title: ov_-2DPA_rep1 RNA-seq

source_name: ovule of -2DPA fruit

value: -2DPA (days post anthesis)


title: ow_-2DPA_rep2 RNA-seq

status: Public on Jan 01 2018

type: SRA

city: Beijing

first: Xia

last: Cui

address: 12 Zhongguancun Nandajie

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig

molecule: total RNA

organism: Solanum lycopersicum

source_name: ovule wall/pericarp of -2DPA fruit

growth_protocol: the tomato plants were grown in greenhouse on soil

extract_protocol:
the fruits of different stages were collected and the ovule and ovary wall were dissected under microscope. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

tag: cultivar

value: Moneymaker

tag: tissue

value: ovary wall/pericarp

tag: Stage


title: exp2_H3K27Ac_dDAVP

status: Public on Jan 02 2018

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

country: USA

institute: Johns Hopkins University School of Medicine

library_source: genomic

data_processing:
Align and transform the .fastq to .sam files using BWA program and mm10 mouse genome:  bwa samse mm10.fa sample.sai sample.fastq > sample.sam bwa aln -t 8 mm10.fa  sample.fastq > sample.sai.
Convert format from Sam to Bam and index the files using Samtools: Samtools view –bhS sample.sam > sample.bam, samtools sort sample.bam sample.sorted; samtools index sample.sorted.bam.
Create bedgraph files using macs2, macs2 callpeak -t sample_filename.sorted.bam -c input_filename.sorted.bam -f BAM -g mm -n output_filename –B –q 0.01 –SPMR
Create a peak txt file from a macs2 peak file
Create a bedGraph file from pile up file of macs2 output
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph and txt files

molecule: genomic DNA

organism: Mus musculus

source_name: mpkCCD cells

growth_protocol: Cultured mouse mpkCCD (clone 11) cells were grown and maintained in complete medium, DMEM/F12 containing 2% dialyzed serum and supplements (5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin), as previously described (Yu MJ, Proc Natl Acad Sci U S A 106:2441-2446, 2009).

extract_protocol:
Shearing of chromatin was carried out by the manufacturer's protocol of truChIP kit (PN 520075, Covaris, Woburn, Massachusetts). All Covaris buffers were provided in kit. Confluent monolayers mpkCCD cells cultured on 100 mm permeable supports of transwell system were treated with dDAVP (0.1 nM) or vehicle for 24 h and then washed in ice-cold PBS followed by cross-linking in 1.11% formaldehyde in Covaris Fixing Buffer (5.5 ml) for 5 min at room temperature with gentle rocking. Cross-linking was terminated by the addition of 0.3 ml of 1X Covaris Quenching Buffer with rocking. The buffer solution was aspirated and ice-cold PBS was added to each plate. Cells were scraped, spun down (200xg, 5 min), and washed twice with ice-cold PBS. Cell pellets were resuspended in 1 ml of 1X Covaris Lysis Buffer for 10 min at 4°C with rocking.  Nuclei were pelleted by spinning at 1,700xg for 5 min at 4°C. Nuclear pellets was resuspended in 1 ml of 1X Covaris Wash Buffer and incubated for 10 min at 4°C with rocking. Samples were spun at 1,700xg for 5 min at 4°C. Nuclear pellets were washed twice with 1 ml of Covaris Non-ionic Shearing Buffer and spun at 1,700xg for 5 min at 4°C. Nuclei were resuspended in 1 ml of Covaris Non-ionic Shearing Buffer. Two 20 ul aliquots of the resuspended pellets were removed prior to shearing to be used as subsequent unsheared controls for immunoblotting and agarose gel electrophoresis. The remaining samples were transferred to AFA tubes (TC12 x 12 mm). Samples were sheared using a Covaris S2 SonoLAB Single system for two minutes (Duty cycle: 5%; Intensity: 4; cycle: 200). Total nuclear protein concentration of each sample in mg/ml was determined with the BCA Protein Assay Kit (Thermo Scientific, Rockford, IL).  To test shearing efficiency, a 20 ul aliquot from each sample was obtained after shearing. The aliquots from the unsheared sample and the sheared sample, were incubated with 100 ul 1X TE buffer, 10 ul 10% SDS, and RNAse A (10 ug/ul, Cell Signaling Technology, Danvers, Massachusetts) for 30 min at 37°C. After adding proteinase K (2 ug), the samples were incubated overnight at 65°C. The DNA was purified using DNA Clean & Concentrator columns (Catalog #: D4013, Zymo Research, Irvine, CA) and ran on an E-gel EX 2% agarose (Invitrogen, Carlsbad, CA). Target fragment sizes for chromatin immunoprecipitation were in the range of 150-700 bp in length with average fragment size of 300 bp.  Immunoprecipitaiton was performed by the manufacturer's instruction (SimpleChIP protocol #9003, Cell Signaling Technology). 'Input' sample (10 ul) was obtained prior to immunoprecipitation.  Chromatin Immunoprecipitation was performed using 30-90 ug of sheared chromatin in 500 uL of 1X Covaris Non-ionic Shearing Buffer with 10 μl anti-H3K27 acetylation antibodies. The mixtures were incubated overnight at 4°C with gentle rotation, followed by incubation with ChIP Grade Protein G Magnet Beads (Catalog #: 9006, Cell Signaling Technology) for 2 h at 4°C with rotation. The beads were washed a total of four times, including three low salt washes followed by one high salt wash for 5 min each at 4°C. Immunoprecipitated chromatin was eluted from the beads with 150 ul of 1X ChIP Elution Buffer for 30 mins at 65°C in a thermomixer. To reverse crosslinks, 6 ul of 5 M NaCl and 2 ul of 20 ug/ul  Proteinase K were added to the chromatin followed by incubation at 65°C overnight. DNA was purified according to the manufacturer's instruction.
Sequencing libraries were prepared according to the manufacturer's instruction (NuGEN Ovation SP Ultralow library system kit). Adaptor-conjugated iibraries were amplified by PCR. The amplified libararies were measured.  A fixed amount of the total measured DNA was used for sequencing in an Illumina Hiseq2000 instrument to obtain single read data.  Libraries were sequenced using an Illumina HiSeq2000, obtaining 1- by 50-bp reads.

treatment_protocol: For dDAVP treatment, cells were transferred to permeable supports (75mm, 0.4um pore, Corning #3419), and grown until confluency as documented transepithelial resistance measurements (Epithelial Volt ohmmeter; WPI). At that point, the complet medium was changed to serum- and hormone-free medium, and cells were maintained for 24 hr. Cells were incubated with the V2 receptor-selective vasopressin analog dDAVP (0.1 nM) or its vehicle (n=2) and harvested after 24 hr.

tag: cell type

value: cultured mouse cortical collecting duct cells (mpkCCD)

tag: passages

tag: chip antibody

value: anti-Histone H3 (acetyl K27) antibody (abcam, ab4729)


title: 203P1

city: Birmingham

first: Eroboghene

last: Ubogu

state: AL

address: 1720 7th Avenue South, SC200

department: Neurology

institute: University of Alabama at Birmingham

data_processing:
Basecalls performed using bcl2fastq version 1.8.4 (for Illumina HiSeq2500) and bcl2fastq version 2.18.0.12 (for NextSeq500)
Reads were aligned to hg19 using RSEM version 1.2.31 with parameters --paired-end; --star; --estimate-rpsd; --append-names; --output-genome-bam; --star-gzipped-read-file
Genes with FPKM values > 0.1 were then further analyzed in gProfiler
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files of FPKM and gProfiler results

organism: Homo sapiens

source_name: Pooled laser capture microdissected endoneurial microvessels from cryopreserved sural nerve (donor 1)

growth_protocol: Primary endoneurial endothelial cells were isolated from sciatic nerves via endoneurial stripping, enzymatic digestion and density centrifugation. Primary endoneurial endothelial cells (1 x 10^6 per 75 cm2 flask) were grown to confluence in specialized pHEndEC growth medium on rat tail collagen-coated Corning CellBIND flasks and RNA extracted using TRIzol

extract_protocol:
Endoneurial microvessels were fluorescently detected in 20 micron thick axial cryosections of human sural nerve biopsies using UEA-1-FITC, and laser capture microdissection performed. Microvessels were stored in extraction buffer at -80oC and RNA isolated using Arcturus Pico Pure Isolation Kit (Thermo Fisher Scientific) or miRNeasy kit (Qiagen, Hilden, Germany). On-column DNase digestion was also performed to remove contaminating genomic DNA using the RNase-free DNase Set (Qiagen).
cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech) and ribosomal cDNA was depleted prior to the final amplification step

value: Sural nerve

tag: passage number

value: Not applicable

tag: age

tag: Sex

value: Female


title: 32P1

source_name: Pooled laser capture microdissected endoneurial microvessels from cryopreserved sural nerve (donor 2)


title: cbp80-1

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: cbp80 mutant - replicate 1

data_processing:
ribosomal and tRNA sequence filtering with Bowtie2  (version 2.1.0), using –fr parameter in addition to default parameters and using unaligned forward and reverse reads later.
Aligning to A. thaliana genome to collect expression data: TopHat (version 2.1.1), with -p 10 -i 10 -I 1000 --library-type fr-secondstrand -G Arabidopsis_thaliana.TAIR10.34.gtf parameters.
Collecting unnormalized read counts from alignment with featureCounts (Subead package, version 1.5.0-p3), with default parameters for paired-end analysis.
Differential expression analysis: DESeq2 (version1.14.1), with default parameters, but using “contrast” argument. Control was always wild-type.
Genome_build: Arabidopsis thaliana: Ensembl Plants release 34 (ftp://ftp.ensemblgenomes.org/pub/release-34/plants/) genome fasta and GTF files, for rRNA/tRNA filering:  Arabidopsis thaliana sequences from tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA
Supplementary_files_format_and_content: “counts_all.txt” output file from featureCounts, ”_all.txt” and  “_005.txt” files for differencial expression data from DESeq2, unfiltered or  filtered values to padj < 0.05.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Plants material were grown on ½ strength MS for 16 days under constant light conditions. Plant material was collected on ice (for apporximately 30 minutes) before snap freezing in liquid nitrogen.

extract_protocol:
RNA for library preparation has been extracted using the RNeasy Plant RNeasy Plant Mini Kit (Qiagen) according to the manufacture’s protocol.
mRNA was isolated using the NEBnext poly(A) mRNA Magnetic Isolation Module (NEB #7490), this was followed by library preparation using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (epicentre). For library preparation mRNA was used as input starting at the fragmentation step in the protocol (step number 5).

treatment_protocol: no treatment

value: whole seedlings

tag: ecotype

tag: genotype

value: cbp80 (CAP-BINDING PROTEIN 80) mutant


title: cbp20-3

description: cbp20 mutant - replicate 3

value: cbp20 (CAP-BINDING PROTEIN 20) mutant


title: 346P1

source_name: Pooled laser capture microdissected endoneurial microvessels from cryopreserved sural nerve (donor 3)

value: Male


title: Parental_ZEB1_ChIP-seq

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description:
parental_1975_zeb1
The line was established in July 1988.

data_processing:
Short reads were aligned to the hg19 genome assembly (National Center for Biotechnology Information Build 37) with Bowtie2 v4.1.2 software for the alignment of short DNA sequences.
Data were analyzed and bound sites (from ChIP followed by deep sequencing) were identified with MACS v1.4.2 (Model-based Analysis for ChIP-Seq) software for peak discovery and next-generation sequencing analysis.
Occupied sites were identified by searching for groups of tags positioned in a sliding window of 500 bp.
Experimental samples were compared against the controls using a Poisson distribution as assigned by the MACS aligner.
The threshold for the number of tags that generated an interacting site was determined for a false-discovery rate of 0.001. Peaks were also required to have at least fourfold more tags (normalized versus total number) than the control samples. Visualization was performed with the IGV v2.3.81 tool.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed

source_name: non-small cell lung cancer, parental cells

growth_protocol: The cell lines were cultured in RPMI-1640 with 10% FBS plus 1% penicillin and streptomycin.

extract_protocol:
In brief, 2x10e7 H1975 and H1975 R2 were fixed in 1% formaldehyde. Sonication was calibrated such that DNA was sheared to between 400 and 1,000 bp. ZEB1 was immunoprecipitated with Cell Signaling TCF8/ZEB1 (D80D3) Rabbit mAb #3396.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters. Barcoded fragments were amplified via PCR. Libraries were sequenced as 40 bp paired end reads on an Illumina NextSeq500 instrument.

treatment_protocol: H1975 R2 cell line was treated with dacomitinib (1uM) every 3~4 days.

tag: cell line

value: lung adenocarcinoma cell line

tag: gender

value: female


title: Resistant_ZEB1_ChIP-seq

description:
resistant_1975_zeb1
The line was established in July 1988.

source_name: non-small cell lung cancer, resistant cells


title: UPN1

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description:
Sample 35
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling. Four fastq files per sample.
The HTG EdgeSeq Parser was used to align reads to the probe list to collate the data. Data are provided as raw counts data and median normalized.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts values.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file includes median normalized values.

source_name: UPN1 cell line

extract_protocol:
Samples were centrifuged for 5 minutes at 1000 RPM, and supernatant was removed without disturbing the cell pellet. Cells were resuspended using 1000 uL of HGT Lysis buffer to maintain original concentration of 4 millions cells per 1000 uL. The lysis buffer cell suspension was placed in 95 degrees Celsius for fifteen (15) minutes. After allowing to cool at room temperature for ten (10) minutes, Proteinase K was added at 1/20 Lysis Buffer volume and samples were incubated at 50 for 180 minutes. Samples were run as singletons. Samples were plated initially at a concentration of 10000 cells per well (10000 cells/35 uL).
Samples submitted were individually barcoded and purified using AMPure XP beads and quantitated using KAPA Library Quantification kit. The library was sequenced at 4pM on an Illumina NextSeq using High Output, 75 cycle, v2 kit with two index reads.


title: VL51

description:
Sample 36
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: VL51 cell line


title: U2932

description:
Sample 34
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: U2932 cell line


title: SUDHL6

description:
Sample 31
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SUDHL6 cell line


title: SUDHL2

description:
Sample 29
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SUDHL2 cell line


title: WSU_DLCL2

description:
Sample 37
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: WSU_DLCL2 cell line


title: SUDHL16

description:
Sample 28
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SUDHL16 cell line


title: TOLEDO

description:
Sample 33
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: TOLEDO cell line

value: TOLEDO


title: TMD8

description:
Sample 32
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: TMD8 cell line


title: SUDHL4

description:
Sample 30
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SUDHL4 cell line


title: ow_-2DPA_rep1 RNA-seq

source_name: ovule wall/pericarp of -2DPA fruit


title: SSK41

description:
Sample 26
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SSK41 cell line


title: SP53

description:
Sample 25
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SP53 cell line


title: SP49

description:
Sample 24
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SP49 cell line


title: OCILY7

description:
Sample 18
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: OCILY7 cell line


title: RCK8

description:
Sample 21
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: RCK8 cell line


title: 347P1

source_name: Pooled laser capture microdissected endoneurial microvessels from cryopreserved sural nerve (donor 4)


title: OCILY1

description:
Sample 15
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: OCILY1 cell line


title: MINO

description:
Sample 14
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: MINO cell line

value: MINO


title: RIVA

description:
Sample 23
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: RIVA cell line

value: RIVA


title: OCILY18

description:
Sample 16
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: OCILY18 cell line


title: OCILY19

description:
Sample 17
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: OCILY19 cell line


title: MAVER1

description:
Sample 12
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: MAVER1 cell line


title: KARPAS422

description:
Sample 11
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: KARPAS422 cell line


title: JEKO1

description:
Sample 8
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: JEKO1 cell line


title: JVM2

description:
Sample 9
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: JVM2 cell line


title: MEC1

description:
Sample 13
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: MEC1 cell line


title: KARPAS1718

description:
Sample 10
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: KARPAS1718 cell line


title: HBL1

description:
Sample 6
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: HBL1 cell line


title: HAIR_M

description:
Sample 5
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: HAIR_M cell line


title: SUDHL10

description:
Sample 27
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: SUDHL10 cell line


title: DOHH2

description:
Sample 2
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: DOHH2 cell line


title: GRANTA519

description:
Sample 4
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: GRANTA519 cell line


title: REC1

description:
Sample 22
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: REC1 cell line


title: DB

description:
Sample 1
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: DB cell line

value: DB


title: FARAGE

description:
Sample 3
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: FARAGE cell line

value: FARAGE


title: HCT116_(-MET)_H3K4me3_ChIPseq_Rep1

city: Durham

first: Jason

middle: W

last: Locasale

state: NC

address: Levine Science Research Center C270

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
HCT116 ChIP-seq: Reads were aligned to a combinational genome consisting of the human reference genome hg19 and the Drosophila reference genome dm6 using Bowtie2. Alignment files were then filtered according to their alignment scores and down-sampled to ensure each file contains the same amount of unique Drosophila reads. Finally, reads mapped to hg19 in the normalized alignment files were kept for peak-calling and other following analyses. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
Mouse liver ChIP-seq: Reads were aligned to a the reference genome mm8 using Bowtie2. Alignment files were then filtered according to their alignment scores and normalized by sequencing depth. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
HCT116 RNA-seq: Raw reads were aligned to the human reference genome hg19 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Mouse liver RNA-seq: Raw reads were aligned to the mouse reference genome mm8 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Genome_build: hg19 (HCT116), mm8 (mouse liver)

growth_protocol: Cells were cultured in RPMI with 10% FBS (containing 30 micromolar methionine).

extract_protocol:
Cross-linked chromatin was collected and flash frozen before sonication with the Covaris M2. Spike-in Drosophila chromatin and spike-in antibody for Drosophila H2Av (Active Motif cat#61686) was mixed with chromatin from the HCT116 cells before the chromatin IP step with a fixed ratio (2:1, Drosophila:HCT116 chromatin) as a reference. Lysates were clarified and protein-DNA complexes were immunoprecipitated with H3K4me3 antibody.
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: Plated cells were first cultured in 100 micromolar methionine (+MET) and switched to 3 micromolar (-MET) for 24 hours upon harvesting lysates.


title: HCT116_(-MET)_H3K4me3_ChIPseq_Rep2


title: OCILY8

description:
Sample 19
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: OCILY8 cell line


title: HCT116_(+MET)_H3K4me3_ChIPseq_Rep2


title: HCT116_InputDNA_Rep2


title: HCT116_(+MET)_H3K4me3_ChIPseq_Rep1


title: E7107 treated - 3

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Alignment to GRCh37 augmented with the Ensembl gene annotation build 78 with STAR version 2.4.1d
Transcript level per-transcript quantification was performed with Sailfish 0.9.0 with 30 bootstrap samples.
Differential expression was called between treatments at the gene level using DESeq2 version 1.12.3
Differential expression was called at the transcript level using Sleuth version 0.28.
Differential expression was called at the event level using MISO version 0.5.3.
Genome_build: GRCh37
Supplementary_files_format_and_content: gene-TPM-E7017.csv: GxM (G: genes, M: samples) matrix of Sailfish TPM values aggregated at the gene level
Supplementary_files_format_and_content: gene-counts-E7107.csv: GxM (G: genes, M: samples) matrix of Sailfish counts aggregated at the gene level
Supplementary_files_format_and_content: transcript-TPM-E7107.csv: TxM (T: transcripts, M: samples) matrix of Sailfish transcript TPM values
Supplementary_files_format_and_content: transcript-counts-E7107.csv: TxM (T: transcripts, M: samples) matrix of Sailfish transcript counts
Supplementary_files_format_and_content: control-vs-E7107.csv: DESeq2 gene level  differential expression results comparing  batch2 control and E7107 treated samples
Supplementary_files_format_and_content: control-vs-E7107-sleuth.csv: Sleuth transcript level differential expression results comparing batch2 control and E7107 treated samples

source_name: MB468 cells

growth_protocol: MB468 cells were cultured in RPMI + 10% FBS supplemented with penicillin G (100 U/ml), streptomycin sulfate (100 mg/ml), HEPES free acid (6 mM), L-glutamine (1.6 mM), beta-mercaptoethanol (50 mM).

extract_protocol:
RNA was extracted using the RNeasy Plus Kit (Qiagen) according to the manufacturer's protocol.
Truseq Stranded mRNA

treatment_protocol: 100,000 cells/well were reverse-transfected with 50 nM siGenome PRPF8, PRPF38A or non-targeting siRNAs using Dharmafect 1 (3 ml/well) in 6-well plates in a 1:1 mixture of WIT-T (Stemgent) and 10% FBS RPMI medium (final volume: 1.2 ml). The transfection medium was replaced with fresh medium (2 ml 10% FBS RPMI) 24 hr after transfection and adherent cells collected 48 hr after transfection.

tag: treatment

value: E7107 treated


title: ow_2DPAe_rep2 RNA-seq

source_name: ovary wall/pericarp of 2DPAe (emasculated) fruit

value: Moneymaker

value: ovary wall/pericarp

value: 2DPA (emasculated at -2DPA)


title: E7107 treated - 4


title: E7107 treated - 2


title: HCT116_InputDNA_Rep1


title: HC_1

description:
Sample 7
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt

source_name: HC_1 cell line


title: untreated control for E7107 - 4

value: untreated


title: untreated control for E7107 - 1


title: untreated control for E7107 - 2


title: ChIP-seq_5F_shEZH1_H3K27me3_rep2

first: Melissa

last: Kinney

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: Streptavidin Dynabeads or Antibodies Millipore 07-449, lot: 2064519

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, and peak bed file

source_name: Human MSCiPS1-derived 5F hematopoietic cells

growth_protocol: MSCiPS1 human induced pluripotent stem cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma).  Puromycin was added at 0.35 ug/mL (ThermoFisher) and G418 was added at 750 ug/mL (Gibco). Media were changed every 3-4 days.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

value: Hematopoietic cells


title: ChIP-seq_5F_shLuc_H3K4me3_rep1

description: Streptavidin Dynabeads or Antibodies: Millipore 04-745, lot: 1997493


title: ChIP-seq_5F_shEZH1_H3K4me3_rep2


title: ChIP-seq_5F_shLuc_H3K27me3_rep1


title: ChIP-seq_5F_shLuc_H3K27me3_rep2


title: ChIP-seq_5F_shLuc_H3K4me3_rep2


title: PRPF8 knockdown_prpf8_2

data_processing:
Alignment to GRCh37 augmented with the Ensembl gene annotation build 78 with STAR version 2.4.1d
Transcript level per-transcript quantification was performed with Sailfish 0.9.0 with 30 bootstrap samples.
Differential expression was called between treatments at the gene level using DESeq2 version 1.12.3
Differential expression was called at the transcript level using Sleuth version 0.28.
Differential expression was called at the event level using MISO version 0.5.3.
Genome_build: GRCh37
Supplementary_files_format_and_content: gene-TPM.csv: GxM (G: genes, M: samples) matrix of Sailfish TPM values aggregated at the gene level
gene-counts.csv: GxM (G: genes, M: samples) matrix of Sailfish counts aggregated at the gene level
transcript-TPM.csv: TxM (T: transcripts, M: samples) matrix of Sailfish transcript TPM values
transcript-counts.csv: TxM (T: transcripts, M: samples) matrix of Sailfish transcript counts
control-vs-prpf8.csv: DESeq2 gene level  differential expression results comparing control and PRPF8 knockdown samples
control-vs-prpf38.csv: DESeq2 gene level  differential expression results comparing control and PRPF38A knockdown samples
control-vs-prpf8-sleuth.csv: Sleuth transcript level differential expression results comparing control and PRPF8 knockdown samples
control-vs-prpf38-sleuth.csv: Sleuth transcript level differential expression results comparing control and PRPF38A knockdown samples
miso.tsv: MISO event-level PSI values for all samples

source_name: MB468_PRPF8 knockdown

value: Triple Negative Breast Cancer Cell line

tag: genotype/variation

value: PRPF8 knockdown


title: PRPF8 knockdown_prpf8_1


title: PRPF8 knockdown_prpf8_3


title: PRPF38A knockdown_prpf38_5

source_name: MB468_PRPF38A knockdown

value: PRPF38A knockdown


title: PRPF38A knockdown_prpf38_2


title: PRPF38A knockdown_prpf38_1


title: PRPF8 knockdown_prpf8_4


title: untreated_control_3

value: control


title: PRPF38A knockdown_prpf38_4


title: untreated_control_5


title: untreated control for E7107 - 3


title: untreated_control_1


title: untreated_control_2


title: ChIP-seq_5F_H3K27me3

description: Streptavidin Dynabeads or Antibodies: Millipore 07-449, lot: 2064519


title: ChIP-seq_5F_H3K4me3


title: ChIP-seq_5F_BirA-Only_rep2

description: Streptavidin Dynabeads or Antibodies: ThermoFisher 65601, lot:123612210


title: ChIP-seq_5F_FB-Ezh1_rep1


title: ChIP-seq_5F_shEZH1_H3K4me3_rep1


title: ChIP-seq_5F_shEZH1_H3K27me3_rep1


title: PRPF38A knockdown_prpf38_3


title: ChIP-seq_5F_FB-Ezh1_rep2


title: ChIP-seq_5F_BirA-Only_rep1


title: untreated_control_4


title: PRPF8 knockdown_prpf8_5


title: E7107 treated - 1


title: ATAC-seq_5F_F8-shLuc-rep2

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly mm9 using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: wig file and peak bed file

growth_protocol: MSCiPS1 human induced pluripotent stem cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma) and puromycin was added at 0.35 ug/mL (ThermoFisher). Cultures were maintained at a density of <1 x106 cells/ml, and media were changed every 3-4 days. AGM tissue was microdissected from E10.5 embryos and dissociated to single cells. AGM hematopoietic cells were sorted for immunophenotypic markers cKit+VE-cadherin+CD45+CD41+.

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human (hg19) or mouse (mm9) genome were retained for downstream data analysis.


title: ChIP-seq_5F_BirA-Only_Input


title: ATAC-seq_5F_D4-shEZH1-rep1


title: Biotin positive 3

city: Cambridge

first: Ang

address: 415 Main St.

institute: Broad Institute

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_3
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt

data_processing:
Short sequencing reads were aligned to the UCSC mm10 transcriptome using Bowtie2 (version 2.1.0; Langmead et al., 2012).
Bowtie2 alignments were used as input in RSEM (version 1.2.8; Li et al., 2011) to quantify gene expression levels.
Data were normalized using R Package DESeq2 (version 1.16.0; Love et al., 2014).
Genes with low read counts, defined as the ones without at least 100 normalized counts in 3 samples, were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized count text files

molecule: polyA RNA

source_name: Dendritic cells

extract_protocol:
Fresh cells were sorted (150 cells/sample) directly into plates containing TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol using a FACS Aria II (BD Biosciences). RNA from sorted populations was isolated using Agencourt RNAClean XP beads (Beckman Coulter).
Full-length cDNA and sequencing libraries were prepared using the Smart-seq2 protocol as described in Picelli et al., 2014. Libraries were sequenced on a Nextseq500 (Illumina) to generate 38 base pair, paired-end reads.

treatment_protocol: Cd40G5/G5 DCs were pulsed with OVA323-339 and transferred subcutaneously (5 x 10^5/footpad) into Cd40G5/G5 recipients. Eighteen hours later, 3 x 10^5 CD40lgSrtA/Y CD4-Cre OT-II CD4+ T cells were transferred intravenously. Biotin-LPETG was administered subcutaneously (300 nmol/footpad) 46 hours post T cell transfer. 48 hours post T cell transfer popliteal lymph nodes were processed and stained for surface markers as above and endogenous biotin+ and biotin- MHC-IIhi CD11c+ CD11b+ XCR1– DCs were sorted. As controls, MHC-IIhi CD11c+ CD11b+ XCR1– DCs were also sorted from Cd40-/- mice treated as above, except that they received WT (instead of Cd40G5/G5) DCs and WT OT-II (instead of CD40lgSrtA/Y CD4-Cre OT-II) CD4+ T cells

tag: strain

value: popliteal lymph node

value: Dendritic cells

tag: population

value: Cd11c-int, Mhc-II-high, Cd11b+, Biotin+


title: CD40 null 1

description:
dendritic cells from Cd40-/- mice
CD40N_1
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt

value: Cd11c-int, Mhc-II-high, Cd11b+


title: Biotin negative 5

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_5
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt

value: Cd11c-int, Mhc-II-high, Cd11b+, Biotin-


title: Biotin negative 6

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_6
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: Biotin negative 2

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_2
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: Biotin negative 4

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_4
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: Biotin negative 1

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_1
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: CD40 null 2

description:
dendritic cells from Cd40-/- mice
CD40N_2
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: Biotin positive 1

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_1
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: Biotin negative 3

description:
dendritic cells unlikely have interacted with T cells via Cd40 ligation
BiotinN_3
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: AB1049_CD8_STAT1 Transgenic_90' 10 ng/ml IFNg

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing:
Adapter Trimmed reads were aligned to mouse genome version GRCm38 and mapped to ensemble gene features (v38.80, current June 2015) using Genomics Workbench software (CLC bio, version 8.0.2). Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Complete read-pairs mapping to specific (10 or fewer) exon locations were counted, Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Using JMP/Genomics software (SAS Institute), raw counts were inflated log-transformed and then normalized by upper quartile scaling
Genome_build: GRCm38
Supplementary_files_format_and_content: per-gene expression as log2(fragment count +1), where fragment count=total exon reads, normalization by Upper Quartile Scaling. Sample s17 filtered out from dataset due to low signal.

source_name: sorted naive CD8 T cells

growth_protocol: CD4+ and CD8+ naïve T cells from LNs of STAT1 Tg (n=4 and 5 respectively) and WT littermate (n=5 and 6 respectively) mice were sorted on a BD FACS Aria based on surface staining of CD8- CD4+ CD44low CD62L+ and CD8+ CD4- CD44low CD62L+ cell populations respectively. A mix of anti-B220, anti-CD49d (clone DX5; BioLegend),anti-Ter119 (clone TER-119; BioLegend), anti-MHC-II (clone M5/114.15.2; eBioscience) and anti-Gr-1 (clone RB6-8C5; BioLegend) was used in PE as a dump channel.

extract_protocol:
The cells were then washed once with PBS before being resuspended in TRIzol (Invitrogen) and stored at −80°C.
Illumina TrueSeq Stranded mRNA Library Prep kit from an input of 500 ng total RNA ("90-minute stimulation" samples)  Illumina True-seq non-stranded mRNA ("overnight stimulation" samples)

treatment_protocol: Sorted cell populations were spun down, adjusted at a concentration of 2x10^6 cells/ml prior to resting overnight for subsequent in vitro stimulation for 90 minutes at 37°C and 5% CO2 in presence or not of rmIL-7 (10 ng/ml) or rmIFN-γ (10 ng/ml; Peprotech).

value: STAT1 Transgenic

tag: stimulus

value: 90' 10 ng/ml IFNg


title: Biotin positive 4

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_4
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt

tag: tissue


title: Biotin positive 6

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_6
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: AB1047_CD8_STAT1 Transgenic_90' media

value: 90' media


title: AB1046_CD4_STAT1 Transgenic_90' 10 ng/ml IFNg

source_name: sorted naive CD4 T cells


title: AB1045_CD4_STAT1 Transgenic_90' 10 ng/ml IL-7


title: AB1048_CD8_STAT1 Transgenic_90' 10 ng/ml IL-7


title: AB1044_CD4_STAT1 Transgenic_90' media


title: AB1042_CD8_WT_90' 10 ng/ml IL-7

value: WT


title: AB1041_CD8_WT_90' media


title: AB1043_CD8_WT_90' 10 ng/ml IFNg


title: ATAC-seq_5F_D6-shEZH1-rep2


title: AB1040_CD4_WT_90' 10 ng/ml IFNg


title: ATAC-seq_5F_C11-shLuc-rep1


title: AB1039_CD4_WT_90' 10 ng/ml IL-7


title: AB1038_CD4_WT_90' media


title: Biotin positive 5

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_5
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: A9846_CD8_IL7Ra449F transgenic_90' media

value: IL7Ra449F transgenic


title: A9847_CD8_IL7Ra449F transgenic_90' 10 ng/ml IL-7


title: Biotin positive 2

description:
dendritic cells likely have interacted with T cells via Cd40 ligation
BiotinP_2
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt


title: A9845_CD4_IL7Ra449F transgenic_90' 10 ng/ml IL-7


title: A9841_CD8_WT_90' media


title: A9833_CD4_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9835_CD8_STAT1 Transgenic_90' media


title: A9840_CD4_WT_90' 10 ng/ml IFNg


title: A9834_CD4_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9842_CD8_WT_90' 10 ng/ml IL-7


title: A9836_CD8_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9837_CD8_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9831_CD8_WT_90' 10 ng/ml IFNg


title: A9839_CD4_WT_90' 10 ng/ml IL-7


title: A9829_CD8_WT_90' media


title: A9832_CD4_STAT1 Transgenic_90' media


title: A9826_CD4_WT_90' media


title: A9830_CD8_WT_90' 10 ng/ml IL-7


title: A9828_CD4_WT_90' 10 ng/ml IFNg


title: A9825_CD8_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9822_CD4_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9823_CD8_STAT1 Transgenic_90' media


title: A9824_CD8_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9821_CD4_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9820_CD4_STAT1 Transgenic_90' media


title: A9844_CD4_IL7Ra449F transgenic_90' media


title: A9819_CD8_WT_90' 10 ng/ml IFNg


title: A9816_CD4_WT_90' 10 ng/ml IFNg


title: A9843_CD8_WT_90' 10 ng/ml IFNg


title: A9818_CD8_WT_90' 10 ng/ml IL-7


title: A9817_CD8_WT_90' media


title: A9838_CD4_WT_90' media


title: A9810_CD4_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9827_CD4_WT_90' 10 ng/ml IL-7


title: FLC ChIP-Seq control rep2

city: Cologne

first: Julieta

last: Mateos

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

data_processing:
For both species, low quality and duplicated reads in the raw sequencing data were filtered out using Parallel-QC v1.0 (Zhou et al., 2013; PLoS ONE). Low quality reads were considered those not having Phred quality scores≥13 in at least 90% of the bases called. Duplicated reads were also removed to achieve a better specificity (fewer false positive peaks) during the peak-calling step at each individual replicate as recommended in Bailey et al. (2013), PLoS Comput. Biol.
Reads kept were then mapped either to the Arabis alpina reference assembly V3 (Willing et al., 2015; Nature Plants) or to the Arabidopsis thaliana TAIR10 using Bowtie v2.0.2 (Langmead et al., 2019; Genome Biol.), reporting alignments under default mode parameters.
The software PeakRanger (Feng et al., 2011; BMC Bioinformatics) was used to identify read-enriched genomic regions (P-value <1e-6, q-value (FDR) < 0.01, rest of parameters default).
Using MULTOVL v1.2 with parameters '-L 1 -u-m 2 -M 0 -s multovl -f BED' (Aszodi A, 2012; Bioinformatics), a total of 173 peak regions present in at least two replicates of PEP1 ChIP-seq or 377peak regions present in the two replicates of FLC ChIP-seq were retained for further processing (the union of overlapping regions was reported, minimum overlap required 1bp). After filtering by peak length (peaks shorter than 1.5kb were kept), we obtained the final peak set for both species, namely 156 peaks in Arabis alpina and 297 peaks in Arabidopsis thaliana.
Genome_build: TAIR10 (A.thaliana); A_alpina_V3 (A.alpina, http://arabis-alpina.org/refseq.html)
Supplementary_files_format_and_content: peak files

source_name: flc-3 FRI above-ground

growth_protocol: For ChIP experiments plants were grown in LD for 2 weeks and above-ground tissue was collected at ZT8.

extract_protocol:
After crosslinking, the ChIP and the ChIP-seq was done as in Mateos et al. (2015) Genome Biol 16:31, for both species.
For ChIP-seq, 10 μl from the eluted chromatin was then used for library preparation using Ovation Ultralow DR Multi- plex System (NuGen, Leek, The Netherlands). Libraries were sequenced using an Illumina Hi-Seq2500 instrument.

treatment_protocol: For ChIP on PEP1 we used Pajares and pep1-1 mutant with 1 µl of PEP1 antiserum raised against the C-terminal domain of PEP1 protein. For ChIP on FLC we analysed the Arabidopsis genotypes Col FRI and flc-3 FRI and 2 µl of FLC antiserum was used. Three independent biological replicates were performed for PEP1 ChIP-seq assays and two for FLC ChIP-seq. For ChIP on PEP1 the Pajares and pep1-1 genotypes were used.

value: above-ground tissue

value: flc-3 FRI


title: A9814_CD4_WT_90' media


title: A9812_CD8_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9811_CD8_STAT1 Transgenic_90' media


title: A9809_CD4_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9808_CD4_STAT1 Transgenic_90' media


title: FLC ChIP-Seq WT rep2

source_name: Col FRI above-ground

value: Col FRI


title: A9813_CD8_STAT1 Transgenic_90' 10 ng/ml IFNg


title: A9807_CD8_WT_90' 10 ng/ml IFNg


title: A9805_CD8_WT_90' media


title: FLC ChIP-Seq WT rep1


title: A9803_CD4_WT_90' 10 ng/ml IL-7


title: Ctrl2_Cr00_mnaseseq

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
Adapter sequences were trimmed from FASTQ during demultipexing step with CASAVA 1.8
Paired-end reads were aligned to mm10 using bowtie 1.1.1 using the parameters (--sam --best --strata)
Duplicates were removed with samtools
wig  files with protein occupancy values at each base pair across the whole genome were created with danpos2
Changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position were created with danpos2
Genome_build: mm10
Supplementary_files_format_and_content: wig files with protein occupancy

growth_protocol: Cells were grown in Alpha-MEM medium (Gibco) supplemented with 5% FBS and 1% Penicillin-Streptomycin solution and passaged at approximately 80% confluency.

extract_protocol:
Cells were washed wjth 1X ice-cold PBS and lysed to release nuclei, which were then re-suspended and treated with 60 units of MNase for 6 minutes.  Following digestion, nucleosomes were separated by electrophoresis in a 1% agarose gel and mononucleosome fragments were excised, deproteinized, and purified.
Library preparation was performed using the PrepX DNA Library kit and Apollo 324 NGS automatic library prep system (WaferGen, Fremont, CA). Overhangs in samples of double-strand DNA fragments (~5 ng) were first blunt-ended, and adenylated at the 3' ends for TA ligation to the sequencing adaptors. The ligated library was enriched by 6 cycles of PCR, followed by automated AMPure XP beads (Beckman Coulte, Brea CA) purification. To check the quality and yield of the library, one µl of purified PCR library was analyzed by Bioanalyzer with DNA High Sensitivity chip. To accurately quantify the library concentration for cluster generation, the library was 1:104 diluted with dilution buffer (10 mM Tris-HCl, pH 8.0 with 0.05% Tween 20), and qPCR analyzed with NEBNext Library Quant Kit (New England Biolabs, Ipswich, MA) using ABI 9700HT real-time PCR system (Lifetech, Grand Island, NY). Individually indexed libraries were proportionally pooled for clustering in the cBot system (Illumina, San Diego, CA). Libraries at the final concentration of 16 pM were clustered onto a flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced for 50 cycles using TruSeq SBS kit on Illumina HiSeq system to generate ~360 M pair-end 2x100 bp reads.

treatment_protocol: Cells were treated with filter-sterilized potassium chromate dissolved in MilliQ-grade water for 72 hours prior to extraction.

value: Mouse Hepatoma Cell Line

tag: chromium dosage

value: 0 µM (Control)

tag: enzyme

value: MNase (Worthington, LS004797)


title: A9804_CD4_WT_90' 10 ng/ml IFNg


title: FLC ChIP-Seq control rep1


title: atphb3.fq

city: Jinan

first: Xiangpei

last: Kong

address: 27 Shanda South Road

institute: Shandong University

data_processing:
RPKM
Supplementary_files_format_and_content: raw counts and RPKM

source_name: root

growth_protocol: Arabidopsis seeds were surface-sterilized with chlorine gas and incubated for 3 d at 4℃ after being plated onto Murashige and Skoog (MS) medium before transfer to a growth room with a 16-h day/8-h night photoperiod at 20°C.

extract_protocol:
Root tips were cut, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
Total RNA was extracted from the shoots and roots with TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

value: primary root

tag: site

value: root tip

tag: number


title: A9806_CD8_WT_90' 10 ng/ml IL-7


title: A9802_CD4_WT_90' media


title: A9815_CD4_WT_90' 10 ng/ml IL-7


title: Ctrl1_Cr00_mnaseseq

tag: cell type


title: Cr2_Cr20_mnaseseq

value: 2 µM


title: A9801_CD8_STAT1 Transgenic_90' 10 ng/ml IL-7


title: A9800_CD8_STAT1 Transgenic_90' media


title: AV74_No_Imput_2

data_processing:
Single reads were aligned to mm10 using bowtie
Insert size was assessed by spp
MACS2 was used to call differentiated peaks between treatments on pooled samples.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with called peaks with macs2

extract_protocol:
Cells were fixed with 1% formaldehyde and the reaction subsequently quenched using 0.125 M glycine.  After fixation, cells were lysed to release nuclei, which were washed and re-suspended in nuclei lysis buffer before sonicating the chromatin using a Diagenode Bioruptor.  Fragmented chromatin was diluted and separated into equivalent aliquots prior to antibody application and complex retrieval.
A ChIP-seq script was selected for sequencing library preparation using PrepX DNA Library kit and Apollo 324 NGS automatic library prep system (WaferGen, Fremont, CA). Overhangs in samples of double-strand DNA fragments (~5 ng) were first blunt-ended, and adenylated at the 3' ends for TA ligation to the sequencing adaptors. The ligated library was enriched by 8 cycles of PCR using index-specific primers, followed by automated AMPure XP beads (Beckman Coulte, Brea CA) purification. To check the quality and yield of the library, one µl of purified PCR library was analyzed by Bioanalyzer with DNA High Sensitivity chip. To accurately quantify the library concentration for cluster generation, the library was 1:104 diluted with dilution buffer (10 mM Tris-HCl, pH 8.0 with 0.05% Tween 20), and qPCR analyzed with NEBNext Library Quant Kit (New England Biolabs, Ipswich, MA) using ABI 9700HT real-time PCR system (Lifetech, Grand Island, NY). Individually indexed libraries were proportionally pooled for clustering in the cBot system (Illumina, San Diego, CA). Libraries at the final concentration of 16 pM were clustered onto a flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced for 50 cycles using TruSeq SBS kit on Illumina HiSeq system. According to Illumina, for studies targeting transcription factors, ~10M reads per sample were generated.

treatment_protocol: Cells were treated with filter-sterilized potassium chromate dissolved in MilliQ-grade water for 90 mins prior to fixation and processing.

value: Total Input

tag: chip antibody

value: CTCF (Cell Signaling, 2899S)


title: A9799_CD8_WT_90' 10 ng/ml IL-7


title: Cr1_Cr20_mnaseseq


title: AV73_No_Imput_1


title: AV55_CTCF_NoTx_2


title: A9797_CD4_STAT1 Transgenic_Unstimulated

value: Unstimulated


title: AV56_CTCF_Cr_2

value: 25 µM


title: A9798_CD8_STAT1 Transgenic_Unstimulated

value: STAT1 Transgenic


title: A9795_CD4_WT_Unstimulated


title: A9796_CD8_WT_Unstimulated


title: AV49_CTCF_NoTx_1


title: Col.fq


title: AV50_CTCF_Cr_1


title: SF8_mouse_atacseq

description:
processed data file:
N503_Cr10_N502_Cr00_q00001_filtered_BL_unique.bed.gz

data_processing:
Adapter sequences were trimmed from FASTQs.
Paired-end reads were aligned to mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align.
Duplicates were removed and library size was estimated using PICARD tools
Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired.
MACS2 (–nomodel –nolambda –keep-dup-all –call-summits) was used to call differentiated peaks between treatments on pooled samples.
Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with called peaks with macs2 after removing blecklisted peaks and duplicated peaks by their summits

extract_protocol:
Cells were lysed to release nuclei, then resuspended in a transposition buffer containing Tn5 Transposase for 30 minutes at 37 ºC prior to eluting DNA fragments using the Qiagen™ MinElute Kit.
The Nextera library was generated using an Illumina Nextera DNA Library Prep Kit (San Diego) after 9 PCR cycles for library amplification and indexing. Following amplification, samples were sequenced using an Illumina HiSeq platform to generate ~75 M pair-end 2x100 bp reads.

value: 1 µM

tag: transposition kit

value: Illumina, FC-121-1037


title: SF7_mouse_atacseq

value: Illumina, FC-121-1036


title: THAP_Riboseq_rep2

city: Ithaca

first: Yumi

last: Woo

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

description: ribosome-footprinted RNA

data_processing:
Library strategy: Ribo-seq
For the RNA-seq data, we used the reads in the last 500 bases of the annotation and generated readcounts, RPKM. For comparison, we generated read counts and RPKMs from the full-length mRNA . We used the cut-off of 10 raw read counts in the RNA-seq dataset. This removes the bimodal distribution of the RPKM readcounts generated by low readcount transcripts.
For the ribosome footprinting normalization, we normalized the reads to total sequenced reads instead of total uniquely mapped reads to account for the global repression in translation.
Genome_build: mm9
Supplementary_files_format_and_content: [bedgraph]  represents the read count positions of the 5' ends of the mapped reads and collapsed reads that have the same UMI at the same 5' end positions.

source_name: THAP, NIH3T3 cells

growth_protocol: NIH3T3 cells were cultured in DMEM (Gibco) media with 10% fetal bovine serum in a humidified 5% CO2 atmosphere at 37 degrees Celsius.

extract_protocol:
For ribosome profiling library, RNase I (100 U/μl) was treated in lysate and incubated at room temperature for 45 min. After nuclease digestion, ribosome footprinted RNAs were purified by sedimenting through a 1 M sucrose cushion and excising the urea gel between 26-34 nucleotides.
For mRNA expression profiling library, TRIzol was added into the supernatant and total RNA was extracted according to the manufacturer's protocol.
Ribo-seq libraries, 3′ end was dephosphorylated by adding PNK and ligated by adding 40 pmol of RA3 adaptor. 5′ end was phosphorylated by adding PNK and ATP and ligated by adding 30 pmol of RA5 adaptor and 50 pmol of RTP primer. After reverse transcription using Superscript II reverse transcriptase (Invitrogen), rRNA products were depleted by hybridization to biotinylated sense-strand oligonucleotides followed by removal of the duplexes through streptavidin bead affinity. Finally, through PCR and gel extraction, the library was generated with 150-160 bp-size.
For mRNA-seq library, poly(A) RNA was isolated using Dynabeads® mRNA purification kit (Ambion) according to the manufacturer’s protocol. After RNA fragmentation with 1 N NaOH at 37°C for 3 min, the final library ranging from 150 to 200 bp-size was generated followed by the same process as producing ribosome profiling library from the step of 3′ dephosphorylation, except for rRNA depletion.

treatment_protocol: For ER stress induction, thapsigargin (THAP, Sigma-Aldrich) was treated with 1 µM for 1 hr 30 min in NIH3T3 cells.

value: Fetus derived cell line from female human embryonic kidney

tag: passages

value: THAP (1µM) for 1.5hr


title: DMSO_Riboseq_rep2

description: ribosome-footprinted RNA

source_name: DMSO, NIH3T3 cells

value: DMSO for 1.5h


title: SF5_mouse_atacseq

description:
processed data file:
N502_Cr05_N502_Cr00_q00001_filtered_BL_unique.bed.gz

value: Mouse Hepatoma Cell Line

value: Illumina, FC-121-1034


title: DMSO_Riboseq_rep1

description: ribosome-footprinted RNA


title: SF4_mouse_atacseq

description:
processed data file:
N502_Cr01_N502_Cr00_q00001_filtered_BL_unique.bed.gz

value: Illumina, FC-121-1033


title: THAP_Riboseq_rep1

description: ribosome-footprinted RNA


title: THAP_RNAseq_rep1

description: TE.norm.txt

data_processing:
For the RNA-seq data, we used the reads in the last 500 bases of the annotation and generated readcounts, RPKM. For comparison, we generated read counts and RPKMs from the full-length mRNA . We used the cut-off of 10 raw read counts in the RNA-seq dataset. This removes the bimodal distribution of the RPKM readcounts generated by low readcount transcripts.
For the ribosome footprinting normalization, we normalized the reads to total sequenced reads instead of total uniquely mapped reads to account for the global repression in translation.
Genome_build: mm9
Supplementary_files_format_and_content: [bedgraph]  represents the read count positions of the 5' ends of the mapped reads and collapsed reads that have the same UMI at the same 5' end positions.
[TE.norm.txt] supplementary table; RPKM from RNA-seq was used to calculate translation efficiency.


title: SF6_mouse_atacseq

value: Illumina, FC-121-1035


title: THAP_RNAseq_rep2

description: TE.norm.txt


title: SF2_mouse_atacseq

value: 0 µM (Control)

value: Illumina, FC-121-1031


title: SF3_mouse_atacseq

value: Illumina, FC-121-1032


title: DMSO_RNAseq_rep1

description: TE.norm.txt

value: DMSO for 1.5hr


title: MouseLiver_InputDNA_(-MET)

source_name: liver

extract_protocol:
Cross-linked chromatin was collected and flash frozen before sonication with the Covaris M2. Lysates were clarified and protein-DNA complexes were immunoprecipitated with H3K4me3 antibody.
Libraries were prepared according to standard Illumina protocols.

treatment_protocol: C57BL/6J mice were fed with either 0.86% (Kcal) methionine control diet or 0.12% (Kcal) methionine MR diet for 12 weeks and fasted before being sacrificed.

value: liver


title: SF1_mouse_atacseq

value: Illumina, FC-121-1030


title: DMSO_RNAseq_rep2

description: TE.norm.txt


title: MouseLiver_InputDNA_(+MET)


title: MouseLiver_(-MET)_H3K4me3_ChIPseq_Rep2


title: SC_cAMP_2

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Ribodepleted RNA
Counts of reads in each gene
Run 1 Fastq Read 1
Run 1 Fastq Read 2
Run 2 Fastq Read 1
Run 2 Fastq Read 2

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the rn6 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
hMeDIP-seq reads and Unprecipitated Input reads were aligned to the rn6 genome assembly using BWA
Peak calling was performed with MACS2
Peaks were filtered using the IDR pipeline from the Encode Project with an IDR cutoff of 0.02.
Number of reads in peaks were counted using HTSeq-count.
Genome_build: rn6
Supplementary_files_format_and_content: Count files were generated using either STAR or HTSeq-count.

organism: Rattus norvegicus

source_name: RNA-seq

extract_protocol:
Qiagen RNEasy or Qiagen DNA Mini
Active Motif hMeDIP or TruSeq RNA Prep kit v2

treatment_protocol: 100 mM cAMP

value: Primary cultured schwann cells

tag: passage

value: 3 to 5


title: SC_cAMP_3


title: MouseLiver_(+MET)_H3K4me3_ChIPseq_Rep2


title: SC_Control_3


title: MouseLiver_(+MET)_H3K4me3_ChIPseq_Rep1


title: ATAC-seq_Ezh1_KO_AGM

source_name: E10.5 AGM cells

value: Hematopoietic cells


title: SC_Control_2


title: SC_Control_1

description:
Ribodepleted RNA
Counts of reads in each gene
Run 1 Fastq Read 1
Run 1 Fastq Read 2


title: SC_cAMP_1


title: ATAC-seq_Ezh1_WT_AGM


title: CS 1

city: Stony Brook

last: McKinnon

address: Nichols Rd

department: Neurobiology and Behavior

institute: Stony Brook University

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to Rnor_6.0 whole genome using Rsubread
Count matrix for Ensembl genes was created using the featureCounts function in Rsubread
Genome_build: Ensembl Rnor_6.0
Supplementary_files_format_and_content: comma delimited text file

source_name: CS, adrenal gland

extract_protocol:
Total RNA was extracted using the RNeasy Miniprep Kit (Qiagen)
cDNA libraries were prepared using the Ultra Directional RNA Library Prep Kit (NEB), Illumina HiSeq sequencer, 50 bp single reads

tag: Sex

value: Male

value: Sprague-Dawley

tag: stress

value: CS

value: Adrenal Gland


title: Control 2

source_name: Control, adrenal gland

value: Control


title: CVS 1

source_name: CVS, adrenal gland

value: CVS


title: CVS 2


title: WT Chronic d8 REP2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA sequencing reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least one library. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. P values from Bayes moderated t-tests were adjusted to control the global false discovery rate (FDR) across all comparisons with the ‘global’ option of the limma package. Genes were called differentially expressed if they achieved a FDR of 0.1 or less and had an expression change of 1.5 folds or greater. The called differentially expressed genes must also have at least 8 RPKMs (reads per kilobase of exon length per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: space-delimited text files include normalized log2-RPKM values for each sample

source_name: spleens and lymph nodes

growth_protocol: P14 CD8 T cell (wildtype [WT] or Irf4+/- [Irf4Het] or Batf+/- [BatfHet]) were transferred into congenically marked host mice, which were subsequently infected with LCMV WE (acute) or LCMV Docile (chronic). Donor P14 cell were sorted from infected mice on either day 8 or day 30 post infection and used for RNA sequencing. Naive (CD62L+, CD44-) CD8 T cells were used as controls.

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: celltype

value: P14 CD8+ T cells

tag: genotype

value: WT

tag: infection

value: Chronic

tag: time

value: 8 days


title: BatfHet Chronic d8 REP1

tag: strain

value: Batf Het


title: Control 3

tag: tissue


title: BatfHet Chronic d8 REP2


title: Control 1


title: WT Acute d8 REP1

value: Acute


title: P8_pHEnd_EC_basal

data_processing:
Basecalls performed using bcl2fastq version 1.8.4 (for Illumina HiSeq2500) and bcl2fastq version 2.18.0.12 (for NextSeq500)
Reads were aligned to hg19 using RSEM version 1.2.31 with parameters --paired-end; --star; --estimate-rpsd; --append-names; --output-genome-bam; --star-gzipped-read-file
Genes with FPKM values > 0.1 were then further analyzed in gProfiler
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files of FPKM and gProfiler results

source_name: Primary endoeneurial endothelial cells (passage 8)

extract_protocol:
Endoneurial microvessels were fluorescently detected in 20 micron thick axial cryosections of human sural nerve biopsies using UEA-1-FITC, and laser capture microdissection performed. Microvessels were stored in extraction buffer at -80oC and RNA isolated using Arcturus Pico Pure Isolation Kit (Thermo Fisher Scientific) or miRNeasy kit (Qiagen, Hilden, Germany). On-column DNase digestion was also performed to remove contaminating genomic DNA using the RNase-free DNase Set (Qiagen).
cDNA libraries were generated using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech) and ribosomal cDNA was depleted prior to the final amplification step

value: Sciatic nerve

tag: passage number

tag: age

value: Female


title: Irf4Het Acute d30 REP3

value: Irf4 Het

value: 30 days


title: WT Chronic d30 REP2


title: P3pHEnd_EC

source_name: Primary endoeneurial endothelial cells (passage 3)


title: WT Acute d8 REP2


title: CS 2


title: MouseLiver_(-MET)_H3K4me3_ChIPseq_Rep1

data_processing:
HCT116 ChIP-seq: Reads were aligned to a combinational genome consisting of the human reference genome hg19 and the Drosophila reference genome dm6 using Bowtie2. Alignment files were then filtered according to their alignment scores and down-sampled to ensure each file contains the same amount of unique Drosophila reads. Finally, reads mapped to hg19 in the normalized alignment files were kept for peak-calling and other following analyses. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
Mouse liver ChIP-seq: Reads were aligned to a the reference genome mm8 using Bowtie2. Alignment files were then filtered according to their alignment scores and normalized by sequencing depth. Processing of alignment files was done using SAMtools. Peaks were called using the --broad mode of MACS2 and filtered with the criterion that enrichment q-value is smaller than 1e-5.
HCT116 RNA-seq: Raw reads were aligned to the human reference genome hg19 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Mouse liver RNA-seq: Raw reads were aligned to the mouse reference genome mm8 using TopHat2. Number of reads mapped to each gene feature was first quantified using HTSeq with the input of GTF files obtained from the UCSC Table Browser and then normalized using DESeq2. Differential expression analysis was done with DESeq2. P-values were adjusted using the Benjamini-Hochberg procedure.
Genome_build: hg19 (HCT116), mm8 (mouse liver)

value: liver


title: CIN3-26613

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Lavage-based self-sample

data_processing:
Each library was indexed in order to multiplex up to 5 samples per sequencing run.
Sequenced reads were analyzed using the miRDeep2 algorithm (Friedländer et al., 2012 Nucl Acids Res). In brief, reads were trimmed for adaptor sequences, and filtered for low-quality sequences and sequences shorter than 18 nucleotides followed by alignment to the human genome (hg19). Input from known miRNAs was obtained from miRBase version 20 (Kozomara et al., 2011, Nucl Acids Res). To avoid multiple counting of miRNA sequences that can originate from several genomic loci, we only counted the expression of miRNA paralogs once.
miRNA read counts were normalized according to the trimmed mean of M values (TMM) normalization strategy (Robinson et al., 2010 Genome Biol). Subsequently, the distribution of miRNA read counts was assessed and samples that depicted an atypical distribution were excluded.
Normalized miRNA read counts were square-root transformed to the quasi Gaussian scale followed by miRNA data standardization. Only those miRNAs that exhibited non-zero read counts in at least 3 samples were included.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include microRNA names and standardized count values for each sample

source_name: Self-sample HPV-positive CIN3_26613

extract_protocol:
Total RNA from self-samples was extracted using Direct-ZolTM RNA Miniprep (Zymo Research, Freiburg, Germany) following the manufacturer's instructions
Preparation of cDNA libraries was performed with equal amount of input RNA per sample (1000ng of total RNA) using the TruSeq Small RNA Sample Preparation Kit according to the manufacturer's instruction (Illumina, San Diego, CA, USA)

tag: histology


title: Irf4Het Chronic d30 REP2


title: CIN3-26488

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_26488


title: WT Chronic.PDL1 d30 REP2


title: CIN3-26174

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_26174


title: CD62L+ Naive d0 REP2

value: CD8+ T cells

value: 0 days


title: WT Chronic d8 REP1


title: CIN3-26115

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_26115


title: CIN3-26038

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_26038


title: CIN3-25924

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_25924


title: WT Acute d30 REP3


title: CIN3-27849

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_27849


title: Irf4Het Acute d30 REP2


title: CIN3-25501

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_25501


title: WT Acute d30 REP1


title: Irf4Het Chronic d30 REP1


title: CIN3-24478

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_24478


title: CD62L+ Naive d0 REP1


title: CIN3-24309

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_24309


title: CIN3-24098

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_24098


title: Irf4Het Acute d30 REP1


title: CIN3-23530

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_23530


title: WT Chronic d30 REP1


title: CIN3-22690

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22690


title: CIN3-22830

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22830


title: CIN3-22938

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22938


title: CIN3-22053

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22053


title: WT Acute d30 REP2

source_name: spleens and lymph nodes


title: CIN3-22363

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22363


title: CIN3-20777

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_20777


title: WT Chronic.PDL1 d30 REP1


title: CIN3-25221

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_25221


title: Control-27059

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_27059

value: normal


title: Control-26658

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26658


title: CIN3-21249

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_21249


title: CIN3-23202

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_23202


title: Control-27491

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_27491


title: Control-27594

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_27594


title: Control-26565

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26565


title: Control-26203

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26203


title: Control-27063

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_27063


title: Control-26221

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26221


title: Control-26864

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26864


title: ATAC-Seq analysis of RxrKO mouse BMDM cells differentiated in the presence of MCSF (24hIL4)

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: bone marrow-derived macrophage

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 (20ng/ul) for 24 hours. Cells were lysed in the following lysis buffer: 10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL.
Nuclei were resuspended in tagmentation reaction mixture (2ul TD enzyme, 25ul 2xTD buffer and 23ul H2O) and incubated for 30 minutes at 37C (Nextera DNA preparation kit: FC-121-1030, index kit: FC-121-1011). Reactions were stopped by the addition of EDTA and purified with Qiagen Minelute DNA preparation kit. Purified DNA was PCR amplified with KAPA PCR mix using 14 PCR cycles. PCR reactions were cleaned up with AMPure XP magnetic beads.

tag: breed

value: 3 months

value: male

tag: method

value: ATAC-seq


title: ATAC-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF


title: Control-26158

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_26158


title: ATAC-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: ATAC-Seq analysis of RxrKO mouse BMDM cells differentiated in the presence of MCSF


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4) 2


title: CIN3-26326

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_26326


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4) 1


title: Control-24934

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24934


title: Control-24928

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24928


title: Control-25709

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_25709


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: ATAC-seq_Ezh1_HET_AGM

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly mm9 using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: wig file and peak bed file

source_name: E10.5 AGM cells

value: Hematopoietic cells


title: CIN3-21638

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_21638


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF 2


title: Control-25025

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_25025


title: CIN3-22926

description: Lavage-based self-sample

source_name: Self-sample HPV-positive CIN3_22926


title: Control-24467

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24467


title: Control-24057

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24057


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hLG268, rep2)

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 20ng/ul) for the indicated period of time and were double crosslinked and lysed. Immunoprecipitation was carried out with antibodies against PU.1 (sc-352), STAT6 (sc-981), RXR (sc-774), PPARγ (Perseus #PP-A3409A), P300 (sc-585), RNAPII-pS2 (ab5095) and RAD21 (ab992). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

tag: chip antibody

value: PolII-pS2 (ab5095)


title: Control-24280

description: Lavage-based self-sample

source_name: Self-sample HPV-positive control_24280


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF 1


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hLG268, rep1)


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hVeh, rep2)


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4 (rep3)


title: RXR ChIP-Seq analysis of Stat6KO mouse BMDM cells differentiated in the presence of MCSF/IL4


title: RXR ChIP-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF/IL4


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4 (rep2)


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hRSG, rep2)


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hVeh, rep1)


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4 (rep1)


title: PPARg ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4

value: PPARg (Perseus #PP-A3409A)


title: HCT116_(-MET)_RNAseq_Rep2

extract_protocol:
Total RNA was extracted using the PARIS kit.
Libraries were prepared according to standard Illumina protocols.


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (rep2)


title: PPARg ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (rep1)


title: HCT116_(+MET)_RNAseq_Rep1


title: PolII pS2 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hRSG, rep1)


title: HCT116_(-MET)_RNAseq_Rep1


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: hsa_kidney_captureseq_rep2

city: Darlinghurst

first: Ira

middle: William

last: Deveson

state: NSW

address: 384 Victoria St

institute: The Garvan Institute

description: human chromosome 21 RNA CaptureSeq

data_processing:
map PacBio reads with GMAP (see Methods)
custom filtering pipeline (see Methods)
concordance with Illumina reads (see Methods)
merge with Gencode v19
Genome_build: hg19
Supplementary_files_format_and_content: known and novel isoforms retireved with single-molecule / short read RNA CaptureSeq on Hsa21

source_name: human kidney

extract_protocol:
For mice tissues, total RNA was extracted in TRIzol reagent (Ambion). Extraction of the aqueous phase was performed using chlorophorm and RNA precipitation was achieved with isopropanol. RNA pellets were washed in ice-cold 75% EtOH and allowed to dry before suspension in DEPC-treated H2O.
Oligonucleotide baits targeting the entire non-repetitive portion of Hsa21 (hg19) and its syntenic regions in the mouse (mm10) genome, obtained using the UCSC Genome Browser liftOver tool, were designed and synthesized by Roche/NimbleGen. In total, the array targeted 25.3 Mb comprising 0.87% of the human genome and 20.3 Mb comprising 0.77% of the mouse genome. According to procedures described previously (Mercer et al., 2014), total RNA samples were assessed for potential gDNA contamination by PCR and accordingly treated with Turbo DNAse (Ambion). Samples were spiked with ERCC RNA spike-in controls (Mix 2) (Jiang et al., 2011) to a final 1% concentration and rRNA-depleted using the Ribo-Zero rRNA removal magnetic kit (Human/Mouse/Rat, Epicentre). Capture enrichment of cDNA libraries was performed as described previously (Mercer et al., 2014). Short-read sequencing libraries were prepared with the Illumina TruSeq stranded mRNA low-template kit. Libraries were sequenced at the Garvan Institute (Sydney, NSW, Australia) on the Illumina HiSeq 2000 or Illumina HiSeq 2500 platforms, generating 2 x 101bp and 2 x 125bp paired-end sequencing, respectively.

value: kidney

tag: Stage

value: adult

tag: type

value: healthy


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: hsa_kidney_captureseq_rep1

description: human chromosome 21 RNA CaptureSeq


title: hsa_testis_captureseq_rep2

description: human chromosome 21 RNA CaptureSeq

source_name: human testis

value: testis


title: hsa_testis_captureseq_rep3

description: human chromosome 21 RNA CaptureSeq


title: hsa_brain_captureseq_rep2

description: human chromosome 21 RNA CaptureSeq

source_name: human brain

value: brain


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: STAT6 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)


title: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (rep3)


title: CRC_26

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Alignment to the hg38 reference genome was performed with Spliced Transcripts Alignment to a Reference (STAR) v2.5
Genome_build: hg38
Supplementary_files_format_and_content: gene count calculations were performed with Spliced Transcripts Alignment to a Reference (STAR) v2.5

source_name: CRC_colonic mucosa

growth_protocol: HILEC were grown and mantained in Endothelial Cell Growth Medium (Lonza)

extract_protocol:
Total RNA has been isolated with the TRIzol® RNA Isolation Reagent (Thermo Fisher Scientific), according to manufacturer's instructions.
Stranded libraries have been prepared from 2 µg of total RNA in accordance with the TruSeq RNA sample preparation guide (Illumina).

tag: subject status

value: Colorectal cancer

tag: cell type

value: Human Intestinal Lymphatic Endothelial cells (HILEC)


title: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)

source_name: bone marrow-derived macrophage

tag: Sex


title: CRC_29


title: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: IgG ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4

value: IgG (Millipore, 12-370)


title: HCT116_(+MET)_RNAseq_Rep2


title: CRC_25


title: CRC_15


title: PU.1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (6hIL4)


title: PU.1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: hsa_testis_captureseq_rep1

description: human chromosome 21 RNA CaptureSeq


title: CRC_9


title: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: CRC_1


title: Healthy_480

source_name: healthy_colonic mucosa

value: Healthy control


title: CRC_2


title: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hIL4)


title: Healthy_478


title: Healthy_475


title: Healthy_466


title: 22_Eed_14d

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: 14 d post-crush

data_processing:
Illumina Pipeline  Casava 1.8.2
Reads were mapped to the Mus musculus genome mm10 using CLC BioWorkbench ver. 9
Genome_build: mm10

source_name: sciatic nerve, Eed cKO, 14 d post-crush

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water. Eed-floxed mice were generated by backcrossing the flox allele for seven generations against the C57BL/6 genetic background and mated to mP0TOTA-Cre (B6N.FVB-Tg(Mpz-cre)26Mes/J, obtained from Jackson Laboratory, RRID: IMSR_JAX:017927).

extract_protocol:
Total RNA was purified using Qiagen Rneasy Lipid Kit
Libraries were prepared using the Illumina TruSeq Stranded total RNA sample preparation kit V2

treatment_protocol: The sciatic nerves of adult mice at the age of 2 months were exposed and transected at the sciatic notch (Hung et al., 2015) or crushed 1 min using fine forceps. As a control, the contralateral limb also received a sham operation consisting of only a skin incision. The nerve tissues distal to the transection or crushed lesions, which were labeled with sterile black ink, and contralateral (sham) nerves were isolated.

value: sciatic nerve

value: Schwann-cell specific knockout of Eed

value: two months


title: hsa_brain_captureseq_rep1

description: human chromosome 21 RNA CaptureSeq


title: CRC_12


title: Healthy_465


title: CRC_17


title: R17_Eed_1d

description: 1d post-cut

source_name: sciatic nerve, Eed cKO, 1d post-cut


title: 24_Eed_14d

description: 14 d post-crush


title: Genome-wide localization analyses of RAD21 binding sites

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were double crosslinked and lysed. Immunoprecipitation was carried out with antibodies against CTCF (Millipore, 07-729) and RAD21 (ab992). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

value: 3 months

value: male


title: R15_Eed_1d

description: 1d post-cut


title: Healthy_447


title: L6_Eed_sham

description: sham

source_name: sciatic nerve, Eed cKO, sham


title: Healthy_301


title: L17_Eed_sham

description: sham


title: 23_wt_14d

description: 14 d post-crush

source_name: sciatic nerve, wt, 14 d post-crush

value: wild type


title: Healthy_443


title: Genome-wide localization analyses of CTCF binding sites

value: CTCF (Millipore, 07-729)


title: MSC-iPS 5F +shLUC C11 day 28 rep 1

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 –o 10)
Then, the cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (--library-type=fr-unstranded --min-intron-length=10 --no-coverage-search --microexon-search --min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene using a htseq-count tool with the following parameters (--stranded=no --idattr=gene_id -t exon -i gene_name).
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing read counts from htseq-count

source_name: Human MSC iPS-derived 5F hematopoietic cells

growth_protocol: Human CD34- and MSC-iPS cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma) and puromycin was added at 0.35 ug/mL (ThermoFisher). Media were changed every 3-4 days. RNA was harvested from bulk day 4 samples, or from sorted CD34+CD38- day 28 samples.  Mouse AGM and YS were microdissected from E10.5 embryos and dissociated to single cells. Cells were then sorted for immunophenotypic markers cKit+VE-Cadherin+CD45+CD41+.

extract_protocol: For 5F cells, we used the NEB ultradirectional kit with 50 ng of input RNA. For mouse YS and AGM cells, we used the Clontech smarterseq kit with 10 ng input RNA.

treatment_protocol: 5F cells were transfected with 2x shRNAs targeting the luciferase (shRNAs F8 and C11) and EZH1(shRNAs D4 and D6) genes. mRNA was collected 4 and 28 days after transfection

value: Hematopoietic cells


title: MSC-iPS 5F +shLUC F8 day 28 rep 1


title: MSC-iPS 5F +shLUC F8 day 28 rep 2


title: 26_wt_14d

description: 14 d post-crush


title: MSC-iPS 5F +shLUC C11 day 28 rep 2


title: L15_Eed_sham

description: sham


title: CRC_20


title: 34-iPS 5F +shLUC F8 day 28 rep 1

source_name: Human CD34 iPS-derived 5F hematopoietic cells


title: Healthy_450


title: R1_wt1d

description: 1d post-cut

source_name: sciatic nerve, wt, 1d post-cut


title: R7_wt1d

description: 1d post-cut


title: 34-iPS 5F +shLUC C11 day 28 rep 2


title: L14_con

description: sham

source_name: sciatic nerve, wt, sham


title: L1_con

description: sham


title: R14_wt1d

description: 1d post-cut


title: 34-iPS 5F +shLUC C11 day 28 rep 1


title: Healthy_464


title: MSC-iPS 5F +shEZH1 D6 day 28 rep 3


title: MSC-iPS 5F +shEZH1 D6 day 28 rep 2


title: R6_Eed_1d

description: 1d post-cut


title: s9_CD4_WT_Unstimulted

data_processing:
Adapter Trimmed reads were aligned to mouse genome version GRCm38 and mapped to ensemble gene features (v38.80, current June 2015) using Genomics Workbench software (CLC bio, version 8.0.2). Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Complete read-pairs mapping to specific (10 or fewer) exon locations were counted, Reads matching (10 or fewer) equally high scoring locations were assigned randomly.
Using JMP/Genomics software (SAS Institute), raw counts were inflated log-transformed and then normalized by upper quartile scaling
Genome_build: GRCm38
Supplementary_files_format_and_content: per-gene expression as log2(fragment count +1), where fragment count=total exon reads, normalization by Upper Quartile Scaling. Sample s17 filtered out from dataset due to low signal.

source_name: sorted naive CD4 T cells

extract_protocol:
The cells were then washed once with PBS before being resuspended in TRIzol (Invitrogen) and stored at −80°C.
Illumina TrueSeq Stranded mRNA Library Prep kit from an input of 500 ng total RNA ("90-minute stimulation" samples)  Illumina True-seq non-stranded mRNA ("overnight stimulation" samples)

tag: genotype/variation

value: WT

tag: stimulus

value: Unstimulted


title: L7_con

description: sham

tag: genotype


title: 21_wt14d

description: 14 d post-crush


title: MSC-iPS 5F +shEZH1 D6 day 28 rep 1


title: s8_CD4_WT_O/N 500 U/ml IFNa4

value: O/N 500 U/ml IFNa4


title: 34-iPS 5F +shLUC F8 day 28 rep 2


title: s6_CD4_WT_O/N 20 ng/ml IL-7

value: O/N 20 ng/ml IL-7


title: s5_CD4_WT_Unstimulted


title: s7_CD4_WT_O/N 10 ng/ml IFNg

value: O/N 10 ng/ml IFNg


title: s4_CD4_WT_O/N 500 U/ml IFNa4


title: MSC-iPS 5F +shEZH1 D4 day 28 rep 2


title: 34-iPS 5F +shEZH1 D6 day 28 rep 2


title: MSC-iPS 5F +shEZH1 D4 day 28 rep 3


title: s3_CD4_WT_O/N 10 ng/ml IFNg


title: s2_CD4_WT_O/N 20 ng/ml IL-7


title: 34-iPS 5F +shEZH1 D4 day 28 rep 1


title: MSC-iPS 5F +shLUC F8 day 4 rep 2


title: MSC-iPS 5F +shLUC F8 day 4 rep 1


title: s16_CD4_STAT1 Transgenic_O/N 20 ng/ml IL-7

value: STAT1 Transgenic


title: s15_CD4_STAT1 Transgenic_Unstimulted


title: 34-iPS 5F +shEZH1 D4 day 28 rep 2


title: MSC-iPS 5F +shLUC C11 day 4 rep 1


title: s14_CD4_STAT1 Transgenic_O/N 20 ng/ml IL-7


title: s13_CD4_STAT1 Transgenic_Unstimulted


title: 34-iPS 5F +shLUC F8 day 4 rep 1


title: s12_CD4_WT_O/N 500 U/ml IFNa4


title: 34-iPS 5F +shLUC C11 day 4 rep 1


title: MSC-iPS 5F +shEZH1 D6 day 4 rep 2


title: s10_CD4_WT_O/N 20 ng/ml IL-7


title: MSC-iPS 5F +shEZH1 D4 day 28 rep 1


title: 34-iPS 5F +shEZH1 D6 day 28 rep 1


title: MSC-iPS 5F +shEZH1 D6 day 4 rep 1


title: s11_CD4_WT_O/N 10 ng/ml IFNg


title: MSC-iPS 5F +shEZH1 D4 day 4 rep 1


title: 34-iPS 5F +shEZH1 D6 day 4 rep 1


title: s17_CD4_STAT1 Transgenic_Unstimulted


title: s1_CD4_WT_Unstimulted


title: 34-iPS 5F +shEZH1 D4 day 4 rep 1


title: MSC-iPS 5F +shEZH1 D4 day 4 rep 2


title: Tumor_2

city: San Francisco

last: Raleigh

state: CA

address: 555 Mission Bay Blvd South

institute: UCSF

data_processing:
Input sequences were analyzed in FASTQ format, with trimming of known adapters and low-quality regions of reads using Fastq-mcf and sequence quality control using FastQC and RSeQC
Alignment to the UCSC mm10 mouse genome assembly was performed using Bowtie 2.2.4, reads were assigned to genes using featureCounts
Gene-level counts were arrived at using Ensembl gene annotation in GTF format
EdgeR was used to calculate differential expression P-values, and p.adjust was used to calculate the false discovery rate for each P-value using the Benjamini-Hochberg method
Genome_build: mm10
Supplementary_files_format_and_content: gene level counts (Raleigh_All_Genes.xlsx)
Supplementary_files_format_and_content: p-value, FDR and fold change values for each gene (Raleigh_processed.xlsx)

source_name: Medulloblastoma

growth_protocol: Mice were aged until P35, at which point samples were collected

extract_protocol:
RNA was extracted according to the manufacturer's protocol using TRIzol (15596026, Thermo Fisher Scientific, Waltham, MA) followed by RNeasy Mini Kit cleanup (74104, QIAGEN, Valencia, CA)
Libraries were constructed according to the manfacturer's protocol using the TruSeq RNA Library Prep Kit v2 (RS-122-2001, Illumina, San Diego, CA)

tag: strain background

value: Math1-Cre SmoM2.c/wt

value: female

value: Medulloblastoma


title: Tumor_1


title: s18_CD4_STAT1 Transgenic_O/N 20 ng/ml IL-7

tag: strain


title: WT_3

source_name: Cerebellum

tag: tissue

value: Cerebellum


title: MSC-iPS 5F +shLUC C11 day 4 rep 2


title: WT_2


title: WT_1