title: Line140_DEX


title: Line14_TUNIC

status: Public on Jun 30 2022

type: SRA

city: Nashville

first: Amanda

middle: Jeanne

last: Lea

state: TN

address: Box 351634 Station B

country: USA

institute: Vanderbilt University

description: Lymphoblastoid cell line from the 1000 Genomes study

library_source: transcriptomic

data_processing:
trimmed each FASTQ file for low quality bases and adapter contamination using "cutadapt"
mapped the trimmed reads to the human reference genome (hg38) using "STAR"
extracted counts of reads mapped to genes using "HTSeq"
removed samples with fewer than 250,000 reads mapped to protein coding genes; if a sample was sequenced twice, kept the sample with the most mapped reads
filtered the per-gene counts matrix to exclude lowly expressed genes, normalized the count data using the R package "limma", and identified 3 surrogate variables that were then regressed out using the R package "sva"
Assembly: hg38
Supplementary files format and content: TXT file of the gene expression values processed as described above

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Lymphoblastoid cell lines (LCLs) were obtained for 544 unrelated individuals included in the 1000 Genomes study. All cells were ordered from Coriell Institute, and live cultures were shipped overnight to Princeton University in randomized batches of 25. Cells were cultured in parallel for 5-11 days until 12 million cells were available to seed (at a density of 1 million cells/2.5mL of media in a 12 well plate).

extract_protocol:
Zymo Quick-RNA
TM3'seq as in PMCID: PMC6945013

treatment_protocol: After an overnight incubation period, 1 of 12 environmental treatments were added to each of the 12 wells.  After 4 hours, cells were washed, harvested, and preserved in lysis buffer for downstream RNA work.

tag: cell type

value: Lymphoblastoid

tag: cell line

tag: treatment

value: Tunicamycin


title: Line14_GARD

value: Gardiquimod


title: Line14_IFNg

value: Interferon Gamma


title: Line14_BAFF

value: B-cell activating factor


title: Line14_DEX

value: Dexamethasone


title: Line14_FSL1


title: Line141_IGF

value: Insulin-like Growth Factor 1


title: Line14_WATER

value: Water


title: Line139_WATER


title: Line139_BAFF


title: Line14_ETOH

value: Ethanol


title: Line139_IGF


title: v3.Line138_ETOH


title: Line139_TUNIC


title: Line139_DEX


title: Line139_IFNg


title: v3.Line138_BAFF


title: Line139_ETOH


title: v3.Line138_WATER


title: Line139_GARD


title: Line138_DEX


title: v6.Line138_BAFF


title: v2.Line138_TUNIC


title: Line138_ETOH


title: Line138_TUNIC


title: v2.Line138_WATER


title: Line138_IGF


title: Line138_BAFF


title: v2.Line138_IFNg


title: v6.Line138_GARD


title: v2.Line138_IGF


title: v6.Line138_DEX


title: v6.Line138_ETOH


title: Line138_WATER


title: v3.Line138_DEX


title: Line138_IFNg


title: v3.Line138_IGF


title: v3.Line138_TUNIC


title: Line138_GARD


title: v3.Line138_GARD


title: v3.Line138_IFNg


title: Line137_IFNg


title: Line137_IGF


title: Line137_GARD


title: Line137_ETOH


title: Line137_BAFF


title: Line137_TUNIC


title: Line136_WATER


title: Line137_DEX


title: Line137_WATER


title: Line136_ETOH


title: Line136_BAFF


title: Line136_DEX


title: Line135_GARD


title: Line136_IGF


title: Line136_GARD


title: Line135_TUNIC


title: Line135_BAFF


title: Line135_ETOH


title: Line135_DEX


title: Line136_TUNIC


title: Line134_IFNg


title: Line135_WATER


title: Line134_BAFF


title: Line136_IFNg


title: Line135_IFNg


title: Line134_WATER


title: Line134_DEX


title: Line134_ETOH


title: Line134_GARD


title: Line134_IGF


title: Line133_DEX


title: Line133_IFNg


title: Line133_IGF


title: Line133_WATER


title: Line133_GARD


title: Line132_WATER


title: Line133_TUNIC


title: Line132_TUNIC


title: Line132_DEX


title: Line133_ETOH


title: Line132_BAFF


title: Line132_GARD


title: Line135_IGF


title: Line132_IGF


title: Line131_IFNg


title: Line131_BAFF


title: Line132_ETOH


title: Line131_WATER


title: Line131_GARD


title: Line131_DEX


title: Line131_IGF


title: Line131_ETOH


title: Line134_TUNIC


title: Line131_TUNIC


title: Line130_ETOH


title: Line130_GARD


title: Line133_BAFF


title: Line130_IFNg


title: Line132_IFNg


title: v3.Line13_ETOH


title: Line130_IGF


title: Line130_TUNIC


title: Line130_BAFF


title: Line13_WATER


title: v3.Line13_TUNIC


title: Line130_WATER


title: v2.Line13_WATER


title: v2.Line13_FSL1


title: v6.Line13_GARD


title: v2.Line13_BAFF


title: v6.Line13_ETOH


title: Line13_IFNg


title: v3.Line13_DEX


title: Line13_BAFF


title: v6.Line13_TUNIC


title: Line13_ETOH


title: v3.Line13_BAFF


title: v6.Line13_DEX


title: v3.Line13_WATER


title: Line130_DEX


title: v2.Line13_IFNg


title: Line13_TUNIC


title: v3.Line13_GARD


title: Line13_FSL1


title: v3.Line13_FSL1


title: Line129_IGF


title: Line129_WATER


title: v3.Line13_IFNg


title: Line129_GARD


title: Line129_BAFF


title: Line129_TUNIC


title: Line129_IFNg


title: Line128_GARD


title: v3.Line128_TUNIC


title: Line129_DEX


title: Line13_GARD


title: Line13_DEX


title: v3.Line128_GARD


title: v2.Line128_WATER


title: v3.Line128_IGF


title: v2.Line128_IFNg


title: v3.Line128_ETOH


title: v3.Line128_WATER


title: v2.Line128_BAFF


title: Line128_WATER


title: v2.Line128_ETOH


title: v6.Line128_DEX


title: Line128_DEX


title: v2.Line128_IGF


title: v6.Line128_GARD


title: Line128_ETOH


title: Line127_IFNg


title: Line128_TUNIC


title: v6.Line128_TUNIC


title: Line127_IGF


title: v3.Line128_DEX


title: Line127_BAFF


title: Line128_IGF


title: Line127_DEX


title: Line127_ETOH


title: Line129_ETOH


title: Line127_TUNIC


title: Line128_IFNg


title: Line127_WATER


title: v3.Line128_IFNg


title: Line128_BAFF


title: v3.Line128_BAFF


title: Line126_DEX


title: Line126_WATER


title: Line126_TUNIC


title: Line126_ETOH


title: Line126_IFNg


title: Line126_GARD


title: Line126_IGF


title: Line126_BAFF


title: Line125_GARD


title: Line125_IFNg


title: Line127_GARD


title: Line125_TUNIC


title: Line125_BAFF


title: Line124_BAFF


title: Line125_DEX


title: Line124_IGF


title: Line124_ETOH


title: Line125_IGF


title: Line125_WATER


title: Line125_ETOH


title: Line124_GARD


title: Line124_TUNIC


title: Line124_WATER


title: Line124_DEX


title: v2.Line123_ETOH


title: Line123_IFNg


title: Line123_WATER


title: Line123_GARD


title: Line123_BAFF


title: v2.Line123_IFNg


title: v6.Line123_TUNIC


title: v6.Line123_BAFF


title: Line123_DEX


title: v6.Line123_IGF


title: Line123_IGF


title: v3.Line123_TUNIC


title: v2.Line123_WATER


title: Line124_IFNg


title: Line123_TUNIC


title: v3.Line123_GARD


title: v3.Line123_WATER


title: v6.Line123_GARD


title: v3.Line123_ETOH


title: v3.Line123_IGF


title: Line122_IFNg


title: v6.Line123_DEX


title: v3.Line123_BAFF


title: Line122_BAFF


title: Line122_GARD


title: v3.Line123_DEX


title: Line122_WATER


title: Line122_IGF


title: Line122_DEX


title: Line122_ETOH


title: Line121_ETOH


title: Line121_TUNIC


title: Line121_DEX


title: Line121_BAFF


title: Line121_IGF


title: v3.Line123_IFNg


title: Line123_ETOH


title: Line121_IFNg


title: Line120_BAFF


title: Line120_DEX


title: Line120_IFNg


title: Line120_ETOH


title: Line120_GARD


title: v2.Line12_BAFF


title: v3.Line12_IFNg


title: Line12_GARD


title: Line122_TUNIC


title: Line120_WATER


title: Line120_TUNIC


title: Line120_IGF


title: Line121_WATER


title: v2.Line12_IFNg


title: v3.Line12_ETOH


title: Line12_ETOH


title: Line121_GARD


title: Line12_IFNg


title: v3.Line12_BAFF


title: v3.Line12_FSL1


title: v3.Line12_DEX


title: v2.Line12_DEX


title: v3.Line12_TUNIC


title: Line12_TUNIC


title: v2.Line12_FSL1


title: v3.Line12_WATER


title: v2.Line12_GARD


title: v2.Line12_ETOH


title: v2.Line12_WATER


title: v3.Line12_GARD


title: v2.Line12_TUNIC


title: Line119_TUNIC


title: Line12_BAFF


title: Line12_DEX


title: Line119_BAFF


title: Line119_GARD


title: Line119_IGF


title: Line12_FSL1


title: Line119_DEX


title: Line119_IFNg


title: Line118_DEX


title: Line118_GARD


title: Line119_ETOH


title: Line12_WATER


title: Line118_BAFF


title: Line118_WATER


title: Line118_IFNg


title: Line118_ETOH


title: Line117_BAFF


title: Line117_DEX


title: Line117_WATER


title: Line117_TUNIC


title: Line117_ETOH


title: Line117_IFNg


title: Line116_GARD


title: Line119_WATER


title: v3.Line116_DEX


title: Line118_IGF


title: v2.Line116_TUNIC


title: v2.Line116_DEX


title: Line116_TUNIC


title: v3.Line116_BAFF


title: v2.Line116_IFNg


title: v2.Line116_IGF


title: v3.Line116_WATER


title: v3.Line116_IFNg


title: Line116_BAFF


title: Line116_ETOH


title: v3.Line116_GARD


title: Line117_GARD


title: v3.Line116_IGF


title: v2.Line116_GARD


title: Line117_IGF


title: Line118_TUNIC


title: v2.Line116_ETOH


title: Line116_IGF


title: v2.Line116_BAFF


title: Line116_DEX


title: Line116_IFNg


title: v2.Line116_WATER


title: Line116_WATER


title: v3.Line116_ETOH


title: v3.Line116_TUNIC


title: Line115_BAFF


title: Line115_IGF


title: Line115_WATER


title: Line115_ETOH


title: Line115_IFNg


title: Line115_GARD


title: Line115_DEX


title: Line114_IFNg


title: Line114_DEX


title: Line114_IGF


title: Line115_TUNIC


title: Line114_WATER


title: Line114_TUNIC


title: Line114_ETOH


title: Line114_BAFF


title: Line113_GARD


title: v2.Line113_BAFF


title: v3.Line113_GARD


title: Line113_DEX


title: v2.Line113_IFNg


title: v3.Line113_TUNIC


title: v2.Line113_TUNIC


title: Line113_WATER


title: v3.Line113_WATER


title: v3.Line113_IFNg


title: Line113_IGF


title: Line113_ETOH


title: v3.Line113_BAFF


title: Line113_TUNIC


title: Line113_BAFF


title: v6.Line113_IGF


title: v3.Line113_ETOH


title: Line114_GARD


title: v2.Line113_GARD


title: v3.Line113_DEX


title: v6.Line113_ETOH


title: v3.Line113_IGF


title: v2.Line113_DEX


title: v2.Line113_WATER


title: Line113_IFNg


title: v3.Line112_BAFF


title: v6.Line112_IGF


title: v3.Line112_TUNIC


title: v2.Line112_GARD


title: Line112_IGF


title: v3.Line112_DEX


title: v6.Line112_TUNIC


title: v3.Line112_IGF


title: v3.Line112_ETOH


title: v3.Line112_IFNg


title: Line112_IFNg


title: Line112_GARD


title: Line112_DEX


title: v3.Line112_GARD


title: v6.Line112_ETOH


title: Line112_ETOH


title: v2.Line112_WATER


title: v3.Line112_WATER


title: v6.Line112_IFNg


title: Line112_TUNIC


title: Line112_WATER


title: Line111_IFNg


title: v6.Line112_DEX


title: Line111_WATER


title: Line111_IGF


title: Line112_BAFF


title: Line111_GARD


title: v6.Line112_BAFF


title: v2.Line111_GARD


title: v3.Line111_TUNIC


title: v3.Line111_ETOH


title: v2.Line111_WATER


title: v2.Line111_BAFF


title: v3.Line111_DEX


title: v3.Line111_WATER


title: v2.Line111_TUNIC


title: Line111_TUNIC


title: v3.Line111_IGF


title: Line111_ETOH


title: v2.Line111_IGF


title: Line111_DEX


title: v2.Line111_IFNg


title: v2.Line111_DEX


title: v2.Line111_ETOH


title: Line110_IGF


title: v3.Line111_IFNg


title: Line110_DEX


title: Line110_BAFF


title: Line11_FSL1


title: Line11_GARD


title: Line11_DEX


title: Line110_WATER


title: Line110_GARD


title: Line110_IFNg


title: Line11_TUNIC


title: Line110_ETOH


title: Line11_IFNg


title: v3.Line111_BAFF


title: Line109_IGF


title: v3.Line111_GARD


title: Line11_WATER


title: Line109_DEX


title: Line109_GARD


title: Line109_WATER


title: Line109_TUNIC


title: Line11_BAFF


title: Line109_ETOH


title: Line110_TUNIC


title: Line11_ETOH


title: Line109_BAFF


title: Line109_IFNg


title: Line108_DEX


title: Line108_TUNIC


title: Line108_GARD


title: Line108_BAFF


title: Line108_IFNg


title: Line108_WATER


title: Line108_IGF


title: Line108_ETOH


title: Line107_IFNg


title: Line107_IGF


title: Line107_TUNIC


title: Line107_WATER


title: Line107_ETOH


title: Line106_TUNIC


title: Line106_IGF


title: Line106_BAFF


title: Line106_DEX


title: Line107_GARD


title: Line106_GARD


title: Line106_ETOH


title: Line106_WATER


title: Line105_GARD


title: Line105_IGF


title: Line105_DEX


title: Line105_ETOH


title: Line105_BAFF


title: Line107_BAFF


title: Line107_DEX


title: Line105_WATER


title: Line105_TUNIC


title: v2.Line104_BAFF


title: Line111_BAFF


title: Line104_ETOH


title: Line104_DEX


title: Line105_IFNg


title: v3.Line104_ETOH


title: v2.Line104_IGF


title: v3.Line104_TUNIC


title: Line106_IFNg


title: v2.Line104_TUNIC


title: v3.Line104_GARD


title: v3.Line104_DEX


title: Line104_TUNIC


title: v3.Line104_WATER


title: v2.Line104_IFNg


title: Line104_WATER


title: v3.Line104_IGF


title: v3.Line104_BAFF


title: v2.Line104_DEX


title: Line104_BAFF


title: v2.Line104_WATER


title: Line104_IGF


title: Line103_TUNIC


title: Line103_ETOH


title: v2.Line104_ETOH


title: v3.Line104_IFNg


title: Line103_GARD


title: Line103_IGF


title: Line103_WATER


title: Line104_GARD


title: v3.Line102_TUNIC


title: v3.Line102_BAFF


title: Line103_IFNg


title: Line102_IGF


title: Line102_IFNg


title: v2.Line102_IGF


title: v2.Line102_BAFF


title: v3.Line102_ETOH


title: v2.Line102_WATER


title: v2.Line102_TUNIC


title: Line104_IFNg


title: v2.Line104_GARD


title: Line102_GARD


title: Line102_DEX


title: Line103_DEX


title: v3.Line102_GARD


title: v2.Line102_ETOH


title: Line103_BAFF


title: v2.Line102_DEX


title: v3.Line102_IFNg


title: v3.Line102_DEX


title: v3.Line102_WATER


title: Line102_TUNIC


title: v2.Line102_IFNg


title: v3.Line102_IGF


title: Line102_ETOH


title: Line102_BAFF


title: v2.Line102_GARD


title: Line101_DEX


title: Line101_GARD


title: Line101_TUNIC


title: Line101_WATER


title: Line101_IFNg


title: Line101_ETOH


title: Line101_IGF


title: Line10_DEX


title: Line10_ETOH


title: Line10_BAFF


title: Line10_WATER


title: Line10_TUNIC


title: Line10_FSL1


title: Line10_IFNg


title: Line10_GARD


title: Line102_WATER


title: Line1_WATER


title: Line1_ETOH


title: Line1_DEX


title: Line1_IFNg


title: Line1_GARD


title: Line1_BAFF


title: V114M

status: Public on Jun 28 2022

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

data_processing:
The paired-end sequencing was conducted on a HiSeq sequencer (Illumina, CA, USA) producing 34.6x2 M raw paired reads sample on average.
We used miARma-Seq pipeline to process the data and perform the analyses.
Raw data were evaluated using FastQC software to analyse the quality of the reads, and afterwards, sequences were aligned to the GRCh38 reference genome with STAR.
Principal component analysis (PCA) and hierarchical clustering of normalized samples were performed to check the similarity of RNA-sequencing samples.
Samples identified as outliers were filtered out from further analyses as well as duplicated samples and those presenting gender discrepancies.
Differential expression analyses were carried out with the edgeR package. Low expressed genes were removed (CPM< 1) and the remaining genes were normalized by the trimmed mean of M-values (TMM) method. Furthermore, we calculated reads per kilobase per million mapped reads (RPKM) and counts per million (CPM) and log2-counts per million (log-CPM) per gene on each sample
All genes with a FDR < 0.05 were statistically significant and designated as differentially expressed genes (DEGs).
To evaluate the contribution of potential confounders such as sex and age, we performed sensitivity analyses. We applied Pearson correlation or Wilcoxon signed-rank test depending on whether the variable of interest was continuous or categorical. Variables with a p-value < 0.05 were considered to significantly contribute to gene expression and were therefore included as covariates in the model.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

molecule: total RNA

source_name: Whole blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were first obtained from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). For subsequent CD14+ monocytes isolation, PBMCs were incubated with CD14-PE and CD15-FITC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes in the dark. Pure monocytes were next isolated by positive selection as CD14+CD15- cells using flow cytometry sorting and were pelleted and stored at -80ºC. Total RNA were extracted  the AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany), according to manufacturer's instructions. RNA were quantified with Nanodrop ND-2100 and Qubit® DNA assay kit (invitrogen). Furthermore, RNA quality was determined by the 2100 Bioanalyzer System (Agilent, CA, USA).
1 μg of excellent quality RNA (RNA integrity number >7) was subjected to the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol.

tag: tissue

value: Whole blood

value: CD14+ Monocytes

value: Monocytes

tag: classification

value: RNT

tag: Sex

value: F

tag: age

tag: sorter day


title: Line1_TUNIC


title: V111M

value: RT

value: M


title: V115M

value: HD


title: V110M


title: V109M


title: Line101_BAFF

value: Lymphoblastoid


title: V108M


title: V106M


title: V105M


title: Line1_FSL1


title: V104M


title: V113M


title: V98M


title: V97M


title: V112M


title: V103M

value: ACT


title: V92M


title: V96M


title: V107M


title: V101M


title: V90M


title: V102M


title: V100M


title: V99M


title: V91M


title: V94M


title: V89M


title: V85M


title: V93M


title: V83M


title: V81M


title: V88M


title: V86M


title: V80M


title: V79M


title: V84M


title: V77M


title: V76M


title: V87M


title: V75M


title: V74M


title: V72M


title: V71M


title: V66M


title: V67M


title: V82M


title: V70M


title: V59M


title: V69M


title: V68M


title: V57M


title: V65M


title: V55M


title: V53M


title: V64M


title: V56M


title: V60M


title: V78M


title: V51M


title: V49M


title: V48M


title: V61M


title: V54M


title: V62M


title: V58M


title: V52M


title: V50M


title: V73M


title: V47M


title: V46M


title: V44M


title: V42M


title: V41M


title: V35M


title: V37M


title: V39M


title: V40M


title: V38M


title: V34M


title: V25M


title: V22M


title: V29M


title: V26M


title: V24M


title: V31M


title: V20M


title: V28M


title: V32M


title: V33M


title: V27M


title: V17M


title: V19M


title: V23M


title: V18M


title: V21M


title: V43M


title: V45M


title: V16M


title: V14M


title: V30M


title: V12M


title: V9M


title: V11M


title: V7M


title: V8M


title: V13M


title: V2M


title: V6M


title: V5M


title: Mta2-DBTBLZ_CD4 replicate 2

status: Public on Jun 10 2022

city: Bethesda

first: Yayi

last: Gao

state: MD

address: 3016 Convert Drive

institute: National Cancer Institute

description:
Mature CD4 thymocyte from recipient mice transplanted with Mta2_DBTBLZ transduced bone marrow
Mta2-DBTBLZ_CD4_2

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: count of RNA reads were performed with Htseq; FPM normalization was performed with the FPM function of the DEseq2 package

organism: Mus musculus

source_name: Thymus

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina) were used for library.   Libraries were pooled and sequenced with paired-end reads of 75bp on a Nexseq to reach 70 million read pairs per sample

tag: strain

tag: cell population

tag: genotype

value: Cd4 Cre+Thpokfl/fl transduced with retrovirus expressing Mta2-DBTBLZ


title: V1M


title: Mta2-DBTBLZ_CD4 replicate 3

description:
Mature CD4 thymocyte from recipient mice transplanted with Mta2_DBTBLZ transduced bone marrow
Mta2-DBTBLZ_CD4_3


title: Mta2-DBTBLZ_CD4 replicate 1

description:
Mature CD4 thymocyte from recipient mice transplanted with Mta2_DBTBLZ transduced bone marrow
Mta2-DBTBLZ_CD4_1


title: V3M


title: V10M


title: Wound healing, lane 3

status: Public on May 28 2022

city: Houston

first: Kenneth

middle: H

last: Hu

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

description:
id,name,read,pattern,sequence,feature_type,condition
BC1,Barcode_1,R2,^(BC),GGAGAAGA,Antibody Capture,D1_2mm
BC2,Barcode_2,R2,^(BC),CCACAATG,Antibody Capture,D1_4mm
BC3,Barcode_3,R2,^(BC),TGAGACCT,Antibody Capture,D1_6mm
BC4,Barcode_4,R2,^(BC),GCACACGC,Antibody Capture,D1_8mm
BC5,Barcode_5,R2,^(BC),AGAGAGAG,Antibody Capture,D3_2mm
BC6,Barcode_6,R2,^(BC),TCACAGCA,Antibody Capture,D3_4mm
BC7,Barcode_7,R2,^(BC),GAAAAGGG,Antibody Capture,D3_6mm
BC8,Barcode_8,R2,^(BC),CGAGATTC,Antibody Capture,D3_8mm
BC9,Barcode_9,R2,^(BC),GTAGCACT,Antibody Capture,D7_2mm
BC10,Barcode_10,R2,^(BC),CGACCAGC,Antibody Capture,D7_4mm
BC11,Barcode_11,R2,^(BC),TTAGCCAG,Antibody Capture,D7_6mm
BC12,Barcode_12,R2,^(BC),GGACCCCA,Antibody Capture,D7_8mm
BC13,Barcode_13,R2,^(BC),CCAACCGG,Antibody Capture,D14_2mm
BC14,Barcode_14,R2,^(BC),TGACCGAT,Antibody Capture,D14_4mm
BC15,Barcode_15,R2,^(BC),GCAACGCC,Antibody Capture,D14_6mm
BC16,Barcode_16,R2,^(BC),CAATCGGT,Antibody Capture,D14_8mm
BC17,Barcode_17,R2,^(BC),ATAGCGTC,Antibody Capture,UW

library_source: transcriptomic single cell

data_processing:
CellRanger 4.0.0 for read counts
deMULTIplex package for R for cell demultiplexing
Seurat v3 package for R
Assembly: mm10-2020-a

source_name: Skin

extract_protocol:
At time of analysis, mice were euthanized, back skin was dissected from mice, excess scapular and inguinal fat was removed, and wounds plus adjacent tissue was excised using an 8 mm biopsy punch. An 8 mm biopsy punch was used to collect unwounded back skin as a day 0 or unwounded control. Four to six 8 mm biopsy punches were pooled from unwounded back skin to collect sufficient cells for downstream analysis. On ice, tissue was finely minced with scissors and then placed in a 2 ml tube containing 1 ml of digestion medium (2 mg/ml collagenase XI, 0.5 mg/ml hyaluronidase, 0.1 mg/ml DNase in RPMI with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 50 µM beta-mercaptoethanol). The tube was placed horizontally in a bacterial shaker for 45 min at 37ºC and 225 rpm. The sample was then filtered through a 100 µm filter and washed with 10 ml cold RPMI. The generated single cell suspension was then processed for further depending on analysis method.
The pool was then split over 5 lanes of a 10X 3’ NEXTGEM chip before encapsulation with a targeted cell number of 12,000 per lane.
Following the MULTI-Seq library construction protocol, additive primer was spiked in during the cDNA amplification step as described in McGinnis et al5, the supernatant was reserved following SPRI cleanup and separately amplified. Finally, libraries were pooled for sequencing using a 1:10 molar ratio of LMO : gene expression (GEX) libraries with approximately equal representation from each lane. Pooled samples were then sequenced using 1 lane of a S4 flowcell for a target of ~3B reads. GEX libraries had total read counts of (493M, 515M, 495M, 452M, 403M) for lanes (1,2,3,4,5) respectively, showing similar order of magnitude representation in read counts. The estimated sequencing saturation ranged from 58-64% (calculated via CellRanger), indicating sequencing depth did not vary appreciably between lanes. LMO libraries had total read counts of (37M, 39M, 38M, 36M, 32M) also showing stable representation from all 5 lanes.

treatment_protocol: All mice used for wounding experiments were between 7-10 weeks old (second telogen hair follicle phase). Two to four days before wounding, back skin was shaved and residual hair was removed using NAIR (Walgreens). On the day of wounding, mice were anesthetized with 3% isofluorane and subcutaneously injected with 50 µl of 0.25% bupivacaine and 50 µl of 50 µg/ml buprenorphine for analgesia. The back skin was then sterilized using a Betadine Solution swab stick (for scRNAseq and imaging experiments) or ChloraPrep (BD Biosciences) (for Mass Cytometry experiments to avoid iodine contamination during sample acquisition). Four full-thickness wounds were generated with a 4 mm biopsy punch. Wound diameter was measured with calipers.

value: Skin

value: primary cells

value: immune (CD45+) and non-immune cells (CD45-)

value: 4 mm punch biopsy for full thickness skin wound


title: Wound healing, lane 2


title: Wound healing, lane 4


title: Wound healing, lane 5


title: Wound healing, lane 1


title: Sympathoadrenal system E16.5 Wnt1-Cre [SS2_19_344]

status: Public on May 27 2022

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

description: corresponding raw files include SS2_19_344 in the filename

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to GRCm39 vM27 genome with ERCC annotations using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
Reads were filtered for only uniquely mapped and were saved in BAM file format; count matrices were subsequently produced using featureCounts.
BAM files from each plate were processed using python command-line velocity tool, using run-smartseq2 command with GENCODE M27 genome and repeat masker annotation files
count matrix was pre-processed using scanpy and scFates python packages, which includes normalization, clustering of cells, and projection on low embedding for visualization
Assembly: mm10
Supplementary files format and content: adata_raw.h5ad contains compiled count data from all plates, plate id is mentioned in cell name. files ending with 'loom' contains spliced and unspliced matrices generated by velocyto pipeline. Other files starting with 'adata' are anndata object at different steps of analysis.

source_name: Sympathoadrenal system

extract_protocol:
Isolated adrenal glands were transferred on a plate with HBSS and cut into small pieces using a clean scalpel. Dissociation was performed using 0,05% Trypsin/0,02% EDTA for 15 minutes at 37°C and triturated with P-1000 and P-200 pipettes tips until complete tissue dissociation. Following the addition of equal volume of 10% FBS, the tissue suspension was centrifugated at 500 g, 5 min, 4°C. Following three washes with 10% FBS the pellet was resuspended in 1xPBS. Cells were sorted using a BD FACSAria III cell sorter into 384-well-plates and stored at -80oC until sequencing took place according to a published protocol (Picelli, Bjorklund et al. 2013).
RNA libraries were prepared according to Smart-seq2 protocol.

value: Wnt1-Cre; R26-Tomato

tag: developmental stage

value: Sympathoadrenal system


title: Sympathoadrenal system E14.5 Wnt1-Cre [SS2_19_342]

description: corresponding raw files include SS2_19_342 in the filename


title: Sympathoadrenal system E16.5 Wnt1-Cre [SS2_19_348]

description: corresponding raw files include SS2_19_348 in the filename


title: Sympathoadrenal system E14.5 Wnt1-Cre [SS2_19_346]

description: corresponding raw files include SS2_19_346 in the filename


title: Sympathoadrenal system E13.5 Wnt1-Cre [SS2_16_250-2]

description: corresponding raw files include SS2_16_250-2 in the filename


title: Sympathoadrenal system E18.5 Wnt1-Cre [SS2_19_358]

description: corresponding raw files include SS2_19_358 in the filename


title: Sympathoadrenal system P2 Wnt1-Cre [SS2_19_360]

description: corresponding raw files include SS2_19_360 in the filename


title: Sympathoadrenal system E12.5 Wnt1-Cre [SS2_16_249-2]

description: corresponding raw files include SS2_16_249-2 in the filename


title: ci8CLC_r4

city: Guangzhou

first: Manqi

last: Chen

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-Sen University

data_processing:
Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC (release 0.11.9) whose results were parsed with MultiQC (release 1.9). Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore (release 0.6.5; default parameter). Trimmed read pairs were aligned to genome with STAR (release 2.7.4a) according to different aims. For alignment of gene, the following command-line arguments were used: --outSAMmultNmax 1 --outFilterMultimapNmax 10; for repeat locus, the arguments included: --outFilterMultimapNmax 1000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 1000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350. We computed the number of mapping reads unambiguously attributed to each gene using the featureCounts package (release 2.0.0; default parameter). Multiple mapped reads were only considered once to quantify expression of repeat locus.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene TPM values for each sample.
Supplementary_files_format_and_content: tab-delimited text files include gene raw counts for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes repeat raw counts generated by mapping reads to genome randomly for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes repeat raw counts generated by mapping reads to genome uniquely for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes repeat TPMs generated by mapping reads to genome randomly for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes repeat TPMs generated by mapping reads to genome uniquely for each sample.

source_name: Embryonic stem cells

growth_protocol: The prEpiSCs are cultured in the GIX medium which contains DMEM/F12 (Thermo Fisher Scientific, catalog. no. 21331020), Neurobasal medium (Thermo Fisher Scientific, catalog. no. 21103049), 2 mM L-glutamine (Thermo Fisher Scientific, catalog. no. 25030081), non-essential amino acids (Thermo Fisher Scientific, catalog. no. 11140050), 1% N2 supplement (Thermo Fisher Scientific, catalog. no. 17502048), 2% B27 supplement (Thermo Fisher Scientific, catalog. no. 12587010, minus vitamin A), 100 mg/ml Vitamin C (Sigma, catalog no. A4403), 50 ng/ml Bovine Albumin Fraction V (Thermo Scientific, cat. no. 15260-037), 20 ng/ml IL6 (PeproTech, catalog. no. AF-200-06), 20 ng/ml sIL-6R (PeproTech, catalog. no. 200-06R),5 ng/ml BMP4 (PeproTech, catalog. no. 120-05ET), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific, catalog. no. 21985023), 0.2 μM GSK112022 (Selleckchem, catalog. no. S2673), 2.5 μM XAV939 (Tocris, catalog. no. 3748), 1 μM Go6983 (Tocris, 2285) and Primocin (InvivoGen, catalog. no. ant-pm-2).To get ci8CLCs, Human prEpiSCs were cultured with the GIX medium plus the chemical cocktail (0.05 μM DZNep, 0.25 μM CBL0137, 0.5 μM AG14361, 1 μM GSK872, and 0.25 μM Ac-EVCD).The medium was changed every other day. The cells were treated with Accutase to dissociate into single cells, and then passaged onto new Matrigel- or feeder-coated plates every 3 - 4 days.

extract_protocol:
Total RNA was extracted from prEpiSCs and ci8CLCs using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: prEpiSCs are culturered in the GIX medium containing a chemical cocktail (0.05-0.1 μM GSK112022, 2.5 μM XAV939, 1 μM Go6983) without any other treatment. Ci8CLCs are cultured in the GIX mdium with the treatment of the chemical cocktail (0.05 μM DZNep, 0.25 μM CBL0137, 0.5 μM AG14361, 1 μM GSK872, and 0.25 μM Ac-EVCD)

value: Embryonic stem cells


title: ci8CLC_r3


title: ci8CLC_r2


title: ci8CLC_r1


title: Sympathoadrenal system P2 Wnt1-Cre [SS2_19_362]

description: corresponding raw files include SS2_19_362 in the filename


title: LEUTX-mCherry+


title: prEpiSC_r2


title: prEpiSC_r1


title: HK104, 30ºC, replicate 2

status: Public on May 22 2022

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

data_processing:
Raw reads were demultiplexed and had their 5' 4 nucleotide barcodes removed using a custom Perl script.
Cutadapt v1.2.1 was used to remove 3' adapters and discard reads that contained at least 14 nucleotides of the 5' adapter. Reads were discarded if, after adapter and barcode trimming, the read was longer than 30 nucleotides or shorter than 17 nucleotides.
FastQC v0.11.8 was used to identify one replicate (HK30-1) with an unusually low read count and a length distribution skewed heavily towards short 17-19 nucleotide reads, and so this replicate was excluded from our results.
Small RNAs were aligned to the C. briggsae genome (the reference genome for AF16 reads, and the reference genome with HK104 variants applied for HK104 reads) using the STAR v2.7.2a read alignment software with the following options: --quantMode GeneCounts --limitBAMsortRAM 30000000000 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1
Aligned small RNA reads from all samples were counted using a custom R pipeline. Mapped reads were counted only if they aligned to the genome (either sense or antisense) without any insertions, deletions, or mismatches, but allowing for gaps due to introns. The number of perfectly-aligned reads in each replicate were defined by their length, first nucleotide, the genomic feature they fully aligned to (microRNA genes, protein-coding genes, pseudogenes, transposable elements, repeat regions, rRNA genes, tRNA genes, other noncoding RNA genes, and unannotated regions), and whether they mapped sense or antisense to this feature.
Assembly: cb4
Supplementary files format and content: For each sample, Excel files give raw counts of small RNA reads aligning to each genomic feature, separated by length and first base of reads. Sheets are separated by feature type. "_AS" sheets indicate reads aligning antisense to features (all other sheets are sense alignments). Fractional counts are due to reads that align to multiple features being divided between those features.

organism: Caenorhabditis briggsae

source_name: whole animal

extract_protocol:
Total RNA from gravid adult hermaphrodites in mass isogenic cultures of each strain-temperature combination was isolated with TRIzol extraction and isopropanol precipitation.
Using the Ambion MirVana kit, we separated the small RNA fractions <200 bp and then isolated small RNAs between 18 and 30 nucleotides using gel extraction from 15% acrylamide gels. The samples were treated with tobacco acid pyrophosphatase to convert triphosphorylated RNA into a monophosphorylated form prior to ligating the 3' linker, followed  by 15% polyacrylamide/7M urea gel extraction. A 5' linker sequence, possessing one of nine 4 nucleotide barcodes at its 3' end, was ligated to the samples to enable multiplexing. This was followed by reverse-transcription cDNA synthesis, and PCR amplification, to add Illumina sequencing adapters with an additional 8 nucleotide indexing barcode on the 3' adapter.

value: whole animal

value: gravid adult

value: reared at 30 C


title: HK104, 30ºC, replicate 3


title: LEUTX-mCherry-


title: HK104, 20ºC, replicate 2

value: reared at 20 C


title: HK104, 20ºC, replicate 3


title: HK104, 30ºC, replicate 1


title: HK104, 20ºC, replicate 1


title: HK104, 14ºC, replicate 3

value: reared at 14 C


title: AF16, 30ºC, replicate 2


title: HK104, 14ºC, replicate 1


title: AF16, 30ºC, replicate 3


title: AF16, 14ºC, replicate 1


title: AF16, 20ºC, replicate 2


title: IL-4/IL-13+TNF L49148_M2_TNF_2_04_J17

status: Public on May 14 2022

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

source_name: Bone marrow

growth_protocol: In the presence of M-CSF

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

value: BMDM


title: AF16, 14ºC, replicate 3


title: AF16, 20ºC, replicate 1


title: AF16, 20ºC, replicate 3


title: HK104, 14ºC, replicate 2


title: IL-4/IL-13+TNF L49146_M2_TNF_2_04_J15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: AF16, 30ºC, replicate 1


title: AF16, 14ºC, replicate 2


title: IL-4/IL-13+TNF L49145_M2_TNF_2_04_J14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49147_M2_TNF_2_04_J16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49143_M2_TNF_2_04_J12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49144_M2_TNF_2_04_J13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49141_M2_TNF_2_04_J10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49139_M2_TNF_2_04_J08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49142_M2_TNF_2_04_J11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49149_M2_TNF_2_04_J18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49140_M2_TNF_2_04_J09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49137_M2_TNF_2_04_J06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49136_M2_TNF_2_04_J05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49138_M2_TNF_2_04_J07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49134_M2_TNF_2_04_J03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49133_M2_TNF_2_04_J02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49131_M2_TNF_2_04_I24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49132_M2_TNF_2_04_J01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49130_M2_TNF_2_04_I23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49129_M2_TNF_2_04_I22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49128_M2_TNF_2_04_I21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49126_M2_TNF_2_04_I19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49127_M2_TNF_2_04_I20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49125_M2_TNF_2_04_I18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49123_M2_TNF_2_04_I16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49124_M2_TNF_2_04_I17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49119_M2_TNF_2_04_I12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49121_M2_TNF_2_04_I14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49122_M2_TNF_2_04_I15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49120_M2_TNF_2_04_I13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49116_M2_TNF_2_04_I09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49118_M2_TNF_2_04_I11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49135_M2_TNF_2_04_J04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49117_M2_TNF_2_04_I10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49115_M2_TNF_2_04_I08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49112_M2_TNF_2_04_I05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49110_M2_TNF_2_04_I03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49109_M2_TNF_2_04_I02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49111_M2_TNF_2_04_I04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49113_M2_TNF_2_04_I06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49108_M2_TNF_2_04_I01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48914_M2_TNF_1_03_P23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48909_M2_TNF_1_03_P18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48913_M2_TNF_1_03_P22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48912_M2_TNF_1_03_P21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48911_M2_TNF_1_03_P20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48910_M2_TNF_1_03_P19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48908_M2_TNF_1_03_P17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48905_M2_TNF_1_03_P14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48906_M2_TNF_1_03_P15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48904_M2_TNF_1_03_P13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48903_M2_TNF_1_03_P12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48907_M2_TNF_1_03_P16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48901_M2_TNF_1_03_P10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48902_M2_TNF_1_03_P11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L49114_M2_TNF_2_04_I07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48899_M2_TNF_1_03_P08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48898_M2_TNF_1_03_P07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48896_M2_TNF_1_03_P05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48891_M2_TNF_1_03_O24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48895_M2_TNF_1_03_P04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48897_M2_TNF_1_03_P06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48915_M2_TNF_1_03_P24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48888_M2_TNF_1_03_O21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48889_M2_TNF_1_03_O22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48886_M2_TNF_1_03_O19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48885_M2_TNF_1_03_O18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48887_M2_TNF_1_03_O20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48880_M2_TNF_1_03_O13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48881_M2_TNF_1_03_O14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48883_M2_TNF_1_03_O16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48879_M2_TNF_1_03_O12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48878_M2_TNF_1_03_O11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48900_M2_TNF_1_03_P09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48877_M2_TNF_1_03_O10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48876_M2_TNF_1_03_O09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48875_M2_TNF_1_03_O08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48870_M2_TNF_1_03_O03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48873_M2_TNF_1_03_O06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48874_M2_TNF_1_03_O07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48869_M2_TNF_1_03_O02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48872_M2_TNF_1_03_O05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48871_M2_TNF_1_03_O04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48866_M2_TNF_1_03_N23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48863_M2_TNF_1_03_N20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48868_M2_TNF_1_03_O01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48864_M2_TNF_1_03_N21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48890_M2_TNF_1_03_O23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48867_M2_TNF_1_03_N24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48884_M2_TNF_1_03_O17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48861_M2_TNF_1_03_N18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48882_M2_TNF_1_03_O15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48858_M2_TNF_1_03_N15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48856_M2_TNF_1_03_N13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48857_M2_TNF_1_03_N14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48855_M2_TNF_1_03_N12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48854_M2_TNF_1_03_N11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48853_M2_TNF_1_03_N10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48852_M2_TNF_1_03_N09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48851_M2_TNF_1_03_N08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48850_M2_TNF_1_03_N07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48865_M2_TNF_1_03_N22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48862_M2_TNF_1_03_N19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48849_M2_TNF_1_03_N06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48843_M2_TNF_1_03_M24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48847_M2_TNF_1_03_N04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48860_M2_TNF_1_03_N17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48841_M2_TNF_1_03_M22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48838_M2_TNF_1_03_M19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48848_M2_TNF_1_03_N05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48846_M2_TNF_1_03_N03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48837_M2_TNF_1_03_M18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48840_M2_TNF_1_03_M21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48842_M2_TNF_1_03_M23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48835_M2_TNF_1_03_M16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48836_M2_TNF_1_03_M17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48845_M2_TNF_1_03_N02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48859_M2_TNF_1_03_N16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48839_M2_TNF_1_03_M20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48834_M2_TNF_1_03_M15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48832_M2_TNF_1_03_M13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48833_M2_TNF_1_03_M14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48829_M2_TNF_1_03_M10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48830_M2_TNF_1_03_M11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48827_M2_TNF_1_03_M08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48844_M2_TNF_1_03_N01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48826_M2_TNF_1_03_M07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: V4M

value: Whole blood

value: CD14+ Monocytes

value: Monocytes

value: RT

value: F


title: IL-4/IL-13+TNF L48822_M2_TNF_1_03_M03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48824_M2_TNF_1_03_M05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48825_M2_TNF_1_03_M06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48823_M2_TNF_1_03_M04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48821_M2_TNF_1_03_M02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48819_M2_TNF_1_03_L24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48820_M2_TNF_1_03_M01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48817_M2_TNF_1_03_L22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48816_M2_TNF_1_03_L21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48818_M2_TNF_1_03_L23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48812_M2_TNF_1_03_L17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48813_M2_TNF_1_03_L18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48814_M2_TNF_1_03_L19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48810_M2_TNF_1_03_L15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48809_M2_TNF_1_03_L14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48831_M2_TNF_1_03_M12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48808_M2_TNF_1_03_L13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48828_M2_TNF_1_03_M09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48811_M2_TNF_1_03_L16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48807_M2_TNF_1_03_L12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48806_M2_TNF_1_03_L11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48803_M2_TNF_1_03_L08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48800_M2_TNF_1_03_L05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48799_M2_TNF_1_03_L04

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48801_M2_TNF_1_03_L06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48797_M2_TNF_1_03_L02

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48815_M2_TNF_1_03_L20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48798_M2_TNF_1_03_L03

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48795_M2_TNF_1_03_K24

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48796_M2_TNF_1_03_L01

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48794_M2_TNF_1_03_K23

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48792_M2_TNF_1_03_K21

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48788_M2_TNF_1_03_K17

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48786_M2_TNF_1_03_K15

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48791_M2_TNF_1_03_K20

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48785_M2_TNF_1_03_K14

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48787_M2_TNF_1_03_K16

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48790_M2_TNF_1_03_K19

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48789_M2_TNF_1_03_K18

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48784_M2_TNF_1_03_K13

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48783_M2_TNF_1_03_K12

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48805_M2_TNF_1_03_L10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48802_M2_TNF_1_03_L07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48782_M2_TNF_1_03_K11

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48781_M2_TNF_1_03_K10

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48780_M2_TNF_1_03_K09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48804_M2_TNF_1_03_L09

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48776_M2_TNF_1_03_K05

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48777_M2_TNF_1_03_K06

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48793_M2_TNF_1_03_K22

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: nuoB/cyoB KO, ALE 4, replicate 2

status: Public on May 06 2022

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie version 1.1.2 with a maximum insert size of 1,000 and a maximum of two maximum mismatches after trimming 3 bp at the 3’ ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the deoxyuridine triphosphate (dUTP) protocol and strict intersection mode
We then estimated the dispersion of each gene using DESeq2
Transcripts per million were calculated by DESeq2.
Assembly: NC_000913.3
Supplementary files format and content: eep_log_tpm.csv contains TPM values for all samples

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Clonal population

growth_protocol: A clone from the endpoints of evolved strains was picked for DNA sequencing and RNA sequencing. The strains were grown in an M9 minimal medium supplemented with 4g/l glucose. Total DNA was sampled from an overnight grown culture and total RNA was sampled from a culture at an A600 ~0.6

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

value: nuoB/cyoB KO, ALE 4

value: Clonal population


title: nuoB/cyoB KO, ALE 4, replicate 1


title: nuoB/cyoB KO, ALE 3, replicate 2

value: nuoB/cyoB KO, ALE 3


title: nuoB/cyoB KO, ALE 3, replicate 1


title: nuoB/cyoB KO, ALE 2, replicate 1

value: nuoB/cyoB KO, ALE 2


title: nuoB/cyoB KO, ALE 2, replicate 2


title: nuoB/cyoB KO, replicate 2

value: nuoB/cyoB KO


title: nuoB/cyoB KO, ALE 1, replicate 1

value: nuoB/cyoB KO, ALE 1


title: nuoB/cyoB KO, replicate 1


title: IL-4/IL-13+TNF L48779_M2_TNF_1_03_K08

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: IL-4/IL-13+TNF L48778_M2_TNF_1_03_K07

description:
IL-4/IL-13+TNF
IL-4/IL-13+TNF


title: ndh/cyoB KO, ALE 3, replicate 2

value: ndh/cyoB KO, ALE 3


title: ndh/cyoB KO, ALE 4, replicate 1

value: ndh/cyoB KO, ALE 4


title: ndh/cyoB KO, ALE 4, replicate 2


title: ndh/cyoB KO, ALE 1, replicate 2

value: ndh/cyoB KO, ALE 1


title: ndh/cyoB KO, ALE 1, replicate 1


title: ndh/cyoB KO, replicate 2

value: ndh/cyoB KO


title: ndh/cyoB KO, replicate 1


title: nuoB/cydB/appC KO, ALE 4, replicate 1

description: eep__BOP27_nuoB_cydB-appC_A16_F57_I1_R1__1

value: nuoB/cydB/appC KO, ALE 4


title: ndh/cyoB KO, ALE 2, replicate 1

value: ndh/cyoB KO, ALE 2


title: nuoB/cydB/appC KO, ALE 3, replicate 2

description: eep__BOP27_nuoB_cydB-appC_A15_F57_I1_R1__2

value: nuoB/cydB/appC KO, ALE 3


title: ndh/cyoB KO, ALE 3, replicate 1


title: nuoB/cydB/appC KO, ALE 3, replicate 1

description: eep__BOP27_nuoB_cydB-appC_A15_F57_I1_R1__1


title: nuoB/cydB/appC KO, ALE 4, replicate 2

description: eep__BOP27_nuoB_cydB-appC_A16_F57_I1_R1__2


title: nuoB/cydB/appC KO, ALE 2, replicate 2

description: eep__BOP27_nuoB_cydB-appC_A14_F58_I1_R1__2

value: nuoB/cydB/appC KO, ALE 2


title: nuoB/cydB/appC KO, ALE 1, replicate 2

description: eep__BOP27_nuoB_cydB-appC_A13_F59_I1_R1__2

value: nuoB/cydB/appC KO, ALE 1


title: nuoB/cydB/appC KO, ALE 1, replicate 1

description: eep__BOP27_nuoB_cydB-appC_A13_F59_I1_R1__1


title: nuoB/cyoB KO, ALE 1, replicate 2


title: nuoB/cydB/appC KO, replicate 2

value: nuoB/cydB/appC KO


title: ndh/cydB/appC KO, ALE 4, replicate 2

description: eep__BOP27_ndh-cydB-appC_A12_F46_I1_R1__2

value: ndh/cydB/appC KO, ALE 4


title: nuoB/cydB/appC KO, replicate 1


title: ndh/cydB/appC KO, ALE 3, replicate 2

description: eep__BOP27_ndh-cydB-appC_A11_F46_I1_R1__2

value: ndh/cydB/appC KO, ALE 3


title: ndh/cydB/appC KO, ALE 4, replicate 1

description: eep__BOP27_ndh-cydB-appC_A12_F46_I1_R1__1

value: Clonal population


title: ndh/cydB/appC KO, ALE 2, replicate 2

description: eep__BOP27_ndh-cydB-appC_A10_F48_I1_R1__2

value: ndh/cydB/appC KO, ALE 2


title: ndh/cydB/appC KO, ALE 3, replicate 1

description: eep__BOP27_ndh-cydB-appC_A11_F46_I1_R1__1


title: ndh/cydB/appC KO, ALE 2, replicate 1

description: eep__BOP27_ndh-cydB-appC_A10_F48_I1_R1__1


title: ndh/cydB/appC KO, ALE 1, replicate 2

description: eep__BOP27_ndh-cydB-appC_A9_F46_I1_R1__2

value: ndh/cydB/appC KO, ALE 1


title: ndh/cyoB KO, ALE 2, replicate 2


title: ndh/cydB/appC KO, ALE 1, replicate 1

description: eep__BOP27_ndh-cydB-appC_A9_F46_I1_R1__1


title: ndh/cydB/appC KO, replicate 2

value: ndh/cydB/appC KO


title: ndh/cydB/appC KO, replicate 1


title: Endometriosis Patient 17 - Eutopic - bulk

status: Public on May 05 2022

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files for all samples were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics GRCh38 reference build (version 3.0.0, GRCh38.93) using 10X Genomics CellRanger count version 3.1.0 for all samples.
A digital counts matrix was generated for each single cell hashtag library using CITE-Seq-Count (https://github.com/Hoohm/CITE-seq-Count), version 1.4.5. This produces a matrix of counts with hashtag labels for rows (available via BioLegend TotalSeq-A antihuman HashTags https://www.biolegend.com/totalseq) and cell barcodes for columns.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
For all bulk RNA-seq samples, data was aligned to the same 10X Genomics GRCh38.93 human reference using nf-core/rnaseq v1.4.2 with the STAR aligner using Nextflow 20.07.1 (build 5412).
In order to further safeguard patients' genomic identities, SNVs relative to the reference genome are masked in all bam files (BAMboozle v0.5.0).
Assembly: GRCh38.93
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market CSR format.  Rows correspond to genes in the order provided in genes.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

growth_protocol: Organoid libraries (EOR01/EOR03) were grown from remaining single cells suspension from tissue dissociation, in 100% Matrigel dome,with expansion media described in Boretto et al. (2019).

extract_protocol:
Single cells were collected through cold active protease dissociation protocol, viable cell sorting strategy. 12,000 single cells were loaded into one lane of a 10X Genomics Chromium controller, targetted 6,000 barcoded single cells. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version 3 chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000 (either an S2 or S4 flow cell) targetting 100,000 raw read pairs per cell.  For Cell Hashing libraries, cells from each input sample were labeled with BioLegend TotalSeq-A anti-human hashtags prior to loading onto the 10X Genomics Chromium system and were sequenced by pooling the gene expression and hashtag libraries at a 20:1 ratio before sequencing on an Illumina NovaSeq 6000, targetting 100k read pairs per cell. For Bulk libraries, fresh tissue were either preserved in RNA Later or flash frozen before extraction. Frozen tissues were submitted to the Genome Technologies core service at the Jackson Laboratory for RNA extraction, and sequenced on NovaSeq6000 (Illumina) with SP 100 cycles single-end reads kit resulting in, on average, 42.7 million reads per sample.
10X Genomics Chromium v3 chemistry
3' single cell RNA-seq

treatment_protocol: Endometriosis patients receiving oral contraceptive treatment were subject to this study.  Endometrial, peroteonial, ovarian tissue were collected immediately upon surgerical ressection.

tag: condition

value: Endometriosis

tag: sample location

value: Eutopic

value: Endometrium

tag: method

value: RNA-seq

tag: library type

value: Gene Expression


title: Endometriosis Patient 16 - Eutopic - bulk


title: Endometriosis Patient 17 - Ectopic - bulk

value: Ectopic

value: Peritoneum


title: nuoB/cydB/appC KO, ALE 2, replicate 1

description: eep__BOP27_nuoB_cydB-appC_A14_F58_I1_R1__1


title: Endometriosis Patient 14 - Ectopic - bulk


title: Endometriosis Patient 16 - Ectopic Ovary - bulk

value: Ectopic Ovary

value: Ovary


title: Endometriosis Patient 14 - Ectopic Ovary - bulk


title: Endometriosis Patient 13 - Eutopic - bulk


title: Endometriosis Patient 17 - Ectopic Ovary - bulk


title: Endometriosis Patient 15 - Eutopic - bulk


title: Endometriosis Patient 13 - Ectopic - bulk


title: Endometriosis Patient 13 - Ectopic Ovary - bulk


title: Endometriosis Patient 10 - Ectopic - bulk


title: Endometriosis Patient 7 - Ectopic Ovary - bulk


title: Control Patient 5 - Control Endometrium - bulk

value: Control


title: Cell Hashing for EOR03

description: Cell Hashing for EOR03

value: Endometriosis + Control

value: Mix

value: Patient-Derived Organoid

value: scRNA-seq

value: Cell Hashing


title: Endometriosis Patient 7 - Eutopic - bulk


title: Endometriosis Patient 9 - Eutopic - bulk


title: Endometriosis Patient 10 - Ectopic Ovary - bulk


title: Control Patient 4 - Control Endometrium - bulk


title: Cell Hashing for EOR01

description: Cell Hashing for EOR01


title: Patient-Derived Organoid - E02/E03/E10

description: Patient-Derived Organoid - E02/E03/E10


title: Control Patient 7 - Control Endometrium - bulk


title: Patient-Derived Organoid - E05/E07/C01/C02


title: Endometriosis Patient 16 - Ectopic - bulk


title: Endometriosis Patient 9 - Ectopic Ovary

description: Endometriosis Patient 9 - Ectopic Ovary


title: Endometriosis Patient 9 - Eutopic

description: Endometriosis Patient 9 - Eutopic


title: Endometriosis Patient 8 - Eutopic

description: Endometriosis Patient 8 - Eutopic


title: Endometriosis Patient 7 - Eutopic

description: Endometriosis Patient 7 - Eutopic


title: Endometriosis Patient 5 - Eutopic

description: Endometriosis Patient 5 - Eutopic


title: Endometriosis Patient 7 - Ectopic

description: Endometriosis Patient 7 - Ectopic


title: Endometriosis Patient 6 - Eutopic

description: Endometriosis Patient 6 - Eutopic


title: Control Patient 1 - Control Endometrium - bulk


title: Endometriosis Patient 3 - Eutopic

description: Endometriosis Patient 3 - Eutopic


title: Endometriosis Patient 7 - Ectopic Ovary

description: Endometriosis Patient 7 - Ectopic Ovary


title: Endometriosis Patient 4 - Eutopic

description: Endometriosis Patient 4 - Eutopic


title: Endometriosis Patient 6 - Ectopic

description: Endometriosis Patient 6 - Ectopic


title: Endometriosis Patient 2 - Eutopic

description: Endometriosis Patient 2 - Eutopic


title: Endometriosis Patient 3 - Eutopic - bulk


title: Control Patient 6 - Control Endometrium - bulk


title: Endometriosis Patient 1 - Eutopic

description: Endometriosis Patient 1 - Eutopic


title: Control Patient 3 - Control Endometrium

description: Control Patient 3 - Control Endometrium


title: Control Patient 2 - Control Endometrium

description: Control Patient 2 - Control Endometrium


title: Control Patient 1 - Control Endometrium

description: Control Patient 1 - Control Endometrium


title: Endometriosis Patient 11 - Ectopic Ovary


title: Maternal-Zygotic wnt11b mutant stage 9 rep1

status: Public on May 02 2022

city: Iowa City

first: Douglas

middle: William

last: Houston

state: IA

department: Dept. of Biology

institute: The University of Iowa

description:
Sample 1
DH1_lane1_20210827000_S1

data_processing:
Base calls and quality scores were generated by NovaSeq System Software; *.cbcl files were converted to FASTQ using bcl2fastq2.
Reads were processed using the CSBB-v3.0 "Process-RNASeq_PairedEnd" module (https://github.com/csbbcompbio/CSBB-v3.0); after fastqc reads were aligned using RSEM v1.3.0 and bowtie2.
bedtools was used to generate and sort .bedgraph files. These were converted to bigwig files using bedGraphToBigWig.
Count matrices were generated using the CSBB-v3.0 TPM_COUNT_Matrix_CSBB.pl script
Genome_build: Xenopus laevis v9.2
Supplementary_files_format_and_content: Matrix of raw counts per sample (.txt) and bigwig files of each sample (.bw)

organism: Xenopus laevis

source_name: stage 9 embryo

growth_protocol: Embryos were raised to the desired stages and then frozen in groups of three embryos per replicate in dry ice.

extract_protocol:
Samples were lysed in RNA lysis buffer containing proteinase K, phenol extracted, isopropanol precipitated and DNAse treated.
RNA libraries were made using the Illumina Stranded mRNA Prep, Ligation kit (catalog #20040532) and  IDT for Illumina RNA UD Indexes Set A (catalog #20040553). Following KAPA qPCR, samples were run in one lane of a NovaSeq 6000 SP flow cell, 2x100 paried end reads.

tag: Stage

value: Nieuwkoop and Faber stage 9

value: embryo

value: Maternal-Zygotic wnt11b mutant


title: Maternal-Zygotic wnt11b mutant stage 9 rep2

description:
Sample 2
DH2_lane1_20210827000_S2


title: Maternal Wildtype Heterozygous stage 10.5 rep 1

description:
Sample 7
DH7_lane1_20210827000_S7

source_name: stage 10.5 embryo

value: Nieuwkoop and Faber stage 10.5

value: Maternal Wildtype Heterozygous


title: Maternal Wildtype Heterozygous stage 9 rep 1

description:
Sample 3
DH3_lane1_20210827000_S3


title: Maternal-Zygotic wnt11b mutant stage 10.5 rep2

description:
Sample 6
DH6_lane1_20210827000_S6


title: Maternal Wildtype Heterozygous stage 9 rep 2

description:
Sample 4
DH4_lane1_20210827000_S4


title: Maternal-Zygotic wnt11b mutant stage 10.5 rep1

description:
Sample 5
DH5_lane1_20210827000_S5


title: Maternal Wildtype Heterozygous stage 10.5 rep 2

description:
Sample 8
DH8_lane1_20210827000_S8


title: Enza_II_TU_140 [19_TU_140_S22_L002]

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

description: sequencing was done in 2 lanes

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
XenofilteR (v.1.5) was used to filter out mouse reads (mm10 as a reference genome) from the xenograft samples.
Genome_build: Human GRCh38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

growth_protocol: Athymic Nude male mice at approximately 4-6 weeks of age were inoculated (VCaP cells) at the study week 0, castrated at the study week 5, allocated to study groups (Enza I and Enza II) and started dosing enzalutamide at the study week 9, and sacrificed at stydy  week 10 (Enza I) and 16 (Enza II) .

extract_protocol:
Total RNA for RNA-seq were extracted from tumor samples using TRIsure (Invitrogen, Carlsbad, CA, USA), and purified using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
Library preparation was done according to Illumina TruSeq® Stranded mRNA kit protocol.

treatment_protocol: At the end of the experiment the mice were sacrificed, and subcutaneous tumors were collected for RNA isolation. Tissue samples were stored at -80 oC after initial freezing in liquid nitrogen.

tag: disease

value: prostate cancer

tag: xenograft

value: subcutaneous

value: VCaP castration-resistant prostate cancer (CRPC)

value: Long term effect of antiandrogen in tumor


title: Enza_I_TU_16 [41_TU_16_S47_L003]

description: sequencing was done in 2 lanes

tag: cell line

tag: treatment

value: Short term effect of antiandrogen in tumor


title: Enza_II_TU_19 [45_TU_19_S49_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_141 [20_TU_141_S24_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_140 [19_TU_140_S22_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_135 [18_TU_135_S21_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_16 [41_TU_16_S47_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_113 [43_TU_113_S48_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_135 [18_TU_135_S21_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_131 [17_TU_131_S20_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_131 [17_TU_131_S20_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_141 [20_TU_141_S24_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_120 [16_TU_120_S19_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_120 [16_TU_120_S19_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_19 [45_TU_19_S49_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_117 [15_TU_117_S18_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_117 [15_TU_117_S18_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_115 [14_TU_115_S17_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_115 [14_TU_115_S17_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_114 [13_TU_114_S16_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_113 [43_TU_113_S48_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_114 [13_TU_114_S16_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_78 [9_TU_78_S53_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_75 [8_TU_75_S52_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_86 [10_TU_86_S15_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_73 [7_TU_73_S51_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_78 [9_TU_78_S53_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_75 [8_TU_75_S52_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_86 [10_TU_86_S15_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_73 [7_TU_73_S51_L002]

description: sequencing was done in 2 lanes


title: Enza_II_TU_55 [4_TU_55_S45_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_63 [6_TU_63_S50_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_63 [6_TU_63_S50_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_15 [1_TU_15_S14_L002]

description: sequencing was done in 2 lanes


title: Tumor,  CD11b+Gr1+

status: Public on Apr 30 2022

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

data_processing:
Data was processed with cellranger pipeline, version 2.0.2
Assembly: mm10 for mouse samples, GRCh38 for human samples
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Ter119+CD71+ splenic cells from anemic mice (A-EPCs), splenic CD45+Ter119+CD71+CD11b-C-kit- cells (T-EPCs), and intratumoral CD45+Ter119+CD71+CD11b+Gr1+ (EDMCs) and CD11b+Gr-1+ (MDSCs) from mice bearing late-stage tumors were sorted by FACS. For patient samples, CD235a+ bone marrow cells from bone-metastasis-free patients with advanced tumors, or CD45+CD235a+CD71+ cells from MPE were sorted by FACS, as indicated. Single cells were suspendend in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA,then the cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller
RNA Libraries were constructed using a Chromium Single Cell 3’ v1 Chemistry kit (10x Genomics) according to the manufacturer’s protocol

tag: tissue

value: Tumor

tag: cell subtype

value: tumor-bearing

tag: cell type

value: MDSCs


title: Enza_II_TU_45 [3_TU_45_S34_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_31 [2_TU_31_S23_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_55 [4_TU_55_S45_L003]

description: sequencing was done in 2 lanes


title: Enza_II_TU_45 [3_TU_45_S34_L002]

description: sequencing was done in 2 lanes


title: Enza_I_TU_15 [1_TU_15_S14_L003]

description: sequencing was done in 2 lanes


title: Enza_I_TU_31 [2_TU_31_S23_L002]

description: sequencing was done in 2 lanes


title: Tumor,  CD45+Ter119+CD71+CD11b+Gr1+

value: EDMCs


title: Spleen, CD45+Ter119+CD71+CD11b-C-kit- 1

source_name: Spleen

value: Spleen


title: Spleen, CD45+Ter119+CD71+CD11b-C-kit- 2


title: BioTAP-Pcl_Input

status: Public on Apr 29 2022

city: Boston

first: Mitzi

last: Kuroda

state: Massachusetts (MA)

address: 77 Ave Louis Pasteur NRB 168

department: Division of Genetics

institute: Brigham and Women’s Hospital

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.36, and quality filtered using FASTX-Tools v0.0.13, removing reads with quality score ≤ 20
ChIP-seq reads were aligned to the UCSC dm3 genome using Bowtie version 1.2.2.
For ChIP-seq log2 ChIP/Input ratio plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, normalized to reads per kilobase per million (RPKM) and reformatted in the bigWig file format using deepTools v3.0.2.
Peaks were called uing MACS v2.1.1 with significance cut-off q-value <=0.05
bigWig files were generated using deepTools. narrowPeak files were generated using MACS v2 using default settings.
Assembly: dm3
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 12-24 hour embryos

extract_protocol:
Embryos expressing BioTAP tagged proteins were homogenized in nuclear extraction buffer including 3% formaldehyde and fixed for 30 minutes. After several washes with PBS, sucrose buffer and glyerol buffer, chromatin was sonicated with Misonix sonicator (power 30%, 3 min 30sec, on time:15 sec, off time:45 sec). Then, tandem affinity purfication were performed by IgG agarose beads, followed by Streptavidin beads.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit and NEBNext Multiplex Oligos for Illumina. End repair, dA-Tailing, and adaptor ligation steps were performed to IP and input DNA. Adaptor ligated DNA was size selected at 250-500 bp in length using 2% SeaPlague GTG agarose  gel (Lonza). Libraries were amplified using 10-12 cycles on the thermocycler and validated using TapeStation or Bioanalyzer.

value: 12-24 hour embryos


title: BioTAP-Pcl_IP B

tag: antibody

value: BioTAP-Pcl


title: BioTAP-Pcl_IP A


title: BioTAP-Jarid2_Input


title: Spleen, Ter119+CD71+

value: tumor-free

value: A-EPCs


title: BioTAP-Jarid2_IP A


title: BioTAP-Jarid2_IP B


title: Intestinal stem cell with OKSM & senolytic overexpression Rep 3

status: Public on Apr 24 2022

city: Singapore

first: Nicholas

last: Tolwinski

address: 16 #01-220, College Ave West

country: Singapore

institute: Yale-NUS College

data_processing:
The raw fastq files were aligned to the dm6 genome (Ensembl v97) using STAR v2.7.1a
The reads were then quantified using RSEM v1.3.1
Assembly: dm6
Supplementary files format and content: genes.results were generated using RSEM v1.3.1 and includes the quantified reads for each sample

source_name: Intestinal Stem Cell

growth_protocol: Drosophila were maintained at standard humidity and temperature (25⁰C) with food containing 6g Bacto agar, 114g glucose, 56g cornmeal, 25g Brewer’s yeast and 20ml of 10% Nipagin in 1L final volume.

extract_protocol:
Adult fly midguts were dissected in 200 µl of 1x PBS in a PYREX™ Spot Plates concave glass dish (FisherScientific). The midguts were rinsed with PBS and stained with 10mg/ml Hoechst 33342 diluted 200 times in 1X PBS for 1min. Subsequently, the guts were carefully transferred onto a small droplet of 1x PBS on a 35mm glass bottom dish. Using fine forceps, the gut was repositioned to resemble its natural orientation. PBS was then removed from the area surrounding the gut, leaving a small amount of excess PBS to hold the gut in place and prevent desiccation. The 3mm glass bottom dish was then mounted onto the Zeiss LSM800 (Carl Zeiss AG, Germany) for imaging. For each construct, midguts from at least 3 flies were dissected and imaged at the 25% percentile from the anterior midgut.
The extracted RNA was quantified using Nanodrop (Thermo Fisher Scientific). Library preparation was performed using 1µg of total RNA and sequencing was performed using Illumina HiSeq 4000 System (2 × 151 bp read length, 40 million reads per sample) by NovogeneAIT Genomics (Singapore).

treatment_protocol: Transgenic flies were maintained under a white light lamp at all times.

value: intestinal stem cells


title: 9973569 Non 4-year follow-up

status: Public on Mar 31 2022

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags are extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 is performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads are collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample are generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference is performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1 combined excel spreadsheet (.xlsx) with two tabs having raw miRNA count values, one with baseline samples and other for 4-year follow-up samples.

source_name: plasma

growth_protocol: No growth

extract_protocol:
RNA is extracted from 200 µL of human plasma using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204).
miRNA libraries are prepared using QIAseq miRNA Library Kit optimized for biofluid samples (QIAseq miRNA, Cat # 331505). Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are multiplexed and sequenced on Illumina NextSeq550 to generate 75bp SE UMI-tagged reads.

treatment_protocol: No treatment

tag: progressor

value: Non

tag: time point

value: 4-year follow-up


title: 9950320 Non 4-year follow-up


title: 9990355 Non 4-year follow-up


title: 9999365 Slow 4-year follow-up

value: Slow


title: Intestinal stem cell with senolytic overepxression Rep 3

tag: genotype

value: Senolytic


title: 9913590 Non 4-year follow-up


title: 9905276 Slow 4-year follow-up


title: Endometriosis Patient 5 - Ectopic - bulk

value: Endometriosis

value: Ectopic

value: Peritoneum

value: RNA-seq

value: Gene Expression


title: 9844581 Slow 4-year follow-up


title: 9847829 Fast 4-year follow-up

value: Fast


title: 9898582 Non 4-year follow-up


title: 9850328 Non 4-year follow-up


title: 9904667 Non 4-year follow-up


title: 9867611 Non 4-year follow-up


title: 9747255 Slow 4-year follow-up


title: 9699399 Non 4-year follow-up


title: 9825304 Non 4-year follow-up


title: 9805234 Non 4-year follow-up


title: 9670760 Non 4-year follow-up


title: 9706954 Non 4-year follow-up


title: 9829221 Slow 4-year follow-up


title: 9842836 Non 4-year follow-up


title: 9752000 Non 4-year follow-up


title: 9806950 Slow 4-year follow-up


title: 9664670 Non 4-year follow-up


title: 9738052 Non 4-year follow-up


title: 9923837 Slow 4-year follow-up


title: 9658152 Fast 4-year follow-up


title: 9650705 Fast 4-year follow-up


title: 9636409 Non 4-year follow-up


title: 9631230 Slow 4-year follow-up


title: 9624154 Fast 4-year follow-up


title: 9629713 Non 4-year follow-up


title: 9623707 Slow 4-year follow-up


title: 9895022 Slow 4-year follow-up


title: 9609732 Fast 4-year follow-up


title: 9612143 Non 4-year follow-up


title: 9568130 Non 4-year follow-up


title: 9502938 Fast 4-year follow-up


title: 9590699 Non 4-year follow-up


title: 9509294 Slow 4-year follow-up


title: 9502727 Slow 4-year follow-up


title: 9445104 Slow 4-year follow-up


title: 9500884 Non 4-year follow-up


title: 9473335 Slow 4-year follow-up


title: 9454100 Non 4-year follow-up


title: 9486748 Slow 4-year follow-up


title: 9494408 Non 4-year follow-up


title: 9443223 Fast 4-year follow-up


title: 9476561 Slow 4-year follow-up


title: 9543020 Fast 4-year follow-up


title: 9423086 Fast 4-year follow-up


title: 9436383 Non 4-year follow-up


title: 9449511 Non 4-year follow-up


title: 9572192 Non 4-year follow-up


title: 9432148 Fast 4-year follow-up


title: 9422008 Slow 4-year follow-up


title: 9453107 Non 4-year follow-up


title: 9409198 Non 4-year follow-up


title: 9406033 Slow 4-year follow-up


title: 9413676 Non 4-year follow-up


title: 9416063 Non 4-year follow-up


title: 9400725 Non 4-year follow-up


title: 9402055 Slow 4-year follow-up


title: 9568618 Non 4-year follow-up


title: 9466897 Non 4-year follow-up


title: 9373786 Slow 4-year follow-up


title: 9378288 Slow 4-year follow-up


title: 9340468 Non 4-year follow-up


title: 9328376 Non 4-year follow-up


title: 9378093 Non 4-year follow-up


title: 9319366 Non 4-year follow-up


title: 9357301 Slow 4-year follow-up


title: 9305065 Slow 4-year follow-up


title: 9254920 Non 4-year follow-up


title: 9222973 Non 4-year follow-up


title: 9258864 Fast 4-year follow-up


title: 9095839 Non 4-year follow-up


title: 9166930 Non 4-year follow-up


title: 9255535 Fast 4-year follow-up


title: 9104620 Slow 4-year follow-up


title: 9282203 Fast 4-year follow-up


title: 9252629 Slow 4-year follow-up


title: 9477362 Non 4-year follow-up


title: 9189553 Slow 4-year follow-up


title: 9153255 Fast 4-year follow-up


title: 9216735 Slow 4-year follow-up


title: 9175275 Non 4-year follow-up


title: 9132486 Non 4-year follow-up


title: 9385984 Fast 4-year follow-up


title: 9387992 Non 4-year follow-up


title: 9362264 Slow 4-year follow-up


title: 9084244 Fast 4-year follow-up


title: 9124024 Non 4-year follow-up


title: 9268052 Slow 4-year follow-up


title: 9081858 Fast 4-year follow-up


title: 9055361 Fast 4-year follow-up


title: 9011949 Non 4-year follow-up


title: 9029791 Slow 4-year follow-up


title: 9088175 Non 4-year follow-up


title: 9895022 Slow baseline

value: baseline


title: 9847829 Fast baseline


title: 9006140 Non 4-year follow-up


title: 9904667 Non baseline


title: 9829221 Slow baseline


title: 9844581 Slow baseline


title: 9842836 Non baseline


title: 9081799 Slow 4-year follow-up


title: 9135902 Fast 4-year follow-up


title: 9867611 Non baseline


title: 9086407 Fast 4-year follow-up


title: 9805234 Non baseline


title: 9825304 Non baseline


title: 9664670 Non baseline


title: 9636409 Non baseline


title: 9631230 Slow baseline


title: 9699399 Non baseline


title: 9629713 Non baseline


title: 9747255 Slow baseline


title: 9806950 Slow baseline


title: 9898582 Non baseline


title: 9706954 Non baseline


title: 9670760 Non baseline


title: 9623707 Slow baseline


title: 9614515 Slow baseline


title: 9738052 Non baseline


title: 9609732 Fast baseline


title: 9658152 Fast baseline


title: 9572192 Non baseline


title: 9624154 Fast baseline


title: 9612143 Non baseline


title: 9650705 Fast baseline


title: 9543020 Fast baseline


title: 9752000 Non baseline


title: 9502938 Fast baseline


title: 9500884 Non baseline


title: 9486748 Slow baseline


title: 9466897 Non baseline


title: 9568618 Non baseline


title: 9502727 Slow baseline


title: 9477362 Non baseline


title: 9432148 Fast baseline


title: 9453107 Non baseline


title: 9423086 Fast baseline


title: 9476561 Slow baseline


title: 9443223 Fast baseline


title: 9445104 Slow baseline


title: 9422008 Slow baseline


title: 9406033 Slow baseline


title: 9402055 Slow baseline


title: 9590699 Non baseline


title: 9387992 Non baseline


title: 9509294 Slow baseline


title: 9400725 Non baseline


title: 9373786 Slow baseline


title: 9378093 Non baseline


title: 9416063 Non baseline


title: 9357301 Slow baseline


title: 9328376 Non baseline


title: 9305065 Slow baseline


title: 9282203 Fast baseline


title: 9255535 Fast baseline


title: 9258864 Fast baseline


title: 9449511 Non baseline


title: 9254920 Non baseline


title: 9378288 Slow baseline


title: 9222973 Non baseline


title: 9252629 Slow baseline


title: 9385984 Fast baseline


title: 9268052 Slow baseline


title: 9880717 Non baseline


title: 9494408 Non baseline


title: 9216735 Slow baseline


title: 9850328 Non baseline


title: 9473335 Slow baseline


title: 9436383 Non baseline


title: 9568130 Non baseline


title: 9454100 Non baseline


title: 9409198 Non baseline


title: 9340468 Non baseline


title: 9189553 Slow baseline


title: 9362264 Slow baseline


title: 9104620 Slow baseline


title: 9413676 Non baseline


title: 9166930 Non baseline


title: 9088175 Non baseline


title: 9095839 Non baseline


title: 9175275 Non baseline


title: 9153255 Fast baseline


title: 9135902 Fast baseline


title: 9172013 Non baseline


title: 9132486 Non baseline


title: 9319366 Non baseline


title: 9081799 Slow baseline


title: 9435600 Non baseline


title: 9055361 Fast baseline


title: 9084244 Fast baseline


title: 9086407 Fast baseline


title: 9950320 Non baseline


title: 9990355 Non baseline


title: 9923837 Slow baseline


title: 9124024 Non baseline


title: 9913590 Non baseline


title: 9905276 Slow baseline


title: 9006140 Non baseline


title: 9011949 Non baseline


title: 2007_C1D1

status: Public on Mar 11 2022

city: Amsterdam

first: Hanneke

last: van Laarhoven

address: Meibergdreef 9

department: Medical Oncology

country: Netherlands

institute: Amsterdam UMC, AMC

data_processing:
The samples were sequenced on an Illumina HiSeq4000 with a single read consisting of 50bp and 100.000.000 reads per sample.
Data went through quality control using FastQC.
RNAseq reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1, and annotated with Gencode v32.
Count files were converted into DESeq_vst values using DESeq2 in R Bioconductor.
DESeq libraries were used for differential expression analysis using the normalized counts in the R2 genome analysis and visualization platform (http://r2.amc.nl).
Assembly: (NCBI37/hg19)
Supplementary files format and content: Table with gene counts for every gene and every sample
Supplementary files format and content: .txt vst file

source_name: Endoscopic tumor biopsy metastatic lesion

extract_protocol:
Fresh-frozen biopsies from metastatic lesions were obtained in the dose-expansion cohort on day 1 and day 15 of cycle 1. RNA was isolated using the RNeasy Mini Kit (QIAgen AllPrep DNA/RNA/miRNA) following the manufacturer’s protocol.
RNA expression analyses were performed by RNA sequencing on an Illumina HiSeq 4000, with a single read consisting of 50 bp and 100 million reads per sample. Data were quality-controlled using FastQC. Reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1 and annotated with Gencode v32

treatment_protocol: Patients received paclitaxel (80 mg/m2) on days 1, 8, and 15 of a 28-day cycle and regorafenib 120mg on day 1-21 in the dose-escalation cohort. In the first cycle, regorafenib was administered from day 2-22 to allow for pharmacokinetic analyses.

tag: timing

value: Baseline

value: Paclitaxel + Regorafenib

value: advanced esophagogastric cancer


title: 2006_C1D1


title: 2005_C1D1


title: 1054_C1D15

value: On-treatment


title: 1052_C1D15


title: 1052_C1D1


title: 1050_C1D1


title: 1050_C1D15


title: 1048_C1D1


title: 1049_C1D15


title: 1047_C1D1


title: 9999365 Slow baseline


title: 9029791 Slow baseline


title: 1046_C1D15


title: 1043_C1D1


title: 1040_C1D1


title: 1047_C1D15


title: 9973569 Non baseline


title: 1049_C1D1


title: 1038_C1D15


title: 1038_C1D1


title: 1035_C1D15


title: 1042_C1D1


title: 1034_C1D15


title: 1034_C1D1


title: 1032_C1D15


title: 1031_C1D1


title: 1032_C1D1


title: 1031_C1D15


title: 1029_C1D1


title: 1028_C1D15


title: 1028_C1D1


title: 1027_C1D15


title: 1027_C1D1


title: 1035_C1D1


title: 1023_C1D1


title: B37_P_35_CD11b

status: Public on Mar 07 2022

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcript counts calculated from Fastq files using Kallisto.
Transcript counts summarized to gene counts using tximport.
Abundance (logTPM) and estimated count measures from tximport normalized using TMM and filtered for expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include normalized values for each Sample.
Supplementary_files_format_and_content: txt files include filtered logTPM values for each Sample.

extract_protocol:
Tumor infiltrating immune cells (TIICs) were obtained from a non-necrotic tumor piece at approximately 2 cm in diameter that could be spared for research purpose after the clinical specimens were prioritized and were dissected by pathologist. RPMI-1640 media were used to resuspend all the cells after disruption and homogenization. The cell suspension was filtered with a 70μm cell strainer and a layer of mononuclear cells that contained TIICs were then isolated using the Ficoll density gradient centrifugation with Ficoll-Paque™ PLUS (Cytiva) as described 39. TIICs were washed three times using 40 ml of the complete RPMI media each time. After the final wash with the RPMI media, isolated TIICs were cryopreserved in the liquid nitrogen freezer or subjected to cell sorting. Peripheral blood mononuclear cells were obtained from patient’s whole blood using the Ficoll-Paque™ PLUS gradient centrifugation to serve as the FACS staining control. TIICs and peripheral blood mononuclear cells were stained with the Zombie Green viability dye (Biolegend), anti-CD4-PE-CF594 (Biolegend), anti-CD8-APC (Biolegend), anti-CD19-PE (Biolegend), and anti-CD11b-BV421 (Biolegend) antibodies. After sorting with the BD FACSAria IIu Cell Sorter (Biosciences), bulk tumor RNA was extracted by using the All Prep DNA/RNA Micro Kit (Qiagen) according to the manufacturer’s instruction and sent to a commercial vendor (BGI Genomics) for whole transcriptomic RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: arm

value: B

tag: os

value: Y


title: B35_P_3_CD4

value: High

value: Low

value: N


title: B39_P_35_CD4


title: B36_P_3_CD8


title: B34_P_3_CD19


title: B32_P_45_CD8

value: A


title: B31_P_45_CD4


title: B28_P_33_CD8


title: B30_P_45_CD19


title: B29_P_45_CD11b


title: B23_P_20_CD4


title: B27_P_33_CD4


title: B24_P_20_CD8


title: B19_P_6_CD4


title: B33_P_3_CD11b


title: B22_P_20_CD19


title: B25_P_33_CD11b


title: B26_P_33_CD19


title: B21_P_20_CD11b


title: B18_P_6_CD19


title: B20_P_6_CD8


title: B17_P_6_CD11b


title: B38_P_35_CD19


title: B40_P_35_CD8


title: B15_P_44_CD4


title: 1024_C1D1


title: B12_P_11_CD8


title: B9_P_11_CD11b


title: B14_P_44_CD19


title: B11_P_11_CD4


title: B8_P_28_CD8


title: B4_P_26_CD8


title: B13_P_44_CD11b


title: B7_P_28_CD4


title: B6_P_28_CD19


title: B2_P_26_CD19


title: B10_P_11_CD19


title: B5_P_28_CD11b


title: Lung_EC

status: Public on Mar 01 2022

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing: Cell Ranger 3.0.2 (10x Genomics) was used to process the raw sequencing data of polyA RNA libraries.

organism: Sus scrofa domesticus

source_name: Lung

growth_protocol: The aorta near to lung was separated and washed with PBS. 5 mL of digestion buffer was injected into the sealed aorta, and left the aorta into water bath at 37 ℃ for 30 mins. Next, the aorta was taken out, and digestion buffer was flowed out. The medium was transferred into a 15 mL Falcon tube and centrifuged at 300 x g for 5 min. The collected cells were washed with 5 mL PBS and centrifuged for culturing within 5 mL PAEC medium.

extract_protocol:
One leaf of pig lung was used for perfusion with PBS from the big vessel on top. After perfusion, the lung was squeezed and made the PBS out. 15 ml of the digestion buffer containing 0.1% collagenase II, 0.25% collagenase IV, 75 μl DNAse I in KnockOutTM DMEM medium was injected into the sealed pig lung. The opening site was closed by sealing clip, and leaved the bag into water bath at 37℃ for 30 mins. Next, the lung was taken out and the digestion buffer was flowed away. 20 mL of PBS was used to wash the lung for 3 times, and the medium was collected for filtering with 100 μm cell strainer afterwards. The medium was transferred into 10 mL Falcon tube and centrifuged at 300 x g for 5 mins. The cells were washed with 10 mL PBS and centrifuged for culturing into 5 mL PAEC medium (DMEM with 10% fetal calf serum, 1 x MEM-NEAA, 1 mM Sodium Pyruvate, 1 x Glutamax, 1 x Penicillin/Streptomycin) in CO2 incubator.
The ployA RNA libraries were prepared following the manufacturer’s instructions of GemCode Single Cell 3’ Gel Bead and Library kit (v3 Chemistry ) from 10x Genomics, Inc. (Pleasanton, CA).

value: Lung