title: EIDD1931_50uM_3_HTB7092_G13

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_G10

status: Public on Oct 25 2024

type: SRA

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

country: USA

institute: University of Louisville

description: TC-83 nsP2-4

library_source: genomic

data_processing:
Basecalling was done using Nanopore Guppy (ver. 5.1.12)
Sequencing reads were checked for read quality and de-multiplexed using 9 nt-long barcode sequence plus adjacent 10 nt primer sequence
Reads were aligned to Venezuelan equine encephalitis virus genome L01443.1 using Minimap2 (version 2.17-r941)
VCF for each sample was generated by SAMtools mpileup function using mapped BAM file.
Assembly: L01443.1
Supplementary files format and content: vcf format

molecule: genomic DNA

organism: Venezuelan equine encephalitis virus (strain TC-83)

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.

tag: cell line

tag: treatment


title: EIDD1931_50uM_3_HTB7092_C6

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_C16

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_O11

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_P2

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_C17

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_J8

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_B9

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_O9

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_O8

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_O21

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_L7

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_L9

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_O3

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_K23

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_L21

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_L3

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_I2

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_I6

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_J6

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_H3

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_F23

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_I22

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_I14

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_P22

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_H17

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_F21

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_F14

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_N14

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_A23

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_P3

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_O13

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_L15

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_P9

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_L20

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7091_K17

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_K8

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_G22

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_G18

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_G20

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_F4

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_H5

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_L13

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_F15

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_B2

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_A16

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_D9

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_E8

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_A10

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_C16

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_D18

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_O4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_P21

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_O10

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_I3

description: TC-83 nsP2-4


title: EIDD1931_50uM_3_HTB7092_G4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_H3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_O3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_J22

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_G7

description: TC-83 nsP2-4


title: 4-cell embryo, control sperm fertilized, rep 11

city: Philadelphia

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Small RNA: Adaptor sequences were trimmed using trimmomatic and sequenced reads were mapped to small RNAs using Bowtie 2 and totaled using Feature counts. Mapped reads were normalized to parts per million for subsequent analysis. mRNA: Reads were mapped using RSEM and normalized to transcripts per million (tpm).
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) with each sheet (tab) containing processed data for each cell type i.e. sperm and embryo

molecule: polyA RNA

organism: Mus musculus

source_name: preimplantation embryo

extract_protocol:
RNA was isolated using RNA-Clean XP beads
Illumina Nextera XT Kit
Sperm pellets were resuspended in lysis buffer supplemented with 33 mM DTT and 0.66 mg/mL Proteinase K and incubated at 60°C for 15 min. After incubation, an equal volume of water and TRIzol was added to each sample. The samples were transferred to phase lock tubes for phase separation and precipitation. Small RNA was purified using denaturing polyacrylamide gel electrophoresis. Single embryos were collected into 1 x TCL buffer with 1% beta-mercaptoethanol and stored at -80°C prior to sequencing. At time of sequencing embryos were further lysed in fresh lysis buffer and RNA was captured using RNA Clean XP beads.
For sperm samples - Illumina Tru-seq Small RNA Library Preparation Kit and single embryo samples - Nextera XT kit (Illumina)

treatment_protocol: Adult (8-12 wk old) male mice were randomly assigned to control sham or heat exposure group. Experimental animals were exposed to increased ambient temperature in an animal intensive care unit for 7 days, using a cycle of 35°C for 8 h and 25°C for 16 h. Sham control animals were housed in identical conditions in the intensive care unit set ata constant temperature of 21°C. Mice were sacrificed on the morning of Day 8 for collection of tissues.

tag: tissue

value: preimplantation embryo

tag: developmental stage

value: control-sperm fertilized embryo


title: 4-cell embryo, control sperm fertilized, rep 14


title: EIDD1931_50uM_1_HTB7082_I4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_F10

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_H12

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_D7

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_D12

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_I12

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_G6

description: TC-83 nsP2-4


title: EIDD1931_50uM_2_HTB7083_F6

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_G20

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_B7

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_B4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_B20

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_C14

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_B10

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7082_G14

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_K3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_K4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_L14

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_K14

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_L13

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_J4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_J17

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_I10

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_H3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_H4

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_F6

description: TC-83 nsP2-4


title: ML336_EIDD1931_0uM_1_HTB7380_A13

description: TC-83 nsP2-4

value: 1uM ML336 + DMSO


title: EIDD1931_50uM_1_HTB7081_G6

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_H6

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_F7

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_A21

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_A10

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_M13

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6009_D3

description: TC-83 nsP2-4

value: 1uM EIDD-1931


title: EIDD1931_1uM_HTB6008_P5

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6009_A10

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6008_O8

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6009_F3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6008_L3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_J9

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_I12

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6008_E14

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6008_H11

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_P20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_P19

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_O17

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_O16

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_O14

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_N20

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_F3

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_C7

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_P3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_L16

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_J4

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_J3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_M21

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_G17

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_H8

description: TC-83 nsP2-4


title: EIDD1931_50uM_1_HTB7081_E13

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_M20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_G14

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_F3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_F19

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_L7

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_G22

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_F13

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_E20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_E10

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_B23

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_B12

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_A7

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_P5

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_P7

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_A5

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_O23

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_O15

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_O1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_N1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_N20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_N8

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_L3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_M1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_M12

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_J19

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_K9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6007_C17

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_K11

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_L1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_I17

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_G9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_H15

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_K16

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_I23

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_H5

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_F11

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_E20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_P20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_D23

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_B9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_A15

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_C10

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_P9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_P14

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_J6

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_K1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_F3

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_N21

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_L2

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_J1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_J12

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_I1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_G20

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_H12

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_I21

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_E18

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_H17

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_H1

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6006_C23

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_H9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_E5

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_F16

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_E16

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_E6

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_D8

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_O4

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_B4

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_E13

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_B21

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_A18

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_N8

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_O19

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_H10

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_M13

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_N21

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_N7

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_M23

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_M4

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_L19

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_L23

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_K9

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_D12

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_J13

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_C17

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_I4

description: TC-83 nsP2-4


title: EIDD1931_1uM_HTB6005_C14

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_H7

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_D9

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_I14

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_D14

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_F4

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_C8

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_E20

description: TC-83 nsP2-4


title: EIDD1931_10uM_HTB6017_O2

description: TC-83 nsP2-4


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title: EIDD1931_1uM-3_HTB6093_H12

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_G7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_D23

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_G1

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_A7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_E7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_E11

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_A16

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_O2

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_O7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_N8

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_K11

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_J7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_I7

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_J18

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_I21

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_I10

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6093_L10

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_G9

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_G23

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_F1

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_F5

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_C6

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_H18

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_E22

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_E1

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_B11

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_A9

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_P19

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_C21

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_P23

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_A14

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_P13

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_O3

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_N15

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_L13

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_I8

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_H21

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_K5

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_H6

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_D9

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_I20

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_F14

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_E8

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_D15

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_D6

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_C1

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_A17

description: TC-83 nsP2-4


title: EIDD1931_1uM-3_HTB6090_A21

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_C15

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_D1

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_A4

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_C2

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_A11

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_A19

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_K2

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_K18

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_I3

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_K17

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_I13

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_H5

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_K16

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_F5

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_E5

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_D8

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_C21

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_C5

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6094_A16

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_B23

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_B1

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_C2

description: TC-83 nsP2-4


title: DMSO_HTB7093_B1

description: TC-83 nsP2-4

value: DMSO


title: EIDD1931_1uM-1_HTB6088_J10

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_A4

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_A18

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_A2

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_A1

description: TC-83 nsP2-4


title: DMSO_HTB7093_D1

description: TC-83 nsP2-4


title: DMSO_HTB7091_F1

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_I2

description: TC-83 nsP2-4


title: DMSO_HTB7093_C1

description: TC-83 nsP2-4


title: DMSO_HTB7092_G1

description: TC-83 nsP2-4


title: DMSO_HTB7093_A1

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_F14

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_F13

description: TC-83 nsP2-4


title: DMSO_HTB7092_H1

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_E20

description: TC-83 nsP2-4


title: DMSO_HTB7092_E1

description: TC-83 nsP2-4


title: DMSO_HTB7092_F1

description: TC-83 nsP2-4


title: DMSO_HTB7081_D1

description: TC-83 nsP2-4


title: DMSO_HTB7081_C1

description: TC-83 nsP2-4


title: DMSO_HTB7081_B1

description: TC-83 nsP2-4


title: DMSO_HTB7083_H1

description: TC-83 nsP2-4


title: DMSO_HTB7081_A1

description: TC-83 nsP2-4


title: DMSO_HTB7091_E1

description: TC-83 nsP2-4


title: DMSO_HTB4860_N11

description: TC-83 nsP2-4


title: DMSO_HTB7083_G1

description: TC-83 nsP2-4


title: DMSO_HTB4860_N3

description: TC-83 nsP2-4


title: DMSO_HTB4860_M14

description: TC-83 nsP2-4


title: DMSO_HTB4860_I21

description: TC-83 nsP2-4


title: DMSO_HTB4860_H3

description: TC-83 nsP2-4


title: DMSO_HTB4860_H17

description: TC-83 nsP2-4


title: DMSO_HTB4860_I24

description: TC-83 nsP2-4


title: EIDD1931_1uM-1_HTB6088_A8

description: TC-83 nsP2-4


title: DMSO_HTB4860_G5

description: TC-83 nsP2-4


title: DMSO_HTB4860_G8

description: TC-83 nsP2-4


title: DMSO_HTB4860_C9

description: TC-83 nsP2-4


title: DMSO_HTB4860_D5

description: TC-83 nsP2-4


title: DMSO_HTB4860_F9

description: TC-83 nsP2-4


title: DMSO_HTB4860_E3

description: TC-83 nsP2-4


title: DMSO_HTB4860_C4

description: TC-83 nsP2-4


title: DMSO_HTB4860_C23

description: TC-83 nsP2-4


title: DMSO_HTB4860_B17

description: TC-83 nsP2-4


title: DMSO_HTB4860_A4

description: TC-83 nsP2-4


title: DMSO_HTB4860_E5

description: TC-83 nsP2-4


title: DMSO_HTB4859_O18

description: TC-83 nsP2-4


title: DMSO_HTB4860_A7

description: TC-83 nsP2-4


title: DMSO_HTB4859_P2

description: TC-83 nsP2-4


title: DMSO_HTB4859_O20

description: TC-83 nsP2-4


title: DMSO_HTB4859_K6

description: TC-83 nsP2-4


title: DMSO_HTB4860_K3

description: TC-83 nsP2-4


title: DMSO_HTB4859_J22

description: TC-83 nsP2-4


title: DMSO_HTB4859_K21

description: TC-83 nsP2-4


title: DMSO_HTB4859_K11

description: TC-83 nsP2-4


title: DMSO_HTB4859_I1

description: TC-83 nsP2-4


title: DMSO_HTB4859_I22

description: TC-83 nsP2-4


title: DMSO_HTB4859_I12

description: TC-83 nsP2-4


title: DMSO_HTB4859_H11

description: TC-83 nsP2-4


title: DMSO_HTB4859_G10

description: TC-83 nsP2-4


title: DMSO_HTB4859_H13

description: TC-83 nsP2-4


title: DMSO_HTB4859_H1

description: TC-83 nsP2-4


title: DMSO_HTB4859_G7

description: TC-83 nsP2-4


title: DMSO_HTB4859_G1

description: TC-83 nsP2-4


title: DMSO_HTB4859_F4

description: TC-83 nsP2-4


title: DMSO_HTB4859_F3

description: TC-83 nsP2-4


title: DMSO_HTB4859_F10

description: TC-83 nsP2-4


title: DMSO_HTB4859_E1

description: TC-83 nsP2-4


title: DMSO_HTB4859_D23

description: TC-83 nsP2-4


title: DMSO_HTB4859_F1

description: TC-83 nsP2-4


title: DMSO_HTB4859_C17

description: TC-83 nsP2-4


title: DMSO_HTB4859_D1

description: TC-83 nsP2-4


title: DMSO_HTB4859_C1

description: TC-83 nsP2-4


title: DMSO_HTB4859_B21

description: TC-83 nsP2-4


title: DMSO_HTB4859_B2

description: TC-83 nsP2-4


title: DMSO_HTB4859_B1

description: TC-83 nsP2-4


title: DMSO_HTB4859_A9

description: TC-83 nsP2-4


title: DMSO_HTB4859_A6

description: TC-83 nsP2-4


title: DMSO_HTB4859_A21

description: TC-83 nsP2-4


title: DMSO_HTB4858_P8

description: TC-83 nsP2-4


title: DMSO_HTB4858_P4

description: TC-83 nsP2-4


title: DMSO_HTB4858_P17

description: TC-83 nsP2-4


title: DMSO_HTB4858_M5

description: TC-83 nsP2-4


title: DMSO_HTB4858_O19

description: TC-83 nsP2-4


title: DMSO_HTB4859_G19

description: TC-83 nsP2-4


title: DMSO_HTB4858_K19

description: TC-83 nsP2-4


title: DMSO_HTB4858_F7

description: TC-83 nsP2-4


title: DMSO_HTB4858_J15

description: TC-83 nsP2-4


title: DMSO_HTB4858_M13

description: TC-83 nsP2-4


title: DMSO_HTB4859_D3

description: TC-83 nsP2-4


title: DMSO_HTB4858_D4

description: TC-83 nsP2-4


title: DMSO_HTB4859_E22

description: TC-83 nsP2-4


title: DMSO_HTB4858_E23

description: TC-83 nsP2-4


title: DMSO_HTB4858_C23

description: TC-83 nsP2-4


title: DMSO_HTB4858_C22

description: TC-83 nsP2-4


title: DMSO_HTB4858_C2

description: TC-83 nsP2-4


title: DMSO_HTB4858_A5

description: TC-83 nsP2-4


title: DMSO_HTB4858_A23

description: TC-83 nsP2-4


title: DMSO_HTB4857_P8

description: TC-83 nsP2-4


title: DMSO_HTB4858_B8

description: TC-83 nsP2-4


title: DMSO_HTB4857_P22

description: TC-83 nsP2-4


title: DMSO_HTB4857_P19

description: TC-83 nsP2-4


title: DMSO_HTB4858_P10

description: TC-83 nsP2-4


title: K36M,EZH2,rep2

city: Boulder

first: Alison

middle: Rae Swearingen

last: Pashos

state: CO

address: 1945 Colorado Avenue

department: MCDB

institute: University of Colorado Boulder

data_processing:
All samples were normalized to background using CPM.
CUT&Tag reads were mapped to the mouse mm10 genome using Bowtie version 2.2.9.
DeepTools v3.0.1 was used with normalization as above to create bigWig files.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: intestinal organoid

growth_protocol: WTH3 and H3K36M organoid samples were grown in ENR with 2 ug/mL doxycycline added for at least 4 weeks before harvest.

extract_protocol:
Organoids were harvested using EDTA to remove matrigel and TrypLE to digest to single cell, at which pointcells were frozen following Heinekoff et al. "Benchtop CUT&Tag".
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: intestinal organoid

tag: genotype


title: K36M,SETD2,rep2


title: K36M,NSD2,rep2


title: DMSO_HTB4857_O14

description: TC-83 nsP2-4


title: K36M,SETD2,rep1


title: DMSO_HTB4858_M17

description: TC-83 nsP2-4


title: K36M,EZH2,rep1


title: DMSO_HTB4857_N19

description: TC-83 nsP2-4


title: WT,SETD2,rep2

value: WT H3


title: DMSO_HTB4857_K4

description: TC-83 nsP2-4


title: DMSO_HTB4857_J17

description: TC-83 nsP2-4


title: WT,NSD2,rep2


title: WT,EZH2,rep2


title: DMSO_HTB4857_K18

description: TC-83 nsP2-4


title: WT,SETD2,rep1


title: DMSO_HTB4857_I16

description: TC-83 nsP2-4


title: WT,NSD2,rep1


title: DMSO_HTB4858_B3

description: TC-83 nsP2-4


title: DMSO_HTB4857_I10

description: TC-83 nsP2-4


title: DMSO_HTB4857_H1

description: TC-83 nsP2-4


title: DMSO_HTB4857_G7

description: TC-83 nsP2-4


title: WT,EZH2,rep1


title: DMSO_HTB4857_I1

description: TC-83 nsP2-4


title: m5d, H3K36me2, rep2

source_name: intestinal epithelium

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Nuclei were isolated from cells following Heinekoff et al. "Benchtop CUT&Tag".
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

treatment_protocol: Mice were irradiated with 12 Gy at day 0 and harvested at 3 and 5 days post-IR.

value: intestinal epithelium

value: WT

value: 5d after irradiation


title: m5d, H3K36me3, rep2


title: K36M,NSD2,rep1


title: DMSO_HTB4857_G14

description: TC-83 nsP2-4


title: DMSO_HTB4857_L2

description: TC-83 nsP2-4


title: DMSO_HTB4857_F1

description: TC-83 nsP2-4


title: m5d, H3K36me2, rep1


title: m3d, H3K36me3, rep2

value: 3d after irradiation


title: m5d, H3K27me3, rep1


title: m5d, H3K27me3, rep2


title: DMSO_HTB4857_E14

description: TC-83 nsP2-4


title: m5d, H3K36me3, rep1


title: DMSO_HTB4857_E1

description: TC-83 nsP2-4


title: DMSO_HTB4857_E24

description: TC-83 nsP2-4


title: m3d, H3K36me2, rep2


title: m3d, H3K36me2, rep1


title: DMSO_HTB4857_D1

description: TC-83 nsP2-4


title: DMSO_HTB4857_C11

description: TC-83 nsP2-4


title: m3d, H3K27me3, rep1


title: DMSO_HTB4857_D17

description: TC-83 nsP2-4


title: m3d, H3K27me3, rep2


title: m3d, H3K36me3, rep1


title: DMSO_HTB4857_C1

description: TC-83 nsP2-4


title: mCtrl, H3K36me3, rep2

value: 0d after irradiation


title: mCtrl, H3K36me2, rep2


title: DMSO_HTB4857_B1

description: TC-83 nsP2-4


title: DMSO_HTB4857_A12

description: TC-83 nsP2-4


title: DMSO_HTB4857_G1

description: TC-83 nsP2-4


title: DMSO_HTB4857_B3

description: TC-83 nsP2-4


title: DMSO_HTB4857_A3

description: TC-83 nsP2-4


title: mCtrl, H3K27me3, rep2


title: mCtrl, H3K36me2, rep1


title: mCtrl, H3K36me3, rep1


title: mCtrl, H3K27me3, rep1


title: DMSO_HTB4856_O4

description: TC-83 nsP2-4


title: DMSO_HTB4856_P22

description: TC-83 nsP2-4


title: m5d,rep1

data_processing:
Sequenced reads were analyzed using nf-core/rnaseq pipeline (v3.8.1).
Raw counts are the output of Salmon from the nf-core/rnaseq pipeline.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: intestine epithelium

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Cells were flash frozen and RNA was isolated using  Direct-zol RNA miniprep kit (Zymo).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: intestine epithelium


title: DMSO_HTB4856_N7

description: TC-83 nsP2-4


title: DMSO_HTB4856_O18

description: TC-83 nsP2-4


title: m3d,rep2


title: DMSO_HTB4856_N22

description: TC-83 nsP2-4


title: m3d,rep1


title: DMSO_HTB4856_N13

description: TC-83 nsP2-4


title: mCtrl,rep2


title: DMSO_HTB4856_K5

description: TC-83 nsP2-4


title: DMSO_HTB4856_M15

description: TC-83 nsP2-4


title: Western diet alcohol, replicate 3, scRNAseq

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

library_source: transcriptomic single cell

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-6.0.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (refdata-gex-mm10-2020-A) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file.

molecule: total RNA

source_name: liver

extract_protocol:
Mouse livers were dissociated by perfusion and collagenase digestion and total non-parenchymal cells were isolated by differential centrifugation. Non parenchymal cells were further purified by FACS and live CD45 positive cells were used for the single cell RNAseq protocol.
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

treatment_protocol: 8 week old mice were fed either normal chow diet, western diet, or western diet with alcohol for 16 weeks.

tag: strain

value: liver

tag: Sex

value: male

tag: cell type

value: Nonparenchymal cells

value: wild-type

value: Western diet alcohol


title: DMSO_HTB4856_I1

description: TC-83 nsP2-4


title: DMSO_HTB4856_I3

description: TC-83 nsP2-4


title: Western diet alcohol, replicate 2, scRNAseq


title: Western diet alcohol, replicate 1, scRNAseq


title: DMSO_HTB4856_H3

description: TC-83 nsP2-4


title: Western diet, replicate 2, scRNAseq

value: Western diet


title: DMSO_HTB4856_H4

description: TC-83 nsP2-4


title: Western diet, replicate 3, scRNAseq


title: Western diet, replicate 1, scRNAseq


title: m5d,rep2


title: DMSO_HTB4856_H1

description: TC-83 nsP2-4


title: DMSO_HTB4856_G16

description: TC-83 nsP2-4


title: Western diet alcohol, replicate 4, scRNAseq


title: DMSO_HTB4856_G1

description: TC-83 nsP2-4


title: Western diet alcohol, DT injections, replicate 4, RNAseq

data_processing:
The read quality was assessed using the FastQC software.
The reads were mapped to the mouse genome (Mus musculus GRCm39; Ensembl release 105) using the STAR software.
Transcript abundance estimates were calculated using the featureCounts software.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file containing raw read counts

extract_protocol:
Mouse livers were dissociated by perfusion and collagenase digestion and total non-parenchymal cells were isolated by differential centrifugation. Non parenchymal cells were further purified by FACS and live CD45 positive cells were used for the single cell RNAseq protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole liver tissue

value: Western diet alcohol, serial DT injections


title: DMSO_HTB4856_F21

description: TC-83 nsP2-4

value: DMSO


title: DMSO_HTB4856_E1

description: TC-83 nsP2-4


title: Chow diet, replicate 2, scRNAseq

value: Chow diet


title: DMSO_HTB4856_F1

description: TC-83 nsP2-4


title: Chow diet, replicate 1, scRNAseq


title: Western diet alcohol, DT injections, replicate 2, RNAseq


title: DMSO_HTB4856_E11

description: TC-83 nsP2-4


title: mCtrl,rep1


title: DMSO_HTB4856_D16

description: TC-83 nsP2-4


title: Western diet alcohol, DT injections, replicate 3, RNAseq


title: DMSO_HTB4856_C1

description: TC-83 nsP2-4


title: Western diet alcohol, saline injections, replicate 3, RNAseq

value: Western diet alcohol, serial saline injections


title: DMSO_HTB4856_B24

description: TC-83 nsP2-4


title: DMSO_HTB4856_D1

description: TC-83 nsP2-4


title: Western diet alcohol, DT injections, replicate 1, RNAseq


title: Western diet alcohol, saline injections, replicate 1, RNAseq


title: Western diet alcohol, saline injections, replicate 2, RNAseq


title: DMSO_HTB4856_C9

description: TC-83 nsP2-4


title: Western diet alcohol, saline injections, replicate 4, RNAseq


title: DMSO_HTB4856_B1

description: TC-83 nsP2-4


title: DMSO_HTB4856_B19

description: TC-83 nsP2-4


title: Chow diet, replicate 2, RNAseq


title: DMSO_HTB4856_B18

description: TC-83 nsP2-4


title: Western diet, replicate 4, scRNAseq


title: Chow diet, replicate 3, RNAseq


title: DMSO_HTB4850_O13

description: TC-83 nsP2-4


title: DMSO_HTB4856_A22

description: TC-83 nsP2-4


title: DMSO_HTB4850_M24

description: TC-83 nsP2-4


title: Chow diet, replicate 1, RNAseq


title: DMSO_HTB4850_L23

description: TC-83 nsP2-4


title: MC38Vir3RT4, MC38, Radiation, VIR

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

data_processing:
Expression counts were quantified using salmon-v1.1.0
Normalization and differential gene expression analysis was conducted using edgeR
Assembly: GRCm38
Supplementary files format and content: comma-separated file includes normalized counts for each sample

growth_protocol: Tumors were implanted subcutaneously into the right flank as follows: C57BL/6 2x105 MC38; BALB/c 2x105 CT26.

extract_protocol:
Tumors were harvested, debulked and immediately flash frozen by rapid immersion in liquid nitrogen. Frozen tumors were crushed, treated with 500µl of RNAlater, then frozen at -80oC. To extract RNA, the samples were thawed on ice, and 500µl of buffer RLT (QIAGEN Cat. No. 79219) was added and samples were homogenized. Following centrifugation, RNA was isolated using a QIAGEN RNeasy Plus Mini Kit (Cat No. 74134), according to the manufacturer’s instructions. Quality was checked on nanodrop (ND-1000) and the quantity of RNA was determined on Qubit 4 flourometer.
To prepare for sequencing, samples were processed using an illumina TruSeq® Stranded mRNA Library Prep kit with with Illumina TruSeq RNA Single Indexes Set A and Set B barcoding kits.
An Illumina NovaSeq 6000 S1 Reagent Kit v1.5 was used to make RNA libraries along with a NovaSeq XP 2-Lane Kit v1.5. RNA libraries were sequenced on NovaSeq 6000.

treatment_protocol: When tumors were approximately 5mm in average diameter at approximately 10-14 days following implantation, mice were randomized to receive treatment with 12Gy radiation to an isocenter within the tumor. The Enpp1 inhibitor VIR3 was delivered through daily oral gavage at 200mg/kg starting 1 day prior to RT until tumor harvest for analysis .

value: Radiation+VIR


title: DMSO_HTB4850_N11

description: TC-83 nsP2-4


title: MC38Vir3RT5, MC38, Radiation, VIR


title: MC38Vir35, MC38, VIR

value: VIR


title: DMSO_HTB4850_L13

description: TC-83 nsP2-4


title: MC38Vir34, MC38, VIR


title: DMSO_HTB4850_J22

description: TC-83 nsP2-4


title: MC38Vir33, MC38, VIR


title: DMSO_HTB4850_J4

description: TC-83 nsP2-4


title: DMSO_HTB4850_H22

description: TC-83 nsP2-4


title: DMSO_HTB4850_K7

description: TC-83 nsP2-4


title: MC38RT5, MC38, Radiation

value: Radiation


title: DMSO_HTB4850_E9

description: TC-83 nsP2-4


title: DMSO_HTB4850_P23

description: TC-83 nsP2-4


title: DMSO_HTB4850_D8

description: TC-83 nsP2-4


title: MC38RT4, MC38, Radiation


title: MC38Vir3RT3, MC38, Radiation, VIR


title: DMSO_HTB4850_D14

description: TC-83 nsP2-4


title: DMSO_HTB4850_D2

description: TC-83 nsP2-4


title: MC38Vir31, MC38, VIR


title: MC38RT1, MC38, Radiation


title: MC38Vir3RT2, MC38, Radiation, VIR


title: DMSO_HTB4850_C22

description: TC-83 nsP2-4


title: MC38RT2, MC38, Radiation


title: MC38Vir3RT1, MC38, Radiation, VIR


title: MC38NT4, MC38, No Treatment

value: No Treatment


title: DMSO_HTB4850_C16

description: TC-83 nsP2-4


title: MC38RT3, MC38, Radiation


title: MC38NT3, MC38, No Treatment


title: MC38NT2, MC38, No Treatment


title: DMSO_HTB4850_B24

description: TC-83 nsP2-4


title: MC38NT1, MC38, No Treatment


title: MC38Vir32, MC38, VIR


title: DMSO_HTB4850_A21

description: TC-83 nsP2-4


title: CT26Vir34, CT26, VIR

value: BALB/c


title: DMSO_HTB4850_A17

description: TC-83 nsP2-4


title: DMSO_HTB4847_O13

description: TC-83 nsP2-4


title: CT26Vir32, CT26, VIR


title: DMSO_HTB4847_O10

description: TC-83 nsP2-4


title: CT26Vir31, CT26, VIR


title: CT26Vir33, CT26, VIR


title: DMSO_HTB4847_L2

description: TC-83 nsP2-4


title: CT26RTVir5, CT26, Radiation, VIR


title: DMSO_HTB4847_L5

description: TC-83 nsP2-4


title: CT26RTVir4, CT26, Radiation, VIR


title: DMSO_HTB4850_C19

description: TC-83 nsP2-4


title: DMSO_HTB4847_K3

description: TC-83 nsP2-4


title: DMSO_HTB4847_M13

description: TC-83 nsP2-4


title: CT26RTVir3, CT26, Radiation, VIR


title: DMSO_HTB4847_K7

description: TC-83 nsP2-4


title: DMSO_HTB4847_J12

description: TC-83 nsP2-4


title: CT26RTVir2, CT26, Radiation, VIR


title: CT26RT4, CT26, Radiation


title: DMSO_HTB4847_K10

description: TC-83 nsP2-4


title: CT26RTVir1, CT26, Radiation, VIR


title: DMSO_HTB4847_I1

description: TC-83 nsP2-4


title: CT26RT2, CT26, Radiation


title: DMSO_HTB4847_H6

description: TC-83 nsP2-4


title: DMSO_HTB4847_J11

description: TC-83 nsP2-4


title: CT26RT3, CT26, Radiation


title: CT26NT5, CT26, No Treatment


title: DMSO_HTB4847_H1

description: TC-83 nsP2-4


title: DMSO_HTB4847_G5

description: TC-83 nsP2-4


title: CT26NT3, CT26, No Treatment


title: CT26NT4, CT26, No Treatment


title: CT26NT2, CT26, No Treatment


title: DMSO_HTB4847_F1

description: TC-83 nsP2-4


title: CT26NT1, CT26, No Treatment


title: DMSO_HTB4847_E1

description: TC-83 nsP2-4


title: DMSO_HTB4847_E7

description: TC-83 nsP2-4


title: DMSO_HTB4847_E9

description: TC-83 nsP2-4


title: Draining (popliteal) lymph nodes WT 2

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.14 package DESeq2 1.34.0, running under R 4.1.3.
Assembly: UCSC mm10 based on GRCm38
Supplementary files format and content: rnaseq_deseq_global_counts_raw.tsv.gz: Per gene and sample raw (integer) counts in tab-separated value (TSV) format
Supplementary files format and content: rnaseq_deseq_global_fpkms.tsv.gz: Per gene and sample DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Draining (popliteal) lymph nodes

extract_protocol:
Draining (popliteal) lymph nodes were isolated and single cell suspensions were prepared. Total RNA was prepared from cell lysates using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen) according to manufacturer’s protocol.
RNA-seq libraries were prepared with the NEBNext Ultra II dirctional RNA preparation kit (New England Bioloabs). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Bioanalyzer Automated Electrophoresis System (Agilent). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using a 50 bp single-read protocol.

treatment_protocol: 6 × 10^5 naïve 2D2-HDAC-On or 2D2-HDAC1-Off CD4+ T cells (CD45.2+) were transferred (i.v.) into CD45.1+ recipient mice. 18 h after cell transfer recipient mice were immunized into the right hind paw with 50 μl of a 1:1 emulsion of 1 mg/ml MOG35-55 peptide (M4939, Sigma Aldrich) in distilled water and complete Freund's adjuvant (incomplete Freund's adjuvant (Sigma) supplemented with 10 mg/ml heat-killed Mycobacterium tuberculosis (strain H37Ra; Difco)).

value: Draining (popliteal) lymph nodes

value: peripheral T cells

value: HDAC1 fl CD4cre-


title: Draining (popliteal) lymph nodes WT 3


title: Gob, rep1

source_name: proximal intestine epithelium

extract_protocol:
Proximal mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Filtered cells were sorted on Sony MA900 and XDP100 machines for cells positive for reporters/antibodies. Sorted cells were flash frozen and RNA was isolated using  miRNeasy Micro kit (Qiagen).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: proximal intestine epithelium


title: DMSO_HTB4847_D10

description: TC-83 nsP2-4


title: DMSO_HTB4847_D23

description: TC-83 nsP2-4


title: EE, rep2


title: DMSO_HTB4847_D1

description: TC-83 nsP2-4


title: CT26RT1, CT26, Radiation


title: DMSO_HTB4847_C1

description: TC-83 nsP2-4


title: Draining (popliteal) lymph nodes catalytically inactive 3

value: HDAC1 fl HDAC1-CI tg/+ CD4cre+


title: EE, rep1


title: Draining (popliteal) lymph nodes WT 1


title: DMSO_HTB4847_C24

description: TC-83 nsP2-4


title: DMSO_HTB4847_B6

description: TC-83 nsP2-4


title: DMSO_HTB4847_B2

description: TC-83 nsP2-4


title: Tuft, rep2


title: Draining (popliteal) lymph nodes catalytically inactive 2


title: Tuft, rep1


title: Pan, rep2

value: Defa4-Cre; tdTom


title: Gob, rep2


title: DMSO_HTB4847_B4

description: TC-83 nsP2-4


title: DMSO_HTB4646_P2

description: TC-83 nsP2-4


title: DMSO_HTB4646_O2

description: TC-83 nsP2-4


title: lgr5, rep2


title: DMSO_HTB4847_B1

description: TC-83 nsP2-4


title: lgr5, rep1


title: DMSO_HTB4646_N15

description: TC-83 nsP2-4


title: DMSO_HTB4646_N2

description: TC-83 nsP2-4


title: DMSO_HTB4646_N3

description: TC-83 nsP2-4


title: DMSO_HTB4646_M3

description: TC-83 nsP2-4


title: Ent, rep2

value: WT


title: DMSO_HTB4646_N14

description: TC-83 nsP2-4


title: DMSO_HTB4646_M14

description: TC-83 nsP2-4


title: DMSO_HTB4646_M2

description: TC-83 nsP2-4


title: Draining (popliteal) lymph nodes catalytically inactive 1


title: e8547-1

type: genomic

city: Memphis

first: Heather

last: Mefford

state: FL

address: 262 Danny Thomas Pl

department: Center for Pediatric Neurological Disease Research

institute: St. Jude Children's Research Hospital

description: DNA methylation array from individual with individuals with pathogenic SCN1A variants

hyb_protocol: Whole genome amplification (*Assay kit with arrays and reagents: Illumina Catalog #WG-317-1001) is performed on the bisulfite converted (and restored, if FFPE) DNA and the amplified material is then end point fragmented and precipitated. The pellets are resuspended and hybridized to the Methylation EPIC 850K array for approximately 20 hours.

scan_protocol: Red and green lasers are used for the excitation of the labeled nucleotides on the arrays and a CCD camera takes images of the sample sections. DMAP files, which must be downloaded for each lot of beadchips purchased from Illumina, are then used to pinpoint the location of each beadchip probe type on the array and extract and register the signal intensities. A variety of files are generated for each array (red and green.idats, .sdf, metrics, qc, and .jpegs). The .sdf, red and green.idats, a .csv (specifying sample and project information and hybridization locations), and the correct 850K EPIC manifest (.bpm) are used to create a project in GenomeStudio 2011.1 (free software).

data_processing: All data were combined and loaded into the R package "minfi" for quality control and normalization (using the preprocessIllumina function). Individual CpG probes that failed (detection p>0.01) in >10% of samples; also, probes overlapping with common SNPs and those previously reported as cross-reactive were removed.

label: Cy3 and Cy5

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Cytosines are converted to Uracils (with the exception of methylated Cytosines) during a three-step sodium bisulfite treatment and column desulphonation (Zymo Research Catalog #D5004).

extract_protocol: DNA were extracted from peripheral-blood DNA samples using standard protocols, includuing the DNeasy Blood and Tissue Kit, the QIAamp DNA Blood Maxi Kit, and the Macherey-Nagel NucleoSpin Blood XL.

value: peripheral blood


title: e8546-1


title: 09A3293


title: T25471


title: DMSO_HTB4646_P7

description: TC-83 nsP2-4


title: DMSO_HTB4646_L8

description: TC-83 nsP2-4


title: DMSO_HTB4646_P3

description: TC-83 nsP2-4


title: DMSO_HTB4646_O3

description: TC-83 nsP2-4


title: T25634


title: Pan, rep1


title: 21A2044


title: DMSO_HTB4646_L3

description: TC-83 nsP2-4


title: Gob, H3K27me3,  rep2

data_processing:
All samples were normalized to background using CPM. All samples were normalized to background signal across the genome.
CUT&Tag reads were mapped to the mouse mm10 genome using Bowtie version 2.2.9.
DeepTools v3.0.1 was used with normalization as above to create bigWig files.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: proximal intestinal epithelium

extract_protocol:
Proximal mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Filtered cells were sorted on Sony MA900 and XDP100 machines for cells positive for reporters/antibodies. Nuclei were isolated following Heinekoff et al. "Benchtop CUT&Tag".
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: proximal intestinal epithelium


title: DMSO_HTB4646_L2

description: TC-83 nsP2-4

value: DMSO


title: 34288


title: Ent, rep1


title: DMSO_HTB4646_K8

description: TC-83 nsP2-4


title: 32935


title: Gob, H3K27me3,  rep1


title: DMSO_HTB4646_K3

description: TC-83 nsP2-4


title: 32923


title: DMSO_HTB4646_K5

description: TC-83 nsP2-4


title: EE, H3K27me3,  rep2


title: EE, H3K27me3,  rep1


title: DMSO_HTB4646_I3

description: TC-83 nsP2-4


title: DMSO_HTB4646_J3

description: TC-83 nsP2-4


title: DMSO_HTB4646_I2

description: TC-83 nsP2-4


title: DMSO_HTB4646_I24

description: TC-83 nsP2-4


title: 32544


title: T25786


title: T25743


title: tuft, H3K27me3,  rep1


title: DMSO_HTB4646_I17

description: TC-83 nsP2-4


title: Pan, H3K27me3,  rep2


title: DMSO_HTB4646_H3

description: TC-83 nsP2-4


title: tuft, H3K27me3,  rep2


title: T24625


title: DMSO_HTB4646_H15

description: TC-83 nsP2-4


title: DMSO_HTB4847_G1

description: TC-83 nsP2-4


title: Pan, H3K27me3,  rep1


title: DMSO_HTB4646_K2

description: TC-83 nsP2-4


title: DMSO_HTB4646_G3

description: TC-83 nsP2-4


title: T23783


title: DMSO_HTB4646_J2

description: TC-83 nsP2-4


title: DMSO_HTB4646_H2

description: TC-83 nsP2-4


title: DMSO_HTB4646_G23

description: TC-83 nsP2-4


title: T23245


title: LGR5, H3K27me3,  rep2


title: T23023


title: DMSO_HTB4646_G2

description: TC-83 nsP2-4


title: DMSO_HTB4646_F3

description: TC-83 nsP2-4


title: DMSO_HTB4646_G11

description: TC-83 nsP2-4


title: DMSO_HTB4646_G18

description: TC-83 nsP2-4


title: LGR5, H3K27me3,  rep1


title: DMSO_HTB4646_F14

description: TC-83 nsP2-4


title: Ent, H3K27me3,  rep2


title: DMSO_HTB4646_F11

description: TC-83 nsP2-4


title: Ent, H3K27me3,  rep1


title: T21674


title: DMSO_HTB4646_F2

description: TC-83 nsP2-4


title: T19196


title: DMSO_HTB4646_E3

description: TC-83 nsP2-4


title: Gob, H3K36me3,  rep2


title: T20704


title: DMSO_HTB4646_D2

description: TC-83 nsP2-4


title: T17775


title: DMSO_HTB4646_C3

description: TC-83 nsP2-4


title: DMSO_HTB4646_C2

description: TC-83 nsP2-4


title: Gob, H3K36me3,  rep1


title: DMSO_HTB4646_D3

description: TC-83 nsP2-4


title: DMSO_HTB4646_C11

description: TC-83 nsP2-4


title: DMSO_HTB4646_B3

description: TC-83 nsP2-4


title: EE, H3K36me3,  rep1


title: EE, H3K36me3,  rep2


title: DMSO_HTB4646_B2

description: TC-83 nsP2-4


title: DMSO_HTB4646_A3

description: TC-83 nsP2-4


title: Tuft, H3K36me3,  rep1


title: Tuft, H3K36me3,  rep2


title: T1588


title: DMSO_HTB4646_A2

description: TC-83 nsP2-4


title: DMSO_HTB4645_P2

description: TC-83 nsP2-4


title: DMSO_HTB4645_P3

description: TC-83 nsP2-4


title: T3611


title: DMSO_HTB4646_E2

description: TC-83 nsP2-4


title: DMSO_HTB4645_O8

description: TC-83 nsP2-4


title: Pan, H3K36me3,  rep2


title: T3595


title: Pan, H3K36me3,  rep1


title: DMSO_HTB4645_O3

description: TC-83 nsP2-4


title: 8707


title: T3147


title: DMSO_HTB4645_O2

description: TC-83 nsP2-4


title: DMSO_HTB4645_N3

description: TC-83 nsP2-4


title: T3028


title: DMSO_HTB4645_N2

description: TC-83 nsP2-4


title: LGR5, H3K36me3,  rep1


title: T3835


title: T2614


title: DMSO_HTB4645_N16

description: TC-83 nsP2-4


title: DMSO_HTB4645_M6

description: TC-83 nsP2-4


title: T3027


title: DMSO_HTB4645_N15

description: TC-83 nsP2-4


title: Ent, H3K36me3,  rep2


title: Ent, H3K36me3,  rep1


title: DMSO_HTB4645_M2

description: TC-83 nsP2-4


title: DMSO_HTB4645_M3

description: TC-83 nsP2-4


title: DMSO_HTB4645_P5

description: TC-83 nsP2-4


title: DMSO_HTB4645_L3

description: TC-83 nsP2-4


title: e4846-1


title: T2657


title: Paneth cell, untreated, 1

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using CellRanger software v3.0.1.
Assembly: mm10
Supplementary files format and content: tab separated barcodes, features, and matrix file.

source_name: proximal small intestine

extract_protocol:
The proximal small intestine (10cm segment within a 2-12cm region from the gastroduodenal junction) from an adult (female 20-week old) Defa4 Cre :Rosa26 tdTomato/tdTomato mouse was removed, rinsed with ice cold PBS, opened longitudinally, and then scraped with a glass slide to remove villi prior to crypt elution using chelation buffer (PBS containing 2mM EDTA and 1mM DTT). To generate a single-cell suspension for flow cytometric analysis and sorting, isolated crypts were incubated with dispase and DNaseI, cell suspensions were filtered through a 40-μm cell strainer and then stained with rat anti-EpCAM–fluorescein isothiocyanate IgG2a antibody  and DAPI. Rat IgG2a–fluorescein isothiocyanate was used as a control. The MoFlo XDP100 cytometer with a 100-μm nozzle was used for single-cell FACS sorting EpCAM+ tdTomato - and EpCAM+ tdTomato + cell populations.
FACS sorted tdTomato+ Defa4 Cre -expressing Paneth cells were loaded onto Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit V2 for complementary DNA library preparation.

value: proximal small intestine

value: Paneth cells

value: Defa4 Cre:Rosa26 tdTomato/tdTomato


title: DMSO_HTB4645_L2

description: TC-83 nsP2-4


title: hEKO-E4KI

city: San Francisco

first: Nuo

last: Chen

state: California

address: 1650 Owens St

department: GIND

institute: Gladstone Institutes

description: contains both cytoplasmic RNA and nuclear RNA

data_processing:
The demultiplexed fastq files for these samples were aligned to the standard mouse reference genome (2020 version, refdata-gex-mm10-2020-A) separately using the 10x Genomics Cell Ranger v7.0.0 count pipeline, as described in the Cell Ranger documentation. The include-introns flag for the count pipeline was set to true to count the reads mapping to intronic regions.
Assembly: The Homo sapiens APOE are genes of interest for this study. Custom mouse reference genome was made using these genes of interest , the reference mouse genome sequence (GRCm38) from Ensembl (release 98) and the mouse gene annotation file from GENCODE (release M23), similar to those used in 10x Genomics Cell Ranger mouse reference package mm10 2020-A.
Supplementary files format and content: Feature-barcode matrix files (zipped) in the Market Exchange Format (MEX Format) (https://www.10xgenomics.com/support/software/cell-ranger/analysis/outputs/cr-outputs-mex-matrices)

source_name: hippocampus

growth_protocol: APOE3 and APOE4 knock-in (E3KI and E4KI) mice on a C57BL/6 background were originally obtained from Taconic. All animals were bred in-house using trio breeding producing 8–10 pups per litter on average, which were weaned at 28 days. Male littermates at 3-5 months of age were randomly assigned to experimental groups. Animals were housed in a pathogen-free barrier facility on a 12 hr light cycle (lights on at 7 am and off at 7 pm) at 19–23°C and 30%–70% humidity. Mice were genotyped by polymerase chain reaction (PCR) of a tail clipping at weaning. All mouse experiments were conducted in accordance with the guidelines and regulations of the National Institutes of Health, the University of California, and the Gladstone Institutes under IACUC protocol AN117112.

extract_protocol:
The hippocampus of each mouse’s left hemi-brain was dissected on ice, rinsed with cold Dissection Buffer, and placed into a pre-chilled 12-well plate with 2 mL/well of Hibernate A Buffer. Hippocampi from 4-6 mice per condition were pooled into one well for further processing. Tissue from each pooled sample was moved to a 100mm dish, minced with a razor blade, then placed in a 5mL Eppendorf tube with 1mL pre-warmed Enzyme Buffer. Samples in Eppendorf tubes were then incubated in a 35°C water bath for 30 minutes, with gentle trituration at the 15-, 25-, and 30-minute timepoints. The homogenate was then filtered (70um MACS SmartStrainers) into a 50mL conical tube and centrifuged and washed at 4°C for a few times. The cells were resuspended in Blocking Buffer (BD Biosciences). After a 5-minute incubation at 4°C, cells were incubated in Antibody Solution (1X DPBS, 0.2% BSA, 1.89ug/mL CD45 PE-Cyanine7 (Thermofisher),  3.53ug/mL CD11b Brilliant Violet 421 (BioLegend)) for 40 minutes at 4°C. After being washed with 1X DPBS with 0.2% BSA and filtered through a 40um Flowmi Cell Strainer (Millipore Sigma) into a pre-chilled 5mL FACS tubes (Stem Cell Technologies), live single cells were identified and gated per standard sorting protocols, then further sorted to isolate a CD11b+/CD45int microglia population (Supp Fig 6) with a BD FACS Aria Fusion I or BD Aria II at 4°C with a 100um nozzle (20 psi). The sorted microglia were centrifuged at 500g at 4°C for 5 minutes, then loaded onto 10x Genomics Next GEM chip G at cell counts of approximately 25,000 cells.
The scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v.3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.

treatment_protocol: Human induced pluripotent stem cell (hiPSC)-derived neurons (at culture days 35-42) were collected and single cells were then centrifuged and resuspended to concentration of 500 cells/nL in 1X HBSS (GIBCO) supplemented with 10 ng/mL BDNF (Peprotech), 10 ng/mL GDNF (Peprotech) and 100 ng/mL DNaseI (Roche) and kept at 4°C until transplantation. Mice were anesthetized with an intraperitoneal injection of ketamine (60 mg/kg) and xylazine (30 mg/kg) and maintained on 0.8%-1.0% isofluorane (Henry Schein). Mice were secured in a stereotaxic alignment system model 940 using earbars and a tooth bar (Kopf Instruments). The scalp was prepared by removing hair with scissors and sterilizing with 70% ethanol. The scalp was then cut open using a scalpel and sterilized with 70% ethanol. Cell suspensions (500 cells/nL) were loaded into 60 μm tip diameter, 30° beveled glass micropipette needles (Nanoject, Drummond Scientific Company). Approximately 30,000 cells per site were injected at 4 sites (2 per hemibrain) at a rate of 25 nL/sec and allowed to diffuse for 1 min. Each mouse received four total cell transplants, two per hemibrain hippocampus. Following surgery, mice were sutured with nylon monofilament non-absorbable 6-0 sutures (Henry Schein), and administered analgesics buprenorphine (0.0375 mg/kg intraperitoneally), ketofen (5 mg/kg subcutaneously), and saline (500µL intraperitoneally). Immunosuppressants were administered immediately after transplantation (day 0) via intraperitoneal injection followed by injections on day 2, 4, and 6 post transplantation.

value: hippocampus

value: Microglia

value: APOE-KO


title: DMSO_HTB4645_J6

description: TC-83 nsP2-4


title: LGR5, H3K36me3,  rep2


title: DMSO_HTB4645_K3

description: TC-83 nsP2-4


title: E4KI


title: DMSO_HTB4645_J2

description: TC-83 nsP2-4


title: T811


title: E3KI


title: DMSO_HTB4645_J16

description: TC-83 nsP2-4


title: DMSO_HTB4645_I3

description: TC-83 nsP2-4


title: hE4-E4KI


title: DMSO_HTB4645_I2

description: TC-83 nsP2-4


title: T1144


title: DMSO_HTB4645_H2

description: TC-83 nsP2-4


title: T25


title: T896


title: DMSO_HTB4645_H3

description: TC-83 nsP2-4


title: DMSO_HTB4645_K2

description: TC-83 nsP2-4


title: T1498


title: hE3-E3KI


title: DMSO_HTB4645_J3

description: TC-83 nsP2-4


title: DMSO_HTB4645_G2

description: TC-83 nsP2-4


title: DMSO_HTB4645_G3

description: TC-83 nsP2-4


title: DMSO_HTB4645_G8

description: TC-83 nsP2-4


title: WT, 4wk,rep2

source_name: organoid

growth_protocol: WT organoid samples were grown in ENR media. H3K36M organoid samples were grown in ENR with 2 ug/mL doxycycline added for 4 weeks before harvest.

extract_protocol:
Organoids were harvested at each timepoint using EDTA to remove matrigel and TrypLE to digest to single cell, at which point RNA was isolated using Zymo Direct-zol RNA Miniprep kit.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: organoid

value: WT H3


title: WT, 8wk,rep2


title: WT, 2wk,rep2


title: T1886


title: DMSO_HTB4645_F2

description: TC-83 nsP2-4


title: DMSO_HTB4645_F6

description: TC-83 nsP2-4


title: DMSO_HTB4645_F3

description: TC-83 nsP2-4


title: T893


title: DMSO_HTB4645_E3

description: TC-83 nsP2-4


title: WT, 1wk,rep2


title: DMSO_HTB4645_E2

description: TC-83 nsP2-4


title: T1895


title: WT, 0wk,rep2


title: DMSO_HTB4645_D7

description: TC-83 nsP2-4


title: DMSO_HTB4645_E14

description: TC-83 nsP2-4


title: T1527


title: T1941


title: WT, 8wk,rep1


title: DMSO_HTB4645_D2

description: TC-83 nsP2-4


title: DMSO_HTB4645_D14

description: TC-83 nsP2-4


title: T1927


title: DMSO_HTB4645_C3

description: TC-83 nsP2-4


title: DMSO_HTB4645_C2

description: TC-83 nsP2-4


title: T24455


title: WT, 4wk,rep1


title: WT, 2wk,rep1


title: DMSO_HTB4645_C13

description: TC-83 nsP2-4


title: 33590


title: 31232


title: WT, 1wk,rep1


title: DMSO_HTB4645_B3

description: TC-83 nsP2-4


title: WT, 0wk,rep1


title: DMSO_HTB4645_B2

description: TC-83 nsP2-4


title: DMSO_HTB4645_B8

description: TC-83 nsP2-4


title: DMSO_HTB4645_B10

description: TC-83 nsP2-4


title: K36M, 8wk,rep2


title: DMSO_HTB4645_A3

description: TC-83 nsP2-4


title: DMSO_HTB4645_A2

description: TC-83 nsP2-4


title: DMSO_HTB4645_A14

description: TC-83 nsP2-4


title: DMSO_HTB4645_D3

description: TC-83 nsP2-4


title: K36M, 4wk,rep2


title: DMSO_HTB4644_P7

description: TC-83 nsP2-4


title: DMSO_HTB4644_P2

description: TC-83 nsP2-4


title: K36M, 1wk,rep2


title: DMSO_HTB4644_O2

description: TC-83 nsP2-4


title: K36M, 0wk,rep2


title: K36M, 2wk,rep2


title: DMSO_HTB4644_O3

description: TC-83 nsP2-4


title: DMSO_HTB4644_N24

description: TC-83 nsP2-4


title: DMSO_HTB4644_N20

description: TC-83 nsP2-4


title: DMSO_HTB4644_N3

description: TC-83 nsP2-4


title: K36M, 4wk,rep1


title: DMSO_HTB4644_N2

description: TC-83 nsP2-4


title: DMSO_HTB4644_P3

description: TC-83 nsP2-4


title: K36M, 8wk,rep1


title: DMSO_HTB4644_N17

description: TC-83 nsP2-4


title: DMSO_HTB4644_M2

description: TC-83 nsP2-4


title: K36M, 1wk,rep1


title: K36M, 2wk,rep1


title: DMSO_HTB4644_M14

description: TC-83 nsP2-4


title: DMSO_HTB4644_L3

description: TC-83 nsP2-4


title: DMSO_HTB4644_L5

description: TC-83 nsP2-4


title: K36M, 0wk,rep1


title: DMSO_HTB4644_L2

description: TC-83 nsP2-4


title: DMSO_HTB4644_L18

description: TC-83 nsP2-4


title: DMSO_HTB4644_J2

description: TC-83 nsP2-4


title: DMSO_HTB4644_J18

description: TC-83 nsP2-4


title: DMSO_HTB4644_K3

description: TC-83 nsP2-4


title: DMSO_HTB4644_I3

description: TC-83 nsP2-4


title: DMSO_HTB4644_M3

description: TC-83 nsP2-4


title: H3K36M, rep2

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Cells were flash frozen and RNA was isolated using  miRNeasy Micro kit (Qiagen).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

treatment_protocol: Doxycycline added to water for 4 weeks before harvest.

value: intestine epithelium


title: DMSO_HTB4644_I2

description: TC-83 nsP2-4


title: WT H3, rep2


title: DMSO_HTB4644_J3

description: TC-83 nsP2-4


title: DMSO_HTB4644_H7

description: TC-83 nsP2-4


title: DMSO_HTB4644_K2

description: TC-83 nsP2-4


title: WT H3, rep1


title: DMSO_HTB4644_H3

description: TC-83 nsP2-4


title: DMSO_HTB4644_H2

description: TC-83 nsP2-4


title: H3K36M, rep1


title: DMSO_HTB4644_G2

description: TC-83 nsP2-4


title: H3K36M, H3K36me2, rep2

data_processing:
H3K36me3 and H3K36me2 samples were normalized to Epicypher K-metstat spike in using in-house scripts to count barcodes.
H3K27me3 samples were normalized to background using CPM.
CUT&Tag reads were mapped to the mouse mm10 genome using Bowtie version 2.2.9.
DeepTools v3.0.1 was used with normalization as above to create bigWig files.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Nuclei were isolated from cells following Heinekoff et al. "Benchtop CUT&Tag"
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

value: intestinal epithelium


title: DMSO_HTB4644_F3

description: TC-83 nsP2-4

extract_protocol:
VEEV TC-83 nsP234 region is PCR-amplified from cDNA synthesized from viral RNA.
For samples sequenced with Nanopore MinION, Nanopore ligation-based sequencing kit was used. For samples sequenced with PacBio Sequel IIe, samples were prepared into SMRTbell template libraries.


title: H3K36M, H3K27me3, rep2


title: DMSO_HTB4644_F2

description: TC-83 nsP2-4


title: DMSO_HTB4644_G3

description: TC-83 nsP2-4


title: H3K36M, H3K27me3, rep1


title: DMSO_HTB4644_F10

description: TC-83 nsP2-4


title: DMSO_HTB4644_F15

description: TC-83 nsP2-4


title: H3K36M, H3K36me3, rep1


title: DMSO_HTB4644_E3

description: TC-83 nsP2-4


title: H3K36M, H3K36me2, rep1


title: DMSO_HTB4644_C3

description: TC-83 nsP2-4


title: WT H3, H3K36me2, rep2


title: H3K36M, H3K36me3, rep2


title: DMSO_HTB4644_E2

description: TC-83 nsP2-4


title: DMSO_HTB4644_D3

description: TC-83 nsP2-4


title: DMSO_HTB4644_D2

description: TC-83 nsP2-4


title: DMSO_HTB4644_B2

description: TC-83 nsP2-4


title: WT H3, H3K36me2, rep1


title: HCT116_LNP-Day2

city: Guangzhou

first: Wenbin

last: Gu

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Chinese Academy of Sciences

country: China

institute: Guangzhou Institutes of Biomedicine and Health

description:
HCT116 cells with LNP treatment at Day 2
HCT116_LNP-Day2

scan_protocol: Polymer-coated chips were image-processed in Illumina iScan scanner.

data_processing: Data were extracted using Illumina GenomeStudio V2011.1 software. Methylation status of each CpG site was presented as beta value based on following definition: beta value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy5 and Cy3

source_name: HCT116, LNP treated, Day2

label_protocol: DNA bisulfite conversion was carried out using EZ DNA Methylation Kit (Zymo Research) by following manufacturer's manual with modifications for Illumina Infinium Methylation Assay. Briefly, 0.5~1.0 ug of genomic DNA was first mixed with 5 ul of M-Dilution Buffer and incubate at 37C for 15 minutes and then mixed with 100 ul of CT Conversion Reagent prepared as instructed in the kit's manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95C for 30 seconds and 50C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification. Concentration of eluted DNA was measured using Nanodrop-1000 spectrometer. Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer's manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

growth_protocol: BeWo cells were maintained in Ham‘s F-12K complete medium.  NCCIT cells were maintained in RPMI 1640 complete medium. HCT116 cells were maintained in McCoy's 5A complete medium, and RKO cells were maintained in MEM complete medium.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer's instructions. Genomic DNA quality was assessed by low concentration agarose gel (0.6%) electrophoresis and spectrometry of OD260/280 and OD 260/230 ratio.

treatment_protocol: BeWo and NCCIT cells were transduced by lentivirus expressing Cas9/sgRNA targeting hSTELLA. The single-cell clones were subsequently selected through serial dilution of these transduced cells, and verified by western blot and sequencing. CRC cells (HCT116 and RKO cells) with lentivirus-mediated stable overexpression of STELLA orthologs were harvested on Day 9 post virus-transduction. HCT116 cells treated with LNP-mRNA or vehicle control were harvested on Days 2, 6 and 10.

tag: tumor type

value: colorectal carcinoma

value: LNP treatment at Day 2


title: HCT116_LNP-mSTELLA-Day6

description:
HCT116 cells with LNP-mSTELLA treatment at Day 6
HCT116_LNP-mSTELLA-Day6

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer's manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

source_name: HCT116, LNP-mSTELLA treated, Day6

value: LNP-mSTELLA treatment at Day 6


title: DMSO_HTB4644_C17

description: TC-83 nsP2-4


title: HCT116_LNP-Day10

description:
HCT116 cells with LNP treatment at Day 10
HCT116_LNP-Day10

source_name: HCT116, LNP treated, Day10

value: LNP treatment at Day 10


title: DMSO_HTB4644_B3

description: TC-83 nsP2-4


title: DMSO_HTB4644_A2

description: TC-83 nsP2-4


title: DMSO_HTB4644_A3

description: TC-83 nsP2-4


title: WT H3, H3K36me3, rep2


title: RKO_EV

description:
RKO cells stably expressing empty vector
RKO_EV

source_name: RKO, empty vector

value: RKO

value: stably expressing empty vector


title: WT H3, H3K27me3, rep1


title: DMSO_HTB4644_A15

description: TC-83 nsP2-4

value: DMSO


title: HCT116_LNP-mSTELLA-Swap1-Day10

description:
HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 10
HCT116_LNP-mSTELLA-Swap1-Day10

source_name: HCT116, LNP-Mstella-Swap1 treated, Day10

value: LNP-mSTELLA-Swap1 treatment at Day 10


title: RKO_mSTELLA-OE

description:
RKO cells stably expressing mSTELLA
RKO_mSTELLA-OE

source_name: RKO, mSTELLA overexpression

value: stably expressing mSTELLA


title: WT H3, H3K36me3, rep1


title: DMSO_HTB4644_C18

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Swap1-Day2

description:
HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 2
HCT116_LNP-mSTELLA-Swap1-Day2

source_name: HCT116, LNP-Mstella-Swap1 treated, Day2

value: LNP-mSTELLA-Swap1 treatment at Day 2


title: HCT116_LNP-Day6

description:
HCT116 cells with LNP treatment at Day 6
HCT116_LNP-Day6

source_name: HCT116, LNP treated, Day6

value: LNP treatment at Day 6


title: M13 phage, NDT codon encoded cyclic peptide library after positive and negative selection, against hIAPP, no replicate

city: Madiso

first: Linwei

last: Yang

state: WI

address: 1101 University Ave

department: Chemistry

institute: UW-Madison

data_processing:
Raw sequencing data were processed using a customized script included in this study to generate sequence distributions.
Assembly: N/A
Supplementary files format and content: Excel sheets that include decoded cyclic peptide sequence, read number for each cyclic peptide sequence, total read number of the library, and read frequency for each cyclic peptide sequence

organism: Inovirus M13

source_name: M13 phage pool

extract_protocol:
M13 phage pool in 2xYT medium was used directly as template for PCRs
M13 phage pool was directly used as template in PCR using appropriate primers specified in this study. Q5 DNA polymerase (from NEB) and buffer were used. Minimal number of cycles was used in PCR reactions to amplify gene of interest from the M13 phage genome. PCR products were purified and pooled as libraries.
Amplicons for NGS using Illumina NovaSeq 6000

value: M13 phage pool


title: DMSO_HTB4644_C2

description: TC-83 nsP2-4


title: DMSO_HTB4643_P3

description: TC-83 nsP2-4


title: DMSO_HTB4643_P13

description: TC-83 nsP2-4


title: HCT116_LNP-mSTELLA-Day10

description:
HCT116 cells with LNP-mSTELLA treatment at Day 10
HCT116_LNP-mSTELLA-Day10

source_name: HCT116, LNP-mSTELLA treated, Day10

value: LNP-mSTELLA treatment at Day 10


title: HCT116_mSTELLA-OE

description:
HCT116 cells stably expressing mSTELLA
HCT116_mSTELLA-OE

source_name: HCT116, mSTELLA overexpression


title: HCT116_LNP-mSTELLA-Day2

description:
HCT116 cells with LNP-mSTELLA treatment at Day 2
HCT116_LNP-mSTELLA-Day2

source_name: HCT116, LNP-mSTELLA treated, Day2

value: LNP-mSTELLA treatment at Day 2


title: DMSO_HTB4643_P2

description: TC-83 nsP2-4


title: WTnoIR,rep2

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Cells were flash frozen and RNA was isolated using  miRNeasy Micro kit (Qiagen). Organoids were harvested using EDTA to remove matrigel and TrypLE to digest to single cell, at which point RNA was isolated using Zymo Direct-zol RNA Miniprep kit.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.

treatment_protocol: Mice were irradiated with 2 Gy at day 0 and harvested at 2 and 3 days post-IR. Organoids were irradiated with 6 Gy and harvested at 24, 48, and 96 hours post-IR.

value: organoid

value: WT H3


title: HCT116_hSTELLA-OE

description:
HCT116 cells stably expressing hSTELLA
HCT116_hSTELLA-OE

source_name: HCT116, hSTELLA overexpression

value: stably expressing hSTELLA


title: DMSO_HTB4643_O3

description: TC-83 nsP2-4


title: DMSO_HTB4643_O23

description: TC-83 nsP2-4


title: M13 phage, NDT codon encoded cyclic peptide library after five rounds of positive selection, against hIAPP, no replicate


title: WTnoIR,rep1


title: DMSO_HTB4644_A10

description: TC-83 nsP2-4


title: DMSO_HTB4643_O2

description: TC-83 nsP2-4


title: HCT116_EV

description:
HCT116 cells stably expressing empty vector
HCT116_EV

source_name: HCT116, empty vector

value: colorectal carcinoma


title: M13 phage, NDT codon encoded cyclic peptide library, against hIAPP, no replicate


title: NCCIT_hSTELLA-KO-c3

description:
Clone 3 from hSTELLA-targeting sgRNA transduced NCCIT cells
NCCIT_hSTELLA-KO-c3

source_name: NCCIT, hSTELLA sgRNA transduced, clone3

value: embryonal carcinoma

value: NCCIT

value: hSTELLA-targeting sgRNA transduced


title: DMSO_HTB4643_N5

description: TC-83 nsP2-4


title: K36M,rep2


title: DMSO_HTB4643_N3

description: TC-83 nsP2-4


title: M13 phage, NNK codon encoded cyclic peptide library after seven rounds of selection, against AB42, no replicate


title: DMSO_HTB4643_M3

description: TC-83 nsP2-4


title: K36M,rep1


title: M13 phage, NNK codon encoded cyclic peptide library, against AB42, no replicate


title: DMSO_HTB4643_N2

description: TC-83 nsP2-4


title: WT H3, H3K27me3, rep2

source_name: intestinal epithelium

value: intestinal epithelium


title: HCT116_LNP-mSTELLA-Swap1-Day6

description:
HCT116 cells with LNP-mSTELLA-Swap1 treatment at Day 6
HCT116_LNP-mSTELLA-Swap1-Day6

source_name: HCT116, LNP-Mstella-Swap1 treated, Day6

value: LNP-mSTELLA-Swap1 treatment at Day 6


title: DMSO_HTB4643_M2

description: TC-83 nsP2-4

value: DMSO


title: DMSO_HTB4643_M11

description: TC-83 nsP2-4


title: M13 phage, NDT codon encoded cyclic peptide library after selection with mutagenesis, against AB42, no replicate


title: RKO_hSTELLA-OE

description:
RKO cells stably expressing hSTELLA
RKO_hSTELLA-OE

source_name: RKO, hSTELLA overexpression

value: RKO


title: IR96,rep1

source_name: organoid


title: DMSO_HTB4643_L3

description: TC-83 nsP2-4


title: DMSO_HTB4643_L2

description: TC-83 nsP2-4


title: M13 phage, NDT codon encoded cyclic peptide library after four rounds of selection, against AB42, no replicate


title: IR48,rep2


title: NCCIT_SCR-c1

description:
Clone 1 from sgSCR transduced NCCIT cells
NCCIT_SCR-c1

source_name: NCCIT, scramble sgRNA transduced, clone1

value: sgSCR transduced


title: DMSO_HTB4643_L14

description: TC-83 nsP2-4


title: IR96,rep2


title: NCCIT_hSTELLA-KO-c1

description:
Clone 1 from hSTELLA-targeting sgRNA transduced NCCIT cells
NCCIT_hSTELLA-KO-c1

source_name: NCCIT, hSTELLA sgRNA transduced, clone1


title: M13 phage, NDT codon encoded cyclic peptide library, against AB42, no replicate


title: DMSO_HTB4643_K3

description: TC-83 nsP2-4


title: DMSO_HTB4643_K2

description: TC-83 nsP2-4


title: nasp_RNAseq_rep3

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (DNBSEQ platform, single-end 50bp).

value: Arabidopsis seedlings

value: nasp-/-

tag: time


title: IR48,rep1


title: DMSO_HTB4643_J3

description: TC-83 nsP2-4


title: NCCIT_SCR-c2

description:
Clone 2 from sgSCR transduced NCCIT cells
NCCIT_SCR-c2

source_name: NCCIT, scramble sgRNA transduced, clone2


title: IR24,rep2


title: nasp_RNAseq_rep2


title: DMSO_HTB4643_J2

description: TC-83 nsP2-4


title: DMSO_HTB4643_I3

description: TC-83 nsP2-4


title: DMSO_HTB4643_I2

description: TC-83 nsP2-4


title: IR24,rep1


title: DMSO_HTB4643_H3

description: TC-83 nsP2-4


title: nasp_RNAseq_rep1


title: DMSO_HTB4643_H2

description: TC-83 nsP2-4


title: msi2msi3nasp_RNAseq_rep3


title: WTnoIR, H3K36me2, regen, rep2

data_processing:
All samples were normalized to background using CPM. H3K36M H3K36me3 and H3K36me2 samples were normalized to Epicypher K-metstat spike in panel using in house scripts to quantify barcodes.
CUT&Tag reads were mapped to the mouse mm10 genome using Bowtie version 2.2.9.
DeepTools v3.0.1 was used with normalization as above to create bigWig files.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Mouse intestine was harvested and epithelial cells were eluted with 20 mM EDTA + 1 mM DTT and filtered through 100 and 40 um cell strainers. Nuclei were isolated from cells following Heinekoff et al. "Benchtop CUT&Tag". Organoids were harvested using EDTA to remove matrigel and TrypLE to digest to single cell, at which point nuclei were isolated following H3inekoff et al. "Benchtop CUT&Tag".
CUT&Tag was performed as in Heinekoff et al. "Benchtop CUT&Tag" for each antibody. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using Agilent High Sensitivity DNA kit.