status: PUBLIC

text: Frontal cortex

tag: attribute

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ArrayExpress-SPECIES

characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Unknown

characteristic: GENDER

text: SC

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Frontal cortex

characteristic: PHENOTYPE

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: title


text: Spleen

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: Spleen

text: house mouse

text: Mus musculus

text: Mus musculus


text: BAT

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: BAT

text: house mouse

text: Mus musculus

text: Mus musculus


text: Ofactory bulb

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: Ofactory bulb

text: house mouse

text: Mus musculus

text: Mus musculus


text: Smooth muscle (colon)

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: Smooth muscle (colon)

text: house mouse

text: Mus musculus

text: Mus musculus


text: Lung

text: unknown

text: Mus musculus

text: Unknown

text: SC

text: public

text: Lung

text: house mouse

text: Mus musculus

text: Mus musculus


text: female

text: Schistosoma mansoni

text: Female

text: SC

text: public

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni


text: male

text: Schistosoma mansoni

text: Male

text: SC

text: public

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni


text: unknown

text: Schistosoma mansoni

text: Unknown

text: SC

text: public

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni


text: Schistosoma mansoni

text: SC

text: public

text: Schistosoma mansoni

text: Schistosoma mansoni

text: Schistosoma mansoni


text: mixed

text: Caenorhabditis quiockensis

text: Mixed

text: SC

text: public

text: Caenorhabditis quiockensis

text: Caenorhabditis quiockensis

text: Caenorhabditis quiockensis


text: Escherichia coli

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: unknown

text: unknown

text: human

text: Unknown

text: SC

text: public

text: unknown

text: human

text: Homo sapiens

text: Homo sapiens


text: Salmonella enterica

text: SC

text: public

text: Salmonella enterica

text: Salmonella enterica

text: Salmonella enterica


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: UCE library plasmid

text: Homo sapiens

characteristic: strain


text: public

text: E-MTAB-13664:D49_Epi_LASP_SLX-20261-20448_SIGAB10

tag: Namespace:Cambridge Stem Cell Institute Department of Pharmacology

unit: year

characteristic: age

characteristic: batch

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: unknown

characteristic: parity

text: 10x 3' v3

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D14_Epi_LASP_SLX-20005-20446_SIGAD3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664:D38_Epi_all_SLX-19902-20449_SIGAF2

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D15_Str_all_SLX-19902-20449_SIGAG1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664:D38_Epi_LASP_SLX-19902-20449_SIGAG2

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D40_Str_all_SLX-19864-20262_SIGAF8

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664:D49_Epi_all_SLX-20261_SIGAA10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

text: unknown

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: unknown

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D18_Str_all_SLX-19902-20449_SIGAD3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664:D39_Str_all_SLX-20005-20446_SIGAC7

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D36_Str_all_SLX-19864-20262_SIGAC8

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664:D45_Epi_all_SLX-20005_SIGAE3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

text: WT

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D28_Epi_all_SLX-20005_SIGAD9

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664:D33_Epi_all_SLX-19902-20446_SIGAH7

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D16_Epi_all_SLX-19902_SIGAH2

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664:D22_Epi_all_SLX-19902_SIGAF3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D29_Epi_LASP_SLX-19902-20449_SIGAF12

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664:D18_Epi_all_SLX-19902-20449_SIGAE11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D12_Epi_all_SLX-19902_SIGAF10

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664:D54_Epi_all_SLX-19902_SIGAE7

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: contralateral

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D29_Epi_all_SLX-19902_SIGAD12

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664:D44_Epi_LASP_SLX-19902_SIGAC11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D23_Epi_all_SLX-19864_SIGAB8

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664:failed_2_Str_all_SLX-20261_SIGAH7

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D22_Epi_LASP_SLX-19902_SIGAG3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664:D48_Epi_LASP_SLX-20005-20446_SIGAG6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

text: unknown

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664:D18_Epi_LASP_SLX-19902-20449_SIGAF11

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664_2:D46_Epi_all_SLX-20005-20446_SIGAE12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

text: WT

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D33_Str_all_SLX-19902-20449_SIGAB3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_2:D44_Epi_all_SLX-19902-20449_SIGAA11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D32_Epi_all_SLX-19902_SIGAB4

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_2:D37_Str_all_SLX-19902-20449_SIGAF1

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D1_Epi_all_SLX-19902_SIGAB1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664_2:D32_Epi_LASP_SLX-19902_SIGAC4

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D15_Epi_all_SLX-19864_SIGAH10

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_2:D25_Str_all_SLX-20005_SIGAH11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D46_Str_all_SLX-20005-20446_SIGAB6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: WT

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_2:D29_Epi_all_SLX-19902_SIGAE12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D1_Epi_LASP_SLX-19902_SIGAC1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664_2:D46_Epi_LASP_SLX-20005_SIGAF12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

text: WT

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D36_Epi_all_SLX-19864_SIGAC7

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_2:D27_Epi_LASP_SLX-19864_SIGAB9

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D19_Str_all_SLX-19902-20449_SIGAE1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_2:D9_Str_live_SLX-19647-20870_SIGAB8

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - live-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_2:D42_Epi_all_SLX-19864_SIGAF4

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_2:D32_Epi_all_SLX-19902-20449_SIGAA4

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D8_Str_all_SLX-20005-20446_SIGAB12

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D3_Epi_LASP_SLX-20005-20446_SIGAH3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: unknown

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D26_Epi_LASP_SLX-19864_SIGAB2

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_3:D44_Epi_all_SLX-19902-20449_SIGAB11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D30_Epi_all_SLX-19902_SIGAE3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_3:D2_Epi_LASP_SLX-20005_SIGAH12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: unknown

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D5_Str_all_SLX-20261-20448_SIGAB1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: unknown

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D48_Str_all_SLX-20261-20448_SIGAH6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

text: unknown

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D40_Epi_LASP_SLX-19864-20262_SIGAD6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_3:D20_Epi_LASP_SLX-19864-20262_SIGAD2

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D14_Str_all_SLX-20261-20448_SIGAD6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


text: public

text: E-MTAB-13664_3:D37_Epi_all_SLX-19864_SIGAF10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D29_Str_all_SLX-19902-20449_SIGAD1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D31_Epi_all_SLX-19902_SIGAA1

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D27_Str_all_SLX-20005-20446_SIGAA7

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_3:D41_Epi_all_SLX-19864_SIGAA6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D49_Str_all_SLX-20261-20448_SIGAC1

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: unknown

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: unknown

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_3:D5_Epi_LASP_SLX-20261_SIGAH2

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: unknown

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D54_Epi_all_SLX-19902_SIGAF7

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: contralateral

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D6_Epi_LASP_SLX-19902_SIGAE10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D2_Str_all_SLX-20005-20446_SIGAC6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: unknown

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_3:D45_Str_all_SLX-20261-20448_SIGAE6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

text: WT

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D34_Epi_all_SLX-20005-20446_SIGAA3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_3:D52_Str_all_SLX-20870_SIGAB9

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: contralateral


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D19_Epi_all_SLX-19902_SIGAH12

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D43_Str_all_SLX-20005-20446_SIGAD6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D35_Epi_all_SLX-20005_SIGAE6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_3:D26_Epi_all_SLX-19864_SIGAA2

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D39_Epi_all_SLX-20005_SIGAA11

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_3:D18_Epi_all_SLX-19902-20449_SIGAD11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D6_Epi_all_SLX-19902-20449_SIGAD10

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D17_Str_all_SLX-20005_SIGAB7

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D11_Str_all_SLX-20261-20448_SIGAB6

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_3:D37_Epi_LASP_SLX-19864_SIGAG10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D45_Epi_LASP_SLX-20005-20446_SIGAF3

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: WT

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_3:D33_Epi_LASP_SLX-19902_SIGAH10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D43_Str_all_SLX-20261-20448_SIGAH9

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_3:D2_Epi_all_SLX-20005-20446_SIGAG12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: unknown

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D1_Str_all_SLX-19864-20262_SIGAH5

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_3:D13_Str_all_SLX-19864-20262_SIGAE10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_3:D50_Epi_LASP_SLX-19864_SIGAB5

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: contralateral

characteristic: title


text: public

text: E-MTAB-13664_4:D7_Epi_LASP_SLX-20005_SIGAD11

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D43_Epi_all_SLX-20005_SIGAA9

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_4:D12_Epi_LASP_SLX-19902_SIGAG10

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D13_Epi_all_SLX-19902_SIGAE4

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_4:D34_Epi_LASP_SLX-20005_SIGAB3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - LASP-sorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D50_Str_all_SLX-20005-20446_SIGAG11

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: contralateral

characteristic: title


text: public

text: E-MTAB-13664_4:D19_Epi_all_SLX-19902_SIGAG12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D17_Epi_LASP_SLX-19864-20262_SIGAD9

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: reduction mammoplasty

characteristic: surgery type


text: public

text: E-MTAB-13664_4:D14_Epi_all_SLX-20005-20446_SIGAC3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: reduction mammoplasty

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D20_Str_all_SLX-20005-20446_SIGAF11

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


text: public

text: E-MTAB-13664_4:D44_Str_all_SLX-19902-20449_SIGAC3

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: All frozen primary human breast tissue was obtained from the Breast Cancer Now Tissue bank (REC 15/EE/0192). Prior to freezing, fresh tissues were minced and digested O/N in 1 mg/mL Collagenase 1A and 1 mg/mL Hyaluronidase in an orbital shaker, washed 2-3 times and sedimented to allow for the separation between epithelial-enriched and stromal fractions, which were then separately cryostored. Frozen vials of epithelial-enriched or stromal-enriched fractions were defrosted, washed in PBS and centrifuged at 400 g for 5 minutes and resuspended in 2 mL of freshly prepared PBS + 0.025% Trypsin and 0.4 mg/mL Deoxyribonuclease 1 (DNase). Samples were then incubated at 37°C with pipetting up and down for 2-3 minutes until smoothly digested or up to a maximum of 10 minutes. Next, samples were washed and centrifuged for 20 minutes at 400 g with slow break. The pellet was resuspended in media + DNase until homogeneous, then diluted and filtered through a 40 μm cell strainer. After centrifugation for 5 minutes at 400 g, the pellet was resuspended by pipetting up and down in 200 μL of Cell Preparation Medium + 10 μL of 10 mg/mL DNase until homogeneous, then washed in 3-6 mL of media. 30,000 cells were resuspended into 48 μL of media and 400 Human mammary epithelial cells (HuMECs, Thermo Fisher Scientific A10565) were added as spike-in, and samples were submitted for scRNA-seq (either stromal-enriched or epithelial-enriched samples). For the epithelial-enriched fraction only, the rest of the processed sample was stained with primary antibodies: CD45-APC, CD31-APC, EPCAM-AF488, CD49f-PE/Cy7. DAPI was used to detect dead cells. Cells were filtered through a cell strainer before sorting. Sorting of cells was done using a FACS Aria Fusion sorter. Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. After doublets, dead cells and contaminating haematopoietic and endothelial cells (referred to as lineage) were gated, up to 30,000 LASPs were sorted for scRNA-seq (with the addition of 400 HuMECs as spike-in). Approximately 30,000 mammary cells per sample were loaded into separate channels of a single Chromium controller (10x Genomics) chip. Consequently, gel bead-in-emulsions (GEMS) were generated using 10X Genomics Single Cell 3’ Reagent Kit v3. Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10X Genomics) and then converted using the NovaSeq 6000 S2 Reagent Kit (Illumina).

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Cambridge Stem Cell Institute Department of Pharmacology

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D31_Str_all_SLX-19864-20262_SIGAG5

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Stroma enriched - unsorted

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


text: public

text: E-MTAB-13664_4:D10_Str_all_SLX-20261-20448_SIGAA1

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: reduction mammoplasty


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D25_Epi_LASP_SLX-19864_SIGAD5

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


text: public

text: E-MTAB-13664_4:D35_Str_all_SLX-20261-20448_SIGAG6

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Stroma enriched - unsorted

characteristic: fraction

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

text: prophylactic mastectomy

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:D39_Epi_LASP_SLX-20005-20446_SIGAB11

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: adult

text: normal

text: Epithelial enriched - LASP-sorted

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: parity

text: 10x 3' v3

characteristic: protocol

text: Homo sapiens

text: female

text: prophylactic mastectomy


text: public

text: E-MTAB-13664_4:D47_Epi_all_SLX-20870_SIGAE9

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Epithelial enriched - unsorted

characteristic: fraction

text: unknown

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: 10x 3' v3

characteristic: sample id

text: Homo sapiens

text: female

characteristic: sex

text: prophylactic mastectomy

characteristic: surgery type


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13664_4:spike-in1_spike-in_SLX-20005-20446_SIGAE10

characteristic: Submitter Id

characteristic: age

characteristic: batch

text: ArrayExpress

text: not collected

text: human

text: normal

text: spike-in

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: 10x 3' v3

text: Homo sapiens

text: female

characteristic: title