title: JJN3-DMSO-2

description:
B0
counts.strict.txt

value: DMSO

value: control


title: JJN3-WNK463-6h-1

status: Public on Apr 16 2024

type: SRA

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

country: USA

institute: University of Massachusetts Medical School

description:
A6
counts.strict.txt

library_source: transcriptomic

data_processing:
OneStopRNAseq server
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to hg38 using STAR
Read count extraction was performed using featureCounts
Assembly: hg38
Supplementary files format and content: counts.strict.txt

molecule: total RNA

organism: Homo sapiens

growth_protocol: JJN3 cells were cultured in 40% DMEM 40% IMDM, and 20% FBS in 37°C supplemented with 10% CO2

extract_protocol:
Trizol following manufacturer's protocol
Novogene

treatment_protocol: Cells were treated with DMSO or WNK463 (5μM) for 2/6 h

tag: cell line

tag: cell type

value: multiple myeloma cell line

tag: genotype

value: WT

tag: treatment

tag: time


title: lib55573

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: counts.txt: Gene count matrix in text file
Supplementary files format and content: tcrs.txt: tab-delimited text file of TCR sequences and accompanying metadata

source_name: CD154+CD69+CD4 T cells

growth_protocol: Cryopreserved PBMC were thawed and rested at 37C for 3h in RPMI with 10% commercial human serum. After resting PBMC were cultures with overlapping peptide libraries (20 aa in length, 12 aa overlap) from the islet proteins GAD65, IGRP, ZnT8, and preproinsulin in the presence of anti-CD40 antibody for 14h.

extract_protocol:
Sorted cells were lysed, followed by reverse transcription (SMART-Seq v1 Ultra Low Input RNA Kit; Takara, Mountain View, CA).
Sequencing libraries were prepared using Nextera XT DNA kits (Illumina, San Diego, CA).

treatment_protocol: After 14h cutlture CD154+ activated T cells were enriched by magnetic bead enrichment and single cell sorted to isolate CD4+CD154+CD69+ T cells. Cells were sorted directly into wells of a 96 w plate containing SMART-seq v1 Ultra Low Input RNA buffer and then processed for library preparation.

value: CD154+CD69+CD4 T cells

value: islet peptide library

tag: donorid


title: Capmatinib_LPS_30

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: ChIPseq

library_source: genomic

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):   For H2K27ac we used peaks identified in ATACseq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant 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

molecule: genomic DNA

organism: Mus musculus

source_name: mouse bone marrow derived macrophages

extract_protocol:
genomic DNA
ChIPseq was carried out as previously described (XXXXXXX). Briefly, 2 x 106 BMDM cells were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Bioruptor® Pico, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 2 μg of H3K27ac antibody (ab4729). After immunoprecipitation, beads were recovered using a magnetic stand and washed six times with FA/SDS buffer (50mM Hepes pH 8, 1% Triton-X, 0.1% Na-deoxycholate, 0.1% SDS, 1mM EDTA, 650mM Nacl), four times with Wash buffer (10mM Tris pH 8, 0.25M LiC, 1mM EDTA, 0.5% NP40, 0.5% Na-deoxycholate), followed by two washes with TEbuffer plus 50mM NaCl. Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Cod.E2670, Promega. DNA libraries were prepared for NextSeq500 sequencing as described (Gualdrini et al 2022). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.

treatment_protocol: Individual samples have been pre-treated with each compound separately for 1h before stimulating the cells with either LPS (10ng/mL) or IL4 (10 ng/mL) for 30minutes, 1h, 2h or 4h.

value: BMDM

value: 1h pre-treatment with Capmatinib followed by 30 LPS 10ng/mL

value: wild type

tag: antibody


title: Capmatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 2h LPS 10ng/mL


title: JJN3-WNK463-2h-1

description:
A2
counts.strict.txt


title: lib55005


title: lib55004


title: lib55582


title: JJN3-DMSO-1

description:
A0
counts.strict.txt


title: Capmatinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 1h LPS 10ng/mL


title: lib55003


title: Capmatinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 4h IL4 10ng/mL


title: lib55002


title: Capmatinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 30 IL4 10ng/mL


title: lib55576


title: lib55001


title: Capmatinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 4h LPS 10ng/mL


title: lib54999


title: lib54998


title: W5Pol2

data_processing:
Reads mapped to hg38 with BWA
Duplicates removed with PICARD
Bigwig files generated with deeptools
Assembly: hg38
Supplementary files format and content: bigwig

source_name: JJN3 human multiple myeloma cell line

extract_protocol:
Protein-DNA complexes were isolated by antibody
Libraries were prepared using DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN) (Cells Signaling Technology) and Multiplex Oligos for Illumina Systems (Single Index Primers) (ChIP-seq, CUT&RUN) (Cells Signaling Technology) following the manufacturer’s protocol

treatment_protocol: Cells were treated with DMSO or WNK463 (5μM) for 4 h

value: multiple myeloma


title: lib55000


title: lib55572


title: W5K272


title: lib54996


title: lib55571


title: Capmatinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 2h IL4 10ng/mL


title: lib54997


title: W5K271


title: lib54995


title: BMS911543_UT_0h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 4h UT


title: Capmatinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Capmatinib followed by 1h IL4 10ng/mL


title: lib54994


title: BMS911543_UT_0h_b

description: ChIPseq


title: lib54992


title: lib54993


title: lib54991


title: W5Input1


title: BMS911543_LPS_4h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 4h LPS 10ng/mL


title: lib54990


title: W5Pol1


title: W0Pol2

value: DMSO


title: lib54989


title: lib54988


title: BMS911543_LPS_30

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 30 LPS 10ng/mL


title: lib54987

value: CD154+CD69+CD4 T cells


title: W0Pol1


title: BMS911543_LPS_2h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 2h LPS 10ng/mL


title: lib54986

value: islet peptide library


title: W0K272


title: lib54985


title: lib54982


title: W0Input2


title: BMS911543_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with BMS911543 followed by 4h IL4 10ng/mL


title: W0K271


title: BMS911543_LPS_1h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 1h LPS 10ng/mL

value: wild type


title: BMS911543_IL4_30

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 30 IL4 10ng/mL


title: lib54984


title: W5Input2


title: lib54983


title: lib54981


title: lib54980


title: lib54979


title: lib54978


title: W0Input1


title: C0S100_Rep1-3

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description:
sample_barcodes.txt.gz
RawCountTable.tsv.gz

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: Uterus

extract_protocol:
30um of tissue sections were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by using Direct-zol Kit (Zymo Research).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

tag: tissue

value: Uterus

value: Carcinosarcoma

tag: disease state


title: BMS911543_IL4_2h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 2h IL4 10ng/mL


title: lib54977


title: BMS911543_IL4_1h

description: ChIPseq

value: 1h pre-treatment with BMS911543 followed by 1h IL4 10ng/mL


title: C10S90_Rep1-3


title: lib54975


title: C30S70_Rep1-3


title: lib54974


title: lib54976


title: lib54973


title: BMS387032_UT_0h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 4h UT


title: BMS387032_UT_0h_b

description: ChIPseq


title: lib54972


title: lib54971


title: lib54970


title: BMS387032_LPS_4h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 4h LPS 10ng/mL


title: BMS387032_LPS_30

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 30 LPS 10ng/mL


title: lib54968


title: lib54967


title: A549 cells_48h_01

description:
TGFb(48hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz

library_source: transcriptomic single cell

data_processing:
Read1(CB) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: Lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Individual cells were sorted into 384 well plate including cell lysis buffer and dT primes with unique cell barcoded.
Individual cells were reverse transcribed in each wells then 384 wells were mixed and purified. CEL-Seq2(Hashimshony T, et al.) method was used for library preparation. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

treatment_protocol: A549 cells were seeded 24 h before induction to reach ~70% confluence and treated with 4 ng/mL TGFb to induce EMT. The medium containing TGFb was replaced every other day.

value: Lung

value: Lung carcinoma

tag: time point

value: TGFb


title: lib54966

value: CD154+CD69+CD4 T cells


title: BMS387032_LPS_1h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 1h LPS 10ng/mL


title: lib54965

value: islet peptide library


title: BMS387032_LPS_2h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with BMS387032 followed by 2h LPS 10ng/mL


title: lib54927


title: BMS387032_LPS_1h_b

description: ChIPseq

value: wild type


title: lib54926


title: A549 cells_24h_01

description:
TGFb(24hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz


title: A549 cells_24h_02

description:
TGFb(24hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: A549 cells_48h_02

description:
TGFb(48hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: BMS387032_IL4_4h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 4h IL4 10ng/mL


title: lib54923


title: A549 cells_12h_02

description:
TGFb(12hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: BMS387032_IL4_30

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 30 IL4 10ng/mL


title: lib54922


title: lib54924


title: lib54925


title: A549 cells_96h_01

description:
TGFb(96hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz


title: A549 cells_12h_01

description:
TGFb(12hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz


title: lib54969


title: lib54920


title: BMS387032_IL4_2h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 2h IL4 10ng/mL


title: A549 cells_96h_02

description:
TGFb(96hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: A549 cells_0.5h_02

description:
TGFb(0.5hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: lib54919


title: BMS387032_IL4_1h

description: ChIPseq

value: 1h pre-treatment with BMS387032 followed by 1h IL4 10ng/mL


title: lib54918


title: A549 cells_0.5h_01

description:
TGFb(0.5hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz


title: lib54916


title: BMS387032_IL4_1h_b

description: ChIPseq


title: lib54917


title: A549 cells_0h_02

description:
TGFb(0hr) treated A549 cell line replicate2
RawCountTable.tsv.gz
384_set1_cb.txt.gz


title: lib54914


title: lib54915


title: A549 cells_0h_01

description:
TGFb(0hr) treated A549 cell line replicate1
RawCountTable.tsv.gz
384_set2_cb.txt.gz


title: lib54913


title: BGT226_LPS_4h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 4h LPS 10ng/mL


title: lib54912


title: lib54921


title: lib54911


title: lib54910


title: lib54964


title: BGT226_LPS_30

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 30 LPS 10ng/mL


title: lib54909


title: BGT226_LPS_2h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 2h LPS 10ng/mL


title: lib54908


title: Poly M395 RES shVARS-1_1

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: POLY-shVARS-51-04-02-20_NGS20-L754_BHKMKVDRXX_S20_L001_R1_001

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 97.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

molecule: polyA RNA

source_name: M395 RES

growth_protocol: M395 RES cells were maintained in RPMI supplemented with 10% fetal bovie serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was haervested from the input or polysomal fractions using the TriPure isolation method (ref. 11667157001, Roche).
RNA libraries were prepared using the TruSeq Stranded mRNA kit (ref. 20020595, Illumina) according to the manufacturer's protocols.

value: M395 RES

value: Primary melanoma culture

value: shVARS

tag: fraction

value: polysomal


title: Poly M395 RES shCTRL_3

description: POLY-shCTRL-31-01-20_NGS20-L749_BHKMKVDRXX_S15_L001_R1_001

value: shCTRL


title: lib54906

value: CD154+CD69+CD4 T cells


title: BGT226_IL4_4h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 4h IL4 10ng/mL


title: BGT226_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with BGT226 followed by 1h LPS 10ng/mL


title: Poly M395 RES shCTRL_1

description: POLY-shCTRL-04-02-20_NGS20-L753_BHKMKVDRXX_S19_L001_R1_001


title: BGT226_IL4_30

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 30 IL4 10ng/mL

value: wild type


title: lib54907

value: islet peptide library


title: Poly M395 RES shCTRL_2

description: POLY-shCTRL-10-02-20_NGS20-L757_BHKMKVDRXX_S23_L001_R1_001


title: lib54901


title: lib54903


title: Poly M395 RES shVARS-1_3

description: POLY-shVARS-51-31-01-20_NGS20-L750_BHKMKVDRXX_S16_L001_R1_001


title: lib54902


title: lib54821


title: BGT226_UT_0h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 4h UT


title: Poly M395 RES shVARS-1_2

description: POLY-shVARS-51-10-02-20_NGS20-L758_BHKMKVDRXX_S24_L001_R1_001


title: lib54820


title: Input M395 RES shVARS-1_3

description: INPUT-shVARS-51-31-01-20_NGS20-L748_BHKMKVDRXX_S14_L001_R1_001

value: input


title: lib54819


title: BGT226_IL4_2h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 2h IL4 10ng/mL


title: lib54905


title: Bafetinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 4h UT


title: lib54817


title: lib54904


title: Input M395 RES shVARS-1_1

description: INPUT-shVARS-51-04-02-20_NGS20-L752_BHKMKVDRXX_S18_L001_R1_001


title: lib54816


title: Input M395 RES shVARS-1_2

description: INPUT-shVARS-51-10-02-20_NGS20-L756_BHKMKVDRXX_S22_L001_R1_001


title: Bafetinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 4h LPS 10ng/mL


title: Input M395 RES shCTRL_3

description: INPUT-shCTRL-31-01-20_NGS20-L747_BHKMKVDRXX_S13_L001_R1_001

value: M395 RES


title: lib54814


title: BGT226_IL4_1h

description: ChIPseq

value: 1h pre-treatment with BGT226 followed by 1h IL4 10ng/mL


title: lib54815


title: Bafetinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 30 LPS 10ng/mL


title: lib54811


title: Bafetinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 2h LPS 10ng/mL


title: lib54813


title: Input M395 RES shCTRL_1

description: INPUT-shCTRL-04-02-20_NGS20-L751_BHKMKVDRXX_S17_L001_R1_001

value: Primary melanoma culture

value: shCTRL


title: lib54810

value: CD154+CD69+CD4 T cells


title: Bafetinib_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Bafetinib followed by 1h LPS 10ng/mL


title: lib54818


title: lib54809


title: Input M395 RES shCTRL_2

description: INPUT-shCTRL-10-02-20_NGS20-L755_BHKMKVDRXX_S21_L001_R1_001


title: Bafetinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 4h IL4 10ng/mL


title: lib54808


title: T47D_AI2m1 _BC.S13

city: London

first: Heena

last: Dhiman

address: 72 Du Cane Road

country: United Kingdom

institute: Imperial College London

description:
BC cDNA
b4_DR

data_processing:
Quantification of genes and expressed barcodes was performed with cellranger count pipeline (v-6.0.2) using GRCh38 as the reference transcriptome and a feature reference corresponding to the Cellecta CloneTracker XP 10M Barcode library.
The unified filtered feature-barcode matrix was imported into Seurat package (v-4.1.0) followed by further filtering and normalization for final data visualization.
Assembly: GRCh38

source_name: T47D 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.
scRNAseq (10X Genomics)

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

value: Oestrogen deprived

tag: Stage

value: Early dormancy

tag: ^sample from all flow cells

tag: sample name from all flow cells


title: T47D_AI2m1 _BC.S4

description:
BC cDNA
b4_DR


title: lib54805

value: islet peptide library


title: lib54806


title: lib54804


title: T47D_AI2m1 _BC.S12

description:
BC cDNA
b4_DR


title: T47D_AI2m1 _BC.S3

description:
BC cDNA
b4_DR


title: Bafetinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 2h IL4 10ng/mL

value: wild type


title: lib54802


title: lib54803


title: Bafetinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 1h IL4 10ng/mL


title: lib54812


title: T47D_AI2m1 _BC.S11

description:
BC cDNA
b4_DR


title: AZD8186_UT_0h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 4h UT


title: lib54800


title: lib54799


title: lib54801


title: lib54797


title: AZD8186_LPS_4h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 4h LPS 10ng/mL


title: lib54807


title: lib54796


title: lib54725


title: AZD8186_LPS_30

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 30 LPS 10ng/mL


title: T47D_AI2m1 _BC.S1

description:
BC cDNA
b4_DR


title: lib54724


title: AZD8186_LPS_2h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 2h LPS 10ng/mL


title: T47D_AI1m1_BC.S4

description:
BC cDNA
b3_DR


title: Bafetinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Bafetinib followed by 30 IL4 10ng/mL


title: lib54722


title: AZD8186_LPS_1h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 1h LPS 10ng/mL


title: lib54721


title: T47D_AI1m1_BC.S3

description:
BC cDNA
b3_DR


title: T47D_AI1m1_BC.S2

description:
BC cDNA
b3_DR


title: AZD8186_IL4_4h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 4h IL4 10ng/mL


title: lib54719

value: CD154+CD69+CD4 T cells


title: lib54718


title: lib54720


title: AZD8186_IL4_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with AZD8186 followed by 30 IL4 10ng/mL


title: lib54798


title: lib54717


title: T47D_AI1m1_BC.S1

description:
BC cDNA
b3_DR


title: T47D_AI2m1 _BC.S2

description:
BC cDNA
b4_DR


title: lib54716


title: T47D_AI2m1 _BC.S10

description:
BC cDNA
b4_DR


title: AZD8186_IL4_2h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 2h IL4 10ng/mL


title: AZD8186_IL4_1h

description: ChIPseq

value: 1h pre-treatment with AZD8186 followed by 1h IL4 10ng/mL


title: lib54713


title: lib54712


title: T47D_AI2m1 _Cell.S3

description:
Cell cDNA
b2_DR

value: Oestrogen deprived

value: Early dormancy


title: lib54715

value: islet peptide library


title: T47D_AI2m1 _Cell.S4

description:
Cell cDNA
b2_DR


title: AZD2014_UT_0h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 4h UT

value: wild type


title: T47D_AI2m1 _Cell.S2

description:
Cell cDNA
b2_DR


title: lib54723


title: lib54711


title: lib54710


title: AZD2014_LPS_4h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 4h LPS 10ng/mL


title: lib54709


title: lib54708


title: T47D_AI2m1 _Cell.S1

description:
Cell cDNA
b2_DR


title: lib54223

source_name: ISLET TMR+ CD8 T cells

value: ISLET TMR+ CD8 T cells


title: T47D_AI1m1_Cell.S9

description:
Cell cDNA
b1_DR


title: T47D_AI1m1_Cell.S13

description:
Cell cDNA
b1_DR


title: lib54222


title: lib54707


title: lib54221


title: T47D_AI1m1_Cell.S8

description:
Cell cDNA
b1_DR


title: lib54220


title: AZD2014_IL4_4h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 4h IL4 10ng/mL


title: lib54218


title: lib54219


title: T47D_AI1m1_Cell.S12

description:
Cell cDNA
b1_DR


title: lib54714


title: T47D_AI1m1_Cell.S7

description:
Cell cDNA
b1_DR


title: lib54214


title: lib54216


title: lib54215


title: lib54213


title: AZD2014_IL4_2h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 2h IL4 10ng/mL


title: lib54212


title: AZD2014_IL4_30

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 30 IL4 10ng/mL


title: AZD2014_LPS_30

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 30 LPS 10ng/mL


title: T47D_AI1m1_Cell.S6

description:
Cell cDNA
b1_DR


title: lib54217


title: AZD2014_LPS_2h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 2h LPS 10ng/mL


title: lib54211


title: T47D_AI1m1_Cell.S11

description:
Cell cDNA
b1_DR


title: AZD2014_LPS_1h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 1h LPS 10ng/mL


title: AZD1208_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with AZD1208 followed by 4h UT


title: T47D_AI1m1_Cell.S10

description:
Cell cDNA
b1_DR


title: T47D_T0_2 _BC.S20

description:
BC cDNA
DR_5

value: Untreated


title: lib54209


title: AZD1208_UT_0h_b

description: ChIPseq


title: lib54159

value: CD154+CD69+CD4 T cells


title: lib54210


title: lib54158


title: AZD1208_LPS_4h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 4h LPS 10ng/mL


title: AZD2014_IL4_1h

description: ChIPseq

value: 1h pre-treatment with AZD2014 followed by 1h IL4 10ng/mL


title: T47D_T0_2 _BC.S19

description:
BC cDNA
DR_5


title: lib54157

value: islet peptide library


title: AZD1208_LPS_30

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 30 LPS 10ng/mL


title: lib54155


title: lib54152


title: lib54153


title: AZD1208_LPS_2h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 2h LPS 10ng/mL

value: wild type


title: lib54154


title: AZD1208_LPS_1h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 1h LPS 10ng/mL


title: T47D_T0_2 _Cell.S8

description:
Cell cDNA
DR_2


title: T47D_T0_2 _BC.S17

description:
BC cDNA
DR_5


title: AZD1208_IL4_4h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 4h IL4 10ng/mL


title: lib54149


title: lib54151


title: T47D_T0_2 _Cell.S7

description:
Cell cDNA
DR_2


title: lib54150


title: lib54148


title: lib54147


title: AZD1208_IL4_30

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 30 IL4 10ng/mL


title: T47D_T0_2 _Cell.S6

description:
Cell cDNA
DR_2


title: T47D_T0_2 _Cell.S5

description:
Cell cDNA
DR_2


title: AZD1208_IL4_2h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 2h IL4 10ng/mL


title: lib54145


title: lib54156


title: lib54146


title: AZD1208_IL4_1h

description: ChIPseq

value: 1h pre-treatment with AZD1208 followed by 1h IL4 10ng/mL


title: lib54143


title: T47D_T0_2 _BC.S18

description:
BC cDNA
DR_5


title: lib54144


title: T47D_T0_1_BC.S16

description:
BC cDNA
DR_4


title: lib54142


title: lib54141


title: Apitolisib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 4h UT


title: lib54140


title: T47D_T0_1_BC.S14

description:
BC cDNA
DR_4


title: lib54139


title: T47D_T0_1_BC.S15

description:
BC cDNA
DR_4


title: lib54137


title: lib54138


title: Apitolisib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 4h LPS 10ng/mL


title: lib54136


title: lib54134


title: T47D_T0_1_Cell.S4

description:
Cell cDNA
DR_1


title: Apitolisib_LPS_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Apitolisib followed by 30 LPS 10ng/mL


title: T47D_T0_1_BC.S13

description:
BC cDNA
DR_4

value: Untreated


title: lib54053

value: ISLET TMR+ CD8 T cells


title: T47D_T0_1_Cell.S3

description:
Cell cDNA
DR_1


title: lib54052


title: lib54051


title: T47D_T0_1_Cell.S2

description:
Cell cDNA
DR_1


title: lib54050


title: Apitolisib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 2h LPS 10ng/mL


title: Apitolisib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 1h LPS 10ng/mL


title: Apitolisib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 4h IL4 10ng/mL


title: Apitolisib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 30 IL4 10ng/mL


title: MCF7_AI_AW2_BC.S24

description:
BC cDNA
DR_6

source_name: MCF7 cell line

value: Oestrogen deprived

value: Awakening


title: lib54046

value: islet peptide library


title: lib54049


title: Apitolisib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 2h IL4 10ng/mL

value: wild type


title: T47D_T0_1_Cell.S1

description:
Cell cDNA
DR_1


title: lib54044


title: lib54135

value: CD154+CD69+CD4 T cells


title: Apitolisib_UT_0h_b

description: ChIPseq


title: Apitolisib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Apitolisib followed by 1h IL4 10ng/mL


title: lib54045


title: lib54043


title: MCF7_AI_AW2_BC.S22

description:
BC cDNA
DR_6


title: lib54042


title: MCF7_AI_AW2_BC.S21

description:
BC cDNA
DR_6


title: lib54041


title: Apatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 4h UT


title: lib54040


title: Apatinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 4h LPS 10ng/mL


title: lib54039


title: lib54037


title: lib54038


title: lib54047


title: Apatinib_LPS_30

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Apatinib followed by 30 LPS 10ng/mL


title: lib54048


title: MCF7_AI_AW2_Cell.S11

description:
Cell cDNA
DR_3


title: lib54036


title: Apatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 2h LPS 10ng/mL


title: MCF7_AI_AW2_Cell.S10

description:
Cell cDNA
DR_3


title: MCF7_AI_AW2_BC.S23

description:
BC cDNA
DR_6


title: lib53993


title: lib53992


title: Apatinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 1h LPS 10ng/mL


title: lib53990


title: MCF7_AI_AW2_Cell.S9

description:
Cell cDNA
DR_3


title: Apatinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 30 IL4 10ng/mL


title: lib53988


title: MCF7_AI_AW3 _BC.S2

description:
BC cDNA
G9


title: Apatinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 2h IL4 10ng/mL


title: lib53987


title: lib53989


title: MCF7_AI_AW3 _BC.S1

description:
BC cDNA
G9


title: lib53986


title: Apatinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Apatinib followed by 1h IL4 10ng/mL


title: lib53985


title: MCF7_AI_AW3 _BC.S4

description:
BC cDNA
G9


title: MCF7_AI_AW2_Cell.S12

description:
Cell cDNA
DR_3


title: AMG208_UT_0h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 4h UT


title: lib53984


title: MCF7_AI_AW3 _BC.S3

description:
BC cDNA
G9

value: Oestrogen deprived


title: MCF7_AI_AW3_Cell.S12

description:
Cell cDNA
F9

value: Awakening


title: lib53983

value: islet peptide library


title: lib53981


title: AMG208_LPS_4h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 4h LPS 10ng/mL


title: lib53980


title: AMG208_LPS_30

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 30 LPS 10ng/mL

value: wild type


title: lib53982

value: CD154+CD69+CD4 T cells


title: lib53991


title: lib53979


title: MCF7_AI_AW3_Cell.S11

description:
Cell cDNA
F9


title: lib53978


title: lib53977


title: MCF7_AI_AW3_Cell.S10

description:
Cell cDNA
F9


title: AMG208_LPS_2h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 2h LPS 10ng/mL


title: lib53976


title: AMG208_LPS_1h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 1h LPS 10ng/mL


title: MCF7_AI_AW3_Cell.S9

description:
Cell cDNA
F9


title: lib53975


title: lib53974


title: lib53973


title: MCF7_TAM_AW3_BC .S19

description:
BC cDNA
D9

value: Tamoxifen treated


title: AMG208_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with AMG208 followed by 4h IL4 10ng/mL


title: MCF7_TAM_AW3_BC .S20

description:
BC cDNA
D9


title: lib53971


title: lib53972


title: AMG208_IL4_30

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 30 IL4 10ng/mL


title: lib53970


title: lib53968


title: lib53966


title: AMG208_IL4_2h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 2h IL4 10ng/mL


title: MCF7_TAM_AW3_BC .S17

description:
BC cDNA
D9


title: Afatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 4h UT


title: lib53967


title: lib53965


title: lib53964


title: lib53969


title: lib53963


title: AMG208_IL4_1h

description: ChIPseq

value: 1h pre-treatment with AMG208 followed by 1h IL4 10ng/mL


title: lib53962


title: MCF7_TAM_AW2_BC .S16

description:
BC cDNA
C9


title: Afatinib_LPS_4h_b

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 4h LPS 10ng/mL


title: Afatinib_LPS_4h

description: ChIPseq


title: MCF7_TAM_AW2_BC .S14

description:
BC cDNA
C9


title: lib53960


title: lib53961


title: Afatinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 30 LPS 10ng/mL


title: MCF7_TAM_AW3_BC .S18

description:
BC cDNA
D9

value: Awakening


title: MCF7_TAM_AW2_BC .S13

description:
BC cDNA
C9


title: lib53959

value: islet peptide library


title: lib53958


title: lib53957


title: lib53955


title: MCF7_TAM_AW3_Cell .S12

description:
Cell cDNA
B9


title: Afatinib_LPS_30_b

description: ChIPseq


title: lib53956


title: lib53954


title: Afatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 2h LPS 10ng/mL


title: MCF7_TAM_AW2_BC .S15

description:
BC cDNA
C9


title: lib53953


title: Afatinib_LPS_2h_b

description: ChIPseq


title: lib53952


title: Afatinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 1h LPS 10ng/mL


title: lib53951


title: MCF7_TAM_AW3_Cell .S10

description:
Cell cDNA
B9


title: MCF7_TAM_AW3_Cell .S11

description:
Cell cDNA
B9


title: lib53950


title: Afatinib_LPS_1h_b

description: ChIPseq

value: wild type


title: lib53949

value: CD154+CD69+CD4 T cells


title: lib53948


title: MCF7_TAM_AW2_Cell .S6

description:
Cell cDNA
A9


title: lib53947


title: Afatinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 4h IL4 10ng/mL


title: lib53946


title: lib53945


title: MCF7_TAM_AW2_Cell .S8

description:
Cell cDNA
A9


title: MCF7_TAM_AW3_Cell .S9

description:
Cell cDNA
B9


title: lib53944


title: MCF7_TAM_AW2_Cell .S7

description:
Cell cDNA
A9


title: Afatinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 2h IL4 10ng/mL


title: lib53941


title: lib53942


title: MCF7_AI_AW4_BC .S8

description:
BC cDNA
H8

value: Oestrogen deprived


title: lib53939


title: AC480_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with AC480 followed by 4h UT


title: AC480_UT_0h_b

description: ChIPseq


title: lib53938


title: Afatinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 1h IL4 10ng/mL


title: lib53936


title: lib53937


title: lib53935


title: AC480_LPS_4h

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 4h LPS 10ng/mL


title: MCF7_AI_AW4_BC .S5

description:
BC cDNA
H8


title: MCF7_TAM_AW2_Cell .S5

description:
Cell cDNA
A9

value: Tamoxifen treated


title: Afatinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Afatinib followed by 30 IL4 10ng/mL


title: MCF7_AI_AW4_BC .S6

description:
BC cDNA
H8


title: lib53934


title: MCF7_AI_AW1_BC .S4

description:
BC cDNA
G8


title: lib53933


title: lib53943


title: lib53940


title: AC480_LPS_2h

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 2h LPS 10ng/mL


title: MCF7_AI_AW4_BC .S7

description:
BC cDNA
H8


title: lib53932


title: lib53930


title: AC480_LPS_30

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 30 LPS 10ng/mL


title: AC480_LPS_1h

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 1h LPS 10ng/mL


title: MCF7_AI_AW1_BC .S3

description:
BC cDNA
G8

value: Awakening


title: lib53931

value: islet peptide library


title: lib53928


title: lib53929


title: lib53927


title: MCF7_AI_AW1_BC .S1

description:
BC cDNA
G8


title: AC480_IL4_30

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 30 IL4 10ng/mL


title: lib53925


title: lib53926


title: MCF7_TAM_AW4_BC .S12

description:
BC cDNA
F8


title: lib53923


title: MCF7_TAM_AW4_BC .S11

description:
BC cDNA
F8


title: lib53922


title: AC480_IL4_2h

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 2h IL4 10ng/mL

value: wild type


title: lib53921

value: CD154+CD69+CD4 T cells


title: AC480_IL4_1h

description: ChIPseq

value: 1h pre-treatment with AC480 followed by 1h IL4 10ng/mL


title: MCF7_TAM_AW4_BC .S10

description:
BC cDNA
F8


title: lib53920


title: lib53919


title: MCF7_TAM_AW4_BC .S9

description:
BC cDNA
F8


title: MCF7_AI_AW1_BC .S2

description:
BC cDNA
G8

value: Oestrogen deprived


title: AC480_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with AC480 followed by 4h IL4 10ng/mL


title: XL413_2hLPS_R3

description: RNAseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Pair-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

extract_protocol:
Total RNA was extracted from BMDM cells using the Zymo Quick-RNA kit (Zymo Research code R1055).
Library preparation was performed following the SMART-seq2 protocol (Picelli et al. 2014b). Briefly, 5 ng of total RNA were reverse transcribed with template-switching using oligo(dT) 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.

treatment_protocol: LPS (10 ng/ml) treatment for 2h

value: 1h pre-treatment with XL413 followed by 2h stimulation with 10ng/mL LPS


title: lib53917


title: lib53918


title: lib53916


title: XL413_2hLPS_R1

description: RNAseq


title: lib53924


title: lib53914


title: MCF7_TAM_AW1_BC .S11

description:
BC cDNA
E8


title: lib53915


title: MCF7_TAM_AW1_BC .S10

description:
BC cDNA
E8


title: X396_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with X396 followed by 2h stimulation with 10ng/mL LPS


title: lib53913


title: lib53912


title: X396_2hLPS_R2

description: RNAseq


title: lib53264

value: ISLET TMR+ CD8 T cells


title: lib53265


title: X396_2hLPS_R1

description: RNAseq


title: lib53266


title: lib53263


title: MCF7_TAM_AW1_BC .S12

description:
BC cDNA
E8

value: Tamoxifen treated


title: MCF7_AI_AW4_Cell .S7

description:
Cell cDNA
D8


title: VX702_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with VX702 followed by 2h stimulation with 10ng/mL LPS


title: lib53260


title: VX702_2hLPS_R2

description: RNAseq


title: lib53261


title: MCF7_AI_AW4_Cell .S6

description:
Cell cDNA
D8


title: lib53259


title: VX702_2hLPS_R1

description: RNAseq


title: lib53258


title: lib53257


title: MCF7_AI_AW4_Cell .S5

description:
Cell cDNA
D8


title: Volasertib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Volasertib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI_AW4_Cell .S8

description:
Cell cDNA
D8


title: lib53255


title: MCF7_TAM_AW1_BC .S9

description:
BC cDNA
E8


title: Volasertib_2hLPS_R2

description: RNAseq


title: MCF7_AI_AW1_Cell .S8

description:
Cell cDNA
C8


title: lib53262


title: XL413_2hLPS_R2

description: RNAseq


title: MCF7_AI_AW1_Cell .S7

description:
Cell cDNA
C8


title: lib53252


title: lib53254


title: lib53253


title: Volasertib_2hLPS_R1

description: RNAseq


title: lib53250


title: lib53249


title: MCF7_AI_AW1_Cell .S6

description:
Cell cDNA
C8


title: Vatalanib_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with Vatalanib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI_AW1_Cell .S5

description:
Cell cDNA
C8

value: Awakening


title: Vatalanib_2hLPS_R3

description: RNAseq


title: lib53248

value: islet peptide library


title: MCF7_TAM_AW4_Cell .S4

description:
Cell cDNA
B8


title: lib53247


title: Vatalanib_2hLPS_R1

description: RNAseq


title: lib53246


title: lib53256


title: MCF7_TAM_AW4_Cell .S3

description:
Cell cDNA
B8


title: lib53245


title: Vandetanib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Vandetanib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_TAM_AW4_Cell .S2

description:
Cell cDNA
B8


title: Vandetanib_2hLPS_R2

description: RNAseq


title: lib53251


title: lib53241


title: lib53240


title: lib53243


title: lib53244


title: lib53239


title: Vandetanib_2hLPS_R1

description: RNAseq


title: lib53242


title: MCF7_TAM_AW4_Cell .S1

description:
Cell cDNA
B8


title: lib53238


title: MCF7_TAM_AW1_Cell .S4

description:
Cell cDNA
A8


title: MCF7_TAM_AW1_Cell .S2

description:
Cell cDNA
A8


title: Ulixertinib_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with Ulixertinib followed by 2h stimulation with 10ng/mL LPS


title: lib53234


title: lib53235


title: Ulixertinib_2hLPS_R1

description: RNAseq

value: wild type


title: MCF7_TAM_AW1_Cell .S1

description:
Cell cDNA
A8


title: lib53233


title: MCF7_AI2m2_BC.S20

description:
BC cDNA
H7

value: Late dormancy


title: lib53232


title: Tofacitinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Tofacitinib followed by 2h stimulation with 10ng/mL LPS


title: Ulixertinib_2hLPS_R3

description: RNAseq


title: lib53231


title: lib53229


title: MCF7_AI2m2_BC.S19

description:
BC cDNA
H7

value: Oestrogen deprived


title: Tofacitinib_2hLPS_R2

description: RNAseq

value: BMDM


title: lib53228


title: lib53230


title: Tofacitinib_2hLPS_R1

description: RNAseq


title: TG100572_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with TG100572 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_TAM_AW1_Cell .S3

description:
Cell cDNA
A8


title: TG100572_2hLPS_R2

description: RNAseq


title: lib53227


title: lib53225


title: lib53237


title: MCF7_AI2m2_BC.S18

description:
BC cDNA
H7


title: lib53236


title: lib53224


title: MCF7_AI2m2_BC.S17

description:
BC cDNA
H7


title: lib53226


title: lib53223


title: lib53222


title: lib53221


title: MCF7_AI1m2_BC.S15

description:
BC cDNA
G7


title: TG100572_2hLPS_R1

description: RNAseq


title: TG100115_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with TG100115 followed by 2h stimulation with 10ng/mL LPS


title: lib53220


title: lib53219


title: TG100115_2hLPS_R2

description: RNAseq


title: MCF7_AI1m2_BC.S14

description:
BC cDNA
G7


title: lib53218


title: lib53217


title: lib53215


title: TG100115_2hLPS_R1

description: RNAseq


title: lib53216


title: MCF7_TAM2m2_BC.S6

description:
BC cDNA
F7


title: lib53211


title: lib53212


title: Telatinib_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with Telatinib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_TAM2m2_BC.S5

description:
BC cDNA
F7


title: lib53209

value: ISLET TMR+ CD8 T cells


title: MCF7_AI1m2_BC.S16

description:
BC cDNA
G7


title: MCF7_TAM2m2_BC.S7

description:
BC cDNA
F7

value: Tamoxifen treated


title: Telatinib_2hLPS_R3

description: RNAseq


title: lib53214


title: MCF7_TAM2m2_BC.S8

description:
BC cDNA
F7


title: lib53208


title: Tanzisertib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Tanzisertib followed by 2h stimulation with 10ng/mL LPS


title: lib53207


title: MCF7_TAM1m2_BC.S33

description:
BC cDNA
E7


title: Tanzisertib_2hLPS_R2

description: RNAseq


title: lib53206


title: lib53210


title: MCF7_TAM1m2_BC.S32

description:
BC cDNA
E7


title: lib53213


title: MCF7_AI1m2_BC.S13

description:
BC cDNA
G7


title: lib53204


title: Tanzisertib_2hLPS_R1

description: RNAseq


title: Telatinib_2hLPS_R1

description: RNAseq


title: MCF7_TAM1m2_BC.S31

description:
BC cDNA
E7


title: Talmapimod_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Talmapimod followed by 2h stimulation with 10ng/mL LPS


title: lib53202


title: lib53203


title: MCF7_TAM1m2_BC.S30

description:
BC cDNA
E7


title: lib53201


title: MCF7_AI2m2_Cell.S12

description:
Cell cDNA
D7


title: lib53200


title: lib53199


title: Talmapimod_2hLPS_R2

description: RNAseq


title: Talmapimod_2hLPS_R1

description: RNAseq


title: lib53198


title: MCF7_AI2m2_Cell.S11

description:
Cell cDNA
D7


title: lib53197


title: SNS314_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with SNS314 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI2m2_Cell.S10

description:
Cell cDNA
D7


title: lib53195


title: lib53205


title: SNS314_2hLPS_R2

description: RNAseq


title: lib53193


title: MCF7_AI1m2_Cell.S4

description:
Cell cDNA
C7


title: lib53192


title: lib53191


title: Silmitasertib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Silmitasertib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI1m2_Cell.S3

description:
Cell cDNA
C7


title: lib53190

value: islet peptide library


title: lib53189


title: MCF7_AI1m2_Cell.S2

description:
Cell cDNA
C7


title: lib53188


title: lib53187


title: lib53196


title: lib53186


title: MCF7_AI1m2_Cell.S1

description:
Cell cDNA
C7


title: lib53185


title: lib53184


title: MCF7_TAM2m2_Cell.S14

description:
Cell cDNA
B7


title: lib53183


title: SGX523_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with SGX523 followed by 2h stimulation with 10ng/mL LPS


title: SGX523_2hLPS_R2

description: RNAseq


title: lib53194


title: Silmitasertib_2hLPS_R1

description: RNAseq


title: SNS314_2hLPS_R1

description: RNAseq


title: lib53182


title: MCF7_TAM2m2_Cell.S13

description:
Cell cDNA
B7


title: lib53181


title: SGX523_2hLPS_R1

description: RNAseq


title: MCF7_AI2m2_Cell.S9

description:
Cell cDNA
D7


title: MCF7_TAM2m2_Cell.S12

description:
Cell cDNA
B7


title: lib53180


title: lib53179


title: lib53178


title: SGI1776_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with SGI1776 followed by 2h stimulation with 10ng/mL LPS


title: Silmitasertib_2hLPS_R2

description: RNAseq

value: wild type


title: MCF7_TAM2m2_Cell.S11

description:
Cell cDNA
B7

value: Late dormancy


title: lib53177


title: SGI1776_2hLPS_R2

description: RNAseq


title: lib53176


title: MCF7_TAM1m2_Cell.S10

description:
Cell cDNA
A7


title: lib53175


title: lib53174


title: MCF7_TAM1m2_Cell.S9

description:
Cell cDNA
A7


title: SGI1776_2hLPS_R1

description: RNAseq


title: Selumetinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Selumetinib followed by 2h stimulation with 10ng/mL LPS


title: lib53173


title: lib53172


title: lib53171


title: MCF7_TAM1m2_Cell.S8

description:
Cell cDNA
A7


title: lib53074

value: CD154+CD69+CD4 T cells


title: Selumetinib_2hLPS_R2

description: RNAseq

value: BMDM


title: Ruxolitinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Ruxolitinib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI2m1_BC.S36

description:
BC cDNA
H6

value: Oestrogen deprived

value: Early dormancy


title: lib53071


title: lib53070


title: Selumetinib_2hLPS_R1

description: RNAseq


title: lib53069


title: MCF7_TAM1m2_Cell.S7

description:
Cell cDNA
A7


title: lib53073


title: Ruxolitinib_2hLPS_R2

description: RNAseq


title: lib53068


title: MCF7_AI2m1_BC.S34

description:
BC cDNA
H6


title: lib53067


title: Ruxolitinib_2hLPS_R1

description: RNAseq


title: MCF7_AI2m1_BC.S33

description:
BC cDNA
H6


title: MCF7_AI2m1_BC.S35

description:
BC cDNA
H6


title: lib53066


title: lib53065


title: Refametinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Refametinib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI1m1_BC.S32

description:
BC cDNA
G6


title: lib53063


title: lib53064


title: lib53062


title: lib53072


title: MCF7_AI1m1_BC.S31

description:
BC cDNA
G6


title: MCF7_AI1m1_BC.S30

description:
BC cDNA
G6


title: lib53059


title: lib53058


title: Poziotinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Poziotinib followed by 2h stimulation with 10ng/mL LPS


title: lib53060


title: MCF7_AI1m1_BC.S29

description:
BC cDNA
G6


title: Refametinib_2hLPS_R1

description: RNAseq


title: lib53061


title: MCF7_TAM2m1_BC.S28

description:
BC cDNA
F6

value: Tamoxifen treated


title: Poziotinib_2hLPS_R2

description: RNAseq


title: lib53055


title: lib53056


title: lib53057


title: MCF7_TAM2m1_BC.S27

description:
BC cDNA
F6


title: lib53053


title: lib53052


title: MCF7_TAM2m1_BC.S26

description:
BC cDNA
F6


title: lib53054


title: lib53051


title: Pimasertib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Pimasertib followed by 2h stimulation with 10ng/mL LPS


title: Refametinib_2hLPS_R2

description: RNAseq


title: Pimasertib_2hLPS_R2

description: RNAseq


title: MCF7_TAM2m1_BC.S25

description:
BC cDNA
F6


title: lib53049


title: Pimasertib_2hLPS_R1

description: RNAseq


title: MCF7_TAM1m1_BC.S24

description:
BC cDNA
E6


title: lib53047


title: lib53048


title: lib53046


title: MCF7_TAM1m1_BC.S23

description:
BC cDNA
E6


title: PH797804_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with PH797804 followed by 2h stimulation with 10ng/mL LPS


title: lib53045


title: Poziotinib_2hLPS_R1

description: RNAseq


title: PH797804_2hLPS_R3

description: RNAseq


title: lib53041


title: MCF7_TAM1m1_BC.S22

description:
BC cDNA
E6


title: PH797804_2hLPS_R1

description: RNAseq


title: MCF7_TAM1m1_BC.S21

description:
BC cDNA
E6


title: PF04691502_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with PF04691502 followed by 2h stimulation with 10ng/mL LPS


title: lib53038

value: islet peptide library


title: MCF7_AI2m1_Cell.S20

description:
Cell cDNA
D6


title: lib53037


title: MCF7_AI2m1_Cell.S19

description:
Cell cDNA
D6


title: lib53050


title: lib53039


title: PF04691502_2hLPS_R1

description: RNAseq


title: MCF7_AI2m1_Cell.S18

description:
Cell cDNA
D6


title: lib53042


title: lib53036


title: lib53035


title: Pacritinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Pacritinib followed by 2h stimulation with 10ng/mL LPS


title: lib53034


title: lib53033


title: MCF7_AI2m1_Cell.S17

description:
Cell cDNA
D6


title: lib53044


title: Pacritinib_2hLPS_R2

description: RNAseq


title: MCF7_AI1m1_Cell.S20

description:
Cell cDNA
C6


title: Pacritinib_2hLPS_R1

description: RNAseq


title: lib53030


title: lib53029


title: MCF7_AI1m1_Cell.S19

description:
Cell cDNA
C6


title: PF04691502_2hLPS_R2

description: RNAseq


title: OSI930_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with OSI930 followed by 2h stimulation with 10ng/mL LPS


title: lib53040


title: lib53043


title: OSI930_2hLPS_R2

description: RNAseq

value: wild type


title: lib53028


title: lib53031


title: lib53026


title: MCF7_AI1m1_Cell.S18

description:
Cell cDNA
C6


title: lib53027


title: lib53025


title: MCF7_AI1m1_Cell.S17

description:
Cell cDNA
C6


title: lib53024


title: MCF7_TAM2m1_Cell.S16

description:
Cell cDNA
B6


title: lib53022


title: ONO4059analogue_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with ONO4059analogue followed by 2h stimulation with 10ng/mL LPS


title: lib53023


title: lib53021


title: lib53010

value: ISLET TMR+ CD8 T cells


title: ONO4059analogue_2hLPS_R2

description: RNAseq


title: lib53032

value: CD154+CD69+CD4 T cells


title: MCF7_TAM2m1_Cell.S14

description:
Cell cDNA
B6


title: lib53008


title: ONO4059analogue_2hLPS_R1

description: RNAseq

value: BMDM


title: MCF7_TAM2m1_Cell.S13

description:
Cell cDNA
B6


title: lib53007


title: lib53006


title: lib53005


title: OSI930_2hLPS_R1

description: RNAseq


title: Omipalisib_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with Omipalisib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_TAM1m1_Cell.S12

description:
Cell cDNA
A6


title: lib53004


title: MCF7_TAM1m1_Cell.S11

description:
Cell cDNA
A6


title: lib53003


title: Omipalisib_2hLPS_R1

description: RNAseq


title: lib53002


title: MCF7_TAM2m1_Cell.S15

description:
Cell cDNA
B6


title: lib53001


title: MCF7_TAM1m1_Cell.S10

description:
Cell cDNA
A6


title: NMS1286937_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with NMS1286937 followed by 2h stimulation with 10ng/mL LPS


title: lib53000


title: MCF7_TAM1m1_Cell.S9

description:
Cell cDNA
A6

value: Early dormancy


title: lib52998


title: NMS1286937_2hLPS_R2

description: RNAseq


title: lib53009


title: MCF7_T0_2 _BC.S16

description:
BC cDNA
DR4

value: Untreated


title: lib52996


title: MCF7_T0_2 _BC.S15

description:
BC cDNA
DR4


title: Omipalisib_2hLPS_R3

description: RNAseq


title: lib52995


title: Neratinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Neratinib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_T0_2 _BC.S14

description:
BC cDNA
DR4


title: lib52987


title: lib52994


title: Neratinib_2hLPS_R2

description: RNAseq


title: lib52986


title: MCF7_T0_2 _BC.S13

description:
BC cDNA
DR4


title: lib52985


title: lib52984


title: Neratinib_2hLPS_R1

description: RNAseq


title: MCF7_T0_1_BC.S12

description:
BC cDNA
DR3


title: Mubritinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Mubritinib followed by 2h stimulation with 10ng/mL LPS


title: lib52999


title: lib52981


title: lib52997


title: lib52982


title: lib52980


title: NMS1286937_2hLPS_R1

description: RNAseq


title: MCF7_T0_1_BC.S11

description:
BC cDNA
DR3


title: MCF7_T0_1_BC.S10

description:
BC cDNA
DR3


title: lib52979


title: Mubritinib_2hLPS_R1

description: RNAseq


title: Mubritinib_2hLPS_R2

description: RNAseq


title: lib52978


title: MCF7_T0_1_BC.S9

description:
BC cDNA
DR3


title: Momelotinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Momelotinib followed by 2h stimulation with 10ng/mL LPS


title: lib52977


title: lib52976


title: MCF7_T0_2 _Cell.S4

description:
Cell cDNA
DR2


title: lib52975


title: Momelotinib_2hLPS_R2

description: RNAseq


title: lib52974


title: lib52983


title: Momelotinib_2hLPS_R1

description: RNAseq


title: lib52972


title: lib52973


title: lib52971


title: MCF7_T0_2 _Cell.S2

description:
Cell cDNA
DR2


title: MK5108_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with MK5108 followed by 2h stimulation with 10ng/mL LPS


title: lib52970


title: lib52969


title: lib52966


title: MCF7_T0_2 _Cell.S1

description:
Cell cDNA
DR2


title: MCF7_T0_1 _Cell.S4

description:
Cell cDNA
DR1


title: lib52967


title: lib52968


title: MK5108_2hLPS_R2

description: RNAseq


title: MK5108_2hLPS_R1

description: RNAseq


title: MCF7_T0_1 _Cell.S2

description:
Cell cDNA
DR1


title: MCF7_T0_1 _Cell.S3

description:
Cell cDNA
DR1


title: lib52965


title: lib52844


title: lib52964


title: MK2461_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with MK2461 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_T0_2 _Cell.S3

description:
Cell cDNA
DR2


title: lib52842

value: islet peptide library


title: lib52843


title: MCF7_T0_1 _Cell.S1

description:
Cell cDNA
DR1


title: MK2461_2hLPS_R1

description: RNAseq


title: T47D_UT5m.3.run2

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

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.

value: 5 months


title: lib52839


title: lib52840


title: MK2206_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with MK2206 followed by 2h stimulation with 10ng/mL LPS


title: T47D_UT5m.3.run1


title: T47D_UT5m.2.run2


title: MK2461_2hLPS_R3

description: RNAseq

value: wild type


title: T47D_UT5m.2.run1


title: lib52836


title: lib52835


title: MK2206_2hLPS_R2

description: RNAseq


title: lib52837


title: lib52834


title: MK2206_2hLPS_R1

description: RNAseq


title: lib52833


title: Midostaurin_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Midostaurin followed by 2h stimulation with 10ng/mL LPS


title: lib52832

value: ISLET TMR+ CD8 T cells


title: lib52831


title: T47D_UT5m.1.run1


title: Midostaurin_2hLPS_R2

description: RNAseq


title: lib52841


title: T47D_UT5m.1.run2


title: Midostaurin_2hLPS_R1

description: RNAseq


title: lib52829


title: T47D_AI.F+30.run2

value: Oestrogen deprived

value: TEP


title: lib52828


title: T47D_AI.F+30.run1


title: Losmapimod_2hLPS_R3

description: RNAseq

value: BMDM

value: 1h pre-treatment with Losmapimod followed by 2h stimulation with 10ng/mL LPS


title: lib52838


title: lib52826


title: Losmapimod_2hLPS_R2

description: RNAseq


title: T47D_AI.E+30.run3


title: lib52825


title: lib52824


title: Losmapimod_2hLPS_R1

description: RNAseq


title: T47D_AI.E+30.run2


title: lib52823


title: lib52822


title: T47D_AI.E+30.run1


title: lib52820


title: lib52819


title: lib52821


title: T47D_AI.D+30.run3


title: Lenvatinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Lenvatinib followed by 2h stimulation with 10ng/mL LPS


title: lib52818


title: lib52830


title: T47D_AI.D+30.run2


title: lib52816


title: lib52817


title: lib52827


title: Lapatinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Lapatinib followed by 2h stimulation with 10ng/mL LPS


title: T47D_AI.D+30.run1


title: lib52815


title: Lenvatinib_2hLPS_R1

description: RNAseq


title: lib52814


title: lib52813


title: Lapatinib_2hLPS_R2

description: RNAseq


title: T47D_AI.C+30.run2


title: lib52812


title: T47D_AI.C+30.run1


title: Lapatinib_2hLPS_R1

description: RNAseq


title: lib52811


title: IMD0354_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with IMD0354 followed by 2h stimulation with 10ng/mL LPS


title: Lenvatinib_2hLPS_R2

description: RNAseq


title: T47D_AI.B+30.run2


title: lib52809


title: lib52806


title: lib52807


title: IMD0354_2hLPS_R2

description: RNAseq


title: lib52805


title: lib52808


title: T47D_AI.A+30


title: IMD0354_2hLPS_R1

description: RNAseq


title: T47D_AI.B+30.run1


title: lib52802


title: lib52803


title: lib52804


title: lib52801


title: lib52800


title: GSK461364_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with GSK461364 followed by 2h stimulation with 10ng/mL LPS


title: GSK461364_2hLPS_R1

description: RNAseq


title: GSK461364_2hLPS_R3

description: RNAseq


title: T47D_AI.F.run1

value: Awakening


title: GSK2110183_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with GSK2110183 followed by 2h stimulation with 10ng/mL LPS


title: T47D_AI.E.run2


title: lib52810


title: lib52796


title: T47D_AI.E.run1


title: lib52798


title: lib52799


title: lib52795


title: lib52797


title: T47D_AI.D.run3


title: lib52793


title: T47D_AI.D.run2


title: lib52794


title: GSK2110183_2hLPS_R2

description: RNAseq


title: T47D_AI.F.run2


title: T47D_AI.D.run1


title: lib52789


title: GDC0994_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with GDC0994 followed by 2h stimulation with 10ng/mL LPS


title: T47D_AI.C.run2


title: lib52787

value: islet peptide library


title: lib52790


title: GDC0994_2hLPS_R1

description: RNAseq


title: lib52788


title: Filgotinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Filgotinib followed by 2h stimulation with 10ng/mL LPS


title: T47D_AI.C.run1


title: lib52786


title: lib52785


title: T47D_AI.B.run1


title: lib52784


title: lib52783


title: Filgotinib_2hLPS_R2

description: RNAseq


title: T47D_AI.B.run2


title: lib52782


title: lib52792


title: GSK2110183_2hLPS_R1

description: RNAseq


title: GDC0994_2hLPS_R3

description: RNAseq


title: lib52781


title: T47D_AI.A


title: lib52791


title: Filgotinib_2hLPS_R1

description: RNAseq


title: Encorafenib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Encorafenib followed by 2h stimulation with 10ng/mL LPS


title: lib52778


title: T47D_UT4m.3.run2

value: Untreated

value: 4 months


title: lib52779

value: ISLET TMR+ CD8 T cells


title: lib52780


title: lib52777


title: Encorafenib_2hLPS_R2

description: RNAseq

value: wild type


title: lib52776


title: T47D_UT4m.3.run1


title: lib52775


title: Encorafenib_2hLPS_R1

description: RNAseq


title: lib52774


title: lib52773


title: DMSOs2_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with DMSO followed by 2h stimulation with 10ng/mL LPS


title: T47D_UT4m.1


title: lib52772


title: DMSOs2_2hLPS_R2

description: RNAseq

value: BMDM


title: lib52771


title: T47D_UT.3

value: 1 month


title: DMSOs2_2hLPS_R1

description: RNAseq


title: T47D_UT.2


title: lib52770


title: lib52769


title: lib52768


title: DMSOs1_2hLPS_R3

description: RNAseq


title: lib52767


title: lib52766


title: DMSOs1_2hLPS_R2

description: RNAseq


title: lib52764


title: T47D_AI30.2

value: Oestrogen deprived

value: Dormancy


title: DMSOs1_2hLPS_R1

description: RNAseq


title: T47D_UT.1


title: lib52763


title: T47D_UT4m.2


title: T47D_AI30.1


title: Capmatinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Capmatinib followed by 2h stimulation with 10ng/mL LPS


title: T47D_T0.4


title: lib52761


title: lib52762


title: lib52760


title: lib52759


title: T47D_T0.3


title: lib52758


title: Capmatinib_2hLPS_R1

description: RNAseq


title: lib52756


title: lib52757


title: BMS911543_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with BMS911543 followed by 2h stimulation with 10ng/mL LPS


title: T47D_T0.2


title: T47D_T0.1


title: lib52755


title: lib52754


title: lib52765


title: BMS911543_2hLPS_R2

description: RNAseq


title: lib52753


title: lib52752


title: BMS911543_2hLPS_R1

description: RNAseq


title: T47D_POT.3

value: POT


title: lib52751


title: T47D_POT.2


title: T47D_POT.1


title: lib52750


title: BMS387032_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with BMS387032 followed by 2h stimulation with 10ng/mL LPS


title: lib52689

value: CD154+CD69+CD4 T cells


title: Capmatinib_2hLPS_R2

description: RNAseq


title: BMS387032_2hLPS_R2

description: RNAseq


title: MCF7_AI.DH.14D.TEP.run2

value: Drug holiday TEP


title: lib52687

value: islet peptide library


title: lib52688


title: MCF7_AI.DH.14D.TEP.run1


title: lib52686


title: lib52685


title: MCF7_AI.DH.7D.TEP.run2


title: lib52684


title: BGT226_2hLPS_R2

description: RNAseq

value: 1h pre-treatment with BGT226 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI.DH.7D.TEP.run1


title: lib52681


title: lib52680


title: lib52679


title: lib52749


title: Bafetinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Bafetinib followed by 2h stimulation with 10ng/mL LPS


title: BGT226_2hLPS_R1

description: RNAseq


title: lib52678


title: MCF7_T.DH.7D.TEP.run1

value: Tamoxifen


title: lib52676


title: Bafetinib_2hLPS_R2

description: RNAseq


title: MCF7_T.DH.7D.TEP.run2


title: MCF7_AI.DH.14D

value: Drug holiday


title: lib52677


title: lib52675


title: BMS387032_2hLPS_R1

description: RNAseq

value: wild type


title: lib52674


title: Bafetinib_2hLPS_R1

description: RNAseq


title: BGT226_2hLPS_R3

description: RNAseq


title: AZD8186_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with AZD8186 followed by 2h stimulation with 10ng/mL LPS


title: lib52673


title: lib52683


title: MCF7_AI.DH.7D.run2


title: lib52671


title: lib52672


title: AZD8186_2hLPS_R2

description: RNAseq

value: BMDM


title: lib52670


title: lib52682


title: MCF7_T.DH.7D


title: lib52669


title: lib52668


title: AZD8186_2hLPS_R1

description: RNAseq


title: MCF7_T.Zeta+30

value: TEP


title: lib52667


title: AZD2014_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with AZD2014 followed by 2h stimulation with 10ng/mL LPS


title: lib52666


title: lib52665


title: lib52664


title: AZD2014_2hLPS_R2

description: RNAseq


title: lib52662


title: MCF7_AI.Gamma+30

value: Oestrogen deprived


title: AZD2014_2hLPS_R1

description: RNAseq


title: MCF7_AI.DH.7D.run1


title: lib52661


title: lib52660


title: AZD1208_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with AZD1208 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI.Beta+30


title: lib52657


title: AZD1208_2hLPS_R2

description: RNAseq


title: lib52658


title: MCF7_AI.Alpha+30


title: AZD1208_2hLPS_R1

description: RNAseq


title: MCF7_T.Beta+30.run2


title: MCF7_T.Beta+30.run1


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

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description: Blood6_PCs_Bmem_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: *.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: BCR-seq

molecule: other

source_name: Peripheral blood

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: Peripheral blood

value: Plasmablasts and Memory B cells

value: Female


title: Apitolisib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Apitolisib followed by 2h stimulation with 10ng/mL LPS


title: Apitolisib_2hLPS_R2

description: RNAseq


title: MCF7_T.Epsilon+30


title: BCR-Seq, BM PC and Bmem, donor 561

description: BM_6_PC_Bmem_BCR.filtered_contig_annotations.csv

source_name: Bone Marrow

value: Bone Marrow

value: Plasma cells and Memory B cells


title: MCF7_T.Alpha+30.run1


title: CITE-Seq, BM PC and Bmem, donor 561

description: BM_6_PC_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

molecule: protein

tag: adt

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

tag: hto

value: TotalSeq™-C0251 anti-human Hashtag 1 Antibody


title: lib52663

value: CD154+CD69+CD4 T cells

value: islet peptide library


title: GEX-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.


title: Apitolisib_2hLPS_R1

description: RNAseq

value: wild type


title: GEX-Seq, BM PC and Bmem, donor 561


title: lib52659


title: GEX-Seq, BM PC and Bmem, donor 559

description: BM_PCs_Bmem_5.filtered_feature_bc_matrix.h5


title: CITE-Seq, BM PC and Bmem, donor 559

value: TotalSeq™-C0257 anti-human Hashtag 7 Antibody


title: Apatinib_2hLPS_R3

description: RNAseq

value: BMDM

value: 1h pre-treatment with Apatinib followed by 2h stimulation with 10ng/mL LPS


title: MCF7_T.Delta+30.run1

value: Tamoxifen

value: TEP


title: BCR-Seq, spike-specific B cells, donor 559

description: BM_blood_Spike_5_BCR.filtered_contig_annotations.csv

source_name: Bone Marrow and peripheral blood

value: Bone Marrow and peripheral blood

value: B cells


title: CITE-Seq, spike-specific B cells, donor 559

description: BM_blood_Spike_5.filtered_feature_bc_matrix.h5

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


title: GEX-Seq, spike-specific B cells, donor 559

value: Female


title: Apatinib_2hLPS_R2

description: RNAseq


title: MCF7_T.Gamma+30.run2


title: Apatinib_2hLPS_R1

description: RNAseq


title: MCF7_T.Gamma+30.run1


title: CITE-Seq, BM PC and Bmem, donor 558

description: BM_PCs_Bmem_4.filtered_feature_bc_matrix.h5

value: Male

value: TotalSeq™-C0259 anti-human Hashtag 9 Antibody


title: MCF7_UT170.3

value: Untreated


title: BCR-Seq, tetanus-specific B cells, donor 558

description: BM_Tetanus_4_BCR.filtered_contig_annotations.csv

value: Bone Marrow


title: MCF7_T.Alpha+30.run2


title: AMG208_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with AMG208 followed by 2h stimulation with 10ng/mL LPS


title: BCR-Seq, BM PC and Bmem, donor 559

description: BM_PCs_Bmem_5_BCR.filtered_contig_annotations.csv

value: Plasma cells and Memory B cells


title: AMG208_2hLPS_R1

description: RNAseq


title: CITE-Seq, tetanus-specific B cells, donor 558

description: BM_Tetanus_4.filtered_feature_bc_matrix.h5

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


title: Afatinib_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with Afatinib followed by 2h stimulation with 10ng/mL LPS

value: wild type


title: CITE-Seq, spike-specific B cells, donor 558

description: BM_Spike_4.filtered_feature_bc_matrix.h5


title: AMG208_2hLPS_R2

description: RNAseq

value: BMDM


title: GEX-Seq, spike-specific B cells, donor 558


title: MCF7_UT170.2.run1


title: MCF7_UT170.2.run2


title: GEX-Seq, tetanus-specific B cells, donor 558


title: BCR-Seq, BM PC and Bmem, donor 558

description: BM_PCs_Bmem_4_BCR.filtered_contig_annotations.csv


title: MCF7_T.Delta+30.run2


title: MCF7_AI.Beta.run2

value: Oestrogen deprived

value: Awakening


title: Afatinib_2hLPS_R1

description: RNAseq


title: GEX-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555

description: BM_PCs-Bmem_3_556-blood555.filtered_feature_bc_matrix.h5


title: MCF7_AI.Beta.run1


title: BCR-Seq, spike-specific B cells, donor 558

description: BM_Spike_4_BCR.filtered_contig_annotations.csv


title: GEX-Seq, BM PC and Bmem, donor 558


title: MCF7_UT170.1


title: BCR-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555

description: BM_PCs_Bmem_3_556_blood555_BCR.filtered_contig_annotations.csv


title: CITE-Seq, BM PC and Bmem, donor 555

description: BM_PCs-Bmem_3_555.filtered_feature_bc_matrix.h5

value: TotalSeq™-C0254 anti-human Hashtag 4 Antibody


title: AC480_2hLPS_R3

description: RNAseq

value: 1h pre-treatment with AC480 followed by 2h stimulation with 10ng/mL LPS


title: MCF7_AI.Gamma


title: Afatinib_2hLPS_R2

description: RNAseq


title: CITE-Seq, BM PC and Bmem, donor 556, blood Bmem, donor 555

value: Bone Marrow and peripheral blood

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


title: AC480_2hLPS_R2

description: RNAseq


title: MCF7_AI.Alpha


title: CITE-Seq, tetanus-specific B cells, donor 555 and 556

description: BM_Tetanus_3.filtered_feature_bc_matrix.h5

value: B cells

value: Female

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


title: GEX-Seq, tetanus-specific B cells, donor 555 and 556


title: AC480_2hLPS_R1

description: RNAseq


title: BCR-Seq, tetanus-specific B cells, donor 555 and 556

description: BM_Tetanus_3_BCR.filtered_contig_annotations.csv


title: GEX-Seq, spike-specific B cells, donor 555 and 556

description: BM_Spike_3.filtered_feature_bc_matrix.h5


title: GEX-Seq, BM PC and Bmem, donor 555


title: MCF7_T.Beta.run1

value: Tamoxifen


title: BCR-Seq, BM PC and Bmem, donor 555

description: BM_PCs_Bmem_3_555_BCR.filtered_contig_annotations.csv

value: Bone Marrow


title: MCF7_T.Beta.run2


title: N134_RHB_met_2_S8

city: New York

first: Nancy

last: Du

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina NovaSeq 6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

growth_protocol: N134 or N134_RHAMMB (N134-RHB) cell lines were S.C. injected or intravenously injected via tail vein into NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice.

extract_protocol: Total RNA was extracted using the miRNasy Mini Kit (Qiagen, 217004) and QIAshredder kit (Qiagen, 79654) according to the manufacturer’s protocol.

treatment_protocol: S.C. tumors and liver metastases were harvested.

value: N134-RHAMMB liver met

tag: host strain


title: N134_RHB_met_3_S9


title: CITE-Seq, spike-specific B cells, donor 555 and 556


title: MCF7_T.Alpha


title: N134_RHB_met_1_S7


title: BCR-Seq, spike-specific B cells, donor 553

description: BM_Spike_2_BCR.filtered_contig_annotations.csv


title: CITE-Seq, spike-specific B cells, donor 553

description: BM_Spike_2.filtered_feature_bc_matrix.h5

value: TotalSeq™-C0260 anti-human Hashtag 10 Antibody


title: GEX-Seq, BM PC and Bmem, donor 553

description: BM_PCs-Bmem_2.filtered_feature_bc_matrix.h5

value: Plasma cells and Memory B cells


title: BCR-Seq, BM PC and Bmem, donor 553

description: BM_PCs_Bmem_2_BCR.filtered_contig_annotations.csv


title: MCF7_T.Delta.run2


title: CITE-Seq, BM PC and Bmem, donor 553

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


title: N134_RHB_SC_2_S5

value: N134-RHAMMB subcutaneous tumor


title: MCF7_T.Gamma


title: GEX-Seq, spike-specific B cells, donor 546, 547 and 548

description: BM_Spike_Pool1.filtered_feature_bc_matrix.h5

value: Female and Male


title: CITE-Seq, spike-specific B cells, donor 546, 547 and 548

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


title: N134_RHB_SC_4_S6


title: N134_RHB_SC_1_S4


title: BCR-Seq, spike-specific B cells, donor 546, 547 and 548

description: BM_Spike_Pool1_BCR.filtered_contig_annotations.csv


title: BCR-Seq, blood Bmem, donor 1684

description: Blood_Bsm_3_BCR.filtered_contig_annotations.csv

value: Peripheral blood

value: Memory B cells

value: Male


title: BCR-Seq, spike-specific B cells, donor 555 and 556

description: BM_Spike_3_BCR.filtered_contig_annotations.csv

value: Bone Marrow and peripheral blood


title: MCF7_UT150.2.run2

value: Untreated


title: BCR-Seq, BM Bmem, donor 1684

description: BM_Bsm_3_BCR.filtered_contig_annotations.csv


title: CITE-Seq, blood Bmem, donor 1684

description: Blood_Bsm_3.filtered_feature_bc_matrix.h5

value: TotalSeq™-C0056 anti-human CD269 (BCMA), TotalSeq™-C0215 anti-human CD268 (BAFF-R), TotalSeq™-C0831 anti-human CD138 (Syndecan-1), TotalSeq™-C0156 anti-human CD95 (Fas), TotalSeq™-C0155 anti-human CD107a (LAMP-1), TotalSeq™-C0366 anti-human CD184 (CXCR4), TotalSeq™-C0897 anti-human CD23, TotalSeq™-C0214 anti-human/mouse integrin β7, TotalSeq™-C0140 anti-human CD183 (CXCR3), TotalSeq™-C0187 anti-human CD79b (Igβ), TotalSeq™-C0389 anti-human CD38, TotalSeq™-C0830 anti-human CD319 (CRACC) TotalSeq™-C0005 anti-human CD80, TotalSeq™-C0073 anti-mouse/human CD44, TotalSeq™-C0166 anti-human CD66b, TotalSeq™-C0050 anti-human CD19, TotalSeq™-C0374 anti-human CD98, TotalSeq™-C0576 anti-human CD49d, TotalSeq™-C0031 anti-human CD40, TotalSeq™-C0181 anti-human CD21, TotalSeq™-C0084 anti-human CD56 (NCAM) Recombinant, TotalSeq™-C0144 anti-human CD185 (CXCR5), TotalSeq™-C0394 anti-human CD71, TotalSeq™-C0577 anti-human CD73 (Ecto-5'-nucleotidase), TotalSeq™-C0007 anti-human CD274 (B7-H1, PD-L1), TotalSeq™-C0386 anti-human CD28, TotalSeq™-C0369 anti-human CD29, TotalSeq™-C0159 anti-human HLA-DR, TotalSeq™-C0008 anti-human CD273 (B7-DC, PD-L2), TotalSeq™-C0070 anti-human/mouse CD49f, TotalSeq™-C0100 anti-human CD20, TotalSeq™-C0147 anti-human CD62L, TotalSeq™-C0006 anti-human CD86, TotalSeq™-C0391 anti-human CD45, TotalSeq™-C0154 anti-human CD27


title: GEX-Seq, blood Bmem, donor 1684


title: CITE-Seq, BM Bmem, donor 1684


title: GEX-Seq, BM Bmem, donor 1684


title: MCF7_T.Delta.run1

value: Awakening


title: N134_SC_2_S2

value: N134 subcutaneous tumor


title: N134_SC_3_S3


title: N134_SC_1_S1


title: CITE-Seq, BM PC, donor 1684

value: Plasma cells


title: MCF7_UT150.1.run1


title: MCF7_UT150.2.run1


title: GEX-Seq, spike-specific B cells, donor 553

value: Bone Marrow

value: B cells

value: Female


title: MCF7_UT150.1.run2


title: NE-4C-Rncr3 exon2/3 deletion-3

city: Boulder

first: Jing

last: Zhang

state: CO

address: 1945 Colorado ave.

department: MCDB

institute: CU Boulder

data_processing:
Samples were run on the Illumina NovaSEQ6000 system at a depth of 80 million paired-end reads.
Following de-multiplexing, fastQ files were assessed for quality using fastQC (version 0.11.8).
Trimgalore (0.4.3) was used to remove adapters; jumping index content unique to Tecan library kit, and sections of reads with low quality with a minimum of 20 bp read length.
Samples were then aligned using tophat2 (version 2.1.1)18 utilizing bowtie2 (version 2.2.9), beyond default options for a sensitive paired end alignment, reads were aligned in reverse to accommodate the first-strand-sense reads unique to the Tecan library prep kit.
Read counts were assessed using htseq (version 0.9.1 under python distribution 3.6.3)21 and options were set for a paired-end reverse alignment. Differential expression was evaluated using deseq2 (version 3.14)22 within Rstudio (version 1.4.1103) utilizing R (version 4.1.2). Deseq2 analysis was performed on all 9 samples simultaneously portioned by design based on transcript knockout length.
Genome_build: mm39
Supplementary_files_format_and_content: tab-delimited xlsx files include log_foldchange and P values for every gene in different genotypes comparison.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: neuroepithelial progenitor cells

growth_protocol: NE-4C cells (ATCC #CRL-2925) and different  CRISPR/Cas9 gene editing clones were grown at 37°C and 5% CO2 under proliferation conditions in MEM (Invitrogen) supplemented with 5% FBS, 1×MEM nonessential amino acids (Invitrogen) and 1×GlutaMax (Invitrogen). PolyA(+) RNA-seq: For sample preparation, three individual clones of CRISPR-Cas9 DNA edited Rncr3 exons 2/3 deletion or Rncr3 full-length deletion in NE-4C cells were used. Three biological replicates of non-manipulated NE-4C cells were used as wild type control. All cell samples were cultured under proliferation conditions for three days and then collected and subjected to total RNA extraction.

extract_protocol:
Cell culture medium were removed and the total RNA was extracted by using Trizol-chloroform system.
1 µg of RNA was used for library preparation (Universal Plus mRNA-Seq with NuQuant, Tecan Genomics, #0520).

value: a neuroepithelial progenitor cell line from cerebral vesicles of embryonic day 9 (E9) mouse embryos, CRISPR/Cas9 gene editing

tag: strain

value: Rncr3 exon2/3 deletion


title: GEX-Seq, BM PC, donor 1684

tag: cell type


title: MCF7_AI.Epsilon.run2

value: Oestrogen deprived


title: BCR-Seq, blood Bmem, donor 1681

description: Blood_Bsm_2_BCR.filtered_contig_annotations.csv

tag: genotype


title: CITE-Seq, blood Bmem, donor 1681

description: Blood_Bsm_2.filtered_feature_bc_matrix.h5


title: NE-4C-Rncr3 exon2/3 deletion-1


title: MCF7_AI.Epsilon.run1

tag: treatment


title: BCR-Seq, BM Bmem, donor 1681

description: BM_Bsm_2_BCR.filtered_contig_annotations.csv


title: GEX-Seq, blood Bmem, donor 1681


title: MCF7_AI.Delta.run2


title: NE-4C-Rncr3 full length KO-3

value: Rncr3 full length KO


title: MCF7_AI.Delta.run1


title: GEX-Seq, BM Bmem, donor 1681


title: CITE-Seq, BM Bmem, donor 1681


title: BCR-Seq, BM PC, donor 1684

description: BM_PCs_3_BCR.filtered_contig_annotations.csv


title: BCR-Seq, BM PC, donor 1681

description: BM_PCs_2_BCR.filtered_contig_annotations.csv


title: NE-4C-Rncr3 full length KO-1


title: MCF7_T.Zeta.run1

value: Tamoxifen


title: TCR-Seq, COVID-19/BNT/BNT, donor C3

description:
10x genomics
COVID_GroupC_d7AB_TCR.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

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: Plasmablasts, Memory B cells and activated T cells

tag: Sex


title: NE-4C-Rncr3 full length KO-2


title: GEX-Seq, COVID-19/BNT/BNT, donor C3

description:
10x genomics
COVID_GroupC_d7AB_Pool1.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: *.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


title: MCF7_T.Zeta.run2


title: GEX-Seq, BM PC, donor 1681

value: Male


title: CITE-Seq, BM PC, donor 1681


title: BCR-Seq, COVID-19/BNT/BNT, donor C3

description:
10x genomics
COVID_GroupC_d7AB_BCR.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: BCR-seq


title: NE-4C_WT-3

value: a neuroepithelial progenitor cell line from cerebral vesicles of embryonic day 9 (E9) mouse embryos

value: wild type


title: NE-4C-Rncr3 exon2/3 deletion-2


title: NE-4C_WT-2


title: MCF7_T.Epsilon.run2


title: MCF7_T.Epsilon.run1


title: MCF7_UT120.2.run2

value: Untreated


title: TCR-Seq, COVID-19/BNT, Pool2, donor C1, C2 and C3

description:
10x genomics
GC_d7_Pool2_TCR.filtered_contig_annotations.csv

value: pooled male and female


title: BCR-Seq, COVID-19/BNT, Pool2, donor C1, C2 and C3

description:
10x genomics
GC_d7_Pool2_BCR.filtered_contig_annotations.csv


title: CITE-Seq, COVID-19/BNT, Pool2, donor C1, C2 and C3

description:
10x genomics
COVID_GroupC_d7_Pool2.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: *.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

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: TCR-Seq, COVID-19/BNT, Pool1, donor C1, C2 and C3

description:
10x genomics
GC_d7_Pool1_TCR.filtered_contig_annotations.csv


title: BCR-Seq, COVID-19/BNT, Pool1, donor C1, C2 and C3

description:
10x genomics
GC_d7_Pool1_BCR.filtered_contig_annotations.csv


title: MCF7_UT120.2.run1


title: CITE-Seq, COVID-19/BNT, Pool1, donor C1, C2 and C3

description:
10x genomics
COVID_GroupC_d7_Pool1.filtered_feature_bc_matrix.h5


title: NE-4C_WT-1


title: GEX-Seq, COVID-19/BNT, Pool2, donor C1, C2 and C3


title: GEX-Seq, COVID-19/BNT, Pool1, donor C1, C2 and C3


title: CITE-Seq, COVID-19/BNT/BNT, donor C3

value: TotalSeq-C0253 anti-human Hashtag 3 Antibody


title: MCF7_UT120.1.run2