title: Tensin Y483F biol rep 3

city: Tampere

first: Paula

last: Turkki

state: Finland

address: Arvo Ylpön katu 34 (Arvo F303)

department: Faculty of Medicine and Life Sciences

country: Finland

institute: Tampere University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In  this step, clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean  data with high quality.  Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website  1      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. We selected Hisat2 as the  mapping tool for that Hisat2 can generate a database of splice junctions based on the gene  model annotation file and thus a better mapping result than other non-splice mapping tools.  Novel transcripts prediction  The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al.  2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as  an optional de novo assembly step to assemble and quantitate fulllength transcripts  representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 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. Filtering: Remove reads with adapter contamination.  Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).  Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read
Differential Gene Expression Analysis: DESeq2 software was used with DEseq as normalization method. The  resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling  the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were  assigned as differentially expressed.
Supplementary files format and content: Excel file that has FPKM values for each Sample
Supplementary files format and content: Excel file that shows the results of Differential Expression Analysis

source_name: cell line

extract_protocol:
total RNA was extracted from cell lysates using Rneasy kit (Qiagen)
Messenger RNAwas purified from total RNA using poly-T oligo-attached magnetic beads.  After fragmentation, the first strand cDNAwas synthesized using random hexamer  primers,followed by the second strand cDNA synthesis using either dUTP for directional  library or dTTP for non-directional library.  For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size  selection, amplification, and purification

value: cell line

value: cell line stably expressing Tensin-2 Y483F


title: Tensin Y483F biol rep 2

status: Public on Jul 20 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: treatment


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35681_rep2

city: Houston

first: James

middle: M.

last: Musser

state: Texas

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

country: USA

institute: Houston Methodist Hospital and Research Institute

data_processing:
Multiplexed libraries were sequenced on an Illumina NextSeq 500 instrument.
Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.
RNA-seq reads from all strains were mapped to reference strain MGCS36044 [National Center for Biotechnology Information (NCBI) Bioproject accession number PRJNA925803], using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Differential expression (DE) analysis was performed with DESeq2 using pcaExplorer and Ideal to streamline RStudio.
DE genes were identified in each of the 38 strains compared to a common reference strain (MGCS36044).
Assembly: MGCS36044, NCBI GenBank accession GCA_029234115.1
Supplementary files format and content: EDGEpro output listing 6 space separated columns: geneID, start_coord, end_coord, average_cov, and RPKM -- determined relative to the reference MGCS36044 genome

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using NEBNext rRNA depletion kit (NEB)
Resultant RNAs were processed using the NEBNext Ultra II directional RNA library prep kit for Illumina (NEB), reverse transcribed to cDNA, tagged with the NEBNext multiplex oligos for Illumina (NEB), pooled and sequenced

treatment_protocol: At the desired growth stage, mid-exponential phase (OD 600nm 1.0), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: genotype


title: Patient AML009, bonemarrow, time point 1, Batch 1

city: Zuerich

first: Yannik

last: Severin

state: ZH

address: Otto-Stern-Weg 3

department: Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).
Assembly: GRCh38, v.93
Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv

molecule: polyA RNA

source_name: bonemarrow

growth_protocol: primary samples

extract_protocol:
Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.
CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033–2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample)

treatment_protocol: not treated

value: bonemarrow


title: ADAM25 KO

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

country: China

institute: xian jiaotong university

data_processing:
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the raw reads were trimmed by using Trim Galore (version 0.5.0_dev, Cutadapt version 1.15) with default parameters. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10), and quantified by using Salmon5. The transcript-level quantification results were converted to the gene-level quantities with tximport R package.
DESeq2 R package was used to normalize the gene-level quantities and followed by differential expression analysis between selected samples with the same package.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: T cells

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and KO CD8+ T cells were sorted from the spleens of recipient mice 7 days after LM-OVA infection in the co-transfer model.

value: T cells

tag: cell type

value: CD8+ T cells

value: KO

tag: time

value: 16 days after LM-OVA infection


title: ADAM22 KO

growth_protocol: WT and KO CD8+ T cells were sorted from the spleens

value: 13 days after LM-OVA infection


title: ADAM21 KO

value: 12 days after LM-OVA infection


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35679_rep3


title: ADAM20 WT

value: WT

value: 10 days after LM-OVA infection


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35679_rep2


title: Col0 roots biol rep 3

city: Mexico City

first: Adriana

last: Garay Arroyo

state: Mexico City

address: C.U., Coyoacán

department: Ecología Funcional

country: Mexico

institute: Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM

data_processing:
For the differential transcript accumulation analysis, raw sequencing data were trimmed with Trimmomatic version 0.39 (Bolger et al., 2014) using the parameters ILLUMINACLIP: 2:30:10 LEADING:3 TRAILING:3 SLIDING WINDOW:4:15 MINLEN:50 HEADCROP:10. The quality of reads was evaluated with FastQC version 0.11.9 (Andrews, 2010) before and after the trimming process. Biological replicates were aligned to the Arabidopsis genome from TAIR10 (https://www.arabidopsis.org/) and the abundance of the transcripts was estimated using Subread version 2.0.1 (Liao et al., 2019). Raw count tables were used for differential transcript accumulation analysis using DESeq2 (Love et al., 2014). Differentially expressed genes (DEGs) were identified with a padj <0.05 and log2 fold change > 1.5.
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: Excel file includes RPKM values and raw counts for each sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown with 0.2X Murashige and Skoog (MS) salts (Murashige and Skoog, 1962) and 1% sucrose on vertical plates in climate chambers at 22°C with the photoperiods (110 mEm22 s21) established at 16 h of light followed by 8 h of dark as described by Tapia- Lopez et al. (2008).

extract_protocol:
Three biological replicates of around 60 plants each were prepared, and the total RNA of 8 dps (days post sowing) roots were extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Irvine, USA), including a DNaseI treatment step to remove any contaminating DNA. The RNA integrity and quantity was checked using a 2100 Bioanalyzer.
The libraries were constructed as indicated by the Illumina TruSeq Stranded mRNA Reference Guide for paired-end sequencing (2017).

value: Root

value: 8-day-old whole roots, excluding hypocotyls and cotyledons

value: MS 0.2X


title: heterozygote embryo-1

type: RNA

city: HangZhou

first: LI

last: XU

state: Zhejiang Province

address: Binwen 7-3-1101,Binwen Road

department: School of Basic Medical Science

institute: Zhejiang Chinese Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: 12 days  embryo

label_protocol: total RNA from each sample was linearly amplified and labeled with Cy3-UTP.The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The animal housing facility is a barrier housing facility, and it is maintained in accordance with the national standards (Laboratory Animal-Requirements of Environment and Housing Facilities, GB 14925–2001).

extract_protocol: Total RNA of tumor tissue were isolated using Trizol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: embryo

tag: strain


title: xal12 roots biol rep 2

value: XAL1 loss of function mutant


title: Col0 roots biol rep 2


title: ADAM18 WT

value: 8 days after LM-OVA infection


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35678_rep2


title: homozygous embryo-2


title: homozygous embryo-1


title: ADAM21 WT

value: 11 days after LM-OVA infection


title: xal12 roots biol rep 1


title: ADAM23 KO

value: 14 days after LM-OVA infection


title: Tensin Y483F biol rep 1

value: cell line

value: cell line stably expressing Tensin-2 Y483F


title: ADAM17 WT

value: T cells

value: CD8+ T cells

value: 7 days after LM-OVA infection


title: PTPR, Z841

status: Public on Jul 19 2024

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

description:
Tumor
204920840045_R04C01

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
R package minfi v1.40.0
Processed data file betas.tsv represents Normalized (preprocessIlumina) Average Beta for the 39 newly profiled samples and the 37 "Third-party reanalysis" samples.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PTPR

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

value: papillary tumor of the pineal region

tag: Sex

value: Male

tag: age

tag: material

value: FFPE


title: Tensin Y483E biol rep 3

value: cell line stably expressing Tensin-2 Y483E


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35679_rep1


title: PTPR, Y983

description:
Tumor
204305120049_R08C01

value: Female


title: PTPR, Y327

description:
Tumor
204088140047_R01C01


title: Tensin Y483E biol rep 2


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35678_rep3


title: ADAM19 WT

value: WT

value: 9 days after LM-OVA infection


title: Col0 roots biol rep 1

value: Root

value: 8-day-old whole roots, excluding hypocotyls and cotyledons

value: MS 0.2X


title: PTPR, Z799

description:
Tumor
204920840052_R02C01


title: PTPR, FA62

description:
Tumor
207534240155_R02C01


title: PTPR, W698

description:
Tumor
203723050022_R02C01


title: Tensin Y483E biol rep 1


title: RNASeq of Streptococcus dysgalactiae subsp. equisimilis isolate MGCS35678_rep1


title: PTPR, MT1324

description:
Tumor
207429040118_R07C01


title: PTPR, Z972

description:
Tumor
204920840138_R04C01


title: PTPR, ER46

description:
Tumor
207429040084_R07C01


title: PTPR, Y322

description:
Tumor
204088140046_R04C01


title: PTPR, Y253

description:
Tumor
204071680089_R06C01


title: PTPR, Y869

description:
Tumor
204295600156_R05C01


title: PTPR, AR17

description:
Tumor
203723190036_R01C01


title: PTPR, MT1322

description:
Tumor
207429040118_R05C01


title: PTPR, MT1327

description:
Tumor
207019370033_R07C01


title: PTPR, DB32

description:
Tumor
206699910146_R02C01


title: PTPR, DW29

description:
Tumor
207278070067_R08C01


title: PTPR, MT1323

description:
Tumor
207429040118_R06C01


title: PTPR, EP50

description:
Tumor
207310410078_R01C01


title: PTPR, U934

description:
Tumor
202835130007_R04C01


title: PTPR, Y193

description:
Tumor
204097730029_R07C01


title: PTPR, DU68

description:
Tumor
207278070129_R04C01


title: PTPR, CB63

description:
Tumor
206382220143_R04C01


title: PTPR, DP18

description:
Tumor
207019360120_R06C01


title: PTPR, BT01

description:
Tumor
206103240067_R03C01


title: PTPR, BA83

description:
Tumor
205624890031_R03C01


title: PTPR, AB29

description:
Tumor
204957740008_R06C01


title: PTPR, DKFZ_PTPR3

description:
Tumor
206184840174_R03C01


title: PTPR, CN35

description:
Tumor
206537460020_R02C01


title: PTPR, DKFZ_PTPR2

description:
Tumor
204361730066_R03C01


title: lung, control, 12 days, rep 3

city: Jeongeup

first: Jinhee

last: Kim

address: 30, Baekhak 1-gil

country: South Korea

institute: Korea institute of toxicology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: lung

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

value: lung


title: PTPR, AO93

description:
Tumor
205379750119_R04C01


title: PTPR, BX20

description:
Tumor
206095950176_R05C01


title: PTPR, CJ17

description:
Tumor
206382220018_R06C01


title: PTPR, AB19

description:
Tumor
204957740149_R07C01


title: lung, control, 12 days, rep 1


title: PTPR, MT1328

description:
Tumor
207019370033_R08C01


title: PTPR, CF35

description:
Tumor
206382220020_R07C01


title: PTPR, DKFZ_PTPR1

description:
Tumor
204001300096_R02C01


title: lung, WCSC 20 mg/mL, 12 days, rep 2


title: lung, WCSC 10 mg/mL, 12 days, rep 3


title: lung, WCSC 20 mg/mL, 12 days, rep 1


title: lung, WCSC 10 mg/mL, 12 days, rep 1


title: lung, control,  6 days, rep 3


title: lung, control,  6 days, rep 2


title: lung, WCSC 5 mg/mL,  12 days, rep 1


title: lung, WCSC 20 mg/mL,  6 days, rep 2


title: lung, control,  6 days, rep 1


title: lung, WCSC 20 mg/mL,  6 days, rep 1


title: lung, WCSC 5 mg/mL,  12 days, rep 3


title: lung, WCSC 10 mg/mL,  6 days, rep 3


title: lung, WCSC 10 mg/mL,  6 days, rep 1


title: lung, WCSC 10 mg/mL, 12 days, rep 2


title: lung, WCSC 20 mg/mL,  6 days, rep 3


title: lung, WCSC 20 mg/mL, 12 days, rep 3


title: lung, control, 12 days, rep 2


title: lung, WCSC 5 mg/mL,  6 days, rep 1


title: lung, WCSC 5 mg/mL,  6 days, rep 3


title: lung, WCSC 10 mg/mL,  6 days, rep 2


title: lung, WCSC 5 mg/mL,  12 days, rep 2


title: MNU_polyA_FF_1µg_rep3 (rna-seq)

city: Paris

first: Jennifer

last: Wong

address: 12 rue lhomond

country: France

institute: Institue Curie

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T3

data_processing:
Reads were aligned to mouse reference genome (mm10) by STAR using ENCODE parameters
Bam files were indexed by samtools
Read counting was done by the function featureCounts from Rsubreads.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files represent the raw counts of each genes generated by featuresCount and the upper quartile normalized count.

source_name: mouse normal urothelium (MNU)

growth_protocol: The mouse bladder cancer cells, BC57, have been culture in DMEM 10% fetal bobine serum. Nine mice were sacrificed and their normal urothelium were removed.

extract_protocol:
Total RNA from FFPE were extracted by using Qiagen RNeasy FFPE. Ten slices of five microns of thickness of FFPE samples were dewaxed using Deparaffinization solution and were extracted according to manufacturer instructions (RNeasy FFPE tissue Handbook). Total RNA from FF samples were extracted with Qiagen RNeasy mini according to manufacturer instructions.
Ovation SoLo NuGEN RNA-seq System: cDNA was synthesized and amplified from 50pg, 250pg, 2ng of total RNA from mouse normal urothelium and mouse bladder cancer cell line using the Ovation SoLo RNA-seq System (NuGEN) which allows to perform a strand specific RNA sequencing. Total RNA underwent a DNAse treatment then random priming allowed to first and the second strand cDNA synthesis end Illumina index was ligated. Before library amplification step, a qPCR was performed to determine the optimal number of library amplification cycles required for a given input and sample type. The depletion of ribosomal sequences was done by the InDA-C technology. PCR amplification was finally achieved to create the final cDNA library. Sequencing was carried out using 2*100 cycles (paired-end reads, 100 nucleotides) on an Illumina HiSeq2000 instrument (high output flow cells) to get around 8M paired reads per sample.
SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian: cDNA was synthesized and amplified from 250pg and 2ng of total RNA from mouse bladder cancer cell line and mouse normal urothelium. This kit uses the SMART technology for Switching Mechanism at 5' End of RNA Template to allow a strand specific RNA sequencing. Total RNA underwent a DNAse treatment and converted to cDNA by SMARTScribe Reverse Transcriptase. When SMARTScribe Reverse Transcriptase reached the 5’ end of RNA fragment, its terminal transferase activity added a few non-templated nucleotides to the 3’ end of the cDNA. The non-templated nucleotides were uses as a primer for the addition of Illumina index adapters through PCR. Next, the ribosomal depletion was carried out by ZapR enzyme, in presence of specific probes recognizing rRNA sequences. PCR amplification was finally achieved to create the final cDNA library. Sequencing was carried out using 2*100 cycles (paired-end reads, 100 nucleotides) on an Illumina HiSeq2000 instrument (high output flow cells) to get around 11M paired reads per sample.
Illumina TruSeq Stranded mRNA: total RNA from FF samples with a RIN > 7 were used for sequencing. RNA sequencing libraries were prepared from 1µg of total RNA from mouse bladder cancer cell line and mouse normal urothelium using Illumina TruSeq Stranded mRNA which allowed to perform a strand specific RNA sequencing. A first step of poly(A) selection using magnetic beads was done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification was finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2*100 cycles (paired-end reads, 100 nucleotides) on an Illumina HiSeq2000 instrument (high output flow cells) to get around 60M paired reads per sample.

treatment_protocol: The normal urothelium of each mouse was divided in two parts, one part was frozen in liquid nitrogen and the other part was conserved in a solution of buffered formalin for 24 hours. Formalin Fixed Paraffin Embedded (FFPE) samples were embedded into wax blocks. The fresh frozen (FF) specimens were conserved in a freezer until the RNA extraction. The mouse bladder cancer cell line (BC57) harvested cell pellet was divided in two parts and underwent the same protocol as the mouse normal urothelium.

value: normal urothelium

tag: rna seq library kit

value: Illumina TruSeq Stranded mRNA (polyA)

tag: rna input quantity

tag: method of sample preservation

value: FF


title: BC57_polyA_FF_1ug_rep2 (rna-seq)

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T5

source_name: mouse bladder cancer cell line, BC57

value: bladder cancer cells


title: MNU_polyA_FF_1µg_rep2 (rna-seq)

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T2


title: BC57_polyA_FF_1ug_rep3 (rna-seq)

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T6


title: BC57_polyA_FF_1ug_rep1 (rna-seq)

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T4


title: BC57_Pico-SM_FF_250pg_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T9

value: SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian (Pico-SM)


title: MNU_polyA_FF_1µg_rep1 (rna-seq)

description:
expCount_raw_count_polyA.txt
expCount_norm_polyA.txt
B221T1


title: MNU_Pico-SM_FFPE_2ng_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T8


title: BC57_Pico-SM_FFPE_2ng_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T7


title: MNU_Pico-SM_FF_2ng_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T4


title: MNU_Pico-SM_FFPE_250pg_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T6


title: BC57_Pico-SM_FFPE_250pg_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T5


title: BC57_Pico-SM_FF_2ng_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T3


title: MNU_Pico-SM_FF_250pg_rep3 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T2


title: BC57_Pico-SM_FFPE_250pg_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T21


title: MNU_Pico-SM_FF_2ng_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T20


title: MNU_Pico-SM_FFPE_2ng_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T24


title: BC57_Pico-SM_FFPE_2ng_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T15


title: lung, WCSC 5 mg/mL,  6 days, rep 2


title: BC57_Pico-SM_FF_250pg_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T17


title: BC57_Pico-SM_FF_2ng_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T19


title: MNU_Pico-SM_FF_2ng_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T12


title: BC57_Pico-SM_FFPE_2ng_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T23


title: MNU_Pico-SM_FFPE_250pg_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T22


title: BC57_Pico-SM_FF_250pg_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T1


title: BC57_Pico-SM_FF_2ng_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T11


title: MNU_Pico-SM_FFPE_2ng_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T16


title: MNU_OVA_NG_FF_250pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T60

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)


title: MNU_Pico-SM_FF_250pg_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T10


title: BC57_Pico-SM_FFPE_250pg_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T13


title: MNU_OVA_NG_FFPE_250pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T54


title: BC57_OVA_NG_FFPE_50pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T51


title: BC57_OVA_NG_FF_250pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T53


title: BC57_OVA_NG_FF_50pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T49


title: MNU_Pico-SM_FFPE_250pg_rep1 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T14


title: MNU_OVA_NG_FF_250pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T52


title: BC57_OVA_NG_FFPE_2ng_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T59


title: BC57_OVA_NG_FF_2ng_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T57


title: BC57_OVA_NG_FFPE_250pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T55


title: MNU_Pico-SM_FF_250pg_rep2 (rna-seq)

description:
expCount_raw_count_smarter.txt
expCount_norm_smarter.txt
A553T18


title: MNU_OVA_NG_FF_2ng_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T56


title: MNU_OVA_NG_FFPE_50pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T45


title: MNU_OVA_NG_FFPE_50pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T50


title: MNU_OVA_NG_FF_250pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T47


title: MNU_OVA_NG_FFPE_2ng_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T58


title: MNU_OVA_NG_FF_2ng_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T39


title: MNU_OVA_NG_FF_50pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T43


title: BC57_OVA_NG_FF_50pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T44


title: BC57_OVA_NG_FF_2ng_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T40


title: MNU_OVA_NG_FF_50pg_rep3 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T48


title: BC57_OVA_NG_FFPE_250pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T38


title: BC57_OVA_NG_FFPE_50pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T46


title: MNU_OVA_NG_FFPE_2ng_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T41


title: BC57_OVA_NG_FF_250pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T36


title: MNU_OVA_NG_FFPE_50pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T34


title: MNU_OVA_NG_FFPE_250pg_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T37


title: BC57_OVA_NG_FF_50pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T33


title: MNU_OVA_NG_FF_50pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T32


title: BC57_OVA_NG_FF_2ng_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T29


title: BC57_OVA_NG_FFPE_2ng_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T31


title: MNU_OVA_NG_FFPE_2ng_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T30


title: MNU_OVA_NG_FF_2ng_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T28


title: BC57_OVA_NG_FFPE_250pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T27


title: MNU_OVA_NG_FFPE_250pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T26


title: BC57_OVA_NG_FF_250pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T25


title: BC57_OVA_NG_FFPE_2ng_rep2 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T42


title: mtstpLii141_late-pupa

city: Atlanta

middle: Gabriel Amor

last: DuBose

state: Georgia

address: 1510 East Clifton Road Northeast 2006

institute: Emory Univeristy

data_processing:
Transcript abundances were quantified using kallisto v.0.46.2.
Assembly: D. plexippus (Dpv3) and O. elektroscirrha (GCA_030141585.1)
Supplementary files format and content: Each processd data file is formatted as the standard kallito output.

organism: Danaus plexippus

source_name: whole body homogenate

extract_protocol:
Promega SV Total Isolation System
Poly-A tail selection

value: whole body homogenate

value: incarnata


title: mtstpLii140_late-pupa


title: mtstpLii138_late-pupa


title: mtstpLii137_late-pupa


title: mtstpLci64_late-pupa

value: curassavica


title: mtstpLci60_late-pupa


title: mtstpLci57_late-pupa


title: mtstpEii125_early-pupa


title: mtstpEii124_early-pupa


title: mtstpEii123_early-pupa


title: mtstpEii122_early-pupa


title: BC57_OVA_NG_FFPE_50pg_rep1 (rna-seq)

description:
expCount_raw_count_nugen.txt
expCount_norm_nugen.txt
A574T35

value: FFPE


title: mtstpEci45_early-pupa


title: mtstpEci43_early-pupa


title: mtstpEci42_early-pupa


title: mtstpEii121_early-pupa


title: mtstpEci41_early-pupa


title: mtstpAii157_adult


title: mtstpAii156_adult


title: mtstpAii154_adult


title: mtstpAci76_adult


title: mtstpAii153_adult


title: mtstpAci74_adult


title: mtstpAii155_adult


title: mtstpAci75_adult


title: mtstpLci58_late-pupa


title: mtstp5ii112_fifth-instar


title: mtstp5ii107_fifth-instar


title: mtstp5ii105_fifth-instar


title: mtstp5ii109_fifth-instar


title: mtstp5ci27_fifth-instar


title: mtstp5ii108_fifth-instar


title: mtstpEci44_early-pupa


title: mtstp5ci26_fifth-instar


title: mtstp3ii89_third-instar


title: mtstp5ci28_fifth-instar


title: mtstp3ci9_third-instar


title: mtstp3ii92_third-instar


title: mtstp3ii90_third-instar


title: mtstp3ii94_third-instar


title: mtstpAci77_adult


title: mtstp3ci10_third-instar


title: mtstp3ci13_third-instar


title: mtstp5ci25_fifth-instar


title: CGND-HRA-03138

city: New York

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

data_processing:
Reads from samples with RIN > = 5.5 were aligned to the hg38 human genome using STAR v2.7.6, allowing for a 4% mismatch rate and up to 100 alignments per read to ensure capture of young transposon sequences. Abundance of gene and transposon sequences was calculated with TEtranscripts v2.2.3
Assembly: hg38
Supplementary files format and content: Text file of gene and transposable element counts

source_name: cervical spinal cord

extract_protocol:
RNA was extracted from flash-frozen patient samples homogenized in Trizol-Chloroform and purified using the QIAGEN RNeasy Mini kit. RNA was assessed using the Bioanalyzer.
RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA Stranded RNA-seq kit with RiboErase for rRNA depletion and Illumina compatible indexes. Pooled libraries were sequenced on an Illumina HiSeq 2500 or NextSeq V1 using a paired end 125 nucleotide

value: cervical spinal cord

tag: disease state

value: ALS

tag: gender

value: Male

tag: subject id


title: mtstp3ci11_third-instar


title: CGND-HRA-03136

value: Female


title: CGND-HRA-03134


title: mtstp3ci12_third-instar


title: CGND-HRA-03131

source_name: lumbar spinal cord

value: lumbar spinal cord


title: CGND-HRA-03137


title: mtstpAci73_adult


title: CGND-HRA-03132


title: CGND-HRA-03126


title: CGND-HRA-03130


title: CGND-HRA-03129


title: CGND-HRA-03123


title: CGND-HRA-03128


title: CGND-HRA-03125


title: CGND-HRA-03124


title: CGND-HRA-03122


title: CGND-HRA-03118


title: CGND-HRA-03117


title: CGND-HRA-03116


title: CGND-HRA-03135


title: CGND-HRA-03114


title: CGND-HRA-03109


title: CGND-HRA-03111


title: CGND-HRA-03133


title: CGND-HRA-03108


title: CGND-HRA-03113


title: CGND-HRA-03115


title: CGND-HRA-03112


title: CGND-HRA-03110


title: CGND-HRA-02954

source_name: spinal cord

value: spinal cord

value: CTL


title: CGND-HRA-02928


title: CGND-HRA-02926


title: CGND-HRA-02952


title: CGND-HRA-02935


title: CGND-HRA-02901


title: CGND-HRA-02906


title: CGND-HRA-02934


title: CGND-HRA-02937


title: CGND-HRA-02907


title: CGND-HRA-02878


title: CGND-HRA-02913

source_name: thoracic spinal cord

value: thoracic spinal cord


title: CGND-HRA-02930

value: NEURCTL


title: CGND-HRA-02922


title: CGND-HRA-02877


title: CGND-HRA-02874


title: CGND-HRA-02870


title: CGND-HRA-02900


title: CGND-HRA-02860


title: CGND-HRA-02869


title: CGND-HRA-02857


title: CGND-HRA-02855


title: CGND-HRA-02881


title: CGND-HRA-02875


title: CGND-HRA-02866


title: CGND-HRA-02940


title: CGND-HRA-02863


title: CGND-HRA-02887


title: CGND-HRA-02839


title: CGND-HRA-02838


title: CGND-HRA-02859


title: CGND-HRA-02829


title: CGND-HRA-02827


title: CGND-HRA-02854


title: CGND-HRA-02828


title: CGND-HRA-02823


title: CGND-HRA-02825


title: CGND-HRA-02822


title: CGND-HRA-02851


title: CGND-HRA-02846


title: CGND-HRA-02804


title: CGND-HRA-02843


title: CGND-HRA-02735


title: CGND-HRA-02727


title: CGND-HRA-02816


title: CGND-HRA-02836


title: CGND-HRA-02835


title: CGND-HRA-02833


title: CGND-HRA-02832


title: CGND-HRA-02718


title: CGND-HRA-02818


title: CGND-HRA-02819


title: CGND-HRA-02815


title: CGND-HRA-02812


title: CGND-HRA-02852


title: CGND-HRA-02811


title: CGND-HRA-02713


title: CGND-HRA-02809


title: CGND-HRA-02712


title: CGND-HRA-02842


title: CGND-HRA-02806


title: CGND-HRA-02808


title: CGND-HRA-02698


title: CGND-HRA-02802


title: CGND-HRA-02800


title: CGND-HRA-02798


title: CGND-HRA-02717


title: CGND-HRA-02795


title: CGND-HRA-02742


title: CGND-HRA-02693


title: CGND-HRA-02689


title: CGND-HRA-02737


title: CGND-HRA-02734


title: CGND-HRA-02684


title: CGND-HRA-02682

value: ALS+FTD


title: CGND-HRA-02685


title: CGND-HRA-02738


title: CGND-HRA-02681


title: CGND-HRA-02726


title: CGND-HRA-02676


title: CGND-HRA-02679


title: CGND-HRA-02645


title: CGND-HRA-02722


title: CGND-HRA-02624-2


title: CGND-HRA-02620


title: CGND-HRA-02708


title: CGND-HRA-02721


title: CGND-HRA-02707


title: CGND-HRA-02629


title: CGND-HRA-02702


title: CGND-HRA-02630


title: CGND-HRA-02614

value: Unknown


title: CGND-HRA-02703


title: CGND-HRA-02694


title: CGND-HRA-02604


title: CGND-HRA-02680


title: CGND-HRA-02594


title: CGND-HRA-02598


title: CGND-HRA-02591


title: CGND-HRA-02636


title: CGND-HRA-02688


title: CGND-HRA-02587


title: CGND-HRA-02619


title: CGND-HRA-02581


title: CGND-HRA-02599


title: CGND-HRA-02592


title: CGND-HRA-02595


title: CGND-HRA-02577


title: CGND-HRA-02573


title: CGND-HRA-02582


title: CGND-HRA-02568


title: CGND-HRA-02562


title: CGND-HRA-02553


title: CGND-HRA-02615


title: CGND-HRA-02552


title: CGND-HRA-02558


title: CGND-HRA-02572


title: CGND-HRA-02567


title: CGND-HRA-02563


title: CGND-HRA-02610


title: CGND-HRA-02603


title: CGND-HRA-02557


title: CGND-HRA-02523


title: CGND-HRA-02586


title: CGND-HRA-02513


title: CGND-HRA-02512


title: CGND-HRA-02547


title: CGND-HRA-02499


title: CGND-HRA-02498


title: CGND-HRA-02491


title: CGND-HRA-02505


title: CGND-HRA-02477


title: CGND-HRA-02484


title: CGND-HRA-02485


title: CGND-HRA-02492


title: CGND-HRA-02472


title: CGND-HRA-02466


title: CGND-HRA-02459


title: CGND-HRA-02460


title: CGND-HRA-02465


title: CGND-HRA-02453


title: CGND-HRA-02530


title: CGND-HRA-02454


title: CGND-HRA-02436


title: CGND-HRA-02435


title: CGND-HRA-02506


title: CGND-HRA-02447


title: CGND-HRA-02448


title: CGND-HRA-02430


title: CGND-HRA-02429


title: CGND-HRA-02423


title: CGND-HRA-02418


title: CGND-HRA-02390


title: CGND-HRA-02386


title: CGND-HRA-02382


title: CGND-HRA-02389


title: CGND-HRA-02381


title: CGND-HRA-02377


title: CGND-HRA-02371


title: CGND-HRA-02368


title: CGND-HRA-02442


title: CGND-HRA-02441


title: CGND-HRA-02361


title: CGND-HRA-02358


title: CGND-HRA-02352


title: CGND-HRA-02353


title: CGND-HRA-02349


title: CGND-HRA-02348


title: CGND-HRA-02344


title: CGND-HRA-02424


title: CGND-HRA-02357


title: CGND-HRA-02337


title: CGND-HRA-02341


title: CGND-HRA-02385


title: CGND-HRA-02331


title: CGND-HRA-02345


title: CGND-HRA-02340


title: CGND-HRA-02320


title: CGND-HRA-02333


title: CGND-HRA-02324


title: CGND-HRA-02318


title: CGND-HRA-02328


title: CGND-HRA-02321


title: CGND-HRA-02376


title: CGND-HRA-02298


title: CGND-HRA-02295


title: CGND-HRA-02296


title: CGND-HRA-02299


title: CGND-HRA-02293


title: CGND-HRA-02292


title: CGND-HRA-02301


title: PTPR, MX1347

description:
Tumor
207831660066_R05C01

value: papillary tumor of the pineal region


title: CGND-HRA-02336


title: CGND-HRA-02285


title: CGND-HRA-02274


title: mTh1, 24h, CREB1, rep2, CUTTag

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

library_source: genomic

data_processing:
Sequenced raw reads were trimmed for adaptor sequence, amplification primers, and masked for low-complexity or low-quality sequence with trim galore V0.6.10.
Clean sequencing reads were mapped to mm10 by bowtie2 V2.3.5.1 with the following parameters: --local --very-sensitive --no-mixed --no-discordant  -I 10 -X 700.
PCR duplicates were removed using Picard (‘MarkDuplicates’, V2.18.29).
Only reads with high mapping quality (MAPQ > 10) were retained by Samtools V1.9.
Bigwig files were generated using deepTools (‘bamCoverage’, V3.5.3).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: spleen

growth_protocol: For T cell in vitro activation, naïve CD4+ T cells were isolated from the spleen of C57BL/6 mice followed with Flow cytometry sorting for CD4+ CD25- CD44- CD62L+ cells. Sorted Naïve CD4+ T cells were activated with plate-bound anti-CD3 (1ug/ml, clone 145-2C11, Bio X Cell) and anti-CD28 (1ug/ml, clone PV-1, Bio X Cell).

extract_protocol:
In vitro cultured CD4+ T cells were harvested and counted before performing CUT&Tag. 200K cells were used for each CUT&Tag assay, and 3 technical resplicates were included for each culture condition. Cells were first labelled with CREB antibody at 4 degree overnight. Then the antibody binding regions were labeled with pA-Tn5-Transposase. The antibody binding genomic DNA was extracted with phenol chloroform isoamyl alcohol.
Extracted genomic DNA was amplified using P5 and P7 primer to do library construction with sample specific index.

treatment_protocol: For T cell in vitro polarization, naïve CD4+ T cells were treated with polarization cytokines under Th0 (without cytokine), Th1 (IL-12, 20ng/mL, R&D Systems) or Th2 (IL-4, 20ng/mL, R&D Systems) conditions. For LCMV infection, mice were perfused intracardially with cold PBS. Spleen was harvested and smashed through 40 um sterile strainers to get single cell suspension for staining and sorting. ACK lysis (Buffer from Lonza) was performed with the spleen for 5 min at RT to remove red blood cells.

value: spleen

value: CD4 T cells

value: Th1 condition


title: CGND-HRA-02273


title: CGND-HRA-02327


title: mTh1, 24h, CREB1, rep1, CUTTag


title: CGND-HRA-02270


title: CGND-HRA-02271


title: CGND-HRA-02268-2


title: CGND-HRA-02267


title: mTh1, 8h, CREB1, rep1, CUTTag


title: mTh1, 8h, CREB1, rep2, CUTTag


title: IgG, rep3, CUTTag


title: IgG, rep1, CUTTag


title: IgG, rep2, CUTTag


title: CGND-HRA-02264-2


title: CGND-HRA-02253


title: CGND-HRA-02258


title: CGND-HRA-02286


title: CGND-HRA-02262-2


title: PTPR, MX1348

description:
Tumor
207831660066_R06C01


title: mTh1, 24h, CREB1, rep3, CUTTag


title: CGND-HRA-02254


title: mTh1, 8h, CREB1, rep3, CUTTag


title: CGND-HRA-02248


title: CGND-HRA-02241


title: CGND-HRA-02235


title: CGND-HRA-02247


title: EHE17 cells, Vehicle control3

city: Cleveland

first: Ajaybabu

last: Pobbati

state: Ohio

address: 9500 Euclid Ave

department: Cancer Biology

institute: Cleveland Clinic Foundation

description:
E17MGHvsE17VC_deg_all.txt
E17DivsE17VC.all_cancer.xls

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
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.
featureCounts v1.5.0-p3 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: 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.
Supplementary files format and content: Excel sheets with sample names, FPKM values, gene ids, among others
Supplementary files format and content: Excel sheets with sample names, FPKM values, gene ids, among others

source_name: tumor cells

growth_protocol: EHE17 cell lines were cultured at 37°C in a humidified atmosphere of 5% CO2 in the c-endo media, which contains DMEM/F12 containing 15 mM HEPES, 20% Fetal Bovine Serum (Gibco, Cat # 10437028), 40 ng/ml endothelial cell growth supplement (Corning, Cat # 356006), 15U/ml heparin (Millipore/Sigma, Cat # H3149), and 50 μg/ml penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research, Cat # R1054), ~ 1 μg total RNA was used for library preparation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP.

treatment_protocol: EHE17 cells were treated with either MGH-CP1 (10 μM) or dinaciclib (300 nM) for 16 h, biological triplicates were used.

value: tumor cells

value: tumor cell line

value: endothelial

value: TC+/+ Cdkn2a -/-

value: vehicle control (DMSO)


title: EHE17 cells, Dinaciclib (300 nM), 1

value: Dinaciclib


title: EHE17 cells, MGH-CP1 (10 μM), 3


title: EHE17 cells, MGH-CP1 (10 μM), 2


title: CGND-HRA-02236

value: lumbar spinal cord

value: ALS

value: Male


title: CGND-HRA-02229

value: cervical spinal cord


title: CGND-HRA-02230


title: EHE17 cells, Vehicle control2


title: CGND-HRA-02224


title: EHE17 cells, MGH-CP1 (10 μM), 1


title: EHE17 cells, Dinaciclib (300 nM), 2


title: EHE17 cells, Dinaciclib (300 nM), 3


title: EHE17 cells, Vehicle control1


title: CGND-HRA-02223


title: CGND-HRA-02178

value: CTL


title: CGND-HRA-02218

value: ALS+FTD


title: CBT_DEG_Spleen3

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

description: SIY-specific CD8+ T cells

library_source: transcriptomic single cell

data_processing:
Raw read processing of scRNA-seq reads was performed as previously described(65). Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI). Then, cells with less than 300 unique genes detected or with greater than 25% mitochondrial gene counts and genes detected in fewer than 5 cells were filtered out. Cell cycle scores for individual cells were computed using CellCycleScoring function in Seurat. Data was then integrated by batch using Seurat v4.1.1(65).  The ScaleData function was then used to regress out the number of RNA features in each cell, as well as S and G2/M cell cycle scores and fraction of mitochondrial gene expression. The number of principal components used for visualization was determined by examination of the elbow plot, and two-dimensional embeddings were generated using uniform manifold approximation and projection (UMAP). Clusters were determined using Louvain clustering, as implemented in the FindClusters function in Seurat. DEG analysis was performed for each cluster and between indicated cell populations using the FindMarkers function. Data was iteratively reclustered to remove clusters with gene expression consistent with naïve T cells, monocytes, and NK cells. Label transfer of cluster labels onto proliferating cell populations was performed using the FindTransferAnchors and TransferData functions in Seurat (65).
Cell hashing data was aligned to HTO barcodes using CITE-seq-Count v1.4.2. First, cells receiving fewer than five total HTO counts were classified as negatives. To establish thresholds for positivity for each HTO barcode, we first performed centered log-ratio normalization of the HTO matrix and then performed k-medoids clustering with k=5 (one for each HTO). This produced consistently five clusters, each dominated by one of the 5 barcodes. For each cluster, we first identified the HTO barcode that was dominant in that cluster. We then considered the threshold to be the lowest value for that HTO barcode among the cells classified in that cluster. To account for the scenario in which this value was substantially lower than the rest of the values in the cluster, we used Grubbs’ test to determine whether this threshold was statistically an outlier relative to the rest of the cluster. If the lower bound was determined to be an outlier at p=0.05, it was removed from the cluster, and the next lowest value was used as the new threshold. This procedure was iteratively applied until the lowest value in the cluster was no longer considered an outlier at p=0.05. Cells were then determined to be “positive” or “negative” for each HTO barcode based on these thresholds. Cells that were positive for multiple HTOs or were negative for all HTOs were excluded from downstream analysis. To account for differences in sequencing depth between samples, these steps were performed separately for each Seq-Well array that was processed. Thresholds calculated for each sample were manually inspected and adjusted if necessary. Cells marked as “doublets” or “negatives” by this procedure were excluded from downstream analysis.
Paired TCR sequencing and read alignment was performed as previously described (66). Briefly, whole transcriptome amplification product from each single-cell library was enriched for TCR transcripts using biotinylated Tcrb and Tcra probes and magnetic streptavidin beads. The enrichment product was further amplified using V-region primers and Nextera sequencing handles, and the resulting libraries were sequenced on an Illumina Novaseq 6000 or Nextseq 550. Processing of raw sequencing reads was performed using the Immcantation software suite (67, 68). First, the FilterSeq.py function was used to remove reads with an average quality score less than 25. Then, reads were aggregated by cell barcode and UMI, and UMI with under 10 reads were discarded ClusterSets.py was used to divide sequences for each UMI into sets of similar sequences. Only sets of sequences that comprised greater than 70% of the sequences obtained for that UMI were considered further. Consensus sequences for each UMI were determined using the BuildConsensus.py function. Consensus sequences were then mapped against TCRV and TCRJ IMGT references sequences with IgBlast (69). Sequences for which a CDR3 sequence could not be unambiguously determined were discarded. UMI for consensus sequences were corrected using a directional UMI collapse, as implemented in UMI-tools. TCR sequences were then mapped to single cell transcriptomes by matching cell barcodes. If multiple Tcra or Tcrb sequences were detected for a single cell barcode, then the corresponding sequence with the highest number of UMI and raw reads was retained. To define clonotypes of cells, we first segregated cells by mouse and unique Tcrb CDR3 junction nucleotide sequences. For each unique combination of mouse and CDR3β junction, we determined the most common TCRα sequence in cells with paired TCR recovery. We then imputed missing beta chains from cells with recovery of only alpha chain by matching to these combinations of mouse, beta chain, and alpha chain.
Assembly: mm10
Supplementary files format and content: WT_DGE.txt.gz: cell/gene UMI count matrix from whole-transcriptome sequencing
Supplementary files format and content: HTO_processed.txt.gz: HTO count matrix
Supplementary files format and content: TCR_processed.txt.gz: aligned and assembeled TCR sequences

source_name: Spleen

growth_protocol: Mice were injected intraperitoneally with anti-CTLA-4 (clone UC10-4F10-11, Bio X Cell) and anti-PD-L1 (clone 10F.9G2, Bio X Cell) antibodies on days 7, 10, 13, and 16 post-tumor inoculation for tumor outgrowth studies, or on days 7 and 10 post-tumor inoculation for day 14 analyses. Each mouse received 100 mg of each antibody per treatment.

extract_protocol:
Prior to staining, cells were washed with FACS staining buffer (chilled PBS containing 1% FBS and 2 mM EDTA). Cells were resuspended in 50 mL of the antibody-containing staining buffer, plus eBioscience Fixable Viability Dye eFluor 780 or eFluor 506 to distinguish live and dead cells and with anti-CD16/CD32 (clone 93, BioLegend) to prevent non-specific antibody binding. Cell surface proteins were stained for 20 min on ice with fluorophore-conjugated antibodies at a 1:200 dilution. Cells were then washed twice and resuspended in eBioscience Fixation/Permeabilization buffer and incubated 30 minutes at room temperature. Cells were then washed twice and resuspended in staining buffer with intracellular antibodies. To obtain absolute counts of cells, Precision Count Beads (BioLegend) were added to samples according to manufacturer’s instructions. Flow cytometry sample acquisition was performed on a LSR Fortessa cytometer (BD), and the collected data was analyzed using FlowJo v10.5.3 software (TreeStar). For cell sorting, the surface staining was performed as described above under sterile conditions, and cells were acquired and sorted into complete medium using a FACSAria III sorter (BD). For CD8+ T cell analysis, cells were pre-gated on FSA and SSC, Live, CD45+, CD45-IV-, CD3+ or TCRbeta+, single cells, CD4-, CD8+. Antibodies used: CD4 clone RM4-5, CD45 clone 30-F11, CD45.1 clone A20, CD45.2 clone 104, CD8a clone 53-6.7, TCRb clone H57-597, CD3 clone 17A2, Thy1.2 clone 53-2.1, CXCR3 clone CXCR3-173, CX3CR1 clone SAO11F11, KLRG1 clone 2F1/KLRG1. SIY-tetramer was obtained from the NIH tetramer core, conjugated to PE, and added at 1:500-1:1,000 to the extracellular staining antibody mix. For scRNA-seq experiments with cell hashing, cells were also stained with Totalseq A anti-mouse hashing antibodies (Biolegend) before FACS.
Sorted cells were then processed for scRNA-seq using the Seq-Well platform with second strand chemistry, as previously described (63, 64). Whole transcriptome libraries were barcoded and amplified using the Nextera XT kit (Illumina) and were sequenced on a Novaseq 6000 (Illumina). Hashtag oligo libraries were amplified as described previously and were sequenced on a Nextseq 550(38).

treatment_protocol: To discriminate vascular T cells from T cells in tissues, tumor-bearing mice were injected retro-orbitally with fluorescently-labeled anti-CD45 antibodies (CD45-IV) 3 minutes prior to euthanasia. Spleens and lymph nodes were dissected from mice and physically dissociated through a 70 µm filter to generate single cell suspensions. Splenocyte suspensions were lysed with ACK lysis buffer (Gibco) for 3 minutes to deplete red blood cells. Subcutaneous tumors were dissected from mice, weighed, and collected in 5 mL DMEM (Gibco) containing the human tumor dissociation kit (Miltenyi) enzymes. Tumors were dissociated using a Mixer HC (USA Scientific) set to 37 degrees Celsius, shaking at 500 RPM for 45 – 60 minutes. Following the digestion, tumors were mashed through a 70 μm filter with a 1 mL syringe plunger to generate a single cell suspension. The dissociated cells were washed 2 times with PBS and were layered over Ficoll (GE). Cells were spun over Ficoll at 450 g for 30 minutes with the lowest settings of acceleration and brakes. The layer at the interface of Ficoll and PBS was collected and washed with PBS.

value: Spleen

value: CD8+ T cell

value: ICB


title: CBT_TCR

description: SIY-specific CD8+ T cells

source_name: Tumor

value: Tumor


title: CGND-HRA-02172

value: Female


title: Untreated_TCR

description: SIY-specific CD8+ T cells

value: Untreated


title: PRE7_UUO_PRE084_day21_biol_rep_1

city: Guadalajara

first: Raquel

last: Echavarria

state: Jalisco

address: Sierra Mojada 800

department: Surgical research

institute: CONACYT- Centro de Investigacion Biomedica de Occidente, IMSS

description:
gene_count_matrix_PRE084.txt
genes_fpkm_expression_PRE084.txt

data_processing:
Cutadapt v1.10 and in-house perl scripts were used to remove low-quality reads.
Sequence quality was verified with FastQC 0.10.1
HISAT2 2.0 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie.
Transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. Transcript expression levels were estimated with StringTie 1.3.4 and ballgown.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (gene)
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample (gene)

source_name: Heart

extract_protocol:
RNA was isolated using TRIzol reagent and ~4 ug was submitted to LC Sciences (Houston, TX, USA) for Sequencing
Poly(A) RNA-seq library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol (Illumina, San Diego, CA, USA) after passing RNA integrity checks (RIN>7).
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads in two rounds.
Quality control and sequencing library quantification were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

treatment_protocol: C57BL/6 male mice were subjected to either sham surgery (n=3), unilateral urinary obstruction (UUO) (n=3), or UUO treated with PRE-084 (1 mg/kg/day) (n=3). After 21 days, the whole heart was removed and processed for RNA extraction.

value: Heart

value: male

value: UUO surgery and PRE-084 (1 mg/kg/day)

value: 21 days


title: CGND-HRA-02217


title: CGND-HRA-02173


title: PRE9_UUO_PRE084_day21_biol_rep_3


title: CBT_DEG_Spleen2

description: SIY-specific CD8+ T cells


title: PRE8_UUO_PRE084_day21_biol_rep_2


title: CBT_DEG_TdLN2

description: SIY-specific CD8+ T cells

source_name: Tumor-draining lymph node

value: Tumor-draining lymph node


title: CBT_DEG_Tumor

description: SIY-specific CD8+ T cells


title: CGND-HRA-02146

value: lumbar spinal cord


title: CGND-HRA-02152

value: ALS


title: CGND-HRA-02145


title: CGND-HRA-02159

value: Male


title: CBT_DEG_Spleen1

description: SIY-specific CD8+ T cells


title: CGND-HRA-02277

value: cervical spinal cord


title: Untreated_DEG_Tumor

description: SIY-specific CD8+ T cells


title: CGND-HRA-02153


title: Untreated_DEG_Spleen2

description: SIY-specific CD8+ T cells


title: Untreated_DEG_Spleen1

description: SIY-specific CD8+ T cells


title: CBT_DEG_TdLN1

description: SIY-specific CD8+ T cells


title: CGND-HRA-01980

value: CTL


title: CBT_HTO_TdLN2

description: SIY-specific CD8+ T cells


title: CGND-HRA-01979


title: CGND-HRA-01944-2


title: CBT_HTO_Tumor

description: SIY-specific CD8+ T cells


title: CGND-HRA-01583


title: Untreated_HTO_Spleen2

description: SIY-specific CD8+ T cells


title: Untreated_DEG_TdLN

description: SIY-specific CD8+ T cells


title: Untreated_HTO_Spleen1

description: SIY-specific CD8+ T cells


title: CBT_HTO_Spleen1

description: SIY-specific CD8+ T cells


title: CGND-HRA-02166


title: CGND-HRA-01595

value: ALS+FTD


title: CGND-HRA-00274

value: NEURCTL


title: CGND-HRA-01767


title: CBT_HTO_Spleen3

description: SIY-specific CD8+ T cells

value: Spleen

value: CD8+ T cell


title: CGND-HRA-01957


title: Untreated_HTO_Tumor

description: SIY-specific CD8+ T cells


title: CGND-HRA-01577


title: CCI_14day_pooled_ATAC

city: Solna

first: Saida

last: Hadjab

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
10x_snMultiomics MO_22_003 (GEX: P26706_8003, ATAC:P27153_3003)
MO_22_003_raw_feature_bc_matrix.h5
MO_22_003_atac_peak_annotation.tsv

library_source: genomic single cell

data_processing:
For 10x snMultiomics, the raw fastq files were processed with Cell Ranger Arc software v2.0.2
For smartseq3, the raw fastq files were process with zUMIs software v2.9.7
Assembly: mm10
Supplementary files format and content: For 10x snMultiomics, the processed files are in h5 (count matrices) and tsv (ATAC fragments) formats.  The files with .h5 format contain the count matrices for both GEX and ATAC modalities within the same file. The atac_peak_annotation.tsv files contain the annotation of the peaks regions in the ATAC count matrices found in .h5 files.
Supplementary files format and content: For smartseq3, the processed files are in h5ad format (count matrix)

source_name: Dorsal Root Ganglia (L4-L6)

extract_protocol:
For snMultiomic: L4-L6 DRGs from mice were collected at 14 days after CCI injury or without injury, and then immediately put on dry ice. Nuclei were extracted from frozen DRG according to a published protocal by the Allen Institute for Brain Science. Pooled nuclei suspension were used for snMultiomic sequencing.
For smartseq3, all DRGs from mice were collected and immediately put on dry ice. Nuclei were extracted from frozen DRG according to a published protocal by the Allen Institute for Brain Science. Nuclei suspension was incubated with anti-NeuN PE conjugated antibody and DAPI. Single NeuN+ and DAPI+ nuclei were sorted into each well of a 384 well plate RNA-for smartseq3 sequencing.
Library was performed according to the manufacter’s instructions (Single Cell Multiome ATAC + Gene Expression protocal, 10x Genomics)
10x snMultiomics

value: Dorsal Root Ganglia (L4-L6)

value: WT

value: CCI model after 14 days (2 males 1 female)


title: CBT_HTO_TdLN1

description: SIY-specific CD8+ T cells

value: ICB


title: CBT_HTO_Spleen2

description: SIY-specific CD8+ T cells


title: CGND-HRA-02996

source_name: frontal cortex

value: frontal cortex


title: CGND-HRA-02986

source_name: motor cortex

value: motor cortex


title: CGND-HRA-00517


title: CGND-HRA-01288-2-2

value: thoracic spinal cord


title: GW3965-diet small intestine

city: Stockholm

last: Fransson

address: Karolinska Institutet

description: Visium (10X)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.2.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Gzip files containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions
Library strategy: Spatial Transcriptomics

source_name: small intestine

extract_protocol:
Spatial transcriptomics protocol was performed according to manufacturer's instructions.
cDNA libraries and post-indexed libraries were prepared accoring to manufacturer's instructions (10X Visium). Visium libraries were sequenced on a NovaSeq S1 flow cell (Illumina) at a depth of ~200 million reads per sample with 28 bases from read 1 and 120 bases from read 2.

treatment_protocol: Wild type C57BL/6J male mice were fed with either a control (standard) diet or a diet with LXR agonist GW3965. After 10 days of diet, small intestines were collected. To prepare the swissroll, the small intestine was rolled from the distal to the proximal and frozen in OCT. Cryo-sectioned (10µm) and placed on the 10X visium provided slide with a barcoded square (6.5mm x 6.5mm). Libraries were prepared according to 10X Visium spatial transcriptomics protocol and submitted for sequencing.

value: small intestine

value: male

tag: diet

value: GW3965 Diet


title: Control_female_pooled_GEX

description:
10x_snMultiomics MO_22_006 (GEX: P26706_8006, ATAC:P27153_3006)
MO_22_006_raw_feature_bc_matrix.h5
MO_22_006_atac_peak_annotation.tsv

molecule: nuclear RNA

tag: tissue

value: Control, Female (3 mice)


title: Control_pooled_GEX

description:
10x_snMultiomics MO_22_004 (GEX: P26706_8004, ATAC:P27153_3004)
MO_22_004_raw_feature_bc_matrix.h5
MO_22_004_atac_peak_annotation.tsv

value: Control, Pooled (2 males 1 female)


title: Control_male_pooled_ATAC

description:
10x_snMultiomics MO_22_008 (GEX: P26706_8008, ATAC:P27153_3008)
MO_22_008_raw_feature_bc_matrix.h5
MO_22_008_atac_peak_annotation.tsv

value: Control, Male (3 mice)


title: Control_female_pooled_ATAC


title: CGND-HRA-02988

value: ALS

value: Female


title: Control_pooled_ATAC


title: CGND-HRA-01589

value: lumbar spinal cord

value: Male


title: CGND-HRA-02977


title: CGND-HRA-02953


title: TAM 10 hi

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
trim adapters with fastp
Align with STAR
featureCounts for counting
edgeR for calling DEGs
Assembly: hg38 or mm10
Supplementary files format and content: txt/rds file containing raw counts

source_name: Tumor Macrophages

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit (Cat# 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor Macrophages


title: CGND-HRA-02970


title: CCI_14day_pooled_GEX

value: Dorsal Root Ganglia (L4-L6)

value: WT


title: CGND-HRA-02955


title: TAM 9 hi


title: CGND-HRA-02951


title: CGND-HRA-02966


title: CGND-HRA-02947


title: Control_male_pooled_GEX


title: TAM 6 hi


title: CGND-HRA-02943


title: CGND-HRA-02945


title: CGND-HRA-02942


title: CGND-HRA-02941


title: TAM 8 lo


title: CGND-HRA-02936


title: TAM 9 lo


title: CGND-HRA-02933


title: CGND-HRA-02979


title: TAM 5 hi


title: TAM 7 lo


title: CGND-HRA-02921


title: CGND-HRA-02939


title: TAM 3 hi


title: TAM 2 hi


title: TAM 7 hi


title: TAM 10 lo


title: CGND-HRA-02925


title: TAM 1 hi


title: TAM 6 lo


title: TAM 4 hi


title: CGND-HRA-02908


title: CGND-HRA-02924


title: CGND-HRA-02919


title: TAM 5 lo


title: CGND-HRA-02910


title: CGND-HRA-02905

source_name: lateral motor cortex

value: lateral motor cortex


title: TAM 3 lo


title: TAM 4 lo


title: CGND-HRA-02923

value: frontal cortex


title: CGND-HRA-02898

source_name: medial motor cortex

value: medial motor cortex


title: TAM 2 lo


title: CGND-HRA-02892

value: motor cortex


title: CGND-HRA-02891


title: MC38 TAM aPD1 3


title: CGND-HRA-02885


title: CGND-HRA-02879


title: CGND-HRA-02876


title: MC38 TAM IgG 3


title: MC38 TAM aPD1 2


title: MC38 TAM IgG 2


title: CGND-HRA-02882


title: CGND-HRA-02868


title: CGND-HRA-02865


title: PFC, EF1_high, scRNASeq, replicate_4

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

institute: University of Iowa

description: 10X Genomics

data_processing:
Using Cell Ranger (version 6.0.0), data was demultiplexed followed by feature quantification and data aggregation. The Cell Ranger software was obtained from here: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
For the supplementary file, SCTransformed counts were imported into DESEq2 and genes with low counts and low variance were removed. Size factors were computed using the "computeSumFactors" function from the scran package for normalization.
Supplementary files format and content: mm10
Supplementary files format and content: Tab separated value and matrix files

source_name: Prefrontal cortex

extract_protocol:
The prefrontal cortex including the prelimbic and infralimbic  cortices were extracted while bathing in artificial cerebrospinal fluid bubbled in carbogen (95% O2/5% CO2) gas. Tissues were digested with in papain prior to creation of single cell suspension by trituration.
Library was contructed as per manufecturer's protocol (10X Genomics, Single Cell 3’ Kit v3.1).

value: Prefrontal cortex

value: 9 weeks


title: CGND-HRA-02864


title: PFC, EF1_low, scRNASeq, replicate_2

description: 10X Genomics


title: PFC, EF1_low, scRNASeq, replicate_3

description: 10X Genomics


title: CGND-HRA-02862


title: MC38 TAM aPD1 1


title: PFC, EF1_high, scRNASeq, replicate_3

description: 10X Genomics

value: 12 weeks


title: CGND-HRA-02858


title: PFC, EF1_medium, scRNASeq, replicate_4

description: 10X Genomics


title: MC38 TAM IgG 1


title: CGND-HRA-02856


title: TAM 1 lo


title: PFC, EF1_medium, scRNASeq, replicate_2

description: 10X Genomics

value: 10 weeks


title: CGND-HRA-02861


title: CGND-HRA-02850


title: CGND-HRA-02853


title: CGND-HRA-02849


title: PFC, EF1_high, scRNASeq, replicate_2

description: 10X Genomics


title: PFC, EF1_medium, scRNASeq, replicate_5

description: 10X Genomics

value: 11 weeks


title: PFC, EF1_medium, scRNASeq, replicate_3

description: 10X Genomics


title: PFC, EF1_medium, scRNASeq, replicate_1

description: 10X Genomics

value: 14 weeks


title: PFC, EF1_high, scRNASeq, replicate_1

description: 10X Genomics


title: CGND-HRA-02845

value: ALS


title: CGND-HRA-02841

value: Female


title: Sorbitol 300mM rep3

city: Detroit

first: Daniel

middle: A

last: Rappolee

state: MI

address: 275 E Hancock St

department: OBGYN

institute: Wayne State University

data_processing:
Data were demultiplexed using Illumina’s CASAVA 1.8.2 software.
Alignment to the mouse genome (mm9) using STAR
Tabulation using htseq-count
Differential expression analysis in edgeR
Assembly: mm9
Supplementary files format and content: Excel files comparing triplicate stimulus data to triplicate Normal Stemness (NS) data.

source_name: REX-1 RFP

growth_protocol: ESC passaged and grown with LIF+ media for ~18hr until ~24% confluence. They were then grown under their corresponding condition.

extract_protocol:
Cells were then washed and lysed using Trizol.
Lexogen 3' Quant-seq protocol

treatment_protocol: Cells were grown under stimulation for 72hr.

value: Embryonic Stem Cell

tag: cell line

value: REX-1 RFP

tag: lif presence

value: positive

tag: condition

value: Sorbitol 300mM

tag: treatment time


title: CGND-HRA-02844

value: Male


title: CGND-HRA-02837


title: CGND-HRA-02834


title: CGND-HRA-02840


title: ND rep3

tag: cell type

value: negative

value: normal differentiation (ND)


title: NS rep3

value: normal stemness (NS)


title: CGND-HRA-02826

value: motor cortex


title: Sorbitol 250mM rep3

value: Sorbitol 250mM


title: Sorbitol 250mM rep2


title: CGND-HRA-02873


title: CGND-HRA-02821


title: Sorbitol 300mM rep2


title: CGND-HRA-02830


title: CGND-HRA-02831


title: CGND-HRA-02820


title: Sorbitol 200mM rep3

value: Sorbitol 200mM


title: CGND-HRA-02824


title: CGND-HRA-02817


title: NS rep2


title: Sorbitol 200mM rep1


title: TAM 8 hi

value: Tumor Macrophages

tag: strain

tag: genotype

value: WT


title: CGND-HRA-02810


title: ND rep1


title: CGND-HRA-02801


title: CGND-HRA-02813


title: NS rep1


title: Sorbitol 200mM rep2


title: CGND-HRA-02814


title: Sorbitol 250mM rep1


title: TregGata3lo cells, rep5

city: Brussels

first: Julie

last: Stockis

address: Avenue Hippocrate 74

department: de Duve Institute

country: Belgium

institute: UCLouvain

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.9)
Raw sequence was trimmed for adapter content using Trimmomatic (version 0.39)
Reads were aligned to the GRCm38.p6 genome using STAR (v 2.7.7a)
Alignment quality was assess using Picard’s CollectAlignmentMetrics, CollectRnaSeqMetrics, MarkDuplicates and CollectInsertSizeMetrics tools (v 2.27.3)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Assembly: Differential gene expression analysis was carried out using DESeq2 (v 1.34.0) [6] in R (v 4.1.2)
Supplementary files format and content: GRCm38.p6
Supplementary files format and content: Tar archive file containing full Salmon output

source_name: Lung

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen) and 5 to 15 ng used as input material for library preparation.
Libraries were generated with the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. The pooled libraries were quantified with KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and sequenced (paired end 150nt) on an Illumina NovaSeq 6000 system (Illumina).

treatment_protocol: Mice were sensitised with 200 ng IL-33 intranasally on day 0 and day 1, and sacrificed on day 6 or 7.

value: Lung

value: Treg Gata3 low

value: Gata3 YFP/YFP Foxp3 RFP/RFP

tag: treatment

tag: mouse id

tag: Sex

value: F


title: CGND-HRA-02793

value: lateral motor cortex

value: ALS

value: Female


title: ND rep2

value: Embryonic Stem Cell

value: REX-1 RFP


title: CGND-HRA-02792

value: medial motor cortex


title: TregGata3lo cells, rep4


title: CGND-HRA-02765

value: frontal cortex

value: Unknown


title: TregGata3lo cells, rep3


title: CGND-HRA-02760

value: Male


title: TregGata3lo cells, rep2


title: PFC, EF1_low, scRNASeq, replicate_1

description: 10X Genomics

value: Prefrontal cortex

tag: age

value: 10 weeks


title: CGND-HRA-02749


title: Sorbitol 300mM rep1

value: positive

value: Sorbitol 300mM


title: TregGata3lo cells, rep1

value: Lung


title: TregGata3hi cells, rep5

value: Treg Gata3 hi


title: Standard diet small intestine

description: Visium (10X)

value: small intestine

value: WT

value: male

value: Standard Diet


title: CGND-HRA-02987

value: ALS


title: CGND-HRA-02763


title: CGND-HRA-02744


title: CGND-HRA-02753


title: TregGata3hi cells, rep4

value: Gata3 YFP/YFP Foxp3 RFP/RFP

value: F


title: TregGata3hi cells, rep1


title: CGND-HRA-02745

value: Female


title: TregGata3hi cells, rep3


title: Th2 cells, rep4


title: CGND-HRA-02739

value: medial motor cortex


title: CGND-HRA-02746

value: frontal cortex


title: CGND-HRA-02725-2

value: motor cortex


title: TregGata3hi cells, rep2


title: Th2 cells, rep3


title: CGND-HRA-02740

value: lateral motor cortex

value: Male


title: CGND-HRA-02733


title: CGND-HRA-02724


title: Th2 cells, rep1


title: Th2 cells, rep2


title: Tconv cells, rep4

value: Tconv


title: Tconv cells, rep5


title: Th2 cells, rep5


title: CGND-HRA-02716


title: Tconv cells, rep3


title: Tconv cells, rep2


title: CGND-HRA-02715


title: CGND-HRA-02719


title: CGND-HRA-02711


title: CGND-HRA-02736


title: CGND-HRA-02710


title: ILC2 cells, rep4


title: CGND-HRA-02705


title: Treg cells, WT, rep6

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.9)
Raw sequence was trimmed for adapter content using Trimmomatic (version 0.39)
Reads were aligned to the GRCm38.p6 genome using STAR (v 2.7.7a)
Alignment quality was assess using Picard’s CollectAlignmentMetrics, CollectRnaSeqMetrics, MarkDuplicates and CollectInsertSizeMetrics tools (v 2.25.1)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Differential gene expression analysis was carried out using DESeq2 (v 1.34.0) [6] in R (v 4.1.2)
Assembly: GRCm38.p6
Supplementary files format and content: Tar archive file containing full Salmon output

value: Spleen

value: Treg

value: Foxp3-Cre OX40 wt/wt

tag: mouse

value: M


title: Treg cells, WT, rep7


title: CGND-HRA-02701

tag: disease state


title: Treg cells, WT, rep5


title: CGND-HRA-02697

tag: gender


title: CGND-HRA-02720

tag: subject id


title: CGND-HRA-02700


title: CGND-HRA-02696


title: Treg cells, KO, rep5

value: Foxp3-Cre OX40 fl/fl


title: Treg cells, WT, rep2


title: CGND-HRA-02692


title: Treg cells, KO, rep2


title: Tconv cells, rep1

value: Lung


title: CGND-HRA-02687-2


title: Treg cells, KO, rep1


title: CGND-HRA-02686


title: CGND-HRA-02683


title: Tconv cells, WT, rep7


title: ILC2 cells, rep5


title: CGND-HRA-02678


title: Tconv cells, WT, rep6


title: Tconv cells, WT, rep2


title: CGND-HRA-02644


title: CGND-HRA-02628


title: Untreated_HTO_TdLN

description: SIY-specific CD8+ T cells

value: Tumor-draining lymph node

value: CD8+ T cell

value: Untreated


title: Treg cells, WT, rep1


title: CGND-HRA-02706

value: ALS


title: Treg cells, KO, rep4


title: CGND-HRA-02675

value: Female


title: Tconv cells, WT, rep5


title: CGND-HRA-02627


title: Tconv cells, WT, rep1


title: CGND-HRA-02691


title: Tconv cells, KO, rep5


title: CGND-HRA-02622


title: Tconv cells, KO, rep4


title: CGND-HRA-02618


title: Tconv cells, KO, rep2


title: Tconv cells, KO, rep1


title: CGND-HRA-02613

value: CTL


title: Standard diet irradiated

description: Visium (10X)

treatment_protocol: Wild type C57BL/6J male mice were fed with either a control (standard) diet or a diet with LXR agonist GW3965. Ten days after diet, mice were exposed to 10Gy total body irradiation (TBI) and SI Swiss rolls (starting from distal SI) were collected on day3 after irradiation (3 dpi), processed and submitted for sequencing. SI Swiss rolls from mice fed with either standard or GW3965 diet but no irradiation (0 dpi) were used as control.

value: WT C57BL/6J

value: small intestine

tag: diet

value: Standard Diet

value: Irradiated (3dpi)


title: CGND-HRA-02608

tag: tissue

value: motor cortex

value: Male


title: Standard diet non-irradiated

description: Visium (10X)

value: Control (no irradaition, 0dpi)


title: Tconv cells, WT, rep3

value: Spleen

value: Tconv

value: Foxp3-Cre OX40 wt/wt


title: GW3965-diet irradiated

description: Visium (10X)

value: GW3965 Diet


title: CGND-HRA-02612

value: frontal cortex


title: GW3965-diet non-irradiated

description: Visium (10X)


title: CGND-HRA-02602


title: CGND-HRA-02601


title: STD_IMM_d0

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.1.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Gzip files containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions

source_name: SI

extract_protocol: SI tissues were digested and epithelial (EpCAM+CD45-, EPI), immune (EpCAM-CD45+, IMM) or stromal cells (EpCAM-CD45-, double negative, DN) cells were sorted and processed for single cell transcriptomics analysis using protocol from 10X genomics.

treatment_protocol: WT mice were fed with either control (standard) or GW3965 containing diet for a period of 10 days. Following this, epithelial (EpCAM+CD45-, EPI), immune (EpCAM-CD45+, IMM) or stromal cells (EpCAM-CD45-, double negative, DN) cells were sorted and proceed for single cell transcriptomics analysis.

value: SI

value: immune (EpCAM-CD45+, IMM)

value: control


title: STD_EPI_d0

value: epithelial (EpCAM+CD45-, EPI)


title: STD_DN_d0

value: stromal cells (EpCAM-CD45-, double negative, DN)


title: CGND-HRA-02597

value: ALS+FTD


title: GW_IMM_d0

value: GW3965 containing diet


title: CGND-HRA-02617

value: ALS

value: Female


title: GW_EPI_d0


title: CGND-HRA-02589


title: CGND-HRA-02590

value: motor cortex


title: GW_DN_d0


title: CGND-HRA-02596

value: Male


title: GW3965 Diet AOM-DSS d43

description: Visium (10X)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.1.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Gzip files containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions
Library strategy: Spatial Transcriptomics

source_name: Colon

treatment_protocol: Wild type C57BL/6J male mice were fed with either a control (standard) diet or a diet with LXR agonist GW3965. Mice were injected with 10mg/kg body weight azoxymethane (AOM). One week after AOM injection, mice were exposed to DSS in drinking water for 7 days followed by 7 days of recovery (DSS-cycle). This DSS cycle was repeated two more times for a total of 3 times with 7 days between each cycle.  Colonic Swiss rolls were collected on day22 or day43 after AOM injection, processed and submitted for sequencing. Colonic Swiss rolls from mice fed with standard (for 43 days, defined as d0 as they were untreated) diet but no AOM or DSS were used as control.

value: WT C57BL/6J

value: Colon

tag: mode

value: AOM-DSS

tag: day


title: CGND-HRA-02607


title: GW3965 Diet AOM-DSS d22

description: Visium (10X)


title: CGND-HRA-02579


title: CGND-HRA-02584


title: Standard Diet AOM-DSS d43

description: Visium (10X)

value: Standard Diet


title: CGND-HRA-02576


title: Standard Diet AOM-DSS d22

description: Visium (10X)


title: Standard Diet no AOM-DSS d43 (day0)

description: Visium (10X)

value: Control


title: CGND-HRA-02575

value: frontal cortex


title: GW3965-treated organoids

data_processing:
Fastq files were processed using CellRanger v 6.0.2 (10X Genomics) to achieve .h5 gene/cell matrix files (filtered_feature_bc_matrix.h5 output from CellRanger).
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with gene/cell matrix for each sample

source_name: Organoids

growth_protocol: SI organoids were grown in Noggin-Rspondin medium using isolated crypts for a period of 5 days before doing single cell analysis.

extract_protocol:
Single cell suspensions of the SI organoids were prepared using TrpLE express, stained and epithelial cells were sorted using flow cytometry before proceeding with single cell RNAseq.
Libraries were constructed according to 10X Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry). Briefly, Gel Bead-In-Emulsions (GEMs) were generated with loaded cells in a Chromium Controller. Reverse transcription was performed in GEMs and beads were dissolved. Barcoded cDNA was purified and amplified, then fragmented, A-tailed, ligated to adaptors and sample indeces, and selected for size. Approx 16,000 cells were loaded to achieve approx 10,000 cells final cell counts. Libraries were sequenced by Novogene UK as 150 BP paired-end on NovaSeq600 platform at 300M reads/sample.

treatment_protocol: SI organoids were either treated with vehicle (DMSO) or 1uM GW3965 for a period of 5 days before being analyzed by single cell RNAseq

value: WT


title: CGND-HRA-02570


title: DMSO-treated organoids

value: DMSO


title: CGND-HRA-02571


title: GW3965 Diet AOM-DSS day70, replicate 3

data_processing:
Fastq files were processed using Kallisto count function.
Genome_build: GRCm38
Supplementary_files_format_and_content: .tsv-files generated by Kallisto count function

extract_protocol:
RNA was extracted from colonic tissues using Qiagen RNeasy Kit according to manufacturer's instructions.
cDNA libraries were constructed and sequenced by Novogene Co Ltd (UK). Sequencing was performed at a depth of 20 million reads per sample using paired-end 150 bp reads on a NovaSeq 6000 sequencer and v1.0 reagent kit.

treatment_protocol: Wild type C57BL/6J male mice were fed with either a control (standard) diet or a diet with LXR agonist GW3965. Mice were injected with 10mg/kg body weight azoxymethane (AOM). One week after AOM injection, mice were exposed to DSS in drinking water for 7 days followed by 7 days of recovery (DSS-cycle). This DSS cycle was repeated two more times for a total of 3 times with 7 days between each cycle. Mice receiving both standard and GW3965 diet but no AOM or DSS were used as controls. Samples were collected on day22, day43 or day70 after AOM injection, processed and submitted for RNA sequencing.

tag: model

value: AOMDSS

value: male

value: Wild type

tag: rin

tag: cage

value: L

value: ~10 weeks

tag: vendor

value: Taconic


title: CGND-HRA-02566

value: ALS


title: GW3965 Diet AOM-DSS day70, replicate 2

tag: strain

tag: genotype

value: K


title: CGND-HRA-02565

value: Male


title: Standard Diet AOM-DSS day70, replicate 3

value: STD

value: I


title: CGND-HRA-02560

value: Female


title: CGND-HRA-02561

value: motor cortex


title: Standard Diet AOM-DSS day70, replicate 2

value: H


title: CGND-HRA-02585


title: CGND-HRA-02555

value: frontal cortex


title: GW3965 Diet no AOM-DSS day43 (day0), replicate 2

value: Control

value: F


title: CGND-HRA-02551


title: CGND-HRA-02580


title: CGND-HRA-02556


title: GW3965 Diet no AOM-DSS day43 (day0), replicate 1


title: CGND-HRA-02550


title: CGND-HRA-02532


title: CGND-HRA-02529

value: lateral motor cortex


title: GW3965 Diet no AOM-DSS day22 (day0), replicate 1

value: male


title: CGND-HRA-02526


title: GW3965 Diet AOM-DSS day43, replicate 3

value: AOMDSS

value: Wild type

value: B


title: GW3965 Diet no AOM-DSS day22 (day0), replicate 2

value: ~10 weeks

value: Taconic


title: CGND-HRA-02522

value: ALS


title: GW3965 Diet AOM-DSS day43, replicate 2


title: GW3965 Diet AOM-DSS day22, replicate 2


title: GW3965 Diet AOM-DSS day70, replicate 1

value: J


title: CGND-HRA-02514

value: Male


title: CGND-HRA-02520


title: GW3965 Diet AOM-DSS day22, replicate 3


title: CGND-HRA-02524


title: CGND-HRA-02508


title: CGND-HRA-02510

value: medial motor cortex


title: CGND-HRA-02504

value: Female


title: GW3965 Diet AOM-DSS day22, replicate 1


title: Standard Diet no AOM-DSS day43 (day0), replicate 1

value: STD

value: E


title: Standard Diet no AOM-DSS day22 (day0), replicate 2


title: Standard Diet AOM-DSS day70, replicate 1

value: G


title: CGND-HRA-02503


title: CGND-HRA-02501

value: frontal cortex


title: CGND-HRA-02497


title: Standard Diet AOM-DSS day43, replicate 3

value: A


title: Standard Diet AOM-DSS day43, replicate 2


title: CGND-HRA-02496


title: Standard Diet AOM-DSS day43, replicate 1


title: CGND-HRA-02494


title: Standard Diet AOM-DSS day22, replicate 3


title: GW3965 Diet AOM-DSS day43, replicate 1


title: Standard Diet AOM-DSS day22, replicate 2


title: CGND-HRA-02489


title: CGND-HRA-02490

value: lateral motor cortex


title: Standard Diet no AOM-DSS day43 (day0), replicate 2

value: Control

value: male


title: CGND-HRA-02487


title: E9

first: Estelle

last: Hirsinger

address: 9 quai Saint Bernard

department: LBD

institute: IBPS

description: 10X Genomics

data_processing:
Sequence analysis with Cell Ranger Single Cell Software Suite 3.0.2 by 10X Genomics
Raw base call files were demultiplexed with the cellranger mkfastq pipeline into library specific FASTQ files.
The FASTQ files for each library were then processed independently with the cellranger count pipeline.
This pipeline used STAR to align cDNA reads to the Gallus gallus genome (Sequence: GRCg6a, Gallus gallus reference).
Assembly: GRCg6ar95
Supplementary files format and content: For each sample, set of 3 files in format 10X (list of cell barcodes, list of genes and expression matrix (raw counts))

organism: Gallus gallus

source_name: Forelimb

extract_protocol:
Forelimbs from X different E7 embryos, Y different E9 embryos were dissected and dissociated by collagenase and mechanical treatments. 5000 cells per conditions were loaded into the 10X Chromium Chip with the Single Cell 3’ Reagent Kit v3 according to the manufacturer’s protocol. Samples were pooled together at each developmental stage (E7 (N=X), E9 (N=Y) ) before making the libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: Forelimb

tag: developmental stage

tag: cell type

value: Limb cells

value: wild-type


title: Standard Diet AOM-DSS day22, replicate 1

value: AOMDSS

tag: Sex

value: Wild type

value: ~10 weeks

value: Taconic


title: E7

description: 10X Genomics


title: Standard Diet no AOM-DSS day22 (day0), replicate 1


title: CGND-HRA-02483

data_processing:
Reads from samples with RIN > = 5.5 were aligned to the hg38 human genome using STAR v2.7.6, allowing for a 4% mismatch rate and up to 100 alignments per read to ensure capture of young transposon sequences. Abundance of gene and transposon sequences was calculated with TEtranscripts v2.2.3
Assembly: hg38
Supplementary files format and content: Text file of gene and transposable element counts

value: ALS

value: Male


title: CGND-HRA-02476


title: CGND-HRA-02482

value: medial motor cortex


title: CGND-HRA-02479


title: CGND-HRA-02469


title: CGND-HRA-02467


title: CGND-HRA-02464


title: CGND-HRA-02463


title: BC57_FFPE_250pg_Pico_SM_rep3 (Nanostring)

hyb_protocol: cDNA or RNA were hybridized overnight in a nCounter Prep Station according to NanoString recommendation

scan_protocol: nCounter Digital Analyzer were used for digital counting

data_processing: Data were normalized using the nSolver software provided by NanoString

label: Fluorescent tag barcode

source_name: mouse bladder cancer cell line (BC57)

label_protocol: Gene of interest are targeted by a specific pair of probe: fluorescently-labeled specific Reporter Tags, and a biotinylated universal Capture Tag. Each report tag has a unique pattern of six spots of color, creating fluorescent barcodes that can be individually resolved and counted   during data collection.

extract_protocol: Total RNA from FFPE were extracted by using Qiagen RNeasy FFPE. Ten slices of five microns of thickness of FFPE samples were dewaxed using Deparaffinization solution and were extracted according to manufacturer instructions (RNeasy FFPE tissue Handbook). Total RNA from FF samples were extracted with Qiagen RNeasy mini according to manufacturer instructions.

value: bladder cancer cells

tag: nanostring amplification method

value: SMARTer Stranded Total RNA-Seq Kit - Pico Input mammelian (Pico-SM)

tag: rna input quantity

tag: method of sample preservation

value: FFPE


title: BC57_FFPE_250pg_Pico_SM_rep1 (Nanostring)


title: BC57_FFPE_250pg_Pico_SM_rep2 (Nanostring)


title: MNU_FFPE_250pg_Pico_SM_rep1 (Nanostring)

source_name: mouse normal urothelium (MNU)

value: normal urothelium


title: MNU_FFPE_250pg_Pico_SM_rep3 (Nanostring)


title: MNU_FFPE_250pg_Pico_SM_rep2 (Nanostring)


title: MNU_FFPE_2ng_Pico_SM_rep2 (Nanostring)


title: CGND-HRA-02457

tag: disease state

tag: gender

tag: subject id


title: CGND-HRA-02470

tag: tissue

value: lateral motor cortex


title: MNU_FFPE_2ng_Pico_SM_rep3 (Nanostring)


title: MNU_FFPE_2ng_Pico_SM_rep1 (Nanostring)


title: CGND-HRA-02455

value: frontal cortex

value: Female


title: BC57_FFPE_2ng_Pico_SM_rep3 (Nanostring)


title: BC57_FFPE_2ng_Pico_SM_rep2 (Nanostring)


title: CGND-HRA-02449


title: CGND-HRA-02452


title: CGND-HRA-02451


title: CGND-HRA-02445


title: MNU_FF_250pg_Pico_SM_rep2 (Nanostring)

value: FF


title: CGND-HRA-02443


title: BC57_FF_250pg_Pico_SM_rep3 (Nanostring)


title: CGND-HRA-02461


title: MNU_FF_250pg_Pico_SM_rep1 (Nanostring)


title: BC57_FFPE_2ng_Pico_SM_rep1 (Nanostring)


title: CGND-HRA-02458


title: BC57_FF_250pg_Pico_SM_rep1 (Nanostring)


title: BC57_FF_250pg_Pico_SM_rep2 (Nanostring)


title: CGND-HRA-02439


title: MNU_FF_250pg_Pico_SM_rep3 (Nanostring)


title: BC57_FF_2ng_Pico_SM_rep3 (Nanostring)


title: CGND-HRA-02440


title: CGND-HRA-02428


title: CGND-HRA-02433


title: CGND-HRA-02425


title: CGND-HRA-02427


title: MNU_FFPE_250pg_SC_rep3 (Nanostring)

value: PCR based approach (SC)


title: MNU_FF_2ng_Pico_SM_rep2 (Nanostring)


title: BC57_FF_2ng_Pico_SM_rep1 (Nanostring)


title: CGND-HRA-02437


title: MNU_FF_2ng_Pico_SM_rep3 (Nanostring)


title: BC57_FF_2ng_Pico_SM_rep2 (Nanostring)


title: CGND-HRA-02446


title: MNU_FFPE_250pg_SC_rep2 (Nanostring)


title: MNU_FF_2ng_Pico_SM_rep1 (Nanostring)


title: CGND-HRA-02422


title: BC57_FFPE_250pg_SC_rep2 (Nanostring)


title: MNU_FFPE_250pg_SC_rep1 (Nanostring)


title: CGND-HRA-02421


title: CGND-HRA-02419


title: CGND-HRA-02431


title: BC57_FFPE_250pg_SC_rep3 (Nanostring)


title: CGND-HRA-02416


title: MNU_FFPE_2ng_SC_rep2 (Nanostring)


title: CGND-HRA-02415


title: BC57_FFPE_250pg_SC_rep1 (Nanostring)


title: CGND-HRA-02413


title: CGND-HRA-02409


title: CGND-HRA-02410


title: BC57_FFPE_2ng_SC_rep3 (Nanostring)


title: MNU_FFPE_2ng_SC_rep3 (Nanostring)


title: CGND-HRA-02403


title: MNU_FFPE_2ng_SC_rep1 (Nanostring)


title: CGND-HRA-02406


title: CGND-HRA-02392

value: ALS+FTD


title: CGND-HRA-02402


title: BC57_FFPE_2ng_SC_rep2 (Nanostring)


title: CGND-HRA-02370

value: motor cortex


title: BC57_FFPE_50pg_SC_rep2 (Nanostring)


title: BC57_FFPE_50pg_SC_rep3 (Nanostring)


title: CGND-HRA-02399

value: CTL


title: BC57_FFPE_2ng_SC_rep1 (Nanostring)


title: CGND-HRA-02396


title: BC57_FFPE_50pg_SC_rep1 (Nanostring)


title: MNU_FFPE_50pg_SC_rep2 (Nanostring)


title: MNU_FF_250pg_SC_rep2 (Nanostring)


title: CGND-HRA-02369


title: CGND-HRA-02367


title: MNU_FF_250pg_SC_rep3 (Nanostring)


title: MNU_FFPE_50pg_SC_rep3 (Nanostring)


title: CGND-HRA-02364


title: MNU_FF_250pg_SC_rep1 (Nanostring)


title: BC57_FF_250pg_SC_rep3 (Nanostring)


title: CGND-HRA-02351


title: CGND-HRA-02356


title: CGND-HRA-02355


title: CGND-HRA-02350


title: CGND-HRA-02346


title: MNU_FF_2ng_SC_rep3 (Nanostring)


title: MNU_FFPE_50pg_SC_rep1 (Nanostring)


title: CGND-HRA-02343


title: BC57_FF_250pg_SC_rep1 (Nanostring)


title: BC57_FF_250pg_SC_rep2 (Nanostring)


title: CGND-HRA-02342


title: CGND-HRA-02338


title: BC57_FF_2ng_SC_rep3 (Nanostring)


title: BC57_FF_2ng_SC_rep2 (Nanostring)


title: CGND-HRA-02339


title: CGND-HRA-02335


title: MNU_FF_2ng_SC_rep2 (Nanostring)


title: CGND-HRA-02326


title: MNU_FF_2ng_SC_rep1 (Nanostring)


title: CGND-HRA-02332


title: MNU_FF_50pg_SC_rep3 (Nanostring)


title: CGND-HRA-02347


title: BC57_FF_50pg_SC_rep3 (Nanostring)


title: MNU_FF_50pg_SC_rep2 (Nanostring)


title: MNU_FF_50pg_SC_rep1 (Nanostring)


title: GM-CSF+ S100A9 + TAK-242 treated mono, biological replicate 4

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data from human monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data was analyzed with R (version 4.3.2). Gene expression profiling was performed using arrays of Human Clariom S from Thermo Fischer Scientific. A Custom CDF Version 25 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: Human monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Human monocytes were isolated from peripheral blood mononuclear cells (PBMC) from buffy coats of healthy donors

extract_protocol: Total RNA from 24h treated monocytes was isolated using Rneasy Kit from Qiagen (Hilden, Germany) according to manufacturer`s instructions. RNA concentration was determined by the microplate reader Tecan Infinite M200 using a Nanoquant plate. The quality of total RNA was confirmed by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Quality and concentration of all samples were checked again on Nanodrop ND-1000, Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany). Microarray experiment were performed at Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ) in Heidelberg, Germany.

treatment_protocol: HSP90a treated monocyte: Human monocytes were treated with recombinant HSP90α (2CD14 monocytes were pre-treated with inhibitors Resatorvid (5 μM) or FPS-ZM1 (30 nM) or DMSO (as control) for 1 hour. They were then stimulated with either rHMGB1 (5 μg/mL) or rS100A9 (10 μg/mL) in the presence of GM-CSF (40 ng/mL) for 72 hours. The control group consisted of monocytes stimulated only with GM-CSF (40 ng/mL).µg/mL) in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h. Control monocytes: Human monocytes were incubated in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h.

value: Peripheral blood

tag: treatment


title: BC57_FF_50pg_SC_rep2 (Nanostring)


title: CGND-HRA-02323

extract_protocol:
RNA was extracted from flash-frozen patient samples homogenized in Trizol-Chloroform and purified using the QIAGEN RNeasy Mini kit. RNA was assessed using the Bioanalyzer.
RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA Stranded RNA-seq kit with RiboErase for rRNA depletion and Illumina compatible indexes. Pooled libraries were sequenced on an Illumina HiSeq 2500 or NextSeq V1 using a paired end 125 nucleotide


title: CGND-HRA-02329


title: BC57_FF_2ng_SC_rep1 (Nanostring)


title: MNU_FFPE_250pg_OVA_NG_rep1 (Nanostring)

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)


title: GM-CSF+ S100A9 + TAK-242 treated mono, biological replicate 1


title: GM-CSF+ S100A9 + TAK-242 treated mono, biological replicate 3


title: CGND-HRA-02322

value: ALS


title: GM-CSF+ S100A9 + TAK-242 treated mono, biological replicate 2


title: GM-CSF+ S100A9 + FPS-ZM1 treated mono, biological replicate 4

value: GM-CSF+ S100A9 + FPS-ZM1


title: GM-CSF+ S100A9 + FPS-ZM1 treated mono, biological replicate 3


title: GM-CSF+ S100A9 treated mono, biological replicate 4

description: Gene expression data from human monocytes incubated in RPMI medium for 24h

value: GM-CSF+ S100A9


title: GM-CSF+ S100A9 + FPS-ZM1 treated mono, biological replicate 2


title: MNU_FFPE_250pg_OVA_NG_rep3 (Nanostring)


title: MNU_FFPE_250pg_OVA_NG_rep2 (Nanostring)


title: GM-CSF+ S100A9 treated mono, biological replicate 2


title: GM-CSF+ S100A9 + FPS-ZM1 treated mono, biological replicate 1


title: CGND-HRA-02307

value: Male


title: GM-CSF+ S100A9 treated mono, biological replicate 3


title: BC57_FF_50pg_SC_rep1 (Nanostring)

value: bladder cancer cells


title: CGND-HRA-02325


title: CGND-HRA-02291


title: CGND-HRA-02297


title: CGND-HRA-02319


title: CGND-HRA-02288


title: BC57_FFPE_250pg_OVA_NG_rep1 (Nanostring)

value: FFPE


title: GM-CSF+ HMGB1+TAK-242 treated mono, biological replicate 4

value: GM-CSF+ HMGB1+TAK-242


title: BC57_FFPE_250pg_OVA_NG_rep2 (Nanostring)


title: MNU_FFPE_2ng_OVA_NG_rep1 (Nanostring)

value: normal urothelium


title: BC57_FFPE_250pg_OVA_NG_rep3 (Nanostring)


title: CGND-HRA-02284


title: GM-CSF+ HMGB1+TAK-242 treated mono, biological replicate 1


title: CGND-HRA-02287

value: frontal cortex


title: GM-CSF+ HMGB1+TAK-242 treated mono, biological replicate 3


title: GM-CSF+ HMGB1+TAK-242 treated mono, biological replicate 2