title: Mouse_ChIP_H3K27AC_130206_WT_GMP

city: Copenhagen N

first: Janus

middle: Schou

last: Jakobsen

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: See publication for FACS isolation regimen

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 (default parameters).
Peaks were called using macs2. To increase the specificity of the enriched regions, we used a control sample prepared using a control anti-body (‘IgG’ control). Further, Irreproducible Discovery Rate (IDR) was used at a false discovery rate of 0.05 to filter out irreproducible regions between the two replicates.
Bigwig files for UCSC genome coverage visualization were generated using Samtools, Bedtools and UCSC wigtobigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: FACS isolated GMP cells, WT, from in vivo

extract_protocol:
Cells were lysed as described previously (Jakobsen JS, Waage J, Rapin N, Bisgaard HC, Larsen FS, Porse BT. Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Res. 2013;23(4):592-603.) in 300 μl lysis buffer,12 applying up/down pipetting 10 times using a 100 ul tip low retention tip. Samples were sonicated using a Bioruptor sonicator plus for 30 cycles, 15/30 seconds on/off, high setting, and debris pelleted by centrifuging cold at 14,000g for 10 minutes. Fragmentation of chromatin was evaluated on extracted DNA using either: 1) a c-Kit enriched 500,000 cell sample processed in parallel (one of six tubes sonicated simultaneously) and agarose gel electrophoresis or, 2) direct sample size inspection of a 20 ul aliquot using a Bioanalyzer. ChIP was performed essentially as described previously (Sandmann T, Jakobsen JS, Furlong EE. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-2855) with ca. 125.000 cells for histone mark and ca. 250.000 cells for CEBPA ChIP. Quanta of used antibodies (CEBPA, Santa Cruz sc-61, lot#J0407, 0.2 ug; H3K27me3, Cell signaling #9733S, lot#2, 1 ul; H3K4me3, Cell signaling #9751S,  lot#2, 1 ul) and protein A beads (Sigma, cat#P9424 , 10 ul 50%/50% beads/RIPA-low salt (140 mM)) were optimized for low input amounts, using siliconized tubes (Biozym, cat#1267-2970).
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB #6200) or NEBNext Ultra I DNA Library Prep Kit for Illumina (NEB #7370), using bacterial carrier DNA as required, see: 'Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq', Jakobsen et al., BMC Genomics 2015

value: Whole bone marrow, cKIT enriched, FACs isolated


title: MA9-CD97_WT_biological_replicate1

status: Public on Jul 30 2019

type: SRA

city: New York

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

country: USA

institute: New York University

description: The Illumina Adapter sequence: 'AGATCGGAAGAGC' was trimmed from the raw fastq file using cutadapt version 1.2.1. and the following parameters:    Maximum trimming error rate: 0.1 (default)  Minimum required adapter overlap (stringency): 3 bp  Minimum required sequence length for both reads before a sequence pair gets removed: 25 bp

library_source: transcriptomic

data_processing:
For RNA-Seq data generated from HL60 cells and MA9 transformed mouse cells, raw fastq files were aligned to the hg19 and mm10 reference genomes, respectively. Read counts were extracted using R with Rsamtools package (v1.24.0) and differentially expressed genes analyzed using the DESeq2 package (v 1.12.3).
Genome_build: hg19 for HL60 RNA-seq
Genome_build: mm10 for MA9 RNA-seq
Supplementary_files_format_and_content: Read count files for i) HL60 RNA-seq data ii) MA9 RNA-seq data

molecule: total RNA

organism: Mus musculus

source_name: Purified HSPCs from wild type (WT) mice transduced with the leukemogenic oncogene MA9.

extract_protocol:
Samples were FACS-sorted into Trizol LS (Thermo Fisher, Rockford, Illinois).
Poly-A selected cDNA libraries were prepared using a SMARTer mRNA amplification kit (Clontech, Mountain View, California).

tag: strain

tag: tissue


title: yFR973_spt16-197_80min37C_H2BvsInput_20170608_Rep2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 2 of 2. H2B occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_861354.bed
A genome browser-ready file for H2B occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

hyb_protocol: Hybridization: Resuspend colored pellet in 110 uL of hybridization mix (100 uL DIG Easy Hyb buffer, 5 uL 10mg/mL Salmon Sperm DNA, 5 uL 8mg/mL yeast tRNA). Put at 95°C for 5 min. Put at 42°C for 10 min (keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocol. Incubate overnight (16-24h) at 42°C in Agilent hybridization oven at 20 rpm rotation speed.  Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 min at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in Wash buffer #2 pre-warmed at 31°C for 5 min on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Stripping: Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 20 to 25 min. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. 1M Potassium phosphate buffer pH 6.6: mix 3.81 mL of 1M K2HPO4 + 6.19 mL of 1M KH2PO4. Dilute 5 mL of this 1M solution in 1 L Milli-Q water to obtain 5 mM Potassium phosphate buffer pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180K. Set the scan as follow: pixel size = 2µm; speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto. Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing:
The ChIP-chip data from individual replicates were normalized by setting the median of log2 ratios to zero. The duplicate were averaged and the data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100bp to generate data points in 10bp intervals as described before (Guillemette et al., 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = median normalized

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Standard Yeast aa-dUTP Labeling. Blunting: Do everything on ice. Add 70 uL of the blunting solution (11 uL NEB Buffer #2, 0.5 uL BSA 10mg/mL, 0.5 uL 20mM dNTPs, 0.2 uL T4 DNA Polymerase 3U/uL, 57.8 uL ddH2O) to 40 uL of the resuspended DNA obtained at the end of the cleanup step. For Inputs, use 4uL + 36uL ddH2O. Incubate 20 min at 12°C. Precipitation: Add 11.5 uL 3M NaOAc pH 5.2 and 0.5 uL Glycogen 20mg/mL and vortex briefly. Extract with 120 uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110 uL to a new tube and add 230 uL of cold 100% EtOH (-20°C). Spin 20 min at 4°C. Wash the pellet with 700 uL of cold 70% EtOH (-20°C) and spin 5 min at 4°C. Resuspend the pellet in 25 uL ddH2O and place on ice. Ligation: Thaw everything and do all manipulations on ice. Add 25 uL of ligase mix (10 uL 5x T4 Ligase Buffer, 6.7 uL 15uM unidirectional linkers, 0.5 uL T4 DNA Ligase (5U/uL), 8 uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16°C. Precipitation: Add 6 uL 3M NaOAc pH 5.2 and vortex. Add 130 uL of cold 100% EtOH (-20°C) and incubate at least 30 min at -20°C. Centrifuge 20 min at 4°C at maximum speed. Wash the pellet (should be a smear on the side of the tube) with 500 uL cold 70% EtOH (-20°C). Spin 5 min at 4°C. Dry the pellet and resuspend in 25 uL ddH2O. Leave on ice for about 20 min, vortex, centrifuge briefly and put on ice. Labeling: Add 15 uL of PCR labeling mix (4 uL 10x ThermoPol Buffer, 2 uL 5mM aa-dUTP mix, 1.25 uL 40uM Oligo FR1, 7.75 uL ddH2O) to the pellet from the ligation step. Start the PCR program and during the first step (4 min at 55°C), add 10 uL of the polymerase mix (1 uL 10x ThermoPol buffer, 1 uL Taq Polymerase 5U/uL, 0.01 uL Pfu Polymerase Turbo 2.5U/uL, 8 uL ddH2O). PCR cycling conditions: 1) 4 min at 55°C; 2) 5 min at 72°C; 3) 2 min at 95°C; 4) 30 sec at 95°C; 5) 30 sec at 55°C; 6) 1 min at 72°C; 7) Repeat steps 4-6 31 more times; 8) 4 min at 72°C; 9) Forever at 4°C. Purify PCR reactions with QIAquick PCR purification kit (Qiagen), following manufacturer's protocol but use a Phosphate Wash buffer and a Phosphate Elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns twice and elute with 50 uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5 uL 0.1M Sodium Carbonate buffer pH 9.0. Add 4.5 uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dyes should be resuspended in 73 uL DMSO. Mix well and incubate at room temperature in the dark for one hour. Add 35 uL 0.1M NaOAc pH 5.2. Purify using the QIAquick PCR purification kit (Qiagen), wash twice and elute in 50 uL. Mix both samples of a pair (Cy5 and Cy3) in the same tube. Speed-vac until 10-20uL are left. Phosphate Wash buffer (100 mL): 0.5 mL 1M KPO4 pH 8.5, 15.25 mL ddH2O, 84.25 mL 95% EtOH. Solution will be cloudy upon mixing. Phosphate Elution buffer (10 mL): 0.04 mL 1M KPO4 pH 8.5, 9.96 mL ddH2O. 1M KPO4 pH 8.5 (10 mL): 9.5 mL 1M K2HPO4, 0.5 mL 1M KH2PO4. 1M Sodium Carbonate buffer pH 9.0 (100 mL): 10.8g Na2CO3, 80 mL ddH2O and pH to 9.0 with concentrated HCl. Adjust volume to 100 mL with ddH2O. Dilute 1:10 when using. Solution will change composition over time. Use only if less than a month old.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose) medium is inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow until it reachs OD600 0.5. Cell cultures are then switched to 37°C and allowed to grow for additional 80 min. Culture is poured in a 50 mL tube containing 1.4 mL 37% formaldehyde for crosslinking, and incubated on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5 mL 2.5M Glycine to quench formaldehyde. Crosslinked cells are pelleted at 4°C, 3000 rpm, resuspended in 40 mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (1 mL) and transferred to 1.5 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cell pellets snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cells are thawed on ice and resuspended in 700 uL Lysis buffer with protease inhibitors. 500 uL of acid-washed glass beads (Sigma) are added and the cells are lysed using a bead-beater (4 x 5 min cycles, with 5 min breaks on ice). The tubes are pierced with an 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2 mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x20sec at output 7 Watts, with a 1 min break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4°C max speed and the supernatant used immediately for ChIP (or saved and frozen at -80°C). Lysis buffer: 50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1mM PMSF, 1mM Benzamidine, 10ug/mL Aprotinin, 1ug/mL Leupeptin, 1ug/mL Pepstatin.
Beads are spun down and supernatant is transferred to a new 1.5 mL tube. 350 uL of a mix of (345 uL TE, 3 uL RNAse A 10mg/mL, 2 uL Glycogen 20mg/mL) is added to the supernatant. Samples are vortexed and incubated at 37°C for 2 hr. 15 uL 10% SDS and 7.5 uL Proteinase K are then added, vortexed and incubated for another 2 hr at 37°C. The samples are then extracted twice with 400 uL phenol/chloroform/isoamyl alcohol (25:24:1). 14 uL of 5M NaCl is added to the final extract of about 350 uL. 1 mL of cold 100% EtOH (-20°C) is added and the samples are centrifuged at maximum speed for 20 min at 4°C. The supernatant is discarded and the pellet is washed with 700 uL of cold 70% EtOH (-20°C) and centrifuged 5 min at 4°C. The supernatant is discarded and the pellet resuspended in 50 uL TE and stored at -20°C.

treatment_protocol:
switch to 37°C for 80 min
H2B ChIP. Antibody from Abcam (ab1790). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (5 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

tag: genotype

value: MATα, leu2Δ1, spt16-197

tag: antibody

value: H2B (Abcam ab1790)

treatment_protocol:
switch to 37°C for 80 min
none


title: RBM8A-WTsib-27hpf-Rep3

city: Columbus

first: Pooja

last: Gangras

state: OH

address: 191 W. 9th Ave, apt A3

department: Molecular Genetics

institute: The Ohio State University

description:
Ribosomal RNA depleted total RNA
ribosomal RNA removed with Ribo-Zero kit (Illumina, Cat# MRZH116) prior to base hydrolysis of RNA. RNA fragments were then used to generate strand-specific libraries using a custom library preparationprotocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28.

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing
Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters -m 20 --discard-untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters -p 12
Multi-mapped reads were removed based on tophat alignment score (< 50) and PCR duplicates were removed only for the RIP-seq data based on random barcodes
RIP-Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters -s -c -F 0.51 -sorted
Genome_build: GRCz10
Supplementary_files_format_and_content: RNA-Seq: FPKM as caculated by DESeq2 for each gene in the samples
Supplementary_files_format_and_content: RIP-seq: RPKM each transcript in the samples

organism: Danio rerio

source_name: Whole embryo

growth_protocol: All embryos were raised at 28.5C upto the required developmental timepoint.

extract_protocol:
RIP-Seq samples were extracted from the IP eluate by Phenol-Chloroform-Isoamyl alcohol extraction. RNA-seq samples were obatined by harvesting whole embryos in TRIZOL.
Libraries were prepared using a custom protocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28. Briefly, a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription (RT) product, which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.

treatment_protocol:
None
NA

tag: developmental stage

value: 27 hpf

tag: rip-antibody

tag: genotype/variation


title: Mouse_ChIP_H3K27AC_050412_WT_GMP

library_source: genomic


title: p35S_Control_6wk_3

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

description: polysomal RNA from PPV infected 6-week-old leaf tissue

data_processing:
Reads were mapped to the Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10 - CLC Bio, Aarhus, Denmark)
Genome_build: Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1)
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, TPM, RPKM, Unique gene reads, Total gene reads, Unique exon reads and Total exon reads.

organism: Prunus domestica

growth_protocol: Transgenic plum trees expressing promoter:His6FLAG-RPL18 were maintained in the plant biosafety level 3 containment facility at the USDA facility at Fort Detrick, Frederick, MD, USA. Plants in the quarantine greenhouse were subjected to a cycle of 60 days of cold dormancy (4°C) followed by 84-90 days of growth at normal greenhouse temperatures (27°C). Leaf samples were collected at two, four, six, and twelve weeks post cold induced dormancy over two consecutive vegatative growth periods

extract_protocol:
Frozen tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA) pH 8.0, 35 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 5 mM dithiothereitol (DTT), 1 mM PMSF, 50 ug/mL cycloheximide, 50 ug/mL chloramphenicol, 0.5 mg/mL heparin) using 10 mL PEB per 5 g of tissue. Samples were centrifuged at 16,000 g for 15 min at 4°C. The supernatant was loaded onto an 8 mL 1.6 M sucrose cushion. The polysome fraction was pelleted by centrifuging the samples at 170,000 g for 18 h at 4 °C. The pellet was resuspended in 1 mL of PEB. 50 μl of Anti-FLAG magnetic beads (Sigma Chemical Company, St. Louis, MO, USA) was added to the resuspended pellet and incubated at 4°C overnight with gentle rocking. The beads were recovered using their magnetic property and were washed four times in wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 35 mM MgCl2, 5 mM DTT, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol). Polysome-RNA complexes were eluted by treatment of the magnetic beads with 100 μl of Elution Buffer (100 μl wash buffer, 10 μl of 5 mg/mL FLAG3 peptide—Sigma Chemical Company, St. Louis, MO USA, 0.5 μl of 2 U/ml RNAse OUT—Thermo Fisher Scientific Cleveland, OH, USA). RLT buffer plus β-mercaptoethanol from the Qiagen RNeasy kit (Qiagen, Valencia, CA, USA) was added to the eluted complexes. A 0.5 × volume of 100% ethanol was then added, and the sample transferred to Qiagen RNeasy columns. Washes and RNA elutions were performed according to the manufacturer’s instructions. Isolated RNA was measured on a NanoDrop 2000 and with the Qubit RNA Assay Kit (Thermo Fisher Scientific, Cleveland, OH, USA). Quality of the RNA was analyzed using an RNA ScreenTape assay (Agilent Technologies, Palo Alto, CA, USA).
Library preparation and paired-end sequencing on the Illumina HiSeq system was done by Genewiz (South Plainfield, NJ, USA).

treatment_protocol: PPV_D isolate Penn7 (EF640935) was used in this study. A Myzus persicae aphid colony was maintained inside containment and transmissions were conducted using symptomatic P. persica cv. GF 305 peach leaves as the inoculum source for aphid transmission to P. domestica L. transgenic plant lines.

tag: cultivar

value: P. domestica L 'President'

value: 6 weeks

tag: infection status

value: healthy control


title: MAGOH-Mutant-21hpf-Rep3

value: 21 hpf

value: MAGOH-Mutant


description:
Biological replicate 1 of 2. H2B occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_944786.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in WT cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H2Bub ChIP. Antibody from Cell Signaling Technology (#5546). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: MATα, leu2Δ1

value: H2Bub (Cell Signaling Technology 5546)


title: yFR971_SPT16-WT_80min37C_H2BvsInput_20170608_Rep2

description:
Biological replicate 2 of 2. H2B occupancy in WT cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_550143.bed
A genome browser-ready file for H2B occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: RBM8A-Mutant-27hpf-Rep3


title: MAGOH-WTsib-21hpf-Rep1

value: MAGOH-WTsib


title: p35S_Control_6wk_2


title: yFR971_SPT16-WT_80min37C_ubH2BvsInput_20170608_Rep2

description:
Biological replicate 2 of 2. H2B occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_944786.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: MA9-CD97_KO_biological_replicate1

source_name: Purified HSPCs from CD97 deficient (CD97-/-) mice transduced with the leukemogenic oncogene MA9.


title: RBM8A-WTsib-27hpf-Rep2


title: yFR974_spt6-1004_80min37C_H3K18acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_165064.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K18ac ChIP. Antibody from Abcam (ab1191). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K18ac (Abcam ab1191)


title: Mouse_ChIP_H3K4ME1_130206_WT_GMP


title: p35S_Control_6wk_1


description:
Biological replicate 1 of 2. H2B occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_861354.bed
A genome browser-ready file for H2B occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: Mouse_ChIP_H3K4ME1_050412_WT_GMP


description:
Biological replicate 1 of 2. H2B occupancy in WT cells treated 80 minutes at 37°C. H2B ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2B and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_550143.bed
A genome browser-ready file for H2B occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: Mouse_ChIP_CEBPA_130419_WT_GMP

description:
See publication for FACS isolation regimen
p30_p42_common_coord_mm9.xlsx

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 (default parameters).
Peaks were called using macs2. To increase the specificity of the enriched regions, we used a control sample prepared using a control anti-body (‘IgG’ control). Further, Irreproducible Discovery Rate (IDR) was used at a false discovery rate of 0.05 to filter out irreproducible regions between the two replicates.
Bigwig files for UCSC genome coverage visualization were generated using Samtools, Bedtools and UCSC wigtobigwig
Genome_build: mm9
Supplementary_files_format_and_content: bigWig; Excel file representing called peak positions (mm9) for CEBPA-ChIP peaks: Lp30 leukemic GMPs only (p30), WT GMPs only (p42) or shared (common)


title: p35S_Control_4wk_4

description: polysomal RNA from PPV infected 4-week-old leaf tissue

value: 4 weeks


title: RBM8A-WTsib-27hpf-Rep1


description:
Biological replicate 1 of 2. H3K18ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_165064.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: RBM8A-Mutant-27hpf-Rep2


title: RBM8A-Mutant-27hpf-Rep1


title: p35S_Control_4wk_2


description:
Biological replicate 1 of 2. H3K14ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_129089.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K14ac ChIP. Antibody from Millipore (07-353). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (3 μL/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K14ac (Millipore 07-353)


title: PL 24,11#32 vs Q 24,11#41 [2]

type: RNA

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

description: TNBC PDX model sensitive (IDB-01S) and resistant (IDB-01R) to docetaxel

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Homo sapiens

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA was isolated by standard procedures using TriPure (Roche, #11667165001)

value: tumor

tag: pdx model

value: IDB-01S model

tag: sensitivity to docetaxel

value: Sensitive

value: IDB-01R model

value: Resistant


title: Mouse_ChIP_III_P30_GMP_H3K4ME1

source_name: FACS isolated p30-GMP-blast cells, from in vivo

value: C57BL/6, Lp30 cells generated from floxed p30 using Mx-cre and Poly-IC injection. Tertiary, transplanted leukemia used for examinations

value: Whole bone marrow, cKIT enriched, FACs isolated


description:
Biological replicate 1 of 2. H2Bub occupancy in WT cells treated 80 minutes at 37°C. H2Bub ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H2Bub and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_ubH2BvsInput_20170608_Rep1-2_MN__S.cerevisiaeApr11_33826.bed
A genome browser-ready file for H2Bub occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: RBM8A-Mutant-21hpf-Rep3


title: p35S_Control_2wk_6

description: polysomal RNA from PPV infected 2-week-old leaf tissue

value: P. domestica L 'President'

value: 2 weeks

value: healthy control


title: p35S_Control_4wk_1


title: yFR974_spt6-1004_80min37C_H3K14acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_129089.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: yFR973_spt16-197_80min37C_H3K18acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_78813.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: Mouse_ChIP_II_P30_GMP_H3K4ME1

description: See publication for FACS isolation regimen


title: p35S_Control_4wk_3


title: Mouse_ChIP_III_P30_GMP_H3K27AC


title: RBM8A-WTsib-21hpf-Rep2

description:
Ribosomal RNA depleted total RNA
ribosomal RNA removed with Ribo-Zero kit (Illumina, Cat# MRZH116) prior to base hydrolysis of RNA. RNA fragments were then used to generate strand-specific libraries using a custom library preparationprotocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28.

value: 21 hpf


title: RBM8A-Mutant-21hpf-Rep2


title: Mouse_ChIP_II_P30_GMP_CEBPA


title: p35S_Control_2wk_4


title: RBM8A-WTsib-21hpf-Rep1


title: Mouse_ChIP_CEBPA_111011_WT_GMP


title: p35S_Control_2wk_5


title: p35S_Control_2wk_3


title: Mouse_ChIP_I_P30_GMP_CEBPA


title: RBM8A-WTsib-21hpf-Rep3


title: Mouse_ChIP_II_P30_GMP_H3K27AC


title: RBM8A-Mutant-21hpf-Rep1


title: Mouse_RNAseq_WT4

data_processing:
The Raw sequencing data was trimmed with Trimmomatic (v 0.32) with the paramters: ILLUMINACLIP:fastqc.fa:2:30:10 HEADCROP:X LEADING:22 SLIDINGWINDOW:4:22 MINLEN:25
The trimmed data was mapped to the genome (hg19, mm9) using TopHat2 (v2.0.9) using the parameters --b2-very-sensitive --library-type=fr-unstranded nd supplying the Enslemble GTF file to the --GTF argument (release 66 for both human and mouse).
The mapped reads were summarized into gene counts using the featureCounts() function, from the Rsubread R package (V1.16.1), using the same GTF file described above and with default parameters apart from isPairedEnd=TRUE.
Filtering and differential expression: Genes with at least 2 fragments uniquely mapping in at least 1 library we tested for differential expression. A gene was deemed differentially expressed if it was called as significant with a False Discovery Rate (FDR) corrected p-value < 0.01 by both edgeR and DESeq. Specifically the exactTest() function from EdgeR (v 3.12.0) (Robinson et al., 2010)[Ref: http://bioinformatics.oxfordjournals.org/content/26/1/139.short ] was used after TMM normalization and estimation of dispersion using both estimateCommonDisp() and estimateTagwiseDisp(). The DESeq() function from DESeq (v 1.18.0) (Anders and Huber, 2010) [Ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/ ] was used with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
Qiagen, RNeasy Mini Kit
Nugen Ovation RNA-Seq System V2


title: yFR973_spt16-197_80min37C_H3K14acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_559617.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K14ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_559617.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: p35S_Control_2wk_2


title: p35S_Control_2wk_1


title: yFR971_SPT16-WT_80min37C_H3K18acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K18ac occupancy in WT cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_819388.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1


description:
Biological replicate 1 of 2. H3K18ac occupancy in WT cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_819388.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: Mouse_RNAseq_WT3


title: RBM8A-RIPSEQ-Rep3

description:
Other (protein-bound RNA)
Input RNA was RNase I footprints of complexes containing Rbm8a protein

value: 24 hpf

value: Human Y14 (Sigma, cat# Y1253)


title: Mouse_RNAseq_WT2


title: pSULTR22_PPV_12wk_2

description: phloem polysomal RNA from PPV infected 12-week-old leaf tissue

value: P. domestica L 'Stanley'

value: 12 weeks

value: PPV infected


title: RBM8A-RIPSEQ-Rep1


title: pSULTR22_PPV_12wk_1


description:
Biological replicate 1 of 2. H3K18ac occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K18ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K18ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K18acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_78813.bed
A genome browser-ready file for H3K18ac occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: H3K18ac (Abcam ab1191)


title: MRWT1_5

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contaminations were removed from reads using cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: Ensembl genebuild 75 (Danio rerio assembly Zv9).
Supplementary_files_format_and_content: matrix_table.xls file contains ENSEMBL gene Ids and TMM-normalized, batch corrected counts per million for each sample.

molecule: polyA RNA

source_name: mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts

growth_protocol: All experiments were conducted with adult zebrafish between 6 and 9 months of age, raised at a density of 3 fish/l.

extract_protocol:
RNA was extracted with PicoPure™ RNA Isolation Kit
Index-tagged cDNA libraries were constructed, in two batches, from total RNA (1 ng) with the TruSeq RNA sample preparation v2 kit (Illumina), after amplification with the NuGen OvationSC RNA-Seq System. Quality, quantity, and size distribution of the Illumina libraries were determined using the DNA-1000 kit (Agilent Bioanalyzer).
RNASeq. Libraries were sequenced (single-end mode and length of 60-61 bp) on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.

treatment_protocol: Four biological replicates consisting of FAC sorted cells, coming from five to seven pooled hearts, were used per phenotype.

tag: phenotype

tag: library batch


title: pSULTR22_PPV_6wk_4

description: phloem polysomal RNA from PPV infected 6-week-old leaf tissue

value: 6 weeks


title: pSULTR22_PPV_6wk_3


description:
Biological replicate 1 of 2. H3K14ac occupancy in WT cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_98488.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: H3K14ac (Millipore 07-353)


title: yFR971_SPT16-WT_80min37C_H3K14acvsInput_20170530_Rep2

description:
Biological replicate 2 of 2. H3K14ac occupancy in WT cells treated 80 minutes at 37°C. H3K14ac ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K14ac and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K14acvsInput_20170530_Rep1-2_MN__S.cerevisiaeApr11_98488.bed
A genome browser-ready file for H3K14ac occupancy (IP/Input) in WT cells treated 80 min at 37°C.


title: Mouse_RNAseq_Lp30_1


title: Mouse_RNAseq_WT1


title: RBM8A-RIPSEQ-Rep2


title: Mouse_RNAseq_Lp30_2


title: MRWT1_4


title: pSULTR22_PPV_6wk_2


title: YAP5SA mutant, Rep#4

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for the first and last 10 bases, then mapped to mm10 using tophat2/2.0.9 with parameters --b2-very-sensitive
Differential expressed genes were determined by cufflinks/2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include related cuffdiff output files
gene_exp.diff: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id
genes.count_tracking: Gene counts. Tracks the summed counts of transcripts sharing each gene_id
genes.fpkm_tracking: Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
genes.read_group_tracking: Gene read group tracking. Tracks the summed expression and counts of transcripts sharing each gene_id in each replicate

source_name: embryonic stomach

extract_protocol:
Embryonic stomach were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

value: E13.5 embryo


title: MRWT1_2


title: YAP5SA mutant, Rep#3


title: MRWT1_1


title: YAP5SA mutant, Rep#2


title: pSULTR22_PPV_6wk_1


title: YAP5SA mutant, Rep#1


title: Wild type, Rep#4

value: wild type


title: MR_4

source_name: mpeg1:mCherry cells from 4dpi hearts


title: MR_5


title: pSULTR22_PPV_4wk_2

description: phloem polysomal RNA from PPV infected 4-week-old leaf tissue

value: 4 weeks


title: pSULTR22_PPV_2wk_2

description: phloem polysomal RNA from PPV infected 2-week-old leaf tissue


title: pSULTR22_PPV_4wk_1


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_966931.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3K4me3 ChIP. Antibody from Abcam (ab8580). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2.5ug/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3K4me3 (Abcam ab8580)


title: MR_2


title: pSULTR22_PPV_2wk_1

value: 2 weeks


title: MR_1


title: yFR971_SPT16-WT_80min37C_H3K4me3vsInput_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_315468.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.


description:
Biological replicate 1 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_484236.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: LOS_#3 Tongue

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
Base-calling was performed using RTA 2.0.
Adapter sequence (TGGAATTCTCGGGTGCCAAGG) were removed using cutadapt v1.18 . Reads with low quality bases (Phred score < 20) were trimmed using the dynamictrim function of SolexaQA++ v3.1.7.1 with Burrows-Wheeler Aligner algorithm.
Trimmed reads were aligned to bovine genome UMD3.1.1 using miRDeep2 v0.0.8 (Bowtie algorithm). mapper.pl was run with parameters (-d -c -i -j -l 17 -m -p -s -t -v). Reads shorter than 17 bases were discarded. miRDeep2.pl was run with parameters (-t -P) to detect known and putative miRNAs.
miRNAs were quantified using quantifier.pl with parameters (-p -m -r -k). One mismatch was allowed within the read by default. Reads aligned to miRNAs with multiple precursors were only counted once for each read per miRNA.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: Abundance measurements files are tab delimited text files containing name of the miRNAs (with miRBase ID indicating known miRNAs), pre-miRNAs (mixed indicating miRNAs with multiple precursors), and raw read counts of miRNAs for each fetus.

organism: Bos indicus x Bos taurus

source_name: ~Day 105 fetal tongue

growth_protocol: Refers to Chen et al., Epigenetics, 2013.

extract_protocol:
Total RNA was isolated from frozen tissues (-80°C) using TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions. RNA samples were stored at -80°C. RNA quality was determined by both spectrometry and fragment analysis.
For each sample, 2 μg RNA was submitted to the University of Missouri DNA Core Facility for library construction. Libraries were prepared with TruSeq® Small RNA Library Prep Kit (Illumina) following the manufacturer’s instructions. Size selection of 140-160 bp were performed on polyacrylamide gel.

tag: disease status

value: LOS

value: ~Day 105 fetus

tag: conception method

value: ART

tag: Sex

value: female

value: tongue


title: pSULTR22_Control_12wk_2

value: P. domestica L 'Stanley'

value: 12 weeks

value: healthy control


description:
Biological replicate 1 of 2. H3K4me3 occupancy in WT cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_SPT16-WT_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_315468.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

value: MATα, leu2Δ1


title: LOS_#5 Tongue

treatment_protocol: Refers to Chen et al., Epigenetics, 2013.

value: male


description:
Biological replicate 1 of 2. H3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_507920.bed
A genome browser-ready file for H3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

treatment_protocol:
switch to 37°C for 80 min
H3 ChIP. Antibody from Abcam (ab1791). Protein G Dynabeads (50uL/ChIP) are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 2 mL PBS + 0.5% BSA. Antibody is added (2 μg/ChIP), and incubated at least 5 hr at 4°C in haematological mixer. Beads are washed twice with 10 mL PBS + 0.5% BSA (freshly made), and resuspended in 30 uL PBS + 0.5% BSA/ChIP. 600 uL of lysate are added to 30 uL beads, and incubated overnight at 4°C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1 mL ice cold Lysis Buffer (no protease inhibitors), twice with 1 mL ice cold Lysis Buffer + additional 360mM NaCl (no protease inhibitors), twice with ice cold Wash Buffer (no protease inhibitors) and once with ice cold TE. Remaining liquid is removed by pipetting after a brief centrifugation at 4°C and 50 uL TE + 1% SDS is added for elution. Beads are incubated overnight at 65°C for elution and to reverse the crosslinking. Note for Inputs: whole cell extracts (WCE) are included in the protocol only at the crosslink reversal step. Add 50 uL TE + 1% SDS to 6 uL (1%) WCE and put overnight at 65°C to reverse the crosslinking. Lysis Buffer: 50 mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1mM EDTA.

value: H3 (Abcam ab1791)


title: p30 replicate 2

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

data_processing:
Sequenced reads (trimmed, quality-controlled by Fasteris) were mapped to E. coli genome + Citrobacter sp. RFL231 Csp231I + cloning vector pBR322 using BWA MEM (version 0.7.17-r1188).
The resulting mapping files were converted into BAM format and sorted using the samtools software (version 1.6).
Significantly differentially expressed gens (DEGs) were detected by using CuffDiff. The expression profiles, normalized to the sample size and transcript length and provided as FPKM (fragments per kilobase per million Mapped reads). CuffDiff was executed with the mapping BAM files as input and default parameters except --no-effective-length-correction -u --max-bundle-frags 50000000000.
Genome_build: NC_000913.3 + AY787793.1 + J01749.1
Supplementary_files_format_and_content: tab-delimited text file including results of CuffDiff analyses of differential gene-level expression

organism: Escherichia coli

source_name: Cultures of E. coli MG1655 carrying pMCsp231 with additional protective MTase gene on ACYC177 derivative, and with plasmid with C-R+ RM (p30)

growth_protocol: LB medium culture

extract_protocol:
At about mid log phase the cells were harvested and resuspanded in RNALater solution (Sigma). Total RNA was extracted with RiboPure (Ambion) in two biological replicates.
RNA libraries were rRNA depleted using Ribo-Zero rRNA Removal Kit (Bacteria) and prepared for sequencing using standard Illumina protocols

value: K-12 substr. MG1655

tag: plasmid

tag: rm system

value: R-M system Csp231I variant with C gene deleted (C- R+)


description:
Biological replicate 1 of 2. H3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_196984.bed
A genome browser-ready file for H3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

tag: strain


title: yFR971_WT_80min37C_H3vsInput_20150721_Rep2

description:
Biological replicate 2 of 2. H3 occupancy in WT cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_588993.bed
A genome browser-ready file for H3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

tag: genotype


title: pSULTR22_Control_12wk_1


title: p30 replicate 1


title: pSULTR22_Control_6wk_3

value: 6 weeks


description:
Biological replicate 1 of 2. H3 occupancy in WT cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR971_WT_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_588993.bed
A genome browser-ready file for H3 occupancy (IP/Input) in WT cells treated 80 min at 37°C.

tag: antibody


title: Wild type, Rep#1

tag: tissue

value: stomach

tag: developmental stage

value: E13.5 embryo

value: wild type


title: p24 replicate 2

source_name: Cultures of E. coli MG1655 carrying pMCsp231 with additional protective MTase gene on ACYC177 derivative, and with plasmid with C+R- RM (p24)

value: R-M system Csp231I variant with no endonuclease activity (C+ R-)


title: LOS_#6 Tongue

value: LOS

value: ~Day 105 fetus


title: yFR974_spt6-1004_80min37C_H3K4me3vsInput_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_966931.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.

value: H3K4me3 (Abcam ab8580)


title: pSULTR22_Control_6wk_2

tag: genotype/variation


title: yFR974_spt6-1004_80min37C_H3vsInput_20150721_Rep2

description:
Biological replicate 2 of 2. H3 occupancy in spt6-1004 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR974_spt6-1004_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_507920.bed
A genome browser-ready file for H3 occupancy (IP/Input) in spt6-1004 temperature-sensitive cells treated 80 min at 37°C.


title: LOS_#1 Tongue

value: ART

value: female

value: tongue


title: p24 replicate 1


title: Wild type, Rep#3


title: yFR973_spt16-197_80min37C_H3vsInput_20150721_Rep2

description:
Biological replicate 2 of 2. H3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3vsInput_20150721_Rep1-2_MN__S.cerevisiaeApr11_196984.bed
A genome browser-ready file for H3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.

value: MATα, leu2Δ1, spt16-197


title: LOS_#2 Tongue


title: LOS_#4 Tongue


title: p18 replicate 2

source_name: Cultures of E. coli MG1655 carrying pMCsp231 with additional protective MTase gene on ACYC177 derivative, and with plasmid with WT RM (p18)

value: R-M system Csp231I WT


title: Wild type, Rep#2


title: OPC cells treated with Quetiapine for 4 days, replicate 3

city: Baltimore

first: Peter

middle: Arthur

last: Calabresi

address: 600 N. Wolfe St

department: Neurology

institute: Johns Hopkins Univbersity

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was proprocessed and normalized using RMA method, and group comparison was performed using the Limma package

label: biotin

organism: Rattus rattus

source_name: oligodendrocyte precursor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After cortex dissection  from rat pups, OPCs were positively selected using A2B5 microbeads, then plated at 250.000 cells per well in SATO media with PDGF 20ng/ml during 4 days.

extract_protocol: RNA was obtained using QIAGEN Rneasy mini kit, following manufacturer protocol, cells were lysated then cDNA was removed through purification columns, ending with total RNA.

treatment_protocol: Plated cells in 6 wells plates, were treated with SATO media with thyroid hormone (45nM), Quetiapine (1uM), a combination of both, or none (control), during 4 days, adding fresh media with the same treatment at the second day.

tag: treatment

value: Quetiapine

tag: concentration

tag: time

value: 4 days

tag: replicate


title: OPC cells treated with T3 and Quetiapine for 4 days, replicate 3

value: 45nM + 1uM


title: OPC cells treated with T3 for 4 days, replicate 3


title: yFR973_spt16-197_80min37C_H3K4me3vsInput_20150409_rep2

description:
Biological replicate 2 of 2. H3K4me3 occupancy in spt16-197 temperature-sensitive cells treated 80 minutes at 37°C. H3K4me3 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against H3K4me3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR973_spt16-197_80min37C_H3K4me3vsInput_20150409_rep1-2_MN__S.cerevisiaeApr11_484236.bed
A genome browser-ready file for H3K4me3 occupancy (IP/Input) in spt16-197 temperature-sensitive cells treated 80 min at 37°C.


title: LOS_#7 Tongue

value: male


title: p18 replicate 1

value: K-12 substr. MG1655


title: pSULTR22_Control_4wk_1

tag: cultivar

value: P. domestica L 'Stanley'

value: 4 weeks

tag: infection status

value: healthy control


title: Control_#9 Tongue

tag: disease status

value: healthy

value: artificial insemination


title: Control_#5 Tongue

value: ~Day 105 fetus

tag: conception method


title: pSUC2_PPV_12wk_5

description: phloem polysomal RNA from PPV infected 12-week-old leaf tissue

value: 12 weeks

value: PPV infected


title: Control_#8 Tongue

tag: Sex


title: pSULTR22_Control_4wk_2


title: pSULTR22_Control_2wk_2

value: 2 weeks


title: Control_#2 Tongue

value: female

value: tongue


title: pSULTR22_Control_2wk_1


title: pSUC2_PPV_12wk_4


title: pSUC2_PPV_12wk_3


title: Control_#4 Tongue


title: pSUC2_PPV_12wk_2


title: PonWT_vs_BC3-10

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

country: Japan

institute: Institute of Fruit Tree Science, NARO

description: CGH analysis to detect the vector construct sequence in the BC3

hyb_protocol: The labeled DNAs were purified with Purification Column (Agilent Technologies) and absorbance was measured with NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA) using Microarray Measurement mode. Mixture of Cy5- and Cy3-labeled DNAs were used for array hybridization at 65°C for 24hr. Standard washing conditions were performed.

scan_protocol: Scanning conditions of array using Agilent Microarry scanner were at 5 m resolution and TIFF 20bit. Image analysis were performed with Agilent Feature Extraction version 12.0.3.1 software.

data_processing: In order to remove systemic biases among each array, normalization was performed by dividing the Cy5/Cy3 values of probes by the median of 13 positive control probes, Dark Corner, SM_01～SM_12 in each array. The normalized value of each probe in arrays no. 2 to 8 was divided with the value in arrays no. 1, the negative controls, to remove the effect of nonspecific hybridization to each probe.

organism: Citrus trifoliata

source_name: wild type of trifoliate orange

label_protocol: 350 ng of genomic DNA was digested with AluI and RsaI, labeled with Cyanine 3 (Cy3) or Cyanine 5 (Cy5) with SureTag Complete DNA Labeling Kit (Agilent Technologies).

growth_protocol: Wild type of trifoliate orange was cultivated in the field of National agriculture and food research organization Institute of Fruit and tea Tree Science (NIFTS), in Okitsu Shizuoka, Japan. Transformans and thier progenies were cultivated in the isolated green house of National agriculture and food research organization Institute of Fruit and tea Tree Science (NIFTS), in Okitsu Shizuoka, Japan.

extract_protocol: Genomic DNA was extracted according to the method described by Dellaporta et al. (1983) Wood J, Hicks JB. A plant DNA minipreparation: Version II. Plant Mol Biol Rep. 1983; 1: 19–21.

value: fresh and fully expaned leaves

source_name: BC3-10: No. 10 individual transgenic segregant with transgene inserted in the genome in back cross generation 3rd


title: PonWT_vs_BC2-19

description: CGH analysis to detect the vector construct sequence in the BC2

source_name: BC2-19: No. 19 individual transgenic segregant with transgene inserted in the genome in back cross generation 2nd


title: PonWT_vs_BC3-8

source_name: BC3-8: No. 8 individual null segregant lacking transgene back cross generation 3rd


title: PonWT_vs_BC2-8

source_name: BC2-8: No. 8 individual null segregant lacking transgene in back cross generation 2nd


title: PonWT_vs_BC2-5


title: Control OPC cells cultured for 4 days, replicate 3

value: Control


title: OPC cells treated with T3 and Quetiapine for 2 days, replicate 3

value: 2 days


title: Control_#3 Tongue


title: OPC cells treated with T3 for 2 days, replicate 3


title: OPC cells treated with T3 for 4 days, replicate 2

value: 4 days


title: OPC cells treated with T3 and Quetiapine for 4 days, replicate 2

value: 45nM + 1uM


title: Control OPC cells cultured for 2 days, replicate 3


title: OPC cells treated with Quetiapine for 4 days, replicate 2

value: Quetiapine


title: PonWT_vs_T0

description: CGH analysis to detect the vector construct sequence in the T0

source_name: T0: transgenic trifoliate orange  with overexpression of citrus FLOWERING LOCUS T (CiFT)  gene by CiFT co-expression vector construct


title: Control_#1 Tongue


title: pSUC2_PPV_6wk_5

description: phloem polysomal RNA from PPV infected 6-week-old leaf tissue

value: P. domestica L 'Stanley'

value: 6 weeks


title: pSUC2_PPV_12wk_1


title: OPC cells treated with Quetiapine for 2 days, replicate 3


title: pSUC2_PPV_6wk_6


title: ART_#4 Liver

data_processing:
Base-calling was performed using RTA 2.0.
Adapter sequence (TGGAATTCTCGGGTGCCAAGG) were removed using the fastq-mcf function of ea-utils v1.04.807. Reads with low quality bases (Phred score < 20) were trimmed using the dynamictrim function of SolexaQA++ v3.1.6 with Burrows-Wheeler Aligner algorithm.
Trimmed reads were aligned to bovine genome UMD3.1.1 using miRDeep2 v0.0.8 (Bowtie algorithm). mapper.pl was run with parameters (-d -c -i -j -l 17 -m -p -s -t -v). Reads shorter than 17 bases were discarded. miRDeep2.pl was run with parameters (-t Cow -P) to detect known and putative miRNAs.
miRNAs were quantified using quantifier.pl with parameters (-p -m -r -k). One mismatch was allowed within the read by default. Reads aligned to miRNAs with multiple precursors were only counted once for each read per miRNA.
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: Abundance measurements files are tab deliminated text files containing name of the miRNAs (with miRBase ID indicating known miRNAs), pre-miRNAs (mixed indicating miRNAs with multiple precursors), and raw read counts of miRNAs for each fetus.

source_name: ~Day 105 fetal liver

value: ART

value: liver


title: Control_#7 Tongue

value: healthy

value: artificial insemination

value: male


title: pSUC2_PPV_6wk_4

value: PPV infected


title: WT24

description:
Ribosomal RNA depleted total RNA
ribosomal RNA removed with Ribo-Zero kit (Illumina, Cat# MRZH116) prior to base hydrolysis of RNA. RNA fragments were then used to generate strand-specific libraries using a custom library preparationprotocol described in detail in Gangras et al., Methods Mol Biol. 2018;1680:1-28.

source_name: Whole embryo

value: 24 hpf

tag: rip-antibody


title: LOS_#3 Muscle

source_name: ~Day 105 fetal skeletal muscle

value: LOS

value: ~Day 105 fetus

value: skeletal muscle


title: E1-2

city: Ithaca

first: JUNG HO

middle: Cornell

last: SHIN

state: NY

address: 363 Weill Hall, Cornell University

department: Microbiology

institute: Weill Institute at Cornell University

data_processing:
The files have been generated by the Illumina pipeline software v2.18. Sequencing data was processed by CLC Genomics Workbench (CLC Bio).
Raw sequencing reads were quality trimmed with the same method with ChIP-Seq reads.
Quality trimmed reads were mapped strand specifically on the reference genome sequence by Transcriptome Analysis Tool with the following parameters: maximum number of mismatches of 2, length fraction, and similarity fraction of both 0.9. Number of mapped reads on each gene was normalized by DESeq2 package in Bioconductor v3.4 (Love et al., 2014). Genes with p-value (padj, DESeq2) lower than 0.001 were scored as differentially expressed genes (DEGs).
Genome_build: (NCBI accession NC_002505.1 and NC_002506.1)
Supplementary_files_format_and_content: gff data files contains total profile and values of reads

organism: Vibrio cholerae O1 biovar El Tor str. N16961

growth_protocol: Cells were grown in LB medium (biological triplicates) until reach to OD600 ∼0.05.

extract_protocol:
RNA was isolated by using TRIzol reagent (Ambion), breifly the pellet resuspended and left at ambient temperature for 5 min. Next, 260 µL of chloroform was added, followed by shaking and centrifugation (11,500 × g, 5 min). The upper (aqueous) phase was transferred to a fresh tube, mixed with an equal volume of chloroform, and centrifuged. The upper phase was then transferred to 600 µL of isopropanol, vortexed, and incubated at room temperature for 10 min, followed by centrifugation (12,000 × g, 15 min, 4 °C). The pellet (total RNA) was washed twice with 75% (vol/vol) ethanol and then resuspended in 100 µL of nuclease-free water (Ambion). DNA was removed using the Turbo DNase kit (Ambion).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies), and the RNA integrity was checked with RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA library preparation and sequencing reactions were conducted by Genewiz. Illumina TruSeq Stranded Total RNA Library Prep Kit, clustering, and sequencing reagents were used throughout the process following the manufacturer’s recommendations. The cDNA library was quantified using Qubit 2.0 Fluorometer (Life Technologies) and by qPCR. The samples were clustered on a flow cell using the cBOT. After clustering, the samples were loaded for sequencing of 1 × 50 single read on the Illumina HiSEq. 2500 instrument.

treatment_protocol: Five milliliters of exponential phase cultures expressing (shaking at 37 °C for 2 h, 250 µM IPTG added at OD600 ∼0.05) either empty plasmid or pHLwigRD78E were pelleted


title: E2-2

source_name: Vibrio cholerae O1 biovar El Tor str. N16961


title: Control_#6 Tongue

value: tongue


title: pSUC2_PPV_6wk_3


title: LOS_#3 Liver


title: E3-2


title: PonWT_vs_PonWT_&_Vector

description: control of CGH analysis to detect the vector construct sequence

value: fresh and fully expaned leaves

source_name: wild type of trifoliate orange and citrus FLOWERING LOCUS T (CiFT) gene co-expression vector construct


title: PonWT_vs_PonWT

description: control of CGH analysis between same samples of wild type of trifoliate orange


title: OPC cells treated with Quetiapine for 2 days, replicate 2

value: 2 days


title: Control OPC cells cultured for 4 days, replicate 2

value: Control

value: 4 days


title: OPC cells treated with T3 for 2 days, replicate 2


title: OPC cells treated with T3 and Quetiapine for 2 days, replicate 2

value: 45nM + 1uM


title: LOS_#4 Muscle


title: C1-2


title: pSUC2_PPV_6wk_2

value: P. domestica L 'Stanley'

value: 6 weeks


title: C3-2


title: C2-2


title: LOS_#3 Kidney

source_name: ~Day 105 fetal kidney

value: ART

value: kidney


title: pSUC2_PPV_6wk_1


title: LOS_#4 Liver

value: liver


title: pSUC2_PPV_4wk_5

description: phloem polysomal RNA from PPV infected 4-week-old leaf tissue

value: 4 weeks


title: pSUC2_PPV_4wk_6

value: PPV infected


title: ChIPVxrBHis100PG3H

data_processing:
The files have been generated by the Illumina pipeline software v2.18. Sequencing data was processed by CLC Genomics Workbench (CLC Bio).
First, raw sequencing reads were quality trimmed using a Trim Sequence Tool with a quality limit of 0.05. Any reads with more than two ambiguous bases were discarded at this step.
Then, quality trimmed reads were mapped onto the V. cholerae reference genome (NCBI accession NC_002505.1 and NC_002506.1) with mismatch cost of 2, insertion/deletion cost of 3, length fraction of 0.9, and similarity fraction of 0.9. Non-specific matches were mapped randomly.
Mapping files (.bam) were submitted to the Model-based Analysis of ChIP-Seq 2 (MACS2) software with a mapping file of a mock sample as a control (Zhang et al., 2008). Peaks were detected with shift size of 50 and q-value cutoff of 10-10.
For motif analysis, peaks with q-value lower than 10-40 were selected and 100 bp DNA sequences centered at peak summits were submitted to MEME Suite software v4.11.4 (Bailey et al., 2009).
Genome_build: (NCBI accession NC_002505.1 and NC_002506.1)
Supplementary_files_format_and_content: gff data files were decompressed from BAM file in-house python script (BAM2GFF_PE) and contains profiles and peaks location

growth_protocol: Cells carrying either 6xHis+VxrB or the native gene were grown in LB medium to mid-logarithmic phase (at an OD600 ~0.5).

extract_protocol:
The cell pellets were resuspended in 1 ml buffer CJ2 [100 mM Na2HPO4, 600 mM NaCl, 0.05% tweenTM, and 30 mM imidazole;pH 8.0] after washing twice with same CJ1 buffer. Cells were then lysed by sonication, followed by addition of Micrococcal nuclease (100 U ml−1, NEB cat# M0247S) and RNase A (1 mg ml−1) for fragmentation of genomic DNA and removal of RNA. 950 μl of supernatant was collected after centrifugation. For DNA-VxrB complex purification, HisPurTM Ni-NTA magnetic beads (cat#88831-Thermo Scientific) were equilibrated with six bed volumes of CJ2 buffer [100 mM Na2HPO4, 600 mM NaCl, 0.05% tweenTM, and 30 mM imidazole;pH 8.0]. 500 μg of crude lysate (protein concentration determined by Bradford assay) was mixed with the Ni-NTA resin and incubated at 4°C for 4 hours on rotation mixer. The bead slurry was recovered via magnetic stand for 5 min standing and washed twice with 400 μl buffer CJ3 [100 mM Na2HPO4, 600 mM NaCl, 0.05% tweenTM, and 50 mM imidazole; pH 8.0]. The VxrB-DNA complexes were then eluted from the beads by addition of CJ4 elution buffer [100 mM Na2HPO4, 600 mM NaCl, 0.05% tweenTM, and 500 mM imidazole;pH 8.0]. Enriched target DNAs were purified by using PCR Clean-Up Kits (Thermo Fisher Scientific) after reversal of crosslinking at 65°C overnight. The desired DNA fragment size (200~300 bps) was then purified by gel extraction.
For illumina HiSeq, each DNA library was constructed with specific barcode sequences, according to the manufacturer’s instruction of TruSeq ChIP Library Preparation Kit (IP-202-1012, Illumina). The constructed libraries were sequenced using 100-bp paired-end read protocol on an Illumina HiSeq 2500 platform (Illumina) at the Biotechnology Resource Center (BRC) at Cornell University.

treatment_protocol: PenG (100 µg/m) was treated into cells for 3 hours, 30 ml aliquots were spun down and the pellets were saved at -80°C.

tag: ChIP


title: LOS_#4 Kidney


title: Control OPC cells cultured for 2 days, replicate 2


title: OPC cells treated with T3 for 4 days, replicate 1


title: ART_#3 Liver

value: healthy


title: ChIPVxrBHis

tag: strain

value: HisPurTM Ni-NTA magnetic beads (cat#88831-Thermo Scientific)


title: ChIPWT100PG3H


title: pSUC2_PPV_4wk_4


title: ART_#1 Liver

value: ~Day 105 fetus


title: pSUC2_PPV_4wk_3


title: OPC cells treated with T3 and Quetiapine for 4 days, replicate 1


title: pSUC2_PPV_4wk_2


title: ART_#2 Liver


title: ChIPWT


title: LOS_#1 Muscle

value: LOS

value: skeletal muscle


title: pSUC2_PPV_2wk_5

description: phloem polysomal RNA from PPV infected 2-week-old leaf tissue

value: 2 weeks


title: Control OPC cells cultured for 4 days, replicate 1


title: OPC cells treated with Quetiapine for 4 days, replicate 1

value: Quetiapine


title: OPC cells treated with Quetiapine for 2 days, replicate 1

value: 2 days


title: InpVxrBHis


title: InpVxrBHis100PG3H


title: OPC cells treated with T3 for 2 days, replicate 1


title: pSUC2_PPV_4wk_1


title: LOS_#1 Liver


title: OPC cells treated with T3 and Quetiapine for 2 days, replicate 1


title: InpWT100PG3H


title: pSUC2_PPV_2wk_4


title: NP37974_Rep2

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

data_processing:
Demultiplexing of reads from superpools into separate pools was performed with bcl2fastq.
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each  PDX  against  non  three pathologic tissue samples
Genome_build: hg19
Supplementary_files_format_and_content: A Excel worksheet  file with normalized read counts for  all samples

source_name: breast tissue

extract_protocol:
Cells isolated from  PDXs and normal breast tissues were used for total RNA  extraction with Zymo Research kit (cat# 1055) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from at least 200 ng of total RNA

tag: cell type

value: non pathologic mammary tissue

tag: disease

tag: patient

value: patient # 37974


title: Control OPC cells cultured for 2 days, replicate 1

value: Control


title: LOS_#1 Kidney

tag: developmental stage

tag: tissue


title: NP37974_Rep1


title: LOS_#2 Muscle


title: InpWT


title: LOS_#2 Liver


title: pSUC2_PPV_2wk_1

value: P. domestica L 'Stanley'

tag: genotype/variation


title: pSUC2_PPV_2wk_3


title: NP37133_Rep2

value: patient # 37133


title: sgVector

city: Nantong

first: Yingcheng

last: Wu

state: Jiangsu

address: No. 19 Qixiu Road, Chongchuan District, Nantong, Jiangsu 226001, China

department: Basic Medical Research Center

country: China

institute: Nantong University

description:
RNA-seq of SgVec  SUM-159 cells.
qcSGV

data_processing:
QC: Fastp v0.19.7
Alignment: Subread-align v1.6.4
Quantification: featureCounts v1.6.4
Genome_build: GENCODE GRCh37 (hg19, version 29, Ensembl 94)
Supplementary_files_format_and_content: RPKM

extract_protocol:
Total RNA is processed by mRNA enrichment or rRNA removal (mRNA enrichment: mRNA with polyA tail enriched with magnetic beads with OligodT; rRNA removal: hybridization of rRNA with DNA probe, selective digestion of DNA/RNA with RNaseH The hybridization strand is digested with DNaseI, and the desired RNA is obtained after purification.).
The obtained mRNA is fragmented by adding an appropriate amount of the interrupting reagent under high temperature conditions, and the stranded cDNA is synthesized by using the broken mRNA as a template, and then the two-stranded cDNA is synthesized by synthesizing the two-stranded synthesis reaction system, and is purified and recovered by using a kit. The 3' end of the cDNA is ligated with the base "A" and ligated to the linker, and then the fragment size is selected and finally amplified by using PCR. The constructed library was examined by Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System and sequenced after passing the test.

value: sgVector

tag: cell line


title: SgPD-L1L2-SE

description:
RNA-seq of PD-L1L2-SE deficient SUM-159 cells.
qcSGCF

value: PD-L1L2-SE deficient


title: NP37974_Rep3


title: LOS_#2 Kidney

value: ART

value: kidney


title: pSUC2_Control_12wk_5

description: phloem polysomal RNA from healthy 12-week-old leaf tissue

value: 12 weeks

value: healthy control


title: NP37133_Rep1


title: pSUC2_Control_12wk_4


title: Control_#4 Muscle

value: healthy

value: ~Day 105 fetus

value: artificial insemination


title: Control_#4 Liver

value: liver


title: NP35438_Rep2

value: patient # 35438


title: NP35438_Rep3


title: pSUC2_Control_12wk_3


title: Control_#4 Kidney


title: RTR1 RRP6 deletion RNA-Seq prep 4

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
For the RNA-seq data, sequence reads were aligned to the reference genome sacCer3 with STAR-2.5.2b.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited excel file includes raw counts, log2 fold change values, p-values and FDR for all samples

source_name: Saccharomyces cerevisiae

growth_protocol: All cells were grown to an OD600 of 0.8

extract_protocol:
Hot acid phenol extraction
Illumina TruSeq Stranded TotalRNA Lib Prep Kit

tag: genotype

value: rtr1-delta rrp6-delta


title: RTR1 RRP6 deletion RNA-Seq prep 2


title: RTR1 RRP6 deletion RNA-Seq prep 1


title: NP37133_Rep3

value: non pathologic mammary tissue


title: Control_#5 Liver


title: pSUC2_Control_12wk_2


title: RTR1 deletion RNA-Seq prep 4


title: MBC7_Rep3

source_name: breast cancer

value: patient derived xenograft cells

value: derived from metastatic mammary adenocarcinoma

tag: subtype

value: TRIPLE NEGATIVE SUBTYPE


title: pSUC2_PPV_2wk_2

tag: cultivar

value: P. domestica L 'Stanley'

value: 2 weeks

value: PPV infected


title: Control_#2 Muscle

value: skeletal muscle


title: Control_#2 Liver


title: RTR1 deletion RNA-Seq prep 3


title: RTR1 deletion RNA-Seq prep 2


title: MBC7_Rep2


title: RTR1 RRP6 deletion RNA-Seq prep 3


title: MBC7_Rep1


title: RTR1 deletion RNA-Seq prep 1


title: pSULTR22_Control_6wk_1

value: 6 weeks

tag: infection status


title: pSUC2_Control_6wk_3

description: phloem polysomal RNA from healthy 6-week-old leaf tissue


title: pSUC2_Control_6wk_2


title: Control_#3 Muscle

tag: disease status


title: Control_#2 Kidney

tag: conception method

value: kidney


title: RRP6 RNA-Seq prep 4


title: MBC3_Rep2

value: LUMINAL B SUBTYPE


title: MBC3_Rep3


title: Control_#3 Liver

value: healthy


title: RRP6 RNA-Seq prep 3


title: MBC3_Rep1


title: pSUC2_Control_4wk_5

description: phloem polysomal RNA from healthy 4-week-old leaf tissue

value: 4 weeks

value: healthy control


title: Control_#3 Kidney

value: ~Day 105 fetus

value: artificial insemination


title: pSUC2_Control_6wk_1


title: pSUC2_Control_12wk_1

value: 12 weeks


title: pSUC2_Control_4wk_4


title: RRP6 RNA-Seq prep 2


title: pSUC2_Control_6wk_4


title: MBC2_Rep3


title: pSUC2_Control_4wk_3


title: Control_#1 Muscle


title: RRP6 RNA-Seq prep 1


title: WT RNA-Seq prep 4

value: wild type


title: NP35438_Rep1

value: non pathologic mammary tissue

value: patient # 35438


title: MBC2_Rep1

value: patient derived xenograft cells

value: derived from metastatic mammary adenocarcinoma

value: TRIPLE NEGATIVE SUBTYPE


title: Control_#1 Liver

value: liver


title: Control_#1 Kidney


title: WT RNA-Seq prep 3


title: MBC26_Rep3


title: pSUC2_Control_4wk_1

value: P. domestica L 'Stanley'


title: WT RNA-Seq prep 2


title: WT RNA-Seq prep 1


title: pSUC2_Control_2wk_5

description: phloem polysomal RNA from healthy 2-week-old leaf tissue

value: 2 weeks


title: MBC26_Rep2


title: MBC26_Rep1


title: pSUC2_Control_2wk_3


title: pSUC2_Control_2wk_4


title: ∆sRNA154 replicate 2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
PolyA removal and sitze filtering by READemption 0.2.3
Read alignment using READemption 0.2.3 and segemehl 0.1.7
Coverage calculation using READemption 0.2.3
Genome_build: NC_003901.1
Supplementary_files_format_and_content: wiggle

organism: Methanosarcina mazei Go1

source_name: mutant_cell culture

growth_protocol: Cells of M. mazei wild type and mutant strains were grown under nitrogen limitation and harvested at mid exponential growth phase

extract_protocol:
RNA isolation was performed using TRI reagent following the manufacturer´s protocol followed by DNaseI treatment and phenol-chloroform precipitation
For cDNA synthesis both RNA fractions were poly(A)-tailed using poly(A) polymerase. This was followed by treatment with TAP to remove the 5' PPP structures. Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNAs. First strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. PCR cycles performed and barcode sequences, which are part of the 3' sequencing adapter. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis. For Illumina sequencing, the cDNAs were pooled in approximately equimolar amounts.

tag: growth condition

value: nitrogen limitation

tag: growth stage

value: mid exponential growth phase


title: 4C seq_KLF5_promoter_bait2

city: Los Angeles

first: Li

last: Chen

state: CA

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

data_processing:
Library strategy: 4C-seq
4C-seq analysed using R package r3CSeq
Each replicate, the raw reads were aligned to masked version of the reference human genome hg19)
Chromosome 7 was selected as the viewpoint, DPnII was used as the restriction enzyme to digest the genome
Genome_build: hg19

growth_protocol: DMEM +10%FBS, 100U/mL penicillin, 100mg/uL streptomyocin

extract_protocol:
4C templates were used for 16 reactions of nested PCR and purified using standard DNA purification kit
sequencing libraries were prepared as per Takara Thruplex DNA seq standard protocol.

treatment_protocol: ESO26 cells were single cell suspended, chromatin crosslinked with 1% formaldehyde  for 10 min at room temperature. Cells were lysed and digested with DpnII, ligated with T4 DNA ligase, second restriction digest with Csp6I, then ligated with T4 DNA ligase

value: esophageal adenocarcinoma cell

tag: bait


title: MBC2_Rep2


title: 4Cseq_ELF3_promoter


title: wildtype replicate 2

source_name: WT_cell culture


title: 4C seq_KLF5_promoter_bait1


title: pSUC2_Control_2wk_1

data_processing:
Reads were mapped to the Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1) using the CLC Genomics Workbench v10.0.1 RNA-seq analysis tool and default parameters (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10 - CLC Bio, Aarhus, Denmark)
Genome_build: Prunus persica v2.0 genome (Verde 2017, The International Peach Genome Initiative 2013, https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1)
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, TPM, RPKM, Unique gene reads, Total gene reads, Unique exon reads and Total exon reads.


title: ∆sRNA154 replicate 1


title: pSUC2_Control_2wk_2


title: wildtype replicate 1


title: pSUC2_Control_4wk_2

value: 4 weeks


title: treated replicate 1

city: LEEDS

first: Milene

last: Volpato

address: St James University Hospital

department: LIRM

country: United Kingdom

institute: University of Leeds

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalisation

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: RPMI, 10% foetal calf serum

extract_protocol: RNEasy kit QIAGEN

treatment_protocol: 50microM EPA-FFA in culture medium for 24h

tag: treatment

value: 24h with 50uM EPA


title: control replicate 3

description: replicate 3

tag: cell type

value: control


title: treated replicate 3

description: replicate 3


title: Flower LMW 2

status: Public on Jul 29 2019

city: Godollo

last: Gyula

state: Pest

address: Szent-Gyorgyi Albert u. 4.

department: Department of Plant Biotechnology

country: Hungary

institute: Hungarian University of Agricultural and Life Sciences

description:
Small RNA
Gel filtrated flower crude extracts; fractions 19–25 in the size range of 66–200 kDa; contains the majority of AGO4.

data_processing:
The Illumina TruSeq Small RNA adapters were trimmed from the raw reads using cutadapt v1.9.1, with a minimum sequencing quality of 20 and a size selection filter that allowed only the 20–25-nt-long sequences to pass. The untrimmed sequences were discarded.
Sequences were mapped to the Arabidopsis thaliana TAIR10 genome (without the mitochondrial and the chloroplastic sequences) using ShortStack v3.4 with the default setting except that the ‘--bowtie_m’ parameter was set to 1000.
Sequences mapped to the Arabidopsis rRNA and tRNA genes, and the secondary alignments were removed from the alignment file using samtools v1.3.1.
The non-redundant, genome-matching reads were collected and their normalized abundances (read per million, RPM) were calculated for every library with an in-house Linux shell script.
The genome browser tracks were created with BEDtools v2.26.0 and can be visualized with the Integrated Genome Browser.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: The bedGraph files contain genome-wide normalized coverage data for sRNAs of a given length. One track contain coverage values for both strands (negative values represent coverage data on the negative strands).

organism: Arabidopsis thaliana

source_name: Flower

growth_protocol: Arabidopsis thaliana Col-0 plants were grown in Jiffy peat blocks and kept under 8 h light/16 h darkness cycles at 21 ˚C for four weeks. Next, these plants were planted in pots and were moved to a light room under 16 h light 8 h darkness at 21 ˚C. Young leaves were harvested from six-weeks-old plants being in the vegetative phase. Young flowers and flower buds were collected from inflorescences which already have 2–6 immature siliques.

extract_protocol:
Crude extracts were purified from leaves and flowers using a buffer containing 50 mM Tris-HCl (pH 7.5), 10 mM NaCl, 5 mM MgCl2 and 4 mM DTT. The extracts were size-fractionated on Sephacryl S-300 columns and fractions were collected. RNA content of the gel-filtration fractions was extracted with Trizolate Reagent (UD-GenoMed, Hungary) and fractions representing the identified sRNA pools were combined. The extracted RNA samples and also 30 μg of total RNA extracted directly from the crude extracts (input) were separated on an 8% denaturing polyacrylamide/urea gel along with RNA size markers, and then the sRNA range was isolated. The pellets were dissolved in 20 μl RNase-free ultrapure water, of which 2.5 μl was used for library preparation.
The sRNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep Kit, according to the manufacturer's instructions.

value: Flower

tag: fraction

value: LMW RISC

tag: replicate


title: control replicate 2

description: replicate 2


title: Flower HMW 2

description:
Small RNA
Gel filtrated flower crude extracts; fractions 6–10 from in the size range of 500–800 kDa; contains the majority of AGO1 and AGO2.

value: HMW RISC


title: Flower HMW 1


title: Flower input 2

description:
Small RNA
Unfractionated flower crude extract

value: Input


title: Flower input 1


title: Flower LMW 1


title: control replicate 1

description: replicate 1


title: Leaf LMW 2

description:
Small RNA
Gel filtrated leaf crude extracts; fractions 19–25 in the size range of 66–200 kDa; contains the majority of AGO4.

source_name: Leaf

value: Leaf


title: Leaf unbound 1

description:
Small RNA
Gel filtrated leaf crude extracts; fractions 29–35 in the size range of 20–40 kDa; containing protein-unbound sRNAs.

value: Protein-unbound


title: SD001-11

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description:
Laser captured NVU from normal individuals
10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each individual 1000 neurovascular unit cells were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Human U133 Plus 2.0 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were normalised using the RMA package in Expression console.

source_name: Laser captured neurovascular unit

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

tag: age group

tag: gender

value: M

tag: age

value: old


title: SD036-12


title: Leaf unbound 2

tag: tissue


title: SD041-10

value: middle


title: SD036-11


title: Leaf LMW 1


title: SD013-09

value: F


title: SD024-12


title: treated replicate 2

description: replicate 2


title: SD037-12


title: SD023-12


title: SD042-12

value: young


title: SD030-12


title: SD030-11


title: SD036-08

source_name: Laser captured motor neurons


title: Flower unbound 1

description:
Small RNA
Gel filtrated flower crude extracts; fractions 29–35 in the size range of 20–40 kDa; containing protein-unbound sRNAs.


title: Flower unbound 2


title: Leaf HMW 1

description:
Small RNA
Gel filtrated leaf crude extracts; fractions 6–10 from in the size range of 500–800 kDa; contains the majority of AGO1 and AGO2.


title: wt_SMC_baseline_12051

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs) using 10X CellRanger 'mkfastq' command.
For cell-gene matrix files, individual matrices were first generated using 10X Cell Ranger 'count' command. Individual matrices were then aggregated using the 10X Cell Ranger 'aggr' command. Sparse matrix was read into Seurat and a dense matrix was exported.
Genome_build: mm10
Supplementary_files_format_and_content: cell-gene readcount matrix; sample identity, corresponding to the 'sample number in processed data' numbers, is appended to each cell barcode column name

extract_protocol:
Cells were enzymatically dissociated from the aortic root and ascending aorta (to the level of the brachiocephalic artery) of experimental mice
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using either the V2 or V3 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

tag: genotype/variation

value: Myh11(cre), ROSA(tdT), ApoE(-/-)

tag: treatment/timepoint

value: baseline

value: aortic root and ascending aorta

tag: smc lineage status

value: SMC lineage

tag: sample number in processed data


title: Leaf input 1

description:
Small RNA
Unfractionated leaf crude extract


title: wt_SMC_16wk_061417

value: 16wk high-fat diet

tag: number of animals included in sample


title: wt_nonSMC_baseline_120518

value: non-SMC


title: wt_SMC_16wk_121217


title: wt_SMC_8wk_051717

value: 8wk high-fat diet


title: wt_nonSMC_16wk_061417


title: ko_nonSMC_8wk_111417

value: Myh11(cre), Tcf21(flx/flx), ROSA(tdT), ApoE(-/-)


title: ko_SMC_16wk_121217


title: wt_nonSMC_8wk_112717


title: ko_SMC_8wk_111417


title: ko_nonSMC_16wk_070617


title: Leaf HMW 2

value: HMW RISC


title: Leaf input 2

value: Input


title: ko_SMC_16wk_070218


title: wt_SMC_8wk_112717


title: ko_nonSMC_16wk_070218


title: Single cell RNAseq from adult male pituitary

city: Montreal

first: Amandine

last: Bemmo

address: 110 Avenue des Pins

institute: IRCM

description:
DROPituitary_02G5MK_7950_S1_L007
Chromium 10X Single cell RNAseq

data_processing:
Reads were aligned on the mm10 mouse reference genome using the default parameters of Cell Ranger to generate unique molecular identifier counts for each genes across the 9269 cells that were profiled. We obtained an average of 25220 reads per cell and we detected 1807 median genes per cell. Using the Cell Ranger pipeline with default parameters, we generated a gene-barcode matrix, principal component analysis and dimensionality reduction using the t-SNE algorithm. Unbiased clustering of single cells was performed using Cell Ranger which combines K-means clustering and graph-based clustering uncovering 12 clusters.
We used Loupe Cell Browser (10X Genomics) to visualize the t-SNE plot with colored cell according to their assigned cluster or colored by gene UMI.
Genome_build: mm10
Supplementary_files_format_and_content: cloupe

source_name: pituitary

extract_protocol:
Mouse pituitary was dissected in 300µl of dissection buffer (DMEM, 10% FBS, HEPES 10mM and DNase 100 U/ml), dissociation was performed at 37°C using 5mg/ml Trypsin for 10 minutes. We then added 2mM EDTA and incubated 5 minutes more. Single cells preparation were obtained by filtration through 40µm filter. Dissociated pituitary cells were diluted at 500 cells per µl and processed using Chromium Single Cell 3′ v2 Reagent (10x Genomics, Pleasanton, CA) following the manufacturer recommendation. Briefly, cells were passed on the channel and 9269 cells were recovered. Pituitary cells were partitioned into gel beads in emulsion for cell lysis and barcoded with oligo-dT priming and reverse transcribed.
cDNA library was amplified fragmented and size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer. Libraries were sequenced on Hiseq 4000 with 100bp paired-end reads.

tag: strain background

tag: Sex

value: male

value: adult

value: pituitary