title: Th1_1_WT

description: total RNA (including small RNAs)


title: In vivo fibrosis GFP low, #30

status: Public on Aug 21 2019

type: RNA

city: Edinburgh

first: Timothy

middle: James

last: Kendall

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised with neqc from the limma package in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Activated hepatic stellate cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA amplifiaction kit (AMIL1791).

extract_protocol: Subpopulations of activated hepatic stellate cells isolated by density centrifugation from WT1GFP/+ animals were obtained sorting by flow cytometry directly into RLT with beta-mercaptoethanol. RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: Activated hepatic stellate cells

tag: gfp status

value: low

tag: genotype

tag: strain

tag: gender

value: Male

tag: activation

value: In vivo


title: 72 hpf, nonskin2, replicate A

type: SRA

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

state: CA

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Demultiplexing: single mismatch to expected 7-mers, only keeping PF=1 spots
Adapter, low quality base trimming: CutAdapt 1.8.1 (-m 21 --trim-n --max-n=2 -q 10,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), then only keeping reads >=47 nt long and only keeping the first 47 nt of those reads
Alignment: STAR 2.5.3a (to genome and transcriptome, single pass mode with known junctions), retaining multiple locations for non-uniquely aligning reads (see paper or BAMs for parameters)
Quantification: Salmon patched 0.10.2 (--numGibbsSamples=1000 --thinningFactor=25 --useVBOpt --libType=U --fldMean=200 --fldSD=200 --rangeFactorizationBins=4 --minAssignedFrags=1 --seqBias --noBiasLengthThreshold), with 1,000 Gibbs samples per experiment
Statistics: see paper; similar to R Bioconductor Sleuth (with Wasabi as importer), but elaborated and with some DESeq2 features incorporated
Genome_build: Ensembl release 92 top-level reference Zebrafish genome (GRCz11 chr1..25 + MT + 847/120 KN/KZ scaffolds) + PhiX, and associated Ensembl genebuild annotations/models
Supplementary_files_format_and_content: GZIP-TAR-Salmon files: GZIP-compressed TAR archives of Salmon transcript quantification output filesystem trees. Supplementary file: Microsoft Excel workbook in XLSX format, with multiple worksheets, containing a comprehensive collection of analysis input data, intermediate steps, and statistical outputs (see column headers as well as Methods and Supplemental methods of the associated journal publication).

molecule: polyA RNA

organism: Danio rerio

source_name: FACS-isolated nonskin cells from whole embryos

growth_protocol: Zebrafish were maintained in 28.5 C and pH 7.5 fish water. Adults were kept in a 14-hour light / 10-hour dark cycle.

extract_protocol:
Dechorionated embryos were transferred into 1.5 ml tubes and rinsed with Ca2+-free Ringer’s solution for 15 min. During this incubation, yolk was removed by gently pipetting embryos through a 200 µl tip (with the end cut off) three to five times. Yolk-free embryos were transferred into a 35 mm petri dish with 5 ml of 0.25% Trypsin-EDTA. Embryos were incubated at 28.5 °C and homogenized with a 200 µl tip every 10 min until most cells were dissociated (20 to 50 min). 55 µl 100 mM CaCl2 and 550 µl FCS were added to stop digestion. Dissociated cells were transferred into a 15 ml tube and centrifuged at 300 g for 5 min at 15 °C. Cells were rinsed once with 10 ml suspension solution (colorless Leibovitz medium L-15 with 0.3 g/L glutamine, 0.8 mM CaCl2, Pen 50U/ml, Strep 0.05 mg/ml, and 1% FCS). Dissociated cells were resuspended in suspension solution to ~10^7 cells/ml and immediately proceeded to cell sorting at the UCLA Broad Stem Cell Research Center Flow Cytometry Core. BD FACS ARIA II SORP instruments sorted cells, using a 488 nm laser for GFP detection and a 561 nm laser for RFP (dsRed) detection.
Sorted cells in suspension solution were immediately lysed using the Qiagen RNeasy kit. Lysis was completed within two hours of dissociating cells. Total RNA was isolated following the Qiagen RNeasy kit and stored at –80 °C. Quality of all samples was assayed with an Agilent Bioanalyzer, and only samples with RNA Integrity Number > 8 were used for creating sequencing libraries. Poly-A bead-purified RNA-Seq libraries were prepared with the Illumina TruSeq RNA Library Prep Kit.

treatment_protocol: Transgenic embryos without further treatment

value: AB+TU

tag: developmental stage

value: 72 hpf

tag: tissue

value: FACS nonskin2

tag: Sex

value: pooled male and female

tag: biomaterial provider

value: Fang Wang (CSUDH)

tag: birth location

value: UCLA


title: In vivo fibrosis GFP low, #8

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 4


title: HEPS_AND1_AF4MLL_Sample1_Rep1

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
Single cell RNA-seq
processed data file: HTSeq_counts.txt

data_processing:
RNA-seq reads were aligned to hg19 using STAR (version 2.4.2a) with parameters (--outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq_counts.txt: HT-Seq counts / gene counts.

organism: Homo sapiens

source_name: Human embryonic stem cells

extract_protocol:
HEPs were FACS-purified from day 15 EBs of EV or MA4-A4M expressing cells into individual wells of a 96-well PCR plate containing lysis buffer (0.2% Triton-X100 and 2.3 U of SUPERase-In RNase Inhibitor; Ambion).
Three independent replicates (50 cells/replicate) per condition were analyzed.
RNA/cDNA was obtained and amplified as per the SMARTSEQ2 protocol.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were sequenced on the Illumina HiSeq 4000 platform.
Libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit.

value: Hemato-endothelial precursors

tag: treatment

tag: day


title: In vivo fibrosis GFP high, #1

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 2

value: high


title: In vitro activation GFP negative, #11

description:
Quiescent heaptic stellate cells from WT1GFP/+ animals were allowed to fully activate by 7 days culture on plastic
Sample 8

value: negative

value: In vitro


title: In vivo fibrosis GFP low, #1

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 1


title: 52 hpf, periderm, replicate B

source_name: FACS-isolated periderm from whole embryos

value: 52 hpf

value: FACS periderm


title: HEPS_AND1_Neo_Sample1_Rep3

value: Control


title: 52 hpf, periderm, replicate A


title: 52 hpf, basal cells, replicate B

source_name: FACS-isolated basal cells from whole embryos

value: FACS basal cells


title: In vivo fibrosis GFP high, #29

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 5

value: Activated hepatic stellate cells


title: Tn_2_KO

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description: total RNA (including small RNAs)

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values from all experiments and gene annotation information for RefSeq transcripts

source_name: T-DKO Tn cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD44-CD4+ naive T cells (Tn), CD44+PSGL1hiCXCR5-CD4+ T cells (Th1), CD44+PSGL1intCXCR5+CD4+ T cells (Tfh) and CD44+PSGL1loCXCR5+CD4+ T cells (GC-Tfh) isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

tag: genotype/variation

value: T cell-specific miR-23~27~24 family KO

value: CD44-CD4+ naive T cells


title: HEPS_AND1_Neo_Sample1_Rep2


title: In vivo fibrosis GFP high, #8

description:
WT1GFP/+ animals were chronically injured with intraperitoneal injection of carbon tetrachloride
Sample 3

value: Male

value: In vivo


title: Tn_1_KO

description: total RNA (including small RNAs)


title: In vitro activation GFP negative, #14

description:
Quiescent heaptic stellate cells from WT1GFP/+ animals were allowed to fully activate by 7 days culture on plastic
Sample 9


title: In vitro activation GFP negative, #3

description:
Quiescent heaptic stellate cells from WT1GFP/+ animals were allowed to fully activate by 7 days culture on plastic
Sample 7


title: 52 hpf, basal cells, replicate A

value: AB+TU


title: 6612Q_Sse9I_1

city: Heidelberg

first: Wei

address: Im Neuenheimer Feld 581

department: Translational Oncology

country: Germany

institute: German Cancer Research Center

description: processed data file: 6612Q_processed_IS.csv

library_source: genomic

data_processing:
Library strategy: Amplicon-Seq
Illumina RTA 1.18.54 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using BWA.
The HIV integration sites were identified and annotated with GENE-IS 1.2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_processed_IS.csv: Comma-separated text files

molecule: genomic DNA

source_name: Primary CD4 positive T cells

growth_protocol: Cells were grown as described in Lucic et al. Nat Communications 2019. Briefly, primary CD4 T cells are isolated from whole blood using RosetteSep Human CD4+ T cell enrichment cocktail beads according to the manufacturer instructions. Cells are then left in resting state or activated with Dynabeads Human T-Activator CD3/CD28 and are grown in RPMI complete medium, 10% FBS, 10ng/ml IL-2.

extract_protocol:
DNA was extracted using the DNeasy Blood & Tissue Kit from QIAGEN.
Linear Amplification Mediated PCR as published as Schmidt et al. 2007, Nature Methods.

treatment_protocol: Cells were infected with the pNL4_3-envFS as described in Nat Communications 2019.

value: Primary CD4 positive T cells

tag: cell state

value: Resting

value: HIV infection

tag: enzyme

tag: replicate


title: 52 hpf, nonskin2, only replicate

value: FACS nonskin2

value: pooled male and female

value: Fang Wang (CSUDH)

value: UCLA


title: HEPS_AND1_Neo_Sample1_Rep1

tag: cell type

value: Hemato-endothelial precursors


title: 6612Q_MseI_2

value: MseI


title: Plate_26

city: Bethesda

first: Anton

last: Schulmann

state: Maryland (MD)

address: 35 Convent Dr

institute: NIH/NIMH

data_processing:
Adapter trimming (cutadapt version 1.16, remove first base and Truseq/Nextera adapters, options -m 20 -n 3 -u 1)
Conversion of fastq to unmapped bam (Picard tools version 1.12, FastqToSam)
Tagging of reads based on cellular and molecular barcodes in read 1 (Drop-seq_tools version 1.13, TagBamWithReadSequenceExtended, cell barcode position 1-8, UMI barcode in position 9-18, FilterBam)
Sorting unmapped tagged bam file and conversion to fastq (Picard tools version 1.12, SortSam, SamToFastq)
Alignment to mouse genome (STAR version 2.5.3, with --limitOutSJcollapsed 5000000)
Sorting mapped bam file and merging alignments and tags (Picard tools version 1.12, SortSam, MergeBamAlignment to merge with tagged unmapped bam file)
Tagging genes with exon and UMI counts per cell for each plate (Drop-seq_tools version 1.13, TagReadWithGeneExon, DigitalExpression, using Ensembl release 85)
Filtering (keep cells with UMI count > 20,000 and detected genes > 2,500)
Genome_build: mm10
Supplementary_files_format_and_content: Transcript counts per gene

source_name: thalamic projection neurons

extract_protocol:
Retrogradely labelled cells were collected as previously described (Hempel et al., Nat Protoc 2007; (Hempel et al., Nat Protoc 2007, PMID 18007629; Sugino et al., eLife 2019, PMID 30977723). Coronal slices (200-300 μm) were cut and incubated for 1 hour with pronases and neural activity blockers in artificial cerebrospinal fluid (ACSF). Thalamic areas were microdissected and the tissue dissociated. Fluorescent neurons were manually sorted, washed, and collected into 8-well strips containing 3 µL Smart-seq2 lysis buffer and frozen at -80ºC.
Samples for single-cell RNAseq were prepared as described previously (Cembrowski et al., Cell 2018, PMID 29681453). Upon thawing, cells were lysed and digested with Proteinase K, and External RNA Controls Consortium (ERCC) spike-ins added at 1:10^7. cDNA was synthesized using the Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) and amplified using the HiFi PCR kit (Kapa Biosystems). Samples were then pooled across strips and purified with Ampure XP beads (Beckman Coulter). These pooled strips were then combined to create a plate-level cDNA pool, and concentration was determined using Qubit High-Sensitivity DNA kit (Thermo Fisher Scientific). Tagmentation and library preparation using 600 pg cDNA from each plate of cells were performed with a modified Nextera XT (Illumina) protocol (Soumillon et al., 2014, bioRxiv 003236), but with the P5NEXTPT5 primer and tagmentation time extended to 15 minutes. Libraries were then purified following the Nextera XT protocol and quantified by qPCR using Kapa Library Quantification (Kapa Biosystems). 6-10 plates were run on a NextSeq 550 flow cell. Read 1 contains the cell barcode and unique molecular identifier (UMI). Read 2 contains a cDNA fragment from the 3’ end of the transcript.

value: thalamus


title: Tn_3_WT

description: total RNA (including small RNAs)

source_name: WT Tn cells

value: WT


title: Tn_2_WT

description: total RNA (including small RNAs)


title: 6612Q_MseI_1


title: Tn_3_KO

description: total RNA (including small RNAs)


title: Plate_24


title: 6612A_Sse9I_2

description: processed data file: 6612A_processed_IS.csv

value: Activated


title: Plate_25


title: Tn_1_WT

description: total RNA (including small RNAs)


title: 3673Q_Mse1_2

description: processed data file: 3673Q_processed_IS.csv


title: 3673Q_Mse1_1


title: 6612A_MseI_2


title: Plate_21


title: 3673Q_Sse9I_1


title: Plate_22


title: 3673A_Mse1_2

description: processed data file: 3673A_processed_IS.csv


title: 3673A_Mse1_1


title: 3673A_Sse9I_2


title: 6612A_MseI_1


title: T1045.3200IV.20.5

city: Singapore

first: Regina

last: Hoo

address: 60, Nanyang Drive

department: School of Biological Science

country: Singapore

institute: Nanyang Technological University

description: in vitro culture derived from CHMI

hyb_protocol: Hybridization of labeled cDNA was performed as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

scan_protocol: Scanning and image acquisition of the hybridized microarray chips was performed using the PowerScannerTM (Tecan) at 10µM resolution under automated photomultiplier (PMT) balancing. Hybridized spots were analysed and preprocessed using GenePix® ProMicroarray Image Analysis Software v6.0 (Axon Instruments).

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium falciparum NF54

source_name: Plasmodium falciparum, CHMI-derived

label_protocol: Labeling of cDNA was performed as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: All P. falciparum isolates were cultivated at 5% haematocrit of O+ erythrocytes. RPMI 1640 medium was completed with 10% Albumax (Gibco), 25mM Hepes Buffer, 2mM L-Glutamine and 0.05mg/ml gentamicin (all PAA Laboratories). Parasites were incubated at 37°C in 90% nitrogen, 5% oxygen and 5% carbon dioxide.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: sample type

value: CHMI-derived

tag: tuchmi id

tag: culture

value: In vitro, blood stage

tag: pfspz dose

tag: gpi

organism: Plasmodium falciparum 3D7

source_name: Plasmodium falciparum, reference

value: Reference

tag: composition

value: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.


title: Plate_23

tag: tissue


title: 6612A_Sse9I_1


title: T1045.3200IV.15

description: in vitro culture derived from CHMI


title: Plate_19


title: T1045.3200IV.41

description: in vitro culture derived from CHMI


title: 34INF_Sse9I_2

description: processed data file: 34INF_processed_IS.csv


title: 34INF_MseI_2


title: Plate_18


title: 34INF_Sse9I_1


title: 3673Q_Sse9I_2


title: 34INF_MseI_1


title: Plate_17


title: 34INF_nr_2

value: Circligase


title: Plate_16


title: T1044.3200IV.18.5

description: in vitro culture derived from CHMI


title: T1044.3200IV.41

description: in vitro culture derived from CHMI


title: 34mockINF_Sse9I_1

description: processed data file: 34mockINF_processed_IS.csv

value: Primary CD4 positive T cells


title: T1045.3200IV.13.5

description: in vitro culture derived from CHMI


title: Plate_20


title: Plate_15


title: T1044.3200IV.15

description: in vitro culture derived from CHMI


title: 3673A_Sse9I_1


title: 34mockINF_Sse9I_2


title: 33INF_Sse9I_1

description: processed data file: 33INF_processed_IS.csv


title: 34mockINF_MseI_1


title: 33INF_MseI_2


title: Plate_14


title: 33INF_MseI_1


title: T1044.3200IV.13.5

description: in vitro culture derived from CHMI


title: Plate_12


title: 33INF_nr_2


title: T1043.3200IV.22

description: in vitro culture derived from CHMI


title: 33INF_nr_1


title: T1043.3200IV.41

description: in vitro culture derived from CHMI


title: T1043.3200IV.15

description: in vitro culture derived from CHMI


title: Plate_11


title: 33mockINF_nr_1

description: processed data file: 33mockINF_processed_IS.csv


title: 33mockINF_nr_2


title: 34INF_nr_1


title: 33mockINF_Sse9I_2


title: 34mockINF_MseI_2


title: T1043.3200IV.13.5

description: in vitro culture derived from CHMI


title: Plate_9


title: 33mockINF_MseI_1


title: 33mockINF_Sse9I_1


title: Plate_10


title: 33mockINF_MseI_2


title: T1041.3200IV.18.5

description: in vitro culture derived from CHMI


title: Plate_8


title: Plate_13


title: T1041.3200IV.42.5

description: in vitro culture derived from CHMI


title: XY5

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

description:
RNA from auto antigen specific CD4+ T cells
SJL.CD4_rawcounts.xlsx

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "SJL.CD4_rawcounts.xlsx" has count values for each Sample

source_name: Lymph node

growth_protocol:
Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.
Lymph node cell suspensions were cultured at a concentration of 4x10^6 cells/mL in 24 well plates in complete RPMI medium with PLP 139-151 (25 ug/mL) for 36 hours.

extract_protocol:
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. The cells were cultured in the presence of autoantigen (PLP 139-151) for 36 hours. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

treatment_protocol:
Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery.
At 8 weeks of age, the mice were immunized with PLP 139-151 peptide (Mimotopes) emulsified in Complete Freund's adjuvant supplemented with mycobacterium tubercusosis H37Ra (Difco Laboratories) for 10 days.

tag: strain

value: SJL

value: Lymph node

value: CD4+ T cell

tag: Sex

value: Female

tag: genotype

value: XY-


title: XY4


title: Plate_7


title: Plate_6


title: XY2


title: Plate_5


title: T1041.3200IV.13.5

description: in vitro culture derived from CHMI


title: T1040.3200IV.45

description: in vitro culture derived from CHMI


title: Plate_4


title: T1041.3200IV.15

description: in vitro culture derived from CHMI


title: XX7

value: XX


title: T1040.3200IV.23

description: in vitro culture derived from CHMI


title: XY1


title: XX6


title: XX4


title: XX5


title: T1040.3200IV.17.5

description: in vitro culture derived from CHMI


title: T1040.3200IV.16

description: in vitro culture derived from CHMI


title: XX1


title: XY-_535

description: RNA from auto antigen specific CD4+ T cells

data_processing:
Data quality check was done on Illumina SAV
De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
R package “QuasR” was used for the read alignment to mouse genome (mm10) followed by the counting at gene level
Genome_build: mm10
Supplementary_files_format_and_content: "B6.CD4_rawcounts.xlsx" has count values for each Sample

growth_protocol: Animals were maintained under standard conditions in a 12 h dark/12 h light cycle with access to food and water ad libitum.

extract_protocol:
Auxillary, brahcial, and inguinal draning lymph nodes were collected and processed into single cell suspensions. The cells were cultured in the presence of autoantigen (MOG 35-55) and IL-12 for 36 hours. Cells were sorted for CD4+ T cells by magnetic negative selection using EasySep Mouse CD4+ T cell isolation kit (STEMCELL). RNA was isolated from CD4+ T cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
Double-stranded cDNA and the sequencing library were made using the Kapa RNA Kit Full kit.

treatment_protocol: Surgery protocol: Young mice (age 4-6 weeks) were gonadectomized (females: ovariectomy, males: castration). Prior to surgery and 24 hours after, the mice received 1.2 mg/mL Carprofen (Zoetis). The mice were given Amoxicillin (50 mg/mL, Virbac) as antibiodic in the water source for 7 days following surgery. Immunization protocol: At 8 weeks of age, the mice were immunized with MOG 35-55 peptide (Mimotopes) emulsified in Complete Freund's adjuvant supplemented with mycobacterium tuberculosis H37Ra (Difco Laboratories) for 10 days. Culture protocol: Lymph node cell suspensions were cultured at a concentration of 4x10^6 cells/mL in 24 well plates in complete RPMI medium with MOG 35-55 (25 ug/mL) and IL-12 (20 ng/mL) for 36 hours.


title: XY3


title: Plate_1


title: Plate_2


title: T1039.3200IV.45

description: in vitro culture derived from CHMI


title: XY-_528


title: XY-_526


title: T1039.3200IV.23

description: in vitro culture derived from CHMI


title: XY-_531


title: T1039.3200IV.17

description: in vitro culture derived from CHMI


title: XY-_525


title: XY-_523


title: OIL3F: Cohort3 Oil

city: Columbus

first: Craig

middle: Joseph

last: Burd

state: OH

address: 460 W. 12th Ave. Rm 920 BRT

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Alignment to mm10 mouse genome using the STAR read aligner.
Read counts were generated using featureCounts and normalized in DESeq2.
Genes with sum of less than 10 reads across all samples were removed.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated text files with normalized read counts

source_name: Mammary gland

extract_protocol:
Fibroblasts were isolated from mammary glands by rapid plating following enzymatic digestion of the tissue.   RNA was purified from fibroblast via Zyme RNA/DNA miniprep kit.
standard illumina library prep

treatment_protocol: pregnant mothers were exposed via ip injection to 25 ug/kg bw BPA or oil control daily from embryonic day 8.5 to 18.5.

value: Primary mammary fibroblasts

tag: age

value: 12 weeks of age primary cells

tag: treatment

value: Oil exposed (control)


title: BPA3F: Cohort3 BPA

value: BPA expossed


title: XX_533


title: XX_530


title: XX_527


title: XX3


title: ESC2_KO_RNA

city: Cambridge

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

institute: University of Cambridge

description:
Illumina HiSeq 4000 platform
ESC_RNA-Seq_FPKM.txt

data_processing:
Raw ChIP-seq fastq were first quality checked with FastQC (version 0.11.5), followed by adapter and base quality trimming with TrimGalore (version 0.2.7).  Reads post-QC were aligned using BWA (v0.6.2).
Potential PCR duplicates were removed with Picard tools (“MarkDuplicates” function)
Peaks were called on mapped data using MACS2 (version 2.1.0) with broad peak option using only uniquely aligned reads (MAPQ>10)
For RNA-seq, reads post-QC were aligned with STAR (v2.5.2, --alignEndsType EndToEnd --outFilterMultimapNmax 300 --outSAMmultNmax 1 --outMultimapperOrder Random)
Genome_build: mm10
Supplementary_files_format_and_content: .bw : bigWig file, .bed : bed file containing ChIP-seq peaks for ZFP57, ESC_RNA-Seq_FPKM.txt : normalised gene expression

source_name: ES cells (zygotic mutants)

growth_protocol: Morula stage embryos were collected at E2.5 and cultured for 2 days in KSOM with inhibitors of Erk and Gsk3 (2i) signaling pathways (PD0325901 and CHIR99021). The trophectoderm was then removed using complement immunosurgery and used for genotyping. The inner cell mass was cultured in N2B27 media supplemented with 2i and LIF until establishment of stable ES cell cultures. Each ES cell line was characterized by staining for alkaline phosphatase activity and expression of Oct-4 (SantaCruz, sc8628) and SSEA1 (Millipore, MAB4301) markers. Finally, each newly established line was karyotyped and screened for mycoplasma contamination prior to use in downstream experiments. ES cells were cultured under 2i/LIF conditions up to a maximum of 15 passages, matching the passage number for WT and KO cells for each experiment.

extract_protocol:
total Trizol extracted RNA (1 µg) was ribodepleted using NEBNext rRNA depletion kit (NEB, E6310L) according to manufacturer’s protocol and purified using Agencourt RNAClean XP beads (Beckman Coulter, A63987). RNA-seq library was prepared using ScripSeq v2 kit (Illumina, SSV21124) with 10 cycles of amplification. Successful ribodepletion was confirmed by post-sequencing QC library analysis.
Paired-end libraries were prepared and sequenced in 150bp reads run according to Illumina instructions.

value: ES cells

value: ZFP57 KO (zygotic)

value: male

tag: antibody


title: XX_524


title: Plate_3

value: thalamus


title: T1039.3200IV.16

description: in vitro culture derived from CHMI

value: CHMI-derived

value: In vitro, blood stage

value: Reference

value: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.


title: T1034.800IV.20

description: in vitro culture derived from CHMI


title: ESC1_KO_RNA


title: XX_522

value: Lymph node


title: T1034.800IV.44.5

description: in vitro culture derived from CHMI


title: DTR-PYR-944V

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the standard Ensembl gtf annotation and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used in union mode to assign tophat-aligned reads to gene entries in the standard Ensembl gtf annotation supplied with the bowtie2 iGenome.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Genome_build: GRCm38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene.  Depth-normalized values were calculated according to DESeq’s library normalization algorithm.

source_name: heart, ventricles

extract_protocol:
Hearts were removed and ventricular apexes were flash-frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.

value: heart, ventricles

value: Male

tag: age (weeks)

value: diphtheria toxin-mediated injury; pyridostigmine-treated


title: T1034.800IV.14.5

description: in vitro culture derived from CHMI


title: DTR-PYR-935V


title: XX_532

value: CD4+ T cell

value: Female

value: XX


title: ESC2_WT_RNA

source_name: ES cells

value: WT


title: ESC3_WT_RNA


title: ESC1_WT_RNA


title: DTR-PYR-390U


title: DTR-PYR-926V


title: T1028.800IV.44.5

description: in vitro culture derived from CHMI


title: DTR-PYR-385U


title: T1034.800IV.12.5

description: in vitro culture derived from CHMI


title: DTR-PBS-917V

value: diphtheria toxin-mediated injury; vehicle (PBS-treated)


title: DTR-PBS-384U


title: DTR-PYR-916V


title: ESC2_KO_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.

extract_protocol:
DNA was extracted using tale lysis buffer (50mM Tris-Cl pH8.5; 5mM EDTA; 200mM Nacl; 0.25% SDS) and 1 µg/ml Proteinase K for 1 hr. The mixture was purified with phenol/chloroform extraction and precipitated with isopropanol.
Paired-end libraries were prepared and sequenced in 150bp reads run according to Illumina instructions.

value: ES cells


title: ESC1_KO_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.

value: ZFP57 KO (zygotic)


title: DTR-PBS-923V


title: T1028.800IV.16

description: in vitro culture derived from CHMI


title: DTR-PBS-388U


title: T1028.800IV.14.5

description: in vitro culture derived from CHMI


title: T1028.800IV.12.5

description: in vitro culture derived from CHMI


title: WT-PYR-391U

value: no diphtheria toxin; pyridostigmine-treated


title: WT-PYR-382U


title: T1027.800IV.44.5

description: in vitro culture derived from CHMI


title: ESC3_WT_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.

value: male


title: DTR-PBS-934V


title: DTR-PBS-943V


title: ESC2_WT_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.


title: WT-PYR-951V


title: WT-PYR-259U


title: WT-PYR-946V


title: ESC_INPUT_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.

value: mixture of WT and ZFP57 KO (zygotic)

value: none (input)


title: ESC2_KO_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.

value: KAP1 (Abcam, ab10483, lot J0809)


title: WT-PBS-379U

value: no diphtheria toxin; vehicle (PBS-treated)


title: bisulphite converted DNA from control placenta

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridized to Illumina HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi package for the R statistical software and in-house R scripts

label: Cy5 and Cy3

source_name: placenta

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from samples using standard phenol/chloroform extraction protocol

value: placenta


title: WT-PBS-258U

value: heart, ventricles


title: WT-PBS-945V

value: Male


title: ESC1_KO_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.


title: T1027.800IV.21

description: in vitro culture derived from CHMI

value: CHMI-derived

value: In vitro, blood stage

value: Reference

value: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.


title: WT-PBS-389U


title: bisulphite converted DNA from tumor

source_name: tumor

value: choriocarcinoma


title: ESC1_WT_H3K9me3_ChIP

description:
Illumina HiSeq 4000 platform
.

value: WT


title: WT-PYR-267U


title: T1022.2500ID.17

description: in vitro culture derived from CHMI


title: T1022.2500ID.15.5

description: in vitro culture derived from CHMI


title: WT-PBS-925V


title: 8 h treatment with 100 ng/mL lipopolysaccharide, repl 3

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Prior to mapping, sequence reads were trimmed to remove adapter sequences introduced by the Diagenode CATS library preparation procedure.  The commands used for read trimming are supplied as a 'processed data file' (remove_CATSadapters_cutadapt.sh)
Sequence reads were mapped to the transcriptome, defined by annotation based on the Ensembl mm10 genes.gtf and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on Ensembl mm10 genes.gtf
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited text file includes htseq-count values for each gene (Ensembl IDs and gene symbols) in each sample.

growth_protocol: Cells were isolated from the peritoneal cavity 4 d after thioglycolate injection.  Adherent cells after 24 h of culture were classed as primary peritoneal macrophages.

extract_protocol:
Medium was aspirated from cultured peritoneal macrophages, and RNA was directly harvested using 1 mL Trizol reagent (Invitrogen) according to the manufacturer's directions.
Diagenode CATS mRNA-seq kit with polyA selection, v2, for Illumina, according to the manufacturer's directions

treatment_protocol: Cells were cultured in DMEM / 10% fetal bovine serum / antibiotics, and treated for the indicated times with the indicated reagents.

value: LPS

tag: timepoint


title: ESC_INPUT_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.

value: ES cells


title: WT-PBS-266U


title: ESC3_WT_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.


title: 8 h treatment with 100 ng/mL lipopolysaccharide, repl 4


title: T1027.800IV.18(rep)

description: in vitro culture derived from CHMI


title: T1027.800IV.14.5

description: in vitro culture derived from CHMI


title: 8 h treatment with 100 ng/mL lipopolysaccharide, repl 1


title: 8 h treatment with 100 ng/mL lipopolysaccharide, repl 2


title: ESC2_WT_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.


title: T1022.2500ID.45

description: in vitro culture derived from CHMI


title: 8 h treatment with 10 ng/mL IL-4, repl 4


title: T1022.2500ID.13.5

description: in vitro culture derived from CHMI


title: 8 h treatment with 10 ng/mL IL-4, repl 3


title: ESC1_WT_KAP1_ChIP

description:
Illumina HiSeq 4000 platform
.


title: T1018.3200IV.42.5

description: in vitro culture derived from CHMI


title: 8 h treatment with 10 ng/mL IL-4, repl 1


title: 8 h culture without medium additions, repl 4


title: T1018.3200IV.22

description: in vitro culture derived from CHMI


title: 8 h culture without medium additions, repl 3


title: T1018.3200IV.15

description: in vitro culture derived from CHMI


title: 8 h culture without medium additions, repl 1


title: 8 h culture without medium additions, repl 2


title: 8 h treatment with 10 ug/mL H9c2 cell extract, repl 4

value: H9c2 cell extracts


title: T1018.3200IV.13.5

description: in vitro culture derived from CHMI


title: 8 h treatment with 10 ug/mL H9c2 cell extract, repl 1


title: T1015.2500ID.45

description: in vitro culture derived from CHMI


title: 8 h treatment with 10 ng/mL IL-4, repl 2


title: 72 h treatment with 100 ng/mL lipopolysaccharide, repl 4


title: 72 h treatment with 100 ng/mL lipopolysaccharide, repl 3


title: 72 h treatment with 100 ng/mL lipopolysaccharide, repl 1


title: 72 h treatment with 100 ng/mL lipopolysaccharide, repl 2


title: 72 h treatment with 10 ng/mL IL-4, repl 4


title: T1015.2500ID.17

description: in vitro culture derived from CHMI


title: 72 h treatment with 10 ng/mL IL-4, repl 3


title: 8 h treatment with 10 ug/mL H9c2 cell extract, repl 3


title: 8 h treatment with 10 ug/mL H9c2 cell extract, repl 2


title: 72 h treatment with 10 ng/mL IL-4, repl 2


title: MMPC6 AFTER co-culture WITH OC

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciances

description:
MMPC6A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an HG-U133-Plus-2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Multiple myeloma plasma cells, 96 hours with osteoclasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MMPCs were cultured with or without osteoclasts for 96 hours.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: multiple myeloma plasma cells

tag: co-culture

value: osteoclasts

tag: patient identfier


title: MMPC8 BEFORE co-culture WITH OC

description:
MMPC8B
Gene expression data from native multiple myeloma plasma cells.

source_name: Multiple myeloma plasma cells, alone

tag: cell type


title: MMPC7 BEFORE co-culture WITH OC

description:
MMPC7B
Gene expression data from native multiple myeloma plasma cells.


title: T1015.2500ID.15.5(rep)

description: in vitro culture derived from CHMI

tag: sample type

tag: tuchmi id


title: T1001.2500ID.45

description: in vitro culture derived from CHMI

tag: culture

tag: pfspz dose


title: MMPC7 AFTER co-culture WITH OC

description:
MMPC7A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: 72 h culture without medium additions, repl 4


title: 72 h culture without medium additions, repl 3


title: MMPC6 BEFORE co-culture WITH OC

description:
MMPC6B
Gene expression data from native multiple myeloma plasma cells.


title: T1001.2500ID.15.5

description: in vitro culture derived from CHMI

tag: gpi

tag: composition


title: T1001.2500ID.22.5

description: in vitro culture derived from CHMI


title: T1015.2500ID.13.5

description: in vitro culture derived from CHMI


title: MMPC5 BEFORE co-culture WITH OC

description:
MMPC5B
Gene expression data from native multiple myeloma plasma cells.


title: MMPC8 AFTER co-culture WITH OC

description:
MMPC8A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: MMPC5 AFTER co-culture WITH OC

description:
MMPC5A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: 72 h culture without medium additions, repl 1

tag: strain


title: 72 h treatment with 10 ug/mL H9c2 cell extract, repl 4


title: 72 h treatment with 10 ug/mL H9c2 cell extract, repl 3


title: T1001.2500ID.13.5

description: in vitro culture derived from CHMI


title: 72 h treatment with 10 ug/mL H9c2 cell extract, repl 2


title: 24 h treatment with 100 ng/mL lipopolysaccharide, repl 3


title: 24 h treatment with 100 ng/mL lipopolysaccharide, repl 4


title: MMPC4 AFTER co-culture WITH OC

description:
MMPC4A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: MMPC4 BEFORE co-culture WITH OC

description:
MMPC4B
Gene expression data from native multiple myeloma plasma cells.


title: 24 h treatment with 100 ng/mL lipopolysaccharide, repl 2


title: NF54_33-21

description: Working cell bank (WCB) that produced the PfSPZ Challenge used for the CHMI.

source_name: Plasmodium falciparum, parental

value: Parental


title: 24 h treatment with 10 ng/mL IL-4, repl 4


title: 24 h treatment with 10 ng/mL IL-4, repl 3


title: 24 h treatment with 100 ng/mL lipopolysaccharide, repl 1


title: MMPC3 AFTER co-culture WITH OC

description:
MMPC3A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: 24 h culture without medium additions, repl 4


title: NF54_32_1-21


title: 24 h treatment with 10 ng/mL IL-4, repl 1


title: Control-3.12

city: Montreal

first: Brenda

middle: Janice

last: Sanchez

state: QC

address: 3655 promenade Sir-William-Osler, Room 915

department: Bichemistry

country: Canada

institute: McGill University

data_processing:
RNA quantity and quality was assessed using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), and a Bioanalyser (Agilent Technology Inc).
The 4 RNA-seq libraries were sequenced on the Illumina NextSeq 500 platform. The reads were trimmed for sequencing adapters.
Trimmed reads were aligned to the reference mouse genome version mm10 (GRCm38) using Tophat version 2.0.10.
Gene quantification was performed on the mapped sequences using the htseq-count software version 0.6.1
Differential expression was analyzed using DESeq2 package, log transformation was used to normalize raw read counts and to calculate normalized expression counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Excel files include Log2FoldChange, Log10pvalue, IfcMLE, IfcSE and padj values for each group (Control/muHuR-KO)

source_name: control_Skeletal Muscle

extract_protocol:
Total RNA from muscle samples was isolated using TRIzo reagent (Invitrogen) according to the manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Muscles were carefully dissected and snap frozen in liquid-nitrogen. Samples were stored at −80°C before processing

tag: strain background

tag: genotype/variation

value: MyoDCre-;LoxP-/-

value: 10 weeks

tag: tissue

value: Skeletal Muscle


title: Control-3.8

tag: age


title: muHuR-KO-3.9

source_name: muHuR-KO_Skeletal Muscle

value: MyoDCre+;LoxP-/-


title: muHuR-KO-1.9


title: MMPC2 AFTER co-culture WITH OC

description:
MMPC2A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: 24 h culture without medium additions, repl 2

tag: treatment


title: ENAP1ox/ein3eil1 4 hour C2H4 RNAseq, rep2

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description: ethylene treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome usingTopHat version 2.0.9 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.2.1
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, generated by Cuffdiff version 2.2.1

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

tag: development stage

value: whole seedling

value: ethylene

value: ENAP1ox/ein3eil1 in COL background


title: 24 h culture without medium additions, repl 1

tag: timepoint


title: HFD_MYC_switch_CTD_3

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
11_VP_HFD_Het_383-4
RNA-seq in Hi-MYC ventral prostate tissues

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: mm9
Supplementary_files_format_and_content: processed data is a tab-delimited table containing normalized FPKM values used for gene expresison analysis

source_name: Hi-MYC ventral prostates

growth_protocol: VB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified control diet (CTD; Harlan Laboratories, TD.130838) consisting of 10% fat, or a high-fat diet (HFD; Harlan Laboratories, TD. 06414) consisting of 60% fat; ingredients were adjusted on a kcal basis. Food was changed on a weekly basis, and mice were weighed every three weeks, starting at weaning. For the dietary intervention experiment, animals were fed a HFD up to 10-week-old and then switched to a CTD. Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutional Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Prior to RNA isolation, cell numbers were determined and total RNA isolation was performed using the miRvana miRNA total RNA isolation kit (ThermoFisher Scientific, AM1560) according to manufacturers instructions. Following isolation, RNA was digested with DNase (Ambion). During isolation, external RNA spike-ins (ERCC, Ambion) were added at the time of cell lysis.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)

tag: cell line

value: ventral prostatic tissues

tag: genotype

value: Hi-MYC

tag: diet

value: 12 weeks

value: FVB


title: ENAP1ox/ein3eil1 4 hour C2H4 RNAseq, rep1

description: ethylene treated for 4 hours


title: 24 h treatment with 10 ug/mL H9c2 cell extract, repl 4

tag: cell type


title: MMPC3 BEFORE co-culture WITH OC

description:
MMPC3B
Gene expression data from native multiple myeloma plasma cells.

tag: co-culture

tag: patient identfier


title: HFD_MYC_switch_CTD_2

description:
10_VP_HFD_Het_383-3
RNA-seq in Hi-MYC ventral prostate tissues


title: 24 h treatment with 10 ug/mL H9c2 cell extract, repl 3


title: MMPC1 AFTER co-culture WITH OC

description:
MMPC1A
Gene expression data from multiple myeloma plasma cells after co-culture with osteoclasts.


title: MMPC2 BEFORE co-culture WITH OC

description:
MMPC2B
Gene expression data from native multiple myeloma plasma cells.


title: ENAP1ox/ein3eil1 4 hour air RNAseq, rep2

description: air treated for 4 hours

value: air


title: 24 h treatment with 10 ng/mL IL-4, repl 2


title: 24 h culture without medium additions, repl 3


title: 24 h treatment with 10 ug/mL H9c2 cell extract, repl 2


title: HFD_MYC_switch_CTD_1

description:
9_VP_HFD_Het_381-2
RNA-seq in Hi-MYC ventral prostate tissues


title: esg[ts]/+ intestinal progenitor cells. C6706ΔvasK infected. biological rep2

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114th St and 87th ave

department: Medical Microbiology and Immunology

institute: University of Alberta

data_processing:
Base calls performed using Cyberduck(FTP)
FASTQC was used to evaluate the quality of raw paired-end sequencing reads. Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic. Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0). The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR. In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6

organism: Drosophila melanogaster

source_name: Drosophila esg[ts]/+ intestinal progenitor cells 24 hour infection

growth_protocol: Flies were raised on standard cornmeal food at 18C before eclosion. Adult flies were transferred to 29C for 5 days to permit establishment of the adult microbiome. Flies were then mock infected or infected with Vibrio cholerae for 24hours.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
For intestinal progenitor cell RNAseq, library construction and sequencing was performed by the Lunenfeld-Tanenbaum Research Institute. For whole gut RNAseq, library construction and sequencing was performed by Novogene: genome sequencing company.

treatment_protocol: After 24 hours of infection, for intestinal progenitor cell RNAseq a total of 100 guts per sample (virgin female) were and for whole gut RNAseq 10 guts per sample were dissected into Trizol and used for RNA extraction.

value: Isolated intestinal progenitor cells

value: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+

tag: infection


title: esg[ts]/+ intestinal progenitor cells. C6706 infected. biological rep3


title: esg[ts]/+ intestinal progenitor cells. C6706 infected. biological rep2


title: NF54_32_2-22.5

tag: sample type

tag: tuchmi id

tag: culture

value: In vitro, blood stage

tag: pfspz dose

tag: gpi

value: Reference

value: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.


title: 210-p6: Phf6-KO MPP3 rep4

city: Taipei

first: Yueh-Chwen

last: Hsu

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Raw reads were aligned to mouse reference genome mm10 and gene-level expression were quantified by STAR algorithm
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene read counts

source_name: bone marrow

extract_protocol:
Mouse bone marrow was harvested from Phf6 wild-type and knockout mice, RBC was lysed and the rest cells were stained with anti-lineage cocktail, anti-Sca-1, anti-cKit, anti-CD150 and anti-CD48.
Libraries were prepared by Nextera XT DNA sample preparation kit (Illumina, CA, USA)

tag: strain

tag: tissue

value: bone marrow

value: Phf6 Knockout


title: ENAP1ox/ein3eil1 4 hour air RNAseq, rep1

description: air treated for 4 hours

tag: treatment

tag: genotype/variation


title: ein3eil1 4 hour air RNAseq, rep2

description: air treated for 4 hours

tag: development stage

value: ein3eil1 in COL background


title: 165-p6: Phf6-KO MPP3 rep3

tag: age


title: 62-p6: Phf6-KO MPP3 rep2

tag: genotype


title: esg[ts]/+ intestinal progenitor cells. C6706 infected. biological rep1


title: Sdc1BleoD21

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
follow default Cellranger 3.0.0.0
Genome_build: mm10
Supplementary_files_format_and_content: .h5

source_name: mouse lung

extract_protocol:
follow standard 10x single cell 3 prime v2 kit manuscript
10x chromium single cell RNAseq

treatment_protocol: Bleomycin treatment for either wild type mice or Sdc-/- mice, collected at Day 21, then compare with untreated wild type mice and Sdc1-/- mice

tag: group


title: WTBleoD21


title: ein3eil1 4 hour C2H4 RNAseq, rep2

description: ethylene treated for 4 hours


title: ein3eil1 4 hour air RNAseq, rep1

description: air treated for 4 hours


title: 55-p6: Phf6-KO MPP3 rep1

tag: cell type


title: esg[ts]/+ intestinal progenitor cells. Mock infected. biological rep3

value: mock


title: 207-p6: WT MPP3 rep4

value: Phf6 Wild-type


title: ein3eil1 4 hour C2H4 RNAseq, rep1

description: ethylene treated for 4 hours

value: whole seedling

value: ethylene


title: ein3eil1_C2H4_ENAP1_input rep2

description: ethylene treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bwa with default parameters
For each ENAP1 binding in each condition,mapped reads were pooled across ChIP-seq replicates as described (Gjoneska, Pfenning et al.Nature, 2015)
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603) following IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr)
Genome_build: tair10
Supplementary_files_format_and_content: the  bdg and narrowPeak (after cutoff according IDR pipeline) files are generated using MACS2 (version 2.1.0.20150603) software.

extract_protocol:
ENAP1 proteins were extracted from seedlings and ENAP1-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

tag: developmental stage

tag: ecotype

value: ethylene treatment

tag: chip antibody


title: esg[ts]/+ intestinal progenitor cells. Mock infected. biological rep2

tag: infection


title: esg[ts]/+ intestinal progenitor cells. C6706ΔvasK infected. biological rep3


title: 162-p6: WT MPP3 rep3


title: mouse_ep2

data_processing:
data processing followed default setting of CellRanger 2.0 pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger software output

source_name: Lung

extract_protocol:
mouse lung are enzymatic digested to generate single cell suspension, epithelial cells then further enriched by FACS
library construction followed 10x chromium 3' V2 kit guideline

value: Lung


title: WTD0


title: MMPC1 BEFORE co-culture WITH OC

description:
MMPC1B
Gene expression data from native multiple myeloma plasma cells.

value: multiple myeloma plasma cells

tag: co-culture

tag: patient identfier


title: FVB KO EC VEGF 3 hours, biological rep5

city: Uppsala

first: Lena

last: Claesson-Welsh

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: PA317_KO6 V3

hyb_protocol: Clariom™ D Mouse Arrays were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the Clariom™ D Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. The data was run in two batches, which was considered in the normalization step.

data_processing: The raw data was normalized to gene and exon level in the Transcription Analysis Console, version 4.0.1.36, provided by Thermo Fisher (http://www.thermofisher.com), using the Signal Space Transformation-Robust Multi-Array Average (SST-RMA) method.

source_name: FVB mouse at postnatal day 7-12

label_protocol: An estimated amount of around 10 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA according to the GeneChip® Pico Reagent Kit User Guide (P/N 703308 Rev. 4, Affymetrix Inc., Santa Clara, CA).

growth_protocol: The isolated ECs were cultured in MV2 medium with supplements in 6-well plates until confluence and then plated in 12-well plates for experiments.

extract_protocol: RNA was isolated immediately by using RNeasy Micro Plus kit (Qiagen). RNA concentration was measured by Nanodrop (ThermoFisher Scientific) and RNA integrity number (RIN) was assessed by Bioanalyzer (Agilent, samples with a RIN>7 were used for microarray).

treatment_protocol: The cells from each mouse were starved for 3 hours in MV2 medium with 0.2% FCS and then either left untreated (basal) or treated with VEGFA (50 ng/mL) for 1 or 3 hours.

tag: strain/background

value: FVB

value: VEGFR2 Y1212F

value: Postnatal day 7-12

value: Lung endothelial cells

value: VEGF

tag: time point

value: 3 hours


title: 59-p6: WT MPP3 rep2

tag: strain

value: 12 weeks


title: 52-p6: WT MPP3 rep1

tag: tissue

value: bone marrow


title: ein3eil1_ENAP1_C2H4_ChIPseq_rep2

description:
ethylene treated for 4 hours
macs2.optimal.C24_C20vsC19_C23.narrowPeak
C24_C20vsC19_C23_control_lambda.bdg
C24_C20vsC19_C23_treat_pileup.bdg

tag: treatment

value: anti-green fluorescent protein (life technologies:A11122)


title: FVB KO EC VEGF 1 hour, biological rep5

description: PA317_KO6 V1

tag: genotype/variation

value: 1 hour


title: Sdc1D0


title: Antennal disc rep 3

city: Baltimore

first: Robert

last: Johnston Jr.

state: MD

address: 3400 N. Charles Street

department: Department of Biology

institute: Johns Hopkins University

data_processing:
FASTQ sequencing datasets were assessed for quality using FastQC
Pseudoalignment with the Drosophila dm6 transcriptome and read quantifications were performed using kallisto
Transcript abundance files generated by kallisto were joined to a file containing the genomic coordinates of all Drosophila mRNA transcripts
The joined transcript coordinate file was compared to a file containing the coordinates of all tested transgenes using the bedtools intersect tool (Quinlan and Hall, 2010). The output file contained a list of all TPMs for each gene contained in each transgene.
Genome_build: dm6
Supplementary_files_format_and_content: tsv files contain TPM values for each gene in the Drosophila transcriptome. bed files contain a list of all genes and TPMs from endogenous genes that are contained in each transgene tested in this study. Note that these samples do not contain the transgenes.

source_name: Antennal disc

extract_protocol:
RNA-seq was performed on three biological replicates, each consisting of 30 third instar larval eye or antennal discs. Eye-antennal discs were dissected in 1X PBS and separated from the mouth hooks. Eye discs and antennal discs were then manually separated and placed directly into 300 mL of Trizol. RNA was purified using a Zymo Direct-zol RNA MicroPrep kit (catalog number R2062).
mRNA libraries were prepared using an Illumina TruSeq Stranded mRNA LT Sample Prep Kit (catalog number RS-122-2101).

value: third instar larvae

value: antennal imaginal disc


title: FVB KO EC Control, biological rep5

description: PA317_KO6 C

value: Untreated

value: Control


title: 211-p7: Phf6-KO MPP2 rep4

value: Phf6 Knockout


title: Antennal disc rep 2


title: Antennal disc rep 1


title: ein3eil1_air_ENAP1_input rep2

description: air treated for 4 hours

value: whole seedling

value: air


title: ein3eil1_air_ENAP1_input rep1

description: air treated for 4 hours


title: FVB KO EC VEGF 1 hour, biological rep4

description: PA317_KO5 V1

value: FVB


title: mouse_ep1

value: Lung


title: esg[ts]/+ intestinal progenitor cells. Mock infected. biological rep1

value: Isolated intestinal progenitor cells

value: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+

value: mock


title: ein3eil1_ENAP1_air_ChIPseq_rep2

description:
air treated for 4 hours
macs2.optimal.50_46vsC17_C21.narrowPeak
50_46vsC17_C21_control_lambda.bdg
50_46vsC17_C21_treat_pileup.bdg


title: FVB KO EC VEGF 3 hours, biological rep3

description: PA317_KO3 V3

value: VEGFR2 Y1212F

value: Postnatal day 7-12

value: Lung endothelial cells

value: VEGF

value: 3 hours


title: FVB KO EC Control, biological rep4

description: PA317_KO5 C


title: Eye disc rep 3

source_name: Eye disc

value: third instar larvae

value: eye imaginal disc


title: ein3eil1_C2H4_ENAP1_input rep1

description: ethylene treated for 4 hours

value: ethylene


title: Eye disc rep 2


title: ein3eil1_ENAP1_air_ChIPseq_rep1

value: anti-green fluorescent protein (life technologies:A11122)


title: 56-p7: Phf6-KO MPP2 rep1

value: bone marrow

value: Phf6 Knockout

value: 12 weeks


title: 166-p7: Phf6-KO MPP2 rep3


title: ein3eil1_ENAP1_C2H4_ChIPseq_rep1

value: whole seedling


title: 208-p7: WT MPP2 rep4

value: Phf6 Wild-type


title: FVB KO EC VEGF 1 hour, biological rep3

description: PA317_KO3 V1

value: FVB

value: 1 hour


title: Eye disc rep 1


title: xrn1_dcr1_1 (small RNA-seq)

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Yeast cells

data_processing:
Adapter sequences were removed using the Atropos software.
Reads were then mapped to the N. castellii and S. pombe reference genomes using the version 2.3.5 of Bowtie (Langmead and Salzberg 2012), using default parameters, with no mismatch in seed alignment.
Subsequent analyses used 22-23 nt reads uniquely mapped on the N. castellii genome.
Densities were normalized on the levels of the centromeric 22-23 nt small RNAs of S. pombe.
Genome_build: The N. castellii reference genome was retrieved from version 7 of the Yeast Gene Order Browser. The S. pombe genome was retrieved from PomBase.
Supplementary_files_format_and_content: Small_RNA_densities_spike.xlsx: For each sample, a single tab-delimited Excel file including normalized tag densities (tag/nt) for each annotated feature (including SUTS, CUTS and XUTs).

organism: Naumovozyma castellii

source_name: xrn1 dcr1 double mutant strain (YAM2796)

growth_protocol: N. castellii strains were grown at 25°C in rich Yeast Extract-Peptone-Dextrose (YPD) medium to mid-log phase.

extract_protocol:
Total RNA was extracted using standard hot-phenol procedure.
For each sample, 50 µg of total RNA were mixed with 2 µg of total RNA from a wild-type strain of S. pombe (the 22-23 nt small RNAs derived from the centromeric repeats in the latter species constituting RNA spike-in used as an internal reference for the subsequent normalization of the small RNA-Seq signals). The small RNAs (<80 nt) fraction was purified on 15% TBE-Urea polyacrylamide gels. Libraries were constructed from 120 ng of purified small RNAs using the NEBNext Multiplex Small RNA Library Preparation Set for Illumina (New England Biolabs). Single-end sequencing (50 nt) of libraries was performed on a HiSeq 2500 system (Illumina).

value: xrn1 dcr1 double mutant

tag: molecule subtype

value: Purified <80 nt small RNAs

tag: biological replicate


title: FVB KO EC Control, biological rep3

description: PA317_KO3 C

value: VEGFR2 Y1212F

tag: age

value: Postnatal day 7-12

value: Untreated

value: Control


title: 60-p7: WT MPP2 rep2

tag: genotype


title: xrn1_dcr1_2 (small RNA-seq)

description: Yeast cells


title: FVB KO EC VEGF 3 hours, biological rep2

description: PA317_KO2 V3

tag: cell type

value: Lung endothelial cells

value: VEGF

value: 3 hours


title: dcr1_2 (small RNA-seq)

description: Yeast cells

source_name: dcr1 mutant strain (YAM2795)

value: dcr1 mutant


title: FVB KO EC VEGF 1 hour, biological rep2

description: PA317_KO2 V1


title: 53-p7: WT MPP2 rep1

value: bone marrow


title: dcr1_1 (small RNA-seq)

description: Yeast cells


title: 212-p8: Phf6-KO LT-HSC rep3

value: LT-HSC

value: Phf6 Knockout


title: FVB KO EC Control, biological rep2

description: PA317_KO2 C


title: xrn1_2 (small RNA-seq)

description: Yeast cells

source_name: xrn1 mutant strain (YAM2479)

value: xrn1 mutant


title: FVB KO EC VEGF 3 hours, biological rep1

description: PA317_KO1 V3


title: xrn1_1 (small RNA-seq)

description: Yeast cells


title: 57-p8: Phf6-KO LT-HSC rep1

value: 12 weeks


title: 61-p8: WT LT-HSC rep2

value: Phf6 Wild-type


title: FVB KO EC VEGF 1 hour, biological rep1

description: PA317_KO1 V1

value: FVB

value: 1 hour


title: WT_2 (small RNA-seq)

description: Yeast cells

source_name: Wild-type strain (YAM2478)

value: Wild-type

value: Purified <80 nt small RNAs


title: 163-p7: WT MPP2 rep3


title: WT_1 (small RNA-seq)

description: Yeast cells


title: 54-p8: WT LT-HSC rep1


title: FVB KO EC Control, biological rep1

description: PA317_KO1 C

value: VEGFR2 Y1212F

value: Postnatal day 7-12


title: FVB WT EC VEGF 3 hours, biological rep5

description: PA317_WT5 V3

value: WT


title: Dcr1-GFP (small RNA-seq)

description: Yeast cells

data_processing:
Adapter sequences were removed using the Atropos software.
Reads were then mapped to the N. castellii and S. pombe reference genomes using the version 2.3.5 of Bowtie (Langmead and Salzberg 2012), using default parameters, with no mismatch in seed alignment.
Subsequent analyses used 22-23 nt reads uniquely mapped on the N. castellii genome.
Densities were normalized on the levels of the centromeric 22-23 nt small RNAs of S. pombe.
Genome_build: The N. castellii reference genome was retrieved from version 7 of the Yeast Gene Order Browser. The S. pombe genome was retrieved from PomBase.
Supplementary_files_format_and_content: Densities_Dcr1_GFP_spike.xlsx: A single tab-delimited Excel file including normalized tag densities (tag/nt) for each annotated feature (including SUTS, CUTS and XUTs).

source_name: Dcr1-GFP strain (YAM2826)


title: HFD_MYC_H4K20me1

description: 12-week-old FVB

data_processing:
For all samples reads were aligned to their indicated build using bowtie2 with parameters -k 1
Bam alignments were converted to bedgraph using bedtools genomecoverage and scaled to million mapped reads
Bigwig files were generated from scaled bedgraphs using UCSC bedGraphTobigWig tool
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in bigwig format and contain whole genome coverage

growth_protocol: FVB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research5. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified control diet (CTD; Harlan Laboratories, TD.130838) consisting of 10% fat, or a high-fat diet (HFD; Harlan Laboratories, TD. 06414) consisting of 60% fat; ingredients were adjusted on a kcal basis. Food was changed on a weekly basis, and mice were weighed every three weeks, starting at weaning. Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutial Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Fresh-frozen VP tissues from 12-week-old mice were pulverized (Cryoprep Impactor, Covaris), resuspended in PBS + 1% formaldehyde, and incubated at room temperature for 20 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration) for 15 minutes at room temperature, then washing in ice cold PBS + EDTA-free protease inhibitor cocktail (PIC; #04693132001, Roche). Multiple biological replicates were combined for each condition in two distinct pools (replicates). Chromatin was isolated by the addition of lysis buffer (0.1% SDS, 1% Triton X-100, 10 mM Tris-HCl (pH 7.4), 1 mM EDTA (pH 8.0), 0.1% NaDOC, 0.13 M NaCl, 1X PIC) + sonication buffer (0.25% sarkosyl, 1 mM DTT) to the samples, which were maintained on ice for 30 minutes. Lysates were sonicated (E210 Focused-ultrasonicator, Covaris) and the DNA was sheared to an average length of ~200-500 bp. Genomic DNA (input) was isolated by treating sheared chromatin samples with RNase (30 minutes at 37°C), proteinase K (30 minutes at 55°C), de-crosslinking buffer (1% SDS, 100 mM NaHCO3 (final concentration), 6-16 hours at 65°C), followed by purification (#28008, Qiagen). DNA was quantified on a NanoDrop spectrophotometer, using the Quant-iT High-Sensitivity dsDNA Assay Kit (#Q33120, Thermo Fisher Scientific). On ice, ChIP-validated H4K20me1 (2 micrograms, #ab9051, Abcam) or PHF8 (5 micrograms, #A301-772A, Bethyl Laboratories) antibodies were conjugated to a mix of washed Dynalbeads protein A and G (Thermo Fisher Scientific), and incubated on a rotator (overnight at 4°C) with 1.5 micrograms (H4K20me1) or 5 micrograms (PHF8) of chromatin. ChIP’ed complexes were washed, sequentially treated with RNase (30 minutes at 37°C), proteinase K (30 minutes at 55°C), de-crosslinking buffer (1% SDS, 100 mM NaHCO3 (final concentration), 6-16 hours at 65°C), and purified (#28008, Qiagen). The concentration and size distribution of the immunoprecipitated DNA was measured using the Bioanalyzer High Sensitivity DNA kit (#5067-4626, Agilent).
Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 2 ng of DNA, using the ThruPLEX DNA-seq kit (#R400427, Rubicon Genomics), according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios, and sequenced to a target depth of 40M reads on an Illumina NextSeq500 run, with single-end 75bp reads.

tag: cell line

value: ventral prostatic tissues

value: Hi-MYC

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: diet

value: HFD


title: 64-p8: Phf6-KO LT-HSC rep2

value: bone marrow


title: Processed RA data at time t30 after BPS addition

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

description: cDNA labelling for W303a strain, t30: 30 min after BPS addition

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: wild type haploid strain

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.2 OD600. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: 30 min after BPS addition


title: FVB WT EC VEGF 1 hour, biological rep5

description: PA317_WT5 V1

value: Lung endothelial cells

value: VEGF


title: FVB WT EC Control, biological rep5

description: PA317_WT5 C

value: Untreated

value: Control


title: xrn1_dcr1 biological replicate 1 (total RNA-seq)

data_processing:
Reads were mapped using version 2.0.9 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns of 2 Kb.
All bioinformatics analyses used uniquely mapped reads. Tag densities were normalized on the ERCC RNA spike-in signal.
Genome_build: The N. castellii reference genome was retrieved from version 7 of the Yeast Gene Order Browser.
Supplementary_files_format_and_content: For each yeast species, a single tab-delimited Excel file including normalized tag densities (tag/nt) for each annotated feature (including SUTS, CUTS and XUTs) in each sample.

extract_protocol:
Total RNA was extracted using standard hot-phenol procedure. For each sample, 1 µg of total RNA was mixed with 2 µl of 1:100 diluted ERCC RNA spike-in (Life Technologies), then ribosomal (r)RNAs were depleted using the RiboMinus Eukaryote v2 Kit (Life Technologies).
Total RNA-Seq libraries were constructed from 50 ng of rRNA-depleted RNA using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina). Paired-end sequencing (2 x 50 nt) was performed on a HiSeq2500 system (Illumina).

value: xrn1 dcr1 double mutant

value: Yeast cells

value: rRNA-depleted RNA


title: HFD_WT_H4K20me1

description: 12-week-old FVB

source_name: WT ventral prostates

value: wild type


title: CTD_MYC_H4K20me1

description: 12-week-old FVB

value: CTD


title: Processed RA data at time t10 after BPS addition

description: cDNA labelling for W303a strain, t10: 10 min after BPS addition

value: 10 min after BPS addition


title: Processed RA data at time t180 after BPS addition

description: cDNA labelling for W303a strain, t180: 180 min after BPS addition

value: 180 min after BPS addition


title: Processed RA data at time t0

description: cDNA labelling for W303a strain, t0: before adding BPS

value: before adding BPS


title: Processed RA data at time t90 after BPS addition

description: cDNA labelling for W303a strain, t90: 90 min after BPS addition

value: 90 min after BPS addition


title: xrn1_dcr1 biological replicate 2 (total RNA-seq)


title: xrn1 biological replicate 2 (total RNA-seq)

value: xrn1 mutant


title: CTD_WT_H4K20me1

description: 12-week-old FVB

value: ventral prostatic tissues

value: Abcam


title: Processed TR data at time t90 after BPS addition

description: GRO labelling for W303a strain, t90: 90 min after BPS addition


title: FVB WT EC VEGF 3 hours, biological rep4

description: PA317_WT4 V3

value: FVB

value: WT

value: Postnatal day 7-12

value: 3 hours


title: Processed TR data at time t30 after BPS addition

description: GRO labelling for W303a strain, t30: 30 min after BPS addition

value: 30 min after BPS addition


title: xrn1 biological replicate 1 (total RNA-seq)


title: Endosperm_nf-yc11_rep3

city: Wuhan

first: Yufei

last: Xiong

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
Illumina CASAVA 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and the raw reads were filtered for adaptors and low-quality reads. Clean reads were mapped to the reference genome of rice (RGAP v. 7.0) using HISAT2 (v.2.0.5).
The gene expression levels were calculated using the FPKM method (expected number of fragments per kilobase of transcript sequence per million base pairs sequenced)
DESeq in R was used to select the differentially expressed genes (DEGs). DEGs were defined as those with an expression change > 1.5-fold and corrected P value < 0.05
Genome_build: RGAP v. 7.0
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each Sample ...

organism: Oryza sativa Japonica Group

source_name: endopserm

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: rice endosperm

value: 7 days after pollination

value: nf-yc11 mutant


title: Processed TR data at time t10 after BPS addition

description: GRO labelling for W303a strain, t10: 10 min after BPS addition


title: FVB WT EC VEGF 1 hour, biological rep4

description: PA317_WT4 V1

value: Lung endothelial cells

value: VEGF

value: 1 hour


title: HFD_MYC_PHF8

description: 12-week-old FVB

value: Hi-MYC

value: Bethyl Laboratories

value: HFD


title: Processed TR data at time t360 after BPS addition

description: GRO labelling for W303a strain, t360: 360 min after BPS addition

value: 360 min after BPS addition


title: Processed TR data at time t180 after BPS addition

description: GRO labelling for W303a strain, t180: 180 min after BPS addition

value: 180 min after BPS addition


title: dcr1 biological replicate 2 (total RNA-seq)

value: dcr1 mutant

value: Yeast cells

value: rRNA-depleted RNA


title: Endosperm_nf-yc11_rep2


title: dcr1 biological replicate 1 (total RNA-seq)


title: FVB WT EC Control, biological rep4

description: PA317_WT4 C

value: FVB

value: WT

value: Postnatal day 7-12

value: Untreated

value: Control


title: WT biological replicate 2 (total RNA-seq)

value: Wild-type


title: CTD_WT_PHF8

description: 12-week-old FVB

value: ventral prostatic tissues

value: wild type

value: CTD


title: WT biological replicate 1 (total RNA-seq)


title: FVB WT EC VEGF 3 hours, biological rep3

description: PA317_WT3 V3

value: Lung endothelial cells

value: VEGF

value: 3 hours


title: HFD_WT_PHF8

description: 12-week-old FVB

value: Bethyl Laboratories

value: HFD


title: Endosperm_WT_rep2

value: rice endosperm

value: 7 days after pollination

value: wildtype


title: FVB WT EC VEGF 1 hour, biological rep3

description: PA317_WT3 V1

value: FVB

value: 1 hour


title: Endosperm_WT_rep1


title: HFD_MYC_2

data_processing:
alignment: bowtie2 using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. See methods for further details
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file matix containing FPKM values for each transcript

extract_protocol:
Fresh VP tissues from 12-week-old mice were dissociated to form a single cell suspension. RNA from an equal number of cells was extracted using the miRNeasy Micro Kit (#217084, Qiagen) coupled with on-column DNAse treatment (#79254, Qiagen). RNA sample concentration was measured and subjected to quality evaluation, using a Bioanalyzer RNA 6000 Nano kit (#5067-1511, Agilent).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using TruSeq Stranded mRNA sample preparation kits (#RS-122-2101, Illumina) according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

value: Hi-MYC


title: Regent mock control sample at 6h pi_rep2

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

description:
Regent treated with mock control at 6h pi
filtered_raw_counts.tsv
sample_48_Regent_m_6hpi

data_processing:
Bcl to fastq conversion using bcl2fastq
Quality control using FastQC
Filtering of adapter containing sequences using Cutadapt
Mapping of remaining reads to Vitis genome using Tophat
Counting of reads to features/genes using HTSeq-count
Genome_build: Vitis vinifera reference genome (12X, INSDC Assembly GCA_000003745.2, Nov 2011) downloaded from Ensembl Plants in January 2018
Supplementary_files_format_and_content: raw counts were filtered to remove genes that had a raw count value < 3 in any of the 10 samples. Counts for remaining genes were summarized in the tsv file "filtered_raw_counts.tsv" which shows raw count values for each sample as separate columns

organism: Vitis vinifera

source_name: leaf

growth_protocol: Potted grapevines were grown under greenhouse conditions (22 °C/day; 18 °C/night; 50 % humidity). Vines were regenerated from canes.

extract_protocol:
leaf discs were recut (1.3 cm diameter) to remove the outer 2 mm wounded edge, immediately prior to freezing in liquid nitrogen. Total RNA was isolated with the Spectrum Plant Total RNA purification kit (Sigma Aldrich), following the manufacturer’s instructions
RNA samples with an RNA integrity number > 7 were used for library preparation. Libraries for next generation sequencing were prepared using the NEBNext Ultra II Directional RNA Preparation Kit with NEBNext Dual Index Oligo’s for Illumina and the NEBNext  Poly A Selection Module (New England Biolabs) according to the manufacturer’s instructions. Single-end sequencing with a length of 75bp for each read was run on an Illumina NextSeq 500 instrument

treatment_protocol: For all infection experiments, leaf discs were excised with a cork borer from the fourth or fifth fully expanded leaves below the shoot apex. Susceptible cultivar (Mueller-Thurgau) was inoculated with avirulent P. viticola isolate and water, resistant cultivar (Regent) was inoculated with an avirulent and a virulent P. viticola isolate and water.

tag: cultivar

value: Regent

tag: phenotype

value: resistant

value: m

tag: inoculation

value: mock control (water)

value: leaf


title: Regent mock control sample at 6h pi_rep1

description:
Regent treated with mock control at 6h pi
filtered_raw_counts.tsv
sample_47_Regent_m_6hpi


title: FVB WT EC Control, biological rep3

description: PA317_WT3 C

tag: strain/background

value: WT

value: Postnatal day 7-12

value: Untreated

tag: time point

value: Control


title: Endosperm Input

data_processing:
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L18 (Length).
Cleaned data were then mapped to the rice reference genome (RGAP v. 7.0) using BWA with default parameters and allowing unique reads only.
Peak calling was generated by MACS version (v2.1.0) (band width = 300；model fold = [5, 50]; qvalue cutoff = 0.05)
Genome_build: RGAP 7.0
Supplementary_files_format_and_content: bigwig files include information of genome-wide signal. MACS2_peaks files include information about peaks called by MACS2, bed file includes the peak summits locations for every peak.

extract_protocol:
Endosperm at 7 DAP was harvested and immediately crosslinked in 1% formaldehyde under vacuum for 30 min and 3 g tissues for each sample were used for chromatin isolation. Chromatin was fragmented to 200-500 bp by sonication. NF-YC11-DNA complexes were isolated with FLAG antibody, and the precipitated DNA was purified and then dissolved in distilled water.
The eluted DNA was uesd to generate Illumina sequencing libraries following the manufacture's protocol.

tag: tissue

tag: developmental stage

tag: chip antibody


title: FVB WT EC VEGF 3 hours, biological rep2

description: PA317_WT2 V3

tag: genotype/variation

value: Lung endothelial cells

tag: treatment

value: VEGF

value: 3 hours


title: HFD_MYC_1

source_name: Hi-MYC ventral prostates

value: ventral prostatic tissues

value: HFD

tag: age

tag: strain


title: FVB WT EC VEGF 1 hour, biological rep2

description: PA317_WT2 V1

value: FVB

tag: cell type


title: Endosperm NF-YC11 ChIP

value: rice endosperm

value: 7 days after pollination

value: anti-FLAG antibody (Sigma, F3165)


title: Processed TR data at time t0

description: GRO labelling for W303a strain, t0: before adding BPS

value: before adding BPS


title: Endosperm_nf-yc11_rep1

tag: genotype

value: nf-yc11 mutant


title: Regent aggressive isolate infected sample at 6h pi_rep2

description:
Regent sample treated with avrRpv3- at 6h pi
filtered_raw_counts.tsv
sample_46_Regent_aggres_6hpi

value: Regent

value: resistant

value: virulent P. viticola isolate avrRpv3-


title: HFD_WT_3

tag: cell line

value: wild type


title: FVB WT EC Control, biological rep2

description: PA317_WT2 C

value: WT

value: Postnatal day 7-12

value: Untreated


title: CTD_MYC_PHF8

description: 12-week-old FVB

value: Hi-MYC

tag: antibody

tag: antibody manufacturer

value: Bethyl Laboratories

tag: antibody catalog number

value: CTD


title: Endosperm_WT_rep3

value: wildtype


title: FVB WT EC VEGF 3 hours, biological rep1

description: PA317_WT1 V3

value: FVB

value: Lung endothelial cells

value: VEGF

value: 3 hours


title: HFD_MYC_3

value: ventral prostatic tissues

tag: diet

value: HFD


title: 72 hpf, all skin, replicate A

city: Los Angeles

first: Shawn

last: Cokus

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

institute: UCLA

data_processing:
Demultiplexing: single mismatch to expected 7-mers, only keeping PF=1 spots
Adapter, low quality base trimming: CutAdapt 1.8.1 (-m 21 --trim-n --max-n=2 -q 10,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), then only keeping reads >=47 nt long and only keeping the first 47 nt of those reads
Alignment: STAR 2.5.3a (to genome and transcriptome, single pass mode with known junctions), retaining multiple locations for non-uniquely aligning reads (see paper or BAMs for parameters)
Quantification: Salmon patched 0.10.2 (--numGibbsSamples=1000 --thinningFactor=25 --useVBOpt --libType=U --fldMean=200 --fldSD=200 --rangeFactorizationBins=4 --minAssignedFrags=1 --seqBias --noBiasLengthThreshold), with 1,000 Gibbs samples per experiment
Statistics: see paper; similar to R Bioconductor Sleuth (with Wasabi as importer), but elaborated and with some DESeq2 features incorporated
Genome_build: Ensembl release 92 top-level reference Zebrafish genome (GRCz11 chr1..25 + MT + 847/120 KN/KZ scaffolds) + PhiX, and associated Ensembl genebuild annotations/models
Supplementary_files_format_and_content: GZIP-TAR-Salmon files: GZIP-compressed TAR archives of Salmon transcript quantification output filesystem trees. Supplementary file: Microsoft Excel workbook in XLSX format, with multiple worksheets, containing a comprehensive collection of analysis input data, intermediate steps, and statistical outputs (see column headers as well as Methods and Supplemental methods of the associated journal publication).

source_name: FACS-isolated all skin cells from whole embryos

extract_protocol:
Dechorionated embryos were transferred into 1.5 ml tubes and rinsed with Ca2+-free Ringer’s solution for 15 min. During this incubation, yolk was removed by gently pipetting embryos through a 200 µl tip (with the end cut off) three to five times. Yolk-free embryos were transferred into a 35 mm petri dish with 5 ml of 0.25% Trypsin-EDTA. Embryos were incubated at 28.5 °C and homogenized with a 200 µl tip every 10 min until most cells were dissociated (20 to 50 min). 55 µl 100 mM CaCl2 and 550 µl FCS were added to stop digestion. Dissociated cells were transferred into a 15 ml tube and centrifuged at 300 g for 5 min at 15 °C. Cells were rinsed once with 10 ml suspension solution (colorless Leibovitz medium L-15 with 0.3 g/L glutamine, 0.8 mM CaCl2, Pen 50U/ml, Strep 0.05 mg/ml, and 1% FCS). Dissociated cells were resuspended in suspension solution to ~10^7 cells/ml and immediately proceeded to cell sorting at the UCLA Broad Stem Cell Research Center Flow Cytometry Core. BD FACS ARIA II SORP instruments sorted cells, using a 488 nm laser for GFP detection and a 561 nm laser for RFP (dsRed) detection.
Sorted cells in suspension solution were immediately lysed using the Qiagen RNeasy kit. Lysis was completed within two hours of dissociating cells. Total RNA was isolated following the Qiagen RNeasy kit and stored at –80 °C. Quality of all samples was assayed with an Agilent Bioanalyzer, and only samples with RNA Integrity Number > 8 were used for creating sequencing libraries. Poly-A bead-purified RNA-Seq libraries were prepared with the Illumina TruSeq RNA Library Prep Kit.

value: AB+TU

value: 72 hpf

value: FACS all skin

tag: Sex

value: pooled male and female

tag: biomaterial provider

value: Fang Wang (CSUDH)

tag: birth location

value: UCLA


title: Regent normal isolate infected sample at 6h pi_rep2

description:
Regent sample treated with avrRpv3+ at 6h pi
filtered_raw_counts.tsv
sample_44_Regent_x_6hpi

tag: cultivar

value: Regent

tag: phenotype

value: resistant

value: x

tag: inoculation

value: avirulent P. viticola isolate avrRpv3+

tag: tissue

value: leaf


title: Regent normal isolate infected sample at 6h pi_rep1

description:
Regent sample treated with avrRpv3+ at 6h pi
filtered_raw_counts.tsv
sample_43_Regent_x_6hpi

tag: treatment


title: HFD_WT_1

tag: genotype/variation

value: wild type

tag: age

value: FVB


title: FVB WT EC VEGF 1 hour, biological rep1

description: PA317_WT1 V1

tag: strain/background

value: WT

value: Postnatal day 7-12

tag: cell type

value: Lung endothelial cells

value: VEGF

tag: time point

value: 1 hour


title: Regent aggressive isolate infected sample at 6h pi_rep1

description:
Regent sample treated with avrRpv3- at 6h pi
filtered_raw_counts.tsv
sample_45_Regent_aggres_6hpi

value: virulent P. viticola isolate avrRpv3-


title: FVB WT EC Control, biological rep1

description: PA317_WT1 C

value: Untreated

value: Control


title: CTD_MYC_3

tag: cell line

value: ventral prostatic tissues

value: Hi-MYC

value: CTD

tag: strain


title: C57 KO EC VEGF 3 hours, biological rep5

description: PA317_C57 KO5 V3

source_name: C57 mouse at postnatal day 7-12

value: VEGFR2 Y1212F

value: 3 hours


title: 72 hpf, nonskin1, replicate A

source_name: FACS-isolated nonskin cells from whole embryos

value: AB+TU

tag: developmental stage

value: 72 hpf

value: FACS nonskin1

value: pooled male and female

value: Fang Wang (CSUDH)

value: UCLA

tag: genotype


title: Mueller mock control sample at 6h pi_rep2

description:
Mueller treated with mock control at 6h pi
filtered_raw_counts.tsv
sample_38_Müller_m_6hpi

value: Mueller

value: susceptible

value: m

value: mock control (water)

value: leaf


title: CTD_MYC_2

tag: diet

value: FVB


title: Mueller mock control sample at 6h pi_rep1

description:
Mueller treated with mock control at 6h pi
filtered_raw_counts.tsv
sample_37_Müller_m_6hpi


title: C57 KO EC Control, biological rep5

description: PA317_C57 KO5 C

value: Postnatal day 7-12

value: Lung endothelial cells

value: Untreated

value: Control


title: C57 KO EC VEGF 1 hour, biological rep5

description: PA317_C57 KO5 V1

value: VEGFR2 Y1212F

value: VEGF

value: 1 hour


title: CTD_WT_3

value: ventral prostatic tissues

value: wild type

value: CTD


title: 52 hpf, all skin, replicate A

value: AB+TU

value: 52 hpf

value: FACS all skin

tag: Sex

value: pooled male and female

tag: biomaterial provider

value: Fang Wang (CSUDH)

value: UCLA


title: 52 hpf, nonskin1, replicate B

value: FACS nonskin1

tag: birth location


title: Mueller normal isolate infected sample at 6h pi_rep2

description:
Mueller treated with avrRpv3+ at 6h pi
filtered_raw_counts.tsv
sample_36_Müller_x_6hpi

tag: cultivar

value: Mueller

tag: phenotype

value: susceptible

value: x

value: avirulent P. viticola isolate avrRpv3+

value: leaf


title: Mueller normal isolate infected sample at 6h pi_rep1

description:
Mueller treated with avrRpv3+ at 6h pi
filtered_raw_counts.tsv
sample_35_Müller_x_6hpi

tag: inoculation

tag: tissue


title: CTD_MYC_1

tag: genotype/variation

value: Hi-MYC

value: FVB


title: 72 hpf, all skin, replicate B

value: 72 hpf


title: HFD_WT_2

value: ventral prostatic tissues

value: wild type

value: HFD

tag: age


title: C57 KO EC VEGF 3 hours, biological rep4

description: PA317_C57 KO4 V3

tag: strain/background

value: VEGFR2 Y1212F

value: Postnatal day 7-12

value: Lung endothelial cells

tag: treatment

value: VEGF

value: 3 hours


title: 52 hpf, nonskin1, replicate A

value: AB+TU

value: 52 hpf

value: FACS nonskin1

value: pooled male and female

value: Fang Wang (CSUDH)

value: UCLA


title: C57 KO EC VEGF 1 hour, biological rep4

description: PA317_C57 KO4 V1

tag: cell type

tag: time point

value: 1 hour


title: 72 hpf, nonskin1, replicate B

tag: strain


title: CTD_WT_1

tag: cell line

value: CTD

value: FVB


title: 20 SS, all skin, replicate B

tag: developmental stage

value: 20 SS

value: FACS all skin

tag: genotype


title: Mlp124499_4

city: Trois-Rivières

first: KarenCristine

last: GonçalvesdosSantos

address: 3351 boulevard des Forges

department: Chemistry, biochemistry and physics

institute: Université du Québec à Trois-Rivières

data_processing:
Trimming and filtering: Trimmomatic - LEADING:4 TRAILING:4 SLIDINGWINDOW:4:20 MINLEN:20
Alignment: TopHat v2.0.14 and TAIR10 - default options;
Counting: R v.3.2.5, annotation obtained from Ensembl Plants with Genomic Features and overlaps found with GenomicAlignments - summarizeOverlaps for paired-ends in union mode
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: .csv files contain read counts for each gene

source_name: Aerial plant tissue

growth_protocol: Soil-grown; 16hs of light/day; 22ᵒC; harvest 15 days after germination

extract_protocol:
Plant Total RNA Mini Kit (Geneaid) using RB buffer following manufacturer’s protocol, with DNase
NeoPrep Library Prep System (Illumina) with the TruSeq Stranded mRNA Library Prep kit (Illumina) using 100 ng of total RNA

treatment_protocol: Stable transgenic lines

tag: transgenic line

value: Mlp124499-GFP and BAR

tag: ecotype


title: Mlp124499_3


title: Mlp124499_2


title: 52 hpf, all skin, replicate B

growth_protocol: Zebrafish were maintained in 28.5 C and pH 7.5 fish water. Adults were kept in a 14-hour light / 10-hour dark cycle.

tag: Sex

tag: biomaterial provider

tag: birth location


title: C57 KO EC VEGF 3 hours, biological rep3

description: PA317_C57 KO3 V3

value: VEGFR2 Y1212F