title: shMETTL3

status: Public on Mar 31 2023

type: SRA

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

country: USA

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
After base calling with Guppy (version 3.6.1+249406c) and mapping to human genome hg19 from the GENCODE database using Minimap2(57) (version 2.22-r1101). We used the machine learning based software nanom6A to detect m6A from nanopore direct RNA-seq with default parameters
Assembly: hg19 for nanopore RNA-seq
Supplementary files format and content: abundance measurements and TPM(Transcript Per Million) for each sample
Supplementary files format and content: bigwig for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: CD4 Tcell

growth_protocol: Human Peripheral Blood CD4+ T Cells were purchased from STEMCELL. Upon activation by ImmunoCult human CD3/CD28/CD2 T Cell activator (STEMCELL), T cells were expanded in ImmunoCult-XF T Cell expansion medium (STEMCELL) with the supplement of human recombinant IL-2 (STEMCELL) at 37 °C and 5% CO2 in a humidified atmosphere. Lentivirus Production and Infection Predesigned lentiviral shRNA vectors targeting METTL3 were purchased from Sigma (shMETTL3-1: TRCN0000289742, shMETTL3-2: TRCN0000289743).

extract_protocol:
The total RNA was extracted from both control and shMETTL3-1 CD4+ T cells using RNeasy Plus Mini Kit (Qiagen) and the mRNA purification was further achieved using PolyATtract mRNA Isolation System (Promega). The mRNA concentration was measured by Qubit RNA HS assay kit (ThermoFisher) and the quality was confirmed by Agilent Bioanalyzer RNA Pico assay chip.
Then, the mRNA was subjected to library construction using Oxford Nanopore direct RNA sequencing kit (SQK-RNA002) according to the manufacturer’s manual. A total of 500 ng mRNA was first annealed and ligated to RT adapter and then reverse-transcribed to form DNA-RNA hybrid products. Then, RNA adapter was ligated to the products and was ready for sequencer loading.
The resulting library was sequenced on R9.4.1 flow cell (FLO-MIN106D) using a MinION sequencer.

tag: cell line

value: CD4 Tcell

tag: cell type

value: T Cell

tag: genotype

tag: treatment


title: shCTRL

value: shCTRL

value: activation by ImmunoCult human CD3/CD28/CD2 T Cell activator


title: lung.NEC.85.normal [miRNA]

type: RNA

city: Madrid

first: GarciaCarbonero

last: Lab

state: Comunidad de Madrid

address: Av/ Córdoba s/n

department: Centro de Oncología Experimental

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

description:
NED288
normal.tissue

data_processing:
Data processing was performed using RT2 Profiler PCR Array Data Analysis versión 3.5 (https://dataanalysis.qiagen.com/mirna/arrayanalysis.php, Qiangen). Ct values for each miRNa was normalized using the mean Ct value of SNORD61, SNORD68, SNORD95, SNORD96A and RNU6B following the formula ∆Ct = Ct (miRNA) - Ct (house-keeping mean).
non-normalized.txt: Non-normalized values
fold-change.txt: Fold Change: Cancer/Normal

label: SYBR Green

molecule: total RNA

label_protocol: PCR assays were performed using the miHS-102Z miScript miRNA PCR Array Human Cancer Pathway Finder (QIAGEN) following the manufacturer’s instructions. Reverse transcription was performed from 250 ng total RNA using the miScript II RT (Qiagen). Quantitative real-time PCR (Applied Biosystems ViiA 7TM Real-Time PCR) were performed with initial activation step at 95oC for 15 minutes and 40 cycles at 94 oC for 15 seconds, 55 oC for 30 seconds and 70oC for 30 seconds.

extract_protocol: Total RNA was extracted from FFPE tissue samples using RecoverAllTM Total Nucleic Acid Isolation de Ambion (Applied Biosystems, Foster City, CA, USA).

value: lung

value: normal

tag: gender

value: male

tag: grade

tag: death


title: lung.NET.84.tumor [miRNA]

description:
NED285
FFPE.tumor.tissue

value: tumor

value: female


title: lung.NET.86.normal [miRNA]

description:
NED377
normal.tissue


title: lung.NET.86.tumor [miRNA]

description:
NED376
FFPE.tumor.tissue


title: lung.NET.84.normal [miRNA]

description:
NED286
normal.tissue


title: lung.NEC.85.tumor [miRNA]

description:
NED287
FFPE.tumor.tissue


title: lung.NET.83.normal [miRNA]

description:
NED284
normal.tissue


title: lung.NET.83.tumor [miRNA]

description:
NED283
FFPE.tumor.tissue


title: lung.NET.82.normal [miRNA]

description:
NED282
normal.tissue


title: lung.NET.82.tumor [miRNA]

description:
NED281
FFPE.tumor.tissue


title: lung.NET.80.normal [miRNA]

description:
NED278
normal.tissue


title: lung.NET.80.tumor [miRNA]

description:
NED277
FFPE.tumor.tissue


title: lung.NET.81.tumor [miRNA]

description:
NED279
FFPE.tumor.tissue


title: lung.NEC.79.normal [miRNA]

description:
NED276
normal.tissue


title: lung.NET.81.normal [miRNA]

description:
NED280
normal.tissue


title: lung.NEC.79.tumor [miRNA]

description:
NED275
FFPE.tumor.tissue


title: lung.NET.78.normal [miRNA]

description:
NED272
normal.tissue


title: lung.NET.76.tumor [miRNA]

description:
NED267
FFPE.tumor.tissue


title: lung.NET.77.tumor [miRNA]

description:
NED269
FFPE.tumor.tissue


title: lung.NET.75.normal [miRNA]

description:
NED266
normal.tissue


title: lung.NEC.74.tumor [miRNA]

description:
NED261
FFPE.tumor.tissue


title: lung.NET.75.tumor [miRNA]

description:
NED265
FFPE.tumor.tissue


title: lung.NET.76.normal [miRNA]

description:
NED268
normal.tissue


title: lung.NET.78.tumor [miRNA]

description:
NED271
FFPE.tumor.tissue


title: lung.NEC.74.normal [miRNA]

description:
NED262
normal.tissue


title: lung.NET.77.normal [miRNA]

description:
NED270
normal.tissue


title: lung.NEC.73.tumor [miRNA]

description:
NED259
FFPE.tumor.tissue


title: lung.NEC.73.normal [miRNA]

description:
NED260
normal.tissue


title: lung.NET.72.normal [miRNA]

description:
NED258
normal.tissue


title: lung.NEC.71.tumor [miRNA]

description:
NED255
FFPE.tumor.tissue


title: lung.NEC.70.tumor [miRNA]

description:
NED253
FFPE.tumor.tissue


title: lung.NET.69.normal [miRNA]

description:
NED252
normal.tissue


title: lung.NET.72.tumor [miRNA]

description:
NED257
FFPE.tumor.tissue


title: lung.NEC.70.normal [miRNA]

description:
NED254
normal.tissue


title: lung.NET.68.tumor [miRNA]

description:
NED249
FFPE.tumor.tissue


title: lung.NET.68.normal [miRNA]

description:
NED250
normal.tissue


title: lung.NET.69.tumor [miRNA]

description:
NED251
FFPE.tumor.tissue


title: lung.NET.67.normal [miRNA]

description:
NED247
normal.tissue


title: lung.NET.66.normal [miRNA]

description:
NED246
normal.tissue


title: lung.NET.65.normal [miRNA]

description:
NED244
normal.tissue


title: lung.NET.62.normal [miRNA]

description:
NED237
normal.tissue


title: lung.NET.64.tumor [miRNA]

description:
NED241
FFPE.tumor.tissue


title: lung.NET.67.tumor [miRNA]

description:
NED248
FFPE.tumor.tissue


title: lung.NEC.71.normal [miRNA]

description:
NED256
normal.tissue


title: lung.NET.66.tumor [miRNA]

description:
NED245
FFPE.tumor.tissue


title: lung.NET.64.normal [miRNA]

description:
NED242
normal.tissue


title: lung.NET.65.tumor [miRNA]

description:
NED243
FFPE.tumor.tissue


title: lung.NEC.58.normal [miRNA]

description:
NED225
normal.tissue


title: lung.NET.59.tumor [miRNA]

description:
NED226
FFPE.tumor.tissue


title: lung.NET.59.normal [miRNA]

description:
NED227
normal.tissue


title: lung.NET.60.tumor [miRNA]

description:
NED230
FFPE.tumor.tissue


title: lung.NEC.61.normal [miRNA]

description:
NED235
normal.tissue


title: lung.NEC.61.tumor [miRNA]

description:
NED234
FFPE.tumor.tissue


title: lung.NEC.57.normal [miRNA]

description:
NED223
normal.tissue


title: lung.NEC.58.tumor [miRNA]

description:
NED224
FFPE.tumor.tissue


title: lung.NET.63.tumor [miRNA]

description:
NED238
FFPE.tumor.tissue


title: lung.NET.62.tumor [miRNA]

description:
NED236
FFPE.tumor.tissue


title: lung.NET.60.normal [miRNA]

description:
NED231
normal.tissue


title: lung.NET.63.normal [miRNA]

description:
NED239
normal.tissue


title: lung.NET.56.normal [miRNA]

description:
NED221
normal.tissue


title: lung.NET.56.tumor [miRNA]

description:
NED220
FFPE.tumor.tissue


title: lung.NEC.55.normal [miRNA]

description:
NED217
normal.tissue


title: lung.NET.53.tumor [miRNA]

description:
NED212
FFPE.tumor.tissue


title: lung.NET.53.normal [miRNA]

description:
NED213
normal.tissue


title: lung.NEC.52.normal [miRNA]

description:
NED211
normal.tissue


title: lung.NET.54.normal [miRNA]

description:
NED215
normal.tissue


title: lung.NET.54.tumor [miRNA]

description:
NED214
FFPE.tumor.tissue


title: lung.NEC.55.tumor [miRNA]

description:
NED216
FFPE.tumor.tissue


title: lung.NET.51.tumor [miRNA]

description:
NED206
FFPE.tumor.tissue


title: lung.NET.50.tumor [miRNA]

description:
NED204
FFPE.tumor.tissue


title: lung.NET.49.normal [miRNA]

description:
NED203
normal.tissue


title: lung.NET.51.normal [miRNA]

description:
NED207
normal.tissue


title: lung.NET.50.normal [miRNA]

description:
NED205
normal.tissue


title: lung.NET.49.tumor [miRNA]

description:
NED202
FFPE.tumor.tissue


title: lung.NET.48.normal [miRNA]

description:
NED201
normal.tissue


title: lung.NEC.45.normal [miRNA]

description:
NED195
normal.tissue


title: lung.NET.44.tumor [miRNA]

description:
NED192
FFPE.tumor.tissue


title: lung.NEC.45.tumor [miRNA]

description:
NED194
FFPE.tumor.tissue


title: lung.NEC.46.tumor [miRNA]

description:
NED196
FFPE.tumor.tissue


title: lung.NEC.57.tumor [miRNA]

description:
NED222
FFPE.tumor.tissue


title: lung.NEC.46.normal [miRNA]

description:
NED197
normal.tissue


title: lung.NET.44.normal [miRNA]

description:
NED193
normal.tissue


title: lung.NEC.43.tumor [miRNA]

description:
NED190
FFPE.tumor.tissue


title: lung.NEC.43.normal [miRNA]

description:
NED191
normal.tissue


title: lung.NEC.41.normal [miRNA]

description:
NED187
normal.tissue


title: lung.NET.42.tumor [miRNA]

description:
NED188
FFPE.tumor.tissue


title: lung.NET.47.tumor [miRNA]

description:
NED198
FFPE.tumor.tissue


title: lung.NET.47.normal [miRNA]

description:
NED199
normal.tissue


title: lung.NET.42.normal [miRNA]

description:
NED189
normal.tissue


title: lung.NET.48.tumor [miRNA]

description:
NED200
FFPE.tumor.tissue


title: lung.NEC.52.tumor [miRNA]

description:
NED210
FFPE.tumor.tissue


title: lung.NEC.41.tumor [miRNA]

description:
NED186
FFPE.tumor.tissue


title: lung.NET.40.normal [miRNA]

description:
NED185
normal.tissue


title: lung.NEC.39.normal [miRNA]

description:
NED183
normal.tissue


title: lung.NET.40.tumor [miRNA]

description:
NED184
FFPE.tumor.tissue


title: lung.NEC.39.tumor [miRNA]

description:
NED182
FFPE.tumor.tissue


title: lung.NET.38.tumor [miRNA]

description:
NED180
FFPE.tumor.tissue


title: lung.NET.38.normal [miRNA]

description:
NED181
normal.tissue


title: lung.NET.37.normal [miRNA]

description:
NED179
normal.tissue


title: lung.NET.37.tumor [miRNA]

description:
NED178
FFPE.tumor.tissue


title: lung.NET.36.normal [miRNA]

description:
NED175
normal.tissue


title: lung.NET.36.tumor [miRNA]

description:
NED174
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.34.normal [miRNA]

description:
NED404
normal.tissue

value: small intestine


title: gastroenteropancreatic.NET.35.tumor [miRNA]

description:
NED418
FFPE.tumor.tissue

value: stomach


title: gastroenteropancreatic.NET.35.normal [miRNA]

description:
NED419
normal.tissue


title: gastroenteropancreatic.NET.33.tumor [miRNA]

description:
NED394
FFPE.tumor.tissue

value: apendix


title: gastroenteropancreatic.NET.34.tumor [miRNA]

description:
NED403
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.31.normal [miRNA]

description:
NED358
normal.tissue

value: pancreas


title: gastroenteropancreatic.NET.30.normal [miRNA]

description:
NED356
normal.tissue

value: colorectal


title: gastroenteropancreatic.NET.33.normal [miRNA]

description:
NED395
normal.tissue


title: gastroenteropancreatic.NEC.32.normal [miRNA]

description:
NED373
normal.tissue


title: gastroenteropancreatic.NET.30.tumor [miRNA]

description:
NED355
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.29.normal [miRNA]

description:
NED354
normal.tissue


title: gastroenteropancreatic.NET.27.normal [miRNA]

description:
NED348
normal.tissue


title: gastroenteropancreatic.NET.29.tumor [miRNA]

description:
NED353
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.28.tumor [miRNA]

description:
NED351
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.28.normal [miRNA]

description:
NED352
normal.tissue


title: gastroenteropancreatic.NET.31.tumor [miRNA]

description:
NED357
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.32.tumor [miRNA]

description:
NED372
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.26.tumor [miRNA]

description:
NED345
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.26.normal [miRNA]

description:
NED346
normal.tissue


title: gastroenteropancreatic.NET.27.tumor [miRNA]

description:
NED347
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.24.normal [miRNA]

description:
NED342
normal.tissue


title: gastroenteropancreatic.NET.25.normal [miRNA]

description:
NED344
normal.tissue


title: gastroenteropancreatic.NET.24.tumor [miRNA]

description:
NED341
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.23.normal [miRNA]

description:
NED340
normal.tissue


title: gastroenteropancreatic.NET.25.tumor [miRNA]

description:
NED343
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.23.tumor [miRNA]

description:
NED339
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.22.normal [miRNA]

description:
NED338
normal.tissue


title: gastroenteropancreatic.NET.20.normal [miRNA]

description:
NED334
normal.tissue


title: gastroenteropancreatic.NET.22.tumor [miRNA]

description:
NED337
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.19.normal [miRNA]

description:
NED332
normal.tissue


title: gastroenteropancreatic.NEC.21.normal [miRNA]

description:
NED336
normal.tissue


title: gastroenteropancreatic.NET.19.tumor [miRNA]

description:
NED331
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.21.tumor [miRNA]

description:
NED335
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.17.normal [miRNA]

description:
NED290
normal.tissue


title: gastroenteropancreatic.NET.17.tumor [miRNA]

description:
NED289
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.16.tumor [miRNA]

description:
NED103
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.20.tumor [miRNA]

description:
NED333
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.14.normal [miRNA]

description:
NED086
normal.tissue


title: gastroenteropancreatic.NET.14.tumor [miRNA]

description:
NED087
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.15.normal [miRNA]

description:
NED096
normal.tissue


title: gastroenteropancreatic.NET.15.tumor [miRNA]

description:
NED097
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.10.tumor [miRNA]

description:
NED041
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.16.normal [miRNA]

description:
NED102
normal.tissue


title: gastroenteropancreatic.NEC.9.tumor [miRNA]

description:
NED039
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.13.tumor [miRNA]

description:
NED078
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.13.normal [miRNA]

description:
NED077
normal.tissue


title: gastroenteropancreatic.NEC.9.normal [miRNA]

description:
NED038
normal.tissue


title: gastroenteropancreatic.NEC.8.normal [miRNA]

description:
NED027
normal.tissue


title: gastroenteropancreatic.NET.12.tumor [miRNA]

description:
NED075
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.8.tumor [miRNA]

description:
NED028
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.12.normal [miRNA]

description:
NED074
normal.tissue


title: gastroenteropancreatic.NEC.10.normal [miRNA]

description:
NED040
normal.tissue


title: gastroenteropancreatic.NET.7.normal [miRNA]

description:
NED025
normal.tissue


title: gastroenteropancreatic.NET.7.tumor [miRNA]

description:
NED026
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.6.tumor [miRNA]

description:
NED024
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.6.normal [miRNA]

description:
NED023
normal.tissue


title: gastroenteropancreatic.NET.5.tumor [miRNA]

description:
NED022
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.4.tumor [miRNA]

description:
NED020
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.5.normal [miRNA]

description:
NED021
normal.tissue


title: gastroenteropancreatic.NET.4.normal [miRNA]

description:
NED019
normal.tissue


title: Sample 24 - LPS, 18h, rep4

city: Bonn

first: Friederike

middle: Sophie

last: Gorki

address: Venusberg-Campus 1

country: Germany

institute: Institute of Innate Immunity

description: Matrix Column R

data_processing:
Using cutadapt version 1.18 (https://cutadapt.readthedocs.io/en/stable/), the reads of the sequencing run were scanned for adapter contaminations, continuous polyA sequences and continuous polyG sequences at the 3’ end and had the contaminations removed if they were found. The reads of the samples prior to adapter trimming and after adapter trimming were analyzed with FastQC version v0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the spike-in complemented Ensembl release 101 of the Mus musculus high coverage assembly GRCm38 from the Genome Reference Consortium. The alignment was performed with the splice-aware aligner STAR version 2.6.1a (https://github.com/alexdobin/STAR)1. The alignments were quantified based on the annotations of Ensembl GRCm38.101 and the spike-in specific annotations of Lexogen with the featureCounts software program version 1.6.4 of the subread analysis package (http://subread.sourceforge.net/).
A differential gene expression analysis was conducted using DESeq2 (version v1.18.1; https://bioconductor.org/packages/release/bioc/html/DESeq2.html ). The analysis used the counts of unique alignments. Significance was determined at adj P<0.1.
Assembly: GRCm38
Supplementary files format and content: tab-separated values (tsv) file including library names, gene IDs and individual normalized counts

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated by culturing bone marrow cells in DMEM supplemented with 10 % FCS, 1 % Penicillin/Streptomycin and 15 % L929 cell-conditioned medium (LCM). On day 6 of differentiation, BMDMs were collected and plated for experiments. Experiments were performed in DMEM supplemented with 10 % FCS and 1 % Penicillin/Streptomycin, unless stated otherwise.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit together with the RNase-free DNase Set for DNA digestion (both Qiagen) according to manufacturer instructions
Libraries were prepared manually according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit. Briefly, 150 ng total RNA was used as input for reverse transcription with oligo(dT) primer containing an Illumina-compatible sequence at its 5’ end. After RNA removal, the second strand of the cDNA was synthesized by a random primer containing an Illumina-compatible linker sequence at its 5’ end. Finally, individual sample barcodes (dual indexing) for multiplexing were introduced via 15 cycles of PCR (determined by qPCR). All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer (Agilent). After pooling the libraries in an equimolar ratio, the concentration and the size distribution of the lane mix was analyzed by Qubit (Thermo Fisher Scientific) and by Fragment Analyzer (Agilent), respectively. A 2 nM dilution of the lane mix was denatured and diluted for sequencing on a NextSeq 2000 instrument

treatment_protocol: For RNA Sequencing, 1 Million BMDMs per condition were left untreated (control), stimulated with 30 µM S14 or 100 ng/mL LPS for 3 h or 18 h before harvesting cells for RNA isolation.

value: Bone marrow-derived macrophages

value: wild-type

value: LPS

tag: time


title: gastroenteropancreatic.NEC.2.normal [miRNA]

description:
NED015
normal.tissue


title: gastroenteropancreatic.NEC.2.tumor [miRNA]

description:
NED016
FFPE.tumor.tissue


title: Sample 22 - LPS, 18h, rep2

description: Matrix Column P


title: gastroenteropancreatic.NET.3.tumor [miRNA]

description:
NED018
FFPE.tumor.tissue


title: gastroenteropancreatic.NEC.1.tumor [miRNA]

description:
NED010
FFPE.tumor.tissue


title: gastroenteropancreatic.NET.3.normal [miRNA]

description:
NED017
normal.tissue


title: gastroenteropancreatic.NEC.1.normal [miRNA]

description:
NED009
normal.tissue


title: Sample 23 - LPS, 18h, rep3

description: Matrix Column Q


title: Sample 20 - S14, 18h, rep4

description: Matrix Column N


title: Sample 19 - S14, 18h, rep3

description: Matrix Column L


title: Sample 21 - LPS, 18h, rep1

description: Matrix Column O


title: Sample 18 - S14, 18h, rep2

description: Matrix Column K


title: Sample 16 - UT, 18h, rep4

description: Matrix Column I

value: untreated


title: Sample 17 - S14, 18h, rep1

description: Matrix Column J


title: Sample 15 - UT, 18h, rep3

description: Matrix Column H


title: Sample 14 - UT, 18h, rep2

description: Matrix Column G


title: Sample 11 - LPS, 3h, rep3

description: Matrix Column D


title: Sample 13 - UT, 18h, rep1

description: Matrix Column F


title: Sample 10 - LPS, 3h, rep2

description: Matrix Column C


title: Sample 12 - LPS, 3h, rep4

description: Matrix Column E


title: Sample 8 - S14, 3h, rep4

description: Matrix Column X


title: Sample 7 - S14, 3h, rep3

description: Matrix Column W


title: Sample 6 - S14, 3h, rep2

description: Matrix Column V


title: Sample 9 - LPS, 3h, rep1

description: Matrix Column Y


title: Sample 3 - UT, 3h, rep3

description: Matrix Column S


title: Sample 2 - UT, 3h, rep2

description: Matrix Column M


title: TE11_shKDM2A_rep2

city: LuZhou

first: Fang

last: Huang

address: No. 25 taiping street

country: China

institute: The Affiliated Hospital of Southwest Medical University

data_processing:
Illumina bcl2fastq 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRch37.p13/GRch38.p13 whole genome using HISAT2 (version 2.1.0) with default parameters
Read counts are aggregated at the gene level using HTseq(version 0.9.1) and then identified DEGs using R package DESeq2
Assembly: GRCh37.p13/GRch38.p13
Supplementary files format and content: tab-delimited text files include raw counts  for each Sample

growth_protocol: Kyse150 and TE11 cells were maintained in  RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated by Trizol and mRNA was enriched by Dynabeads Oligo (dT)25 beads
RNA libraries for RNA-seq were prepared using the VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina (NR601, Vazyme, Nanjing, China) with 3 independent replicates following manufacturer's protocols.One hundred and fifty bp paired-end sequencing was performing using Illumina HiSeq Xten.

value: Esophageal cells

value: KDM2A knockdown


title: Sample 1 - UT, 3h, rep1

description: Matrix Column B


title: TE11_shKDM2A_rep1


title: TE11_shNC_rep2

value: Control


title: Kyse150_shKDM2A_rep2


title: Kyse150_shKDM2A_rep1


title: Kyse150_shNC_rep2


title: TE11_shNC_rep1


title: TE11_shNC_rep3


title: NC2, Bulk RNA-Seq

city: Su Zhou

first: Shiyou

last: Wang

state: Jiang Su

address: Chong Wen street

department: Suzhou Institute of Systems Medicine

institute: Peking Union Medical College

data_processing:
To estimate gene expression changes, the raw RNA-seq data were preprocessed using Trimmomatic to remove reads of low quality and adaptor contamination.
The high-quality reads were further aligned to the mouse genome (mm10) using HISAT2 with default parameters.
Only uniquely mapped reads were retained for gene expression quantification at the count level using feature counts based on mouse gene annotation of Ensembl.
mm10
tab-delimited text files include RPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted using the Simply P Total RNA Extraction Kit (BioFlux).
Total RNA was prepared into a cDNA library according to the standard Illumina RNA-seq instructions.

tag: tissue

value: cell line

value: MOVAS

value: Smooth muscle cell

value: WT

value: siRNA(Ctrl)


title: Kyse150_shNC_rep1


title: H73WCBBXY_5_IDT-DUI-NXT-96

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

institute: IDIBAPS

data_processing:
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx (Raw counts for each cell)

source_name: Tetramer+ CD4+ T cells

extract_protocol:
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)

treatment_protocol: Mice that have received intravenously 10 doses of InsB13-21-CT-R1/IAg7-NPs.

tag: strain

value: NOD

value: T cell

value: pMHCII-NPs

tag: sample type

value: Tetramer+ CD4+ T cells from InsB13-21-CT-R2/IAg7-NP-treated


title: ChIP-seq_H1KO_HA_tetR_EED_targeting_H3K27me3_rep2

city: Beijing

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph files

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol:
ChIP-seq:  mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.
ChOR-seq:  mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq:  Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChIP-seq:  H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.
ChOR-seq:  Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChOR-seq:  H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: mouse embryonic stem cells

tag: chip antibody


title: H73WCBBXY_5_IDT-DUI-NXT-95


title: H73WCBBXY_5_IDT-DUI-NXT-93


title: NC1, Bulk RNA-Seq

description: Simply P Total RNA Extraction Kit (BioFlux)


title: SiYT1, Bulk RNA-Seq

value: siYAP/TAZ


title: SiYT2, Bulk RNA-Seq


title: H73WCBBXY_5_IDT-DUI-NXT-94


title: Sample 4 - UT, 3h, rep4

description: Matrix Column T

value: Bone marrow-derived macrophages

value: wild-type


title: H73WCBBXY_5_IDT-DUI-NXT-88


title: Sample 5 - S14, 3h, rep1

description: Matrix Column U


title: H73WCBBXY_5_IDT-DUI-NXT-89


title: H73WCBBXY_5_IDT-DUI-NXT-87


title: H73WCBBXY_5_IDT-DUI-NXT-86


title: H73WCBBXY_5_IDT-DUI-NXT-90


title: H73WCBBXY_5_IDT-DUI-NXT-83


title: H73WCBBXY_5_IDT-DUI-NXT-81


title: H73WCBBXY_5_IDT-DUI-NXT-78


title: H73WCBBXY_5_IDT-DUI-NXT-8


title: H73WCBBXY_5_IDT-DUI-NXT-79


title: H73WCBBXY_5_IDT-DUI-NXT-76


title: H73WCBBXY_5_IDT-DUI-NXT-92


title: H73WCBBXY_5_IDT-DUI-NXT-91


title: H73WCBBXY_5_IDT-DUI-NXT-75


title: H73WCBBXY_5_IDT-DUI-NXT-73


title: H73WCBBXY_5_IDT-DUI-NXT-72


title: H73WCBBXY_5_IDT-DUI-NXT-74


title: H73WCBBXY_5_IDT-DUI-NXT-9


title: H73WCBBXY_5_IDT-DUI-NXT-70


title: H73WCBBXY_5_IDT-DUI-NXT-7


title: H73WCBBXY_5_IDT-DUI-NXT-69


title: H73WCBBXY_5_IDT-DUI-NXT-85


title: H73WCBBXY_5_IDT-DUI-NXT-67


title: H73WCBBXY_5_IDT-DUI-NXT-66


title: H73WCBBXY_5_IDT-DUI-NXT-84


title: H73WCBBXY_5_IDT-DUI-NXT-62


title: H73WCBBXY_5_IDT-DUI-NXT-63


title: H73WCBBXY_5_IDT-DUI-NXT-68


title: H73WCBBXY_5_IDT-DUI-NXT-65


title: H73WCBBXY_5_IDT-DUI-NXT-82


title: H73WCBBXY_5_IDT-DUI-NXT-61


title: H73WCBBXY_5_IDT-DUI-NXT-80


title: H73WCBBXY_5_IDT-DUI-NXT-77


title: H73WCBBXY_5_IDT-DUI-NXT-58


title: H73WCBBXY_5_IDT-DUI-NXT-55


title: H73WCBBXY_5_IDT-DUI-NXT-54


title: H73WCBBXY_5_IDT-DUI-NXT-71


title: H73WCBBXY_5_IDT-DUI-NXT-51


title: H73WCBBXY_5_IDT-DUI-NXT-52


title: H73WCBBXY_5_IDT-DUI-NXT-64


title: H73WCBBXY_5_IDT-DUI-NXT-5


title: H73WCBBXY_5_IDT-DUI-NXT-49


title: H73WCBBXY_5_IDT-DUI-NXT-47


title: H73WCBBXY_5_IDT-DUI-NXT-46


title: H73WCBBXY_5_IDT-DUI-NXT-45


title: H73WCBBXY_5_IDT-DUI-NXT-43


title: H73WCBBXY_5_IDT-DUI-NXT-41


title: H73WCBBXY_5_IDT-DUI-NXT-6


title: H73WCBBXY_5_IDT-DUI-NXT-60


title: H73WCBBXY_5_IDT-DUI-NXT-40


title: H73WCBBXY_5_IDT-DUI-NXT-4


title: H73WCBBXY_5_IDT-DUI-NXT-39


title: H73WCBBXY_5_IDT-DUI-NXT-38


title: H73WCBBXY_5_IDT-DUI-NXT-59


title: H73WCBBXY_5_IDT-DUI-NXT-57


title: H73WCBBXY_5_IDT-DUI-NXT-37


title: H73WCBBXY_5_IDT-DUI-NXT-36


title: H73WCBBXY_5_IDT-DUI-NXT-56


title: H73WCBBXY_5_IDT-DUI-NXT-35


title: H73WCBBXY_5_IDT-DUI-NXT-33


title: H73WCBBXY_5_IDT-DUI-NXT-34


title: H73WCBBXY_5_IDT-DUI-NXT-53


title: H73WCBBXY_5_IDT-DUI-NXT-50


title: H73WCBBXY_5_IDT-DUI-NXT-32


title: H73WCBBXY_5_IDT-DUI-NXT-48


title: H73WCBBXY_5_IDT-DUI-NXT-3


title: H73WCBBXY_5_IDT-DUI-NXT-30


title: H73WCBBXY_5_IDT-DUI-NXT-44


title: H73WCBBXY_5_IDT-DUI-NXT-29


title: H73WCBBXY_5_IDT-DUI-NXT-42


title: H73WCBBXY_5_IDT-DUI-NXT-27


title: H73WCBBXY_5_IDT-DUI-NXT-26


title: H73WCBBXY_5_IDT-DUI-NXT-24


title: H73WCBBXY_5_IDT-DUI-NXT-25


title: H73WCBBXY_5_IDT-DUI-NXT-23


title: H73WCBBXY_5_IDT-DUI-NXT-17


title: H73WCBBXY_5_IDT-DUI-NXT-21


title: H73WCBBXY_5_IDT-DUI-NXT-15


title: H73WCBBXY_5_IDT-DUI-NXT-2


title: H73WCBBXY_5_IDT-DUI-NXT-16


title: H73WCBBXY_5_IDT-DUI-NXT-14


title: H73WCBBXY_5_IDT-DUI-NXT-22


title: H73WCBBXY_5_IDT-DUI-NXT-19


title: H73WCBBXY_5_IDT-DUI-NXT-13


title: H73WCBBXY_5_IDT-DUI-NXT-1


title: H73WCBBXY_5_IDT-DUI-NXT-10


title: H73WCBBXY_5_IDT-DUI-NXT-11


title: H73WCBBXY_5_IDT-DUI-NXT-31


title: HC5H7BBXY_7_IDT-DUI-NXT-288

treatment_protocol: Mice that have received intravenously 10 doses of InsB12-20-CT-R1/IAg7-NPs.

value: Tetramer+ CD4+ T cells from InsB12-20-CT-R1/IAg7-NP-treated


title: H73WCBBXY_5_IDT-DUI-NXT-28


title: HC5H7BBXY_7_IDT-DUI-NXT-286


title: HC5H7BBXY_7_IDT-DUI-NXT-287


title: HC5H7BBXY_7_IDT-DUI-NXT-285


title: HC5H7BBXY_7_IDT-DUI-NXT-282


title: HC5H7BBXY_7_IDT-DUI-NXT-278


title: H73WCBBXY_5_IDT-DUI-NXT-20


title: HC5H7BBXY_7_IDT-DUI-NXT-279


title: HC5H7BBXY_7_IDT-DUI-NXT-277


title: HC5H7BBXY_7_IDT-DUI-NXT-283


title: H73WCBBXY_5_IDT-DUI-NXT-12


title: HC5H7BBXY_7_IDT-DUI-NXT-280


title: HC5H7BBXY_7_IDT-DUI-NXT-281


title: HC5H7BBXY_7_IDT-DUI-NXT-270


title: HC5H7BBXY_7_IDT-DUI-NXT-274


title: HC5H7BBXY_7_IDT-DUI-NXT-275


title: H73WCBBXY_5_IDT-DUI-NXT-18


title: HC5H7BBXY_7_IDT-DUI-NXT-267


title: HC5H7BBXY_7_IDT-DUI-NXT-272


title: HC5H7BBXY_7_IDT-DUI-NXT-263


title: HC5H7BBXY_7_IDT-DUI-NXT-273


title: HC5H7BBXY_7_IDT-DUI-NXT-271


title: HC5H7BBXY_7_IDT-DUI-NXT-265


title: HC5H7BBXY_7_IDT-DUI-NXT-266


title: HC5H7BBXY_7_IDT-DUI-NXT-269


title: HC5H7BBXY_7_IDT-DUI-NXT-261


title: HC5H7BBXY_7_IDT-DUI-NXT-259


title: HC5H7BBXY_7_IDT-DUI-NXT-260


title: HC5H7BBXY_7_IDT-DUI-NXT-264


title: HC5H7BBXY_7_IDT-DUI-NXT-268


title: HC5H7BBXY_7_IDT-DUI-NXT-256


title: HC5H7BBXY_7_IDT-DUI-NXT-284


title: HC5H7BBXY_7_IDT-DUI-NXT-255


title: HC5H7BBXY_7_IDT-DUI-NXT-257


title: HC5H7BBXY_7_IDT-DUI-NXT-254


title: HC5H7BBXY_7_IDT-DUI-NXT-276


title: HC5H7BBXY_7_IDT-DUI-NXT-258


title: HC5H7BBXY_7_IDT-DUI-NXT-262


title: HC5H7BBXY_7_IDT-DUI-NXT-249


title: HC5H7BBXY_7_IDT-DUI-NXT-244


title: HC5H7BBXY_7_IDT-DUI-NXT-247


title: HC5H7BBXY_7_IDT-DUI-NXT-251


title: HC5H7BBXY_7_IDT-DUI-NXT-252


title: HC5H7BBXY_7_IDT-DUI-NXT-253


title: HC5H7BBXY_7_IDT-DUI-NXT-250


title: HC5H7BBXY_7_IDT-DUI-NXT-243


title: HC5H7BBXY_7_IDT-DUI-NXT-241


title: HC5H7BBXY_7_IDT-DUI-NXT-240


title: HC5H7BBXY_7_IDT-DUI-NXT-239


title: HC5H7BBXY_7_IDT-DUI-NXT-236


title: HC5H7BBXY_7_IDT-DUI-NXT-238


title: HC5H7BBXY_7_IDT-DUI-NXT-237


title: HC5H7BBXY_7_IDT-DUI-NXT-235


title: HC5H7BBXY_7_IDT-DUI-NXT-246


title: HC5H7BBXY_7_IDT-DUI-NXT-248


title: HC5H7BBXY_7_IDT-DUI-NXT-245


title: HC5H7BBXY_7_IDT-DUI-NXT-242


title: HC5H7BBXY_7_IDT-DUI-NXT-232


title: HC5H7BBXY_7_IDT-DUI-NXT-234


title: HC5H7BBXY_7_IDT-DUI-NXT-231


title: HC5H7BBXY_7_IDT-DUI-NXT-233


title: HC5H7BBXY_7_IDT-DUI-NXT-229


title: HC5H7BBXY_7_IDT-DUI-NXT-230


title: HC5H7BBXY_7_IDT-DUI-NXT-228


title: HC5H7BBXY_7_IDT-DUI-NXT-227


title: HC5H7BBXY_7_IDT-DUI-NXT-223


title: HC5H7BBXY_7_IDT-DUI-NXT-225


title: HC5H7BBXY_7_IDT-DUI-NXT-224


title: HC5H7BBXY_7_IDT-DUI-NXT-221


title: HC5H7BBXY_7_IDT-DUI-NXT-226


title: HC5H7BBXY_7_IDT-DUI-NXT-220


title: HC5H7BBXY_7_IDT-DUI-NXT-222


title: HC5H7BBXY_7_IDT-DUI-NXT-217


title: HC5H7BBXY_7_IDT-DUI-NXT-216


title: HC5H7BBXY_7_IDT-DUI-NXT-219


title: HC5H7BBXY_7_IDT-DUI-NXT-213


title: HC5H7BBXY_7_IDT-DUI-NXT-215


title: HC5H7BBXY_7_IDT-DUI-NXT-210


title: HC5H7BBXY_7_IDT-DUI-NXT-208


title: HC5H7BBXY_7_IDT-DUI-NXT-204


title: HC5H7BBXY_7_IDT-DUI-NXT-205


title: HC5H7BBXY_7_IDT-DUI-NXT-209


title: HC5H7BBXY_7_IDT-DUI-NXT-218


title: HC5H7BBXY_7_IDT-DUI-NXT-214


title: HC5H7BBXY_7_IDT-DUI-NXT-203


title: HC5H7BBXY_7_IDT-DUI-NXT-211


title: HC5H7BBXY_7_IDT-DUI-NXT-206


title: HC5H7BBXY_7_IDT-DUI-NXT-212


title: HC5H7BBXY_7_IDT-DUI-NXT-207


title: HC5H7BBXY_7_IDT-DUI-NXT-201


title: HC5H7BBXY_7_IDT-DUI-NXT-200


title: HC5H7BBXY_7_IDT-DUI-NXT-202


title: HC5H7BBXY_7_IDT-DUI-NXT-198


title: HC5H7BBXY_7_IDT-DUI-NXT-199


title: HC5H7BBXY_7_IDT-DUI-NXT-197


title: HC5H7BBXY_7_IDT-DUI-NXT-196


title: HC5H7BBXY_7_IDT-DUI-NXT-193


title: HC5H7BBXY_7_IDT-DUI-NXT-195


title: HC5H7BBXY_7_IDT-DUI-NXT-194


title: H73J2BBXY_3_IDT-DUI-NXT-97


title: H73J2BBXY_3_IDT-DUI-NXT-99


title: H73J2BBXY_3_IDT-DUI-NXT-98


title: H73J2BBXY_3_IDT-DUI-NXT-191


title: H73J2BBXY_3_IDT-DUI-NXT-190


title: H73J2BBXY_3_IDT-DUI-NXT-189


title: H73J2BBXY_3_IDT-DUI-NXT-188


title: H73J2BBXY_3_IDT-DUI-NXT-187


title: H73J2BBXY_3_IDT-DUI-NXT-186


title: H73J2BBXY_3_IDT-DUI-NXT-185


title: H73J2BBXY_3_IDT-DUI-NXT-183


title: H73J2BBXY_3_IDT-DUI-NXT-184


title: H73J2BBXY_3_IDT-DUI-NXT-182


title: H73J2BBXY_3_IDT-DUI-NXT-177


title: H73J2BBXY_3_IDT-DUI-NXT-176


title: H73J2BBXY_3_IDT-DUI-NXT-173


title: H73J2BBXY_3_IDT-DUI-NXT-181


title: H73J2BBXY_3_IDT-DUI-NXT-179


title: H73J2BBXY_3_IDT-DUI-NXT-172


title: H73J2BBXY_3_IDT-DUI-NXT-180


title: H73J2BBXY_3_IDT-DUI-NXT-174


title: H73J2BBXY_3_IDT-DUI-NXT-178


title: H73J2BBXY_3_IDT-DUI-NXT-175


title: H73J2BBXY_3_IDT-DUI-NXT-169


title: H73J2BBXY_3_IDT-DUI-NXT-170


title: H73J2BBXY_3_IDT-DUI-NXT-171


title: H73J2BBXY_3_IDT-DUI-NXT-192


title: H73J2BBXY_3_IDT-DUI-NXT-165


title: H73J2BBXY_3_IDT-DUI-NXT-168


title: H73J2BBXY_3_IDT-DUI-NXT-167


title: H73J2BBXY_3_IDT-DUI-NXT-166


title: H73J2BBXY_3_IDT-DUI-NXT-162


title: H73J2BBXY_3_IDT-DUI-NXT-161


title: H73J2BBXY_3_IDT-DUI-NXT-164


title: H73J2BBXY_3_IDT-DUI-NXT-163


title: H73J2BBXY_3_IDT-DUI-NXT-160


title: H73J2BBXY_3_IDT-DUI-NXT-158


title: H73J2BBXY_3_IDT-DUI-NXT-159


title: H73J2BBXY_3_IDT-DUI-NXT-156


title: H73J2BBXY_3_IDT-DUI-NXT-157


title: H73J2BBXY_3_IDT-DUI-NXT-154


title: H73J2BBXY_3_IDT-DUI-NXT-155


title: H73J2BBXY_3_IDT-DUI-NXT-153


title: H73J2BBXY_3_IDT-DUI-NXT-152


title: H73J2BBXY_3_IDT-DUI-NXT-151


title: H73J2BBXY_3_IDT-DUI-NXT-150


title: H73J2BBXY_3_IDT-DUI-NXT-147


title: H73J2BBXY_3_IDT-DUI-NXT-149


title: H73J2BBXY_3_IDT-DUI-NXT-144


title: H73J2BBXY_3_IDT-DUI-NXT-142


title: H73J2BBXY_3_IDT-DUI-NXT-143


title: H73J2BBXY_3_IDT-DUI-NXT-146


title: H73J2BBXY_3_IDT-DUI-NXT-140


title: H73J2BBXY_3_IDT-DUI-NXT-148


title: H73J2BBXY_3_IDT-DUI-NXT-141


title: H73J2BBXY_3_IDT-DUI-NXT-145


title: H73J2BBXY_3_IDT-DUI-NXT-137


title: H73J2BBXY_3_IDT-DUI-NXT-139


title: H73J2BBXY_3_IDT-DUI-NXT-138


title: H73J2BBXY_3_IDT-DUI-NXT-134


title: H73J2BBXY_3_IDT-DUI-NXT-131


title: H73J2BBXY_3_IDT-DUI-NXT-135


title: H73J2BBXY_3_IDT-DUI-NXT-136


title: H73J2BBXY_3_IDT-DUI-NXT-132


title: H73J2BBXY_3_IDT-DUI-NXT-133


title: H73J2BBXY_3_IDT-DUI-NXT-129


title: H73J2BBXY_3_IDT-DUI-NXT-130


title: H73J2BBXY_3_IDT-DUI-NXT-127


title: H73J2BBXY_3_IDT-DUI-NXT-128


title: H73J2BBXY_3_IDT-DUI-NXT-126


title: H73J2BBXY_3_IDT-DUI-NXT-124


title: H73J2BBXY_3_IDT-DUI-NXT-123


title: H73J2BBXY_3_IDT-DUI-NXT-122


title: H73J2BBXY_3_IDT-DUI-NXT-125


title: H73J2BBXY_3_IDT-DUI-NXT-121


title: H73J2BBXY_3_IDT-DUI-NXT-120


title: H73J2BBXY_3_IDT-DUI-NXT-119


title: H73J2BBXY_3_IDT-DUI-NXT-115


title: H73J2BBXY_3_IDT-DUI-NXT-118


title: H73J2BBXY_3_IDT-DUI-NXT-116


title: H73J2BBXY_3_IDT-DUI-NXT-117


title: H73J2BBXY_3_IDT-DUI-NXT-114


title: H73J2BBXY_3_IDT-DUI-NXT-113


title: H73J2BBXY_3_IDT-DUI-NXT-109


title: H73J2BBXY_3_IDT-DUI-NXT-110


title: H73J2BBXY_3_IDT-DUI-NXT-112


title: H73J2BBXY_3_IDT-DUI-NXT-111


title: H73J2BBXY_3_IDT-DUI-NXT-107


title: H73J2BBXY_3_IDT-DUI-NXT-108


title: H73J2BBXY_3_IDT-DUI-NXT-104


title: H73J2BBXY_3_IDT-DUI-NXT-102


title: H73J2BBXY_3_IDT-DUI-NXT-101


title: H73J2BBXY_3_IDT-DUI-NXT-105


title: H73J2BBXY_3_IDT-DUI-NXT-100


title: H73WCBBXY_6_IDT-DUI-NXT-99

treatment_protocol: Mice that have received intravenously 10 doses of InsB10-23-CT-R1/IAg7-NPs.

value: Tetramer+ CD4+ T cells from InsB10-23-CT-R3/IAg7-NP-treated


title: H73J2BBXY_3_IDT-DUI-NXT-103


title: H73J2BBXY_3_IDT-DUI-NXT-106


title: H73WCBBXY_6_IDT-DUI-NXT-98


title: H73WCBBXY_6_IDT-DUI-NXT-192


title: H73WCBBXY_6_IDT-DUI-NXT-191


title: H73WCBBXY_6_IDT-DUI-NXT-190


title: H73WCBBXY_6_IDT-DUI-NXT-188


title: H73WCBBXY_6_IDT-DUI-NXT-189


title: H73WCBBXY_6_IDT-DUI-NXT-97


title: H73WCBBXY_6_IDT-DUI-NXT-187


title: H73WCBBXY_6_IDT-DUI-NXT-186


title: H73WCBBXY_6_IDT-DUI-NXT-185


title: H73WCBBXY_6_IDT-DUI-NXT-183


title: H73WCBBXY_6_IDT-DUI-NXT-182


title: H73WCBBXY_6_IDT-DUI-NXT-184


title: H73WCBBXY_6_IDT-DUI-NXT-180


title: H73WCBBXY_6_IDT-DUI-NXT-181


title: H73WCBBXY_6_IDT-DUI-NXT-179


title: H73WCBBXY_6_IDT-DUI-NXT-175


title: H73WCBBXY_6_IDT-DUI-NXT-177


title: H73WCBBXY_6_IDT-DUI-NXT-174


title: H73WCBBXY_6_IDT-DUI-NXT-176


title: H73WCBBXY_6_IDT-DUI-NXT-178


title: H73WCBBXY_6_IDT-DUI-NXT-172


title: H73WCBBXY_6_IDT-DUI-NXT-171


title: H73WCBBXY_6_IDT-DUI-NXT-173


title: H73WCBBXY_6_IDT-DUI-NXT-169


title: H73WCBBXY_6_IDT-DUI-NXT-166


title: H73WCBBXY_6_IDT-DUI-NXT-170


title: H73WCBBXY_6_IDT-DUI-NXT-168


title: H73WCBBXY_6_IDT-DUI-NXT-164


title: H73WCBBXY_6_IDT-DUI-NXT-163


title: H73WCBBXY_6_IDT-DUI-NXT-162


title: H73WCBBXY_6_IDT-DUI-NXT-160


title: H73WCBBXY_6_IDT-DUI-NXT-158


title: H73WCBBXY_6_IDT-DUI-NXT-159


title: H73WCBBXY_6_IDT-DUI-NXT-157


title: H73WCBBXY_6_IDT-DUI-NXT-154


title: H73WCBBXY_6_IDT-DUI-NXT-153


title: H73WCBBXY_6_IDT-DUI-NXT-150


title: H73WCBBXY_6_IDT-DUI-NXT-149


title: H73WCBBXY_6_IDT-DUI-NXT-151


title: H73WCBBXY_6_IDT-DUI-NXT-144


title: H73WCBBXY_6_IDT-DUI-NXT-167


title: H73WCBBXY_6_IDT-DUI-NXT-146


title: H73WCBBXY_6_IDT-DUI-NXT-165


title: H73WCBBXY_6_IDT-DUI-NXT-143


title: H73WCBBXY_6_IDT-DUI-NXT-142


title: H73WCBBXY_6_IDT-DUI-NXT-145


title: H73WCBBXY_6_IDT-DUI-NXT-141


title: H73WCBBXY_6_IDT-DUI-NXT-139


title: H73WCBBXY_6_IDT-DUI-NXT-147


title: H73WCBBXY_6_IDT-DUI-NXT-138


title: H73WCBBXY_6_IDT-DUI-NXT-137


title: H73WCBBXY_6_IDT-DUI-NXT-140


title: H73WCBBXY_6_IDT-DUI-NXT-161


title: H73WCBBXY_6_IDT-DUI-NXT-156


title: H73WCBBXY_6_IDT-DUI-NXT-135


title: H73WCBBXY_6_IDT-DUI-NXT-155


title: H73WCBBXY_6_IDT-DUI-NXT-133


title: H73WCBBXY_6_IDT-DUI-NXT-131


title: H73WCBBXY_6_IDT-DUI-NXT-152


title: H73WCBBXY_6_IDT-DUI-NXT-129


title: H73WCBBXY_6_IDT-DUI-NXT-148


title: H73WCBBXY_6_IDT-DUI-NXT-128


title: H73WCBBXY_6_IDT-DUI-NXT-127


title: H73WCBBXY_6_IDT-DUI-NXT-125


title: H73WCBBXY_6_IDT-DUI-NXT-126


title: H73WCBBXY_6_IDT-DUI-NXT-123


title: H73WCBBXY_6_IDT-DUI-NXT-120


title: H73WCBBXY_6_IDT-DUI-NXT-136


title: H73WCBBXY_6_IDT-DUI-NXT-121


title: H73WCBBXY_6_IDT-DUI-NXT-118


title: H73WCBBXY_6_IDT-DUI-NXT-115


title: H73WCBBXY_6_IDT-DUI-NXT-119


title: H73WCBBXY_6_IDT-DUI-NXT-114


title: H73WCBBXY_6_IDT-DUI-NXT-117


title: H73WCBBXY_6_IDT-DUI-NXT-112


title: H73WCBBXY_6_IDT-DUI-NXT-111


title: H73WCBBXY_6_IDT-DUI-NXT-134


title: H73WCBBXY_6_IDT-DUI-NXT-110


title: H73WCBBXY_6_IDT-DUI-NXT-132


title: H73WCBBXY_6_IDT-DUI-NXT-108


title: H73WCBBXY_6_IDT-DUI-NXT-130


title: H73WCBBXY_6_IDT-DUI-NXT-107


title: H73WCBBXY_6_IDT-DUI-NXT-106


title: H73WCBBXY_6_IDT-DUI-NXT-105


title: H73WCBBXY_6_IDT-DUI-NXT-103


title: H73WCBBXY_6_IDT-DUI-NXT-122


title: H73WCBBXY_6_IDT-DUI-NXT-124


title: H73WCBBXY_6_IDT-DUI-NXT-101


title: H73WCBBXY_6_IDT-DUI-NXT-116


title: H73WCBBXY_6_IDT-DUI-NXT-113


title: H73J2BBXY_2_IDT-DUI-NXT-384


title: H73J2BBXY_2_IDT-DUI-NXT-383


title: H73J2BBXY_2_IDT-DUI-NXT-380


title: H73J2BBXY_2_IDT-DUI-NXT-381


title: H73WCBBXY_6_IDT-DUI-NXT-109


title: H73J2BBXY_2_IDT-DUI-NXT-377


title: H73J2BBXY_2_IDT-DUI-NXT-378


title: H73J2BBXY_2_IDT-DUI-NXT-371


title: H73J2BBXY_2_IDT-DUI-NXT-372


title: H73J2BBXY_2_IDT-DUI-NXT-368


title: H73J2BBXY_2_IDT-DUI-NXT-373


title: H73J2BBXY_2_IDT-DUI-NXT-374


title: H73J2BBXY_2_IDT-DUI-NXT-375


title: H73J2BBXY_2_IDT-DUI-NXT-370


title: H73J2BBXY_2_IDT-DUI-NXT-369


title: H73WCBBXY_6_IDT-DUI-NXT-104


title: H73WCBBXY_6_IDT-DUI-NXT-100


title: H73J2BBXY_2_IDT-DUI-NXT-365


title: H73J2BBXY_2_IDT-DUI-NXT-364


title: H73WCBBXY_6_IDT-DUI-NXT-102


title: H73J2BBXY_2_IDT-DUI-NXT-363


title: H73J2BBXY_2_IDT-DUI-NXT-382


title: H73J2BBXY_2_IDT-DUI-NXT-362


title: H73J2BBXY_2_IDT-DUI-NXT-361


title: H73J2BBXY_2_IDT-DUI-NXT-379


title: H73J2BBXY_2_IDT-DUI-NXT-360


title: H73J2BBXY_2_IDT-DUI-NXT-357


title: H73J2BBXY_2_IDT-DUI-NXT-359


title: H73J2BBXY_2_IDT-DUI-NXT-355


title: H73J2BBXY_2_IDT-DUI-NXT-356


title: H73J2BBXY_2_IDT-DUI-NXT-376


title: H73J2BBXY_2_IDT-DUI-NXT-358


title: H73J2BBXY_2_IDT-DUI-NXT-367


title: H73J2BBXY_2_IDT-DUI-NXT-354


title: H73J2BBXY_2_IDT-DUI-NXT-353


title: H73J2BBXY_2_IDT-DUI-NXT-350


title: H73J2BBXY_2_IDT-DUI-NXT-351


title: H73J2BBXY_2_IDT-DUI-NXT-366


title: H73J2BBXY_2_IDT-DUI-NXT-348


title: H73J2BBXY_2_IDT-DUI-NXT-346


title: H73J2BBXY_2_IDT-DUI-NXT-344


title: H73J2BBXY_2_IDT-DUI-NXT-349


title: H73J2BBXY_2_IDT-DUI-NXT-345


title: H73J2BBXY_2_IDT-DUI-NXT-343


title: H73J2BBXY_2_IDT-DUI-NXT-342


title: H73J2BBXY_2_IDT-DUI-NXT-341


title: H73J2BBXY_2_IDT-DUI-NXT-340


title: H73J2BBXY_2_IDT-DUI-NXT-337


title: H73J2BBXY_2_IDT-DUI-NXT-338


title: H73J2BBXY_2_IDT-DUI-NXT-336


title: H73J2BBXY_2_IDT-DUI-NXT-339


title: H73J2BBXY_2_IDT-DUI-NXT-334


title: H73J2BBXY_2_IDT-DUI-NXT-333


title: H73J2BBXY_2_IDT-DUI-NXT-332


title: H73J2BBXY_2_IDT-DUI-NXT-352


title: H73J2BBXY_2_IDT-DUI-NXT-328


title: H73J2BBXY_2_IDT-DUI-NXT-329


title: H73J2BBXY_2_IDT-DUI-NXT-331


title: H73J2BBXY_2_IDT-DUI-NXT-347


title: H73J2BBXY_2_IDT-DUI-NXT-326


title: H73J2BBXY_2_IDT-DUI-NXT-330


title: H73J2BBXY_2_IDT-DUI-NXT-323


title: H73J2BBXY_2_IDT-DUI-NXT-325


title: H73J2BBXY_2_IDT-DUI-NXT-320


title: H73J2BBXY_2_IDT-DUI-NXT-321


title: H73J2BBXY_2_IDT-DUI-NXT-317


title: H73J2BBXY_2_IDT-DUI-NXT-319


title: H73J2BBXY_2_IDT-DUI-NXT-322


title: H73J2BBXY_2_IDT-DUI-NXT-315


title: H73J2BBXY_2_IDT-DUI-NXT-316


title: H73J2BBXY_2_IDT-DUI-NXT-313


title: H73J2BBXY_2_IDT-DUI-NXT-335


title: H73J2BBXY_2_IDT-DUI-NXT-318


title: H73J2BBXY_2_IDT-DUI-NXT-314


title: H73J2BBXY_2_IDT-DUI-NXT-312


title: H73J2BBXY_2_IDT-DUI-NXT-311


title: H73J2BBXY_2_IDT-DUI-NXT-310


title: H73J2BBXY_2_IDT-DUI-NXT-308


title: H73J2BBXY_2_IDT-DUI-NXT-309


title: H73J2BBXY_2_IDT-DUI-NXT-327


title: H73J2BBXY_2_IDT-DUI-NXT-324


title: H73J2BBXY_2_IDT-DUI-NXT-307


title: H73J2BBXY_2_IDT-DUI-NXT-306


title: H73J2BBXY_2_IDT-DUI-NXT-305


title: H73J2BBXY_2_IDT-DUI-NXT-304


title: H73J2BBXY_2_IDT-DUI-NXT-301


title: H73J2BBXY_2_IDT-DUI-NXT-300


title: H73J2BBXY_2_IDT-DUI-NXT-302


title: H73J2BBXY_2_IDT-DUI-NXT-303


title: H73J2BBXY_2_IDT-DUI-NXT-299


title: H73J2BBXY_2_IDT-DUI-NXT-298


title: H73J2BBXY_2_IDT-DUI-NXT-295


title: H73J2BBXY_2_IDT-DUI-NXT-297


title: H73J2BBXY_2_IDT-DUI-NXT-292


title: H73J2BBXY_2_IDT-DUI-NXT-296


title: H73J2BBXY_2_IDT-DUI-NXT-291


title: H73J2BBXY_2_IDT-DUI-NXT-294


title: H73J2BBXY_2_IDT-DUI-NXT-289


title: H73J2BBXY_2_IDT-DUI-NXT-293


title: HC5HWBBXY_7_IDT-DUI-NXT-381

value: Control Tetramer- CD4+ T cells from InsB12-20-CT-R1/IAg7-NP-treated


title: H73J2BBXY_2_IDT-DUI-NXT-290


title: HC5HWBBXY_7_IDT-DUI-NXT-382


title: HC5HWBBXY_7_IDT-DUI-NXT-380


title: HC5HWBBXY_7_IDT-DUI-NXT-377


title: HC5HWBBXY_7_IDT-DUI-NXT-383


title: HC5HWBBXY_7_IDT-DUI-NXT-379


title: HC5HWBBXY_7_IDT-DUI-NXT-384


title: HC5HWBBXY_7_IDT-DUI-NXT-376


title: HC5HWBBXY_7_IDT-DUI-NXT-378


title: HC5HWBBXY_7_IDT-DUI-NXT-372


title: HC5HWBBXY_7_IDT-DUI-NXT-374


title: HC5HWBBXY_7_IDT-DUI-NXT-371


title: HC5HWBBXY_7_IDT-DUI-NXT-373


title: HC5HWBBXY_7_IDT-DUI-NXT-369


title: HC5HWBBXY_7_IDT-DUI-NXT-375


title: HC5HWBBXY_7_IDT-DUI-NXT-370


title: HC5HWBBXY_7_IDT-DUI-NXT-367


title: HC5HWBBXY_7_IDT-DUI-NXT-368


title: HC5HWBBXY_7_IDT-DUI-NXT-366


title: HC5HWBBXY_7_IDT-DUI-NXT-365


title: HC5HWBBXY_7_IDT-DUI-NXT-362


title: HC5HWBBXY_7_IDT-DUI-NXT-363


title: HC5HWBBXY_7_IDT-DUI-NXT-361


title: HC5HWBBXY_7_IDT-DUI-NXT-364


title: HC5HWBBXY_7_IDT-DUI-NXT-360


title: HC5HWBBXY_7_IDT-DUI-NXT-359


title: HC5HWBBXY_7_IDT-DUI-NXT-358


title: HC5HWBBXY_7_IDT-DUI-NXT-355


title: HC5HWBBXY_7_IDT-DUI-NXT-354


title: HC5HWBBXY_7_IDT-DUI-NXT-353


title: HC5HWBBXY_7_IDT-DUI-NXT-356


title: HC5HWBBXY_7_IDT-DUI-NXT-357


title: HC5HWBBXY_7_IDT-DUI-NXT-352


title: HC5HWBBXY_7_IDT-DUI-NXT-346


title: HC5HWBBXY_7_IDT-DUI-NXT-347


title: HC5HWBBXY_7_IDT-DUI-NXT-344


title: HC5HWBBXY_7_IDT-DUI-NXT-350


title: HC5HWBBXY_7_IDT-DUI-NXT-349


title: HC5HWBBXY_7_IDT-DUI-NXT-348


title: HC5HWBBXY_7_IDT-DUI-NXT-345


title: HC5HWBBXY_7_IDT-DUI-NXT-351


title: HC5HWBBXY_7_IDT-DUI-NXT-341


title: HC5HWBBXY_7_IDT-DUI-NXT-343


title: HC5HWBBXY_7_IDT-DUI-NXT-342


title: HC5HWBBXY_7_IDT-DUI-NXT-339


title: HC5HWBBXY_7_IDT-DUI-NXT-338


title: HC5HWBBXY_7_IDT-DUI-NXT-340


title: HC5HWBBXY_7_IDT-DUI-NXT-336


title: HC5HWBBXY_7_IDT-DUI-NXT-333


title: HC5HWBBXY_7_IDT-DUI-NXT-337


title: HC5HWBBXY_7_IDT-DUI-NXT-330


title: HC5HWBBXY_7_IDT-DUI-NXT-335


title: HC5HWBBXY_7_IDT-DUI-NXT-334


title: HC5HWBBXY_7_IDT-DUI-NXT-329


title: HC5HWBBXY_7_IDT-DUI-NXT-328


title: HC5HWBBXY_7_IDT-DUI-NXT-327


title: HC5HWBBXY_7_IDT-DUI-NXT-331


title: HC5HWBBXY_7_IDT-DUI-NXT-326


title: HC5HWBBXY_7_IDT-DUI-NXT-323


title: HC5HWBBXY_7_IDT-DUI-NXT-322


title: HC5HWBBXY_7_IDT-DUI-NXT-325


title: HC5HWBBXY_7_IDT-DUI-NXT-324


title: HC5HWBBXY_7_IDT-DUI-NXT-320


title: HC5HWBBXY_7_IDT-DUI-NXT-318


title: HC5HWBBXY_7_IDT-DUI-NXT-321


title: HC5HWBBXY_7_IDT-DUI-NXT-317


title: HC5HWBBXY_7_IDT-DUI-NXT-316


title: HC5HWBBXY_7_IDT-DUI-NXT-315


title: HC5HWBBXY_7_IDT-DUI-NXT-319


title: HC5HWBBXY_7_IDT-DUI-NXT-314


title: HC5HWBBXY_7_IDT-DUI-NXT-311


title: HC5HWBBXY_7_IDT-DUI-NXT-313


title: HC5HWBBXY_7_IDT-DUI-NXT-310


title: HC5HWBBXY_7_IDT-DUI-NXT-309


title: HC5HWBBXY_7_IDT-DUI-NXT-308


title: HC5HWBBXY_7_IDT-DUI-NXT-332


title: HC5HWBBXY_7_IDT-DUI-NXT-307


title: HC5HWBBXY_7_IDT-DUI-NXT-301


title: HC5HWBBXY_7_IDT-DUI-NXT-312


title: HC5HWBBXY_7_IDT-DUI-NXT-303


title: HC5HWBBXY_7_IDT-DUI-NXT-300


title: HC5HWBBXY_7_IDT-DUI-NXT-305


title: HC5HWBBXY_7_IDT-DUI-NXT-296


title: HC5HWBBXY_7_IDT-DUI-NXT-306


title: HC5HWBBXY_7_IDT-DUI-NXT-302


title: HC5HWBBXY_7_IDT-DUI-NXT-299


title: HC5HWBBXY_7_IDT-DUI-NXT-304


title: HC5HWBBXY_7_IDT-DUI-NXT-297


title: HC5HWBBXY_7_IDT-DUI-NXT-293


title: HC5HWBBXY_7_IDT-DUI-NXT-294


title: HC5HWBBXY_7_IDT-DUI-NXT-295


title: HC5HWBBXY_7_IDT-DUI-NXT-298


title: HC5HWBBXY_7_IDT-DUI-NXT-292


title: HC5HWBBXY_7_IDT-DUI-NXT-290


title: H73J2BBXY_3_IDT-DUI-NXT-96


title: H73J2BBXY_3_IDT-DUI-NXT-95


title: HC5HWBBXY_7_IDT-DUI-NXT-291


title: HC5HWBBXY_7_IDT-DUI-NXT-289


title: H73J2BBXY_3_IDT-DUI-NXT-94


title: H73J2BBXY_3_IDT-DUI-NXT-91


title: H73J2BBXY_3_IDT-DUI-NXT-90


title: H73J2BBXY_3_IDT-DUI-NXT-93


title: H73J2BBXY_3_IDT-DUI-NXT-89


title: H73J2BBXY_3_IDT-DUI-NXT-87


title: H73J2BBXY_3_IDT-DUI-NXT-92


title: H73J2BBXY_3_IDT-DUI-NXT-88


title: H73J2BBXY_3_IDT-DUI-NXT-9


title: H73J2BBXY_3_IDT-DUI-NXT-86


title: H73J2BBXY_3_IDT-DUI-NXT-84


title: H73J2BBXY_3_IDT-DUI-NXT-83


title: H73J2BBXY_3_IDT-DUI-NXT-8


title: H73J2BBXY_3_IDT-DUI-NXT-77


title: H73J2BBXY_3_IDT-DUI-NXT-85


title: H73J2BBXY_3_IDT-DUI-NXT-75


title: H73J2BBXY_3_IDT-DUI-NXT-71


title: H73J2BBXY_3_IDT-DUI-NXT-70


title: H73J2BBXY_3_IDT-DUI-NXT-69


title: H73J2BBXY_3_IDT-DUI-NXT-67


title: H73J2BBXY_3_IDT-DUI-NXT-65


title: H73J2BBXY_3_IDT-DUI-NXT-64


title: H73J2BBXY_3_IDT-DUI-NXT-82


title: H73J2BBXY_3_IDT-DUI-NXT-59


title: H73J2BBXY_3_IDT-DUI-NXT-61


title: H73J2BBXY_3_IDT-DUI-NXT-63


title: H73J2BBXY_3_IDT-DUI-NXT-81


title: H73J2BBXY_3_IDT-DUI-NXT-57


title: H73J2BBXY_3_IDT-DUI-NXT-80


title: H73J2BBXY_3_IDT-DUI-NXT-58


title: H73J2BBXY_3_IDT-DUI-NXT-56


title: H73J2BBXY_3_IDT-DUI-NXT-55


title: H73J2BBXY_3_IDT-DUI-NXT-53


title: H73J2BBXY_3_IDT-DUI-NXT-54


title: H73J2BBXY_3_IDT-DUI-NXT-79


title: H73J2BBXY_3_IDT-DUI-NXT-51


title: H73J2BBXY_3_IDT-DUI-NXT-78


title: H73J2BBXY_3_IDT-DUI-NXT-52


title: H73J2BBXY_3_IDT-DUI-NXT-50


title: H73J2BBXY_3_IDT-DUI-NXT-5


title: H73J2BBXY_3_IDT-DUI-NXT-76


title: H73J2BBXY_3_IDT-DUI-NXT-74


title: H73J2BBXY_3_IDT-DUI-NXT-73


title: H73J2BBXY_3_IDT-DUI-NXT-72


title: H73J2BBXY_3_IDT-DUI-NXT-45


title: H73J2BBXY_3_IDT-DUI-NXT-48


title: H73J2BBXY_3_IDT-DUI-NXT-7


title: H73J2BBXY_3_IDT-DUI-NXT-68


title: H73J2BBXY_3_IDT-DUI-NXT-62


title: H73J2BBXY_3_IDT-DUI-NXT-66


title: H73J2BBXY_3_IDT-DUI-NXT-4


title: H73J2BBXY_3_IDT-DUI-NXT-39


title: H73J2BBXY_3_IDT-DUI-NXT-60


title: H73J2BBXY_3_IDT-DUI-NXT-6


title: H73J2BBXY_3_IDT-DUI-NXT-49


title: H73J2BBXY_3_IDT-DUI-NXT-32


title: H73J2BBXY_3_IDT-DUI-NXT-33


title: H73J2BBXY_3_IDT-DUI-NXT-47


title: H73J2BBXY_3_IDT-DUI-NXT-44


title: H73J2BBXY_3_IDT-DUI-NXT-46


title: H73J2BBXY_3_IDT-DUI-NXT-41


title: H73J2BBXY_3_IDT-DUI-NXT-43


title: H73J2BBXY_3_IDT-DUI-NXT-42


title: H73J2BBXY_3_IDT-DUI-NXT-27


title: H73J2BBXY_3_IDT-DUI-NXT-29


title: H73J2BBXY_3_IDT-DUI-NXT-25


title: H73J2BBXY_3_IDT-DUI-NXT-40


title: H73J2BBXY_3_IDT-DUI-NXT-24


title: H73J2BBXY_3_IDT-DUI-NXT-22


title: H73J2BBXY_3_IDT-DUI-NXT-37


title: H73J2BBXY_3_IDT-DUI-NXT-36


title: H73J2BBXY_3_IDT-DUI-NXT-20


title: H73J2BBXY_3_IDT-DUI-NXT-34


title: H73J2BBXY_3_IDT-DUI-NXT-30


title: H73J2BBXY_3_IDT-DUI-NXT-31


title: H73J2BBXY_3_IDT-DUI-NXT-3


title: H73J2BBXY_3_IDT-DUI-NXT-28


title: H73J2BBXY_3_IDT-DUI-NXT-26


title: H73J2BBXY_3_IDT-DUI-NXT-18


title: H73J2BBXY_3_IDT-DUI-NXT-14


title: H73J2BBXY_3_IDT-DUI-NXT-13


title: H73J2BBXY_3_IDT-DUI-NXT-15


title: H73J2BBXY_3_IDT-DUI-NXT-23


title: H73J2BBXY_3_IDT-DUI-NXT-38


title: H73J2BBXY_3_IDT-DUI-NXT-21


title: H73J2BBXY_3_IDT-DUI-NXT-35


title: H73J2BBXY_3_IDT-DUI-NXT-2


title: KO DCM2

city: Nanjing

first: Qi

last: Chen

state: Jiangsu Province

address: 101 Longmian Avenue

department: Department of Pathophysiology

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v.2.6.1b
All downstream statistical analyses were performed using R (v3.5.1). After RNA-seq data was aligned to the transcriptome, counts were transformed to TPM (transcript per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM/FPKM values for each Sample …

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

value: post natal week 8

tag: duration of drug treatment


title: WT DCM3

value: wild type


title: H73J2BBXY_3_IDT-DUI-NXT-19


title: H73J2BBXY_3_IDT-DUI-NXT-11


title: KO DCM3


title: KO DCM1


title: WT DCM1


title: cKO 12h 1Gy I18_1045_11_3367

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

description:
cKO 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_11_3367

data_processing:
Illumina Casava software used for basecalling.
Reads were quality trimmed and good quality reads were mapped to the reference genome GRCm38 (mm10) with the RNA-Seq Analysis toolbox within CLC Genomics Workbench v11.0.1 (Qiagen Co., Ltd.) using the default parameters.
The expression was normalized to Reads Per Kilobase of exon model per Million (RPKM) by dividing the total exon reads over the mapped reads (in millions) and exon length (in kilobase). Differential expression analysis was performed between the samples’ genome mapped reads using CLC differential analysis for RNAseq tool box, using ANOVA like analysis.  Differentially expressed genes (DEGs) were generated based on a false discovery rate - corrected p-value (FDR) <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: brain

growth_protocol: All the mice were housed under standard laboratory conditions with 12-h light/dark cycle. Food and water were available ad libitum. Female mice were coupled during a 2-h time period in the morning, at the start of the light phase (07:30 am) in order to ensure synchronous timing of embryonic development. The morning of coupling was counted as E0.

extract_protocol:
Fetal cortices were dissected and stored in RLT Plus lysis buffer (Qiagen) at -80°C until RNA extraction using the RNeasy Mini Kit (Qiagen). RNA quality was determined using the RNA nano assay on a 2100 Bioanalyzer (Agilent Technologies). All samples had RNA Integrity Numbers >9.10.
Triplicate RNA-Seq libraries were prepared according to the TruSeq stranded mRNA protocol (Illumina). Briefly, 200 ng of total RNA was purified using poly-T oligo-attached magnetic beads to end up with poly-A containing mRNA. The poly-A tailed mRNA was fragmented and cDNA was synthesized using SuperScript II and random primers in the presence of Actinomycin D. cDNA fragments were end repaired, purified with AMPure XP beads, A-tailed using Klenow exo-enzyme in the presence of dATP. Paired end adapters with dual index (Illumina) were ligated to the A-tailed cDNA fragments and purified using AMPure XP beads. The resulting adapter-modified cDNA fragments were enriched by PCR using Phusion polymerase as followed: 30 s at 98°C; 15 cycles of 10 s at 98°C, 30 s at 60°C, 30 s at 72°C; 5 min at 72°C. PCR products were purified using AMPure XP beads and eluted in 30 µl of resuspension buffer. One microliter was loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and for quality check.

treatment_protocol: Pregnant dams at E11 were given a single dose of whole-body radiation (1 Gy), by using an X-Strahl 320 kV (0.13 Gy/min, inherent filtration: 3 mm of Be, additional filtration: 3.8 mmAl + 1.4 mm Cu + DAP, tube voltage: 250 kV, tube current: 12 mA, sample distance: 100 cm, beam orientation: vertical) in accordance to ISO 4037. Control mice were taken as well to the radiation facility but were not placed within the radiation field (sham-irradiation).

value: Trp53 brain conditional knock-out obtained by breeding Trp53fl/fl mice to Emx1IRES cre mice

value: Fetal cortices

value: embryonic day 11, 12 hours post 1Gy irradiation

value: knock-out


title: H73J2BBXY_3_IDT-DUI-NXT-10

value: NOD

value: T cell


title: WT 12h 0Gy I18_1045_04_3865

description:
WT 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_04_3865

value: embryonic day 11, 12 hours post sham-irradiation


title: H73J2BBXY_3_IDT-DUI-NXT-12

value: pMHCII-NPs


title: KO CONTROL


title: WT 12h 0Gy I18_1045_03_3865

description:
WT 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_03_3865


title: H73J2BBXY_3_IDT-DUI-NXT-1


title: WT 12h 0Gy I18_1045_01_3099

description:
WT 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_01_3099


title: H73J2BBXY_3_IDT-DUI-NXT-16


title: WT DCM2


title: cKO 12h 0Gy I18_1044_12_3099

description:
cKO 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_12_3099


title: WT 12h 1Gy I18_1045_10_3367

description:
WT 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_10_3367


title: cKO 6h 1Gy I18_1044_11_3780

description:
cKO 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_11_3780

value: embryonic day 11, 6 hours post 1Gy irradiation


title: cKO 12h 1Gy I18_1045_09_3098

description:
cKO 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_09_3098


title: H73J2BBXY_3_IDT-DUI-NXT-17


title: WT 12h 1Gy I18_1045_07_3098

description:
WT 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_07_3098


title: WT 12h 1Gy I18_1045_06_3098

description:
WT 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_06_3098


title: cKO 12h 1Gy I18_1045_08_3098

description:
cKO 12h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_08_3098


title: cKO 12h 0Gy I18_1045_05_3865

description:
cKO 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_05_3865


title: cKO 12h 0Gy I18_1045_02_3865

description:
cKO 12h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1045_02_3865


title: cKO 6h 0Gy I18_1044_01_3781

description:
cKO 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_01_3781

value: embryonic day 11, 6 hours post sham-irradiation


title: cKO 6h 0Gy I18_1044_03_3771

description:
cKO 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_03_3771


title: WT CONTROL


title: cKO 6h 1Gy I18_1044_10_3780

description:
cKO 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_10_3780


title: cKO 2h 1Gy I18_1043_12_3776

description:
cKO 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_12_3776

value: embryonic day 11, 2 hours post 1Gy irradiation


title: WT 6h 1Gy I18_1044_09_3780

description:
WT 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_09_3780


title: WT 6h 0Gy I18_1043_13_3781

description:
WT 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_13_3781


title: WT 2h 1Gy I18_1043_10_3776

description:
WT 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_10_3776


title: WT 6h 1Gy I18_1044_06_3866

description:
WT 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_06_3866


title: cKO 6h 1Gy I18_1044_08_3780

description:
cKO 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_08_3780


title: WT 2h 0Gy I18_1043_06_3368

description:
WT 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_06_3368

value: embryonic day 11, 2 hours post sham-irradiation


title: cKO 6h 0Gy I18_1044_02_3781

description:
cKO 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_02_3781


title: cKO 2h 1Gy I18_1043_11_3776

description:
cKO 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_11_3776


title: WT Arabidopsis thaliana-2

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

data_processing:
Raw FASTQ files were converted to FASTA format.
Reads containing unassigned nucleotides were excluded.
The 3’ adapter was trimmed by using first 8 nucleotide of the 3’ HiSeq 2500 adapter (TGGAATTC).
The HD reads were mapped (no mismatch allowed) to A. thaliana genome (TAIR10 reference genome) using PatMaN.
The HD signatures (four assigned degenerate nucleotides at the ligating ends) of the reads were also trimmed.
Read per million approach was used for the normalization of the sRNA libraries.
To identify differentially expressed sRNA, offset of 10 was added to normalised counts between different conditions. This was done to correct for low expression level counts, to avoid false positive results.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read per million approach was used for the normalization of the sRNA libraries.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

growth_protocol: Wild-type A. thaliana and rdr1 mutant A. thaliana were grown for 16 hours of daylight in a growth room at constant 22°C temperature.

extract_protocol:
Total RNA from the leaf samples were isolated by TRIzol reagent (Invitrogen)
sRNA cDNA-libraries were prepared  using HD adapters. sRNA libraries were generated from the total RNA isolated from wild-type and rdr1 mutant Arabidopsis thaliana.
Illumina HiSeq 2500 platform (50 bp, single-end)

value: Wild type

value: No treatment

value: Leaf sample


title: WT 2h 1Gy I18_1043_09_3776

description:
WT 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_09_3776


title: T_Cell_rep3-0min

data_processing:
RNA-seq reads were mapped to the human reference genome hg19 using topHat[45]. Read counts of the annotated genes were obtained by the Python software HTSeq-count[46]. The edgeR package was used to identify differentially expressed genes (DEGs) from RNA-seq with two biological replicates[47]. Genes with at least 1.5-fold change in expression levels and false discovery rate (FDR) less than 0.05 were considered to be differentially expressed. The adaptor sequences in raw data were removed using cutadapt, then an all-in-one small noncoding RNA annotation pipeline AASRA was applied to process the mapping and count the raw count for each small noncoding RNA.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw counts for 12 Samples of RNA-seq.

source_name: T cell

growth_protocol: For T cell RNA-seq, the T cell were collected from the patient blood and separated using apheresis method. The cells were cultured in complete median and treated the with transcription inhibition ActD at 4 different time points, 0-hour, 0.25-hour, 1 hour and 2 hours.

extract_protocol:
Total RNA was isolated from cells using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research) with the procedure provided by the manufacturer.  RNA libraries were prepared for sequencing using standard Illumina protocols
For RNA-seq, total RNA was isolated from cells using RNeasy Plus Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the DNBseq platform.For small RNA-seq, small RNA was extracted from cells using miRNeasy Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the Hiseq platform.

treatment_protocol: no

value: Blood T cell


title: T_Cell_rep3-120min


title: T_Cell_rep2-60min


title: WT 2h 1Gy I18_1043_08_3101

description:
WT 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_08_3101

value: wild type


title: T_Cell_rep1-60min


title: T_Cell_rep1-15min


title: WT 2h 0Gy I18_1043_03_3094

description:
WT 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_03_3094


title: cKO 2h 1Gy I18_1043_07_3101

description:
cKO 2h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_07_3101

value: Trp53 brain conditional knock-out obtained by breeding Trp53fl/fl mice to Emx1IRES cre mice


title: cKO 2h 0Gy I18_1043_05_3368

description:
cKO 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_05_3368

value: Fetal cortices


title: T_Cell_rep1-120min


title: cKO 2h 0Gy I18_1043_04_3094

description:
cKO 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_04_3094


title: rdr1 mutant Arabidopsis thaliana-2

value: rdr1 mutant


title: rdr1 mutant Arabidopsis thaliana-1


title: WT 6h 1Gy I18_1044_07_3866

description:
WT 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_07_3866


title: T_Cell_rep3-60min


title: WT 2h 0Gy I18_1043_02_3094

description:
WT 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_02_3094


title: WT 6h 0Gy I18_1044_05_3771

description:
WT 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_05_3771


title: rdr1 mutant Arabidopsis thaliana-3


title: cKO 2h 0Gy I18_1043_01_3094

description:
cKO 2h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1043_01_3094

value: knock-out


title: B11_WK2_oTAU

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

data_processing:
Each sequencing library was demultiplexed based on the sample index read to generate FASTQ files for the RNA pair-end reads using Cell Ranger V3.1.0.
Gene-cell barcode matrices for RNA count data were generated using 10X genomics CellRanger V3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file for 10X RNA-UMI count data

source_name: human induced pluripotent stem cell derived neurons and astrocytes

growth_protocol: Human induced pluripotent stem cell derived neural progenitor cells  (Stem Cell Technologies) were differentiated to neurons (hiNCs) and astrocytes (hiACs) and combined in microwells at a 1:1 ratio to form self-aggregating spheroids (asteroids).

extract_protocol:
A single cell suspension of asteroid cultures was prepared by Accutase dissociation and 20 uM filtration.
scRNA-seq libraries were prepared following 10X Genomics Chromium Single Cell 3’ V3 scRNA-seq method.

treatment_protocol: hiNCs were treated with 0.04 mg/mL oligomeric tau to induce pathology in oTAU samples. Asteroids were treated for 72 hrs with 1 uM PU-H71 before timepoint collection in drug treated samples.

tag: time point

value: week 2

tag: agent

value: oligomeric tau


title: B11_WK2_Control

value: Control


title: B11_WK1_oTAU

value: week 1


title: WT 6h 0Gy I18_1044_04_3771

description:
WT 6h 0Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_04_3771


title: WT Arabidopsis thaliana-3


title: Twins040A

city: Granada

first: Martin

last: Munoz-Lopez

state: GRANADA

address: C/ Ilustración

institute: GENYO

data_processing:
Library strategy: RC-seq (Retrotransposon Capture Sequencing)
Computational analysis of reads was implemented according to the RC-seq pipeline described by Shuckla et al. (Shukla et al., 2013). Briefly, the RC-seq pipeline is conducted to search for split reads that represent a L1-insertion junction, being constituted by an L1-end and a flanking DNA sequence. Flanking DNA sequences are aligned to the Human Genome Reference Sequence (hg19) using SOAP (Li et al., 2009) (parameters –M 4 –v 2 –r 1 –p 8) and the L1-end characterized by mapping to the human active L1 consensus sequences (L1Hs-Ta/L1Hs-preTa) using LAST (Kielbasa et al., 2011) (parameters –s 2 –l 11 –d 30 –q 3 –e 30) (alignment at >95% identity and spanning at least 33 nucleotides of the read end). To assess the reliability of RC-seq, we determined the percentage of L1Hs copies annotated in hg19 (available from euL1db at http://eul1db.unice.fr/, contains 1544 reference L1Hs copies annotated) that were detected by RC-seq in the different WGA-gDNA samples. As an additional control, we also compared recovered insertions in H9-hESCs and hEMBs with the L1Hs-Ta subset of reference L1Hs (485 copies). Finally, L1-insertions were further filtered with respect to reference L1-insertions annotated in hg19 and to reported polymorphic L1-insertions (from euL1db database (Mir et al., 2015) and from recent publications not included yet in this database (Tubio et al., 2014)).

source_name: blood

extract_protocol:
Genomic DNA was purified using the QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s instructions.
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)

value: blood

tag: individual


title: Twins055B


title: Twins040B


title: WT Arabidopsis thaliana-1


title: T_Cell_rep2-15min


title: B11_WK3_oTAU

value: week 3


title: Trio-109_child-133


title: T_Cell_rep2-120min


title: T_Cell_rep3-15min


title: Trio-109_mother-131


title: Trio-109_father-130


title: Individual_23710_muscle

source_name: muscle

extract_protocol:
Genomic DNA purification was carried out using the Blood & Cell Culture DNA Midi Kit (Qiagen) following the manufacturer’s instructions.
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)

value: muscle


title: P240_placenta

source_name: chorion frondosum

extract_protocol:
Genomic DNA purification from extraembryonic tissues was carried out using the Blood & Cell Culture DNA Midi Kit (Qiagen) following the manufacturer’s instructions. Genomic DNA from blood samples was purified using the QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s instructions.
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) and following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)

value: chorion frondosum


title: Twins056B


title: T_Cell_rep2-0min


title: P240_mother


title: Twins050B


title: Twins056A


title: Twins050A


title: Twins055A


title: P224_mother


title: P222_newborn


title: P222_mother


title: T_Cell_rep1-0min


title: P220_newborn


title: P224_newborn


title: Trio-48_child-22


title: Trio-48_mother-20


title: P220_mother


title: P213_newborn


title: P217_mother


title: Trio-48_father-21


title: B11_WK3_Control


title: B11_WK1_Control


title: Individual_24154_muscle


title: P212_newborn


title: Individual_24154_brain

value: brain


title: Individual_23710_brain


title: P240_newborn


title: P225_placenta


title: P225_newborn


title: P225_mother


title: P224_placenta


title: P222_placenta


title: P220_placenta


title: P217_placenta


title: P217_newborn


title: P213_placenta


title: P213_mother


title: P212_placenta


title: P212_mother


title: XC_2298_2

city: Mishima

first: Toyoyuki

last: Takada

state: Shizuoka-ken

country: Japan

institute: National Institute of Genetics

description: Gene expression data from liver at 10-week-old male

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip scanner 3000 (Affymetrix).

data_processing: The data were analyzed with DFW (Chen et al. Bioinformatics, 2007).

label: biotin

source_name: B6-ChrXCMSM_mouse liver

label_protocol: Biotinylated cRNA were prepared from 10ug total RNA by using GeneChip 3'IVT express kit (Affymetrix) according to the standard Affymetrix protocol.

extract_protocol: Livers were immersed in RNAlater (life technologies) and stored at -20C. Total RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Samples were collected after a fasting period of four hours.

value: male

value: liver


title: Y_1482_2

source_name: B6-ChrYMSM_mouse liver


title: MSM_1269_1

source_name: MSM_mouse liver

value: MSM


title: XT_1898_2

source_name: B6-ChrXTMSM_mouse liver


title: Y_1482_1


title: mt_2374_2

source_name: B6-mtMSM_mouse liver


title: XC_1638_1


title: mt_2415_2


title: XT_2006_1


title: XT_1898_1


title: Y_1486_2


title: XC_2298_1


title: mt_2415_1


title: XC_1638_2


title: XT_2006_2


title: C9_1626_2

source_name: B6-Chr9MSM_mouse liver


title: Y_1486_1


title: MSM_1269_2


title: KPC HAPLN1 biol. Rep. 2

city: Heidelberg

first: Lena

last: Wiedmann

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
Bioinformatics analysis of RNA-sequencing data sets was performed using the software R using the DESeq2 package. Plots were created using ggplot2 or EnhancedVolcano. apeglm package was used for LFC shrinkage.
Assembly: mm10
Supplementary files format and content: featureCounts.csv lists the normalized read counts assessed by RNAseq of all samples listed.

source_name: solid tumor

growth_protocol: tumor cells were cultured in 10 % FBS DMEM. They were injected into mice in PBS after washing. Extraction 11 days later.

extract_protocol:
tumor cells and fibroblasts were extracted from solid tumors after digestion by cell sorting using flow cytometry. Tumor cells in ascites were isolated without digestion also by cell sorting with flow cytometry.
Libraries and multiplexes were prepared with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7600S) and NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, E6420S).

value: solid tumor

tag: cell line

value: KPC

value: tumor cell

value: KrasG12D Trp53R172H Elas-CreER, HAPLN1 overexpression


title: KPC HAPLN1 biol. Rep. 3

tag: cell type


title: KPC biol. Rep. 1

tag: genotype

value: KrasG12D Trp53R172H Elas-CreER


title: MSM_1261_2


title: MSM_1261_1


title: C9_0833_3


title: C9_0833_1


title: mt_2374_1


title: C7T_0186_1

source_name: B6-Chr7TMSM_mouse liver


title: C8_1282_2

source_name: B6-Chr8MSM_mouse liver


title: C7C_2457_2

source_name: B6-Chr7CMSM_mouse liver


title: C7T_1197_2


title: C7T_0186_2


title: C8_1682_1


title: C7_2070_2

source_name: B6-Chr7MSM_mouse liver


title: C9_1626_1


title: C8_1682_2


title: KPC biol. Rep. 3

tag: treatment


title: KPC biol. Rep. 2


title: KPC HAPLN1_ascites biol. Rep. 1

source_name: ascites

value: ascites


title: fibroblasts_KPC biol. Rep. 3

value: primary CAFs

value: fibroblast

value: wildtype


title: C8_1282_1

tag: gender


title: C7_2070_1


title: fibroblasts_KPC biol. Rep. 1


title: fibroblasts_KPC HAPLN1 biol. Rep. 3

description:
fibroblasts_KPC HAPLN1_3
wildtype fibroblasts in a tumor that contains modified tumor cells


title: C7_2058_2


title: C7T_1197_1


title: C7_2058_1


title: SMP2

city: Haerbin

first: Chen

last: Jian

state: China

address: College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, P.R. China

institute: Northeast Agricultural University

data_processing:
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Stringtie was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: gut

extract_protocol:
A total amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.

value: gut

value: SMP


title: SMP3


title: Con3

value: Control


title: C7C_2457_1


title: KPC HAPLN1 biol. Rep. 1


title: KPC HAPLN1_ascites biol. Rep. 3


title: C6T_2054_2

source_name: B6-Chr6TMSM_mouse liver


title: C7C_2440_2


title: Con1


title: C6T_0805_2


title: KPC HAPLN1_ascites biol. Rep. 2


title: C7C_2440_1


title: C6C_0713_1

source_name: B6-Chr6CMSM_mouse liver


title: fibroblasts_KPC biol. Rep. 2


title: fibroblasts_KPC HAPLN1 biol. Rep. 2

description:
fibroblasts_KPC HAPLN1_2
wildtype fibroblasts in a tumor that contains modified tumor cells


title: fibroblasts_KPC HAPLN1 biol. Rep. 1

description:
fibroblasts_KPC HAPLN1_1
wildtype fibroblasts in a tumor that contains modified tumor cells


title: C5_2119_2

source_name: B6-Chr5MSM_mouse liver


title: SMP1


title: C5_2119_1


title: Con2


title: DD-BFD1∆bfd2_vehicle_1b_rep3

first: Sebastian

last: Lourido

address: 455 Main Street, Rm 555

institute: Whitehead Institute

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v.3.6
Alignment to the T. gondii genome was performed with STAR v.2.7.0a.
Differential expression analysis was done using the DESeq2 package (v. 1.12.3) in R
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: xls files include i) relative mRNA abundance in BFD2-knockout parasites (DD-BFD1∆bfd2) relative to their parental strain (DD-BFD1) in both the presence and absence of Shield-1, and ii) within either strain, the relative change in mRNA abundance induced by treatment with Shield-1. FPKM values for each sample are also provided.
Supplementary files format and content: xls file includes the following processed data, annotated as indicated in brackets:
Supplementary files format and content: i) Log2(fold-change) in mRNA abundance in BFD2 knockouts (DDBFD1_dBFD2) relative to their parental strain (DDBFD1), under both Shield-1 (S1) and vehicle (V) treatment [i.e. L2FC.DDBFD1_dBFD2_S1.v.DDBFD1_S1]
Supplementary files format and content: ii) Log2(fold-change) in mRNA abundance either strain after treatment with Shield-1 [i.e. L2FC.DDBFD1_S1.v.DDBFD1_V]
Supplementary files format and content: iii) Corresponding negative log-transformed p-values for differential expression analysis [i.e. nL10p.DDBFD1_dBFD2_S1.v.DDBFD1_S1]
Supplementary files format and content: iv) Log-transformed FPKM values as genered within each comparison using the DeSeq2 fpkm() function [i.e. L10FPKM.DDBFD1_S1].

organism: Toxoplasma gondii

source_name: intracellular protozoan parasite, cultured in HFFs

growth_protocol:
For routine maintenance, parasites were cultured in human foreskin fibroblasts (HFFs) grown at 37°C under 5% CO2 in standard medium, consisting of DMEM (GIBCO) supplemented with 3% heat-inactivated fetal bovine serum (IFS), 2 mM L-glutamine, and 10 μg/mL gentamicin.
Passaging was performed on a 2-3 day cycle—prior to lysis of host cell monolayers—by scraping and transfer to fresh HFFs.

extract_protocol:
Parasites were isolated from host cells by syringe-release (described above) and filtering through a Millex filter unit (5 μm pore size, Merck Millipore) to remove host cell debris. RNA was isolated using the Rneasy mini plus kit (Qiagen).
Libraries for RNA-seq were prepared using the Swift Low-Input Library Prep Kit with poly(A) enrichment following manufacturer's protocols.

treatment_protocol:
To establish infection, parasites were mechanically released from host cells by passage through a 27-gauge needle and innoculated onto confluent HFFs in standard  medium.
After 4h, infected monolayers were washed twice with PBS, and the medium was replaced with new standard media containing either 3µM Shield-1 or an equivalent volume of vehicle.  Experiments were harvested after an additional 48 hr of culture.

value: standard medium, +vehicle

tag: replicate information

value: Biological replicate 3, Technical replicate 2


title: C5_2125_2

value: male


title: C6T_0805_1

value: liver


title: C4_1294_1

source_name: B6-Chr4MSM_mouse liver


title: DD-BFD1∆bfd2_Shield_1b_rep3

value: intracellular protozoan parasite, cultured in HFFs

value: standard medium, +3uM Shield-1


title: DD-BFD1_vehicle_1b_rep3


title: C6T_2054_1


title: DD-BFD1∆bfd2_Shield_1a_rep3

value: Biological replicate 3, Technical replicate 1


title: DD-BFD1∆bfd2_Shield_1b_rep2

value: Biological replicate 2, Technical replicate 2


title: C3_1245_1

source_name: B6-Chr3MSM_mouse liver


title: DD-BFD1∆bfd2_vehicle_1a_rep3


title: C6C_0713_2


title: C6C_0440_1


title: C4_1029_1


title: C2T_1694_2

source_name: B6-Chr2TMSM_mouse liver


title: C3_0544_1


title: DD-BFD1_Shield_1b_rep3


title: DD-BFD1_Shield_1a_rep3


title: DD-BFD1_Shield_1b_rep2


title: DD-BFD1∆bfd2_vehicle_1a_rep2

value: Biological replicate 2, Technical replicate 1


title: DD-BFD1∆bfd2_Shield_1a_rep2


title: DD-BFD1_vehicle_1a_rep3


title: C4_1294_2


title: C2T_1694_1


title: C5_2125_1


title: DD-BFD1∆bfd2_vehicle_1b_rep2


title: C6C_0440_2


title: C4_1029_2


title: C3_0544_2


title: DD-BFD1∆bfd2_vehicle_1b_rep1

value: Biological replicate 1, Technical replicate 2


title: DD-BFD1∆bfd2_Shield_1a_rep1

value: Biological replicate 1, Technical replicate 1


title: C3_1245_2


title: C2T_1686_1


title: DD-BFD1_vehicle_1b_rep2


title: DD-BFD1∆bfd2_Shield_1b_rep1


title: DD-BFD1∆bfd2_vehicle_1a_rep1


title: DD-BFD1_vehicle_1a_rep2


title: C2C_1185_1

source_name: B6-Chr2CMSM_mouse liver


title: C19_0262_2

source_name: B6-Chr19MSM_mouse liver


title: C2C_1173_1


title: DD-BFD1_Shield_1b_rep1


title: DD-BFD1_vehicle_1b_rep1


title: DD-BFD1_vehicle_1a_rep1


title: C2C_1185_2


title: DD-BFD1_Shield_1a_rep1


title: ∆bfd2_standard_3b

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v.3.6
Alignment to the T. gondii genome was performed with STAR v.2.7.0a.
Differential expression analysis was done using the DESeq2 package (v. 1.12.3) in R.
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: xls file includes the following processed data, annotated as shown in brackets:
Supplementary files format and content: i) Log2(fold-change) in mRNA abundance in ∆bfd2 and wildtype parasites after treatment with alkaline stress [i.e. L2FC.∆bfd2_S.v.∆bfd2_US]
Supplementary files format and content: ii) Log2(fold-change) in mRNA abundance in ∆bfd2 as compared to its wildtype parebtal strain, under either stressed or unstressed conditions [i.e. L2FC.∆bfd2_S.v.WT_S]
Supplementary files format and content: iii) Corresponding negative log-transformed p-values for differential expression analysis [i.e. nL10p.∆bfd2_S.v.∆bfd2_US]
Supplementary files format and content: iv) Log-transformed FPKM values as genered within each comparison using the DeSeq2 fpkm() function [i.e. L10FPKM.WT_S].

treatment_protocol:
To establish infection, parasites were mechanically released from host cells by passage through a 27-gauge needle and innoculated onto confluent HFFs in standard  medium.
After 4h, infected monolayers were washed twice with PBS, and either switched to alkaline-stress medium (RPMI 1640 supplemented with 1% IFS, 10 μg/mL gentamicin, 50 mM HEPES, and pH-adjusted to 8.1 with 10 N NaOH) under ambient CO2 or returned to standard conditions for an additional 48 h before harvest..

tag: condition

value: standard culture media, 5% CO2


title: ∆bfd2_stress_3b

value: alkaline stress media, ambient CO2


title: ∆bfd2_stress_3a


title: ∆bfd2_standard_3a


title: WT_stress_3b


title: C2C_1173_2


title: WT_stress_3a


title: C18_2406_2

source_name: B6-Chr18MSM_mouse liver


title: C19_0250_1


title: C2T_1686_2


title: DD-BFD1_Shield_1a_rep2


title: C18_3277_2


title: C17_1350_2

source_name: B6-Chr17MSM_mouse liver


title: C17_1346_1


title: C19_0250_2


title: C18_3277_1


title: C18_2406_1


title: C17_1346_2


title: WT_standard_3a


title: WT_standard_3b


title: ∆bfd2_stress_2a


title: C16_1037_2

source_name: B6-Chr16MSM_mouse liver


title: C19_0262_1


title: C16_0885_1


title: ∆bfd2_standard_2a


title: C17_1350_1


title: ∆bfd2_standard_2b


title: C16_0885_2


title: WT_stress_2b


title: WT_stress_2a


title: WT_standard_2b


title: WT_standard_2a


title: ∆bfd2_stress_1b


title: ∆bfd2_stress_1a


title: C15_0845_2

source_name: B6-Chr15MSM_mouse liver


title: C15_0845_1


title: C15_0049_1


title: C14_0468_2

source_name: B6-Chr14MSM_mouse liver


title: ∆bfd2_standard_1b


title: ∆bfd2_standard_1a


title: C14_0452_1


title: C14_0452_2


title: C13T_0238_1

source_name: B6-Chr13TMSM_mouse liver


title: C14_0468_1


title: WT_stress_1b


title: WT_stress_1a


title: C13T_0230_1


title: C13T_0230_2


title: C13T_0238_3


title: ∆bfd2_stress_2b


title: C13C_0645_2

source_name: B6-Chr13CMSM_mouse liver


title: C13C_0645_1


title: WT_standard_1b


title: pt235_PBMC_prestimulation

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: We obtained PBMCs from COVID-19 positive donors and stimulated with SARS-CoV-2 virus; some were enriched for cytotoxic lymphocytes via cytokine stimulation

hyb_protocol: 30ng DNase-treated RNA was used as input for PanCancer immune gene expressional panel from NanoString Technologies. Hybridization with reporter CodeSet and capture ProbeSet was performed according to manufacturer's protocol for 16 hours at 65 degrees C. Hybridized samples were then processed on the nCounter MAX/FLEX prep station using high sensitivity setting.

scan_protocol: Cartridges were scanned on nCounter digital analyzer at Max setting (555 fields of view).

data_processing: Digital counts were normalized using a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane. All normalization techniques were applied in nSolver software according to manufacturer's protocol. The 'NS_CANCERIMMUNE_V1.1.COVID19.csv' is an excel template which contains individual RCC data files produced by the nCounter digital analyzer into a single spreadsheet.

label: Nanostring

source_name: PBMC from COVID-19 positive donor

label_protocol: standard NanoString protocol

extract_protocol: RNA was extracted from frozen cell pellets using mirVana™ miRNA Isolation Kit (Thermo Fisher) per manufacturer’s instructions. RNA was DNase-treated using Zymo RNA clean/concentrator protocol.

tag: age (years)

tag: Sex


title: pt235_PBMC_peptide_stimulation

value: stimulation with PepTivator peptide pools of SARS-CoV-2


title: WT_standard_1a

tag: strain


title: pt235_viral_CTLs

value: stimulation with PepTivator peptide pools of SARS-CoV-2 plus enrichment of cytotoxic lymphocytes via the CliniMACS cytokine capture system


title: C13C_0637_2

tag: tissue


title: pt234_viral_CTLs

value: female


title: C12T_1201_2

source_name: B6-Chr12TMSM_mouse liver


title: C13C_0637_1


title: pt234_PBMC_peptide_stimulation


title: 311100-mNG-mAID_Veh._REP2

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v.3.6
Alignment to the T. gondii genome was performed with STAR v.2.7.0a.
Differential expression analysis was done using the DESeq2 package (v. 1.12.3) in R
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: The corresponding xls file includes the following processed data, annotated as indicated in brackets:
Supplementary files format and content: i) log2(fold-change) in mRNA abundance in parasites depleted for each factor (i.e. treated with IAA) as compared to the IAA-treated parental TIR1 strain [L2FC.TargetedGeneID_IAA.v.TIR1_IAA]
Supplementary files format and content: ii) negative log-transformed p-values for differential expression analysis [nL10p.TargetedGeneID_IAA.v.TIR1_IAA]
Supplementary files format and content: iii) normalized transcript levels in each knockdown strain, expressed as log-transformed Fragments per Kilobase Mapped [L10FPKM.TargetedGeneID_IAA]

treatment_protocol:
To establish infection, parasites were mechanically released from host cells by passage through a 27-gauge needle and innoculated onto confluent human foreskin fibroblasts in standard  medium.
After 4h, infected monolayers were washed twice with PBS, switched to alkaline-stress medium (RPMI 1640 supplemented with 1% IFS, 10 μg/mL gentamicin, 50 mM HEPES, and pH-adjusted to 8.1 with 10 N NaOH), and treated with either 5uM 3-indole-acetic acid (IAA) or an equivalent volume of vehicle.
Cultures were maintained under their respective treatment condition for 96h before harvest, with fresh stress medium provided on day 2.

value: 96hr alkaline stress

value: Vehicle (PBS)


title: pt224_PBMC_peptide_stimulation


title: pt234_PBMC_prestimulation


title: C12T_1201_1


title: 306620-mNG-mAID_+IAA_REP2

value: 50uM IAA


title: 311100-mNG-mAID_+IAA_REP2


title: f2_110_42S3

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

institute: South Dakota State University

data_processing:
Fastq files were generated and multiplexed with bcl2fastq.
Quality of raw sequence reads were checked using FastQC.
Sequence reads were trimmed for adapters, length of 20 nucleotides, quality of 20 nucleotides using cutadapt and prinseq respectively.
Cleaned sequence reads were aligned to the Vitis vinifera 12X.V1 genome using Tophat and Gene expression levels in FPKM were quantified using Cufflinks.
Differential gene expression analysis was performed using EdgeR
Genome_build: 12X.V1
Supplementary_files_format_and_content: Tab-delimited text files

organism: Vitis

source_name: F2 110 short day at 42 days

growth_protocol: F2 040 and F2 110 genotypes were previously described as part of a larger F2 population (Fennell et al., 2005, Acta Hort 689:533-539).  Spur-pruned grapevines were grown under long days until shoots reached 12-15 nodes and then randomized into a continued long (LD, 15 h) or short photoperiod (13 h) for 28 or 42 days (George et al. 2018, J.Prot:187:13-24)

extract_protocol:
RNA was extracted at 28 and 42 days of long day and short day photoperiod.
Single end RNAseq libraries were prepared with TruSeq Stranded RNA Sample Prep Kit.

treatment_protocol: Spur-pruned F2 040 and 110 grapevines were grown under long days until shoots reached 12-15 nodes, vines were randomized into LD (15 h) or SD (13 h) treatment, grown for an additional 28 or 42 days prior to bud harvest.

tag: photoperiod

value: Short


title: 224630-mNG-mAID_+IAA_REP2


title: C12T_1181_2

value: male

value: liver

tag: age


title: 224630-mNG-mAID_Veh._REP2

value: intracellular protozoan parasite, cultured in HFFs


title: 306620-mNG-mAID_Veh._REP2


title: f2_110_42S2


title: C12T_1181_1


title: C12C_0993_1

source_name: B6-Chr12CMSM_mouse liver


title: C12C_1550_1


title: WT1 (CONTROL)

type: genomic

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

institute: Ulster University

description:
WThTERT replicate one
SAMPLE 1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2 and RnBeads (v1.6.1) through R (v3.3)

label: Cy5 and Cy3

source_name: WT1 (CONTROL)

label_protocol: Standard Illumina Protocol

growth_protocol: The wild-type (hTERT1604) lung fibroblast cell line (Ouellette et al., 2000) and derivatives were cultured in 4.5g/l glucose DMEM with 10% FBS and 2× NEAA (all Thermo-Fisher Scientific, Loughborough, UK).

extract_protocol: The genomic DNA isolated was assessed for purity and integrity prior to quantification using the Picogreen fluorescent assay.

treatment_protocol: Depletion of UHRF1 in hTERT1604 (U5/U10/UH4 lines) for this study used GIPz Lentiviral shRNAmir (Thermo-Fisher Scientific) according to the manufacturer’s instructions.

value: Male

tag: sample type

value: hTERT

tag: disease state

value: WT hTERT


title: UH3

description:
UH4 replicate three
SAMPLE 5

value: UHRF1 KD hTERT


title: WT10A

description:
UH+R10 replicate one
SAMPLE 6

value: UHRF1 Rescue 10 hTERT


title: 253790-mNG-mAID_Veh._REP2

source_name: intracellular protozoan parasite, cultured in HFFs


title: f2_110_42S1


title: 253790-mNG-mAID_+IAA_REP2


title: f2_110_42L3

source_name: F2 110 long day at 42 days

value: Long


title: 208020-mNG-mAID_+IAA_REP2


title: f2_110_42L2


title: WT10B

description:
UH+R10 replicate two
SAMPLE 7


title: C12C_1550_3


title: pt224_PBMC_prestimulation


title: 208020-mNG-mAID_Veh._REP2