title: Ffar2 agonist 2

city: MA

first: Sena

last: Bae

address: Boston

institute: Harvard T.H. Chan School of Public Health

data_processing:
Low quality reads were filtered by using sickle version 1.33
Alignment to the NCBI GRCm38/mm10 mouse genome using the STAR aligner version 2.7 with default setting
Reads per gene counts using HTSeq version 0.11.1
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: MLN

extract_protocol:
MLNs (2 MLNs pooled/sample, n=2) were removed from WT C57BL/6J mice and were crushed through a 40 micron strainer. CD11c+ cells were sorted from MLN samples using a CD11c magnetically activated cell sorting (MACS) kit (Miltenyi Biotec cat#: 130-108-338). CD11c+ cells from each sample (~9x104 cells) were then split into two wells and resuspended in RPMI (Sigma) with 10%FBS and cultured in with either control (H2O) or with Ffar2 agonist (10μM) at 37C for 6hr. After incubation, the cells were resuspended in RLT buffer and RNA was immediately isolated using an RNeasy Micro kit (Qiagen cat#: 74004).
RNA quality verification, library preparation, and sequencing were performed at BPF Next-Gen Sequencing Core Facility at Harvard Medical School. RNA samples showed an average 9.0 of RNA integrity number (RIN) and libraries were generated using SMART-seq v4 Ultra Low Input RNA kit (Takara Bio Inc.).

value: MLN

value: 10μM of Ffar2 agonist treatment

tag: strain

value: WT C57BL/6J


title: BD04_04: Biparental diploid bio rep4 tech rep4

status: Public on Jan 16 2020

type: SRA

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic

data_processing:
Sequencing performed by: Bielefeld University, CeBiTec & Faculty of Biology
Sequenced reads were trimmed for adaptor sequences with trimmomatic version 0.38 using the paramters SE -phred33 ILLUMINACLIP:adapter_sequences.fasta:2:30:10
Low quality regions were removed using trimmomatic version 0.38 with parameters: SE -phred33 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to protein coding sequences using STAR version 2.6.0c with parameters: --alignIntronMin 20 --alignIntronMax 50000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 50 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode TranscriptomeSAM
Read assignment was done by salmon version 0.11.3 with the parameters: quant –libType U –gcBias –seqBias –useErrorModel
Normalization of counts was performed with DESeq2 version 1.22
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: semicolon separated files contain DESeq2 library size normalized counts (deseq2_norm), regularized log transformed counts (deseq2_rlog), and TPM normalized expression values for each biological replicate

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: aerial tissues of 18 DAS plants

growth_protocol: The plant materials were grown in a Conviron MTPS growth chamber under long-day conditions (16 hours light/8 hours dark) at 23 ̊C.

extract_protocol:
The aerial tissues of 18 DAS plants were frozen and grinded in pre-cooled EP tubes with metal beads and total RNA was isolated following the procedure of GeneMATRIX Universal RNA purification kit.
750 ng total RNA per sample was used to prepare sequencing libraries according to the Illumina TruSeq RNA Sample Preparation v2 Guide. Purification of the poly-A containing mRNA was performed using two rounds of poly-T Oligos attached to magnetic beads. During the second elution of the poly-A RNA, the RNA was fragmented and primed for cDNA synthesis. After cDNA synthesis the fragments were end-repaired and A-tailing was performed. Multiple indexing adapters were ligated to the ends of the cDNA fragments and the adapter ligated fragments were enriched by 10 cycles of PCR. After quali- and quantification the resulting sequencing libraries were pooled equimolar and sequenced 75 bp single-read on an Illumina NextSeq500.

treatment_protocol:
For all the crosses, ein3-1 mutants were used as female plant. Triparental triploids (TT) were obtained from double pollination as previously described (Nakel et al. Nat Comm. 2017), while biparental triploids (BT) were recovered from a cross of 2n female with 4n male pollen donor pRPS5a::mGAL4-VP16/-; pUAS::BAR-YFP/-. Biparental diploids (BD) were generated from a cross of 2n female with 2n pollen donor pRPS5a::mGAL4-VP16/-; pUAS::BAR-YFP/-.
Seeds that contain TT, BT and BD were selected on 0.5 MS medium containing 25 mg/l Glufosinate-ammonium (PPT, Sigma), and the seedlings were transferred to soil 9 days after sowing (DAS). YFP and ploidy analysis was carried out 17 DAS to confirm TT, BT and BD profile.

tag: tissue

value: aerial tissues of 18 DAS plants

tag: genotype/variation

value: Biparental diploid


title: BD02_02: Biparental diploid bio rep2 tech rep2


title: Ctrl 2

country: USA

molecule: total RNA

organism: Mus musculus

tag: treatment

value: no treatment


title: BD01_04: Biparental diploid bio rep1 tech rep4


title: 3018R4

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
Trimming of data using cutadapt
Alignment of data using HISAT2
Read count by HTSeq
Filtering of protein-coding genes
Calculation of transcripts per million values from raw read counts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include Gene expression (in transcripts per million)

source_name: placenta

extract_protocol:
Fetal placental tissue was microdissected at e12.5
RNA libraries were prepared for sequencing using standard Illumina protocols and the NextSeq 500 instrument

treatment_protocol: Female mice were fed daily a Nabisco Nilla Wafer containing either:  200ug/kg body weight BPA reconstituted in ethanol; 200ug/kg body weight BPS reconstituted in ethanol; or a wafer containing 70% ethanol (control). They were provided these wafers for two weeks prior to breeding and up until the time of placental collections.

value: placenta

value: BPA

tag: gender

value: Female

tag: developmental stage


title: Ffar2 agonist 3


title: BD01_03: Biparental diploid bio rep1 tech rep3


title: BD01_02: Biparental diploid bio rep1 tech rep2


title: 3015L4

value: Male


title: 3004L2

value: BPS


title: BD02_01: Biparental diploid bio rep2 tech rep1


title: BD01_01: Biparental diploid bio rep1 tech rep1


title: 3018R3


title: 3004L3


title: 3002R3


title: TT01_02: Triparental triploid bio rep1 tech rep2

value: Triparental triploid


title: Parental cells study dox/no-dox comparison control replicate 3 3'end tag-Seq

city: Columbus

first: Ralf

last: Bundschuh

state: OH

address: 191 West Woodruff Avenue

department: Department of Physics

institute: The Ohio State University

description:
cytoplasmic RNA isolates
No Dox 3

data_processing:
REV Human Lexogen QuantSeq pipeline 2.2.3
Genome_build: hGRC38
Supplementary_files_format_and_content: space delimited text files with read counts for each gene

organism: Homo sapiens

source_name: U2OS-TR cell line - control

growth_protocol: 3x10^6 cells were split into a 10 cm dish.

extract_protocol:
Twenty-four hours later cells were rinsed once with ice cold phosphate buffered saline (PBS) and suspended in 1 ml of PBS with a cell scraper. The recovered cells were centrifuged at 2,500 xg for 5 minutes at 4°C, washed once with 1 ml PBS and centrifuged again at 2,500 xg for 5 minutes at 4°C. The pelleted cells were resuspended in 5 volumes of lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 0.2% NP-40, 80 U/ml RNaseOUT (Invitrogen)) and incubated on ice for 10 minutes. Nuclei were removed by centrifugation at 12,000 xg for 10 minutes at 4°C. The supernatant fraction was used for western blot analysis and for RNA isolation using Direct-zol RNA MiniPrep Kit (Zymo Research R2053) including an in-column DNAse I digestion. Purified RNA was eluted in RNAse free water.
Sequencing libraries were prepared from 2 μg of cytoplasmic RNA from uninduced or 24 hr doxycycline-treated (induced) cells carrying the ΔN-RNMT transgene (n=5 for each) or parental U2OS-TR cells (n=3 for each) using the QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina (Lexogen) according to manufacturer’s protocol. The final concentration of each library was determined using Qubit 2.0 Fluorometer (Invitrogen).

treatment_protocol: After 48 hr, 1 μg/ml of doxycycline was added.

tag: cell line

value: bone

tag: disease

value: osteosarcoma


title: 2001L2


title: 3002R2


title: Parental cells study dox/no-dox comparison with dox replicate 3 3'end tag-Seq

description:
cytoplasmic RNA isolates
With Dox 3

source_name: U2OS-TR cell line + dox


title: 34


title: Parental cells study dox/no-dox comparison with dox replicate 1 3'end tag-Seq

description:
cytoplasmic RNA isolates
With Dox 1


title: PBMC mRNA-seq

city: San Francisco

first: Jesse

last: Zhang

state: CA

department: BTS

institute: UCSF

library_source: genomic

data_processing:
Basecalling was done with bcl2fastq v2.20
Bead barcode was extracted from position 1-12 of Read 1 and UMI was extracted from position 13-20 of Read 1.
For mRNA reads: Read2 was aligned to a reference human or mouse genome using STAR.
For coordinate reads: Read2 was aligned to a known list of well index sequences using CITEseq-Count
Digital gene expression matrices were created by, for each bead barcode group, counting the number of unique UMIs for each gene or well index sequence.
To link beads to nanowell position: UMI counts for each bead are scaled based on the number of total UMIs on the bead. Next, the off-target noise of each well index is estimated based on the average expression across all beads and subtracted from scaled UMI counts. The top x, y, and z well index captured on each bead is then extracted. Beads which the top well index is not at least 5 times as abundant as the next most abundant well index for any of the sets of x, y, and z well indexes are removed. The remaining beads are assigned to a nanowell position by matching the most abundant x, y, and z indexes on the bead to a lookup table of the expected x, y, and z positions at each nanowell position. Following position assignment, the bead barcodes of all beads matched at each nanowell position are collected. The columns on the gene expression matrix of all beads matched at the same nanowell position are merged, yielding a revised matrix where the columns represented nanowell positions instead of individual beads.
The gene expression matrix is then annotated by recorded cell fluorescence values obtained during printing.
Genome_build: hg18
Supplementary_files_format_and_content: Digital gene expression matricies by nanowell position (.csv)
Supplementary_files_format_and_content: Indexed flow cytometry data by nanowell position (.csv)

molecule: genomic DNA

source_name: human peripheral blood mononuclear cells

growth_protocol: PBMCs were obtained from a human donor (Stemcell Technologies)

extract_protocol:
Cell-containing drops were merged with lysis buffer drops containing coordinate oligos and barcoded poly dT beads within microwells. Beads were then processed using the Drop-Seq protocol, using the modified CITE-seq/Cell hashing protocol to separate coordinate oligo reads from mRNA reads.
The coordinate library directly had sequencing adapters added with PCR. The mRNA library underwent tagmentation and sequencing adapter addition using the Illumina Nextera XT sample preparation kit. A custom Read 1 primer used in Drop-Seq was used during the sequencing of both libraries.
Drop-Seq; CITE-Seq/Cell hashing

treatment_protocol: PBMCs were thawed and resuspended. PBMCs were labeled with antibodies against CD14 and CD16 . Cells were then encapsulated in 80-um droplets.

value: primary human PBMCs


title: Parental cells study dox/no-dox comparison control replicate 1 3'end tag-Seq

description:
cytoplasmic RNA isolates
No Dox 1


title: 2001L3


title: Parental cells study dox/no-dox comparison with dox replicate 2 3'end tag-Seq

description:
cytoplasmic RNA isolates
With Dox 2


title: Parental cells study dox/no-dox comparison control replicate 2 3'end tag-Seq

description:
cytoplasmic RNA isolates
No Dox 2


title: Ctrl 3


title: 32


title: coordinate reads for PBMC mRNA-seq

organism: synthetic construct

source_name: synthetic DNA


title: 48h_bradyzoites_rep3_tech1

city: CAMBRIDGE

first: Benjamin

middle: S

last: Waldman

state: MA

address: 455 Main Street Rm. 555

department: Biology

institute: Whitehead Institute

data_processing:
STAR_2.6.1a: STAR  --genomeDir "path/to/genome/dir"   --sjdbGTFfile "/path/to/GTF" --quantMode GeneCounts --readFilesIn $r1_read $r2_read --outFileNamePrefix $sample
DESeq2 1.21.16: design = ~replicate + growth condition, contrast = stress, unstress
Genome_build: ToxoDB-36_TgondiiME49
Supplementary_files_format_and_content: Counts files as output by STAR --quantMode GeneCounts

organism: Toxoplasma gondii

source_name: Toxoplasma gondii bradyzoites

growth_protocol: Parasites were allowed to invade and replicate inside host cells for 24 h in standard medium, and then switched to either standard or alkaline stress medium. For FACS, parasites were mechanically released from host cells using a 27- followed by a 30-gauge syringe needle, and passed through a 3 µm filter. At 24 and 48 h post medium change, ~1 x 10e5 unstressed mNG– or stressed mNG+ parasites were sorted directly into TRIzol LS and frozen on dry ice. Sorting was done using a BD FACS Aria II

extract_protocol:
RNA was extracted by TRIzol-chloroform according to manufacturer’s protocol, DNaseI digested, and TRIzol-chloroform extracted again. RNA quality was assessed using a BioAnalyzer or Fragment analyzer. When possible, two samples were prepared per replicate and timepoint and treated as technical replicates in downstream processing. Libraries were generated using the SMARTseq low-input v4 kit, and sequenced on two lanes of a HiSeq 2000.
Smart Seq v4 low input

tag: Stage

value: bradyzoites

tag: biological replicate

tag: growth condition

value: stress

tag: timepoint

value: 48 hr


title: 27

value: CTL


title: 29


title: 30


title: 33


title: 28


title: 24h_tachyzoites_rep3_tech1

source_name: Toxoplasma gondii tachyzoites

value: tachyzoites

value: unstress

value: 24 hr


title: 24h_tachyzoites_rep2_tech2


title: 3015L3


title: 48h_bradyzoites_rep2_tech2


title: 24h_tachyzoites_rep2_tech1


title: 24


title: 25


title: 48h_bradyzoites_rep1_tech2


title: 48h_bradyzoites_rep1_tech1


title: 23


title: 24h_tachyzoites_rep1_tech2


title: 26


title: 48h_bradyzoites_rep2_tech1


title: 18


title: 20


title: 21


title: 17


title: 24h_tachyzoites_rep1_tech1


title: 16


title: 19


title: 15


title: 13


title: 14


title: 12


title: 10


title: 9


title: 22


title: Tumor-3

type: RNA

city: Wuhan

first: balu

last: wu

address: Donghu Road

country: China

institute: Wuhan University

description: miRNA expression data from breast cancer tissue.

hyb_protocol: 1. Completely thaw and then heat the 20X Eukaryotic Hybridization Controls (bioB, bioC, bioD, cre fromGeneChip Eukaryotic Hybridization Control Kit) for 5 minutes at 65°C.  2. Add the following components to the 21.5μl biotin-labeled sample in the order listed, to prepare the array  hybridization cocktail:  50μl 2X Hybridization Mix (from GeneChip Hyb, Wash and Stain Kit)  15μl 27.5% Formamide (Vial 12)  10μl DMSO (from GeneChip Hyb, Wash and Stain Kit)  5μl 20X Eukaryotic Hybridization Controls (from GeneChip Eukaryotic Hyb Control Kit)  1.7μl Control Oligonucleotide B2, 3nM (from GeneChip Eukaryotic Hyb Control Kit)  3. The volume will be 103.2μl. Incubate at 99C for 5 minutes, then 45C for 5 minutes.  4. Aspirate 100μl and inject into an array.  5. Remove the pipet tip from the upper right septum of the array.  6. Cover both septa with 1/2 Tough-Spots to minimize evaporation and/or prevent leaks.  7. Place the arrays into hybridization oven trays.  8. Load the trays into the hybridization oven.  9. Incubate the arrays at 48°C and 60 rpm for 16 hours.

scan_protocol: The instructions for using the scanner and scanning arrays can be found in the Affymetrix Command Console  Software User Manual in Chapter 6 (http://www.affymetrix.com).

data_processing: Use the free miRNA QC Tool software for data summarization, normalization, and quality control.

label: tissue

source_name: Breast cancer tissue

label_protocol: Genisphere FlashTag™ Biotin HSR RNA Labeling

growth_protocol: The tissue that were harvested individually from patients

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

treatment_protocol: The tissue were stored at  liquid nitrogen

tag: patient diagnosis

value: breast cancer

value: breast cancer tissue

tag: Sex

value: female


title: Normal-3

description: miRNA expression data from normal breast tissue.

source_name: Breast tissue

value: adjacent normal breast tissue


title: 6

value: placenta

value: BPA

value: Male


title: Tumor-1


title: Tumor-2


title: 4

value: BPS

value: Female


title: 5


title: 1


title: 2


title: CBZ_3

city: Nagoya

first: Reo

last: Kawata

address: 65 Tsurumai-cho, Showa-ku, Nagoya, Japan

department: Drug Safety Sciences

country: Japan

institute: Nagoya university

data_processing:
FASTQ files generated by the Illumina MiSeq System were analyzed with CLC Genomics Workbench (Qiagen). Adaptor sequences were trimmed, and sequences with a length less than 15 or more than 35 bp were discarded before counting. Trimmed data were mapped to the rat mature miRNA sequences in miRbase ver. 22.1 allowing two-base mismatches, after that, the unmapped data were mapped to the rat ncRNAs sequences other than miRNA and piRNA: tRNA, ribosomal RNA (rRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), etc. in GtRNAdb and Ensemble Rattus norvegicus 6.0 ncRNA with perfect match, and then the unmapped data were mapped to the rat piRNA sequences that was hit with “rat piRNA” filtered at 0-35 bases on NCBI Nucleotide with perfect match. The remained unmapped data were identified as “unannotated reads”. Small RNAs with a total read count in samples less than 10 were filtered out. In the read counts mapped to miRNA, tRNA or piRNA, normalization and statistical analysis were performed by edgeR package using TCC-GUI (Su et al., 2019). Differentially expressed small RNA genes (DEGs) compared with each vehicle group were identified at q value < 0.25.
Supplementary_files_format_and_content: xlsx files containing raw and normalized read counts in individual files.

organism: Rattus norvegicus

source_name: Serum exosome

growth_protocol: Male Sprague-Dawley rats (8-weeks-old) were obtained from Japan SLC (Hamamatsu, Japan). The animals were housed under a 12-hour light/dark cycle in a controlled environment (maintained at 23 ± 2°C with a relative humidity of 55 ± 10%) in the institutional animal facility with ad libitum access to food and water. All procedures performed on the animals were approved by the Animal Care Committee of Nagoya University Graduate School of Medicine and were carried out in accordance with the guidelines established by the Institute for Laboratory Animal Research of the Medical School of Nagoya University, Japan.

extract_protocol:
The serum was centrifuged at 16,500 g for 20 min at 4°C, and the supernatant was obtained (pretreated serum). The pretreated serum (2.7 mL) was centrifuged at 208,000 g for 70 min at 4°C and the supernatant was discarded. The exosome pellet was resuspended in PBS and centrifuged again at 208,000 g for 70 min at 4°C. The supernatant was discarded, and then QIAzol Lysis Reagent were added to the exosome pellet for RNA extraction. The total RNA was extracted using miRNeasy Serum/Plasma Kit according to the manufacturer’s protocol.
cDNA libraries for small-RNA sequencing were synthesized with a NEBNext Multiplex Small RNA Library Prep Set for illumina and quantified with a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA) using Qubit dsDNA HS Assay Kit (Life Technologies) according to the manufacturer’s protocol. Small-RNA sequencing was performed with an Illumina MiSeq System using MiSeq Reagent Kit v3. For the improved cluster formation, denatured PhiX Control v3 was added to the cDNA libraries.

treatment_protocol: Rats (9-weeks-old) were orally administered a single dose of 2000 mg/kg EGME diluted in water (10 mL/kg), 400 mg/kg CBZ suspended to corn oil (5 mL/kg), 500 mg/kg NF to 0.5% CMC (10 mL/kg) or 60 mg/kg 1,3-DNB to corn oil (5 mL/kg). The rats in each control group were orally administered a single dose of each vehicle. Blood sample was obtained from the caudal vena cava under isoflurane anesthesia 24 h after administration of each testicular toxicant. The obtained blood was incubated overnight at 4°C to clot, and then centrifuged at 1,000 g for 15 min at 4°C to obtain serum.

value: Sprague-Dawley

tag: age

tag: drug

value: CBZ

value: Serum exosome


title: CBZ_2


title: CBZ_1


title: Normal-2


title: Normal-1


title: WT_Shield1_Rep3

data_processing:
STAR_2.6.1a: STAR  --genomeDir "path/to/genome/dir"   --sjdbGTFfile "/path/to/GTF" --quantMode GeneCounts --readFilesIn $r1_read $r2_read --outFileNamePrefix $sample
DESeq2 1.21.16: design = ~genotype_growthcondition, contrast = 2B4_Shield1, 2B4_EtOH
Genome_build: ToxoDB-36_TgondiiME49
Supplementary_files_format_and_content: Counts files as output by STAR --quantMode GeneCounts

source_name: Toxoplasma gondii parasites isolated from host cells

growth_protocol: Parasites were allowed to invade and replicate inside host cells for 4 hours before being shifted to normal medium containing 3 µM Shield-1 or an equal volume of vehicle (100% EtOH). Parasites were allowed to grow for another 48 hours before being mechanically released from host cells using a 27- followed by a 30-gauge syringe needle, and passed through a 5 µm filter.

extract_protocol:
RNA was extracted by TRIzol-chloroform according to manufacturer’s protocol and DNA removed using Turbo DNase. Libraries were generated using the NEBNext Ultra II Directional RNA kit following the polyA mRNA workflow, and were sequenced on a NextSeq 500.
NEBNext Ultra II Directional RNA kit

tag: genotype

value: WT (ME49{delta}KU80)

tag: replicate


title: Oil_3

tag: strain

value: Oil

tag: tissue


title: EV-exposed keratinocyte 2

city: Linköping

first: Petra

middle: Karolin

last: Wäster

address: Linköpings Universitet

country: Sweden

institute: Linköping University

description: EV-exposed

hyb_protocol: Hybridisation was performed with the Affymetrix Human Genome Microarray (WT GeneTitan ST1.1; Plate type, HuGene-2_1-st-v1-16; Array type, HuGene-1_1-st-v1) according to the manufacturer’s protocols (Affymetrix Inc., CA, USA)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix). The data were processed using the Agilent GeneSpring GX 13 software package (Agilent Technologies, Santa Clara, CA, USA).

label: biotin

source_name: keratinocyte

label_protocol: Biotin. Labelling was performed with the Affymetrix Human Genome Microarray (WT GeneTitan ST1.1; Plate type, HuGene-2_1-st-v1-16; Array type, HuGene-1_1-st-v1) according to the manufacturer’s protocols (Affymetrix Inc., CA, USA)

growth_protocol: Keratinocytes were obtained from Caucasian donors (0-3 years of age) by means of foreskin circumcisions. The keratinocytes were cultured in DMEM/F12 with supplements and incubated at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: After isolation of total RNA (TRIzol, Sigma), the quality was controlled using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: Evs were isolated from UVA irradiated melanocytes and added to keratinocytes.

value: foreskin

tag: cell type

value: keratinocyte


title: 8

tag: treatment

tag: gender


title: WT_Shield1_Rep2

value: Toxoplasma gondii parasites isolated from host cells


title: vHip63-cKO

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

description:
processed data file: controlVscKO_VentralHipAllRunsGLM.differential_expression_edgeR.txt
Three runs were performed for this Sample. NS68 fastq file corresponds to _1 in the processed data file, NS78 fastq file corresponds to _2 in the processed data file, and NS85 fastq file corresponds to _3 in the processed data file.

data_processing:
Raw reads were trimmed using cutadapt with a Phred-quality threshold of 30, and resulting reads smaller than 25 bases are discarded.
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using hisat2 with default parameters.
Gene expression was quantified with featureCounts. Reads mapping to multiple locations of the genome are discarded from this analysis.
Differential expression analysis was performed using edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing raw and normalised read counts, and results from the differential expression analysis. Replicates in the files represent multiple runs of the same sample. The differential expression analysis was performed using the pooled data for each sample.

source_name: Ventral hippocampus

extract_protocol:
RNA was extracted using Trizol® reagent (Invitrogen).
RNA-Seq libraries were generated from 500 ng of total RNA using the Quant-Seq 3‘mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: To induce Tet3 ablation, six-week-old mice were injected intraperitoneally with 50 mg/kg of tamoxifen twice a day for 5 consecutive days, with 7 days break followed by injections for 5 additional consecutive days.

tag: genotype/variation

value: Tet3fl/fl; Camk2a-CreERT2

value: Adult

value: Ventral hippocampus


title: EV-exposed keratinocyte 4

description: EV-exposed


title: Control keratinocyte 4

description: control


title: EV-exposed keratinocyte 3

description: EV-exposed


title: vHip50-Control


title: EV-exposed keratinocyte 1

description: EV-exposed


title: vHip49-Control


title: Oil_2


title: vHip41-Control


title: Control keratinocyte 3

description: control


title: Control keratinocyte 2

description: control


title: Control keratinocyte 1

description: control


title: WT_Shield1_Rep1


title: vHip40-cKO


title: vHip64-cKO


title: dHip64-cKO

description:
processed data file: controlVscKO_DorsalHipAllRunsGLM.differential_expression_edgeR.txt
Three runs were performed for this Sample (one was excluded from the analysis). NS68 fastq file corresponds to _1 in the processed data file, and NS85 fastq file corresponds to _3 in the processed data file.

source_name: Dorsal hippocampus

value: Dorsal hippocampus


title: Oil_1


title: WT_EtOH_Rep3

value: vehicle


title: dHip71-Control

description:
processed data file: controlVscKO_DorsalHipAllRunsGLM.differential_expression_edgeR.txt
Three runs were performed for this Sample. NS68 fastq file corresponds to _1 in the processed data file, NS78 fastq file corresponds to _2 in the processed data file, and NS85 fastq file corresponds to _3 in the processed data file.


title: dHip49-Control


title: EGME_3

value: EGME


title: WT_EtOH_Rep2


title: EGME_2

value: Male


title: dHip43-cKO


title: WT_EtOH_Rep1


title: dHip41-Control


title: KO_Shield1_Rep3


title: dHip40-cKO


title: EGME_1


title: KO_Shield1_Rep2


title: KO_Shield1_Rep1


title: Water_3

value: Water


title: EpCAM_2

city: Boston

first: Lora

last: Bankova

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Illumina NextSeq500
Each sample’s sequences were aligned utilizing STAR v2.4.2a (Dobin, Davis et al. Bioinformatics 2013) and the following parameters: --twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. Alignments were processed using Picard v1.1073 tools to add read groups and other sequencing information, reorder the BAM file to the reference, and mark duplicate sequences.
The data was assessed for quality using RNA-SeQC (DeLuca, Levin et al.Bioinformatics 2012). TPM were quantified using RSEM v1.2.21 (Li and Dewey BMC Bionformatics 2011) with the paired-end option. Raw counts for differential expression analysis were generated using the FeatureCounts function of Rsubread (Liao, Smyth et al.Nucleic Acids Res 2013)
Differential expression analysis was conducted using the DEseq2 package (Love, Huber et al. Genome Biol 2014). Genes were considered to be significantly differentially regulated based on a fold change in expression of > 4-fold and a false discovery rate of <0.05 based on a Benjamini-Hochberg adjusted p-value to correct for multiple comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized counts from Deseq2 analysis

source_name: nose

extract_protocol:
Nasal epithelial cell suspensions were derived through a 2 step protocol: incubation with high dose dispase followed by papain digestion. Brush cells were identified flow cytometrically as CD45-EpCAM+eGFP+ cells, and subset to FSClow and FSChigh based on their FSC and SSC by FACS. EpCAM+ cells were identified as CD45−EpCAM+ChAT-eGFP- after dead cell exclusion with propidium iodide. Cells were sorted into TCL buffer supplemented with RNAprotect Cell Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nasal ChAT-eGFP- epithelial cells


title: EpCAM_5


title: Water_2

value: Sprague-Dawley


title: EpCAM_4


title: Water_1


title: EpCAM_1


title: ChATeGFP_FSClow_9

value: nasal ChAT-eGFP+ FSClow/SSClow epithelial cells


title: 2B4_Shield1_Rep2


title: RNA-seq of Homo sapiens: normal P120_N

city: Guangzhou

first: Changxi

last: Wang

state: Guangdong

address: No.74, Zhongshan second road

institute: Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using hisat2.
Read count for each gene was calculated using htseq-count software. Then fragments per kilobase of exon model per million reads mapped (FPKM) were calculated using stringtie.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: Osteosarcoma

extract_protocol:
Sarcoma specimens including tumor, adjacent normal tissues and paired blood samples were obtained from osteosarcoma patients.RNA was extracted using Trizol reagent.
RNA libraries were construncted for sequencing using standard Illumina protocols

value: normal

value: male

tag: kshv infection

value: negative


title: RNA-seq of Homo sapiens: normal P21_N


title: ChATeGFP_FSClow_8


title: 10X_Etv2_heterozygous_20ss

city: Tampa

first: Saulius

last: Sumanas

state: Florida

address: 560 Channelside Dr

institute: University of South Florida

data_processing:
All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters
Raw basecall files were assembled into fastq files using 'mkfastq' function
The 'count' function was used to align Fastq files to zebrafish genome v.9  and to obtain the gene expression matrices
Genome_build: GRCz10
Supplementary_files_format_and_content: mtx matrix files

organism: Danio rerio

source_name: FACS-sorted GFP+ endothelial cells

extract_protocol:
Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: 20-somite stage

value: FACS-sorted GFP+ endothelial cells


title: RNA-seq of Homo sapiens: tumor P16_T

value: tumor


title: ChATeGFP_FSClow_7


title: 2B4_EtOH_Rep3

value: Toxoplasma gondii parasites isolated from host cells


title: RNA-seq of Homo sapiens: normal P16_N


title: WT-2 [RNA-seq]

city: Guang zhou

first: siyuan

last: feng

address: 74 zhongshan 2nd road

description:
Mycobacterium smegmatis mc2155
processed data file: RNA-seq_DE_no_filter.txt

data_processing:
All raw sequence reads by RNA-Seq were initially pre-processed by Trimmomatic (v0.36) to trim the adaptor sequences and remove low-quality sequences. The remaining clean reads were mapped to the M. smegmatis mc2 155 genomes using Tophat2. The alignment results were input into Cufflinks (v2.2.1). Unless otherwise stated, the unit of expression level in our analyses is FPKM. Cuffdiff (v2.2.1) was used to test for differential expression. We defined genes as differentially expressed using the following criteria: FPKM > 10 and FDR < 0.001. The data for visualization was generated by R (R Development Core Team, Vienna, Austria).
The genome sequences and the annotations of M. smegmatis mc2 155 were obtained from the GenBank (https://www.ncbi.nlm.nih.gov/genbank/). We analyzed differences in the enrichment of Gene Ontology (GO) categories and KEGG pathways for the DEGs using the DAVID (v6.8) functional annotation analysis tool (https://david.ncifcrf.gov).
The obtained FASTQ files were filtered according to read quality, and adapter sequences were trimmed using the Trimmomatic software (Usadel Lab; Aachen University, Aachen, Germany). The filtered FASTQ files were mapped to the genome of M. smegmatis strain mc2 155 (from GenBank) using the BWA v0.7.12 (Burrows-Wheeler aligner), and the Bwa mem algorithm was applied. The bam files were sorted and indexed. Then, the bam files for the ChIP and input samples were subjected to MACS analysis (MACS2 software) for ChIP-Seq peak detection. Peak calling was performed without building a model using a shift size of 150 bp. The ChIP-Seq peaks were uploaded into the R environment as bed files, and the peaks were annotated ChIP-Seq data.
Then the bam files for the ChIP and input samples were subjected to MACS analysis (MACS2 software) for ChIP-Seq peak detection. Peak calling was performed without building a model using a shift size of 150 bp. The ChIP-Seq peaks were uploaded into the R environment as bed files, and the peaks were annotated ChIP-Seq data.
Genome_build: NC_008596.1
Supplementary_files_format_and_content: *.bw: bigWig files include ChIP-Seq peaks for each sample.
Supplementary_files_format_and_content: *.bed: BED files include peak scores for flag1 and flag2.
Supplementary_files_format_and_content: RNA-seq_DE_no_filter.txt: Tab-delimited text file includes log CPM.

organism: Mycolicibacterium smegmatis MC2 155

source_name: bacteria

growth_protocol: Wild-type M. smegmatis mc2155 as well as the greA deletion strain were grown to the log-phase (OD600, 0.4) in Middlebrook 7H9-ADC.

extract_protocol:
Total RNA was prepared from wild-type and mutant strains using TRIzol reagent (Invitrogen), followed by DNase I treatment. Approximately 1-μg total RNA samples were treated by the Ribo-Zero rRNA removal procedure (Illumina) to enrich for mRNA.
Approximately 1μg of RNA was used for library preparation using a ScriptSeq (v2) RNA-seq kit and high-throughput sequencing on an Illumina HiSeq platform.

treatment_protocol: No treatment.

value: wild type


title: WT-3 [RNA-seq]


title: 2B4_Shield1_Rep1


title: EpCAM_3


title: RNA-seq of Homo sapiens: tumor P21_T

value: positive


title: ChATeGFP_FSClow_6


title: RNA-seq of Homo sapiens: tumor P14_T


title: 2B4_EtOH_Rep2


title: 2B4_Shield1_Rep3


title: RNA-seq of Homo sapiens: tumor P20_T


title: WT-1 [RNA-seq]


title: ChATeGFP_FSClow_5


title: RNA-seq of Homo sapiens: normal P14_N


title: ChATeGFP_FSClow_4


title: 2B4_EtOH_Rep1


title: greA-3 [RNA-seq]

description:
Mycobacterium smegmatis mc2155
ΔgreA
processed data file: RNA-seq_DE_no_filter.txt

value: <delta>greA


title: ChATeGFP_FSClow_3


title: 10X_Etv2_homozygous_20ss


title: Isotype_control

data_processing:
Library strategy: CUT&RUN
adaptor trimming using trim_galore (v. 0.4.1)
alignment with bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 (v. 2.3.4.1)
peak calling with MACS2 -g 65668394 --nomodel -B –extsize 183 (v. 2.1.1)
Genome_build: ToxoDB-45_TgondiiME49
Supplementary_files_format_and_content: BedGraphs of BFD1 or isotype control fragments, and MACS2 narrowPeak files for two different fragment sizes - Extsize183 used for peak identification, and Extsize 119 used for motif analysis

growth_protocol: ∆BFD1::BFD1-Ty parasites were grown for 24 h in normal medium before being shifted to alkaline stress conditions and grown for an additional 48 hours before being mechanically released from host cells using two 27- followed by a 30-gauge syringe needle, and passed through a 5 µm filter. Parasites were then processed according to a modified version of the protocol used by Skene and Henikoff (2017), as detailed in the methods of the accompanying paper.

extract_protocol:
Parasite nuclei were isolated and bound to Concanalin A coated magnetic beads, and incubated with either anti-Ty (BB2) antibody or an isotype control. pAG-Mnase was then added and incubated to allow for antibody-targeted cleavage of DNA into  fragments. These fragments were allowed to diffuse out of the nucleus, and extracted by phenol-chloroform-isoamyl alcohol followed by ethanol precipitation.
Following end-repair, phosphorylation, and polyA-tailing, fragments were ligated with TruSeq Illumina indexed adapters and further amplified by PCR.

tag: antibody

value: Mouse IgG Isotype control

value: Toxoplasma gondii bradyzoites


title: greA-2 [RNA-seq]


title: BFD1

value: Anti-Ty (BB2)


title: greA-1 [RNA-seq]


title: Muscle_4

city: New York

first: Gregory

middle: Robert

last: Smith

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

data_processing:
Cell Ranger 2.0.1 used for data demultiplexing and alignment to the hg19 genome
Seurat 2.3 used for filtering cells with less than 200 discovered genes and filtering genes expressed in fewer than 3 cells. Cells were further filtered to remove those with high mitochondrial gene counts
Genome_build: hg19
Supplementary_files_format_and_content: csv files of raw UMI counts per sample

source_name: Vastus Lateralis Biopsy Mononuclear Cells

extract_protocol:
Four individual samples of dissociated cryopreserved cells (non-fiber cells only) obtained from a single human muscle biopsy were thawed based on the 10X Genomics Demonstrated Protocol (Manual Part Number CG00039 Rev C). Briefly, cryovials were removed from liquid nitrogen storage and immediately thawed in a 37°C waterbath for 2 minutes. 1ml of the thawed cells were transferred into individual tubes, the cryovials were rinsed with 1ml of warm complete growth medium and the rinse medium was added dropwise (1 drop per 5 sec) to each tube containing the thawed cells. The cells were serially diluted with complete growth medium a total of 3 times by 1:1 volume dropwise additions with 1 minute wait before each addition. Next the cells were centrifuged at 300 rcf for 5 minutes and resuspended in complete growth medium. Cells were filtered through a 40μm cell strainer, counted, and the volume of medium was adjusted for the final concentration to be 1,000 cells/μl
Single-cell encapsulation with beads using the 10X Genomics Chromium Single Cell 3’ v2 kit (PN 120235 and PN 120234 Module 1) was performed following manufacturer instructions (User Guide Rev A, 10X Genomics, Pleasanton, CA, USA). Briefly, 4 wells of a 10X microfluidic chip (PN 120236) were loaded each with an individual sample to target 5,000 cells per sample. Single-cell gel beads in emulsion (GEMs) were generated and reverse-transcription was performed in the emulsion prior to 12 cycles of cDNA amplification. Quality control and quantification of the amplified cDNA were assessed by Bioanalyzer. Libraries were constructed according to manufacturer instructions (PN 120234 Module 2). Each library was tagged with a different index for multiplexing (PN 120262) during sequencing. Library quality controls were assessed by Bioanalyzer and quantified by Qubit and quantitative PCR (KAPA Biosystems Quantification for Illumina platforms). Sequencing was performed on an HiSeq 2500 (Illumina, Inc., San Diego, CA) using the following read length: 26 bp Read1 (cell barcode(first 16 nt) + UMI(next 10 nt)), 8 bp i7 index (sample index), and 98 bp Read2 (insert).

value: skeletal muscle

tag: freezing medium

value: Commercial (Recovery Cell Culture Freezing Medium (Gibco/Thermofisher #12648-010, 10% DMSO))

tag: sample size


title: Muscle_3

value: Vastus Lateralis Biopsy Mononuclear Cells

value: Homemade (40% DMEM, 50% FBS, 10% DMSO)


title: ChATeGFP_FSClow_2

value: nasal ChAT-eGFP+ FSClow/SSClow epithelial cells


title: Muscle_2


title: WT-2 [ChIP-seq]

description: Mycobacterium smegmatis mc2155

growth_protocol: ChIP was performed using log-phase (OD600, 0.4) liquid medium grown cultures of M. smegmatis strains producing GreA-FLAG. As a negative control, WT log-phase culture was used.

extract_protocol:
The cells were fixed with 1% formaldehyde for 30 min, the reaction was quenched with 150 mM glycine for 15 min, and then the cells were washed three times with cold PBS (54,000 rpm, 5 min, 4 °C) and frozen at -80 °C. To prepare lysates, pellets were resuspended in FA-1 buffer (HEPES-KOH at 50 mM [pH 7.5], NaCl at 140 mM, EDTA at 1 mM, Triton X-100 at 1%, and protease inhibitor cocktail [Sigma-Aldrich]), disintegrated with silica beads (0.1 mm) for 45 min, and sonicated on ice using ten cycles of a 10-s pulse followed by a 50-s pause. The obtained lysates were centrifuged (5 min, 12,000 rpm, 4 °C) and frozen at -80 °C in 5% glycerol. For immunoprecipitation, 200 μg of total protein was incubated on a rotary shaker (Thermo Fisher Scientific, China Co., Ltd.) for four hours at 4 °C with a 15-μl packed-gel volume of anti-FLAG M2 magnetic beads (Sigma-Aldrich) and then washed twice with FA-1 buffer. Samples were processed in a final volume of 0.5 ml in two biological replicates, with input DNA controls (200 μg of total protein alone) included for each replicate. Samples were washed using a magnetic separator with sequential applications of FA-1 buffer, FA-2 buffer (HEPES-KOH at 50 mM [pH 7.5], NaCl at 500 mM, EDTA at 1 mM, Triton X-100 at 1%, and protease inhibitor cocktail), and Tris-EDTA buffer solution (TE) (Tris-HCl at 10 mM [pH 8.0], EDTA at 1 mM). Immunoprecipitated samples were de-cross-linked overnight in TE containing 1% SDS at 65 °C and then digested with proteinase K (final concentration, 0.05 mg/ml) for 1.5 h at 55 °C. The immunoprecipitated DNA was extracted using Cycle-Pure Kit (OMEGA Bio-tek, Inc.).
The library of DNA fragments was prepared using a QIAseq Ultralow Input library kit (Qiagen). Briefly, the protocol includes DNA end-repair, sequencing adapter ligation, cleanup, and PCR amplification. At the end of the procedure, quantification and quality evaluations were done using a NanoPhotometer® spectrophotometer (IMPLEN), a Qubit® 2.0 Fluorometer (Life Technologies), and a 2100 Bioanalyzer (Agilent). Second-generation sequencing was performed using a HiSeq 1500 sequencing platform (Illumina).

tag: chip magnetic beads

value: Anti-FLAG beads (Millipore, M8823)


title: GreA-FLAG-2 [ChIP-seq]

description: Mycobacterium smegmatis mc2155

value: greA-flag


title: Muscle_1


title: WT_stress_72h_array2

data_processing:
R1: technical (barcode is 1-12, UMI is 13-20). R2: biological.
FastqToSam: from picard-tools 1.0
Drop-seq_script.sh: From https://github.com/broadinstitute/Drop-seq/releases, Drop-Seq tools v.2.1.0 zip. Modified slightly by replacing refflat variable in tag_with_gene_exon with appropriate GTF (ToxoDB-41_TgondiiME49 gff, converted to gtf by gffread
DetectBeadSynthesisErrors v2.1.0 with: NUM_BARCODES=20000 PRIMER_SEQUENCE=AAGCAGTGGTATCAACGCAGAGTAC
DigitalExpression v.2.1.0 with: MIN_NUM_GENES_PER_CELL=100
Genome_build: ToxoDB-41_TgondiiME49
Supplementary_files_format_and_content: Digital Gene Expression (DGE) files are matrices, where extracted cell barcodes are columns and genes are rows. Values are of Unique Molecular Identifers (UMIs) detected, a proxy for unique transcripts captured.

source_name: T. gondii purified from host HFFs

growth_protocol: Parasites were inoculated onto host HFFs at an MOI of 1, allowed to invade for 4 hours, and then placed under unstressed (DMEM + 3% IFS, 5% CO2) or stressed (RPMI 1640 pH 8.1 + 1% IFS, ambient CO2) conditions for 24, 48 or 72 hours.

extract_protocol:
Seq-Well was performed as previously described  (Gierahn et al., 2017) , with the following amendments to the protocol. Following Exonuclease I treatment, second strand synthesis was performed.
Nextera XT library reactions were done using 1 ng of WTA input, 11 μL TD and 4 μL ATM per reaction.
instrument model: NovaSeq S2

treatment_protocol: Single cell suspensions of Toxoplasma were prepared by syringe release of parasites from host cells with a 27 followed by a 30-gauge needle, followed by filtering through a 5 µm filter and counting on a haemocytometer. Approximately 12,000 parasites were loaded per array, with two arrays per strain and timepoint used for stressed samples, and one array per strain for unstressed. At the 48 h timepoint, one wild-type stressed and one ∆BFD1 stressed array failed to seal correctly, resulting in only one array per strain and growth condition at this timepoint.

value: WT

tag: growth condition

value: stress

tag: timepoint

value: 72 hr


title: L2 bulk brady 7d

description: genomic DNA/amplicon

data_processing:
gRNAs were quantified by aligning the first 20 base pairs of the read against a list of library gRNAs. Only exact matches to the input library were considered and counted. A sample script to do this operation is available from Sidik, Huet, and Lourido (2018, Nature Methods) - https://www.ncbi.nlm.nih.gov/pubmed/29323662
Supplementary_files_format_and_content: Processed data files contain a list of all gRNAs in the screen alongside an absolute count of times that gRNA was perfectly observed in sequencing data. gRNAs were quantified using a custom perlscript, equivalent to aligning the first 20 base pairs of the read against a known list of possible gRNAs with no mismatches allowed.

source_name: integrated gRNAs

growth_protocol: Reporter strain parasites were grown up in ~10 15-cm plates per screen. 10 transfections were performed for each library as described previously, with 50 μg of library transfected into approximately 2.6 x 10e7 parasites in 400 µL cytomix for each reaction (Sidik et al., 2014). Transfections were pooled and split between four 15-cm dishes. Medium was changed the following day to standard media supplemented with 3 μM pyrimethamine and 10 μg/mL DNaseI (Sigma-Aldrich). At each passage of the screen, plates were scraped and parasites were mechanically released with a 27-gauge needle. For the second passage of the screen, all parasites were passed into four 15-cm plates without counting. All subsequent passages were performed at a multiplicity of infection (MOI) of ~1 (6 x 10e6 parasites per plate). Plates lysed every 2–3 days under unstressed growth in standard media supplemented with 3 µM pyrimethamine. At fourth passage (14 days post-transfection), parasites were inoculated into seven 15-cm plates, and medium was changed after 4 hours to standard medium supplemented with 3 µM pyrimethamine (3 plates) or alkaline stress media (4 plates). Unstressed parasites were passaged at an MOI of 1 every 2–3 days into one or two 15-cm plates, in standard medium supplemented with 3 µM pyrimethamine. Parasites under stressed conditions did not lyse out and were not passaged for the duration of the experiment, and medium was changed every 2 days to fresh alkaline stress medium. At each passage of unstressed parasites, 1–4 x 10e7 parasites were frozen down. At 10 days post media change, stressed populations were scraped, parasites were mechanically released, passed through a 3 µm filter, and sorted based on green fluorescence. Sorting was done using a BD FACS Aria II. At final timepoints for stressed parasites, both bulk populations (~2 x 10e5 parasites) and mNG+-sorted populations (~7 x 10e5) were frozen.

extract_protocol:
DNA was isolated using the Qiagen Blood and Tissue kit, following the protocol for blood cells. Integrated gRNAs were amplified, barcoded, pooled by QuBit and sequenced on an Illumina MiSeq.
We assembled two libraries, each targeting ~100 potential nucleic acid-binding proteins, with 5 gRNAs per gene. Library 1 (L1) largely consists of genes identified as differentially regulated in our preliminary RNA-seq experiment. Library 2 (L2) contains genes with DNA-binding domains commonly found in transcription factors, such as zinc finger and Myb-like domains. Across both libraries, all 67 members of the ApiAP2 transcription factor family are targeted, along with 151 putative nucleic acid-binding proteins. As controls, each library additionally contains 10 genes known to be essential, 10 genes known to be dispensable, 10 non-cutting gRNAs, and 5 gRNAs against the mNG reporter itself. Oligonucleotide pools were ordered from agilent, and assembled by Gibson assembly.

tag: sample type

value: unsorted bradyzoite

value: stressed

value: L2 bulk bradyzoites, 7d post alkaline stress


title: L2 mNG+ 10d

description: genomic DNA/amplicon

value: sorted bradyzoite

value: L2 sorted mNG+ bradyzoites, 10d post alkaline stress


title: ChATeGFP_FSClow_1


title: ChATeGFP_FSChi_4

value: nasal ChAT-eGFP+ FSChi/SSChi epithelial cells


title: ChATeGFP_FSChi_3


title: L2 p8

description: genomic DNA/amplicon

value: tachyzoites

value: unstressed

value: L2 eigth passage tachyzoites


title: GreA-FLAG-1 [ChIP-seq]

description: Mycobacterium smegmatis mc2155


title: WT_stress_72h_array1


title: WT_stress_24h_array2

value: 24 hr


title: ChATeGFP_FSChi_1


title: ChATeGFP_FSChi_2


title: L2 bulk brady 10d

description: genomic DNA/amplicon

value: unsorted bradyzoites

value: L2 bulk bradyzoites, 10d post alkaline stressed


title: Whib6-3xfl (DespM)/MSP-espM Rep 2, part 2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Reads from each lane were combined into individual files using standard UNIX commands
Trimmomatic (v0.33)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie (v1.1.2) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
HTSeq software suite (v0.6.0) was used to analyze aligned and determine counts per gene feature in the M. tuberculosis CDC1551 genome
edgeR (v3.2) was used to normalize data by estimating effective library sizes using trimmed mean M-values
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the GLM functionality edgeR package
Genome_build: Mycobacterium marinum M reference genome (GCA_000018345.1)
Supplementary_files_format_and_content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates

organism: Mycobacterium marinum

source_name: Bacterial Cell

growth_protocol: M Marinum M based strains (Wild type, epsM mutant and complemented overexpressor strain) were cultured in 5mL 7H9 and 0.1% Tween-80 for two days, then moved to 25mL 7H9 and 0.1% Tween-80 for two days. All strains were then subcultured in Sauton’s media 0.01% Tween-80 at an OD of 0.8  for 48 hours.

extract_protocol:
The cultures were collected by centrifugation and stored at -80 for 24 hours. Cells were lysed using a bead beater. Total RNA was prepared from the pellets using the Qiagen RNeasy kit, as described by Bosserman et al., PNAS, 2017.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: Cells were untreated

value: M strain (ATCC BAA-535)

value: espM deletion mutant, complemented


title: ChATeGFP_FSChi_5


title: WT_stress_48h_array1

value: WT

value: 48 hr


title: L2 p7

description: genomic DNA/amplicon

value: tachyzoite

value: L2 seventh passage tachyzoites


title: Whib6-3xfl (DespM)/MSP-espM Rep 1, part 2


title: L2 p6

description: genomic DNA/amplicon

value: L2 sixth passage tachyzoites


title: gDNA

city: Birmingham

first: Rui

last: Monteiro

address: Medical School, Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Sequencing was performed on a NextSeq machine, using two 75bp paired-end chips loaded with the same Master-Library mix. Reads were combined to one raw data set.
Sequences were aligned to the Zebrafish Genome Zv10 with BWA (Version 0.7.12) with default parameters. Aligned read features were counted using Subread tool: featureCounts method (version 1.4.5-p1).
Peaks were identified using MAC2 software (Version 1.4.2), using the genomic DNA as input to define background, and ChrM peaks were filtered out. Differential peaks analysis was carried out using DiffBind (Bioconductor Package).  tool).
Quadruplicates were analysed for consistency by PCA and correlation analysis and two replicates have been removed for Kdrl-GFPhigh due to coverage issues. Using DiffBind (EdgeR method), a list of DE peaks between Kdrl-GFPhigh and Kdrl-GFPneg were identified. The threshold for differential peaks was p<0.05
“De novo analysis” for transcription factor binding site has been carried out using the TSS, intergenic, and intron peaks list with “findMotifsGenome.pl” in Homer software package. The peak list has been filtered according the gene present in the Differential Expressed gene list. From an RNAseq experiment performed in endothelial cells from Tg(kdrl:GFP) transgenic embryos profiling  expression at 26-28hpf. The data used from this table are been filtered by FC > 1.3
Genome_build: Zv9
Supplementary_files_format_and_content: DE_Peacks_kdrlPos_kdrlNeg_componed_peacks_annotations.txt

source_name: whole embryo

growth_protocol: Tg(Kdrl:GFP)s843 transgenic zebrafish embryos were raised to 26-27 hpf.

extract_protocol:
whole embryos were prepaired for FACsorting. 40000-50000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation
Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218), but with 1.5 µl Tn5 transposase (Illumina) in a 50 µl reaction volume. DNA was purified using the QIAquick PCR purification kit (Qiagen). Fragments were amplified for 16 cycles.

tag: Stage

value: FACS isolated cells

value: Genomic control DNA was isolated from 30.000 cells using the DNeasy Blood & Tissue kit (Qiagen) and eluted with EB buffer.


title: L2 mNG+ 7d

description: genomic DNA/amplicon

value: sorted bradyzoite

value: stressed

value: L2 sorted mNG+ bradyzoites, 7d post alkaline stress


title: WT_stress_24h_array1

tag: genotype

value: stress


title: WT-1 [ChIP-seq]

description: Mycobacterium smegmatis mc2155

value: wild type

value: Anti-FLAG beads (Millipore, M8823)


title: L2 p4

description: genomic DNA/amplicon

value: unstressed

value: L2 fourth passage tachyzoites


title: WT_unstress_72h_array1

value: unstress

value: 72 hr


title: Whib6-3xfl (DespM) Rep 2, part 2

value: M strain (ATCC BAA-535)

value: espM deletion mutant


title: Kdrl-GFPneg_sample6

source_name: non-endothelial tissue


title: Whib6-3xfl (DespM) Rep 2, part 1


title: L2 input library

description: genomic DNA/amplicon

source_name: plasmid library

value: L2 intial library


title: Kdrl-GFPneg_sample4


title: L1 mNG+ 10d

description: genomic DNA/amplicon

value: L1 sorted mNG+ bradyzoites, 10d post alkaline stress


title: Whib6-3xfl (DespM)/MSP-espM Rep 2, part 1

value: espM deletion mutant, complemented


title: WT_unstress_24h_array1

value: WT

value: 24 hr


title: KO_stress_72h_array2


title: L1 mNG+ 7d

description: genomic DNA/amplicon

value: sorted bradyzoite

value: L1 sorted mNG+ bradyzoites, 7d post alkaline stress


title: Whib6-3xfl (DespM) Rep 1, part 2


title: Whib6-3xfl (DespM) Rep 1, part 1


title: L1 bulk brady 10d

description: genomic DNA/amplicon

value: unsorted bradyzoite

value: stressed

value: L1 bulk bradyzoites, 10d post alkaline stressed


title: KO_stress_24h_array2

value: stress


title: Kdrl-GFPneg_sample2

value: FACS isolated cells

value: wild type


title: WT (WhiB6-3xfl) Rep 2, part 2

value: Wild Type (expressing WhiB6-FLAG)


title: Kdrl-GFP+_sample1

source_name: endothelial tissue


title: L2 p5

description: genomic DNA/amplicon

value: tachyzoite

value: unstressed

value: L2 fifth passage tachyzoites


title: Whib6-3xfl (DespM)/MSP-espM Rep 1, part 1

value: M strain (ATCC BAA-535)


title: L1 bulk brady 7d

description: genomic DNA/amplicon

value: L1 bulk bradyzoites, 7d post alkaline stress


title: Kdrl-GFP+_sample3


title: KO_stress_72h_array1

value: 72 hr


title: Kdrl-GFP+_sample7


title: L1 p8

description: genomic DNA/amplicon

value: L1 eigth passage tachyzoites


title: KO_stress_48h_array1

value: 48 hr


title: WT (WhiB6-3xfl) Rep 2, part 1


title: VC-4

city: harbin

first: Ningning

last: Song

address: No.678. Haping Road

institute: Harbin Veterinary Research Institute

data_processing:
step1:Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
step2：Obtained clean reads were mapped to the Mycobacterium bovis BCG_str_Tokyo_172 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
step3:The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: Mycobacterium bovis BCG_str_Tokyo_172
Supplementary_files_format_and_content: raw read count and FPKM

organism: Mycobacterium tuberculosis variant bovis

source_name: BCG culture

growth_protocol: Mycobacterium bovis BCG str. Tokyo 172 strain was grown in Middlebrook 7H9 medium Becton Dickinson supplemented with 0.05% Tween 80(V/V), 10% ADC (Albumin-Dextrose-Catalase, BD) and 0.2% (V/V) glycerol. The bacteria were incubated at 100 rpm 37℃ until the culture reached an exponential phase.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vc was added at a final concentration of 5 mM in 7H9 liquid medium.


title: WT (WhiB6-3xfl) Rep 1, part 2


title: WT_unstress_48h_array1

value: WT

value: unstress


title: VC-3


title: WT (WhiB6-3xfl) Rep 1, part 1


title: KO_stress_24h_array1

value: 24 hr


title: L1 p6

description: genomic DNA/amplicon

value: L1 sixth passage tachyzoites


title: L1 p7

description: genomic DNA/amplicon

value: L1 seventh passage tachyzoites


title: KO_unstress_72h_array1


title: Ca150

city: Qingdao

first: Ning

last: Ma

address: No.7 Nanhai Road

institute: The Institute of Oceanology, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia). After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Raw data of fastq format were firstly processed through in-house perl scripts.Then clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GCA_001606005.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Brevibacterium linens

source_name: brevibacterium linens cells

extract_protocol:
Total RNAs were extracted using the RNApure Bacteria Kit (DNase I) (CWBio, China). A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The Brevibacterium lines cells were treated with 0 mM, 50 mM or 150 mM CaCl2 for 24 h.

tag: treated with


title: control 3

tag: strain


title: KO_unstress_48h_array1


title: L1 p5

description: genomic DNA/amplicon

value: L1 fifth passage tachyzoites


title: Ca50

value: 50 mM  Ca2+


title: KO_unstress_24h_array1


title: L1 p4

description: genomic DNA/amplicon

value: L1 fourth passage tachyzoites


title: HeLa, Myc depletion 3

status: Public on Jan 15 2020

city: Turku

first: Jukka

last: Westermarck

address: Tykistokatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Human GRCh38
Supplementary_files_format_and_content: tab delimited text file containing the genewise read counts for each sample

source_name: Myc depletion

growth_protocol: Growth mediums were supplemented with 10% heat-inactivated FBS (Gibco), 2 mmol/L L-glutamine, and penicillin (50 units/mL)/streptomycin (50 mg/mL). HeLa cells were cultured in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using NucleoSpin® RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation was done according to Illumina TruSeq® Stranded mRNA kit protocol.

treatment_protocol: The HeLa cell were transfected with relevant siRNAs for 72 hours.

tag: cell line

value: HeLa

tag: tissue

value: cervix

tag: disease

value: cervical adenocarcinoma

tag: genotype (rna interference)

value: Myc knockdown by siRNA


title: HeLa, UBR5 depletion 1

description: sequencing was done in 1 lane

source_name: UBR5 depletion

value: UBR5 knockdown by siRNA


title: HeLa, UBR5 depletion 2

description: sequencing was done in 1 lane


title: HeLa, Negative control 2

description: sequencing was done in 1 lane

source_name: Negative control

value: Scrambled siRNA


title: HeLa, Myc depletion 2

description: sequencing was done in 1 lane


title: HeLa, Myc depletion 1

description: sequencing was done in 1 lane


title: HeLa, UBR5 depletion 3

description: sequencing was done in 1 lane


title: HeLa, Negative control 1

description: sequencing was done in 1 lane

value: none siRNA


title: VC-2


title: L4_DH12_Bone__RefRNA

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

description:
RefRNA
S1500 TempOseq RNA
L4_DH12_S384_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

data_processing:
.gz files were concatenated from Lane1/2.
Reads Aligned against s1500+ Manifest (BioSpyder) Human. This was a TempOseq experiment with the s1500+ probeset (January 2018).
Unambiguous Counts assigned for n = 2977 Probes.
Supplementary_files_format_and_content: TCTC_Mapped_Reads.csv: Comma-separated file

source_name: TE-Bone, 3D Osteoblasts

extract_protocol:
Cell lysates from plates or 3D tumors were prepared using lysis buffer (provided with TempO-seq probes). After 10-min incubation at room temperature, lysates were stored at −80 °C until testing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: TE-Bone, 3D Osteoblasts


title: L4_DH06_Bone/Tumor_MAP_P16C4

description:
P16C4
S1500 TempOseq RNA
L4_DH06_S372_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

source_name: TE-Tumor, 3D Osteoblasts and Ewing's Sarcoma

tag: exposure

value: MAP

tag: treatment concentration

value: high


title: L4_DH05_Bone/Tumor_Vincristine_P15A4

description:
P15A4
S1500 TempOseq RNA
L4_DH05_S370_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: TE-Tumor, 3D Osteoblasts and Ewing's Sarcoma

value: Vincristine


title: L4_DH03_Bone/Tumor_Dexamethasone_P12C4

description:
P12C4
S1500 TempOseq RNA
L4_DH03_S366_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Dexamethasone


title: L4_DH02_Bone/Tumor_Dexamethasone_P11A4

description:
P11A4
S1500 TempOseq RNA
L4_DH02_S364_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DH01_Bone/Tumor_Cisplatin_P10B2

description:
P10B2
S1500 TempOseq RNA
L4_DH01_S362_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Cisplatin


title: control 2


title: L4_DG05_Bone/Tumor_Vincristine_P15C2

description:
P15C2
S1500 TempOseq RNA
L4_DG05_S322_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG06_Bone/Tumor_MAP_P16B4

description:
P16B4
S1500 TempOseq RNA
L4_DG06_S324_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: MCF10A timecourse

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

data_processing:
cellranger ranger2.1.1  used for processing and mapping the raw sequnce reads
Genome_build: hg38
Supplementary_files_format_and_content: rds; matrix.mtx, barcodes.tsv, genes.tsv

molecule: nuclear RNA

source_name: Mammary epithelium

growth_protocol: The cells were grown in DMEM/F12(1:1)

extract_protocol:
RNA-Seq library was prepared using 10x Chromium Single Cell 3' –end Reagent Kits User Guide (v2 Chemistry)
Libraries were sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on the Illumina HiSeq 2500

treatment_protocol: Normal human mammary epithelial cell MCF10A was stimulated with TGFbeta for 0,1,2,3,4,5,6,7 days (8 time points) and all samples were pooled before loading into 10x Genomics. Single-cell 3'RNA-seq library was prepared according to the manufacturer's instructions.

value: mammary epithelial cell MCF10A

tag: treatment

value: TGFbeta

tag: time

value: mixed sample [0,1,2,3,4,5,6,7 days (8 time points)]


title: L4_DG12_Bone/Tumor_Control_Water

description:
Water
S1500 TempOseq RNA
L4_DG12_S336_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Control


title: control 1


title: L4_DG04_Bone/Tumor_Methotrexate_P14A2

description:
P14A2
S1500 TempOseq RNA
L4_DG04_S320_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Methotrexate


title: L4_DG02_Bone/Tumor_Cisplatin_P11C2

description:
P11C2
S1500 TempOseq RNA
L4_DG02_S316_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG03_Bone/Tumor_Dexamethasone_P12B4

description:
P12B4
S1500 TempOseq RNA
L4_DG03_S318_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1 input library

city: CAMBRIDGE

first: Benjamin

last: Waldman

address: 455 Main Street Rm. 555

description: genomic DNA/amplicon

value: L1 intial library


title: L4_DF12_Bone_Control_LysisBuffer

description:
LysisBuffer
S1500 TempOseq RNA
L4_DF12_S288_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG01_Bone/Tumor_Cisplatin_P10A2

description:
P10A2
S1500 TempOseq RNA
L4_DG01_S314_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF05_Bone/Tumor_Vincristine_P15B2

description:
P15B2
S1500 TempOseq RNA
L4_DF05_S274_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF04_Bone/Tumor_Methotrexate_P13C4

description:
P13C4
S1500 TempOseq RNA
L4_DF04_S272_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF02_Bone/Tumor_Cisplatin_P11B2

description:
P11B2
S1500 TempOseq RNA
L4_DF02_S268_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF01_Bone/Tumor_Control_P9C4

description:
P9C4
S1500 TempOseq RNA
L4_DF01_S266_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE05_Bone/Tumor_Vincristine_P15A2

description:
P15A2
S1500 TempOseq RNA
L4_DE05_S226_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE06_Bone/Tumor_MAP_P16C2

description:
P16C2
S1500 TempOseq RNA
L4_DE06_S228_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: low


title: L4_DF06_Bone/Tumor_MAP_P16A4

description:
P16A4
S1500 TempOseq RNA
L4_DF06_S276_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF03_Bone/Tumor_Dexamethasone_P12A4

description:
P12A4
S1500 TempOseq RNA
L4_DF03_S270_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DH04_Bone/Tumor_Methotrexate_P14B2

description:
P14B2
S1500 TempOseq RNA
L4_DH04_S368_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE03_Bone/Tumor_Dexamethasone_P12C2

description:
P12C2
S1500 TempOseq RNA
L4_DE03_S222_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE02_Bone/Tumor_Cisplatin_P11A2

description:
P11A2
S1500 TempOseq RNA
L4_DE02_S220_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE04_Bone/Tumor_Methotrexate_P13B4

description:
P13B4
S1500 TempOseq RNA
L4_DE04_S224_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE01_Bone/Tumor_Control_P9B4

description:
P9B4
S1500 TempOseq RNA
L4_DE01_S218_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD06_Bone/Tumor_MAP_P16B2

description:
P16B2
S1500 TempOseq RNA
L4_DD06_S180_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD04_Bone/Tumor_Methotrexate_P13A4

description:
P13A4
S1500 TempOseq RNA
L4_DD04_S176_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD02_Bone/Tumor_Cisplatin_P10C4

description:
P10C4
S1500 TempOseq RNA
L4_DD02_S172_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD01_Bone/Tumor_Control_P9A4

description:
P9A4
S1500 TempOseq RNA
L4_DD01_S170_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC05_Bone/Tumor_Vincristine_P14B4

description:
P14B4
S1500 TempOseq RNA
L4_DC05_S130_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC02_Bone/Tumor_Cisplatin_P10B4

description:
P10B4
S1500 TempOseq RNA
L4_DC02_S124_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC06_Bone/Tumor_MAP_P16A2

description:
P16A2
S1500 TempOseq RNA
L4_DC06_S132_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC01_Bone/Tumor_Control_P9C3

description:
P9C3
S1500 TempOseq RNA
L4_DC01_S122_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DB05_Bone/Tumor_Vincristine_P14A4

description:
P14A4
S1500 TempOseq RNA
L4_DB05_S82_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DB06_Bone/Tumor_Vincristine_P15C4

description:
P15C4
S1500 TempOseq RNA
L4_DB06_S84_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC04_Bone/Tumor_Methotrexate_P13C2

description:
P13C2
S1500 TempOseq RNA
L4_DC04_S128_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: Ca0

value: 0 mM Ca2+


title: L4_DD03_Bone/Tumor_Dexamethasone_P12B2

description:
P12B2
S1500 TempOseq RNA
L4_DD03_S174_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DB02_Bone/Tumor_Cisplatin_P10A4

description:
P10A4
S1500 TempOseq RNA
L4_DB02_S76_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DB03_Bone/Tumor_Dexamethasone_P11C4

description:
P11C4
S1500 TempOseq RNA
L4_DB03_S78_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DB01_Bone/Tumor_Control_P9B3

description:
P9B3
S1500 TempOseq RNA
L4_DB01_S74_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DA06_Bone/Tumor_Vincristine_P15B4

description:
P15B4
S1500 TempOseq RNA
L4_DA06_S36_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DA05_Bone/Tumor_Methotrexate_P14C2

description:
P14C2
S1500 TempOseq RNA
L4_DA05_S34_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DA02_Bone/Tumor_Cisplatin_P10C2

description:
P10C2
S1500 TempOseq RNA
L4_DA02_S28_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD05_Bone/Tumor_Vincristine_P14C4

description:
P14C4
S1500 TempOseq RNA
L4_DD05_S178_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DA01_Bone/Tumor_Control_P9A3

description:
P9A3
S1500 TempOseq RNA
L4_DA01_S26_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DA04_Bone/Tumor_Methotrexate_P13A2

description:
P13A2
S1500 TempOseq RNA
L4_DA04_S32_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AH09_Bone_Doxorubicin_TC_P8_C2

description:
TC_P8_C2
S1500 TempOseq RNA
L4_AH09_S353_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Doxorubicin


title: L4_AG10_Bone_Linsitinib_TC_P4_B2

description:
TC_P4_B2
S1500 TempOseq RNA
L4_AG10_S307_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Linsitinib


title: L4_AG09_Bone_Doxorubicin_TC_P8_B2

description:
TC_P8_B2
S1500 TempOseq RNA
L4_AG09_S305_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: TE-Bone, 3D Osteoblasts


title: L4_DC03_Bone/Tumor_Dexamethasone_P12A2

description:
P12A2
S1500 TempOseq RNA
L4_DC03_S126_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AF09_Bone_Doxorubicin_TC_P8_A2

description:
TC_P8_A2
S1500 TempOseq RNA
L4_AF09_S257_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AF10_Bone_Linsitinib_TC_P4_A2

description:
TC_P4_A2
S1500 TempOseq RNA
L4_AF10_S259_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AE09_Bone_Doxorubicin Control_TC_P6_C2

description:
TC_P6_C2
S1500 TempOseq RNA
L4_AE09_S209_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Doxorubicin Control


title: L4_DB04_Bone/Tumor_Methotrexate_P13B2

description:
P13B2
S1500 TempOseq RNA
L4_DB04_S80_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: HeLa, Negative control 3

description: sequencing was done in 1 lane

value: HeLa

value: cervix

value: cervical adenocarcinoma

value: Scrambled siRNA


title: L4_AD10_Bone_Linsitinib Control_TC_P2_B2

description:
TC_P2_B2
S1500 TempOseq RNA
L4_AD10_S163_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Linsitinib Control


title: L4_AD09_Bone_Doxorubicin Control_TC_P6_B2

description:
TC_P6_B2
S1500 TempOseq RNA
L4_AD09_S161_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AC09_Bone_Doxorubicin Control_TC_P6_A2

description:
TC_P6_A2
S1500 TempOseq RNA
L4_AC09_S113_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DH09_Bone/Tumor_Linsitinib_TC-P7-C2

description:
TC-P7-C2
S1500 TempOseq RNA
L2_DH09_S378_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AC10_Bone_Linsitinib Control_TC_P2_A2

description:
TC_P2_A2
S1500 TempOseq RNA
L4_AC10_S115_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DF09_Bone/Tumor_Linsitinib_TC-P7-A2

description:
TC-P7-A2
S1500 TempOseq RNA
L2_DF09_S282_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: TE-Tumor, 3D Osteoblasts and Ewing's Sarcoma


title: L4_DA03_Bone/Tumor_Dexamethasone_P11B4

description:
P11B4
S1500 TempOseq RNA
L4_DA03_S30_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Dexamethasone


title: L2_DG09_Bone/Tumor_Linsitinib_TC-P7-B2

description:
TC-P7-B2
S1500 TempOseq RNA
L2_DG09_S330_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AH10_Bone_Linsitinib_TC_P4_C2

description:
TC_P4_C2
S1500 TempOseq RNA
L4_AH10_S355_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DE09_Bone/Tumor_Linsitinib Control_TC-P5-C2

description:
TC-P5-C2
S1500 TempOseq RNA
L2_DE09_S234_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DC09_Bone/Tumor_Linsitinib Control_TC-P5-A2

description:
TC-P5-A2
S1500 TempOseq RNA
L2_DC09_S138_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DD09_Bone/Tumor_Linsitinib Control_TC-P5-B2

description:
TC-P5-B2
S1500 TempOseq RNA
L2_DD09_S186_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CH09_Bone/Tumor_Doxorubicin_TC-P7-C2

description:
TC-P7-C2
S1500 TempOseq RNA
L1_CH09_S354_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CE09_Bone/Tumor_Doxorubicin Control_TC-P5-C2

description:
TC-P5-C2
S1500 TempOseq RNA
L1_CE09_S210_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CF09_Bone/Tumor_Doxorubicin_TC-P7-A2

description:
TC-P7-A2
S1500 TempOseq RNA
L1_CF09_S258_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CD09_Bone/Tumor_Doxorubicin Control_TC-P5-B2

description:
TC-P5-B2
S1500 TempOseq RNA
L1_CD09_S162_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DH10_Tumor_Vincristine_ES34F

description:
ES34F
S1500 TempOseq RNA
L4_DH10_S380_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

source_name: Ewing's Sarcoma Cells 2D

value: Ewing's Sarcoma Cells 2D

value: Vincristine


title: L4_DH07_Tumor_Cisplatin_ES26F

description:
ES26F
S1500 TempOseq RNA
L4_DH07_S374_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Cisplatin


title: L4_DH08_Tumor_Dexamethasone_ES46E

description:
ES46E
S1500 TempOseq RNA
L4_DH08_S376_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_AE10_Bone_Linsitinib Control_TC_P2_C2

description:
TC_P2_C2
S1500 TempOseq RNA
L4_AE10_S211_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CG09_Bone/Tumor_Doxorubicin_TC-P7-B2

description:
TC-P7-B2
S1500 TempOseq RNA
L1_CG09_S306_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CC09_Bone/Tumor_Doxorubicin Control_TC-P5-A2

description:
TC-P5-A2
S1500 TempOseq RNA
L1_CC09_S114_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DH11_Tumor_MAP_ES210E

description:
ES210E
S1500 TempOseq RNA
L4_DH11_S382_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: MAP


title: L4_DH09_Tumor_Methotrexate_ES14G

description:
ES14G
S1500 TempOseq RNA
L4_DH09_S378_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Methotrexate


title: L4_DG11_Tumor_Vincristine_ES38G

description:
ES38G
S1500 TempOseq RNA
L4_DG11_S334_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG07_Tumor_Cisplatin_ES26E

description:
ES26E
S1500 TempOseq RNA
L4_DG07_S326_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF11_Tumor_Vincristine_ES38F

description:
ES38F
S1500 TempOseq RNA
L4_DF11_S286_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG08_Tumor_Dexamethasone_ES44G

description:
ES44G
S1500 TempOseq RNA
L4_DG08_S328_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG10_Tumor_Vincristine_ES34E

description:
ES34E
S1500 TempOseq RNA
L4_DG10_S332_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: U87MG_F

city: Dalian

first: Weifeng

last: Mao

address: 9 Lvshun South Rd,

institute: Dalian Medical University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence ( SeqPrep ), and masked for low-complexity or low-quality sequence ( Sickle ) , then mapped to GRCh38 using TopHat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: brain

growth_protocol: The U87MG  cells were cultured in DMEM medium containing 10% fetal bovine serum and 1% Penicillin-Streptomycin in an environment of 5% CO2 at 37˚C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 5 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate radioresistant cells, we plated U87MG cells (1×10^6) in 10 cm culture dishes and irradiated them with 2 Gy of X-rays using a X-RAD 320ix Biological irradiation system (Precision X-ray, Inc.). Immediately after irradiation, the culture medium was renewed, and the cells were cultured in the incubator. When the cells reached approximately 90% confluence, they were counted and passaged into new culture dishes. The cells were treated again with 2 Gy of X-rays at about 60% confluence. These procedures were repeated 5 times in a period of 1 month, in a total dose of 10 Gy. The parental U87MG cells were trypsinized, counted, and passaged under the same conditions without irradiation. The screened radioresistant cells were named U87MG_F.

value: Glioblastoma

tag: x-ray radiation

value: 2 Gy of X-rays for 5 times


title: U87MG


title: L4_DF10_Tumor_Methotrexate_ES18G

description:
ES18G
S1500 TempOseq RNA
L4_DF10_S284_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF09_Tumor_Methotrexate_ES14E

description:
ES14E
S1500 TempOseq RNA
L4_DF09_S282_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DF08_Tumor_Dexamethasone_ES44F

description:
ES44F
S1500 TempOseq RNA
L4_DF08_S280_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 12w.1d.rep2

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

data_processing:
For ease of use R2 sequence was concatenated to header of R1.
Samples were aligned to mouse genome mm9 using HISAT aligner.
Sam files were filtered for PCR duplication using 8N UMI (unique molecular identifier) found in header after sample barcode.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized table of expression was created using Homer, normalization was done to 10M reads.

source_name: HSC KSL Flt3- CD48- CD150+

growth_protocol: 6-8 weeks old WT C57BL/6 mice at the time of the first injection.

extract_protocol:
8000 sorted HSC KSL Flt3- CD48- CD150+ from pool of 3-8 mice were directly sorted in lysis buffer. RNA extraction has been done as described in Lara-Astiaso et al., 2014.
Library amplification using nextera kit has been done as described in Lara-Astiaso et al., 2014.

treatment_protocol: Mice were injected I.P. with 100 µl PBS or 125 ug in 100 µl of LPS. 1 day after the last injection, bone marrow was harvested, then mature cells were depleted and HSC KSL Flt3- were FACS-sorted. Samples are from pool of 3-8 mice.

value: 12 weeks and 1 day

value: HSC KSL Flt3- CD48- CD150+ bone marrow


title: 12w.1d.rep1


title: 4w.1d.rep2

value: 4 weeks and 1 day


title: L4_DF07_Tumor_Cisplatin_ES24G

description:
ES24G
S1500 TempOseq RNA
L4_DF07_S278_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 4w.1d.rep1


title: 12w.rep2

value: 12 weeks


title: L4_DE12_Tumor_MAP_ES310G

description:
ES310G
S1500 TempOseq RNA
L4_DE12_S240_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: high


title: 12w.rep1


title: L4_DE11_Tumor_Vincristine_ES38E

description:
ES38E
S1500 TempOseq RNA
L4_DE11_S238_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DG09_Tumor_Methotrexate_ES14F

description:
ES14F
S1500 TempOseq RNA
L4_DG09_S330_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 1d.rep2

value: 1 day


title: 4w.rep1

value: 4 weeks


title: 1d.rep1


title: 1d.rep3


title: L4_DE09_Tumor_Dexamethasone_ES48G

description:
ES48G
S1500 TempOseq RNA
L4_DE09_S234_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE08_Tumor_Dexamethasone_ES44E

description:
ES44E
S1500 TempOseq RNA
L4_DE08_S232_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD12_Tumor_MAP_ES310F

description:
ES310F
S1500 TempOseq RNA
L4_DD12_S192_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE07_Tumor_Cisplatin_ES24F

description:
ES24F
S1500 TempOseq RNA
L4_DE07_S230_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD11_Tumor_Vincristine_ES36G

description:
ES36G
S1500 TempOseq RNA
L4_DD11_S190_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 0.rep2

value: no LPS


title: L4_DD09_Tumor_Dexamethasone_ES48F

description:
ES48F
S1500 TempOseq RNA
L4_DD09_S186_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 12w.ATAC-Seq

data_processing:
Tophat2 was used to align sequences on mm9 genome.
Reads from .bam files were then filtered according mapping quality value (mapq value, option -q 10).
Bedgraph files were generated by macs2.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated from bedgraph files thanks to bdg2bw script (https://gist.github.com/taoliu/2469050).

source_name: HSC KSL Flt3-

extract_protocol:
40-50 000 sorted HSC KSL Flt3- from pool of 4-8 mice were lyzed in lysis buffer. After centrifugation, nuclei were resuspend in reaction buffer containing Tn5 transposase. Tagmented DNA was purified using SPRI beads.
Library amplification using nextera kit has been done as described in Lara-Astiaso et al., 2014.

treatment_protocol: Mice were injected I.P. with 100 µl PBS or 125 ug in 100 µl of LPS. At the indicated time after injection, bone marrow was harvested, then mature cells were depleted and HSC KSL Flt3- were FACS-sorted. Samples are from pool of 4-8 mice.

value: Lin- Sca+ Kit- Flt3- bone marrow


title: 0.rep1


title: L4_DD10_Tumor_Methotrexate_ES18E

description:
ES18E
S1500 TempOseq RNA
L4_DD10_S188_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD08_Tumor_Cisplatin_ES28G

description:
ES28G
S1500 TempOseq RNA
L4_DD08_S184_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DD07_Tumor_Cisplatin_ES24E

description:
ES24E
S1500 TempOseq RNA
L4_DD07_S182_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 0.ATAC-Seq


title: 4w.ATAC-Seq


title: L4_DC11_Tumor_Vincristine_ES36F

description:
ES36F
S1500 TempOseq RNA
L4_DC11_S142_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DE10_Tumor_Methotrexate_ES18F

description:
ES18F
S1500 TempOseq RNA
L4_DE10_S236_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L4_DC10_Tumor_Methotrexate_ES16G

description:
ES16G
S1500 TempOseq RNA
L4_DC10_S140_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: 4w.rep2


title: L4_DC09_Tumor_Dexamethasone_ES48E

description:
ES48E
S1500 TempOseq RNA
L4_DC09_S138_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Dexamethasone


title: L4_DC08_Tumor_Cisplatin_ES28F

description:
ES28F
S1500 TempOseq RNA
L4_DC08_S136_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Ewing's Sarcoma Cells 2D


title: L4_DC07_Tumor_Control_ES32G

description:
ES32G
S1500 TempOseq RNA
L4_DC07_S134_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Control


title: L4_DB12_Tumor_MAP_ES210G

description:
ES210G
S1500 TempOseq RNA
L4_DB12_S96_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: low


title: Primary neurons, PBS

city: Lausanne

first: Hilal

last: Lashuel

address: Station 19, AI2142, Batiment AI

country: Switzerland

institute: EPFL

data_processing:
RNA-seq reads were aligned to the mm10 mouse reference genome (GRCm38.p5) with STAR (version 2.5).
Abundance measurements was done from uniquely mapped reads, using HTSeq-count (version 0.9). All protein-coding and antisense RNA genes from the gencode primary assembly (v16) were considered, representing a total of 23,057 studied genes.
Lowly expressed genes (CPM < 5) and genes present in less than three samples were excluded prior to further processing.
Normalization and differential expression analysis of the remaining 11,767 genes were done with the R package DEseq2 (version 1.2), using the internal DEseq. Genes with an absolute log2 fold-change greater than 1 and an FDR less than 0.01 were considered as significantly differentially expressed.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: file combined_DEseq2_FC1_FDR_0_01_full.csv contains results for all samples, and reports the mean counts and mean normalised expressions of gene cross replicates; 1 column per time point (T, D1, D3, D7, D14 and D21). Differential expression results are reported with 3 columns per comparison: log2 Fold change (log2FC), fdr (BH) and the status of the gene for the current filtering criteria (referred as “PF_”, for “PassFilter”: abs(log2FC)>1 and fdr < 0.01). Values for this column are “up”, “down” or “no” if the gene does not satisfy the significant criteria.

source_name: Primary neurons

growth_protocol: Primary hippocampal neurons were prepared from P0 pups of WT mice (C57BL/6JRccHsd, Harlan) or α-syn KO mice (C57BL/6J OlaHsd, Harlan) and cultured as previously described(2, 3). All procedures were approved by the Swiss Federal Veterinary Office (authorization number VD 3392). Briefly, the cerebral hippocampi were isolated stereoscopically in Hank's Balanced Salt Solution (HBSS) and digested by papain (20U/mL, Sigma-Aldrich, Switzerland) for 30 minutes at 37 ̊C. After inhibition of the papain activity by a trypsin inhibitor (Sigma-Aldrich, Switzerland), the tissues were dissociated by mechanical trituration. The cells were finally resuspended in adhesion media (MEM, 10% Horse Serum, 30% glucose, L-glutamine and penicillin/streptomycin) (Life Technologies, Switzerland) and plated in 24- or 6-well plates previously treated with poly-L-lysine 0.1% w/v in water (Brunschwig, Switzerland) at a density of 300,000 cells/mL (for biochemistry analysis) or 250,000 cells/ml (for ICC/confocal microscopy analysis). After 3 hours, adhesion media was removed and replaced by Neurobasal medium (Life Technologies, Switzerland) containing B27 supplement (Life Technologies, Switzerland), L-glutamine and penicillin/streptomycin (100U/mL, Life Technologies, Switzerland) (table 1).

extract_protocol:
Primary hippocampal neurons were treated with WT PFFs or PBS buffer for 7, 14, and 21 days. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Switzerland) according to the manufacturer's protocol. The concentration of each sample was measured using a NanoDrop (NanoDrop Technologies, Wilmington, DE, USA), and the purity was confirmed using the ratios at (260/280) nm and (260/230) nm.
Libraries for mRNA-seq were prepared according to manufacturer’s instructions with the TruSeq stranded mRNA kit (Illumina) starting from 300 ng of good-quality total RNAs (RNA quality scores >8.9 on the TapeStation 4200). Libraries were subsequently loaded at 1.44 pM on two High Output flow cells (Illumina) and sequenced in a NextSeq 500 instrument (Illumina) according to manufacturer instructions, yielding 75 nt paired-end reads.

treatment_protocol: As morphological, physiological, gene expression and proteome changes are observed during the different developmental stages of primary neurons in culture (Days In vitro, DIV), we have adapted the time-course of the PFFs treatment in primary neurons to be able to analyze the spatio-temporal effects of the seeding mechanism at the biochemical, proteomic, transcriptomic and ultrastructural level uncoupled to the intrinsic changes related to neuronal development and maturation. Therefore, in our seeding model, the PFFs were added to the neuronal cell culture media at different DIV and PFFs-treated neurons were all harvested at the DIV 26 (See Figure S1F). This ensures that the developmental stage of primary neurons in culture was similar at the harvest time. For the control neurons, PBS was added at DIV 5The day of the treatment, PFFs were thawed at RT and diluted to a final concentration of 70 nM using the Neurobasal media collected from wells containing the plated neurons (see table 2). The Neurobasal media left in the wells with neurons was then aspirated and replaced by the diluted PFFs. Treated neurons were cultured for up to 21 days without any further media changes until the end of the treatment (see previous section on primary culture conditions for further information).

value: WT

value: Hippocampus

value: Primary neurons

tag: age

value: Pups P0-P1

value: PBS buffer

value: control


title: Primary neurons, D1

value: preformed fibrils (PFFs)


title: Primary neurons, D21

value: 21 days


title: Primary neurons, D14

value: 14 days


title: L4_DB09_Tumor_Dexamethasone_ES46G

description:
ES46G
S1500 TempOseq RNA
L4_DB09_S90_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: Lats2 cKO replicate 2

city: Muenster

first: Kishor Kumar

last: Sivaraj

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

description: processed data file: Lats2_FPKM.txt

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat-2 v2.0.13 with parameters -g 2
HTSeq was used to count the aligned reads on a per gene basis (Version: HTSeq-0.6.1). The count data were normalized, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Lats2 cKO

extract_protocol:
Endothelial cells isolated by FACS. RNA was isolated with RNeasy Plus Micro kit(QIAGEN). Illumina TruSeq Stranded Total RNA Library Prep Kit (Cat#RS-122-2203) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genetype/variation

value: Lats2flx/flx; Cdh5CreERT2 positive

value: bone

value: FACS-sorted bone endothelial cells


title: Primary neurons, D7

value: 7 days


title: Primary neurons, D3

value: 3 days


title: L4_DB07_Tumor_Control_ES32F

description:
ES32F
S1500 TempOseq RNA
L4_DB07_S86_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Ewing's Sarcoma Cells 2D


title: L4_DB10_Tumor_Methotrexate_ES16F

description:
ES16F
S1500 TempOseq RNA
L4_DB10_S92_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Methotrexate


title: Lats2 cKO replicate 1

description: processed data file: Lats2_FPKM.txt


title: Lats2 Cont replicate 1

description: processed data file: Lats2_FPKM.txt

source_name: Lats2 Cont

value: Lats2flx/flx; Cdh5CreERT2 negative


title: L4_DB11_Tumor_Vincristine_ES36E

description:
ES36E
S1500 TempOseq RNA
L4_DB11_S94_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Vincristine


title: Lats2 Cont replicate 2

description: processed data file: Lats2_FPKM.txt