RIGHT COLON (mid-ascending colon).
• Collect using Jumbo forceps (endoscopy provider to determine forceps size)
• Make sure formalin jars (provided by BRPC) and cryovials are labelled prior to processing
o Split biopsies will be labeled using an alphanumerical order
Example: R1A and R1B is the same biopsy. R1A is ½ of the biopsy and R1B is the other ½.
This is referred to as a paired sample. The second paired biopsy will be labeled as R2A and
• Place four of the biopsies in a petri dish for washing in PBS (see below for processing
o choose the 2 larger biopsies to split (butterflied)
• The fifth biopsy is for Dr. Roper’s lab (see below for processing)
Two Biopsies for splitting
• Transfer the two largest biopsies into another petri dish for splitting:
o One CRC will hold each biopsy stable with forceps/needle
o A second CRC will cut in half with a razor blade or scalpel
• ½ of each paired biopsy sample (R1A and R2A) will go into 10% buffered formalin for FFPE (each right colon biopsy will go into separate formalin jars)
o Label each jar with the GI repository subject ID and accordingly as R1A or R2A
o Place both R1A and R2A in biohazard lab bag
o Copy the transport form and place it in the bag
o Place the GI repository sticker (A1) on the transport form
o Deliver to BRPC for processing
• ½ of each paired biopsy sample (R1B and R2B) will go into Liquid nitrogen for single nuclear ATAC seq. (each right colon biopsy will go into separate cryovials)
o Prior to collection: Label each jar with the GI repository subject ID and accordingly as R1B or
o Cryovials will be dropped into a dewar of liquid nitrogen
o Copy transport form and deliver with samples
o Place the GI repository sticker (C1) on the transport form
o Deliver dewar/samples to BRPC
• Clean instruments under running water per BRPC/pathology standard process
Two Biopsies (mid-ascending colon – proximal transverse colon if unable to obtain ascending)
• Label cryovial with GI repository subject ID # and sticker (C2)
• Collected and will also be washed in PBS with samples above
• Place the two biopsies into one cryovial filled with 1mL Bambanker Cell Freezing Medium for cryopreservation.
• Place cryovial in Mr. Frosty to slowly freeze for 24 hours
• Email CRC to pick up sample the next day or on Monday (if collected on Friday)
One Biopsy (mid-ascending right colon – proximal transverse colon if unable to obtain ascending)
• Place biopsy (not washed in PBS) into cryo media provided by Dr. Roper’s lab for colonic organoids and Dr. Roper
• Label cryovial with GI repository sticker (A2)
• Contact Ghada Mohamed 646-675-1869 for pick up
LEFT COLON (mid-descending colon).
• Collect using Jumbo forceps (endoscopy provider to determine forceps size)
• Make sure formalin jars (provided by BRPC) and cryovials are labelled prior to processing
o Split biopsies will be labeled using an alphanumerical order
Example: L1A and L1B is the same biopsy. L1A is ½ of the biopsy and L1B is the other ½. This is
referred to as a paired sample. The second paired biopsy will be labeled as L2A and L2B.
• Place four of the biopsies in a petri dish for washing in PBS (see below for processing
o Choose the 2 larger biopsies to split (butterflied)
• The fifth biopsy is for Dr. Roper’s lab (see below for processing)
Two Biopsies for splitting
• Transfer the two largest biopsies into another petri dish for splitting:
o One CRC will hold each biopsy stable with forceps/needle
o A second CRC will cut in half with a razor blade or scalpel
• ½ of each paired biopsy sample (L1A and L2A) will go into 10% buffered formalin for FFPE (each left colon biopsy will go into separate formalin jars)
o Label each jar with the GI repository subject ID and accordingly as L1A or L2A
o Place both L1A and L2A in biohazard lab bag
o Copy the transport form and place it in the bag
o Place the GI repository sticker (B1) on the transport form
o Deliver to BRPC for processing
• ½ of each paired biopsy sample (L1B and L2B) will go into Liquid nitrogen for single nuclear ATAC seq. (each left colon biopsy will go into separate cryovial)
o Prior to collection: Label each jar with the GI repository subject ID and accordingly as L1B or L2B
o Cryovials will be dropped into a dewar of liquid nitrogen
o Place GI repository sticker (D1) on the transport form
o Deliver dewar/samples with transport form to BRPC
• Clean instruments under running water per BRPC/pathology standard process
Two Biopsies (descending colon – sigmoid if unable to obtain descending)
• Label cryovial with GI repository subject ID # and sticker (D2)
• Collected and will also be washed in PBS with samples above
• Place the two biopsies into one cryovial filled with 1mL Bambanker Cell Freezing Medium for cryopreservation.
• Place cryovial in Mr. Frosty to slowly freeze for 24 hours
• Email CRC to pick up sample the next day or on Monday (if collected on Friday)
• Copy of transport form to be retained for these samples
One Biopsy (mid-descending left colon)
• Place biopsy (not washed in PBS) into cryo media provided by Dr. Roper’s lab for colonic organoids
• Label cryovial with GI repository sticker (A2)
• Contact Ghada Mohamed 646-675-1869 for pick up
Special Note: If unable to use JUMBO forceps, protocol will be altered as follows and NO splitting will be attempted:
Right colon: Ascending colon or proximal transverse:
• One large biopsy in formalin for spatial
• One large biopsy from adjacent tissue in cryovial and snap frozen in liquid nitrogen
• Two large biopies cryopreserved in Bambanker Cell Freezing Media
• One large biopsy for Roper lab into media for organoids
Left colon: Descending colon or sigmoid colon:
• One large biopsy in formalin for spatial
• One large biopsy from adjacent tissue in cryovial and snap frozen in liquid nitrogen
• Two large biopies cryopreserved in Bambanker Cell Freezing Media
• One large biopsy for Roper lab into media for organoids
GI REPOSITORY LABELING (ALL tubes will be labelled with GI repository ID #)
A1: Placed on the transport form given to BRPC on day of collection.
• Two formalin jars for right colon samples (2)
A2: Placed on the cryovial with Roper’s media
• One cryovial with right colon samples (2)
B1: Placed on the transport form given to BRPC on day of collection.
• Two formalin jars for left colon samples (2)
B2: Placed on the cryovial with Roper’s media
• One cryovial with right colon samples (2)
C1: Placed on the transport form given to BRPC on day of collection.
• One cryovial in liquid nitrogen for right colon samples (2)
C2: Placed on the cryovial with bambanker media
• One cryovial with right colon samples (2)
D1: Placed on the transport form given to BRPC on day of collection.
• One cryovial in liquid nitrogen for left colon samples (2)
D2: Placed on the cryovial with bambanker media
• One cryovial with left colon samples (2)
F1: Placed on the transport form given to SSCRS on day of collection
• 3 ACD and 1 purple top blood tubes
F2: Placed on the GI repository sample acquisition form per normal practice