title: ERM_s6G_IN_rep4


title: NCCLu-181

status: Public on Jan 03 2022

type: SRA

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National cancer center

library_source: transcriptomic

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer patient derived cells

growth_protocol: Pleural effusions, pericardium effusions, ascites and tissues were obtained by lung cancer patients at National Cancer Center. All experiments utilizing human material were approved by NCC IRB. For liquid samples, effusions were transferred to conical tube and centrifuged at 120 x g for 10 min. The cell pellet was resuspended in RPMI and carefully layered onto LSM (Lymphocyte Separation Medium, #091692249 MP Biomedicals, France). After centrifugation at 400 x g for 30 min at room temperature, interphase layer between RPMI and LSM including tumor cells was harvested and washed with RPMI. For tissue sample, tumor tissues were minced finely and washed with RPMI. After washing, cells from effusion or tissue were cultured in AR-5 medium (5% FBS, 1 X GlutaMAX (Thermo Fisher Scientific), 1 X ITS (Insulin-Transferrin-Selenium, Thermo Fisher Scientific), 1% Penicillin/streptomycin, 50 nM hydrocortisone, 1 mM Sodium Pyruvate and 1 ng/ml EGF in RPMI) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was purified from cultured cell using RNeasy® mini kit, and AllPrep DNA/RNA Mini kit (Qiagen, German) and handled by QIAcube automatic instrument (Qiagen, German).
For RNA-seq analysis, we prepared mRNA sequencing libraries as paired-end reads with a length of 100 bases using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturers’ protocols. Briefly, mRNA molecules were purified and fragmented from 2 μg of total RNA. The libraries were sequenced as paired-end reads (2 × 150 bp) using the NovaSeq 6000 (Illumina).

treatment_protocol: non-treatment

tag: tissue

value: Pleural fluid

tag: disease

value: Lung cancer

tag: histopathology

value: Adenocarcinoma


title: cervix_distant_recurrence_6

type: RNA

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Hybridization was performed at 65°C for 17 hours using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

source_name: cervix

extract_protocol: RNA was isolated using the RNeasy® FFPE Kit (Qiagen, Hilden, Q15 Germany) according to the manufacturer’s directions. RNA concentrations and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA).  To correct for degradation of the RNA, the percentage of fragments of 300-4000 nucleotides was used to calculate the corrected concentrations. For each sample, 300 ng of total RNA, with a maximum of 7 mL (>42.8 ng/mL), was used.

value: cervix

tag: stage at last follow-up

value: Death

tag: age

tag: surgical approach

value: Open

tag: histological subtype

value: squamous

tag: lvsi

value: yes

tag: tnm-stage

tag: hpv

tag: adjuvant therapy

value: radiotherapy

tag: time to recurrence


title: cervix_distant_recurrence_5

value: Alive


title: NCCLu-178


title: cervix_distant_recurrence_4


title: ERM_s6G_IN_rep1

city: Beijing

first: Ran

last: Li

address: Yiheyuan Road No.5

country: China

institute: Peking University

data_processing:
The RNA-seq reads were initially performed adaptor removal by our own script with phred quality score over 33. The reads were then mapped using hisat2 (v2.1.0) to the human genome assembly GRCh38 (hg38) with Homo_sapiens.GRCh38.87.gtf annotations (http://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens), using the following command: hisat2 -p 8 -x ~/genome/Homo_sapiens/hisat2_index/Homo_hisat2 -1 $clean_file1 -2 $clean_file2|samtools view -b > $output.bam
The mapped reads were then sorted by name using samtools: samtools sort -n $output.bam -o $output.sortname.bam
The sorted reads were counted by HTSEQ (v0.7.2): htseq-count -s no -f bam $output.sortname.bam ~/genome/Homo_sapiens/Homo_sapiens.GRCh38.87.chr.gtf > $output.txt
The mapped data was visualized using WashU Epigenome Browser or Integrative Genomics Viewer. The mapped reads were generated from mapped BAM file to BigWig file using bamCoverage (v2.5.3) and normalized all mitochondrial counts to 2,000,000 for MITO MERR APEX-seq samples or and normalized all mitochondrial counts to 200,000 for LMNB1 MERR APEX-seq samples: bamCoverage -b $out.bam -o $out.bw --scaleFactor
The BigWig files of two biological replicates were merged into one bedGraph file using bigWigMerge (v2): bigWigMerge $input1.bw $input2.bw $out.bedGraph
BedGraph files were converted to BigWig files using bedGraphToBigWig (v4): bedGraphToBigWig $input.bedGraph ~/genome/Homo_sapiens/chromosome.sizes $output.bw
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminted text files include count data from Hisat2 and HTSEQ; quantified expression values in TPM (Transcripts Per Million); or DESeq2 log2foldchanges and P-value or Padjusted values for each gene.
Supplementary_files_format_and_content: BigWig files contain normalized expression signal merged by 2 replicates.

molecule: polyA RNA

source_name: human embryonic kidney 293T cells

growth_protocol: HEK293T cells (passages < 25) were cultured in DMEM supplemented with 10% fetal bovine serum at 37℃ under 5% CO2.

extract_protocol:
HEK293T cells under labeling and unlabeling in 6-well plate were extracted by 1 mL TRIzol reagent following the manufacture protocol after MERR APEX labeling. The extracted total RNA was eluted into ultrapure water.  Total RNA was treated 1 µL DNase I (NEB) to remove residual DNA and incubated at 37℃ for 15 min. Then, RNA was purified by RNA clean and concentrator kit (Zymo). RNA integrity was analyzed by Fragment Analyzer (Agilent). Only RNA with a RQN (RNA quality number) > 8.0 was used for subsequent experiments as INPUT. INPUT samples were enriched by 10 µL Dynabeads MyOne Streptavidin C1 (Invitrogen). RNA afer enrichment was purified by TRIzol reagent and dissolved in 20 µL ultrapure water as ENRICH samples.
cDNA libraries for RNA-seq were constructed from ~300 ng INPUT samples and 5 µL ENRICH samples (enriched from 6.5 μg INPUT) using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) with Poly(A) mRNA Magnetic Isolation Module (NEB) selection. PolyA RNA was fragmented at 94℃ for 12 min. cDNA was amplified 11 cycles for INPUT and 15 cycles for ENRICH samples. The prepared libraries were quality-controlled by Fragment Analyzer (Agilent). Good libraries with most cDNA range from 250 bp to 350 bp were sequenced on the Illumina HiSeq X Ten platform at ~10 million paired (2 x 150) reads per library.

treatment_protocol: HEK293T cells at 60-70% confluency were treated with 100 µM s6G or 100 µM s4U for 4.5 hr as described at 37℃ under 5% CO2. Then, cells were performed APEX labeling by adding 0.5 mM biotin-phenol in culture medium for 30 min incubation. After that, 1 mM H2O2 was added and gently rotated for 1 min. The reaction was quenched with 10 mM NaAsc, 5 mM trolox and 10 mM NaN3 in PBS by replacing medium three times before further cell fixation or RNA extraction. Negative controls were processed identically, except s6G, s4U or BP addition steps were omitted.

tag: cell compartment

value: endoplasmid reticulum membrane

tag: treatment

value: treated with 100 µM s6G for 5 hr

tag: cell line


title: MITO_ctrl_EN_rep2

value: mitochondrial matrix

value: untreated


title: MITO_ctrl_EN_rep1


title: NCCLu-175


title: QPCTL-deficient and proficient TMEs

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

institute: Sanquin

data_processing:
Raw data were processed by Cell Ranger 3.1.0.
Resulting 10x files were combined into a Seurat object in the R environment, and hashtag assignment was performed using HTOdemux
Subsequent analysis was performed using the MetaCell package in the R environment.
Specific filtering and analysis steps are described in detail in the manuscript
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: seurat_object.rds: Seurat object containing all unfiltered data from the experiment. seurat.immune.rds: All filtered Immune cells. seurat.Fibr.rds: All filtered Fibroblasts. seurat.Tum.rds: All filtered tumor cells
Supplementary_files_format_and_content: g2g_correlations.txt: gene-gene correlations across all feature-genes in the data-set. gene_modules.tsv: Gene-modules identified using gene-gene correlations. Imm_gene_clusters_pseudotime.tsv: Gene-clusters found to associate with pseudotime in the monocyte/macrophage MetaCells

organism: Mus musculus

source_name: Tumor microenvironment

extract_protocol:
3 TMEs were harvested from QPCTL-KO mice innoculated with QPCTL-KO B16F10 tumor cells, and 3 TMEs were harvested from QPCTL-WT mice innoculated with QPCTL-WT B16F10 tumor cells. Single cell suspensions were made, and live cells were FACS sorted. Each sample was  stained with sample hashtags individually, and subsequently pooled into a single sample. Library preperation was performed in according the manufacturers protocol of the 10X genomics Chromium Single Cell 3' kit. Sequencing was performed on Next-Seq550 (Illumina)
Library preperation was performed in according the manufacturer's protocol of the 10X Genomics Chromium Single Cell 3' kit (V3)

tag: strain

value: QPCTL-KO C57/Bl6JR

tag: time point

value: 14 days post tumor innoculation

tag: cell type

value: TME (Immune cells, Fibroblasts, Tumor cells)


title: NCCLu-173

tag: tissue

value: Pleural fluid

tag: disease

value: Miscellaneous


title: cervix_local_recurrence_1

tag: stage at last follow-up

value: adeno

value: Follow up


title: MITO_ctrl_IN_rep2


title: NCCLu-171

value: Lung cancer

tag: histopathology

value: Adenocarcinoma


title: MITO_ctrl_IN_rep1


title: NCCLu-170


title: cervix_distant_recurrence_2

value: cervix

value: Death

tag: age

tag: surgical approach

value: Open

value: squamous

value: chemoradiation


title: cervix_distant_recurrence_1

value: Alive

tag: histological subtype

tag: lvsi

value: no

value: radiotherapy


title: MITO_RNA_EN_rep2

value: mitochondrial matrix

value: untreated


title: NCCLu-168


title: ERM_s6G_EN_rep2

value: endoplasmid reticulum membrane

value: treated with 100 µM s4U for 5 hr


title: hepatocytes, flox-HFS 3

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

country: USA

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: isolated hepatocytes

extract_protocol:
Hepatocytes were isolated and RNA was extracted using Trizol reagent.
Illumina TruSeq Total RNA-Seq Library Prep

treatment_protocol: Mice were fed either regular chow or HFS diet for up to 6 weeks

value: isolated hepatocytes

tag: group

value: flox HFS

tag: genotype

value: control

value: high fat sugar (HFS) diet


title: hepatocytes, KO-HFS 1

value: KO HFS

value: liver-specific XBP1 deletion


title: NCCLu-166

value: Pleural fluid

value: Lung cancer

value: Adenocarcinoma


title: ERM_s6G_IN_rep3

value: treated with 100 µM s6G for 5 hr


title: MITO_RNA_EN_rep1


title: hepatocytes, flox-HFS 2


title: ERM_s6G_IN_rep2


title: MITO_RNA_IN_rep2


title: NCCLu-158


title: hepatocytes, flox-HFS 1


title: NCCLu-157


title: cervix_distant_recurrence_3

value: cervix

value: Alive

value: Open

value: squamous

value: yes

tag: tnm-stage

tag: hpv

tag: adjuvant therapy

tag: time to recurrence


title: hepatocytes, KO-chow 2

tag: strain

value: KO chow

tag: treatment

value: chow


title: MITO_RNA_IN_rep1

tag: cell compartment

value: mitochondrial matrix

value: untreated

tag: cell line


title: hepatocytes, KO-HFS 3

tag: cell type

value: isolated hepatocytes


title: hepatocytes, KO-HFS 2

value: high fat sugar (HFS) diet


title: MITO_s4U_EN_rep2

value: treated with 100 µM s4U for 5 hr


title: hepatocytes, KO-chow 1

value: liver-specific XBP1 deletion


title: NCCLu-156

tag: tissue

value: Pleural fluid

tag: disease

value: Miscellaneous


title: MITO_s4U_EN_rep1


title: NCCLu-155

value: Pericardial fluid

value: Lung cancer

tag: histopathology

value: Adenocarcinoma


title: MITO_s4U_IN_rep2


title: A2780 paclitaxel resistant 2, biological rep 3

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data

hyb_protocol: Biotin-labeled miRNA were hybridized to Applied Biosystems™ miRNA 4.1 Array Strip (20 h, 48 °C). Then, the microarrays were subjected to a washing and staining procedure, according to the technical protocol, using the Affymetrix GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: human ovarian carcinoma A2780 cell line

label_protocol: The complete procedure for preparing miRNA for hybridization was performed using the FlashTagTM Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, Waltham, MA, USA). 150 ng of previously isolated miRNA was subjected to poly(A) tailing and biotin ligation procedure, according to producer protocol.

growth_protocol: All cell lines were maintained as a monolayer in the complete medium [MEM medium supplemented with 10% (v/v) fetal bovine serum, 2 pM L-glutamine, penicillin (100 U/ml), streptomycin (100 U/ml) and amphotericin B (25 µg/ml)] at 37˚C in a 5% CO2 atmosphere

extract_protocol: miRNA was isolated using Qiagen reagent kit following the producer's protocol. The concentration and quality of isolated miRNA was quantified by measuring absorbance at 260 nm and 280 nm. The 260/280 nm ratio was used to estimate the degree of protein contamination. In all samples, the 260/280 nm ratio ranged from 1.8 to 2.0

treatment_protocol: The human ovarian carcinoma A2780 cell line was purchased from ATCC. A2780 sublines that were resistant to CIS [A2780CR1, A2780CR2 (A2780 cisplatin resistant)], and PAC [A2780PR1 and A2780PR2 (A2780 paclitaxel resistant)] were obtained by exposing A2780 cells to the relevant drugs at gradually increasing concentrations. The final con-centrations used to select the resistant cells were 1000 ng/ml of CIS for both A2780CR1 and A2780CR2 cell lines, 300 ng/ml of PAC for A2780PR1 cell line and 1100 ng/ml of PAC for A2780PR2 cell line

tag: cell subline

value: paclitaxel resistant

value: human ovarian carcinoma A2780 cell line


title: hepatocytes, flox-chow 2

value: flox chow

value: control


title: NCCLu-154


title: MITO_s4U_IN_rep1


title: A2780 paclitaxel resistant 2, biological rep 1

description: Gene expression data


title: hepatocytes, flox-chow 1


title: MITO_s6G_EN_rep2

value: treated with 100 µM s6G for 5 hr


title: NCCLu-150

value: tissue


title: D3 Corticotrophs 28d recovery

city: Edinburgh

first: Thomas

middle: James Gray

last: Chambers

address: Little France Crescent

country: United Kingdom

institute: University of Edinburgh

data_processing:
Nextera adapters were removed from paired end FASTA files using trimgalore v0.6.5 using the flags –paired and –2colour
Trimmed reads were aligned to the mouse genome (GRCm38 release 98) using STAR v2.7.1a
Aligned reads were quantified using featureCounts v2.0.0 using the flags -p (paired end), -Q 20 (mapping quality >20) and -s 2 (reverse stranded)
Count files were then normalised by TMM  using EdgeR
Genome_build: GRCm38 release 98
Supplementary_files_format_and_content: CPM

source_name: Corticotrophs

extract_protocol:
Qiagen RNeasy Plus Universal Mini kit
Ultra-low input RNA sequencing library preparation used the Clontech SMART-V4 kit for cDNA Synthesis from 10 pg-10 ng total RNA and polyA amplification. Illumina Nextera XT kit was used to prepare the final DNA libraries according to manufacturer’s instructions.

treatment_protocol: Mice had drinking water switched with dexamethasone 2.5microg/ml for the duration of the treatment period. Water was repalced weekly.

value: DEX

tag: time point (day)

value: POMC-GFP


title: MITO_s6G_EN_rep1

value: mitochondrial matrix


title: A2780 paclitaxel resistant 2, biological rep 2

description: Gene expression data


title: NCCLu-143

value: Ascites


title: D1 Corticotrophs 28d recovery


title: A2780 paclitaxel resistant 1, biological rep 3

description: Gene expression data


title: MITO_s6G_IN_rep2


title: MITO_s6G_IN_rep1


title: A2780 cisplatin resistant 2, biological rep 3

description: Gene expression data

value: cisplatin resistant


title: hepatocytes, flox-chow 3

value: isolated hepatocytes

value: chow


title: C3 Corticotrophs 7 d recovery


title: NCCLu-142

value: Pleural fluid


title: A2780 cisplatin resistant 2, biological rep 2

description: Gene expression data


title: A2780 paclitaxel resistant 1, biological rep 1

description: Gene expression data


title: A2780 paclitaxel resistant 1, biological rep 2

description: Gene expression data


title: NCCLu-141


title: D2 Corticotrophs 28d recovery


title: C2 Corticotrophs 7d recovery


title: NCCLu-153


title: NCCLu-139


title: C1 Corticotrophs 7d recovery


title: A2780 cisplatin resistant 2, biological rep 1

description: Gene expression data


title: tumor tissue treated without DAC from PDX model (WGBS)

city: Shanghai

first: Ganjun

last: Yu

state: Shanghai

address: 800 Xiangyin Road, Shanghai, China.

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

description: microsatellite stability

library_source: genomic

data_processing:
Adapter were trimmed using TrimGalore! v0.6.6 and masked for low-complexity or low-quality sequence
Raw sequencing reads were aligned to the human genome (GRCm38) using bismark .
Methylation levels called using bismark.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated for each cytosine position in CpG, CHG, and CHH contexts (with H corresponding to A, C, or T nucleotides).
Genome_build: GRCm38
Supplementary_files_format_and_content: a comma-separated text file containing a matrix of methylation levels determined for CpG positions each Sample.

molecule: genomic DNA

source_name: fresh tumor from the same patient inoculataed into NPG mice

extract_protocol:
Genomic DNA was isolated from the control and the DAC-treated CT26 cells and PDX tumors using a QIAamp genomic DNA Kit (Qiagen, Stockach, Germany) according to the instructions.
The bisulfite-treated DNA was purified on a spin column and used to prepare the sequencing library using an EpiGnome Kit (Epicentre, Wisconsin, USA).In this procedure,bisulfite-treated single-stranded DNA was random-primed using a polymerase able to read uracil nucleotides to synthesize DNA that contained a specific sequence tag. The 3′ ends of the newly synthesized DNA strands were then selectively tagged with a second specific sequence, which resulted in doubly tagged DNA molecules with known sequence tags at their 5′ and 3′ ends.

value: colorectal cancer

value: non DAC-treated


title: CXCR4-exo-2

first: Hui

last: Hu

address: #600, Yishan Rd

department: Institute of Diagnostic and Interventional Radiology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

description: All.miRNA.mature.Counts.exp.txt

data_processing:
RNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA-seq: Hisat2 2.0.4 mapping to reference genome
RNA-seq: count counting
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo Sapiens miRNA database and GRCh38.p7 genome.
miRNA-seq: count counting
Genome_build:  hg19_GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: endothelial progenitor cells

growth_protocol: HUVEC and EPC were cultured in endothelial growth medium-2 (EGM-2; Lonza) containing 5% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
miRNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
miRNA-seq and RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EPC exosomes were harvested from conditioned media after 24-40 hours of incubation. Exosomes (1×1011 particles/mL) or PBS were added to HUVEC (T25 flask) and incubated in serum-free EGM media for 24 hours.

value: CXCR4-overexpressed HUCB endothelial progenitor cells

tag: passages

value: passages :4-6

value: human umbilical cord blood


title: CXCR4-exo-1

description: All.miRNA.mature.Counts.exp.txt


title: NCCLu-144

value: Pericardial fluid

value: Lung cancer

value: Adenocarcinoma


title: A2780 cisplatin resistant 1, biological rep 1

description: Gene expression data

value: human ovarian carcinoma A2780 cell line


title: B3 Corticotrophs DEX

value: DEX


title: A2780 cisplatin resistant 1, biological rep 2

description: Gene expression data


title: tumor tissue treated with DAC from PDX model (WGBS)

description: microsatellite stability

source_name: fresh tumor from patient inoculataed into NPG mice

value: DAC-treated


title: A2780 cisplatin resistant 1, biological rep 3

description: Gene expression data


title: A2780 cell line, biological rep 3

description: Gene expression data

value: parental


title: B2 Corticotrophs DEX

value: POMC-GFP


title: NCCLu-137


title: A2780 cell line, biological rep 2

description: Gene expression data


title: EPC-exo-1

description: All.miRNA.mature.Counts.exp.txt

value: HUCB-drived endothelial progenitor cells


title: A2780 cell line, biological rep 1

description: Gene expression data


title: B1 Corticotrophs DEX


title: NCCLu-135


title: HUVEC(CXCR4-exo)-3

description: all.counts.exp.txt

source_name: human umbilical veinendothelial cell

value: CXCR4-exo-treated human umbilical veinendothelial cell

value: passages :4-5

value: human umbilical vein


title: HUVEC(CXCR4-exo)-2

description: all.counts.exp.txt


title: A3 Corticotrophs control

value: CTL


title: NCCLu-134

value: Pleural fluid


title: HUVEC(CXCR4-exo)-1

description: all.counts.exp.txt


title: NCCLu-132


title: 38-Caco-2-5-8-sample-1-B6_S32_R1_001

city: Gent

first: Amar

middle: van

last: Laar

address: Coupure Links, 653

country: Belgium

institute: Ghent University

description: NormCounts_2 (sample 18)

data_processing:
Illumina Real-Time Analysis (RTA) version 2.4.11
cutadapt v1.18
STAR v2.6.0 --quantMode TranscriptomeSAM
Genome_build: GRCh38

source_name: Colon carcinoma cells (ATCC)

growth_protocol: Caco-2 and HepG2 cells were cultured in cell culture flasks (T25/T75) and on DMEM with respectively 25mM and 5.5 mM glucose

extract_protocol:
Qiagen RNeasy plus mini kit
QuantSeq 3' mRNA-Seq Library Prep

treatment_protocol: Caco-2 cells were exposed to sugars at 55 mM for 24 hours in a coculture setup, allowing transport to the HepG2 cells

value: L-arabinose

tag: experiment day


title: 40-Caco-2-5-8-sample-3-D6_S31_R1_001

description: NormCounts_2 (sample 20)


title: 37-Caco-2-16-4-sample-2-A6_S21_R1_001

description: NormCounts_2 (sample 17)


title: 39-Caco-2-5-8-sample-2-C6_S1_R1_001

description: NormCounts_2 (sample 19)


title: A2 Corticotrophs Control

tag: genotype


title: NCCLu-131


title: HUVEC(EPC-exo)-3

description: all.counts.exp.txt

value: EPC-exo-treated human umbilical veinendothelial cell


title: 36-Caco-2-16-4-sample-1-H5_S9_R1_001

description: NormCounts_2 (sample 16)


title: HUVEC(EPC-exo)-2

description: all.counts.exp.txt


title: 35-Caco-2-5-8-sample-3-G5_S36_R1_001

description: NormCounts_2 (sample 15)

value: Fructose


title: NCCLu-130


title: Gdown1 KO 3 RNA-Seq Rep 3

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2 (PRO-Seq and ChIP-Seq) or hisat2 (RNA-Seq)
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing pileup of normalized RNA-Seq, PRO-Seq, and ChIP-data

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM (Gibco 11965-092) supplemented with 10% FBS.

extract_protocol:
Rapid nuclei isolation steps for PRO-Seq were performed on wet ice using ice-cold buffers as previously described (Nilson et. al. 2017; Ball et. al. 2019). Modifications described in the text were made for harvesting mitotic cells for PRO-Seq. For RNA-Seq, cells were directly lysed in Trizol, and extracted and DNase treated prior to quality control analysis as described in the text.
Details of library construction for each type of assay are provided in the methods.

treatment_protocol: Parental and HA-FKBP-Gdown1 HeLa cells in a T-150 flask were treated with 400 nM dTAGV-1 or DMSO vehicle control for 4 h prior to harvesting nuclei for PRO-Seq.

value: HeLa

value: Gdown1 KO

value: Untreated

tag: chip antibody


title: NCCLu-138

value: Lung cancer

value: Adenocarcinoma


title: EPC-exo-2

description: All.miRNA.mature.Counts.exp.txt

value: passages :4-6

value: human umbilical cord blood


title: NCCLu-129


title: Gdown1 KO 2 RNA-Seq Rep 2


title: HUVEC(EPC-exo)-1

description: all.counts.exp.txt


title: 34-Caco-2-5-8-sample-2-F5_S37_R1_001

description: NormCounts_2 (sample 14)


title: 33-Caco-2-5-8-sample-1-E5_S7_R1_001

description: NormCounts_2 (sample 13)


title: NCCLu-128


title: HUVEC(Con)-2

description: all.counts.exp.txt

value: PBS-treated human umbilical veinendothelial cell


title: Gdown1 KO 2 RNA-Seq Rep 1


title: NCCLu-124


title: Gdown1 KO 1 RNA-Seq Rep 3


title: 32-Caco-2-16-4-sample-2-D5_S24_R1_001

description: NormCounts_2 (sample 12)


title: HUVEC(Con)-1

description: all.counts.exp.txt


title: NCCLu-123


title: Gdown1 KO 1 RNA-Seq Rep 2


title: NCCLu-121


title: 31-Caco-2-16-4-sample-1-C5_S22_R1_001

description: NormCounts_2 (sample 11)


title: Gdown1 KO 1 RNA-Seq Rep 1


title: Mobp-TDP43 KO B147-2

city: Baltimore

first: Dwight

last: Bergles

state: MD

address: 725 North Wolfe St., WBSB 1001

department: Neuroscience

institute: Johns Hopkins University

description: Mobp-TDP43 KO

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 refSeq using the STAR spliced read aligner
Fragment counts were derived using HTS-seq program using mm10 Ensembl transcripts as model.
Differentially expressed genes were identified using edgeR which were then considered and ranked based on adjusted p-values (FDR) of ≤ 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file including raw counts, normalized counts, and FPKM for each samples as well as DEG analysis between each condition

source_name: Oligodendrocytes

extract_protocol:
QIAGEN RNeasy micro kit
NuGEN Ovation single-cell RNAseq kit

value: Cortex

tag: age

tag: Sex

value: F


title: Mobp-TDP43 Control B144-1

description: Mobp-TDP43 Control


title: 30-Caco-2-5-8-sample-1-B5_S38_R1_001

description: NormCounts_2 (sample 10)

value: Glucose


title: NCCLu-120


title: Parental RNA-Seq Rep 3

value: parental


title: NCCLu-119


title: Mobp-TDP43 Control B133-16

description: Mobp-TDP43 Control

value: M


title: A1 Corticotrophs Control

value: CTL

value: POMC-GFP


title: Mobp-TDP43 KO B132-13

description: Mobp-TDP43 KO


title: 29-Caco-2-14-8-sample-2-A5_S10_R1_001

description: NormCounts_2 (sample 9)


title: 27-Caco-2-16-4-sample-2-G4_S25_R1_001

description: NormCounts_2 (sample 7)


title: HUVEC(Con)-3

description: all.counts.exp.txt

value: passages :4-5

value: human umbilical vein


title: 28-Caco-2-14-8-sample-1-H4_S23_R1_001

description: NormCounts_2 (sample 8)


title: Parental RNA-Seq Rep 1

value: HeLa


title: NCCLu-118

value: Pleural fluid

value: Miscellaneous


title: Mog-TDP43 KO A68-2

description: Mog-TDP43 KO


title: Parental RNA-Seq Rep 2

value: Untreated


title: NCCLu-116

value: Lung cancer

value: Adenocarcinoma


title: BT20_CRISPRscreen_T0

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

description: BT20 (TNBC cell line) CRISPRscreen T0 untreated

data_processing:
Library strategy: CRISPR screen
barcode and adapter removal: FASTX toolkit (v0.0.14)
quality filtering: FastQC (v0.11.8)
alignment: EdgeR, No mismatches between sgRNA sequences and GeCKOv2 library
DESeq2(1.26.0), Controls (DMSO); Treatment (ERLOTINIB); parametric
Collapsed sgRNA level to single gene-level scores
Calculated empiric p-value and did FDR-adjustment
Genome_build: GeCKOv2 library
Supplementary_files_format_and_content: sgRNA-level counts; Gene level collapsed L2FC & FDR-adjusted pvalues for comparisons

organism: synthetic construct

growth_protocol: BT20 cells were cultured with MEM + FBS + glutamine + penicillin/streptomycin

extract_protocol:
Phenol-chloroform extraction of whole gDNA
Two consecutive PCRs to amplify sgRNAs in gDNA and add barcodes

treatment_protocol: Treatment with either DMSO (v/v%) or ERLOTINIB (10uM)

tag: agent


title: Mog-TDP43 Control A66-1

description: Mog-TDP43 Control


title: NCCLu-114


title: 26-Caco-2-16-4-sample-1-F4_S8_R1_001

description: NormCounts_2 (sample 6)

tag: strain


title: BT20_CRISPRscreen_ERLOTINIB_Rep3

description: Replicate 3: BT20 (TNBC cell line) CRISPRscreen Erlotinib (10uM) treatment

value: ERLOTINIB


title: 25-Caco-2--5-8-sample-3-E4_S28_R1_001

description: NormCounts_2 (sample 5)

tag: treatment

value: Mannitol


title: NCCLu-113


title: BT20_CRISPRscreen_ERLOTINIB_Rep2

description: Replicate 2: BT20 (TNBC cell line) CRISPRscreen Erlotinib (10uM) treatment


title: 24-Caco-2-5-8-sample-2-D4_S39_R1_001

description: NormCounts_2 (sample 4)


title: Mog-TDP43 KO A58-7

description: Mog-TDP43 KO

value: Cortex


title: BT20_CRISPRscreen_ERLOTINIB_Rep1

description: Replicate 1: BT20 (TNBC cell line) CRISPRscreen Erlotinib (10uM) treatment


title: NCCLu-109


title: Escalating Morphine 3

city: Palo Alto

first: Gregory

last: Scherrer

state: CA

address: 1050 Arastradero Rd

department: Anesthesiology

institute: Stanford University

data_processing:
Reads were mapped to the UCSC mouse reference genome mm10 via the Galaxy platform (http://usegalaxy.org) using HISAT2 version 2.0.5.1.
FPKM (fragments per kilobase of transcript sequence per million mapped fragments) values were obtained using Cufflinks version 2.2.1.
Reads were quantified using featureCounts version 1.4.6.p5
Differential expression analysis was conducted in R with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM for all samples
Supplementary_files_format_and_content: excel spreadsheet with Deseq2 output for all groups

source_name: Lumbar spinal cord microglia

extract_protocol:
Mice were perfused with ice cold PBS, caudal lumbar cord was dissection and manually dissociated then subjected to MACS myelin removal and CD11b selection. Total RNA was extracted from CD11b-positive cells using the RNeasy Micro Kit
Libraries were prepared using Smart-Seq2 and modified for sequencing using the Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: Mice received one of 2 chronic morphine dosing strategies (fixed or escalating) or one of three peripheral nerve injuries - sciatic nerve transection (SNT), chronic constriction injury (CCI), or spared nerve injury (SNI). Controls received saline or no treatment/injury

value: Lumbar spinal cord microglia

tag: condition

value: Morphine

tag: timepoint or dose

value: escalating


title: 23-Caco-2-5-8-sample-1-C4_S11_R1_001

description: NormCounts_2 (sample 3)


title: NCCLu-107

value: Ascites


title: BT20_CRISPRscreen_DMSO_Rep3

description: Replicate 3: BT20 (TNBC cell line) CRISPRscreen DMSO (v/v%) treatment

value: DMSO

tag: cell line


title: Escalating Morphine 2

tag: tissue


title: NCCLu-106

tag: disease


title: BT20_CRISPRscreen_DMSO_Rep2

description: Replicate 2: BT20 (TNBC cell line) CRISPRscreen DMSO (v/v%) treatment


title: Escalating Morphine 1


title: NCCLu-100

tag: histopathology


title: BT20_CRISPRscreen_DMSO_Rep1

description: Replicate 1: BT20 (TNBC cell line) CRISPRscreen DMSO (v/v%) treatment


title: 21-Caco-2-16-4-sample-1-A4_S13_R1_001

description: NormCounts_2 (sample 1)


title: NCCLu-096


title: 19-HepG2-5-8-sample-2-C3_S15_R1_001

description: NormCounts_1 (sample 19

source_name: Hepatoma cells (ATCC)

value: L-arabinose


title: Control_ChIP Technical 2

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: SNU-398 input sample done as control for ChIP-Seq

data_processing:
raw fastq files were passed to ChIP-AP v4.1 and processed. Refer to the ChIP-AP Github for pipeline details.
ChIP-AP processed settings table can be found as a processed data file in this entry or as a supplemental table in the published manuscript.
Briefly, QC and cleanup was done by clumpify, bbduk and trimmomatic.  Alignment was done by bwa mam.  Peak calling was done by MACS2, HOMER, GEM and Genrich
Genome_build: hg38

source_name: cell line

growth_protocol: SNU-398 cell line was obtained from the American Type Culture Collection (ATCC). The cells were maintained in RPMI medium supplemented with 10% foetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2 as recommended by ATCC.

extract_protocol:
20 million SNU-398 cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. The reaction was terminated by adding 2M glycine to a final concentration of 125mM. Cells were then washed with 1´PBS and resuspended in 1mL of cell lysis buffer (20mM Tris pH8.0, 85mM KCl, 0.5% nonidet P-40, protease inhibitor). After 10 minutes of incubation on ice, cells were spun down and cell pellet was resuspended in another 1mL of cell lysis buffer. After another 5 minutes of incubation on ice, cells were spun down and cell pellet was resuspended in 1mL of nuclear lysis buffer (10mM Tris-HCl pH7.5, 1% nonidet P-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitor). After 10 minutes of incubation on ice, chromatin was sheared to 500bp. Antibody‑protein A/G Dynabead conjugate was prepared by adding 0.75µg of SALL4 rabbit monoclonal antibody (Cell Signaling Technology #8459) to pre-washed 50µL of protein A/G Dynabeads (Life Techonlogies) with one hour incubation at 4°C with rotation. Sheared chromatin was then added to antibody-protein A/G conjugate and incubated overnight at 4°C with rotation. After overnight incubation, the beads were washed sequentially with the following buffers: twice with RIPA/500mM NaCl buffer (0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 500mM NaCl, 1mM EDTA, 20mM Tris-HCl pH8.1), twice with LiCl buffer (0.25M LiCl, 1% nonidet P-40, 1% sodium deoxycholate, 1mM EDTA, 10mM Tris-HCl pH8.1), twice with TE buffer (10mM Tris-HCl pH8.0, 1mM EDTA pH8.0). Protein complexes were reverse cross-linked with 50µL of ChIP Elution Buffer (10mM Tris-HCl pH8.0, 5mM EDTA, 300mM NaCl, 0.1% SDS) and 8µL of Reverse Crosslink Mix (250mM Tris-HCl pH6.5, 1.25M NaCl, 62.5mM EDTA, 5mg/mL proteinase K, 62.5µg/mL RNase A) at 65°C for 5 hours. Reverse cross-linked DNA was cleaned up using SPRI beads (Beckman Coulter) and eluted in 10mM Tris-HCl pH 8.0.
To generate libraries for deep sequencing, the eluted DNA was end‑repaired using End-It DNA End-Repair Kit (Epicenter #ER0720) and A-tailing was then carried using Klenow (3’-5’ exo-) enzyme (New England Biolabs). Illumina sequencing adaptors were ligated to the DNA fragments and adaptor-ligated DNA fragments were enriched with 14 cycles of PCR. DNA libraries were gel purified and analyzed on Bioanalyzer (Agilent) for their size distribution. Libraries were sequenced on Illumina HiSeq 2500 sequencer with single-end 35bp settings.

tag: antibody

value: control


title: Fixed Morphine 3

value: fixed


title: NCCLu-089

source_name: Lung cancer patient derived cells


title: 18-HepG2-5-8-sample-1-B3_S33_R1_001

description: NormCounts_1 (sample 18)


title: Fixed Morphine 2


title: Mog-TDP43 Control A64-6

description: Mog-TDP43 Control

value: M


title: NCCLu-088

value: Pleural fluid

value: Small cell lung cancer


title: SALL4 ChIP-Seq Biological Replicate 2 Technical 2

description: SNU-398 sample undergone ChIP-Seq targetting the oncogene SALL4

value: chip done using SALL4 rabbit monoclonal Ab (Cell Signaling Technology #8459)


title: 17-HepG2-16-4-sample-2-A3_S26_R1_001

description: NormCounts_1 (sample 17)


title: Fixed Morphine 1


title: NCCLu-086

value: Lung cancer


title: SALL4 ChIP-Seq Biological Replicate 2 Technical 1


title: NCCLu-082

value: Pericardial fluid

value: Adenocarcinoma


title: SALL4 ChIP-Seq Biological Replicate 1 Technical 2


title: 16-HepG2-16-4-sample-1-H2_S29_R1_001

description: NormCounts_1 (sample 16)


title: 15-HepG2-5-8-Sample-3-G2_S30_R1_001

description: NormCounts_1 (sample 15)

value: Fructose


title: CCI 7dpi 1

value: CCI


title: 22-Caco-2-16-4-sample-2-B4_S12_R1_001

description: NormCounts_2 (sample 2)

value: Mannitol


title: SALL4 ChIP-Seq Biological Replicate 1 Technical 1


title: NCCLu-078


title: 14-HepG2-5-8-Sample-2-F2_S2_R1_001

description: NormCounts_1 (sample 14)


title: CCI 2dpi 2

value: Lumbar spinal cord microglia


title: NCCLu-076


title: BL41 Proton 5gy 12hr rep9 [Ger3_Bl41_Proton5]

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Ger3_Bl41_Proton5
processed data file: DATASET-Bl41_Normalized.xlsx

data_processing:
The FASTQ files were aligned to the human (hg19) or mouse (mm10) genome and transcriptome using TopHat2. From the resulting BAM files, read mapping, expression quantification and differential expression analysis were performed using AltAnalyze version 2.1.0. Prior to differential expression analysis, batch effects were observed by principal component analysis. To correct for batch effects, we explicitly normalized the expression of each gene within each batch relative to its average expression (log2 geometric median normalized). A single-replicate of each cell line RNA-Seq sample was processed in the same manner in each batch, with the same cell lines represented. No batch effects were evident following PCA analysis on the batch corrected data. Differential expression was performed on the batch corrected data.
Differential expression was performed on the batch corrected data using the AltAnalyze supplied empirical Bayes moderated t-test, following Benjamini-Hochberg adjustment for false discovery (FDR), with a cutoff of p<0.05 (FDR) and fold change≥1.3.Gene ontology enrichment analysis was carried out using the ToppFun function of Toppgene64 with the Biological Process database.
Genome_build: hg19 for BL41 samples and mm10 for J3D  samples
Supplementary_files_format_and_content: Differential Expression

source_name: BL41 Proton 5gy 12hr

growth_protocol: Human BL41and mouse J3D lymphoma cell lines were maintained in RPMI 1640 media complemented with 10% FBS and Penicillin and Streptomycin.

extract_protocol:
Total RNA was puriﬁed with the SurePrep RNA/DNA/Protein purification kit from samples at 12hr after irradiation.
RNA libraries were prepared for sequencing using standard Illumina protocols by the CCHMC DNA sequencing and genotyping core.

treatment_protocol: Cell lines were re-suspended at 1x106 cells/ml at 6hr before irradiation. For proton irradiation the same SOBP constraints were utilized by energies ranging between 129.3-148.2 MeV/u and median LET: 3.5 keV/µm (ranging from 2.9-7.9 keV/µm) (SuppFig.1). Cells were place in the center area of the SOBP. All proton irradiations were carried out using a raster-scanning technique. Photon Irradiation was performed on a LINAC Artist 6mV system from Siemens. Sham un-irradiated were kept outside incubator at room temperature in parallel of irradiated cells.

tag: tumor type

value: Burkitt lymphoma

tag: passage

tag: irradiation

value: Proton 5Gy

tag: harvest time


title: Fixed Morphine 4

value: Morphine


title: 20-HepG2-5-8-sample-3-D3_S14_R1_001

description: NormCounts_1 (sample 20)

value: L-arabinose

tag: experiment day


title: CCI 2dpi 1


title: SNT 7dpi 2

value: SNT


title: 12-HepG2-16-4-sample-2-D2_S27_R1_001

description: NormCounts_1 (sample 12)


title: BL41 Proton 5gy 12hr rep8 [Ger2_Bl41_Proton5]

description:
Ger2_Bl41_Proton5
processed data file: DATASET-Bl41_Normalized.xlsx


title: BL41 Proton 5gy 12hr rep7 [Ger1_Bl41_Proton5]

description:
Ger1_Bl41_Proton5
processed data file: DATASET-Bl41_Normalized.xlsx


title: NCCLu-064


title: Control_ChIP Technical 1

value: control


title: SNT 7dpi 1


title: 11-HepG2-16-4-sample-1-C2_S17_R1_001

description: NormCounts_1 (sample 11)


title: 10-HepG2-5-8-sample-1-B2_S18_R1_001

description: NormCounts_1 (sample 10)

value: Glucose


title: SNT 4dpi 2


title: NCCLu-049

value: Pleural fluid


title: NCCLu-046


title: CCI 7dpi 2


title: BL41 Xray 5gy 12hr rep6 [Ger3_Bl41_Xray5]

description:
Ger3_Bl41_Xray5
processed data file: DATASET-Bl41_Normalized.xlsx

source_name: BL41 Xray 5gy 12hr

value: Xray 5Gy


title: 9-HepG2-14-8-sample-2-A2_S3_R1_001

description: NormCounts_1 (sample 9)


title: SNT 4dpi 1


title: BL41 Xray 5gy 12hr rep5 [Ger2_Bl41_Xray5]

description:
Ger2_Bl41_Xray5
processed data file: DATASET-Bl41_Normalized.xlsx


title: 8-HepG2-14-8-sample-1-H1_S4_R1_001

description: NormCounts_1 (sample 8)


title: BL41 Xray 5gy 12hr rep4 [Ger1_Bl41_Xray5]

description:
Ger1_Bl41_Xray5
processed data file: DATASET-Bl41_Normalized.xlsx


title: NCCLu-045


title: SNT 2dpi 2


title: NCCLu-042


title: BL41 untreated rep3 [Ger3_Bl41_Ctrl]

description:
Ger3_Bl41_Ctrl
processed data file: DATASET-Bl41_Normalized.xlsx

source_name: BL41 untreated

value: Sham


title: 13-HepG2-5-8-Sample-1-E2_S16_R1_001

description: NormCounts_1 (sample 13)


title: 7-HepG2-16-4-sample-2-G1_S19_R1_001

description: NormCounts_1 (sample 7)


title: SNT 2dpi 1


title: BL41 untreated rep2 [Ger2_Bl41_Ctrl]

description:
Ger2_Bl41_Ctrl
processed data file: DATASET-Bl41_Normalized.xlsx


title: NCCLu-041

value: Lung cancer

value: Miscellaneous


title: 6-HepG2-16-4-sample-1-F1_S34_R1_001

description: NormCounts_1 (sample 6)


title: SNT 1dpi 2


title: NCCLu-061

value: Adenocarcinoma


title: NCCLu-025

value: Pericardial fluid


title: 5-HepG2-5-8-sample-3-E1_S35_R1_001

description: NormCounts_1 (sample 5)


title: SNT 1dpi 1


title: NCCLu-027


title: NMuMG cells with UGCG knock out (Replicate #3)

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

data_processing:
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCm39 mouse reference genome.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”.
The gene annotation used for quantification was Ensembl version 104.
Genome_build: GRCm39
Supplementary_files_format_and_content: raw read count in TSV file

source_name: mouse mammary gland

growth_protocol: Mouse NMuMG epithelial cells were cultured in Dulbecco’s modified Eagle medium (DMEM, 11965092, Thermo) with 10% fetal bovine serum (FBS, S1860-500, BioWest) and 100 U/mL penicillin-streptomycin (15140148, Thermo).

extract_protocol:
Total RNA extraction was prepared using the NucleoSpin RNA II kit (740955, BIOKE´). The mouse sgRNAs of UGCG (Forward: 5’-CACCTCGTGCTCTTCGTGGTGCTG-3’; Reverse: 5’-AAACCAGCACCACGAAGAGCACGA-3’) were cloned into the lentiviral vectors lentiCRISPR_v2 (Addgene). The design and cloning of sgRNA were performed according to the general protocols obtained from the Feng Zhang lab. The pLV-Cas9-blasticidin plasmid (CAS9BST, Sigma) was used as a negative control. The stable NMuMG cells with UGCG knock out were generated by Cas9 and sgRNAs of UGCG lentivirus infection and subsequently selection with 4 μg/mL of blasticidin.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in China using DNBSEQ platform.

treatment_protocol: No treatment

tag: cell type

value: nontransformed mouse mammary gland (NMuMG) epithelial cell line

tag: genotype

value: NMuMG cells with UGCG knock out


title: 4-HepG2-5-8-sample-2-D1_S40_R1_001

description: NormCounts_1 (sample 4)

value: Mannitol


title: Control 9

value: Lumbar spinal cord microglia

value: saline

value: escalating


title: 3-HepG2-5-8-sample-1-C1_S5_R1_001

description: NormCounts_1 (sample 3)


title: NMuMG cells with UGCG knock out (Replicate #2)


title: NCCLu-019

first: namhee

last: yu

address: 323, Ilsan-ro, Ilsandong-gu

institute: National cancer center

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Total RNA was purified from cultured cell using RNeasy® mini kit, and AllPrep DNA/RNA Mini kit (Qiagen, German) and handled by QIAcube automatic instrument (Qiagen, German).
For RNA-seq analysis, we prepared mRNA sequencing libraries as paired-end reads with a length of 100 bases using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturers’ protocols. Briefly, mRNA molecules were purified and fragmented from 2 μg of total RNA. The libraries were sequenced as paired-end reads (2 × 150 bp) using the NovaSeq 6000 (Illumina).


title: NCCLu-017

value: Small cell lung cancer


title: Control 8


title: Control 7


title: 2-HepG2-16-4-sample-2-B1_S20_R1_001

description: NormCounts_1 (sample 2)


title: NMuMG cells with UGCG knock out (Replicate #1)


title: 1-HepG2-16-4-sample-1-A1_S6_R1_001

description: NormCounts_1 (sample 1)


title: NMuMG cells expressing Cas9 (Replicate #3)

value: NMuMG cells with Cas9 expression


title: NCCLu-015


title: Control 4

value: fixed


title: NMuMG cells expressing Cas9 (Replicate #2)


title: NMuMG cells expressing Cas9 (Replicate #1)


title: tumor tissue treated with DAC from PDX model

description: microsatellite stability

data_processing:
Raw data (raw reads) were processed using Trim Galore and FastQC(v0.11.5). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using STAR(2.5.3a) software.
FPKM value of each gene was calculated using stringtie and cufflinks.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample.

extract_protocol:
The total RNA was isolated with TRIzol (Sigma, St Louis, US) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer

value: DAC-treated


title: NCCLu-009

value: Pleural fluid


title: Control 3


title: tumor tissue treated without DAC from PDX model

description: microsatellite stability

value: non DAC-treated


title: BL41 untreated rep1 [Ger1_Bl41_Ctrl]

description:
Ger1_Bl41_Ctrl
processed data file: DATASET-Bl41_Normalized.xlsx

value: Burkitt lymphoma

value: Sham


title: TPP3308

status: Public on Jan 02 2022

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Genome_build: hg19
Supplementary_files_format_and_content: csv file include raw count values for each cell

source_name: NC

growth_protocol: tissues collected were transferred into pre-warmed DMEM medium containing 2 mg/ml collagenase P (Roche) and 10 U/µl DNase I (Roche).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We gently pipetted the mixture and then digested for 60 min at 37 °C to fully release single cells. The cell suspension solution was filtered and centrifuged. The pellet was resuspended and 2 mM ethylene diamine tetraacetic acid in phosphate-buffered saline. We employed fluorescence activated cell sorting (FACS) to ensure the living cell selections.

tag: disease state

value: Cervical cancer (CC)

value: normal tissue (NC)


title: Control 2

tag: strain


title: TPP3307

source_name: TT

value: primary tumour tissue (TT)


title: TPP3306

source_name: TP

value: paracarcinoma tissue (TP)


title: TPP3305


title: TPP3304


title: TPP3303


title: TPP3302


title: TPP3296


title: TPP3293


title: TPP3297


title: TPP3294


title: TPP3298


title: NCCLu-012

value: Lung cancer

value: Adenocarcinoma


title: TPP3295


title: TPP3289


title: TPP3291


title: TPP3300


title: TPP3292


title: TPP3290


title: TPP3286


title: TPP3288


title: TPP3285


title: TPP3287


title: TPP2758


title: TPP2757


title: TPP3309


title: TPP2755


title: TPP2754


title: TPP2756


title: TPP2752


title: TPP2753


title: TPP2751


title: TPP2750


title: TPP2749


title: TPP3301


title: TPP3299


title: TPP2748


title: TPP2747


title: TPP2745


title: TPP2744


title: TPP2743


title: TPP2742


title: ICH438IS

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
hg38
Supplementary_files_format_and_content: STAR raw count matrix, DESeq2 normalized count matrix

source_name: CD Intestinal biopsy fibrotic

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
polyA-enriched RNA-Seq: Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: diagnosis

value: CD

value: Intestinal biopsy

value: fibrotic


title: ICH441IM

source_name: CD Intestinal biopsy notfibrotic

value: notfibrotic


title: ICH463IS


title: ICH432IM


title: ICH473IS


title: ICH424IS


title: ICH424IM


title: ICH421IM


title: ICH414CS


title: ICH413IS


title: ICH412IM


title: ICH398IS


title: ICH408IS


title: ICH412IS


title: ICH396IS


title: ICH398IM


title: ICH406IS


title: ICH397IM


title: ICH393IM


title: ICH393IS


title: ICH384IS


title: TPP2746


title: ICH390IM


title: ICH373IS


title: ICH381IM


title: ICH362IM


title: ICH373IM


title: ICH451IS


title: TPP2741


title: ICH449IM


title: ICH328IS


title: ICH338IS


title: ICH316IS


title: ICH328IM


title: ICH324IM


title: ICH308IM


title: ICH336IM


title: ICH257IM


title: ICH260IS


title: ICH259CM


title: ICH251IM


title: Sample_GMP110

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description: ***Submitter states that raw data will be submitted to dbGaP for controlled access***

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were aligned to the Human reference genome build hg19, using Tophat2 RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and differential expression analysis is performed between relapsed and baseline samples using the DEseq2 package.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Gene-Level Read Count files

source_name: GMP  HD

extract_protocol:
Total RNA from sorted HSPC populations with greater than or equal to 250 cells was purified using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific)
cDNA libraries were prepared using Ovation SoLo RNA-Seq System

value: Bone marrow

tag: age

value: Female

value: GMPs


title: Sample_GMP111


title: Sample_GMP19


title: Sample_GMP21


title: DMSO_3

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the human genome (hg19) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

growth_protocol: A375 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy extraction kit
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp single-end reads.

treatment_protocol: A375 cells were treated with 200nM A-366 for 48h

value: Melanoma

tag: treatment

value: DMSO


title: A366_4

tag: cell line


title: Sample_GMP18

tag: tissue

value: Male


title: DMSO_1


title: DMSO_4


title: DMSO_2


title: Sample_GMP95

source_name: GMP  BG


title: Sample_GMP17


title: A366_2


title: A366_1


title: Sample_GMP75


title: Sample_GMP22


title: Sample_GMP127


title: Sample_GMP120


title: ICH256IM


title: Sample_GMP66


title: Sample_GMP92

source_name: GMP  BC


title: Sample_GMP71


title: Sample_GMP72


title: Sample_GMP90


title: Sample_GMP104


title: Sample_GMP39


title: A366_3


title: Sample_GMP23


title: Sample_GMP20


title: Sample_GMP64


title: Sample_GMP48


title: Sample_CMP23

source_name: CMP  HD

value: CMPs


title: Sample_GMP32


title: Sample_CMP18


title: Sample_CMP21


title: Sample_CMP111


title: Sample_CMP95

source_name: CMP  BG


title: Sample_CMP110


title: St Foxp3_WT2

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
RNA-seq reads are trimmed using Trim Galore v0.4.4 using default parameters to remove the Nextera adapter sequence
Mapping is performed using STAR (2.6) against the mouse NCBIM37 genome, guided by gene models from Ensembl annotation release 68
Quantification and generation of gene expression matrices were performed with the function featureCounts, implemented in the R package Rsubread
Aligned fragments are imported into RStudio and before statistical analysis, the function filterbyExpr, implemented in the R package edgeR was used to determine genes with enough counts for further analyse
Differential gene expression analysis is performed using the DESeq2 algorithm within R and RStudio
Genome_build: mouse NCBIM37 genome, guided by gene models from Ensembl annotation release 68
Supplementary_files_format_and_content: DESeq2 output

source_name: St Foxp3_WT

extract_protocol:
Purified CD8+ T cells were resuspended in 100 μL of Lysis/Binding Buffer (Ambion), vortexed and stored at -80°C until further processing.
Poly-A RNA was purified and reverse-transcribed with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent) using poly-dT oligos carrying a 7 bp-index  and subjected to linear amplification by IVT using HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Next, aRNA was fragmented into 250-350 bp fragments with RNA Fragmentation Reagents (Ambion) and dephosphorylated with FastAP (Thermo) following manufacturer´s instructions. Partial Illumina adaptor sequences  were ligated with T4 RNA Ligase 1 (New England Biolabs), followed by a second RT reaction. Full Illumina adaptor sequences were added during final library amplification with KAPA HiFi DNA Polymerase (Kapa Biosystems). RNA-seq libraries quality controls consisted in quantification with Qubit 3.0 Fluorometer (Life Technologies) and size profiles examination with Agilent’s 4200 TapeStation System. Libraries were sequenced in an Illumina NextSeq 500 at a sequence depth of 10 million reads per sample.

treatment_protocol: When indicated 8St) cells were stimulated in the presence of SIINFEKL peptide for 6 h

value: CD45.2+ C57BL/6 J mice

value: mixed BM from OT-1 Foxp3wt CD45.1+/2+ and from CD45.2+ donor mice

value: Two months after bone marrow reconstitution

value: Highly purified fresh CD8 T cells from BM chimeric mice

value: stimulated with SIINFEKL peptide for 6h


title: St Foxp3_WT3


title: Sample_GMP87


title: Sample_CMP90


title: Sample_CMP92


title: Sample_CMP86


title: St Foxp3_WT1


title: St Foxp3_Scurfy3

source_name: St  Foxp3_Scurfy

value: mixed BM from OT-1 Foxp3Scurfy CD45.1+/2+ and from CD45.2+ donor mice


title: St Foxp3_Scurfy1

source_name: St Foxp3_Scurfy


title: Uns Foxp3_WT3

source_name: Uns Foxp3_WT


title: St Foxp3_Scurfy2


title: Sample_CMP25


title: Sample_CMP120


title: Sample_CMP117


title: Uns Foxp3_WT2


title: Uns Foxp3_WT1


title: Uns Foxp3_Scurfy3

source_name: Uns Foxp3_Scurfy

value: Mixed bone marrow chimera   from OT-1 Foxp3Scurfy CD45.1+/2+ and from CD45.2+ donor mice


title: Sample_CMP75

source_name: CMP  BC


title: Sample_CMP72


title: Sample_CMP69


title: Sample_CMP66


title: Sample_GMP12-1


title: Sample_CMP20


title: Uns Foxp3_Scurfy2


title: Sample_CMP19


title: Uns Foxp3_Scurfy1


title: Sample_CMP17


title: Sample_CMP62


title: Sample_CMP48


title: Enos WT retina rep 2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_wt_705

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with kb-python on reference GRCm38
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters. This represent the filtered RNA count data from seurat V3 command GetAssayData(object = Seurat_object, assay = "RNA", slot = "counts"). Saved using write.table(RNAcounts, "Seurat_object.RNAcounts_P14retina_ENOSproject.txt", sep="\t", row.names=TRUE, col.names =NA)
Supplementary_files_format_and_content: Meta data file. Compressed, flat text files with tab delimiters. Saved using write.table(Seurat_object@meta.data, "Seurat_object.metadata_P14retina_ENOSproject.txt", sep="\t", row.names=TRUE, col.names =NA)

source_name: retina

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

treatment_protocol: Mouse Oxygen-induced retinopathy (OIR)

value: ENOS WT

tag: condition

value: Oxygen-induced retinopathy

value: Post natal day 14

tag: replicate


title: Enos WT retina rep 3

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_wt_706


title: Sample_CMP64

value: Bone marrow


title: Sample_CMP39


title: Sample_CMP32

value: Female


title: Enos KO retina rep 3

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_enos_704

value: ENOS KO


title: Enos WT retina rep 1

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_wt_703


title: Enos KO retina rep 2

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_enos_702


title: Sample_CMP12-1


title: Enos KO retina rep 1

description:
Read 1 and Read 2 on 4 lanes of single-cell RNAseq library
Sample_NX_Joyal_enos_701


title: A549-sp-3_Count

city: chengdu

first: hong

last: wu

address: 55 renmin south road

institute: sichuan cancer hospital

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung cancer cell

growth_protocol: A549 cells were cultured in DMEM medium

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cancer cells were cultured in DMEM/F12 stem cell medium containing basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), and B-27 for 1 week

value: A549-Sphere cell

value: Tumorsphere-formation assay


title: Sample_CMP104

value: Male


title: RC4

description:
Sample_56
Paired-end RNA-Seq

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility.
The raw reads were aligned to the Human reference genome build hg19, using Tophat2 RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and differential expression analysis is performed between relapsed and baseline samples using the DEseq2 package.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Gene-Level Read Count files.

source_name: Relapsed

extract_protocol:
Total RNA from sorted HSPC populations with greater than or equal to 250 cells was purified using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
cDNA libraries were prepared using Ovation SoLo RNA-Seq System.

value: Myelodysplastic syndromes (MDS)

tag: group

value: Relapsed

value: Bone marrow LT-HSCs

tag: gender

tag: batch


title: A549-sp-2_Count


title: A549-sp-1_Count


title: RC2

description:
Sample_35--2
Paired-end RNA-Seq


title: RC1

description:
Sample_2--3
Paired-end RNA-Seq


title: RC3

description:
Sample_83
Paired-end RNA-Seq


title: A549-3_Count

value: untreated


title: A549-2_Count


title: BC5

description:
Sample_72
Paired-end RNA-Seq

source_name: Baseline

value: Baseline


title: PTB_IP_2

city: Beijing

first: Wei

last: Han

address: Dongdansantiao 5

institute: CAMS&PUMC

data_processing:
The filtered effective reads were compared to the reference genome using HISAT2 software.
The distribution density of all reads (total mapped reads) aligned to the genome on each chromosome (divided into positive and negative chains) is counted. The specific mapping method is as follows: take 10kb as the interval unit length, divide the chromosome into multiple small windows, count the number of reads aligned to each window, and take log2.
The binding targets of PTBP1 and IGF2BP2 proteins were analyzed by eCLIP-seq. The high-throughout sequencing was conducted by Illumina Nextseq. CLIPper software was used for peak scanning in the transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: By analyzing the location information of the genome where peak is located and the sequence information of peak region, the peak related genes are screened out, which indicates the target genes that the target protein may participate in the regulation to a certain extent.

extract_protocol:
After SDS-PAGE gel electrophorylation and membrane transfer, we excised the areas from ~55 kDa to ~130 kDa (PTBP1 eCLIP) and from ~65 kDa to ~140 kDa (IGF2BP2 eCLIP), and then treated them with proteinase K (P8107S, New England Biolabs) to release RNA.
Reverse transcription, DNA adapter ligation, PCR amplification were performed to construct the DNA libraries. The DNA libraries were purifed by 3% low melting temp agarose gels (50070, Lonza), cutting gel slices 175~350 bp, and were eluted by Qiagen MinElute gel extraction kit as previously described. All eCLIP experiments were performed twice.

value: glioma cell


title: A549-1_Count


title: BC2

description:
Sample_32
Paired-end RNA-Seq


title: BC4

description:
Sample_71
Paired-end RNA-Seq


title: PTB_input_2


title: BC3

description:
Sample_48
Paired-end RNA-Seq


title: BC1

description:
Sample_12
Paired-end RNA-Seq


title: Half food 5

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

institute: IDAEA-CSIC

description:
half food 5
Agilent-079797 Daphnia magna DGC v2

hyb_protocol: according to manufacturer protocols Low input Quick Amp lebelling

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:079797_D_F_20151120)to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: Daphnia magna gut

growth_protocol: daphnias were cultured and grown according to Barata and Baird, 200

extract_protocol: Total RNA was extracted using Trizol according to Soetaert et al. 2007

treatment_protocol: water exposures according to the manuscript linked

value: Dissected guts


title: Starving 4

description:
starving 4
Agilent-079797 Daphnia magna DGC v2

scan_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: Starving 5

description:
starving 5
Agilent-079797 Daphnia magna DGC v2

label_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: PTB_input_1


title: RG5

description:
MLP166-1
Paired-end RNA-Seq

data_processing:
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility.
The raw reads were aligned to the Human reference genome build hg19, using Tophat2 RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and differential expression analysis is performed between relapsed and baseline samples using the DEseq2 package.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Gene-Level Read Count files.

value: Bone marrow LMPPs


title: Copper Low 4

description:
Copper H2 4
Agilent-079797 Daphnia magna DGC v2


title: Half food 3

description:
half food 3
Agilent-079797 Daphnia magna DGC v2


title: IMP2_IP_2


title: RG6

description:
MLP189-1
Paired-end RNA-Seq


title: RG4

description:
MLP141-2
Paired-end RNA-Seq


title: Copper Low 1

description:
Copper H2 1
Agilent-079797 Daphnia magna DGC v2


title: Starving 2

description:
starving 2
Agilent-079797 Daphnia magna DGC v2


title: Copper Low 5

description:
Copper H2 5
Agilent-079797 Daphnia magna DGC v2


title: IMP2_input_2


title: RG3

description:
MLP101-1
Paired-end RNA-Seq


title: PTB_IP_1


title: IMP2_input_1


title: RG2

description:
MLP75-4
Paired-end RNA-Seq


title: Cadmium Low 3

description:
Cadmium 8 3
Agilent-079797 Daphnia magna DGC v2


title: RG1

description:
MLP34-1
Paired-end RNA-Seq


title: AML 882 PDX + BMS-345541

description: CD45+ sAML cells from a mouse PDX treated with BMS-345541

data_processing:
Sample preparation and sequencing were performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were mapped to the human reference genome (GRCh38) using the cellranger count pipeline
The digital expression matrix was extracted from the filtered_feature_bc_matrix folder outputted by the cellranger count pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcript-Level Read Count files

source_name: CD45+ CD3- cells

extract_protocol:
TheLin-CD34+ cells of BM samples were sorted by FACS. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific)
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented.

tag: sampletype

value: Case


title: MEG01_GFI1B

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

data_processing:
Sequencing reads were aligned to the human genome hg19 using bwa and sum_bed.pl was used for making wiggle files for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

growth_protocol: MEG-01 cells were cultured in RPMI 1640 (GIBCO) supplemented with 10% heat inactivated FCS, at 37˚C and 5% CO2.

extract_protocol:
MEG01 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature at a concentration of 15x106 cells/ml. The fixed cells were sonicated for 4 minutes (30 sec on; 30 sec off) using the Diagnode Bioruptor and centrifuged at maximum speed for 10 minutes. Chromatin of about 5x105 cells was incubated overnight in dilution buffer (167mM NaCl, 16,7 mM Tris (pH 8), 1,2mM EDTA, 1% Triton X-100) with 1 µg antibody at 4C. ProtA/G beads were blocked and incubated with the chromatin-Ab for one hour at 4C. Beads were washed with three different wash buffers and chromatin was eluted from the beads. DNA-proteins were de-crosslinked (200mM NaCl and 4 µl proteinase K (10mg/ml)), by incubation for four hours at 65C and samples were purified using the Qiaquick MinElute PCR purification kit according manufacturer’s protocol.
Sequencing samples were prepared according to the manufacturer's protocol (Illumina). End repair was performed using the precipitated DNA using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ~300 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR and used for cluster generation on the Solexa genome analyzer. Tags were mapped to the human genome HG19 using BWA (Li and Durbin, 2009). For processing and manipulation of SAM/BAM files SAMtools was used (Li et al., 2009). For each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window and visualized in the UCSC genome browser (Kent et al., 2002).

treatment_protocol: no treatment

tag: antibody

value: GFI1B B7 antibody (Santa Cruz, sc-28356)

tag: sample collection (day)


title: AML 882 PDX + Vehicle

description: CD45+ sAML cells from a mouse PDX

value: Control


title: Copper High 3

description:
Copper H 3
Agilent-079797 Daphnia magna DGC v2


title: AML 476 PDX + ABT-199

description: CD45+ sAML cells from a mouse PDX  treated with ABT-199

value: Bone marrow


title: Copper High 5

description:
Copper H 5
Agilent-079797 Daphnia magna DGC v2


title: BG6

description:
MLP151-1
Paired-end RNA-Seq

tag: cell type

value: Female


title: BG3

description:
MLP120
Paired-end RNA-Seq


title: Cadmium Low 2

description:
Cadmium 8 2
Agilent-079797 Daphnia magna DGC v2


title: Planktothrix Low 5

description:
Planktothrix L 5
Agilent-079797 Daphnia magna DGC v2


title: Cadmium High 1

description:
Cadmium 32 1
Agilent-079797 Daphnia magna DGC v2


title: Copper High 4

description:
Copper H 4
Agilent-079797 Daphnia magna DGC v2


title: Half food 2

description:
half food 2
Agilent-079797 Daphnia magna DGC v2


title: Cadmium High 2

description:
Cadmium 32 2
Agilent-079797 Daphnia magna DGC v2


title: Cadmium High 4

description:
Cadmium 32 4
Agilent-079797 Daphnia magna DGC v2


title: Planktothrix Low 3

description:
Planktothrix L 3
Agilent-079797 Daphnia magna DGC v2


title: BG5

description:
MLP141-1
Paired-end RNA-Seq


title: AML 476 PDX + Vehicle

description: CD45+ sAML cells from a mouse PDX

tag: genotype


title: BG4

description:
MLP127-1
Paired-end RNA-Seq


title: Patient 11 GML

city: Amsterdam

first: Anne-Marie

last: Dam

state: Noord Holland

address: De Boelelaan 1108

department: Anatomy and Neurosciences

institute: Amsterdam UMC, location VUmc

description:
Patient 11
Sample 43

data_processing:
Quality control of the raw FASTQ files was performed with FASTQC.
Bad quality bases were trimmed with TrimGalore version 0.4.5. Sequences were aligned using HiSat2 version 2.1 to the H. Sapiens (GRCh38.92) reference template obtained from Ensembl and quantified with featureCounts.
A quality check of aligned data was performed with FASTQC and MultiQC.
Genome_build: GRCh38.92
Supplementary_files_format_and_content: Counts per Million (edgeR)

source_name: Brain

extract_protocol:
Leukocortical areas were extracted using laser capture microscopy. Samples were collected in lysis buffer of the PicoPure ARCTURUS® PicoPure® RNA Isolation Kit and RNA was isolated according to the manufacturers protocol. Only samples with a RIN > 6 before the LCM procedure were included in the sequencing.
Sequencing libraries were prepared with the Quant Seq 3' mRNA-Seq Library Prep Kit FWD

tag: area

value: GML

value: m


title: Patient 10 NAWM

description:
Patient 10
Sample 37

value: NAWM

value: f


title: BG2

description:
MLP87
Paired-end RNA-Seq

value: Myelodysplastic syndromes (MDS)

value: Male


title: Planktothrix Low 2

description:
Planktothrix L 2
Agilent-079797 Daphnia magna DGC v2


title: BG1

description:
MLP86
Paired-end RNA-Seq


title: Planktothrix High 4

description:
Planktothrix H 4
Agilent-079797 Daphnia magna DGC v2


title: Patient 11 NAGM

description:
Patient 11
Sample 42

value: NAGM


title: Planktothrix High 1

description:
Planktothrix H 1
Agilent-079797 Daphnia magna DGC v2


title: F_144h

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

data_processing:
FASTQ sequence files were generated using the Illumina Casava pipeline version 1.8.3. Initial quality assessment was based on data passing the Illumina Chastity filtering.
Reads containing PhiX control signal were removed. Reads containing (partial) adapters were clipped up to minimum read length of 50bp.
The second quality assessment was based on the remaining reads using the FASTQC quality control tool version 0.10.0.
FASTQ sequence reads were trimmed to their first 50 nucleotides, in order to limit the chance of reads mapping to more than one gene.
Trimmed read sequences were mapped to the E88 chromosome and plasmid reference sequence using bowtie2 (version 2.2.4) with default settings, after which a table with the number of counts per gene was obtained using samtools (version 1.1).
Genome_build: NC_004557.1 (chromosome) and NC_004565.1 (plasmid)
Supplementary_files_format_and_content: Countdata.xlsx: count data per sample plus gene annotation

organism: Clostridium tetani

source_name: bacterial cells

growth_protocol: Clostridium tetani batch cultures were grown at Sanofi-Pasteur under different small-scale batch fermentation conditions. The cultures were performed during two studies; the second study served as a confirmation as well as an expansion of the first study. In the first study, cultures were performed in duplicate. Bacterial samples were taken at five time points if possible.

extract_protocol:
10mL samples of cell suspension were collected and centrifuged (5 min at 4500 g). After supernatant removal, cell pellet was put in suspension with 500 μL of fresh medium. For RNA preservation, 1 mL of RNA-protect Bacteria reagent (Qiagen) was added. After homogenization, samples were stored at 5 °C for 5 min to 1 hour and then stored at -70 °C until RNA extraction. After thawing, a maximum of 10^9 cells were collected for RNA extraction. Cell content was not enough for certain samples, in this case the totality of sample was used. RNA extraction and purification were performed by using the RiboPure™-Bacteria kit from Life technologies (ref. AM1925) and the RiboPure Bacteria procedure (Part Number 1925M Rev. D). RNA QC was performed to determine the concentration and the integrity (RIN number).
For the first study, RNA-Seq was performed at RIVM. Library preparation was performed using the TruSeq Stranded mRNA Library Prep kit (Illumina). Additional reagents used were the Ribo-Zero rRNA removal kit for Gram-Positive Bacteria (Illumina), RNA clean & concentrator-5 (Baseclear), and the Baseline-ZERO DNase (Immunosource). Libraries combined with 1% PhiX Control v3 (Illumina) were sequenced using Illumina NextSeq 500 equipment and the NextSeq 500/550 High Output Kit v2.5.  For the second study, RNA-Seq was performed at BaseClear, using their Illumina-based protocols for bacterial RNA-Seq.

treatment_protocol: Growth conditions included: (A) normal (34°C, pH 7.3, 150rpm stirring); (B) no agitation; (C) 36 °C; (D) 32 °C; (E) pH 7.8; (F) increased N2 flux in headspace

value: increased N2 flux

tag: time point

tag: study number


title: Planktothrix High 3

description:
Planktothrix H 3
Agilent-079797 Daphnia magna DGC v2


title: Petient 10 GML

description:
Petient 10
Sample 39

tag: age


title: fluoranthrene Low 3

description:
fluoranthrene L 3
Agilent-079797 Daphnia magna DGC v2


title: Patient 10 NAGM

description:
Patient 10
Sample 38


title: Patient 9 GML

description:
Patient 9
Sample 35


title: fluoranthrene Low 2

description:
fluoranthrene L 2
Agilent-079797 Daphnia magna DGC v2


title: Patient 11 NAWM

description:
Patient 11
Sample 41


title: F_120h


title: Patient 9 NAWM

description:
Patient 9
Sample 33


title: Fluoranthrene High 2

description:
fluoranthrene H 2
Agilent-079797 Daphnia magna DGC v2


title: F_096h


title: Cyalothrin Low 1

description:
cyalo L 1
Agilent-079797 Daphnia magna DGC v2


title: Patient 11 WML

description:
Patient 11
Sample 40

value: WML


title: fluoranthrene Low 4

description:
fluoranthrene L 4
Agilent-079797 Daphnia magna DGC v2


title: Fluoranthrene High 4

description:
fluoranthrene H 4
Agilent-079797 Daphnia magna DGC v2


title: Patient 8 GML

description:
Patient 8
Sample 31


title: fluoranthrene High 5

description:
fluoranthrene H 5
Agilent-079797 Daphnia magna DGC v2


title: Patient 8 NAGM

description:
Patient 8
Sample 30


title: Patient 9 NAGM

description:
Patient 9
Sample 34


title: F_072h


title: Patient 9 WML

description:
Patient 9
Sample 32


title: F_048h


title: E_144h

value: high pH (7.8)


title: E_096h


title: Patient 8 NAWM

description:
Patient 8
Sample 29


title: Patient 8 WML

description:
Patient 8
Sample 28


title: Cyalothrin Low 3

description:
cyalo L 3
Agilent-079797 Daphnia magna DGC v2

value: Dissected guts


title: E_072h


title: D_072h

value: lower temperature (32 degrees)


title: Cyalothrin Low 4

description:
cyalo L 4
Agilent-079797 Daphnia magna DGC v2


title: Cyalothrin High 4

description:
cyalo H 4
Agilent-079797 Daphnia magna DGC v2


title: CT cyalothryn fluoranthener 4

description:
ct cyalo fluor 4
Agilent-079797 Daphnia magna DGC v2


title: Cyalothrin High 5

description:
cyalo H 5
Agilent-079797 Daphnia magna DGC v2


title: CT cyalothryn fluoranthene 5

description:
ct cyalo fluor 5
Agilent-079797 Daphnia magna DGC v2


title: Patient 7 NAGM

description:
Patient 7
Sample 26


title: Cyalothrin High 1

description:
cyalo H 1
Agilent-079797 Daphnia magna DGC v2


title: D_120h


title: Patient 6 NAGM

description:
Patient 6
Sample 22


title: D_096h


title: CT  cyalothryn fluoranthene 1

description:
ct cyalo fluor 1
Agilent-079797 Daphnia magna DGC v2


title: Patient 7 GML

description:
Patient 7
Sample 27


title: E_048h


title: IMP2_IP_1

value: glioma cell


title: Patient 6 GML

description:
Patient 6
Sample 23


title: Patient 7 WML

description:
Patient 7
Sample 24


title: Patient 6 NAWM

description:
Patient 6
Sample 21


title: D_048h


title: Patient 7 NAWM

description:
Patient 7
Sample 25


title: C2_089h

value: higher temperature (36 degrees)


title: CT control copper and Planktothrix 5

description:
control cu Plank 5
Agilent-079797 Daphnia magna DGC v2


title: CT control copper and Planktothrix 1

description:
control cu Plank 1
Agilent-079797 Daphnia magna DGC v2


title: C2_065h


title: Patient 6 WML

description:
Patient 6
Sample 20


title: CT control cadmium 5

description:
control cd 5
Agilent-079797 Daphnia magna DGC v2


title: Patient 5 GML

description:
Patient 5
Sample 19


title: Whole trochophore larvae

city: Vienna

first: David

middle: Andrés

last: Salamanca-Díaz

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

data_processing: Reads were mapped to the previously published genome with Cell Ranger v3.1.0

organism: Dreissena rostriformis

source_name: Whole trochophore larvae

extract_protocol: cDNA generation was performed using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Sequencing libraries were generated using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).

value: 13-15 hours post fertilization


title: CT control copper and Planktothrix 2

description:
control cu Plank 2
Agilent-079797 Daphnia magna DGC v2


title: C2_041h


title: Patient 5 NAGM

description:
Patient 5
Sample 18


title: Patient 5 NAWM

description:
Patient 5
Sample 17


title: C1_089h


title: Chsy3KO-2

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: nucleus pulposus cells

growth_protocol: Nucleus pulposus tissue were dissected under microscopy, and nucleus pulposus tissue were further digested using Type II & IV collagenase for 2h and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 2 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus pulposus

tag: passage

value: Passage 2

value: 8 week

tag: Sex

value: male


title: C1_065h


title: CT control cadmium 2

description:
control cd 2
Agilent-079797 Daphnia magna DGC v2

tag: tissue


title: CT control cadmium 1

description:
control cd 1
Agilent-079797 Daphnia magna DGC v2


title: CT full food 5

description:
full food 5
Agilent-079797 Daphnia magna DGC v2


title: CT full food 1

description:
full food 1
Agilent-079797 Daphnia magna DGC v2


title: CT full food 2

description:
full food 2
Agilent-079797 Daphnia magna DGC v2


title: CT control cadmium 3

description:
control cd 3
Agilent-079797 Daphnia magna DGC v2


title: C1_041h

tag: condition


title: Patient 4 GML

description:
Patient 4
Sample 16

value: GML


title: Patient 4 NAGM

description:
Patient 4
Sample 15

value: f


title: B2_113h

value: no agitation

tag: replicate


title: Chsy3HE-2

value: Chsy3 heterozygous


title: B2_136h


title: Patient 4 NAWM

description:
Patient 4
Sample 14

value: NAWM


title: Chsy3HE-1


title: Chsy3WT-2

value: wild type


title: Chsy3KO-1


title: B2_065h


title: B2_041h


title: Chsy3WT-1


title: Patient 3 GML

description:
Patient 3
Sample 12


title: Patient 4 WML

description:
Patient 4
Sample 13

value: WML


title: B2_089h


title: Patient 3 NAWM

description:
Patient 3
Sample 10


title: B1_136h


title: Patient 3 WML

description:
Patient 3
Sample 9


title: Patient 3 NAGM

description:
Patient 3
Sample 11

value: NAGM


title: B1_113h


title: Patient 2 GML

description:
Patient 2
Sample 8


title: B1_089h


title: A4

first: Kunshan

last: Zhang

address: 389 Xincun Rd.

department: Tongji Hospital

institute: Tongji University

data_processing:
Reads were mapped to mouse genome (mm9) by using of hisat2(v2.1).
Gene counts were estimated by HTSeq (0.11).
Genome_build: mm9
Supplementary_files_format_and_content: A Tab-separated values file including gene counts of each sample.

source_name: Spleen Treg

extract_protocol:
Total RNA was extracted from cells using TRIZOL, then checked for a RIN number to inspect RNA integrity by the Spectrophotometer NanoDrop ND-1000 and an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4+GFP+ Treg cells from the liver and spleen of Foxp3GFP knock-in mice (12-day-old) were purified by flow cytometry.

value: Spleen

value: CD4+GFP+ Treg cells

tag: genotype/variation

value: Foxp3GFP knock-in


title: A5

source_name: Liver Treg

value: Liver


title: A3


title: A6


title: B1_041h


title: B1_065h


title: Patient 2 NAGM

description:
Patient 2
Sample 7

tag: gender


title: Patient 2 NAWM

description:
Patient 2
Sample 6


title: A2


title: A1


title: HUDEP WT_rep2

city: Vellore

first: Nithin Sam

last: R

state: TamilNadu

address: Bagayam

department: Center for Stem Cell Research

country: India

institute: Christian Medical College

data_processing:
All the raw data in .FASTq format was analyzed using NFCORE - RNASeq pipeline
Genome_build: GrCH38
Supplementary_files_format_and_content: Normalized TMM Values

source_name: umbilical cord blood

growth_protocol: HUDEP-2 cell lines were cultured in StemSpan™ SFEM II (STEMCELL Technologies) supplemented with 50 ng/ml SCF (ImmunoTools), 3 U/ml EPO (Zyrop 4000 IU Injection), 1x Pen-Strep, 1 uM dexamethasone (Alfa Aesar), 1 μg/ml doxycycline (Sigma-Aldrich) and 1x L-Glutamine 200 mM (Gibco™). Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions.

extract_protocol:
RNA was extracted with Macherey-Nagel’s NucleoSpin RNA kit. Illumina TruSeq RNA Sample Preparation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus production: Transfections were performed About 1x106 HEK 293T cells were seeded in a 10cm cell culture dish with DMEM (HyClone) containing 10% FBS and 1 % Pen-Strep. After achieving 80% confluency, 2.5 μg of pMD2.G, 3.5 μg of psPAX2 along with 4 μg (construct with gRNA) or 5 μg (Construct with ABE/CBE/Cas9) of lentiviral-vector were transfected using FuGENE-HD as per manufacturer's protocol. After 48 hours the viral supernatant was collected and concentrated using Lenti-X Concentrator (Takara). The concentrated pellet was resuspended in 200 μl 1xPBS and stored in -80oC for downstream use. Transduction: HUDEP-2 or K562 cells were taken in 6 well plate (0.5 million cells per well) along with 6 μg/ml Polybrene (Sigma-Aldrich), 1% HEPES 1M buffer (Gibco) and 100 μl of desired Lentivirus and centrifuged at 800g for 30 min at RT. The lentivirus containing the pLenti-FNLS-P2A-Puro or pLenti-ABERA-P2A-Puro or pLenti-ABE8e-Puro or lentiCRISPR V2 1.1 were used to prepare respective stable lines followed by puromycin selection (1 μg/ml) (Sigma-Aldrich) after 48 hours of transduction till ten days. While for transducing desired gRNA in the respective stable, pLKO5.sgRNA.EFS.GFP/RFP construct was used and the transduction efficiency was analyzed by FACS for GFP/RFP after 48 hours.

value: human erythroid progenitor cell

tag: cell line

value: Wild type

tag: treatment


title: C57BL/6 - Ep1_4_fpkm

city: Kaifeng

first: Haigang

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the mm8 hole genome using bowtie v0.12.2 with parameters set as defaults.
FPKM data
Genome_build: mm8

source_name: C57BL/6 brain tissue

extract_protocol:
Cell samples were lyzed and harvested using Trizol reagent. THe purification of RNA was performed using protocol provided by extracting kits (Total RNA Extraction Kit, Cat. R1200, Solarbio life science, China).
RNA library were prepared for sequencnig using standard illumina protocols

value: Brain microvessel endothelial cells

tag: strain

value: treated with PDT with 20 J/cm2


title: A2_136h

value: standard


title: A2_113h


title: Patient 2 WML

description:
Patient 2
Sample 5


title: Patient 1 GML

description:
Patient 1
Sample 4

value: GML


title: HUDEP WT_rep1


title: A2_089h


title: CBE 11_rep2

value: CBE expressing stable

value: treated with gRNA 11


title: CBE 11_rep1


title: CBE Control_rep2

value: Control


title: Patient 1 NAGM

description:
Patient 1
Sample 3

value: f


title: Patient 1 NAWM

description:
Patient 1
Sample 2

value: NAWM


title: C57BL/6 - Ep1_2_fpkm

value: treated with PDT with 10 J/cm2


title: CBE 2_rep2

value: treated with gRNA 2


title: A2_065h


title: C57BL/6 - Ep1_1_fpkm


title: Patient 1 WML

description:
Patient 1
Sample 1

value: WML


title: C57BL/6 - Ctrl_4_fpkm

value: untreated


title: CBE Control_rep1


title: A2_041h


title: A1_136h


title: ABE Control_rep2

value: ABE expressing stable


title: C57BL/6 - Ctrl_3_fpkm


title: ABE Control_rep1


title: CBE 2_rep1


title: A1_113h


title: C57BL/6 - Ctrl_2_fpkm


title: C57BL/6 - Ep1_3_fpkm


title: IN vacc

city: Berkeley

first: Robyn

middle: M

last: Jong

address: 500E Li Ka Shing, 1951 Oxford St mc3370, UC Berkeley

department: Molecular and Cell Biology

institute: Stanley Lab, UC Berkeley

data_processing:
Reads were aligned to the mouse transcriptome mm10 with the 10x Cell Ranger analysis pipeline
After filtering, barcode counting, and UMI counting, the Scanpy toolkit was used to preprocess the data.
The single cell variational inference (scVI) approach was utilized to project the data from both vaccinated and naïve mice into a shared lower-dimensional latent space. Uniform manifold approximation and projection (UMAP) and Leiden clustering were then applied on the k-Nearest-Neighbor graph of the latent space for visualization and clustering of the data. Leiden clusters that expressed high levels of myeloid, B cell, or CD8 T cell markers were excluded from the data before utilizing the scVI model a second time.
The filtered data was annotated using signature genes from CD4 T cell subset in cellxgene, a single-cell data exploration tool.
Scanpy was used to visualize data and test differential expression of genes between samples and CD4 T cell subsets. The single-cell ANnotation using Variational Inference (scANVI) variant of scVI was used to assign annotations to unassigned cells based on high-confidence seed labels annotated on cellxgene.
Genome_build: mm10
Supplementary_files_format_and_content: PBSctrl_filtered_feature_bc_matrix.h5 and INvacc_filtered_feature_bc_matrix.h5 are HDF5 files aligned to the mouse mm10 transcriptome using the 10x Cell Ranger analysis pipeline, before concatenation of the data from both samples.
Supplementary_files_format_and_content: Supplementary file adata_counts is a cells x genes count matrix containing normalized read counts of PBS control and IN vacc sample after utilizing the scVI approach to concatenate the datasets, identify and exclude contaminating non-CD4 T cell populations, and utilizing the scVI approach a second time.
Supplementary_files_format_and_content: Supplementary file adata_meta is a meta data file of cells x observations matrix containing annotations derived from data processing, clustering, manual annotations, seeds for the scANVI approach, and scANVI results.

source_name: lung CD4 T cells

extract_protocol:
The second largest lung lobes were pooled from three mock or i.n. H1/ML-RR-cGAMP vaccinated mice, tissue dissociated in RPMI containing liberase and DNase I in gentleMACS C tubes using the gentleMACS dissociator and strained through a 70μm filter for sorting on a Sony SH-800 sorter using a 100μm nozzle. Sorted CD4 T cells were washed in RPMI and counted. 5000-6000 CD4 T cells per sample were used for single cell RNA sequencing (scRNA-seq) according to the 10x Genomics protocol.
Single cell suspensions were partitioned into Gel Beads in emulsion (GEMs) using the 3’ Chromium Next GEM single Cell v3.1 system. 10x barcoded primers were used to reverse transcribe poly-adenylated mRNA to produce barcoded, full-length cDNA. Purified DNA was amplified, fragmented, and amplified again to attach Illumina adapter sequences by the Functional Genomics Laboratory at UC Berkeley. Libraries were sequenced on an Illumina NovaSeq SP 100SR and demultiplexed.

treatment_protocol: 5 μg ML-RR-cGAMP and 3 μg fusion antigen protein (5Ag or H1) were formulated in PBS for intranasal (i.n.) delivery. Mice were vaccinated three times at 4-week intervals with 20 μL vaccine or mock vacine (PBS) i.n. Twelve weeks after the initial vaccine injection, mice were infected via the aerosol route with M. tuberculosis strain Erdman.

tag: vaccine

value: i.n. H1/ML-RR-cGAMP

value: lung

value: CD4 T cells


title: ABE 11_rep2

tag: cell type

value: human erythroid progenitor cell


title: C57BL/6 - Ctrl_1_fpkm

value: Brain microvessel endothelial cells


title: ABE 11_rep1

tag: genotype


title: Healthy donor 1

description: Healthy donor CD34+ cells

source_name: CD34+ cells

extract_protocol:
TheLin-CD34+ cells of BM samples were sorted by FACS. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific)
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented.
Single Cell RNAseq

value: Bone marrow

value: Male

tag: sampletype


title: CMP pattern MDS

description: Baseline GMP pattern MDS CD34+ cells

value: Case


title: Healthy donor 2

description: Healthy donor CD34+ cells


title: A1_065h

value: standard

tag: time point


title: A1_041h

tag: study number


title: PBS ctrl

value: mock


title: AML 881 PDX run 2

description: CD45+ sAML cells from a mouse PDX