title: SNC: L4 DRG sciatic nerve crush

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

description: single cell

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: matrix.mtx, barcodes.tsv, genes.tsv

source_name: L4 DRG sciatic nerve crush

extract_protocol:
Whole DRG’s were dissociated with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 40-micron cell strainer and FACS sorted using live/dead staining. Sorted cells were loaded on the 10X Chromium system.
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.  Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/). libraries were then constructed using standard instrutions of the 10x plaform.

treatment_protocol: 3 days post sciatic nerve crush, dorsal root crush and spinal cord injury

value: Dorsal root ganglion (L4)

value: 8-12 weeks

value: sciatic nerve crush


title: LV3R4R DMSO-treated rep 1

status: Public on Sep 12 2021

type: SRA

city: La Jolla

first: Robert

last: Rissman

state: California

address: 9500 Gillman Drive

country: USA

institute: University of California, San Diego

description:
3R4R_only_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

library_source: transcriptomic

data_processing:
Paired-end FASTQ files. Extra sequencing was done on another lane to add sequencing depth; this can be found in the "L001" files, which can be merged with corresponding the "L004" files. In the raw file name, the lentiviral infection is listed (ex. "3R", "4R", "3R4R", "Ctrl"), then the treatment ("AB" = amyloid beta; "only" = DMSO), then the biological replicate ("1", "2", or "3"). "R1" and "R2" are the different paired-end files.
FastQC was run before and after adapter trimming with Bbduk (BBMap_38.73).
FASTQ files were mapped to the GRCh38 human reference genome available from Ensembl using STAR 2.7.3a and release number 98 of the GTF.
featureCounts (Subread 1.6.4) was used to determine gene counts, which were then analyzed for differential expression using DESeq (1.26.0).
GO analysis was carried out using clusterProfileR.
For transposable element quantification and analysis, TEcounts (2.0.3) was used for a global view of transposable element expression (i.e. not at locus level), while TElocal (0.1.0) was used to analyze locus-level differential expression of transposable elements. Both programs are available from Molly Hammell's lab at Cold Spring Harbor Laboratory. Genome indices and GTFs for GRCh38 that are custom-made by the Hammell lab were used in analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing gene counts output from featureCounts. File is called "featurecounts_matrix.txt".
Supplementary_files_format_and_content: csv file containing raw counts for both genes and transposable elements from TEcount. File is "TEcount_cells_raw_counts_all.csv".
Supplementary_files_format_and_content: csv file containing raw counts of only transposable elements from TEcount. File is "TEcount_cells_raw_counts_TEs_only.csv".
Supplementary_files_format_and_content: csv file containing raw counts for both genes and transposable elements from TElocal. File is "TElocal_cells_raw_counts_all.csv".
Supplementary_files_format_and_content: csv file containing raw counts of only transposable elements from TElocal. File is "TElocal_cells_raw_counts_TEs_only.csv".

molecule: polyA RNA

organism: Homo sapiens

source_name: Neuroblastoma SHSY-5Y cells

growth_protocol: Undifferentiated SY5Y cells underwent fewer than 20 passages, were passaged weekly, and were maintained with media composed of 10% fetal bovine serum and a 1:1 mixture of Eagle’s Minimum Essential Medium (MEM) and Ham’s F12 (F12).

extract_protocol:
Cells were gently scraped and RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentiviral infection with respective tau or control lentiviruses at MOI 20 at time of plating. Following plating, cells were differentiated into neurons and fed daily using 15 nM retinoic acid in 1:1 MEM:F12 with 3% fetal bovine serum. For 24 hours prior to collection, cells were incubated with either 50nM amyloid-beta oligomers or 50 nM DMSO (as a control).

tag: cell type

value: Retinoic acid-differentiated SHSY-5Y cells

tag: lentiviral infection

value: 0N3R and 1N4R tau lentivirus (1:1), MOI 20 each at time of plating

tag: agent

value: DMSO (Control group) for 24 hours prior to collection


title: Keratinocytes_baby_rep1

type: RNA

city: Val-de-Reuil

first: Cécilia

last: Brun

address: Campus de Maigremont

department: Translational Science - Essential Health

country: France

institute: Johnson & Johnson Santé Beauté France

hyb_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.

data_processing: A background correction followed by a quantile normalization (QN) was applied using the RMA framework as implemented in the limma R package. Quality-check was performed to properly evaluate the impact of the QN and filtering using extensive data visualization before and after normalization.

molecule: total RNA

source_name: Keratinocytes - Foreskin

growth_protocol: Human primary keratinocytes were provided by Sterlab (Sophia Antipolis, France) from 6 baby and 6 adult volunteers. Briefly, keratinocytes were isolated from foreskin and from abdominoplasty, for babies and adults respectively. Then, Keratinocytes were cultured in KGM gold basal medium supplemented with KGM-Gold Keratinocyte SingleQuots Kit (Lonza).

extract_protocol: One passage after thawing, RNAs were extracted using RNeasy 96 QIAcube HT Kit (Qiagen) and supernatants were collected.

tag: gender

value: Male

tag: age

value: Baby

tag: tissue

value: Keratinocytes - Foreskin


title: pro-B cell line transfected with empty vector rep1

city: Isehara

first: Katsuto

last: Hozumi

state: Kanagawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai University School of Medicine

hyb_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent), according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

scan_protocol: Scaned using microarray scanner G2690D

data_processing: All scanned images were analyzed using Agilent feature extraction software (v11.5.1.1). Raw data were imported with GeneSpring GX software (v14.9, Agilent Technologies, CA, USA) with adapted by 75 percentile shift normalization

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the Low Input Quick Amp WT Labeling Kit, One-Color*3 (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using NucleoSpin RNA XS (Takara, Japan) and quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: B cell line


title: LV4R DMSO-treated rep 3

description:
4R_only_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 1N4R tau lentivirus, MOI 20 at time of plating


title: HSC3_siDLEU1_H3K4me3

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

library_source: genomic

data_processing:
Basecalls and alignment to the hg19 genome assembly were performed by Torrent Suite software.
Peakcalling and creation of bedgraph files were perfomed by MACS2 software.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

source_name: HSC3 cells

growth_protocol: HSC3 cells were maintained in RPMI supplemented with 10% fatal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library construction was performed according to the manufacturer's instructions. Briefly, input DNA or the immunoprecipitate was ligated to adapters and PCR amplified using a Ion Plus Fragment Library Kit (Thermo Fisher Scientific). Template preparation and chip loading were carried out using a Ion Chef System (Thermo Fisher Scientific).

treatment_protocol: HSC3 cells were transfected with siDLEU1 or Control siRNA for 72 hours.

tag: cell line

value: HSC3 cells

value: oral squamous cell carcinoma

tag: chip-antibody

value: H3K4me3 (Upstate, clone MC315)

tag: sirna

tag: transfection

value: HSC3 cells transfected with siDLEU1


title: Keratinocytes_adult_rep6

scan_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.

source_name: Keratinocytes - Abdominoplasty

value: Female

value: Adult

value: Keratinocytes - Abdominoplasty


title: LV4R DMSO-treated rep 2

description:
4R_only_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: HSC3_siDLEU1_H3K27ac

value: H3K27ac (Active Motif, #39133)


title: Keratinocytes_adult_rep5

label_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.


title: HSC3_siDLEU1_Input


title: Keratinocytes_adult_rep4


title: DRC: L4 DRG dorsal root crush

description: single cell

source_name: L4 DRG dorsal root crush

tag: strain

value: Dorsal root ganglion (L4)

value: 8-12 weeks

tag: treatment

value: dorsal root crush


title: SCI2: L4 DRG spinal cord injury

description: single cell

source_name: L4 DRG spinal cord injury

value: spinal cord injury


title: HSC3_siCONT_H3K27ac

value: siCONT

value: HSC3 cells transfected with siCONT


title: 155A

city: Tucson

first: Ritu

last: Pandey

state: Arizona

address: 1515 N Campbell Ave.,

department: Cellular and Molecular Medicine, Arizona Cancer Center

institute: University of Arizona

data_processing:
Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark.
Differential methylation was estimated using MethylKit (v. 1.11)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Text file containg percent methylation scores of bisulfite converted cytosines (T’s, unmethylated C’s) and  non-converted Cs (methylated C’s)

source_name: Organoid

extract_protocol: none provided by the submitter

value: prostate

value: organoid

value: Control


title: HSC3_siCONT_H3K4me3

value: HSC3 cells


title: Keratinocytes_adult_rep3


title: DRC2: L4 DRG dorsal root crush

description: single cell


title: LV3R DMSO-treated rep 2

description:
3R_only_2
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: Retinoic acid-differentiated SHSY-5Y cells

value: 0N3R tau lentivirus, MOI 20 at time of plating

value: DMSO (Control group) for 24 hours prior to collection


title: LV3R DMSO-treated rep 1

description:
3R_only_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: Keratinocytes_adult_rep1

value: Female


title: HSC3_siCONT_Input

value: oral squamous cell carcinoma


title: SCI: L4 DRG spinal cord injury

description: single cell


title: LV3R DMSO-treated rep 3

description:
3R_only_3
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv


title: H3K27ac_HiChIP_OCI-Ly7_control_rep2

status: Public on Sep 11 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
LY7_H3K27ac_control7
Control replicate 2

data_processing:
Library strategy: HiChIP
HiC-Pro was used for aligning reads and generated contact maps.
mcool files were generated from validPairs files using "cooler" as part of the HiC-Pro pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Contact maps provided as mcool files.
Supplementary_files_format_and_content: LY7_H3K27ac_controlpooled_5000.mcool: This file represents processed files for pooled replicates samples: H3K27ac_HiChIP_OCI-Ly7_control_rep1, H3K27ac_HiChIP_OCI-Ly7_control_rep2, and H3K27ac_HiChIP_OCI-Ly7_control_rep3.
Supplementary_files_format_and_content: LY7_H3K27ac_OCABipooled_5000.mcool: This file represents processed files for pooled replicates samples: H3K27ac_HiChIP_OCI-Ly7_OCABi_rep1, H3K27ac_HiChIP_OCI-Ly7_OCABi_rep2.

growth_protocol: OCI-Ly7 cells were cultured in medium containing 80% Iscove’s Modified Dulbecco’s Medium with 20% FBS, 1% glutamine, and 1% penicillin/streptomycin. CRISPRi cells were generated by lentiviral transduction of pHR-SFFV-dCas9-BFP-KRAB (46911, Addgene).

extract_protocol:
H3K27ac HiChIP was performed using 10 million cells.
Following biotin pull-down, samples were tagmented with Tn5 and libraries were generated using 6-8 cycles of PCR amplifications. After dual size selection with Ampure XP beads, libraries size was measured by BioAnalyzer.
HiSeq4000 platform on PE50 mode.

treatment_protocol: gRNA constructs targeting POU2AF1 or non-targeting controls were lentivirally transduced into OCI-Ly7 CRISPRi cell lines.

value: control non-targeting sgRNAs

tag: transgene

tag: hichip pulldown


title: LV4R DMSO-treated rep 1

description:
4R_only_1
Ensembl_Reversely_stranded.txt
TEcount_cells_raw_counts_all.csv
TEcount_cells_raw_counts_TEs_only.csv
TElocal_cells_raw_counts_all.csv
TElocal_cells_raw_counts_TEs_only.csv

value: 1N4R tau lentivirus, MOI 20 at time of plating


title: Keratinocytes_adult_rep2

value: Adult

value: Keratinocytes - Abdominoplasty


title: H3K27ac_HiChIP_OCI-Ly7_OCABi_rep2

description:
LY7_H3K27ac_OCABi2
OCAB knockdown replicate 2

value: sgRNAs targeting OCAB (POU2AF1)


title: H3K27ac_HiChIP_OCI-Ly7_OCABi_rep1

description:
LY7_H3K27ac_OCABi1
OCAB knockdown replicate 1


title: Ca9-22 with a control vector

description: Ca9-22 with a control vector

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: Ca9-22 cells were cultured in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Ca9-22 cells were infected with a DLEU1 lentiviral vector or a control vector and selected with 6mg/ml of Blasticidin for 2 weeks.

tag: vector

value: control


title: Ca9-22 with a DLEU1 vector

description: Ca9-22 with a DLEU1 vector


title: NAI2: L4 DRG uninjured

description: single cell

source_name: L4 DRG uninjured

value: Dorsal root ganglion (L4)

value: 8-12 weeks

value: uninjured


title: H3K27ac_HiChIP_OCI-Ly7_control_rep3

description:
LY7_H3K27ac_control8
Control replicate 3


title: OCI-Ly7_OCT2i_rep6

description:
Sample_LY7_OCT2i_4_s0
mRNA

data_processing:
Read adapter trimming using fastp.
Transcript quantification with decoy-aware transcriptome using Salmon version 1.5.1.
Genome_build: GRCh38.p13; Transcriptome build Gencode Release 38.
Supplementary_files_format_and_content: Salmon quant.sf files containing transcript quantifications.

growth_protocol: OCI-Ly7 cells were cultured in medium containing 80% Iscove’s Modified Dulbecco’s Medium with 20% FBS, or 90% RPMI-1640 with 10% FBS (SU-DHL-4), each supplemented with 1% glutamine and 1% penicillin/streptomycin. CRISPRi cells were generated by lentiviral transduction of pHR-SFFV-dCas9-BFP-KRAB (46911, Addgene).

extract_protocol:
Trizol
Illumina TruSeq stranded mRNA.
Paired-end

treatment_protocol: gRNA constructs targeting POU2F2, POU2AF1, or non-targeting controls were lentivirally transduced into OCI-Ly7 or SU-DHL-4 CRISPRi cell lines.

tag: crispri knock down

tag: batch


title: OCI-Ly7_OCT2i_rep5

description:
Sample_LY7_OCT2i_3_s0
mRNA


title: SUDHL4_OCT2i_rep2

description:
su4.oct2.3
mRNA


title: OCI-Ly7_OCT2i_rep2

description:
Sample_LY7_OCT2i2_s2
mRNA


title: OCI-Ly7_OCT2i_rep7

description:
Sample_LY7_OCT2i_s2
mRNA


title: OCI-Ly7_OCT2i_rep8

description:
Sample_LY7_OCT2i_s3
mRNA


title: OCI-Ly7_OCT2i_rep4

description:
Sample_LY7_OCT2i_2_s0
mRNA


title: OCI-Ly7_OCT2i_rep3

description:
LY7_OCT2i_48h
mRNA


title: OCI-Ly7_OCT2i_rep1

description:
Sample_LY7_OCT2_3_s1
mRNA


title: H3K27ac_HiChIP_OCI-Ly7_control_rep1

description:
LY7_H3K27ac_control10
Control replicate 1


title: NAI: L4 DRG uninjured

description: single cell


title: OCI-Ly7_control_rep7

description:
Sample_LY7_sg81_s0
mRNA


title: OCI-Ly7_control_rep9

description:
Sample_LY7_sg81_s3
mRNA


title: OCI-Ly7_control_rep8

description:
Sample_LY7_sg81_s2
mRNA


title: Differentially expressed genes by knocking down of HELLS in EBC-1

city: Kagoshima

first: Kengo

last: Tanigawa

address: 8-35-1 Sakuragaoka

department: Pulmonary Medicine

institute: Kagoshima university

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (5188-5242: Agilent) and Gene Expression Wash Pack (5187-5327: Agilent) according to manufacturer protocols.

scan_protocol: Microarray slides were scanned with Agilent SureScan Microarray Scanner G4900DA (Agilent Technologies). Images were quantified using Feature Extraction 12. 1. 1. 1.

data_processing: Data was analyzed by GeneSpring ver. 14.9.1. LOWESS normalization for microarray was performed.

source_name: mock

label_protocol: Starting with 100 ng total RNA, amplification and labeling with Cy3 or Cy5 was performed using the Low Input Quick Amp Labeling Kit Two-Color (5190-2306: Agilent).

growth_protocol: Normal cell culture medium RPMI 1640 or EMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell type

value: lung squamous cell carcinoma

value: no transfection

source_name: si-HELLS-3 transfected cell line

value: si-HELLS-3 transfection


title: SUDHL4_OCT2i_rep1

description:
su4.oct2.2
mRNA


title: OCI-Ly7_OCABi_rep5

description:
Sample_LY7_OCABi_s0
mRNA


title: OCI-Ly7_OCABi_rep4

description:
LY7.OCABi.D
mRNA


title: OCI-Ly7_OCABi_rep3

description:
LY7.OCABi.48hrs
mRNA


title: OCI-Ly7_control_rep3

description:
LY7.sg81.48hrs
mRNA

value: Control


title: OCI-Ly7_OCABi_rep6

description:
Sample_LY7_OCABi_s2
mRNA


title: OCI-Ly7_OCABi_rep2

description:
LY7.OCABi.B
mRNA


title: SUDHL4_control_rep2

description:
SU4.sg81b
mRNA


title: Differentially expressed genes by knocking down of HELLS in SK-MES-1


title: SUDHL4_control_rep1

description:
SU4.sg81a
mRNA


title: OCI-Ly7_control_rep2

description:
LY7.sg81b
mRNA


title: SUDHL4_OCABi_rep1

description:
SU4.OCABi.Aa
mRNA


title: 3x_mrc1_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Cells in ethanol (1-3x107 per plug) were pelleted in round bottom 2 ml tubes by centrifuging 30 s 20,000 g, washed once in 1 ml PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) and resuspended in 60 µl same with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH7, 50% glycerol, Merck >2000 U/mg L2524). Samples were heated to 50°C for 1-10 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE was buffer containing 10 µl 17 U/µl lyticase and incubated 1 hour at 37°. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE Plugs were stored in 1xTE.

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified %reverse reads in 1kb windows
Genome_build: S. cerevisiae R64-1-1
TrAEL-seq report: A tab delimited Seqmonk annotated probe report. The quantification show % reverse reads in 1% windows.

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
1/2 an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

value: yeast

tag: growth media

value: SC 2percent glucose

tag: fixed/unfixed

value: Fixed - 70percent ethanol


title: SUDHL4_OCABi_rep2

description:
SU4.OCABi.Ab
mRNA


title: 3x_mrc1_1


title: 3x_2


title: OCI-Ly7_OCABi_rep1

description:
LY7.OCABi.A
mRNA


title: CH12 T9 C unsorted

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
library strategy: CRISPR seq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the mTKO FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

source_name: B cells

growth_protocol: CH12F3-2 cells were cultured in RPMI (as indicated) supplemented with 10%FBS and 1x P/S and 50uM BME

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) or QIAamp DNA mini kit according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

treatment_protocol: Cells transduced with mTKO were treated with C.I.T cocktail for 3 days,and stained for surface expression of IgA, followed by FACS sorting to separates IgA+ from IgA- populations.

tag: crispr library

value: mTKO

value: CIT treatment and unsorted

value: RPMI+10% FBS+1XP/S+50uM BME

tag: molecule subtype

value: gRNA amplicon


title: CH12 T9 B unsorted


title: CH12 T9 A unsorted


title: OCI-Ly7_control_rep1

description:
LY7.sg81a
mRNA


title: OCI-Ly7_OCABi_rep2 [ATAC-seq]

data_processing:
Complete processing pipeline available at https://github.com/DoaneAS/atacflow
Read adapter trimming using ngtrim.
Alignment to GRCh38 using bowtie2.
PCR duplicate removal by piccard tools.
Peak calling using genrich.
Genome_build: GRCh38
Supplementary_files_format_and_content: NarrowPeak files contain ATAC-seq peaks.
Supplementary_files_format_and_content: bigWig files contain binned ATAC-seq fragments normalized to reads in peaks using a consensus peak atlas.

extract_protocol:
Omni-ATAC-seq https://www.nature.com/articles/nmeth.4396
Illumina Nextera per protocol https://www.nature.com/articles/nmeth.4396
Paired-end


title: OCI-Ly7_Control_rep3 [ATAC-seq]

value: Non-targeting Control


title: OCI-Ly7_OCABi_rep3 [ATAC-seq]


title: OCI-Ly7_OCABi_rep1 [ATAC-seq]


title: SUDH4_Control_rep1 [ATAC-seq]


title: OCI-Ly7_OCT2i_rep1 [ATAC-seq]


title: CH12 T9 B IgA-

value: CIT treatment and FACS sorted, IgA-


title: OCI-Ly7_Control_rep2 [ATAC-seq]


title: CH12 T9 A IgA-


title: OCI-Ly7_OCABi_rep4 [ATAC-seq]


title: 3x_1


title: OCI-Ly7_Control_rep1 [ATAC-seq]


title: CH12 T9 C IgA+

value: CIT treatment and FACS sorted, IgA+


title: GCT0085

type: genomic

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
tumor DNA from germ cell tumor specimen
8942351030_R03C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Data was analyzed using the minfi package in R. All samples were quantile normalized together using preprocessQuantile(). Probes with snps were removed with getSnpInfo() and  dropLociWithSnps(quanNormAll, snps = c("SBE","CpG"), maf = 0). Beta values were extracted from normalize data with getBeta(). Identificatuon of DMRs was done with bumphunter() using type = "Beta", B = 200 nullMethod = "bootstrap" and cutoffs specific to the test.
Quantile normalized Beta value for each probe
Quantile normalized probe value for each probe

label: cy3, cy5

source_name: tumor DNA

label_protocol: Standard Illumina Protocol

extract_protocol: FFPE slides extracted with Zymo PinPoint Slide DNA isolation kit

tag: Sex

value: male

tag: tumor histology

value: MMGCT

tag: tumor location

value: Testis

tag: age at diagnosis

tag: tissue type

value: Frozen


title: SUDH4_Control_rep2 [ATAC-seq]

tag: cell line


title: GCT0109

description:
tumor DNA from germ cell tumor specimen
8942351030_R04C01


title: CH12 T9 B IgA+

tag: treatment


title: GCT0089

description:
tumor DNA from germ cell tumor specimen
8942351030_R02C02

value: female

value: Germinoma

value: Ovary


title: CH12 T9 C IgA-


title: CH12 T9 A IgA+


title: SUDH4_OCT2i_rep2 [ATAC-seq]


title: GCT0090

description:
tumor DNA from germ cell tumor specimen
8942351030_R02C01


title: GCT0091

description:
tumor DNA from germ cell tumor specimen
8942351030_R01C02


title: SUDH4_OCABi_rep2 [ATAC-seq]


title: SUDH4_OCABi_rep1 [ATAC-seq]


title: GCT0093

description:
tumor DNA from germ cell tumor specimen
8942351029_R06C01


title: GCT0097

description:
tumor DNA from germ cell tumor specimen
8942351029_R05C02


title: GCT0106

description:
tumor DNA from germ cell tumor specimen
8942351029_R06C02


title: OCI-Ly7_OCT2i_rep2 [ATAC-seq]


title: GCT0095

description:
tumor DNA from germ cell tumor specimen
8942351029_R05C01

value: Extragonadal


title: GCT0104

description:
tumor DNA from germ cell tumor specimen
8942351029_R04C02


title: SUDH4_OCT2i_rep1 [ATAC-seq]


title: IMR5 LP MOI 2 CHD5 MOI 5_rep 2

city: Ulm

first: Christian

last: Beltinger

address: Eythstr. 24

department: Dept. of Pediatrics and Adolescent Medicine

country: Germany

institute: University Medical Center Ulm

data_processing:
Sequencing reads were aligned to the hg38 genome using bowtie2 (v 2.3.5.1)
Aligned files were sorted using samtools sort (version 1.9) and read counting was performed using htseq-count from htseq (v 0.9.1)
Genome_build: hg38
Supplementary_files_format_and_content: readcounts

growth_protocol: Cells were cultured (typically ~5 × 10^6 cells into a T75 flask) on uncoated plastic in RPMI 1640 medium (Gibco, #31870025) supplemented with 20% FCS, 1% Penicillin/Streptomycin and 1% L-Glutamine.

extract_protocol:
4 x 10^6 cells were seeded on 10cm culture dishes and grown over night. RNA was harvested using Trizol reagent and further isolated with the Direct-zol RNA MiniPrep Kit (Zymo, #R2050).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were constantly selected with 9,75 µg/mL Blasticidin.

value: neuroblastoma-derived cell line

tag: primary site

value: Abdomen

tag: genotype

value: CHD5 overexpressing


title: IMR5 LP MOI 2 CHD5 MOI 5_rep 3


title: B182: dsRdRP3_rep3

city: NARA

first: Katsutomo

last: Okamura

address: 8916-5 Takayama, Ikoma, NARA 630-0192 JAPAN

institute: Nara Institute of Science and Technology

description: Total RNAseq data, library construction using  stranded TruSeq mRNA Library Prep Kit (Illumina), sequencing on Hiseq4000.

data_processing:
The adaptor sequences were trimmed using Cutadapt (version 1.18) with the default quality cutoff value (20).
Gene expression was quantified by salmon (v1.5.0) using the Vectorbase IscaI1.0 annotation
Differential gene expression analysis was done using DESeq2 package (version 1.26.0), with cut-off adjusted-p value set to 0.05.
genome build: Vectorbase IscaI1.0 annotation
processed data files format and content: The file "Processed_data_file_TotalRNASeq.xlsx" contains the results of DGE analysis using the total RNAseq libraries by the Salmon-DESeq2 pipeline.Sheet1: Ago-16 KD vs GFP control, Sheet2 RdRP1 KD vs GFP control, Sheet3: RdRP3 KD vs GFP control, Sheet4: TPM values for individual libraries.

organism: Ixodes scapularis

growth_protocol: Ixodes scapularis embryonic 6 (ISE6)  cells were obtained from ATCC and cultured according to the published protocol at 34 degrees C (Munderloh and Kurtti, 1989). Cells were seeded at 1x10^6 /ml in 2ml fresh L-15B medium on a 6-well plate.

extract_protocol:
Total RNA was extracted from ISE6 cells using Trizol-LS (Invitrogen) according to the manufacturer’s instructions.For small RNA libraries of ISE6 cells depleted of small RNA factors and their control samples, 1ug total RNA was used for library construction. For 5’-tri-P libraries, the small RNA fraction (~15-35nt) was isolated by gel extraction and RNA species bearing 5’-OH were monophosphorylated by T4 polynucletide kinase (NEB). This was followed by treatment by a terminator exonuclease (Epicentre), dephosphorylation by Calf Intestine Phosphatase (NEB) and re-phosphorylation by T4 polynucletide kinase (NEB). For the oxidized small RNA library, small RNAs (~15-35nt) from 50ug total RNA was isolated by gel extraction and treated with 25mM NaIO4 dissolved in 60mM Borax buffer and incubated for 30 minutes at room temperature in the dark. For total RNAseq analysis, three sets of knockdown experiments were performed independently, and total RNA samples extracted by Trizol-LS (Invitrogen) were sent to BGI (Hongkong) for ribosomal RNA depletion using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Epicentre).
For small RNA libraries of ISE6 cells depleted of small RNA factors and their control samples, 1ug total RNA was used for library construction using the TruSeq Small RNA Library Preparation kit (Illumina). Both 5’-tir-P enriched and oxidized samples were subjected to a small RNA library construction by the TruSeq Small RNA Library Preparation kit (Illumina). For total RNAseq analysis,  library construction used non-stranded (Replicate 1) or stranded (Replicates 2 and 3) TruSeq mRNA Library Prep Kit (Illumina).

treatment_protocol: The dsRNA transfection was performed using Effectene (QIAGEN). 400ng dsRNA was diluted in in 100ul Buffer EC and 3.2ul Enhancer was added. The mixture was incubated for 2-5min at room temperature. Then, 10ul Effectene was added and incubated for 5-10min at room temperature. The mixture was added to the culture and the cells were incubated for 7-10 days. After the first incubation, the dsRNA transfection procedure was repeated again and incubated for 7-10 days to ensure the maximal efficacy of RNAi.

value: transfection with dsRdRP3


title: B181: dsRdRP1_rep3

source_name: Ixodes scapularis embryonic 6 (ISE6)  cells

value: transfection with dsRdRP1


title: GCT0098

description:
tumor DNA from germ cell tumor specimen
8942351029_R01C02


title: GCT0115

description:
tumor DNA from germ cell tumor specimen
8942351029_R02C02

value: YST


title: IMR5 LP MOI 2 CHD5 MOI 5_rep 1


title: GCT0123

description:
tumor DNA from germ cell tumor specimen
8942351029_R02C01


title: CH12 T0  ctrl

value: mTKO

value: untreated

value: RPMI+10% FBS+1XP/S+50uM BME

value: gRNA amplicon


title: GCT0079

description:
tumor DNA from germ cell tumor specimen
8784233115_R06C02

value: GD


title: B179: dsAgo-16_rep3

value: Ixodes scapularis embryonic 6 (ISE6)  cells

value: transfection with dsAgo-16


title: IMR5 LP MOI 2 RFP MOI 5_rep 3

value: control


title: GCT0122

description:
tumor DNA from germ cell tumor specimen
8784233115_R05C02

value: male

value: Testis

value: Frozen


title: IMR5 LP MOI 2 RFP MOI 5_rep 2

value: neuroblastoma-derived cell line


title: B178: dsGFP_rep3

value: transfection with dsGFP


title: IMR5 LP MOI 2 RFP MOI 5_rep 1

value: Abdomen


title: GCT0049

description:
tumor DNA from germ cell tumor specimen
8784233115_R04C01

value: female

value: Ovary


title: GCT0001

description:
tumor DNA from germ cell tumor specimen
8784233115_R04C02

value: YST

value: Missing


title: B177: dsRdRP3_rep2

value: transfection with dsRdRP3


title: GCT0062

description:
tumor DNA from germ cell tumor specimen
8784233115_R03C02

value: Teratoma

value: Extragonadal


title: GCT0009

description:
tumor DNA from germ cell tumor specimen
8784233115_R02C02


title: GCT0118

description:
tumor DNA from germ cell tumor specimen
8942351029_R01C01


title: OCI-Ly7_OCABi_INPUT_rep2

description: Input

data_processing:
Adapter trimming using Trime Galore!
Alignment using BWA.
Mark duplicate reads using picard.
Filtering to remove reads mapping to blacklisted regions, reads marked as duplicates and unmapped reads.
Call narrowPeaks and generate fold enrichment / input bigWig files using MACS2.
Genome_build: GRCh38
Supplementary_files_format_and_content: NarrowPeak file and fold enrichment / input bigWig.

growth_protocol: Primary lymphocytes were isolated by gradient centrifugation and naive and germinal center B cell populations were isolated by FACS. OCI-Ly7 cells were cultured in medium containing 80% Iscove’s Modified Dulbecco’s Medium with 20% FBS, or 90% RPMI-1640 with 10% FBS (SU-DHL-4), each supplemented with 1% glutamine and 1% penicillin/streptomycin. CRISPRi cells were generated by lentoviral transduction of pHR-SFFV-dCas9-BFP-KRAB (46911, Addgene).

extract_protocol:
10 million cells were fixed in 1% formaldehyde for 10 min at room temperature, and fragmentation of fixed chromatin was obtained from isolated nuclei by sonication. To enrich for short chromatin fragments (200 - 700 bp), 5μg of antibody was added to the chromatin lysate and incubated overnight at 4 °C. The following day, Dynabeads protein A was added and incubated with rotation at 4 °C for 1.5 hours. Enriched DNA was isolated through extensive wash steps, subsequent reverse cross-linking, and purification using DNA Clean & Concentrator Kit.
ChIP-seq libraries were prepared from 2-5 ng ChIP DNA. After end-repair, A-tailing, and ligation with barcodes, barcoded DNA was amplified by 12 cycles of PCR using Phusion® High-Fidelity DNA Polymerase.
50bp single-end.

tag: knock down

tag: chip antibody


title: GCT0042

description:
tumor DNA from germ cell tumor specimen
8784233115_R06C01

value: MMGCT

tag: batch


title: GCT0005

description:
tumor DNA from germ cell tumor specimen
8784233115_R02C01


title: OCI-Ly7_OCABi_INPUT_rep1

description: Input


title: B176: dsRdRP1_rep2

value: Ixodes scapularis embryonic 6 (ISE6)  cells

value: transfection with dsRdRP1


title: GCT0008

description:
tumor DNA from germ cell tumor specimen
8784233044_R06C02


title: GCT0057

description:
tumor DNA from germ cell tumor specimen
8784233115_R01C01


title: OCI-Ly7_control_INPUT_rep1

description: Input

value: control


title: OCI-Ly7_control_INPUT_rep2

description: Input


title: GCT0120

description:
tumor DNA from germ cell tumor specimen
8784233044_R02C02

value: male


title: GCT0014

description:
tumor DNA from germ cell tumor specimen
8784233044_R03C01


title: GCT0034

description:
tumor DNA from germ cell tumor specimen
8784233044_R03C02

value: Testis


title: B172: dsRdRP3_rep1

description: Total RNAseq data, library construction using non-stranded TruSeq mRNA Library Prep Kit (Illumina), sequencing on Hiseq4000.


title: GCT0012

description:
tumor DNA from germ cell tumor specimen
8784233044_R06C01

value: Frozen


title: B173: dsGFP_rep2

description: Total RNAseq data, library construction using  stranded TruSeq mRNA Library Prep Kit (Illumina), sequencing on Hiseq4000.


title: OCI-Ly7_OCABi_OCT2_rep2

description: OCT2 ChIP-seq


title: GCT0071

description:
tumor DNA from germ cell tumor specimen
8784233044_R04C02


title: B171: dsRdRP1_rep1


title: OCI-Ly7_OCABi_OCT2_rep1

description: OCT2 ChIP-seq


title: GCT0083

description:
tumor DNA from germ cell tumor specimen
8784233044_R01C02

value: Germinoma


title: B169: dsAgo-16_rep1

value: transfection with dsAgo-16


title: B168: dsGFP_rep1

value: transfection with dsGFP


title: GCT0125

description:
tumor DNA from germ cell tumor specimen
8784233044_R01C01


title: OCI-Ly7_control_OCT2_rep2

description: OCT2 ChIP-seq


title: GCT0032

description:
tumor DNA from germ cell tumor specimen
8784233115_R01C02


title: B174: dsAgo-16_rep2


title: GCT0018

description:
tumor DNA from germ cell tumor specimen
8784233023_R05C01

value: female


title: OCI-Ly7_Input

description: Input


title: GCT0063

description:
tumor DNA from germ cell tumor specimen
8784233023_R06C02

value: missing


title: OCI-Ly7_control_OCT2_rep1

description: OCT2 ChIP-seq


title: GCT0023

description:
tumor DNA from germ cell tumor specimen
8784233023_R05C02

value: YST


title: OCI-Ly7_OCT2

description: OCT2 ChIP-seq


title: GCT0017

description:
tumor DNA from germ cell tumor specimen
8784233023_R03C02


title: GCT0080

description:
tumor DNA from germ cell tumor specimen
8784233023_R04C02


title: GCT0045

description:
tumor DNA from germ cell tumor specimen
8784233044_R02C01


title: OCI-Ly7_OCAB

description: OCAB ChIP-seq

value: OCAB


title: GCT0003

description:
tumor DNA from germ cell tumor specimen
8784233023_R04C01

value: Missing


title: GCT0058

description:
tumor DNA from germ cell tumor specimen
8784233023_R02C01


title: GCT0030

description:
tumor DNA from germ cell tumor specimen
8784233023_R01C02


title: GCT0002

description:
tumor DNA from germ cell tumor specimen
8784233023_R02C02


title: GCT0065

description:
tumor DNA from germ cell tumor specimen
8784233009_R04C01

value: Teratoma


title: GCB_Input

description: Input

source_name: germinal center B-cells

tag: tissue

value: tonsil

tag: cell type

value: germinal center B-cells


title: GCT0073

description:
tumor DNA from germ cell tumor specimen
8784233009_R03C02

value: Extragonadal


title: GCT0048

description:
tumor DNA from germ cell tumor specimen
8784233009_R05C01

value: MMGCT


title: GCT0033

description:
tumor DNA from germ cell tumor specimen
8784233009_R06C02


title: GCB_OCAB

description: OCAB ChIP-seq


title: SCC4 Hemophilus parainfluenzae treated-Biological Replicate2

city: Philadelphia

first: Nezar

last: Al-hebshi

state: Pennsylvania

address: 3223, North Broad Street, Mauice H. Kornberg School of Dentistry

department: Oral Health Sciences

institute: Temple University

hyb_protocol: Hybridization was performed on a GeneChip™ WT cartridge arrays (Affymetrix, Santa Clara, CA) using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix cat #900720). Hybridization was performed with rotation at 60 rpm for 16 hr at 45°C using a  GeneChip™ Hybridization Oven 645

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara, CA) using default parameters.

data_processing: Arrays were analyzed using Summarization SST-RMA algorithm1 in Transcriptome Analysis Console (TAC) Software.

label: Biotin

source_name: H. parainfluenzae treated SCC4

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed using GeneChip™ WT Terminal Labeling Kit (Affymetrix cat# 900670) according to manusfacturer's instructions.

growth_protocol: Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 2.5 mM L-glutamine was used for growing CAL27. A 1:1 mixture of DMEM and Ham's F12 medium containing 2.5 mM L-glutamine, 400 ng/ml hydrocortisone and 10% FBS was used for growing cell lines SCC4 and SCC25.

extract_protocol: The culture medium was removed, the cells were washed with PBS, and RNA was isolated using the PureLink RNA extraction kit (Invitrogen, USA) following manufacturer's instructions.  Contaminating DNA was digested using the Turbo DNA-freeTM kit (Invitrogen).

treatment_protocol: OSCC cells were seeded at 25,000–35,000 cells/well depending on the cell line in 48 well plates (TPP, Switzerland). The cells were allowed to attach for 24 h before the bacteria were added. After 24 h actively growing bacteria in their mid-log stage were added at Multiplicity of Infection (MOI) of 100 to the OSCC cells. Only cell line CAL 27 treated with S. mitis was an exception where MOI of 10 was added.

value: Tongue

tag: disease

value: Squamous Cell Carcinoma

value: oral squamous cell carcinoma (OSCC) cells

value: Hemophilus parainfluenzae treated


title: SCC4 Hemophilus parainfluenzae treated-Biological Replicate1


title: SCC25 Streptococcus mitis treated-Biological Replicate2

source_name: S. mitis treated SCC25

value: Streptococcus mitis treated


title: SCC4 Hemophilus parainfluenzae treated-Biological Replicate3


title: GCT0064

description:
tumor DNA from germ cell tumor specimen
8784233023_R01C01

value: male

value: Testis

value: Frozen


title: NB_OCT2

description: OCT2 ChIP-seq

source_name: naïve B-cells

value: naive B-cells


title: SCC25 Streptococcus mitis treated-Biological Replicate1


title: GCT0037

description:
tumor DNA from germ cell tumor specimen
8784233009_R01C01

value: YST


title: GCT0026

description:
tumor DNA from germ cell tumor specimen
8784233009_R03C01

value: missing


title: NB_Input

description: Input


title: RA09-HFD WT

city: Los Angeles

first: Bangyan

last: Stiles

state: CA

address: 1985 Zonal Ave.

department: PPSI

institute: University of Southern California

data_processing: Partek Flow

source_name: islets from mice fed high fat diet

extract_protocol: Islet isolated, RNA extracted with Trizol

treatment_protocol: HFD for 4 month

tag: strain

value: Isolated Islets

tag: diet

value: mice fed high fat diet


title: GCT0075

description:
tumor DNA from germ cell tumor specimen
8784233009_R04C02

tag: Sex


title: GCT0010

description:
tumor DNA from germ cell tumor specimen
8784233009_R01C02

value: female

tag: tumor histology

value: Missing


title: GCT0011

description:
tumor DNA from germ cell tumor specimen
8784233009_R02C02

tag: tumor location


title: GCB_OCT2

description: OCT2 ChIP-seq

value: tonsil

value: germinal center B-cells


title: GCT0081

description:
tumor DNA from germ cell tumor specimen
8784233009_R02C01

value: Extragonadal

tag: age at diagnosis


title: GCT0019

description:
tumor DNA from germ cell tumor specimen
8784233004_R06C02

tag: tissue type


title: RA08-HFD WT


title: GCT0051

description:
tumor DNA from germ cell tumor specimen
8784233004_R06C01

value: MMGCT


title: RA07-HFD WT


title: SCC4 Neisseria flavescens treated-Biological Replicate3

source_name: N. flavescens treated SCC4

value: Tongue

value: Squamous Cell Carcinoma

tag: cell line

value: oral squamous cell carcinoma (OSCC) cells

value: Neisseria flavescens treated


title: GCT0067

description:
tumor DNA from germ cell tumor specimen
8784233004_R04C02

value: male

value: Germinoma

value: Testis


title: SCC4 Neisseria flavescens treated-Biological Replicate1

tag: treatment


title: SCC4 Neisseria flavescens treated-Biological Replicate2


title: BS14-NC WT

source_name: islets from mice fed normal chow

value: mice fed normal chow


title: GCT0066

description:
tumor DNA from germ cell tumor specimen
8784233004_R04C01

value: YST

value: Ovary

value: Frozen


title: SCC4 Porphyromonas gingivalis treated-Biological Replicate3

source_name: P. gingivalis treated SCC4

value: Porphyromonas gingivalis treated


title: GCT0015

description:
tumor DNA from germ cell tumor specimen
8784233004_R03C02

value: female


title: GCT0021

description:
tumor DNA from germ cell tumor specimen
8784233004_R01C02

value: Missing


title: GCT0036

description:
tumor DNA from germ cell tumor specimen
8784233004_R01C01


title: GCT0074

description:
tumor DNA from germ cell tumor specimen
8784233004_R03C01


title: GCT0116

description:
tumor DNA from germ cell tumor specimen
8784233004_R02C01


title: GCT0059

description:
tumor DNA from germ cell tumor specimen
8784233004_R05C02


title: BS13-NC WT

value: Isolated Islets


title: 118

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

data_processing:
Adapter sequences were removed using cutadapt (adapter sequence : AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Trimmed reads were aligned to the human genome (hg19) with bismark (using bowtie) (parameters :   -q --phred33-quals -n 1 -l 35 -k 2 --best --chunkmbs 1024)
Information on each citosine was extracted with bismark_methylation_extractor
Citosines in the top 1% most highly covered were removed to avoid including PCR duplicates in the calculations.
Citosines with a read coverage of less than 5 were removed as their signal is unreliable when calculating methylation percentages
Genome_build: hg19
Supplementary_files_format_and_content: tabulation separated table containing the methylation ratio and read coverage over each specified citosine. Only citosines with a coverage of 5 or more reads in at least one sample were kept.

source_name: Case_post-mortem dosolateral caudate

extract_protocol:
20 mg of frozen dosolateral caudate tissue was homogenized and DNA was extracted using Qiagen DNA MiniKits.
RRBS libraries were prepared from 1ug genomic DNA using MspI digestion, end-repair and adapter ligation before bisulfite conversion.

tag: subject status

value: Case

tag: age

tag: ethnicity

value: HispanicCaucasian

tag: smoker status

value: Non-smoker

tag: alcohol present at death

value: yes

value: Brain

tag: post mortem interval

tag: tissue ph


title: SCC4 Porphyromonas gingivalis treated-Biological Replicate2

tag: tissue

value: Tongue

tag: disease

value: Squamous Cell Carcinoma

tag: cell type

value: oral squamous cell carcinoma (OSCC) cells


title: GCT0041

description:
tumor DNA from germ cell tumor specimen
8784233001_R06C02

tag: Sex

tag: batch


title: GCT0007

description:
tumor DNA from germ cell tumor specimen
8784233001_R03C02

tag: tumor histology

value: Blue cell tumor

tag: tumor location


title: GCT0029

description:
tumor DNA from germ cell tumor specimen
8784233001_R05C02

tag: age at diagnosis

tag: tissue type


title: GCT0070

description:
tumor DNA from germ cell tumor specimen
8784233001_R04C02

value: Teratoma

value: Extragonadal


title: GCT0072

description:
tumor DNA from germ cell tumor specimen
8784233001_R02C01

value: male

value: MMGCT

value: Testis


title: SCC4 Porphyromonas gingivalis treated-Biological Replicate1

tag: cell line

tag: treatment

value: Porphyromonas gingivalis treated


title: GCT0078

description:
tumor DNA from germ cell tumor specimen
8784233001_R01C02

value: female

value: Germinoma

value: Missing

value: Frozen


title: BS12-NC WT

tag: strain

value: Isolated Islets

tag: diet

value: mice fed normal chow


title: SCC4 Streptococcus mitis treated -Biological Replicate2

source_name: S. mitis treated SCC4

value: Streptococcus mitis treated


title: SCC25 Hemophilus parainfluenzae treated-Biological Replicate2

source_name: H. parainfluenzae treated SCC25

value: Tongue

value: Hemophilus parainfluenzae treated


title: GCT0038

description:
tumor DNA from germ cell tumor specimen
8784233001_R05C01

value: YST


title: SCC4 Streptococcus mitis treated -Biological Replicate3

value: Squamous Cell Carcinoma

value: oral squamous cell carcinoma (OSCC) cells


title: SCC25 Hemophilus parainfluenzae treated-Biological Replicate3


title: SCC4 Streptococcus mitis treated -Biological Replicate1


title: GCT0020

description:
tumor DNA from germ cell tumor specimen
8784225079_R06C02

value: Ovary


title: GCT0052

description:
tumor DNA from germ cell tumor specimen
8784225079_R05C02

value: male

value: Teratoma

value: Extragonadal


title: SCC25 Hemophilus parainfluenzae treated-Biological Replicate1


title: 114

source_name: Control_post-mortem dosolateral caudate

tag: subject status

value: Control

tag: age

tag: ethnicity

value: Caucasian

tag: smoker status

value: Non-smoker

value: no

value: Brain


title: 116

tag: alcohol present at death

tag: tissue

tag: post mortem interval

tag: tissue ph


title: GCT0013

description:
tumor DNA from germ cell tumor specimen
8784225079_R04C02

tag: Sex

value: Frozen

tag: batch


title: SCC25 Neisseria flavescens treated-Biological Replicate3

source_name: N. flavescens treated SCC25

tag: disease

tag: cell type

value: Neisseria flavescens treated


title: 119

value: Case

value: HispanicCaucasian


title: 112


title: GCT0068

description:
tumor DNA from germ cell tumor specimen
8784225079_R05C01

tag: tumor histology

value: Germinoma

tag: tumor location

value: Testis

tag: age at diagnosis

tag: tissue type


title: GCT0050

description:
tumor DNA from germ cell tumor specimen
8784225079_R03C02

value: MMGCT


title: GCT0039

description:
tumor DNA from germ cell tumor specimen
8784225079_R04C01

value: YST


title: 108

value: Smoker


title: GCT0054

description:
tumor DNA from germ cell tumor specimen
8784225079_R02C02

value: GD

value: Missing


title: GCT0016

description:
tumor DNA from germ cell tumor specimen
8784233001_R02C02

value: male


title: GCT0069

description:
tumor DNA from germ cell tumor specimen
8784225079_R01C02


title: 110

value: Control


title: GCT0022

description:
tumor DNA from germ cell tumor specimen
8784225079_R02C01


title: GCT0053

description:
tumor DNA from germ cell tumor specimen
8784225079_R01C01


title: 106


title: GCT0035

description:
tumor DNA from germ cell tumor specimen
8221932159_R06C02

value: female

value: Ovary


title: 104

value: no


title: 117

value: Non-smoker

value: Brain


title: GCT0025

description:
tumor DNA from germ cell tumor specimen
8221932159_R05C01

value: Extragonadal

value: Frozen


title: 102

value: HispanicCaucasian


title: 100


title: GCT0040

description:
tumor DNA from germ cell tumor specimen
8221932159_R03C02


title: GCT0061

description:
tumor DNA from germ cell tumor specimen
8221932159_R03C01


title: GCT0124

description:
tumor DNA from germ cell tumor specimen
8221932159_R02C02


title: GCT0027

description:
tumor DNA from germ cell tumor specimen
8221932159_R06C01


title: GCT0060

description:
tumor DNA from germ cell tumor specimen
8221932159_R04C01


title: GCT0463

description:
tumor DNA from germ cell tumor specimen
200069280215_R06C01

value: FFPE


title: GCT0006

description:
tumor DNA from germ cell tumor specimen
8221932159_R01C02

value: Blue cell tumor


title: 98


title: GCT0464

description:
tumor DNA from germ cell tumor specimen
200069280215_R06C02


title: 94

value: Caucasian


title: 96


title: GCT0462

description:
tumor DNA from germ cell tumor specimen
200069280215_R05C02

value: YST


title: 92


title: GCT0024

description:
tumor DNA from germ cell tumor specimen
8221932159_R04C02

value: Testis


title: GCT0460

description:
tumor DNA from germ cell tumor specimen
200069280215_R04C01


title: GCT0458

description:
tumor DNA from germ cell tumor specimen
200069280215_R03C01


title: GCT0459

description:
tumor DNA from germ cell tumor specimen
200069280215_R03C02


title: 90


title: GCT0457

description:
tumor DNA from germ cell tumor specimen
200069280215_R02C01

value: MMGCT


title: 86


title: GCT0456

description:
tumor DNA from germ cell tumor specimen
200069280215_R01C02


title: 88


title: GCT0453

description:
tumor DNA from germ cell tumor specimen
200069280209_R06C01


title: GCT0452

description:
tumor DNA from germ cell tumor specimen
200069280209_R05C02

value: Germinoma

value: Intracranial


title: GCT0461

description:
tumor DNA from germ cell tumor specimen
200069280215_R05C01

value: male


title: GCT0455

description:
tumor DNA from germ cell tumor specimen
200069280215_R01C01

value: female


title: SCC25 Streptococcus mitis treated-Biological Replicate3

value: Tongue

value: Squamous Cell Carcinoma

tag: cell line

value: oral squamous cell carcinoma (OSCC) cells

tag: treatment

value: Streptococcus mitis treated


title: CAL27 Hemophilus parainfluenzae treated-Biological Replicate3

source_name: H. parainfluenzae treated CAL27

value: Hemophilus parainfluenzae treated


title: SCC25 Neisseria flavescens treated-Biological Replicate1

value: Neisseria flavescens treated


title: CAL27 Neisseria flavescens treated-Biological Replicate2

source_name: N. flavescens treated CAL27


title: CAL27 Neisseria flavescens treated-Biological Replicate3


title: CAL27 Neisseria flavescens treated-Biological Replicate1


title: CAL27 Porphyromonas gingivalis treated-Biological Replicate1

source_name: P. gingivalis treated CAL27

value: Porphyromonas gingivalis treated


title: CAL27 Porphyromonas gingivalis treated-Biological Replicate2


title: 84

tag: subject status

value: Control

tag: age

value: Non-smoker

value: no

value: Brain


title: SCC25 Neisseria flavescens treated-Biological Replicate2


title: SCC25 Porphyromonas gingivalis treated -Biological Replicate3

source_name: P. gingivalis treated SCC25


title: 82

tag: ethnicity

tag: smoker status


title: SCC25 Porphyromonas gingivalis treated -Biological Replicate2

tag: tissue


title: CAL27 Hemophilus parainfluenzae treated-Biological Replicate1


title: GCT0451

description:
tumor DNA from germ cell tumor specimen
200069280209_R05C01

source_name: tumor DNA

value: Ovary

value: FFPE


title: CAL27 Porphyromonas gingivalis treated-Biological Replicate3


title: SCC25 Porphyromonas gingivalis treated -Biological Replicate1


title: GCT0454

description:
tumor DNA from germ cell tumor specimen
200069280209_R06C02

value: MMGCT


title: GCT0449

description:
tumor DNA from germ cell tumor specimen
200069280209_R04C01

value: Testis


title: GCT0448

description:
tumor DNA from germ cell tumor specimen
200069280209_R03C02

value: male


title: CAL27 Hemophilus parainfluenzae treated-Biological Replicate2


title: GCT0450

description:
tumor DNA from germ cell tumor specimen
200069280209_R04C02

value: female

value: YST


title: 80

value: HispanicCaucasian

tag: alcohol present at death

tag: post mortem interval


title: GCT0447

description:
tumor DNA from germ cell tumor specimen
200069280209_R03C01

tag: Sex


title: GCT0446

description:
tumor DNA from germ cell tumor specimen
200069280209_R02C02

tag: batch


title: 78

tag: tissue ph


title: GCT0444

description:
tumor DNA from germ cell tumor specimen
200069280209_R01C02


title: GCT0440

description:
tumor DNA from germ cell tumor specimen
200069280197_R05C02


title: CAL27 Streptococcus mitis treated-Biological Replicate2

source_name: S. mitis treated CAL27

value: Tongue

tag: disease

value: Squamous Cell Carcinoma

tag: cell type

value: oral squamous cell carcinoma (OSCC) cells


title: GCT0443

description:
tumor DNA from germ cell tumor specimen
200069280209_R01C01

tag: tumor histology

tag: tumor location

value: Extragonadal


title: GCT0442

description:
tumor DNA from germ cell tumor specimen
200069280197_R06C02

tag: age at diagnosis

tag: tissue type


title: SCC4 control-Biological Replicate4

source_name: Untreated SCC4

tag: cell line

tag: treatment

value: control


title: GCT0437

description:
tumor DNA from germ cell tumor specimen
200069280197_R04C01

value: Germinoma

value: Frozen


title: CAL27 Streptococcus mitis treated-Biological Replicate1

value: Streptococcus mitis treated


title: GCT0439

description:
tumor DNA from germ cell tumor specimen
200069280197_R05C01


title: GCT0436

description:
tumor DNA from germ cell tumor specimen
200069280197_R03C02


title: SCC4 control-Biological Replicate3


title: 68

tag: subject status

value: Case

tag: age

value: Smoker

value: no

value: Brain


title: CAL27 Streptococcus mitis treated-Biological Replicate3


title: SCC4 control-Biological Replicate2


title: 72

value: Control

tag: ethnicity

tag: smoker status


title: GCT0434

description:
tumor DNA from germ cell tumor specimen
200069280197_R02C02


title: GCT0445

description:
tumor DNA from germ cell tumor specimen
200069280209_R02C01

value: MMGCT

value: Ovary

value: FFPE


title: GCT0441

description:
tumor DNA from germ cell tumor specimen
200069280197_R06C01

value: female

value: YST


title: 74

value: male

value: HispanicCaucasian

value: Non-smoker

tag: alcohol present at death

tag: tissue


title: SCC25 control-Biological Replicate4

source_name: Untreated SCC25

value: Tongue

value: Squamous Cell Carcinoma

value: oral squamous cell carcinoma (OSCC) cells

value: control


title: SCC4 control-Biological Replicate1


title: 70

tag: Sex

tag: post mortem interval


title: SCC25 control-Biological Replicate3


title: GCT0433

description:
tumor DNA from germ cell tumor specimen
200069280197_R02C01

value: Testis

tag: batch


title: 76

value: yes

tag: tissue ph


title: GCT0422

description:
tumor DNA from germ cell tumor specimen
200069280197_R01C01

value: Germinoma

value: Frozen


title: 64

value: Case

value: Smoker

value: no

value: Brain


title: GCT0421

description:
tumor DNA from germ cell tumor specimen
200069280176_R06C02

value: female

value: MMGCT

value: Extragonadal

value: FFPE


title: 60

value: male


title: GCT0419

description:
tumor DNA from germ cell tumor specimen
200069280176_R05C02

value: Ovary


title: GCT0438

description:
tumor DNA from germ cell tumor specimen
200069280197_R04C02

value: YST


title: GCT0420

description:
tumor DNA from germ cell tumor specimen
200069280176_R06C01


title: GCT0418

description:
tumor DNA from germ cell tumor specimen
200069280176_R05C01


title: GCT0416

description:
tumor DNA from germ cell tumor specimen
200069280176_R04C01

value: Intracranial


title: 58


title: SCC25 control-Biological Replicate1

value: Tongue

tag: disease

value: Squamous Cell Carcinoma

tag: cell type

value: oral squamous cell carcinoma (OSCC) cells

value: control


title: GCT0415

description:
tumor DNA from germ cell tumor specimen
200069280176_R03C02

tag: tumor histology

tag: tumor location

value: Testis

value: Frozen


title: 56

value: Case

value: Smoker


title: GCT0414

description:
tumor DNA from germ cell tumor specimen
200069280176_R03C01

tag: age at diagnosis

tag: tissue type


title: 54

value: yes

value: Brain


title: SCC25 control-Biological Replicate2

tag: cell line

tag: treatment


title: 52

tag: subject status

tag: age

value: Non-smoker

value: no


title: GCT0413

description:
tumor DNA from germ cell tumor specimen
200069280176_R02C02

value: female

value: Teratoma


title: GCT0411

description:
tumor DNA from germ cell tumor specimen
200069280176_R01C01

value: male


title: GCT0412

description:
tumor DNA from germ cell tumor specimen
200069280176_R02C01

value: Germinoma


title: GCT0417

description:
tumor DNA from germ cell tumor specimen
200069280176_R04C02

value: YST

value: Extragonadal


title: 50

tag: ethnicity

tag: smoker status


title: GCT0410

description:
tumor DNA from germ cell tumor specimen
200069280175_R06C02

value: Intracranial


title: CAL27 control-Biological Replicate4

source_name: Untreated CAL27

tag: tissue

value: Tongue

value: Squamous Cell Carcinoma

value: oral squamous cell carcinoma (OSCC) cells


title: GCT0409

description:
tumor DNA from germ cell tumor specimen
200069280175_R06C01

tag: Sex

value: Frozen


title: CAL27 control-Biological Replicate2

value: control


title: CAL27 control-Biological Replicate3


title: GCT0408

description:
tumor DNA from germ cell tumor specimen
200069280175_R05C02

value: Ovary


title: CAL27 control-Biological Replicate1


title: 46

value: Case

value: Smoker

tag: alcohol present at death

tag: post mortem interval


title: GCT0407

description:
tumor DNA from germ cell tumor specimen
200069280175_R05C01

value: MMGCT

value: Testis

tag: batch


title: GCT0404

description:
tumor DNA from germ cell tumor specimen
200069280175_R03C02

value: female


title: GCT0405

description:
tumor DNA from germ cell tumor specimen
200069280175_R04C01


title: 44

value: HispanicCaucasian

value: Non-smoker

value: no

value: Brain

tag: tissue ph


title: GCT0403

description:
tumor DNA from germ cell tumor specimen
200069280175_R03C01


title: GCT0406

description:
tumor DNA from germ cell tumor specimen
200069280175_R04C02

value: male

value: Teratoma


title: 42

value: Caucasian


title: U87MG P-bi-TAT  Rep. TREATED 2 24h

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

label: biotin

source_name: U87MG cell line

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human glioblastoma multiforme GBM 10181360 cells (generous gift from the University of Pittsburgh Medical Center, Department of Neurosurgery) and U87MG cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

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

treatment_protocol: Cells were treated with P-bi-TAT (30 µM) for 24 h and 48 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

tag: p-bi-tat treatment

value: Treated, 24h

value: U87MG cell line


title: U87MG P-bi-TAT  Rep. TREATED 1 48h

value: Treated, 48h


title: U87MG P-bi-TAT  Rep. TREATED 2 48h


title: GCT0402

description:
tumor DNA from germ cell tumor specimen
200069280175_R02C02

tag: tumor histology

value: YST

value: Extragonadal

value: Frozen


title: U87MG P-bi-TAT  Rep. TREATED 1 24h


title: GCT0401

description:
tumor DNA from germ cell tumor specimen
200069280175_R02C01

tag: tumor location

value: Ovary


title: 40

value: Case

value: Smoker


title: GCT0400

description:
tumor DNA from germ cell tumor specimen
200069280175_R01C01

value: MMGCT

value: Testis

tag: age at diagnosis


title: 48

value: HispanicCaucasian

value: Non-smoker


title: 38

value: no

value: Brain


title: 36

value: male


title: GBM 10181360 P-bi-TAT  Rep. TREATED 2 48h

source_name: GBM 10181360 cell line

value: GBM 10181360 cell line


title: 32


title: 30


title: GBM 10181360 P-bi-TAT  Rep. TREATED 2 24h

value: Treated, 24h


title: GBM 10181360 P-bi- 48hTAT  Rep. TREATED 1


title: 28


title: Acute-on-chronic liver failure Liver biopsy (LM131)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: The standard Affymetrix hybridization protocol was used

scan_protocol: Standard Affy scanning protocol

data_processing: Standard RMA processing using affyPLM bioconductor R package(v.3.6)

source_name: Liver Biopsy

label_protocol: Samples were labeled using the Affymetrix Labeling Kit as per manufacturer's protocols.

extract_protocol: mRNA was isolated from fresh human liver tissues using Trizol and following manufacturer’s manual instructions (Invitrogen, Carlsbad, CA, USA).

tag: disease state

value: Acute-on-chronic liver failure


title: 26

source_name: Case_post-mortem dosolateral caudate


title: U87MG CONTROL Rep. 2 48h

treatment_protocol: Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: PBS, 48h

tag: cell line

value: U87MG cell line


title: Acute-on-chronic liver failure Liver biopsy (LM083)


title: U87MG CONTROL Rep. 2 24h

tag: treatment

value: PBS, 24h


title: U87MG CONTROL Rep. 1 48h


title: Acute-on-chronic liver failure Liver biopsy (LM016)


title: GBM 10181360 P-bi-TAT  Rep. TREATED 1 24h


title: Acute-on-chronic liver failure Liver biopsy (LM134)


title: GBM 10181360 CONTROL Rep. 1 48h

source_name: GBM cell line


title: Acute-on-chronic liver failure Liver biopsy (LM124)


title: Decompesated Cirrhosis Liver biopsy (LM013)

value: Decompesated Cirrhosis


title: Acute-on-chronic liver failure Liver biopsy (LM100)


title: GBM 10181360 CONTROL Rep. 2 48h


title: Decompesated Cirrhosis Liver biopsy (LM035)


title: Decompesated Cirrhosis Liver biopsy (LM005)


title: 20

tag: subject status

value: Caucasian

value: yes


title: 16

value: Case

tag: age


title: Decompesated Cirrhosis Liver biopsy (LM023)


title: Decompesated Cirrhosis Liver biopsy (LM054)


title: U87MG CONTROL Rep. 1 24h


title: Acute-on-chronic liver failure Liver biopsy (LM017)


title: Decompesated Cirrhosis Liver biopsy (LM009)


title: 18

tag: ethnicity

value: Smoker


title: Acute-on-chronic liver failure Liver biopsy (LM021)


title: 14

tag: smoker status


title: B061: 5'TriP enriched

description: small RNA library, sequencing on a Hiseq2000.

data_processing:
Adaptor sequences were removed by using fastx_clipper(Part of FASTX Toolkit 0.0.14) and collapsed by fastx_collapser(Part of FASTX Toolkit 0.0.14) and converted by fasta_formatter(Part of FASTX Toolkit 0.0.14).
The fasta files were used for mapping using the ISE6 genome sequence (IscaI1) (Miller et al., 2018) using bowtie1.3.0  without allowing any mismatches.
For identification of sRNA sources, genome-mapping reads were mapped to the following reference sequences: 1. miRNAs (miRbase Release 22.1) (Kozomara et al., 2019), RNAP III transcripts (downloaded from RNAcentral) (Sweeney et al., 2021), rRNAs from NCBI and mRNAs (Vectorbase IscaI1.0) (Miller et al., 2018).
Python scripts were used to quantify reads that belong to different categories.
R script was used to normalize the data with RPM.
genome build: IscaI1
processed data files format and content: The file "Processed_data_file_sRNA_category.xlsx" contains summary of sRNA analysis:
processed data files format and content: Sheets1-13: sRNA read counts for each category. Each sheet report the numbers in each of the libraries.
processed data files format and content: Sheet14: Normalized counts of sRNAseq and total RNAseq reads mapping to the persistently present viruses.

source_name: Ixodes scapularis embryonic 6 (ISE6)  cells

value: 5'TriP enriched


title: 66

tag: tissue


title: B060: oxidized

value: Ixodes scapularis embryonic 6 (ISE6)  cells

value: oxidized RNA


title: GCT0435

description:
tumor DNA from germ cell tumor specimen
200069280197_R03C01

tag: Sex

value: female

value: MMGCT

value: Ovary

tag: tissue type

value: Frozen


title: GBM 10181360 CONTROL Rep. 2 24h

value: GBM 10181360 cell line


title: Decompesated Cirrhosis Liver biopsy (LM077)


title: 12

value: male

value: HispanicCaucasian

tag: alcohol present at death

value: no

value: Brain

tag: post mortem interval


title: Decompesated Cirrhosis Liver biopsy (LM036)

value: Decompesated Cirrhosis


title: 10

source_name: Control_post-mortem dosolateral caudate

value: Control

value: Caucasian

tag: tissue ph


title: B058: dsRdRP3

value: transfection with dsRdRP3


title: GBM 10181360 CONTROL Rep. 1 24h

value: PBS, 24h


title: K562  treated 2 with fB-PMT Rep. 16B

source_name: K562, AML cell line

growth_protocol: Human glioblastoma multiforme GBM 10181360 cells (generous gift from the University of Pittsburgh Medical Center, Department of Neurosurgery) and U87MG cells (ATCC, Manassas, VA), Bladder cancer (JBV253), skin cancer (A375) and  Acute Myelod Leukemia (AML)  (KG1A  and K562  cells) were obtained from  (ATCC, Manassas, VA). All the cells were  cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

treatment_protocol: Cells were treated with fb-PMT (30 µM) for 24 h or 48h as indicated. Control cells were exposed to PBS, pH 7.4, for the same period of time.

tag: fb-pmt treatment

value: Treated, 48h

value: K562, AML cell line


title: B057: dsRdRP1

value: Ixodes scapularis embryonic 6 (ISE6)  cells

value: transfection with dsRdRP1


title: 8

value: Non-smoker


title: 6

value: Smoker


title: Decompesated Cirrhosis Liver biopsy (LM012)


title: B056: dsAGO3-2

value: transfection with dsAGO3-2


title: Decompesated Cirrhosis Liver biopsy (LM018)


title: Decompesated Cirrhosis Liver biopsy (LM002)


title: B055: dsAGO3-1

value: transfection with dsAGO3-1


title: K562 treated 1 with fB-PMT  Rep. 16A


title: Decompesated Cirrhosis Liver biopsy (LM050)


title: B059: No treatment

value: No treatment control


title: K562  CONTROL Rep. 15B

value: PBS, 48h


title: Compensated Cirrhosis Liver biopsy (LM057)

value: Compensated Cirrhosis


title: 2

value: male

value: HispanicCaucasian

value: no

value: Brain


title: B054: dsAub2

value: transfection with dsAub2


title: B053: dsAgo-78

value: transfection with dsAgo-78


title: Compensated Cirrhosis Liver biopsy (LM144)


title: KG1A cells treated 2 with fB-PMT Rep. 14B

source_name: KG1A, AML cell line

value: Treated, 48h

value: KG1A, AML cell line


title: B052: dsAgo-96

value: Ixodes scapularis embryonic 6 (ISE6)  cells

value: transfection with dsAgo-96


title: 4

value: Control


title: B051: dsAgo-30

value: transfection with dsAgo-30


title: B050: dsAgo-16

value: transfection with dsAgo-16


title: B049: dsGFP

value: transfection with dsGFP


title: Compensated Cirrhosis Liver biopsy (LM051)


title: KG1A cells CONTROL Rep. 13B


title: Veh (HSC20)

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (rn6) and the quantification of genes and transcripts were done with the RSEM program using ensembl ( Rattus_norvegicus.Rnor_6.0.91.chr.gtf)
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rattus norvegicus (rn6)
Supplementary_files_format_and_content: RSEM expected counts

organism: Rattus norvegicus

source_name: Rat hepatic stellate cells (HSC)

growth_protocol: Primary HSC were isolated by differential gradient centrifugation protocol from cirrhotic rats induced by chronic CCl4 inhalation

extract_protocol:
RNAqueous-Micro kit (Ambion)
TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E)

treatment_protocol: HSC were co-cultured with hAMSC or hAEC (15.000 viable cells) using Transwell membrane inserts for 24h.

tag: cell type

value: Rat hepatic stellate cells (HSC)

tag: co-cultured with

value: Veh


title: Veh (HSC19)


title: A375 cells cells treated 1 with FB-PMT  Rep. 12A

source_name: A375 Skin Cancer cell line

value: A375 Skin Cancer cell line


title: Compensated Cirrhosis Liver biopsy (LM030)

value: Compensated Cirrhosis


title: KG1A cells treated 1 with fB-PMT  Rep. 14A


title: A375 cells CONTROL Rep. 11A

value: PBS, 48h


title: Compensated Cirrhosis Liver biopsy (LM022)


title: K562  CONTROL Rep. 15A

value: K562, AML cell line


title: Mtb (#2)

city: Seoul

first: Sung Jae

last: Shin

address: 50-1 Yonsei-ro

department: Department of Microbiology

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Primary cell

growth_protocol: Isolated mouse bone marrow cells were diffrentiated into BMDMs using L929-conditioned medium at 37°C in the presence of 5% CO2 for 6 days. The culture medium consisted of Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% L929 supernatant, 10% heat-inactivated fetal bovine serum (FBS), and 100 units/ml of penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: BMDMs were infected with M. tuberculosis H37Rv at one bacterium per cell in antibiotic-free DMEM supplemented with 10% L929 supernatant and 10% FBS, and incubated for 4 h. After infection, BMDMs were washed twice with PBS and treated with colchicine of 2.5 mM for 4 h.

tag: strain

value: Bone marrow-dereived macrophages

tag: gender

value: female

tag: infection

value: M. tuberculosis H37Rv ATCC 27294

value: Non


title: Mtb (#3)

tag: treatment


title: Naïve (#3)


title: Compensated Cirrhosis Liver biopsy (LM029)

tag: disease state


title: Mtb-Col (#3)

value: Colchicine (4h)


title: Mtb-Col (#2)


title: Naïve (#2)


title: A375 cells CONTROL Rep. 11B

tag: cell line


title: eCLD Liver biopsy (LM071)

description: eCLD Liver biopsy (LM071)

value: eCLD


title: Mtb-Col (#1)


title: JBV253 cells treated 2 with FB-PMT Rep. 10B

source_name: JBV253 Bladder Cancer cell line

value: Treated, 48h

value: JBV253 Bladder Cancer cell line


title: eCLD Liver biopsy (LM068)

description: eCLD Liver biopsy (LM068)


title: Veh (HSC18)


title: Compensated Cirrhosis Liver biopsy (LM047)


title: KG1A cells CONTROL Rep. 13A

value: KG1A, AML cell line


title: JBV253 cells treated 1 with FB-PMT  Rep. 10A


title: Mtb (#1)


title: JBV253 CONTROL Rep. 9B


title: Veh (HSC17)


title: Compensated Cirrhosis Liver biopsy (LM027)


title: eCLD Liver biopsy (LM118)

description: eCLD Liver biopsy (LM118)


title: A375 cells cells treated 2 with FB-PMT Rep. 12B


title: Naïve (#1)


title: eCLD Liver biopsy (LM040)

description: eCLD Liver biopsy (LM040)


title: hAMSC (HSC8)

value: hAMSC


title: Lcn2_neg_8w_Ccl4_3

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

data_processing:
Generation of the fastq files and removal of adapters were completed using the Illumina demultiplexing and conversion software bcl2fastq [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html]. Subsequently, we performed RNA-Seq primary analysis with the RNA-Seq pipeline of nf.core [1] using standard parameters. For instance, quality control of the sequenced transcripts were done with fastqc available online (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), library complexity was measured with preseq [2]. Adapter and quality trimming was performed using TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Subsequently, the reads were aligned to the mm10 reference genome sequence using STAR [3] with default parameters. In the quantification step, reads were counted with featureCounts [4] from the subread package available online (http://subread.sourceforge.net).
Differential expression analysis was then performed in R using the DESeq function of the DESeq2 v1.30.0 package [5], with local fit type (fitType="local"), without LFC modulation (betaPrior=False) and using the Wald Test as significance test. Genes with log fold change > .56 (FC >= 1.5) and corrected p-value <= 0.05 are considered as differentially expressed.
GO enrichment analyses for each of the comparisons were performed with the gprofiler2 package [6] v0.2.0, using the package’s gost function, making an ordered query (genes sorted by significance) with an adjusted p-value threshold of 0.05 and the multiple test correction method gSCS. To ensure reproducibility, the script of the advanced analysis (DEA and GOA and various QC’s and all plots used in this manuscript)
Genome_build: mm10
Supplementary_files_format_and_content: Table for each of the differential expression analyses of the four comparisons in excel format, containing a list of genes which respective Log Fold Change information and Significance values (p-values) as well as additional statistical information.
Supplementary_files_format_and_content: Table for each of the GO enrichment analyses in excel format, containing a list of gene set which enrichment significance values (p-values) as well as additional statistical information and gene information.
Supplementary_files_format_and_content: All results are in Excel format.

growth_protocol: Eight-week-old female C57BL/6 wild type and Lcn2−/− mice (4) were subjected to intraperitoneal (i.p.) injection of 0.8 ml/kg body weight CCl4 diluted in mineral oil twice weekly for 8 weeks. The mineral oil vehicle was applied to control animals. Mice were sacrificed 48 hours upon the last injection

extract_protocol:
Total RNA was isolated as described previously through phenol-chloroform extraction, isopropanol precipitation and DNAse digestion followed by subsequent RNA clean up with PureLink RNA Mini kits
The cDNA libraries were generated using rapid Mace Kit (GenxPro)

treatment_protocol: Liver tissue was homogenized in QIAzol lysis reagent (Qiagen, Hilden, Germany) in a Mixer Mill MM400 homogenizer (Retsch, Haan, Germany).

value: liver

tag: genotype


title: hAMSC (HSC15)

value: Rat hepatic stellate cells (HSC)


title: Lcn2_neg_Oil_3

source_name: Lcn2-/- (Oil)

value: oil


title: Lcn2_neg_Oil_2


title: Lcn2_neg_Oil_1


title: hAMSC (HSC7)


title: hAEC (HSC12)

value: hAEC


title: hAMSC (HSC16)


title: Lcn2_neg_8w_Ccl4_1


title: U87MG fB-PMT  Rep. TREATED 2 48h

value: U87MG cell line


title: hAEC (HSC11)


title: Healthy Liver biopsy (LMS6)

description: Healthy Liver biopsy (LMS6)

value: Healthy


title: JBV253 CONTROL Rep. 9A

value: PBS, 48h


title: Healthy Liver biopsy (LMS5)

description: Healthy Liver biopsy (LMS5)


title: U87MG FB-PMT  Rep. TREATED 1 24h

value: Treated, 24h


title: U87MG fB-PMT  Rep. TREATED 1 48h


title: Healthy Liver biopsy (LMS4)

description: Healthy Liver biopsy (LMS4)


title: U87MG FB-PMT  Rep. TREATED 2 24h


title: GBM 021913 FB-PMT  Rep. 8B

source_name: GBM 021913 cell line

value: GBM 021913 cell line


title: Lcn2_neg_8w_Ccl4_2


title: CP_0_3

city: Galveston

first: Yingzi

last: Cong

state: TX

address: 301 University Boulevard

institute: University of Texas Medical Branch at Galveston

description:
20 µm CpdA
CP_0_3

data_processing:
Raw data processing and quality assessment: 1. Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). 2.Base Quality and Phred score relationship in illumina Casava 1.8. 3.GC-content is used to detect potential AT/GC separation. 4. Raw reads filtering conditions are as follows:(1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Aligment: 1. Mapping reads to reference genome. 2.Reads is mapped to exon, intron and intergenic. 3. Distribution of mapped reads on chromosome.
Gene expression level analysis: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: tab-delimited text file includes readcount and FPKM values for each Sample

source_name: CD4+ T cells

growth_protocol: 1 × 106 Cells were cultured in 1640 RPMI medium supplemented with 10% FBS, 1 mM sodium pyruvate, and 0.05mM 2-ME.

extract_protocol:
mRNA from T cells is isolated by using Trizol reagent. All samples need to pass through the following three steps before library construction: (1) Nanodrop: for RNA purity (OD260/OD280). (2) Agarose gel electrophoresis: for RNA integrity and potential contamination. (3) Agilent 2100: check RNA integrity again.
1 µg of RNA was used for cDNA library constuction at Novogene using an NEBNext@ Utra RNA library Prep Kit for Illumina@ (cat# E7420S, New England Biolabs, lpswich, MA, USA) according to the manufacturer's protocol.

treatment_protocol: Cells were activated with antiCD3 and antiCD28 treated with or without CpdA for 2 days

value: Spleen

tag: agent

value: 20 microm CpdA


title: B6_Oil_3

source_name: Wild type (Oil)

tag: tissue

value: wild type


title: B6_Oil_2


title: CP_0_2

description:
20 µm CpdA
CP_0_2


title: B6_Oil_1


title: GBM 021913 FB-PMT  Rep. 8A


title: CP_0_1

description:
20 µm CpdA
CP_0_1


title: Healthy Liver biopsy (LMS1)

description: Healthy Liver biopsy (LMS1)


title: GBM 021913 CONTROL Rep. 7B


title: Healthy Liver biopsy (LMS2)

description: Healthy Liver biopsy (LMS2)


title: Healthy Liver biopsy (LMS3)

description: Healthy Liver biopsy (LMS3)


title: eCLD Liver biopsy (LM039)

description: eCLD Liver biopsy (LM039)

value: eCLD


title: Top Internode section of the maize stem, rep 2

city: IRAPUATO

first: Stewart

last: Gillmor

state: GUANAJUATO

address: CARR. LEON-IRAPUATO

department: UNIDAD DE GENOMICA AVANZADA

country: Mexico

institute: CINVESTAV

data_processing:
RNA-seq read quality was assessed with FastQC v0.11.2 and cleaned using the Trimmomatic software (Bolger, Lohse & Usadel, 2014).
Reads were aligned to the maize B73 reference genome (ZmB73_RefGen_v3.25, www.maizegdb.org) using the TopHat v2.0.13 software.
The expression level was calculated in fragments per kilobase of transcript per million fragments mapped (FPKM) as described previously (Trapnell, Pachter & Salzberg, 2009; Trapnell et al., 2012).
Data analysis were updated using CLC Genomics Workbench 20.0 (QIAGEN) software mapping to the B73 reference genome v4 .
Only the genes with FPKM results that met the criteria of FDR <0.05 and fold change > |2| between the two conditions were considered to be significantly differentially expressed
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample including FPKM values
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Updated expression data with CLC Workbench software. Tab-delimited text file with expression values including FPKM

organism: Zea mays

source_name: Puma hybrid maize

growth_protocol: Puma hybrid maize plants were grown in 10 L plastic pots containing 1/1 v/v peatmoss and vermiculite sterile soil mixture under greenhouse conditions. Plants were collected at early reproductive stage R1 (60 DAS). Tissues collected were the top internode section of the stem, TI. And the female inflorescences (FI) which were bagged prior to silk emergence. Samples were frozen, milled with Restch mill in liquid nitrogen and storage at -80°C.

extract_protocol:
Total RNA from female inflorescences (FI) and top internodes of the stem (TI) at 60 DAS were extracted using the PureLink RNA-micro-to-midi Kit (Invitrogen Corp., Carlsbad, CA, USA) as described by the manufacturer. The purity and integrity of RNA samples were evaluated by electrophoresis on 2% RNase-free agarose gels, spectrophotometry (A260/A280 and A260/A230 ratios) using a NanoDrop 2000 (Thermo Scientific) and quality analysis using the Agilent 2100 Bioanalyzer system (Agilent technologies, Inc, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Puma hybrid

tag: developmental stage

value: 60 DAS before pollination

value: Top internode section of the stem


title: Top Internode section of the maize stem, rep 1


title: hAEC (HSC3)


title: GBM 10181360 FB-PMT  Rep. TREATED 2 48h

source_name: GBM 10181360 cell line

value: Treated, 48h

value: GBM 10181360 cell line


title: GBM 021913 CONTROL Rep. 7A


title: NT_0_3 Medium alone

value: Medium aone


title: B6_8w_Ccl4_3

source_name: Wild type (CCl4)

value: liver


title: NT_0_2 Medium alone


title: Female inflorescence rep 1

value: Female inflorescence


title: B6_8w_Ccl4_1


title: Ag-PVP80-2

status: Public on Sep 10 2021

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

country: China

institute: Chinese Academy of Sciences

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using cutadapt 2.10.
The filtered reads were mapped to the T. thermophila genome using HISAT.
Assembled the transcriptomes using StringTie.
The CUFFCOMPARE was used to compare all the assemblies to the genome annotation of T. thermophila.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by RSEM.
Genome_build: Tetrahymena thermophila
Supplementary_files_format_and_content: xls files include FPKM values for each Sample.

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila total RNA

growth_protocol: Colonial cultures were maintained in the SSP medium

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: three replicates was silver nanoparticles treated for 24 hours.

value: treated with Ag-PVP80 for 24 hours


title: Ag-PVP80-3


title: NT_0_1 Medium alone

value: Medium alone


title: Ag-Cit80-3

value: treated with Ag-Cit80 for 24 hours


title: Ag-Cit80-2


title: Ag-PVP80-1


title: hAEC (HSC4)

value: Rat hepatic stellate cells (HSC)

value: hAEC


title: Ag-Cit10-2

value: treated with Ag-Cit10 for 24 hours


title: AgNO3-3

value: treated with Ag+ for 24 hours


title: Ag-Cit10-3


title: Ag-Cit80-1


title: GBM 10181360 FB-PMT  Rep. TREATED 1 48h


title: AgNO3-2


title: GBM 10181360 FB-PMT  Rep. TREATED 2 24h

value: Treated, 24h


title: Control-2

value: untreated


title: GBM 10181360 FB-PMT  Rep. TREATED 1 24h


title: Female inflorescence rep 2

value: Puma hybrid


title: Control-3


title: CTCF_depleted_5

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
processed data files:
nanog_CTCF_merged_uniq_chimeric.txt
oct4_CTCF_merged_uniq_chimeric.txt
prdm14_CTCF_merged_uniq_chimeric.txt
sox2_CTCF_merged_uniq_chimeric.txt

data_processing:
Library strategy: Tiled-Micro-Capture-C
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Genome_build: mm10
Supplementary_files_format_and_content: chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions

source_name: E14 mouse embryonic stem cells

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

extract_protocol: Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

tag: genetic modification

value: CTCF-AID

value: auxin

value: E14 mouse embryonic stem cells


title: CTCF_depleted_4


title: B6_8w_Ccl4_2

value: wild type


title: CTCF_depleted_3


title: RAD21-depleted_5

description:
processed data files:
nanog_rad21_merged_uniq_chimeric.txt
oct4_rad21_merged_uniq_chimeric.txt
prdm14_rad21_merged_uniq_chimeric.txt
sox2_rad21_merged_uniq_chimeric.txt


title: Control-1


title: RAD21-depleted_3


title: Ag-Cit10-1


title: CTCF_depleted_2


title: RAD21-depleted_6


title: untreated_3

description:
processed data files:
nanog_untr_merged_uniq_chimeric.txt
oct4_untr_merged_uniq_chimeric.txt
prdm14_untr_merged_uniq_chimeric.txt
sox2_untr_merged_uniq_chimeric.txt


title: RAD21-depleted_4


title: PreB-Lig4-Rev1-18hrs-AsisI-ENDseq

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
library strategy: END-seq
END-seq reads were aligned to mm10 using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization at UCSC genome browser
.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson-transformed murine pre-B cells were grown in DMEM supplemented by 5% FBS, 1% pen/strep, 1% glutamine, 1% sodium pyruvate, 1% nonessential amino acids, and 55 μM β-mercaptoethanol

extract_protocol:
Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: For G0/G1 cell cycle arrest, asynchronously cycling cells were treated with 3 μM imatinib/STI (Selleckchem, S2475) for 48 hr at 1x106 cells/mL. To induce AsiSI-ER cutting, cells were treated with 3 μg/mL doxycycline for 24 hr, followed by 1 μM 4-hydroxytamoxifen for an additional 18 hr

value: Abelson-transformed pre-B cell

value: NT

tag: asisi induction


title: untreated_4


title: untreated_2


title: PreB-Lig4-Rev1-18hrs-AsisI-ENDseq-rep2

institute: Center for Excellence in Molecular Cell Science


title: CTCF_depleted_1


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-DNA2i-EXO1i-rep2

value: 2uM DNA2I+20uM EXO1i


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-DNA2i-rep2

value: 2uM DNA2i


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-EXO1i-rep2

value: 20uM EXO1i


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-control-for-DNA2i-EXO1i-rep2


title: PreB-Lig4-12hrs-AsisI-ENDseq-EXO1i-rep2


title: PreB-Lig4-12hrs-AsisI-ENDseq-DNA2i-rep2


title: PreB-Lig4-12hrs-AsisI-ENDseq-DNA2i-EXO1i-rep2


title: PreB-Lig4-12hrs-AsisI-ENDseq-control-for-DNA2i-EXO1i-rep2


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-EXO1i


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-DNA2i-EXO1i


title: untreated_1


title: PreB-Lig4-12hrs-AsisI-ENDseq-DNA2i-EXO1i


title: PreB-Lig4-12hrs-AsisI-ENDseq-EXO1i


title: PreB-Lig4-53BP1-12hrs-AsisI-ENDseq-control-for-DNA2i-EXO1i


title: PreB-Lig4-12hrs-AsisI-ENDseq-DNA2i


title: RAD21-depleted_1


title: PreB-WT-asyn-6hrs-AsisI-ENDseq-APH

value: asynchronized+5uM APH

value: WT


title: PreB-WT-asyn-6hrs-AsisI-ENDseq

value: asynchronized+NT


title: PreB-Lig4-G2-6hrs-AsisI-ENDseq-APH

value: G2 arrested+5uM APH


title: PreB-Lig4-asyn-6hrs-AsisI-ENDseq-APH


title: PreB-Lig4-12hrs-AsisI-ENDseq-control-for-DNA2i-EXO1i


title: PreB-Lig4-G2-6hrs-AsisI-ENDseq

value: G2 arrested+NT


title: PreB-Lig4-asyn-6hrs-AsisI-ENDseq


title: PreB-Lig4-53BP1-18hrs-AsisI-ENDseq-clone2-POLAi

value: 1uM POLAi