title: Sperm Nico-9 RRBS

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) Reads were trimmed using Trim Galore! v0.4.3 with the --rrbs flag.
2) Trimmed reads were mapped to rn6 (release 92, Ensembl) and methylation levels estimated using Bismark v0.18.1 and Bowtie2 v2.2.5 on default settings.
3) The SNPs (dbSNP, build 149, Rnor_6.0) overlapping with CpGs were filtered out.
4) CpGs with coverage larger than 10 times the 95-percentile of coverage in each sample are filtered out.
5) CpGs with a minimum of 10 counts were considered for differential methylation analysis.
6) Differential methylation analysis was performed by edgeR v3.24.0.
Genome_build: rn6
Supplementary_files_format_and_content: Coverage (cov) files contain the coverage per sample (data processing step 2)

organism: Rattus norvegicus

source_name: Epididymal spermatozoa

extract_protocol:
QIAamp® DNA Mini Kit (Qiagen, Germany, Cat. No. 51304) according to the instructions of the manufacturer
Genomic DNA was incubated with MspI (NEB, Frankfurt, Germany) restriction enzyme overnight for fragmentation. Adenylation step was performed using dNTP and Klenow fragment followed by an AMpure Bead clean-up (Beckman Coulter, Copenhagen, Denmark) and ligation to TruSeq adapters (Illumina, CA, USA). All samples were pooled and subjected to bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Freiburg, Germany). The library pool was amplified by PCR (2 min 95ºC [30 s 95ºC, 30 s 65ºC; 45 s 72ºC] × 20 cycles; 7 min 72ºC) with PfuTurbo Hotstart DNA polymerase (Agilent, Glostrup, Denmark). PCR products were purified using the AMPure Bead clean-up. Libraries were sequenced on a NextSeq 2500 system (Illumina), on a 75-bp single-end sequencing mode.

treatment_protocol: First time pregnant, young adult Sprague Dawley rat dams received either placebo (saline, n = 3) or nicotine (1 mg/kg, n = 4) subcutaneously from embryonic day 6 of gestation to postnatal day 21. The dams were pair-fed according to the previous day’s food consumption by the nicotine-treated group and pups were weaned at postnatal day 21. At postnatal day 60, ten animals (3 = 4  litters) from each group were processed for epidydimal DNA and lung RNA and protein extactions.

value: Sprague Dawley

value: Epididymal spermatozoa

tag: treatment group

value: Nicotine


title: Sperm Nico-10 RRBS

status: Public on May 17 2021

type: SRA

library_source: genomic

molecule: genomic DNA

tag: strain

tag: tissue


title: Sperm Nico-6 RRBS


title: Sperm Nico-8 RRBS


title: Sperm Nico-7 RRBS


title: ESC_HIRAKO_ATAC_rep2

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

country: USA

institute: UT Southwestern Medical Center

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on gelatin-coated plates under standard conditions (KO-DMEM, 2mM Glutamax, 15% ES grade fetal bovine serum, 0.1mM 2-mercaptoethanol, 1x Pen/Strep, 1x NEAA and leukemia inhibitory factor).

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

tag: cell line

value: ESC

tag: genotype

value: HIRA-/-


title: Sperm Nico-4 RRBS


title: 8_YBJCNT_Parabiosis_RNASeq [8_S24]

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

library_source: transcriptomic

data_processing:
Fastq files were ran through fastqc to check for sequencing quality. 5 of 35 samples (numbers 6, 15, 16, 27, 35) were omitted due to poor quality and / or low coverage. QC was visualized using MultiQC (Ewels et al Bioinformatics 2016)
Salmon (Patro et al Nature Methods 2017) was used to generate an index of the CHR Gencode mouse transcriptome (gencode.vM20.trasncripts.fa)
Salmon was used to quanitfy transcripts against the mouse transcriptome reference. Flags used were for automatic library type detection -l A (unstranded, single-end), --seqBias, --gcBias, and --validateMappings
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Genome_build: Read alignment was not utlized for this analysis. Gencode utilizes the GRCm38 primary assembly genome sequence as the reference for their transcriptome annotation.
Supplementary_files_format_and_content: Differential expression files include log2 fold changes generated by DESeq2 for each indicated comparison (with all samples from a given group identified by parabiont status utilized in the differential expression test). These files are listed as .csv files. A counts file is also provided with all the gene level counts for each sample that are used as the input for DESeq2, also as a .csv file.

molecule: total RNA

source_name: Young BoyJ control

extract_protocol:
Hematopoietic stem cells were isolated from the bone marrow of mice through a standardized process of bone marrow extraction, creation of a single cell suspension, and flow cytometry based cell sorting. RNA was isolated using the PicoPure RNA Isolation Kit from ThermoFisher.
Purified RNA was used as input for the Nugen Ovation Trio low input RNA library preparation kit. Samples were processed on an automated robot system at the NYU Genome Technology Center

tag: age at procedure

value: 8-12 weeks

tag: parabiont status

value: Young BoyJ control

tag: Sex

value: Male

tag: cell type

value: Hematopoietic stem cells


title: Sperm Nico-5 RRBS


title: ESC_ATRXKO_ATAC_rep2

value: ATRX-/-


title: EC_DNA_AGM_cell177

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

source_name: aorta-gonad-mesonephros (AGM)

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)

tag: antibody


title: ESC_DAXXKO_ATAC_rep2

value: DAXX-/-


title: Sperm Nico-3 RRBS


title: 7_YISOBJ_Parabiosis_RNASeq [7_S23]

source_name: Young isochronically parabiosed BoyJ

value: Young isochronically parabiosed BoyJ


title: 4_OHETB6X_Parabiosis_RNASeq [4_S21]

source_name: Old heterochronic B6 lodged in young BM niche

value: 22 months old


title: EC_DNA_AGM_cell176


title: Sperm Nico-2 RRBS


title: EC_DNA_AGM_cell175


title: ESC_WT_ATAC_rep2

value: wildtype


title: EC_DNA_AGM_cell174


title: 2_YHETBJ_Parabiosis_RNASeq [2_S19]

source_name: Young heterochronically parabiosed BoyJ

value: Young heterochronically parabiosed BoyJ


title: 3_YHETBJ_Parabiosis_RNASeq [3_S20]


title: ESC_DAXXKO_ATAC_rep1


title: ESC_ATRXWT_ATRX

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Crosslink ChIP was performed as described (Law et al. 2010; Truch et al. 2018). Briefly, cell were harvested and crosslinked in 2mM EGS for 45min and 1% PFA for 10min. Chromatin was then sheared to 150-500 bp. Chromatin was isolated and used for ChIP-seq according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: For genertating ATRX-GFP mouse ESCs, TagGFP2 were knocked-into the c-teminal of ATRX locus by CRISPR/Cas9-mediated homology directed repair. For generating ctrl, SSRP1 KD and SPT16 KD mouse ESCs, cells were infected with lentivirus containing non-targeting, SSRP1 and SPT16 shRNA plasmid (Dharmacon). The next day, the media was replaced with complete mESC culture media containing 1 μg/ml puromycin. After 3 days of selection, mESCs were used for downstream analysis.

value: ATRX (ab97508, Abcam)

tag: ChIP

value: Crosslink


title: Sperm Ctrl-9 RRBS

value: Sprague Dawley

value: Epididymal spermatozoa

value: Ctrl


title: Sperm Nico-1 RRBS

value: Nicotine


title: EC_DNA_AGM_cell173


title: Arabidopsis roots - ctl1-2 R2

city: Zürich

first: Susanne

last: Dora

address: Universitätsstrasse 2

department: D-Biology, Institute for molecular plant biology

country: Switzerland

institute: ETH Zürich

data_processing:
sequenced reads were trimmed for low-quality bases with Trimmomatic, version 0.36
sequencing adapters were removed with Flexbar, version 3.0.3
Reads were mapped against the Arabidopsis thaliana genome (TAIR10) with STAR version 2.6.1c
Uniquely mapped reads were counted by featureCounts, based on the R package Rsubread (version 1.32.1)
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files include the raw counts of reads mapped uniquely against the reference genomes in .txt format.
Supplementary_files_format_and_content: Processed data files include the normalized counts per million for the samples and time points used afterwards to draw conclusions (counts were normalized using trimmed means of M-values (TMM) normalization in EdgeR version 3.24.3; Robinson and Oshlack, 2010)

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Arabidopsis thaliana accession Col-0 and ctl1-2 plants were grown for 14d under long-day conditions (16h light, 8h dark) with optimized light intensity (130-150 μE m-2 s-1) at 20-22 °C. Seeds were either gas or liquid-sterilized and grown on 60µm nylon mesh ½ MS media (Duchefa; catalog number M0222.0025) supplemented with 1% (w/v) sucrose (when indicated) and 0.9% bacteriological grade agar (Difco; catalog number 214530).

extract_protocol:
Roots from 14 days-old seedlings grown on plates  were harvested and immediately frozen in liquid N2. Three independent replicates were used for the transcriptome assay. Root material was ground with mortar and pestle in liquid N2. 50 -100 mg of ground material was used for RNA extraction using the RNeasy plant mini Kit (Qiagen). Extraction was performed according to the user manual provided by the supplier (RNeasy Mini Kit handbook, Fourth edition, June 2012, Qiagen). Extraction buffer RLC with 10 µl/ml β-mercaptoethanol freshly added was used to extract the RNA. An on-column DNA digestion (RNase-Free DNase Set, Qiagen) was performed. Before elution of the RNA the column was incubated 1 min with 30 µl RNAse-free water to resolve the RNA.
3’mRNA-libraries were prepared using the 3’mRNA-Seq library Prep Kit (QuantSeq, Lexogen). The manual from the supplier was followed with the following modifications. At least 1 µg RNA was used as input. For first strand synthesis of cDNA the incubation time at step 4 was increased to 60 min. For library indexing and amplification 13-17 amplification cycles of the given PCR were used depending on the amount of input RNA. 17 µl of the purified library was transferred to a fresh tube. The finished libraries were stored at -20° C until quality control and pooling.

tag: ecotype

value: ctl1-2 mutant

value: whole root


title: Arabidopsis roots - ctl1-2 R3


title: ESC_ATRXKO_ATAC_rep1

value: ESC


title: Arabidopsis roots - ctl1-2 R1


title: EC_DNA_AGM_cell172


title: EC_DNA_AGM_cell170


title: ESC_WT_ATAC_rep1


title: Sperm Ctrl-10 RRBS


title: Sperm Ctrl-7 RRBS


title: RNAseq_neurons_BANP_dTAG_6h_r3

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: mRNA_knownGene_mm10_neuronsdegronTimeCourse_II.csv

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

source_name: Ngn2-induced neurons

growth_protocol: For neural differentiation, dishes were coated with sterile filtered (0.22μm) Poly-D-lysine hydrobromide (0.5mg/ml, Sigma, P-7886-100MG) diluted in Borate Buffer (50mM, pH 8.5) for 24 hours at 37oC, washed 3x with sterile water and coated for at least 2 hours with Laminin (6.65ug/ml, Sigma, L2020-1MG) in PBS at 37oC. Wild-type BANP-dTAG ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008), trypsinated and plated at a density of 2x106 per 10cm dish in proliferation medium supplemented with 1μg/ml Doxycycline for three days to generate neurons.

extract_protocol:
RNA for RNA-seq was isolated using Direct-zol RNA Purification Kit (Zymo), following the manufacturer’s instructions.
Sequencing libraries were prepared from 100ng of purified total RNA for three biological replicates using TruSeq stranded Total RNA Library Prep (Illumina).

treatment_protocol: For RNA-seq, cells (2x10e5) were seeded into 6 well plates for neural generation three days before the experiment. Neurons were then treated with the dTAG13 compound to remove BANP over a time course of: 1, 2, 4 and 6 hours.

value: Ngn2-induced neurons

value: Ngn2 insertion, BANP dTag

tag: treatment

value: Dox, dTag 6h


title: Sperm Ctrl-8 RRBS


title: EC_DNA_AGM_cell171

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: RNAseq_neurons_BANP_dTAG_6h_r1


title: EC_DNA_AGM_cell168


title: RNAseq_neurons_BANP_dTAG_6h_r2


title: RNAseq_neurons_BANP_dTAG_4h_r3

value: Dox, dTag 4h


title: EC_DNA_AGM_cell167


title: Arabidopsis roots - Col-0 R3

value: wild type


title: Sperm Ctrl-6 RRBS


title: EC_DNA_AGM_cell169


title: Sperm Ctrl-5 RRBS


title: T_Spinal3

city: xi'an

first: Erliang

last: Li

address: xin si street

institute: tangdu hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and Ballgown were used to perform expression level for genes by calculating FPKM.
Genome_build: rattus_norvegicus ensembl release101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

source_name: spinal cord

growth_protocol: Wistar female rats of 8 weeks of age (From SPF (Beijing) Biotechnology Co., Ltd, China) weighing between 200 and 230 g were group housed in cages (n = 3/group) and maintained in an environmentally controlled room (22 – 24 ° C) with a 12-h light/dark cycle and were provided with adequate food and water.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA(1ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the poly(A) RNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded mRNA Library Prep Kit(Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

treatment_protocol: T_Spinal group was subjected to 3ml MED oral treatments once daily by oral gavage after spinal cord injury, whereas the C_Spinal group was intragastrically administered with distilled water after spinal cord injury.

value: spinal cord

tag: injure

value: yes

tag: teratment

value: treated with MED


title: Arabidopsis roots - Col-0 R2


title: Sperm Ctrl-4 RRBS

value: Sprague Dawley


title: T_Spinal1


title: RNAseq_neurons_BANP_dTAG_2h_r3

value: Dox, dTag 2h


title: Sperm Ctrl-2 RRBS

value: Epididymal spermatozoa

value: Ctrl


title: C_Spinal3

value: untreated


title: Sperm Ctrl-1 RRBS


title: RNAseq_neurons_BANP_dTAG_2h_r1


title: C_Spinal2


title: RNAseq_neurons_BANP_dTAG_4h_r1


title: EC_DNA_AGM_cell163


title: RNAseq_neurons_BANP_dTAG_4h_r2


title: T_Spinal2


title: lox5-11_0hai_3

city: Nanjing

first: wang

last: yinying

state: Jiangsu

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

department: College of Agriculture

institute: Nanjing Agricultural University

data_processing:
alignment: Hisat2 software version 2.1.0
assemble: stringtie software version 1.3.5
calculate DEG: DESeq2 version
Genome_build: B73 AGPv4.59 reference genome
Supplementary_files_format_and_content: format: csv, content: genes reads count

organism: Zea mays

source_name: seedling stalk

growth_protocol: B73 (wild type, medium resistant) and lox5-3 (mutant in B73 background, susceptible) seedling  are planted at 26 ± 2 °C during a 14/10 h light/dark cycle, with the light density of 600 LUX, a  humidity approximately 75%.

extract_protocol:
RNA was extracted from the seedling stems at different time points inoculated with F. graminearum using TRIzol reagent (Invitrogen), then purified with the RNeasy
RNA samples were subject to quality control prior to the library construction using Illumina TruSeq RNA library prep kit v2

treatment_protocol: 20 μl of 1.0ⅹ10 6 /ml Fusarium graminearum  spore suspensions  in 0.001% Tween-20 were inoculated to the B73  and lox5-3 seedling stem，and the seedling stalk of B73  and lox5-3 were  harvested at 0h，12h and 24h. with  materials at 0h as control.

value: stem

tag: developmental stage

value: seeding

value: CK

tag: hours post inoculated

value: mutant


title: EC_DNA_AGM_cell165


title: RNAseq_neurons_BANP_dTAG_2h_r2

value: Ngn2-induced neurons

value: Ngn2 insertion, BANP dTag


title: EC_DNA_AGM_cell166

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell164


title: Sperm Ctrl-3 RRBS

tag: treatment group


title: EC_DNA_AGM_cell161

tag: strain


title: RNAseq_neurons_BANP_dTAG_1h_r2

value: Dox, dTag 1h


title: Arabidopsis roots - Col-0 R1

value: wild type

tag: tissue

value: whole root


title: C_Spinal1

value: spinal cord

value: yes


title: Sham3

value: no


title: lox5-10_24hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: RNAseq_neurons_BANP_dTAG_1h_r1


title: EC_DNA_AGM_cell160


title: lox5-9_12hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: Sham2


title: EC_DNA_AGM_cell159


title: lox5-7_24hai_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: EC_DNA_AGM_cell162


title: Sham1


title: RNAseq_neurons_BANP_dTAG_UT_r3

value: Dox


title: RNAseq_neurons_BANP_dTAG_1h_r3


title: RNAseq_neurons_BANP_dTAG_UT_r2


title: lox5-6_24hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: Array fnr_anaerobic_NO3_10

type: RNA

city: Greifswald

first: Christian

last: Kohler

address: Ferdinand Sauerbruch Strasse 1

department: Friedrich Loeffler Institue of Medical Microbiology

country: Germany

institute: University Medicine Greifswald

description: This sample is of Dfnr mutant of Burkholderia pseudomallei E8 and the one of three Dfnr mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.

hyb_protocol: Microarray hybridizations were performed at 65°C in a MAUI hybridization station (BioMicro Systems, USA) for 17hrs.

scan_protocol: The slides were washed, dried in a centrifuge at 500rpm for 2mins, and scanned on an Axon Genepix 4000B scanner (Molecular Devices, USA) at a resolution of 5 microns

data_processing:
The raw data (.pair file) was subjected to Robust Multi-array Average (RMA) procedure as implemented in Roche NimbleGen (USA) and normalized using the quantile normalization method developed from Bolstad et al. (2005) (Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003). "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias". Bioinformatics. 19 (2): 185–93.
processed data: RMA-normalized, averaged gene-level signal intensity

organism: Burkholderia pseudomallei

source_name: Burkholderia pseudomallei Dfnr mutant

label_protocol: 1.5 µg of obtained cDNA were used for the labeling procedure using the ULSTM arrayCGH Labeling Kit (Leica Microsystem) according to the manufacturer´s instructions.

growth_protocol: B. pseudomallei was cultivated in 60 ml Lysogeny broth at 37 °C and 140 rpm OD650nm 0.5 under aerobic conditions. Aerobic samples (1-6) were taken at this time point. Samples  7-42 were also grown aerobically to OD650nm 0.5 but then either incubated anaerobically (tightly closed  Falcon tubes) without nitrate (samples 7-12, 19-24, 31-36) or with 50 mM nitrate (samples 13-18, 24-30, 37-42) for 30 min under various agitation.

extract_protocol: 50 ml of cell suspension were harvested and centrifuged at 2°C at 10,000 g for 5 min. The cell pellets were quickly resuspended in 1 ml of Trizol Reagent (Invitrogen). After the RNA extraction procedure according to manufacturer's instructions, the integrity of the RNA was assessed by agarose gel electrophoresis and tested for the absence of DNA contamination by PCR.

treatment_protocol: 100 µg total RNA per sample were treated with DNA-freeTM Kit from Ambion (USA) according to the manufacturer's instructions to obtain DNA-free RNA. After precipitation of the RNA with ethanol and resuspension in nuclease free water, 10 µg per sample were subjected to ribosomal RNA depletion using the MICROBExpressTM kit from Ambion (USA) according to the manufacturer's instructions. Afterwards, 2 µg of purified mRNA were used for cDNA synthesis utilizing Superscript II Reverse Transcriptase (Life Technologies).

tag: phenotype

value: virulent


title: EC_DNA_AGM_cell158


title: EC_DNA_AGM_cell157


title: Array fnr_anaerobic_NO3_9


title: RNAseq_ESC_Ngn2_uninduced_BANP_dTAG_UT_r3

source_name: embryonic stem cells

value: embryonic stem cells

tag: genotype

value: untreated


title: RNAseq_neurons_BANP_dTAG_UT_r1


title: EC_DNA_AGM_cell156


title: lox5-8_0hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

value: stem

value: seeding


title: EC_DNA_AGM_cell155


title: Array fnr_anaerobic_NO3_8


title: lox5-5_12hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

value: mutant


title: RNAseq_ESC_Ngn2_uninduced_BANP_dTAG_UT_r2


title: lox5-3_12hai_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: Array wild type_anaerobic_NO3_10

description: This sample is of wild-type Burkholderia pseudomallei E8 and the first of one wild-type biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.

source_name: Burkholderia pseudomallei wild type E8


title: EC_DNA_AGM_cell154


title: B73_0hai_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

value: CK


title: Array wild type_anaerobic_NO3_9


title: RNAseq_ESC_Ngn2_uninduced_BANP_dTAG_UT_r1

value: Ngn2 insertion, BANP dTag


title: EC_DNA_AGM_cell153

value: endothelial cells


title: RNAseq_ESC_wt_r6


title: B73_24hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: Array wild type_anaerobic_NO3_8


title: EC_DNA_AGM_cell152

value: aorta-gonad-mesonephros (AGM)


title: Array fnr_anaerobic_9

description: This sample is of Dfnr mutant of Burkholderia pseudomallei E8 and the one of three Dfnr mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition without nitrate.


title: RNAseq_ESC_wt_r5


title: B73_12hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: lox5-4_0hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: RNAseq_ESC_wt_r4


title: B73_0hai_2

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: EC_DNA_AGM_cell150


title: Array fnr_anaerobic_8


title: Array fnr_anaerobic_7


title: RNAseq_ESC_tko_dTAG_6h_r2

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_6h_R2

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

treatment_protocol: Cells (2.5x105) were seeded into 6 well plates the day before the experiment. DNMT TKO cells were teated with the dTAG13 compound to remove Banp over a time course of: 1, 2, 4 and 6 hours.

value: Dnmt triple knock-out, dTag

value: 6h treated


title: Array wild type_anaerobic_8

description: This sample is of wild-type Burkholderia pseudomallei E8 and the one of three wild-type biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition without nitrate.


title: EC_DNA_AGM_cell149


title: Array wild type_anaerobic_9


title: B73_24hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区

value: wild type


title: RNAseq_ESC_tko_dTAG_6h_r3

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_6h_R3


title: EC_DNA_AGM_cell148


title: Array wild type_anaerobic_7


title: EC_DNA_AGM_cell147


title: B73_0hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: RNAseq_ESC_tko_dTAG_4h_r2

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_4h_R2

value: 4h treated


title: B73_24hai_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: B73_12hai_1

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: EC_DNA_AGM_cell151


title: Array narL_anaerobic_NO3_7

description: This sample is of DnarL mutant of Burkholderia pseudomallei E8 and the one of three DnarL mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.

source_name: Burkholderia pseudomallei DnarL mutant


title: RNAseq_ESC_tko_dTAG_4h_r3

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_4h_R3


title: Array narL_anaerobic_NO3_6


title: EC_DNA_AGM_cell146


title: RNAseq_ESC_tko_dTAG_4h_r1

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_4h_R1


title: RNAseq_ESC_tko_dTAG_6h_r1

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_6h_R1


title: B73_12hai_3

address: 江苏省南京市玄武区卫岗1号南京农业大学卫岗校区


title: EC_DNA_AGM_cell143


title: EC_DNA_AGM_cell142


title: OP50_12h_rep3 [miRNA-seq]

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were analyzed using mirDeep2 (ver. 2.0.1.1, (Friedländer et al., 2012)) aligned to the C. elegans miRbase (Kozomara et al., 2019) reference (WBcel235).
Raw reads counts are from mirDeep2.
Genome_build: WBcel235
Supplementary_files_format_and_content: miRNA_rawcounts.txt: Tab-delimited text file includes raw counts for each Sample.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: N2 worm populations were synchronized and, when reaching the L4 larval stage, were exposed to the different Bt strains in 9 cm peptone-free NGM (PFM) plates inoculated with 250 µl of Bt spore solution diluted with E. coli OP50 OD 5.

extract_protocol:
Worms were centrifuged and washed in M9 buffer three times and then transferred to TRIzol lysis Reagent™ (Invitrogen). Worms were cyclically thawed and frozen four times using liquid nitrogen and a heating block at 37°C to allow the TRIzol reagent to enter the cells and better preserve the RNA. miRNA were simultaneously extracted using the NucleoSpin® miRNA purification kit (Macherey-Nagel) and stored at -80°C.
miRNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Worms were exposed to OP50 and BT at the stage L4. The experiments with BT were performed at 20°C.

value: whole body

value: E. coli OP50

tag: timepoint

value: 12 hour


title: RNAseq_ESC_tko_dTAG_2h_r1

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_2h_R1

value: 2h treated


title: EC_DNA_AGM_cell141


title: OP50_12h_rep1 [miRNA-seq]


title: EC_DNA_AGM_cell139


title: EC_DNA_AGM_cell140


title: 9_OHETB6_Parabiosis_RNASeq [9_S25]

source_name: Old heterochronically parabiosed B6

tag: age at procedure

value: 22 months old

tag: parabiont status

value: Old heterochronically parabiosed B6

value: Male

value: Hematopoietic stem cells


title: EC_DNA_AGM_cell145

tag: cell type


title: RNAseq_ESC_tko_dTAG_2h_r3

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_2h_R3

value: embryonic stem cells


title: OP50_12h_rep4 [miRNA-seq]


title: Array narL_anaerobic_6

description: This sample is of DnarL mutant of Burkholderia pseudomallei E8 and the one of three DnarL mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition without nitrate.

value: virulent


title: RNAseq_ESC_tko_dTAG_UT_r3

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_UT_R3

value: untreated


title: EC_DNA_AGM_cell138

value: endothelial cells

tag: antibody


title: RNAseq_ESC_tko_dTAG_UT_r2

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_UT_R2


title: BT679_12h_rep4 [miRNA-seq]


title: EC_DNA_AGM_cell144

value: aorta-gonad-mesonephros (AGM)


title: Array narL_anaerobic_NO3_5


title: Array wild type_anaerobic_6


title: BT679_12h_rep3 [miRNA-seq]


title: Array wild type_anaerobic_4


title: BT679_12h_rep2 [miRNA-seq]


title: BT407_12h_rep1 [miRNA-seq]


title: OP50_12h_rep2 [miRNA-seq]


title: EC_DNA_AGM_cell134


title: Array wild type_anaerobic_NO3_6

description: This sample is of wild-type Burkholderia pseudomallei E8 and the one of three wild-type biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.


title: BT679_12h_rep1 [miRNA-seq]


title: BT247_12h_rep4 [miRNA-seq]


title: RNAseq_ESC_tko_r6

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_R6

value: Dnmt triple knock-out


title: RNAseq_ESC_tko_r3

description:
mRNA_knownGene_mm10_tkowt.csv
EyTKO_R3


title: RNAseq_ESC_tko_dTAG_1h_r2

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_1h_R2

value: Dnmt triple knock-out, dTag

value: 1h treated


title: BT407_12h_rep4 [miRNA-seq]

value: wild type


title: Array wild type_anaerobic_NO3_5


title: BT247_12h_rep3 [miRNA-seq]

value: whole body


title: EC_DNA_AGM_cell131


title: RNAseq_ESC_tko_dTAG_1h_r1

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_1h_R1


title: BT247_12h_rep2 [miRNA-seq]


title: BT407_12h_rep3 [miRNA-seq]


title: Array narL_anaerobic_5


title: BT407_12h_rep2 [miRNA-seq]


title: Array regA_anaerobic_NO3_1

description: This sample is of DregA mutant of Burkholderia pseudomallei E8 and the one of four DregA mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.

source_name: Burkholderia pseudomallei DregA mutant

value: avirulent


title: RNAseq_ESC_tko_dTAG_2h_r2

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_2h_R2


title: EC_DNA_AGM_cell130


title: RNAseq_ESC_wt_r3

description:
mRNA_knownGene_mm10_tkowt.csv
Eywt_R3


title: Array wild type_anaerobic_NO3_7


title: Array narL_anaerobic_4


title: RNAseq_ESC_tko_r2

description:
mRNA_knownGene_mm10_tkowt.csv
EyTKO_R2


title: EC_DNA_AGM_cell137


title: RNAseq_ESC_tko_dTAG_UT_r1

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_dTAG_UT_R1


title: EC_DNA_AGM_cell136


title: RNAseq_ESC_wt_r1

description:
mRNA_knownGene_mm10_tkowt.csv
Eywt_R1


title: EC_DNA_AGM_cell135


title: Array regA_anaerobic_NO3_4


title: RNAseq_ESC_tko_r4

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_R4


title: OP50_6h_rep3 [miRNA-seq]

value: E. coli OP50

value: 6 hour


title: RNAseq_ESC_tko_r5

description:
mRNA_knownGene_mm10_tkodegronTimeCourse.csv
EyTKO_R5


title: Array wild type_anaerobic_NO3_2

description: This sample is of wild-type Burkholderia pseudomallei E8 and the one of four wild-type biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition with 50 mM nitrate.


title: Array wild type_anaerobic_5

description: This sample is of wild-type Burkholderia pseudomallei E8 and the one of three wild-type biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition without nitrate.


title: EC_DNA_AGM_cell133


title: EC_DNA_AGM_cell126


title: OP50_6h_rep1 [miRNA-seq]


title: OP50_6h_rep2 [miRNA-seq]


title: Array regA_anaerobic_NO3_2


title: EC_DNA_AGM_cell132


title: RNAseq_ESC_tko_r1

description:
mRNA_knownGene_mm10_tkowt.csv
EyTKO_R1


title: EC_DNA_AGM_cell124


title: Array wild type_anaerobic_NO3_4


title: Array regA_anaerobic_NO3_3


title: BT247_12h_rep1 [miRNA-seq]

value: 12 hour


title: EC_DNA_AGM_cell129


title: BT407_6h_rep2 [miRNA-seq]


title: RNAseq_ESC_wt_r2

description:
mRNA_knownGene_mm10_tkowt.csv
Eywt_R2


title: EC_DNA_AGM_cell122


title: OP50_6h_rep4 [miRNA-seq]


title: Array wild type_anaerobic_NO3_3


title: Array wild type_anaerobic_3


title: Array regA_aerobic_3

description: This sample is of DregA mutant of Burkholderia pseudomallei E8 and the one of three DregA mutant biological replicates used in this experiment, each from separate cultures. Aerobic growth condition.


title: BT679_6h_rep4 [miRNA-seq]


title: EC_DNA_AGM_cell120


title: EC_DNA_AGM_cell128


title: Array wild type_anaerobic_NO3_1


title: Array regA_anaerobic_3

description: This sample is of DregA mutant of Burkholderia pseudomallei E8 and the one of three DregA mutant biological replicates used in this experiment, each from separate cultures. Anaerobic growth condition without nitrate.


title: BT679_6h_rep3 [miRNA-seq]


title: EC_DNA_AGM_cell125


title: BT407_6h_rep4 [miRNA-seq]


title: Array regA_aerobic_2


title: BT679_6h_rep1 [miRNA-seq]


title: EC_DNA_AGM_cell118


title: EC_DNA_AGM_cell127


title: Array wild type_anaerobic_2


title: Array regA_anaerobic_1


title: Array wild type_anaerobic_1


title: EC_DNA_AGM_cell123


title: BT247_6h_rep4 [miRNA-seq]


title: EC_DNA_AGM_cell119


title: EC_DNA_AGM_cell121


title: Array regA_anaerobic_2


title: Array wild type_aerobic2

description: This sample is of wild-type Burkholderia pseudomallei E8 and the one of three wild-type biological replicates used in this experiment, each from separate cultures. Aerobic growth condition.


title: EC_DNA_AGM_cell116


title: EC_DNA_AGM_cell115


title: Array wild type_aerobic1


title: BT247_6h_rep2 [miRNA-seq]


title: BT679_6h_rep2 [miRNA-seq]


title: Array regA_aerobic_1


title: BT407_6h_rep1 [miRNA-seq]


title: BT407_6h_rep3 [miRNA-seq]


title: EC_DNA_AGM_cell117


title: Array wild type_aerobic3


title: ATACseq_ESC_dTAG_4h_r2

description: 4h treated

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ATAC-seq reads were trimmed using cutadapt version 1.18, (Martin, M. EMBnet.journal 17, 10 (2011)) with parameters -a CTGTCTCTTATACACA -A CTGTCTCTTATACACA -m 5 --overlap=1 and then mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters.
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 and pairedAsSingle=TRUE . The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

extract_protocol: DNA was purified using the MinElute PCR Purification Kit (Qiagen).

treatment_protocol: Wild-type ES cells and Banp degron tagged ES cells were teated with the dTAG13 compound to remove Banp over a time course of: 1, 2, 4, 6 and 20 hours. ATAC-seq was performed according to the previously described protocol(Corces, M. R. et al. Nat. Methods, 2017) with modifications. Briefly, 5x104 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500g for 5 min in a pre-chilled (4°C). Cell pellets were suspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g (4°C). Nuclei were suspended in 50 μl of Tn5 transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 rpm. Reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen). The eluted transposed DNA was subjected to PCR amplification using Q5 High-Fidelity Polymerase (NEB) for 7 cycles.

value: Banp degron tagged

tag: time point

tag: agent

value: dTag


title: BT247_6h_rep3 [miRNA-seq]

tag: treatment


title: ATACseq_ESC_dTAG_20h_r2

description: 20h treated


title: EC_DNA_AGM_cell114


title: BT247_6h_rep1 [miRNA-seq]


title: EC_DNA_AGM_cell110


title: EC_DNA_AGM_cell113


title: ATACseq_ESC_dTAG_UT_r2

description: untreated


title: ATACseq_ESC_dTAG_6h_r2

description: 6h treated


title: OP50_2h_rep4 [miRNA-seq]

value: 2 hour


title: EC_DNA_AGM_cell112


title: BT407_2h_rep4 [miRNA-seq]


title: EC_DNA_AGM_cell111


title: OP50_2h_rep3 [miRNA-seq]


title: ATACseq_ESC_dTAG_2h_r2

description: 2h treated

value: embryonic stem cells


title: BT407_2h_rep3 [miRNA-seq]


title: ATACseq_ESC_dTAG_1h_r2

description: 1h treated


title: 3D7-A Control gDNA Replicate 2

type: genomic

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

hyb_protocol: Microarray hybridizations were carried out using a MAUI hybridization system (BioMicro Systems) as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].

scan_protocol: Scanning was performed with a GenePix Pro 6.0 (Axon Instruments) as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].

data_processing: Microarray background for each channel (635 nm for Cy5 and 532 nm for Cy3) was calculated as the minimum between the median intensity of the 100 spots with lowest intensity and the median of the local background of all spots in the microarray. Spots with a signal in both channels lower than 1.5 fold times the background were eliminated. When a spot had intensity higher than 1.5 times the background in only one of the two channels, the other channel was assigned a value of 1.5 times the background of this channel, to avoid extreme ratio values. Background was subtracted before normalization. Log2(Cy5/Cy3) was normalized using LOESS.

organism: Plasmodium falciparum

label_protocol: Test sample, Cy5; reference pool, Cy3. Labeling was carried out as previously described [Bozdech Z et al Genome biol 2003, 4(2):R9].

growth_protocol: Parasites were cultured under standard conditions in media containing Albumax II  and no human serum, in a 5% CO2, 3% O2, 92% N2 atmosphere. Tight synchronization was achieved by Percoll or magnet purification of schizonts followed by sorbitol lysis 5 h later, to obtain a population of a defined age window of 0–5 h post- invasion. Parasites were cultured undisturbed for different periods of time (8, 16, 24, 32 and 40 h) before collecting in TRIzol for total RNA extraction.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions. For genomic DNA (gDNA) extraction, parasites were lysed with SDS and gDNA purified by double phenol/chloroform extraction and ethanol precipitation, followed by mild sonication.

treatment_protocol: All cultures (control and previously heat shock-adapted lines) were maintained at 37 ºC for the transcriptome characterization.

tag: status

value: Control

tag: age (hpi)

value: mix

tag: replicate

value: Biological replicate 2

source_name: 3D7-A genomic DNA

value: Mixed states


title: 3D7-A Heat Shock gDNA Replicate 2

value: Heat shock-adapted


title: BT407_2h_rep2 [miRNA-seq]


title: ATACseq_ESC_dTAG_6h_r1

description: 6h treated


title: ATACseq_ESC_dTAG_20h_r1

description: 20h treated


title: OP50_2h_rep2 [miRNA-seq]


title: ATACseq_ESC_wt_r2

description: untreated


title: OP50_2h_rep1 [miRNA-seq]


title: 3D7-A Heat Shock gDNA Replicate 1

value: Biological replicate 1


title: EC_DNA_AGM_cell108

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell109


title: EC_DNA_AGM_cell107


title: ATACseq_ESC_dTAG_4h_r1

description: 4h treated


title: EC_DNA_AGM_cell106


title: EC_DNA_AGM_cell105


title: BT407_2h_rep1 [miRNA-seq]

value: wild type

value: whole body


title: EC_DNA_AGM_cell104


title: ATACseq_ESC_dTAG_1h_r1

description: 1h treated


title: BT679_2h_rep4 [miRNA-seq]


title: 3D7-A Heat Shock, 24h Replicate 2

source_name: 3D7-A mixed stage Reference Pool

value: Samples of synchronized cultures covering the whole asexual cycle.


title: EC_DNA_AGM_cell103

source_name: aorta-gonad-mesonephros (AGM)


title: 3D7-A Control gDNA Replicate 1


title: 3D7-A Heat Shock, 36h Replicate 2


title: BT679_2h_rep3 [miRNA-seq]


title: 3D7-A Heat Shock, 40h Replicate 2


title: ATACseq_ESC_dTAG_UT_r1

description: untreated


title: BT679_2h_rep2 [miRNA-seq]


title: ATACseq_ESC_wt_r1

description: untreated


title: 3D7-A Heat Shock, 16h Replicate 2


title: EC_DNA_AGM_cell102


title: MNaseseq_ESC_dTAG_4h_r2

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. MNase-seq reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.

extract_protocol:
DNA was purified using a PCR Purification Kit (Qiagen).
Sequencing libraries were prepared from 1 μg of MNase digested DNA using the NEBNext Ultra Library Preparation Kit (NEB) with 4 PCR amplification cycles.

treatment_protocol: Wild-type cells were teated with the dTAG13 compound to remove Banp over a time course of: 1 and 4 hours. A custom MNase protocol was used combining previously published methods(Gaidatzis, D. et al. PLoS Genet., 2014); Cui, K. & Zhao, K. Methods Mol. Biol., 2012); Barisic, D. et al. Nature, 2019). In brief, 250,000 cells were resuspended in 250 μl of Buffer 1 (0.3M Sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 2mM EDTA, 0.5mM DTT, 1x Complete Protease Inhibitor Cocktail (PIC, Roche), 0.2mM spermine, 1mM spermidine) with detergent (Buffer 1 + 0.02% NP-40) and incubated on ice for 5min. Nuclei were then pelleted (300g, 5min, 4°C). Nuclei were gently suspended in 250 μl of Buffer 2 (0.3M Sucrose, 15mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.5mM DTT, 1 x PIC, 0.2mM spermine, 1mM spermidine). Nuclei integrity was checked at this point using the TC20 cell analyzer (BioRad). We made sure to recover at least 75% of nuclei compared to the starting cell number. Nuclei were pelleted (5min, 300g, 4°C) and suspended in 100 μl MNase buffer (0.3M Sucrose, 50mM Tris pH 7.5, 4mM MgCl2, 1mM CaCl2, 1 x PIC). 1U of MNase S7 micrococcal nuclease (Roche) was added. Nuclei were incubated (30min, 37°C). The reaction was stopped by adding EDTA to a final concentration of 5 mM. SDS (to a final concentration 1%) and Proteinase K (200 μg/mL) were then added to the samples, followed by incubation at 55°C for 1h with shaking. DNA was purified using a PCR Purification Kit (Qiagen). Purified DNA was loaded on a 1% agarose gel or on the Agilent Bioanalyzer to determine digestion efficiency.

value: 4h treated


title: EC_DNA_AGM_cell101


title: 3D7-A Control, 40h Replicate 2


title: BT247_2h_rep4 [miRNA-seq]


title: BT679_2h_rep1 [miRNA-seq]


title: MNaseseq_ESC_dTAG_4h_r1


title: BT247_2h_rep3 [miRNA-seq]


title: 3D7-A Heat Shock, 8h Replicate 2


title: ATACseq_ESC_dTAG_2h_r1

description: 2h treated


title: 3D7-A Control, 36h Replicate 2


title: MNaseseq_ESC_dTAG_1h_r2

value: 1h treated


title: BT247_2h_rep2 [miRNA-seq]


title: 3D7-A Control, 24h Replicate 2


title: EC_DNA_AGM_cell98


title: MNaseseq_ESC_dTAG_1h_r1


title: BT247_2h_rep1 [miRNA-seq]


title: MNaseseq_ESC_dTAG_UT_r2

value: untreated


title: MNaseseq_ESC_dTAG_UT_r1


title: 3D7-A Control, 8h Replicate 2


title: 3D7-A Control, 16h Replicate 2


title: EC_DNA_AGM_cell96


title: EC_DNA_AGM_cell100


title: 3D7-A Heat Shock, 40h Replicate 1


title: 3D7-A Heat Shock, 36h Replicate 1


title: EC_DNA_AGM_cell95


title: SLAMseq_ESC_wt_dTag_20h_SLAM_r3

description: mRNA_knownGene_mm10_wtdegronTimeCourse.csv, EISA_exon_knownGene_mm10_wtdegronTimeCourse.csv, EISA_intron_knownGene_mm10_wtdegronTimeCourse.csv, SLAM_conversionT_knownGene_mm10_wtdegronTimeCourse.csv

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. slamdunk (version 0.3.4, Neumann et al, BMC Bioinformatics, 2019) was run with the following parameters: slampdunk map -5 0, slamdunk filter -mi 0.9, slamdunk snp -c 1 -f 0.2. Finally, slamdunk count was run on exonic segments as defined by the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.10.0).
Supplementary_files_format_and_content: Exonic (EISA_exon_knownGene_mm10_wtdegronTimeCourse.csv) and intronic counts (EISA_intron_knownGene_mm10_wtdegronTimeCourse.csv) for exon-intron split analysis (EISA) were determined as described (Gaidatzis, Burger, Stadler et al, Nature Biotech 2015). SLAM_conversionT_knownGene_mm10_wtdegronTimeCourse.csv: Number of Ts converted to Cs on exonic segments. mRNA_knownGene_mm10_wtdegronTimeCourse.csv: Alignments overlapping any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
Cells were lysed directly in TRIzol (500 μl, Invitrogen). Samples were processed according to the SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen). Briefly, added 100 µl chloroform:isoamyl alcohol mix (24:1) to TRIzol lysate, shake tube vigorously (15 sec), incubate at RT for 3 min. Centrifuge at (16,000g, 15 min, 4°C) Transfer the aqueous phase to a new tube. Measure the volume of the aqueous phase using a pipette. Add 1 µl of Carrier Substance, 1/1,000th volumes of Reducing Agent, and 1 volume of 2-propanol. Vortex well. Incubate for at RT (10 min) and centrifuge at (16,000g, 20 min, 4°C). Wash pellet with 500 µl 75 % EtOH and 0.5 µl of Reducing Agent. Vortex well and centrifuge (7,500g, 5 min, 4°C). Remove supernatant, let pellet dry for 5-10 min, and resuspend it in 16 µl of Elution Buffer. Incubate for 10 min, 55°C and measure the concentration by NanoDrop. Prepare a mastermix containing 5 µl of freshly prepared 100 mM Iodoacteamide, 25 µl of Organic Solvent, and 5 µl of Sodium Phosphate per sample.
Sequencing libraries were prepared from 100ng of purified total RNA for three biological replicates using TruSeq stranded Total RNA Library Prep (Illumina).

treatment_protocol: Wild-type ES cells and Banp degron tagged RS cells were teated with the dTAG13 compound to remove Banp over a time course of: 1, 2, 4, 6 and 20 hours. Nascent RNA was pulse labeled with 4-thiouridine correspondingly for: 0.5, 1.5, 2, 2 and 2 hours. Cells (5x105) were seeded into 6 well plates the day before the experiment. The media was exchanged to induce Banp degradation by the addition of the dTAG13 compound (500 nM, Sigma) for at least 30 min. After this time, nascent RNA transcripts were pulse labeled by the addition of 4-thiouridine (s4U) (200 μM, Lexogen) to the medium for a minimum of 30 min and up to 2 hours across the Banp degradation time course.

value: wild type, dTag

value: dTag 20h, s4U 2h


title: EC_DNA_AGM_cell94


title: EC_DNA_AGM_cell93


title: SLAMseq_ESC_wt_dTag_20h_SLAM_r2

value: embryonic stem cells


title: 3D7-A Heat Shock, 16h Replicate 1


title: EC_DNA_AGM_cell99


title: EC_DNA_AGM_cell97


title: SLAMseq_ESC_wt_dTag_20h_SLAM_r1


title: EC_DNA_AGM_cell92


title: 3D7-A Control, 40h Replicate 1

value: Control


title: 3D7-A Heat Shock, 8h Replicate 1


title: SLAMseq_ESC_wt_dTag_6h_SLAM_r3

value: dTag 6h, s4U 2h


title: 3D7-A Heat Shock, 24h Replicate 1


title: SLAMseq_ESC_wt_dTag_6h_SLAM_r2


title: EC_DNA_AGM_cell90


title: EC_DNA_AGM_cell91


title: 3D7-A Control, 36h Replicate 1


title: Treg_rapamycin_A

city: Napoli

first: Paola

last: De Candia

address: via Pansini 5

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI NAPOLI FEDERICO II - Dipartimento di Medicina molecolare e Biotecnologie mediche

description:
raw data file:
210410 slide 251485043437  Area 3  Cy3 A 25 plus rapa  Cy5 B 25.gpr
Gene expression from Treg cells that were isolated from peripheral blood, pre-treated for 1 hour with rapamycin and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

hyb_protocol: 5µg of each differentially labelled aaRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's Homo sapiens Microarray Kit 4x44k for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing and drying on the Axon 4200AL Scanner using three color scan setting for 4x44k array slides.

data_processing: The microarray images were segmented and the median intensity of each spot was estimated by the software GenePixPro® 6.0 (Axon). The data were then imported into R software and preprocessed by the BioConductor package Limma.

organism: Homo sapiens

source_name: Treg cells treated with rapamycin

label_protocol: The samples (500–1000 ng) were indirectly labeled using the T7 amplification method (Amino Allyl MessageAmp II amplified RNA (Johnston et al.) Amplification Kit; Ambion, USA), according to the manufacturer’s recommendations. RNA (5 μg/sample) was labeled using monoreactive Cy3 and Cy5 dyes (GE Healthcare, U.K.) or monoreactive Alexa Fluor 488 (Invitrogen, USA), followed by purification according to the manufacturer’s instructions. Labeled aRNAs (800 ng/sample) were hybridized onto Agilent Whole Human Genome 4x44K, according to the manufacturer’s recommendations. The slides were then washed and scanned by an Axon GenePix 4200 AL scanner (Molecular Devices, USA).

growth_protocol: Human Treg (CD4+CD25high) and Tconv (CD4+CD25−) cells were purified from PBMCs from buffy coats of human healthy donors by magnetic cell separation. Cells were immediately collected (freshly isolated condition) or cultured for 12 hours in RPMI 1640 medium supplemented with 100 U/ml penicillin and 100 μg/ml streptomycin and with 5% AB human serum. They were stimulated with anti-CD3 and anti-CD28-coated beads (0.2 beads per cell). For transient mTOR inhibition, T cells were pretreated in vitro for 1 h with rapamycin at a final concentration of 100 nM. Cells were washed extensively with serum-free culture medium and cultured, as previously described.  For in vitro leptin blocking experiments, we used human anti-leptin neutralizing mAb at a final concentration of 20 μg/ml.

extract_protocol: Total RNA was isolated from human T cells using the RNAqueous-4PCR Kit (Ambion, USA), following the manufacturer’s instruction. RNA was quantified by NanoDrop, and the amount and its quality were confirmed in an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

value: peripheral blood isolated Treg cells

tag: disease state

value: healthy


title: SLAMseq_ESC_wt_dTag_6h_SLAM_r1


title: 3D7-A Control, 16h Replicate 1


title: Treg_leptin mAb_B

description:
raw data file:
210410 slide 251485043437  Area 3  Cy3 A 25 plus rapa  Cy5 B 25.gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation and a leptin blocking antibody

source_name: Treg cells treated with leptin mAb

treatment_protocol: For transient mTOR inhibition, T cells were pretreated in vitro for 1 h with rapamycin at a final concentration of 100 nM. Cells were washed extensively with serum-free culture medium and cultured, as previously described.  For in vitro leptin blocking experiments, we used human anti-leptin neutralizing mAb at a final concentration of 20 μg/ml.


title: 14-091E1_CRPC_LUNG

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC lung metastasis

extract_protocol:
Total RNA was isolated from CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: lung

tag: patient

tag: molecular phenotype


title: SLAMseq_ESC_wt_dTag_4h_SLAM_r1

tag: genotype

value: dTag 4h, s4U 2h

tag: strain


title: SLAMseq_ESC_wt_dTag_4h_SLAM_r2


title: Gamma irradiation sample 3

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

data_processing:
Base-calling by bcl2fastq (v2.19.0.316)
Adapter clipping by adapterremoval (v2.3.0), Parameters: –trimns  –trimqualities  –minquality '20'  and –minlength '30'
Read alignment by HISAT2 (v2.1.0), Parameters: –fr and rna-strandness: RF
Read counting by htseq-count (v0.11.2), Parameters –mode intersection-strict –stranded yes and –type exon
Genome_build: human genome hg38 (GENCODE release 31)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CAR-123-NK-92 cells

growth_protocol: CD123-directed NK-92 cells were cultured in X-VIVOTM 10 medium with recombinant transferrin and L-glutamine, without gentamicin and phenol red, xeno-free, (Biozym Scientific GmbH), supplemented with 5 % heat-inactivated human serum and 100 IU/mL IL-2

extract_protocol:
Cell pellets from 10^6 cells per sample were solved and frozen in Qiazol. RNA was extracted according to the miRNeasy mini protocol (Qiagen) followed by two steps of DNase-digestion (TURBO DNA free Kit, Ambion)
Truseq-Stranded mRNA Sample Prep kit (Illumina, Inc, San Diego, CA) according to manufacturers’ protocol. Molarity of each library was calculated and equal amounts were pooled and used for sequencing (10 pM).

treatment_protocol: Cells were LEE-irradiated using a custom-built irradiation device, equipped with an electron emitter. Cells were placed into sterile bags and processed at a bag transportation velocity of 5 mm/s through the LEEI-area. LEE-irradiation corresponded to a dose of 11 Gy. Gamma irradiation was performed at a dose of 10 Gy, using a Cs-137 source. For both LEEI and gamma irradiation, up to 1.5 × 108 cells were irradiated in a volume of 20 mL of cell culture medium. Directly after irradiation, the cell concentration was adjusted to 0.3 × 106 viable cells/mL with fresh cell culture medium. In order to check for irradiation-independent effects, control cells were processed in parallel without applying irradiation.

value: CAR-123-NK-92 cells

value: Gamma irradiated with 10Gy

tag: cultivation

value: 2h cultivation following irradiation


title: Treg_rapamycin_C

tag: tissue


title: EC_DNA_AGM_cell86

tag: cell type

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: 3D7-A Control, 8h Replicate 1

value: Biological replicate 1

value: Samples of synchronized cultures covering the whole asexual cycle.


title: Treg_medium_B

description:
raw data file:
210410 slide 251485043437  Area 2 Cy3 A 25 plus 3 28  Cy5 B 25 .gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli

source_name: Treg cells unstimulated


title: EC_DNA_AGM_cell89

tag: antibody


title: Treg_fresh_C

description:
raw data file:
210410 slide 251485043437  Area 2 Cy3 A 25 plus 3 28  Cy5 B 25 .gpr
Gene expression from Treg cells immediately upon peripheral blood isolation

source_name: Treg cells freshly isolated


title: SLAMseq_ESC_wt_dTag_4h_SLAM_r3

value: wild type, dTag


title: Treg_anti-CD3CD28_A

description:
raw data file:
210410 slide 251485043437  Area 2 Cy3 A 25 plus 3 28  Cy5 B 25 .gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

source_name: Treg cells anti-CD3/CD28 stimulated


title: Treg_anti-CD3CD28_C

description:
raw data file:
210410 slide 251485043437  Area 1 Cy3 A 25 plus med  Cy5 B 25 p.gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation


title: Treg_medium_A

description:
raw data file:
210410 slide 251485043437  Area 1 Cy3 A 25 plus med  Cy5 B 25 p.gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli


title: 13-101K3_CRPC_LN

source_name: CRPC lymph node (LN) metastasis

value: lymph node (LN)


title: Gamma irradiation sample 2


title: Treg_anti-CD3CD28_B


title: EC_DNA_AGM_cell88


title: EC_DNA_AGM_cell87


title: SLAMseq_ESC_wt_dTag_2h_SLAM_r3

source_name: embryonic stem cells

value: embryonic stem cells

value: dTag 2h, s4U 1.5h


title: 01-002N1_CRPC_LN


title: 3D7-A Control, 24h Replicate 1

value: Control


title: EC_DNA_AGM_cell85


title: Gamma irradiation sample 1


title: LEEI irradiation sample 3

value: LEEI irradiated with 200keV 0.05mA


title: SLAMseq_ESC_wt_dTag_2h_SLAM_r1


title: EC_DNA_AGM_cell84


title: SLAMseq_ESC_wt_dTag_1h_SLAM_r3

value: dTag 1h, s4U 30min


title: Treg_rapamycin_B

description:
raw data file:
210410 slide 251485043436  Area 3 Cy3 A 25 plus a lep Cy5 B 25 plus rapa  .gpr
Gene expression from Treg cells that were isolated from peripheral blood, pre-treated for 1 hour with rapamycin and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

value: peripheral blood isolated Treg cells

value: healthy


title: Treg_medium_C

description:
raw data file:
210410 slide 251485043436  Area 2 Cy3 A 25 plus fresh Cy5 B 25 minus rapa .gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli


title: Treg_leptin mAb_C

description:
raw data file:
210410 slide 251485043436  Area 3 Cy3 A 25 plus a lep Cy5 B 25 plus rapa  .gpr
Gene expression from Treg cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation and a leptin blocking antibody


title: Treg_leptin mAb_A


title: EC_DNA_AGM_cell82


title: EC_DNA_AGM_cell83


title: LEEI irradiation sample 1


title: EC_DNA_AGM_cell81


title: Control sample 3

value: Not irradiated

value: cultivation for 2h


title: LEEI irradiation sample 2

value: CAR-123-NK-92 cells


title: SLAMseq_ESC_wt_dTag_1h_SLAM_r1


title: SLAMseq_ESC_wt_dTag_2h_SLAM_r2


title: Control sample 2


title: EC_DNA_AGM_cell80


title: EC_DNA_AGM_cell79


title: Control sample 1


title: SLAMseq_ESC_wt_dTag_UT_SLAM_r1

value: dTag untreated, s4U 2h


title: Treg_fresh_A

description:
raw data file:
210410 slide 251485043436  Area 2 Cy3 A 25 plus fresh Cy5 B 25 minus rapa .gpr
Gene expression from Treg cells immediately upon peripheral blood isolation


title: EC_DNA_AGM_cell78

value: endothelial cells


title: Tconv_rapamycin_A

description:
raw data file:
210410 slide 251485043436  Area 1 Cy3 A 25 minus rapa Cy5 B 25 .gpr
Gene expression from Tconv cells that were isolated from peripheral blood, pre-treated for 1 hour with rapamycin and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

source_name: Tconv cells treated with rapamycin

value: peripheral blood isolated Tconv cells


title: SLAMseq_ESC_wt_dTag_1h_SLAM_r2


title: Treg_fresh_B

description:
raw data file:
210410 slide 251485043436  Area 1 Cy3 A 25 minus rapa Cy5 B 25 .gpr
Gene expression from Treg cells immediately upon peripheral blood isolation


title: EC_DNA_AGM_cell77

value: aorta-gonad-mesonephros (AGM)


title: Tconv_rapamycin_C


title: SLAMseq_ESC_wt_SLAM_r3

value: wild type

value: s4U 2h


title: SLAMseq_ESC_wt_SLAM_r2


title: Tconv_rapamycin_B

description:
raw data file:
210410 slide 251485043436  Area 2 Cy3 A 25 plus fresh Cy5 B 25 minus rapa .gpr
Gene expression from Tconv cells that were isolated from peripheral blood, pre-treated for 1 hour with rapamycin and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation


title: EC_DNA_AGM_cell76


title: SLAMseq_ESC_wt_SLAM_r1


title: Tconv_fresh_C

description:
raw data file:
210410 slide 251485043435  Area 4 Cy3 A 25 minus a lep Cy5 B 25 minus 3 28.gpr
Gene expression from Tconv cells immediately upon peripheral blood isolation

source_name: Tconv cells freshly isolated


title: SLAMseq_ESC_wt_dTag_UT_SLAM_r2

value: wild type, dTag


title: EC_DNA_AGM_cell75


title: EC_DNA_AGM_cell73


title: SLAMseq_ESC_wt_r3

value: embryonic stem cells

value: untreated


first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

description:
RPF RNA
Lucap 145 Tumor sample, Ribosome bound RNA, replicate2
LUCAP_145_RP_rep2

data_processing:
Library strategy: RiboSeq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and employed a single-end, 50 base read length (SE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: Prostate cancer tissue

growth_protocol: Tissues were obtained as frozen chunks, and manually pulverized before lysis

extract_protocol:
Total RNA and ribosome-protected RNA were extracted following the protocol in the TruSeq Ribo Profile kit from Illumina
RNA libraries were prepared for sequencing following the protocol in the TruSeq Ribo Profile kit from Illumina

value: tumor sample


title: EC_DNA_AGM_cell74

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.


title: IFN-gamma-positive Lung N. brasiliensis day 8 rep 2

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

description: Normalized counts per peak

data_processing:
Raw data from the sequencer was demultiplexed and FASTQ files were generated using Illumina bcl2fastq conversion software (version 2.17).
Nextera TruSight adapters were trimmed using skewer (version 0.2.2), which by default removes reads with fewer than 18nt.
BAM files were generated by mapping to the GRCm38 mouse genome with Bowtie2 (version 2.3.2) with options with options --very-sensitive --no-dovetail -X 2000.
Any reads that were either unmapped, not in proper pairs, had a mapping quality score of less than 10, or mapped to the mitochondrial chromosome, non-canonical contigs, or the ENCODE3 blacklisted regions (accession ENCFF759PJK) were removed.
Peaks summits were called on individual repliactes with MACS2 (version 2.1.1, March 9, 2016) with parameters --keep-dup auto --nomodel --nolambda.
Peak summits from individual replicates were expanded to regions of 200bp width and overlapping regions from all samples were merged.
Peaks on the Y chromosome, as well as within ENCODE blacklisted regions (accession ENCFF547MET) were excluded from further analysis.
Reads overlapping each peak were computed with summarizeOverlaps from the R package GenomicAlignments (verion 1.14.2) for all replicates.
Reads per peak were normalized with voom from the limma package (version 3.38.3) in R (version 3.5.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: gzipped tab-separated text; peak coordinates and for each sample the normalized counts of reads overlapping each peak

source_name: Lung

extract_protocol:
50,000 cells from each sample were washed in cold PBS, lysed, and transposed for 40 minutes at 37°C using Nextera Tn5 transposase enzyme (Illumina).
Transposed DNA fragments were amplified 10-15 cycles and barcoded using Illumina compatible indexed primers purchased from IDTdna.com. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and size selection was using AMPureXP beads (Beckman Coulter). Libraries were quantified and size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: N. brasiliensis was prepared as previously described by Voehringer et al. (2006, doi: 10.1084/jem.20052448). Mice were infected with 500 L3 larvae in 200 uL PBS subcutaneously in the lower back.

value: Lung

value: CD4+ T cells, IFN-gamma+

value: N. brasiliensis infection

tag: time

value: 8 days post infection

tag: reporter mouse

value: IFN-gamma-Great YFP reporter mouse

tag: reporter phenotype

value: YFP+


title: EC_DNA_AGM_cell72

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.


title: Tconv_anti-CD3CD28_B

description:
raw data file:
210410 slide 251485043435  Area 4 Cy3 A 25 minus a lep Cy5 B 25 minus 3 28.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

source_name: Tconv cells anti-CD3/CD28 stimulated

value: healthy


title: Tconv_anti-CD3CD28_A

description:
raw data file:
210410 slide 251485043435  Area 3 Cy3 A 25 minus 3 28 Cy5 B 25 minus a lep.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation


title: Tconv_leptin mAb_B

description:
raw data file:
210410 slide 251485043435  Area 3 Cy3 A 25 minus 3 28 Cy5 B 25 minus a lep.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation and a leptin blocking antibody

source_name: Tconv cells treated with leptin mAb


title: Tconv_leptin mAb_A

description:
raw data file:
210410 slide 251485043435  Area 4 Cy3 A 25 minus a lep Cy5 B 25 minus 3 28.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation and a leptin blocking antibody


title: EC_DNA_AGM_cell71


title: SLAMseq_ESC_wt_r1

description: mRNA_knownGene_mm10_wtdegronTimeCourse.csv, EISA_exon_knownGene_mm10_wtdegronTimeCourse.csv, EISA_intron_knownGene_mm10_wtdegronTimeCourse.csv, SLAM_conversionT_knownGene_mm10_wtdegronTimeCourse.csv

tag: treatment


title: Tconv_medium_C

description:
raw data file:
210410 slide 251485043435  Area 3 Cy3 A 25 minus 3 28 Cy5 B 25 minus a lep.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli

source_name: Tconv cells unstimulated


description:
total RNA
Lucap 145 Tumor sample, total RNA, replicate1
LUCAP_145_RNA_rep1


title: Tconv_leptin mAb_C

description:
raw data file:
210410 slide 251485043435  Area 2 Cy3 A 25 minus med Cy5 B 25 minus fresh .gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation and a leptin blocking antibody


title: SLAMseq_ESC_wt_r2


title: EC_DNA_AGM_cell70

source_name: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell69


title: EC_DNA_AGM_cell68


description:
RPF RNA
Lucap 92 Tumor sample, Ribosome bound RNA, replicate1
LUCAP_92_RP_rep1


title: IL-4-positive Lung N. brasiliensis day 8 rep 2

description: Normalized counts per peak

value: CD4+ T cells, IL4+

value: IL-4-4get GFP reporter mouse

value: GFP+


description:
RPF RNA
Lucap 145 Tumor sample, Ribosome bound RNA, replicate1
LUCAP_145_RP_rep1


description:
total RNA
Lucap 92 Tumor sample, total RNA, replicate2
LUCAP_92_RNA_rep2


title: IL-4-positive Lung N. brasiliensis day 8 rep 3

description: Normalized counts per peak


description:
RPF RNA
Lucap 92 Tumor sample, Ribosome bound RNA, replicate2
LUCAP_92_RP_rep2


title: IL4-positive lymph node N. brasiliensis day 8 rep 2

description: Normalized counts per peak

source_name: Mediastinal lymph node

value: Mediastinal lymph node


description:
total RNA
Lucap 145 Tumor sample, total RNA, replicate2
LUCAP_145_RNA_rep2


title: IL-4-positive Lung N. brasiliensis day 8 rep 1

description: Normalized counts per peak


description:
total RNA
Lucap 92 Tumor sample, total RNA, replicate1
LUCAP_92_RNA_rep1


title: IFN-gamma-positive Lung N. brasiliensis day 8 rep 1

description: Normalized counts per peak


title: Tconv_anti-CD3CD28_C

description:
raw data file:
210410 slide 251485043435  Area 1 Cy3 A 25 minus fresh Cy5 B 25 minus mebd.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the presence of anti-CD3/CD28 stimulation

value: peripheral blood isolated Tconv cells


title: Tconv_medium_A

description:
raw data file:
210410 slide 251485043435  Area 2 Cy3 A 25 minus med Cy5 B 25 minus fresh .gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli


title: Tconv_fresh_A

description:
raw data file:
210410 slide 251485043435  Area 1 Cy3 A 25 minus fresh Cy5 B 25 minus mebd.gpr
Gene expression from Tconv cells immediately upon peripheral blood isolation


description:
RPF RNA
Lucap 81 Tumor sample, Ribosome bound RNA, replicate2
LUCAP_81_RP_rep2


title: EC_DNA_AGM_cell66

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: Tconv_fresh_B

description:
raw data file:
210410 slide 251485043435  Area 2 Cy3 A 25 minus med Cy5 B 25 minus fresh .gpr
Gene expression from Tconv cells immediately upon peripheral blood isolation


title: 10E_pfap2-hs 2h post HS, HS-exposed

hyb_protocol: Hybridization performed as previously described (Painter, H. et al., 2013. PMID: 22990780).

scan_protocol: Microarrays images were obtained using the Agilent G2505C Microarray Scanner.

data_processing: Initial data processing of microarray data, including normalization, was performed using the GE2_1105_Oct12 extraction protocol in Agilent Feature Extraction 11.5.1.1 software. The next steps of the analysis were performed using Bioconductor in an R environment (R version 3.5.3). For each individual microarray, we calculated Cy3 and Cy5 background signal as the median of the 100 lowest signal probes for each channel. Probes with both Cy3 and Cy5 signals below three times the array background were excluded (set to NA). Gene level log2(Cy5/Cy3) values and statistical estimation of parasite age were computed as described (Rovira-Graells et al., 2012). Genes with missing values or genes that in all samples had expression values within the lowest 20th percentile of intensity (Cy5 channel) were excluded from downstream analysis, including identification of differentially expressed genes, because differences in genes expressed at near-background levels are of low confidence. To account for the progression delay induced by HS exposure, which can be a major confounder in the downstream analysis, we estimated the age (hours post-invasion, hpi) of each microarray sample by calculating the most likely time post-invasion along the asexual cycle compared to the HB3 transcriptome as reference, using a statistical likelihood method as previously described [Lemieux et al., 2009, PMID: 19376968].

source_name: 10E pfap2-hs knockout

label_protocol: Test sample, Cy5; reference pool, Cy3. As previously described (Painter, H. et al., 2013. PMID: 22990780)

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based media containing Albumax II without human serum, in a 5% CO2, 3% O2, balance N2 atmosphere at 35ºC. Tight synchronization (5 h age window) was achieved by Percoll purification followed by sorbitol treatment 5 h later. Given the slower developmental progression of 10E_pfap2-hs, cultures of this parasite line were synchronized to 0-5 hpi 3 h earlier than 10E and 10G cultures, such that at the time of starting HS (in parallel for all lines) all cultures were the same age.

extract_protocol: RNA was purified using the TRIzol method following the manufacturer intructions.

treatment_protocol: Tightly synchronized cultures were exposed to heat shock at 30-35 hpi (10E and 10G) or 33-38 hpi (10E_pfap2-hs). For this, the full incubation chamber was transferred to an incubator at 41.5 ºC for 3 h, and then placed back to 35 ºC. The chamber with the control cultures was always maintained at 35 ºC.

value: HS-exposed

tag: timepoint

value: 2 h post

tag: estimated age (hpi)

source_name: 3D7-A mixed stage Reference Pool

tag: time-point

value: 3 samples of synchronized cultures covering the whole asexual cycle.


title: EC_DNA_AGM_cell65


title: IL4-positive lymph node N. brasiliensis day 8 rep 1

description: Normalized counts per peak


description:
RPF RNA
Lucap 81 Tumor sample, Ribosome bound RNA, replicate1
LUCAP_81_RP_rep1

value: tumor sample


title: EC_DNA_AGM_cell64


title: 6 dpt inf R1.1

data_processing:
sequenced reads were trimmed for low-quality bases with Trimmomatic, version 0.36
sequencing adapters were removed with Flexbar, version 3.0.3
Reads were mapped against the Arabidopsis thaliana genome (TAIR10) with STAR version 2.6.1c
Reads were mapped against the Fusarium oxysporum 5176 genome (Fokkens et al., 2020, G3) with STAR version 2.6.1c
Uniquely mapped reads were counted by featureCounts, based on the R package Rsubread (version 1.32.1)
Genome_build: ASM1311235v1
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files include the raw counts of reads mapped uniquely against the reference genomes in .txt format.
Supplementary_files_format_and_content: Processed data files include the normalized counts per million for the samples and time points used afterwards to draw conclusions (counts were normalized using trimmed means of M-values (TMM) normalization in EdgeR version 3.24.3; Robinson and Oshlack, 2010)
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Fusarium oxysporum 5176 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Arabidopsis thaliana Col-0 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.

source_name: Roots

growth_protocol: Arabidopsis seeds were germinated at 24° C, long day conditions, on 2 mm foam plugs suspended on 200 ml  ½ MS + 1% sucrose media in 330ml pots at pH 5.7 adjusted by KOH. The media was exchanged 6 days after germination to ½ MS and seedlings were further grown.

extract_protocol:
For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.
3’mRNA-libraries were prepared using the 3’mRNA-Seq library Prep Kit (QuantSeq, Lexogen). The manual from the supplier was followed with the following modifications. At least 1 µg RNA was used as input. For first strand synthesis of cDNA the incubation time at step 4 was increased to 60 min. For library indexing and amplification 13-17 amplification cycles of the given PCR were used depending on the amount of input RNA. 17 µl of the purified library was transferred to a fresh tube. The finished libraries were stored at -20° C until quality control and pooling.

treatment_protocol: For hydroponic infections, the roots of 10-day-old seedlings were infected with 20µl of a solution containing 107 microconidia/ml Fo5176. All pots were incubated for 30 minutes at 100 rpm on a rotary shaker. The media of the infected plants was then replaced with fresh ½ MS media. The plants were further grown under the same conditions until the roots were harvested for RNA extraction or for imaging at 0, 1, 2, 3, 4, and 6 days post treatment. For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.

tag: ecotype

value: whole root

value: Fusarium oxysporum 5176

tag: days post treatment


description:
total RNA
Lucap 81 Tumor sample, total RNA, replicate2
LUCAP_81_RNA_rep2


description:
total RNA
Lucap 81 Tumor sample, total RNA, replicate1
LUCAP_81_RNA_rep1


title: EC_DNA_AGM_cell62

treatment_protocol: Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.


title: EC_DNA_AGM_cell63


title: 4 dpt inf R1.1


title: 10E_pfap2-hs 2h post, Control

value: Control


title: 10E_pfap2-hs 3h HS, HS-exposed

value: 3 h


title: 10E_pfap2-hs 3h, Control


title: EC_DNA_AGM_cell67


title: 6 dpt inf R4


title: Tconv_medium_B

description:
raw data file:
210410 slide 251485043435  Area 1 Cy3 A 25 minus fresh Cy5 B 25 minus mebd.gpr
Gene expression from Tconv cells that were isolated from peripheral blood and cultured for 12 hours in the absence of additional stimuli

tag: disease state


title: 4 dpt inf R4


title: 4 dpt mock R4

value: untreated


description:
RPF RNA
Lucap 78 Tumor sample, Ribosome bound RNA, replicate2
LUCAP_78_RP_rep2


title: EC_DNA_AGM_cell61


title: 10E_pfap2-hs 1.5h HS, HS-exposed


description:
RPF RNA
Lucap 78 Tumor sample, Ribosome bound RNA, replicate1
LUCAP_78_RP_rep1


title: EC_DNA_AGM_cell60


description:
total RNA
Lucap 78 Tumor sample, total RNA, replicate2
LUCAP_78_RNA_rep2


title: 10E_pfap2-hs 1.5h, Control


title: EC_DNA_AGM_cell59


title: 3 dpt mock R4


title: 10E_pfap2-hs Pre HS

value: 0 h


title: 293T prostate cancer cells, totalRNA, replicate2

description:
total RNA
293T prostate cancer cells , totalRNA, replicate2

data_processing:
Library strategy: RiboSeq
The libraries were sequenced employing a paired-end, 100 base read length (PE100) sequencing strategy on a HiSeq 2500 (Illumina). Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.66.3 software, followed by demultiplexing of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4.
Sequencing targeted only the barcode region of each sample ensuring that the barcode was completely contained within, and at a fixed offset from the 3’end of the second 100nt read in each pair. Barcodes were extracted from this fixed position, subject to the constraint that a short sequence (4nt) on both sides match the expected sequence as a check on improper barcode length or placement. Using this method barcodes were extracted from 80% of the reads in each sample
Genome_build: hg19
Supplementary_files_format_and_content: the total number of barcodes observed for each 5’ UTR in each sample were counted and tab-delimited text files include raw values for each barcode per sample.

source_name: human embryonic kidney HEK293T cells

growth_protocol: Sequencing libraries were generated by performing 1st and 2nd round PCRs on each DNA, and cDNA generated from total RNA and polysome RNA samples.

extract_protocol:
1st round PCR primers contain target-specific sequences flanking the 30-bp randomer barcode and Illumina adaptor sequences, producing a product of 215 bp (see Supplementary Table 7f).  The 1st round PCR reaction was performed using 2x Phusion Flash Mastermix (ThermoFisher) in a 50 µL reaction. The PCR reaction consisted of 5 µL of DNA or cDNA template, 2 µL of forward primer (10 µM), 2 µL of reverse primer (10 µM) and 25 µL of Phusion Flash Mastermix. Thermal cycling conditions were at 95°C for 3 min, 20 cycles of (98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec), followed by 72°C at 5 min. A small portion (3 µL) of the PCR products and negative controls were run on a 1.5% agarose gel for visual inspection. The 1st round PCR products were purified using a 0.8x AMPure XP (Beckman Coulter) cleanup following the manufacturer’s protocol with 80% ethanol
Following cleanup, 4 µL of the purified 1st round PCR product was used as a template in the 2nd round PCR reaction.  The forward primer contains the Illumina adaptor sequence, as well as the flow cell attachment sequence, the reverse primer contains an 8-bp index between the adaptor sequence and flow cell attachment sequence. The 2nd round PCR reaction was carried out in a 50 µL reaction similarly, using Phusion Flash Mastermix (ThermoFisher), with 5 µL of each forward and reverse primer (0.5 µM).  Thermal cycling conditions were at 95°C for 3 min, 8 cycles of (95°C for 30 sec, 55°C for 30 sec, 72°C for 30 sec), followed by 72°C at 5 min. PCR products were purified using a 0.8x AMPure XP (Beckman Coulter) cleanup following the manufacturer’s protocol with 80% ethanol. A sample (3 µL) of the purified PCR products were run on a 1.5% agarose gel for visual inspection. Each sample was quantified by qPCR using the KAPA Library Universal Quantification kit (KAPA Biosystems) according to the manufacturer’s instructions and pooled in equimolar amounts for multiplex sequencing. The final pool was denatured and diluted to a loading concentration of 7.5pM as per Illumina protocol. The PhiX control library (Illumina) was spiked in at 20% to add diversity for improved cluster imaging.

tag: cell line


title: 10G 2h post HS, HS-exposed

source_name: 10G (3D7-A subclone)


title: 10G 3h HS, HS-exposed


title: 10G 3h, Control


title: 3 dpt inf R4


description:
total RNA
Lucap 78 Tumor sample, total RNA, replicate1
LUCAP_78_RNA_rep1


title: 6 dpt mock R4


title: 2 dpt inf R4


title: EC_DNA_AGM_cell56


title: 293T prostate cancer cells, totalRNA, replicate1

description:
total RNA
293T prostate cancer cells , totalRNA, replicate1


title: 293T prostate cancer cells, totalRNA, replicate3

description:
total RNA
293T prostate cancer cells , totalRNA, replicate3


title: 2 dpt mock R4


title: 1 dpt inf R4


title: EC_DNA_AGM_cell54


title: EC_DNA_AGM_cell55


title: 10G 2h post, Control


title: EC_DNA_AGM_cell58


title: EC_DNA_AGM_cell57


title: 10G 1.5h HS, HS-exposed


title: 1 dpt mock R4


title: EC_DNA_AGM_cell53


title: 293T prostate cancer cells, polysome, replicate3

description:
polysome
293T prostate cancer cells , polysome, replicate3


title: 293T prostate cancer cells, polysome, replicate2

description:
polysome
293T prostate cancer cells , polysome, replicate2


title: 10G Pre HS


title: 10G 1.5h, Control


title: 0 dpt inf R4


title: EC_DNA_AGM_cell50


title: 293T prostate cancer cells, polysome, replicate1

description:
polysome
293T prostate cancer cells , polysome, replicate1


title: 293T prostate cancer cells, DNA, replicate2

description:
DNA
293T prostate cancer cells , DNA, replicate2


title: 293T prostate cancer cells, DNA, replicate1

description:
DNA
293T prostate cancer cells , DNA, replicate1


title: EC_DNA_AGM_cell52


title: 0 dpt mock R4


title: 293T prostate cancer cells, DNA, replicate3

description:
DNA
293T prostate cancer cells , DNA, replicate3


title: EC_DNA_AGM_cell48


title: 10E 2h post HS, HS-exposed

source_name: 10E (3D7-A subclone)


title: 10E 3h HS, HS-exposed


title: EC_DNA_AGM_cell51


title: 10E 2h post, Control


title: 10E 3h, Control


title: 4 dpt mock R3


title: 6 dpt mock R3


title: 6 dpt inf R3


title: PC3 prostate cancer cells, totalRNA, replicate2

description:
total RNA
PC3 prostate cancer cells , totalRNA, replicate2

source_name: PC3 prostate cancer cells


title: EC_DNA_AGM_cell49


title: 4 dpt inf R3


title: PC3 prostate cancer cells, totalRNA, replicate3

description:
total RNA
PC3 prostate cancer cells , totalRNA, replicate3


title: EC_DNA_AGM_cell47


title: 3 dpt inf R3


title: PC3 prostate cancer cells, totalRNA, replicate1

description:
total RNA
PC3 prostate cancer cells , totalRNA, replicate1


title: 10E 1.5h, Control


title: 3 dpt mock R3


title: EC_DNA_AGM_cell46


title: PC3 prostate cancer cells, polysome, replicate2

description:
polysome
PC3 prostate cancer cells , polysome, replicate2


title: 2 dpt mock R3


title: On-liver-rep1

city: Cambridge

first: Sudhakaran

last: Prabakaran

address: Downing Site, CB2 3EH, UK

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

data_processing:
HISAT2 2.1.0 for the alignment of reads to their respective genomes.
The aligned reads were assembled using Stringtie and their respective reference genome. The assembled transcriptomes for each biological replicate were merged using Stringtie merge utility to produce one transcriptome per tissue per species.
The assembled transcriptomes were filtered to remove unexpressed and duplicated transcripts. Ballgown's v2.10.0 k-mean clustering was used to reduce the number of highly similar transcripts. The transcripts were clustered within each locus and transcripts within each cluster were merged by taking union of the exon-coordinates of the individual transcripts. The minimum number of clusters was used at each locus such that at least 90% of the within-locus variation was retained.
Genome_build: ASM185804v2, PunNye1.0
Supplementary_files_format_and_content: ctab files generated by Stringtie are tab seprated files that include FPKM estimates

organism: Oreochromis niloticus

source_name: On-liver

growth_protocol: Tank-reared, P. nyererei (generation 1; Lake Victoria) and O. niloticus (generation ~93; Manzala, Egypt)

extract_protocol:
Total RNA was isolated using TRIzol (ThermoFisher) and then treated with DNase (TURBO DNase, ThermoFisher) to remove any DNA contamination.
Quality and quantity of total RNA extracts were determined using NanoDrop spectrophotometer (ThermoFisher), Qubit (ThermoFisher) and BioAnalyser (Agilent). Following ribosomal RNA depletion (RiboZero, Illumina), stranded rRNA-depleted RNA libraries (Illumina) were prepped and sequenced (paired-end 75bp-long reads) on HiSeq2500 V4 (Illumina). On average, 11.82±0.42Mio paired-end reads were generated.

treatment_protocol: 5-10mg of fresh liver tissue were snap-frozen upon dissection and were homogenized and used for RNA extraction.

tag: generation

tag: location

value: Manzala, Egypt

tag: Sex

value: male

value: liver


title: PC3 prostate cancer cells, polysome, replicate1

description:
polysome
PC3 prostate cancer cells , polysome, replicate1


title: 10E 1.5h HS, HS-exposed

tag: strain


title: EC_DNA_AGM_cell45

tag: cell type

tag: tissue


title: On-liver-rep3


title: 1 dpt inf R3


title: 10E Pre HS


title: On-liver-rep2


title: EC_DNA_AGM_cell43

tag: antibody


title: EC_DNA_AGM_cell44


title: 2 dpt inf R3


title: PC3 prostate cancer cells, DNA, replicate3

description:
DNA
PC3 prostate cancer cells , DNA, replicate3


title: 1 dpt mock R3


title: PC3 prostate cancer cells, DNA, replicate2

description:
DNA
PC3 prostate cancer cells , DNA, replicate2


title: PC3 prostate cancer cells, polysome, replicate3

description:
polysome
PC3 prostate cancer cells , polysome, replicate3


title: EC_DNA_AGM_cell42


title: PC3 prostate cancer cells, DNA, replicate1

description:
DNA
PC3 prostate cancer cells , DNA, replicate1


title: F. nucleatum delta-carR Rep 2

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

institute: Bielefeld University

data_processing:
Base calling with Illumina CASAVA
quality trimming with trimmomatic v0.36 from both ends with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
reverse complementing of R1 reads
mapping with bowtie2 2.2.7, --ff read orientation, default parameters
converting SAM to BAM with samtools 1.2
visualization and read counting with readXplorer 2.2.3
Analysis of differentially transcribed genes with DESeq2 in default parameters
Genome_build: ASM17889v1
Supplementary_files_format_and_content: List_of_differentially_transcribed_genes.xlsx contains raw counts, normalized read counts and log2foldchanges and adjusted p-values for each gene.

organism: Fusobacterium nucleatum subsp. nucleatum

source_name: bacterial culture

growth_protocol: F. nucleatum were grown in tryptic soy broth (TSB) supplemented with 1% BactoTM peptone plus 0.25% freshly made cysteine (TSPC) or on TSPC agar plates in an anaerobic chamber (10% CO2, 10% H2 and 80% N2).

extract_protocol:
F. nucleatum RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacture’s protocol. Fusobacterial cell pellets from 3 ml log-phase culture (OD600 ~ 0.6) were harvested and resuspended into 200 μl of chilled 10 mM RNA-free TE (10 mM Tris-HCl, pH 8; 1 mM EDTA). Each suspension was transferred to a fast-protein tube (Q BIOgene), which contained 700 μl RLT buffer (RNeasy Mini Kit, Qiagen) and 7 μL β-mercaptoethanol (BME) (ThermoFischer Scientific. Cells were lysed by using Ribolyser (Hybaid), and supernatants were obtained by centrifugation at 13000 x g for 5 min at 4°C. RNA was then purified from the supernatant accordingly, and purified RNA was treated with DNAse (Qiagen) and cleaned by using an RNeasy clean up kit (Qiagen). Quality of RNA samples was determined RNA Integrity Number (RIN) values greater than 8 using an Agilent 2100 Bioanalyzer (Agilent Technologies).
2 µg total RNA from F.nucleatum parent and mutant strains were used. Stable RNAs were depleted with the RiboZero Kit according to manufacturer's instructions (Epicentre). Afterwards the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality with the Bioanalyzer (Agilent). Fragmentation of mRNA, reverse transcription to cDNA, adenylation of 3' ends, adapter ligation and PCR amplification were performed according to TrueSeq Stranded mRNA library instructions (Illumina). Prior to paired-end sequencing of the whole transcriptome cDNA libraries on an Illumina MiSeq, the quality and concentration of the libraries were checked using the Bioanalyzer (Agilent).

value: Genes galK and carR deleted

tag: growth phase

value: exponential growth


title: F. nucleatum delta-carR Rep 1


title: 0 dpt inf R3


title: WT_5_RP

description: Wild type sample, Ribosome bound RNA, replicate5

data_processing:
Library strategy: Ribo-Seq
Library strategy: Ribo-Seq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: Normal prostate tissue

value: Normal prostate

tag: genotype/variation

value: wild type/ normal


title: EC_DNA_AGM_cell41

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: F. nucleatum Parent Strain Rep 3

tag: treatment

value: Gene galK deleted


title: EC_DNA_AGM_cell39


title: 0 dpt mock R3


title: F. nucleatum delta-carR Rep 3


title: EC_DNA_AGM_cell40


title: F. nucleatum Parent Strain Rep 1


title: F. nucleatum Parent Strain Rep 2


title: WT_3_RP

description: Wild type sample, Ribosome bound RNA, replicate3


title: 6 dpt mock R2


title: 4 dpt inf R2


title: WT_4_RP

description: Wild type sample, Ribosome bound RNA, replicate4


title: EC_DNA_AGM_cell36


title: WT_1_RP

description: Wild type sample, Ribosome bound RNA, replicate1


title: EC_DNA_AGM_cell37


title: EC_DNA_AGM_cell35