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Design: Single cell RNA-seq and BCR-seq of peritoneal B cells
Study: Single cell RNA-seq and BCR-seq of peritoneal B cells
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B1 cells account for the majority of B cell population in the peritoneal cavity, and are essential for the innate immune responses and maintaining the homeostasis. The origin of the B1 cells and how to form the B1 cells pool in the postnatal life remain unknown. And the heterogeneity of B1 cells can largely affect the functions of B1 cells. Until now, nobody has performed the single cell RNA-seq of peritoneal B cells. In order to reveal the characteristics of peritoneal B cells, we have performed the scRNA-seq and scBCR-seq of the peritoneal B cells of mouse from different stages.
Sample: E scBCR-seq
SAMEA8002304 • ERS5689554 • All experiments • All runs
Organism: Mus musculus
Name: E scBCR-seq_p
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Selection: Oligo-dT
Layout: PAIRED
Construction protocol: Adult and elderly sample collection: 1. The mice were sacrificed by cervical dislocation, spraying it with 70% ethanol. 2. Use a scissors and forceps to cut the outer skin of the peritoneum and gently pull it back to expose the inner skin lining the peritoneal cavity. 3. Inject 10 ml of ice cold PBS (with 2% FCS) into the peritoneal cavity with a 27g needle. Push the needle slowly in the peritoneum. 4. After injection, gently massage the peritoneum to dislodge any attached cells into the PBS solution. 5. Insert a 25 g needle, bevel up, attached to a 10 ml syringe in the peritoneum and collect the fluid while moving the tip of the needle gently to avoid clogging by the fat tissue or other organs. Collect as much fluid as possible and depositing the collected cell suspension in tubes kept on ice after removing the needle from the syringe. 6. Repeat step 3-5. 7. Make an incision in the inner skin of the peritoneum and use a pipette to aspirate the fluid. 8. Spin the collected cell suspension at 400 x g for 8 minutes, 9. Red blood cells were removed using the ACK Lysing Buffer 10. Centrifuge the lavage fluid of the peritoneal cells at 400 x g for 6 minutes and resuspending the cell pellet in 90 μl MACS Buffer which is prepared by dissolving bovine serum protein with auto MACS Rinsing Solution to form a 0.5% BSA solution. 11. Then the CD19 MicroBeads were added to the suspention, and the mixture was incubated at 4℃ for 10 minutes. 12. Applying the cell suspention onto the MS column placed in the magnetic field of a MACS Separator. And the labeled CD19 positive cells were retained on the column. 13. Collecting the positive selected cells for further research by removing the column from the magnetic field and flushing the column with MACS buffer. 14. The collected CD19 positive cells were filterd with 30-μm Cell Strainer and then were counted with the cell auto counter. 15. Centrifuging the cells and resuspending the cells with suitable volume buffer to ensure that the concentration is 3 x 105 – 1 x 106 cells/ml. (5')GEM generation and reverse transcription1. GEMs are generated by combining barcoded Single Cell 5' Gel Beads, a Master Mix with cells, and Partitioning Oil on a microfluidic chip. To achieve single cell resolution, the cells are delivered at a limiting dilution, such that the majority (~90 – 99%) of generated GEMs contains no cell, while the remainder largely contain a single cell. Immediately following generation of a GEM, the Single Cell 5' Gel Bead is dissolved and any co-partitioned cell is lysed.2. Upon dissolution of the Single Cell 5' Gel Bead in a GEM, oligonucleotides containing (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a 13 nt Switch Oligo are released and mixed with cell lysate and a Master Mix that contains reverse transcription (RT) reagents and poly(dT) primers. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, the GEMs are broken and the pooled post GEM-RT reaction mixtures are recovered.3. The pooled post GEM-RT reaction mixture contains barcoded first-strand cDNA from poly-adenylated mRNA, as well as leftover biochemical reagents and primers. Silane magnetic beads are used to purify the cDNA from this mixture. Barcoded, full-length V(D)J segments can then be directly enriched from the purified post GEM-RT product by TCR/Ig constant region-specific PCR amplification prior to library construction. Alternatively, the entire purified post GEM-RT product can be amplified by PCR and aliquoted prior to enriching for barcoded, full-length V(D)J segments. (BCR-seq)BCR region enriched library construction1. Perform the cDNA amplification, and clean up the products.2. Amplified cDNA underwent two rounds of target enrichment using nested primer pairs specific for mouse BCR constant regions.3. Clean up the BCR target enrichment 2 from amplified cDNA reaction with the SPRIselect Reagent.4. Quality control were performed on the Alilent Bioanalyser.Enriched Library construction1. Dispense the appropriate volume for 50 ng (Enrichment from cDNA) into each well of a PCR 8-tube strip on a chilled metal block resting on ice.2. Prepare a thermal cycler with the following incubation protocol and initiate the 4°C precool block step prior to assembling the Fragmentation Mix. The incubation protocol is: 4 °C holding, 32 °C for 2 min, 65 °C for 30 min, 4 °C holding.3. Vortex the Fragmentation Buffer. Prepare the Fragmentation Mix on ice. Add the reagents in the order (Nuclease-free water, Fragmentation Buffer, FragmentationEnzyme Blend). Pipette mix thoroughly and centrifuge briefly.4. Dispense 30 µl Fragmentation Mix into each tube containing 20 µl Target Enrichment 2 product. Pipette mix 15 times on ice and centrifuge briefly before returning the tube strip to a chilled metal block resting on ice.5. Transfer the chilled tube strip into the pre-cooled thermal cycler (4°C) and press “SKIP” to initiate the Fragmentation protocol.Adaptor Ligation6. Prepare Adaptor Ligation Mix by adding the reagents in the order (Nuclease-Free Water, Ligation Buffer, DNA Ligase, Adaptor Mix).7. Remove tube strip containing Fragmentation, End-Repair & A-tailing Product from the thermal cycler.8. Add 50 µl Adaptor Ligation Mix to each tube containing 50 µl sample from the Fragmentation, End Repair and A-tailing Reaction. Pipette mix 15 times and centrifuge briefly.9. Incubate in a thermal cycler at 20 °C for 15 min.Post Ligation Cleanup – SPRIselect10. Vortex the SPRIselect Reagent until fully resuspended. Add 80 μl SPRIselect Reagent (0.8X) to each sample in the tube strip and pipette mix 15 times.11. Incubate the tube strip at room temperature for 5 min.12. Place the tube strip in a 10x™ Magnetic Separator in the High position until the solution is clear. Carefully remove and discard the supernatant.13. Add 200 µl 80% ethanol to the pellet and stand for 30 sec. 14. Carefully remove and discard the ethanol wash. Repeat this step.15. Centrifuge the tube strip briefly and return it to a 10x Magnetic Separator in the low position.16. Remove and discard any remaining ethanol and allow the samples to air dry for 2 min.17. Remove the tube strip from the 10x Magnetic Separator and add 30.5 µl Buffer EB.Pipette mix 15 times.18. Incubate the tube strip at room temperature for 2 min.19. Place the tube strip in a 10x Magnetic Separator in the Low position until the solution is clear.20. Transfer 30 µl of sample to a new tube strip.Sample Index PCR21. Prepare Sample Index PCR Mix by adding the reagents in the order (Nuclease-Free Water, Amplification Master Mix, SI-PCR Primer). Pipette mix thoroughly and centrifuge briefly.22. Add 60 µl Sample Index PCR Mix to each tube containing 30 µl purified Post Ligation sample.23. Add 10 µl of an individual Chromium i7 Sample Index to each well and record theirassignment. Pipette mix 5 times (pipette set to 90 μl) and centrifuge briefly.24. Index the library DNA in a thermal cycler with the following protocol. The protocol is: 98 °C for 45 s, 9 cycles of 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20s, 72 °C for 1 min, and 4 °C holding.25. Store the tube strip at 4°C for up to 72 h or proceed directly to Post Sample Index PCR Cleanup.26. Clean up the sample index PCR product with SPRIselect Reagent.27. Perform the quality control of the cDNA library.
Experiment attributes:
Experimental Factor: age: 70
Runs: 1 run, 38.8M spots, 5.8G bases, 1.9Gb
Run# of Spots# of BasesSizePublished


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