Process raw data for single-cell multiome ATAC + Gene Expression data

Mouse Model: SMMHCCreERT2;R26RtdTomato;Ren1cYFP

FASTQ file names (unprocessed)

Naming conventions of FASTQ files.

Untreated (control)

  1. Untreated for 1 month (3mo of age mouse)

    ATAC raw data:
    - Control_3_months_ATAC_S1_L001_R1_001.fastq.gz
    - Control_3_months_ATAC_S1_L001_R2_001.fastq.gz
    - Control_3_months_ATAC_S1_L001_R3_001.fastq.gz
    - Control_3_months_ATAC_S1_L001_I1_001.fastq.gz

    RNA raw data:
    - Control_3_months_GEX_S1_L001_I1_001.fastq.gz
    - Control_3_months_GEX_S1_L001_I2_001.fastq.gz
    - Control_3_months_GEX_S1_L001_R1_001.fastq.gz
    - Control_3_months_GEX_S1_L001_R2_001.fastq.gz

  2. Untreated for 3 months (5mo of age mouse)

    ATAC raw data:
    - Control_5_months_ATAC_S1_L001_R1_001.fastq.gz
    - Control_5_months_ATAC_S1_L001_R2_001.fastq.gz
    - Control_5_months_ATAC_S1_L001_R3_001.fastq.gz
    - Control_5_months_ATAC_S1_L001_I1_001.fastq.gz

    RNA raw data:
    - Control_5_months_GEX_S1_L001_I1_001.fastq.gz
    - Control_5_months_GEX_S1_L001_I2_001.fastq.gz
    - Control_5_months_GEX_S1_L001_R1_001.fastq.gz
    - Control_5_months_GEX_S1_L001_R2_001.fastq.gz

  3. Untreated for 6 months (8mo of age mouse)

    ATAC raw data:
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_ATAC_S1_L001_I1_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_ATAC_R1_L001_I1_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_ATAC_R2_L001_I1_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_ATAC_R3_L001_I1_001.fastq.gz

    RNA raw data:
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_GEX_S21_L004_I1_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_GEX_S21_L004_I2_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_GEX_S21_L004_R1_001.fastq.gz
    - SMMHCtdTomatoYFP_6_months_Control_Multiome_GEX_S21_L004_R2_001.fastq.gz

Captopril-treated

  1. Captopril-treated for 1 month (3mo of age mouse)

    ATAC raw data:
    - 1m_captopril_ATAC_S3_L001_I1_001.fastq.gz
    - 1m_captopril_ATAC_S3_L001_R1_001.fastq.gz
    - 1m_captopril_ATAC_S3_L001_R2_001.fastq.gz
    - 1m_captopril_ATAC_S3_L001_R3_001.fastq.gz

    RNA raw data:
    - 1m_captopril_GEX_S7_L003_I1_001.fastq.gz
    - 1m_captopril_GEX_S7_L003_I2_001.fastq.gz
    - 1m_captopril_GEX_S7_L003_R1_001.fastq.gz
    - 1m_captopril_GEX_S7_L003_R2_001.fastq.gz

  2. Captopril-treated for 3 months (5mo of age mouse)

    ATAC raw data:
    - 3m_captopril_ATAC_S4_L001_I1_001.fastq.gz
    - 3m_captopril_ATAC_S4_L001_R1_001.fastq.gz
    - 3m_captopril_ATAC_S4_L001_R2_001.fastq.gz
    - 3m_captopril_ATAC_S4_L001_R3_001.fastq.gz

    RNA raw data:
    - 3m_captopril_GEX_S8_L003_I1_001.fastq.gz
    - 3m_captopril_GEX_S8_L003_I2_001.fastq.gz
    - 3m_captopril_GEX_S8_L003_R1_001.fastq.gz
    - 3m_captopril_GEX_S8_L003_R2_001.fastq.gz

  3. Captopril-treated for 6 months (8mo of age mouse)

    ATAC raw data:
    - 8_months_ATAC_S5_L001_I1_001.fastq.gz
    - 8_months_ATAC_S5_L001_R1_001.fastq.gz
    - 8_months_ATAC_S5_L001_R2_001.fastq.gz
    - 8_months_ATAC_S5_L001_R3_001.fastq.gz

    RNA raw data:
    - 8_months_GEX_S9_L003_I1_001.fastq.gz
    - 8_months_GEX_S9_L003_I2_001.fastq.gz
    - 8_months_GEX_S9_L003_R1_001.fastq.gz
    - 8_months_GEX_S9_L003_R2_001.fastq.gz

Run Cell Ranger ARC (v. cellranger-arc-2.0.2)

Run FASTQ files through 10X Cell Ranger ARC pipeline.

Untreated (control)

  1. 1mo

    console cellranger-arc count --id=captopril-ctrl_1mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-ctrl_1mo_libraries.csv \ --localcores=4 \ --localmem=24

  2. 3mo

    console cellranger-arc count --id=captopril-ctrl_3mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-ctrl_3mo_libraries.csv \ --localcores=4 \ --localmem=24

  3. 6mo

    console cellranger-arc count --id=captopril-ctrl_6mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-ctrl_6mo_libraries.csv \ --localcores=4 \ --localmem=24

Captopril-treated

  1. 1mo

    console cellranger-arc count --id=captopril-trt_1mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-trt_1mo_libraries.csv \ --localcores=4 \ --localmem=24

  2. 3mo

    console cellranger-arc count --id=captopril-trt_3mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-trt_3mo_libraries.csv \ --localcores=4 \ --localmem=24

  3. 6mo

    console cellranger-arc count --id=captopril-trt_6mo \ --reference=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \ --libraries=/data/captopril_multiome/captopril-trt_6mo_libraries.csv \ --localcores=4 \ --localmem=24

Processed file names

  1. Captopril-treated for 1 month (3mo of age mouse)

    • 1m_captopril_atac_fragments.tsv.gz
    • 1m_captopril_atac_fragments.tsv.gz.tbi
    • 1m_captopril_barcodes.tsv.gz
    • 1m_captopril_features.tsv.gz
    • 1m_captopril_matrix.mtx.gz
    • 1m_captopril_per_barcode_metrics.csv
    • 1m_untreated_atac_fragments.tsv.gz
    • 1m_untreated_atac_fragments.tsv.gz.tbi
    • 1m_untreated_barcodes.tsv.gz
    • 1m_untreated_features.tsv.gz
    • 1m_untreated_matrix.mtx.gz
    • 1m_untreated_per_barcode_metrics.csv


  2. Captopril-treated for 3 months (5mo of age mouse)

    • 3m_captopril_atac_fragments.tsv.gz
    • 3m_captopril_atac_fragments.tsv.gz.tbi
    • 3m_captopril_barcodes.tsv.gz
    • 3m_captopril_features.tsv.gz
    • 3m_captopril_matrix.mtx.gz
    • 3m_captopril_per_barcode_metrics.csv
    • 3m_untreated_atac_fragments.tsv.gz
    • 3m_untreated_atac_fragments.tsv.gz.tbi
    • 3m_untreated_barcodes.tsv.gz
    • 3m_untreated_features.tsv.gz
    • 3m_untreated_matrix.mtx.gz
    • 3m_untreated_per_barcode_metrics.csv


  3. Captopril-treated for 6 months (8mo of age mouse)

    • 6m_captopril_atac_fragments.tsv.gz
    • 6m_captopril_atac_fragments.tsv.gz.tbi
    • 6m_captopril_barcodes.tsv.gz
    • 6m_captopril_features.tsv.gz
    • 6m_captopril_matrix.mtx.gz
    • 6m_captopril_per_barcode_metrics.csv
    • 6m_untreated_atac_fragments.tsv.gz
    • 6m_untreated_atac_fragments.tsv.gz.tbi
    • 6m_untreated_barcodes.tsv.gz
    • 6m_untreated_features.tsv.gz
    • 6m_untreated_matrix.mtx.gz
    • 6m_untreated_per_barcode_metrics.csv

Process raw data for single-cell RNA-seq data

Mouse Model - Wildtype (ReninWT): Ren1c+/-;Ren1cCre;R26RmTmG - Knockout (ReninKO or Reninnull): Ren1c-/-;Ren1cCre;R26RmTmG

FASTQ file names (unprocessed)

Naming conventions of FASTQ files.

Wildtype (control)

Wildtype mice (1mo of age)

RNA raw data:
- Ren1cPosPos_Ren1cCre_mTmG_1mo_S12_L001_I1_001.fastq.gz
- Ren1cPosPos_Ren1cCre_mTmG_1mo_S12_L001_I2_001.fastq.gz
- Ren1cPosPos_Ren1cCre_mTmG_1mo_S12_L001_R1_001.fastq.gz
- Ren1cPosPos_Ren1cCre_mTmG_1mo_S12_L001_R2_001.fastq.gz

Knockout

Knockout mice (1mo of age)

RNA raw data:
- Ren1cKO_Ren1cCre_mTmG_1mo_S6_L003_I1_001.fastq.gz
- Ren1cKO_Ren1cCre_mTmG_1mo_S6_L003_I2_001.fastq.gz
- Ren1cKO_Ren1cCre_mTmG_1mo_S6_L003_R1_001.fastq.gz
- Ren1cKO_Ren1cCre_mTmG_1mo_S6_L003_R2_001.fastq.gz

Run Cell Ranger (v. cellranger-7.2.0)

Run FASTQ files through 10X Cell Ranger pipeline.

Wildtype mouse (ReninWT)

cellranger count --id=ren1c_1mo \
  --transcriptome=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \
  --fastqs=/data/lucas/ren1c \
  --sample=Ren1cPosPos_Ren1cCre_mTmG_1mo \
  --localcores=4 \
  --localmem=24

Knockout mouse (ReninKO)

cellranger count --id=ren1cKO_1mo \
  --transcriptome=/data/genomes/mouse/refdata-cellranger-arc-mm10-2020-A-2.0.0 \
  --fastqs=/data/lucas/ren1c \
  --sample=Ren1cKO_Ren1cCre_mTmG_1mo \
  --localcores=4 \
  --localmem=24

Processed file names

  1. Phenotypically WT mice (Ren1c+/-)
    • Ren1cKO_Ren1cCre_mTmG_1mo_barcodes.tsv.gz
    • Ren1cKO_Ren1cCre_mTmG_1mo_features.tsv.gz
    • Ren1cKO_Ren1cCre_mTmG_1mo_matrix.mtx.gz

  2. Renin KO mice (Ren1c-/-)
    • Ren1cPosPos_Ren1cCre_mTmG_1mo_barcodes.tsv.gz
    • Ren1cPosPos_Ren1cCre_mTmG_1mo_features.tsv.gz
    • Ren1cPosPos_Ren1cCre_mTmG_1mo_matrix.mtx.gz