eedfl/-


title: Eedfl/- Blastocyst Rep 3


title: Eedfl/- Blastocyst Rep 2


title: Eedfl/- Blastocyst Rep 1


title: LA-NPC_M6

value: Nasopharyngeal carcinoma


title: LA-NPC_M11


title: LA-NPC_M1


title: LA-NPC_M5


title: LA-NPC_M3


title: LA-NPC_M7


title: CFTRneg_Nontreated_2


title: CFTRpos_Treated_2

value: NonCF


title: CFTRpos_Treated_3


title: H9hESCs_OCT4

value: Santa Cruz Biotechnology


title: CFTRpos_Treated_1


title: LA-NPC_M4

value: yes


title: CFTRpos_Nontreated_3


title: CFTRneg_Treated_2


title: Rhode Island Red-RIR_W46 [reanalyzed]

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

institute: China Agricultural University

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 array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

label: Biotin

organism: Gallus gallus

source_name: Rhode Island Red

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: chickens were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Blood


title: Rhode Island Red-RIR_W43 [reanalyzed]


title: Rhode Island Red-RIR_W49 [reanalyzed]


title: Rhode Island Red-RIR_W48 [reanalyzed]


title: Rhode Island Red-RIR_W42 [reanalyzed]


title: Rhode Island Red-RIR_W47 [reanalyzed]


title: Rhode Island Red-RIR_W50 [reanalyzed]


title: Rhode Island Red-RIR_W45 [reanalyzed]


title: Rhode Island Red-RIR_W44 [reanalyzed]


title: Rhode Island Red-RIR_W41 [reanalyzed]


title: CFTRpos_Nontreated_2


title: Rhode Island Red-RIR_W40 [reanalyzed]


title: Rhode Island Red-RIR_W39 [reanalyzed]


title: CFTRpos_Nontreated_1


title: cll_vs_wce_bam

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

data_processing:
ChIP-seq data were processed according to the ENCODE Histone ChIP-seq Data Standards and Processing Pipeline (https://www.encodeproject.org/chip-seq/histone/). Raw reads were mapped to the Human genome GRCh37 assembly using Burrows-Wheeler Aligner (BWA v0.7.17). Duplicate reads were removed using Picard (https://broadinstitute.github.io/picard/) and bigwig files were created for visualization. Peaks were identified with Macs2 (v2.0.10) with a q-value threshold of 0.01 and de novo motif enrichment analyses were performed using Homer against JASPAR CORE database. Peaks overlapping with Satellite repeat regions and Encode Blacklist were discarded. All ChIP-seq reads were normalized and displayed as read counts per million mapped reads.
Raw reads were mapped to the human genome GRCh37 using STAR (v2.5.2a) aligner49. We used several QC metrics for the RNA-seq library, including intron–exon ratio, intragenic reads fraction and GC bias. We quantified exon and gene expression using Salmon50 against the Homo sapiens transcriptome GRCh37.
Genome_build: GRCh37

source_name: CLL

growth_protocol: Human subjects, sample collection and genotyping. The study was approved by the local ethics committee and by the Institutional Review Board (IRB) and conducted in accordance to the Declaration of Helsinki protocol. Blood samples were collected in EDTA blood collection tubes (BD Biosciences) from patient and healthy adult volunteers enrolled on clinical research protocols at the Dana-Faber/Harvard Cancer Center (DF/HCC), Memorial Sloan Kettering Cancer Center (MSKCC), and NewYork-Presbyterian/Weill Cornell Medical Center (NYP/WCMC). We note that the IRB does not permit collection of demographic information of healthy donors. The diagnosis of CLL according to World Health Organization (WHO) criteria was confirmed in all cases by flow cytometry, or by lymph node or bone marrow biopsy. Peripheral blood mononuclear cells (PBMCs) from normal donors and patients were isolated by Ficoll-Paque Plus (GE Healthcare) density gradient centrifugation. PBMCs were cryopreserved in 50%FBS/40%RPMI/10% DMSO and stored in vapor-phase liquid nitrogen until the time of analysis. Informed consent on DFCI and WCM IRB-approved protocols for genomic sequencing of patients’ samples was obtained prior to the initiation of sequencing studies. Immunoglobulin heavy-chain variable (IGHV) homology (unmutated was defined as greater than or equal to 98% homology to the closest germline match) were determined44. Cytogenetics were primarily evaluated by FISH analysis for the most common CLL abnormalities [del(13q), trisomy 12, del(11q), del(17p), del(6p)]

extract_protocol:
A minimum of 2 million purified human cells were used. Briefly, cells were fixed in a 1% methanol-free formaldehyde solution and then resuspended in sodium dodecyl sulfate (SDS) lysis buffer. Lysates were sonicated in an E220 focused-ultrasonicator (Covaris, Woburn, MA) to a desired fragment size distribution of 100–500 base pairs. Immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells. ChIP assays were processed on an SX-8G IP-STAR Compact Automated System (Diagenode, Denville, NJ) using a direct ChIP protocol as previously described. Eluted chromatin fragments were then de-crosslinked and the DNA fragments purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adaptors (Illumina) according to the manufacturer’s protocol on an SX-8G IP-STAR Compact Automated System (Diagenode). Phusion High-Fidelity DNA Polymerase (New England Biolabs) and TruSeq PCR Primers (Illumina, San Diego, CA) were used to amplify the libraries, which were then purified to remove adaptor dimers using AMPure XP beads and multiplexed on the HiSeq 2000 (Illumina, San Diego, CA).
dodecyl sulfate (SDS) lysis buffer. Lysates were sonicated in an E220 focused-ultrasonicator (Covaris, Woburn, MA) to a desired fragment size distribution of 100–500 base pairs. Immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells. ChIP assays were processed on an SX-8G IP-STAR Compact Automated System (Diagenode, Denville, NJ) using a direct ChIP protocol as previously described45. Eluted chromatin fragments were then de-crosslinked and the DNA fragments purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adaptors (Illumina) according to the manufacturer’s protocol on an SX-8G IP-STAR Compact Automated System (Diagenode). Phusion High-Fidelity DNA Polymerase (New England Biolabs) and TruSeq PCR Primers (Illumina, San Diego, CA) were used to amplify the libraries, which were then purified to remove adaptor dimers using AMPure XP beads and multiplexed on the HiSeq 2000 (Illumina, San Diego, CA). RNA was extracted using Qiagen (Hilden, Germany) RNeasy columns according to the manufacturer’s instructions. Subsequently, 500 ng of total RNA was used for polyA selection and TruSeq library preparation according to the instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 125 bp paired-end mode, using the TruSeq SBS Kit v.3 (Illumina, San Diego, CA). An average of 75 million paired reads was generated per sample.

treatment_protocol: Untreated

value: Peripheral Blood

tag: cell type

value: CLL IGHV mutated

tag: antibody

value: wce


title: WT_H3K4me3_BR1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic v. 0.3.6 with the following command "trimmomatic-0.36.jar  SE -threads 24 -phred33 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 -p 18 --very-sensitive" against the genome of Arabidopsis thaliana (TAIR10).
Filtering step: Mapped reads were sorted with with samtools v. 1.6 with the command "samtools sort -m 6G -@ 4" and the files indexed with "samtools index".
Duplicate filtering: duplicated reads were removed with sambamba markdup v. 0.6.6 with the command "sambamba markdup -r "
Bigwig generation: read density was scored over 10-bp non-overlapping bins and normalized to 1x genome woverage with deepTools v. 3.0.0 with the command "bamCoverage -p 8 --normalizeTo1x 120000000 -bs 10 -of bigwig"
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.

source_name: 5 day-old Seedlings

extract_protocol:
Chromatin extraction and immunoprecipitation was carried out as in Bourbousse et al., PLoS Genetics (2012). Chromatin was extracted from Arabidopsis seedlings. 100μg of Arabidopsis chromatin was immunoprecipiated with an anti-H3K4me3 antibody (Millipore, 07-473).
The resulting DNA then was used for library preparation with NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) . The ChIP libraries were sequenced in SE75 mode on a NextSeq500 Illumina machine.

value: wild-type

value: anti-H3K4me3 (Millipore, 07-473)


title: HUB1_H3K4me3_BR1

value: hub1-3 mutant


title: WT_H3K4me3_BR2


title: cll_vs_h3k9me3_bam

value: CLL IGHV unmutated


title: HUB1_Input_BR2


title: Rhode Island Red-RIR_W38 [reanalyzed]


title: Rhode Island Red-RIR_W37 [reanalyzed]


title: HUB1_H3K4me3_BR2


title: A2B5+ iOPC(H)_OCT4_Rep1

source_name: Foreskin fibroblasts

value: Foreskin fibroblasts

value: A2B5+ iOPCs(H)


title: cll_vs_h3k36me3_bam


title: Rhode Island Red-RIR_W36 [reanalyzed]


title: WT_Input_BR2


title: Rhode Island Red-RIR_W33 [reanalyzed]


title: Rhode Island Red-RIR_W34 [reanalyzed]


title: cll_vs_h3k27me3_bam


title: WT_Input_BR1


title: cll_ho_wce_bam


title: cll_vs_h3k27ac_bam


title: Rhode Island Red-RIR_W32 [reanalyzed]


title: cll_ho_h3k4me3_bam


title: Rhode Island Red-RIR_W30 [reanalyzed]


title: cll_ho_h3k36me3_bam


title: Rhode Island Red-RIR_W31 [reanalyzed]


title: gr2.ID8.17.g_08_C2

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: late  stage tumor tissue from mouse 7

data_processing: TMM normalization and voom transform, excluding genes with very low signals

source_name: ID8 late tumor

growth_protocol: 5x106 ID8 Luc expressing cells were injected intraperitoneally in C57/BL6 mice. Tumor were harvested at 3 weeks (early-stage) or 6 weeks (late-stage) post inoculation.

extract_protocol: Total RNA was isolated from 100 to 500 mg of frozen tissue with TRIzol reagent (Invitrogen, Carlsbad, CA). Samples were treated with RNase-free DNase (Invitrogen) before eluted total RNA was obtained

tag: development stage

value: late-stage tumor tissue


title: gr2.ID8.18.g_09_C2

description: late stage tumor tissue from mouse 8


title: cll_ho_h3k4me1_bam

tag: tissue


title: HUB1_Input_BR1


title: gr2.ID8.16.g_07_C2

description: late  stage tumor tissue from mouse 6


title: cll_ho_h3k9me3_bam


title: cll_vs_h3k4me3_bam


title: Rhode Island Red-RIR_W29 [reanalyzed]


title: gr2.ID8.14.g_05_C2

description: late  stage tumor tissue from mouse 5


title: CFTRneg_Nontreated_1

value: Colonic adenocarcinoma-derived cell line

value: CFTR null


title: cll_ho_h3k27ac_bam


title: Rhode Island Red-RIR_W28 [reanalyzed]


title: gr2.ID8.13.g_09_C1

description: late  stage tumor tissue from mouse 4


title: cll_ho_h3k27me3_bam


title: Rhode Island Red-RIR_W27 [reanalyzed]


title: gr2.ID8.12.g_08_C1

description: late  stage tumor tissue from mouse 3


title: gr2.ID8.15.g_06_C2

description: late  stage tumor tissue from mouse 5


title: Rhode Island Red-RIR_W35 [reanalyzed]


title: cll_7528t_h3k27me3_bam


title: Rhode Island Red-RIR_W26 [reanalyzed]


title: gr2.ID8.11.g_07_C1

description: late stage tumor tissue from mouse 2


title: gr2.ID8.10.g_06_C1

description: late stage tumor tissue from mouse 1


title: gr1.ID8.09.g_04_C2

description: early stage tumor tissue from mouse 8

source_name: ID8 early tumor

value: early-stage tumor tissue


title: Rhode Island Red-RIR_W25 [reanalyzed]


title: cll_5268t_h3k27me3_bam


title: Mouse 14

city: Chapel Hill

first: Marcus

middle: Luis

last: Basiri

state: NC

address: 115 Mason Farm Road

institute: UNC Chapel Hill

description:
internal sample name: BE
sequencing pool: 1
Drop-seq

data_processing:
Demultiplexing was performed with 1 mismatch allowed using Illumina bcl2fastq v2.18.0.12.
R1 contains cell barcode (bases 1-12) and UMI (bases 13-20).
Read 2 was aligned to mm10 using STAR v2.4.2a with 72 GB of RAM and 16 threads.
Aligned reads were tagged with mate-pair UMI and cell barcodes using Drop-seq_tools v1.12 and Picard Tools v2.2.4.
Aligned exonic reads were tagged with a mapped gene name.
A count expression matrix was made by counting UMIs for each gene for each cell barcode.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: paired-end fastq files and processed  gene count expression matrices are provided for each sample.

source_name: lateral hypothalamus tissue punch

growth_protocol: Animals were housed on a reverse 12 hr./12 hr. day/light cycle with ad libitum access to water and high fat diet or taste-matched control chow.

extract_protocol:
Single cell suspensions were prepared from lateral hypothalamic area tissue punches and processed through the standard dropseq protocol to generate single-cell cDNA libraries attached to barcoded beads. Beads were counted, PCR amplified and indexed at the 3' end for sequencing using a modified Nextera XT protocol. Two sequencing pools were made and sequenced on separate lanes of an Illumina HiSeq 2500 in rapid-run mode using paired-end sequencing with 20x8x50 cycles.
Drop-seq

value: lateral hypothalamus

value: wildtype

tag: Sex

value: male

tag: group

value: high fat diet


title: Rhode Island Red-RIR_W24 [reanalyzed]

value: Blood


title: Mouse 13

description:
internal sample name: BD
sequencing pool: 1
Drop-seq

value: control


title: cll_5268t_h3k27ac_bam

value: Peripheral Blood

value: CLL IGHV mutated


title: gr1.ID8.08.g_03_C2

description: early stage tumor tissue from mouse 7


title: Rhode Island Red-RIR_W23 [reanalyzed]


title: Mouse 11

description:
internal sample name: BB
sequencing pool: 2
Drop-seq


title: Mouse 12

description:
internal sample name: BC
sequencing pool: 2
Drop-seq


title: Rhode Island Red-RIR_W21 [reanalyzed]


title: gr1.ID8.07.g_02_C2

description: early stage tumor tissue from mouse 6


title: Rhode Island Red-RIR_W22 [reanalyzed]


title: gr1.ID8.06.g_01_C2

description: early stage tumor tissue from mouse 5


title: Mouse 10

description:
internal sample name: BA
sequencing pool: 2
Drop-seq


title: gr1.ID8.05.g_05_C1

description: early stage tumor tissue from mouse 5


title: Mouse 9

description:
internal sample name: AZ
sequencing pool: 2
Drop-seq


title: cll_7528t_h3k27ac_bam


title: cll_51_h3k4me3_bam


title: gr1.ID8.04.g_04_C1

description: early stage tumor tissue from mouse 4


title: cll_51_h3k27me3_bam


title: gr1.ID8.03.g_03_C1

description: early stage tumor tissue from mouse 3


title: Rhode Island Red-RIR_W19 [reanalyzed]


title: cll_51_wce_bam

value: wce


title: cll_51_h3k27ac_bam


title: Rhode Island Red-RIR_W20 [reanalyzed]


title: Mouse 8

description:
internal sample name: AS
sequencing pool: 1
Drop-seq


title: cll_4605t_h3k27me3_bam


title: Mouse 7

description:
internal sample name: AQ
sequencing pool: 2
Drop-seq


title: Rhode Island Red-RIR_W17 [reanalyzed]


title: cll_4605t_h3k27ac_bam


title: Rhode Island Red-RIR_W16 [reanalyzed]


title: cll_32545t_h3k27me3_bam


title: gr1.ID8.01.g_01_C1

description: early stage tumor tissue from mouse 1


title: Rhode Island Red-RIR_W15 [reanalyzed]


title: s2lb_rep1

data_processing:
Read Filtering and Mapping: RNA sequencing data were aligned to TAIR10 reference genome using STAR v.2.5.4b with the following configurations "--sjdbGTFfile Araport11_GFF3_genes_transposons.201606.gtf --sjdbOverhang 100 --outSAMstrandField intronMotif --quantMode GeneCounts --outSAMtype SortedByCoordinate --outFilterIntronMotifs RemoveNoncanonical"
RNA-seq Analysis: Raw read counts were based on Araport11 gene models. Normalization of read counts and differential expression analysis were performed using DESeq2.
Genome_build: TAIR10

source_name: 6 day-old

extract_protocol:
Total RNAs from ~12 seedlings were extracted using the RNEasy MiniPrep kit (Qiagen). 1µg of RNA was used for library preparation.
The resulting cDNA then was used for strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina) NextSeq High kit. The RNA libraries were sequenced in SE50 mode on a HiSeq 1500 machine.


title: Mouse 5

description:
internal sample name: AO
sequencing pool: 1
Drop-seq


title: WT_rep2

value: wild type


title: cll_253_wce_bam

value: CLL IGHV unmutated


title: Mouse 3

description:
internal sample name: AL
sequencing pool: 1
Drop-seq


title: Rhode Island Red-RIR_W14 [reanalyzed]


title: cll_253_h3k4me3_bam


title: Rhode Island Red-RIR_W13 [reanalyzed]


title: Rhode Island Red-RIR_W12 [reanalyzed]


title: IP-antiGFP-S2LB_GFP_hub1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic v. 0.3.6 with the following command  java -jar trimmomatic-0.36.jar PE -threads 24 -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 -p 24 --very-sensitive" against the genome of Arabidopsis thaliana (TAIR10).
Filtering step: Mapped reads were sorted with with samtools v. 1.6 with the command "samtools sort -m 20G " and indexed with "samtools index".
Duplicate filtering: duplicated reads were removed with sambamba markdup v. 0.6.6 with the command "sambamba markdup -r "
Bigwig generation: read density was scored over 10-bp non-overlapping bins and normalized to 1x genome woverage with deepTools v. 3.0.0 with the command "bamCoverage -p 8 -bs 100 --normalizeTo1x 120000000 -of bigwig --extendReads  "
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.

extract_protocol:
Chromatin extraction and immunoprecipitation was carried out as in Bourbousse et al., PLoS Genetics (2012) using an additional crosslinking step with EGS. Chromatin was extracted from Arabidopsis seedlings. 100μg of Arabidopsis chromatin was immunoprecipiated with an anti-H3K4me3 antibody (Millipore, 07-473).
The resulting DNA then was used for library preparation with NextSeq High kit . The ChIP libraries were sequenced in SE50 mode on a NextSeq High machine.

tag: genotype/variation

value: anti-GFP


title: Mouse 1

description:
internal sample name: AJ
sequencing pool: 1
Drop-seq


title: cll_253_h3k27me3_bam


title: cll_253_h3k4me1_bam


title: IP-antiGFP-S2LB_GFP


title: WT_rep1


title: Rhode Island Red-RIR_W10 [reanalyzed]


title: Rhode Island Red-RIR_W11 [reanalyzed]


title: gr1.ID8.02.g_02_C1

description: early stage tumor tissue from mouse 2


title: cll_253_h3k27ac_bam


title: IP-antiGFP-WT

value: wild-type


title: s2lb_rep2


title: Rhode Island Red-RIR_W9 [reanalyzed]


title: cll_32545t_h3k27ac_bam


title: KO cell Ploy (I:C) treated 3

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

description: 10 ug/ml poly(I:C)_6 hr

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Mus musculus GRCm38.p4 genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: connective tissue - MEFs

growth_protocol: The  β-actin−/− MEFs (KO) from Dr. Christophe Ampe, University of Gent, Belgium, were cultured in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin (all from Millipore-Sigma), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: MEFs were staimulated by 10 ug/ml Poly(dA:dT) (AT treatment) or Poly(I:C) (IC treatment) using Lipofectamine 2000 (Invitrogen) as transfection regaent in Opti-MEM medium for 6 hours. Mock groups were treated only with transfection regaent.

value: MEFs

value: BALB/c

tag: age

value: 10.5 day old embryos

value: beta-actin knockout

value: 10 ug/ml poly(I:C)_6 hr


title: Mouse 4

description:
internal sample name: AN
sequencing pool: 2
Drop-seq

value: lateral hypothalamus

tag: strain

value: wildtype


title: IP-antimyc-SDG2

value: anti-myc


title: KO cell Ploy (I:C) treated 2

description: 10 ug/ml poly(I:C)_6 hr


title: Mouse 6

description:
internal sample name: AP
sequencing pool: 1
Drop-seq

value: male

value: high fat diet


title: Rhode Island Red-RIR_W7 [reanalyzed]

value: Blood


title: cll_248_h3k4me3_bam

value: Peripheral Blood


title: cll_248_h3k27me3_bam


title: inputWT


title: Rhode Island Red-RIR_W5 [reanalyzed]


title: KO cell Ploy (dA-dT) treated 2

description: 10 ug/ml poly(dA:dT)_6 hr

value: 10 ug/ml poly(dA:dT)_6 hr


title: KO cell Ploy (dA-dT) treated 3

description: 10 ug/ml poly(dA:dT)_6 hr


title: 4h3k4me3_ip (rep 4)

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
s_4h3k4me3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.

data_processing:
Image analysis was performed with Illumina RTA 1.18.61. Basecalling was performed with Illumina bcl2fastq 1.8.3.
Primary analysis pipeline was run with CASAVA 1.8.2.
Reads were aligned to sacCer3 from UCSC using bowtie2 version 2.1.0 with -k 1.
Data was read into R 3.1.0 for visualization and analysis.
rpm (reads per million) normalized bigWig files were generated in R by taking the running mean (101-base window) of the reads per million mapped reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: *.rpm.smoothed.101.bw: BigWig format files of 101-base smoothed rpm values.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown in 200 ml YPD media at 30°C until OD600 of 0.5-0.7.

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 Illumina HiSeq 2500 following the manufacturer's protocols.

tag: strain/background

value: H3K4me3 (Millipore, 07-473)


title: Rhode Island Red-RIR_W4 [reanalyzed]


title: cll_242_wce_bam

value: CLL IGHV mutated

value: wce


title: 3h3k4me3_ip (rep 3)

description:
s_3h3k4me3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.

tag: chip antibody


title: KO cell Mock sample 3

description: Transfection reagent alone_6 hr

value: Transfection reagent alone_6 hr


title: Mouse 2

description:
internal sample name: AK
sequencing pool: 1
Drop-seq


title: Rhode Island Red-RIR_W3 [reanalyzed]


title: cll_248_wce_bam

value: CLL IGHV unmutated


title: KO cell Mock sample 2

description: Transfection reagent alone_6 hr

value: MEFs

value: BALB/c


title: 1h3k4me3_ip (rep 1)

description:
s_1h3k4me3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.


title: cll_242_h3k27me3_bam


title: cll_242_h3k4me3_bam


title: KO cell Ploy (I:C) treated 1

description: 10 ug/ml poly(I:C)_6 hr

value: 10.5 day old embryos

value: beta-actin knockout


title: Rhode Island Red-RIR_W2 [reanalyzed]


title: KO cell Ploy (dA-dT) treated 1

description: 10 ug/ml poly(dA:dT)_6 hr


title: Rhode Island Red-RIR_W1 [reanalyzed]


title: Rhode Island Red-RIR_R48 [reanalyzed]


title: KO cell Mock sample 1

description: Transfection reagent alone_6 hr


title: NMuMG RNA-seq PBKD low glucose replicate 3

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

data_processing:
RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using HISAT2 in paired-end mode. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed using edgeR with a FDR threshold of 0.05. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for HK2. mm10 for NmuMG.
Supplementary_files_format_and_content: For RNA-seq, the raw counts matrix is provided as a tab-delimted text file. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.

source_name: NMuMG cells

growth_protocol: HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stress treatments were performed immediately prior to RNA extraction. For peroxide stress, cells were treated with media containing 200 µM H2O2 for two hours. For low-glucose stress, cell media was replaced with glucose-free media for six hours.

value: Lentiviral transfection of shPBRM1 with low glucose stress


title: Rhode Island Red-RIR_W6 [reanalyzed]


title: IP-antimyc-WT

city: Paris

first: Lorenzo

last: Concia

address: 46 Rue d'Ulm

institute: École Normale Supérieure

value: wild-type


title: cll_22526t_h3k27me3_bam


title: NMuMG RNA-seq PBKD low glucose replicate 2


title: Rhode Island Red-RIR_R47 [reanalyzed]


title: cll_248_h3k27ac_bam


title: 2h3_ip (rep 2)

description:
s_2h3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.

value: H3 (Abcam, ab1791)


title: Rhode Island Red-RIR_R46 [reanalyzed]


title: 1h3_ip (rep 1)

description:
s_1h3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.


title: 4h3_ip (rep 4)

description:
s_4h3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.


title: cll_242_h3k27ac_bam


title: Rhode Island Red-RIR_R45 [reanalyzed]


title: cll_21626t_h3k27me3_bam


title: NMuMG RNA-seq vector low glucose replicate 2

value: Lentiviral transfection of empty vector with low glucose stress


title: Set1_input


title: NMuMG RNA-seq PBKD low glucose replicate 1


title: Set1_ip

value: Anti-FLAG M2 (Sigma-Aldrich, F1804-1MG)


title: Rhode Island Red-RIR_R44 [reanalyzed]

value: Blood


title: cll_20792t_h3k27ac_bam

value: Peripheral Blood


title: NMuMG RNA-seq vector low glucose replicate 1


title: Rhode Island Red-RIR_R42 [reanalyzed]


title: NMuMG RNA-seq vector low glucose replicate 3


title: Rhode Island Red-RIR_R43 [reanalyzed]


title: 3h3_ip (rep 3)

description:
s_3h3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.


title: 2h3k4me3_ip (rep 2)

description:
s_2h3k4me3_ip
Since the final results are the ratio of H3K4me3/H3, there is no Input samples for the H3 and H3K4me3 IP samples.


title: wt_input


title: cll_20788t_h3k27me3_bam


title: cll_20788t_h3k27ac_bam


title: NMuMG RNA-seq PBKD H2O2 replicate 2

value: Lentiviral transfection of shPBRM1 with H2O2 stress


title: cll_21626t_h3k27ac_bam


title: Rhode Island Red-RIR_R40 [reanalyzed]


title: Rhode Island Red-RIR_R41 [reanalyzed]


title: cll_20792t_h3k27me3_bam


title: NMuMG RNA-seq vector H2O2 replicate 2

value: Lentiviral transfection of empty vector with H2O2 stress


title: Rhode Island Red-RIR_R38 [reanalyzed]


title: Rhode Island Red-RIR_R39 [reanalyzed]


title: wt_ip


title: NMuMG RNA-seq vector H2O2 replicate 3


title: cll_189_h3k4me3_bam

value: CLL IGHV mutated


title: NMuMG RNA-seq PBKD replicate 3

value: Lentiviral transfection of shPBRM1


title: NMuMG RNA-seq vector H2O2 replicate 1


title: cll_189_h3k27me3_bam


title: NMuMG RNA-seq PBKD H2O2 replicate 1


title: cll_189_h3k36me3_bam


title: Rhode Island Red-RIR_R36 [reanalyzed]


title: cll_189_h3k27ac_bam


title: NMuMG RNA-seq PBKD replicate 2


title: Rhode Island Red-RIR_R35 [reanalyzed]


title: cll_175_wce_bam

value: wce


title: NMuMG RNA-seq PBKD replicate 1


title: cll_189_wce_bam


title: LSC RH-RAS/ Brd4

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

data_processing:
All reads were mapped to the mouse genome (mm9) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.  Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and the Integrative Genomics Browser (IGB, Affymetrix).  The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The bedGraph files, which were generated by MACS2 software with default parameters, report the number of ChIP-Seq sequencing reads in a genomic interval (normalized to a read depth of 1 million reads).

source_name: RH-RAS LSCs

extract_protocol: Lysates were clarified from sonicated nuclei and DNMT3A R882H- or histone-DNA complexes were isolated with indicated antibodies.  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 following the manufacturer's protocols.

value: RH-RAS LSCs

value: BRD4 (Sigma, HPA015055)


title: MEF, biological rep1

city: Izmir

first: Hani

last: Alotaibi

address: Dokuz Eylül University Health Campus

country: Turkey

institute: Izmir Biomedicine and Genome Center

description: E13.5 MEF

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: CEL files were analyzed using the Bioconductor package oligo V. 1.46.0

source_name: MEF, biological rep1

label_protocol: Affymetrix

growth_protocol: Keratinocytes were isolated from new born mice (P0)  and MEFs were isolated from E13.5 mice.

extract_protocol: MEF isolation Protocol 1. dissect 10-15 embryos (E13.5-E14.5) of the desired strain (DR-4) in PBS 2. discard head and all inner organs (liver, lungs, gut, kidneys,…) 3. wash rest of the embryo by several washing steps in PBS to remove blood 4. get rid of most of the PBS and transfer embryos onto a 90 mm dish lid 5. cut them with two scalpels into small pieces 6. transfer pieces into 50 ml Falcon tube and add Trypsin (2.0 - 2.5 ml per embryo) 7. incubate over night on ice in the coldroom, gently shaking 8. transfer cell suspension into 37°C incubator for 10-20’, invert tube every 5’ 9. add equal volume of feeder medium and resuspend cells by pipetting 10.add 2000-4000 U of crude DNase (Sigma Cat No.: DN-25) and incubate 37°C 5’ 11. spin cells 10’ 1000 rpm 12.drain supernatent and wash cells once in PBS 13.resuspend cells in 20 ml feeder medium and count cells 14.plate 5x106 cells per 150 mm plate 15.change medium after 24h and grow to confluency 16.freeze each plate down as P1 stock or split 1/5 to new 150 mm plates (if a frozen P1 vial is thawn, first grow again to confluency on one 150 mm plate and then split)   Keratinocytes Isolation Protocol 1. transfer P0 newborns to a box with paper towels for isolation 2. prepare 1 cuvette with 200 ml saturated iodine, 1 cuvette with 70 % EtOH, 2-3 ml Dispase-solution per pup in 3 cm plates on ice, 20 ml Gentamycin/PBS (10 ml per 90 cm plate) and Scissors/Forceps in 70% EtOH 3. Take newborns one by one, kill them by deception and transfer bodies/skin from iodine to medium 4. Incubate in iodine solution 2-5 min 5. Incubate in 70% EtOH 2-5 min 6. Remove limbs and cut off tail for genotyping (1.5 ml tube), lyse with tail lysis buffer 7. On the side of the chest the skin is cut from neck to tail using forceps to lift the loose skin and allow space to fit the scissor in 8. Turn the body facing the back up and peal off the skin using two sets of curved forceps; start at shoulders 9. Place the skin in 90 cm dish with genatamycin/PBS and incubate for 10 min 10.Transfer skin to second plate with genatamycin/PBS and incubate for 10 min 11.Place the skin in 3 cm plate with Dispase-medium over night at 4°C to allow separation of epidermis from dermis (ON)   12.Prepare 2-4 3 cm plates with 2 ml CnT-07 and several 6 cm plates with a 500 µl drop of TrypLE 13.Wash and place skin in CnT-07 plate (reuse) to remove excess of dispase; with the two curved forceps detach epidermis from dermis and transfer epidermis on top of the drop of TrypLE in 3 cm plate (basal layer downward) 14.After the last sample incubate all plates at 37°C for 10 min 15.Tilt each plate and rub the skin on the ground to remove single cells 16.Add 1.5 ml medium and resuspend in 15 ml Falcon tube, add another 1 ml and repeat step 15, transfer remaining cells to the Falcon tube and pool cells of the same genotype 17.Spin down 1000 rpm 5 min 18.plate 4-5x104 per cm2 in CnT-07 (1x106 cells per 6 cm TPP plate) 19.Grow til confluency, wash with PBS and add 1 ml TrypLE 20.Incubate 20 min at 37°C and resuspend cells with 4 ml medium and spin down at 1000 rpm for 5 min 21.Resuspend in CnT-07 and split 1:2 to new 6 cm plates (plate 6x105 per 6 cm plate (3x104/cm2) 22.Freeze down confluent plates or split accordingly   Materials and Solutions: - Pen-Strep  Gibco - Dispase II   Roche 10165859001 0.5U/mg - Keratinocyte medium  CellnTec CnT-07/CellnTec CnT-02  (undiff./differentiation-Ca2+ switch) - Collagen IV  Sigma C-5533 - Genatmycin B  Gibco 10 mg/ml - Iodine   Sigma - TrypLE Select  Invitrogen   - Keratinocyte medium: 500 ml Medium CnT-07, 5 ml Pen./Strep. + Suppl. A,B,C   - Keratinocyte medium without suppl.: 500 ml Medium CnT-07, 5 ml Pen/Strep, or Gibco Medium +5 µl Choleratoxin (10-10M)   - Saturated iodine - 70% EtOH - Gentamycin B/PBS (50 µg/ml; 1:200) - Dispase-medium: 4 mg/ml Dispase II in Keratinocyte medium without suppl.   - optional: Collagen-solution: 1 mg/ml Stock (dissolve in 0.1M HAc (0.6%)); dilute 1:20 with PBS (50 µg/ml) working dilution   - Forceps & Scissors (FST): 2x 11271-30 1x 14001-14 1x 11000-16 1x 11200-14 1x 14090-09   RNA isolation Protocol RNA was isolated using the Nucleospin RNA II kit (Macherey-Nagel) as recommended by the manufacturer. RNA quality was checked with the Agilent Bioanalyzer. RNA with RIN values above 9 was used in the microarray protocol.

treatment_protocol: No treatment was applied

value: MEF


title: Keratinocytes, biological rep2

description: p0 keratinocytes

source_name: Keratinocytes, biological rep2

value: Keratinocytes


title: MEF, biological rep3

description: E13.5 MEF

source_name: MEF, biological rep3


title: MEF, biological rep2

description: E13.5 MEF

source_name: MEF, biological rep2


title: cll_175_h3k4me3_bam


title: NMuMG RNA-seq vector replicate 3

value: Lentiviral transfection of empty vector


title: Rhode Island Red-RIR_R33 [reanalyzed]


title: cll_175_h3k27me3_bam


title: Rhode Island Red-RIR_R37 [reanalyzed]


title: Keratinocytes, biological rep3

description: p0 keratinocytes

source_name: Keratinocytes, biological rep3


title: NMuMG RNA-seq vector replicate 2


title: Keratinocytes, biological rep1

description: p0 keratinocytes

source_name: Keratinocytes, biological rep1