title: Day 8 of repigmentation

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

description:
8 day depigmentation animals plus 8 days back in the dark
8 days repig (X05) CPM+1

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Differential gene expression was simply measured by fold-change comparisons between control day 0 (wild-type) and white animals after 8 days of depigmentation treatment.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: CPM

organism: Schmidtea mediterranea

source_name: Wildtype animals

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol:
All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: Animals were fed 3 times control(RNAi), apc(RNAi), or Smed-Bcatenin1(RNAi) every 3 days. Animals were amputated 3 days following their final feed. RNA was extracted from >5 regenerating tail fragments at days 1, 2, 3, 4, 5 and 6 post amputation. In total, 54 samples (3 RNAi conditions with 6 time points, biologically replicated 3 times) were sequenced to a depth of >43 million reads per mixed sample.

tag: strain

value: Asexual CIW4

value: Whole animals

tag: treatment

value: repigmentation

tag: time point

value: 8 days


title: 1375-B12_GTAGAGGA-CTCTCTAT_L001

status: Public on Dec 01 2017

type: SRA

city: NEW YORK

first: Cecilia

last: Berin

state: NY

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
processed data file:
peanut_gene_raw_counts
peanut_1r1c_RLE_normalized_RPKM

library_source: transcriptomic

data_processing:
RNAseq reads were aligned to hg38 using star
Genes were quantified using featurecount
Cells with reads<5e5 were removed and genes with counts<1 in <cell were removed.
RPKM were calcuated after RLE normalizaiton within EdgeR
Genome_build: hg38
Supplementary_files_format_and_content:
peanut_gene_raw_counts: raw counts for each Sample
peanut_1r1c_RLE_normalized_RPKM: normalized RPKM for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: peanut-responsive T cells_peanut allergic subject_1375

growth_protocol: PBMCs were isolated by density centrifugation with Ficoll-Paque Plus (GE Healthcare) and cultured in AIM V® medium (Gibco) with 2.5% autologous plasma.

extract_protocol:
Sorted Tregs and CD154+ T cells were resuspended and loaded onto a Fluidigm C1TM Single-Cell Auto Prep IFC for Fluidigm C1TM processing as per manufacturer protocols (Fluidigm). Single-cells were visualized by microscopy and wells containing >1 cell were noted and excluded from further steps. cDNA was generated according to Fluidigm C1TM protocols with SMARTer® UltraTM Low RNA Kit for the Fluidigm C1TM System reagents (Clontech Laboratories). Resultant cDNA from Fluidigm C1TM processing was subsequently assessed for quantity and quality using a Qubit Fluorometer 3.0 (Thermo Fisher Scientific) and 2100 Bioanalyzer or 2200 TapeStation (Agilent Technologies).
cDNA which passed QC were subsequently processed for library construction using the Nextera XT DNA Library Prep and Nextera XT Index Kits (all from Illumina).

treatment_protocol: PBMCs were stimulated with 100 μg/mL crude peanut extract (CPE) or 5μL/mL anti-CD3/CD28 beads (Invitrogen) for 18 hours. For surface CD154 staining (sorting), blocking anti- CD40 antibody (Miltenyi Biotec) was added to the culture to maintain CD154 at the surface. PBMCs stimulated for 18h were harvested and enriched for CD154+ cells using the CD154 MicroBead Kit (Miltenyi Biotec). Enriched cells were stained with CD3 APC-Cy7 (Clone SK7, eBioscience), CD4 Alexa Fluor 488 (Clone OKT4, BioLegend) and CD154 streptavidin PE (Clone 24-31, eBioscience). CD3+CD4+CD154+ T cells were sorted on the BD FACSAria IIu (BD Biosciences) in Mount Sinai’s Flow Cytometry Core Facility, and resuspended according to manufacturer protocols (Fluidigm, South San Francisco, CA).

tag: subject id

tag: allergies

value: Peanut

tag: stimulation

tag: tissue/cell type

value: blood; peripheral blood mononuclear cells (PBMCs)

tag: cell subtype


title: Day 2 of repigmentation

description:
8 day depigmentation animals plus 2 days back in the dark
2 days repig (X04) CPM+1

tag: tissue

value: 2 days


title: Day 1 of repigmentation

description:
8 day depigmentation animals plus 1 day back in the dark
1 day repig (X03) CPM+1

value: 1 day


title: 1402-B7_CTCTCTAC-CTCTCTAT_L005

source_name: polyclonally activated T cells_peanut allergic subject_1402


title: 1375-C8_CAGAGAGG-TATCCTCT_L001


title: 1375-A11_AAGAGGCA-GCGTAAGA_L001


title: 1430-E6_TAGGCATG-GTAAGGAG_L006

source_name: polyclonally activated T cells_peanut allergic subject_1430


title: 1407-G4_TCCTGAGC-AAGGAGTA_L004

source_name: peanut-responsive T cells_peanut allergic subject_1407


title: 1401-F5_GGACTCCT-ACTGCATA_L002

source_name: peanut-responsive T cells_peanut allergic subject_1401


title: 1403-B10_CGAGGCTG-CTCTCTAT_L003

source_name: peanut-responsive T cells_peanut allergic subject_1403

value: Peanut & Egg & Milk


title: 1402-B6_TAGGCATG-CTCTCTAT_L005


title: 1430-E8_CAGAGAGG-GTAAGGAG_L006


title: 1407-F9_GCTACGCT-ACTGCATA_L004


title: 1375-A4_TCCTGAGC-GCGTAAGA_L001


title: 1435-B9_GCTACGCT-CTCTCTAT_L007

value: Tregs


title: 1403-C7_CTCTCTAC-TATCCTCT_L003


title: 1430-F6_TAGGCATG-ACTGCATA_L006


title: 1375-B1_TAAGGCGA-CTCTCTAT_L001


title: 1407-E9_GCTACGCT-GTAAGGAG_L008


title: 1435-F10_CGAGGCTG-ACTGCATA_L008


title: 1430-G5_GGACTCCT-AAGGAGTA_L006


title: 1401-H3_AGGCAGAA-CTAAGCCT_L002


title: Day 8 of depigmentation

description:
wild-type animals plus 8 days of depigmentation treatment
8 day depig (X02) CPM+1

value: depigmentation


title: 1375-A5_GGACTCCT-GCGTAAGA_L001


title: 1407-F10_CGAGGCTG-ACTGCATA_L004


title: control WT animals

description:
control animals in the dark
WT (X01) CPM+1


title: 1375-D3_AGGCAGAA-AGAGTAGA_L001


title: 1430-E12_GTAGAGGA-GTAAGGAG_L006


title: 1407-E8_CAGAGAGG-GTAAGGAG_L008


title: 1402-B4_TCCTGAGC-CTCTCTAT_L005


title: 1407-E1_TAAGGCGA-GTAAGGAG_L004


title: 1401-E2_CGTACTAG-GTAAGGAG_L008


title: HD53-D1_TAAGGCGA-AGAGTAGA_L007

source_name: Tregs_healthy control_HD53


title: 1375-D2_CGTACTAG-AGAGTAGA_L001


title: HD54-D7_CTCTCTAC-AGAGTAGA_L007

source_name: Tregs_healthy control_HD54


title: 1402-B2_CGTACTAG-CTCTCTAT_L005


title: 1401-E5_GGACTCCT-GTAAGGAG_L008


title: 1430-G7_CTCTCTAC-AAGGAGTA_L006


title: Nanoblades_RNA_content

city: Lyon

first: Emiliano

middle: P

last: Ricci

address: 46 allée d'Italie

department: Centre International de Recherche en Infectiologie

country: France

institute: INSERM

data_processing:
Image analysis and base calling were performed using bcl2fastq v1.8.4
5’ in sequence barcode and 3′-adaptor sequences were removed from reads when present. Reads were then aligned to a custom set of sequences corresponding to ribosomal RNA and tRNA as well as to the human Refseq transcriptome from UCSC (hg19 assembly) using RSEM/1.2.19 with parameters: --strand-specific --forward-prob 1 --seed-length 10 --bowtie2 --bowtie2-sensitivity-level very_sensitive --calc-ci --ci-memory 2048 --fragment-length-mean 40 --fragment-length-sd 30
Genome_build: hg19
Supplementary_files_format_and_content: Nanoblades_mRNA_rRNA_tRNA_sgRNA_counts_genes.csv reports gene counts for endogenous cellular mRNAs, ribosomal RNAs, tRNAs and the CRISPR/Cas9 sgRNA expressed in producer cells.

source_name: Purified Murine-Leukemia Virus-like particles loaded with the Cas9 protein and a single-guideRNA targeting the YFP coding sequence.

growth_protocol: HEK293T Lenti-X cells (Clontech) were transfected with plasmids coding for Murine Leukemia virus Gag/Pro-Pol, a Gag::Cas9 fusion, a single-guideRNA targeting the YFP coding sequence, the vesicular stomatitis virus G-protein (VSVG) and the Baboon endogenous retrovirus envelope (BaeV). 48 hours after transfection, the supernatant is collected, cellular debris removed by centrifugation and virus-like particles purified on a sucrose cushion.

extract_protocol:
Total RNA was extracted from purified virus-like particles using Trizol.
Total RNA was fragmented to ~40nt using Ambion RNA fragmentation reagent (AM8740). RNA fragments were dephosphorylated at their 3’ end and libraries prepared as described in Heyer E et al., 2015 Nucleic Acids Research (doi: 10.1093/nar/gku1235)

tag: cell line

value: HEK293T Lenti-X

tag: transfection

value: plasmids coding for MLV Gag/Pro-Pol, a Gag::Cas9 fusion, a single-guideRNA targeting the YFP coding sequence, VSVG, BaeV

tag: purification


title: 1402-A4_TCCTGAGC-GCGTAAGA_L005


title: 1407-E7_CTCTCTAC-GTAAGGAG_L008


title: 1403-A7_CTCTCTAC-GCGTAAGA_L007


title: 1403-B7_CTCTCTAC-CTCTCTAT_L003


title: 1401-E4_TCCTGAGC-GTAAGGAG_L002


title: Aneurysm_061

city: Buffalo

first: Hui

last: Meng

address: 875 Ellicott Street

institute: University at Buffalo

data_processing:
All samples were subjected to 50-cycle, single-read sequencing in the HiSeq2500 (Illumina) and were demultiplexed using Bcl2Fastq v2.17.1.14 (Illumina)
Gene expression analysis was completed using the Tuxedo Suite. Gene expression levels were calculated using fragments per kilobase of transcript per million mapped reads (FPKM) normalization in CuffLinks v2.2.1
Short RNA fragment data were compiled in FASTQ format and aligned to the human reference genome (human genome 19 [hg19]) using TopHat v2.1.13
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: neutrophils

growth_protocol: Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA)

tag: sample id

tag: cohort

value: Replication

tag: age

tag: Sex

value: Male

tag: smoker (y/n)

value: Y

tag: hypertension (presence; 0=no,1=yes)

tag: hyperlipidemia (presence; 0=no,1=yes)

tag: coronary artery disease (presence; 0=no,1=yes)

tag: stroke history (presence; 0=no,1=yes)

tag: diabetes mellitus (presence; 0=no,1=yes)

tag: osteoarthritis (presence; 0=no,1=yes)


title: Aneurysm_066

value: Female

value: N


title: 1407-E6_TAGGCATG-GTAAGGAG_L004

tag: subject id

tag: allergies

tag: stimulation

tag: tissue/cell type


title: 1407-E6_TAGGCATG-GTAAGGAG_L008

tag: cell subtype


title: Aneurysm_059


title: Aneurysm_058


title: Aneurysm_057


title: 1402-C12_GTAGAGGA-TATCCTCT_L005


title: 1407-F5_GGACTCCT-ACTGCATA_L004


title: 1375-D4_TCCTGAGC-AGAGTAGA_L001


title: 1436-G6_TAGGCATG-AAGGAGTA_L008


title: Control_XL


title: Control_042


title: Control_LXII


title: Control_043


title: 1430-G11_AAGAGGCA-AAGGAGTA_L006


title: 1407-E3_AGGCAGAA-GTAAGGAG_L004


title: 1401-E3_AGGCAGAA-GTAAGGAG_L002


title: Aneurysm_042

value: Original


title: Control_040


title: Aneurysm_024


title: Aneurysm_019


title: HNE1_ETS2-1

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description: HNE1 cells with siRNA against ETS2

data_processing:
Raw paired fastq files were aligned with STAR aligner and expression was measured in terms of FPKM with cufflinks or stringtie (ensemble gtf) for samples treated with DMSO or THZ1. For samples with scramble or siRNA, fastq files were aligned with kallisto and differental expresion analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values as measured by stringtie or cufflinks. TPM and counts from kallisto.

molecule: polyA RNA

source_name: Nasopharyngeal Carcinoma cell line

growth_protocol: C666-1 cell line was cultured in RPMI-1640 medium; HK1 and HNE1 were maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). All media were supplemented with 10% fetal bovine serum (Hyclone), penicillin (100 U/mL) and streptomycin (100 mg/mL), respectively. Cells were grown at 37°C and 5% CO2.

extract_protocol:
QIAGEN RNA extract kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: condition

value: siRNA targeting ETS2


title: Aneurysm_022

tag: sample id

tag: cohort


title: HNE1_THZ1

description: HNE1 cells were treated with 200nM THZ1 for 6 hours

value: treated with 200nM THZ1 for 6 hours


title: HNE1_SCRAMBLE

description: HNE1 cells with scrambled shRNA

value: scramble shRNA


title: HK1_THZ1

description: HK1 cells were treated with 200nM THZ1 for 6 hours


title: HNE1_DMSO

description: HNE1 cells were treated with DMSO for 6 hours

value: DMSO treated


title: HK1_DMSO

description: HK1 cells were treated with DMSO for 6 hours


title: C666-1_DMSO

description: C666-1 cells were treated with DMSO for 6 hours


title: C666-1_THZ1

description: C666-1 cells were treated with 200nM THZ1 for 6 hours


title: Aneurysm_017

tag: age

tag: Sex


title: Aneurysm_016

tag: smoker (y/n)

tag: hypertension (presence; 0=no,1=yes)


title: HNE1_ETS2-4

description: HNE1 cells with siRNA against ETS2


title: Aneurysm_020

tag: hyperlipidemia (presence; 0=no,1=yes)

tag: coronary artery disease (presence; 0=no,1=yes)


title: HNE1_H3K4Me1

library_source: genomic

data_processing:
Raw fastq files were aligned to reference genome using bowtie aligner with parameters -e 70 -m 2 -k 2 -n 2 –best –strata
Peak calling was done using MACS2 with parameters –nomodel --extsize 200 -B –SPMR.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files normalized to RPM

molecule: genomic DNA

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

tag: antibody


title: Aneurysm_014

tag: stroke history (presence; 0=no,1=yes)

tag: diabetes mellitus (presence; 0=no,1=yes)

tag: osteoarthritis (presence; 0=no,1=yes)


title: Control_037


title: Aneurysm_008


title: Aneurysm_003


title: HNE1_H3K4Me3


title: Aneurysm_XX


title: HNE1_Input


title: HNE1_H3K27Ac


title: Control_034


title: HK1_Input


title: Control_028


title: Control_025


title: C666-1_Pol2


title: Control_017


title: Control_015


title: Control_019


title: C666-1_ATAC


title: Control_023


title: Control_013


title: HK1_H3K27Ac


title: HK1_H3K4Me3


title: C666-1_Input


title: Control_006


title: Control_014


title: C666-1_H3K4Me3


title: C666-1_H3K4Me1


title: Coronary-Soft-3

city: Philadelphia

first: Daniel

last: Rader

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

description: Barcode: GTCCGC

data_processing:
Sequencing reads were mapped against hg19 using STAR against a genome generated using GENCODE v19 annotations.
Alignment files were filtered for high quality reads (score >=30) and sorted using SAMtools.
Counts per gene were determined using HTSeq against human GENCODE v19 annotations
Count normalization and differential expression testing were done using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw count data from HTSeq-count for each GENCODE annotated gene per row for each sample

source_name: Coronary-Soft

growth_protocol: Human primary aortic (Ao) and coronary (Co) artery smooth muscle cells were cultured with smooth muscle growth medium-2 (SmGM2, Lonza) with all supplements

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini Kit (QIAGEN) and TRIzol reagent following the manufacturer’s instructions. Ribosomal RNA was depleted using Illumina Ribo-Zero Gold
Libraries were prepared using a strand-specific TruSeq RNA library Prep kit (Illumina)

treatment_protocol: VSMCs were serum-starved for 48 hours in smooth muscle basal medium (SmBM, Lonza) supplemented with heat-inactivated fatty acid-free bovine serum albumin (1 mg/mL) before plating on hydrogels with SmGM2. Physiologically soft (2-4 KPa) and pathologically stiff (20-25 KPa) hydrogel matrices coated with 5ug/mL human fibronectin were fabricated. VSMCs were cultured on hydrogels for 24 hours before RNA collection

tag: cell type

value: Primary Coronary Artery Vascular Smooth Muscle Cell

tag: tissue

value: Vascular Smooth Muscle

tag: tissue source

value: Coronary Artery

tag: fibronectin coated hydrogel matrix

value: Soft


title: Coronary-Soft-4

description: Barcode: GAGTGG


title: WT WGBS

city: New York

first: Nipun

last: Verma

address: 430 East 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
WGBS data were aligned to the bisulfite-converted hg19 reference genome using Bismark v0.13.0.
We extracted the methylation status with the bismark_methylation_extractor script in Bismark. Only CpGs with at least 3 covered reads were used for downstream analysis.
DMRs were defined as regions containing at least five differentially methylated CpGs (DMCs, false discover rate=20%, Chi square test) and whose total methylation difference was more than 10%.
For whole genome bisulfite sequencing only one replicate was used but the use of five or more DMCs partially overcomes the statistical limitation of individual Chi square tests based on a n=1 sample, as the latter should be cautiously interpreted in the absence of multiple measurements from independent samples.
DMRs were annotated using ChIPseeqerAnnotate from ChIPseeqer package10. Methylation of a specific region was calculated by averaging the methylation levels of all covered CpGs in that region.
Genome_build: hg19
Supplementary_files_format_and_content: WGBS_cpg.WT.mincov3.txt cpg reads
Supplementary_files_format_and_content: WGBS_cpg.TKO.mincov3.txt cpg reads
Supplementary_files_format_and_content: WGBS_DMR.TKO_WT differentially methylated regions when comparing TKO and WT samples

source_name: HUES8 human embryonic stem cells (hESCs)

growth_protocol: HUES8 (NIHhESC-09-0021) hESCs were cultured on irradiated mouse embryonic fibroblasts (iMEFs) feeder layers in DMEM/F12 medium (Life Technologies, 12500-062) supplemented with 20% KnockOut Serum Replacement (Life Technologies, 10828028), 1X MEM Non-Essential Amino Acids (Life Technologies, 11140050), 1X GlutaMAX (Life Technologies, 35050079), 100U/ml Penicillin and 100 μg/ml Streptomycin (Gemini, 15070063), 0.055 mM 2-mercaptoethanol (Life Technologies, 21985023) and 10 ng/ml recombinant human bFGF (EMD Millipore, GF003AF). Cells were incubated at 37 °C with 5% (vol/vol) CO2, and media was changed daily. Cultures were passaged at a 1:6 - 1:12 split ratio every 4 - 6 days using TrypLE (Life Technologies, 12563-029). 5 µM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the culture medium when passaging or thawing cells. Cells are regularly confirmed to be mycoplasma-free by the MSKCC Antibody & Bioresource Core Facility.

extract_protocol:
For WGBS genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines
Genomic DNA was sheared using E220 focused-ultrasonicator (Covaris) to 250-350bp fragments. After end-repair and TruSeq adapter (Illumina) ligation the DNA-libraries were denatured followed by treatment with bisulfite (Zymo Research, D5020) for 30 min at 65C. Single stranded DNA was purified using silica gel columns and amplified using HiFi Uracil+ polymerase (Kapa biosciences, KK2802). The amplified libraries were quantified and mixed equimolarly for sequencing.

treatment_protocol: No treatments were applied prior to genomic DNA extraction

tag: cell line

value: HUES8 hESCs

tag: genotype

value: Wild type sequence


title: TKO WGBS

value: Inactivating mutations in TET1, TET2 and TET3


title: Coronary-Soft-1

description: Barcode: CCGTCC


title: input (5hmC)

data_processing:
FASTQ sequence files were aligned to Bowtie.
The best alignment and reporting option was used for all conditions, corresponding to no more than 2 bp mismatches across each 38 bp read.
5-hmC peak identification was performed using nonduplicate reads with Model-based Analysis of ChIP-Seq data (MACS)
Genome_build: hg19
Supplementary_files_format_and_content: WT_Input_peak.txt Genomic coordinates of identified peaks
Supplementary_files_format_and_content: TKO_Input.peak.txt Genomic coordinates of identified peaks

extract_protocol:
For 5hmC profiling genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines.
40 μg of genomic DNA was sonicated to ~200-400bp fragments using a Diagenode Bioruptor Sonicator. Sonicated DNA was then labeled with azide glucose in a 1 hr reaction at 37°C catalyzed by recombinant -GT utilizing UDP-6-N3-glucose as the sugar donor. The reactions were cleaned up using a Zymo DNA Clean & Concentrator kit (Zymo, D4003), then a biotin moiety was added to the azide-labeled DNA via a copper-free click chemistry reaction with DBCO-S-S-PEG3-Biotin in water at 37°C for 1 hr. Reactions were once again cleaned with the Zymo kit and then bound to Dynabeads MyOne Streptavidin C1 beads (Life Technologies, 65001) for 15 minutes at RT and washed 5 times with binding buffer (5mM Tris-HCl, pH7.5, 0.5mM EDTA, 1M NaCl, 0.01% Tween 20). Bound DNA was eluted by reducing the disulfide in the biotin linker with 100mM DTT for 2h at RT with gentle rotation. Eluted DNA was cleaned on a Micro Bio-spin Column (BioRad, 7326204) to remove DNA and then purified by the Zymo kit. Libraries were constructed from eluted DNA by end repair, A-tailing, and adapter ligation, followed by 4 cycles of PCR, size selection via agarose gel electrophoresis, 12 additional PCR cycles, and a final size selection via agarose gel electrophoresis. Library quantity and quality were analyzed by Bioanalyzer prior to sequencing.

tag: sample type


title: QKO ERRBS rep1

data_processing:
RRBS data were aligned to the bisulfite-converted hg19 reference genome using Bismark v0.13.0.
We extracted the methylation status with the bismark_methylation_extractor script in Bismark. Only CpGs with at least 3 covered reads were used for downstream analysis.
DMRs were defined as regions containing at least five differentially methylated CpGs (DMCs, false discover rate=20%, Chi square test) and whose total methylation difference was more than 10%.
DMRs were annotated using ChIPseeqerAnnotate from ChIPseeqer package10. Methylation of a specific region was calculated by averaging the methylation levels of all covered CpGs in that region.
Genome_build: hg19
Supplementary_files_format_and_content: ERRBS_cpg1 cpg reads from reduced representation bisulfite sequencing
Supplementary_files_format_and_content: ERRBS_cpg2.txt cpg reads from reduced representation bisulfite sequencing
Supplementary_files_format_and_content: ERRBS_DMR.QKO_TKO_1 List of differntially methylated regions between QKO and TKO, first replicate.
Supplementary_files_format_and_content: ERRBS_DMR.QKO_TKO_2 List of differntially methylated regions between QKO and TKO, second replicate.
Supplementary_files_format_and_content: ERRBS_DMR.QKO_WT_1 List of differntially methylated regions between QKO and WT, first replicate.
Supplementary_files_format_and_content: ERRBS_DMR.QKO_WT_2 List of differntially methylated regions between QKO and WT, second replicate.
Supplementary_files_format_and_content: ERRBS_DMR.TKO_WT_1 List of differntially methylated regions between TKO and WT, first replicate.
Supplementary_files_format_and_content: ERRBS_DMR.TKO_WT_2 List of differntially methylated regions between TKO and WT, second replicate.

extract_protocol:
For RRBS genomic DNA was isolated from HUES8 WT and HUES8 TKO hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines.
Illumina Tru-Seq adaptor construction

value: Inactivating mutations in TET1, TET2, TET3 and DNMT3B.


title: Coronary-Soft-2

description: Barcode: ATGTCA


title: Coronary-Stiff-3

description: Barcode: GTGAAA

source_name: Coronary-Stiff

value: Stiff


title: TKO ERRBS rep2


title: QKO ERRBS rep2


title: HK1_H3K4Me1


title: Coronary-Stiff-4

description: Barcode: GTTTCG


title: Coronary-Stiff-2

description: Barcode: AGTCAA


title: WT ERRBS rep2


title: WT ERRBS rep1


title: Aortic-Soft-3

description: Barcode: GCCAAT

source_name: Aortic-Soft

value: Primary Human Aortic Vascular Smooth Muscle Cells

value: Ascending Aorta


title: Coronary-Stiff-1

description: Barcode: AGTTCC


title: Aortic-Soft-4

description: Barcode: CTTGTA


title: Aortic-Soft-1

description: Barcode: TTAGGC


title: C666-1_H3K27Ac


title: TKO ERRBS rep1


title: Day30.y

city: los angeles

first: matteo

last: pellegrini

state: CA

address: 610 charles young drive east

institute: UCLA

description: replicate A

data_processing:
Read-Alignment: Short-read sequences generated from Illumina Sequencer were aligned to the UCSC human reference genome hg19 downloaded from support.Illumina.com (http://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat from the Tuxedo Tools.
Abundance measurements: Counts/gene expression matrices were generated using HTSeq which quantified the reads per transcript
Normalization of abundance measurements: The expression matrices were log transformed and normalized using the rlog function in Deseq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files include expression values for annotated features in each sample

source_name: cardiac progenitor cells

extract_protocol:
TRIZOL (TheroFisher) and RNeasy kit (QIAGEN)
500 ng of DNaseI-treated RNA was used as input material for library preparation using the Illumina TruSeq mRNA kit (Illumina, RS-122-2001)

value: ES-derived cardiac progenitor cells


title: Day14.x

description: replicate A


title: Day15.y

description: replicate B


title: Aortic-Soft-2

description: Barcode: TGACCA


title: Aortic-Stiff-4

description: Barcode: CAGATC

source_name: Aortic-Stiff


title: Day5.y

description: replicate B


title: Aortic-Stiff-2

description: Barcode: ATCACG


title: Aortic-Stiff-3

description: Barcode: ACAGTG


title: Day2.y

description: replicate B


title: Aortic-Stiff-1

description: Barcode: CGATGT


title: Day0.y

description: replicate B


title: Day2.x

description: replicate A


title: Day0.x

description: replicate A


title: WT RNA-Seq rep1

data_processing:
RNA-seq data was aligned to the hg19 reference genome using Bowtie.
Read counts were derived from HTSeq.scripts.count module in HTSeq-0.6.0 with default parameters. in a non-directional model
Differentially expressed genes were generated by DESeq2-1.4.5 in R.
Up regulated genes were decided by logFC > 2 and p-adj < 0.1 (n=153).
Downregulated genes were decided by logFC < -2 and p-adj < 0.1 (n=233).
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq_WT1.counts Counts for WT sample, first replicate.
Supplementary_files_format_and_content: RNASeq_WT2.counts Counts for WT sample, second replicate.
Supplementary_files_format_and_content: RNASeq_TKO1.counts Counts for TKO sample, first replicate.
Supplementary_files_format_and_content: RNASeq_TKO2.counts Counts for TKO sample, second replicate.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74136). DNA was removed from RNA samples using genomic DNA eliminator spin columns.
Illumina Truseq kit PolyA method non stranded

treatment_protocol: No treatments were applied prior to RNA extraction


title: TKO RNA-Seq rep2


title: TKO RNA-Seq rep1


title: WT RNA-Seq rep2


title: HD5_AD

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode against the Homo_sapiens.GRCh38.79.gtf annotation table from http://www.ensembl.org.
Genome_build: hg38
Supplementary_files_format_and_content: The raw read counts

source_name: Extracellular Vesicle

extract_protocol:
Qiazol-Chloroform extraction performed, and RNA purified by miRNeasy mini kit according to the manufacturers protocol. (Qiagen, Valencia, MA)
Amplified cDNA was synthesized from RNA extracted from captured extracellular vesicle products using the SMARTer Ultra Low Input RNA Kit for Sequencing - v4 kit (Clontech Laboratories). PCR amplification following second strand synthesis was run for 18 cycles. 1 ng of amplified cDNA was loaded into the Nextera XT kit. Normalization was done using the KAPA SYBR® FAST Universal qPCR Kit (Kapa Biosystems) rather than the bead-based normalization in the Nextera XT kit.

tag: group

value: Healthy donor controls

value: EVHB-Chip captured Extracellular vesicles

tag: biofluid

value: Plasma


title: HD6_AD


title: lo:100_D130_CXCR5_POS_lo_AIT_RSS19_16

city: La Jolla

first: Bjoern

last: Peters

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
RNA-Seq data was mapped against hg19 reference genome using tophat (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome bioinformatics site.
The alignment results (sam files) were converted into bam files and sorted by using samtools.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] file reports raw counts of sequencing reads per gene generated by HTSeq-count

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, CXCR5+  T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Sorted cell subsets were defined as the combination of CD4+CD45RO+CXCR5hi and  CD4+CD45RO+CXCR5lo populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Microscaled (SmartSeq2) cDNA amplification.
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: individual

tag: disease group

value: Allergen-specific immunotherapy

value: T cell

tag: cell subset

value: CXCR5 low


title: lo:95_D106_CXCR5_POS_lo_AIT_RSS19_11


title: lo:98_D155_CXCR5_POS_lo_AIT_RSS19_14


title: hi:112_D146_CXCR5_POS_hi_AIT_RSS19_28

value: CXCR5 high


title: lo:108_D111_CXCR5_POS_lo_AIT_RSS19b_24


title: hi:96_D106_CXCR5_POS_hi_AIT_RSS19_12


title: lo:105_U34_CXCR5_POS_lo_Allergic_RSS19b_21

value: Allergic


title: HD2_AD


title: HD3_AD


title: Day5.x

description: replicate A


title: lo:92_U149_CXCR5_POS_lo_Allergic_RSS19_8


title: HD1_AD

value: Serum


title: lo:86_U161_CXCR5_POS_lo_Allergic_RSS19_2


title: lo:89_D90_CXCR5_POS_lo_Allergic_RSS19_5


title: GBM_A6

value: Glioblastoma Multiforme patients


title: GBM_A7


title: GBM_A5


title: hi:93_U149_CXCR5_POS_hi_Allergic_RSS19_9


title: hi:90_D90_CXCR5_POS_hi_Allergic_RSS19_6


title: GBM_A4


title: hi:109_D111_CXCR5_POS_hi_AIT_RSS19_25


title: HD4_AD


title: GBM_A2


title: lo:102_D73_CXCR5_POS_lo_Allergic_RSS19b_18


title: hi:87_U161_CXCR5_POS_hi_Allergic_RSS19_3


title: PT6_AD


title: GBM_A1


title: DOX_rep1

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to human genome (hg19) whole genome using tophat v2.0.10 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.2.1) with the provision of a GTF annotation file (hg19).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Total RNA was harvested using RNeasy Mini Kit (QIAGEN); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gata4 status

value: Overexpressed GATA4


title: DOX_rep2


title: noDOX_rep2

value: Normal level of GATA4


title: GATA4

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were aligned to the hg9 genome assembly using bowtie version 1.0.0 with the following parameters -k 1 --best -v 2
Data were filtered using the following specifications…
peaks were called using MACS version 2.0.10 with the defult setting
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using makeUCSCfile and normalized to 10M reads.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody

value: GATA4(Thermo fisher,MA5-15532)


title: PT2_AD


title: hi:106_U34_CXCR5_POS_hi_Allergic_RSS19b_22


title: PT3_AD


title: PT1_AD


title: GBM_A8


title: noDOX_rep1


title: hi:103_D73_CXCR5_POS_hi_Allergic_RSS19b_19


title: PT4_AD


title: HPAFII Gem 3

first: Meghan

middle: Morrison

last: Joly

address: Sears Lab, CLSB 4N079, Oregon Health & Science University 2730 SW Moody Ave

department: Molecular and Medical Genetics

data_processing:
Base calling - using Illumina RTA version 2.4.11.
Conversion to FASTQ using bcl2fastq version 2.17.1.14
Reads were trimmed to 44 bases (first 5 bases were discarded, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to hg19 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
R scripts were used to count tags that aligned to the exons of UCSC RefSeq gene models and calculate RPKM values.  Processed files contain the in exon tag counts and the RPKM nomalized values for each RefSeq gene model.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files with tag counts and RPKM values for each RefSeq gene model.

source_name: HPAFII cell line

growth_protocol: Cells were maintained and plated in DMEM with 10% FBS and pen/strep

extract_protocol: Total RNA was extracted using Qiagen Rneasy kit as per manufacturer's protocol.

treatment_protocol: Cells were plated, grown to 50% confluence and treated with PBS or gemcitabine (10 µM) for 72 hours.

value: HPAFII

value: pancreatic cancer

tag: treatment

value: Gemcitabine (10 µM)


title: HPAFII Gem 2


title: HPAFII Gem 1


title: GFP-Normal rep 2

first: Ruifeng

last: Li

address: Haidian

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Aligned using the TopHat (v2.0.13) with the Ensembl Drosophila_melanogaster.BDGP5.78.gtf as a reference.
The transcription analysis was performed using Cufflinks (v2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: U2OS cell line

extract_protocol:
Total RNA from U2OS cells overexpressing actin mutant G13R and those expressing GFP as control, at both normal-growth and serum-stimulation conditions. Poly(A)+ mRNAs were enriched using Dynabeads oligo (dT) beads (NEB). RT reactions and purification of cDNA templates were performed following the RNA-seq sample preparation protocol from Illumina. Each cDNA sample was sequenced on an IlluminaHiseq 2500 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: GFP

tag: condition

value: Normal


title: GFP-Serum rep 1


title: GFP-Serum rep 2


title: HPAFII PBS 3

value: PBS


title: PT5_AD

tag: cell type

value: EVHB-Chip captured Extracellular vesicles

value: Plasma


title: PRDM1 ChIP-Seq

city: Tampa

first: Kenneth

last: Wright

state: Florida

address: 12902 Magnolia Dr

department: Immunology

institute: H Lee Moffitt Cancer Center

data_processing:
Base calling was done using CASAVA 1.8.2
ChIP-Seq reads were aligned to h19 using BowTie 0.12.7.  Paired end fastq files aligned as single-read with settings --best --strata -m 1 --seedlen 28 --threads 32 --chunkmbs 256
Peaks were identified using the MACS v1.4 peak-finding software, bandwith = 300,
Peaks were enriched for 50 or more mapped reads with a False Discovery rate of less than 5%
Genome_build: h19
Supplementary_files_format_and_content: .bed files in MACS v1.4 format including

source_name: Mutiple Myeloma cell line

growth_protocol: U266 cell lines were passaged every 3 days at respectively 0.1-0.2 x 106/ml cells supplemented with 10% FBS, 1% Pen-Strep and 55μM 2-Mercaptoethanol for the NCI-H929.

extract_protocol:
Purified nuclei were sonicated and PRDM1- or unbound DNA complexes were isolated utilizing PRDM1 antibody
The library was prepared using the Illumina TruSeq Library preparation Kit according to manufacturer protocol (Illumina, Inc.)

value: Plasma cell lymphoma

tag: chip-antibody

value: PRDM1 (C14A4) rabbit mAb (Cell Signaling Tecnology)


title: IgG

value: IgG(Santa Cruz,sc-2025)


title: HPAFII PBS 2

tag: tissue


title: G13R-Serum rep1


title: Input ChIP-Seq


title: HPAFII PBS 1


title: G13R-Normal rep2


title: G13R-Normal rep1


title: 22Rv1-M4-tumor_02

city: Taipei

first: Chin-Hsien

last: Tsai

state: Others

address: Nan-Kang

department: ABRC

country: Taiwan

institute: Academia Sinica

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using Tophat version 2.0.13 with parameters -p 12 --library-type fr-firststrand
Cufflinks verson 2.2.1 was then applied to assemble transcripts and quantify their abundance in terms of FPKM (fragments per kilobase of transcript per million fragments mapped)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Xenograft

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using Zymo research RNA kit.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kits.

value: Human prostate cancer cell line


title: 22Rv1-M4-tumor_01


title: HUES8 TET TKO DNMT3B ChIP-Seq

description: ChIP-seq

data_processing:
FASTQ sequence files were aligned using Bowtie.
Peaks identification was performed using nonduplicate reads with Model-based Analysis of ChIP-Seq data (MACS).
Genome_build: hg19
Supplementary_files_format_and_content: peak files in .txt format

extract_protocol:
ChIP-Seq was performed for TET1 (WT hESCs) and DNMT3B (WT and TKO hESCs). WT and TKO hESCs were cultured in standard hESC media, as described above. ~5 × 107 cells were fixed, washed and snap-frozen according to the Cell Fixation protocol from Active Motif (http://www.activemotif.com/documents/1848.pdf).
Immunoprecipitation and library prep were performed by Active Motif Epigenetic Services (https://www.activemotif.com/catalog/704/epigenetic-services)

treatment_protocol: No treatments were applied prior to chromatin isolation and fixation.

value: HUES8 hESCs

value: Inactivating mutations in TET1, TET2 and TET3

tag: antibody


title: 22Rv1-M4-tumor_03


title: 22Rv1-tumor_03


title: 22Rv1-tumor_02


title: G13R-Serum rep2

value: Serum


title: HUES8 TKO ChIP-Seq Input

description: ChIP-seq

tag: cell line


title: HUES8 WT ChIP-Seq Input

description: ChIP-seq

tag: genotype

value: Wild type sequence


title: GFP-Normal rep 1


title: HUES8 WT DNMT3B ChIP-Seq

description: ChIP-seq


title: 22Rv1-tumor_01


title: HUES8 WT TET1 ChIP-Seq

description: ChIP-seq


title: 22Rv1-Luc2

source_name: cell line


title: PC-3_WCE_03

description: Sample 6

tag: treatment duration

value: 10 weeks

tag: host strain

value: nude mice


title: R191H.TRE.2.4.B

city: Cambridge

first: Ofir

last: Cohen

state: Massachusetts

address: 415 Main St, Cambridge, MA 02142

department: Cancer Program

institute: Broad Institute

description: Parental cell line with R191H ERK2 over-expression treated with trametinib

data_processing:
Illumina RNASeq libraries were prepared from 100 ng of bulk RNA using the TruSeq RNA Sample Prep Kit (v2, Illumina).
mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, as 75bp paired-end reads
Reads were mapped with STAR aligner (Dobin et al. 2013)
Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation
Supplementary_files_format_and_content: csv file with raw counts

source_name: Melanoma

growth_protocol: A375 cells were grown in RPMI media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit per the manufacturer's instructions.
Illumina TruSeq

treatment_protocol: Expression of ERK alleles was induced with 1ug/ml doxycycline. Twenty-four hours post induction, half of replicates were treated for 4 hours with 4nM trametinib.

tag: replicate


title: PC-3_WCE_02

description: Sample 5


title: MEKDD.TRE.2.4.B

description: Parental cell line with MEKDD ERK2 over-expression treated with trametinib


title: S142L.TRE.2.4.B

description: Parental cell line with S142L ERK2 over-expression treated with trametinib


title: P58L.TRE.2.4.B

description: Parental cell line with P58L ERK2 over-expression treated with trametinib


title: P58G.TRE.2.4.B

description: Parental cell line with P58G ERK2 over-expression treated with trametinib


title: PC-3_Vehicle_03

description: Sample 3


title: E81K.TRE.2.4.B

description: Parental cell line with E81K ERK2 over-expression treated with trametinib


title: PC-3_Vehicle_02

description: Sample 2


title: E322V.TRE.2.4.B

description: Parental cell line with E322V ERK2 over-expression treated with trametinib


title: D321V.TRE.2.4.B

description: Parental cell line with D321V ERK2 over-expression treated with trametinib


title: PC-3_Vehicle_01

description: Sample 1


title: E322K.TRE.2.4.B

description: Parental cell line with E322K ERK2 over-expression treated with trametinib


title: rdr2-ros1_rosette_BSseq

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
For all libraries: Low quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32
All libraries were mapped using bismark v0.16.1 with parameters -N 1 and -L 40
Mapped bisulfite reads were further filtered to remove presumed PCR duplicates using a custom script provided with Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/),  Methylation information was then extracted using bismark_methylation_extractor.  Resulting data were processed into BED-like format (see processed data files) with separate files for methylation in the following sequence contexts: CpG, CHG or CHH.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files with per-cytosine methylation information for each sample in each context (CpG, CHG and CHH), in BED format.  First three fields indicate location of the cytosine (BED-like format, 0-based), fourth field is number of unmethylated reads at that position, fifth is number of methylated reads and sixth is % reads methylated.

organism: Arabidopsis thaliana

source_name: 3-week old whole rosette

growth_protocol: Plants were grown in a growth chamber with 16h light at 21C.

extract_protocol:
Illumina Truseq DNA methylation protocol with index ACTTGA
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

treatment_protocol: no treatment

value: rdr2; ros1 mutant

value: 3-week old whole rosette

tag: molecule subtype

value: bisulfite-treated genomic DNA


title: ros1_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index TGACCA
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

value: ros1 mutant


title: K54R.TRE.2.4.B

description: Parental cell line with K54R ERK2 over-expression treated with trametinib


title: rdr2_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index TTAGGC
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

value: rdr2 mutant


title: EZH2 + Vehicle rep1

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using Tophat 2.0.10 with parameters -G. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by edgeR with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample ...

source_name: tamoxifen-sensitive breast cancer cells

growth_protocol: Cells were cultured in regular RPMI 1640 (10%  FBS + 1% PSG [Penicillin-Streptomycin-L-Glutamine]) and hormone stripped in phenol-red-free RPMI 1640  (10% charcoal stripped FBS + 1% PSG) for 3 days before hormone treatment.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 (Cat.# RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MCF-7 cells were stably transfected with pLenti-CMV-hygro-GFP or pLenti-HA-EZH2. Hormone stripped cells were treated with either vehicle (EtOH) or 4-OHT (100 nM) for 6 hr.

tag: transfection

value: Vehicle


title: EZH2 + Tamoxifen rep3

value: Tamoxifen


title: EZH2 + Tamoxifen rep4


title: WT.TRE.2.4.B

description: Parental cell line with WT ERK2 over-expression treated with trametinib


title: A375.TRE.2.4.B

description: Parental cell line treated with trametinib


title: EZH2 + Tamoxifen rep2


title: Col0_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index ATCACG
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

value: wild type


title: BRmut18_T4_rosette_BSseq

value: control lines in which ROS1 is mutated


title: R191H.2.4.B


title: BRmut11_T4_rosette_BSseq


title: MEKDD.2.4.B


title: EV + Vehicle rep2

value: pLenti-CMV-hydro-GFP


title: S142L.2.4.B


title: EV + Vehicle rep1


title: BR35_T4_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index TAGCTT
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

value: broken rheostat (BR) line


title: EZH2 + Vehicle rep2


title: P58L.2.4.B


title: BR35_T4_leaves_BSseq

source_name: Leaves 5 & 6 from 3-week old plant

extract_protocol:
Illumina Truseq DNA methylation protocol with index GGCTAC
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.

value: Leaves 5 & 6 from 3-week old plant


title: EV + Tamoxifen rep3


title: EV + Tamoxifen rep4


title: BR35_T3_leaves_BSseq


title: P58G.2.4.B


title: E81K.2.4.B


title: EV + Tamoxifen rep1


title: EV + Tamoxifen rep2


title: BR35_T2_leaves_BSseq


title: BR24_T4_leaves_BSseq


title: BR32_T4_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index CTTGTA
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.


title: BR24_T4_rosette_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index GCCAAT
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.


title: PC-3_WCE_01

description: Sample 4

value: Human prostate cancer cell line


title: BR24_T3_leaves_BSseq


title: K54R.2.4.B


title: BR24_T2_leaves_BSseq


title: shCtrl rep2

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using Tophat 2.0.10 with parameters -G. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by edgeR with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: tamoxifen-resistant breast cancer cells

growth_protocol: Cells were cultured in phenol-red-free RPMI 1640 supplemented with 10% charcoal stripped FBS and 1% PSG (Penicillin-Streptomycin-L-Glutamine).  100 nM of 4-hydroxytamoxifen was added to maintain the tamoxifen resistant feature. Cells were 1:3 split twice per week.

treatment_protocol: TamR MCF-7 cells were stably transfected with shCtrl and shEZH2 and maintained in phenol-red-free RPMI 1640 supplemented with 100 nM of 4-OHT.

value: TamR MCF-7

value: Cells were infected with scrambled control shRNAs


title: shEZH2 rep1

value: Cells were infected with EZH2-specific shRNAs


title: E322V.2.4.B


title: WT.2.4.B


title: shCtrl rep1


title: EZH2 + Tamoxifen rep1


title: A375.2.4.B


title: BR23_T4_leaves_BSseq

extract_protocol:
Illumina Truseq DNA methylation protocol with index ACAGTG
DNA was isolated using the CTAB procedure.
200 ng DNA was bisulfite treated using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were constructed using the Illumina TruSeq DNA methylation kit. Reads were sequenced on an Illumina HiSeq 2000.


title: BR23_T4_rosette_BSseq


title: G25-3

description: replicate C

extract_protocol:
TRIZOL (TheroFisher) and RNeasy kit (QIAGEN)
Libraries for RNA-Seq in Figure 1G and H were prepared with KAPA Stranded RNA-Seq Kit

value: ES-derived cardiac progenitor cells

value: Glucose 25 mM


title: MEKDD.TRE.2.3.B


title: G25-2

description: replicate B


title: BR23_T3_leaves_BSseq


title: E322K.2.4.B


title: D321V.2.4.B


title: BR23_T2_leaves_BSseq


title: G25-1

description: replicate A


title: R191H.TRE.2.3.B


title: shEZH2 rep2


title: S142L.TRE.2.3.B


title: P58L.TRE.2.3.B


title: p35S:miRGUS

city: Cold Spring Harbor

first: Damianos

last: Skopelitis

address: One Bungtown Rd

department: Cancer Biology

institute: Cold Spring Harbor Laboratory

description: p35S:miRGUS seedlings express from the ubiquitous 35S CaMV promoter, an artificial miRNA (miRGUS) in the p35S:GUS rdr6 background.

data_processing:
The RNA adapter AGATCGGAAGAGCACACGTCT for 'No miRGFP' Libraries and TGGAATTCTCGGGTGCCAAGG for all the rest of the Libraries were removed from the 3' end, using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
For both Libraries trimmed reads 19- to 25-nt in length were selected.
Trimmed reads 19- to 25-nt in length were aligned to the Arabidopsis reference genome (TAIR10) including the eGFP coding sequence or the GUS coding sequence, using the Burrows-Wheeler Aligner, allowing for a single mismatch for miRGFP and 3 mismatches for the miRGUS to accommodate mismatches at the target sites of their GFP or GUS target sequence.
For comparison of small RNA levels across samples, read counts were normalized per million mapped reads (reads per million) using SAM Tools (Li, H. & Durbin, R., 2009).
Genome_build: Arabidopsis TAIR10 Build including the coding sequence of eGFP (atggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccctgacctacggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggccatgatgagctttacaagtaa) or GUS (atggtccgtcctgtagaaaccccaacccgtgaaatcaaaaaactcgacggcctgtgggcattcagtctggatcgcgaaaactgtggaattgatcagcgttggtgggaaagcgcgttacaagaaagccgggcaattgctgtgccaggcagttttaacgatcagttcgccgatgcagatattcgtaattatgcgggcaacgtctggtatcagcgcgaagtctttataccgaaaggttgggcaggccagcgtatcgtgctgcgtttcgatgcggtcactcattacggcaaagtgtgggtcaataatcaggaagtgatggagcatcagggcggctatacgccatttgaagccgatgtcacgccgtatgttattgccgggaaaagtgtacgtatcaccgtttgtgtgaacaacgaactgaactggcagactatcccgccgggaatggtgattaccgacgaaaacggcaagaaaaagcagtcttacttccatgatttctttaactatgccggaatccatcgcagcgtaatgctctacaccacgccgaacacctgggtggacgatatcaccgtggtgacgcatgtcgcgcaagactgtaaccacgcgtctgttgactggcaggtggtggccaatggtgatgtcagcgttgaactgcgtgatgcggatcaacaggtggttgcaactggacaaggcactagcgggactttgcaagtggtgaatccgcacctctggcaaccgggtgaaggttatctctatgaactgtgcgtcacagccaaaagccagacagagtgtgatatctacccgcttcgcgtcggcatccggtcagtggcagtgaagggcgaacagttcctgattaaccacaaaccgttctactttactggctttggtcgtcatgaagatgcggacttacgtggcaaaggattcgataacgtgctgatggtgcacgaccacgcattaatggactggattggggccaactcctaccgtacctcgcattacccttacgctgaagagatgctcgactgggcagatgaacatggcatcgtggtgattgatgaaactgctgctgtcggctttaacctctctttaggcattggtttcgaagcgggcaacaagccgaaagaactgtacagcgaagaggcagtcaacggggaaactcagcaagcgcacttacaggcgattaaagagctgatagcgcgtgacaaaaaccacccaagcgtggtgatgtggagtattgccaacgaaccggatacccgtccgcaaggtgcacgggaatatttcgcgccactggcggaagcaacgcgtaaactcgacccgacgcgtccgatcacctgcgtcaatgtaatgttctgcgacgctcacaccgataccatcagcgatctctttgatgtgctgtgcctgaaccgttattacggatggtatgtccaaagcggcgatttggaaacggcagagaaggtactggaaaaagaacttctggcctggcaggagaaactgcatcagccgattatcatcaccgaatacggcgtggatacgttagccgggctgcactcaatgtacaccgacatgtggagtgaagagtatcagtgtgcatggctggatatgtatcaccgcgtctttgatcgcgtcagcgccgtcgtcggtgaacaggtatggaatttcgccgattttgcgacctcgcaaggcatattgcgcgttggcggtaacaagaaagggatcttcactcgcgaccgcaaaccgaagtcggcggcttttctgctgcaaaaactggacgctggcatgaacttcggtgaaaaaccgcagcagggaggcaaacaataa).
Supplementary_files_format_and_content: tab-delimited txt file with normalized reads (rpm) for miRGFP (21nt) and the endogenous miR390 and miR156 for Libraries pCLV3:miRGFP, pSUC2:miRGFP and pRbcS:miRGFP. tab-delimited txt file with normalized reads (rpm) for miRGFP in shoot and root samples of pRbcS:miRGFP and "no miRGFP" control Libraries.  tab-delimited txt file with normalized reads (rpm) for miRGUS (21nt) in p35S:miRGUS Library.
Supplementary_files_format_and_content: tdf format file generated with IGVtools for the processed p35S:miRGUS library alligned to Reference genome including the GUS sequence, showing no production of GUS-derived secondary siRNAs.
Supplementary_files_format_and_content: Reference genome including GUS sequence in Fasta format

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown at 22°C under long-day conditions in 1% agar plates containing 1x Murashige and Skoog (MS) medium supplemented with 1% sucrose.

extract_protocol:
Total RNA was extracted from 10 day-old Arabidopsis seedlings using TRIzol reagent (Invitrogen). Small RNA libraries were prepared from 1 µg of total RNA. The 'No miRGFP' small RNA Libraries was constructed using the NEBNext Multiplex Small RNA Library Kit for Illumina (New England Biolabs). All the rest small RNA Libraries was constructed using the TruSeq Small RNA Library Kit from Illumina.
Small RNA Libraries prepared using standard Illumina protocols.

value: whole seedlings

tag: age

value: 10 day-old seedlings

tag: background


title: p35S:3xNLS-GFP (No miRGFP) Root

description: Isolated root sample from the control p35S:3xNLS-GFP (no miRGFP) seedlings express ubiquitously from the 35S CaMV promoter, a nuclear localized GFP sequence, in an rdr6 null mutant background, defective in secondary siRNA production.

value: root


title: G-3

description: replicate C

value: Glucose 0 mM for 5 days and back to Glucose 25 mM for 5 days


title: p35S:3xNLS-GFP (No miRGFP) Shoot

description: Isolated shoot sample from the control p35S:3xNLS-GFP (no miRGFP) seedlings express ubiquitously from the 35S CaMV promoter, a nuclear localized GFP sequence, in an rdr6 null mutant background, defective in secondary siRNA production.

value: shoot


title: P58G.TRE.2.3.B


title: D321V.TRE.2.3.B


title: pRbcS:miRGFP Root

description: Isolated root sample from pRbcS:miRGFP seedlings expressing from the RbcS promoter, which is transcriptionally active in the mesophyll cells, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.


title: G0-3

description: replicate C

value: Glucose 0 mM


title: E81K.TRE.2.3.B


title: G-1

description: replicate A


title: G0-2

description: replicate B


title: E322K.TRE.2.3.B


title: pRbcS:miRGFP

description: pRbcS:miRGFP seedlings express from the pRbcS promoter, which is transcriptionally active in the mesophyll cells, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.


title: E322V.TRE.2.3.B


title: K54R.TRE.2.3.B


title: G0-1

description: replicate A


title: pRbcS:miRGFP Shoot

description: Isolated shoot sample from pRbcS:miRGFP seedlings expressing from the RbcS promoter, which is transcriptionally active in the mesophyll cells, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.


title: pSUC2:miRGFP

description: pSUC2:miRGFP seedlings express from the SUC2 promoter, which is transcriptionally active in the companion phloem cells of vascular tissue, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.


title: WT.TRE.2.3.B


title: pwr_27_2hrs_Rep2

city: Melbourne

first: Avilash

last: Singh Yadav

state: Victoria

address: Innovation Walk 18, Monash University Clayton Campus

department: School of Biological Sciences

country: Australia

institute: Monash University

data_processing:
Sequenced reads were trimmed for adaptor sequences
Initial quality check of the RNA-Seq data was performed using FASTQC
SortmeRNA used to filter the rRNA sequences from the datasets,using its default rRNA  databases comprising of 16S, 18S 23S and 28S rRNAs
Reads were mapped to Arabidopsis thaliana TAIR 10 genome using Tophat2 (v2.1.0) and bowtie2 (v2.1.0) with parameters -r 50 -p 4 -i 20 -I 5000
Raw reads counts were generated using featureCounts (v1.4.5) using parameters -T 4 -p  -B
Normalized read counts were generated from raw read counts using  DESeq2 (v1.14.1) differential expression analysis pipeline
Genome_build: TAIR 10
Supplementary_files_format_and_content: Normalized_read_counts_all_samples.csv: Normalized count measurement from DESeq2 (v1.14.1)
Supplementary_files_format_and_content: Matrix table containing the normalized read counts generated by DeSeq2. Normalized counts for each sample for each gene is mentioned under the corresponding header for each sample.
Supplementary_files_format_and_content: 27_2hrs_raw_counts.csv: Raw read counts output from featureCounts (v1.4.5)
Supplementary_files_format_and_content: Matrix table containing the raw read counts generated by featurecounts for samples grown at 27°C  2 hrs. Raw reads counts are recorded in columns under the corresponding  header for each sample. First column contains gene IDs. Second column contains corresponding gene length (in bps)
Supplementary_files_format_and_content: 23_2hrs_raw_counts.csv: Raw read counts output from featureCounts (v1.4.5)
Supplementary_files_format_and_content: Matrix table containing the raw read counts generated by featurecounts for samples grown at 23°C  2 hrs. Raw reads counts are recorded in columns under the corresponding  header for each sample. First column contains gene IDs. Second column contains corresponding gene length (in bps)

source_name: Whole Seedlings

growth_protocol: About one hundred six day old seedlings were grown in in growth chambers (GR-36, Percival Scientific, Canada) at 23°C in short days (8hrs light/ 16 hours dark cycle). Half of the samples were then shifted to 27°C short days for 2 hours

extract_protocol:
Two biological replicates were used. Each biological replicate constituted of about a hundred seedlings. Total RNA was extracted from whole seedlings using Isolate II RNA plant kit (Bioline Pty Ltd, Australia).
Illumina HiSeqTM 2000 platform using paired-end sequencing of 90 bp in length at BGI-Shenzen (Beijing Genomics Institute).

value: 6 day old

tag: ecotype

value: pwr-2 mutant

tag: growth temperature

tag: photoperiodic lighting

value: short day (8h light/16h dark)


title: A375.TRE.2.3.B


title: MEKDD.2.3.B

description: Parental cell line with MEKDD ERK2 over-expression treated with trametinib


title: G-2

description: replicate B

data_processing:
Read-Alignment: Short-read sequences generated from Illumina Sequencer were aligned to the UCSC human reference genome hg19 downloaded from support.Illumina.com (http://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat from the Tuxedo Tools.
Abundance measurements: Counts/gene expression matrices were generated using HTSeq which quantified the reads per transcript
Normalization of abundance measurements: The expression matrices were log transformed and normalized using the rlog function in Deseq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files include expression values for annotated features in each sample

tag: treatment


title: pCLV3:miRGFP

description: pCLV3:miRGFP seedlings express in stem cells from the CLV3 promoter, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.


title: pwr_23_2hrs_Rep2


title: pwr_23_2hrs_Rep1


title: P58L.2.3.B

description: Parental cell line with P58L ERK2 over-expression treated with trametinib


title: E81K.2.3.B

description: Parental cell line with E81K ERK2 over-expression treated with trametinib


title: R191H.2.3.B

description: Parental cell line with R191H ERK2 over-expression treated with trametinib


title: P58G.2.3.B

description: Parental cell line with P58G ERK2 over-expression treated with trametinib


title: D321V.2.3.B

description: Parental cell line with D321V ERK2 over-expression treated with trametinib


title: Col_23_2hrs_Rep2

value: Wild Type


title: Col_27_2hrs_Rep2


title: E322K.2.3.B

description: Parental cell line with E322K ERK2 over-expression treated with trametinib


title: E322V.2.3.B

description: Parental cell line with E322V ERK2 over-expression treated with trametinib


title: K54R.2.3.B

description: Parental cell line with K54R ERK2 over-expression treated with trametinib


title: p35SmiRGFP

description: p35SmiRGFP seedlings express ubiquitously from the 35S CaMV promoter, an artificial miRNA (miRGFP) in the p35S:3xNLS-GFP rdr6 background.

data_processing:
The RNA adapter AGATCGGAAGAGCACACGTCT for 'No miRGFP' Library and TGGAATTCTCGGGTGCCAAGG for 'p35SmiRGFP' Library were removed from the 3' end, using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
For both Libraries trimmed reads 19- to 25-nt in length were selected.
Trimmed reads 19- to 25-nt in length were aligned to the Arabidopsis reference genome (TAIR10) including the eGFP coding sequence, using the Burrows-Wheeler Aligner (Li, H. & Durbin, R., 2009), allowing a single mismatch to accommodate the mismatch at position 20 of miRGFP relative to its GFP target.
For comparison of small RNA levels across samples, read counts were normalized per million mapped reads (reads per million) using SAM Tools (Li, H. & Durbin, R., 2009).
Alignments of Small RNA Libraries to Reference Genome, including the eGFP coding sequence, were visualized using the Integrative Genomics Viewer (Thorvaldsdottir, H. et al. 2013).
Genome_build: Arabidopsis TAIR10 Build including the coding sequence of eGFP (atggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccctgacctacggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttcttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaagatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccactacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggccatgatgagctttacaagtaa).
Supplementary_files_format_and_content: tab-delimited txt files with normalized reads (rpm) for miRGFP (21nt) and other GFP-derived secondary siRNAs.
Supplementary_files_format_and_content: tdf format files generated with IGVtools for the processed libraries aligned to Reference genome.

extract_protocol:
Total RNA was extracted from 10 day-old Arabidopsis seedlings using TRIzol reagent (Invitrogen). Small RNA libraries were prepared from 1 µg of total RNA. The 'No miRGFP' small RNA Library was constructed using the NEBNext Multiplex Small RNA Library Kit for Illumina (New England Biolabs). The 'p35SmiRGFP' small RNA Library was constructed using the TruSeq Small RNA Library Kit from Illumina.
Small RNA Libraries prepared using standard Illumina protocols.

tag: background ecotype


title: MEKDD.TRE.2.2.B


title: R191H.TRE.2.2.B


title: pwr_27_2hrs_Rep1


title: S142L.TRE.2.2.B

description: Parental cell line with S142L ERK2 over-expression treated with trametinib


title: P58L.TRE.2.2.B


title: P58G.TRE.2.2.B


title: D321V.TRE.2.2.B


title: E81K.TRE.2.2.B


title: E322K.TRE.2.2.B


title: S142L.2.3.B


title: Col_27_2hrs_Rep1


title: Col_23_2hrs_Rep1


title: K54R.TRE.2.2.B


title: A375.TRE.2.2.B

description: Parental cell line treated with trametinib


title: MEKDD.2.2.B


title: R191H.2.2.B


title: WT.TRE.2.2.B

description: Parental cell line with WT ERK2 over-expression treated with trametinib


title: P58L.2.2.B


title: P58G.2.2.B


title: p35S:3xNLS-GFP (No miRGFP)

description: The control p35S:3xNLS-GFP (no miRGFP) seedlings express ubiquitously from the 35S CaMV promoter, a nuclear localized GFP sequence, in an rdr6 null mutant background, defective in secondary siRNA production.


title: WT.2.3.B


title: A375.2.3.B


title: E81K.2.2.B


title: D321V.2.2.B


title: E322K.2.2.B


title: salmIR IFM 1d rep 1

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

description:
DESeq2_IFMvssalm_1d.txt
DESeq2_salm_1dvs72h.txt
Mfuzz_salm_4TP_inputdata.xlsx
previously submitted as GSM1555988

data_processing:
basecalling and demultiplexing by the VBCF (Vienna, Austria) using Illumina software
quality assessment of the raw data using fastqc v.0.11.2
filtering and trimming of adapter residues and low quality reads with fthe FASTX toolkit v.0.0.14 and cutadapt v.1.4.1
Sequenced reads were mapped to the Ensembl BDGP6.80 whole genome using STAR v.2.4.2a
mapped reads were sorted and indexed using samtools v.1.2
bam files were converted into bigwig for visualisation on the UCSC server
Counting the mapped reads on the gene and exon level using featureCounts v.1.4.6
run the differentail expression analysis using the R package DESeq2 v.1.8.2
run the clustering using the R package Mfuzz v.2.28.0
Genome_build: BDGP6.80 from ENSEMBL

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol: flies were grown on standard cornmeal medium using a standard fly husbandry protocol

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP
RNA libraries were prepared for sequencing by the VBCF (Vienna, Austria) using standard Illumina protocols

treatment_protocol: dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction

value: indirect flight muscle

tag: developmental stage

value: 1d adult

value: Mef2-Gal4, UAS-T3029 (salmIR)

tag: growth protocol

value: grown at 27C from cross until eclosion

tag: barcode

value: TAGCTT


title: WT IFM 72h APF rep 1

description:
DESeq2_IFM_90hvs72h.xlsx
DESeq2_IFM_72hvs48h.xlsx
DESeq2_IFM_72hvs30h.xlsx
DESeq2_IFMvssalm_72h.txt
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555982

tag: tissue

value: 72h APF

value: Mef2-Gal4, UAS-GMA-GFP

value: grown at 27C, staged 0h white pre-pupae

value: CGATGT


title: WT IFM 72h APF rep 2

description:
DESeq2_IFM_90hvs72h.xlsx
DESeq2_IFM_72hvs48h.xlsx
DESeq2_IFM_72hvs30h.xlsx
DESeq2_IFMvssalm_72h.txt
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555983

tag: genotype

value: TTAGGC


title: FRTsalmFRT mut IFM 1d rep 1

description:
DESeq2_IFMvssalm_1d.txt
DESeq2_salm_1dvs72h.txt
Mfuzz_salm_4TP_inputdata.xlsx
previously submitted as GSM1555989

value: UAS-Flp; mef2-Gal4, salm1/FRT-salm-FRT

value: grown at 18C, shifted to 30C at crawling 3rd instar stage until eclosion

value: GGCTAC


title: E322V.TRE.2.2.B

tag: cell line


title: K54R.2.2.B


title: WT IFM 30h APF rep 2

description:
DESeq2_IFM_72hvs30h.xlsx
DESeq2_IFM_48hvs30h.xlsx
DESeq2_IFM_30hvs24h.xlsx
DESeq2_IFMvssalm_30h.txt
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555981

value: 30h APF


title: WT IFM 30h APF rep 1

description:
DESeq2_IFM_72hvs30h.xlsx
DESeq2_IFM_48hvs30h.xlsx
DESeq2_IFM_30hvs24h.xlsx
DESeq2_IFMvssalm_30h.txt
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555980

value: ATCACG


title: A375.2.2.B


title: WT.2.2.B


title: WT IFM 1d rep 2

description:
DESeq2_IFMvssalm_1d.txt
DESeq2_IFM_1dvs90h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555979

value: TGACCA


title: WT IFM 1d rep 1

description:
DESeq2_IFMvssalm_1d.txt
DESeq2_IFM_1dvs90h.xlsx
Mfuzz_IFMTC_8TP_inputdata.txt
Mfuzz_IFMTC_8TP_genes_975iterations.txt
Mfuzz_IFMTC_8TP_genes_1064iterations.txt
Mfuzz_IFMTC_8TP_genes_1118iterations.txt
Mfuzz_IFMTC_8TP_plots_975iterations.pdf
Mfuzz_IFMTC_8TP_plots_1064iterations.pdf
Mfuzz_IFMTC_8TP_plots_1118iterations.pdf
previously submitted as GSM1555978


title: S142L.2.2.B


title: MEKDD.TRE.2.1.B

description: Parental cell line with MEKDD ERK2 over-expression treated with trametinib


title: R191H.TRE.2.1.B

description: Parental cell line with R191H ERK2 over-expression treated with trametinib


title: P58L.TRE.2.1.B

description: Parental cell line with P58L ERK2 over-expression treated with trametinib


title: E322K.TRE.2.1.B

description: Parental cell line with E322K ERK2 over-expression treated with trametinib


title: K54R.TRE.2.1.B

description: Parental cell line with K54R ERK2 over-expression treated with trametinib


title: P58G.TRE.2.1.B

description: Parental cell line with P58G ERK2 over-expression treated with trametinib


title: D321V.TRE.2.1.B

description: Parental cell line with D321V ERK2 over-expression treated with trametinib


title: E322V.TRE.2.1.B

description: Parental cell line with E322V ERK2 over-expression treated with trametinib


title: E81K.TRE.2.1.B

description: Parental cell line with E81K ERK2 over-expression treated with trametinib


title: MEKDD.2.1.B


title: E322V.2.2.B


title: S142L.TRE.2.1.B

description: Parental cell line with S142L ERK2 over-expression treated with trametinib


title: A375.TRE.2.1.B

description: Parental cell line treated with trametinib


title: P58G.2.1.B


title: WT.TRE.2.1.B

description: Parental cell line with WT ERK2 over-expression treated with trametinib


title: R191H.2.1.B


title: P58L.2.1.B


title: S142L.2.1.B


title: E81K.2.1.B


title: D321V.2.1.B


title: E322V.2.1.B


title: E322K.2.1.B


title: K54R.2.1.B


title: WT.2.1.B


title: A375.2.1.B


title: MEKDD.TRE.1.4.A


title: R191H.TRE.1.4.A


title: P58L.TRE.1.4.A


title: P58G.TRE.1.4.A


title: S142L.TRE.1.4.A


title: D321V.TRE.1.4.A


title: E81K.TRE.1.4.A


title: E322V.TRE.1.4.A


title: A375.TRE.1.4.A


title: K54R.TRE.1.4.A


title: WT.TRE.1.4.A


title: R191H.1.4.A


title: MEKDD.1.4.A


title: S142L.1.4.A


title: P58L.1.4.A


title: E81K.1.4.A


title: E322K.1.4.A


title: K54R.1.4.A


title: P58G.1.4.A


title: E322V.1.4.A


title: D321V.1.4.A


title: WT.1.4.A


title: A375.1.4.A


title: R191H.TRE.1.3.A


title: MEKDD.TRE.1.3.A


title: E322V.TRE.1.3.A


title: S142L.TRE.1.3.A


title: E81K.TRE.1.3.A


title: P58G.TRE.1.3.A


title: E322K.TRE.1.4.A


title: WT.TRE.1.3.A


title: E322K.TRE.1.3.A


title: A375.TRE.1.3.A


title: K54R.TRE.1.3.A


title: MEKDD.1.3.A


title: R191H.1.3.A


title: ko2 hypothalamus

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

institute: Murdoch University

description: ko2 hypothalamus

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: mm10
Supplementary_files_format_and_content: counts data

organism: Mus musculus

source_name: hypothalamus

growth_protocol: Mice were sacrificed by cervical dislocation, hippocampi and hypothalami were dissected out from the brain and snap-frozen in liquid nitrogen. Total RNA was extracted from hippocampus and hypothalamus using mirVana miRNA Isolation Kit (Life Technologies/Thermo Fisher Scientific Inc, Waltham, MA, USA) according to the manufacturer’s protocol. For hippocampus 4 animals and for hypothalamus 5 animals were used from both genotypes. During the purification DNase I treatment was performed on column according to manufacturers’ protocol (Qiagen Inc, Valencia, CA, USA). The RNA quality was assessed using Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc, Santa Clara, CA, USA).

extract_protocol:
mirVana miRNA Isolation Kit
For hypothalami whole transcriptome sequencing cDNA was synthesized using Ovation RNA-Seq System V2 (NuGEN Technologies Inc, San Carlos, CA, USA), 50 ng of total RNA was used. SOLiD DNA Fragment library kit (cDNA input 2 µg) was used to generate libraries and quality was controlled with the Agilent Bioanalyzer 2100 (Agilent Technologies Inc, Santa Clara, CA, USA) before sequencing. The libraries were marked with different barcodes and pooled together for the following template preparation. The automated SOLiD EZ Bead System and SOLiD EZ Bead E80 System Consumables (Life Technologies/Thermo Fisher Scientific Inc, Waltham, MA, USA) were applied for the template preparation. For sequencing the SOLiD 5500xl System and paired end (75 bp forward and 35 bp reverse) chemistry for DNA sequencing was applied (Life Technologies/Thermo Fisher Scientific Inc, Waltham, MA, USA).

tag: mutant gene

tag: strain

value: homozygous


title: ko3 hypothalamus

description: ko3 hypothalamus


title: ko4 hypothalamus

description: ko4 hypothalamus


title: S142L.1.3.A

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit per the manufacturer's instructions.
Illumina TruSeq

tag: replicate


title: P58L.1.3.A


title: P58G.1.3.A


title: hz2 hypothalamus

description: hz2 hypothalamus

value: heterozygous


title: P58L.TRE.1.3.A


title: hz3 hypothalamus

description: hz3 hypothalamus


title: E81K.1.3.A


title: hz1 hypothalamus

description: hz1 hypothalamus


title: E322V.1.3.A


title: ko1 hypothalamus

description: ko1 hypothalamus


title: D321V.1.3.A


title: hz4 hypothalamus

description: hz4 hypothalamus


title: D321V.TRE.1.3.A


title: wt3 hypothalamus

description: wt3 hypothalamus

value: wild-type


title: wt5 hypothalamus

description: wt5 hypothalamus


title: K54R.1.3.A


title: WT.1.3.A


title: wt2 hypothalamus

description: wt2 hypothalamus


title: A375.1.3.A


title: MEKDD.TRE.1.2.A


title: S142L.TRE.1.2.A


title: R191H.TRE.1.2.A


title: wt1 hypothalamus

description: wt1 hypothalamus


title: P58L.TRE.1.2.A


title: E322V.TRE.1.2.A


title: E81K.TRE.1.2.A


title: D321V.TRE.1.2.A


title: E322K.TRE.1.2.A


title: K54R.TRE.1.2.A


title: WT.TRE.1.2.A


title: A375.TRE.1.2.A


title: MEKDD.1.2.A


title: E322K.1.3.A


title: P58L.1.2.A


title: S142L.1.2.A


title: R191H.1.2.A


title: E81K.1.2.A


title: E322V.1.2.A


title: K54R.1.2.A


title: E322K.1.2.A


title: WT.1.2.A


title: D321V.1.2.A


title: MEKDD.TRE.1.1.A


title: A375.1.2.A


title: R191H.TRE.1.1.A


title: S142L.TRE.1.1.A


title: P58G.TRE.1.1.A


title: P58G.TRE.1.2.A


title: D321V.TRE.1.1.A


title: E322K.TRE.1.1.A


title: WT.TRE.1.1.A


title: P58G.1.2.A


title: S142L.1.1.A


title: MEKDD.1.1.A


title: R191H.1.1.A


title: P58L.1.1.A


title: P58G.1.1.A


title: E322K.1.1.A


title: D321V.1.1.A


title: E322V.1.1.A


title: K54R.1.1.A


title: E81K.TRE.1.1.A


title: P58L.TRE.1.1.A


title: E322V.TRE.1.1.A


title: K54R.TRE.1.1.A


title: A375.1.1.A


title: CSB_WT_8h

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called by Macs1.4.2 and were annotated by Homer v4.8 and with Ensembl release 75
Genome_build: hg19
Supplementary_files_format_and_content: Excel table with macs1 peak calling result and Ensembl 75 gene annotations

growth_protocol: DMEM/HamF10 (1:1) + 10 % FCS and 40 mg/ml gentamycin

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA-containing complexes were isolated with antibody.
Diagenode MicroPlex Library Preparation kit v2

tag: cell type

value: dermal fibroblasts, immortolized

tag: treatments

tag: chip antibody

value: CSB (rabbit polyclonal, #3222)


title: PSMD1_8h

value: UV-C, 12 J/m2 + lactacystin 3h

value: PSMD-1 (Abcam, ab140682)


title: CSA_WT_8h

value: CSA (Abcam, ab137033)


title: A375.TRE.1.1.A


title: MDM2_WT_8h

value: MDM2 (Santa Cruz, sc-965x)


title: Input

value: no


title: CSA_WT_0h


title: PSMB5_8h

value: PSMB5 (Santa Cruz, sc-55009)


title: CSB_WT_0h


title: pol2_mut_24h

value: RNA Pol II (Santa Cruz, sc-9001x)


title: pol2_WT_24h


title: ATF3_mut_24h

value: ATF3 (Santa Cruz, sc-188x)


title: pol2_WT_8h


title: CD11b rep2

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
trim reads for quality with trm galore (-q 20)
quasi mapping with salmon (--numBootstraps 30)
DEG at gene level with R tximport and DESeq2 packages compare CD11b to CD103 samples
Genome_build: mm10
Supplementary_files_format_and_content: CD11b_vs_CD103_gene_res_exp_TPM_ann.xls contains TPM and counts for the samples and p-values and statistics comparing CD11b to CD103 samples

extract_protocol:
RNeasy Micro kit (Qiagen)
RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq kit (Roche) according to manufacturer’s instruction. First, poly A RNA was isolated from 100ng total RNA using oligo-dT magnetic beads. Purified RNA was then fragmented at 85C for 6 min., targeting fragments range 250-300bp. Fragmented RNA is reverse transcribed with an incubation of 25C for 10mins, 42C for 15mins and an inactivation step at 70C for 15mins. This was followed by second strand synthesis at 16C, 60mins. Double stranded cDNA fragments were purified using Ampure XP beads (Beckman). The dscDNA were then A-tailed, and ligated with illumina adaptors. Adaptor-ligated DNA was purified using Ampure XP beads. This is followed by 10 cycles of PCR amplification. The final library was cleaned up using AMpure XP beads. Sequencing was performed on Illumina NextSeq platform generating paired end reads of 76bp.

treatment_protocol: LPS inhalation followed 18 hours later by sorting on DC susbets in mediastinal LNs

value: Mediastinal lymph node


title: pol2_WT_0h


title: E81K.1.1.A


title: CD11b rep3


title: CD11b rep1


title: WT.1.1.A


title: CD103 rep3


title: ATF3_WT_24h


title: CD103 rep2


title: ATF3_WT_8h


title: ATF3_WT_0h


title: MDM2_WT_0h


title: CD103 rep1


title: upf3b-ASO-dose2-rep6

city: Carlsbad

first: Sagar

middle: S

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

data_processing:
demultiplexing and base-calling was performed by Illumina bcl2fastq2 software (version 2.17.1.14)
reads were associated to transcripts using a quasi-mapping based mode of Salmon  (version 0.7.2)
gene-level TPM was computed by normalizing number of reads mapped per transcript by number of mapped reads, using gene models from mouse ensembl build 81
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma-separated files containing gene symbol and TPM for genes

growth_protocol: mouse 8-14 weeks

extract_protocol:
Animal tissues were homogenized in guanidine isothiocyanate solution (Invitrogen) supplemented with 8% 2-mercaptoethanol (Sigma-Aldrich). Total RNA was prepared using the RNeasy mini Kit (Qiagen).
Digital gene expression (DGE) was performed by sequencing fragment libraries from purified total RNA as described previously (Patro et al., Nat Methods, 2017) using the QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen

treatment_protocol: 6 doses of ASOs were administrated subcutaneously at a volume of 10 µl/g, every 5 days

tag: dose

value: 20 mg/kg weekly dosing

tag: Sex

value: F

tag: age

value: adult

value: liver


title: upf3b-ASO-dose2-rep4

tag: treatment

value: M


title: upf3b-ASO-dose2-rep5


title: CSA_0h

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Tophat 2.0.10 and Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Quantiifcation of gene expression has been performed using HTSeq-0.6.1
Read counts have then been normalized across libraries with the method proposed by Anders and Huber
Genome_build: hg19
Supplementary_files_format_and_content: Excel table with raw expression, normalized expression values and foldchange values

extract_protocol:
RNA was harvested and isolated using a QIAGEN RNA purification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dermal fibroblasts, immortalized


title: CSA_24h


title: CS1AN_24h


title: CS1AN_0h


title: CSB_24h


title: upf3b-ASO-dose2-rep1


title: CSB_8h


title: CS3BE_0h


title: CS3BE_24h


title: upf3b-ASO-dose1-rep5

value: 10 mg/kg weekly dosing


title: upf3b-ASO-dose1-rep1


title: upf1-ASO-dose1-rep3


title: upf3b-ASO-dose1-rep2


title: upf3b-ASO-dose1-rep3


title: upf1-ASO-dose1-rep1


title: PBS-rep8

source_name: PBS

value: DPBS

value: 0 mg/kg weekly dosing


title: PBS-rep10


title: PBS-rep9


title: upf3b-ASO-dose1-rep4


title: Ventral half st10-st12

city: Los Angeles

first: Edward

middle: M

last: De Robertis

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

data_processing:
After sequencing, adaptors were first trimmed from the RNA reads and RNA reads of low quality filtered. The clean RNA reads were mapped using Tophat (Version 2.09, default parameters) against the Xenopus laevis JGI9.1 (Xenbase) transcript sequences.
Transcripts counts were normalized using DESeq package in R . RPKM (Reads Per Kilobase per Million mapped reads) for transcripts was calculated in R.
Human gene names were assigned to transcripts using an annotation file obtained by blasting the JGI9.1 peptide sequences to human reference protein sequences.
Genome_build: Xenopus Laevis J-strain Version 9.1
Supplementary_files_format_and_content: Excel tables that include RPKM and fold induction values of genes for each sample

organism: Xenopus laevis

source_name: Vental halves of embryos cut at st10 and developed until st12

growth_protocol: The embryos were cultured in 0.1x Marc's Modified Ringers (MMR) and staged according to Nieuwkoop and Faber (1967).

extract_protocol:
RNA  was isolated with an Absolutely RNA miniprep Kit (Agilent).
Libraries were constructed with the Illumina TruSeq RNA Library Preparation Kit V2 according to manufacturer’s protocol. Briefly, 1 µg total RNA  was used for input RNA. Then mRNA was purified through polyA+ selection. After fragmentation of the mRNA, first strand and second strand synthesis, double strand cDNA (ds cDNA) was obtained. The ds cDNA was then further processed for A-tailing, end repair and ligation of appropriate adaptors. Finally, the ds cDNA with adaptors was amplified by PCR to generate libraries. After measurement of the length and concentration of the libraries by Bioanalyser and Qubit, the libraries were sent for sequencing on Illumina Hi-Seq 2000 using standard methods to generate 100-bp single end reads by the Broad Stem Cell Research Center at UCLA.

treatment_protocol: mRNAs were injected at 2-4 cell stage; Animal caps are cut and dissociated at st9 and cultured till st12; Dorsal and ventral halves were dissected at stage 10 in 1x Barth’s solution and cultured to stage 12 in 0.3 x Barth's solution.

value: Nasco

value: ventral half embryo

value: embryo, stage 12


title: PBS-rep11


title: PBS-rep7


title: Xnr2 AC st12

source_name: animal caps injected with 200 pg Xnr2 mRNA cut at st 9 and cultured until st12

value: animal caps


title: PBS-rep6


title: upf3b-ASO-dose2-rep2


title: PBS-rep5


title: PBS-rep4


title: PBS-rep1


title: FGF8 AC st12

source_name: animal caps injected with 200 pg FGF8 mRNA cut at st 9 and cultured until st12


title: Dorsal half st10-st12

source_name: Dorsal halves of embryos cut at st10 and developed until st12

value: dorsal half embryo


title: PBS-rep2


title: con AC st12 #4

source_name: animal caps cut at st9  and cultured until st12; control for FGF8 AC st12, Xnr2 AC st12 and Wnt8 Xnr2 AC st12.


title: Wnt8 Xnr2 AC st12

source_name: animal caps injected with 200 pg Xnr2 mRNA and 16 pg of xWnt8 mRNA cut at st 9 and cultured until st12


title: Cer AC st12

source_name: animal caps injected with 400 pg Cerberus mRNA cut at st 9 and cultured until st12


title: ctrl-ASO-dose2-rep6

value: Control-GalNAc-ASO


title: ctrl-ASO-dose2-rep5


title: ctrl-ASO-dose2-rep4


title: dis AC st12 #2

source_name: animal caps cut and dissociated at st 9 and cultured until st12.


title: dis AC st12 #3


title: ctrl-ASO-dose2-rep2


title: chrd AC st12

source_name: animal caps injected with 400 pg Chrd mRNA cut at st 9 and cultured until st12


title: ctrl-ASO-dose2-rep1


title: con AC st12 #2

source_name: animal caps cut at st9  and cultured until st12; control for dis AC st12 #2


title: ctrl-ASO-dose2-rep3


title: ctrl-ASO-dose1-rep4

value: 15 mg/kg weekly dosing


title: Wnt AC st12

source_name: animal caps injected with 16 pg xWnt8 mRNA cut at st 9 and cultured until st12


title: PBS-rep3


title: ctrl-ASO-dose1-rep3


title: ko18 hippocampus

source_name: hippocampus

extract_protocol:
mirVana miRNA Isolation Kit
For hippocampi whole transcriptome sequencing 10 mg of total RNA was taken and treated with RiboMinus Eukaryote Kit for RNA-seq (Invitrogen/Thermo Fisher Scientific Inc, Waltham, MA, USA) to eliminate ribosomal RNA from the rest of the transcriptome. The SOLiD Total RNA-Seq Kit and 500 ng of ribodepleted RNA was used (according to the manufacturer’s protocol; (Life Technologies/Thermo Fisher Scientific Inc, Waltham, MA, USA)) for whole transcriptome RNA-seq library preparation. The libraries were marked with different barcodes and pooled together for the following template preparation. The sequencing was performed with SOLiD 4 platform ((Life Technologies/Thermo Fisher Scientific Inc, Waltham, MA, USA) and paired-end DNA sequencing chemistry (50 bp forward and 35 bp reverse).

value: homozygous


title: EPZ_mESC_serum_1_lane3

city: Edinburgh

first: J

last: Thomson

address: Crewe Road

department: IGMM

country: United Kingdom

institute: University of Edinburgh

data_processing:
Paired ends aligned using FASTQ paired-end parser
Quality control and Tophat 2 Alignment
General sequence statistics calculated
Genome_build: mm9
Supplementary_files_format_and_content: .bw

growth_protocol: Dnmt1 tet/tet mESCs (R1 strain)  were cultured in DMEM supplemented with 15% foetal calf serum, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 1% penicillin/streptomycin, 2mM L-glutamine, 0.1mM beta-mercaptoethanol and LIF at 1000U/mL. mESCS were passaged every 2-3 days with trypsin/EDTA and plated on 0.2% gelatin coated flasks.

extract_protocol:
RNA extracted usisng RNeasy kit (Qiagen).  For RNA quantification, samples were treated with DNase (Ambion) and random hexamer cDNA synthesized by reverse transcription.  Assays-on-demand gene expression TaqMan® MGB 6FAM dye-labeled products (Applied Biosystems) were used for relative quantification of cDNA.
Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out on a NextSeq-550 sequencer

treatment_protocol: Dnmt1 tet/tet mESCs (R1 strain) were treated with 10µM EPZ6438 for 9 days prior to harvesting.

tag: culture condition

value: Serum + EPZ

tag: strain/cell type

value: J1 mESC

value: EPZ


title: con AC st12 #1

source_name: animal caps cut at st9  and cultured until st12; control for dis AC st12 #1, BMP4 AC st12 and chrd AC st12.

tag: developmental stage


title: EPZ_mESC_serum_1_lane4


title: EPZ_mESC_serum_1_lane1


title: dis AC st12 #1


title: ctrl-ASO-dose1-rep2

value: adult

value: liver


title: control_mESC_serum_1_lane4

value: Serum


title: EPZ_mESC_serum_1_lane2


title: wt9 hippocampus

value: wild-type


title: ko17 hippocampus


title: wt10 hippocampus


title: wt8 hippocampus


title: ko15 hippocampus


title: ctrl-ASO-dose1-rep1

value: F


title: control_mESC_serum_1_lane2


title: con AC st12 #3

source_name: canimal caps cut at st9  and cultured until st12; control for dis AC st12 #3, Wnt AC st12 and Cer AC st12.


title: BMP4 AC st12

source_name: animal caps injected with 200 pg BMP4 mRNA cut at st 9 and cultured until st12


title: Cyst biol. rep. 2

city: Bloomington

first: Elizabeth

middle: Ann

last: Malinich

state: IN

address: 212 S Hawthorne Dr Rm313

department: Biology

institute: Indiana University

data_processing:
Quality Control: reads were trimmed with Trimmomatic on a sliding window of 5:25, minimum read length of 40bp
Aligned with Bowtie2 to A. brasilense sp7 genome; NCBI assembly GCF_001315025.1
Gene counts quantified with HTSeq
Differential gene expression analysized with DESeq2 in R
Genome_build: ASM131501v1
Supplementary_files_format_and_content: Excel files include gene number and associatd KEGG identification with the basemean, log2fold change of vegetative expression over cyst expression, p-value of change, and false discovert rate adjusted p-value.

organism: Azospirillum brasilense

source_name: Cyst

extract_protocol:
RNA extraction via acid phenol:cholorform and precipitated with 2mM LiCl and 100% ETOH; RNA cleaned with RNAeasy Qiagen Clean up Kit
cDNA prepared from Bacterial Scripting Complete Kit (Illumina)
RNA-seq; Illumina NextSeq on High Output 75 cycle


title: MycER_MEFs_YAP2S + Y27 rep2

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts (RPKMs) over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing expression quantification (reads per kilobase per million exonic mapped reads: eRPKM) of genes in MEF cells (WT and YAP2s) not treated and treated with Y27, OHT or both

source_name: MycER_MEFs_YAP2S + Y27 rep2

growth_protocol: murine fibroblast were grown in DMEM medium supplemented with 10% tetracyclin-free serum, penicillin/streptomycin and 2mM L-Gln

extract_protocol:
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)

treatment_protocol: ROCK inhibitor Y27632 (used 50µM), MycER was activated by OHT (400nM).

value: mouse embryonic fibroblasts


title: control_mESC_serum_1_lane3


title: control_mESC_serum_1_lane1


title: wt7 hippocampus


title: ko16 hippocampus


title: MycER_MEFs_YAP2S + Y27 rep1

source_name: MycER_MEFs_YAP2S + Y27 rep1


title: Cyst biol. rep. 1


title: Vegetative biol. rep. 3

source_name: Vegetative


title: Vegetative biol. rep. 2


title: MycER_MEFs_YAP2S + OHT + Y27 rep2

source_name: MycER_MEFs_YAP2S + OHT + Y27 rep2


title: MycER_MEFs_YAP2S + OHT rep2

source_name: MycER_MEFs_YAP2S + OHT rep2


title: Cyst biol. rep. 3


title: MycER_MEFs_YAP2S rep1

source_name: MycER_MEFs_YAP2S rep1


title: MycER_MEFs + Y27 rep2

source_name: MycER_MEFs + Y27 rep2

value: MycER


title: MycER_MEFs_YAP2S + OHT+ Y27 rep1

source_name: MycER_MEFs_YAP2S + OHT+ Y27 rep1


title: MycER_MEFs_YAP2S rep2

source_name: MycER_MEFs_YAP2S rep2


title: MycER_MEFs + OHT + Y27 rep1

source_name: MycER_MEFs + OHT + Y27 rep1


title: Vegetative biol. rep. 1


title: MycER_MEFs rep1

source_name: MycER_MEFs rep1


title: MycER_MEFs + OHT + Y27 rep2

source_name: MycER_MEFs + OHT + Y27 rep2


title: MycER_MEFs rep2

source_name: MycER_MEFs rep2


title: MycER_MEFs + Y27 rep1

source_name: MycER_MEFs + Y27 rep1


title: MycER_MEFs + OHT rep1

source_name: MycER_MEFs + OHT rep1