title: mouse female arc IP replicate 2

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_f_arc_ip2_AH


title: mouse female arc IP replicate 1

status: Public on Jun 01 2021

type: SRA

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

country: USA

institute: Baylor College of Medicine

description:
total RNA enriched for translating mRNA in Kiss1 neurons
mouse_f_arc_ip1_AH

library_source: transcriptomic

data_processing:
Basecalls performed by Real-Time Analysis software RTA v2
BCL files converted to fastq and demultiplexing performed by bcl2fastq v2.20.0.422 using options --minimum-trimmed-read-length 0 --mask -short-adapter-reads 0 –no-lane-splitting
The first 5 base calls were then trimmed and low quality reads filtered out using FASTX-Toolkit v0.0.14 with  zcat original_file.fastq.gz | fastx_trimmer -f 6 -v -Q33 | fastq_quality_filter -q 25 -p 80 -v -Q33 -z -o filtered_file.fastq.gz; done
trimmed and filtered fastq files were aligned using Tophat2 v2.1.1 to create bam files
Bam files were used to calculate raw counts, scaled counts, and FPKMs using cuffnorm from cufflinks v2.2.1 using options --no-update-check --output-format cuffdiff
Genome_build: UCSC mm10
Supplementary_files_format_and_content: raw counts, scaled counts, FPKMs in tab delimited text file

molecule: total RNA

organism: Mus musculus

source_name: IP arc hypothalamus brain

extract_protocol:
Circular 2 mm-punches containing the RP3V area or the ARC from groups of four RiboTag expressing mice were pooled and homogenized in 1 ml of buffer as described previously (Sanz et al., 2019; Sanz et al., 2015). Briefly, 4 μl of anti-HA antibody (Clone 16B12, BioLegend) were added to 800 μl of the cleared lysate and incubated for 4 h at 4°C. A sample of total lysate (80 μl) was saved as an input. After incubation, 200 μl of protein A/G magnetic beads (Thermo Fisher Scientific) were added and incubated overnight at 4°C with rotation. Immunoprecipitates (IPs) were washed in high salt buffer and RNA from inputs and IPs extracted using the RNeasy micro kit (Qiagen).
NuGEN Ovation RNA-Seq System V2 (Catalog # 7102)(NuGEN, San Carlos, CA) in combination with Ovation Ultralow Library Systems (Catalog #s 0330, 0331) (NuGEN) and 2-10ng of total RNA were used to make cDNA libraries. Libraries were quantified with NEBNext Library Quant Kit for Illumina (Catalog # E7630, New England BioLabs, Ipswich, MA) before sequencing them on a NextSeq500 (Illumina, San Diego, CA) using NextSeq500 High-Output v2 75 cycles consumables (FC-404-2005; Illumina). Libraries were sequenced 75 cycles using single-ended reads with 6 additional reads for barcodes.

tag: strain

tag: Sex

value: female

tag: genotype

tag: treatment

tag: target of treatment

tag: tissue

value: ARC of hypothalamus of brain


title: FPI Astro rep 1

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Reads were demultiplexed and converted to fastq format using Illumina's 'bcl2fastq'.  Fastq rna-seq data were processed using the 'bcbio-nextgen.py' pipeline.
bcbio-nextgen.py' (v1.0.8) was run in "RNA-seq" mode with reference genome set to "mm10" referencing the Ensembl GRCm38.p6 v94 build.  'hisat2' (v2.1.0) in soft-clipping mode was used for full alignment and 'featureCounts' was used to generate processed "counts" tables.  "salmon" (v0.9.1) was also used for quantification against the transcriptome.
Genome_build: "mm10" (Ensembl GRCm38.p6 v94 / GENCODE M19)
Supplementary_files_format_and_content: text format (counts from FeatureCounts)

source_name: Ipsilateral forebrain

extract_protocol:
Microglia and astrocytes were isolated by FACS sorting, mRNA was extracted using the Qiagen RNAeasy Plus Micro kit.
Sequencing libraries were prepared using the Clontech SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian Kit following the manufacturer’s recommendations. All libraries were sequenced on the NovaSeq S4 2x150-bp flow cell.

tag: cell type

value: Astrocyte

tag: protocol

value: traumatic brain injury

tag: time point

value: 7-days post sham/FPI


title: FPI Astro rep 2


title: LNCaPabl-Abi_Ctrl_rep1

type: RNA

city: Innsbruck

first: Martin

last: Puhr

address: Anichstrasse 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

description: gene expression profiling of treated prostate cancer cell lines

hyb_protocol: The generated target RNA was loaded onto the Affymetrix Clariom S human array cartridge and hybridized for 16 hours at 45°C using GeneTitan Hybridization modul

scan_protocol: Array were scanned in the GeneChip Scanner 7G. The image files were imported into the Affymetrix Expression Console software.

data_processing: Preprocessing were performed with Affymetrix Expression Console software and RMA was used for background modeling, quantile normalization, and probe summarization. Analysis were performed on the gene level (with Refseq annotation) and differentially expressed genes were identified using moderated t-test with limma R package.

label: biotin

organism: Homo sapiens

source_name: Epithelial prostate cancer cell line (LNCaPabl-Abi) treated with DMSO

label_protocol: A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).

growth_protocol: LNCaP were cultured in RPMI 1640 supplemented with 10% fetal calf serum (FCS) (Biowest, MI, USA), 1% penicillin/streptomycin (Szabo Scandic, Vienna, Austria), and 1x glutamax (ThermoFisher Scientific, Vienna).

extract_protocol: Total RNA from cell lines was isolated with the EXTRACTME TOTAL RNA KIT (DNA-Gdansk) according to manufacturer’s instructions. Quality and amount of isolated RNA were determined on a Nanodrop2000 system (ThermoFisher Scientific).

treatment_protocol: 5 Mio epithelial LNCaPabl-Abi/Enza were seeded into T175 tissue flasks. On the next day specific treatments were performed as followed. Epitelial cells : Group 1: vehicle Ctrl was treated with DMSO for 24h. Group 2: 100 nM dexamethasone for 24h.

value: DMSO

tag: concentration

value: Control


title: Col_H3K27me3_rep2

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq version 2.16.
Adapter and low-quality sequences were trimmed, and the clean reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.4.2) allowing one mismatch.
The reads that fell in the DMR regions were counted with the BEDTools package.
The H3K27me3 levels of hypo-DMRs were evaluated by RPKM (reads per kilobase per million mapped reads).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23ºC and 8 h of darkness at 21ºC.

extract_protocol:
For H3K27me3 antibody (ab6002, Abcam), the resin was washed with low salt wash buffer (150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, and 20 mM Tris-HCl pH 8.0), high salt wash buffer (500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, and 20 mM Tris-HCl pH 8.0), LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% sodium doxycholate,1 mM EDTA pH 8.0, and 10 mM Trish-HCl pH 8.0), TE wash buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA).
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing)

treatment_protocol: The 11-day-old seedlings grown on MS plates were harvested and subjected to  ChIP analysis.

value: wild type

tag: chip antibody

value: Abcam, ab6002


title: Col_H3K27me3_rep1


title: Sham Astro rep 5

value: sham control


title: (ATACseq) RNF2I53A/I53A Mutant Knockin Tumor Replicate #2

city: Winston-Salem

first: Swapan

last: Das

state: NC

address: Bowman Gray Center for Medical Education, 475 Vine St

department: Department of Internal Medicine, Section of Endocrinology and Metabolism

institute: Wake Forest School of Medicine

data_processing:
ATAC-seq reads were aligned to mm10 with BWA version 0.7.12 with default setting.
All samples were normalized by randomly down-sampling read pairs to the same number.
Peaks were called with MACS2 version 2.1.0 with options --nomodel -g 1.87e9 --bw 200.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files, peak files generated by MACS2

source_name: Breast tumor tissue

growth_protocol: These cells were cultured in vitro in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin before being injected into mice

extract_protocol:
400,000 cells suspended in 100 µL HBSS were injected into 4th mammary pads of the left side of BALB/c mice. 7 days later, tumors were removed and each tumor was cut into small pieces (<3mm) and incubated in 3ml dissociation solution (PBS supplemented with 2% FBS, 1mg/ml collagenase/Dispase and 0.5 mg/ml DNase I) for 1 hour at 37°C with gentle shaking. Cell suspension was then passed through a 70 µm cell strainer and washed with DMEM/2% FBS followed by flow cytometry analysis. Single cell suspension was first stained with the fixable viability dye (Biolegend) at 1:1000 in PBS for 10 min. After washed with FACS buffer (PBS/2% FBS), cells were then incubated with Fc block (anti-mouse CD16/32 antibody) at 1:100 for 10 min, followed by incubation with CD45 antibody for 30 min before washing and flow cytometry analysis. Then CD45- populations were collected and frozen in 70% DMEM supplemented with 20% FBS and 10% DMSO until further processed.
Libraries were prepared with standard Illumina protocols.

treatment_protocol: Untreated

value: Breast Cancer (Triple Negative)

value: RNF2I53A/I53A Mutant Knockin

value: BALB/c


title: T12.WGS

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Library strategy: WGS
FastQC (v0.11.7) was used to assess the quality of sequence reads.
Adapters and low-quality reads were removed from raw sequencing reads by Trimmomatic (v0.36) using following paramaters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:75
Clean reads from each species were mapped to respective reference genome after quality control, and then conduct SNP calling using GATK workflow.
MUMmer (v3.0) was used to examine all the single nucleotide polymorphism (SNPs) between reference genomes of T. pseudospiralis and other eleven Trichinella species. SNPs from uniquely aligned regions and with homozygous genotypes constituted the final set of SNVs.
Genome_build: The genomic data resources of the twelve Trichinella species were downloaded from NCBI BioProject database with the following accession codes: PRJNA12603 for T. spiralis,  PRJNA451013 for T. pseudospiralis, and PRJNA257433 for other ten Trichinella species.

organism: Trichinella patagoniensis

source_name: T. patagoniensis

extract_protocol:
DNA was extracted using the phenol chloroform extraction method.
High molecular DNA from 12 Trichinella genotypes were extracted from freshly collected muscle larvae. Qubit Fluorometer dsDNA HS Kit (Invitrogen) was used to determine total DNA amounts, followed by measurement of integrity by by agarose gel electrophoresis and using a BioAnalyzer (2100, Agilent). Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform, according to instructions provided by Illumina.

tag: passages

value: Muscle larvae


title: Sham Astro rep 4


title: Individual 20 203723180102_R01C01

type: genomic

city: Hanover

first: Nasim

last: Azizgolshani

state: NH

address: Dartmouth College

department: Christensen Lab

institute: Dartmouth College

description:
203723180102_R01C01 is theBS treated version  and 203723180102_R04C01 is the BS treated version of the same sample from Individual 20
Individual 20

hyb_protocol: BS and oxBS conversions were performed with 1.2 -1.4 _g of DNA according to the TrueMethyl protocol. ssDNA was recovered and quantified with Qubit and processed on Illumina EPIC methylation arrays at the Diagenode Genomics Facility using standard Illumina protocol.

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

data_processing: We extracted signal intensity from both BS (5hmC and 5mC beta values) and OxBS files (5mC only),  minfi funnorm used,  Fortin et al Bioinformatics 2016, for normalization. In our literature, these beta values were used to calculate 5hmC levels (BS-OxBS)

label: Cy5 and Cy3

source_name: tumor tissue

label_protocol: Standard Illumina Protocol

growth_protocol: human fresh frozen brain tissue

extract_protocol: Tumor DNA was extracted with the QIAmp DNeasy tissue kit (Qiagen) according to the manufacturer instructions

tag: subject

value: no

tag: slide

tag: array

tag: age (years)

value: F

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

tag: sample brain region

value: infratentorial

tag: sample brain lobe location

value: 4TH VENTRICLE

tag: condition

value: BS

tag: sample label

value: Ependymoma


title: (ATACseq) RSF1 KO Tumor Replicate #2

tag: cell type

tag: genotype

value: RSF1 KO

tag: strain


title: T10.WGS

organism: Trichinella papuae

source_name: T. papuae


title: (ATACseq) RSF1 KO Tumor Replicate #1


title: T5.WGS

organism: Trichinella murrelli

source_name: T. murrelli


title: Sham Astro rep 3

value: Astrocyte

tag: protocol

tag: time point

value: 7-days post sham/FPI


title: Sham Astro rep 2


title: T3.WGS

organism: Trichinella britovi

source_name: T. britovi

tag: passages


title: Individual 20 203723180102_R04C01

description:
203723180102_R04C01 is theOxBS treated version  and 203752100011_R08C01 is the BS treated version of the same sample from Individual 20
Individual 20

tag: subject

tag: Sex

value: OxBS


title: (ATACseq) RNF2 KO Tumor Replicate #2

value: RNF2 KO


title: gumB-3

city: Pittsburgh

first: Robert

middle: MQ

last: Shanks

state: PA

address: EEI 1020, 203 Lothrop st.

department: Ophthalmology

institute: University of Pittsburgh

description:
RNA later Qiagen; RT-PCR
processed data file: Differential_expression_analysis_table_gumB.txt

data_processing:
Sequence reads were trimmed to remove adaptor sequence using Trimmomatic v.0.36.
Trim reads were mapped to K904 ORFs using Bowtie2 aligner v.2.2.6. BAM files were generated.
Unique read hit counts were calculated using featureCounts from Subread package v.1.5.2.
Differential gene expression was performed using DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Genome_build: Mapped with strain K904 genome, with annotations substituted with the reference genome S. marcescens Db11 (HG326223.1).
Supplementary_files_format_and_content: Differential_expression_analysis_table_gumB.txt: Tab-delimited text file includes log2 counts per million (CPM) values for each Sample.

organism: Serratia marcescens

source_name: bacterial RNA

growth_protocol: Cultures were grown to OD=1.0 in Lysogeny Broth.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen), treated twice with DNase I, and concentrated with a spin concentrator (Monarch, New England Biolabs).
Libraries were made by GeneWiz, Steps include: ribosomal RNA depletion, RNA fragmentation and random priming, first and second strand cDNA synthesis, end repair, 5' phosphorylation and dA-tailing, adaptor ligation, PCR enrichment, and sequencing.

treatment_protocol: 400µl aliquots were treated with RNAprotect and frozen at -80˚C.

tag: background strain

tag: genotype/variation

value: gumB mutant


title: Individual 19 203752110002_R04C01

description:
203752110002_R04C01 is theBS treated version  and 203723190041_R02C01 is the BS treated version of the same sample from Individual 19
Individual 19

value: yes

tag: slide

tag: array

tag: age (years)

tag: vital status(alive=1)

value: POSTERIOR FOSSA

value: Embryonal


title: (ATACseq) RNF2I53A/I53A Mutant Knockin Tumor Replicate #1

value: Breast Cancer (Triple Negative)

value: RNF2I53A/I53A Mutant Knockin

value: BALB/c


title: Sham Astro rep 1

value: sham control


title: FPI MG rep 5

value: Microglia

value: traumatic brain injury


title: (ATACseq) RNF2 KO Tumor Replicate #1


title: Individual 17 203723050029_R07C01

description:
203723050029_R07C01 is theBS treated version  and 203723050029_R02C01 is the BS treated version of the same sample from Individual 17
Individual 17

value: no

value: M

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

tag: sample brain region

value: infratentorial

tag: sample brain lobe location

value: BS


title: Individual 19 203723190041_R08C01

description:
203723190041_R08C01 is theOxBS treated version  and 203723180102_R01C01 is the BS treated version of the same sample from Individual 19
Individual 19

value: F

tag: condition

value: OxBS

tag: sample label


title: (ATACseq) Control Tumor Replicate #2

tag: cell type

tag: genotype

value: Control

tag: strain


title: Individual 21 203752100011_R08C01

description:
203752100011_R08C01 is theBS treated version  and 203752100011_R01C01 is the BS treated version of the same sample from Individual 21
Individual 21

tag: subject

value: SUPRASELLAR

value: Glioma


title: gumB-1

value: gumB mutant


title: Individual 19 203723190041_R02C01

description:
203723190041_R02C01 is theBS treated version  and 203723190041_R08C01 is the BS treated version of the same sample from Individual 19
Individual 19

value: yes

tag: Sex

value: POSTERIOR FOSSA

value: Embryonal


title: (ATACseq) Control Tumor Replicate #1

value: Breast Cancer (Triple Negative)

value: BALB/c


title: K904-3

tag: background strain

value: wild-type


title: Individual 17 203723050029_R02C01

description:
203723050029_R02C01 is theOxBS treated version  and 203751380056_R08C01 is the BS treated version of the same sample from Individual 17
Individual 17

value: no

value: Ependymoma


title: FPI MG rep 2

value: Microglia

tag: protocol

value: traumatic brain injury

tag: time point

value: 7-days post sham/FPI


title: K904-2

tag: genotype/variation


title: 7dpi_sample1

city: Miami

first: James

last: Choi

state: FL

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

data_processing:
Illumina NextSeq 500 used for base-calling
CellRanger pipeline (10X Genomics) used for base-cell demultiplexing, alignment, read filtering, and UMI counting.
Cell barcode calling performed on unfiltered gene-barcode matrices using DropletUtils R package.
Low quality cells removed based on total UMI count, number of uniquely expressed genes, mitochondrial percentage, ribosomal percentage, doublet scores (Scrublet python package), and presence of hemoglobin gene counts.
Software: CellRanger (2.2.0, 3.0.1, and 4.0.0), DropletUtils Bioconductor package (1.8.0).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file of gene-barcode matrix for each sample, with genes along rows and cell-barcodes along columns.

source_name: Spinal cord

extract_protocol:
An 8mm section of spinal cord centered at the injury site (or the corresponding location in uninjured tissue) was dissected. After removal of the meninges, tissue was chopped using a razor blade, washed with 5mL CSF solution, and centrifuged at 300g for 5min at 4°C. The pelleted cells were processed using the Miltenyi Neural Tissue Dissociation Kit (P) (Cat #: 130-092-628) following manufacturer’s suggested protocol to obtain a single cell suspension. In brief, the pellets were incubated in a 2mL of Enzyme Mixture 1 for 30min at 37°C (50µL Enzyme P in 1.9mL Buffer X) with gentle shaking by hand every 5 minutes. 30µL of Enzyme Mixture 2 (10 µL Enzyme A in 20 µL Buffer Y) was added to the cell suspensions and manually triturated (slowly, 10 times per sample) with a large (1000µm diameter) opening fire-polished pipette. After 10min incubation at 37°C, suspensions were triturated with a medium and then small (750µm and 500µm diameter respectively) opening fire-polished pipette to produce single cell suspensions. Suspensions were strained through a 70µM cell strainer and washed with 10mL CSF solution. Suspensions were centrifuged at 300g for 5min and supernatants were discarded. Cell pellets were incubated in 10µl Miltenyi Myelin Removal Beads II (Cat #: 130-096-733)  and 90µL MACS Buffer (0.5% BSA in HBSS w/o Ca2+/Mg2+) for 15min at 4°C. Cells were washed with 10mL MACS Buffer and centrifuged at 300g for 5min. Supernatants were discarded and pellets were resuspended in 1 mL MACS buffer. Suspensions were then applied onto equilibrated LS Miltenyi MACS Magnetic Bead Columns (Cat #: 130-042-401). Columns were washed with 2mL MACS buffer, flow through was centrifuged at 300g for 5min, and supernatants were discarded. Due to the low number of astrocytes recovered in our first set of replicates, we enriched our second set of replicates with astrocytes by pooling from two spinal cord samples. We processed two spinal cords from each injury time point in parallel as described above to yield two suspensions per time point. One suspension from each time point was kept on ice while the was further processed with the Miltenyi Anti-ACSA-2 MicroBead kit according to manufacturer’s instructions. In brief, suspensions were incubated with Miltenyi ACSA2 Beads for 15mins at 4°C and subsequently washed with 1mL of MACS buffer. Suspensions were applied to LS Miltenyi MACS Magnetic Bead Columns and remaining cells were flushed from each column using LS Miltenyi column syringes and collected in separate tubes. ACSA-2 enriched flow throughs were then pooled with the single cell suspension from the other tissue. Combined suspensions were centrifuged at 300g for 5min and the pellets were resuspended in Red Blood Cell Lysis buffer (155 mM NH4Cl, 10 mM KHCO3, 0.09 mM Na4-EDTA) and incubated at room temperature for 1min. After washing with 5mL MACS Buffer, suspensions were centrifuged at 300 g for 5 min and supernatants were discarded. Pellets were resuspended in 50µl FACS buffer (1% BSA + 0.05% sodium azide in HBSS w/o Ca2+/Mg2+) and processed for scRNA-seq. Before submitting for sequencing, each sample underwent a quality control assessment which included cell viability and number. Briefly, cell suspensions were incubated with ViaStain AOPI Staining Solution and cell concentration/viability was assessed using the Nexcelom Cellometer K2. Each submitted sample met a viability cutoff of 80% or higher. Each sample was diluted accordingly to achieve a target cell capture of 10,000 cells, with our actual capture for the two replicates totaling 12488 for Uninjured, 21010 for 1dpi, 17491 for 3dpi, and 15189 for 7dpi.
Sample libraries were prepared according to Chromium Single Cell 3’ Library and Gel Bead Kit instructions. V2 Gel Bead kits were used for all but two samples (10X Genomics, PN-120237). One uninjured sample and one 1dpi sample were prepared using V3 Gel Bead kits (PN-1000075). All samples were indexed with Chromium i7 Multiplex Kits (10X Genomics, PN-120262) and single-cell suspensions were processed according to manufacturer’s instructions to construct final libraries for Illumina sequencing For sequencing, libraries were loaded at recommended loading concentrations onto an Illumina NextSeq 500 flow cell and paired-end sequenced under recommended settings (R1: 28 cycles; i7 index: 8 cycles; i5 index: none; R2: 91 cycles). After sequencing, Illumina output was processed using CellRanger’s recommended pipeline to generate gene-barcode count matrices. In brief, base call files for each sample were demultiplexed into FASTQ reads and then aligned to the mouse mm10 reference genome using STAR splice-aware aligner. Reads that confidently intersected at least 50% with an exon were considered exonic and further aligned with annotated transcripts. Reads were then filtered to remove UMIs and barcodes with single base substitution errors and finally used for UMI counting.

tag: tissue

value: T8 spinal cord

value: Standard


title: FPI MG rep 1


title: 7dpi_sample2

value: ACSA-2 Enriched


title: gumB-2


title: FPI MG rep 3


title: Individual 18 203751380056_R01C01

description:
203751380056_R01C01 is theOxBS treated version  and 203752110002_R08C01 is the BS treated version of the same sample from Individual 18
Individual 18

tag: slide

tag: array

tag: age (years)

value: M

tag: vital status(alive=1)

value: FF

value: infratentorial

value: TEMPORAL LOBE

value: OxBS


title: Individual 15 203751380056_R07C01

description:
203751380056_R07C01 is theBS treated version  and 203751380056_R02C01 is the BS treated version of the same sample from Individual 15
Individual 15

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location

value: FRONTAL LOBE

value: BS

value: Glioma


title: K904-1

value: wild-type


title: Individual 15 203751380056_R02C01

description:
203751380056_R02C01 is theOxBS treated version  and 203723050029_R07C01 is the BS treated version of the same sample from Individual 15
Individual 15

value: no

tag: condition

tag: sample label


title: 3dpi_sample2

tag: strain


title: Sham MG rep 5

tag: cell type

value: sham control


title: sczA_Cu4

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq (version 2.18.0.12) was used for basecalling
Read quality check was conducted using FastQC (version 0.11.7) and adaptors were trimmed using Trim Galore (version 0.4.2) with parameters --path_to_cutadapt cutadapt --fastqc --keep --output_dir.
EDGE-pro (version 1.3.1) workflow was used for read processing by using implemented Bowtie2 (version 2.3.4.3) to map trimmed reads to the reference genome and to determine read coverage and count for each gene with edge.pl script with parameters -g GCF_002289205.1_ASM228920v1_genomic.fna -p GCF_002289205.1_ASM228920v1.ptt -r GCF_002289205.1_ASM228920v1.rnt -u $SAMPLE.fq.gz -t 2.
Output files from EDGE-pro were formatted using edgeToDeseq.perl script provided in the EDGE-pro and used as input file for DESeq2 (version 1.26.0) to normalize the counts and determine diffential expression between conditions.
Genome_build: Streptococcus agalactiae 874391 (RefSeq assembly accession: GCF_002289205.1).
Supplementary_files_format_and_content: Tab delimited Excel file including raw counts for each gene in each sample.

organism: Streptococcus agalactiae

source_name: Streptococcus agalactiae 874391

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2791 were back-diluted 1/100 in 100mL of THB + 0.5 mM Cu (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

extract_protocol:
Total RNA SV kit (Promega) and removal of trace DNA using Turbo DNA-free (Life Technologies).
Library construction consisted of random fragmentation of the poly(A) mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired and A-tailed, and adaptors were ligated for indexing (with up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, Massachusetts) prior to cluster generation. Clusters were generated to yield approximately 725K–825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed.

treatment_protocol: RNA quality was analysed by RNA LabChip using GX Touch (Perkin Elmer). RNase-free DNase-treated RNA that passed Bioanalyzer 2100 (Agilent) analysis was used for RNA sequencing (RNA-seq) using the Illumina NextSeq 500 platform. We used TruSeq library generation kits (Illumina, San Diego, California).

tag: genotype

value: sczA-

tag: treatment

value: THB + 0.5 mM Cu


title: 3dpi_sample1


title: sczA_Cu3


title: Individual 18 203751380056_R08C01

description:
203751380056_R08C01 is theBS treated version  and 203751380056_R01C01 is the BS treated version of the same sample from Individual 18
Individual 18

tag: subject

tag: Sex


title: Sham MG rep 4

value: Microglia

tag: protocol

tag: time point

value: 7-days post sham/FPI


title: Sham MG rep 3


title: sczA_Cu2


title: 1dpi_sample2

tag: tissue

value: T8 spinal cord


title: Individual 19 203752110002_R08C01

description:
203752110002_R08C01 is theOxBS treated version  and 203752110002_R04C01 is the BS treated version of the same sample from Individual 19
Individual 19

value: yes

tag: slide

tag: array

tag: age (years)

value: F

value: POSTERIOR FOSSA

value: Embryonal


title: Individual 13 203752110002_R01C01

description:
203752110002_R01C01 is theOxBS treated version  and 203752110002_R02C01 is the BS treated version of the same sample from Individual 13
Individual 13

value: M

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

value: infratentorial

value: OCCIPITAL LOBE


title: 1dpi_sample3

value: ACSA-2 Enriched


title: sczA_Cu1


title: Sham MG rep 2


title: FPI MG rep 4

value: traumatic brain injury


title: sczA_Zn4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2791 were back-diluted 1/100 in 100mL of THB + 0.25 mM Zn (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: THB + 0.25 mM Zn


title: Individual 14 203752110071_R02C01

description:
203752110071_R02C01 is theBS treated version  and 203752110071_R06C01 is the BS treated version of the same sample from Individual 14
Individual 14

value: no

tag: sample brain region

tag: sample brain lobe location

value: TEMPORAL LOBE

tag: condition

value: BS

value: Glioma


title: Individual 12 203723190041_R03C01

description:
203723190041_R03C01 is theBS treated version  and 203752110002_R01C01 is the BS treated version of the same sample from Individual 12
Individual 12

tag: sample label


title: 1dpi_sample1

tag: strain

value: Standard


title: Sham MG rep 1

tag: cell type

value: Microglia

value: sham control

value: 7-days post sham/FPI


title: sczA_Zn3

tag: genotype

value: sczA-

tag: treatment


title: Individual 11 203752100068_R07C01

description:
203752100068_R07C01 is theBS treated version  and 203752100068_R05C01 is the BS treated version of the same sample from Individual 11
Individual 11

tag: subject

tag: Sex

value: F

value: Ependymoma


title: Individual 12 203723190041_R07C01

description:
203723190041_R07C01 is theOxBS treated version  and 203723190041_R03C01 is the BS treated version of the same sample from Individual 12
Individual 12

value: M

value: FF

value: POSTERIOR FOSSA

value: OxBS

value: Embryonal


title: uninj_sample3

value: Uninjured

tag: tissue

value: T8 spinal cord

value: ACSA-2 Enriched


title: Individual 13 203752110002_R02C01

description:
203752110002_R02C01 is theBS treated version  and 203752110071_R02C01 is the BS treated version of the same sample from Individual 13
Individual 13

value: no

tag: slide

value: infratentorial

value: OCCIPITAL LOBE

value: BS


title: Individual 11 203752100068_R05C01

description:
203752100068_R05C01 is theOxBS treated version  and 203723190041_R07C01 is the BS treated version of the same sample from Individual 11
Individual 11

tag: array


title: uninj_sample2


title: T4,D1_WT_Total

city: New York

first: Eric

last: Klann

state: NY

address: 4 Washington Pl

institute: New York University

data_processing:
Trimmed reads were aligned to mm10 using STAR aligner.
Reads mapped to genes annotated in the Gencode primary assembly were counted using featureCounts.
Modeling and differential expression analysis were carried using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Gene x sample matrix with raw counts, and gene level log2 fold changes in CSV format for IP and Total.

molecule: polyA RNA

source_name: Striatum

extract_protocol:
Trap-Seq was carried out as described in (Heiman et al., 2014). Briefly, striata from WT (n=6) and FXS (n=5) model mice expressing the EGFP-tagged Rpl10a protein in dopamine receptor Drd1-expressing medium spiny neurons were lysed by dounce homogenization (40 strokes) in 25 mM Hepes-HCl (pH 7.3), 150 mM KCl, 10 mM MgCl2, 0.5 mM DTT, 100 μgml−1 Cycloheximide, 10 μlml−1 RNasin (Promega, Madison, WI) and 10 μlml−1 Superase-In (Life Technologies) RNase inhibitors, and 1X Halt protease/phosphatase inhibitor on ice. Nuclei were pelleted by centrifuging the lysates at 2000g. NP-40 (Sigma) and DHPC (Avanti Polar Lipids, Alabaster, AL) were each added to the supernatant to a final concentration of 1%, following which the lysates were centrifuged at 20,000g in order to pellet insoluble membranes. A small aliquot of the supernatant was saved for RNA-Seq (input). EGFP- tagged ribosomal protein L10a was precipitated by incubating the remaining supernatant overnight (4◦C) with 100 μg of monoclonal anti-EGFP antibodies (50 μg each of clones 19C8 and 19F7) bound to biotinylated-Protein L (Pierce, Thermo Fisher, Waltham, MA) coated streptavidin-conjugated magnetic beads (Life Technologies). The magnetic beads were then washed four times in high-salt buffer consisting of 10 mM Hepes-HCl (pH 7.3), 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM DTT, 100 μgml−1 Cycloheximide, and RNasin and Superase-In RNase inhibitors (Promega). Bound RNA was eluted and purified using the Absolutely RNA Nanoprep kit (Agilent, Santa Clara, CA).
Sequencing libraries (non strand-specific) from the IP and input RNA were prepared using the Nugen Ovation Trio Low Input RNA kit at the NYUMC Genome Technology Center. Libraries were sequenced on the Illumina NovaSeq S1 100 Cycle Flow Cell to generate 50-cycle paired-end reads. All pulldowns and sequencing were carried out in a single batch.

value: Striatum

value: WT

tag: assay

value: Input

value: D1 neurons


title: T20,D1_WT_Total


title: uninj_sample1

value: Standard


title: T3,D1_KO_Total

value: FMRP mutant


title: T9,D1_KO_Total


title: sczA_Zn1

value: sczA-

value: THB + 0.25 mM Zn


title: hepatocyte_WCE

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

description: Background WCE control for H3K27ac ChIPmentation in 1 million hepatocytes extracted from 8 week old C57BL/6 mouse liver

data_processing:
FASTQ files were processed using the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specification created by the Kundaje lab (github.com/NHLBI-BCB/TF_chipseq_pipeline).
Alignments were performed on the GRCm38 (mm10) reference genomes.
MACS 1.4.3 was used to generate .wig processed files
Genome_build: mm10
Supplementary_files_format_and_content: .wig aligned read pileup

extract_protocol:
Briefly, hepatocytes were extracted from the livers of 8-week old C57BL/6 mice using the protocol described in Foretz et al.,24. 1 million hepatocytes were cross-linked and sonicated for 6 cycles in order to shear chromatin in ~200-400bp length fragments.
Mouse liver H3K27ac ChIP-seq was performed for this study using the ChIPmentation protocol described at http://www.medical-epigenomics.org/papers/schmidl2015/ ChIPmentation was performed according to protocol and post amplification libraries were cleaned using AMPure bead size selection yielding a library of DNA fragments between 200-500bp.
Library was sequenced on an Illumina Next-Seq 500 to generate raw reads. 75bp single end reads

value: liver hepatocyte

tag: chip antibody


title: sczA_Ctrl4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2791 were back-diluted 1/100 in 100mL of THB (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: THB


title: hepatocyte_H3K27AC

description: ChIPmentation for H3K27ac in 1 million hepatocytes extracted from 8 week old C57BL/6 mouse liver

value: anti-H3K27ac (abcam ab4729)


title: T2,D1_KO_Total


title: T14,D1_WT_Total


title: sczA_Ctrl2


title: T13,D1_WT_Total


title: sczA_Ctrl1


title: GW.DA.rep5

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative read per unique molecular identifier using a custom python script.
Gene expression was quantified using salmon v1.1.0 using a transcriptome prepared from the mouse mm10 primary genome assembly and the ensembl version 98 annotation. The resulting counts were summarized to the gene level using R (version 3.6.2) running tximport (version 1.12.3, Soneson et al., 2015) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.26.8, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space
Genome_build: mm10 with ensembl v98 annotation
Supplementary_files_format_and_content: mmana_2020_IntCt.txt.gz is a text file of integer count data
Supplementary_files_format_and_content: mmana_2020_l2cpm.txt.gz is a text file of log2 tpm data with a plus 1 offset

source_name: Intestinal stem cell organoids

growth_protocol: Following crypt isolation, crypts were embedded in 65% matrigel and treated with Vehicle (0.1%DMSO) or GW501516 (1uM, Sigma  SML1491). Organoids were propagated for 8 days, encompassing two passages before final collection.

extract_protocol:
Sigma Aldrich TRI reagent
High Throughput 3'DGE

value: Ppard-fl/fl; Ppara-null


title: GW.A.rep5

value: Ppara-null


title: GW.D.rep3

value: Ppard-fl/fl


title: Individual 14 203752110071_R06C01

description:
203752110071_R06C01 is theOxBS treated version  and 203751380056_R07C01 is the BS treated version of the same sample from Individual 14
Individual 14

value: no

tag: age (years)

value: F

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

value: FF

value: infratentorial

value: TEMPORAL LOBE

value: OxBS

value: Glioma


title: Individual 10 203723180102_R08C01

description:
203723180102_R08C01 is theBS treated version  and 203723180102_R03C01 is the BS treated version of the same sample from Individual 10
Individual 10

value: yes

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location

value: POSTERIOR FOSSA

value: BS


title: T12,D1_WT_Total

value: Striatum

value: WT

value: Input

value: D1 neurons


title: Individual 10 203723180102_R03C01

description:
203723180102_R03C01 is theOxBS treated version  and 203752100068_R07C01 is the BS treated version of the same sample from Individual 10
Individual 10

tag: condition

tag: sample label


title: Individual 9  203752100068_R08C01

description:
203752100068_R08C01 is theBS treated version  and 203752110071_R07C01 is the BS treated version of the same sample from Individual 9
Individual 9

value: Embryonal


title: GW.WT.rep5

tag: strain

tag: genotype

value: Wildtype


title: T11,D1_KO_Total

value: FMRP mutant

tag: cell type


title: covR_Cu3

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2400 were back-diluted 1/100 in 100mL of THB + 0.5 mM Cu (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: covR-

tag: treatment

value: THB + 0.5 mM Cu


title: Veh.A.rep5

value: 0.1% DMSO

value: Ppara-null


title: T10,D1_KO_Total

tag: tissue


title: Individual 9  203752100068_R02C01

description:
203752100068_R02C01 is theOxBS treated version  and 203752100068_R08C01 is the BS treated version of the same sample from Individual 9
Individual 9

tag: subject

tag: slide

tag: Sex

value: F

value: FF

value: infratentorial


title: sczA_Ctrl3

value: sczA-

value: THB


title: Individual 9  203723060072_R02C01

description:
203723060072_R02C01 is theBS treated version  and 203752100068_R02C01 is the BS treated version of the same sample from Individual 9
Individual 9

value: yes

tag: array

value: POSTERIOR FOSSA

value: BS


title: Individual 10 203752110071_R07C01

description:
203752110071_R07C01 is theBS treated version  and 203752110071_R03C01 is the BS treated version of the same sample from Individual 10
Individual 10

tag: age (years)

value: ARACHNOID METASTASIS

value: Glioma


title: sczA_Zn2

value: THB + 0.25 mM Zn


title: Veh.D.rep5

value: Ppard-fl/fl


title: Individual 10 203752110071_R03C01

description:
203752110071_R03C01 is theOxBS treated version  and 203723180102_R08C01 is the BS treated version of the same sample from Individual 10
Individual 10

tag: vital status(alive=1)

value: OxBS


title: T1,D1_WT_Total

value: Striatum

value: WT

tag: assay

value: Input

value: D1 neurons


title: covR_Cu2

value: covR-

value: THB + 0.5 mM Cu


title: covR_Cu4


title: covR_Cu1


title: Individual 8  203752100011_R07C01

description:
203752100011_R07C01 is theBS treated version  and 203752100011_R05C01 is the BS treated version of the same sample from Individual 8
Individual 8

value: no

value: M

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

value: infratentorial


title: Veh.WT.rep5

value: 0.1% DMSO

value: Wildtype


title: I9,D1_KO_IP

value: FMRP mutant

value: IP


title: covR_Zn4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2400 were back-diluted 1/100 in 100mL of THB + 0.25 mM Zn (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: THB + 0.25 mM Zn


title: GW.DA.rep4

value: Ppard-fl/fl; Ppara-null


title: I4,D1_WT_IP


title: Individual 9  203723060072_R08C01

description:
203723060072_R08C01 is theOxBS treated version  and 203723060072_R02C01 is the BS treated version of the same sample from Individual 9
Individual 9

value: yes

value: F

tag: sample brain region

tag: sample brain lobe location

value: POSTERIOR FOSSA

value: OxBS

value: Embryonal


title: covR_Zn3

value: covR-


title: GW.A.rep4

value: Ppara-null


title: I3,D1_KO_IP

value: Striatum

value: D1 neurons


title: GW.WT.rep4


title: covR_Zn1


title: covR_Zn2


title: Veh.DA.rep4


title: covR_Ctrl4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2400 were back-diluted 1/100 in 100mL of THB (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: THB


title: I14,D1_WT_IP

value: WT


title: covR_Ctrl3


title: Individual 8  203752100011_R05C01

description:
203752100011_R05C01 is theOxBS treated version  and 203723060072_R08C01 is the BS treated version of the same sample from Individual 8
Individual 8

value: no

value: M

value: FF

value: infratentorial

tag: condition

tag: sample label

value: Glioma


title: I20,D1_WT_IP

tag: genotype

value: IP


title: Individual 7  203752110002_R05C01

description:
203752110002_R05C01 is theBS treated version  and 203752100011_R07C01 is the BS treated version of the same sample from Individual 7
Individual 7

value: BS

value: Ependymoma


title: covR_Ctrl2

tag: strain


title: Individual 6  203723050029_R03C01

description:
203723050029_R03C01 is theOxBS treated version  and 203752110002_R07C01 is the BS treated version of the same sample from Individual 6
Individual 6

value: yes

value: F

value: PARIETO-TEMPORAL LOBE


title: Veh.WT.rep4

tag: treatment

value: 0.1% DMSO

value: Wildtype


title: I12,D1_WT_IP

tag: tissue

value: Striatum

tag: cell type


title: covR_Ctrl1

value: covR-


title: Individual 7  203752110002_R07C01

description:
203752110002_R07C01 is theOxBS treated version  and 203752110002_R05C01 is the BS treated version of the same sample from Individual 7
Individual 7

tag: subject

tag: slide

value: POSTERIOR FOSSA

value: OxBS


title: GW.DA.rep3

value: Ppard-fl/fl; Ppara-null


title: I13,D1_WT_IP

value: WT

value: D1 neurons


title: Veh.A.rep4

value: Ppara-null


title: copY_Cu4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2857 were back-diluted 1/100 in 100mL of THB + 0.5 mM Cu (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: copY-

value: THB + 0.5 mM Cu


title: Individual 6  203723060072_R01C01

description:
203723060072_R01C01 is theBS treated version  and 203723060072_R06C01 is the BS treated version of the same sample from Individual 6
Individual 6

tag: array

tag: Sex

value: FF

value: infratentorial

value: BS

value: Embryonal


title: Individual 6  203752100068_R01C01

description:
203752100068_R01C01 is theOxBS treated version  and 203752100068_R04C01 is the BS treated version of the same sample from Individual 6
Individual 6

value: yes

tag: age (years)

value: F

tag: vital status(alive=1)

value: PARIETO-TEMPORAL LOBE

value: Ependymoma


title: I10,D1_KO_IP

value: Striatum

value: FMRP mutant

tag: assay

value: IP


title: I2,D1_KO_IP


title: GW.D.rep2

value: Ppard-fl/fl


title: copY_Cu3


title: GW.WT.rep3

value: Wildtype


title: I11,D1_KO_IP

value: D1 neurons


title: Veh.D.rep4

value: 0.1% DMSO


title: Individual 6  203752100068_R04C01

description:
203752100068_R04C01 is theBS treated version  and 203752100068_R06C01 is the BS treated version of the same sample from Individual 6
Individual 6

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)


title: Individual 6  203723060072_R06C01

description:
203723060072_R06C01 is theOxBS treated version  and 203723050029_R05C01 is the BS treated version of the same sample from Individual 6
Individual 6

tag: sample brain region

tag: sample brain lobe location

value: OxBS


title: copY_Cu2

value: copY-

value: THB + 0.5 mM Cu


title: Veh.A.rep3

value: Ppara-null


title: High Fat Diet Mouse 3 Proximal

first: Constantine

middle: Nicholas

last: Tzouanas

address: 45 Carleton St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Proximal Small Intestine

growth_protocol: Mice were grown under the husbandry care of Department of Comparative Medicine in the Koch Institute for Integrative Cancer Research

extract_protocol:
Cells were processed according to the Seq-Well protocol with second strand synthesis (Hughes*, Wadsworth*, Gierahn*, et al., Immunity, doi.org/10.1016/j.immuni.2020.09.015).
Library construction followed from the protocol above (Hughes et al.)

treatment_protocol: High fat diet mice were supplied 60% kcal from fats (Research Diets D12492). Control mice were provided purified Control diet (10 kcal% fats, matching sucrose, Research Diets,  635 D12450J)

tag: age

tag: diet

value: High Fat Diet

tag: organ

value: Proximal Small Intestine


title: copY_Cu1

tag: strain

tag: genotype

tag: treatment


title: Veh.DA.rep3

value: Ppard-fl/fl; Ppara-null


title: Individual 5  203752100072_R06C01

description:
203752100072_R06C01 is theOxBS treated version  and 203752100068_R03C01 is the BS treated version of the same sample from Individual 5
Individual 5

tag: subject

value: no

value: M

value: FF

value: infratentorial

value: POSTERIOR FOSSA

tag: condition

tag: sample label

value: Glioma


title: copY_Ctrl4

growth_protocol: 1mL overnight THB starter cultures of S. agalactiae GU2857 were back-diluted 1/100 in 100mL of THB (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: THB


title: Veh.D.rep3

value: Ppard-fl/fl


title: Individual 6  203723050029_R05C01

description:
203723050029_R05C01 is theBS treated version  and 203723050029_R03C01 is the BS treated version of the same sample from Individual 6
Individual 6

value: yes

tag: slide

tag: array

tag: Sex

value: F

value: PARIETO-TEMPORAL LOBE

value: BS

value: Embryonal


title: copY_Ctrl3

value: copY-


title: High Fat Diet Mouse 3 Distal

source_name: Distal Small Intestine

value: High Fat Diet

value: Distal Small Intestine


title: High Fat Diet Mouse 3 Colon

source_name: Colon

value: Colon


title: Individual 6  203752100068_R03C01

description:
203752100068_R03C01 is theBS treated version  and 203752100068_R01C01 is the BS treated version of the same sample from Individual 6
Individual 6

tag: age (years)

tag: vital status(alive=1)

value: Ependymoma


title: I1,D1_WT_IP

tag: tissue

value: Striatum

value: WT

tag: assay

value: IP

tag: cell type

value: D1 neurons


title: Individual 4  203723050029_R08C01

description:
203723050029_R08C01 is theBS treated version  and 203752100072_R02C01 is the BS treated version of the same sample from Individual 4
Individual 4

value: no

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

tag: sample brain region

value: infratentorial

tag: sample brain lobe location

value: POSTERIOR FOSSA

value: Glioma


title: Individual 3  203723190041_R05C01

description:
203723190041_R05C01 is theBS treated version  and 203723050029_R04C01 is the BS treated version of the same sample from Individual 3
Individual 3

value: yes

value: M


title: Bcdim2rid2_3

first: Chang

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Resources

institute: Institute of Botany, the Chinese Academy of Sciences

description: incubated on PDB liquid media

data_processing:
Sequencing was performed using the HighSeq2000.
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs.
After filtering, the clean data was then mapped to the reference genome by BSMAP.
Methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Genome_build: Botrytis cinerea B05.10 RefSeq Genome

organism: Botrytis cinerea

source_name: genomic DNA from Bcrid2dim2 mutant

growth_protocol: The 12 sampless were incubated with PDB liquid media for 24 hours.

extract_protocol:
Genomic DNA was extracted with CTAB reagent from 24 hours old mycelia.
The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end; finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the HighSeq4000 or other Illumina platforms.

treatment_protocol: On rocking shaker at 22 oC.

tag: strain

value: Bcdim2rid2 mutant

tag: growth stage

value: mycelium

tag: incubation time

value: 24 hours


title: Individual 6  203752100068_R06C01

description:
203752100068_R06C01 is theOxBS treated version  and 203723060072_R01C01 is the BS treated version of the same sample from Individual 6
Individual 6

tag: subject

value: F

value: PARIETO-TEMPORAL LOBE

tag: condition

value: OxBS


title: Veh.WT.rep3

tag: treatment

value: 0.1% DMSO

tag: genotype

value: Wildtype


title: High Fat Diet Mouse 2 Proximal

tag: age

tag: diet

value: High Fat Diet

tag: organ

value: Proximal Small Intestine


title: GW.A.rep3

value: Ppara-null


title: copY_Ctrl2

value: copY-

value: THB


title: Bcdim2rid2_2

description: incubated on PDB liquid media


title: copY_Ctrl1


title: Bcdim2rid2_1

description: incubated on PDB liquid media


title: High Fat Diet Mouse 2 Colon

value: Colon


title: Veh.A.rep2


title: Veh.D.rep2

value: Ppard-fl/fl


title: Individual 5  203752100072_R02C01

description:
203752100072_R02C01 is theBS treated version  and 203752100072_R06C01 is the BS treated version of the same sample from Individual 5
Individual 5

value: no

tag: slide

tag: array

tag: age (years)

tag: Sex

tag: vital status(alive=1)

value: FF

value: infratentorial

value: POSTERIOR FOSSA

value: BS

tag: sample label

value: Glioma


title: Bcrid2_3

description: incubated on PDB liquid media

source_name: genomic DNA from Bcrid2 mutant

value: Bcrid2 mutant

value: mycelium

value: 24 hours


title: High Fat Diet Mouse 1 Proximal


title: WT_Cu3

growth_protocol: 1mL overnight THB starter cultures were back-diluted 1/100 in 100mL of THB + 0.5 mM Cu (prewarmed; 37°C in 250mL Erlenmeyer flasks). Cultures were grown shaking (200rpm) at 37°C; after exactly 2.5h, 10-50mL volumes containing approximately 500 million mid-log bacteria were removed and the RNA was preserved by addition of 0.4 volumes of ice-cold 95% ethanol/5% phenol (vol/vol) and incubated on ice for 30min. Cells were stored at -80 ºC until lysis at 37ºC for 1h in 100 µL TE buffer (RNase-free, Sigma-Aldrich) containing 100U mutanolysin (Sigma-Aldrich) and 30mg/mL lysozyme (Sigma-Aldrich). RNA was isolated using a Total RNA SV kit (Promega) and successful removal of trace DNA using Turbo DNA-free (Life Technologies) was confirmed by PCR.

value: wild type

value: THB + 0.5 mM Cu


title: Bcrid2_2

description: incubated on PDB liquid media


title: High Fat Diet Mouse 2 Distal

value: High Fat Diet

value: Distal Small Intestine


title: Veh.WT.rep2

value: 0.1% DMSO

value: Wildtype


title: WT_Cu4


title: High Fat Diet Mouse 1 Distal


title: WT_Cu2


title: Individual 4  203723050029_R04C01

description:
203723050029_R04C01 is theOxBS treated version  and 203723050029_R08C01 is the BS treated version of the same sample from Individual 4
Individual 4

value: F

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location

value: OxBS


title: Bcrid2_1

description: incubated on PDB liquid media

tag: strain

tag: growth stage

tag: incubation time


title: GW.A.rep2

tag: treatment

tag: genotype

value: Ppara-null


title: High Fat Diet Mouse 1 Colon

tag: age

tag: diet

value: Colon


title: Control Diet Mouse 2 Proximal

value: Control Diet

tag: organ

value: Proximal Small Intestine


title: WT_Cu1


title: Bcdim2_3

description: incubated on PDB liquid media

source_name: genomic DNA from Bcdim2 mutant

value: Bcdim2 mutant


title: GW.DA.rep2

value: Ppard-fl/fl; Ppara-null


title: 899_liver

city: New Orleans

first: Victoria

last: Belancio

state: LA

address: 1430 Tulane Avenue

department: Structural and Cellular Biology

institute: Tulane University School of Medicine

data_processing:
We used Bowtie1 to concordantly map read pairs (-X 600) with a single preferred mapping location (-m 1) with the tryhard switch (-y) that forces it to exhaustively search each read pair against the reference genome. The same alignment parameters were used in this study with either mm10 or rn6 genomes.
The generated bam file was strand separated and then intersected with the same-oriented annotation for full-length L1s. Manual curation of resulting L1 loci with greater than 10 mapped reads was performed using IGV
After aligning the .fastq sequences to the appropriate reference genome (mm10 or rn6), we used a list of LINE-1 element genomic coordinates downloaded from L1 base (http://l1base.charite.de/) to quantify how many reads from the aligned files overlapped with annotated LINE-1 element coordinates. This was performed using 'bedtools coverage'. L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.
L1Base - L1Resources<http://l1base.charite.de/>
L1Resources. This web portal is dedicated to putatively active LINE-1 elements. What are LINE-1s? LINE-1 (Long Interspersed Nucleotide Element 1, L1) are the only autonomous retrotransposons in the group of non-LTR retrotransposons.
All scripts and protocols used in this analysis are available in our previous publication RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level (doi: 10.3791/59771).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.

molecule: cytoplasmic RNA

source_name: liver

extract_protocol:
Organ samples of approximately 10 mm3 were bluntly dissected and then homogenized in 0.5-1mL of lysis buffer (150 mM NaCl, 50 mM HEPES pH 7.4, 25 ug/mL digitonin with 1000 U/mL SUPERase-In Rnase inhibitor added just prior to application) to lyse the cytoplasmic membrane. The mixture was lightly homogenized in a dounce homogenizer with an autoclaved B pestle, incubated on ice for 5 minutes and then centrifuged for 2 min at 1000 rpm at 4oC. Supernatant, containing the cytoplasmic fraction, was mixed with pre-chilled 7.5 mL of Trizol and 1.5 mL of chloroform and then centrifuged for 35 min at 4000 rpm at 4oC. The aqueous portion was transferred to 4.5 mL of chilled chloroform, mixed and centrifuged for 10 min at 4000 rpm at 4oC. The resulting aqueous portion was precipitated with 4.5 mL of isopropanol overnight in 80oC, centrifuged for 45 min at 4oC at 4000 rpms, washed with 10 mL of ethanol and re-suspended in RNAse-free water.
Cytoplasmic RNA samples were submitted to BGI Genomics for selection of polyadenylated RNAs, and strand-specific, paired-end library preparation. During this study, we used two methods of RNA sequencing with the same read depth: BGI DNA nanoball sequencing (DNBseq), which produces 150 bp read lengths, and Illumina sequencing, which produces 100 bp read lengths. For samples sequenced using Illumina sequencing, samples were pooled in groups of 5-7 and applied to a single lane of an Illumina HiSeq 2500/4000 instrument.

value: liver

value: Male


title: Control Diet Mouse 2 Distal


title: Bcdim2_2

description: incubated on PDB liquid media

value: mycelium

value: 24 hours


title: GW.WT.rep2


title: Individual 3  203723190041_R06C01

description:
203723190041_R06C01 is theOxBS treated version  and 203723190041_R05C01 is the BS treated version of the same sample from Individual 3
Individual 3

tag: subject

value: yes

tag: slide

tag: array

value: M

value: FF

value: infratentorial

value: POSTERIOR FOSSA

tag: condition

value: Ependymoma


title: 899_brain

source_name: brain

value: brain

tag: Sex


title: 831_repro

source_name: repro

value: repro


title: Bcdim2_1

description: incubated on PDB liquid media


title: Control Diet Mouse 2 Colon

value: Colon


title: B05.10_3

description: incubated on PDB liquid media

source_name: genomic DNA from B05.10 strain


title: Individual 3  203752100011_R02C01

description:
203752100011_R02C01 is theOxBS treated version  and 203752100072_R04C01 is the BS treated version of the same sample from Individual 3
Individual 3

source_name: tumor tissue

tag: age (years)

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

value: OxBS

tag: sample label


title: GW.D.rep1

tag: strain

value: Ppard-fl/fl


title: Control Diet Mouse 1 Proximal

value: Control Diet

value: Proximal Small Intestine


title: Individual 3  203751380056_R05C01

description:
203751380056_R05C01 is theOxBS treated version  and 203723190041_R06C01 is the BS treated version of the same sample from Individual 3
Individual 3

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location


title: Veh.DA.rep2

tag: treatment

value: 0.1% DMSO

tag: genotype

value: Ppard-fl/fl; Ppara-null


title: Control Diet Mouse 1 Distal

tag: age

tag: diet

value: Distal Small Intestine


title: 830_repro

tag: organ

value: Male


title: B05.10_1

description: incubated on PDB liquid media

tag: growth stage

value: mycelium

tag: incubation time

value: 24 hours


title: Veh.D.rep1


title: Control Diet Mouse 1 Colon


title: ΔmetR methionine1 rep2

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Tophat 2.1.1 and Bowtie 2.3.1
Reads per kilobase transcriptome per million mapped reads (RPKM) were calculated
Genome_build: Streptococcus pneumoniae R6 (accession NC_003098.1, assembly GCA_000007045.1) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 2)

growth_protocol: Both strains were grown in 8 ml of TSB to OD620 = 0.5; spin in microfuge (1.8 ml/tube x 4) and wash 2 times with Ringer's solution; suspended the final pellet in 1 ml of ringer's solution and adjusted the OD620 to 0.5 with ringer's solution  in a 20-ml glass tube. Mix 300 ul of  bacterial suspension with 30 ml of fresh (not prewarmed) chemically defined medium supplemented with 1 ug/ml methionine. Spit the suspension into 4 20-ml glass tubes (7 ml/tube). Incubated at 37 ℃ with 5 % CO2 for 5.5 hrs.

extract_protocol:
Total RNA was purified from cultures at the 5.5 hr point. Total RNA was extracted using TIANGEN kit (TIANGEN, Beijing, China) and purified using QIAGEN kit (QIAGEN, Beijing, China).
The ribosomal RNA was removed from total RNA (~1.5 µg) using poly-T oligo-attached magnetic beads. Fragmentation of mRNAs and sequencing libraries were generated using NEBNext® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The cDNA molecules were ligated with the NEBNext Adaptor, and further processed for selected, purifed, and sequence amplification.

tag: antibiotic resistance

value: rpsL1 (StreptomycinR)

tag: culture time

value: 5.5 hours


title: Veh.WT.rep1

value: Wildtype


title: 831_liver

value: liver

tag: Sex


title: B05.10_2

description: incubated on PDB liquid media


title: Individual 3  203752100011_R03C01

description:
203752100011_R03C01 is theBS treated version  and 203752100011_R02C01 is the BS treated version of the same sample from Individual 3
Individual 3

tag: subject

value: yes

tag: slide

tag: array

tag: age (years)

value: M

tag: vital status(alive=1)

value: FF

value: infratentorial

value: POSTERIOR FOSSA

tag: condition

value: BS

value: Ependymoma


title: SiCNN3-3

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

data_processing:
Off-Line Base Caller software, version 1.8
Illumina NovaSeq 6000 sequencer was used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) was calculated by Ballgown,version 3.5.0
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: C2C12 cells

growth_protocol: The C2C12 (Stem Cell Bank, Chinese Academy of Sciences, Shanghai, China) was cultured in Dulbecco’s modified Eagle’s medium (DMEM) high glucose supplemented with 10% fetal bovine serum, 100 U/ml of penicillin, and 100 μg/ml of streptomycin in 5% CO2 at 37˚C. When the cells reached 80-90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum.

extract_protocol:
Total RNA was extracted from cells using TRIZOL reagent (Life Technologies, NY, USA), in accordance with the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C2C12 cells were transfected with CNN3 siRNA and NC siRNA

value: transfect with CNN3 siRNA

tag: cell type

value: mouse myotube

tag: cell line


title: Individual 3  203752100072_R08C01

description:
203752100072_R08C01 is theOxBS treated version  and 203751380056_R06C01 is the BS treated version of the same sample from Individual 3
Individual 3

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

tag: sample brain lobe location

value: OxBS

tag: sample label


title: ΔmetR methionine1 rep1

source_name: Streptococcus pneumoniae D39 ΔmetR cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 1)

tag: strain


title: SiCNN3-2

tag: treatment


title: Individual 3  203752100072_R04C01

description:
203752100072_R04C01 is theBS treated version  and 203752100072_R08C01 is the BS treated version of the same sample from Individual 3
Individual 3


title: GW.DA.rep1

tag: genotype

value: Ppard-fl/fl; Ppara-null


title: 829_liver

tag: organ

tag: age

tag: Sex

value: Male


title: Individual 3  203751380056_R06C01

description:
203751380056_R06C01 is theBS treated version  and 203751380056_R05C01 is the BS treated version of the same sample from Individual 3
Individual 3

tag: subject

tag: slide

tag: array


title: SiCNN3-1


title: 829_repro

value: repro


title: 830_liver


title: WT methionine1 rep2

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 2)

tag: antibiotic resistance

value: rpsL1 (StreptomycinR)

tag: culture time


title: GW.A.rep1

value: Ppara-null


title: Veh.A.rep1

value: 0.1% DMSO


title: 1540_ovary

source_name: ovary

value: ovary

value: Female


title: WT methionine1 rep1

source_name: Streptococcus pneumoniae D39 WT cultured in CDM with 1 µg/ml methionine for 5.5 hours (replicate 1)

value: 5.5 hours


title: Individual 1  203723060072_R04C01

description:
203723060072_R04C01 is theBS treated version  and 203723190041_R04C01 is the BS treated version of the same sample from Individual 1
Individual 1

value: no

tag: age (years)

value: M

tag: vital status(alive=1)

value: FF

value: FRONTAL LOBE

tag: condition

value: Glioma


title: Individual 2  203723190041_R01C01

description:
203723190041_R01C01 is theOxBS treated version  and 203752100011_R03C01 is the BS treated version of the same sample from Individual 2
Individual 2

value: F

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

tag: sample brain region

value: infratentorial

value: POSTERIOR FOSSA

value: Embryonal


title: GW.D.rep4

source_name: Intestinal stem cell organoids

tag: strain

value: Ppard-fl/fl; Ppara-null


title: SiNC-3

tag: treatment

value: transfect with NC siRNA

tag: cell type

value: mouse myotube

tag: cell line


title: 1540_lung

source_name: lung

tag: organ

value: lung

tag: age


title: SiNC-2


title: 1540_brain

value: brain

tag: Sex


title: Individual 2  203723190041_R04C01

description:
203723190041_R04C01 is theBS treated version  and 203723190041_R01C01 is the BS treated version of the same sample from Individual 2
Individual 2

tag: subject

tag: slide

tag: sample brain lobe location

value: BS

tag: sample label


title: Veh.DA.rep1

value: 0.1% DMSO

tag: genotype


title: SiNC-1


title: 1535_ovary

value: ovary

value: Female


title: Vav-Ezh2-WT17

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

data_processing:
Sequencing reads from ATAC-SEQ samples quality checked with FASTQC; all bases with less than PHRED of 20 were removed.
Adapter sequences were removed using FASTX-Toolkit
Remaining sequences were mapped to genome with bowtie2.v2.2.1
SAM files were processed with samtools (v1.3.1) to remove unmapped, multimapped and mitochondrial reads.
Duplicate reads removed with MarkDuplicates function from Picard.v.1.96 package
Uniquely mapped reads that have a corresponding pair with a mapping quality of atleast 20 were retained and used to generate BAM files and indexed
BAM files processed with MACS2 v2.1.2 to identify genome-wide open chromatin regions
Parameters used: --shift 100 --extsize 200 --qvalue 0.01 --keep-dup 1 --slocal 1000 --SPMR --bdg
Homer (v4.10) used to annotate significant peaks
TSS/genebody profiles were generated by ngsplot v2.61
Differential chromatin modification analysis performed with diffReps.v.1.55.4 with negative binomial statistical tests
Genome_build: mm10
Supplementary_files_format_and_content: Differential binding sites; a cut-off of 1.5 fold (increased or decreased) was applied to identified differentially-regulated sites. Annotations is based on +/- 5 kb from TSS

source_name: E10.5 yolk sac erythro-myeloid progenitors

extract_protocol:
500 erythro-myeloid progenitors were sorted into a 0.5-ml DNA LoBind tube (Eppendorf #022431005) containing 23.75 μl of transposition mix (8.25 μl PBS, 2.5 μl water, 12.5 μl 2× TD Buffer, 0.25 μl 1% digitonin and 0.25 μl 10% Tween-20). 1.25 μl Tn5 transposase was added to the tube and incubated at 37 °C for 30 min in a thermomixer with shaking at 300 r.p.m. Reactions were cleaned up with Qiagen MinElute Kit.
The transposed DNA was pre-amplified/indexed with 14 cycles of PCR with NEBNext High-Fidelity 2x PCR master mix. Samples were sequenced using the Illumina NextSeq 500/550 platform.

value: erythro-myeloid progenitors

tag: developmental stages

tag: tissue

value: yolk sac

value: Ezh2fl/fl; Vav-Cre+/+  Wild type


title: 1535_lung


title: Vav-Ezh2-WT16


title: RGG1518-Galactose-R2

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: rgg1518 mutant vs WT in galctose R2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios  were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F635 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in CDM supplemented either with 55 mM galactose or mannose. Cells were grown until early exponential phase (OD600 0.3).

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: growth

value: Grown in Galactose

value: wild type

source_name: F532 Mean

value: spd_1518 mutant


title: Vav-Ezh2-WT2


title: RGG1518-Galactose-R1

description: rgg1518 mutant vs WT in galctose R1


title: 1534_ovary


title: 1534_uterus

source_name: uterus

value: uterus


title: GW.WT.rep1

value: Wildtype


title: Vav-Ezh2-KO18

value: Ezh2fl/fl; Vav-CreTg/+  Ezh2 KO


title: Vav-Ezh2-KO13


title: RGG1518-Mannose-R2

description: rgg1518 mutant vs WT in mannose R2

source_name: F550 Mean

value: Grown in Mannose

source_name: F650 Mean


title: siNIPBL 1h Dex rep#1 GR HiCHIP

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

institute: NIH

data_processing:
Library strategy: HiChIP
Alignment was performed by HiC pro with the mm10 reference genome using MBOI restriction enzyme as digestion genome reference
Hic data were generated by HiC pro script: hicprp2juicebox
Genome_build: mm10
Supplementary_files_format_and_content: hic

source_name: cell line derived from mouse mammary epithelial tissues

growth_protocol: Two days in CSS medium

extract_protocol:
After crosslinking, nuclei were isolated and HiCHIP was performed
TN5 on beads library preparation

treatment_protocol: To achieve an effective knockdown, 5 million 3134 cells were transfected during log phase growth, by electroporation (140V, 10ms, 3pulses) with 10ug of each siRNA against NIPBL, SMC1 or RAD21. Smartpool siRNAs were purchased by Dharmacon. Cells were treated with vehicle or dexamethasone after 48 and 72hrs after electroporation.

value: Dexamethasone

tag: concentration

tag: time

tag: replicate

value: replicate 1

tag: antibody

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1006

tag: sirna

value: siNIPBL


title: Vav-Ezh2-KO1

tag: cell type

tag: strain


title: siCTRL 1h Dex rep#1 GR HiCHIP

tag: cell line

tag: treatment

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1005

value: siCTRL


title: 1534_lung

tag: organ

value: lung

tag: age

tag: Sex

value: Female


title: RGG1518-Mannose-R1

description: rgg1518 mutant vs WT in mannose R1


title: untreated rep1 GR HiChIP

value: untreated

value: GR coctail:Thermo MA1-510, Santa Cruz #SC-1004

value: ethanol


title: Individual 1   203723060072_R07C01

description:
203723060072_R07C01 is theOxBS treated version  and 203723060072_R04C01 is the BS treated version of the same sample from Individual 1
Individual 1

growth_protocol: human fresh frozen brain tissue

tag: subject

value: no

tag: slide

tag: array

tag: age (years)

value: M

tag: vital status(alive=1)

tag: duration of clinical follow up (years)

tag: fresh frozen (ff)

value: FF

tag: sample brain region

value: infratentorial

tag: sample brain lobe location

value: FRONTAL LOBE

tag: condition

value: OxBS

tag: sample label

value: Glioma


title: Tie2-Ezh2-WT12

tag: cell type

value: erythro-myeloid progenitors

tag: developmental stages

tag: strain

tag: tissue

value: yolk sac

tag: genotype

value: Ezh2fl/fl; Tie2-Cre+/+  Wild type


title: 1535_brain

source_name: brain

tag: organ

value: brain

tag: age

tag: Sex


title: LA_Treatment 2

city: Baltimore

first: Stephen

middle: A

last: Semick

address: 655 W Baltimore St S

institute: University of Maryland School of Medicine

description: Injury refers to Gulf War Illness exposure (GWE) which was a combination of lipopolysaccharide, pyridostigmine, and chronic unpredictable stress. Treatment refers to Gulf War Exposure with rosiglitazone prophylaxis (GWE-ROSI). FC: frontal cortex. LA: lateral amygdala.

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing: Data were normalized (SST-RMA) and log transformed using Transcriptome Analysis Console (TAC) with downstream statistical analyses performed in R.

organism: Rattus norvegicus

source_name: LA

label_protocol: Following manufacturer's protocol

extract_protocol: total RNA was isolated by Trizol, as per manufacturer's protocol

tag: region

value: LA

value: Treatment


title: Tie2-Ezh2-KO11

value: Ezh2fl/fl; Tie2-CreTg/+  Ezh2 KO


title: LA_Treatment 3


title: LA_Treatment 1


title: 1534_brain

value: Female


title: 1338_ovary

value: ovary


title: 1338_uterus

value: uterus


title: p300-KO_289

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description:
Mouse genotype is Crebbp+/+;Ep300fl/fl;Cg1cre/+ (Ep300-KO)
counts_deseq2_normalized.txt.gz

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC mm10) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5.
Reads were mapped to exons using featureCounts to produce abundance tables.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of DESeq2 normalized counts

source_name: Sorted germinal center B cells

growth_protocol: Mice were immunized by intraperitoneal injection of sheep red blood cells. Analysis was performed 12 days after immunization.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA XS kit (Machery Nagel), according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Germinal center B cells (B220+/PNA+/CD95+)  were isolated by cytofluorimetric sorting.

value: Spleen

value: germinal center (GC) B cells


title: p300-KO_287


title: Tie2-Ezh2-KO10


title: LA_Control 3

value: Control


title: LA_Injury 2

value: Injury


title: Tie2-Ezh2-KO9


title: 1338_lung

value: lung


title: LA_Injury 1


title: 1338_brain


title: p300-KO_18


title: CBP-KO_1

description:
Mouse genotype is Crebbpfl/fl;Ep300+/+;Cg1cre/+ (Crebbp-KO)
counts_deseq2_normalized.txt.gz

value: CBP-KO


title: 1337_ovary


title: Tie2-Ezh2-KO5


title: CBP-KO_55


title: LA_Control 2


title: 1337_lung


title: Tie2-Ezh2-KO7


title: LA_Control 1


title: Tie2-Ezh2-WT3


title: CBP-KO_53


title: 1337_brain


title: Tie2-Ezh2-WT2


title: FC_Treatment 2

source_name: FC

value: FC


title: FC_Treatment 3


title: TAM-14dOV_mononuclear_cells

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

data_processing:
Raw sequencing data were processed using Cell Ranger 3.0.2 (10X Genomics) using the mm10 mouse transcriptome (release 93)
Genome_build: mm10 with tdTomato

source_name: plantaris muscle

extract_protocol:
Plantaris muscles were harvested and dissociated mechanically and enzymatically to yield a mononuclear cell suspension. Cells were loaded onto 10X Chromium controller and Chromium Single Cell Gene Expression Solution was used for generating 3'-droplet-based RNA-seq libraries.
Single-cell RNA-seq libraries were prepared for sequencing using 10X Chromium Single Cell Gene Expression kit v3.

value: plantaris muscle

value: mononuclear cells

tag: treatment

value: tamoxifen-treated


title: WT_288

description:
Mouse genotype is Crebbp+/+;Ep300+/+;Cg1cre/+ (Crebbp/Ep300 WT). Mice are littermates obtained by crossing Crebbp+/-;Cg1cre/+ and Crebbp+/- Cg1+/+mice.
counts_deseq2_normalized.txt.gz

value: WT


title: 1209_liver

source_name: liver

value: liver

value: Male


title: cko_rs3: Ewsr1_CKO_RS_rep2

city: Bar Harbor

first: Hui

last: Tian

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Adapter of RNA-seq fastq filles trimmed using Trimmatics. Then the trimmed fastq filles were aligned to mouse genome mm10 by Bowtie2
Fragments per kilobase million (FPKM) was calculated and normalized by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file include FRKM values for each Sample ...

source_name: round spermatids

extract_protocol:
Germ cells were isolated from 8 weeks Ewsr1 control and conditional knockout mice and then sorted using FASC to extract 4C late spermatocytes and 2C round spermatids. KAPA RNA Hyper Prep Kit was used to construct RNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell tyes

value: round spermatids

value: 8 weeks

value: Ewsr1 loxP/-;Hspa2-Cre


title: 1209_brain

value: brain


title: WT_7

value: Spleen


title: cko_rs2: Ewsr1_CKO_RS_rep1


title: WT_4

value: germinal center (GC) B cells


title: FC_Injury 2


title: FC_Treatment 1

value: Treatment


title: 1111_liver


title: cko_p3: Ewsr1_CKO_PD_rep2

source_name: pachynema and diplonema

value: pachynema and diplonema


title: 1111_repro

source_name: repro

value: repro


title: FC_Injury 1

value: Injury


title: cko_p2: Ewsr1_CKO_PD_rep1


title: 1110_repro


title: WT_46


title: 1110_liver


title: 3F_P

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Quality control (QC) of FASTQ files was performed using FastQC Toolkit (v0.11.5) [http://www.bioinformatics.babraham.ac.uk/projects/fastqc]
Paired-end reads were aligned against Dp_genome_v3
the reference genome of Danaus plexippus [Zhan and Reppert 2013] using HISAT2 (v2.0.5) [Kim et al. 2015]
The latest version of monarch GTF (OGS2.0) consisting of 15130 expressed gene models was downloaded from MonarchBase [http://monarchbase.umassmed.edu/geneset.html] for gene expression quantification
The paired-end reads mapped to the genome assembly were summarized using featureCounts (v1.5.2) [Liao et al. 2014]
Differential expression analysis at the gene-level was carried out using limma-voom [Law et al. 2014] open source R packages.
Trimmed mean of M-values (TMM) normalization [Robinson and Oshlack 2010] was carried out to determine normalization factors for all samples.
Genome_build: Dp_genome_v3 the reference genome of Danaus plexippus [Zhan and Reppert 2013]
Supplementary_files_format_and_content: TEXT - Raw Gene Counts

organism: Danaus plexippus

source_name: proboscis

growth_protocol: The monarch butterflies were caught in the field.

extract_protocol:
The frozen tissue was thawed, and then total RNA was harvested using Trizol reagent following Qiagen RNeasy protocol. RNA concentration and RNA IQ (integrity and quality) score were determined using a Qubit 4 Fluorometer (Thermo Fischer).
Illumina TruSeq Stranded mRNAseq Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries, following the manufactor's protocols.

treatment_protocol: The caught monarch butterflies were sex-identified and dissected to separate and collect antennae, legs and proboscis tissues. The collected tissues were stored at -80C until RNA isolation.

tag: animal id

tag: batch

tag: developmental stage

value: adult

value: female

tag: female state

value: gravid


title: 3F_L

source_name: legs


title: FC_Control 3

value: FC

tag: condition

value: Control


title: het_rs3: Ewsr1_het_RS_rep2

value: Ewsr1 loxP/+;Hspa2-Cre


title: 1071_repro

value: Male


title: FC_Control 2


title: FC_Control 1


title: 3F_A

source_name: antennae


title: het_p3: Ewsr1_het_PD_rep2


title: 1071_liver

value: liver


title: het_rs2: Ewsr1_het_RS_rep1

value: round spermatids

value: 8 weeks


title: 2M_P

value: male


title: 2M_L


title: het_p2: Ewsr1_het_PD_rep1


title: WT_41

value: Spleen

value: WT


title: 1006_uterus

value: uterus

value: Female


title: 1006_ovary

source_name: ovary

value: ovary


title: T1.WGS

first: Yayan

last: Feng

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Library strategy: WGS
FastQC (v0.11.7) was used to assess the quality of sequence reads.
Adapters and low-quality reads were removed from raw sequencing reads by Trimmomatic (v0.36) using following paramaters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:75
Clean reads from each species were mapped to respective reference genome after quality control, and then conduct SNP calling using GATK workflow.
MUMmer (v3.0) was used to examine all the single nucleotide polymorphism (SNPs) between reference genomes of T. pseudospiralis and other eleven Trichinella species. SNPs from uniquely aligned regions and with homozygous genotypes constituted the final set of SNVs.
Genome_build: The genomic data resources of the twelve Trichinella species were downloaded from NCBI BioProject database with the following accession codes: PRJNA12603 for T. spiralis,  PRJNA451013 for T. pseudospiralis, and PRJNA257433 for other ten Trichinella species.

organism: Trichinella spiralis

source_name: T. spiralis

extract_protocol:
DNA was extracted using the phenol chloroform extraction method.
High molecular DNA from 12 Trichinella genotypes were extracted from freshly collected muscle larvae. Qubit Fluorometer dsDNA HS Kit (Invitrogen) was used to determine total DNA amounts, followed by measurement of integrity by by agarose gel electrophoresis and using a BioAnalyzer (2100, Agilent). Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform, according to instructions provided by Illumina.

tag: passages

value: Muscle larvae


title: T8.RNA-seq.NBL

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

organism: Trichinella sp. T8

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

value: Newborn larvae


title: 2M_A

value: adult


title: T8.RNA-seq.ML


title: 1F_P

value: female

value: gravid


title: 1006_lung

source_name: lung

value: lung


title: 1F_L


title: 1006_brain

value: brain


title: IMR-90_TGFb-YAPi-TAZi_rep2

city: Rochester

first: Daniel

middle: J.

last: Tschumperlin

state: MN

address: 200 First St SW, AL 4-184

department: Physiology and Biomedical Engineering

institute: Mayo Clinic

description: Gene expression data from IMR-90 cells treated with TGFb and combined YAP and TAZ siRNA

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on 3. GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP and TAZ siRNA, rep2

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

growth_protocol: IMR-90 cells (ATCC) were maintained in EMEM (ATCC) containing 10% FBS, 10,000 U/mL of penicillin, 10,000 μg/mL of streptomycin, and 25 μg/mL of amphotericin B in a humidified 37 °C, 5% CO2 incubator.

extract_protocol: RNA was extracted and isolated using a RNAeasy micro kit (Qiagen) according to manufacturer’s instructions containing at least 200 ng of purified RNA per sample.

treatment_protocol: IMR-90 cells were treated with TGFβ1 (2 ng/ml)  and transfected with siRNA (ON-TARGETplus SMARTpool; Dharmacon) targeting YAP and TAZ alone or in combination, or scrambled control for 72 hours, using Lipofectamine® RNAiMAX (Invitrogen).

tag: sample type

value: cultured cells

tag: cell line


title: T8.RNA-seq.AD

tag: strain

value: Adult


title: 1F_A


title: IMR-90_TGFb-YAPi-TAZi_rep1

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP and TAZ siRNA, rep1


title: T8.WGBS.NBL

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag


title: IMR-90_TGFb-YAPi_rep2

description: Gene expression data from IMR-90 cells treated with TGFb and YAP siRNA

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP siRNA, rep2


title: IMR-90_TGFb-YAPi-TAZi_rep3

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP and TAZ siRNA, rep3


title: IMR-90_TGFb-YAPi_rep3

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP siRNA, rep3


title: 1004_uterus

source_name: uterus


title: 16M_P


title: 1004_ovary


title: T8.WGBS.ML


title: 16M_L


title: T8.WGBS.AD


title: 16M_A


title: T7.RNA-seq.NBL

organism: Trichinella nelsoni

source_name: T. nelsoni


title: 12M_P


title: 1004_brain

organism: Mus musculus

source_name: brain


title: T7.RNA-seq.ML


title: T7.RNA-seq.AD


title: IMR-90_TGFb-YAPi_rep1

organism: Homo sapiens

source_name: IMR-90 cells, 2ng/ml TGFb treatment with YAP siRNA, rep1


title: IMR-90_TGFb-TAZi_rep3

description: Gene expression data from IMR-90 cells treated with TGFb and TAZ siRNA

source_name: IMR-90 cells, 2ng/ml TGFb treatment with TAZ siRNA, rep3


title: IMR-90_TGFb-TAZi_rep2

source_name: IMR-90 cells, 2ng/ml TGFb treatment with TAZ siRNA, rep2


title: IMR-90_TGFb-nontarget_rep3

description: Gene expression data from IMR-90 cells treated with TGFb and non-targeting siRNA

source_name: IMR-90 cells, 2ng/ml TGFb treatment, rep3


title: 1004_lung


title: IMR-90_TGFb-TAZi_rep1

source_name: IMR-90 cells, 2ng/ml TGFb treatment with TAZ siRNA, rep1


title: IMR-90_TGFb-nontarget_rep2

source_name: IMR-90 cells, 2ng/ml TGFb treatment, rep2


title: T7.WGBS.NBL


title: T7.WGBS.ML


title: 11F_P

source_name: proboscis


title: 11F_L

source_name: legs


title: 11F_A

source_name: antennae


title: 12M_L


title: T7.WGBS.AD


title: T6.RNA-seq.NBL

organism: Trichinella sp. T6


title: 12M_A


title: 27FP


title: T6.RNA-seq.ML


title: IMR-90_TGFb-nontarget_rep1

source_name: IMR-90 cells, 2ng/ml TGFb treatment, rep1


title: 27FL


title: T6.RNA-seq.AD


title: 27FA


title: IMR-90_Control_rep3

description: Gene expression data from IMR-90 control cells

source_name: IMR-90 cells, control treatments, rep3