title: Follow-up HN30 shKMT2D – rep 3

value: KMT2D knockdown


title: Hv_nsp1_-P+N_rep3

status: Public on Oct 06 2022

type: SRA

city: Cambridge

first: Darius

last: Zarrabian

address: 93 Lawrence Weaver Rd

department: Plant Sciences

country: United Kingdom

institute: Crop Science Centre, University of Cambridge

library_source: transcriptomic

data_processing:
Quality control was conducted with FastQC software
Resultant raw fastq data were mapped to the M. truncatula reference genome version 4.0 or the H. vulgare cv. Golden Promise reference genome with STAR software
The raw count values were calculated with featureCounts in R package Rsubread
Assembly: Mt4.0v1, Hordeum vulgare cv. Golden  Promise
Supplementary files format and content: tab separated files with raw count values

molecule: total RNA

organism: Hordeum vulgare

source_name: whole root

extract_protocol:
H. vulgare total RNA was extracted using the Spectrum™ Plant Total RNA kit (SigmaAldrich) and M. truncatula total RNA was isolated with the RNeasy PlantMini Kit (Qiagen),  following the manufacturer’s instructions.
Poly A enrichment

tag: tissue

value: whole root

tag: genotype

value: nsp1-1 mutant in Golden Promise background

tag: treatment

value: -P+N

tag: time

value: 21 days


title: Sample_37DC

city: Indianapolis

first: Kunal

last: Gupta

state: IN

address: 355 W 16th St

country: USA

institute: Indiana Universitty

data_processing:
NextSeq reads were trimmed using fastp (version 0.20.1) with parameters “-l 17 --detect_adapter_for_pe -g -p”
The resulting reads were mapped against GRCm39 using HISAT2 (version 2.2.1) with parameters “--rna-strandness F“
Read counts for each gene were created using featureCounts from the Subread package (version 1.6.4) with the parameters “-O -M --primary -p --largestOverlap -s 2 -B” and Gencode M28 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.32.0) in R/Bioconductor (R version 4.1.1)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Contralateral dentate gyrus

extract_protocol:
Samples were prepared for extraction using the standard protocol for lipid-rich samples described in the QIAsymphony RNA Handbook (issued November 2020).  Tissue disruption and homogenization was carried out using a Qiagen Tissuelyser II.  RNA extraction was performed using a QIAsymphony SP (protocol: RNA_CT_800_V7, kit: QIAsymphony RNA Kit (192), catalog no. 931636).  RNA was eluted into 100 µL of RNase-free water and analyzed using an Agilent 4200 TapeStation.
Libraries were prepared by Illumina TruSeq Stranded mRNA Library Preparation Kit protocol (catalog no. 20020595).  The libraries were analyzed by Agilent 4200 TapeStation, and pooled.  The pooled libraries were loaded on a NextSeq 500/550 High Output v2.5 run with a 75-cycle sequencing module (catalog no. 20024906) to generate paired-end reads.  The demultiplexing of the reads was performed with bcl2fastq version 2.20.0

value: Contralateral dentate gyrus

tag: strain

value: Saline

value: Day 3


title: Sample_30DC

value: Kainate


title: Follow-up HN30 shKMT2D – rep 2

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

institute: UW Health

data_processing:
raw reads were aligned to the hg19 genome using STAR v2.7.2b and quality checked using FastQC v0.11.8
Counts were generated using featureCounts from subread v1.6.3 80
Downstream normalization and differential expression analysis were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample. Samples as columns, genes as rows.

organism: Homo sapiens

growth_protocol: Human HNSCC cell lines were acquired and characterized as previously described [59]. Briefly, cell lines were cultured in DMEM supplemented with 10% FBS, L-glutamine, sodium pyruvate, nonessential amino acids, vitamins, and 1% penicillin-streptomycin. All cell lines were cultured at 37 °C in an atmosphere of 5% CO2

extract_protocol:
RNA extraction was performed using an RNeasy Mini Kit per manufacturer’s instructions (Qiagen). Isolation of mRNA was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module
libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs). Library quality was checked on an Agilent TapeStation 4150 and quantified by Qubit 2000 fluorometer (Invitrogen). Libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq6000 SP runs with paired-end 100-bp reads at the The Advanced Technology Genomics Core (ATGC) at MD Anderson Cancer Center.

treatment_protocol: Human KMT2D knockdown experiments were performed in the HN30 cell line using KMT2D-specific shRNAs described previously (Maitituoheti et al., 2020).

tag: cell type

value: head and neck squamous cell carcinoma cell line

tag: status


title: S106foxo_control_fb_2

city: LONDON

first: MengJia

last: Li

state: Please Select

address: flat38 midhopse house, midhope street

institute: University College London

data_processing:
Read quality assessed with FastQC
Aligned to D. melanogaster genome by HiSAT2, sorted by Samtools
Counted with featurecounts
Analysed with DESeq2
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_foxo_switch_RNA.xlsx: Excel file containing read counts for genes analysed in gut and fat body.

organism: Drosophila melanogaster

source_name: Adult female Fat body

growth_protocol: Flies reared on 10% yeast, 5% sucrose

extract_protocol:
Gut and fat body dissection, Trizol-chloroform extraction, NextFlex Poly(A) beads (PerkinElmer NOVA-512981) for polyA enrichment.
NextFlex Rapid Directional qRNAseq v2 reagents, (barcode sets C and D, PerkinElmer NOVA-5130-14 and NOVA-5130-15 )  and 16 cycles of PCR.

treatment_protocol: Mated 48h, separated from males, fed 200 µM RU486 for 21 days, and switch to control food for 7 days.

tag: Sex

value: female

tag: age

value: 30 days

tag: induction


title: Sample_38DI

source_name: Ipsilateral dentate gyrus

value: Ipsilateral dentate gyrus


title: Hv_nsp1_-P+N_rep2


title: WT_switch_fb_1

value: RU486+ 3weeks, then RU- 1 week


title: Hv_nsp1_-P+N_rep1


title: Follow-up HN30 shKMT2D – rep 1


title: Sample_38DC


title: HN30 shNT – rep 2

data_processing:
raw reads were aligned to the hg19 genome using STAR v2.7.2b and quality checked using FastQC v0.11.8
Counts were generated using featureCounts from subread v1.6.3 80
Downstream normalization and differential expression analysis were performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file with raw gene counts for every gene and every sample. Samples as columns, genes as rows.

extract_protocol:
RNA extraction was performed using an RNeasy Mini Kit per manufacturer’s instructions (Qiagen).
libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs). and sequenced on Illumina HiSeq4000 runs with paired-end 76-bp reads at Novogene.

value: Non-targeting control


title: WT_control_fb_5


title: HN30 shNT – rep 3


title: NOD.Idd2 Dendritic cells_2

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

description:
DC_NOD_Idd2_2
Isolated DC cells from the spleen of NOD.Idd2 mice

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 transcriptome using STAR v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: normalized counts

source_name: Isolated splenic Dendritic cells

extract_protocol:
Trizol
KAPA RNA HyperPrep PolyA

value: Spleen

value: 12 weeks


title: WT_control_fb_4


title: Hv_nsp1_+P-N_rep3

value: +P-N


title: NOD.Idd2 Dendritic cells_3

description:
DC_NOD_Idd2_3
Isolated DC cells from the spleen of NOD.Idd2 mice


title: Sample_29DC


title: Hv_nsp1_+P-N_rep2

value: whole root


title: HN30 shNT – rep 1


title: NOD.Idd2 Dendritic cells_1

description:
DC_NOD_Idd2_1
Isolated DC cells from the spleen of NOD.Idd2 mice


title: WT_control_fb_2


title: Hv_nsp1_+P-N_rep1

value: nsp1-1 mutant in Golden Promise background


title: HN30 shKMT2D – rep 3

value: KMT2D knockdown


title: NOD Dendritic cells_3

description:
DC_NOD_3
Isolated DC from the spleen of NOD mice

value: NOD


title: WT_switch_fb_2


title: Hv_nsp1_+P+N_rep3

value: +P+N

value: 21 days


title: WT_control_fb_1


title: HN30 shKMT2D – rep 2


title: NOD Dendritic cells_2

description:
DC_NOD_2
Isolated DC from the spleen of NOD mice


title: Hv_nsp1_+P+N_rep2


title: switch_gut_3

library_source: genomic

data_processing:
Read quality assessed with FastQC
Read trimmed with trimmomatic
Aligned to D. melanogaster genome by MACS2
Counted with featurecounts
Analysed with DESeq2
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_foxo_switch_ATAC.xlsx: Excel file containing read counts for peaks analysed in gut and fat body.

molecule: genomic DNA

source_name: Adult female gut

extract_protocol:
Gut and fat body dissection, Nuclei separted and washed. Tagmentation with Tn5 transposase and Illumina buffer TD (Illumina Nextera kit)
NEBNext Ultra II Q5 Master Mix for PCR

value: Adult


title: NOD Dendritic cells_1

description:
DC_NOD_1
Isolated DC from the spleen of NOD mice


title: NOD.Idd2 B cells_3

description:
Idd2_3
Isolated B cells from the spleen of NOD.Idd2 mice

source_name: Isolated splenic B cells


title: HN30 shKMT2D – rep 1


title: switch_gut_2


title: WT_control_fb_3


title: WT_switch_gut_3


title: High Fractality (HF) 4

city: Milwaukee

first: Ulrich

last: Broeckel

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: AmpliSeq based expression data for High Fractality sample 4

data_processing:
The raw reads in FASTQ format were aligned to the human hg19 reference genome using bwa mem with default parameters: bwa mem -M -t 8 -R "@RG\tID:SampleName\tPL:ILLUMINA\tSM:SampleName" -L 5
Gene quantification was done using HTSeq using the default parameters: htseq-count -f bam -r pos -s no Sorted.bam Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf
Differential gene expression was analyzed using the DESeq2 (v.1.26.0) R/Bioconductor package
Genome_build: hg19, custom annotation GTF file for targeted transcripts (Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf) received from the manufacturer
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts for targeted genes.

source_name: primary human fetal kidney podocytes, Lonza CC-7224

growth_protocol: Primary human podocytes were seeded at an initial density of 30,000 cells/cm2, using RPMI 1640 basal medium with GlutaMAX and HEPES, supplemented with 10% FBS, 1% ITS, and 0.5% GA-1000. Primary cells were rinsed with HEPES-BSS during subculture and rinsing steps.

extract_protocol:
Cells were rinsed once with warm PBS prior to RNA extraction and isolation using the PicoPure RNA isolation Kit (Thermo Fisher Scientific, #KIT0204). 50 µL lysis buffer was added to each scaffold top, placed on a shaker for 5 min at room temperature, and gently scraped with a pipette tip and liquid collected while avoiding bubbles. Samples were incubated at 42˚C for 30 minutes on a heating block in microtubes. Manufacturer’s protocols were followed, with the inclusion of a DNAse treatment step (Qiagen, #79254). 21 µL of elution buffer was used in the last step, and a DeNovix spectrophotometer was used to approximate sample RNA concentration and quality. Extraction and isolation were performed in the same sitting. Isolated RNA was kept frozen at -80˚C.
Targeted whole transcriptome sequencing was done using the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, Inc) following manufacturer’s recommendations.

treatment_protocol: Groups are treated by the topographic pattern of the scaffold on which they are grown: (NT) No Topography, (RT) Round Topography, (HF) High Fractal topography. Scaffolds were coated with Porcine kidney ECM (Xylyx Bio, NativeCoat Kidney ECM surface coating kit #MTSKY201) according to manufacturer's instructions prior to cell seeding.

value: Human fetal kidney podocytes


title: Hv_GP_-P-N_rep3

value: wildtype Golden Promise cultivar

value: -P-N


title: switch_gut_1

value: female


title: High Fractality (HF) 2

description: AmpliSeq based expression data for High Fractality sample 2


title: Hv_GP_-P-N_rep2


title: NOD.Idd2 B cells_1

description:
Idd2_1
Isolated B cells from the spleen of NOD.Idd2 mice


title: Hv_GP_-P-N_rep1


title: NOD B cells_2

description:
NOD_2
Isolated B cells from the spleen of NOD mice


title: High Fractality (HF) 1

description: AmpliSeq based expression data for High Fractality sample 1


title: Hv_GP_-P+N_rep3

value: -P+N


title: control_gut_1


title: No Topography (NT) 4

description: AmpliSeq based expression data for No Topography sample 4


title: control_gut_2


title: NOD B cells_3

description:
NOD_3
Isolated B cells from the spleen of NOD mice


title: Hv_GP_-P+N_rep2


title: switch_fb_3

value: RU486+ 3weeks, then RU- 1 week


title: No Topography (NT) 3

description: AmpliSeq based expression data for No Topography sample 3


title: NOD B cells_1

description:
NOD_1
Isolated B cells from the spleen of NOD mice


title: switch_fb_2


title: Hv_nsp1_+P+N_rep1


title: High Fractality (HF) 3

description: AmpliSeq based expression data for High Fractality sample 3


title: endometrium-non-adenomyosis-rep3

type: RNA

city: Zhengzhou

first: Yan

last: Zhang

state: Henan

address: No. 1 Jianshe East Road, Erqi District

department: Department of Gynecology

country: China

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level” and “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.
Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: endometrium, non-adenomyosis (IP)

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: Endometrium in both adenomyosis patients(Adenomyosis group) and non-adenomyosis patients(Control group) was surgically obtained and preserved in -80℃ refrigerator.

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

tag: gender

value: endometrium, non-adenomyosis

source_name: endometrium, non-adenomyosis (SUP)


title: NOD.Idd2 B cells_2

description:
Idd2_2
Isolated B cells from the spleen of NOD.Idd2 mice

value: Spleen


title: Hv_GP_+P-N_rep3


title: endometrium-non-adenomyosis-rep2


title: Hv_GP_+P-N_rep2


title: No Topography (NT) 1

description: AmpliSeq based expression data for No Topography sample 1


title: Hv_GP_-P+N_rep1


title: Round Topography (RT) 4

description: AmpliSeq based expression data for Round Topography sample 4


title: switch_fb_1


title: No Topography (NT) 2

description: AmpliSeq based expression data for No Topography sample 2


title: control_gut_3


title: endometrium-non-adenomyosis-rep1


title: control_fb_3


title: Hv_GP_+P-N_rep1


title: Hv_GP_+P+N_rep3


title: endometrium-adenomyosis-rep3

source_name: endometrium, adenomyosis (IP)

value: endometrium, adenomyosis

source_name: endometrium, adenomyosis (SUP)


title: endometrium-adenomyosis-rep2


title: Round Topography (RT) 2

description: AmpliSeq based expression data for Round Topography sample 2


title: control_fb_1


title: fresh, td, 1

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description: td' indicates the samples are from transgenic mice bred with the 'tdTomato' construct.

library_source: transcriptomic single cell

data_processing:
Processing of  scRNAseq reads was performed using the 10X Genomics Cell Ranger pipeline (v5.0.0) and visualized in R with the Seurat package (v4.0.5). Briefly, FASTQ files were generated using cellranger mkfastq with default parameters and cellranger count was run using the reference genome and annotation supplied (mm10-2.1.0) for each sample, counting UMIs for each gene. The output for each sample was integrated using cellranger aggr with default options and imported into R using Seurat for further analysis.
Assembly: mm10-2.1.0
Supplementary files format and content: *_filtered_feature_bc_matrix.h5: gene-cell barcode matrices in hdf5 format. Filtering was performed using default parameters in cellranger.

source_name: BM

growth_protocol: Femurs and tibias isolated from Tie2-CreERT2;Rosa26-tdTomato mice were collected into sterile cold PBS with 2% FBS and gently crushed using a mortar and pestle. In order to avoid damaging ECs, especially those ones localized just beneath of the bones, crushing was performed very gently upon reducing each bone in 2-3 pieces. Cell suspensions were then filtered into a 50 mL tube on ice using a 70 um cell strainer while the crushed bone pieces were incubated at 37°C with gentle agitation (150 rpm) in 1-2 mL/mouse of bone digestion buffer containing DMEM supplemented with 20 mM HEPES, 3 mg/mL collagenase I, BSA 1 mg/mL, and 0.1 mg/mL DNase I. After 10 minutes, the bone digested mixture was brought to a 10 mL volume in PBS containing 2% FBS and filtered again via the 70 um cell strainer and into the 50 mL tube used previously. A further 1-2 mL of digestion media was added to the bone pieces and the mixture was incubated at 37°C in agitation (150 rpm) for additional 30 minutes. The cell suspension derived from the bone digestion was washed again in PBS with 2% FBS and added to the previous 50 mL tube after filtration through the same 70 um cell strainer on ice. The digested bone pieces were collected back into the mortar and further crushed in PBS/2% FBS. The supernatant was passed through the same 70 um cell strainer and gathered into the same 50 mL tube on ice. The whole cell suspension was centrifuged at 1200 rpm for 5 minutes and the cell pellet was dissolved in EGM-2 medium for counting.

extract_protocol: For scRNA-seq, DAPI-CD45-Ter119-tdTomato+ sorted cells from the fresh (without culture) bone marrows of two 4-month-old Tie2-CreERT2;Rosa26-tdTomato mice were loaded on the Chromium controller (10XGenomics) based on the number provided by the sorting equipment. The libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ GEM, Library & Gel Bead Kit v3 (PN-1000075), Chromium Chip B Single Cell Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics) and following the Chromium Single Cell 3′ Reagent Kits (v3) User Guide (manual part no. CG000183 Rev A). Libraries were run on an Illumina HiSeq 2500 as 150-bp paired-end reads, at 20,000 read pairs per cell.

value: BM

value: fresh (without culture)

value: BMEC


title: endometrium-adenomyosis-rep1


title: Round Topography (RT) 1

description: AmpliSeq based expression data for Round Topography sample 1


title: P0, td, 1

value: primary culture

tag: passage


title: Hv_GP_+P+N_rep1

value: whole root


title: control_fb_2


title: B11deletion replicate 3 [MAB_KOB11_3]

status: Public on Oct 05 2022

city: Worcester

first: Scarlet

middle: Sara

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

data_processing:
Raw fastq files were demultiplexed using Cutadapt as in DOI 10.14806/ej.17.1.200.
Reads were aligned using BWA mem (DOI 10.1093/bioinformatics/btp324).
Reads aligned to genes were quantified using FeatureCounts (DOI 10.1093/bioinformatics/btt656).
Assembly: NC_010397.1.gbk
Supplementary files format and content: Mab_B11_FeatureCounts.xlsx contains the output from running FeatureCounts on bam files generated from these fastq files. The FeatureCounts table can be used as input for DESeq2 for differential expression analysis.

organism: Mycobacteroides abscessus ATCC 19977

source_name: Log phase growth cell culture

growth_protocol: Strains were growth to OD 0.6-0.75 in 7H9 supplemented with ADC and glycerol. All complemented strains had the addition of 150 ug/ml kanamycin in the media.

extract_protocol:
Pellets were resuspended in Trizol and lysed by bead-beating. RNA was extracted with a Zymo Direct-zol kit, treated with DNase, and purified with a Zymo Clean and Concentrate kit.
rRNA was depleted using a set of biotinylated oligos designed as described in DOI 10.1128/mBio.00010-20. Paired-end Illumina sequencing libraries were constructed as described in DOI 10.1128/mBio.02012-21

tag: strain background

value: Log phase growth cell culture

value: ATCC_19977 with deletion of B11


title: B11 deletion complement with B11 with loop 2 insertion mutation replicate 3 [MAB_KOB11_L2_3]

value: ATCC_19977 with deletion of B11 transformed with an integrating plasmid expressing B11 with insertion of a single "C" into the 7-C tract in loop 2


title: B11 deletion complement with B11 with loop 2 insertion mutation replicate 1 [MAB_KOB11_L2_1]


title: Wildtype replicate 3 [MAB_WT_3]

value: Wildtype ATCC_19977


title: B11 deletion wildtype complement replicate 3 [MAB_KOB11_B11_3]

value: ATCC_19977 with deletion of B11 transformed with an integrating plasmid expressing wildtype B11


title: B11 deletion wildtype complement replicate 2 [MAB_KOB11_B11_2]


title: B11 deletion complement with B11 with loop 2 insertion mutation replicate 2 [MAB_KOB11_L2_2]


title: B11 deletion wildtype complement replicate 1 [MAB_KOB11_B11_1]


title: B11 deletion complement with B11 with loop 1 deletion mutation replicate 3 [MAB_KOB11_L1_3]

value: ATCC_19977 with deletion of B11 transformed with an integrating plasmid expressing B11 with a deletion of a single "C" from the 6-C tract in loop 1


title: B11 deletion complement with B11 with loop 1 deletion mutation replicate 1 [MAB_KOB11_L1_1]


title: B11 deletion complement with B11 with loop 1 deletion mutation replicate 2 [MAB_KOB11_L1_2]


title: B11deletion replicate 1 [MAB_KOB11_1]


title: Wildtype replicate 2 [MAB_WT_2]


title: B11deletion replicate 2 [MAB_KOB11_2]


title: Wildtype replicate 1 [MAB_WT_1]


title: Round Topography (RT) 3

description: AmpliSeq based expression data for Round Topography sample 3

value: Human fetal kidney podocytes


title: Hv_GP_+P+N_rep2

value: wildtype Golden Promise cultivar

value: +P+N

value: 21 days


title: paternal_P6_lateral_septum

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

data_processing:
Basecalling and demultiplexing was done using Illumina bcl2fastq v2.20.
Raw reads were first processed for quality filtering and adapter trimming with fastp (v0.20.0) with adapter trimming, base correction (-p option), and polyX tail trimming (-x option). The final quality of reads was then verified using FastQC (v0.11.8).
Filtered reads were then pseudo-aligned and quantified using Salmon (v0.14.1) with -g, --numBootstraps 1000, --validateMappings, --rangeFactorizationBins 4, --seqBias, --gcBias, and --recoverOrphans parameters.
Genome_build: MicOch1.0 Ensembl Release 97 + GenBank #AF069304.2
Supplementary_files_format_and_content: Matrix of reads counts (not normalized) for each gene in each sample as computed by DESeq2 (tab-delimited txt file).

organism: Microtus ochrogaster

extract_protocol:
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial preoptic nucleus, nucleus accumbens, and lateral septum. Total RNA was then extracted using TRI-Reagent according to the manufacturer's protocol (Molecular Research Center, #TR 118), followed by DNAse I treatment to remove any eventual DNA contamination and clean-up (RNA Clean & Concentrator, Zymo Research, Irvine, CA, USA).
RNA-seq libraries were prepared by the Florida State University NGS Library Facility following poly(A) mRNA purification from total RNA based on magnetic beads, cDNA synthesis using random hexamers, and final amplification using barcoded primers (New England Biolabs, Ipswich, MA, USA). The resulting barcoded and unstranded libraries were quantified using a KAPA qPCR library quantification kit (KAPA Biosystems, Boston, MA, USA) and the absence of adapters or primers contamination was verified on an Agilent TapeStation (Agilent Technologies, Santa Clara, CA, USA).

tag: group

value: paternal


title: paternal_P5_nucleus_accumbens


title: paternal_P4_nucleus_accumbens


title: paternal_P5_medial_preoptic_nucleus


title: paternal_P6_nucleus_accumbens


title: paternal_P5_lateral_septum


title: paternal_P4_medial_preoptic_nucleus


title: paternal_P4_lateral_septum


title: paternal_P3_nucleus_accumbens


title: paternal_P3_lateral_septum


title: paternal_P3_medial_preoptic_nucleus


title: paternal_P2_nucleus_accumbens


title: paternal_P2_lateral_septum


title: paternal_P1_nucleus_accumbens


title: paternal_P1_lateral_septum


title: mothers_M6_medial_preoptic_nucleus

value: mothers


title: mothers_M6_lateral_septum


title: mothers_M5_nucleus_accumbens


title: mothers_M4_medial_preoptic_nucleus


title: mothers_M4_nucleus_accumbens


title: mothers_M6_nucleus_accumbens


title: mothers_M3_medial_preoptic_nucleus


title: mothers_M3_lateral_septum


title: mothers_M5_medial_preoptic_nucleus


title: paternal_P1_medial_preoptic_nucleus


title: mothers_M2_nucleus_accumbens


title: mothers_M3_nucleus_accumbens


title: mothers_M2_medial_preoptic_nucleus


title: mothers_M2_lateral_septum


title: mothers_M4_lateral_septum


title: mothers_M1_nucleus_accumbens


title: mothers_M1_medial_preoptic_nucleus


title: fathers_F4_medial_preoptic_nucleus

value: fathers


title: fathers_F5_medial_preoptic_nucleus


title: fathers_F4_nucleus_accumbens


title: fathers_F6_lateral_septum


title: fathers_F6_medial_preoptic_nucleus


title: mothers_M5_lateral_septum


title: fathers_F4_lateral_septum


title: fathers_F3_nucleus_accumbens


title: fathers_F2_nucleus_accumbens


title: fathers_F3_medial_preoptic_nucleus


title: fathers_F3_lateral_septum


title: fathers_F2_medial_preoptic_nucleus


title: fathers_F2_lateral_septum


title: fathers_F1_medial_preoptic_nucleus


title: attackers_A6_medial_preoptic_nucleus

value: attackers


title: fathers_F1_lateral_septum


title: attackers_A6_nucleus_accumbens


title: mothers_M1_lateral_septum


title: attackers_A5_lateral_septum


title: attackers_A6_lateral_septum


title: attackers_A5_medial_preoptic_nucleus


title: attackers_A4_medial_preoptic_nucleus


title: attackers_A5_nucleus_accumbens


title: fathers_F5_nucleus_accumbens


title: fathers_F5_lateral_septum


title: attackers_A4_lateral_septum


title: fathers_F6_nucleus_accumbens


title: attackers_A3_nucleus_accumbens


title: attackers_A2_medial_preoptic_nucleus


title: attackers_A3_lateral_septum


title: attackers_A2_lateral_septum


title: attackers_A3_medial_preoptic_nucleus


title: attackers_A2_nucleus_accumbens


title: attackers_A1_nucleus_accumbens


title: fathers_F1_nucleus_accumbens


title: attackers_A1_medial_preoptic_nucleus


title: attackers_A4_nucleus_accumbens


title: Patient 24

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

country: Australia

institute: Liverpool Hospital

hyb_protocol: As Per Nanostring nCounter System

scan_protocol: As Per Nanostring nCounter System

data_processing: Normalized and Analyzed using Nsolver (Nanostring)

label: Nanostring CodeSet

source_name: Hidradenitis Suppurativa

label_protocol: As Per Nanostring nCounter System

extract_protocol: Total RNA extracted using Quiagen RNeasy

tag: response to il-23 antagonism

value: Non-Responder

value: lesional skin


title: Patient 19


title: Patient 17

value: Responder


title: Patient 16


title: Patient 15


title: Patient 11


title: Patient 22


title: Patient 13


title: Patient 21


title: Patient 25


title: Patient 20


title: Patient 23


title: Patient 10


title: Patient 26


title: Patient 14


title: Patient 9


title: Patient 8


title: Patient 18


title: Patient 7


title: Patient 6


title: Patient 2


title: Patient 3


title: Patient 4


title: Patient 1


title: Bovine intercotyledonary placenta, replicate 2, snRNAseq

city: Pullman

first: Kimberly

middle: M

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: Intercotyledonary placenta

extract_protocol:
Nuclei were isolated from fresh tissue following the 10X Genomics protocol
Libraries were consructed according to the 10X Genomics manufacterer's instructions

value: Intercotyledonary placenta


title: Bovine intercotyledonary placenta, replicate 1, snRNAseq

description: 10X Genomics


title: Bovine cotyledon, replicate 2, snRNAseq

description: 10X Genomics

source_name: Cotyledon

value: Cotyledon


title: Bovine cotyledon, replicate 1, snRNAseq

description: 10X Genomics


title: Patient 12


title: D10_d0_VDJ [scRNA-seq]

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

data_processing:
Library strategy: TCR repertoire sequencing
The raw scRNA-seq data were demultiplexed, aligned to the Human (GRCh38) reference and the feature-barcode matrix was quantified using Cell Ranger (v3.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5). Cells were subjected to QC filters based on the number of detected genes, number of UMIs and proportion of UMIs mapped to mitochondrial and ribosomal genes per cell. The thresholds filters for each variable were selected based on their distribution within each of the single cell libraries and visual inspection of quality control scatter plots. Genes detected in fewer than three cells and cells where fewer than 150 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 10% and more than 40% mitochondrial or ribosomal content respectively, were also discarded. In addition, cells with more than the 97.5th percentile of detected genes per sample, were discarded to remove likely doublet or multiplet captures.
Each dataset was subjected to normalization, identification of highly variable genes and removal of unwanted sources of variation using Seurat (v3.1.5). Integration of all the dataset was based on Seurat’s canonical correlation analysis. Different resolution parameters for unsupervised clustering were examined to determine the optimal number of clusters. For this study, the first 40 PCs and 3000 highly variable genes identified by Seurat were used for sample integration and unsupervised clustering analysis with the resolution set to 0.8, yielding a total of 23 cell clusters. Non-linear dimensional reduction was performed using t-distributed stochastic neighbour embedding (t-SNE) and UMAP.
TCR V(D)J sequence assembly, paired clonotype calling, TCR diversity and clonality analysis. TCR reconstruction and paired TCR clonotype analysis was performed using Cell Ranger v3.0.2 for V(D)J sequence assembly. The CDR3 motif was located, and the productivity was determined for each single cell. The clonotype landscape was then assessed, and the clonal fraction of each identified clonotype was calculated. The TCR clonotype diversity matrix was calculated using the tcR R package. TCR clonality was defined as 1-Peilou’s evenness and was calculated on productive rearrangements as previously described. Clonality values approaching 0 indicate a very even distribution of clone frequencies, whereas values approaching 1 indicate an increasingly.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell recovered as per Cell Ranger (v3.0.1). barcodes.tsv (10X Genomics Chromium Raw Gene BC Cellular Barcodes), features.tsv (10X Genomics Chromium Raw Gene BC Cellular Genes), matrix.mtx (10X Genomics Chromium Raw Gene BC Cellular Matrix) files.
Supplementary_files_format_and_content: *VDJ.csv: Comma-separated text files.

source_name: Donor cells

growth_protocol: PBMCs were isolated from peripheral blood of healthy donors using Ficoll-PaqueTM Plus (GE Healthcare) and then CD4+ and CD8+ cells were isolated using CD4 and CD8 MicroBeads (Miltenyi Biotec) in the AutoMACS Pro Separator (Miltenyi Biotec). Isolated T cells were cultured at a concentration of 1×10^6 cells/ml in RPMI 1640 culture medium (Lonza) supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin (Gibco) and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec), and activated with 10 µl/ml T cell TransAct (Miltenyi Biotec).

extract_protocol:
FACS-sorted CAR T cells (BFP+ cells) from three independent donors were interrogated using the 10X Chromium platform for simultaneous transcriptome and TCR profiling, with 28,117 cells (range, 7,416-10,5093 cells/donor) passing our quality control (QC) thresholds and taken into subsequent analysis. These cells were sequenced to an average depth of 42,296 reads/cell, yielding an average of 2,541 genes/cell.
scRNA-seq was performed using the Chromium Single Cell 5′ Reagent Kit (10X Genomics) according to the manufacturer’s instructions. Briefly, CAR T cells were sorted in 100µl 1X PBS, 0.04% BSA and their concentration and viability were determined using Nexcelom’s Cellometer K2 Fluorescent Cell Counter. Cell concentration was adjusted to 700 to 1200 cells/µl to maximize the likelihood of achieving the desired cell recovery target. Then single-cell suspension was mixed with RT Master Mix and loaded together with barcoded single-cell 5′ gel beads and partitioning oil into separate single cell A Chips to generate Gel Beads in Emulsion (GEMs) using Chromium Controller. Thus, individual cells were lysed and the polyadenylated RNA was reverse-transcribed and barcoded inside each GEM. Barcoded complementary DNA (cDNA) was recovered through post GEM-RT cleanup and PCR-amplified. cDNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its profile examined using High Sensitivity D5000 ScreenTape Assay (Agilent Technologies). Fifty nanograms of double-stranded cDNA were used for 5′ Gene Expression library construction. cDNA was fragmented, end-repaired, A-tailed and ligated to an adaptor. A final PCR-amplification with barcoded primers was performed for sample indexing.
Single-cell TCR repertoire sequencing. TCRTCR α/β sequencing was performed with 10X Genomics Single Cell V(D)J Immune Profiling Solution (10× Genomics). Briefly, full-length V, D and J gene segments were amplified from barcoded cDNA using a Chromium Single Cell V(D)J Enrichment Kit (human T cells) by means of two sequential PCRs with primers targeting the adaptor and the gene constant region. Enriched cDNA was quantified as described above and 50 ng were further used for library construction as described above. After quality control and quantification, Single Cell V(D)J enriched libraries were pooled and sequenced in an Illumina’s HiSeq X (Read1: 150 cycles; Read2: 150 cycles, i7 index: 8 cycles) at an average depth of 5000 reads per cell.

treatment_protocol: After 48h, T cells were infected with the CAR lentiviral vector at MOI 2 and 10 µl/ml of LentiBoost (Sirion Biotech), to enhance viral infection. CAR T cells were expanded in RPMI 1640 culture medium (Lonza) supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin (Gibco) and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec). CAR T cells were counted, and the concentration was adjusted to 1×10^6 cells/ml every two days until day 13-14 of the production.

tag: diagnosis

value: Healthy

value: Blood

value: BFP+ CAR T cells


title: Patient 5


title: D18_d0_VDJ [scRNA-seq]


title: D14_d0_VDJ [scRNA-seq]


title: 2B

city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

data_processing:
Single cell RNA-seq library were prepared using 10x Genomics Chromium (human, ~3000 cells target, v3.1).
Sequencing were performed on the DNBSEQ System, in a 2x150bp paired-end (PE) configuration Read 1 (28bp) + i7  index (8bp) + i5 index (0bp) + Read2 (91bp) per lane, with ~350M paired-read per lane, 0.5 lane(s) per sample.
Interactive differential gene expression were analysed through the 10X Genomics Cell Ranger (human, --force-cell=FALSE, aggregation).
Genome_build: hg38

source_name: human induced pluripotent stem cells

growth_protocol: The hPSCs were cultured in StemFlex (Thermo Fisher Scientific) on a plate coated with Matrigel (Corning  ). For passaging hPSCs, 1mM EDTA and 10 mM Y-27632 (StemCell Technologies) were added to the culture  medium and maintained 24 h.

extract_protocol:
RNA extract and libraries were prepared for sequencing using standard protocols of HiSeq X Ten by Genewiz.
Single cell RNA-Seq

value: male

value: iPS cells


title: BJ


title: EDOM

value: female


title: SEES6

source_name: human embryonic stem cells

value: ES cells


title: A549-I_1

city: Beijing

state: Not Applicable

address: Dongdajie street

institute: Beijing institute of Biotechnology

description: ATAC on A549 cells in interphase replicate 1

data_processing:
Raw paired-end reads were trimmed for adaptors and checked for quality using fastp.  Clean data were aligned to hg38 using Bowtie2 with parameters "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700".  PCR duplicates were discarded using Picard.   Biological replicates were combined for further presentation.   DeepTools were used to produce bigWig tracks for ATAC-seq signals, and create heatmaps for scores associated with genomic regions.  Peaks were calling by MACS3 with parameters "-f BAMPE --call-summits".
Genome_build: GRCh38
Supplementary_files_format_and_content: bed format of narrowpeak

source_name: A549 cells

growth_protocol: A549 (ATCC CCL-185) and HeLa-S3 (ATCC CCL-2.2) Cells were grown in standard DME/F12 1:1 media (HyClone #SH30023.01) with 10% Bovine serum (Gibco #16170078), 1% PenStrep (Gibco #15140).

extract_protocol:
Cells were harvested as non-synchrous without treatment or arrested in mitosis using Thymidine treatment and Nocodazole.
For each sample, ATAC-seq was performed following a previously published protocol (Buenrostro et al, 2015).

treatment_protocol: 48 hours prior to synchronization, cells were plated on 15 cm plates at 50% confluence. First, cells were incubated with media containing 2 mM Thymidine (Sigma T1895-10G) for 24 hours, washed twice with 10 ml 1x PBS and released into standard media for 3 hours. Media were then substituted with media containing 100ng/ml nocodazole (Sigma #M1404) for 12h. At the end of the incubation, media with floating mitotic cells was collected.

tag: protocol

value: ATAC

value: A549 cells

tag: cell cycle

value: interphase


title: HeLaS3-I_2

description: ATAC on HeLaS3 cells in interphase replicate 2

source_name: HeLaS3 cells

value: HeLaS3 cells


title: HeLaS3-I_1

description: ATAC on HeLaS3 cells in interphase replicate 1


title: A549-I_3

description: ATAC on A549 cells in interphase replicate 3


title: HeLaS3-M_2

description: ATAC on HeLaS3 cells in mitosis replicate 2

value: mitosis


title: A549-M_2

description: ATAC on A549 cells in mitosis replicate 2


title: A549-M_3

description: ATAC on A549 cells in mitosis replicate 3


title: A549-I_2

description: ATAC on A549 cells in interphase replicate 2


title: SEES4


title: SEES3


title: SEES2


title: SEES1


title: HeLaS3-M_1

description: ATAC on HeLaS3 cells in mitosis replicate 1


title: SEES7


title: SEES5


title: Input

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg38 whole genome using STAR with default parameters
MACS2 was used to call the peaks of SOX4 binding using default parameters.
Genome_build: Hg38
Supplementary_files_format_and_content: pileup peaks

source_name: decidualized human stromal cells

growth_protocol: Immortalized hEnSCs were maintained in DMEM/F12 without phenolic red (Gibco) at the present of 10%charcoal stripped fetal bovine serum (CS-FBS, Biological Industries), glucose (3.1 g/L), sodium pyruvate (1 mM, Sigma); sodium bicarbonate (1.5 g/L, Sigma), Penicillin-Streptomycin (50 mg/ml, Solarbio); insulin-transferrin-selenium (ITS, 1%, Thermo Fisher) and puromycin (500 ng/ml). The primary cultured cells were maintained only in DMEM/F12 (Gibco) without phenolic red and CS-FBS 10%. For decidualization, hESCs were cultured in medium at the present of estrogen (E2, 10nM, Sigma), medroxyprogesterone acetate (MPA, 1 mM, Sigma), and dibutyl cyclophospsinoside (db-cAMP, 0.5 mM, MCE) in 2% CS-FBS with different days. All the cells were cultured in 5% CO2, 95% air, 100% humidity at 37 C and culture medium was replaced every 48 h.

extract_protocol:
hEnSCs cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

value: Human uterus

tag: tissue

value: Endoemtrium stromal cells


title: RNAseq.Gli1-rep2

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

description: RNAseq_counts_per_gene.Glis1_Amrh2.txt.gz

data_processing:
ATACseq processing: Raw reads were filtered to exclude pairs with mean base quality <20.  Filtered read pairs were mapped against  mm10  via Bowtie v1.2 with parameters "-m 1 -X 2000 --chunkmbs 1024".  Reads mapped to chrM were discarded via samtools v1.3.1. Duplicate mapped read pairs were removed by Picard tools MarkDuplicates.jar v1.110.  Only the 9bp at the 5’ end of each read were retained for downstream analysis.
ATACseq signal tracks: Coverage tracks for genome browser views were generated with BEDtools v2.24.0 "genomecov -bg", depth-normalized to 40 million read ends per sample, then converted to bigWig format with UCSC utility bedGraphToBigWig.
ATACseq peaks: Peak calls per sample were made by MACS2 v2.1.1 with parameters "callpeak -g mm -q 0.0001 --keep-dup=all --nomodel --extsize 9" followed by combining nearby peaks with BEDTools v2.24.0 "merge -d 200".  A single set of unified peaks was defined by collapsing called peaks from all samples and identifying only peak regions that overlap from 2 or more samples via BEDtools v2.24.0 "unionbedg", followed by combining nearby peaks with BEDTools v2.24.0 "merge -d 200". Unified peaks less than 50bp in width were discarded.
RNAseq processing: Raw reads were filtered to exclude those with mean base quality <20. Filtered read pairs were mapped against mm10 via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".  Raw counts per gene per sample were collected by featureCounts (Subread v1.5.0-p1) with parameters "-s0" for the E14/E16 dataset (which is single-end and unstranded) or "-s2 -Sfr -p" for the E19 dataset (which is paired-end and stranded).
RNAseq signal tracks:  Coverage tracks were generated by STAR v2.5 with parameters “--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigNorm RPM" and "--outWigStrand Stranded" or "--outWigStrand Unstranded" as appropriate, then converted to bigWig format with UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: signal or coverage tracks in bigWig format; raw counts per gene in tab-delimited text format; peaks in BED format

source_name: Neonatal uterus

extract_protocol:
RNA extractions were performed using PicoPure RNA Isolation kit.
For sorted Gli1+ mesenchymal cells, 250 ng RNA were used to generate libraries using Truseq RNA non-stranded kit (Illumina); For sorted Gli1+ and Amhr2+ cell from E19.5 uterus, TruSeq Stranded mRNA kit was used to generate libraries; For ATAC-seq on sorted Gli1+ mesenchymal cells,  Illumina Nextera DNA preparation kit was used to generate the libraries.

treatment_protocol: Tamoxifen (1 mg per dam) was given intraperitoneally on E12.5 and 13.5 to dams carrying embryos with Gli1-CreER; Rosa-Tomato or Amhr2-Cre; Rosa-Tomato. Fetal mesonephros or neontal uterus were freshly frozen for RNA extraction or enzymatically dissociated with TrypLE express (Gibco, 12604-013 - no phenol red) for cell sorting.

tag: cell population


title: HA-SOX4 in decidualized stromal cells

tag: chip antibody

value: HA-Tag (C29F4) Rabbit mAb , vendor:Cell signaling Technology (CST); catalog number:#3724;  lot/batch number:4


title: RNAseq.Gli1-rep3


title: RNAseq.Gli1-rep1


title: A549-M_1

description: ATAC on A549 cells in motisis replicate 1


title: ADSC


title: RNAseq.Amhr2-rep3


title: H3K27ac-4-cell-rep2

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
Library strategy: CUT&Tag
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.4.4 with with options: –local –very-sensitive -local –no-unal –nomixed –no-discordant –phred33 -I 10 -X 700
Cut&tag peaks were called on merged replicates and normalized to input using MACS2 version 2.1.1.20160309
Peak comparisons and overlaps were done using the BedTools suite for autosomal chromosomes only
RPKM values were calculated using merged replicate bam files by bamCoverage from deepTools
Genome_build: mm10

source_name: mouse embryos

extract_protocol: After removing the zona pellucida, embryonic cells were washed with PBS. CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901; Vazyme Biotech, Nanjing, China). Embryos were incubated in 50 μL of antibody buffer; 0.5 μg antibody was added and the mixture was cultured for 1.5 h at room temperature. After washing twice with dig-wash buffer, 150 μL dig-wash buffer with 0.7 μg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 μL dig-wash buffer, 0.3 μL pG–Tn5 and 50 μL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h and then washed twice with 100 μL dig-wash buffer. We added 200 μL of tagmentation buffer and the samples were incubated at 37°C for 1 h. The reaction was stopped with 7 μL 0.5 M ethylenediaminetetraacetic acid (EDTA), 2 μL 10% sodium dodecyl sulfate (SDS) and 1.7 μL 20 mg/ml proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following cycling conditions: 72°C for 5 min, 98°C for 30 s, 17 cycles of 98°C for 10 s, and 60°C for 30 s, followed by a final extension at 72°C for 1 min and holding at 4°C. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (N411; Vazyme Biotech), and libraries were incubated with beads for 10 min at room temperature, washed gently in 80% ethanol, and eluted in 20 μL water. All libraries were sequenced using the Illumina NovaSeq 6000 platform according to the manufacturer’s instructions.

treatment_protocol: Embryos were collected from superovulated female ICR mice treated with 6.5 IU of pregnant mare serum gonadotropin (PMSG); after 45–47 h, they were treated with 5 IU of human chorionic gonadotropin (hCG) and crossed to ICR males. Embryos were collected at the following times post-hCG injection: 24 h for the zygote stage, 34 h for the early 2-cell stage, 41 h for the middle 2-cell stage, 48 h for the late 2-cell stage, 58 h for the 4-cell stage, 69 h for the 8-cell stage, and 94 h for the blastocyst stage. Additionally, zygotes were collected at the following times: 12 h for the PN0 stage, 15 h for PN1, 18 h for PN2, 21 h for PN3, 24 h for PN4, and 27 h for PN5. Embryos were cultured in KSOM medium (MR-121-D; Merck, Kenilworth, NJ, USA) under mineral oil at 37°C in a 5% CO2 incubator.

tag: developmental stage

value: mouse 4-cell

value: mouse embryos

value: H3K27ac (active motif, cat.39034)

tag: treatment

value: untreated


title: H3K27ac-4-cell-rep1

tag: cell type


title: RNAseq.E16M-rep3

source_name: Mesonephros

tag: Sex


title: RNAseq.Amhr2-rep1

tag: age


title: H3K27ac-4-cell-FK866-NMN-rep1

value: treated with FK866-NMN


title: H3K27ac-late-2-cell-Sirt1-rep2

value: mouse late 2-cell

value: treated with Sirt1


title: H3K27ac-4-cell-FK866-rep2

value: treated with FK866


title: H3K27ac-4-cell-FK866-rep1


title: RNAseq.E14M-rep2

value: male


title: RNAseq.E14M-rep3


title: RNAseq.E16M-rep2


title: H3K27ac-late-2-cell-Sirt1-rep1


title: RNAseq.E16F-rep2

value: female


title: H3K27ac-late-2-cell-TSA-rep2

value: treated with TSA


title: RNAseq.E16F-rep3


title: H3K27ac-late-2-cell-FK866-NMN-rep2


title: RNAseq.E14M-rep1


title: H3K27ac-late-2-cell-FK866-NMN-rep1


title: H3K27ac-late-2-cell-FK866-rep2


title: H3K27ac-late-2-cell-FK866-rep1


title: RNAseq.E14F-rep3


title: RNAseq.E14F-rep2


title: H3K27ac-late-2-cell-rep2


title: RNAseq.Amhr2-rep2


title: H3K27ac-4-cell-FK866-NMN-rep2


title: RNAseq.E14F-rep1


title: H3K27ac-late-2-cell-rep1


title: RNAseq.E16M-rep1


title: H3K27ac-late-2-cell-TSA-rep1


title: RNAseq.E16F-rep1


title: ATACseq.E16M-rep1

description: ATACseq-unified.peaks.bed.gz


title: ATACseq.E16F-rep2

description: ATACseq-unified.peaks.bed.gz


title: ATACseq.E14M-rep1

description: ATACseq-unified.peaks.bed.gz


title: ATACseq.E16F-rep1

description: ATACseq-unified.peaks.bed.gz


title: ATACseq.E14F-rep2

description: ATACseq-unified.peaks.bed.gz


title: ATACseq.E14M-rep2

description: ATACseq-unified.peaks.bed.gz


title: H3K27ac-Zygote-rep2

value: mouse zygote


title: H3K27ac-early-2-cell-rep2

value: mouse early 2-cell


title: H3K27ac-Sperm-rep2

value: mouse sperm


title: H3K27ac-early-2-cell-rep1


title: H3K27ac-MII-rep1

value: mouse MII


title: ATACseq.E14F-rep1

description: ATACseq-unified.peaks.bed.gz


title: H3K27ac-Zygote-rep1


title: H3K27ac-Sperm-rep1


title: Round3rep2

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: Third round of infection with IBV (replicate 2)

data_processing:
The reads were mapped to the CRISPR Calabrese sgRNA library and raw reads for each sgRNA were counted using the MAGeCK pipeline
Supplementary files format and content: Raw reads from the sequenced sgRNA amplicons mapped to the Calabrese sgRNA library
Supplementary files format and content: Reads shown are of each replicate of the screen from the transduced library input and after each round of infection with influenza B virus

growth_protocol: A549 cells were maintained throughout the screen in DMEM supplemented with 10% FBS, Glutamax, and Pen/Strep

extract_protocol:
Surviving cells were collected, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers. PCR amplified libraries were generated with independent barcodes to allow multiplexing.
OTHER: CRISPR Screen

treatment_protocol: Cells were transduced with the Calabrese sgRNA library at an MOI of 0.5, then repeatedly infected with influenza B virus

tag: cell line


title: Round3rep1

description: Third round of infection with IBV (replicate 1)


title: Round2rep1

description: Second round of infection with IBV (replicate 1)


title: ATACseq.E16M-rep2

description: ATACseq-unified.peaks.bed.gz


title: Round2rep2

description: Second round of infection with IBV (replicate 2)


title: Round1rep2

description: First round of infection with IBV (replicate 2)


title: Round1rep1

description: First round of infection with IBV (replicate 1)


title: TransInputRep2

description: Uninfected transduced library input (replicate 2)


title: H3K27ac-MII-rep2


title: TFK-1, HOXA5 overexpression, Flag, CST

city: Wuhan

first: Fei

last: Xiong

state: Hubei

address: Jiefang Road No.1095

institute: Huazhong University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting.
Bowtie2 software was used to compare Clean Reads with the reference genome for analysis; DeepTools' computeMatrix module was used to analyze the Reads distribution in the upstream and downstream 3kb regions of transcription start sites (TSS).
MACS2 software was used to complete Peak detection in genome-wide range, and CHIPseeker software R package was used to analyze and calculate the distribution of Peak in each functional area.
MACS2 software is used to compare the Peaks of different experimental groups in two groups, so as to obtain the Peaks difference between different experimental groups. For a candidate difference peaks region, it is required to be enriched in at least one sample, and its likelihood ratio (log10 Likelihood ratio) is used to determine whether there is a difference.
Assembly: GRCh38
Supplementary files format and content: txt, narrowPeak

extract_protocol:
CUT & Tag assay was performed with the Hyperactive Universal CUT&Tag Assay Kit (Vazyme). 1×106 TFK-1 cells were harvested and their nuclei were extracted. The extracted nuclei were immobilized with activated concanavalin A‐coated magnetic beads and reacted with anti-Flag antibodies (1:50) in 100 μL DIG buffer overnight at 4℃. After being washed, the bound antibodies were reacted with secondary antibodies (1:50) for 1 h at room temperature and incubated with 100 μl Hyperactive pA/G-Transposon adapter complex (0.04 μM) for 1 h at room temperature. The precipitated immunocomplex was diluted in Trueprep Tagment Buffer L and after proteinase K digestion, the DNA fragments were extracted and stored at -80 ℃.
A DNA library was constructed using the TruePrep Index Kit V2 (Vazyme). The DNA fragments were mixed with N5XX and N7XX and amplified by PCR at 72 ℃ for 3 min, 95 ℃ for 3 min, and subsequent 10 cycles of 98 ℃ for 10 sec and 60 ℃ for 5 sec, 72 ℃ for 1 min and hold at 4 ℃. The library was extracted by VAHTS DNA Clean Beads (Vazyme). Average insert size of the molecules sequenced in T1 sample is 461. Average insert size of the molecules sequenced in T1 sample is 447. The specific gene sequences with paired ends were analyzed with DNA sequencing in an Illumina PE150 platform (Illumina)

value: Extrahepatic cholangiocarcinoma

value: Flag (14793S, CST)

value: HOXA5 overexpression


title: TransInputRep1

description: Uninfected transduced library input (replicate 1)


title: CalInfA2

data_processing:
The reads were mapped to the CRISPR Calabrese sgRNA library and raw reads for each sgRNA were counted using the MAGeCK pipeline.
sgRNA enrichment was determined using the MAGeCK analysis pipeline.

source_name: human hepatoma Huh7 cell line

growth_protocol: Huh7 cells were cultured with DMEM containing 10% FBS

extract_protocol:
Genomic DNA in control and survival cells were both extracted with QIAamp DNA Blood Maxi Kit (QIAGEN, catalog no. 51192) and the sgRNA sequences were amplified via PCR.
Illumina adaptors and barcodes were incorporated into the PCR primers. PCR amplified libraries were generated with independent barcodes to allow multiplexing.

treatment_protocol: Huh7-dCas9 cells were transduced with CRISPR activation sgRNA library (Calabrese set A, Addgene#92379) at 0.5 MOI in two replicates. Two days later, cells were placed under 1 µg/mL puromycin selection. Next, half of the cells were collected as control and the other half of cells were infected with HCoV-229E (MOI=0.02). The infected cells were cultured and expanded for seven weeks.

value: infected


title: TFK-1, Nornal control, Flag, CST

value: Normal control


title: CalInfA1


title: CalTransA2

value: Uninfected


title: 4TFs-c-myc-1 RPE cells

city: Shanghai

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Genome_build: hg38
Supplementary_files_format_and_content: RNA-SEQ FPKM.TXT

source_name: Dedifferentiated iPSC-RPE cells

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: 4TFs-c-myc-1 RPE


title: 4TFs-c-myc-2 RPE cells

value: 4TFs-c-myc-2 RPE


title: TFK-1, H3

description: TFK-1 cells (HOXA5 overexpression VS Normal control)

hyb_protocol: 10 ug of Cy5-labeled aRNA was hybridized to the Phalanx Human OneArray 6.1 by Phalanx Hybridization System according to the Phalanx Hybridization Protocol.

scan_protocol: After hybridization, the arrays were washed, scanned and the gene expression results were extracted by DNA Microarray Scanner G2565B (Agilent), according to the manufacturer’s instructions.

data_processing:
Raw fluorescence intensity values were normalized and log-transformed using GeneSpring GX 10 software (Agilent).
Expression value normalized and log-transformed by GeneSpring GX 10 software

source_name: Extrahepatic cholangiocarcinoma cell line

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Cy5-labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000.

growth_protocol: TFK-1 was maintained in RPMI-1640 with 10% FBS.

extract_protocol: Total RNA was extracted from individual cell samples using RNA Extraction Reagent (Vazyme) according to the instructions. The samples were resuspended with nuclease-free water.RNA quantity and purity was assessed using NanoDrop ND-1000.

treatment_protocol: TFK-1 cells were transduced with specific lentiviruses at a multiplicity of infection (MOI) of 20 in the presence of HistransG (Genechem) for 24 h. The cells were cultured in complete medium for two days and treated with 1 μg/ml of puromycin for the establishment of stable cell lines.

value: extrahepatic cholangiocarcinoma cell

tag: genotype


title: CalTransA1


title: TFK-1, H2


title: 4TFs-nr2e1-1 RPE cells

value: 4TFs-nr2e1-1 RPE


title: 4TFs-mitf-a-2 RPE cells

value: 4TFs-mitf-a-2 RPE


title: 4TFs-mitf-a-1 RPE cells

value: 4TFs-mitf-a-1 RPE


title: LMH cells, PFT, PFTV4

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Assembly: Gallus_gallus-4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: LMH

growth_protocol: LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Separated cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LMH cells with or without ILTV infection were treated with Nutlin dissolved in DMSO at a final concentration of 10 μM or PFT-α dissolved in DMSO at a final concentration of 20 μM. Control groups were treated with DMSO at the same volumes, and the final concentration of DMSO in the cell culture studies was 0.1% or less.

value: LMH

value: liver cells

tag: infection

value: ILTV

value: PFT

tag: ILTV infection


title: LMH cells, PFT, PFTV2


title: LMH cells, PFT, PFTV3


title: TFK-1, N3


title: TFK-1, N2


title: TFK-1, N1


title: 5-azacytidine-treated SK-HEP-1 cells

first: Xing-Xing

last: He

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

description:
US80803205_251911813821_S02_2_3
MiRNA expression in SK-HEP-1 cells treated with 5μM 5-azacytidine for 24 h.

hyb_protocol: See manufacturer's web site at http://www.agilent.com/.

scan_protocol: Images were scanned with the Agilent microarray scanner, and the results were obtained by Agilent Feature Extraction software, Scan resolution 5μm, PMT 100%, 5%.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software. The raw intensity data were quantile normalized and further analyzed using GeneSpring10.0 software.

source_name: human hepatoma cell line SK-HEP-1, 5μM 5-azacytidine, 24 h

growth_protocol: The human hepatoma cell line SK-HEP-1 was cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 ℃ with 5% carbon dioxide.

extract_protocol: The MirVana miRNA Isolation Kit (Ambion, AM1560) was used to isolate total RNA (including miRNA) according to the manufacturer’s protocol.

treatment_protocol: Exponentially growing SK-HEP-1 cells were treated with 5μM 5-azacytidine for 24 hours.

value: hepatocellular carcinoma cells

value: 5μM 5-azacytidine

tag: treatment duration

value: 24 hr


title: TFK-1, H1

value: HOXA5 overexpression


title: 4TFs-crx-2 RPE cells

value: 4TFs-crx-2 RPE


title: LMH cells, PFT, PFTV1


title: 4TFs-crx-1 RPE cells

value: 4TFs-crx-1 RPE


title: iPRE-3 cells


title: LMH cells, PFT, PFT4

value: control

tag: no infection


title: LMH cells, PFT, PFT3


title: LMH cells, PFT, PFT2


title: iPRE-2 cells


title: iPRE-1 cells


title: 4TFs-nr2e1-2 RPE cells

value: 4TFs-nr2e1-2 RPE


title: De-iPSC-RPE-3 cells

source_name: iPSC-RPE cells


title: LMH cells, PFT, PFT1


title: De-iPSC-RPE-2 cells


title: De-iPSC-RPE-1 cells


title: LMH cells, Nutlin, NV3

value: Nutlin


title: iPSC-RPE-1 cells

source_name: Human iPSCs


title: LMH cells, Nutlin, NC4


title: LMH cells, Nutlin, NC3


title: LMH cells, Nutlin, NV2


title: LMH cells, Nutlin, NC2


title: LMH cells, Nutlin, NC1


title: LMH cells, DMSO, DV3

value: DMSO


title: LMH cells, Nutlin, NV1


title: LMH cells, DMSO, DV4


title: Donor 6, IL-2v polypeptide

city: Marseille

first: Eric

last: Vivier

address: 117 Avenue de Luminy BP 30191

country: France

institute: Innate Pharma

data_processing:
Demultiplexing of sequencing data containing unique molecular identifers (UMIs) was performed following guidelines provided by IDT. Briefly, extraction of sample barcodes for every read in every sequencer lane, demultiplexing each lane of bcl files and creation of per-sample unaligned BAM including UMI data, conversion of BAM files to fastq.gz files, mapping of fastq.gz reads and finally merging of sorted aligned BAM files with sorted unaligned BAM files with UMI data. The Picard software suite v2.18.29 was used (Broad Institute 2019).
The reads were mapped to the human genome (GRCh38) release 98 and to the mouse genome (GRCm38) release 98 using STAR v2.7.0 (Dobin et al., 2013).
PCR replicates were removed with Picard UmiAwareMarkDuplicatesWithMateCigar program (Broad Institute 2019).
Gene expression was calculated by featureCounts in SubReads package v1.6.4 (Liao et al., 2014).
Assembly: GRCh38
Supplementary files format and content: BAM files are alignement files where technical duplicated reads (identified by UMIs) were removed
Supplementary files format and content: TSV files include raw counts and TMM-normalized counts

source_name: blood

extract_protocol:
Total RNA was extracted using RNeasy micro kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was assessed using the Qubit RNA HS Assay kit (Thermofisher).
RNA-Seq libraries were prepared from 80ng to 200ng of total RNA using the KAPA RNA HyperPrep kit (Roche). mRNAs were enriched with oligo dT magnetic beads and then fragmented for 5min30 at 94°C. Cleaved mRNA fragments were used as templates for double stranded DNA synthesis followed by A-tailing. The 8 bp UMI containing TruSeq Compatible Duplex Y adapters UDI-UMI, (Unique dual index - Unique molecular identifier) from IDT were then ligated on both sides of the cDNA. After bead-based purification, libraries were amplified by PCR for 10-12 cycles. Cleaned-up libraries were quantified using the Qubit 1X dsDNA HS Assay kit (Thermofisher) and quality was assessed using TapeStation.

treatment_protocol: Purified NK cells from blood were activated with tetraspecific ANKET, trispecific aNKp46/Fc/aCD20, the Fc-enhanced anti-CD20 mAb  obinutuzumab or an IL-2v polypeptide (IL2v/IC/Fc null/IC) in the presence of CD20+ tumor target cells.

value: blood

value: NK cells from healthy donors stimulated by transfected murine B16F10 cells expressing the human CD20 antigen

value: tetraspecific ANKET


title: Donor 6, trispecific aNKp46/Fc/aCD20


title: Donor 6, combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: LMH cells, DMSO, DV1

value: LMH


title: Donor 5, tetraspecific ANKET

value: combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: Donor 5, obinutuzumab


title: Donor 6, unstimulated condition


title: Donor 6, obinutuzumab


title: Donor 5, IL-2v polypeptide


title: LMH cells, DMSO, DC3

value: liver cells


title: LMH cells, DMSO, DC4


title: LMH cells, Nutlin, NV4

value: ILTV


title: Donor 5, combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: Donor 5, trispecific aNKp46/Fc/aCD20


title: LMH cells, DMSO, DC2


title: DC1

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assembly was  finished by Cufflinks 2.2.1.
The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.
Genome_build: The reference genome and annnotation is download form http://ftp.ensembl.org/pub/release-73/fasta/gallus_gallus/dna/.
Supplementary_files_format_and_content: normalized counts

extract_protocol:
Sample was treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LMH cells were collected and RNA was extracted for RNA-seq.

value: Chick embryo liver


title: Donor 6, tetraspecific ANKET


title: iPSC-RPE-2 cells


title: Donor 4, tetraspecific ANKET

value: obinutuzumab


title: Donor 4, obinutuzumab


title: Donor 4, IL-2v polypeptide


title: Donor 4, combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: RPMI+B27-treated biowire tissue, stimulated, rep3

city: Toronto

first: Neal

middle: I

last: Callaghan

state: Ontario

address: 661 University Ave

department: Institute of Biomedical Engineering

institute: University of Toronto

description:
rpmi_bw_stim_3
biowire_counts.xlsx

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to GR.Ch38 using Salmon in mapping-based mode with default settings.
Gene-level read counts were obtained from Salmon output files using Tximeta.
Assembly: GR.Ch38
Supplementary files format and content: Excel files containing raw read counts for each sample

source_name: PGPC-17 induced pluripotent stem cells

extract_protocol:
Total RNA was extracted from iPSC-CM monolayers using the Qiagen RNeasy Micro kit. Total RNA was extracted from Biowire II tissues using the PicoPure™ kit (Thermo-Fisher).
For iPSC-CM monolayer samples, RNA libraries for RNA-seq were prepared using the Stranded Total RNA Prep kit (Illumina Inc, USA). For Biowire samples, RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit (Takara Bio Inc., Japan).

value: PGPC-17 induced pluripotent stem cells

value: cardiomyocyte

value: WT

tag: media

tag: culture format

value: Biowire


title: RPMI+B27-treated biowire tissue, unstimulated, rep1

description:
rpmi_bw_unstim_1
biowire_counts.xlsx


title: RPMI+B27-treated biowire tissue, stimulated, rep2

description:
rpmi_bw_stim_2
biowire_counts.xlsx


title: RPMI+B27-treated biowire tissue, unstimulated, rep3

description:
rpmi_bw_unstim_3
biowire_counts.xlsx


title: RPMI+B27-treated biowire tissue, unstimulated, rep2

description:
rpmi_bw_unstim_2
biowire_counts.xlsx


title: Donor 4, trispecific aNKp46/Fc/aCD20

tag: tissue


title: RPMI+B27-treated biowire tissue, stimulated, rep1

description:
rpmi_bw_stim_1
biowire_counts.xlsx


title: c16-treated biowire tissue, unstimulated, rep3

description:
c16_bw_unstim_3
biowire_counts.xlsx


title: c16-treated biowire tissue, unstimulated, rep4

description:
c16_bw_unstim_4
biowire_counts.xlsx


title: Donor 4, unstimulated condition


title: NF62 TR ChIP

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

data_processing:
We conducted quality processing on raw reads (fastq) files from each sample to remove poor quality bases  and adapter sequences using fastp (v0.20.1). Quality assessments on raw and trimmed reads were  performed using FastQC (v0.11.9).
Processed reads were aligned to the Xenopus tropicalis genome (v9.1), Ensembl release 101, using bwa-mem (v0.7.17) and default parameters.
Alignments were then sorted, indexed using samtools (v1.13). Duplicates were marked using Picard (v2.18.2). Unmapped reads, secondary alignments, PCR or optical duplicates, and mappings with a quality below 30 were filtered out with samtools (v1.13).
Read depth-normalized bigwig files were created from sorted files using bamCoverage from deepTools (v3.5.1).
Areas of enriched TR binding were identified using MACS2 (v2.2.6) with the sharp peak type. For binding sites within 10 kb upstream of a transcription start site (TSS) or witin a gene-body, ChIPPeakAnno  (v3.26.4) the peak was annoated with: the corresponding gene name, the distance from the peak to the gene, and the relative position of the peak relative to the gene feature (ie., upstream, internal).
Assembly: v9.1, Ensembl release 101
Supplementary files format and content: MAC2 output file, annotated with (for binding sites within 10 kb upstream of a tss) the corresponding gene name, the distance from the peak to the gene, and the relative position of the peak relative to the gene feature. Columns are the peak name, the chromosome, the start position of the peak on the chromosome, the end position of the peak on the chromosome, the width of the peak, the strand, macs2 score, enrichment score, negative log10 p-value, log10 false-discovery rate, base pair of the of the absolute peak, gene id, gene start position, gene end position, gene length, strand the gene is on,  distance from peak to gene, position of peak relative to gene (inside, overlap, upstream, etc.), distance from peak to gene, gene symbol, full gene name.

organism: Xenopus tropicalis

source_name: Brain (POA/hypothalamus/thalamus)

growth_protocol: We obtained wildtype (WT) Xenopus tropicalis frogs from NASCO and reared them in dechlorinated tap water at 25C under a 13L:11D photoperiod, and fed them frog brittle (NASCO, Fort Atkinson, WI) or Sera Micron plankton food (tadpoles only).

extract_protocol:
We isolated chromatin from NF stage 62 X. tropicalis tadpole brain. The isolated chromatin was cross-linked with formaldehyde, fragmented by sonication, then precipitated (5 µg per reaction) using a polyclonal antiserum to Xenopus TRs (PB antiserum provided by Yun-Bo Shi) and the Magna ChIP A/G kit (Millipore) following the manufacturer's protocol.
The sequencing libraries were constructed on the Apollo instrument (an automated system) using IntegenX reagents (now Wafergen, Fremont, CA) at the University of Michigan DNA sequencing core.

value: Wild type

value: brain

tag: brain region

value: middle brain region containing the preoptic area/hypothalamus/thalamus

value: anti-TR


title: Donor 3, tetraspecific ANKET

value: blood

value: trispecific aNKp46/Fc/aCD20


title: Donor 3, obinutuzumab

value: NK cells from healthy donors stimulated by transfected murine B16F10 cells expressing the human CD20 antigen


title: c16-treated biowire tissue, unstimulated, rep2

description:
c16_bw_unstim_2
biowire_counts.xlsx


title: LMH cells, DMSO, DV2

value: LMH

value: DMSO


title: Donor 3, trispecific aNKp46/Fc/aCD20


title: Donor 3, IL-2v polypeptide


title: Donor 3, combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: Donor 3, unstimulated condition


title: c16-treated biowire tissue, unstimulated, rep1

description:
c16_bw_unstim_1
biowire_counts.xlsx


title: Donor 5, unstimulated condition

value: combination of the trispecific aNKp46/Fc/aCD20 and the IL-2v polypeptide


title: NF62 Input

tag: chip antibody

value: none (input)


title: c16-treated biowire tissue, stimulated, rep4

description:
c16_bw_stim_4
biowire_counts.xlsx


title: Donor 2, trispecific aNKp46/Fc/aCD20

value: IL-2v polypeptide


title: shrek1_3

city: Qingdao

first: hui

last: liu

state: Shandong

address: 72 Binhai Road, Jimo, Qingdao, P.R. China

institute: Shandong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data, then mapped to the reference genome Zm-B73-REFERENCE-NAM-5.0 by HISAT2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is used  for estimating gene expression levels.
Genome_build: Zm-B73-REFERENCE-NAM-5.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: FPKM values for each sample

organism: Zea mays

source_name: Kernels

growth_protocol: The maize plants were grown in the experimental filed of Shandong University under natural conditions.

extract_protocol:
Kernel at 13DAP was peeled the pricarp and frozen immediately by liquid nitrogen. RNA was extracted by Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: geneotype

value: Kernels

tag: timepoint

value: 13 days after pollination


title: c16-treated biowire tissue, stimulated, rep3

description:
c16_bw_stim_3
biowire_counts.xlsx

value: PGPC-17 induced pluripotent stem cells

tag: cell type

value: cardiomyocyte


title: Donor 1, tetraspecific ANKET

tag: treatment

value: No treatment


title: Donor 1, unstimulated condition


title: c16-treated biowire tissue, stimulated, rep2

description:
c16_bw_stim_2
biowire_counts.xlsx

value: WT

value: Biowire


title: Donor 1, trispecific aNKp46/Fc/aCD20


title: c16-treated biowire tissue, stimulated, rep1

description:
c16_bw_stim_1
biowire_counts.xlsx


title: shrek1_1


title: pre-treatment monolayer, d20, rep3

description:
d20_3
monolayer_counts.xlsx

value: Control

value: Monolayer


title: WT_2

value: wild-type


title: WT_1


title: D9_Low_CD8_S14_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

data_processing:
ATAC-seq reads were analyzed for quality control measures prior alignment to the human genome assembly (GRCh38) using Bowtie2 (v2.3.4).
For each sample, mitochondrial reads, ummapped reads and low mappability (< 30) reads were filtered out using samtools (v1.9). Library complexity and removal of PCR duplicates were done with Picard tools (v2.18.17). Reads in blacklisted genomic regions as defined by ENCODE for human were removed. All downstream analyses were performed on these filtered reads.
BigWig files were generated with deepTools.
Peak calling from each individual replicate was performed with MACS2 (v.2.1.0).
Differential accessible analysis was analyzed with Csaw R package.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files

source_name: Donor cells

extract_protocol:
Accessible chromatin mapping was performed using FAST-ATAC-seq (56) with minor modifications. Briefly, 10000 CD4+ or CD8+ CARHigh T or CARLow T cells from six independent donors were sorted in 1X PBS, 0.05% BSA and pelleted by centrifugation at 500 rcf for 5 min at 4 °C with low acceleration and brake settings in a pre-cooled swinging-bucket rotor centrifuge. All the supernatant but 5 µL was removed. Next, 25 µL of transposase mix (15 µL of 2x TD buffer (Illumina); 1 µL of TDE1 (Illumina), 0.25 µL of 5% digitonin (Promega); 8.75 µL of nuclease- free water) were added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37 °C for 30 min in an Eppendorf ThermoMixer with shaking at 450 rpm. Reactions were stopped at 4 °C for 5 min. In order to release tagmented DNA, samples were incubated at 40 °C for 30 min with 5 µL of clean up buffer (900 mM NaCl (Sigma), 30 mM EDTA (Millipore), 2 µL of 5% SDS (Millipore) and 2 µL of Proteinase K (NEB)). DNA was purified using a 2X SPRI beads cleanup kit (Agencourt AMPure XP, Beckman Coulter).
CRs were performed using KAPA HiFi DNA Polymerase and customized Nextera PCR indexing primers (IDT). The conditions of the first PCR were: 5 min at 72 °C and 2 min at 98 °C followed by 9 cycles of 20 secs at 9 °C, 30 secs at 63 °C, and 1 min at 72 °C. Depending on the library concentration in this first PCR, a second PCR (2 min at 98 °C followed by 4 to 6 cycles of 20 secs at 98 °C, 30 secs at 63 °C, and 1 min at 72 °C) was performed aiming for a library concentration in the range of 2 to 10 ng/µL. PCR products were purified using a 2X SPRI beads cleanup. Libraries were quantified and their size profiles examined as described above. Sequencing was carried out in an Illumina NextSeq500 using paired-end, dual-index sequencing (Read1: 38 cycles; Read2: 38 cycles; i7 index: 8 cycles; i5 index: 8 cycles).

tag: diagnosis

value: Healthy

value: Blood

value: D9_Low_CD8 CAR T cells


title: LMH cells, overexpression of chicken p53 with flag, Input3

data_processing:
Basecalls were performed using bcl2fastq2 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the Gallus_gallus-4.0 genome using Bowtie version 2.1.0. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01. bigWig files were generated using the genomicRanges R package.
Assembly: Gallus_gallus-4.0
Supplementary files format and content: bigWig

extract_protocol:
LMH cells were fixed in 1% formaldehyde for 10 min and then with 0.125 M glycine. Each ChIP experiment was performed with sheared chromatin samples and indicated antibody. The immunoprecipitated DNA was purified using a QIAquick PCR Purification Kit (28106, QIAGEN, Valencia, CA).
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit following manufacturer's protocols.

tag: cell line

value: LMH

value: liver cells

value: p53 overexpression


title: Donor 2, tetraspecific ANKET

value: blood

value: NK cells from healthy donors stimulated by transfected murine B16F10 cells expressing the human CD20 antigen

value: IL-2v polypeptide


title: pre-treatment monolayer, d20, rep1

description:
d20_1
monolayer_counts.xlsx

value: PGPC-17 induced pluripotent stem cells


title: D9_Low_CD4_S13_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D9_Low_CD4 CAR T cells


title: STEMCELL-treated monolayer, d20 + 6 weeks, rep3

description:
sc_3
monolayer_counts.xlsx

value: cardiomyocyte

value: STEMCELL


title: STEMCELL-treated monolayer, d20 + 6 weeks, rep2

description:
sc_2
monolayer_counts.xlsx

value: WT


title: D8a_Low_CD4_S7_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D8a_Low_CD4 CAR T cells


title: LMH cells, overexpression of chicken p53 with flag, Input4


title: LMH cells, overexpression of chicken p53 with flag, Input1


title: LMH cells, overexpression of chicken p53 with flag, Input2


title: STEMCELL-treated monolayer, d20 + 6 weeks, rep1

description:
sc_1
monolayer_counts.xlsx

value: Monolayer


title: shrek1_2

value: Kernels

value: 13 days after pollination


title: D8a_Low_CD8_S8_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: Healthy

value: Blood

value: D8a_Low_CD8 CAR T cells


title: Donor 2, unstimulated condition


title: D9_High_CD4_S17_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D9_High_CD4 CAR T cells


title: D8a_High_CD4_S11_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D8a_High_CD4 CAR T cells


title: RPMI+B27-treated monolayer, d20 + 6 weeks, rep3

description:
rpmi_3
monolayer_counts.xlsx


title: LMH cells, overexpression of chicken p53 with flag, Flag3

value: LMH

value: liver cells

value: p53 overexpression

value: Flag（GenScript, #A00187）


title: D7_Low_CD8_S2_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D7_Low_CD8 CAR T cells


title: D7_Low_CD4_S1_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D7_Low_CD4 CAR T cells


title: RPMI+B27-treated monolayer, d20 + 6 weeks, rep2

description:
rpmi_2
monolayer_counts.xlsx

value: PGPC-17 induced pluripotent stem cells

value: cardiomyocyte


title: WT_3

value: wild-type


title: LMH cells, overexpression of chicken p53 with flag, Flag2


title: D7_High_CD8_S6_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D7_High_CD8 CAR T cells


title: D7_High_CD4_S5_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D7_High_CD4 CAR T cells


title: D9_High_CD8_S18_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D9_High_CD8 CAR T cells


title: D18_Low_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: Healthy

value: D18_Low_CD8_d0 CAR T cells


title: RPMI+B27-treated monolayer, d20 + 6 weeks, rep1

description:
rpmi_1
monolayer_counts.xlsx

value: WT

value: Monolayer


title: LMH cells, overexpression of chicken p53 with flag, Flag1


title: D18_Low_CD4_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: Blood

value: D18_Low_CD4_d0 CAR T cells


title: iCell-treated monolayer, d20 + 6 weeks, rep3

description:
icell_3
monolayer_counts.xlsx

value: iCell


title: D18_High_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D18_High_CD8_d0 CAR T cells


title: D14_Low_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D14_Low_CD8_d0 CAR T cells


title: iCell-treated monolayer, d20 + 6 weeks, rep2

description:
icell_2
monolayer_counts.xlsx


title: D18_High_CD4_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D18_High_CD4_d0 CAR T cells


title: LMH cells, overexpression of chicken p53 with flag, Flag4

value: LMH

value: liver cells

value: p53 overexpression

value: Flag（GenScript, #A00187）


title: iCell-treated monolayer, d20 + 6 weeks, rep1

description:
icell_1
monolayer_counts.xlsx

value: PGPC-17 induced pluripotent stem cells

value: cardiomyocyte


title: D14_High_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D14_High_CD8_d0 CAR T cells


title: D14_Low_CD4_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: Healthy

value: D14_Low_CD4_d0 CAR T cells


title: D8a_High_CD8_S12_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D8a_High_CD8 CAR T cells


title: C16-treated monolayer, d20 + 6 weeks, rep3

description:
c16_3
monolayer_counts.xlsx

value: WT

value: Monolayer


title: D14_High_CD4_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: Blood

value: D14_High_CD4_d0 CAR T cells


title: D10_Low_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D10_Low_CD8_d0 CAR T cells


title: C16-treated monolayer, d20 + 6 weeks, rep2

description:
c16_2
monolayer_counts.xlsx


title: D10_Low_CD4_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D10_Low_CD4_d0 CAR T cells


title: C16-treated monolayer, d20 + 6 weeks, rep1

description:
c16_1
monolayer_counts.xlsx


title: D10_High_CD8_d0_R1_001 [ATAC-seq]

description: FAST-ATAC-seq

value: D10_High_CD8_d0 CAR T cells


title: T3

city: Linfen

first: lin

middle: jin

last: feng

state: Shanxi

address: gongyuan 1 street

department: College of Life Sciences

institute: Shanxi Normal University

data_processing:
Clean data were obtained by removing reads containing adapters, calls marked as N, and low-quality reads from the raw data.
The high-quality reads were mapped to the Arabidopsis TAIR10 genome using Hisat2 v2.0.5.
The expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced for each gene was calculated based on the length of the gene and read count mapped to the gene.
Assembly: Arabidopsis TAIR10 genome
Supplementary files format and content: Alignment information from reads to reference sequences.
Supplementary files format and content: gene_fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: TreatmentvsControl_deg_all.txt: Tab-delimited text file

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) from the treatment group and the control group seedlings.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: seedlings

value: MS Medium with 20 mM yttrium oxide nanoparticles

tag: time

value: 6 h


title: T2

tag: genotype


title: T47D_WT_clone2_mimic_neg_ctrl

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Reads were aligned to the human genome using HISAT2.
Sam files were then converted to bam files and sorted via Samtools.
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package.
Normalization and differential expression analysis were performed using DeSeq2.
Assembly: hg19
Supplementary files format and content: Raw gene counts in a text file

growth_protocol: Cells were cultured in RPMI1640 Media (ThermoFisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
24 hours post-transfection, cells were collected, washed with PBS, then treated with RLT Plus lysis buffer supplemented with 1% BME. RNA was extracted using a Quick-RNA RNA Miniprep kit (Zymo Research).
Poly-A selected RNA-seq libraries were generated using a KAPA Stranded mRNA-Seq kit (KAPA Biosystems) and 500ng RNA per sample as starting material.

treatment_protocol: T-47D cells were grown in 100mm plates in hormone-deprived media for four days then plated into 12-well plates at approximately 50% confluence and allowed to adhere for 24 hours. Cells were then transfected with a miRNA mimic or inhibitor for a given miRNA or with a mimic or inhibitor negative control at a 10nM final concentration.

value: mammary gland ductal carcinoma

tag: esr1 genotype

value: mimic negative control


title: D10_High_CD4_d0_R1_001 [ATAC-seq]

institute: CIMA

description: FAST-ATAC-seq

value: D10_High_CD4_d0 CAR T cells


title: T47D_WT_clone1_mimic_neg_ctrl


title: T47D_WT_clone2_mimic_miR_181c_5p

value: hsa-miR-181c-5p mimic


title: sc5_D14_BCMA_d0 [scRNA-seq]

data_processing:
The raw scRNA-seq data were demultiplexed, aligned to the Human (GRCh38) reference and the feature-barcode matrix was quantified using Cell Ranger (v3.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5). Cells were subjected to QC filters based on the number of detected genes, number of UMIs and proportion of UMIs mapped to mitochondrial and ribosomal genes per cell. The thresholds filters for each variable were selected based on their distribution within each of the single cell libraries and visual inspection of quality control scatter plots. Genes detected in fewer than three cells and cells where fewer than 150 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 10% and more than 40% mitochondrial or ribosomal content respectively, were also discarded. In addition, cells with more than the 97.5th percentile of detected genes per sample, were discarded to remove likely doublet or multiplet captures.
Each dataset was subjected to normalization, identification of highly variable genes and removal of unwanted sources of variation using Seurat (v3.1.5). Integration of all the dataset was based on Seurat’s canonical correlation analysis. Different resolution parameters for unsupervised clustering were examined to determine the optimal number of clusters. For this study, the first 40 PCs and 3000 highly variable genes identified by Seurat were used for sample integration and unsupervised clustering analysis with the resolution set to 0.8, yielding a total of 23 cell clusters. Non-linear dimensional reduction was performed using t-distributed stochastic neighbour embedding (t-SNE) and UMAP.
TCR V(D)J sequence assembly, paired clonotype calling, TCR diversity and clonality analysis. TCR reconstruction and paired TCR clonotype analysis was performed using Cell Ranger v3.0.2 for V(D)J sequence assembly. The CDR3 motif was located, and the productivity was determined for each single cell. The clonotype landscape was then assessed, and the clonal fraction of each identified clonotype was calculated. The TCR clonotype diversity matrix was calculated using the tcR R package. TCR clonality was defined as 1-Peilou’s evenness and was calculated on productive rearrangements as previously described. Clonality values approaching 0 indicate a very even distribution of clone frequencies, whereas values approaching 1 indicate an increasingly.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell recovered as per Cell Ranger (v3.0.1). barcodes.tsv (10X Genomics Chromium Raw Gene BC Cellular Barcodes), features.tsv (10X Genomics Chromium Raw Gene BC Cellular Genes), matrix.mtx (10X Genomics Chromium Raw Gene BC Cellular Matrix) files.
Supplementary_files_format_and_content: *VDJ.csv: Comma-separated text files.

extract_protocol:
FACS-sorted CAR T cells (BFP+ cells) from three independent donors were interrogated using the 10X Chromium platform for simultaneous transcriptome and TCR profiling, with 28,117 cells (range, 7,416-10,5093 cells/donor) passing our quality control (QC) thresholds and taken into subsequent analysis. These cells were sequenced to an average depth of 42,296 reads/cell, yielding an average of 2,541 genes/cell.
scRNA-seq was performed using the Chromium Single Cell 5′ Reagent Kit (10X Genomics) according to the manufacturer’s instructions. Briefly, CAR T cells were sorted in 100µl 1X PBS, 0.04% BSA and their concentration and viability were determined using Nexcelom’s Cellometer K2 Fluorescent Cell Counter. Cell concentration was adjusted to 700 to 1200 cells/µl to maximize the likelihood of achieving the desired cell recovery target. Then single-cell suspension was mixed with RT Master Mix and loaded together with barcoded single-cell 5′ gel beads and partitioning oil into separate single cell A Chips to generate Gel Beads in Emulsion (GEMs) using Chromium Controller. Thus, individual cells were lysed and the polyadenylated RNA was reverse-transcribed and barcoded inside each GEM. Barcoded complementary DNA (cDNA) was recovered through post GEM-RT cleanup and PCR-amplified. cDNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its profile examined using High Sensitivity D5000 ScreenTape Assay (Agilent Technologies). Fifty nanograms of double-stranded cDNA were used for 5′ Gene Expression library construction. cDNA was fragmented, end-repaired, A-tailed and ligated to an adaptor. A final PCR-amplification with barcoded primers was performed for sample indexing.
Single-cell TCR repertoire sequencing. TCRTCR α/β sequencing was performed with 10X Genomics Single Cell V(D)J Immune Profiling Solution (10× Genomics). Briefly, full-length V, D and J gene segments were amplified from barcoded cDNA using a Chromium Single Cell V(D)J Enrichment Kit (human T cells) by means of two sequential PCRs with primers targeting the adaptor and the gene constant region. Enriched cDNA was quantified as described above and 50 ng were further used for library construction as described above. After quality control and quantification, Single Cell V(D)J enriched libraries were pooled and sequenced in an Illumina’s HiSeq X (Read1: 150 cycles; Read2: 150 cycles, i7 index: 8 cycles) at an average depth of 5000 reads per cell.

value: Healthy

value: BFP+ CAR T cells


title: T47D_WT_clone1_mimic_miR_181c_5p


title: T1


title: C3

value: MS Medium


title: sc5_D10_BCMA_d0 [scRNA-seq]