title: Treg NT STAT4 rep1

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Anti-CD3 + anti-CD28, IL-2, no IL-12.
Treg.NT.STAT4.e2b1.narrowPeak

data_processing:
Adapters were trimmed using TrimGalore  (ver 0.6.4_dev using Cutadapt version 4.2)
FASTQ files were aligned using bowtie2 (ver 2.5.1) with the parameters “--very-sensitive –no-discordant -5 0 -3 0” to GRCh38 and duplicates were marked using Picard MarkDuplicates and removed using samtools, along with any reads mapping to unplaced scaffolds or the GRCh38 blacklist.
bigWigs for each STAT4 IP replicate were generated using DeepTools bamCoverage -of bigwig --binSize 1 --normalizeUsing CPM --extendReads
Peaks for STAT4 IP samples were called using macs3 in narrow peak mode with IgG used as background.
Assembly: GRCh38
Supplementary files format and content: Normalized bigWig files represent STAT4 IP.
Supplementary files format and content: Peak files generated by macs3, STAT4 IP as treatment with IgG as the control.
Library strategy: CUT&RUN

source_name: cord blood

growth_protocol: Freshly isolated naive Treg cells (7.5 × 10˄4 cells per well) from cord blood or PBMCs were cultured at 37 ºC in serum-free AIM-V with 2 µL Dynabeads Human T-Activator CD3/CD28 and recombinant human IL-2. Naive conventional CD4 T cells were also cultured with the conditions above, but 4 ng/mL IL-7 instead of IL-2. No splitting was required for naive conventional CD4 T cells.

extract_protocol:
Cells were fixed wih 0.1% formaldehyde for 1 minute. After quenching, nuclei were extracted and permeabilized using 0.01% digitonin. Chromatin was digested with Mnase and released via incubation at 37ºCfor 30 minutes.
CUT&RUN libraries were prepared via the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were amplified for 15 cycles on a thermocycler and verified via agarose gel electrophoreses

treatment_protocol: 20 ng/mL recombinant human IL-12 at 2.5 days of culture. After 1 hour of treatment cells were harvested for CUT&RUN experiment.

value: cord blood

value: Treg

tag: cut&run antibody

tag: cell description

value: Live CD4+CD45RO-CD25HiCD127Lo/-CXCR5-.


title: Treg NT STAT4 rep2

status: Public on Apr 16 2024

type: SRA

country: USA

description:
Anti-CD3 + anti-CD28, IL-2, no IL-12.
Treg.NT.STAT4.e2b2.narrowPeak

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

tag: tissue

value: peripheral blood

tag: cell type

tag: treatment


title: Treg NT STAT4 rep3

description:
Anti-CD3 + anti-CD28, IL-2, no IL-12.
Treg.NT.STAT4.e2b3.narrowPeak


title: BCR-Seq, Spike-specific B cells, COVID-19, donor C1, C2 and C3

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description:
10x genomics
GC_d7_SPIKE_BCR.filtered_contig_annotations.csv

library_source: other

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files contain the BCR and/or TCR sequencing information for each sample, if available
Supplementary files format and content: *.h5 files contain barcode, matrix, and feature information for each sample as well as the Cite-seq reads for each sample
Library strategy: BCR-seq

molecule: other

source_name: Peripheral blood

extract_protocol:
Cells were enriched directly from blood by simultaneously using StraightFrom Whole Blood and Bone Marrow CD138 MicroBeads, StraightFrom Whole Blood CD19 MicroBeads and StraightFrom Whole Blood CD3 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions. Enriched cells were incubated with Fc Blocking Reagent (Miltenyi Biotec) following manufacturer’s instructions and subsequently stained for 30 min at 4°C with fluorophore-coupled anti-human antibodies. Simultaneously, cells were incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). DAPI was added before sorting to allow dead cell exclusion. Live CD3- CD14- CD38high CD27high lymphocytes (plasmablasts),  live CD3- CD14- CD38-/int CD27+ lymphocytes (memory B cells) and live CD14- CD3+ CD38+ HLA-DR+ lymphocytes (activated T cells) were subsequently sorted by FACS. These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (v1.1, single index) following the manufacturer’s instructions. Some samples were additionally stained with fluorophore-coupled tetanus toxoid and SARS-CoV-2 Spike Protein tetramers for the sorting and sequencing of antigen-specific cells.
The purified cDNA was amplified and then used for 5’ gene expression (GEX), CITE-Seq and BCR/TCR library preparation using the Single Cell 5’ Library & Gel Bead Kit (v1.1, 10x Genomics). BCR/TCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human B or T cells. Through fragmentation, adapter ligation and index PCR the final GEX and BCR/TCR libraries were obtained. The CITE-Seq libraries were obtained only by index PCR. The quality of single cell 5’ GEX, CITE-Seq and BCR/TCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq2000 device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 98nt, index1: 8nt, index2: 0) and NextSeq 1000/2000 P3 reagent kits (300 Cycles, Illumina) for BCR/TCR libraries (read1: 151nt, read2: 151nt, index1: 8nt, index2: 0, 20% PhiX spike-in).

value: Peripheral blood

value: B cells

tag: Sex

value: pooled male and female


title: Treg NT IgG rep3

value: IgG


title: Treg NT IgG rep2


title: GEX-Seq, Spike-specific B cells, COVID-19, donor C1, C2 and C3

description:
10x genomics
COVID_GroupC_Spike.filtered_feature_bc_matrix.h5

library_source: transcriptomic

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files contain the BCR and/or TCR sequencing information for each sample, if available
Supplementary files format and content: *.h5 files contain barcode, matrix, and feature information for each sample as well as the Cite-seq reads for each sample

molecule: polyA RNA


title: TCR-Seq, DTP 6mo, donor T2 and T7

description:
10x genomics
Tetanus_6Mo_Pool3_hTCR.filtered_contig_annotations.csv

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files contain the BCR and/or TCR sequencing information for each sample, if available
Supplementary files format and content: *.h5 files contain barcode, matrix, and feature information for each sample as well as the Cite-seq reads for each sample
Library strategy: TCR-seq

value: Plasmablasts, Memory B cells and activated T cells

value: DTP


title: CITE-Seq, Spike-specific B cells, COVID-19, donor C1, C2 and C3

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files contain the BCR and/or TCR sequencing information for each sample, if available
Supplementary files format and content: *.h5 files contain barcode, matrix, and feature information for each sample as well as the Cite-seq reads for each sample
Library strategy: CITE-seq

molecule: protein

tag: adt

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

tag: hto

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: MCF7_AI90.2.run1

city: London

first: Heena

last: Dhiman

address: 72 Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Raw reads were trimmed for adapters and quality (Phred Quality>=30) with trim_galore.
Processed reads were mapped to the Cellecta CloneTracker XP 10M Barcode library with BWA mem using default settings. The alignment maps were then parsed with samtools to filter out all the reads with supplementary alignments and alignment quality less than 30. The filtered and sorted alignment maps were used to count number of reads per barcode.
Assembly: Cellecta CloneTracker XP 10M Barcode library

source_name: MCF7 cell line

growth_protocol: Differentially barcoded cells were expanded for 13 days from 1x105 cells to reach a POT population of ~90x106 cells and plated based on the following scheme: 1) 34 hyperflasks were seeded (1.2x106 and 2.8x106 cells for -E2 and TAM conditions respectively) 2) 2x106 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 8x106 were expanded to 90x106 and harvested as triplicate POT samples. Harvesting of each HYPERflask was performed at the indicated time points. Following awakening, TAMɑ-𝝵 and AIɑ-ε samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs).

extract_protocol:
Cells were collected at the indicated time points (T0, early and late dormancy and awakening) and resuspended in HBSS buffer (Invitrogen, 14065049) supplemented with 0,037% Sodium Bicarbonate (Gibco), 10mM HEPES (Gibco) and 0.5% BSA.  Single cell suspensions were generated by passing the cells multiple times through 30um and 20um separation filters (miltenyi) in succession.
10K single cells were loaded into Chromium Single Cell Platform (10X Genomics). Library preparation was performed following Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 manual.

treatment_protocol: Cell treatment of the 34 aliases, with either E2 or TAM, started 48 hours after seeding.

value: Oestrogen deprived

tag: Stage

value: Dormancy


title: BCR-Seq, DTP 6mo, donor T2 and T7

description:
10x genomics
Tetanus_6Mo_Pool3_hBCR.filtered_contig_annotations.csv


title: MCF7_UT120.1.run1

value: Untreated


title: MCF7_AI90.2.run2


title: CITE-Seq, DTP 6mo, donor T2 and T7

description:
10x genomics
Tetanus_6Mo_Pool3.filtered_feature_bc_matrix.h5

value: TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: GEX-Seq, DTP 6mo, donor T2 and T7


title: TCR-Seq, DTP 6mo, donor T4, T5 and T6

description:
10x genomics
Tetanus_6Mo_Pool2_hTCR.filtered_contig_annotations.csv


title: Treg NT IgG rep1


title: MCF7_AI90.1


title: CITE-Seq, blood PB and Bmem, donor 561

description: Blood6_PCs_Bmem.filtered_feature_bc_matrix.h5

data_processing:
CellRanger v5.0.0 functions count and aggr were used in default settings
Assembly: hg19
Supplementary files format and content: *.h5 files containing the information needed to evaluate date in R using Seurat (e.g.)
Supplementary files format and content: *.fasta files containing the DNA information for the samples
Supplementary files format and content: *.csv files containing the B-cell receptor informations for the samples.
Library strategy: CITE-seq

extract_protocol:
Bone marrow samples were fragmented and transferred to a 50mL tube where they were vortexed to separate cells from bone fragments. Samples were subsequently rinsed through a 70µM filter with PBS/1% BSA/5mM EDTA/2µg/mL actinomycin D to obtain a cell suspension. Cells were enriched from bone marrow, or when available, blood, using StraightFrom Whole Blood and Bone Marrow CD138 MicroBeads and StraightFrom Whole Blood CD19 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions. Enriched cells were incubated with Fc Blocking Reagent (Miltenyi Biotec) following manufacturer’s instructions and subsequently stained for 30 min at 4°C with fluorophore-coupled anti-human antibodies. Simultaneously, cells were incubated with DNA barcoded antibodies for Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq). DAPI was added before sorting to allow dead cell exclusion. Live CD3- CD14- CD38highCD27high or CD38highCD138+ lymphocytes (plasma cells) and live CD3- CD14- CD38-/intCD27high lymphocytes (memory B cells) were subsequently sorted by FACS. These were then applied to the 10X Genomics platform using the Single Cell 5’ Library & Gel Bead Kit (v2, dual index) following the manufacturer’s instructions. Some bone marrow and blood samples were additionally stained with fluorophore-coupled tetanus toxoid and SARS-CoV-2 Spike Protein tetramers for the sorting and sequencing of antigen-specific cells. In this case, antigen-specific live CD3- CD14- CD27+ lymphocytes were sorted first and CD38high CD27high lymphocytes (plasma cells) and CD38-/int CD27high lymphocytes (memory B cells) were sorted from antigen-negative cells.
The purified cDNA was amplified and then used for 5’ gene expression (GEX), CITE-Seq and BCR library preparation using the Single Cell 5’ Library & Gel Bead Kit (v2, 10x Genomics). BCR target enrichment was achieved using the Chromium Single Cell V(D)J Enrichment Kit for Human B cells. Through fragmentation, adapter ligation and index PCR the final GEX and BCR libraries were obtained. The CITE-Seq libraries were obtained only by index PCR. The quality of single cell 5’ GEX, CITE-Seq and BCR libraries was assessed by Qubit quantification and Bioanalyzer fragment analysis (HS DNA Kit, Agilent).
The sequencing was performed on a NextSeq2000 device (Illumina) using NextSeq 1000/2000 P3 reagent kits (200 Cycles, Illumina) with the recommended sequencing conditions for 5’ GEX and Cite-Seq libraries (read1: 26nt, read2: 90nt, index1: 10nt, index2: 10nt) and NextSeq 1000/2000 P3 reagent kits (300 Cycles, Illumina) for BCR libraries (read1: 151nt, read2: 151nt, index1: 10nt, index2: 10nt, 20% PhiX spike-in).

value: Plasmablasts and Memory B cells

tag: genotype

value: Female

value: TotalSeq™-C0831 anti-human CD138 (Syndecan-1), TotalSeq™-C0156 anti-human CD95 (Fas), TotalSeq™-C0366 anti-human CD184 (CXCR4), TotalSeq™-C0389 anti-human CD38, TotalSeq™-C0140 anti-human CD183 (CXCR3), TotalSeq™-C0144 anti-human CD185 (CXCR5), TotalSeq™-C0053 anti-human CD11c, TotalSeq™-C0394 anti-human CD71, TotalSeq™-C0100 anti-human CD20, TotalSeq™-C0154 anti-human CD27, TotalSeq™-C0006 anti-human CD86, TotalSeq™-C0384 anti-human IgD, TotalSeq™-C0136 anti-human IgM

value: TotalSeq™-C0252 anti-human Hashtag 2 Antibody


title: Treg IL12 STAT4 rep3

description:
Anti-CD3 + anti-CD28, IL-2, IL12.
Treg.IL12.STAT4.e2b3.narrowPeak

value: cord blood

value: Treg

value: Live CD4+CD45RO-CD25HiCD127Lo/-CXCR5-.


title: CITE-Seq, DTP 6mo, donor T4, T5 and T6

description:
10x genomics
Tetanus_6Mo_Pool2.filtered_feature_bc_matrix.h5

value: Peripheral blood

value: pooled male and female

value: TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody


title: MCF7_T.Eta

value: Tamoxifen

value: Awakening


title: Treg IL12 STAT4 rep2

description:
Anti-CD3 + anti-CD28, IL-2, IL12.
Treg.IL12.STAT4.e2b2.narrowPeak

value: peripheral blood


title: MCF7_T.Theta.run2


title: MCF7_T.Theta.run1


title: Treg IL12 STAT4 rep1

description:
Anti-CD3 + anti-CD28, IL-2, IL12.
Treg.IL12.STAT4.e2b1.narrowPeak


title: TCR-Seq, DTP 6mo, donor T1 and T3

description:
10x genomics
Tetanus_6Mo_Pool1_hTCR.filtered_contig_annotations.csv

value: Plasmablasts, Memory B cells and activated T cells

value: DTP


title: BCR-Seq, DTP 6mo, donor T1 and T3

description:
10x genomics
Tetanus_6Mo_Pool1_hBCR.filtered_contig_annotations.csv


title: CITE-Seq, DTP 6mo, donor T1 and T3

description:
10x genomics
Tetanus_6Mo_Pool1.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: GEX-Seq, DTP 6mo, donor T1 and T3


title: Treg IL12 IgG rep3

value: IgG


title: BCR-Seq, Tetanus-specific B cells, DTP d7, donor T1, T2, T5 and T7

description:
10x genomics
Tetanus_specificBcells_BCR.filtered_contig_annotations.csv


title: MCF7_T14.2.run2

value: Latency


title: Treg IL12 IgG rep2


title: MCF7_UT90.2

value: Untreated


title: MCF7_AI60.2.run2

value: Oestrogen deprived

value: Dormancy


title: Treg IL12 IgG rep1

description:
Anti-CD3 + anti-CD28, IL-7, no IL-12.
Treg.IL12.STAT4.e2b1.narrowPeak

value: cord blood

value: Treg


title: Tnaive NT STAT4 rep3

description:
Anti-CD3 + anti-CD28, IL-7, no IL-12.
Tnaive.NT.STAT4.e2b3.narrowPeak

value: Tnaive

value: Live CD4+CD45RO-CD25-CD127+.


title: BCR-Seq, DTP d7, donor T2, T3 and T6

description:
10x genomics
Tetanus_Pool3_BCR.filtered_contig_annotations.csv

value: Peripheral blood

value: pooled male and female


title: CITE-Seq, Tetanus-specific B cells, DTP d7, donor T1, T2, T5 and T7

description:
10x genomics
Tetanus_specificBcells.filtered_feature_bc_matrix.h5

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: BCR-Seq, DTP 6mo, donor T4, T5 and T6

description:
10x genomics
Tetanus_6Mo_Pool2_hBCR.filtered_contig_annotations.csv


title: MCF7_AI60.2.run1


title: CITE-Seq, DTP d7, donor T2, T3 and T6

description:
10x genomics
Tetanus_Pool3.filtered_feature_bc_matrix.h5

value: TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody


title: TCR-Seq, DTP d7, donor T5 and T7

description:
10x genomics
Tetanus_Pool2_TCR.filtered_contig_annotations.csv

value: Plasmablasts, Memory B cells and activated T cells


title: GEX-Seq, DTP 6mo, donor T4, T5 and T6

value: DTP


title: CITE-Seq, DTP d7, donor T5 and T7

description:
10x genomics
Tetanus_Pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: Tnaive NT STAT4 rep2

description:
Anti-CD3 + anti-CD28, IL-7, no IL-12.
Tnaive.NT.STAT4.e2b2.narrowPeak

value: peripheral blood


title: Tnaive NT STAT4 rep1

description:
Anti-CD3 + anti-CD28, IL-7, no IL-12.
Tnaive.NT.STAT4.e2b1.narrowPeak


title: MCF7_AI60.1.run1


title: GEX-Seq, DTP d7, donor T2, T3 and T6


title: BCR-Seq, DTP d7, donor T5 and T7

description:
10x genomics
Tetanus_Pool2_BCR.filtered_contig_annotations.csv


title: Tnaive NT IgG rep3

value: IgG


title: TCR-Seq, DTP d7, donor T1 and T4

description:
10x genomics
Tetanus_Pool1_TCR.filtered_contig_annotations.csv


title: MCF7_T60.2

value: Tamoxifen


title: BCR-Seq, DTP d7, donor T1 and T4

description:
10x genomics
Tetanus_Pool1_BCR.filtered_contig_annotations.csv


title: TCR-Seq, DTP d7, donor T2, T3 and T6

description:
10x genomics
Tetanus_Pool3_TCR.filtered_contig_annotations.csv


title: CITE-Seq, DTP d7, donor T1 and T4

description:
10x genomics
Tetanus_Pool1.filtered_feature_bc_matrix.h5

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: GEX-Seq, Tetanus-specific B cells, DTP d7, donor T1, T2, T5 and T7


title: GEX-Seq, DTP d7, donor T5 and T7


title: Tnaive NT IgG rep2


title: TCR-Seq, BNT/BNT/BNT d7, donor 27

description:
10x genomics
G11_7Mo_Pool3_TCR.filtered_contig_annotations.csv

value: Female

value: Comirnaty/Comirnaty/Comirnaty


title: MCF7_UT60.2.run2

value: Untreated


title: GEX-Seq, DTP d7, donor T1 and T4


title: MCF7_AI60.1.run2

value: Oestrogen deprived

value: Dormancy


title: Tnaive IL12 STAT4 rep3

description:
Anti-CD3 + anti-CD28, IL-7, IL12
Tnaive.IL12.STAT4.e2b3.narrowPeak

value: cord blood

value: Tnaive

value: Live CD4+CD45RO-CD25-CD127+.


title: BCR-Seq, BNT/BNT/BNT d7, donor 27

description:
10x genomics
G11_7Mo_Pool3_BCR.filtered_contig_annotations.csv

value: Peripheral blood


title: Tnaive NT IgG rep1


title: CITE-Seq, BNT/BNT/BNT d7, donor 27

description:
10x genomics
COVID_G11_Pool3.filtered_feature_bc_matrix.h5

value: Plasmablasts, Memory B cells and activated T cells

value: TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: MCF7_UT60.1.run2


title: Tnaive IL12 STAT4 rep2

description:
Anti-CD3 + anti-CD28, IL-7, IL12
Tnaive.IL12.STAT4.e2b2.narrowPeak


title: MCF7_UT60.2.run1


title: GEX-Seq, BNT/BNT/BNT d7, donor 27


title: TCR-Seq, BNT/BNT/BNT d7, donor 25

description:
10x genomics
G11_7Mo_Pool2_TCR.filtered_contig_annotations.csv


title: Tnaive IL12 STAT4 rep1

description:
Anti-CD3 + anti-CD28, IL-7, IL12
Tnaive.IL12.STAT4.e2b1.narrowPeak


title: CITE-Seq, BNT/BNT/BNT d7, donor 25

description:
10x genomics
COVID_G11_Pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: GEX-Seq, BNT/BNT/BNT d7, donor 25


title: BCR-Seq, BNT/BNT/BNT d7, donor 25

description:
10x genomics
G11_7Mo_Pool2_BCR.filtered_contig_annotations.csv


title: Tnaive IL12 IgG rep3


title: MCF7_UT60.1.run1


title: TCR-Seq, BNT/BNT/BNT d7, donor 11

description:
10x genomics
G11_7Mo_Pool1_TCR.filtered_contig_annotations.csv

value: Male


title: MCF7_T60.1


title: MCF7_AI30.2


title: BCR-Seq, BNT/BNT/BNT d7, donor 11

description:
10x genomics
G11_7Mo_Pool1_BCR.filtered_contig_annotations.csv


title: GEX-Seq, BNT/BNT/BNT d7, donor 11

description:
10x genomics
COVID_G11_Pool1.filtered_feature_bc_matrix.h5


title: CITE-Seq, BNT/BNT/BNT d7, donor 11

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody


title: Tnaive IL12 IgG rep2

value: peripheral blood

value: IgG


title: MCF7_AI30.1


title: Tnaive IL12 IgG rep1


title: MCF7_T30.2

value: Tamoxifen


title: BCR-Seq, Spike-specific B cells, BNT/BNT 7mo, donor 31 and 32

description:
10x genomics
G10_7Mo_Spike_BCR.filtered_contig_annotations.csv

value: B cells

value: pooled male and female

value: Comirnaty/Comirnaty


title: GEX-Seq, Spike-specific B cells, BNT/BNT 7mo, donor 31 and 32

description:
10x genomics
G10_7Mo_Spike.filtered_feature_bc_matrix.h5


title: TCR-Seq, BNT/BNT 7mo, donor 31 and 32

description:
10x genomics
G10_7Mo_Pool1_TCR.filtered_contig_annotations.csv


title: MCF7_T30.1

value: Dormancy


title: CITE-Seq, BNT/BNT 7mo, donor 31 and 32

description:
10x genomics
G10_7Mo_Pool1.filtered_feature_bc_matrix.h5

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody


title: MCF7_UT30.2

value: Untreated


title: GEX-Seq, BNT/BNT 7mo, donor 31 and 32


title: Very Heavy-10252 VTA Expression 30 Day Abstinence

city: Nashville

first: Cody

last: Siciliano

state: TN

address: 2222 Pierce Avenue, 410 Robinson Research Building

department: Pharmacology

institute: Vanderbilt University

data_processing:
Paired-end RNA sequencing reads (150bp long) were trimmed and filtered for quality using Trimgalore v0.6.7 (Krueger et al. 2021).
Trimmed reads were quantified using Salmon(Patro et al., 2017) v1.9.0 with the Mmul10 Macaca mulatta genome.
Sample read counts were normalized using DESeq2 v1.36.0(Love et al., 2014).
Assembly: Mmul10
Supplementary files format and content: excel file containing normalized and variance stabilized counts for genome aligned with Salmon and processed using deseq
Supplementary files format and content: excel file containing raw counts for genome aligned with Salmon and processed using deseq

molecule: total RNA

organism: Macaca mulatta

source_name: Brain VTA Punch

extract_protocol: Nugen Universal Plus mRNA

treatment_protocol: Monkeys (17 alcohol drinkers and 11 calorically-yoked or housing controls) were trained to obtain fluids and their meals from an operant panel that replaced one of the walls of their home cage, as described previously(Grant et al., 2008; Vivian et al., 2001). Briefly, the panels had two spouts, one to each side of a 15-inch video display screen. Near each spout, the display showed a set of three stimulus lights (white, red, and green) that indicated an active session or food or fluid availability, respectively. A centrally located recessed dowel activated the fluid spouts, and an infrared finger poke activated the pellet dispenser (env-203-1000; Med Associates). Each spout was connected via Nalgene tubing to a 1 L fluid reservoir set on a digital scale (Adventurer Pro Balances AV4101C; Ohaus). Dowel pulls, finger pokes, and fluid consumption were recorded every 500 ms via a computerized system (Dell Optiplex) using custom hardware and programming using a National Instruments interface and Labview software. Schedule-induced polydipsia, as described previously(Grant et al., 2008; Vivian et al., 2001), was used to induce alcohol self-administration in daily 16 h sessions. Briefly, a 1 g banana food pellet (Research Diets) was dispensed every 300 s (fixed time, 300 s) until a water volume equivalent to 1.5 g/kg of 4% (w/v) ethanol was consumed. Following at least 30 days of water induction, 4% ethanol replaced water. In 30-day increments, each animal consumed increasing doses of 4% ethanol: 0.5 g/kg/d, 1.0 g/kg/d, then 1.5 g/kg/d. Following consumption of the programmed volume, water was immediately available, and any remaining pellets were available on a fixed-ratio 1 (FR-1) schedule after a 2 h time-out. Following completion of ethanol induction, daily 22 h open access sessions were performed, during which water and ethanol were concurrently available. Food pellets were available on a FR-1 schedule in at least three daily meals in 2 h intervals starting at the session onset. Data were downloaded, husbandry tasks were performed, food and fluids were replenished, and fresh fruit was provided each day by technicians during the 2 h break.After drinking was initiated, subjects had 12 months of open access to alcohol for 22 hours a day. 6 months into this period, an endocrine profile was collected. After 12 months of alcohol access, subjects underwent a one-month abstinence period. Following this abstinence period, subjects returned to open access alcohol exposure for three months, then underwent another one-month withdrawal period, returned to three months of open access alcohol exposure, and finally underwent one month of withdrawal at the end of which subjects were necropsied. During open access blood was collected weekly for blood ethanol concentration measurements.

tag: drinking phenotype

value: Very Heavy

value: Brain VTA Punch

value: Bulk Tissue

value: WT

value: Ethanol


title: MCF7_UT30.1


title: Very Heavy-10249 VTA Expression 30 Day Abstinence


title: BCR-Seq, BNT/BNT 7mo, donor 24 and 25

description:
10x genomics
G9_8Mo_Pool2_BCR.filtered_contig_annotations.csv

value: Peripheral blood

value: Plasmablasts, Memory B cells and activated T cells

value: Female


title: TCR-Seq, BNT/BNT 7mo, donor 24 and 25

description:
10x genomics
G9_8Mo_Pool2_TCR.filtered_contig_annotations.csv


title: exosome control

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: U87MG delta EGFR cells

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Cells were cultured in DMEM contaiing 10 % exosome-depleted fetal bovine serum in 5 % CO2 incubator.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: Cells were exposed to 25ppm p-Boronophenylalanine-fructose complex for two hous and irradiated with thermal neutrons. After Irrdiation, cells were cultured in the medium, and  the medium was collected three days after irradiation.

tag: cell line

value: U87MG delta EGFR

value: glioblastoma

value: non-treated control


title: Very Heavy-10248 VTA Expression 30 Day Abstinence


title: BCR-Seq, BNT/BNT 7mo, donor 31 and 32

description:
10x genomics
G10_7Mo_Pool1_BCR.filtered_contig_annotations.csv


title: CITE-Seq, BNT/BNT 7mo, donor 24 and 25

description:
10x genomics
G9_7Mo_Pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: Very Heavy-10247 VTA Expression 30 Day Abstinence


title: BCR-Seq, BNT/BNT 7mo, donor 11 and 27

description:
10x genomics
G9_8Mo_Pool1_BCR.filtered_contig_annotations.csv

value: pooled male and female

value: Comirnaty/Comirnaty


title: CITE-Seq, Spike-specific B cells, BNT/BNT 7mo, donor 31 and 32

value: B cells

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody


title: TCR-Seq, BNT/BNT 7mo, donor 11 and 27

description:
10x genomics
G9_8Mo_Pool1_TCR.filtered_contig_annotations.csv


title: MCF7_AI14.2

value: Oestrogen deprived

value: Latency


title: MCF7_AI14.1


title: Very Heavy-10242 VTA Expression 30 Day Abstinence

value: Very Heavy

value: Brain VTA Punch

value: Bulk Tissue


title: GEX-Seq, BNT/BNT 7mo, donor 11 and 27

description:
10x genomics
G9_7Mo_Pool1.filtered_feature_bc_matrix.h5

value: Peripheral blood


title: CITE-Seq, BNT/BNT 7mo, donor 11 and 27

value: Plasmablasts, Memory B cells and activated T cells

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: MCF7_T14.2.run1

value: Tamoxifen


title: Very Heavy-10244 VTA Expression 30 Day Abstinence

value: WT

value: Ethanol


title: BCR-Seq, AZ/BNT d7, donor 54, 55, 56 and 57

description:
10x genomics
G5_day7AB_Pool2_BCR.filtered_contig_annotations.csv

value: Vaxzevria/Comirnaty


title: TCR-Seq, AZ/BNT d7, donor 54, 55, 56 and 57

description:
10x genomics
G5_day7AB_Pool2_TCR.filtered_contig_annotations.csv


title: exosome BNCT

value: U87MG delta EGFR

value: glioblastoma

value: BNCT


title: MCF7_T14.1


title: CITE-Seq, AZ/BNT d7, donor 54, 55, 56 and 57

description:
10x genomics
G5_day7AB_Pool2.filtered_feature_bc_matrix.h5

value: pooled male and female

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: Very Heavy-10215 VTA Expression 30 Day Abstinence


title: GEX-Seq, AZ/BNT d7, donor 51, 53 and 58

description:
10x genomics
G5_day7AB_Pool1.filtered_feature_bc_matrix.h5


title: GEX-Seq, AZ/BNT d7, donor 54, 55, 56 and 57


title: CITE-Seq, AZ/BNT d7, donor 51, 53 and 58

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: CITE-Seq, AZ d14, donor 53, 54, 57 and 58

description:
10x genomics
gr5_d14_pool2.filtered_feature_bc_matrix.h5

value: Vaxzevria

value: TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: BCR-Seq, AZ/BNT d7, donor 51, 53 and 58

description:
10x genomics
G5_day7AB_Pool1_BCR.filtered_contig_annotations.csv


title: MCF7_UT14.1

value: Untreated

value: Latency


title: TCR-Seq, AZ d14, donor 53, 54, 57 and 58

description:
10x genomics
G5_day14_Pool_2_TCR.filtered_contig_annotations.csv

value: Peripheral blood

value: Plasmablasts, Memory B cells and activated T cells


title: MCF7_T7.2

value: Tamoxifen


title: TCR-Seq, AZ/BNT d7, donor 51, 53 and 58

description:
10x genomics
G5_day7AB_Pool1_TCR.filtered_contig_annotations.csv


title: Very Heavy-10212 VTA Expression 30 Day Abstinence

value: Very Heavy

value: Brain VTA Punch

value: Bulk Tissue

value: WT


title: BCR-Seq, AZ d14, donor 53, 54, 57 and 58

description:
10x genomics
G5_day14_Pool_2_BCR.filtered_contig_annotations.csv


title: GEX-Seq, AZ d14, donor 53, 54, 57 and 58


title: GEX-Seq, BNT/BNT 7mo, donor 24 and 25

value: Female

value: Comirnaty/Comirnaty


title: CITE-Seq, AZ d14, donor 51, 52, 55 and 56

description:
10x genomics
gr5_d14_pool1.filtered_feature_bc_matrix.h5

value: pooled male and female

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 AntibodyTotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody


title: MCF7_T7.1


title: Heavy-10213 VTA Expression 30 Day Abstinence

value: Heavy

value: Ethanol


title: BCR-Seq, AZ d14, donor 51, 52, 55 and 56

description:
10x genomics
G5_day14_Pool_1_BCR.filtered_contig_annotations.csv

value: Vaxzevria


title: MCF7_UT7.2


title: Very Heavy-10214 VTA Expression 30 Day Abstinence


title: MCF7_UT14.2


title: GEX-Seq, AZ d14, donor 51, 52, 55 and 56


title: TCR-Seq, AZ d14, donor 51, 52, 55 and 56

description:
10x genomics
G5_day14_Pool_1_TCR.filtered_contig_annotations.csv


title: Low-10210 VTA Expression 30 Day Abstinence

value: Low

value: Ehanol


title: TCR-Seq, AZ d7, donor 58

description:
10x genomics
G5_day7_Pool_3_TCR.filtered_contig_annotations.csv

value: Male


title: MCF7_UT7.1

value: Untreated


title: MCF7_AI7.2

value: Oestrogen deprived

value: Latency


title: MCF7_AI7.1


title: BCR-Seq, AZ d7, donor 58

description:
10x genomics
G5_day7_Pool_3_BCR.filtered_contig_annotations.csv

value: Peripheral blood

value: Plasmablasts, Memory B cells and activated T cells


title: MCF7_T0.3


title: CITE-Seq, AZ d7, donor 58

description:
10x genomics
gr5_d7_pool3.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: Heavy-10251 VTA Expression 30 Day Abstinence

value: Brain VTA Punch

value: Bulk Tissue

value: WT


title: Heavy-10208 VTA Expression 30 Day Abstinence


title: BCR-Seq, AZ d7, donor 55, 56 and 57

description:
10x genomics
G5_day7_Pool_2_BCR.filtered_contig_annotations.csv

value: pooled male and female


title: GEX-Seq, AZ d7, donor 58


title: MCF7_T0.1


title: Control-10250 VTA Expression 30 Day Abstinence

value: Control


title: TCR-Seq, AZ d7, donor 55, 56 and 57

description:
10x genomics
G5_day7_Pool_2_TCR.filtered_contig_annotations.csv


title: CITE-Seq, AZ d7, donor 55, 56 and 57

description:
10x genomics
gr5_d7_pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: Heavy-10211 VTA Expression 30 Day Abstinence

value: Heavy

value: Ethanol


title: T47D_T47D_U150.3_R2

data_processing:
Raw reads were trimmed for adapters and quality with trim_galore followed by alignment to hg38 human genome reference with bwa mem.
After removal of PCR duplicates, post-processing and variant identification were performed using the Genome Analysis Toolkit best practices. Joint variant calling was performed using Platypus and variant annotation was done using VEP.
Assembly: hg38

source_name: T47D cell line

growth_protocol: For MCF7, differentially barcoded cells were expanded for 13 days from 1x105 cells to reach a POT population of ~90x106 cells and plated based on the following scheme: 1) 34 hyperflasks were seeded (1.2x106 and 2.8x106 cells for -E2 and TAM conditions respectively) 2) 2x10^6 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 8x10^6 were expanded to 90x10^6 and harvested as triplicate POT samples. Harvesting of each HYPERflask was performed at the indicated time points. Following awakening, TAMɑ-𝝵 and AIɑ-ε samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs). For T47D, differentially barcoded cells were expanded for 12 days to reach a POT population of ~20x106 cells and plated based on the following scheme: 1) 8 HYPERflasks were seeded (1.1x106 cells) for -E2, 1.1x106 cells were kept in culture as untreated arm (UT, 3 replicates), 3) 3.5x106 were expanded to 20x106 and harvested as triplicate POT samples (5x106 cells each) with rest of the barcoded population frozen 4) 4.4x106 cells were used for plating of four T0 samples (1.1x106 )and collected after 48 hours. Oestrogen deprivation of the 8 HYPERflask carbon copies (-E2) started 48 hours after seeding.Harvesting of each HYPERflask was performed at the indicated time points (shared timepoints for 2 replicates of 1 month and diverging time points for individual awakenings). Following awakening, AI A-F samples were further cultured for 1 month in T150 flasks (Corning) with cell passaging giving rise to Terminal End Points (TEPs).

extract_protocol:
At time of collection, cells were snap-frozen in multiple pellets for subsequent DNA extraction using DNeasy Blood and Tissue DNA extraction kit (Qiagen) according to manufacturer’s recommendations. Qubit (Life Technologies) was used for quantification.
Quality control and library preparation (all samples exluding a29 and a30 were prepared using PCR-free library protocol) were performed by Novogene (Cambridge, UK) where 150 bp paired-end sequencing (30X coverage) was performed on the Illumina NovaSeq6000 platform.
MCF7: Whole Genome Sequencing, T47D: Targeted genome sequencing (targeted panel available on request)

value: Untreated equivalent for awakening

tag: rep


title: CITE-Seq, AZ d7, donor 51, 52, 53, 54 and 55

description:
10x genomics
gr5_d7_pool1.filtered_feature_bc_matrix.h5

value: Vaxzevria

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody


title: Control-10245 VTA Expression 30 Day Abstinence


title: TCR-Seq, AZ d7, donor 51, 52, 53, 54 and 55

description:
10x genomics
G5_day7_Pool_1_TCR.filtered_contig_annotations.csv


title: Control-10223 VTA Expression 30 Day Abstinence


title: Heavy-10209 VTA Expression 30 Day Abstinence


title: GEX-Seq, AZ d7, donor 55, 56 and 57


title: T47D_T47D_U150.3_R1

value: Untreated


title: GEX-Seq, AZ d7, donor 51, 52, 53, 54 and 55


title: T47D_T47D_U150.2_R2


title: Control-10222 VTA Expression 30 Day Abstinence


title: TCR-Seq, BNT/BNT d7, donor 31, 32 and 33

description:
10x genomics
G3_day7AB_Pool_1_TCR.filtered_contig_annotations.csv

value: Comirnaty/Comirnaty


title: BCR-Seq, BNT/BNT d7, donor 31, 32 and 33

description:
10x genomics
G3_day7AB_Pool_1_BCR.filtered_contig_annotations.csv

value: Peripheral blood


title: MCF7_T0.2


title: GEX-Seq, BNT/BNT d7, donor 31, 32 and 33

description:
10x genomics
gr3_d7AB_pool1.filtered_feature_bc_matrix.h5

value: Plasmablasts, Memory B cells and activated T cells


title: T47D_T47D_U150.1_R2


title: TCR-Seq, BNT d14, donor 31, 32 and 33

description:
10x genomics
G3_day14_Pool_1_TCR.filtered_contig_annotations.csv

value: Comirnaty


title: CITE-Seq, BNT/BNT d7, donor 31, 32 and 33

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: Control-10221 VTA Expression 30 Day Abstinence

value: Brain VTA Punch

value: Bulk Tissue


title: BCR-Seq, AZ d7, donor 51, 52, 53, 54 and 55

description:
10x genomics
G5_day7_Pool_1_BCR.filtered_contig_annotations.csv

value: pooled male and female


title: Control-10241 VTA Expression 30 Day Abstinence

value: Control

value: WT


title: Control-10220 VTA Expression 30 Day Abstinence


title: T47D_T47D_U150.1_R1


title: Control-10219 VTA Expression 30 Day Abstinence


title: BCR-Seq, BNT d14, donor 31, 32 and 33

description:
10x genomics
G3_day14_Pool_1_BCR.filtered_contig_annotations.csv


title: CITE-Seq, BNT d14, donor 31, 32 and 33

description:
10x genomics
gr3_d14_pool1.filtered_feature_bc_matrix.h5


title: GEX-Seq, BNT d14, donor 31, 32 and 33


title: CITE-Seq, Spike-specific B cells, BNT/BNT d7, donor 21, 22, 23, 24, 25, 26, 27 and 28

description:
10x genomics
G2_RBD.filtered_feature_bc_matrix.h5

value: B cells

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: GEX-Seq, Spike-specific B cells, BNT/BNT d7, donor 21, 22, 23, 24, 25, 26, 27 and 28


title: BCR-Seq, Spike-specific B cells, BNT/BNT d7, donor 21, 22, 23, 24, 25, 26, 27 and 28

description:
10x genomics
G2_day7AB_RBD_BCR.filtered_contig_annotations.csv


title: T47D_T74D_AI.F.TEP_R1

value: Oestrogen deprivation

value: TEP


title: Control-10217 VTA Expression 30 Day Abstinence


title: TCR-Seq, BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_day7_pool_2_TCR.filtered_contig_annotations.csv


title: BCR-Seq, BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_day7_pool_2_BCR.filtered_contig_annotations.csv


title: Control-10216 VTA Expression 30 Day Abstinence


title: CITE-Seq, BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_day7_Pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: T47D_T74D_AI.E.TEP_R1


title: T47D_T74D_AI.E.TEP_R2


title: T47D_T47D_U150.2_R1

value: Untreated

value: Untreated equivalent for awakening


title: Binge-10246 VTA Expression 30 Day Abstinence

value: Binge

value: Ethanol


title: T47D_T74D_AI.D.TEP_R2


title: T47D_T74D_AI.D.TEP_R1


title: Binge -10243 VTA Expression 30 Day Abstinence


title: T47D_T74D_AI.F.TEP_R2


title: CITE-Seq, BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_day7_Pool1.filtered_feature_bc_matrix.h5

value: Peripheral blood

value: Plasmablasts, Memory B cells and activated T cells

value: Comirnaty

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0254 anti-human Hashtag 4 Antibody


title: Control-10218 VTA Expression 30 Day Abstinence

value: Brain VTA Punch

value: Bulk Tissue


title: T47D_T74D_AI.C.TEP_R2


title: TCR-Seq, BNT/BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_day7AB_pool_2_TCR.filtered_contig_annotations.csv

value: pooled male and female

value: Comirnaty/Comirnaty


title: TCR-Seq, BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_day7_pool_1_TCR.filtered_contig_annotations.csv


title: GEX-Seq, BNT d7, donor 21, 22, 23 and 24


title: CITE-Seq, BNT/BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_d7AB_pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154


title: T47D_T74D_AI.C.TEP_R1


title: clec-35_ext_biol rep 3^

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

data_processing:
Reads were aligned to C. elegans genome WS283
Reads were counted using Kallisto
Transcript abundance was quantified using the Sleuth and Wald test
Assembly: WormBase Release WS283
Supplementary files format and content: H5 files having raw TPM counts for all genes

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: All worm strains were prepared by bleaching gravid adults to isolate embyros which were grown until L4 stage where extract (or water control) treatment was performed for 4 hours before collecting for RNA isolation.

extract_protocol:
TRIzol (Life Technologies)
By Novogene

treatment_protocol: Nematode Growth Media agar plates supplemented with E. coli OP50 at 20°C

value: Whole animal

value: L4 stage_20°C


title: TCR-Seq, BNT/BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_day7AB_pool_1_TCR.filtered_contig_annotations.csv


title: clec-35_ext_biol rep 1^


title: BCR-Seq, BNT/BNT d7, donor 25, 26, 27 and 28

description:
10x genomics
G2_day7AB_pool_2_BCR.filtered_contig_annotations.csv


title: GEX-Seq, BNT/BNT d7, donor 25, 26, 27 and 28


title: GEX-Seq, BNT d7, donor 25, 26, 27 and 28


title: BCR-Seq, BNT/BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_day7AB_pool_1_BCR.filtered_contig_annotations.csv


title: clec-35_biol rep 3^


title: T47D_T74D_AI.B.TEP_R1

value: Oestrogen deprivation

value: TEP


title: CITE-Seq, BNT/BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_d7AB_pool1.filtered_feature_bc_matrix.h5


title: clec-35_biol rep 2^


title: GEX-Seq, BNT/BNT d7, donor 21, 22, 23 and 24


title: T47D_T74D_AI.A.TEP_R2


title: TCR-Seq, BNT d14, donor 25, 26, 27 and 28

description:
10x genomics
G2_day14_pool_2_TCR.filtered_contig_annotations.csv


title: BCR-Seq, BNT d7, donor 21, 22, 23 and 24

description:
10x genomics
G2_day7_pool_1_BCR.filtered_contig_annotations.csv


title: BCR-Seq, BNT d14, donor 25, 26, 27 and 28

description:
10x genomics
G2_day14_pool_2_BCR.filtered_contig_annotations.csv


title: T47D_T74D_AI.A.TEP_R1


title: clec-35_biol rep 1^


title: CITE-Seq, BNT d14, donor 25, 26, 27 and 28

description:
10x genomics
G2_d14_pool2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: GEX-Seq, BNT d14, donor 25, 26, 27 and 28


title: clec-27_ext_biol rep 3^


title: TCR-Seq, BNT d14, donor 21, 22, 23 and 24

description:
10x genomics
G2_day14_pool_1_TCR.filtered_contig_annotations.csv


title: clec-35_ext_biol rep 2^


title: CITE-Seq, BNT d14, donor 21, 22, 23 and 24

description:
10x genomics
G2_day14_Pool1.filtered_feature_bc_matrix.h5


title: clec-27_ext_biol rep 2^


title: BCR-Seq, BNT d14, donor 21, 22, 23 and 24

description:
10x genomics
G2_day14_pool_1_BCR.filtered_contig_annotations.csv


title: GEX-Seq, BNT d14, donor 21, 22, 23 and 24


title: T47D_T74D_AI.E

value: Awakening


title: TCR-Seq, BNT d7, donor 14, 15, 16 and 17

description:
10x genomics
G1_day7_pool_2_TCR.filtered_contig_annotations.csv

value: Male


title: CITE-Seq, BNT d7, donor 14, 15, 16 and 17

description:
10x genomics
d7_pool_2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: T47D_T74D_AI.B.TEP_R2


title: BCR-Seq, BNT d7, donor 14, 15, 16 and 17

description:
10x genomics
G1_day7_pool_2_BCR.filtered_contig_annotations.csv

value: Peripheral blood


title: clec-27_biol rep 3^


title: T47D_T74D_AI.C


title: GEX-Seq, BNT d7, donor 14, 15, 16 and 17

value: Plasmablasts, Memory B cells and activated T cells


title: T47D_T74D_AI.D


title: TCR-Seq, BNT d7, donor 11, 12 and 13

description:
10x genomics
G1_day7_pool_1_TCR.filtered_contig_annotations.csv

value: Comirnaty


title: BCR-Seq, BNT d7, donor 11, 12 and 13

description:
10x genomics
G1_day7_pool_1_BCR.filtered_contig_annotations.csv


title: T47D_T74D_AI.B


title: clec-27_ext_biol rep 1^


title: clec-27_biol rep 2^


title: clec-27_biol rep 1^


title: T47D_T74D_AI.A


title: CITE-Seq, BNT d7, donor 11, 12 and 13

description:
10x genomics
d7_pool_1.filtered_feature_bc_matrix.h5

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody


title: BCR-Seq, BNT/BNT d7, donor 12, 13, 15 and 16

description:
10x genomics
G1_day7AB_pool_1_BCR.filtered_contig_annotations.csv


title: GEX-Seq, BNT d7, donor 11, 12 and 13


title: T47D_T74D_AI.F


title: T47D_T47D_POT.2_R2

value: Treatment naïve

value: POT


title: N2_ext_biol rep 3^

value: WT


title: N2_ext_biol rep 2^


title: GEX-Seq, BNT/BNT d7, donor 12, 13, 15 and 16

description:
10x genomics
d7_AB_pool_1.filtered_feature_bc_matrix.h5

value: Comirnaty/Comirnaty


title: CITE-Seq, BNT/BNT d7, donor 12, 13, 15 and 16

value: TotalSeq-C0831 anti-human CD138 (Syndecan-1), TotalSeq-C0100 anti-human CD20, TotalSeq-C0045 anti-human CD4, TotalSeq-C0046 anti-human CD8, TotalSeq-C0087 anti-human CD45RO, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0085 anti-human CD25, TotalSeq-C0390 anti-human CD127 (IL-7Rα), TotalSeq-C0032 anti-human CD154

value: TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody


title: TCR-Seq, BNT d14, donor 13, 16 and 17

description:
10x genomics
G1_day14_pool_2_TCR.filtered_contig_annotations.csv


title: T47D_T47D_POT.1_R1


title: N2_ext_biol rep 1^

value: Whole animal

value: L4 stage_20°C


title: N2_biol rep 3^


title: BCR-Seq, BNT d14, donor 13, 16 and 17

description:
10x genomics
G1_day14_pool_2_BCR.filtered_contig_annotations.csv


title: CITE-Seq, BNT d14, donor 13, 16 and 17

description:
10x genomics
d14_pool_2.filtered_feature_bc_matrix.h5

value: TotalSeq-C0253 anti-human Hashtag 3 Antibody, TotalSeq-C0257 anti-human Hashtag 7 Antibody, TotalSeq-C0258 anti-human Hashtag 8 Antibody


title: GEX-Seq, BNT d14, donor 13, 16 and 17


title: MCF7_AI90.2_R2

value: Oestrogen deprivation

value: Dormancy


title: MCF7_AI90.2_R1


title: TCR-Seq, BNT d14, donor 11, 12, 14 and 15

description:
10x genomics
G1_day14_pool_1_TCR.filtered_contig_annotations.csv

value: Male


title: GEX-Seq, BNT d14, donor 11, 12, 14 and 15

description:
10x genomics
d14_pool_1.filtered_feature_bc_matrix.h5


title: CITE-Seq, BNT d14, donor 11, 12, 14 and 15

value: TotalSeq-C0251 anti-human Hashtag 1 Antibody, TotalSeq-C0252 anti-human Hashtag 2 Antibody, TotalSeq-C0255 anti-human Hashtag 5 Antibody, TotalSeq-C0256 anti-human Hashtag 6 Antibody


title: N2_biol rep 2^


title: ceh-37_ext_biol rep 3


title: MCF7_AI90.1_R2


title: N2_biol rep 1^


title: T47D_T47D_POT.3_R3


title: TCR-Seq, BNT/BNT d7, donor 12, 13, 15 and 16

description:
10x genomics
G1_day7AB_pool_1_TCR.filtered_contig_annotations.csv

value: Peripheral blood


title: HEK293T-DECOR-MALAT1-REP1

city: Chicago

first: Hao

last: Yan

state: Illinois

address: 929 E 57th St, GCIS E535

institute: University of Chicago

description: read 1 62 cycles, read 2 160 cycles

data_processing:
R2 reads were trimmed to 97 nt by Cutadapt
Aligned to the hg19 (GRCh37) reference genome using STAR 2.6.1b
A-to-G RNA editing call with REDItools2.0
Assembly: hg19 (GRCh37)
Supplementary files format and content: tab-delimited text files include A-to-G RNA editing rate for each Sample

source_name: Embryonic Kidney

growth_protocol: HEK293T cell lines were cultured in Dulbecco’s Modified Eagle Medium with high glucose, sodium pyruvate, and L-Glutamine (Corning) supplemented with 10% fetal bovine serum (Corning). Cells were maintained in 5% CO2 and passaged regularly at a confluency of 80%.

extract_protocol:
Total RNA extraction with TRIzol (Invitrogen), mRNA was enriched by a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs)
Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: Embryonic Kidney

value: epithelial


title: HEK293T-DECOR-MALAT1-REP2

description: read 1 62 cycles, read 2 160 cycles


title: MCF7_AI90.1_R1


title: ceh-37_ext_biol rep 2


title: HEK293T-DECOR-KRAS-REP2

description: read 1 62 cycles, read 2 160 cycles


title: MCF7_AI.gamma_R2


title: HEK293T-DECOR-KRAS-REP1

description: read 1 62 cycles, read 2 160 cycles


title: ceh-37_ext_biol rep 1


title: HEK293T-dCas13d-ADAR-EZH2 -REP2

description: read 1 25 cycles, read 2 97 cycles


title: HEK293T-dCas13d-ADAR-EZH2 -REP1

description: read 1 25 cycles, read 2 97 cycles


title: MCF7_AI.gamma_R1


title: ceh-37_biol rep 3


title: HEK293T-dCas13d-ADAR-NT-REP2

description: read 1 25 cycles, read 2 97 cycles


title: BCR-Seq, BNT d14, donor 11, 12, 14 and 15

description:
10x genomics
G1_day14_pool_1_BCR.filtered_contig_annotations.csv

value: Plasmablasts, Memory B cells and activated T cells

value: Comirnaty


title: MCF7_AI.delta_R3

value: Awakening


title: HEK293T-Repair.t1-EZH2_A22-REP2

description: read 1 25 cycles, read 2 97 cycles


title: HEK293T-Repair.t1-EZH2_A22-REP1

description: read 1 25 cycles, read 2 97 cycles


title: HEK293T-Repair.t1-NT-REP2

description: read 1 25 cycles, read 2 97 cycles


title: ceh-37_biol rep 1


title: MCF7_AI.delta_R2


title: N2_ext_biol rep 3

value: WT


title: MCF7_AI.delta_R1


title: HEK293T-dCas13d-ADAR-NT-REP1

description: read 1 25 cycles, read 2 97 cycles


title: HEK293T-Repair.v2-EZH2_A22-REP2

description: read 1 25 cycles, read 2 97 cycles


title: MCF7_AI.epsilon_R4


title: HEK293T-Repair.t1-NT-REP1

description: read 1 25 cycles, read 2 97 cycles


title: HEK293T-Repair.v2-NT-REP2

description: read 1 25 cycles, read 2 97 cycles


title: MCF7_AI.epsilon_R3


title: HEK293T-Repair.v2-NT-REP1

description: read 1 25 cycles, read 2 97 cycles


title: N2_ext_biol rep 2


title: N2_ext_biol rep 1


title: MCF7_AI.epsilon_R2


title: N2_biol rep 3


title: MCF7_AI.epsilon_R1


title: DKOWT2

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description:
mA3-AID double knockout B6 mouse TBLV-WT derived tumor
snp_counts_nanopore.csv

data_processing:
*library strategy: DNA amplicon
Aligned against provided reference using BWA mem
Duplicates marked using Picard MarkDuplicates
Marked duplicates filtered out using samtools
Mapped read counts quantified by position using bam-readcount (https://github.com/genome/bam-readcount)
Resulting positional counts analyzed using custom Python and R scripts
Alternative base frequencies were dichotomized using a cutoff of 3%.For each pair (reference base to alternate base), the dichotomized alternate calls were modeled as a function of sample group (TBLV-SD versus TBLV-WT in wild-type, AID-knockout, or mA3/AID double-knockout B6 mice).A mixed-effects logistic regression approach was used, incorporating a random effect that accounted for sample variation within the group.
Assembly: Custom TBLV (T-cell tropic MMTV) sequence
Supplementary files format and content: csv file containing readcount results

organism: Mus musculus

source_name: lymphoma

extract_protocol:
For MiSeq sequencing, genomic DNA extracted from tumors induced by TBLV-WT and TBLV-SD at the higher dose (3 tumors each) in wild-type and Aicda-/- B6 mice was used for PCR with primers env7254(+) (5’-ATC GCC TTT AAG AAG GAC GCC TTC T-3’) and LTR9604(-) (5’-GGA AAC CAC TTG TCT CAC ATC-3’), resulting in ~2 kb amplicon of the envelope-LTR junction region. Reactions were performed with JumpStart RED Accutaq LA polymerase (Sigma-Aldrich) in the supplied buffer, 1 µg of tumor DNA, 50 pmol of each primer, and 0.5 mM deoxynucleoside triphosphates in 20 µl.  PCR parameters were: 94oC for 1 min, then 10 cycles at 94oC for 10 sec, 53oC for 30 sec, and 68oC for 2 min followed by 25 cycles of 95oC for 15 sec, 50oC for 30 sec, and 68oC for 2 min with a final incubation at 68oC for 7 min. Sixteen independent reactions for each tumor sample were pooled, and DNA was sheared to a size of approximately 400 bp using a Covaris ultrasonicator at the UT Austin Genomic Sequencing and Analysis Facility (GSAF). For Nanopore sequencing, genomic DNA extracted from tumors from B6, B6 AID (Aicda)-knockout, or B6 mA3-AID double-knockout mice induced by TBLV-WT or TBLV-SD was used for PCR with primers env7254(+) (5’-ATC GCC TTT AAG AAG GAC GCC TTC T-3’) and LTR9604(-) (5’-GGA AAC CAC TTG TCT CAC ATC-3’) for the region spanning the envelope-LTR junction. PCRs were performed in 25 µl with JumpStart RED Accutaq LA polymerase (Sigma-Aldrich, cat# D8045) in the supplied buffer, 500 ng of tumor DNA, 25 to 50 pmol of each primer, and 0.5 mM deoxynucleoside triphosphates.  PCR parameters were: 94oC for 1 min, 10 cycles at 94oC for 10 sec, 53oC for 30 sec, 68oC for 2 min followed by 25 cycles of 95oC for 15 sec, 50oC for 30 sec, and 68oC for 2 min with a final incubation at 68oC for 7 min. The fragment size for the env-LTR junction was ~2kb.
For MiSeq sequencing, fragmented DNA was end repaired and used for dA-tailing and ligation with Illumina adapters (unique to each tumor sample). Adapter-ligated DNA was amplified using these PCR parameters: 98oC for 30 sec, 6 cycles at 98oC for 10 sec, 65oC for 30 sec, and 72oC for 30 sec with a final incubation at 72oC for 5 min. Library preparations were submitted for sequencing on the MiSeq platform at the UT Austin Genome Sequencing and Analysis Facility (GSAF). Nanopore sequencing was employed for high-throughput sequence analysis of TBLV proviruses from the tumors induced by low-dose infection. The extracted PCR fragment used for Sanger sequencing was purified using a Zymoclean Gel DNA Recovery Kit (Zymo Research, cat# D4002). DNA (~1 µg) was prepared for Nanopore long amplicon sequencing by the University of Wisconsin Biotechnology Center.

treatment_protocol: For each strain of mice, age-matched weanlings 4-to-6 weeks of age were injected intraperitoneally with either 1 x 106 (low dose) or 2 x 107 (high dose) stably transfected Jurkat T cells. Infectious clones were used for transfection of Jurkat cells and selected for three weeks in hygromycin  and then screened for production of equivalent amounts of TBLV-WT or TBLV-SD (Rem-null) as judged by Western blotting with antibodies to MuLV capsid protein. Mice were monitored for the development of thymic and/or splenic tumors for a period of 9-12 months

value: lymphoma

tag: strain

value: mA3-AID double knockout B6

value: TBLV-WT


title: DKOWT3


title: DKOWT4


title: DKOSD3

description:
mA3-AID double knockout B6 mouse TBLV-SD derived tumor
snp_counts_nanopore.csv

value: TBLV-SD


title: ceh-37_biol rep 2

value: Whole animal

value: L4 stage_20°C


title: DKOSD2


title: N2_biol rep 2


title: MCF7_AI.betaTEP_R3

value: Oestrogen deprivation

value: Terminal end point


title: DKOSD1


title: N2_biol rep 1


title: B6WT30

description:
C57BL/6 (B6) mouse TBLV-WT derived tumor
snp_counts_nanopore.csv


title: MCF7_AI.betaTEP_R2


title: B6WT45A


title: B6WT45B


title: HEK293T-Repair.v2-EZH2_A22-REP1

description: read 1 25 cycles, read 2 97 cycles


title: B6SD46A

description:
C57BL/6 (B6) mouse TBLV-SD derived tumor
snp_counts_nanopore.csv


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 20 hr rep2

city: Beijing

first: Xue

last: Han

address: Zhongguancun North Street

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
Raw reads of ChIP-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For Pol II ChIP-seq with 293T spike-in, we additionally mapped the raw reads to human genome hg19, which is DNA spike-in, and normalized to spike-in reads.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, cell number normalized reads count

source_name: AID-FBEXOSC2 ESCs

growth_protocol: AID-FBEXOSC2 ESCs were maintained in a complete ESC culture medium that consisted of DMEM (Corning) supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX (100× stock, Gibco), Penicillin-Streptomycin Solution (100× stock, Corning), MEM nonessential amino acids (100× stock, Gibco), nucleoside mix (100× stock, Millipore), 0.1 mM 2-mercaptoethanol (Gibco), and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, Millipore). The mESCs were seeded onto 0.1% gelatin-coated dishes. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and subjected to immunoprecipitation. After elution and reverse-crosslinking, the DNA was purified using DNA Clean-up Kit (CWBIO). We added cross-linked 293T cells as spike-in to cross-linked AID-FBEXOSC2 ESCs and then performed cell lysis and all downstream procedures to indicate cell number.
ChIP-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

treatment_protocol: EXOSC2 degradation was induced by treatment of IAA (0.5 mM, Sigma, Cat#: I5148) for indicated hours to adherent ESCs.

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: IAA

tag: time

value: 20 hour

tag: chip antibody

value: Ser2P Pol II (CST, Cat#:13499)


title: B6SD341


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 20 hr rep1


title: B6AIDKOWT45A

description:
AID-knockout B6 mouse TBLV-WT derived tumor
snp_counts_nanopore.csv

value: AID-knockout B6


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 4 hr rep2

value: 4 hour


title: B6SD348


title: MCF7_AI.beta_R3

value: Awakening


title: MCF7_AI.betaTEP_R1


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 4 hr rep1


title: B6AIDKOWT322


title: MCF7_AI.beta_R4


title: MCF7_AI.beta_R2


title: B6AIDKOWT321


title: B6AIDKOSD356

description:
AID-knockout B6 mouse TBLV-SD derived tumor
snp_counts_nanopore.csv


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 0 hr rep2

value: 0 hour


title: MCF7_AI.beta_R1


title: B6AIDKOSD48B

value: lymphoma


title: B6AIDKOSD351


title: MCF7_AI.gammaTEP_R3


title: Sorted spermatocytes, Paf1L homozygous mutant, NOT rRNA-depleted, rep3

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

description:
C_216637_mRNA_216646_rRNA_spermatocyte_GFP_Cdc73L_CG12674_A2_7_rep3
GeTMM_per_gene_Spermatocyte_RNAseq.txt

data_processing:
After trimming to bases 5-45, RNA-Seq reads were mapped to the Drosophila melanogaster genome (dm6, r6.40) using STAR (for genome-mapping) or to Drosophila melanogaster mRNA sequences using Salmon (for transcriptome quasi-mapping)
Normalization between samples was done based on the number of genome-unique mapping reads for each sample (for STAR-based mapping)
For gene expression quantification, Gene length corrected TMM (GeTMM) values were calculated using edgeR (v3.34.0)
Differential Gene Expression analysis was performed on Salmon analysis output using DESeq2
The scripts used for RNAseq analysis and visualization as well as related processed data files are available at GitLab: https://gitlab.com/AndersenGermlineLab/tpaf_vilstrup_2024
Assembly: dm6, r6.40
Supplementary files format and content: tab-delimited text files with GeTMM gene expression estimates for all annotated genes in each sample (one table for bulk testis RNA-seq and one for spermatocyte RNA-seq)

organism: Drosophila melanogaster

source_name: Testis

growth_protocol: D. melanogaster strain maintenance, as well as experiments, were done on standard medium at 25°C at 70% humidity with 12:12 hrs light/dark cycle unless otherwise stated.

extract_protocol:
For bulk testis RNA-seq samples: RNA was isolated from testis tissues of 1-3 days old transheterozygous tPAF mutants and control (w1118) flies. Tissues were dissected in cold 1x PBS on ice. Samples were homogenized and lysed in 1mL TRIzol and extracted according to standard procedure.  For RNA-seq of sorted spermatocytes: For spermatocyte isolation, testis tissues were dissected from 1-3 days old knock-in LAP-Cdc73L flies (control or in combination with Paf1L or Leo1L mutant alleles) into cold Schneider's medium on ice. Following, the medium was removed and the tissue was homogenized with a plastic pestle and lysis buffer (560 µL PBS, 70 µl 1x trypsin, 70 µl 2% collagenase) was added. Samples were rotated at room temperature for 30 minutes followed by careful pipetting with a p1000 tip. The cell suspension was then drawn through a 40 µm mesh cell strainer into 500 µL Schneider's medium. 100 µL additional Schneider's medium was drawn through the cell strainer to collect the remaining cells. Samples were centrifuged at 1200 rpm for 7 minutes at 4°C and the supernatant was removed. Then, the cells were resuspended in 200 µL Schneider’s medium, and DNA was stained with bisbenzimide Hoechst 33342 (Sigma). GFP-expressing cells were then isolated by fluorescence-activated cell sorting (FACS) on a FACSAria III machine (BD Biosciences, FACS Core Facility at Aarhus University, www.facs.au.dk). Flowjo software (Treestar) was used for data analysis. The preparation and FACS sorting of control and mutant spermatocytes were performed in three independent experiments. To this end, we isolated control and mutant spermatocytes with a purity of at least 85% by FACS sorting and characterized their transcriptome by RNA-seq. Wildtype testes were used to clearly identify the GFP-expressing spermatocyte population during flow cytometry. RNA isolation and library preparation were done in the same manner as for whole testis.
Library construction for bulk testis RNA-seq: Genomic DNA was removed from the purified RNA samples using RNA Clean & Concentrator™-5 columns with on-column DNase digest (Zymo Research, R1014). For rRNA-depleted samples, rRNA was removed with RNase H using a modified version of the original protocol in (Morlan et al. 2012) as described in (ElMaghraby et al. 2019). Briefly, rRNA depletion was performed using a mixture of antisense oligos complementary to the mature Drosophila melanogaster rRNA transcripts. The oligo pool was mixed with 1 μg DNAse-free total RNA in RNase H Buffer (20 mM Tris-HCl pH 8, 100 mM NaCl) and annealed over a temperature gradient from 95°C to 45°C. The RNA-DNA hybrids were then digested with thermostable RNase H (NEB, M0523S) at 45°C for 1 hour. Next, RNA was purified and the DNA oligos were removed from samples using RNA Clean & Concentrator™-5 columns with on-column DNase digest (Zymo Research, R1014) according to the manufacturer’s instructions. rRNA depletion was verified by qPCR. Library preparation was done with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7770L), following the recommended kit protocol. Amplified libraries were purified by SPRI beads and library quality was assessed with Bioanalyzer High Sensitivity DNA Analysis (Agilent Technologies, 5067-4626). Samples were sequenced on a NovaSeq 6000 sequencing system  (Illumina).  Library construction for sorted spermatocyte RNA-seq: Sorted spermatocyte RNA-seq libraries were prepared for each sample with and without rRNA depletion to minimize technical biases from working with small sample amounts. For the analyses, both library variants were pooled and analyzed together (see also the section on Analysis of RNA-seq data). Otherwise, the library preparation was performed as described above for whole testis RNA-seq.

value: Testis

value: Sorted spermatocytes

value: Paf1L FS1 mutant genotype combined with endogenously GFP-tagged Cdc73L

value: male


title: EXOSC2 AID ESCs, S2P Pol II, spikein, 0 hr rep1


title: Sorted spermatocytes, Paf1L homozygous mutant, NOT rRNA-depleted, rep1

description:
C_216631_mRNA_216640_rRNA_spermatocyte_GFP_Cdc73L_CG12674_A2_7_rep1
GeTMM_per_gene_Spermatocyte_RNAseq.txt


title: Sorted spermatocytes, PafL homozygous mutant, rRNA-depleted, rep3


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 20 hr rep2

value: Ser5P Pol II (CST, Cat#:13523)


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 20 hr rep1


title: Sorted spermatocytes, PafL homozygous mutant, rRNA-depleted, rep2

description:
C_216634_mRNA_216643_rRNA_spermatocyte_GFP_Cdc73L_CG12674_A2_7_rep2
GeTMM_per_gene_Spermatocyte_RNAseq.txt


title: MCF7_AI.gammaTEP_R2

value: Oestrogen deprivation


title: MCF7_AI.gammaTEP_R1

value: Terminal end point


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 4 hr rep2

value: AID-FBEXOSC2 ESCs


title: Sorted spermatocytes, PafL homozygous mutant, rRNA-depleted, rep1


title: MCF7_AI.alphaTEP_R3


title: Sorted spermatocytes, Leo1L homozygous mutant, NOT rRNA-depleted, rep2

description:
B_216633_mRNA_216642_rRNA_spermatocyte_GFP_Cdc73L_CG10887_A12_3_rep2
GeTMM_per_gene_Spermatocyte_RNAseq.txt

value: Leo1L FS1 mutant genotype combined with endogenously GFP-tagged Cdc73L


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 4 hr rep1

value: mouse embryonic stem cell

value: IAA


title: Sorted spermatocytes, Leo1L homozygous mutant, NOT rRNA-depleted, rep1

description:
B_216630_mRNA_216639_rRNA_spermatocyte_GFP_Cdc73L_CG10887_A12_3_rep1
GeTMM_per_gene_Spermatocyte_RNAseq.txt


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 0 hr rep2


title: MCF7_AI.alphaTEP_R2


title: Sorted spermatocytes, Leo1L homozygous mutant, rRNA-depleted, rep1


title: Sorted spermatocytes, Leo1L homozygous mutant, rRNA-depleted, rep2


title: Sorted spermatocytes, control (w1118), NOT rRNA-depleted, rep3

description:
A_216635_mRNA_216644_rRNA_spermatocyte_GFP_Cdc73L_rep3
GeTMM_per_gene_Spermatocyte_RNAseq.txt

value: Control (w1118) genotype combined with endogenously GFP-tagged Cdc73L


title: MCF7_AI.alpha_R2


title: Sorted spermatocytes, control (w1118), NOT rRNA-depleted, rep2

description:
A_216632_mRNA_216641_rRNA_spermatocyte_GFP_Cdc73L_rep2
GeTMM_per_gene_Spermatocyte_RNAseq.txt


title: Sorted spermatocytes, Paf1L homozygous mutant, NOT rRNA-depleted, rep2


title: MCF7_AI.alpha_R1


title: Sorted spermatocytes, control (w1118), NOT rRNA-depleted, rep1

description:
A_216629_mRNA_216638_rRNA_spermatocyte_GFP_Cdc73L_rep1
GeTMM_per_gene_Spermatocyte_RNAseq.txt


title: EXOSC2 AID iMEFs, RNA, 20 hr, rep2

data_processing:
Raw reads of RNA-seq were mapped to mouse genome mm10 by TopHat (version 2.0.11).
FPKM was calculated by Cufflinks (version 2.0.2) using Gencode vM16 annotation with redundant genes removed (a list containing 52,885 annotated genes).
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count
Supplementary files format and content: tab-delimited text file includes FPKM values for RNA-seq samples

growth_protocol: AID-FBEXOSC2 iMEFs were fibroblasts derived from AID-FBEXOSC2 ESCs. The ESCs (3*104 cells per 10 cm dish) were treated with 1 μM retinoic acid for 10 days in LIF-withdrawal ESC medium with medium refreshed every day. The differentiated cells, which formed a monolayer, were trypsinized and replated in an uncoated cell culture dish where fibroblasts quickly attach within 1 hour. Other types of cells floating in the medium were removed. The attached cells, mainly composed of fibroblasts, named iMEFs, were then trypsinized, re-seeded to uncoated dishes and cultured in LIF-withdrawal ESC medium. All cultured cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA were extracted by TRIzol reagent according to manufacturer's instruction. Purified total RNA were subjected to ribosomal RNA depletion by Ribo-Zero rRNA removal kits (Illumina) according to manufacturer's instruction.
RNA-seq libraries were constructed by NEBNext Ultra II directional RNA library prep kits (NEB) following manufacturer’s protocols.

value: mouse embryonic fibroblast

value: 20 hour


title: EXOSC2 AID iMEFs, RNA, 20 hr, rep1


title: Sorted spermatocytes, control (w1118), rRNA-depleted, rep2


title: MCF7_T.eta_R3

value: Tamoxifen treated

value: Awakening


title: Sorted spermatocytes, control (w1118), rRNA-depleted, rep1


title: Bulk testis, Paf1L transheterozygous mutants, rep3

description:
G_Paf1L_TH_mut_rep3_191912
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Bulk testis

value: Paf1L TH2 mutants


title: Sorted spermatocytes, Leo1L homozygous mutant, rRNA-depleted, rep3

description:
B_216636_mRNA_216645_rRNA_spermatocyte_GFP_Cdc73L_CG10887_A12_3_rep3
GeTMM_per_gene_Spermatocyte_RNAseq.txt

value: Testis

value: Sorted spermatocytes


title: MCF7_T.eta_R2


title: Bulk testis, Paf1L transheterozygous mutants, rep2

description:
G_Paf1L_TH_mut_rep2_191911
GeTMM_per_gene_Bulk_RNAseq.tsv

value: male


title: EXOSC2 AID iMEFs, RNA, 4 hr, rep2

value: 4 hour


title: Sorted spermatocytes, Leo1L homozygous mutant, NOT rRNA-depleted, rep3


title: MCF7_T.eta_R1


title: EXOSC2 AID ESCs, S5P Pol II, spikein, 0 hr rep1

value: 0 hour

value: Ser5P Pol II (CST, Cat#:13523)


title: Bulk testis, Leo1L transheterozygous mutants (inverted cross), rep3

description:
F_Leo1L_2_TH_mut_rep3_191909
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Leo1L TH1 mutants (inverted cross)


title: Bulk testis, Leo1L transheterozygous mutants (inverted cross), rep2

description:
F_Leo1L_2_TH_mut_rep2_191908
GeTMM_per_gene_Bulk_RNAseq.tsv


title: EXOSC2 AID iMEFs, RNA, 0 hr, rep2

value: AID-FBEXOSC2 ESCs


title: EXOSC2 AID iMEFs, RNA, 4 hr, rep1


title: Bulk testis, Paf1L transheterozygous mutants, rep1

description:
G_Paf1L_TH_mut_rep1_191910
GeTMM_per_gene_Bulk_RNAseq.tsv


title: Bulk testis, Leo1L transheterozygous mutants (inverted cross), rep1

description:
F_Leo1L_2_TH_mut_rep1_191907
GeTMM_per_gene_Bulk_RNAseq.tsv


title: MCF7_T.theta_R3


title: MCF7_AI.alphaTEP_R1

value: Oestrogen deprivation

value: Terminal end point


title: Bulk testis, Leo1L transheterozygous mutants, rep3

description:
E_Leo1L_TH_mut_rep3_191906
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Leo1L TH1 mutants


title: EXOSC2 AID iMEFs, RNA, 0 hr, rep1

value: mouse embryonic fibroblast


title: MCF7_T.theta_R2


title: Bulk testis, Leo1L transheterozygous mutants, rep2

description:
E_Leo1L_TH_mut_rep2_191905
GeTMM_per_gene_Bulk_RNAseq.tsv


title: Bulk testis, Leo1L transheterozygous mutants, rep1

description:
E_Leo1L_TH_mut_rep1_191904
GeTMM_per_gene_Bulk_RNAseq.tsv


title: MCF7_T.theta_R1


title: Bulk testis, Ctr9L transheterozygous mutants, rep2

description:
D_Ctr9L_TH_mut_rep2_191902
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Ctr9L TH2 mutants


title: Bulk testis, Ctr9L transheterozygous mutants, rep1

description:
D_Ctr9L_TH_mut_rep1_191901
GeTMM_per_gene_Bulk_RNAseq.tsv


title: Sorted spermatocytes, control (w1118), rRNA-depleted, rep3

value: Control (w1118) genotype combined with endogenously GFP-tagged Cdc73L


title: EXOSC2 AID ESCs, total Pol II, 4 hr, rep1

data_processing:
Raw reads of ChIP-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and subjected to immunoprecipitation. After elution and reverse-crosslinking, the DNA was purified using DNA Clean-up Kit (CWBIO).
ChIP-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

value: mouse embryonic stem cell

value: IAA

value: total Pol II  (CST, Cat#:14958)


title: EXOSC2 AID ESCs, total Pol II, 0 hr, rep2


title: EXOSC2 AID ESCs, total Pol II, 4 hr, rep2


title: Bulk testis, Cdc73L transheterozygous mutants, rep3

description:
C_Cdc73L_TH_mut_rep3_191900
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Testis

value: Bulk testis

value: Cdc73L TH1 mutants


title: Bulk testis, Ctr9L transheterozygous mutants, rep3

description:
D_Ctr9L_TH_mut_rep3_191903
GeTMM_per_gene_Bulk_RNAseq.tsv

value: male


title: MCF7_T.zetaTEP_R1

value: Tamoxifen treated


title: MCF7_T.zetaTEP_R2


title: Bulk testis, control (w1118 iso), rep2

description:
B_w1118_iso_rep2_191920
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Control (w1118)


title: Bulk testis, control (w1118), rep3

description:
A_w1118_rep3_191918
GeTMM_per_gene_Bulk_RNAseq.tsv


title: EXOSC2 AID ESCs, total Pol II, 0 hr, rep1

value: 0 hour


title: Bulk testis, control (w1118 iso), rep1

description:
B_w1118_iso_rep1_191919
GeTMM_per_gene_Bulk_RNAseq.tsv


title: Bulk testis, Cdc73L transheterozygous mutants, rep1

description:
C_Cdc73L_TH_mut_rep1_191898
GeTMM_per_gene_Bulk_RNAseq.tsv


title: Bulk testis, control (w1118 iso), rep3

description:
B_w1118_iso_rep3_191921
GeTMM_per_gene_Bulk_RNAseq.tsv


title: MCF7_T.epsilonTEP_R4


title: Bulk testis, control (w1118), rep2

description:
A_w1118_rep2_191917
GeTMM_per_gene_Bulk_RNAseq.tsv


title: EXOSC2 AID ESCs, S5P Pol II, 4 hr, rep1

value: AID-FBEXOSC2 ESCs

value: 4 hour

value: Ser5P Pol II (CST, Cat#:13523)


title: MCF7_T.zeta_R1

value: Awakening


title: HFL-1, shPEX5-2, D3 Rep3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

data_processing:
Alignment to hg38 performed using Hisat2. SAMtools toolkit was applied to produce mapped reads in SAM format from the Hisat2-generated BAM file. Read counts for genes were assigned using featureCounts (subread package version 1.6.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Lung

growth_protocol: Human fetal lung fibroblasts were maintained in DMEM (HyClone) supplemented with 10% FBS, 100 units/mL penicillin G sodium, and 100 μg/mL streptomycin sulfate.

extract_protocol:
Total RNA were extracted using Trizol reagenet according to the manufactural protocol
Libraries were prepared according to the instructions for the VAHTSTM mRNA-Seq V2 Library Prep Kit (Vazyme Biotech) for Illumina and purified using Beckman.

treatment_protocol: Human fetal lung fibroblasts were infected with lentivirus supernatants for 24 hours and then cultured in a complete medium for 2 days.

value: Lung

value: Human fetal lung fibroblasts

value: PEX5 knockdown

value: shPEX5-2 treated O/N


title: HFL-1, shPEX5-2, D3 Rep2


title: EXOSC2 AID ESCs, S5P Pol II, 4 hr, rep2

value: mouse embryonic stem cell

value: IAA


title: MCF7_T.zetaTEP_R3

value: Terminal end point


title: Bulk testis, control (w1118), rep1

description:
A_w1118_rep1_191916
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Testis

value: Bulk testis


title: EXOSC2 AID ESCs, S5P Pol II, 0 hr, rep1


title: MCF7_T.epsilonTEP_R3


title: EXOSC2 AID ESCs, S5P Pol II, 0 hr, rep2


title: EXOSC2 AID ESCs, ATAC, 20 hr, rep3 (2nd batch)

data_processing:
Raw reads of ATAC-seq were mapped to mouse genome mm10 by Bowtie2 (version 2.2.6). All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed.
Normalized reads count was calculated by Bedtools.
Assembly: mm10
Supplementary files format and content: bigWig, normalized reads count

extract_protocol:
~1,500 cells were lysed followed by tagmentation using Tn5 transposase (Vazyme, TD502) following manufacturer’s protocols. The samples were then subjected to PCR amplification and purification for sequencing.
ATAC-seq libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

value: 20 hour


title: HFL-1, shPEX5-1, D3 Rep2

value: shPEX5-1 treated O/N


title: HFL-1, shPEX5-1, D3 Rep3


title: MCF7_T.zeta_R2

value: Tamoxifen treated


title: HFL-1, shPEX5-2, D3 Rep1


title: MCF7_T.epsilonTEP_R1


title: EXOSC2 AID ESCs, ATAC, 20 hr, rep1 (2nd batch)


title: EXOSC2 AID ESCs, ATAC, 20 hr, rep2 (2nd batch)


title: MCF7_T.epsilon_R4


title: EXOSC2 AID ESCs, ATAC, 4 hr-2, rep3 (2nd batch)


title: Bulk testis, Cdc73L transheterozygous mutants, rep2

description:
C_Cdc73L_TH_mut_rep2_191899
GeTMM_per_gene_Bulk_RNAseq.tsv

value: Cdc73L TH1 mutants

value: male


title: MCF7_T.epsilon_R3


title: HFL-1, shPEX5-1, D3 Rep1


title: MCF7_T.epsilonTEP_R2


title: EXOSC2 AID ESCs, ATAC, 4 hr-2, rep1 (2nd batch)

value: AID-FBEXOSC2 ESCs

value: 4 hour


title: HFL-1, PEX5, D3 Rep2

value: PEX5 overexpression

value: PEX5 treated O/N


title: EXOSC2 AID ESCs, ATAC, 4 hr-2, rep2 (2nd batch)


title: HFL-1, Flag, D3 Rep2

value: Lung

value: Human fetal lung fibroblasts

value: Flag control

value: Flag treated O/N


title: HFL-1, shNC, D3 Rep1

value: shNC control

value: shNC treated O/N


title: EXOSC2 AID ESCs, ATAC, 0 hr-2, rep2 (2nd batch)

value: mouse embryonic stem cell

value: 0 hour


title: HFL-1, shNC, D3 Rep3


title: HFL-1, PEX5, D3 Rep1


title: HFL-1, Flag, D3 Rep3


title: MCF7_T.gammaTEP_R2

value: Terminal end point


title: MCF7_T.gammaTEP_R1


title: dpf61_Ov_wt_1

city: Research Triangle Park

first: Ciro

middle: Maurizio

last: Amato

state: NC

address: 111 Tw Alexander Dr

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

data_processing:
Data were pseudoaligned with Kallisto.
Assembly: GRCz11
Supplementary files format and content: tab-delimited file that has raw counts for each sample.

organism: Danio rerio

source_name: Ovary

growth_protocol: WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14-hour(h) light and 10h dark photoperiod, lights on at 8:30am, lights off at 10:30pm; at water temperature of 28.5°C, pH of approximately 7.2, and salinity/conductivity ranging from 500 to 1,200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.

extract_protocol:
Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at -800C till purification. Total RNA was purified following the manufacturer’s protocol
cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA-Seq library kit for 47 and 61dpf samples.

value: Ovary

tag: age

value: dpf 61

value: wildtype


title: EXOSC2 AID ESCs, ATAC, 4 hr-1, rep2 (1st batch)

value: IAA


title: MCF7_T.epsilon_R2

value: Tamoxifen treated

value: Awakening


title: dpf61_Ov_mt_2

value: mutant


title: HFL-1, PEX5, D3 Rep3

value: PEX5 overexpression

value: PEX5 treated O/N


title: MCF7_T.epsilon_R1


title: dpf61_Ov_wt_3


title: EXOSC2 AID ESCs, ATAC, 2 hr, rep2 (1st batch)

value: AID-FBEXOSC2 ESCs

value: 2 hour


title: dpf61_Ov_mt_3


title: EXOSC2 AID ESCs, ATAC, 0 hr-2, rep3 (2nd batch)


title: HFL-1, Flag, D3 Rep1

value: Lung

value: Human fetal lung fibroblasts

value: Flag control

value: Flag treated O/N


title: MCF7_T.beta_R1


title: dpf61_Ov_mt_1


title: HFL-1, shNC, D3 Rep2

value: shNC control

value: shNC treated O/N


title: dpf47_Ov_wt_2

value: Ovary

value: dpf 47


title: EXOSC2 AID ESCs, ATAC, 0 hr-2, rep1 (2nd batch)

value: mouse embryonic stem cell

value: 0 hour


title: dpf61_Ov_wt_2

value: dpf 61

value: wildtype


title: MCF7_T.alphaTEP_R2

value: Tamoxifen treated

value: Terminal end point


title: MCF7_T.beta_R3

value: Awakening


title: MCF7_T.alpha_R4


title: dpf47_Ov_wt_1


title: treatment2

city: Los Angeles

first: Yoshihiro

last: Sakano

state: CA

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

growth_protocol: Cells were freshly isolated from the lungs and cultured for 18 hours with isotype control or cd226 antibody

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

treatment_protocol: Isotype control or CD226 antiboy (5µg/mL)  were used for treatment

value: lung

value: sorted ILC2s

value: BALB/c

value: anti-CD226 antibody


title: iso1

value: isotype control


title: dpf47_Ov_mt_2

value: mutant


title: dpf47_Ov_mt_1


title: dpf47_Ov_wt_3


title: MCF7_T.alpha_R3


title: UTR_R2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Chromatin Associated RNA

library_source: transcriptomic single cell

data_processing:
Reads were quality filtered according to the illumina pipeline
Single-end reads were mapped after adapter trimming to the mouse genome assembly mm10 (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html), and the Refseq transcript annotation (ncbiRefSeqCurated 2017/11/16) using topHat2 (TopHat v2.1.1) (Trapnell et al. 2012) with parameters: --max-multihits 1 --b2-very-sensitive).
Reads mapping to the ENCODE black-list regions (https://github.com/Boyle-Lab/Blacklist) (Amemiya et al. 2019) were removed using standard bedtools operations (bedtools v2.29.2).
Per gene read counts were retrieved using standard R/Bioconductor packages (e.g. GenomicRanges and GenomicAlignment together with the proper GFF Refseq annotation ncbiRefSeqCurated 2017/11/16).
Sample normalization was achieved by selecting invariant genes across samples/conditions (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.  Differentially regulated genes were selected using DESEq2 (R/Bioconductor package version 1.26.0; R version 3.6.2) after turning off the default normalization DESEq2 applies.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

source_name: mouse bone marrow derived macrophages

extract_protocol:
chromatin-associated-RNA-seq libraries were prepared for NextSeq500 sequencing following standard protocols.
Library preparation was performed following the SMART-seq2 protocol (Picelli et al. 2014b). Briefly, 5 ng of chromatin associated RNA were reverse transcribed with template-switching using random primers and an LNA-containing template-switching oligo (TSO). The resulting cDNA was pre-amplified, purified and tagmented with Tn5 transposase produced in-house. cDNA fragments generated after tagmentation were gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina NextSeq500 sequencing.
RNAseq_Smartseq2

treatment_protocol: LPS (10 ng/ml) treatment for 30min, 1h, 2h or 4h, IL4 (10 ng/ml) for 30min, 1h, 2h or 4h

value: BMDM

value: 1h DMSO followed by UNTREATED

value: wild type


title: K5_D1_cTECs

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extremities
Expression values were computed using a pseudo-alignment to the reference transcriptome described in Ensembl version 99 using Kallisto version 0.43.0
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file where columns are: Ensembl transcript identifier, transcript lengh, effective length, estimated read count and TPM values

source_name: Thymus

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hypreprep Kit and were further amplified for sequencing.

value: Thymus

value: cortical thymic epithelial cells

tag: reference genome

tag: strand orientation

value: forward


title: MCF7_T.alphaTEP_R1


title: treatment1

tag: tissue


title: EXOSC2 AID ESCs, ATAC, 0 hr-1, rep1 (1st batch)

value: AID-FBEXOSC2 ESCs

tag: cell type

value: mouse embryonic stem cell

value: 0 hour


title: UTR_R1

description: Chromatin Associated RNA

tag: treatment


title: UTR_R3

description: Chromatin Associated RNA


title: LPS_4h_R3

description: Chromatin Associated RNA

value: 1h DMSO followed by 4h LPS 10ng/mL


title: MCF7_T.beta_R2

value: Tamoxifen treated

value: Awakening


title: K5_D1_mTECs

value: medullary thymic epithelial cells


title: EXOSC2 AID ESCs, ATAC, 1 hr, rep1 (1st batch)

value: IAA

value: 1 hour


title: iso2

value: lung

value: sorted ILC2s

value: BALB/c

value: isotype control


title: MCF7_T.alpha_R2


title: EXOSC2 AID ESCs, ATAC, 4 hr-1, rep1 (1st batch)

value: 4 hour


title: MCF7_T.deltaTEP_R4

value: Terminal end point


title: LPS_30_R3

description: Chromatin Associated RNA

value: BMDM

value: 1h DMSO followed by 30min LPS 10ng/mL

value: wild type


title: MCF7_T.alpha_R1


title: MCF7_T.deltaTEP_R3


title: EXOSC2 AID ESCs, H3K9me3, 20 hr, rep2

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: 20 hour

value: H3K9me3 (Abclonal, Cat#:A2360)


title: EXOSC2 AID ESCs, H3K9me3, 0 hr, rep2

value: 0 hour


title: EXOSC2 AID ESCs, ATAC, 0 hr-1, rep2 (1st batch)


title: EXOSC2 AID ESCs, ATAC, 1 hr, rep2 (1st batch)


title: LPS_4h_R2

description: Chromatin Associated RNA

value: 1h DMSO followed by 4h LPS 10ng/mL


title: EXOSC2 AID ESCs, ATAC, 2 hr, rep1 (1st batch)

value: IAA

value: 2 hour


title: EXOSC2 AID ESCs, H3K9me3, 20 hr, rep1


title: LPS_30_R1

description: Chromatin Associated RNA


title: EXOSC2 AID ESCs, H3K9me3, 0 hr, rep1


title: LPS_30_R2

description: Chromatin Associated RNA


title: LPS_2h_R2

description: Chromatin Associated RNA

value: 1h DMSO followed by 2h LPS 10ng/mL


title: LPS_2h_R1

description: Chromatin Associated RNA


title: MCF7_T.deltaTEP_R2

value: Tamoxifen treated


title: LPS_1h_R3

description: Chromatin Associated RNA

value: 1h DMSO followed by 1h LPS 10ng/mL


title: LPS_1h_R2

description: Chromatin Associated RNA


title: LPS_1h_R1

description: Chromatin Associated RNA


title: MCF7_T.delta_R1

value: Awakening


title: dpf47_Ov_mt_3

value: Ovary

value: dpf 47

value: mutant


title: EXOSC2 AID ESCs, H3K27me3, 20 hr, rep2

value: H3K27me3 (Active Motif, Cat#:39155)


title: MCF7_T.deltaTEP_R1

value: Terminal end point


title: IL4_4h_R1

description: Chromatin Associated RNA

value: BMDM

value: 1h DMSO followed by 4h IL4 10ng/mL

value: wild type


title: IL4_30_R3

description: Chromatin Associated RNA

value: 1h DMSO followed by 30min IL4 10ng/mL


title: LPS_4h_R1

description: Chromatin Associated RNA


title: MCF7_T.betaTEP_R3


title: IL4_30_R2

description: Chromatin Associated RNA


title: MCF7_T.delta_R2


title: EXOSC2 AID ESCs, H3K27me3, 4 hr, rep2

value: AID-FBEXOSC2 ESCs

value: mouse embryonic stem cell

value: 4 hour


title: IL4_4h_R3

description: Chromatin Associated RNA


title: LPS_2h_R3

description: Chromatin Associated RNA


title: EXOSC2 AID ESCs, H3K27me3, 0 hr, rep2

value: 0 hour


title: IL4_4h_R2

description: Chromatin Associated RNA


title: MCF7_T.betaTEP_R2


title: IL4_30_R1

description: Chromatin Associated RNA


title: EXOSC2 AID ESCs, H3K27me3, 4 hr, rep1

value: IAA


title: MCF7_T.delta_R3

value: Tamoxifen treated


title: IL4_2h_R1

description: Chromatin Associated RNA

value: 1h DMSO followed by 2h IL4 10ng/mL


title: EXOSC2 AID ESCs, H3K4me3, 20 hr, rep2

value: 20 hour


title: EXOSC2 AID ESCs, H3K27me3, 20 hr, rep1


title: MCF7_T.gamma_R2

value: Awakening


title: EXOSC2 AID ESCs, H3K4me3, 20 hr, rep1


title: IL4_2h_R2

description: Chromatin Associated RNA


title: IL4_2h_R3

description: Chromatin Associated RNA


title: IL4_1h_R3

description: Chromatin Associated RNA

value: 1h DMSO followed by 1h IL4 10ng/mL


title: EXOSC2 AID ESCs, H3K27me3, 0 hr, rep1


title: MCF7_T.betaTEP_R1


title: EXOSC2 AID ESCs, H3K4me3, 0 hr-2, rep2 (ctrl for 20 hr)


title: MCF7_T.gamma_R1


title: ATAC_control_UT_R2

description:
ATACseq
ATAC_reference_peaks.bed
ATAC_reference_peaks_extended.bed
ATAC_reference_summits.bed

data_processing:
Reads were quality filtered according to the illumina pipeline
Following adapter trimming, single end reads were trimmed with trimmomatic (Bolger et al. 2014) (version 0.39 flags: EADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:38).
Resulting reads were mapped with ShortStack (Axtell 2013).
Resulting bam files were then filtered using SAMtools (version 1.9) in order to remove unmapped reads, failing quality or mapping to mitochondrial chromosome.
Reads were then shifted of 4nt on the positive strand and -5nt on the negative strand using basic awk operations (Buenrostro et al. 2013).
Peak calling was performed using MACS2 (version 2.2.6; options --nomodel --extsize 146 --nolambda --keep-dup 'all' --call-summits). A reference set of peaks was created by selecting peaks called in each samples/replicate with qvalue ≤ 0.01 and being consistent between replicates (overlapping area of at least 50% between replicates).
The resulting set of peaks was used to count reads in each sample using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013).
Sample normalization was achieved by selecting invariant ATAC peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

extract_protocol:
genomic DNA
5 × 104 BMDM cells were pelleted by centrifugation and resuspended in 50 µl of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM MgCl2, 0.1% Igepal CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation for 10 min at 500g at 4 °C and resuspended in 25 µl of reaction buffer containing 1 µl of Tn5 transposase made in-house using a described protocol (Picelli et al. 2014a), 5 µl of 5x transposase buffer (50 mM Tris-HCl, (pH 8.4) and 25 mM MgCl2), and 19 µl of milliQ water. The tagmentation mix was incubated at 37 °C for 60 min gently shaking, in order to avoid precipitation of nuclei. The reaction was stopped by the addition of 5 µl of cleanup buffer (900 mM NaCl, 30 mM EDTA), 2 µl of 5% SDS and 2 µl of Proteinase K (20 µg /µl) (Merck cod. P2308) and incubation for 30 min at 40 °C. Tagmented DNA was isolated using 2× Agencourt Ampure Xp beads (Beckman cod.A63881) and amplified by PCR with the HotStart Kapa HiFi enzyme (Roche cod. 07958889001). Fragments smaller than 600 bp were isolated by negative size selection (using 0.65× Agencourt Ampure Xp beads) and then purified with 1.8× Agencourt Ampure Xp beads. Libraries were single-end sequenced (76 bp) on an Illumina NextSeq500 platform.

value: 1h DMSO followed by UNTREATED


title: IL4_1h_R2

description: Chromatin Associated RNA


title: ATAC_control_LPS_4h_R2

value: 1h DMSO followed by 4h LPS 10ng/mL


title: ATAC_control_UT_R1


title: MCF7_U150.3_R3

value: Untreated

value: Untreated equivalent for awakening


title: MCF7_U150.3_R2


title: ATAC_control_LPS_4h_R1

value: BMDM


title: ATAC_control_LPS_30_R2

value: 1h DMSO followed by 30min LPS 10ng/mL

value: wild type


title: EXOSC2 AID ESCs, H3K4me3, 0 hr-2, rep1 (ctrl for 20 hr)

value: AID-FBEXOSC2 ESCs


title: EXOSC2 AID ESCs, H3K4me3, 4 hr, rep2

value: mouse embryonic stem cell


title: MCF7_U150.3_R1


title: ATAC_control_LPS_30_R1


title: ATAC_control_LPS_2h_R1

value: 1h DMSO followed by 2h LPS 10ng/mL


title: MCF7_U150.2_R4


title: ATAC_control_IL4_4h_R2

value: 1h DMSO followed by 4h IL4 10ng/mL


title: EXOSC2 AID ESCs, H3K4me3, 4 hr, rep1

value: IAA

value: 4 hour