title: Wild type (cv Money Maker) biological replicate 3 Breaker stage

description: not applicable

source_name: wilde tipe breaker stage

value: wild type


title: Transgenic line LCY3 (cv Money Maker) biological replicate 1 Breaker stage

status: Public on Jan 01 2020

type: RNA

city: Rome

first: sarah

last: frusciante

address: Via Anguillarese 301

country: Italy

institute: ENEA Italian National Agency for New Technologies, Energy and Sustainable Development

description: not applicable

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Eu-TOM3 (custom exon) was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0001 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 72 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Image acquisition, processing: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters.

data_processing:
Data were processed using RobiNA v2.0 software. Normalization method: rma; P-value correction method: fdr; Multiple testing strategy: global; P-value cut-off value for significant differential expression: 0.05; Genes that showed a log2-fold change smaller than two ignored: yes
probe group file: eutom3gene_v2_ucprobes
meta-probeset file: EUTOM3_funcion_GO.tsv

label: Biotin

molecule: total RNA

organism: Solanum lycopersicum

source_name: transgenic line breaker stage

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). The sense strand cDNA was synthesized with the same kit, then it was fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown in a greenhouse under a long photoperiod (16-h light/24°C and 8-h dark/20°C) and irradiance (150 mmol m22 s21). Fruit were labeled at the Mature Green stage of ripening and collected at Mature Green, Breaker and 10 days later Breaker. Pericarps was frozen in liquid nitrogen and stored at -80°C for subsequent analyses.

extract_protocol: Briefly, total RNA isolation was performed using a Tris-Borate/phenol-chloroformisoamyl alcohol 25:24:1-based extraction followed by Potassium Acetate/Lithium Chloride/Sodium Chloride precipitation steps (Lopez-Gomez and Gomez-Lim, 1992) and DNAse I purification at 37°C for 20’. RNA quality was determined by using a Nanodrop ND-1000 (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer: only RNAs showing A260/A280 and A260/230 ratios between, respectively, 1.8-2.0 and 2.0-2.2 and with a 28S/18S ratio between 1.5 and 2.0 were selected.

tag: genotype/variation

tag: Stage

value: breaker stage

tag: tissue

value: pericarp


title: M9 1

type: SRA

city: Memphis

first: Richard

middle: E

last: Lee

state: Tennessee

address: 262 Danny Thomas Place

department: Chemical Biology and Therapeutics

country: USA

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Ribosomal RNA sequences filtered out using BBDuk {https://jgi.doe.gov/data-and-tools/bbtools/}
Reads aligned to the reference Escherichia coli str. K-12 substr. MG1655 genome (NCBI) using Rockhopper {23716638} to generate the gene counts
DESeq2 analysis package {25516281} in the R statistical computing environment used for differential gene expression analysis
Genome_build: GenBank: U00096.3
Supplementary_files_format_and_content: CSV format containing locus tag and read count

organism: Escherichia coli

source_name: ATCC 2511 broth_DMSO

growth_protocol: For each of three bioreplicates, a single colony of Escherichia coli K12 MG1655 was used to inoculate an overnight culture in either ATCC 2511 broth (M9) or the ATCC 2511 media with a molar equivalent of magnesium chloride used to replace magnesium sulfate and taurine used to as the sole sulfur source (M9T). The next day, overnight cultures were diluted 1:100 into fresh M9 or M9T.  The cultures were allowed to reach a mid-log OD600 and then treated.

extract_protocol:
10 mL RNAprotect Bacteria Reagent was immediately added and mixed with the drugged cultures and pelleted at 5,000XG for 10 minutes.  The supernatant was discarded and the pellets were flash frozen.  For RNA extraction, pellets of E. coli K12 were re-suspended in 100 µL of 1 mg/mL lysozyme and incubated at 37°C for 10 minutes with 5 seconds vortex every 2 minutes. Subsequent steps were carried out using the RNeasy extraction kit (Qiagen) according to protocol. RNA was eluted in 40-50 µL of supplied elution buffer. Residual genomic DNA contamination was depleted using RNA Clean and Concentrator kit (Zymo Research) following the manufacture’s protocol. Samples were eluted in 50 µL of DNase/Rnase-Free water. Quality of RNA samples were measured using an Agilent 2100 Bioanalyzer and RIN values were all > 7.0.
ScriptSeq™ v2 RNA-Seq Library Preparation Kit, standard protocol.

treatment_protocol: 50 μL of either DMSO or 50 μL of 1.56 mg/mL 2-((1H-1,2,3-triazol-4-yl)thio)-N-(2-fluorophenyl)acetamide was added to a 50 mL conical tube.  When E. coli cultures reached mid-log, 5 mL of culture was added to each tube and allowed to incubate with shaking at 37°C and 225 RPM.

tag: strain

tag: media

value: ATCC 2511 broth

tag: treatment

value: 1% DMSO


title: 70.NOD2.CCCP

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted txt files were analyzed further using R and the associated BioConductor limma package. Background correction ( normexp) and normalization between arrays  (quantile) was used,control probe were removed. Within-array replicate features were condensed with their average by avereps.

organism: Homo sapiens

source_name: HeLa NOD2 cells, 4hr, replicate 2

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: HeLa inducible NOD1 or NOD2 cells were grown in DMEM medium supplemented with 10% FBS, 1mM Sodium Pyruvate and 2mM L-Glutamine overnight. To induce NOD1 or NOD2 expression, HeLa NOD1 or NOD2 cells were treated in absence or presence of 0.5 µg/mL or 0.25 µg/mL doxycyclin overnight, respectively.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: After doxycycline treatment, medium was replaced with fresh DMEM full medium. Then HeLa NOD1 or NOD2 cells were treated with various stimuli for 4 hrs.

tag: cell line

value: HeLa

tag: inducible gene

value: CCCP (5 µM)

tag: sample purification

value: ok


title: 72.NOD2.2MC


title: 69p.NOD2.Actin

value: Actinonin (50 µM)

value: phenol


title: Wild type (cv Money Maker) biological replicate 2 Breaker stage

description: not applicable


title: Wild type (cv Money Maker) biological replicate 1 Breaker stage

description: not applicable


title: taur 3

source_name: ATCC 2511 broth_taurine_DMSO

value: ATCC 2511 modified to have taurine as the sole sulfur source


title: gDNA from subject PASRUJ

type: genomic

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum  concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours.  Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode.

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

molecule: genomic DNA

source_name: AML, pre-treatment

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

tag: group

value: tumor

tag: age at diagnosis (days)

tag: gender

value: Male


title: Transgenic line LCY3 (cv Money Maker) biological replicate 3 Mature Green stage

description: not applicable

source_name: transgenic line immature fruit

value: mature green


title: Male Right Anterior Dorsal Head [6M_RA]

city: Bloomington

first: David

middle: M

last: Linz

state: IN

address: Myers Hall 3rd Street

institute: Indiana University

description:
6M_RA
M_RA_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

data_processing:
Trimming: Trimmomatic v0.32 parameters: ‘2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:36’
Alignment: Bowtie2 v2.3.2
Counting: RSEM v1.3.0
DE Analysis: DESeq2
Genome_build: O. taurus NCBI Genome Assembly v2.0 (GCF_000648695.1, Otau_2.0)
Supplementary_files_format_and_content: OnthophagusHeadCounts.tsv.gz: Raw mapped fragment counts matrix for O. taurus transcripts (NCBI genome assembly v2.0 gene models ) in TSV format.

organism: Onthophagus taurus

source_name: Male Right Anterior Dorsal Head epithelium

extract_protocol:
Qiagen RNeasy Plus Micro Kit.
Illumina TruSeq Stranded mRNA Sample Preparation Kit.

value: Dorsal head

tag: head compartment

value: Right Anterior

tag: developmental stage

value: Pre-pupae (larval stage)

tag: Sex


title: Male Right Posterior Dorsal Head [6M_RP]

description:
6M_RP
M_RP_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Male Right Posterior Dorsal Head epithelium

value: Right Posterior


title: Male Medial Posterior Dorsal Head [6M_MP]

description:
6M_MP
M_MP_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Male Medial Posterior Dorsal Head epithelium

value: Medial Posterior


title: 67p.NOD2.Nig

value: Nigericin (5 µM)


title: 68.NOD2.Etop

value: Etoposide (5 µM)


title: Male Medial Anterior Dorsal Head [6M_MA]

description:
6M_MA
M_MA_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Male Medial Anterior Dorsal Head epithelium

value: Medial Anterior


title: Transgenic line LCY3 (cv Money Maker) biological replicate 2 Mature Green stage

description: not applicable

value: pericarp


title: gDNA from subject PASPKE

value: Female


title: 66p.NOD2.Nocad

value: HeLa

value: Nocadazole (10 µM)


title: Male Left Posterior Dorsal Head [6M_LP]

description:
6M_LP
M_LP_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Male Left Posterior Dorsal Head epithelium

value: Left Posterior


title: Male Left Anterior Dorsal Head [6M_LA]

description:
6M_LA
M_LA_rep6
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Male Left Anterior Dorsal Head epithelium

value: Left Anterior


title: gDNA from subject PASRTP

value: tumor


title: SLB-1_DMSO_16h_rep2

city: Musashimurayama-shi

first: Emi

last: Ikebe

state: Tokyo

address: 4-7-1, Gakuen

country: Japan

institute: National Institute of Infectious Diseases

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

label: biotin

extract_protocol: RNeasy Mini Kit

value: DMSO 16h


title: gDNA from subject PASNDA

value: Male


title: 65p.NOD2.CHX

value: Cycloheximide (50 µM)

value: phenol


title: Transgenic line LCY1 (cv Money Maker) biological replicate 3 Mature Green stage

description: not applicable

value: mature green


title: 63p.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: Transgenic line LCY3 (cv Money Maker) biological replicate 1 Mature Green stage

description: not applicable


title: Male Right Posterior Dorsal Head [5M_RP]

description:
5M_RP
M_RP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Right Posterior

value: Pre-pupae (larval stage)


title: Male Right Anterior Dorsal Head [5M_RA]

description:
5M_RA
M_RA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior


title: gDNA from subject PASMPC


title: Day1_KO9

city: Chuncheon-si

first: Yoon Mee

last: Yang

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using version 2.2.5 with parameters--phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase Million(FPKM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

organism: Mus musculus

source_name: Hepatic stellate cell

growth_protocol: Primary hepatic stellate cells were isolated from male aSMA-HAS2 Tg and HSC-specific Has2 knockout mice. The isolated primary hepatic stellate cells were incubated in DMEM medium containing 10% FBS, and supplemented with Antibiotic-Antimycotic for 4 hr. After cell attachment, the culture media was refreshed and incubated for another 14 hr.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and purified using RNA isolation kit (Macherey-Nagel). Beijing Genomics Institute (BG) (Beijing, China) performed the RNA sequencing.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: 24-week-old male ASMA-human HAS2 transgenic mice and hepatic stellate cell-specific Has2 knockout mice generated by the Lrat-Cre/loxP system were used. All procedures were approvd by the Institutional Animal Care and Use Committee at Cedars-Sinai Medical Center. Hepatic stellate cells were isolated from the mice in a 2-step process: collagenase-pronase perfusion of mouse livers followed by Nycodenz 2-layer discontinuous density gradient centrifugation. We further depleted contaminated liver macrophages by magnetic antibody cell sorting (Miltenyi Biotec) using Cd11b-conjugated microbeads (Miltenyi Biotec).

tag: cell type

value: Primary hepatic stellate cell

tag: genotype

value: HSC-specific Has2 KO


title: 64p.NOD2.Vinbl

value: HeLa

value: Vinblastine (10 µM)


title: Male Medial Posterior Dorsal Head [5M_MP]

description:
5M_MP
M_MP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Posterior


title: gDNA from subject PASLYX

value: Female


title: Wild type (cv Money Maker)  biological replicate 2 Mature Green stage

description: not applicable

source_name: wild type immature fruit

tag: genotype/variation

value: wild type

value: pericarp


title: 62p.NOD2.Jasp

value: Jasplanokinolid (0.2 µM)


title: Transgenic line LCY1 (cv Money Maker) biological replicate 2 Mature Green stage

description: not applicable

tag: Stage


title: Transgenic line LCY1 (cv Money Maker)  biological replicate 1 Mature Green stage

description: not applicable

tag: tissue


title: 61.NOD2.Control

value: Ctr (DMSO)

value: ok


title: gDNA from subject PASLTF

value: tumor

value: Male


title: Wild type (cv Money Maker)  biological replicate 3 Mature Green stage

description: not applicable

value: mature green


title: Male Left Posterior Dorsal Head [5M_LP]

description:
5M_LP
M_LP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Left Posterior


title: Male Medial Anterior Dorsal Head [5M_MA]

description:
5M_MA
M_MA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Anterior

value: Pre-pupae (larval stage)


title: 59.NOD1.5F

source_name: HeLa NOD1 cells, 4hr, replicate 2


title: Wild type (cv Money Maker) biological replicate 1 Mature Green stage

description: not applicable


title: Transgenic line LCY3 (cv Money Maker) biological replicate 1 Breaker+10 stage

description: not applicable

source_name: transgenic line mature fruit

value: breaker+10 stage


title: 58.NOD1.Tg

value: HeLa

value: Thapsigargin (5 µM)


title: Male Left Anterior Dorsal Head [5M_LA]

description:
5M_LA
M_LA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior


title: Day1_KO8

tag: strain

value: Primary hepatic stellate cell

value: HSC-specific Has2 KO


title: 60.NOD1.6G


title: Male Right Posterior Dorsal Head [4M_RP]

description:
4M_RP
M_RP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Posterior


title: WT non-involved 2

city: Miami

first: Juan

middle: F

last: Burgueno

address: 1011 NW 15th St, Gautier Bldg. suite 534B

institute: University of Miami

hyb_protocol: The slides were hybridized for 16-18 hours under constant rotation in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: Slides were scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Non-flagged spots were selected and probe intensities were transformed into Log2 data. Transformed probe intensities were subsequently normalized and selected when above negative controls (TPT99) in at least two samples. 15308 probes with positive signal were analyzed by ANOVA or t-test. Microarray and analysis were performed by Ocean Ridge Biosciences

label: Streptavidin-Alexa 647

source_name: Non-involved colon tissue

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared from total RNA by the method of Van Gelder et al., US Patent 7049102. Briefly, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence was used to prime reverse transcription of RNA catalyzed by Superscript II (Invitrogen, Carlsbad, CA). Double-stranded cDNA was prepared from the 1st strand product by the method of Gubler & Hoffman (1983), and purified on a PCR purification column (Qiagen, Valencia, CA). The double-stranded cDNA was then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion) and including biotin-16-UTP (Ambion) in the reaction mixture

growth_protocol: Mice bred in a C57Bl6 background

extract_protocol: tissue was stored in RNA later and subsequently homogenized in TRIzol. Phenol-chloroform isolation protocol was used to obtain total RNA

treatment_protocol: Mice were injected with 7.4 mg/kg AOM on day 0. On day 7, mice underwent a cycle of 1.5-3% DSS for 7 days. Two weeks after, mice underwent a second cycle of 1.5-3% DSS for 5 days

value: colon

value: WT littermate

value: female

tag: age

value: 10 weeks at beginning of exp

tag: dss


title: gDNA from subject PASJXN

value: tumor

value: Female


title: 57.NOD1.Tm

tag: cell line

tag: treatment

value: Tunicamycin (5 µg/mL)

value: ok


title: WT non-involved 1


title: gDNA from subject PASLTS


title: U87_ABCB7_3

city: Seoul

first: Jung Yun

last: Kim

address: 145 Anam-ro, Seungbuk-gu

institute: Korea University

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-delimited text file which includes contents; 1) NCBI gene accession ID, 2) Gene length, 3) Means of FPKM values for each experimental sets, 4) Log2 ratio of gene expression, 5) Probability value (PA), 6) Gene symbol, 7) Gene description, 8) KEGG orthology, 9) GO component, 10) GO function, 11) GO process, 12) Blast nr

source_name: U87MG cell line

growth_protocol: U87MG cells were grown in DMEM medium supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50 μg/ml).

extract_protocol:
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using CG RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) coporation.

value: Glioblastoma cells

value: Brain

value: Male


title: gDNA from subject PASHWN


title: U87_ABCB7_2


title: villin-TLR4 non-involved 2

value: male


title: Male Medial Posterior Dorsal Head [4M_MP]

description:
4M_MP
M_MP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Medial Posterior

value: Pre-pupae (larval stage)


title: 56.NOD1.AnisoM

value: HeLa

tag: inducible gene

value: Anisomycin (1 µM)

tag: sample purification


title: villin-TLR4 non-involved 1

value: colon


title: U87_ABCB7_1


title: Male Medial Anterior Dorsal Head [4M_MA]

description:
4M_MA
M_MA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Anterior


title: Male Right Anterior Dorsal Head [4M_RA]

description:
4M_RA
M_RA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior


title: U87_Con_3


title: WT non-involved 3

value: WT littermate

value: female

value: 10 weeks at beginning of exp


title: 55.NOD1.BFA

value: BrefeldinA (0.2 µg/mL)


title: 54.NOD1.Lov

value: Lovastatin (30 µM)

value: ok


title: Male Left Posterior Dorsal Head [4M_LP]

description:
4M_LP
M_LP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: U87_Con_2

value: Glioblastoma cells

value: Brain

value: Male


title: Male Left Anterior Dorsal Head [4M_LA]

description:
4M_LA
M_LA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Left Anterior


title: 53.NOD1.LB42708

value: HeLa


title: 52.NOD1.2MC


title: Male Right Posterior Dorsal Head [3M_RP]

description:
3M_RP
M_RP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Posterior

value: Pre-pupae (larval stage)


title: U87_Con_1


title: Male Right Anterior Dorsal Head [3M_RA]

description:
3M_RA
M_RA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: PfRrp6-DD-4C_R_rep2_RNA-seq

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

country: China

institute: Tongji University

description:
PfRrp6-DD clone line PfRrp6-DD-4C
RRP6-DD_rep3_Raw_Counts_sense_and_antisense_RNA.xlsx

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0)  with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1)  with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

organism: Plasmodium falciparum

growth_protocol: Parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin. The vector line was selected and cultured with 2.5nM WR99210. The 5mM GlcN was added in the inducible knock down culture.

extract_protocol:
Highly synchronous parasites were harvested at the ring stage (10 h after invasion), Total RNA was isolated using TRIzol (Life) according to the manufacturer’s manual and further purified using the Direct-zol RNA Kit (ZYMO RESEARCH) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
The RNA isolation, mRNA enrichment and library construction were performed as described using 15 cycles of library amplification. The mRNA was enriched by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).

treatment_protocol: Parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments ((Lambros and Vanderberg, 1979)

tag: development stage

value: Ring

value: Pf 3D7

tag: host

value: Homo sapiens


title: gDNA from subject PASDIR

tag: group

value: tumor

tag: age at diagnosis (days)

tag: gender


title: Male Medial Posterior Dorsal Head [3M_MP]

description:
3M_MP
M_MP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

tag: head compartment

value: Medial Posterior

tag: developmental stage

tag: Sex


title: Male Medial Anterior Dorsal Head [3M_MA]

description:
3M_MA
M_MA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Anterior


title: RUF6-OE_S_rep2_RNA-seq

description:
RUF6 member overexpression in Pf 3D7 lilne
RUF6-OE_rep1_rep2_Raw_Counts_sense_and_antisense_RNA.xlsx

value: Schizont

tag: genotype


title: gDNA from subject PASDET


title: PfMaf1-OE-10_S_rep2_RNA-seq

description:
PfMaf1-OE line selected by 10 nM durg (WR)
MAF1-OE_rep1_rep2_Raw_Counts_sense_and_antisense_RNA.xlsx


title: PfMaf1-OE-10_T_rep2_RNA-seq

value: Trophozoite


title: Male Left Anterior Dorsal Head [3M_LA]

description:
3M_LA
M_LA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

tag: tissue


title: 51.NOD1.2BP

value: ok


title: Male Right Posterior Dorsal Head [2M_RP]

description:
2M_RP
M_RP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: 49.NOD1.Actin

value: Actinonin (50 µM)


title: PfMaf1-OE-10_R_rep2_RNA-seq

tag: strain


title: 48.NOD1.Etop

value: Etoposide (5 µM)


title: 50.NOD1.CCCP

value: CCCP (5 µM)


title: gDNA from subject PASEGC

value: Female


title: 45.NOD1.CHX

value: Cycloheximide (50 µM)


title: 47.NOD1.Nig

value: HeLa

value: Nigericin (5 µM)


title: 46.NOD1.Nocad

value: Nocadazole (10 µM)


title: 44.NOD1.Vinbl

value: Vinblastine (10 µM)


title: PfMaf1-OE-2.5_S_rep2_RNA-seq

description:
PfMaf1-OE line selected by 2.5 nM durg (WR)
MAF1-OE_rep1_rep2_Raw_Counts_sense_and_antisense_RNA.xlsx

value: Pf 3D7


title: gDNA from subject PASAUN

value: Male


title: 43.NOD1.CytoD

value: Cytoclasin D (5 µM)


title: Male Right Anterior Dorsal Head [2M_RA]

description:
2M_RA
M_RA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Right Anterior

value: Pre-pupae (larval stage)


title: PfRrp6-DD-1B_R_rep2_RNA-seq

description:
PfRrp6-DD clone line PfRrp6-DD-1B
RRP6-DD_rep3_Raw_Counts_sense_and_antisense_RNA.xlsx

value: Ring

value: Homo sapiens


title: PfMaf1-OE-2.5_T_rep2_RNA-seq

value: Trophozoite


title: Male Medial Posterior Dorsal Head [2M_MP]

description:
2M_MP
M_MP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Posterior


title: Male Left Posterior Dorsal Head [3M_LP]

description:
3M_LP
M_LP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: 42.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)

value: ok


title: Male Medial Anterior Dorsal Head [2M_MA]

description:
2M_MA
M_MA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Anterior


title: gDNA from subject PARZPD

value: tumor

value: Female


title: PfMaf1-OE-2.5_R_rep2_RNA-seq


title: PfRrp6-DD-1C-GlcN+_S_rep2_RNA-seq

description:
PfRrp6-DD clone line PfRrp6-DD-1C cultured with 5 nM GlcN
RRP6-DD-GlcN+_rep1_rep2_Raw_Counts_sense_and_antisense_RNA.xlsx

value: Schizont


title: Male Left Posterior Dorsal Head [2M_LP]

description:
2M_LP
M_LP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: gDNA from subject PARZGM


title: PfRrp6-DD-1C-GlcN+_T_rep2_RNA-seq

value: Pf 3D7


title: Male Left Anterior Dorsal Head [2M_LA]

description:
2M_LA
M_LA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior

value: Male


title: gDNA from subject PARZHI


title: gDNA from subject PASAMY


title: PfRrp6-DD-1C-GlcN+_R_rep2_RNA-seq


title: Male Right Posterior Dorsal Head [1M_RP]

description:
1M_RP
M_RP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Right Posterior


title: gDNA from subject PARVZU


title: gDNA from subject PARVUC


title: Male Right Anterior Dorsal Head [1M_RA]

description:
1M_RA
M_RA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior

value: Pre-pupae (larval stage)


title: GFP_T_rep2_RIP-seq

description: transgenic parasite line of GFP-HAx3-Ty1x3,no-crosslink

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0)  with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1)  with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

growth_protocol: Parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin. The GFP parasite line was cultured in presence of 2.5nM WR99210 (WR).

extract_protocol:
An equivalent of 5 x 109 PfRrp6, PfRrp4 and GFP parasites were grown to 15–20 h ring stages in RPMI complete medium. Free parasites were collected by saponin lysis. The resulting parasite pellet was lysed under non-denaturing conditions (50mM Tris-Cl pH7.4, 150mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100/NP-40, Proteinase inhibitor, RNase inhibitor) for 2h at 4℃ with rotator, then the supernatant was collected by centrifugation at 13,000rpm for 15min at 4℃, and subjected to immunoprecipitation analysis with mouse anti-Ty1 antibodies for 3h at 4 ℃, then incubated with the protein G magnetic beads (Thermo) overnight at 4 ℃. After washing the beads twice with IPP500 (500 mM NaCl, 10 mM Tris-Cl, pH 8.0, 0.05% NP-40, Proteinase inhibitor, RNase inhibitor) and once with 1 x PBS, bounded RNA was eluted by TRIzol reagent for 10min with rotator at 4℃, then RNA was extracted by phenol-chloroform method and treated with DNaseI for 10min at room temperature. IPed RNA was directly used to prepare strand-specific RNA-seq libraries(see below), without poly(A) enrichment. A minimum of two biological replicates was sequenced for each experimental and control immunoprecipitation.
The IPed RNA was fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).

tag: rip antibody

value: mouse anti-Ty1,Sigma SAB4800032-50 ug

value: wild type

value: Homo sapiens


title: Male Medial Posterior Dorsal Head [1M_MP]

description:
1M_MP
M_MP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Posterior


title: Male Medial Anterior Dorsal Head [1M_MA]

description:
1M_MA
M_MA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: Male Left Posterior Dorsal Head [1M_LP]

description:
1M_LP
M_LP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: Male Left Anterior Dorsal Head [1M_LA]

description:
1M_LA
M_LA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: gDNA from subject PARSXZ


title: Female Right Posterior Dorsal Head [5F_RP]

description:
5F_RP
F_RP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Right Posterior Dorsal Head epithelium


title: gDNA from subject PASLDL


title: Female Right Anterior Dorsal Head [5F_RA]

description:
5F_RA
F_RA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Right Anterior Dorsal Head epithelium


title: RUF6-OE_HM-H3K9Ac_R_rep2_ChIP-seq

library_source: genomic

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

growth_protocol: Parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin.

extract_protocol:
Ring-stage (10 hr post invasion ±5 hr) synchronized 3D7-G7 and PfRrp6-DD-1C lines were used in ChIP assay. Parasites culture (1x109 rings) was harvested and cross-linked immediately with 1% paraformaldehyde with rotation for 10 min at 37℃, and quenched with 0.125 M glycine for 5 min on ice. The fixed culture was washed twice with cold 1xPBS, and the parasites were released from iRBC with 0.15% saponin for 15min on ice. After washed with cold 1xPBS, nuclei were isolated by incubation with 2 ml cold Lysis Buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1 mM EDTA pH8.0, 0.1mM EGTA pH8.0, 1mM DTT, 0.25% NP40, 1x protease inhibitors cocktail) for 30 min on ice, and followed by dounce homogenization for 200 strokes. After centrifuge at 10,000 rpm for 10 min at 4 ℃, the nuclei was resuspended in 150μl SDS Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH8.0) for sonication. Chromatin was sheared into 200-500 bp fragments with Bioruptor (BioruptorTM UCD-200) of highest power for 4x4 min at 30 sec intervals. The resulting chromatin was diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 150 mM NaCl, 1x protease inhibitors cocktail). Pre-clear the chromatin solution with 50 μl/ml of salmon sperm DNA/protein A/G agarose slurry for 2h at 4℃ with agitation. After centrifugation, per 250μl chromatin supernatant was incubated with 3μg of Rabbit polyclonal H3K9me3 (abcam, ab8898), 3μg of Rabbit polyclonal H3K9Ac (Millipore, 07-352) and  3μg of Rabbit polyclonal HP1 for each IP overnight at 4℃ and rabbit IgG (Sigma) as control. To collect immune complexes, the sample was incubated with 50μl of Salmon sperm DNA/protein A/G slurry for 2h at 4℃ with agitation. After extensive washes, immunoprecipitated chromatin was eluted with ChIP Elution Buffer (1% SDS, 0.1 M NaHCO3), and reverse crosslinked at 65℃ for 16 h in the presence of 200 mM NaCl, then added RNase A at 37℃ for 30min and incubated with the proteinase K at 45℃ for 2h. DNA was purified by Phenol/chloroform/isoamylic alcohol extraction for ChIP-seq.
To prepare sequencing libraries, 10 ng of input DNA, 3-5ng IPed DNA were end repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific). Libraries were amplified using an optimized KAPA protocol using KAPA HiFi HotStart ready mix (KAPA Biosystems) and the following PCR program: 98°C for 3 min followed by 14 cycles of 98°C for 20 sec, 65°C for 30 s; 68°C for 30s; finally extended 68°C for 5min. Amplified libraries were size-selected for 300-600 bp using 2% agarose gels. ChIP-seq libraries were sequenced on the HiSeq X Ten machine.

value: Ring

tag: chip antibody

value: H3K9ac, Millipore, 07-352


title: PfRrp6-DD-1C_HP1_R_rep2_ChIP-seq

description: antibody was provided by Institut Pasteur,Paris

value: HP1 antibody, rabbit


title: PfRrp6-DD-1C_HM-H3K9Ac_R_rep2_ChIP-seq


title: RUF6-OE_HP1_R_rep2_ChIP-seq


title: PfRrp6-DD-1C_HM-H3K9me3_R_rep2_ChIP-seq

value: H3K9me3, abcam, ab8898


title: WT_3D7-G7_HM-H3K9me3_R_rep2_ChIP-seq


title: Female Medial Posterior Dorsal Head [5F_MP]

description:
5F_MP
F_MP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Medial Posterior Dorsal Head epithelium

value: Female


title: gDNA from subject PARJYP

source_name: AML, pre-treatment

value: tumor


title: WT_3D7-G7_HM-H3K9Ac_R_rep2_ChIP-seq

value: Pf 3D7


title: gDNA from subject PARKGB

value: Male


title: RUF6-OE_HM-H3K9me3_R_rep2_ChIP-seq


title: Female Left Posterior Dorsal Head [5F_LP]

description:
5F_LP
F_LP_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Left Posterior Dorsal Head epithelium

value: Dorsal head


title: WT_3D7-G7_R_rep2_HiC-seq

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then the clean reads were processed using HiC-Pro (v2.11.1) as described. In brief, each end of read pairs was mapped to Plasmodium falciparum 3D7 genome (Pf 3D7 v32) using bowtie2 with default parameters in HiC-Pro setting files.
The alignment results were save in a bam format file, respectively. On the basis of the alignment results, the reads were re-paired to remove singleton, multi-hits, low-MAPQ and unmapped reads. The pairable reads were assigned to DpnII restriction fragments for filtering dangling-end, self-circle ligation and PCR duplicates.
The raw contact matrix was generated for each sample of each replicate at a resolution of 2500 bp and 5000 bp, respectively.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The matrix of interaction frequency was applied to plot heatmap using JuiceBox (v1.11.08) .In brief, the script ‘hicpro2juicebox’ in HiC-Pro was used to transfer ‘allValidPairs’ files into two files ‘resfrag.juicebox’ and ‘pre_juicebox_sorted’. These files were input to juicer_tools (v1.9.9) transferred to ‘hic’ files that were further visualized by JuiceBox.

extract_protocol:
Ring-stage (10 hr post invasion ±5 hr) synchronized 3D7-G7 lines was used in ChIRP assay. Parasites culture (1x109 rings) was harvested and cross-linked immediately with 1% paraformaldehyde with rotation for 10 min at 37℃, and quenched with 0.125 M glycine for 5 min on ice. The fixed culture was washed twice with cold 1xPBS, crosslinked parasite pellets were resuspended in 1 ml of ice-cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, protease inhibitor cocktail). Parasite membranes were disrupted by passing the lysate through 30G needle 15 times using a syringe. Samples were spun at 4000 g for 5 min at 4 °C. Pellets were resuspended in 36μl of ice cold 10x NEBuffer 3.1 and 324μl pure water, samples were mixed with 38μl of 1% SDS to a final concentration of 0.1% and incubated at 65°C for 10 minutes. Samples were mixed with 43μl of 10% Triton X-100 to a final concentration 1%, then added 9.3 µl of 10x NEBuffer 3.1. 100U (2 µl of 50 units/µl) DpnII was added to digest the DNA overnight at 37°C on a rocking platform in a total volume of 434.3µl .  Day 2. The sample quality was assessed by running on 0.75% agarose gel, the 10 µl digested DNA should run as a smear between 200-300bp. The sample was incubated at 65˚C for 20 mins, then put it on ice until cooled to room temperature. 60 µl Biotin Fill-in MaseterMix (6 µl 10x NEBuffer 3.1, 2 µl 5 mM dCTP, 2 µl 5 mM dGTP, 2 µl 5 mM dTTP, 25 µl 0.4 mM biotin-14-dATP, 10 µl 5 U/µl DNA polymerase I Klenow, 13µl milliQ) and 50.7 µl 1x NEBuffer 3.1 were added to each tube. Samples were incubated at 37°C for 3h in Rocker and placed on ice immediately after incubation. Tubes were centrifuged for 5 min at 2500g at 4°C and the supernatant was discarded, then the samples were mixed with 500 µl ligation mix (50 µl 10x ligation buffer NEB, 50 µl 10% Triton X-100, 2.5 µl 20 mg/ml BSA, 2µl T4 DNA ligase NEB, 395.5 µl water) and incubated at 16°C for overnight.  Day 3. Each sample was incubated at 65°C for at least 2h by adding 25µl 20 mg/ml proteinase K, another 25µl 20 mg/ml proteinase K was added to each tube and samples were incubated at 65°C overnight.  Day 4. DNA was extracted with the an equal volume of phenol : chloroform : isoamyl alcohol (25:24:1), The aqueous phase was mixed with sodium chloride and glycogen to a final concentration of 200 mM and 25 µg/ml, respectively. DNA was precipitated by adding equal volume Isopropanol and incubated at -80°C for 2h. Precipitated DNA was pelleted by centrifugation at 16,000g for 15min at 4°C. Pellets was washed twice with cold 75% ethanol and resuspended in 100 µl TLE buffer (10 mM Tris-HCl, 0.1mM EDTA, dH2O pH 8.0). DNA was incubated for 30 min at 37°C by adding 1 µl RNAse A (1mg/ml). After ligation check on 0.75% agarose gel, 5 μg of Hi-C DNA sample was added to 5 μl 10x NEBuffer 2.1, 0.125 μl 10 mM dATP, 0.125 μl 10 mM dGTP and 15 Units T4 DNA polymerase (NEB) in a total volume of 50 μl  and incubated at 20°C for 4 h. Reaction was stopped at 75°C for 20 min. DNA was subsequently purified with TIAGEN Purification Kit (5 μg/column). DNA pellets were resuspended and pooled in a total of 200 μl water and divided into 2 tubes for sonication. The DNA was sheared to a size of 300-500 bp and run 1 μl with glycerol on 2% agarose gel.
The Hi-C sample was purified with the AMpure XP mixture (Beckman Coulter Fullerton, CA) and eluted with 40 μl TLE buffer. The DNA ends were repaired by adding 6 μl 10x ligation buffer (NEB), 6 μl 2.5 mM dNTP mix, 6 μl ATP, 2 μl Enzyme mix (NEB) and incubated at 20°C for 45min, 75°C for 20min. The biotin tagged Hi-C DNA was bound to Dynabeads MyOne Streptavin C1 Beads (Invitrogen) as follows. 10 μl of resuspended Streptavidin beads were washed twice with 400 μl Tween Wash Buffer (TWB) (5 mM Tris-HCl pH8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween) by incubating for 3 minutes at RT with rotation. After this and for all subsequent incubations or washes of Streptavidin beads, the beads were reclaimed by holding against a magnetic particle concentrator (Invitrogen) for 1 minute and the supernatant was removed. These reclaimed beads were then resuspended in 400 μl 2x Binding Buffer (BB) (10 mM Tris- HCl pH8.0, 1 mM EDTA, 2 M NaCl) and combined with 390 μl Hi-C DNA(330 μl TLE). The mixture was incubated at RT for 15 minutes with rotation. The supernatant was removed and the DNA bound Streptavidin beads were resuspended in 400 μl 1x BB and transferred to a new tube. The beads were washed with 100 μl 1x TLE, transferred to a new tube before a final resuspension in 40 μl 1x TLE. An 'A' was added to the 3' ends of the end repaired DNA by addition of 5 μl 10x NEBuffer2.1, 2 μl 5 mM dATP and 3 μl Klenow (5 U/μl exo-) (NEB) . The reaction was incubated at 37°C for 30 minutes followed by 65°C for 20 minutes to inactivate Klenow (exo-). The reactions were cooled on ice and the beads were washed with 400 μl 1x ligation buffer and resuspended in 38.9 μl 1x ligation buffer. 6 μl of Illumina Paired End adapters (Illumina, San Diego, CA) were ligated to the Hi-C DNA for 2 hours at 22°C in the presence of 1x ligation buffer and 5 μl Quick ligase (Ambion, Austin, TX). The ligated Hi-C DNA was isolated by holding against the magnet and washed with 400 μl of 1x TWB to remove non-ligated Paired End adapters. The beads were resuspended in a further 400 μl 1x TWB and the mixture was transferred to a new tube and the Streptavidin beads were recovered. This wash step was repeated with 200 μl 1x BB and finally 20 μl 1x NEBuffer 2.1. The beads were resuspended in 5 μl 1x NEBuffer 2.1. Next, test PCR reactions were performed to determine the optimal PCR cycles needed to generate enough library for sequencing. 5 μl Streptavidin bead bound Hi-C library was mixed with 0.5 μl primers (12.5 nM), 15 μl KAPA HiFi 2x mix buffer and 9 μl dH2O in a total volume of 30 μl. The temperature profile was 120 s at 95°C followed by 10 cycles of 20 s at 95°C, 30 s at 62°C, 150 s at 65°C and a final 5min extension at 65°C. 5μl PCR reactions were run on a 2% gel after 10 cycles and the optimal cycle number was determined. The remain sample was PCR with the chosen cycles. The PCR product was purified by mixing with 1.5x volume Ampure beads (Beckman Coulter, Fullerton, CA). The mixture was held against a magnet to separate the PCR product bound to the Ampure beads and the supernatant was discarded. The Hi-C library bound Ampure beads were washed twice with 1 ml 70% ethanol while the tube remained against the magnet. After air-drying the beads, the DNA was eluted by resuspending the beads in 30 μl of TLE buffer. The tube was held against a magnet and the supernatant containing the purified PCR products was transferred to a new tube. The amount of DNA in the Hi-C library was quantified on the 2% agarose gel. 10 ng Hi-C product was digested with ClaI to estimate the portion of molecules with valid biotinylated junctions and incubated at 37°C for 30 min. The entire volume of the reaction was run on a 2% agarose gel. Finally, the Hi-C library was sequenced with Illumina paired end sequencing.

tag: enzyme

value: DpnII


title: Female Left Anterior Dorsal Head [5F_LA]

description:
5F_LA
F_LA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Left Anterior Dorsal Head epithelium

value: Left Anterior


title: gDNA from subject PARJGD


title: WT_3D7-G7_R_rep1_HiC-seq


title: gDNA from subject PARJET


title: 39.NOD2.5F

source_name: HeLa NOD2 cells, 4hr, replicate 1

tag: cell line

value: HeLa

tag: treatment

value: ok


title: gDNA from subject PARHVK


title: SLB-1_DMSO_16h_rep1

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

value: DMSO 16h


title: 41.NOD1.Control

tag: inducible gene

value: Ctr (DMSO)

tag: sample purification


title: Female Medial Anterior Dorsal Head [5F_MA]

description:
5F_MA
F_MA_rep5
PolyA RNA
OnthophagusHeadCounts.tsv.gz

source_name: Female Medial Anterior Dorsal Head epithelium

value: Medial Anterior

value: Pre-pupae (larval stage)


title: 33.NOD2.LB42708


title: 31.NOD2.2BP


title: 38.NOD2.Tg

value: Thapsigargin (5 µM)


title: gDNA from subject PARHJV


title: CP-PfRrp6-DD-1C_R_rep2_ChIRP-seq

description: Complementary probes were designed on the sense strand of RUF6 ncRNAs

data_processing:
Library strategy: ChIRP-seq
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9)  was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
ChIRP peaks were predicted by MACS2 (v2.1.1)  with Q-value < 0.01 and the parameter: -c.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

extract_protocol:
Ring-stage (15 hr post invasion ±5 hr) synchronized 3D7-G7 and the PfRrp6-DD-1C line were used in ChIRP assay. Parasites culture (1x109 rings) were cross-linked as the ChIP arrays. After three washes with cold 1 x PBS, the parasite pellets were lysed with the swelling buffer (0.1M Tris pH 7.0, 10mM KOAc, 15mM MgOAc, 1% NP-40, 1mM DTT, protease inhibitor, and RNase inhibitor) at 4℃ for 10min with rotator. After centrifuge at 10,000 rpm for 10 min at 4 ℃, the parasites were resuspended in 150μl SDS Lysis Buffer ( 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0 ) for sonication. Chromatin was sheared into 200-500 bp fragments with Bioruptor (BioruptorTM UCD-200) of highest power for 4x4 min at 30 sec intervals. Chromatin is diluted in 2 times volume of hybridization buffer (500mM NaCl, 1%SDS, 100mM Tris 7.0, 10mM EDTA, 15% Formamide, add DTT, PMSF, P.I, and RNase inhibitor fresh). 100 pmol probes were added to each reaction, which was mixed by end to-end rotation at 37℃ for 4 hours. Streptavidin-magnetic T1 beads were washed three times in lysis buffer, blocked with 500ng/μl yeast total RNA and 1mg/ml BSA for 1 hour at 37℃, and washed three times again in lysis buffer before resuspended in its original volume. 100μl washed/blocked T1 beads were added per 100 pmol of probes, and the whole reaction was mixed for another 45min at 37℃. Beads : biotin -probes : RNA : chromatin products were captured by magnets (Invitrogen) and washed five times with 40x beads volume of wash buffer (2 x SSC, 0.5% SDS, add DTT and PMSF fresh). After last wash buffer was removed carefully with P-10 pipette, beads were resuspended in 3x original volume DNA elution buffer (50mM NaHCO3, 1%SDS, 200mM NaCl), and DNA was eluted with 100μg/ml RNase A and 0.1U/μl RNase H. RNase elution was carried out twice at 37 ℃ with end-to-end rotation. Then chromatin was reverse-crosslinked with  0.2U/μl protease K at 65℃ overnight. DNA was then extracted with equal volume of phenol : chloroform : isoamyl. Eluted DNA was subject to high-throughput sequencing.
To prepare sequencing libraries, 10 ng of input DNA, 3-5ng IPed DNA were end repaired, extended with 3′ A-overhangs and ligated to barcoded NextFlex adapters (Bio Scientific). Libraries were amplified using an optimized KAPA protocol using KAPA HiFi HotStart ready mix (KAPA Biosystems) and the following PCR program: 98°C for 3 min followed by 14 cycles of 98°C for 20 sec, 65°C for 30 s; 68°C for 30s; finally extended 68°C for 5min. Amplified libraries were size-selected for 300-600 bp using 2% agarose gels. ChIP-seq libraries were sequenced on the HiSeq X Ten machine.

tag: development stage

value: Ring

tag: host

value: Homo sapiens


title: gDNA from subject PARHBA

tag: group

tag: age at diagnosis (days)


title: CP-PfRrp6-DD-1C_R_rep1_ChIRP-seq


title: Female Medial Posterior Dorsal Head [4F_MP]

description:
4F_MP
F_MP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

tag: head compartment

value: Medial Posterior


title: Female Right Posterior Dorsal Head [4F_RP]

description:
4F_RP
F_RP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Posterior

tag: developmental stage

value: Female


title: gDNA from subject PARGTL

value: tumor

tag: gender


title: 29.NOD2.Actin

value: Actinonin (50 µM)


title: CP-PfRrp6-DD-1C-Input_R_rep1_ChIRP-seq

value: Pf 3D7

tag: genotype


title: WT_3D7-G7_HP1-input_R_rep2_ChIP-seq

value: wild type


title: Female Medial Anterior Dorsal Head [4F_MA]

description:
4F_MA
F_MA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

tag: tissue

value: Dorsal head

tag: Sex


title: 37.NOD2.Tm

value: HeLa

value: Tunicamycin (5 µg/mL)


title: 27.NOD2.Nig

value: Nigericin (5 µM)

value: ok


title: 35.NOD2.BFA

value: BrefeldinA (0.2 µg/mL)


title: 36.NOD2.AnisoM

value: Anisomycin (1 µM)


title: Female Right Anterior Dorsal Head [4F_RA]

description:
4F_RA
F_RA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior

value: Pre-pupae (larval stage)


title: gDNA from subject PARFZP

value: Male


title: Female Left Posterior Dorsal Head [4F_LP]

description:
4F_LP
F_LP_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: Female Left Anterior Dorsal Head [4F_LA]

description:
4F_LA
F_LA_rep4
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior


title: gDNA from subject PARDZW

value: Female


title: Female Right Posterior Dorsal Head [3F_RP]

description:
3F_RP
F_RP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Posterior


title: gDNA from subject PARDDA

value: tumor


title: WT_3D7-G7_HP1_R_rep2_ChIP-seq

value: Ring

tag: strain

value: Pf 3D7

value: HP1 antibody, rabbit

value: Homo sapiens


title: RUF6-OE_HM-HP1-input_R_rep1_ChIP-seq

tag: chip antibody


title: RUF6-OE_HP1_R_rep1_ChIP-seq


title: 34.NOD2.Lov

value: HeLa

value: Lovastatin (30 µM)


title: Female Right Anterior Dorsal Head [3F_RA]

description:
3F_RA
F_RA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head


title: 25.NOD2.CHX

value: Cycloheximide (50 µM)

value: ok


title: RUF6-OE_HM-H3K9Ac_R_rep1_ChIP-seq

value: H3K9ac, Millipore, 07-352


title: gDNA from subject PARCIN


title: Female Medial Posterior Dorsal Head [3F_MP]

description:
3F_MP
F_MP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Posterior

value: Pre-pupae (larval stage)


title: PfRrp6-DD-1C_HM-HP1-input_R_rep1_ChIP-seq


title: Female Medial Anterior Dorsal Head [3F_MA]

description:
3F_MA
F_MA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Medial Anterior


title: Female Left Posterior Dorsal Head [3F_LP]

description:
3F_LP
F_LP_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: 23.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: PfRrp6-DD-1C_HP1_R_rep1_ChIP-seq

description: antibody was provided by Institut Pasteur,Paris


title: gDNA from subject PARBVE

value: Male


title: Female Left Anterior Dorsal Head [3F_LA]

description:
3F_LA
F_LA_rep3
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior

value: Female


title: PfRrp6-DD-1C_HM-H3K9Ac_R_rep1_ChIP-seq

value: Ring

value: Pf 3D7


title: 21.NOD2.Control

value: Ctr (DMSO)


title: 17.NOD1.Tm

source_name: HeLa NOD1 cells, 4hr, replicate 1

value: HeLa

value: Tunicamycin (5 µg/mL)


title: Female Right Posterior Dorsal Head [2F_RP]

description:
2F_RP
F_RP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Right Posterior


title: 15.NOD1.BFA

value: BrefeldinA (0.2 µg/mL)

value: ok


title: gDNA from subject PARCEV

value: tumor


title: 18.NOD1.Tg

value: Thapsigargin (5 µM)


title: 19.NOD1.5F


title: gDNA from subject PARBCV


title: RUF6-OE_HM-H3K9me3_R_rep1_ChIP-seq

value: H3K9me3, abcam, ab8898

value: Homo sapiens


title: 32.NOD2.2MC


title: gDNA from subject PARCAU


title: PfRrp6-DD-1C_HM-H3K9me3_R_rep1_ChIP-seq


title: 16.NOD1.AnisoM

value: Anisomycin (1 µM)


title: 14.NOD1.Lov

value: Lovastatin (30 µM)


title: 30.NOD2.CCCP

value: CCCP (5 µM)


title: Female Right Anterior Dorsal Head [2F_RA]

description:
2F_RA
F_RA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior

value: Pre-pupae (larval stage)

value: Female


title: 26.NOD2.Nocad

value: Nocadazole (10 µM)


title: 28.NOD2.Etop

value: HeLa

value: Etoposide (5 µM)


title: 12.NOD1.2MC


title: 24.NOD2.Vinbl

value: Vinblastine (10 µM)


title: 13.NOD1.LB42708


title: 10.NOD1.CCCP


title: WT_3D7-G7_HP1_R_rep1_ChIP-seq

value: Ring

value: Pf 3D7

value: HP1 antibody, rabbit

value: wild type


title: WT_3D7-G7_HM-input_R_rep1_ChIP-seq


title: Female Medial Anterior Dorsal Head [2F_MA]

description:
2F_MA
F_MA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Medial Anterior


title: WT_3D7-G7_HP1-input_R_rep1_ChIP-seq

value: Homo sapiens


title: gDNA from subject PARANT

value: tumor

value: Male


title: Female Left Posterior Dorsal Head [2F_LP]

description:
2F_LP
F_LP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: Female Left Anterior Dorsal Head [2F_LA]

description:
2F_LA
F_LA_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior


title: WT_3D7-G7_HM-H3K9me3_R_rep1_ChIP-seq

value: H3K9me3, abcam, ab8898


title: WT_3D7-G7_HM-H3K9Ac_R_rep1_ChIP-seq

value: H3K9ac, Millipore, 07-352


title: gDNA from subject PARBFJ


title: 9.NOD1.Actin

value: Actinonin (50 µM)

value: ok


title: 11.NOD1.2BP

value: HeLa


title: Female Right Posterior Dorsal Head [1F_RP]

description:
1F_RP
F_RP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Posterior

value: Pre-pupae (larval stage)

value: Female


title: GFP-CL_R_rep1_RIP-seq

source_name: transgenic parasite line of GFP-HAx3-Ty1x3,crosslink

value: Ring

value: Pf 3D7

tag: rip antibody

value: mouse anti-Ty1,Sigma SAB4800032-50 ug


title: gDNA from subject PARAIC


title: gDNA from subject PAPZYS


title: PfRrp6-CL_R_rep1_RIP-seq

source_name: transgenic parasite line of Pfrrp6-Ty1x3,crosslink

value: wild type


title: Female Medial Posterior Dorsal Head [2F_MP]

description:
2F_MP
F_MP_rep2
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

value: Medial Posterior


title: Female Right Anterior Dorsal Head [1F_RA]

description:
1F_RA
F_RA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Right Anterior


title: Female Medial Posterior Dorsal Head [1F_MP]

description:
1F_MP
F_MP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz


title: GFP-input_T_rep1_RIP-seq

source_name: transgenic parasite line of GFP-HAx3-Ty1x3,no-crosslink

value: Trophozoite

value: Homo sapiens


title: gDNA from subject PAPZTC

value: tumor


title: GFP-input_R_rep1_RIP-seq


title: GFP_T_rep1_RIP-seq


title: gDNA from subject PAPZLT

value: Male


title: GFP_R_rep2_RIP-seq


title: Female Left Posterior Dorsal Head [1F_LP]

description:
1F_LP
F_LP_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Posterior


title: Female Left Anterior Dorsal Head [1F_LA]

description:
1F_LA
F_LA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Left Anterior


title: 7.NOD1.Nig

tag: cell line

value: HeLa

value: Nigericin (5 µM)

value: ok


title: HCT116_DACSB

city: Rehovot

last: Brocks

state: Bavaria

address: Herzlstreet 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
CASAVA
Read pairs missing the constant part of the template switch oligo (defined by a hamming distance to TTTCTTATATGGG greater than 4) were excluded.
Filtered reads were processed with the cell-ranger analysis software version 2.1.0 and aligned against the human GRCh38-1.2.0 reference with the following parameters: chemistry = SC5P-PE; r1_length = 100; r2_length = 50; and outFilterMultimapScoreRange: 2 (STAR aligner specific)
Genome_build: hg38
Supplementary_files_format_and_content: Summarized molecule counts in a unique molecular identifier (UMI) matrix U = [Ufi] on features f and cells i

molecule: polyA RNA

growth_protocol: H1299 cells were cultured in RPMI 1640 and HCT116 cells were grown in heat-inactivated McCoy’s 5A medium, both supplemented with 10% Fetal Bovine Serum, 0.4% Penicillin-Streptomycin and 1% L-glutamine.

extract_protocol:
10x Genomics 5' single-cell RNA-seq
Please note that the first 26 positions of R1 contain the barcode (1:16) and UMI (17:26) sequences, followed by a constant part and biological sequence. R2 is purely biological and the I file contains the indices.

treatment_protocol: Cells were treated with 500-nM DAC + 500-nM SB939 for a total of 72 and 18 h, respectively. Compound-containing media was refreshed every 24 h.

tag: cell type

value: Colorectal cancer

tag: passage

tag: treatment

value: DAC+SB


title: Chip_GCN5

city: New Delhi

first: Sunita

last: Verma

state: Delhi

address: JNU Campus

department: School of Computational and Integrative Sciences

country: India

institute: Jawaharlal Nehru Univesity

description: Sample

data_processing:
The high quality paired end ChIP seq reads generated through hi-throughput sequencing were mapped with the reference genome (PlasmoDB-41_Pfalciparum 3D7) using Bowtie2 (v2.1.0).
PfGCN5 peak calling using MACS2 (v2.1.2) with 0.05 p-value cutoff.
Genome_build: Plasmodium_falciparum_3D7, version=2015-06-18
Supplementary_files_format_and_content: GCN5_NP.bedgraph file contains chromosome name, peaks start site, peaks end site and score value.
Supplementary_files_format_and_content: GCN5_NP_peaks.narrowPeak

organism: Plasmodium falciparum 3D7

source_name: Asynchronous-asexual stage parasites

growth_protocol: Parasites were cultivated in O+ human erythrocytes at 3% haematocrit in RPMI 1640 medium supplemented with 0.5% Albumax II, 0.2% sodium bicarbonate, 27.2 mg/litre hypoxanthine and 50 mg/litre Gentamycin. The parasites were grown at 37°C in an atmosphere of 5% CO2, 5% O2 and 90% nitrogen. Synchronization of parasites was carried out using 5% sorbitol treatment.

extract_protocol:
Parasites were resuspended in ice cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) supplemented with PMSF (100μM/ml) and protease inhibitor cocktail for 10 minutes on ice. Parasite lysate was then sonicated to generate the sheared chromatin of ~500bp and centrifuged at 1000g for 15 minutes. After the removal of debris from the lysate, the lysate was further diluted 10 times in ChIP dilution buffer (0.01% SDS, 0.1% Triton-X 100, 1.2mM EDTA, 16.7mM Tris, pH 8.1, and 150mM NaCl). Subsequently, the parasite lysates were precleared using protein A sepharose beads at 4°C for 1 hour. Cleared chromatins were incubated with pre-immune sera and immune GCN5 sera for overnight at 4°C on rotating wheel.
The paired-end sequencing library was prepared using Illumina TruSeq Nano DNA LT Library Preparation Kit. 200ng of each DNA was fragmented by Covaris S2. Covaris shearing generates DNA fragments with 3' or 5' overhangs. The fragments were then subjected to end-repair. This process converts the overhangs resulting from fragmentation into blunt ends using End Repair Mix. The 3' to 5' Exonuclease activity of this mix removes the 3' overhangs and the 5' to 3' polymerase activity fills in the 5' overhangs. A single "A" nucleotide is added to the 3' ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. A corresponding single "T" nucleotide on the 3' end of the adapter provides a complementary overhang for ligating the adapter to the fragment. This strategy ensures a low rate of chimera (concatenated template) formation. Indexing adapters were ligated to the ends of the DNA fragments, preparing them for hybridization onto a flow cell. The ligated products were purified using Ampure XP beads. The product was PCR amplified as described in the kit protocol.

treatment_protocol: Asynchronous stage parasites (trophozoite and schizont enriched) with 10% parasitemia were harvested and fixed with 1% formaldehyde at 37°C for 10 minutes. To prevent the over crosslinking, excess formaldehyde was quenched by addition of glycine to a final concentration of 150 mM. After that, the parasitized RBC’s were washed twice with 1x PBS followed by saponin lysis to remove the RBCs.

value: Whole body (trophozoite and schizont enriched)

tag: Stage

value: Asexual

value: Polyclonal antibodies against PfGCN5-C-termini


title: 6.NOD1.Nocad

tag: inducible gene

value: Nocadazole (10 µM)

tag: sample purification


title: gDNA from subject PAPZIZ

tag: group

tag: age at diagnosis (days)


title: PfRrp4-input_T_rep1_RIP-seq

source_name: transgenic parasite line of Pfrrp4-HAx3-Ty1x3,no-crosslink

tag: development stage

value: Pf 3D7

value: wild type

tag: host


title: HCT116_DMSO

value: DMSO


title: GFP_R_rep1_RIP-seq

value: Ring

value: mouse anti-Ty1,Sigma SAB4800032-50 ug

tag: genotype

value: Homo sapiens


title: 2.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)


title: treatment-4 rep3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the sequencing platform were cleaned with the Cutadapt program to trim off sequencing adaptors, low quality bases, and potential errors introduced during sequencing or library preparation. Reads with a quality Phred-like score < 20 and read length < 40 bases were excluded from RNAseq analysis.
The NCBI Genome database transcripts of Bos taurus (80,896 sequences) was used as a reference for RNAseq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the bowtie2 mapper (v. 2.2.3) with a “3 mismatches a read” allowance. The mapping results were processed with the samtools and scripts developed in-house at the University of Florida Interdisciplinary Center for Biotechnology Research to remove potential PCR duplicates and choose uniquely mapped reads for gene expression analysis. Differentially expressed genes (DEGs) in bacteria infused heifers (compared to vehicle infused heifers) were identified at each time point (day 4 or day 60) by counting the number of mapped reads for each transcript. Differentially expressed genes were defined using the P-value and log2 fold change (FC) ≥ 2 or ≤ -2. Adjusted P-values ≤ 0.1 were used initially in addition to non-adjusted P-values ≤ 0.05.
Pathway analysis was performed using Ingenuity Pathway Analysis (IPA, Qiagen). Differentially expressed genes with the criteria of log2 FC ≥ 2 or ≤ -2, and a non-adjusted P-value ≤ 0.05 were used for IPA analysis. These criteria were applied in order to maintain uniformity throughout the investigation due to the disparity in the number of DEGs following false discovery rate analysis using the adjusted P-value. Represented canonical pathways with a -log P-value > 1.3 were determined with corresponding z-scores to describe predicted activation status. Represented gene networks were determined by assessing the number of DEGs in each gene network. Upstream regulators of specific gene networks and upstream regulators of DEGs were predicted using IPA algorithms. Predicted upstream regulators of DEGs were assigned an activation z-score to predict either upregulation or down regulation of various downstream DEGs. A z-score ≥ 2 or ≤ -2 was assumed to be a significant prediction of activation or inhibition, respectively.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Bos taurus

growth_protocol: To avoid confounding effects of periparturient problems, lactation and metabolic stress, we used virgin Holstein heifers, 11 to 13 months old.

extract_protocol:
Total RNA was extracted in oocytes of vehicle (n = 5) and bacteria (n = 3) infused heifers at day 4, and vehicle (n = 6) and bacteria (n = 3) infused heifers at day 60. Oocytes were thawed and suspended in 350 μL RLT buffer for the extraction of total RNA using the RNeasy Micro kit (Qiagen) according to the manufacturer’s instructions. Total RNA concentration was determined using a Qubit 2.0 Fluorometer (Fisher Scientific) and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA).
To produce RNAseq libraries for sequencing, 200 pg of total RNA was used for library construction using SMARTer Universal Low input RNA kit (Takara Bio, Mountain View, CA), combined with Illumina Nextera DNA Library Preparation Kit (Illumina, San Diego, CA), according to the manufacturer's instructions. Briefly, first strand cDNA was primed by a modified N6 primer (the SMART N6 CDS primer), then base-paired with additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting in single-stranded cDNA containing sequences that are complementary to the SMARTer oligonucleotide. The SMARTer anchor sequence and the N6 sequence then served as universal priming sites for DNA amplification by PCR for 10 cycles. A total of 125 pg of cDNA was then fragmented by a tagementation reaction and adapter sequences were added to the template cDNA by PCR amplification.

treatment_protocol: Estrous cycles were synchronized by administering 100 mg i.m. of GnRH (gonadorelin diacetate tetrahydrate; Ovacyst, Bayer) followed by 25 mg i.m. of PGF2α (dinoprost tromethamine; Prostamate, Bayer) administered 5 and 6 d later. Eight days following initial GnRH, heifers received a final dose of 100 mg of GnRH i.m. Starting on the day following the end of the synchronization protocol, heifers received 200 mg i.m. of progesterone in corn oil (50 mg/mL; Sigma-Aldrich, St Louis MO) daily for 7 days. Heifers were randomly assigned to receive intrauterine infusion of vehicle control (n = 6) or live pathogenic bacterial infusion (n = 4). Intrauterine infusion (day 0) was performed 3 days after the end of the synchronization protocol. Briefly, endometrial scarification preceded the intrauterine infusion of either vehicle medium (30 mL of sterile Luria-Bertani (LB) broth) or pathogenic bacteria (10 mL of 4.64 × 107 CFU/mL of Escherichia coli MS499, 10 mL of 3.38 × 107 CFU/mL Trueperella pyogenes MS249 followed by 10 mL of sterile LB broth). Ovum pick-up was performed using transvaginal ultrasound-guided follicle aspiration performed on days 4 and 60. Briefly, heifers received a caudal epidural injection of 60 mg of lidocaine hydrochloride 2% (Aspen Veterinary Resources, Greely CO), and the perineum and vulva were cleaned and disinfected with povidone followed by 70% ethanol. A vaginal lavage using 100 mL of 0.2% chlorohexidine in saline followed by two 100 mL lavages using sterile 0.9% saline were employed to wash the vagina.

tag: tissue

value: Oocyte

tag: location

value: University of Florida Dairy Unit

tag: age

value: 11-13 months, female


title: 3.NOD1.CytoD

value: HeLa

value: Cytoclasin D (5 µM)

value: ok


title: 1.NOD1.Control

value: Ctr (DMSO)


title: H1299_DACSB

value: Non-small cell lung cancer

value: DAC+SB


title: control-4 rep5


title: 4.NOD1.Vinbl

value: Vinblastine (10 µM)


title: gDNA from subject PAPZCL

value: tumor

tag: gender

value: Male


title: 8.NOD1.Etop

value: Etoposide (5 µM)


title: PfRrp4-input_R_rep1_RIP-seq

value: Ring

tag: strain

value: Pf 3D7

tag: rip antibody

value: wild type


title: treatment-4 rep2


title: Chip_Input

description: Input

value: Whole body (trophozoite and schizont enriched)

value: Asexual

tag: chip antibody


title: Female Medial Anterior Dorsal Head [1F_MA]

description:
1F_MA
F_MA_rep1
PolyA RNA
OnthophagusHeadCounts.tsv.gz

value: Dorsal head

tag: head compartment

value: Medial Anterior

tag: developmental stage

value: Pre-pupae (larval stage)

tag: Sex

value: Female


title: PfRrp4_T_rep2_RIP-seq

value: Trophozoite

value: mouse anti-Ty1,Sigma SAB4800032-50 ug

value: Homo sapiens


title: control-4 rep4

value: Oocyte

value: University of Florida Dairy Unit

value: 11-13 months, female


title: B3-Black_skin

city: Chengdu

first: LiRui

last: Zhao

state: Sichuan

address: HuiMing road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description: domestic pig

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3).
Transcripts were assembled by Stringtie version 1.3.3.
Mapped reads were merged by Cuffmerge (part of Cufflinks, version 2.2.1) .
Remove coding gene transcripts by Coffcompare (part of Cufflinks, version 2.2.1)  (marked by ‘c’ for partial match or ‘=’ for full match), then transcripts longer than 200bp or more than two exons were kept.
Compared each transcript sequence with Pfam-27 database and trimmed out transcripts with p-value<10-4 by Hmmscan.
Compared with uniref and nr database and trim out transcripts with p-value<10-10 by BLASTX (https://blast.ncbi.nlm.nih.gov/)
Predict and calculate coding protential of the remainly transcripts by CPC
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Sus scrofa

source_name: skin tissue

extract_protocol:
Total RNA (3ug each sample) was isolated  with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA (each sample) and the Oligo(dT) magnetic head were used for generating RNA-Seq cDNA libraries , and then, RNA -seq was conducted following the manufacturer's standard procedures.

tag: breed

value: Bama

value: adult

value: skin

value: 2 year old

tag: skin color

value: black


title: B3-White_skin

description: domestic pig

value: white


title: treatment-4 rep1


title: PfRrp4_R_rep2_RIP-seq

value: Ring

value: Pf 3D7

value: wild type


title: B2-Black_skin

description: domestic pig


title: control-4 rep3


title: B2-White_skin

description: domestic pig


title: PfRrp4_R_rep1_RIP-seq


title: H1299_DMSO

tag: cell line

tag: cell type

value: Non-small cell lung cancer

tag: passage

tag: treatment

value: DMSO


title: B1-Black_skin

description: domestic pig

tag: development stage


title: B1-White_skin

description: domestic pig

tag: tissue


title: PfRrp6-input_R_rep1_RIP-seq

source_name: transgenic parasite line of Pfrrp6-Ty1x3,no-crosslink

tag: genotype

tag: host


title: PfRrp6-input_T_rep1_RIP-seq

value: Trophozoite


title: control-4 rep1

tag: location

tag: age


title: control-4 rep2


title: treatment-60 rep3


title: PfRrp6_T_rep2_RIP-seq

tag: strain

tag: rip antibody

value: mouse anti-Ty1,Sigma SAB4800032-50 ug


title: gDNA from subject PAPUNR

tag: group

value: tumor

tag: age at diagnosis (days)

tag: gender

value: Female


title: PfRrp6_R_rep2_RIP-seq

value: Homo sapiens


title: treatment-60 rep2

value: Oocyte

value: University of Florida Dairy Unit

value: 11-13 months, female


title: control-60 rep5


title: PfRrp6_T_rep1_RIP-seq


title: PfRrp4_T_rep1_RIP-seq


title: PfRrp6_R_rep1_RIP-seq


title: control-60 rep4


title: gDNA from subject PAPSCM


title: control-60 rep3


title: TX9631

city: Galveston

first: Daniele

last: Swetnam

state: TX

address: 301 University Blvd

department: Experimental Pathology

institute: University of Texas Medical Branch

data_processing:
Aptmers and poor quality bases (q< 20) were removedwith Trimmomatic
reads were aligned to the reference (AF196835) with bowtie2 under the sensitive local parameters
a consensus sequence was extracted using the mpileup function in samtools
alignment was repaired by realigning to the new consensus sequence in Bowtie2 under the very sensitive local parameters
reads were sorted by coordinate by the SamSort function of picard tools
Duplicates were removed with the MarkDuplicate function of picard tools
Single nucleotide variants were identified with V-phaser2
Genome_build: AF196835
Supplementary_files_format_and_content: variant caller summary; Each variant entry consists of the following: the reference position (coordinate starts at 1), predicted variant, consensus base, strand-bias p-value, type of variant (Single nucleotide polymorphism (SNP) or Length polymorphism (LP)), frequency of the variant and the profile, where each entry consists of three values: the base, its count in the forward strand, and its count in the reverse strand, separated by Colons.

organism: West Nile virus

source_name: Cyanocitta cristata (Blue Jay)

growth_protocol: virus was isolated from the brain  homogenate  of dead birds by passageing on vero cells

extract_protocol:
RNA was extracted from the supernatant of infected vero cells using the QIAamp Viral RNA Mini kit according to the manufacturer’s recommendations
Libraries were generated with a TruSeq RNA v2 kit (Illumina) according the the manufactures instructions

tag: source tissue

value: dead bird brain homogenate

value: USA:TX, Spring (77379)

tag: collection date

tag: molecule subtype

value: viral RNA


title: PfRrp6-DD-1B_R_rep1_RNA-seq

source_name: PfRrp6-DD clone line PfRrp6-DD-1B


title: control-60 rep6


title: KD_0h

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description: Gene expression in chronic ethanol-fed liver

hyb_protocol: Affymetrix gene chips, Mouse Clariom S were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail. Target denaturation was performe at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization with rotation 60 rpm for 16 hour at 45°C. Arrays were then wash and stained using Gene chip Fluidic Station 450, using Affymetrix GeneChip hybridization wash & stain kit.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.  Quality Control of the experiment was perform by Expression Console Software v 1.4.1.

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

source_name: Mcu knockdown mouse liver sample

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the GeneChip WT Plus kit.

extract_protocol: Total RNA was isolated using  Animal Tissue RNA Purification Kit (Norgen Biotek, ) and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100.

treatment_protocol: To generate liver-specific MCU KD 10-12 weeks old MCUloxp/loxp male mice were injected via the tail vein with AAV8-TBG-Cre (1.3x1011 pfu/mouse) (Penn Vector Core). AAV8-TBG-Null injected littermates were used as controls. 5 weeks after injection mice were subjected to 70% partial hepatectomy, remnant tissue was collected 30h after the surgery. Liver tissue  was freeze-clamped in liquid nitrogen and stored at -80 degrees C.

tag: timepoint

value: 0h (control)

tag: background strain

value: male

value: liver


title: control-60 rep2


title: gDNA from subject PANKBX

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.


title: control-60 rep1


title: gDNA from subject PANHWD


title: RUF6-OE_S_rep1_RNA-seq

source_name: RUF6 member overexpression in Pf 3D7 lilne

value: Schizont

value: Pf 3D7


title: TX9604

value: USA:TX, Harris Co. (77065)


title: KD_30h

description: Gene expression in chronic ethanol-fed liver 1h after PHx

tag: treatment


title: TX9614

source_name: Tyrannus forficatus (Scissor-Tailed Flycatcher)

value: USA:TX, Houston (77087)


title: WT_30h

source_name: Wild type mouse liver sample

value: Wild type


title: treatment-60 rep1


title: RUF6-OE_T_rep1_RNA-seq

tag: development stage

value: Trophozoite


title: RUF6-OE_T_rep2_RNA-seq


title: WT_0h

tag: tissue


title: PHZ3

city: Chicago

first: Peng

last: Ji

state: Illinois

address: 303E,Chicago Avenue, Ward3-240

institute: Northwestern University

description: PHZ-Expression

data_processing:
Clean reads were mapped to reference genome using HISAT.
SNP and Indel were called by GATK.
Gene expression level was calculated for each sample with RSEM
NOIseqand PossionDis algorithms were used to detect the differentially expression genes
Genome_build: rn6
Supplementary_files_format_and_content: txt files including the gene expression and annotation

organism: Rattus norvegicus

source_name: PHZ_c-kit+ cell

extract_protocol:
Bone marrow c-kit+ cells were purification and RNAs were extracted by Trizol
poly A RNA libraries were constructed in BGI

treatment_protocol: 6-8 weeks ACI rats were treated with 100mg/kg PHZ via I.P.

value: ACI

tag: Sex

value: female

value: 6-8 weeks

value: 100mg/Kg PHZ treated for 36h

value: bone marrow

tag: cell type

value: c-kit+ cell


title: TX9597

source_name: Mimus polyglottos (Mocking Bird)

value: dead bird brain homogenate

tag: location

value: USA:TX, Atascocita (77339)


title: TX9611

value: USA:TX, Kingswood (77339)

value: viral RNA


title: gDNA from subject PANZXI

source_name: AML, pre-treatment

value: tumor

value: Male


title: gDNA from subject PANXWX

value: Female


title: PHZ2

description: PHZ-Expression

value: male

tag: age


title: PfRrp6-DD-4C_R_rep1_RNA-seq

source_name: PfRrp6-DD clone line PfRrp6-DD-4C

value: Ring

tag: strain

value: Pf 3D7

tag: genotype

tag: host

value: Homo sapiens


title: RUF6-OE_R_rep2_RNA-seq


title: RUF6-OE_R_rep1_RNA-seq


title: PHZ1

description: PHZ-Expression

value: ACI


title: TX9437

source_name: Passer domesticus (House Sparrow)

value: USA:TX, Baytown (77521)


title: V05417

source_name: Culex Quinquefasciatus

value: Mosquito pool

value: USA:TX,  Houston


title: gDNA from subject PANTXR

tag: group

tag: age at diagnosis (days)


title: PBS3

description: PBS-Expression

source_name: PBS_c-kit+ cell

value: female

value: 6-8 weeks

value: PBS treated for 36h

value: bone marrow


title: vector_S_rep1_RNA-seq

source_name: vector transfected in Pf 3D7 line as control

value: Schizont

value: vector contorl


title: vector_S_rep2_RNA-seq


title: gDNA from subject PANTIV

value: tumor

tag: gender


title: PBS1

description: PBS-Expression

value: c-kit+ cell


title: vector_T_rep2_RNA-seq

value: Trophozoite


title: PBS2

description: PBS-Expression

value: male


title: vector_T_rep1_RNA-seq


title: TX10108

tag: source tissue

value: dead bird brain homogenate

value: USA:TX,  Houston (77070)

tag: collection date

value: viral RNA


title: gDNA from subject PANRWM

value: Male


title: 100d/WB

city: New Orleans

first: XiaoChing

last: Li

state: LA

address: 2020 Gravier St.

department: Neuroscience Center

institute: LSU School of Medicine

data_processing:
Illumina Casava1.7 software used for demultiplexing and base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to zrbra finch whole genome
Genome_build: zebra finch genome (3.2.4/taeGut1)
Supplementary_files_format_and_content: read count

organism: Taeniopygia guttata

source_name: whole brain sample/100 days old

extract_protocol:
HVC tissue was dissected and RNA was isolated with Trizol reagents
Used a NuGEN Ovation RNAseq V1 kit following manufacturer’s instructions

value: whole brain


title: TX9981

value: USA:TX, Cypress (77433)

tag: molecule subtype


title: vector_R_rep2_RNA-seq

value: Ring

value: Pf 3D7

value: Homo sapiens


title: gDNA from subject PANKEF


title: 45d/WB

source_name: whole brain sample/45 days old


title: TX9410

value: USA:TX, Houston (77204)


title: gDNA from subject PANUTX


title: TX9968

source_name: Cardinalis cardinalis (Northern Cardinal)

value: USA:TX, Houston (77084)


title: vector_R_rep1_RNA-seq


title: gDNA from subject PANKCE


title: TX9971

source_name: Cyanocitta cristata (Blue Jay)

value: USA:TX, Baytown (77521)


title: gDNA from subject PANFMG


title: 100d/HVC

source_name: HVC region/100 days old

value: avian brain region


title: TX9967

value: USA:TX, Baytown (77520)


title: PfMaf1-OE-10_S_rep1_RNA-seq

source_name: PfMaf1-OE line selected by 10 nM durg (WR)

value: Schizont


title: 45d/HVC2

source_name: HVC region/45 days old


title: TX9966

value: USA:TX, Houston (77018)


title: PfMaf1-OE-10_T_rep1_RNA-seq

value: Trophozoite


title: 45d/HVC1


title: TX9963

value: dead bird brain homogenate

value: USA:TX, Houston (77055)


title: gDNA from subject PANPKN

value: tumor


title: PfMaf1-OE-10_R_rep1_RNA-seq


title: TX9962

value: viral RNA


title: PC 3

city: Vancouver

first: Martha

last: Liu

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to the bacilis mobilis genome using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.

organism: Bacillus mobilis

source_name: bacterial culture

growth_protocol: 1.0 μL of log phase B. mobilis ML-A2C4 at an OD600 of 0.02 was spotted onto the center of  3 different conditions of MH 1.5% agar plates (control, plates spread with 1.5mL of 10% skim milk powder (milk), and plates spread with 0.5mL of 2% PC in 50% EtOH (PC)). The plates were incubated aerobically at 30 °C for 24 hours.

extract_protocol:
Cells were scraped from the outermost edges of the growing control or filamentous colonies at 24 h post inoculation directly into RNA Protect Bacterial Reagent (QIAGEN), 1.8 OD 600 was pelleted, and pellets were stored at -80 °C. Pellets were resuspended in 1 ml buffer RLT (QIAGEN) supplemented with 1/100 β-mercaptoethanol and transferred to tubes containing lysing matrix B (MP Biomedicals). Samples were bead bashed in the Bead Ruptor 24 (Omni International) once at speed 7 for 30 s and twice at speed 8 for 30 s, with chilling on ice in between. After a brief spin, the supernatant was mixed with 700 μl 70% EtOH. RNA isolation then proceeded according to the manufacturer’s instructions using the RNeasy Mini Kit (QIAGEN). Eluted RNA was further purified with the TURBO DNA-free kit (Thermo Fisher). RNA samples were depleted of rRNA using the RiboZero Bacteria Kit (Illumina). Libraries were prepared using the KAPA Stranded Total RNA Kit (Kapa Biosystems) prior to sending for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacterial culture

tag: motility/medium

value: Swarming on phosphatidylcholine


title: PfMaf1-OE-2.5_S_rep1_RNA-seq

source_name: PfMaf1-OE line selected by 2.5 nM durg (WR)


title: PC 2


title: WT3_SL

city: Beijing

first: Huimin

last: Chen

state: Beijing

address: No. 20 Nanxin Village, Xiangshan, Haidian District, Beijing

department: State Key Laboratory of Systematic and Evolutionary Botany

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
Raw reads were filtered to obtain clean reads using NGSToolkit(V2.3.3) and Trimmomatic(V0.36) software
Clean reads were aligned with Populus trichocarpa genome (https://phytozome.jgi.doe.gov/pz/portal.html#!bulk?org=Org_ Ptrichocarpa_er) using the HISAT (V2.0.5) software with default parameters
The reads which mapped to transcripts was quantified by using HTSeq (V2.2.1) package
The differential expression genes(DEGs) were identified using edgeR (V3.16.5) package. The screening criteria are as follows: |log2FC| ≥ 1 and FDR < 0.05
Genome_build: Ptrichocarpa_444_v3.1
Supplementary_files_format_and_content: tab-delimited text files include ht-count values for each Sample

organism: Populus tomentosa

source_name: Shoot

growth_protocol: P.tomentosa were micro propagated on 5‰ agar-solidified Lloyd & McCown woody plant basal medium (WPM) with 1.5% sucrose and 1mg/L NAA. The growth chamber conditions were set as follows: 24°C, 16h of light per day and photon flux density of approximately 50 μmol m-2 s-1. Micro propagated plants which had the same developmental stage (~10 cm shoot length) were selected and transferred to WPM solution.

extract_protocol:
RNA isolation and extraction were carried out at Biomarker technologies company (Beijing, China) with three biological replicates
Library construction were carried out at Biomarker technologies company (Beijing, China) with three biological replicates

treatment_protocol: Plants were divided into two groups on average and transferred to new WPM solution containing 100μM Fe (Fe-sufficient group) and 0μM Fe (Fe-deficient group), respectively.

value: Shoot

value: Fe-deficient

tag: developmental stage

value: Seedling stage


title: Milk 3

value: Swarming on milk


title: PfMaf1-OE-2.5_T_rep1_RNA-seq

tag: development stage

value: Pf 3D7

value: Homo sapiens


title: PC 1

tag: tissue


title: TX9950


title: WT2_SL


title: TX9961

source_name: Accipiter cooperii (Cooper's Hawk)

value: USA:TX, Houston (77095)


title: PfMaf1-OE-2.5_R_rep1_RNA-seq

value: Ring


title: Milk 2


title: PfRrp6-DD-1C-GlcN+_S_rep1_RNA-seq

source_name: PfRrp6-DD clone line PfRrp6-DD-1C cultured with 5 nM GlcN

value: Schizont


title: TX9959


title: TX9388

value: USA:TX, Humble (77346)


title: CK3_SL

value: Fe-sufficient


title: Milk 1


title: CK1_SL


title: TX9943

value: dead bird brain homogenate


title: PfRrp6-DD-1C-GlcN+_T_rep1_RNA-seq

value: Trophozoite


title: WT1_SL


title: Nonswarm 3

value: Non-swarming


title: TX9919

value: USA:TX, Houston (77080)

value: viral RNA


title: PfRrp6-DD-1C_S_rep2_RNA-seq

source_name: PfRrp6-DD clone line PfRrp6-DD-1C


title: Poplar_G798-T08

source_name: Root

value: Root


title: TX9901

source_name: Mimus polyglottos (Mocking Bird)

value: USA:TX, Spring (77379)


title: Nonswarm 2

value: bacterial culture


title: PfRrp6-DD-1C_S_rep1_RNA-seq


title: Nonswarm 1


title: PfRrp6-DD-1C_T_rep2_RNA-seq


title: CK2_SL

value: Shoot

value: Seedling stage


title: Poplar_G798-T07

value: Fe-deficient


title: TX9907

value: USA:TX, Baytown (77521)