title: WTA_rep1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
bcl2fastq v2 for basecalling
Adaptors and the last nucleotide (the number 51) were removed and reads where mapped to mm9 using tophat (v2.1.1) with parameters  --no-coverage-search --library-type fr-unstranded
PCR duplicates were removed using picard tools (1.62) and read counts per gene were calculated using Htseq-count (v0.7.2) with parameters -q -t exon --stranded=no --mode=intersection-nonempty using the Refseq gtf from UCSC
Genes with 0 counts in all samples were removed and differential analysis was performed using DESeq2 (v3.7) with default parameters. Genes with an absolute log2FC >= 2 and FDR <= 0.1 were considered as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Counts2Deseq2.txt contains raw counts from Htseq-count output that were used as DESeq2 input
Supplementary_files_format_and_content: Normalized_countTable.txt contains the normalized counts produced by DESeq2
Supplementary_files_format_and_content: WTAvsRes4.txt contains the output of DESeq2 plus a column indicating if a gene is differentially expressed using the threshold determined for the study ( abs (log2fc) >= 2 and fdr =< 0.1 )

molecule: polyA RNA

source_name: Cancer-associated fibroblast (CAF)

extract_protocol:
mRNA-seq library preparation from 4 μg of total RNA was performed with TruSeq RNA Sample Prep Kit V2 (Illumina) according to the manufacturer’s instructions.
RNA-seq was carried out using the SMART-seq2 protocol (PMID:24385147) with minor modifications. Briefly, the poly-A containing mRNA molecules from 5 ng of total RNA were copied into first strand cDNA by reverse transcription and template-switching using oligo(dT) primers and an LNA-containing template-switching oligo (TSO). The resulting cDNA was pre-amplified, purified and tagmented with Tn5 transposase produced in-house using a described protocol (PMID:25079858). cDNA fragments generated after tagmentation were gap-repaired, enriched by PCR and purified to create the final cDNA library.

value: Cancer-associated fibroblast (CAF)

tag: phenotype

value: Normal tumor associated


title: CA40_GNF_2 (rna-seq)

status: Public on Jul 06 2018

type: SRA

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

description: counts.txt

library_source: transcriptomic

data_processing:
Sequences were aligned to hg38 genome with Tophat (2.0.14)
Raw counts were calculated with subread (1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: tab separated file with raw counts for each sample in the columns

molecule: total RNA

organism: Homo sapiens

source_name: lymphoblastoid cell line

growth_protocol: Gown in RPMI 1640 + 15% FBS +1% P/S; passaged by spinning down at 120g for 5 minutes and resuspended in growth media; cultured in 37C with 5% CO2

extract_protocol:
Cells were pelleted at 300g for 5 minutes at 4C, resuspended in ice cold phosphate buffered saline and pelleted again.  RNA was extracted using the miRNeasy RNA extraction kit.
TruSeq RNA Library Prep Kit v2

treatment_protocol: Cells treated with 1uM 3-MC, 1uM GNF-351 or 0.1% DMSO in fresh media for 24 hours

tag: treatment

tag: cell line


title: WTA_rep2

organism: Mus musculus

tag: cell type


title: UT-SCC-43 [HumanHT-12 V4.0]

type: RNA

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

description:
9234921026E
HNSCC.UT-SCC-43

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The gene expression data were quantile normalized using the lumi R package

label: biotin

source_name: head and neck cancer cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina total prep RNA Amplification kit

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine, 10% fetal bovine serum, non-essential amino acids solution, penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in an atmosphere of 5% CO2 (all reagents were purchased from Lonza BioWhittaker, Allendale, NJ, USA)

extract_protocol: Total RNA was isolated using a Macherey-Nagel (Düren, Germany) Nucleospin RNA II kit. The quality of total RNA was assessed with a 2100 Agilent Bioanalyzer

treatment_protocol: No treatment was carried out for the cells

value: Head and neck squamous cell carcinoma cell line

tag: site-of-origin

value: gingiva of mandib.


title: RES4_rep1

value: Tumor resistant associated


title: CA64_3MC_1 (rna-seq)

description: counts.txt


title: CA64_DMSO_1 (rna-seq)

description: counts.txt

value: DMSO


title: Single cell 45 16-cell embryo 1

city: Princeton

first: Nicholas

last: Treen

state: NJ

address: Carl Icahn Laboratory,, Princeton University, Washington Rd

country: USA

institute: Princeton University

description:
Single isolated cell
Full length cDNA from single-cell lysate

data_processing:
Base calling software: HiSeq Control Software, Version: 2.2.58, defualt paramaters
Data filtering by Illumina default parameters
Data demultiplexed by unique barcodes and trimmed of illumina adaptors and polyA tails
Genome_build: Ciona intestinalis KH2012
Supplementary_files_format_and_content: Gene expression level determined by RPKM

organism: Ciona intestinalis

source_name: 16-cell embryo 1

growth_protocol: Dechorionated Ciona embryos were developed in artificial sea water

extract_protocol:
For single cells, cDNA was prepared directly from cell lysate. For pooled embryos total RNA was purified using Trizol.
cDNA was synthesized and amplified from the poly-A containing RNA transcripts in the single-cell lysate using the Smart-Seq2 method. cDNA from cells at 4-cell stage was amplified by 15 cycles of PCR, while 16 cycles of PCR was applied on the cDNA from cells of 8-cell and 16-cell stage embryos. The amplified cDNA samples were cleaned up with Ampure XP beads (Beckman Coulter, CA, USA), quantified by Qubit fluorometer (Invitrogen, CA, USA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA, USA) for size distribution. Nextera DNA library prep kit (Illumina, CA, USA) was used to convert the cDNA samples to Illumina sequencing libraries. For pooled embryo samples, cDNA synthesis and sequencing was performed as described for single-cells with the exception that 12 cycles of PCR were performed.

treatment_protocol: Single cells were hand dissected in calcium/magnesium free sea water following a brief protease treatment.

tag: cell identity

value: A5.1 cell

tag: developmental stage

value: 16-cell embryo


title: Single cell 20 8-cell embryo 1

source_name: 8-cell embryo 1

value: B4.1 cell

value: 8-cell embryo


title: UT-SCC-16A [HumanHT-12 V4.0]

description:
9234921014A
HNSCC.UT-SCC-16A

value: tongue


title: UT-SCC-24A [HumanHT-12 V4.0]

description:
9234921014G
HNSCC.UT-SCC-24A


title: UT-SCC-6A [HumanHT-12 V4.0]

description:
9234921026H
HNSCC.UT-SCC-6A

value: larynx


title: UT-SCC-11 [HumanHT-12 V4.0]

description:
9234921026K
HNSCC.UT-SCC-11


title: UT-SCC-2 [HumanHT-12 V4.0]

description:
9234921044G
HNSCC.UT-SCC-2

value: baseos oris


title: CA40_DMSO_2 (rna-seq)

description: counts.txt


title: RES4_rep2


title: UT-SCC-8 [HumanHT-12 V4.0]

description:
9234921026J
HNSCC.UT-SCC-8


title: Single cell 17 8-cell embryo 1

value: a4.2 cell


title: CA40_3MC_2 (rna-seq)

description: counts.txt


title: Single cell 16 8-cell embryo 1


title: WT rep2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the   raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

source_name: Thymus

extract_protocol:
Ter119–Gr1–CD19–NK1.1–CD4–CD8–TCRb–TCRgd–CD44–; representative of DN3-DN4 cells were sorted into culture medium, spun down, and re-suspended in 100 μl of 1 x PBS + 0.04% BSA.
Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate 6000 single cell  GEMs (gel beads in emulsion) per sample. Libraries were prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x  Genomics)

tag: tissue

value: thymus

tag: age

value: 6-10 weeks

tag: genotype

value: wild type


title: Rptor KO rep2

value: Rptor-/-


title: Rptor KO rep3


title: WT rep1


title: Single cell 21 8-cell embryo 2

source_name: 8-cell embryo 2


title: CA40_3MC_1 (rna-seq)

description: counts.txt


title: Single cell 15 8-cell embryo 1

value: A4.1 cell


title: CA29_GNF_2 (rna-seq)

description: counts.txt


title: CA29_DMSO_2 (rna-seq)

description: counts.txt


title: Single cell 19 8-cell embryo 1


title: CA40_GNF_1 (rna-seq)

description: counts.txt


title: Rptor KO rep1


title: CA40_DMSO_1 (rna-seq)

description: counts.txt


title: Single cell 14 8-cell embryo 1

value: b4.2 cell


title: Single cell 13 8-cell embryo 1


title: CA29_DMSO_1 (rna-seq)

description: counts.txt


title: Single cell 12 4-cell embryo 3

source_name: 4-cell embryo 3

value: B3 cell

value: 4-cell embryo


title: Single cell 18 8-cell embryo 1


title: Single cell 11 4-cell embryo 3


title: CA29_3MC_1 (rna-seq)

description: counts.txt


title: Single cell 9 4-cell embryo 3

value: A3 cell


title: SpragueDawley_oocyte_RNAseq_rep2

city: Vancouver

first: Matthew

middle: C

last: Lorincz

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
RNA-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using STAR v.2.4.0.i. Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1. PCR duplicates were filtered out. Sequence alignment maps were converted to bedGraph and wiggle formats using Bedtools v2.22.1 and UCSC binary bedGraphToBigWig.
Genome_build: rn6
Supplementary_files_format_and_content: bigWig

organism: Rattus norvegicus

source_name: GVO

extract_protocol:
RNA-seq: total RNA was isolated from 100-200 mouse or rat oocytes using TriReagent, and ribosomal RNA was depleted using NEB Next rRNA Depletion kit according to manufacturer’s instruction. Double stranded cDNA was synthesized using NEB Next first strand and second strand synthesis modules.
Libraries were constructed using a custom protocol (Brind’Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer’s protocols.

tag: strain

value: Sprague Dawley

value: oocyte

value: GV

tag: chip antibody


title: CA23_GNF_2 (rna-seq)

description: counts.txt


title: Single cell 8 4-cell embryo 2

source_name: 4-cell embryo 2


title: CA23_GNF_1 (rna-seq)

description: counts.txt


title: SpragueDawley_oocyte_RNAseq_rep1


title: Arabidopsis heso1-1 miR1510

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
The adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the Pigeon pea,  mung bean, and Arabidopsis genomes.
Genome_build: Pigeon pea Cc1.0; mung bean Vr1.0; Arabidopsis thaliana TAIR10.
Supplementary_files_format_and_content: Tag count file

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis and mung bean were grown in a growth chamber or greenhouse  with a light cycle of 16 h light / 8 h dark, at 22 to 23 °C. Pigeon pea plants were grown  in a greenhouse with a light cycle of 16 h light / 8 h dark, at 24 to 28 °C.

value: 2-week old

value: leaf

tag: ecotype


title: Single cell 7 4-cell embryo 2


title: Arabidopsis urt1-1 miR1510


title: CA29_GNF_1 (rna-seq)

description: counts.txt


title: off_target_odd

city: Urbana

first: Alan

last: Luu

state: Illinois

address: 1110 W Green St.

department: Physics

institute: University of Illinois at Urbana Champaign

description: Human embryonic kidney cell culture

library_source: genomic

data_processing:
Library strategy: DNA-seq
Sequenced reads were mapped to GrCh38 whole genome using Bowtie2 v2.3.3.1 with parameters -x -1 -2 -S
Sam files converted to bam files using SAMtools v1.6 view function with parameters -S -b
Bam files sorted with SAMtools v1.6 sort function with parameter -o
Bed file containing on and off-target coordinates created manually
mpileup files created from sorted bam files using SAMtools v1.3.1 mpileup function with parameters --skip-indels -d 10000 -u -v -t AD,ADF,ADR  -l -f -o
SNP’s called using using binomial test with null hypothesis p parameter estimated from sequencing noise in control sample.
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab delimited files displaying SNPs called

molecule: genomic DNA

source_name: Sequencing data of treated sample for 9 on-target sites not covered in even sample and their 36 respective off-target sites

growth_protocol: According to ATCC recommendations (ATCC CRL-3216)

extract_protocol:
EarthOx Animal Genomic DNA Mini Preparation
Target regions were amplified using Kapa 2G Robust PCR kit (Roche), purified with the Zymoclean gel DNA recovery kit, and pooled evenly. Shotgun libraries were prepared with the Hyper Library construction kit from Kapa Biosystems without shearing.

treatment_protocol: Transfected with plasmids to express a BE3 variant and an sgRNA targeting splice acceptor sequence using lipofectamine 2000, and cultured for 6 days

tag: passage

value: Embryonic Kidney


title: off_target_even

description: Human embryonic kidney cell culture

source_name: Sequencing data of treated sample for 9 on-target sites and their 36 respective off-target sites


title: RELA_exon10_gDNA_BE3_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G16

data_processing:
Library strategy: DNA-seq
Sequenced reads were mapped to GrCh38 whole genome using Bowtie2 v2.3.3.1 with parameters -x -1 -2 -S
Sam files converted to bam files using SAMtools v1.6 view function with parameters -S -b
Bam files sorted with SAMtools v1.6 sort function with parameter -o
Sorted bam files visualized using IGV v2.4.4 and base distribution manually counted
Genome_build: GrCh38
Supplementary_files_format_and_content: The processed data file is an xlsx spreadsheet file with four sheets, each containing data on a single exon. Base distribution counts at the positions spanned by the protospacer and PAM are given in the second table. These counts are then converted into base percentages in the third table. The fourth table averages the percentages. The first table simply conveys the information in the fourth table but as a figure appropriate for publication.

source_name: BE3 treated sample for CRISPR-SKIP experiment targeting RELA exon 10

extract_protocol:
EarthOx Animal Genomic DNA Mini Preparation
Target region was amplified using Kapa 2G Robust PCR kit (Roche), and purified with the Zymoclean gel DNA recovery kit. Shotgun libraries were prepared with the Hyper Library construction kit from Kapa Biosystems without shearing.

treatment_protocol: Transfected with plasmids to express SaBE3-KKH and sgRNA targeting splice acceptor sequence using lipofectamine 2000, and cultured for 6 days


title: CA23_DMSO_1 (rna-seq)

description: counts.txt

value: DMSO


title: off_target_control

description: Human embryonic kidney cell culture

source_name: Sequencing data of control sample for 18 on-target sites and 72 off-target sites

treatment_protocol: Transfected with GFP control plasmid using Lipofectamine 2000, and cultured for 6 days


title: Single cell 5 4-cell embryo 2


title: Single cell 4 4-cell embryo 1

source_name: 4-cell embryo 1


title: RELA_exon10_gDNA_BE3_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G15


title: RELA_exon10_gDNA_control_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G14

source_name: Control sample for CRISPR-SKIP experiment targeting RELA exon 10


title: RELA_exon10_gDNA_control_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G13


title: BRCA2_exon26_gDNA_BE3_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G12

source_name: BE3 treated sample for CRISPR-SKIP experiment targeting BRCA exon 26

treatment_protocol: Transfected with plasmids to express SpBE3-VQR and sgRNA targeting splice acceptor sequence using lipofectamine 2000, and cultured for 6 days


title: CA29_3MC_2 (rna-seq)

description: counts.txt

source_name: lymphoblastoid cell line


title: Single cell 3 4-cell embryo 1


title: CA23_3MC_2 (rna-seq)

description: counts.txt


title: BRCA2_exon26_gDNA_BE3_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G11


title: CA12_GNF_2 (rna-seq)

description: counts.txt


title: Single cell 10 4-cell embryo 3


title: BRCA2_exon26_gDNA_control_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G10

source_name: Control sample for CRISPR-SKIP experiment targeting BRCA exon 26


title: CA23_DMSO_2 (rna-seq)

description: counts.txt


title: CA12_GNF_1 (rna-seq)

description: counts.txt


title: Single cell 2 4-cell embryo 1


title: BRCA2_exon26_gDNA_control_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G9


title: PIK3CA_exon5_gDNA_BE3_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G7

source_name: BE3 treated sample for CRISPR-SKIP experiment targeting PIK3CA exon 5

treatment_protocol: Transfected with plasmids to express SpBE3 and sgRNA targeting splice acceptor sequence using lipofectamine 2000, and cultured for 6 days


title: PIK3CA_exon5_gDNA_control_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G6

source_name: Control sample for CRISPR-SKIP experiment targeting PIK3CA exon 5


title: CA12_DMSO_2 (rna-seq)

description: counts.txt


title: Single cell 1 4-cell embryo 1


title: Single cell 6 4-cell embryo 2


title: CA23_3MC_1 (rna-seq)

description: counts.txt


title: PIK3CA_exon5_gDNA_control_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G5


title: CA12_3MC_2 (rna-seq)

description: counts.txt


title: RELA_exon7_gDNA_control_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G2

source_name: Control sample for CRISPR-SKIP experiment targeting RELA exon 7


title: RELA_exon7_gDNA_BE3_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G3

source_name: BE3 treated sample for CRISPR-SKIP experiment targeting RELA exon 7


title: RELA_exon7_gDNA_control_1

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G1


title: CA12_3MC_1 (rna-seq)

description: counts.txt


title: CA12_DMSO_1 (rna-seq)

description: counts.txt


title: Leptin-overexpressing rep3

city: changsha

first: junchen

last: chen

address: 87 Xiangya Road, Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.

department: 1Department of Dermatology, Xiangya Hospital, Central South University

country: China

description:
F1_14
processed data file: processed_data.txt

data_processing:
The raw data was checked by FastQC v.
Clean reads were aligned to the pig genome using STAR 2.5.
The expression of the transcript was calculated by FPKM using Cuffnorm.
Differentially expressed transcripts were determined using DESeq v1.22.1.
Function and signaling pathway enrichment analysis using GO and KEGG database.
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: processed_data.txt: Tab-delimited text file includes FPKM values for all Samples.

organism: Sus scrofa

source_name: PBMC

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina).

tag: breed

value: Yorkshire

tag: genotype/variation

value: Leptin-overexpressing

value: 6 months

value: PBMC


title: Leptin-overexpressing rep1

institute: 1Department of Dermatology, Xiangya Hospital, Central South University

description:
F1_3
processed data file: processed_data.txt


title: RELA_exon7_gDNA_BE3_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G4


title: RELA_exon10_RNA_BE3_1

description:
sample name in processed data file:
R15
Human embryonic kidney cell culture

data_processing:
Sequenced reads were mapped to GrCh38 whole genome using TopHat v2.1.1 with parameters -o
Bam files sorted using SAMtools v1.6 sort function with parameters -o
Forward and reverse reads combined and junctions mapped using HTSeq
Isoform quantification performed by looking at ratio between exon-skipped junction and canonical junction at 5' end of exon to be skipped
Genome_build: GrCh38
Supplementary_files_format_and_content: Tab delimited file containing counts and percentages of wild type and exon-skipped reads calculated in three different ways

extract_protocol:
Qiagen Rneasy Plus Mini Kit with Qiashredder step, Followed by Quantabio qScript cDNA synthesis
Target region was amplified using Kapa 2G Robust PCR kit (Roche), and purified with the Zymoclean gel DNA recovery kit. Shotgun libraries were prepared with the Hyper Library construction kit from Kapa Biosystems without shearing.


title: CA12_DMSO_1_input (chip-seq)

description: OverlappedPeaksUniq.bed.gz

data_processing:
Sequences were mapped to hg19 genome with BWA
Duplicates were removed
MACS2 was used to call narrow peaks
Bedtools was used to identify common peaks
Genome_build: hg19
Supplementary_files_format_and_content: tab separated bed of peaks in common between all four samples

extract_protocol:
Cells were pelleted at 300g for 5 minutes at 4C, resuspended in ice cold phosphate buffered saline and pelleted again.  RNA was extracted using the miRNeasy RNA extraction kit. ChIP DNAs were extracted as described previously (PMID: 29268714).
ChIP-seq libraries were prepared according to manufacturer’s instructions in the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI). The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: Cells treated with 1uM 3-MC or 0.1% DMSO in fresh media for 24 hours


title: CA12_DMSO_2 (chip-seq)

description: OverlappedPeaksUniq.bed.gz

value: D5S6H-lot 1 (Cell Signaling Technology)


title: Leptin-overexpressing rep2

description:
F1_4
processed data file: processed_data.txt


title: RELA_exon10_RNA_BE3_2

description:
sample name in processed data file:
R16
Human embryonic kidney cell culture


title: RELA_exon10_RNA_control_2

description:
sample name in processed data file:
R14
Human embryonic kidney cell culture


title: WT rep3

description:
F1_9
processed data file: processed_data.txt

value: WT


title: WT rep2

description:
F1_5
processed data file: processed_data.txt


title: RELA_exon10_RNA_control_1

description:
sample name in processed data file:
R13
Human embryonic kidney cell culture


title: BRCA2_exon26_RNA_BE3_2

description:
sample name in processed data file:
R12
Human embryonic kidney cell culture


title: PIK3CA_exon5_gDNA_BE3_2

description:
Human embryonic kidney cell culture
gDNA_counts.xlsx
sample name in processed data:
G8


title: BRCA2_exon26_RNA_control_2

description:
sample name in processed data file:
R10
Human embryonic kidney cell culture


title: BRCA2_exon26_RNA_BE3_1

description:
sample name in processed data file:
R11
Human embryonic kidney cell culture


title: CA12_DMSO_1 (chip-seq)

description: OverlappedPeaksUniq.bed.gz


title: 11L-BaP rep 4

city: Mérida

first: Reyna

middle: Cristina

last: Colli-Dula

state: Yucatán

address: Km. 6 Ant Carretera a Progreso

department: Recursos del Mar

country: Mexico

institute: CINVESTAV

description:
MTL.txt
Sample11_Ind12-35335561

data_processing:
Tilapia RNA-Seq reads were trimmed (adaptor sequences) and reads of low quality (< 12 bp) were eliminated. The reference genome from O. niloticus (Orenil2.0) were downloaded from the Ensembl web site (http://www.ensembl.org/Oreochromis_niloticus/Info/Index). Clean reads were aligned to the reference genome using Tophat and the resulting Binary Sequence Alignment/Map (BAM) files were quantified for gene/transcript expression. Differential expression (DE) analysis of the clean reads was performed by testing the BaP treated read counts against controls read counts using exact test with R package EdgeR with a significance threshold of p < 0.05; fold change greater than ± 1. Pathway analysis was performed using PathwayStudioTM V9 (Elsevier, Inc., Rockville, MD, USA) operating with the ResNet 10.0 database. The gene set enrichment analysis (GSEA) and sub-network enrichment analysis (SNEA) using the Mann-Whitney test with an alpha level of p < 0.05 were used to identified potential pathways altered by BaP exposure.
Genome_build: Orenil2.0

organism: Oreochromis niloticus

source_name: Liver

growth_protocol: Adult male tilapias (378.8 ± 9.63 g in weight and 27.7 ± 0.214 cm in length) were selected from one year old tilapia fish stocks maintained at CINVESTAV-Merida. After selection, the fish were kept for a four-week acclimation period in a 300 l aquarium at ~ 28°C with aerated water, natural photoperiod and flow-through conditions.

extract_protocol:
Total RNA was isolated from ~0.5 mg of liver or testis tissues using the Trizol reagent method according to the manufacturer's procedure (Invitrogen™, Carlsbad CA,USA). The RNA pellet was resuspended in 20–50 μl of RNAsecureTM Reagent (Ambion Austin, TX, USA) and DNAse was-treated with Turbo DNA-free (Ambion Austin, TX, USA). RNA cleanup was performed using Phenol-chloroform (1:1) extraction, followed by sodium acetate (3M) and ethanol (100 %) precipitation (Chomczynski et al., 1987).
RNA libraries were prepared for sequencing using standard Illumina protocols. Samples were processed following the manufacturer’s protocol for NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England, Biolabs (NEB), lpswich, MA, USA) in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1)

treatment_protocol: Tilapia were randomly assigned to the BaP-treated or control groups (n = 24 each) and kept distributed in four experimental aquariums (2 for control group and 2 for BaP-treated with 12 fish per aquarium). Male adult tilapia received 5 separate i.p injections (a single injection every 6 days) of BaP (3 mg/kg) or DMSO + corn oil as the carrier solution. Two days after the 5th injection (Day 26), six fish from each BaP-treated and control groups were euthanized using an overdose of 0.5 g/l MS-222 (Sigma Aldrich, Inc). Liver and testis were excised, weighed, snap frozen in liquid nitrogen and then stored at -80 °C for subsequent molecular analyses.

value: Liver

value: One year old

tag: Sex

value: male


title: CA12_3MC_2_input (chip-seq)

description: OverlappedPeaksUniq.bed.gz


title: BRCA2_exon26_RNA_control_1

description:
sample name in processed data file:
R9
Human embryonic kidney cell culture


title: PIK3CA_exon5_RNA_BE3_2

description:
sample name in processed data file:
R8
Human embryonic kidney cell culture


title: 14L-BaP rep 3

description:
MTL.txt
Sample14_Ind5-35349448


title: PIK3CA_exon5_RNA_BE3_1

description:
sample name in processed data file:
R7
Human embryonic kidney cell culture


title: CA12_3MC_2 (chip-seq)

description: OverlappedPeaksUniq.bed.gz


title: PIK3CA_exon5_RNA_control_2

description:
sample name in processed data file:
R6
Human embryonic kidney cell culture


title: RELA_exon7_RNA_BE3_2

description:
sample name in processed data file:
R4
Human embryonic kidney cell culture


title: RELA_exon7_RNA_BE3_1

description:
sample name in processed data file:
R3
Human embryonic kidney cell culture


title: 15L-BaP rep 2

description:
MTL.txt
Sample15_Ind11-35352441


title: CA12_3MC_1 (chip-seq)

description: OverlappedPeaksUniq.bed.gz


title: PIK3CA_exon5_RNA_control_1

description:
sample name in processed data file:
R5
Human embryonic kidney cell culture


title: 16L-BaP rep 1

description:
MTL.txt
Sample16_Ind8-35350457


title: RELA_exon7_RNA_control_2

description:
sample name in processed data file:
R2
Human embryonic kidney cell culture


title: 17L-CTRL rep 4

description:
MTL.txt
Sample17_Ind10-35366331


title: WistarHan_oocyte_RNAseq_rep2

source_name: MII

value: Wistar Han

value: MII


title: WistarHan_oocyte_RNAseq_rep1

value: oocyte


title: Pigeon pea leaf

organism: Cajanus cajan

source_name: Leaf


title: 18L-CTRL rep 3

description:
MTL.txt
Sample18_Ind7-35356419


title: RELA_exon7_RNA_control_1

description:
sample name in processed data file:
R1
Human embryonic kidney cell culture


title: WT rep1

description:
F1_2
processed data file: processed_data.txt


title: 19L-CTRL rep 2

description:
MTL.txt
Sample19_Ind6-35353466


title: Mung bean leaf

organism: Vigna radiata


title: 20L-CTRL rep1

description:
MTL.txt
Sample20_Ind9-35347447


title: Solvent + OGG1 Inhibitor + TNF

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

description: SAMPLE 4

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/us/shop/genes-and-pathways/data-analysis-center-overview-page/
For the normalization it uses the average of five housekeeping genes: Gusb, Hprt, Hsp90ab1, Gapdh, Actb.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change table  reports test/control (i.e., solvent + TNF / solvent) ratios.

label: SYBR Green

source_name: Cell lysate

label_protocol: PCR assays were performed using the Mouse Inflammatory Cytokines & Receptors PCR array PAMM-011ZA (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 1µg total RNA using the Superscript® IIIFirst Strand Synthesis System (Invitrogen)

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Cells were exposed to solvent or OGG1 inhibitor for 1 hour, and treated with 20 ng/ml TNF for 30 minutes.

value: Solvent + OGG1 Inhibitor + TNF


title: Solvent + TNF (20 ng/ml)

description: SAMPLE 3

value: Solvent + TNF (20 ng/ml)


title: 15G-BaP rep 3

description:
MTG.txt
Sample5_Ind13-35352447

source_name: Testis

value: Testis


title: 14G-BaP rep 2

description:
MTG.txt
Sample4_Ind4-35349452


title: Solvent

description: SAMPLE 1

value: Solvent


title: Solvent + OGG1 Inhibitor

description: SAMPLE 2

value: Solvent + OGG1 Inhibitor


title: 11G-BaP rep 1

description:
MTG.txt
Sample1_Ind3-35349451


title: degradome of mixed sample1 and sample2

city: Hangzhou

first: Xiaojiao

last: Han

state: Zhejiang

address: Daqiao Road 73#

department: The Research Institute of Subtropical of Forestry

institute: Chinese Academy of Forestry

data_processing:
Raw sequencing reads were obtained from related Illumina’s analysis software. All clean and unique sRNAs read sequences were queried using the BLAST algorithm to search against the relevant non-coding RNAs deposited in the Rfam and NCBI GenBank databases to remove rRNA, tRNA, snRNA and snoRNA sequences.
Genome_build: Salix matsudana Koidz full-length transcriptome data; MTL_quivered_hq.fasta
Supplementary_files_format_and_content: xlsx files include miRNA sequences and other relevant information

organism: Salix matsudana

source_name: untreated and salt stress samples mixed

growth_protocol: untreated by 100mmol salt

extract_protocol:
Total RNA was isolated by the Total RNA Purification Kit (NORGEN, Thorold, Canada). All RNA samples were treated with DNase I (TaKaRa, Dalian, China) to remove genomic DNA.
Small RNA (sRNA) libraries were constructed following the standard protocol (Illumina, San Diego, USA)

treatment_protocol: treated by 100mmol salt

value: 30-day-old plants

tag: sample type

value: untreated and salt stress samples mixed

value: roots and stems


title: 20G-CTRL rep 3

description:
MTG.txt
Sample9_Ind18-35337542


title: 18G-CTRL rep 1

description:
MTG.txt
Sample7_Ind14-35363335


title: sample 2_two days after salt treatment

source_name: salt stress

tag: exposed to

value: salt solution (100 mmol L-1 NaCl) for 2 days


title: sample 1_untreated control

source_name: untreated

value: none (untreated control)


title: 19G-CTRL rep 2

description:
MTG.txt
Sample8_Ind16-35365336


title: Plasma-CC7 (healthy control group)-Rep1

city: Weifang

first: zhengjun

last: Yi

state: Shandong

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine

department: Department of Laboratory Medicine

institute: Weifang Medical University

description: CircRNA expression in plasma isolated from healthy controls

hyb_protocol: Arraystar Human Circular RNA Microarray V2 (8x15K, Arraystar Inc., MD, USA) covers 13,617 human circRNAs and was used to identify circRNAs with differential expression between active TB samples and controls. Briefly,1 μg of each labeled cRNA was fragmented by adding 10×Blocking Agent (5 μl) and 25×Fragmentation Buffer (1 μl), then the mixture was heated at 60°C for 30 min, finally 2 × Hybridization buffer (25 μl) was added to dilute the labeled cRNA. The resulting hybridization solution (50 μl) was dispensed into the gasket slide and then assembled to the circRNA expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were kept for subsequent differential analysis.

source_name: Plasma,CC7 (one of three healthy control subjects), replicate 1

label_protocol: Sample labeling was performed utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar Inc., MD, USA). Briefly, total RNA from each sample was treated with RNase R (EpicentreInc., Madison, WI, USA) to remove linear RNAs and enrich circRNAs. Then, the enriched circRNAs were amplified and transcribed into fluorescently-labeled cRNAs utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar Inc., MD, USA). The labeled cRNAs were purified with a RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were then quantified with a NanoDrop ND-1000 spectrophotometer.

extract_protocol: For RNA preparation,total RNA was isolated from plasma with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Total RNA concentration and quality of each sample were determined with NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). RNA integrity and DNA contamination were measured by electrophoresis on a denaturing agarose gel. Only RNA samples with high quality were used for subsequent microarray analysis.

treatment_protocol: Plasma samples from active TB patients and healthy controls were collected by centrifugation, immediately aliquoted and stored in liquid nitrogen until further use. All the TB patients had no history of radiotherapy or chemotherapy before blood collection.

value: Plasma

tag: gender

value: Male

tag: disease state

value: healthy control


title: Plasma-CC8 (healthy control group)-Rep1

source_name: Plasma,CC8 (one of three healthy control subjects), replicate 1


title: EGD1(Δ1-33bp), EGD2 -GFP:: kanMX4, Btt1:: natNT2, IP translatome, replicate 1

status: Public on Jul 05 2018

city: Haifa

first: Ayala

last: Shiber

address: Emerson building, Technion City

country: Israel

institute: Technion, Israel institute of technology

data_processing:
Library strategy: Ribosome profiling
Barcode and linker removal using Cutadapt 1.8.3
Alignment to rRNA using Bowtie2.2.5.0
Alignment to genome using TopHat2.0.13
center weighting of ribosomal footprints (custom python script)
normalization to total read number per sample (custom python script)
Genome_build: NCBI build3.1
Supplementary_files_format_and_content: GeneExpression (tab-delimited text files include RPKM values for each gene.  column1: Gene systematic name, column2: chromosome number, column3: nt start position, column4: chromosome number,  column4: nt stop position, column5: plus or minus strand, column6: normalized reads in RPKM, column6: excluded  or included in analysis, based on a 64 reads per orf threshold)
Supplementary_files_format_and_content: mix_FAS1-GFP_W_FAS2-TAP_tags file (tab-delimited text file include RPM ratio values for each codon along FAS2-TAP tag orf.  column1: codon number,  column2:  IP/T ratio replicate 1  column3:  IP/T ratio replicate 2)
Supplementary_files_format_and_content: EGD1del11aa_EGD1.txt (tab-delimited text file include RPM ratio values for each nt along EGD1 orf, in EGD2-GFP.  column1: nt position,  column2:  IP/T ratio)
Supplementary_files_format_and_content: EGD1del11aa_EGD2.txt (tab-delimited text file include RPM  ratio values for each nt along EGD2 orf, in EGD1-GFP.  column1: nt position,  column2:  IP/T ratio)
Supplementary_files_format_and_content: NAA20_GFP_NAA25.txt (tab-delimited text file include RPM ratio values for each nt along NAA25 orf, in NAA20-GFP.  column1: nt position,  column2:  IP/T ratio)
Supplementary_files_format_and_content: NAA20_GFP_NAA20.txt (tab-delimited text file include RPM  ratio values for each nt along NAA20 orf, in NAA20-GFP.  column1: nt position,  column2:  IP/T ratio)
Supplementary_files_format_and_content: NAA25_GFP_NAA20.txt (tab-delimited text file include RPM  ratio values for each nt along NAA20 orf, in NAA25-GFP.  column1: nt position,  column2:  IP/T ratio)
Supplementary_files_format_and_content: NAA10_GFP_NAA15.txt (tab-delimited text file include RPM  ratio values for each nt along NAA15 orf, in NAA10-GFP.  column1: nt position,  column2:  IP/T ratio)

organism: Saccharomyces cerevisiae BY4741

source_name: Yeast

growth_protocol: Cultures were grown in YPD, except for TRP2/3-GFP strains, grown on SD-trp and CPA1/2-GFP strains grown on SD-arg, at 30°C and 150 rpm. MPT deletion strains growth media was supplanted with fatty acids.

extract_protocol:
RNA was extracted using the hot acid phenol method (for details see Becker et al. 2013)
DNA libraries were generated following previously published protocoles (Ingolia et al. 2009, Becker et al. 2013)

treatment_protocol: Cultures were filtered, flash frozen and lysed in frozen state using a mixer mill. Total and IP samples were taken. For total samples, ribosomes were pelleted through a sucrose cushion and resuspended.  IP samples   were subjected to GFP-tagged subunit purification using a GFP-antibody coupled to sepharose-beads. Then both Total and IP were used for RNA extraction.

value: whole organism


title: EGD1(Δ1-33bp), EGD2 -GFP:: kanMX4, Btt1:: natNT2, Total translatome, replicate 1


title: EGD1(Δ1-33bp) -GFP:: kanMX4, Btt1:: natNT2, IP translatome, replicate 1


title: NAA25-GFP, IP translatome, replicate 1


title: NAA25-GFP, Total translatome, replicate 1


title: EGD1(Δ1-33bp) -GFP:: kanMX4, Btt1:: natNT2, Total translatome, replicate 1


title: NAA20-GFP, Total translatome, replicate 1


title: Plasma-BC10 (active TB group)-Rep1

description: CircRNA expression in plasma isolated from patients with active TB

source_name: Plasma, BC10 (one of three active TB patients), replicate 1

value: TB


title: NAA20-GFP, IP translatome, replicate 1


title: NAA15-GFP, IP translatome, replicate 1


title: Plasma-CC6 (healthy control group)-Rep1

source_name: Plasma,CC6 (one of three healthy control subjects), replicate 1

value: Female


title: Plasma-BC1 (active TB group)-Rep1

source_name: Plasma, BC1 (one of three active TB patients), replicate 1


title: Plasma-BC2 (active TB group)-Rep1

source_name: Plasma, BC2 (one of three active TB patients), replicate 1


title: NAA15-GFP, Total translatome, replicate 1


title: SUI3-GFP, Total translatome, replicate 1


title: NAA10-GFP, Total translatome, replicate 1


title: GCD11-GFP, IP translatome, replicate 1


title: GCD11-GFP, Total translatome, replicate 1


title: SUI2-GFP, IP translatome, replicate 1


title: NAA10-GFP, IP translatome, replicate 1


title: SUI2-GFP, Total translatome, replicate 1


title: SUI3-GFP, IP translatome, replicate 1


title: CPA2-GFP, Total translatome, replicate 1


title: CPA1-GFP, IP translatome, replicate 1


title: CPA2-GFP, IP translatome, replicate 1


title: TRP2-GFP, Total translatome, replicate 1


title: PFK2-GFP, IP translatome, replicate 2


title: PFK2-GFP, Total translatome, replicate 2


title: PFK2-GFP, IP translatome, replicate 1


title: PFK2-GFP, Total translatome, replicate 1


title: TRP2-GFP, Total translatome, replicate 2


title: TRP3-GFP, IP translatome, replicate 1


title: CPA1-GFP, Total translatome, replicate 1


title: TRP2-GFP, IP translatome, replicate 1


title: TRP3-GFP, Total translatome, replicate 1


title: PFK1-GFP, IP translatome, replicate 2


title: TRP2-GFP, IP translatome, replicate 2


title: PFK1-GFP, IP translatome, replicate 1


title: PFK1-GFP, Total translatome, replicate 2


title: PFK1-GFP, Total translatome, replicate 1


title: ARC1-GFP, Total translatome, replicate 1


title: ARC1-GFP, IP translatome, replicate 2


title: MES1-GFP, IP translatome, replicate 2


title: ARC1-GFP, IP translatome, replicate 1


title: ARC1-GFP, Total translatome, replicate 2


title: GUS1-GFP, IP translatome, replicate 2


title: MES1-GFP, IP, translatome replicate 1


title: MES1-GFP, Total translatome, replicate 1


title: GUS1-GFP, IP translatome, replicate 1


title: GUS1-GFP, Total translatome, replicate 1


title: MES1-GFP, Total translatome, replicate 2


title: mix: FAS1-GFP & FAS2-TAP,IP translatomes, replicate 2


title: mix: FAS1-GFP &  FAS2-TAP,Total translatomes, replicate 2


title: Mnemiopsis_iChip_H3K4me2

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

data_processing:
scRNA-seq:
.Read_1 files were mapped into the corresponding species genome assembly (see below) using bowtie2, using default parameters.
.Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651)
iChIP:
.Paired reads files were mapped into the corresponding species genome assembly (see below) using bowtie2, using default parameters.
.Duplicate reads were removed using samtools.
.deepTools bamCoverage was used to generate bigWig coverage files, using a total extension of 220bps from the read start position, and a scaleFactor parameter of 0.1
Genome_build: : https://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index
Genome_build: : https://research.nhgri.nih.gov/mnemiopsis/download/download.cgi?dl=genome
Genome_build: Trichoplax adhaerens: https://genome.jgi.doe.gov/Triad1/Triad1.home.html

organism: Mnemiopsis leidyi

source_name: Adult comb jelly

extract_protocol:
MARSseq RNA capture: single-cells were FACS-sorted directedly into a lysis solution in 384-well plates. Plates were forzen at -80C, lysis solution (ddH2O, 0.1%triton, RNAse inhibitors) was evaporated and reverse transcription was performed directly in the wells.
MARSseq library prepartion was performed as described in  Jaitin et al. 2014 (10.1126/science.1247651). Briefly, cDNA from different cells (barcoded in the Reverse Transcripiton step) was pooled and amplified by in vitro-transcription. Amplified RNA was then fragmented, reverse transcribed, and Illumina adaptors were added by PCR (14 cycles).
iChIP experiments were performed starting from 200,000 cells, following the iChIP protocol originally described in Lara-Astiaso et al. 2014 (10.1126/science.1256271). Briefly, cells were cross-linked in FA 1% for 10 min and cross-linked chromatin was sonicated using 45 cycles (30"ON/30"OFF). Then chromatin was immobilized using anti-H3 antibody and barcoded, followed by immunoprecipitation using specific anti-H3K4me2 and anti-H3K4me3 antibodies.

tag: stage/cell type

value: Adult

value: Wild type

value: anti-H3K4me2:Abcam #ab3236


title: GUS1-GFP, Total translatome, replicate 2


title: mix: FAS1-GFP &  FAS2-TAP,IP translatomes, replicate 1


title: Mnemiopsis_iChip_input


title: 5mC-BC1N

type: genomic

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: 5mC level in adjacent normal breast tissue from patient BC1

hyb_protocol: genomic DNA was bisulfite-converted using an EZ DNA methylation Kit (ZYMO research). DNA methylation level was measured using the Illumina Infinium HD Methylation Assay. Bisulfite converted DNA was hybridized with the Illumina HumanMethylation450 BeadChip 450K array (12 samples/chip), as described previously. (Dedeurwaerder et al, Epigenomics 2011).

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

data_processing: Raw data were first filtered using a detection p-value <0.05. Cross-reactive, SNP-containing and heterochromosomes-located probes were filtered out using the extended annotation provided by Price et al (Epigenetics chromatin, 2013). β-values were computed using the following formula: β-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. The β-values were corrected for type I and type II bias using the peak-based correction.

source_name: Breast tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted using the Qiagen AllPrep DNA/RNA micro or mini kit according to the manufacturer's instructions.Nucleic acid concentration and purity was 1.81 (1.73-1.91).

tag: tumor status

value: Adjacent normal

tag: patient id

tag: tet1 qpcr level


title: Mnemiopsis_iChip_H3K4me3

value: anti-H3K4me3:Millipore #07-473


title: 5mC-BC3T

description: 5mC level in TET1-low primary breast tumor from patient BC3

value: Primary tumor

value: Low


title: Mnemiopsis_Adult_scRNAseq


title: 5mC-BC1T

description: 5mC level in TET1-low primary breast tumor from patient BC1


title: FAS1-GFP, FAS2 deletion of MPT domain segment (Δ1-282bp),Total translatome, replicate 2

tag: tissue


title: DRG Sham week 3 -1

city: Camden

first: Jaroslav

last: Jelinek

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: DRG 3 weeks after sham operation

data_processing:
Fastq files were trimmed to remove Illumina adapters and aligned to the bisulfite-converted Rattus norvegicus genome (rn4) using Bismark v0.18.1  and Bowtie2.
Methylation values were extracted using Bismark v0.18.1.
We used methylKit v1.3.3 to analyze differential methylation.
Genome_build: rn4
Supplementary_files_format_and_content: tab delimited text file with chromosome, postion, coverage, and percent of methylated (freqC) and unmethylated (freqT) CpG sites

source_name: DRG

extract_protocol: Genomic DNA from dorsal a root ganglia (DRGs) was analyzed for DNA methylation changes by reduced representation bisulfite sequencing (RRBS) (Gu et al. Nature Protocols 2011, doi:10.1038/nprot.2010.190). We followed the NEB protocol for methylated adaptors. Briefly, 1 microgram of genomic DNA was spiked 100 picograms of lambda phage DNA as the unmethylated standard and digested with MspI. Ends of restriction fragments were filled in, 3’-dA tailed and methylated adaptors (NEB E7535) were ligated to the ends of restriction fragments. Bisulfite treatment using the Epitect kit (Qiagen) followed. Bisulfite-converted libraries were amplified using EpiMark Taq DNA polymerase (NEB) and primers with barcode indices. The libraries were pooled and sequenced at Fox Chase Cancer Center Genomics Facility on Illumina HiSeq2500 instrument using single end reads of 50 bases. We used Bismark v0.18.1 to align the sequences to hg19 human genome assembly. We used methylKit v1.3.3 to analyze differential methylation.

treatment_protocol: Spinal nerve ligation (SNL) in male Sprague-Dawley rats (8-9 weeks old, ± 220 g; Harlan Sprague-Dawley, Indianapolis, IN) was used for this study as the neuropathic pain model. Animals were anesthetized with 2-3% isoflurane, and the left L5 and L6 spinal nerves were isolated and ligated tightly with 4.0-silk suture under a surgical microscope. Sham surgery (without nerve ligation) was performed on the contralateral side as the control.

value: Sprague-Dawley

value: dorsal root ganglion

tag: age

value: adult

tag: procedure

value: 3 weeks after sham operation


title: DRG Sham week 3 -2

description: DRG 3 weeks after sham operation

tag: strain


title: DRG Sham week 3 -3

description: DRG 3 weeks after sham operation


title: mix: FAS1-GFP & FAS2-TAP,Total translatomes, replicate 1


title: 5mC-BC3N

description: 5mC level in adjacent normal breast tissue from patient BC3


title: FAS1-GFP, FAS2 deletion of MPT domain segment (Δ1-282bp), IP translatome, replicate 1


title: FAS1-GFP, FAS2 deletion of MPT domain segment (Δ1-282bp), IP translatome, replicate 2


title: DRG SNL week 3 -3

description: DRG 3 weeks after spinal nerve ligation

value: 3 weeks after spinal nerve ligation


title: DRG SNL week 3 -2

description: DRG 3 weeks after spinal nerve ligation


title: 5mC-BC6N

description: 5mC level in adjacent normal breast tissue from patient BC6


title: DRG SNL week 3 -1

description: DRG 3 weeks after spinal nerve ligation


title: FAS1 deletion of MPT domain segment (Δ4989-6153bp), GFP tagged, IP translatome, replicate 2


title: FAS2-GFP, IP translatome, replicate 2


title: FAS2-GFP, IP translatome, replicate 1


title: 5mC-BC5T

description: 5mC level in TET1-high primary breast tumor from patient BC5

value: High


title: FAS1 deletion of MPT domain segment (Δ4989-6153bp), GFP tagged, IP translatome, replicate 1


title: FAS1 deletion of MPT domain segment  (Δ4989-6153bp), GFP tagged,  Total translatome, replicate 2


title: 5mC-BC6T

description: 5mC level in TET1-high primary breast tumor from patient BC6


title: FAS2-GFP, Total translatome, replicate 2


title: FAS1-GFP, FAS2 deletion of MPT domain segment (Δ1-282bp),Total translatome, replicate 1


title: FAS1 deletion of MPT domain segment (Δ4989-6153bp), GFP tagged, Total translatome, replicate 1


title: FAS1-GFP, IP translatome, replicate 2


title: FAS2-GFP, total translatome, replicate 1


title: FAS1-GFP, Total translatome, replicate 2


title: FAS1-GFP, Total translatome, replicate 1


title: FAS1-GFP, IP translatome, replicate 1


title: Stimulated CKO

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Reads were converted to fastq files and were trimmed and filtered using FASTX-Toolkit
Reads were mapped to mm10 using STAR guided by GTF version
Calculating insert size and standard deviation performed using Picard v.1.126
read counting performed using HT-seq v0.6.0
Normalization and Deferential expression analysis performed using DESeq
BAM to bedgraph performed using bedtools v2.17.0
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.1.1
Genome_build: mm10

source_name: Stimulated CKO CD4+CD62L+T Cell

extract_protocol:
RNA extraction was performed with PureLink RNA  Mini Kit
Libraries were prepared according to the standard SOLiD protocol.

treatment_protocol: For stimulation, cells resuspended in RPMI-1640 and added to a plate coated with anti-CD3 and anti-CD28 antibodies.  After 12 hours, the cells were collected and RNA was extracted.

value: Zfx T cell conditional knockout

tag: treatment

value: stimulated


title: CKO

source_name: CKO CD4+CD62L+T Cell


title: Stimulated Control

source_name: Stimulated Control CD4+CD62L+T Cell

value: control


title: Control

source_name: Control CD4+CD62L+T Cell


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Ovary_individual24

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Ovary_dsDNTM1_RNA_S4_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

data_processing:
Gene expression. Raw RNA-seq FASTQ reads were trimmed for adapters and preprocessed to remove low-quality reads using Trimmomatic v0.33 (arguments: LEADING:10 TRAILING:10 MINLEN:30) prior to mapping to the O. fasciatus v1.1 genome assembly. Reads were mapped using TopHat v2.1.1 supplied with a reference General Features File (GFF) to the O. fasciatus v1.1 genome assembly, and with the following arguments: -I 20000 --library-type fr-firststrand --b2-very-sensitive.
genome_build: O. fasciatus: v1.1 (https://www.hgsc.bcm.edu/arthropods/i5k), B. germanica: v1 (https://www.hgsc.bcm.edu/arthropods/i5k)
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers.

organism: Oncopeltus fasciatus

source_name: Ovary

growth_protocol: Oncopeltus fasciatus cultures were originally purchased from Carolina Biologicals (Burlington, NC). Mass colonies were maintained in incubators under a 12 h:12 h light/dark cycle at 27°C. Colonies and individual experimental animals were fed organic raw sunflower seeds and provided with ad libitum deionized water. Late instar nymphs were separated from the mass colonies and housed under the same conditions. Nymph colonies were checked daily for newly emerged adults. Adults were separated by sex and kept with food and water for 7–10 days until females reached sexual maturity.

extract_protocol:
Gene expression. RNA-seq libraries for RNA extracted from three DNMT1 knocked down and three control individuals were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
Tissue was flash frozen in liquid nitrogen and stored at -80°C until processing. Total RNA and genomic DNA was extracted using a Qiagen RNAeasy micro kit (Qiagen, Venlo, The Netherlands) per manufacturer’s instructions with Qiagen Qiazol as the lysis buffer. Complementary DNA (cDNA) was synthesized from 500 ng RNA with qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD).

treatment_protocol: RNAi. Template for the in vitro transcription of reactions was prepared from a PCR reaction in which T7 phage promoter sequences were added to the gene-specific DNMT1 primers. For our control sequence, we used the red fluorescent protein (RED) sequence used in previous parental RNAi experiments in O. fasciatus. Sense and anti-sense RNA was synthesized in a single reaction using the Ambion MEGAscript kit (ThermoFisher Sci, Waltham, MA). After purification, the double-stranded RNA (dsRNA) concentration was adjusted to 2 μg/μL in injection buffer (5 mM KCl, 0.1 mM NaH2PO4). Females were injected with 5 μL of dsRNA between the abdominal sternites using an insulin syringe. Following injection, females were paired with an un-injected male to stimulate oviposition and fertilize eggs.  Individual females with their mate were housed in petri dishes with sunflower seeds, water and cotton wool as an oviposition site. The parental RNAi protocol has been reported to result in 100% penetrance by the third clutch of eggs and this was also our experience. Eggs were collected between days 4–10 post-injection and assessed for development. Oncopeltus fasciatus embryos change from a creamy white color to orange as they develop, which indicates viability. Thus, color change is a useful tool for assessing healthy development. We examined the number of developing eggs at 5 days post-oviposition, at which point viable eggs are clearly distinguishable from inviable eggs, as well as hatching rate of eggs from females injected with double-stranded DNMT1 (dsDNMT1) and double-stranded RED (dsRED).

value: Ovary

tag: developmental stage

value: Adult female post-mating

tag: genotype

value: Carolina Biologicals


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Thorax_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Thorax_dsDNMT1_RNA_S17_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

source_name: Thorax

value: Thorax


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Thorax_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Thorax_dsDNTM1_RNA_S16_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Ovary_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Ovary_dsDNTM1_RNA_S5_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Gut_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Gut_dsDNMT1_RNA_S11_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

source_name: Gut

value: Gut


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Head_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Head_dsDNMT1_RNA_S23_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

source_name: Head

value: Head


title: liver - male - pesticide - rep5

city: Toulouse

first: laurence

last: Gamet-Payrastre

address: 180 chemin de Tournefeuille

department: Human alimentation

country: France

institute: INRA ToxAlim

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34183 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31532 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Thirty-six males and 36 females were housed in the laboratory animal room (23 ± 2 ºC) and segregated into 2 groups, each including 18 females and 18 males, fed the pesticides-enriched or the control diet for 52 weeks.

treatment_protocol: The experimental work on animals was conducted in the Toxalim Unit, INRA, Toulouse (France), followed the European Union guidelines for laboratory animal use and care, and was approved by an independent ethics committee. Eight weeks-old female and male C57 BL/6J mice were purchased from Janvier Laboratories, France. Mean body weights were 18.9 and 23.1g for females and males respectively. The animals were allowed to acclimatise to laboratory conditions for 2 weeks before starting the experiment.

value: male

value: pesticide

value: 68 weeks


title: liver - male - control - rep5


title: liver - male - control - rep6


title: liver - female - pesticide - rep4

value: female


title: liver - female - control - rep5


title: liver - female - control - rep6


title: liver - female - pesticide - rep6


title: liver - male - pesticide - rep6


title: 5mC-BC5N

description: 5mC level in adjacent normal breast tissue from patient BC5

value: Adjacent normal


title: liver - female - pesticide - rep5


title: liver - male - pesticide - rep4


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Head_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Head_dsDNMT1_RNA_S22_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: liver - male - control - rep4


title: Adult hippocampus CBP cKO (cre+), biological rep3

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

institute: ISABIAL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray data were background corrected, normalized, summarized, and statistically analyzed using R (http://www.r-project.org/; The R Development Core Team) and Bioconductor (Gentleman et al, 2004). Mouse Gene 1.0 ST arrays were read using oligo package, using RMA algorithm as normalization method.

source_name: Hippocampus CBPf/f : Camk2-creERT2

label_protocol: standard Affymetrix protocol

growth_protocol: The transgenic strains N171-82Q (Tg(HD82Gln)81Gschi, http://www.informatics.jax.org/reference/allele/MGI:2670626) and R6/1 (Tg(HDexon1)61Gpb, MGI:2389466) were acquired from Jackson Laboratories (Sacramento, CA, USA) and maintained in a DBA and C57BL/6J mixed background (50:50) and pure C57BL/6J background, respectively. Experimental protocols were consistent with European regulations and approved by the Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted separately from individual hippocampi using TRI reagent (Sigma-Aldrich) following manufacturers' instructions. Equal amounts of total RNA from 3-4 animals were pooled and treated with RNAse-free DNaseI (Qiagen) treatment and a cleaned up using RNeasy RNA purification columns (Qiagen).

treatment_protocol: Animals were sacrificed by cervical dislocation and brains were immediately removed. Brain areas were dissected and placed into RNAlater solution (Qiagen) until RNA purification.

value: Hippocampus

value: 4 months

value: Male

value: CBPf/f :Camk2-creERT2

tag: genetic background


title: liver - female - control - rep4


title: Adult hippocampus CBP cKO (cre+), biological rep2


title: liver - female - control - rep3


title: Adult hippocampus CBP cKO (cre+), biological rep1


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Head_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Head_dsDNMT1_RNA_S21_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Gut_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Gut_dsDNMT1_RNA_S9_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Thorax_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Thorax_dsDNMT1_RNA_S15_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Ovary_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Ovary_dsDNMT1_RNA_S3_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: liver - male - pesticide - rep3


title: liver - male - control - rep2


title: liver - female - pesticide - rep3


title: liver - female - pesticide - rep2


title: liver - male - control - rep3


title: liver - male - pesticide - rep2


title: liver - female - control - rep1


title: liver - female - control - rep2


title: Oncopeltus_fasciatus_buffer_RNA-seq_Ovary_individual34

description:
11 days post-injection of buffer (control)
TS_34_Ovary_buffer_RNA_S6_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_buffer_RNA-seq_Head_individual34

description:
11 days post-injection of buffer (control)
TS_34_Head_buffer_RNA_S24_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_buffer_RNA-seq_Gut_individual34

description:
11 days post-injection of buffer (control)
TS_34_Gut_buffer_RNA_S12_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_buffer_RNA-seq_Thorax_individual34

description:
11 days post-injection of buffer (control)
TS_34_Throax_buffer_RNA_S18_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

source_name: Throax


title: Oncopeltus_fasciatus_ds-dnmt1_RNA-seq_Gut_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Gut_dsDNMT1_RNA_S10_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: liver - female - pesticide - rep1


title: liver - male - pesticide - rep1


title: Adult hippocampus control (cre-), biological rep3

source_name: Hippocampus CBPf/f

value: CBPf/f


title: liver - male - control - rep1

value: control


title: UACC62_day6_replicate3

city: Madrid

first: Karras

last: Panagiotis

state: Madrid

address: Calle Melchor Fdez Almagro

department: Molecular Oncology

institute: CNIO

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 1.65 µg. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on a G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Bioconductor's limma package was used for data processing. Data were normalized using loess. Normexp method was applied for background correction.

source_name: UACC62, shp62, day 6

label_protocol: Amount of nucleic acid labeled: 500ng. Amplification: by RNA polymerases. Commercial One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90040 Ver 5.7 March 2008.

growth_protocol: All the cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Lonza, cat. No. BE12-604F/U1) supplemented with 10% fetal bovine serum (FBS, Lonza, cat. No. DE14-801F) and 100 μg/mL Penicillin/Streptomycin (Invitrogen, cat. No. 15070-063).

extract_protocol: RNA extraction (QIAshredder Cat No 79654 and RNeasy Mini Kit Cat No 74104, with DNase treatment).

treatment_protocol: Stable depletion of p62 was achieved by lentiviral-driven gene silencing using shRNA purchased from Sigma-Aldrich (TRCN0000007237) in two different melanoma cell lines (SK-Mel-103 and UACC-62, respectively) at two different time points (day 3 and 6). Controls included non-targeting shRNA from Sigma (CAACAAGATGAAGAGCACCAA). Lentiviruses were produced in 293FT cells and infections were performed as previously described (Denoyelle et al., 2006). RNA extraction was achieved using QIAshredder (Cat No 79654) and RNeasy Mini Kit (Cat No 74104) with DNase treatment.

tag: cell line

tag: shRNA

tag: time

value: Day 6

source_name: UACC62, shControl, day 6

value: shControl


title: Juvenile cerebellum wt (control for 82Q), biological rep2

source_name: Cerebellum wt (control for 82Q)

value: Cerebellum

value: 6 weeks

tag: gender

value: wild type

value: DBA :C57BL/6J


title: Oncopeltus_fasciatus_buffer_RNA-seq_Thorax_individual2

description:
11 days post-injection of buffer (control)
TS_2_Thorax_buffer_RNA_S14_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

value: Thorax

value: Adult female post-mating

value: Carolina Biologicals


title: Juvenile cerebellum N171-82Q, biological rep2

source_name: Cerebellum N171-82Q


title: Adult hippocampus control (cre-), biological rep2


title: Juvenile cerebellum N171-82Q, biological rep3


title: Juvenile cerebellum N171-82Q, biological rep1


title: Oncopeltus_fasciatus_buffer_RNA-seq_Ovary_individual2

description:
11 days post-injection of buffer (control)
TS_2_Ovary_buffer_RNA_S2_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

value: Ovary


title: Oncopeltus_fasciatus_buffer_RNA-seq_Head_individual2

description:
11 days post-injection of buffer (control)
TS_2_Head_buffer_RNA_S20_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

value: Head


title: Adult hippocampus control (cre-), biological rep1

value: Hippocampus


title: Juvenile cerebellum wt (control for 82Q), biological rep3


title: Tfh from TONS 1 [exon-level]

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

institute: INSERM UMR1236

description:
Gene expression from tonsil CD4 Tfh cells
Tfh1.CEL

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Transcriptome Array 2.0 (Affymetrix)

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels

source_name: Ex-vivo Tfh cells

label_protocol: Biotinylated double strand cDNA targets were prepared with the NuGEN Ovation PicoSL WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kitaccording to manufacturer recommendations

extract_protocol: RNA was extracted using AllPrep ARN/ADN kit (Qiagen, Valencia, CA)

tag: pathology

value: Tonsillectomy

value: Untreated


title: Tfh from TONS 3 [exon-level]

description:
Gene expression from tonsil CD4 Tfh cells
Tfh3.CEL


title: Memory  T CD4 from TONS 1 [exon-level]

description:
Gene expression from tonsil naive CD4 T cells
N1.CEL

source_name: Ex-vivo memory CD4 T cells


title: Juvenile cerebellum wt (control for 82Q), biological rep1

value: Male


title: Juvenile hippocampus N171-82Q, biological rep3

source_name: Hippocampus N171-82Q


title: Oncopeltus_fasciatus_buffer_RNA-seq_Thorax_individual1

description:
11 days post-injection of buffer (control)
TS_1_Throax_buffer_RNA_S13_R1_001
processed data file:
thorax.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Memory T CD4 from TONS 2 [exon-level]

description:
Gene expression from tonsil naive CD4 T cells
N2.CEL


title: UACC62_day6_replicate2


title: UACC62_day3_replicate2

source_name: UACC62, shp62, day 3

value: Day 3

source_name: UACC62, shControl, day 3


title: Oncopeltus_fasciatus_buffer_RNA-seq_Gut_individual2

description:
11 days post-injection of buffer (control)
TS_2_Gut_buffer_RNA_S8_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

value: Gut


title: Juvenile hippocampus N171-82Q, biological rep2


title: Oncopeltus_fasciatus_buffer_RNA-seq_Head_individual1

description:
11 days post-injection of buffer (control)
TS_1_Head_buffer_RNA_S19_R1_001
processed data file:
head.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: Oncopeltus_fasciatus_buffer_RNA-seq_Gut_individual1

description:
11 days post-injection of buffer (control)
TS_1_Gut_buffer_RNA_S7_R1_001
processed data file:
gut.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx


title: SK-Mel-103_day6_replicate3

source_name: SK-Mel-103, shp62, day 6

value: Day 6

source_name: SK-Mel-103, shControl, day 6


title: UACC62_day3_replicate3

value: shControl


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Thorax_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Thorax_dsDNMT1_BS_S4_R1_001
processed data file:
allc_TS_26_Thorax_dsDNMT1_BS_S4_R1_001.tsv

data_processing:
DNA methylation. Reads generated from MethylC-seq were aligned to the O. fasciatus v1.1 genome assembly or B. germanica v1 genome assembly using the latest version of methylpy (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). MethylC-seq analysis was performed as described in Schmtiz et al. (2013; doi:10.1101/gr.152538.112).
genome_build: O. fasciatus: v1.1 (https://www.hgsc.bcm.edu/arthropods/i5k), B. germanica: v1 (https://www.hgsc.bcm.edu/arthropods/i5k)
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers. TSV file is included in tar archive on the series record.

source_name: Thorax

extract_protocol:
DNA methylation. MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate.
Tissue was flash frozen in liquid nitrogen and stored at -80°C until processing. Total RNA and genomic DNA was extracted using a Qiagen RNAeasy micro kit (Qiagen, Venlo, The Netherlands) per manufacturer’s instructions with Qiagen Qiazol as the lysis buffer. Complementary DNA (cDNA) was synthesized from 500 ng RNA with qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD).


title: Tfh from TONS 2 [exon-level]

description:
Gene expression from tonsil CD4 Tfh cells
Tfh2.CEL


title: UACC62_day6_replicate1


title: Memory  T CD4 from TONS 3 [exon-level]

description:
Gene expression from tonsil naive CD4 T cells
N3.CEL


title: SK-Mel-103_day6_replicate1


title: UACC62_day3_replicate1


title: SK-Mel-103_day3_replicate3

source_name: SK-Mel-103, shp62, day 3

source_name: SK-Mel-103, shControl, day 3


title: Oncopeltus_fasciatus_buffer_RNA-seq_Ovary_individual1

description:
11 days post-injection of buffer (control)
TS_1_Ovary_buffer_RNA_S1_R1_001
processed data file:
ovary.RNAprocessed.ds-dnmt1_16_24_26.control_1_2_34.xlsx

source_name: Ovary


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Ovary_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Ovary_dsDNTM1_BS_S3_R1_001
processed data file:
allc_TS_26_Ovary_dsDNTM1_BS_S3_R1_001.tsv


title: SK-Mel-103_day6_replicate2


title: Juvenile hippocampus wt (control for 82Q), biological rep3

source_name: Hippocampus wt (control for 82Q)


title: SK-Mel-103_day3_replicate1


title: Juvenile hippocampus wt (control for 82Q), biological rep2


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R2_Head_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Head_dsDNMT1_BS_S8_R2_001
processed data file:
allc_TS_26_Head_dsDNMT1_BS_S8_R1_R2_001.tsv

source_name: Head


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R1_Head_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Head_dsDNMT1_BS_S8_R1_001
processed data file:
allc_TS_26_Head_dsDNMT1_BS_S8_R1_R2_001.tsv


title: Juvenile hippocampus N171-82Q, biological rep1


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Ovary_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Ovary_dsDNTM1_BS_S2_R1_001
processed data file:
allc_TS_24_Ovary_dsDNTM1_BS_S2_R1_001.tsv


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R2_Thorax_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Thorax_dsDNTM1_BS_S3_R2_001
processed data file:
allc_TS_24_Thorax_dsDNTM1_BS_S3_R1_R2_001.tsv


title: Juvenile striatum N171-82Q, biological rep2

source_name: Striatum N171-82Q

value: Striatum


title: Juvenile striatum wt (control for 82Q), biological rep1

source_name: Striatum wt (control for 82Q)

value: 6 weeks


title: SK-Mel-103_day3_replicate2


title: Juvenile hippocampus wt (control for 82Q), biological rep1

value: wild type


title: Juvenile striatum wt (control for 82Q), biological rep3

value: DBA :C57BL/6J


title: Juvenile striatum N171-82Q, biological rep3


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R1_Thorax_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Thorax_dsDNTM1_BS_S3_R1_001
processed data file:
allc_TS_24_Thorax_dsDNTM1_BS_S3_R1_R2_001.tsv

value: Thorax


title: Juvenile striatum wt (control for 82Q), biological rep2


title: Juvenile striatum N171-82Q, biological rep1


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Thorax_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Thorax_dsDNMT1_BS_S10_R1_001
processed data file:
allc_TS_16_Thorax_dsDNMT1_BS_S10_R1_001.tsv

value: Adult female post-mating


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R2_Head_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Head_dsDNMT1_BS_S7_R2_001
processed data file:
allc_TS_24_Head_dsDNMT1_BS_S7_R1_R2_001.tsv

value: Carolina Biologicals


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Gut_individual26

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_26_Gut_dsDNMT1_BS_S8_R1_001
processed data file:
allc_TS_26_Gut_dsDNMT1_BS_S8_R1_001.tsv

source_name: Gut


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Ovary_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Ovary_dsDNMT1_BS_S2_R1_001
processed data file:
allc_TS_16_Ovary_dsDNMT1_BS_S2_R1_001.tsv

value: Ovary


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R1_Head_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Head_dsDNMT1_BS_S6_R1_001
processed data file:
allc_TS_16_Head_dsDNMT1_BS_S6_R1_R2_001.tsv

value: Head


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R2_Head_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Head_dsDNMT1_BS_S6_R2_001
processed data file:
allc_TS_16_Head_dsDNMT1_BS_S6_R1_R2_001.tsv


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_R1_Head_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Head_dsDNMT1_BS_S7_R1_001
processed data file:
allc_TS_24_Head_dsDNMT1_BS_S7_R1_R2_001.tsv


title: Juvenile cortex N1710-82Q, biological rep2

source_name: Prefrontal cortex N1710-82Q

value: Prefrontal cortex

value: Transgenic (HD)


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Gut_individual24

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_24_Gut_dsDNMT1_BS_S7_R1_001
processed data file:
allc_TS_24_Gut_dsDNMT1_BS_S7_R1_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R2_Thorax_individual34

description:
11 days post-injection of buffer (control)
TS_34_Throax_buffer_BS_S4_R2_001
processed data file:
allc_TS_34_Thorax_buffer_BS_S4_R1_R2_001.tsv


title: Oncopeltus_fasciatus_ds-dnmt1_MethylC-seq_Gut_individual16

description:
11 days post-RNAi injection targeting Dnmt1 (treatment)
TS_16_Gut_dsDNMT1_BS_S6_R1_001
processed data file:
allc_TS_16_Gut_dsDNMT1_BS_S6_R1_001.tsv


title: Juvenile cortex N1710-82Q, biological rep3


title: Juvenile cortex wt (control for 82Q), biological rep2

source_name: Prefrontal cortex wt (control for 82Q)


title: Juvenile cortex N1710-82Q, biological rep1


title: Juvenile cortex wt (control for 82Q), biological rep1


title: Juvenile cerebellum R6/1, biological rep3

source_name: Cerebellum R6/1

value: Cerebellum

value: 7.5 weeks


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R1_Thorax_individual34

description:
11 days post-injection of buffer (control)
TS_34_Throax_buffer_BS_S4_R1_001
processed data file:
allc_TS_34_Thorax_buffer_BS_S4_R1_R2_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R2_Head_individual34

description:
11 days post-injection of buffer (control)
TS_34_Head_buffer_BS_S9_R2_001
processed data file:
allc_TS_34_Head_buffer_BS_S9_R1_R2_001.tsv


title: Juvenile cerebellum wt (control for R6/1), biological rep3

source_name: Cerebellum wt (control for R6/1)

value: Male


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Ovary_individual34

description:
11 days post-injection of buffer (control)
TS_34_Ovary_buffer_BS_S4_R1_001
processed data file:
allc_TS_34_Ovary_buffer_BS_S4_R1_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R1_Head_individual34

description:
11 days post-injection of buffer (control)
TS_34_Head_buffer_BS_S9_R1_001
processed data file:
allc_TS_34_Head_buffer_BS_S9_R1_R2_001.tsv


title: Juvenile cerebellum wt (control for R6/1), biological rep2


title: Juvenile cerebellum R6/1, biological rep1


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Gut_individual34

description:
11 days post-injection of buffer (control)
TS_34_Gut_buffer_BS_S9_R1_001
processed data file:
allc_TS_34_Gut_buffer_BS_S9_R1_001.tsv

value: Gut


title: Juvenile cortex wt (control for 82Q), biological rep3


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Ovary_individual2

description:
11 days post-injection of buffer (control)
TS_2_Ovary_buffer_BS_S1_R1_001
processed data file:
allc_TS_2_Ovary_buffer_BS_S1_R1_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Thorax_individual2

description:
11 days post-injection of buffer (control)
TS_2_Thorax_buffer_BS_S3_R1_001
processed data file:
allc_TS_2_Thorax_buffer_BS_S3_R1_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R2_Head_individual2

description:
11 days post-injection of buffer (control)
TS_2_Head_buffer_BS_S5_R2_001
processed data file:
allc_TS_2_Head_buffer_BS_S5_R1_R2_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R1_Head_individual2

description:
11 days post-injection of buffer (control)
TS_2_Head_buffer_BS_S5_R1_001
processed data file:
allc_TS_2_Head_buffer_BS_S5_R1_R2_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R1_Gut_individual2

description:
11 days post-injection of buffer (control)
TS_2_Gut_buffer_BS_S1_R1_001
processed data file:
allc_TS_2_Gut_buffer_BS_S1_R1_R2_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R2_Gut_individual2

description:
11 days post-injection of buffer (control)
TS_2_Gut_buffer_BS_S1_R2_001
processed data file:
allc_TS_2_Gut_buffer_BS_S1_R1_R2_001.tsv


title: Juvenile cerebellum R6/1, biological rep2


title: Juvenile hippocampus R6/1, biological rep1

source_name: Hippocampus R6/1

value: Hippocampus


title: Juvenile hippocampus wt (control for R6/1), biological rep3

source_name: Hippocampus wt (control for R6/1)


title: Juvenile hippocampus wt (control for R6/1), biological rep1


title: Juvenile striatum R6/1, biological rep3

source_name: Striatum R6/1


title: Juvenile cerebellum wt (control for R6/1), biological rep1


title: Juvenile hippocampus R6/1, biological rep2


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R2_Thorax_individual1

description:
11 days post-injection of buffer (control)
TS_1_Throax_buffer_BS_S2_R2_001
processed data file:
allc_TS_1_Thorax_buffer_BS_S2_R1_R2_001.tsv


title: Oncopeltus_fasciatus_buffer_MethylC-seq_R1_Thorax_individual1

description:
11 days post-injection of buffer (control)
TS_1_Throax_buffer_BS_S2_R1_001
processed data file:
allc_TS_1_Thorax_buffer_BS_S2_R1_R2_001.tsv


title: Juvenile hippocampus R6/1, biological rep3


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Head_individual1

description:
11 days post-injection of buffer (control)
TS_1_Head_buffer_BS_S11_R1_001
processed data file:
allc_TS_1_Head_buffer_BS_S11_R1_001.tsv


title: Juvenile hippocampus wt (control for R6/1), biological rep2


title: Juvenile striatum wt (control for R6/1), biological rep3

source_name: Striatum wt (control for R6/1)


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Gut_individual1

description:
11 days post-injection of buffer (control)
TS_1_Gut_buffer_BS_S5_R1_001
processed data file:
allc_TS_1_Gut_buffer_BS_S5_R1_001.tsv


title: Oncopeltus_fasciatus_dsRED_RNA-seq_biological_rep_2_of_3

description:
11 days post-RNAi injection targeting RED (control)
B2_8_dsRED_11day_RNA_S2_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

data_processing:
Gene expression. Raw RNA-seq FASTQ reads were trimmed for adapters and preprocessed to remove low-quality reads using Trimmomatic v0.33 (arguments: LEADING:10 TRAILING:10 MINLEN:30) prior to mapping to the O. fasciatus v1.1 genome assembly. Reads were mapped using TopHat v2.1.1 supplied with a reference General Features File (GFF) to the O. fasciatus v1.1 genome assembly, and with the following arguments: -I 20000 --library-type fr-firststrand --b2-very-sensitive.
Genome_build: O. fasciatus: v1.1 (https://www.hgsc.bcm.edu/arthropods/i5k), B. germanica: v1 (https://www.hgsc.bcm.edu/arthropods/i5k)
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers.

source_name: Ovary_individual 8

extract_protocol:
Ovaries were removed from each female, flash frozen in liquid nitrogen and stored at -80°C until processing. Total RNA and genomic DNA was extracted from pairs of ovaries (from a single female) using a Qiagen RNAeasy micro kit (Qiagen, Venlo, The Netherlands) per manufacturer’s instructions with Qiagen Qiazol as the lysis buffer. Complementary DNA (cDNA) was synthesized from 500 ng RNA with qScript cDNA SuperMix (Quanta Biosciences, Gaithersburg, MD).
DNA methylation. MethylC-seq libraries were prepared using the protocol described in Urich et al. (2015; doi:10.1038/nprot.2014.114). Lambda phage DNA was used as a control for the sodium bisulfite non-conversion rate. Gene expression. RNA-seq libraries for RNA extracted from three DNMT1 knocked down and three control individuals were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.


title: Oncopeltus_fasciatus_dsRED_RNA-seq_biological_rep_3_of_3

description:
11 days post-RNAi injection targeting RED (control)
B2_9_dsRED_11day_RNA_S3_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

source_name: Ovary_individual 9


title: Oncopeltus_fasciatus_buffer_MethylC-seq_Ovary_individual1

description:
11 days post-injection of buffer (control)
TS_1_Ovary_buffer_BS_S1_R1_001
processed data file:
allc_TS_1_Ovary_buffer_BS_S1_R1_001.tsv


title: Tfh from TONS 3 [gene-level]

description:
Gene expression from tonsil CD4 Tfh cells
Tfh3.CEL

source_name: Ex-vivo Tfh cells

value: Tonsillectomy

value: Untreated


title: Juvenile striatum R6/1, biological rep1

value: Striatum


title: Juvenile striatum wt (control for R6/1), biological rep2

value: wild type


title: Tfh from TONS 2 [gene-level]

description:
Gene expression from tonsil CD4 Tfh cells
Tfh2.CEL


title: Oncopeltus_fasciatus_dsDNMT1_RNA-seq_biological_rep_3_of_3

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2_17_dsDMNT1_11day_RNA_S6_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

source_name: Ovary_individual 17


title: Oncopeltus_fasciatus_dsDNMT1_RNA-seq_biological_rep_1_of_3

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2_13_dsDMNT1_11day_RNA_S4_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

source_name: Ovary_individual 13


title: Oncopeltus_fasciatus_dsDNMT1_RNA-seq_biological_rep_2_of_3

description:
11 days post-RNAi injection targeting DNMT1 (treatment)
B2_14_dsDMNT1_11day_RNA_S5_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

source_name: Ovary_individual 14


title: Trichoplax_iChip_H3K4me3

organism: Trichoplax adhaerens

source_name: Adult placozoan

tag: stage/cell type

value: Adult

value: Wild type

tag: chip antibody

value: anti-H3K4me3:Millipore #07-473


title: Memory T CD4 from TONS 2 [gene-level]

description:
Gene expression from tonsil naive CD4 T cells
N2.CEL

source_name: Ex-vivo memory CD4 T cells


title: Juvenile striatum R6/1, biological rep2


title: Juvenile cortex R6/1, biological rep3

source_name: Prefrontal cortex R6/1


title: Juvenile cortex R6/1, biological rep1


title: Juvenile striatum wt (control for R6/1), biological rep1


title: Juvenile cortex wt (control for R6/1), biological rep1

source_name: Prefrontal cortex wt (control for R6/1)


title: Juvenile cortex wt (control for R6/1), biological rep3


title: Juvenile cortex R6/1, biological rep2


title: Memory  T CD4 from TONS 3 [gene-level]

description:
Gene expression from tonsil naive CD4 T cells
N3.CEL


title: Juvenile cortex wt (control for R6/1), biological rep2


title: RNA seq - PEN- WT

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
processed data file: normalized_RNA_seq.csv
Sample name in processed data file: Sample 6

data_processing:
RNA-seq reads of each sample were mapped using the STAR_2.4.0i with default parameters.
Gene expression was called by featureCounts v1.5.0-p1. Normalization between the samples was based on the proportionality of the numbers of the mapped reads, and normalized counts are further log2 transformed with the trimming of minimal counts to 10.
Genome_build: hg19
Supplementary_files_format_and_content: text file with the log2 normalized read count.

source_name: Hepatocarcinoma cell

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq samples, cells were treated with 30μM of PEN, PEN-MUT, PEN-WT, or PEN-FFW for 8hrs

tag: cell type

value: Hepatocarcinoma

value: SNU398 was treated with 30uM PEN-WT  peptides for 8hrs


title: RNA seq - PEN-MUT

description:
processed data file: normalized_RNA_seq.csv
Sample name in processed data file: Sample 5

value: SNU398 was treated with 30uM PEN-MUT  peptides for 8hrs


title: RNA seq - PEN- FFW

description:
processed data file: normalized_RNA_seq.csv
Sample name in processed data file: Sample 7

value: SNU398 was treated with 30uM PEN-FFW peptides for 8hrs


title: Tfh from TONS 1 [gene-level]

description:
Gene expression from tonsil CD4 Tfh cells
Tfh1.CEL


title: Memory  T CD4 from TONS 1 [gene-level]

description:
Gene expression from tonsil naive CD4 T cells
N1.CEL


title: Oncopeltus_fasciatus_dsRED_RNA-seq_biological_rep_1_of_3

description:
11 days post-RNAi injection targeting RED (control)
B2_5_dsRED_11day_RNA_S1_R1_001
GSE109199_ovary.RNAprocessed.ds-dnmt1_13_14_17.control_5_8_9.xlsx

source_name: Ovary_individual 5

value: Ovary

value: Adult female post-mating

value: Carolina Biologicals


title: Trichoplax_iChip_H3K4me2

value: anti-H3K4me2:Abcam #ab3236


title: SNU398 Input

data_processing:
The paired-end ChIP-seq reads are mapped by bowtie2 to the human reference genome GRCh38 (hg38).
PCR duplicates are filtered out from the resulting BAM files using samtools rmdup.
Alignments with mapping quality below 20 are also filtered out.
Peak calling is performed by macs2. The options for calling SALL4 peaks are: macs2 callpeak -g hs -B -q 0.05.
For calling histone mark peaks, the options are: macs2 callpeak —broad -g hs —broad-cutoff 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. The ChIP-seq signal will be shrunk to fit the size of its control if the control is smaller in size.

extract_protocol:
Cell were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 100 to 500 base pair and protein-DNA complexes were pulled down by antbodies
Libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing

value: none (input)


title: Oncopeltus_fasciatus_dsRED_MethylC-seq_fastq_4_of_4

description:
11 days post-RNAi injection targeting RED (control)
B2-5-dsRED-day-11-deep_S1_L004_R1_001

data_processing:
DNA methylation. Reads generated from MethylC-seq were aligned to the O. fasciatus v1.1 genome assembly or B. germanica v1 genome assembly using the latest version of methylpy (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). MethylC-seq analysis was performed as described in Schmtiz et al. (2013; doi:10.1101/gr.152538.112).
Genome_build: O. fasciatus: v1.1 (https://www.hgsc.bcm.edu/arthropods/i5k), B. germanica: v1 (https://www.hgsc.bcm.edu/arthropods/i5k)
Supplementary_files_format_and_content: Tab delimited; please see metadata file for column headers.

source_name: Ovary


title: SNU398 H3K27Ac ChIP