title: p279_ENL_R2_(230817_DJ_Hs_p279_ENL_R2_230801)

description: AutoCUTnTag for ENL Replicate 2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital


title: p454_K4me3_R1_(230817_DJ_Hs_p454_K4me3_R1_230801)

status: Public on Sep 27 2024

type: SRA

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

country: USA

institute: Van Andel Institute

description: AutoCUTnTag for H3K4me3 Replicate 1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

library_source: genomic

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: infant BALL sample p454

extract_protocol:
AutoCUTnTag DOI: dx.doi.org/10.17504/protocols.io.bgztjx6n
Specified separately for each sample, see above.
PMID 31036827

tag: cell type

value: infant BALL sample p454

tag: group

tag: antibody

value: Rabbit H3K4me3 Active Motif 39159


title: p279_ENL_R1_(230817_DJ_Hs_p279_ENL_R1_230801)

description: AutoCUTnTag for ENL Replicate 1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

source_name: infant B-ALL lineage-switching sample p279

value: Rabbit ENL Cell Signaling Technologies D9M4B


title: p279_Dot1L_R1_(230817_DJ_Hs_p279_Dot1L_R1_230801)

description: AutoCUTnTag for Dot1L Replicate 1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: infant B-ALL lineage-switching sample p279

value: Rabbit Dot1L Cell Signaling Technologies D4O2T


title: SEM_AFF1_1_(240410_DJ_Hs_SEM_AFF1_1_05T_040324)

description: AutoCUTnRUN for AFF1-1 in SEM cells. This sample contains the KMT2A-AFF1 translocation and is a B-ALL cell line; gift from Marie Bleakley lab

source_name: pedatric B-ALL cell line SEM

extract_protocol:
AutoCUTnRUN DOI: dx.doi.org/10.17504/protocols.io.ufeetje
Specified separately for each sample, see above.
PMID 31036827

value: pedatric B-ALL cell line SEM

value: Mouse AFF1-1 MyBioSource MBS190886


title: p279_AFF1_1_(240410_DJ_Hs_p279_AFF1_1_05T_040324)

description: AutoCUTnRUN for AFF1-1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital


title: R3652_KMT2A_N2_(240410_DJ_Hs_5652_KMT2A_N2_05T_040324)

description: AutoCUTnRUN for KMT2A-N2 in R3652. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3595) from Seattle Children's Hospital

source_name: infant B-ALL lineage-switching sample R3652

value: Rabbit KMT2A-N2 CST D2M7U


title: R3652_KMT2A_N1_(240410_DJ_Hs_5652_KMT2A_N1_05T_040324)

description: AutoCUTnRUN for KMT2A-N1 in R3652. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3595) from Seattle Children's Hospital

value: infant B-ALL lineage-switching sample R3652

value: Mouse KMT2A-N1 Millipore 05-764


title: p454_AFF1_1_(240410_DJ_Hs_p454_AFF1_1_05T_040324)

description: AutoCUTnRUN for AFF1-1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital


title: R3652_KMT2A_C2_(240410_DJ_Hs_5652_KMT2A_C2_05D_040324)

description: AutoCUTnRUN for KMT2A-C2 in R3652. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3595) from Seattle Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765


title: R3652_IgG_(240410_DJ_Hs_5652_IgG_05T_040324)

description: AutoCUTnRUN for IgG in R3652. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3595) from Seattle Children's Hospital

value: Rabbit IgG abcam ab46540


title: SEM_AFF1_2_(240410_DJ_Hs_SEM_AFF1_2_05T_040324)

description: AutoCUTnRUN for AFF1-2 in SEM cells. This sample contains the KMT2A-AFF1 translocation and is a B-ALL cell line; gift from Marie Bleakley lab

value: Rabbit AFF1-2 Thermo Fisher Scientific PA5-77068


title: R3595_KMT2A_C2_(240410_DJ_Hs_5395_KMT2A_C2_05T_040324)

description: AutoCUTnRUN for KMT2A-C2 in R3595. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3652) from Seattle Children's Hospital

source_name: infant B-ALL lineage-switching sample R3595


title: R3595_KMT2A_C1_(240410_DJ_Hs_5395_KMT2A_C1_05T_040324)

description: AutoCUTnRUN for KMT2A-C1 in R3595. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3652) from Seattle Children's Hospital

value: infant B-ALL lineage-switching sample R3595

value: Mouse KMT2A-C1 SantaCruz H10


title: R3595_IgG_(240410_DJ_Hs_5395_IgG_05T_040324)

description: AutoCUTnRUN for IgG in R3595. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3652) from Seattle Children's Hospital


title: R3595_KMT2A_N2_(240410_DJ_Hs_5395_KMT2A_N2_05T_040324)

description: AutoCUTnRUN for KMT2A-N2 in R3595. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3652) from Seattle Children's Hospital


title: p318_Dot1L_R2_(230817_DJ_Hs_p318_Dot1L_R2_230801)

description: AutoCUTnTag for Dot1L Replicate 2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

source_name: infant AML lineage-switching sample p318


title: 152985_Menin_R2_(240423_DJ_Hs_152985_Menin_R2_041624)

description: AutoCUTnTag for Menin Replicate 2 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital

source_name: infant AML lineage-switching sample 152985 treated with the Menin inhibitor

value: Rabbit Menin Bethyl Labs A300-115A


title: R3595_KMT2A_N1_(240410_DJ_Hs_5395_KMT2A_N1_05T_040324)

description: AutoCUTnRUN for KMT2A-N1 in R3595. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3652) from Seattle Children's Hospital


title: 152985_KMT2A_N1_(240515_DJ_Hs_DJ8_152985_500K_KMT2A_N1_240416)

description: AutoCUTnRUN for KMT2A-N1 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital

value: infant AML lineage-switching sample 152985 treated with the Menin inhibitor


title: 152985_KMT2A_C2_(240515_DJ_Hs_DJ10_152985_500K_KMT2A_C2_240416)

description: AutoCUTnRUN for KMT2A-C2 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 152985_ENL_R2_(240423_DJ_Hs_152985_ENL_R2_041624)

description: AutoCUTnTag for ENL Replicate 2 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 152985_KMT2A_N2_(240515_DJ_Hs_DJ4_152985_500K_KMT2A_N2_240416)

description: AutoCUTnRUN for KMT2A-N2 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 152985_ENL_R1_(240423_DJ_Hs_152985_ENL_R1_041624)

description: AutoCUTnTag for ENL Replicate 1 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 152985_KMT2A_C1_(240515_DJ_Hs_DJ9_152985_500K_KMT2A_C1_240416)

description: AutoCUTnRUN for KMT2A-C1 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 148752_Menin_R2_(240423_DJ_Hs_148752_Menin_R2_041624)

description: AutoCUTnTag for Menin Replicate 2 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital

source_name: infant B-ALL lineage-switching sample 148752 treated with the Menin inhibitor


title: 152985_Dot1L_R1_(240423_DJ_Hs_152985_Dot1L_R1_041624)

description: AutoCUTnTag for Dot1L Replicate 1 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 152985_Menin_R1_(240423_DJ_Hs_152985_Menin_R1_041624)

description: AutoCUTnTag for Menin Replicate 1 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 148752_KMT2A_N1_(240515_DJ_Hs_DJ5_148752_500K_KMT2A_N1_240416)

description: AutoCUTnRUN for KMT2A-N1 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital

value: infant B-ALL lineage-switching sample 148752 treated with the Menin inhibitor


title: 148752_KMT2A_C2_(240515_DJ_Hs_DJ7_148752_500K_KMT2A_C2_240416)

description: AutoCUTnRUN for KMT2A-C2 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: R3652_KMT2A_C1_(240410_DJ_Hs_5652_KMT2A_C1_05D_040324)

description: AutoCUTnRUN for KMT2A-C1 in R3652. This sample contains the KMT2A-EPS15 translocation and is an infant BALL lineage-switching sample (paired with R3595) from Seattle Children's Hospital


title: 152985_Dot1L_R2_(240423_DJ_Hs_152985_Dot1L_R2_041624)

description: AutoCUTnTag for Dot1L Replicate 2 in 152985. This sample contains the KMT2A-ENL translocation and is an infant AML lineage-switching sample treated with the Menin inhibitor (paired with 148752) from Texas Children's Hospital


title: 148752_Menin_R1_(240423_DJ_Hs_148752_Menin_R1_041624)

description: AutoCUTnTag for Menin Replicate 1 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: 148752_ENL_R2_(240423_DJ_Hs_148752_ENL_R2_041624)

description: AutoCUTnTag for ENL Replicate 2 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: 148752_ENL_R1_(240423_DJ_Hs_148752_ENL_R1_041624)

description: AutoCUTnTag for ENL Replicate 1 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: 148752_Dot1L_R2_(240423_DJ_Hs_148752_Dot1L_R2_041624)

description: AutoCUTnTag for Dot1L Replicate 2 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: p454_KMT2A_N2_(230626_DJ_Hs_p454_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

data_processing:
Genome_build: hg38
1. We used cutadapt 4.1 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg38 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg38 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg38 track which is the fraction of counts at each base pair scaled by the size of the hg38 reference sequence (3210038034) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg38.bw)

source_name: AutoCUTnRUN

extract_protocol:
http://dx.doi.org/10.17504/protocols.io.ufeetje
CUT&RUN libraries are prepared on a Biomek via End-Repair, A-tailing and barcoded Y-adapter ligation, followed by PCR .

tag: sample

value: Rabbit KMT2A-N2 CST D2M7U; p454; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p454_KMT2A_C2_(230626_DJ_Hs_p454_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p454; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p454_KMT2A_N1_(230626_DJ_Hs_p454_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p454; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p454_KMT2A_C1_(230626_DJ_Hs_p454_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p454; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p454_IgG_(230626_DJ_Hs_p454_IgG_230613)

description: AutoCUTnRUN for IgG in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p454; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p247_KMT2A_N1_(230626_DJ_Hs_p247_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p247. This sample contains the KMT2A-AFF1 translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p247; KMT2A-AFF1; pediatric BALL; Texas Children's Hospital


title: p247_KMT2A_C2_(230626_DJ_Hs_p247_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p247. This sample contains the KMT2A-AFF1 translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p247; KMT2A-AFF1; pediatric BALL; Texas Children's Hospital


title: p247_KMT2A_C1_(230626_DJ_Hs_p247_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p247. This sample contains the KMT2A-AFF1 translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p247; KMT2A-AFF1; pediatric BALL; Texas Children's Hospital


title: 148752_KMT2A_N2_(240515_DJ_Hs_DJ2_148752_500K_KMT2A_N2_240416)

description: AutoCUTnRUN for KMT2A-N2 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U


title: p214_KMT2A_N2_(230626_DJ_Hs_p214_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p214. This sample contains the KMT2A-ENL translocation and is a pediatric BALL from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p214; KMT2A-ENL; pediatric BALL; Texas Children's Hospital


title: p214_KMT2A_N1_(230626_DJ_Hs_p214_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p214. This sample contains the KMT2A-ENL translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p214; KMT2A-ENL; pediatric BALL; Texas Children's Hospital


title: 148752_KMT2A_C1_(240515_DJ_Hs_DJ6_148752_500K_KMT2A_C1_240416)

description: AutoCUTnRUN for KMT2A-C1 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital


title: p247_IgG_(230626_DJ_Hs_p247_IgG_230613)

description: AutoCUTnRUN for IgG in p247. This sample contains the KMT2A-AFF1 translocation and is a pediatric BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p247; KMT2A-AFF1; pediatric BALL; Texas Children's Hospital


title: p214_KMT2A_C1_(230626_DJ_Hs_p214_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p214. This sample contains the KMT2A-ENL translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p214; KMT2A-ENL; pediatric BALL; Texas Children's Hospital


title: p214_KMT2A_C2_(230626_DJ_Hs_p214_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p214. This sample contains the KMT2A-ENL translocation and is a pediatric BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p214; KMT2A-ENL; pediatric BALL; Texas Children's Hospital


title: p214_IgG_(230626_DJ_Hs_p214_IgG_230613)

description: AutoCUTnRUN for IgG in p214. This sample contains the KMT2A-ENL translocation and is a pediatric BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p214; KMT2A-ENL; pediatric BALL; Texas Children's Hospital


title: p186_KMT2A_C1_(230626_DJ_Hs_p186_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p186. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p186; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p186_KMT2A_N2_(230626_DJ_Hs_p186_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p186. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p186; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p179_KMT2A_C1_(230626_DJ_Hs_p179_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p179. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p179; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p179_KMT2A_N2_(230626_DJ_Hs_p179_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p179. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p179; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p179_KMT2A_C2_(230626_DJ_Hs_p179_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p179. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p179; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: 148752_Dot1L_R1_(240423_DJ_Hs_148752_Dot1L_R1_041624)

description: AutoCUTnTag for Dot1L Replicate 1 in 148752. This sample contains the KMT2A-ENL translocation and is an infant BALL lineage-switching sample treated with the Menin inhibitor (paired with 152985) from Texas Children's Hospital

value: infant B-ALL lineage-switching sample 148752 treated with the Menin inhibitor

value: Rabbit Dot1L Cell Signaling Technologies D4O2T


title: p179_IgG_(230626_DJ_Hs_p179_IgG_230613)

description: AutoCUTnRUN for IgG in p179. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p179; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p186_KMT2A_C2_(230626_DJ_Hs_p186_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p186. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p186; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p186_KMT2A_N1_(230626_DJ_Hs_p186_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p186. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p186; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: RCC18, C2

status: Public on Nov 26 2024

city: Houston

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The fastq files from single-cell sequencing were preprocessed using Cell Ranger software (version 7.1.0)32 with default parameters. Reads were aligned to the human reference genome hg38 (version 2020-A, 10x Genomics) to calculate the expression matrix, which contained the number of unique molecular identifiers (UMIs) for every cell and gene. To ensure high-quality data for downstream analysis, careful selection of samples and cells was performed. Cells with gene expression of fewer than 500 genes were removed to eliminate cell debris, empty drops, and low-quality cells. Cells with a mitochondrial versus endogenous genes expression ratio exceeding 25% were also discarded. Additionally, genes expressed in fewer than 3 cells were excluded from the expression matrix. Subsequently, the Seurat package33 was used for data preprocessing. The raw expression matrix was log2 transformed with the NormalizeData function, scaled with the ScaleData function using default parameters, and the top 2000 genes with the highest standardized variance were identified using the FindVariableFeatures function. Principal component analysis (PCA) was performed using the RunPCA function with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Lung

extract_protocol:
Tumor biopsy samples were thoroughly minced to size < 1mm and transferred to 2.0ml Eppendorf tube containing 0.1 mg/ml Liberase TM and 0.2 mg/ml DNase I (MillieporeSigma) in RPMI1640/0.1% BSA. Tubes were then incubated at 37 degrees Celsius for 15 minutes with gentle rotation. Samples were filtered through 70 µm filters, spun down, and red blood cell lysis was performed with ACK lysis buffer (ThermoFisher, catalog #A1049201). Cell viability will be determined with Trypan blue exclusion assay. Only the samples with >60% viability were further processed on Chromium iX (10x Genomics) to generate 5' v2 gel beads-in-emulsions (GEMs).
The barcoded cDNA was purified and amplified for the final generation of 10x single cell RNA sequencing (scRNAseq) libraries. After quantification with a high sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent), the libraries were sequenced as recommended by the manufacturer (approximately 50,000 reads per cell) on a NovaSeq 6000 system.

tag: tissue

value: Lung

tag: disease state

value: clear cell renal cell carcinoma


title: p186_IgG_(230626_DJ_Hs_p186_IgG_230613)

description: AutoCUTnRUN for IgG in p186. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p186; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p179_KMT2A_N1_(230626_DJ_Hs_p179_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p179. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p179; KMT2A-AFF1; infant BALL; Texas Children's Hospital


title: p160_KMT2A_N1_(230626_DJ_Hs_p160_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p160. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p160; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p247_KMT2A_N2_(230626_DJ_Hs_p247_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p247. This sample contains the KMT2A-AFF1 translocation and is a pediatric BALL from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p247; KMT2A-AFF1; pediatric BALL; Texas Children's Hospital


title: p160_IgG_(230626_DJ_Hs_p160_IgG_230613)

description: AutoCUTnRUN for IgG in p160. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p160; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p160_KMT2A_C2_(230626_DJ_Hs_p160_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p160. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p160; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: p160_KMT2A_C1_(230626_DJ_Hs_p160_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p160. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p160; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: TB995291_KMT2A_N2_(220413_JS_Hs_032922_JS2212)

description: AutoCUTnRUN for KMT2A-N2 in TB-99-5291. This sample contains the KMT2A-ENL translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB995291_KMT2A_C2_(220413_JS_Hs_032922_JS2214)

description: AutoCUTnRUN for KMT2A-C2 in TB-99-5291. This sample contains the KMT2A-ENL translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB995291_KMT2A_C1_(220413_JS_Hs_032922_JS2213)

description: AutoCUTnRUN for KMT2A-C1 in TB-99-5291. This sample contains the KMT2A-ENL translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB995291_KMT2A_N1_(220413_JS_Hs_032922_JS2211)

description: AutoCUTnRUN for KMT2A-N1 in TB-99-5291. This sample contains the KMT2A-ENL translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB995291_IgG_(220413_JS_Hs_032922_JS2215)

description: AutoCUTnRUN for IgG in TB-99-5291. This sample contains the KMT2A-ENL translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB986292_KMT2A_N1_(220412_JS_Hs_032922_JS2151)

description: AutoCUTnRUN for KMT2A-N1 in TB-98-6292. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-98-6292; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB986292_KMT2A_N2_(220412_JS_Hs_032922_JS2152)

description: AutoCUTnRUN for KMT2A-N2 in TB-98-6292. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-98-6292; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB986292_KMT2A_C1_(220412_JS_Hs_032922_JS2153)

description: AutoCUTnRUN for KMT2A-C1 in TB-98-6292. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-98-6292; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB986292_KMT2A_C2_(220412_JS_Hs_032922_JS2154)

description: AutoCUTnRUN for KMT2A-C2 in TB-98-6292. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-98-6292; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB971992_KMT2A_N2_(220412_JS_Hs_032922_JS2170)

description: AutoCUTnRUN for KMT2A-N2 in TB-97-1992. This sample contains the KMT2A-ENL translocation and is an infant TALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-97-1992; KMT2A-ANL; infant TALL; St. Jude Children's Hospital


title: TB971992_KMT2A_N1_(220412_JS_Hs_032922_JS2169)

description: AutoCUTnRUN for KMT2A-N1 in TB-97-1992. This sample contains the KMT2A-ENL translocation and is an infant TALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-97-1992; KMT2A-ANL; infant TALL; St. Jude Children's Hospital


title: TB971992_KMT2A_C2_(220412_JS_Hs_032922_JS2172)

description: AutoCUTnRUN for KMT2A-C2 in TB-97-1992. This sample contains the KMT2A-ENL translocation and is an infant TALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-97-1992; KMT2A-ANL; infant TALL; St. Jude Children's Hospital


title: TB971992_KMT2A_C1_(220412_JS_Hs_032922_JS2171)

description: AutoCUTnRUN for KMT2A-C1 in TB-97-1992. This sample contains the KMT2A-ENL translocation and is an infant TALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-97-1992; KMT2A-ANL; infant TALL; St. Jude Children's Hospital


title: TB920488_KMT2A_N2_(220412_JS_Hs_032922_JS2164)

description: AutoCUTnRUN for KMT2A-N2 in TB-92-0488. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-92-0488; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB971992_IgG_(220412_JS_Hs_032922_JS2173)

description: AutoCUTnRUN for IgG in TB-97-1992. This sample contains the KMT2A-ENL translocation and is an infant TALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-97-1992; KMT2A-ANL; infant TALL; St. Jude Children's Hospital


title: TB920488_KMT2A_N1_(220412_JS_Hs_032922_JS2163)

description: AutoCUTnRUN for KMT2A-N1 in TB-92-0488. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-92-0488; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB920488_KMT2A_C1_(220412_JS_Hs_032922_JS2165)

description: AutoCUTnRUN for KMT2A-C2 in TB-92-0488. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-92-0488; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB920488_IgG_(220412_JS_Hs_032922_JS2167)

description: AutoCUTnRUN for IgG in TB-92-0488. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-92-0488; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: p160_KMT2A_N2_(230626_DJ_Hs_p160_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p160. This sample contains the KMT2A-ENL translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p160; KMT2A-ENL; infant BALL; Texas Children's Hospital


title: TB051939_KMT2A_N2_(220412_JS_Hs_032922_JS2182)

description: AutoCUTnRUN for KMT2A-N2 in TB-05-1939. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-05-1939; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB051939_KMT2A_N1_(220412_JS_Hs_032922_JS2181)

description: AutoCUTnRUN for KMT2A-N1 in TB-05-1939. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-05-1939; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB051939_KMT2A_C2_(220412_JS_Hs_032922_JS2184)

description: AutoCUTnRUN for KMT2A-C2 in TB-05-1939. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-05-1939; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB051939_IgG_(220412_JS_Hs_032922_JS2185)

description: AutoCUTnRUN for IgG in TB-05-1939. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-05-1939; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB040576_KMT2A_C1_(220413_JS_Hs_032922_JS2201)

description: AutoCUTnRUN for KMT2A-C1 in TB-04-0576. This sample contains the KMT2A-AF9 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-04-0576; KMT2A-AF9; infant Pre-BALL; St. Jude Children's Hospital


title: TB040576_KMT2A_N2_(220413_JS_Hs_032922_JS2200)

description: AutoCUTnRUN for KMT2A-N2 in TB-04-0576. This sample contains the KMT2A-AF9 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-04-0576; KMT2A-AF9; infant Pre-BALL; St. Jude Children's Hospital


title: TB040576_KMT2A_C2_(220413_JS_Hs_032922_JS2202)

description: AutoCUTnRUN for KMT2A-C2 in TB-04-0576. This sample contains the KMT2A-AF9 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-04-0576; KMT2A-AF9; infant Pre-BALL; St. Jude Children's Hospital


title: TB051939_KMT2A_C1_(220412_JS_Hs_032922_JS2183)

description: AutoCUTnRUN for KMT2A-C1 in TB-05-1939. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-05-1939; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB000694_KMT2A_N1_(220412_JS_Hs_032922_JS2187)

description: AutoCUTnRUN for KMT2A-N1 in TB-00-0694. This sample contains the KMT2A-AF10 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB000694_KMT2A_N2_(220412_JS_Hs_032922_JS2188)

description: AutoCUTnRUN for KMT2A-N2 in TB-00-0694. This sample contains the KMT2A-AF10 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: TB920488_KMT2A_C2_(220412_JS_Hs_032922_JS2166)

value: Mouse KMT2A-C2 Millipore 05-765; TB-92-0488; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB040576_IgG_(220413_JS_Hs_032922_JS2203)

description: AutoCUTnRUN for IgG in TB-04-0576. This sample contains the KMT2A-AF9 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-04-0576; KMT2A-AF9; infant Pre-BALL; St. Jude Children's Hospital


title: TB986292_IgG_(220412_JS_Hs_032922_JS2155)

description: AutoCUTnRUN for IgG in TB-98-6292. This sample contains the KMT2A-AFF1 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-98-6292; KMT2A-AFF1; infant Pre-BALL; St. Jude Children's Hospital


title: TB000694_KMT2A_C1_(220412_JS_Hs_032922_JS2189)

description: AutoCUTnRUN for KMT2A-C1 in TB-00-0694. This sample contains the KMT2A-AF10 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: A95941_KMT2A_N2_(220413_JS_Hs_032922_JS2236)

description: AutoCUTnRUN for KMT2A-N2 in A95941. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: TB000694_KMT2A_C2_(220412_JS_Hs_032922_JS2190)

description: AutoCUTnRUN for KMT2A-C2 in TB-00-0694. This sample contains the KMT2A-AF10 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: A95941_KMT2A_N1_(220413_JS_Hs_032922_JS2235)

description: AutoCUTnRUN for KMT2A-N1 in A95941. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: A95941_KMT2A_C2_(220413_JS_Hs_032922_JS2238)

description: AutoCUTnRUN for KMT2A-C2 in A95941. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: A93949_KMT2A_N2_(220413_JS_Hs_032922_JS2224)

description: AutoCUTnRUN for KMT2A-N2 in A93949. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center


title: A95941_KMT2A_C1_(220413_JS_Hs_032922_JS2237)

description: AutoCUTnRUN for KMT2A-C1 in A95941. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: A93949_KMT2A_C2_(220413_JS_Hs_032922_JS2226)

description: AutoCUTnRUN for KMT2A-C2 in A93949. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center


title: A93949_KMT2A_C1_(220413_JS_Hs_032922_JS2225)

description: AutoCUTnRUN for KMT2A-C1 in A93949. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center


title: A93949_IgG_(220413_JS_Hs_032922_JS2227)

description: AutoCUTnRUN for IgG in A93949. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: TB040576_KMT2A_N1_(220413_JS_Hs_032922_JS2199)

description: AutoCUTnRUN for KMT2A-N1 in TB-04-0576. This sample contains the KMT2A-AF9 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; TB-04-0576; KMT2A-AF9; infant Pre-BALL; St. Jude Children's Hospital


title: A93692_KMT2A_N1_(221118_DJ_Hs_A93692_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A93692. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A93692; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A93692_KMT2A_C1_(221118_DJ_Hs_A93692_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A93692. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A93692; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A93692_KMT2A_N2_(221118_DJ_Hs_A93692_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A93692. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A93692; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A93692_KMT2A_C2_(221118_DJ_Hs_A93692_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A93692. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A93692; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A89691_KMT2A_N1_(221118_DJ_Hs_A89691_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A89691. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A89691; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A93692_IgG_(221118_DJ_Hs_A93692_IgG_221101)

description: AutoCUTnRUN for IgG in A93692. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A93692; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A89691_KMT2A_C2_(221118_DJ_Hs_A89691_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A89691. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A89691; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A89691_KMT2A_C1_(221118_DJ_Hs_A89691_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A89691. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A89691; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A82485_KMT2A_N2_(221118_DJ_Hs_A82485_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A82485. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A82485; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A82485_KMT2A_C2_(221118_DJ_Hs_A82485_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A82485. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A82485; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A82485_KMT2A_N1_(221118_DJ_Hs_A82485_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A82485. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A82485; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A82485_IgG_(221118_DJ_Hs_A82485_IgG_221101)

description: AutoCUTnRUN for IgG in A82485. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A82485; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A80956_KMT2A_N2_(221118_DJ_Hs_A80956_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A80956. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A80956; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A80956_KMT2A_N1_(221118_DJ_Hs_A80956_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A80956. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A80956; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A95941_IgG_(220413_JS_Hs_032922_JS2239)

description: AutoCUTnRUN for IgG in A95941. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center


title: A93949_KMT2A_N1_(220413_JS_Hs_032922_JS2223)

description: AutoCUTnRUN for KMT2A-N1 in A93949. This sample contains the KMT2A-AF9 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A93949; KMT2A-AF9; pediatric AML; Fred Hutch Cancer Center


title: A80956_KMT2A_C2_(221118_DJ_Hs_A80956_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A80956. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A80956; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A82485_KMT2A_C1_(221118_DJ_Hs_A82485_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A82485. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A82485; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A73051_KMT2A_N2_(221118_DJ_Hs_A73051_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A73051. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A73051; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A80956_KMT2A_C1_(221118_DJ_Hs_A80956_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A80956. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A80956; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A73051_KMT2A_N1_(221118_DJ_Hs_A73051_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A73051. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A73051; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A73051_KMT2A_C2_(221118_DJ_Hs_A73051_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A73051. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A73051; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A70498_KMT2A_N2_(221118_DJ_Hs_A70498_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A70498. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A70498; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A89691_KMT2A_N2_(221118_DJ_Hs_A89691_KMT2A_N2_221101)

description: AutoCUTnRUN for KMT2A-N2 in A89691. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit KMT2A-N2 CST D2M7U; A89691; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A73051_KMT2A_C1_(221118_DJ_Hs_A73051_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A73051. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A73051; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A70498_KMT2A_N1_(221118_DJ_Hs_A70498_KMT2A_N1_221101)

description: AutoCUTnRUN for KMT2A-N1 in A70498. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-N1 Millipore 05-764; A70498; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A73051_IgG_(221118_DJ_Hs_A73051_IgG_221101)

description: AutoCUTnRUN for IgG in A73051. This sample contains the KMT2A-AF10 translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A73051; KMT2A-AF10; pediatric AML; Fred Hutch Cancer Center


title: A70498_KMT2A_C2_(221118_DJ_Hs_A70498_KMT2A_C2_221101)

description: AutoCUTnRUN for KMT2A-C2 in A70498. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C2 Millipore 05-765; A70498; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: p318_KMT2A_N2_(230626_DJ_Hs_p318_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p318; KMT2A-AFF1; infant AML lineage-switching sample; Texas Children's Hospital


title: A70498_KMT2A_C1_(221118_DJ_Hs_A70498_KMT2A_C1_221101)

description: AutoCUTnRUN for KMT2A-C1 in A70498. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Mouse KMT2A-C1 SantaCruz H10; A70498; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: A89691_IgG_(221118_DJ_Hs_A89691_IgG_221101)

description: AutoCUTnRUN for IgG in A89691. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A89691; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: p318_KMT2A_N1_(230626_DJ_Hs_p318_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p318; KMT2A-AFF1; infant AML lineage-switching sample; Texas Children's Hospital


title: p318_KMT2A_C2_(230626_DJ_Hs_p318_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p318; KMT2A-AFF1; infant AML lineage-switching sample; Texas Children's Hospital


title: p318_KMT2A_C1_(230626_DJ_Hs_p318_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p318; KMT2A-AFF1; infant AML lineage-switching sample; Texas Children's Hospital


title: A70498_IgG_(221118_DJ_Hs_A70498_IgG_221101)

description: AutoCUTnRUN for IgG in A70498. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A70498; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: TB000694_IgG_(220412_JS_Hs_032922_JS2191)

description: AutoCUTnRUN for IgG in TB-00-0694. This sample contains the KMT2A-AF10 translocation and is an infant Pre-BALL from St. Jude Children's Hospital

value: Rabbit IgG abcam ab46540; TB-00-0694; KMT2A-AF10; infant Pre-BALL; St. Jude Children's Hospital


title: p279_KMT2A_N2_(230626_DJ_Hs_p279_KMT2A_N2_230613)

description: AutoCUTnRUN for KMT2A-N2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: Rabbit KMT2A-N2 CST D2M7U; p279; KMT2A-AFF1; infant B-ALL lineage-switching sample; Texas Children's Hospital


title: p318_IgG_(230626_DJ_Hs_p318_IgG_230613)

description: AutoCUTnRUN for IgG in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p318; KMT2A-AFF1; infant AML lineage-switching sample; Texas Children's Hospital


title: p279_IgG_(230626_DJ_Hs_p279_IgG_230613)

description: AutoCUTnRUN for IgG in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: Rabbit IgG abcam ab46540; p279; KMT2A-AFF1; infant B-ALL lineage-switching sample; Texas Children's Hospital


title: p279_KMT2A_N1_(230626_DJ_Hs_p279_KMT2A_N1_230613)

description: AutoCUTnRUN for KMT2A-N1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: Mouse KMT2A-N1 Millipore 05-764; p279; KMT2A-AFF1; infant B-ALL lineage-switching sample; Texas Children's Hospital


title: p279_KMT2A_C2_(230626_DJ_Hs_p279_KMT2A_C2_230613)

description: AutoCUTnRUN for KMT2A-C2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: Mouse KMT2A-C2 Millipore 05-765; p279; KMT2A-AFF1; infant B-ALL lineage-switching sample; Texas Children's Hospital


title: p279_KMT2A_C1_(230626_DJ_Hs_p279_KMT2A_C1_230613)

description: AutoCUTnRUN for KMT2A-C1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: Mouse KMT2A-C1 SantaCruz H10; p279; KMT2A-AFF1; infant B-ALL lineage-switching sample; Texas Children's Hospital


title: A80956_IgG_(221118_DJ_Hs_A80956_IgG_221101)

description: AutoCUTnRUN for IgG in A80956. This sample contains the KMT2A-AFDN translocation and is a pediatric AML from Fred Hutch Cancer Center

value: Rabbit IgG abcam ab46540; A80956; KMT2A-AFDN; pediatric AML; Fred Hutch Cancer Center


title: JLat106 NFkB AZD5582+IBET151 vRNA Rep1

status: Public on Sep 17 2024

city: Seattle

first: Michael

last: Emerman

state: Washington

address: 1110 Fairview Ave N

institute: Fred Hutch Cancer Research Center

library_source: other

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis (RTA) v3.9.2 for NextSeq data and RTA v1.18.54.4 for MiSeq data. This was followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v2.20.
Adapter trimming was performed using Cutadapt.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform guide-level quantification followed by differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: Samples 1 through 12 were aligned against the HuEpi guide RNA library generated by Emerman lab. The library targets 841 human epigenome genes and 252 non-targeting controls. Samples 13 through 15 were aligned against the RelB library from Emerman lab, which consists of 503 genes and 163 non-targetting controls.
Supplementary files format and content: Tab delimited files with read counts for each guide sequence
Library strategy: CRISPR Screen

molecule: other

source_name: Peripheral blood

growth_protocol: J-Lat 10.6 ZAP KO and J-Lat 5A8 ZAP KO are grown in RPMI-1640 supplemented with 10% FBS, 10nM HEPES, and Pen/Strep. Cells are passaged between 2 x 10^5 cells/mL and 2 x 10^6 cells/mL.

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen, Cat No 52904). Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen, Cat No 51183).
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the 5,309 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: For HuEpi and NFkB: 3 x 10^6 (>500X coverage) J-Lat 10.6 ZAP KO and J-Lat 5A8 ZAP KO cells were each transduced with the HuEpi library (MOI of 0.4) and selected in  0.4 ug/mL puromycin for 10-14 days. For each cell line, knockout cell pools are treated with: all HuEpi screens were performed with 10 nM AZD5582 & 100 nM I-BET151 for 48 hrs whereas all NFkB screens were performed with 1 nM AZD5582 & 2.5uM I-BET151 for 24hrs.

value: Peripheral blood

tag: cell line

value: Jurkat

tag: genotype

value: NFkB Library KO

tag: treatment


title: JLat5A8 HuEpi DMSO gDNA Rep2

value: J-Lat 5A8

value: HuEpi Library KO

value: DMSO


title: JLat106 NFkB AZD5582+IBET151 vRNA Rep2


title: JLat106 NFkB AZD5582+IBET151 gDNA


title: JLat5A8 HuEpi DMSO vRNA Rep1


title: JLat5A8 HuEpi DMSO gDNA Rep1


title: JLat106 HuEpi DMSO gDNA Rep2


title: JLat5A8 HuEpi DMSO vRNA Rep2


title: JLat106 HuEpi DMSO gDNA Rep1


title: JLat106 HuEpi AZD5582+IBET151 vRNA Rep2


title: JLat5A8 HuEpi AZD5582+IBET151 vRNA Rep2


title: JLat106 HuEpi DMSO vRNA Rep1


title: JLat5A8 HuEpi AZD5582+IBET151 vRNA Rep1


title: BMMC_Chol_rep4

status: Public on Sep 10 2024

type: genomic

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

description:
Unsorted monocytes from cultured BMMCs
Chol4

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.14.2
Normalized average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

organism: Mus musculus

source_name: Cultured BMMCs, cholesterol

label_protocol: Standard Illumina Protocol

growth_protocol: In vitro bone marrow monocyte (BMMC) LPS exhaustion experiments were performed as previously described (Pradhan et al., 2021, Front. Immunol.). Briefly, bone marrow cells were harvested from 6- to 8-week-old C57BL/6 WT female mice, seeded at a density of 3x10^5 cells/cm2, and cultured in complete RPMI 1640 media (10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine) supplemented with 10 ng/mL M-CSF (PeproTech). Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous low-dose 100 pg/mL lipopolysaccharide (LPS; Sigma-Aldrich) or 10 µg/mL cholesterol (Sigma-Aldrich) stimulation.

extract_protocol: Cultured BMMCs were harvested by manual disruption and processed for genomic DNA using a DNeasy Blood and Tissue Kit (Qiagen).

tag: Sex

value: Female

tag: age

tag: strain

value: Cholesterol

value: Cultured primary bone marrow monocytes


title: BMMC_Chol_rep2

description:
Unsorted monocytes from cultured BMMCs
Chol2

treatment_protocol: Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous low-dose 100 pg/mL lipopolysaccharide (LPS; Sigma-Aldrich) or 10 µg/mL cholesterol (Sigma-Aldrich) stimulation.


title: BMMC_Chol_rep3

description:
Unsorted monocytes from cultured BMMCs
Chol3


title: JLat106 HuEpi AZD5582+IBET151 vRNA Rep1


title: BMMC_lowLPS_rep2

description:
Unsorted monocytes from cultured BMMCs
lowLPS2

source_name: Cultured BMMCs, low-dose LPS

value: Low-dose LPS


title: BMMC_lowLPS_rep4

description:
Unsorted monocytes from cultured BMMCs
lowLPS4


title: BMMC_lowLPS_rep1

description:
Unsorted monocytes from cultured BMMCs
lowLPS1


title: Female, never-smoker, GEX, subject4

status: Public on Aug 14 2024

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

description:
polyA nuclear RNA
10X Genomics
FN4_GEX

data_processing:
The demultiplexing, barcode processing, and alignment to human genome reference sequences (GRCh38) were performed using Cell Range ARC software (10x Genomics, v.2.0.1 or 2.0.0)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: Seurat object including cell type annotation, sample information, expression levels, and chromatin accessibility peaks.

molecule: polyA RNA

source_name: Tumor-distant normal lung

extract_protocol:
The tissues were collected at a ~2 cm3 size and put in MACS Tissue Storage Solution (Miltenyl biotec cat.130-100-008) within 30 mins of surgical dissection. Samples were kept at 4°C and processed within 3 hours of dissection. Tissues were chopped into 2 mm diameter pieces within a dissociation tube to reduce the cell loss. Multi Tissue Dissociation Kit 1 and gentleMACS Octo Dissociator (Miltenyi Biotec) were used for dissociation of the tissue into single-cell suspension with a reduced amount of enzyme R (25% of the regular amount). Red blood cells were removed using Red Blood Cell Lysis Solution (Miltenyl biotec cat.130-094-183). Single-cell suspension of samples was frozen using 90% FBS and 10% DMSO and stored in liquid nitrogen until further processing except for the time of transfer in dry ice. The dissociated single-cell suspensions were thawed and filtered using a 70 μm cell strainer (Miltenyi Biotec) to remove debris. The filtered cells were labelled with cell viability marker (DAPI) and antibody markers of EPCAM, CD31, and CD45. Live single-cells (DAPI-negative) were sorted into lysis plates based on three gates: EPCAM+CD45- (designated “epithelial”), EPCAM-CD45+ (designated “immune”), and EPCAM-CD45- (designed “endothelial or stromal”). To enrich epithelial cells, which are considered to have key roles in lung cancer etiology, we collected all “epithelial” cells from EPCAM+CD45- gates and balanced the ratios to 6:3:1 (“epithelial”: “immune”: “endothelial or stromal”). Nuclei isolation was performed based on “Low Cell Input Nuclei Isolation” protocol (CG000365-Rev C, 10X Genomics) with a modification of the 1X lysis buffer treatmenet time (3-second duration).
Isolated nuclei were used for single-cell capture and sequencing library preparation using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits following the manufacturer’s guidelines (CG000338- Rev E, 10X Genomics, USA).

value: Tumor-distant normal lung

tag: subject status

value: never-smoker

tag: subject id


title: BMMC_lowLPS_rep3

description:
Unsorted monocytes from cultured BMMCs
lowLPS3


title: BMMC_Chol_rep1

description:
Unsorted monocytes from cultured BMMCs
Chol1


title: Female, never-smoker, GEX, subject1

description:
polyA nuclear RNA
10X Genomics
FN1_GEX


title: Female, never-smoker, GEX, subject2

description:
polyA nuclear RNA
10X Genomics
FN2_GEX


title: Female, smoker, GEX, subject2

description:
polyA nuclear RNA
10X Genomics
FS2_GEX

value: smoker


title: Female, smoker, GEX, subject1

description:
polyA nuclear RNA
10X Genomics
FS1_GEX


title: Male, never-smoker, GEX, subject2

description:
polyA nuclear RNA
10X Genomics
MN2_GEX

value: Male


title: Male, never-smoker, GEX, subject3

description:
polyA nuclear RNA
10X Genomics
MN3_GEX


title: JLat106 HuEpi DMSO vRNA Rep2


title: Male, smoker, GEX, subject4

description:
polyA nuclear RNA
10X Genomics
MS4_GEX


title: Male, never-smoker, GEX, subject1

description:
polyA nuclear RNA
10X Genomics
MN1_GEX


title: Male, smoker, GEX, subject3

description:
polyA nuclear RNA
10X Genomics
MS3_GEX


title: Male, smoker, GEX, subject2

description:
polyA nuclear RNA
10X Genomics
MS2_GEX


title: Male, smoker, GEX, subject1

description:
polyA nuclear RNA
10X Genomics
MS1_GEX


title: ChIP2, Tal1(ddm1), Rep2

status: Public on Aug 08 2024

city: Bunkyo-ku

first: Sayuri

last: Tsukahara

state: Tokyo

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

data_processing:
ChIP-seq reads were mapped on the Col-CEN genome using Bowtie2 (ver. 2.4.4). The read count for each 10 kb bins was calculated using the coverage function of BEDTools (ver. 2.26.0).
For ONT, R9 reads were filtered for length and accuracy using Filtlong (Version 0.2.0) (--min_mean_q 90, --min_length 5000). Methylation prediction for the CG, CHG, and CHH contexts were called using DeepSignal-plant (v1.6.1) using the model: model.dp2.CNN.arabnrice2-1_120m_R9.4plus_tem.bn13_sn16.both_bilstm.epoch6.ckpt.
Assembly: Col-CEN_v1.2
Supplementary files format and content: bedgraph for ChIP-seq, tsv for ONT

organism: Arabidopsis thaliana

source_name: 2-week-old seedlings

growth_protocol: Plants were grown on plates of 0.5 x MS medium.

extract_protocol:
For ChIP-seq, ground tissue samples were fixed with 1% formaldehyde for 10 min. After quencing and cell lysis, chromatin was sonicated using a bioruptor pico (Diagenode).
ChIP-seq libraries were constructed using ThruPLEX DNA-seq Kit (Clontech).

value: 2-week-old seedlings

value: CENH3 ChIP


title: ChIP1, CENH3-OX-2


title: ChIP1, wild type

value: WT


title: ChIP1, CENH3-OX-1


title: ChIP1, CENH3-OX-3


title: ChIP2, Tal1(ddm1), Rep3


title: Female, never-smoker, GEX, subject3

description:
polyA nuclear RNA
10X Genomics
FN3_GEX


title: ChIP2, Tal1(WT)


title: Female, smoker, GEX, subject3

description:
polyA nuclear RNA
10X Genomics
FS3_GEX


title: Female, smoker, GEX, subject4

description:
polyA nuclear RNA
10X Genomics
FS4_GEX


title: A549 + LKB1 High methionine plus Carboplatin

status: Public on Jul 19 2024

city: LEXINGTON

first: Christine

middle: Fillmore

last: Brainson

state: KY

address: 1095 VA Drive

department: Toxicology and Cancer Biology

institute: University of Kentucky

description:
12LKB1_High_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv

library_source: transcriptomic

data_processing:
Sequencing and base-calling were performed by BGI (Beijing Genomics Institute)
Sequencing reads were trimmed and filtered using Trimmomatic(V0.39) to remove adapters and low quality reads. Reads from samples were mapped to Ensembl GRCh37 transcripts annotation, using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Assembly: GRCh37R75
Supplementary files format and content: TPM data: gene.TPM.annotated.tsv
Supplementary files format and content: Count data: gene.count.annotated.tsv

source_name: Lung tumor cell line

growth_protocol: A549 cells with and without LKB1 were grown in low, regular, or high methionine media

extract_protocol:
Cells were collected by removing cells from plates with trypsin. Trypsin was neutralized and RNA was extracted using Absolutely RNA Nanoprep kits (Agilent).
RNA libraries were prepared for sequencing using BGI protocols.

treatment_protocol: A549 cells with and without LKB1 were sensitized to low (58µM), regular (115µM), and high (575µM) methionine media (RPMI) for 5 days, they were then treated for 4 days with either vehicle control or 60 µM carboplatin, cells were collected on day 4 of carboplatin treatment

value: Lung tumor cell line

value: lung adenocarcinoma

value: High methionine

value: Carboplatin


title: A549 + LKB1 Low methionine plus Carboplatin

description:
8LKB1_Low_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv

value: Low methionine


title: A549 + LKB1 High methionine no Carboplatin

description:
11LKB1_High_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv

value: Vehicle


title: Male, never-smoker, GEX, subject4

description:
polyA nuclear RNA
10X Genomics
MN4_GEX


title: A549 + pBABE EV High methionine no Carboplatin

description:
5pBABE_High_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv

value: pBABE EV


title: A549 + pBABE EV High methionine plus Carboplatin

description:
6pBABE_High_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: A549 + LKB1 Low methionine no Carboplatin

description:
7LKB1_Low_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: A549 + pBABE EV Regular methionine plus Carboplatin

description:
4pBABE_Reg_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv

value: Regular methionine


title: A549 + pBABE EV Regular methionine no Carboplatin

description:
3pBABE_Reg_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: ChIP1, CENH3-OX-4


title: ChIP2, Tal1(ddm1), Rep1


title: A549 + pBABE EV Low methionine no Carboplatin

description:
1pBABE_Low_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: PDX-G266, Xe4MeCF3 + Docetaxel , LWHR40

status: Public on Jul 18 2024

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads preprocessing steps were performed using cutadapt 1.10, reads were mapped onto the hg38 assembly of Homo sapiens genome using STAR version 2.5.3a. Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 108 and “union” mode. Only non-ambiguously assigned reads were retained for further analyses. Read counts were normalized across libraries by published method
Assembly: hg38
Supplementary files format and content: alldata_count.tsv

source_name: PDX-G266 mice, a model of CRPC

extract_protocol: P2830 : RNA-Seq libraries were generated according to manufacturer's instructions from 300 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94oC for 8 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

value: castration-resistant prostate cancer (CRPC)

value: Xe4MeCF3 + Docetaxel


title: PDX-G266, Xe4MeCF3 + Docetaxel , LWHR39


title: PDX-G266, Vehicle, LWHR35


title: ChIP2, ddm1


title: A549 + LKB1 Regular methionine plus Carboplatin

description:
10LKB1_Reg_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: PDX-G266, Vehicle, LWHR34


title: PDX-G266, Vehicle, LWHR33


title: ChIP2, wild type


title: A549 + LKB1 Regular methionine no Carboplatin

description:
9LKB1_Reg_0
gene.count.annotated.tsv
gene.TPM.annotated.tsv


title: PDX-G266, Xe4MeCF3 + Docetaxel , LWHR37


title: BMMC, LPS, IgG Control, rep3

status: Public on Mar 05 2024

data_processing:
Paired-end CUT&RUN reads were mapped to the mm10 and E. coli (MG1655) genomes using bowtie2 (2.5.2; parameters: --local –very-sensitive –no-mixed –no-discordant –dovetail)
Low quality mapped reads (-q 30) and PCR duplicates were removed using samtools, and peak calling was performed using SEACR (parameters: norm, stringent)
CUT&RUN coverage was determined using deepTools (3.5.2; function: bamCompare), with coverage values normalized to E. coli spike-in controls
bigwig files were prepared using bedGraphToBigWig (UCSC)
Assembly: mm10
Supplementary files format and content: biwgwig, bed (SEACR formatted: <chr> <start> <end> <total signal> <max signal> <max signal region>)
Library strategy: CUT&RUN

source_name: Cultured primary bone marrow monocytes

growth_protocol: In vitro bone marrow monocyte (BMMC) LPS exhaustion experiments were performed as previously described (Pradhan et al., 2021, Front. Immunol.). Briefly, bone marrow cells were harvested from 6- to 8-week-old C57BL/6 WT female mice, seeded at a density of 3x105 cells/cm2, and cultured in complete RPMI 1640 media (10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine) supplemented with 10 ng/mL M-CSF (PeproTech). Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation or PBS control conditions, with fresh media changes at days 2 and 4 of culture.

extract_protocol:
Cultured BMMCs were harvested by manual disruption and immediately processed for CUT&RUN using a CUTANA ChIC/CUT&RUN Kit (EpiCypher) according to the manufacturer’s protocol. Briefly, live cells were permeabilized in 0.01% digitonin in the presence of ConA beads. K-MetStat Panel spike-in was added to each reaction, and samples were incubated overnight at 4˚C in the presence of H3K4me1 (EpiCypher #13-0057), H3K4me3 (EpiCypher #13-0041), or IgG negative control (EpiCypher #13-0042) antibodies. Following PAG-MNase digestion and chromatin release, 0.5ng of E. coli spike-in DNA were added to each reaction, and DNA samples were purified using CUTANA kit reagents.
Purified DNA was quantified using a Qubit dsDNA HS Assay Kit (Invitrogen), and 1-5 ng of purified DNA were used as input for CUTANA CUT&RUN Library Prep Kit (EpiCypher) according to the manufacturer’s protocol. Library fragment sizes were analyzed using Tapestation DNA ScreenTape analysis (Agilent) at the Fralin Life Sciences Institute at Virginia Tech Genomics Sequencing Center.

treatment_protocol: BMMCs were cultured for 5 days under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation or PBS control conditions

value: Cultured primary bone marrow monocytes

value: Female

value: LPS

value: IgG (EpiCypher #13-0042)


title: K562 WT replicate 2

status: Public on May 29 2024

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

data_processing:
For gene expression analysis, reads were pseudoaligned using kallisto.
Differential gene expression was determined using the DESeq2 package.
For splicing analysis, RSEM v1.2.4 was used to map all RNA-seq reads to this transcriptome annotation.
Remaining unaligned reads were then mapped a database of all possible junctions between annotated 5' and 3' splice sites of the transcriptome annotation, as well as to the genome sequence, with TopHat v2.0.8b, and the resulting aligned reads were merged with the RSEM output
The expression levels of isoforms annotated in MISO v2.0’s annotation were estimated with MISO v2.0.
To identify events that were differentially spliced, we defined the metric deltaPSI (ΔPSI) as the isoform ratio (absolute percentage of mRNA) in SF3B1-mutant samples - isoform ratio in SF3B1-WT cells, and computed a significance statistic using Wagenmakers’s Bayesian framework for single-sample comparisons or the Mann-Whitney U test for group comparisons. An event was classified as differentially spliced if it exhibited an absolute change of ΔPSI ≥ 10% and Bayes factor ≥ 5 or p < 0.05.
Assembly: For splicing analysis, transcriptome annotation for the hg19/GRCh37 human genome assembly was created by merging gene annotations from Ensembl v71.1, the UCSC knownGene track, and MISO v2.0 isoform annotations.
Assembly: For gene expession analysis, hg38 reference genome was used.
Supplementary files format and content: comma-separated values file including splicing analysis for CB CD34+ HSPCs including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including splicing analysis for PB CD34+ HSPCs including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including splicing analysis for PB CD34+ HSPCs (SMARTSeq v4 Ultra Low Input RNA Kit) including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including normalised counts for CD34+ HSPCs.
Supplementary files format and content: comma-separated values file including paiwise comparison between SF3B1 mutant and AAVS1 control CD34+ HSPCs.
Supplementary files format and content: comma-separated values file including splicing analysis for K562 cells including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including normalised counts for K562 cells.
Supplementary files format and content: comma-separated values file including paiwise comparison between SF3B1 mutant and wild-type K562 cells.

source_name: Hematopoietic

growth_protocol:
HSPCs were cultured in StemSpan SFEM II (StemCell Technologies), 100 U/mL penicillin/streptomycin (Fisher), 100 ng/ml SCF, 100 ng/ml FLT3, 100 ng/ml TPO, 100 ng/ml IL-6 (all Peprotech), 35 nM UM171 (Apexbio Technology) and 0.75 μM SR1 (Cellagen Technology). Cell density was maintained between 4 x 10^5 and 1 x10^6 per ml.
SF3B1-mutant (K700E) and wild-type control K562 cells (25) were grown in Iscove’s modified Dulbecco’s media (IMDM) with 10% FBS and 100 U/mL penicillin/streptomycin (Fisher), and cultures were maintained at <1.5 x 10^6 cells/ml.

extract_protocol:
Cells were resuspended in Trizol (ThermoFisher, cat. #15596026), and RNA extracted per manufacturer protocol.
RNA sequencing was performed at Omega Bioservices with TruSeq Stranded mRNA kit with polyA selection. PB BFP+CD34+ gene edited HSPCs were additionally sequenced with SMARTSeq v4 Ultra Low Input RNA Kit.

treatment_protocol: HSPCs were CRISPR-edited using the Lonza 4D Nucleofection system and the Human Primary Cell Nucleofection Kit (Lonza). RNP complexes were generated by combining Cas9 protein and sgRNA (Synthego) at 1:2.5 molar ratio in P3 Primary Cell Nucleofector Solution with Supplement 1 (Lonza). CD34+ HSPCs were electroporated using Lonza 4D (DZ-100 program) and returned to HSPC media containing AAV particles comprising < 20% culture volume, as recommended. HSPCs were washed 16-24 hours later and plated in HSPC media for 48 hours.

value: Hematopoietic


title: PDX-G266, Vehicle, LWHR32


title: BMMC, LPS, H3K4me3, rep2

value: H3K4me3 (EpiCypher #13-0041)


title: BMMC, PBS, H3K4me3, rep3

value: PBS


title: BMMC, LPS, IgG Control, rep2


title: K562 WT replicate 1

description: TruSeq Stranded mRNA kit with polyA selection


title: Age3, SV, svRNA-seq

status: Public on May 16 2024

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation Street

department: BMB

institute: Umass Chan Medical School

description: 10x Genomics

data_processing:
Seurat was used for clustering single-cell data. We filtered cells that have a number of unique features (genes) less than 500, a number of unique molecular identifiers (UMI) less than 200, and a percentage of mitochondrial genes over 1%. After filtering, we have total 47,804 cells and 19,601 features (genes) with average 6053 UMI per cell. Filtered data was normalized with SCTransform as described in {Choudhary, 2022 #3428}. Transformed data across conditions were then integrated with canonical correlation analysis. Genes from the FindVariableFeatures function were used as input for the initial principal component analysis (PCA). The number of principal components (PCs) was chosen based on the Seurat ElbowPlot function. We set resolution parameters from 0.1 to 1.4 and examined the clustering quality based on DoHeatmap function and clustree. We identified significantly differentially expressed markers in each cluster by running the default FindAllMarkers function. We annotated cell types based on well-established markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and mitrix files.

source_name: Seminal vesicle

extract_protocol:
After euthanizing the mice, the urogenital system was exposed. The entire urogenital system was taken out of the mouse abdominal cavity and placed into a 60 mm Petri dish containing 5 ml complete medium (CM) composed of IMDM (Invitrogen), 10% FBS (Sigma), and Antibotica-Antimycotic (invitrogen). Under a dissection microscope, carefully remove the surrounding organs and tissues. Open the seminal vesicle longitudinally with a scissor and let seminal vesicle fluid out of the organ. Transfer the tissue to another dish and gently remove any loose coagulated seminal vesicle fluid without disturbing the epithelial cell layer.  After washing, the tissue was transferred into a 15 ml conical tube with 2 ml CM and 2 ml extracellular matrix digestion media (ECM) containing collagenase (Sigma), DNase (Sigma), collagenase/hyaluronidase (Stem Cell), and collagenase/dispase (Sigma). The tissue was incubated in a water bath at 300 rpm for 30 minutes at 35 C. After incubation, 10 ml IMDM-DNase media was added to the tube and centrifuged at 300 g for 5 minutes at room temperature. Wash the pellet once with 8 ml IMDM-DNase media. Resuspend the pellet with 3 ml TrypLEtm express (Gibco), and digested the tissue in the water bath at 300 rpm for 5 minutes at 35 C. Fill the tube with 10 ml CM and filter the cell suspension through a series of 100 μm, 70 μm, and 40 μm cell strainers. Pellet the cells by centrifuging for 5 minutes at 300 g. Resuspend the pellet with 3 ml CM. The cell suspension was then placed on the top of OptitPrep (Sigma) gradient followed by centrifuging at 800 g for 15 minutes. The gradient was composed of 3 ml of 67%, 50%, and 36% OptiPrep in CM, respectively. Interface fractions were collected and cells were pelleted, washed 1X with CM, and resuspended in 1 ml CM. The samples with cell viability over 80% were used for sequencing library preparation.
Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics), as per the manual.

treatment_protocol: Mice were housed under a controlled lighting regimen (12-h light: 12 h dark) at 21 to 22 °C and supplied with food and water ad libitum.

value: Seminal vesicle

value: male

value: Wild type

value: aging


title: BMMC, LPS, H3K4me1, rep2

value: H3K4me1 (EpiCypher #13-0057)


title: BMMC, LPS, H3K4me3, rep3


title: BMMC, PBS, IgG Control, rep2


title: BMMC, LPS, H3K4me1, rep3


title: BMMC, PBS, H3K4me3, rep2


title: BMMC, PBS, H3K4me1, rep2


title: A549 + pBABE EV Low methionine plus Carboplatin

description:
2pBABE_Low_Plus
gene.count.annotated.tsv
gene.TPM.annotated.tsv

value: Lung tumor cell line

value: lung adenocarcinoma

value: Low methionine

value: Carboplatin


title: BMMC, LPS, IgG Control, rep1


title: BMMC, PBS, H3K4me1, rep3


title: PDX-G266, Xe4MeCF3 + Docetaxel , LWHR36

value: castration-resistant prostate cancer (CRPC)

value: Xe4MeCF3 + Docetaxel


title: BMMC, LPS, H3K4me3, rep1

value: Cultured primary bone marrow monocytes

value: Female


title: BMMC, LPS, H3K4me1, rep1

value: LPS


title: BMMC, PBS, H3K4me1, rep1


title: BMMC, PBS, IgG Control, rep1

value: IgG (EpiCypher #13-0042)


title: BMMC, PBS, H3K4me3, rep1

value: H3K4me3 (EpiCypher #13-0041)


title: Food2, SV, scRNA-seq

description: 10x Genomics

value: FVB/NJ

value: diet


title: BMMC, PBS, IgG Control, rep3

value: PBS


title: BMMC_Ticam2_PBS_rep2

description:
Total monocytes (not FACS sorted)
TICAM2_PBS_2
matrix_signal.xlsx

data_processing: SeSAMe software v1.14.2

source_name: Cultured BMMCs, Ticam2-/-, PBS control

growth_protocol: In vitro bone marrow monocyte (BMMC) LPS exhaustion experiments were performed as previously described (Pradhan et al., 2021, Front. Immunol.). Briefly, bone marrow cells were harvested from 6- to 8-week-old C57BL/6 WT female mice, seeded at a density of 3x105 cells/cm2, and cultured in complete RPMI 1640 media (10% fetal bovine serum, 1% penicillin-streptomycin, 1% L-glutamine) supplemented with 10 ng/mL M-CSF (PeproTech). Cells were cultured for 5 days at 37˚C in a humidified 5% CO2 atmosphere under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation or PBS control conditions, with fresh media changes at days 2 and 4 of culture. For trehalose 6,6’-dimycolate (TDM; invivoGen) experiments, cells were maintained in TDM (10 µg/mL) for the full 5 day LPS exhaustion time course.

extract_protocol: Cultured BMMCs were harvested by manual disruption and either directly processed for genomic DNA extraction (total monocytes) or FACS sorted based on Ly6C expression (Ly6C-low, -int, and -high). Bone marrow monocytes from in vivo experiments were isolated using LS columns (Miltenyi). Genomic DNA was prepared for all samples using a DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: BMMCs were cultured for 5 days under continuous high-dose 100 ng/mL lipopolysaccharide (LPS; Sigma-Aldrich) stimulation or PBS control conditions. For trehalose 6,6’-dimycolate (TDM; invivoGen) experiments, cells were maintained in TDM (10 µg/mL) for the full 5 day LPS exhaustion time course. For in vivo experiments, sepsis was induced by intraperitoneal injection of cecal slurry in 6- to 8-week-old C57BL/6 WT male mice as previously described. Briefly, whole ceca were dissected from 12-week-old C57BL/6 mice euthanized by cervical dislocation. Cecal contents were extracted and mixed with sterile water (250 µg/µL), sequentially filtered through 860 µm and 190 µm mesh strainers, mixed with an equal volume of 30% glycerol in PBS (final concentration 125 µg/µL), and placed in -80˚C storage. For cecal slurry injections, frozen cecal slurry (CS) stock was rapidly thawed in 37˚C water bath and injected (0.9 mg/g mouse weight) into the peritoneal cavity of recipient mice. After 5 days, mice were injected with a second 0.9 mg/g dose of CS, and then euthanized by cervical dislocation 1, 2, or 7 days later. Bone marrow cells were collected as previously described and used for flow cytometry analysis or LS column purification (Miltenyi) of bone marrow monocytes following the manufacturer’s protocol.

tag: ly6c subtype

tag: cs experimental day


title: BMMC_CSd12_PBS_rep1

description:
Total monocytes (not FACS sorted)
CSd12_BMMC_1
matrix_signal.xlsx

source_name: Cultured BMMCs, CSd12, PBS control

value: Male

value: Day 12


title: BMMC_CSd12_PBS_rep3

description:
Total monocytes (not FACS sorted)
CSd12_BMMC_3
matrix_signal.xlsx


title: BMMC_Ticam2_PBS_rep4

description:
Total monocytes (not FACS sorted)
TICAM2_PBS_4
matrix_signal.xlsx


title: BM_CTRL_rep7

description: Total monocytes, LS column purified

source_name: Bone marrow monocytes, CTRL mice

value: CTRL

value: Bone marrow monocytes


title: BMMC_Ticam2_LPS_rep4

description:
Total monocytes (not FACS sorted)
TICAM2_LPS_4
matrix_signal.xlsx

source_name: Cultured BMMCs, Ticam2-/-, LPS


title: BM_CTRL_rep5

description: Total monocytes, LS column purified


title: BMMC_CSd12_PBS_rep2

description:
Total monocytes (not FACS sorted)
CSd12_BMMC_2
matrix_signal.xlsx


title: BM_CSd12_rep4

description: Total monocytes, LS column purified

source_name: Bone marrow monocytes, CS mice, day 12

value: CS


title: BM_CSd6_rep4

description: Total monocytes, LS column purified

source_name: Bone marrow monocytes, CS mice, day 6

value: Day 6


title: BM_CSd12_rep2

description: Total monocytes, LS column purified


title: BMMC_Ticam2_PBS_rep1

description:
Total monocytes (not FACS sorted)
TICAM2_PBS_1
matrix_signal.xlsx


title: BMMC_Ticam2_LPS_rep1

description:
Total monocytes (not FACS sorted)
TICAM2_LPS_1
matrix_signal.xlsx


title: BM_CSd7_rep4

description: Total monocytes, LS column purified

source_name: Bone marrow monocytes, CS mice, day 7

value: Day 7


title: BM_CSd6_rep3

description: Total monocytes, LS column purified


title: BM_CSd7_rep2

description: Total monocytes, LS column purified


title: BM_CSd7_rep6

description: Total monocytes, LS column purified


title: BMMC_Ticam2_LPS_rep3

description:
Total monocytes (not FACS sorted)
TICAM2_LPS_3
matrix_signal.xlsx


title: BM_CSd7_rep1

description: Total monocytes, LS column purified


title: BMMC_Ticam2_LPS_rep2

description:
Total monocytes (not FACS sorted)
TICAM2_LPS_2
matrix_signal.xlsx


title: BM_CTRL_rep4

description: Total monocytes, LS column purified


title: BM_CSd12_rep1

description: Total monocytes, LS column purified


title: BMMC_CSd12_PBS_rep4

description:
Total monocytes (not FACS sorted)
CSd12_BMMC_4
matrix_signal.xlsx


title: BM_CSd7_rep5

description: Total monocytes, LS column purified


title: BMMC_Ticam2_PBS_rep3

description:
Total monocytes (not FACS sorted)
TICAM2_PBS_3
matrix_signal.xlsx


title: BM_CSd7_rep3

description: Total monocytes, LS column purified


title: BM_CTRL_rep6

description: Total monocytes, LS column purified


title: BM_CSd6_rep1

description: Total monocytes, LS column purified


title: BM_CSd6_rep2

description: Total monocytes, LS column purified


title: BM_CTRL_rep2

description: Total monocytes, LS column purified


title: BM_CSd12_rep3

description: Total monocytes, LS column purified


title: BM_CTRL_rep1

description: Total monocytes, LS column purified


title: BMMC_LPS-TDM_rep4

description: Total monocytes (not FACS sorted)

source_name: Cultured BMMCs, LPS with TDM


title: g4_wt_fl_E125_r2

status: Public on Mar 04 2024

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: bulk limb

data_processing:
Reads from RNA-seq were mapped using the STAR 2.7.2b mapper with default settings to the GRCm39/mm39 genome
Assembly: mm39
Supplementary files format and content: BigWig

source_name: embryonic limb bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA from 1,5 x10^5 cells was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina NovaSeq 6000 sequencer.

value: embryonic limb bud

value: embryonic limb cell

value: WT


title: BMMC_LPS-TDM_rep3

description: Total monocytes (not FACS sorted)

value: Female

value: Cultured primary bone marrow monocytes


title: g4_wt_fl_E125_r1

description: bulk limb


title: Sample 19 Control

status: Public on Feb 29 2024

city: Winnipeg

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

data_processing:
Raw reads were quality and adapter trimmed using cutadapt and then aligned to the Hg38 reference genome using STAR
Gene count matrix generated using FeatureCounts
Assembly: Hg38
Supplementary files format and content: csv file with raw counts for each sample

source_name: Lung

extract_protocol:
RNA extracted from lung tissue stored in RNAlater using Ambion PureLink RNA Mini Kit
Illumina's TruSeq mRNA Stranded kit

treatment_protocol: E-cigarette habits were collected by questionnaire

value: Lung

value: Control


title: BM_CTRL_rep3

description: Total monocytes, LS column purified


title: Sample 18 Control


title: BMMC_LPS-TDM_rep1

description: Total monocytes (not FACS sorted)

value: LPS


title: BMMC_LPS_rep4

description: Total monocytes (not FACS sorted)

source_name: Cultured BMMCs, LPS


title: Sample 21 Control


title: BMMC_PBS_rep3

description: Total monocytes (not FACS sorted)

source_name: Cultured BMMCs, PBS control


title: BMMC_LPS_rep3

description: Total monocytes (not FACS sorted)


title: BMMC_LPS-TDM_rep2

description: Total monocytes (not FACS sorted)


title: Sample 17 E-cig

value: E-cig


title: Sample 16 Control


title: BMMC_PBS_Ly6C-low_rep1

description: FACS sorted for Ly6C-low monocytes

source_name: Cultured BMMCs, PBS control, Ly6C-low

value: PBS


title: BMMC_PBS_Ly6C-low_rep3

description: FACS sorted for Ly6C-low monocytes


title: Sample 9 Control


title: Sample 10 Control


title: BMMC_LPS_rep1

description: Total monocytes (not FACS sorted)


title: BMMC_PBS_rep4

description: Total monocytes (not FACS sorted)


title: Sample 4 E-cig


title: Sample 7 E-cig


title: Sample 3 Control


title: BMMC_LPS_Ly6C-high_rep3

description: FACS sorted for Ly6C-high monocytes

source_name: Cultured BMMCs, LPS, Ly6C-high


title: Sample 2 Control


title: BMMC_PBS_rep1

description: Total monocytes (not FACS sorted)


title: BMMC_LPS_Ly6C-int_rep3

description: FACS sorted for Ly6C-int monocytes

source_name: Cultured BMMCs, LPS, Ly6C-int


title: BMMC_LPS_Ly6C-low_rep1

description: FACS sorted for Ly6C-low monocytes

source_name: Cultured BMMCs, LPS, Ly6C-low


title: Sample 5 E-cig


title: Sample 1 Control


title: BMMC_LPS_Ly6C-low_rep3

description: FACS sorted for Ly6C-low monocytes


title: BMMC_LPS_rep2

description: Total monocytes (not FACS sorted)


title: BMMC_LPS_Ly6C-low_rep2

description: FACS sorted for Ly6C-low monocytes


title: BMMC_PBS_rep2

description: Total monocytes (not FACS sorted)


title: BMMC_LPS_Ly6C-high_rep1

description: FACS sorted for Ly6C-high monocytes


title: Subject_2_Tissue

status: Public on Feb 08 2024

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

description: 10X Genomics

data_processing:
Cell Ranger software v7.0.0 was used for basecalling, demultiplexing and initial analyses to create the single cell count matrix (Subject_1_Blood, Subject_1_Tissue, Subject_2_Blood, Subject_2_Tissue). cellranger mkfastq and cellranger count were used for this purpose with default parameters.
H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample
The CellPlex data were demultiplexed using Cell Ranger software v7.0.0
The cell count were analyzed using cellranger multi (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi) using CMO constructs and associated barcodes (Subject_5_Blood = 303, Subject_5_Tissue = 304)
Assembly: GRCh38
Supplementary files format and content: H5 files were created using cellranger multi to get the general multiplexing and demultiplexed output per samples

molecule: cytoplasmic RNA

source_name: Periprosthetic soft tissue

extract_protocol: Leukocytes were collected from whole blood using Histopaque and periprosthetic tissue was dissociated using a mortar and pestle in ice-cold HBSS + 10% FBS to obtain a single cell suspension. The resulting cell suspensions were passed through a 70um filter to remove aggregates and processed for FACS.

value: Periprosthetic soft tissue

value: Leukocytes


title: Subject_2_Blood

description: 10X Genomics

source_name: Blood

value: Blood


title: Subject_1_Blood

description: 10X Genomics


title: Subject_1_Tissue

description: 10X Genomics


title: AC Emerson spikeletes 7 days post inoculation with F. graminearum 2

status: Public on Jan 24 2024

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

institute: Agriculture and AgriFood Canada

data_processing:
Illumina Casava1.7 software used for basecalling
reads trimmed using trimmomatic v0.36 for adapter sequences and low-quality reads
trimmed reads mapped to T. aestivum and F. graminearum using hisat2
count data generated using featureCounts
Differential expression analysis performed using DESeq2
Assembly: T. aestivum IWGSC release 56 ,F. graminearum PH-1 (ASM24013v3)
Supplementary files format and content: tab delimited count data sheets

organism: Triticum aestivum

source_name: wheat spikelet

growth_protocol: seeds were sown in 4” pots with a mixture of 50% Sunshine #5 soilless mix (Sungro, Horticulture Canada, Seba Beach, AB, Canada) and 50% soil, plus 6 g of Osmocote slow release fertilizer (14-14-14; Everris NA, Dublin Ohio, United States). Wheat plants were grown in controlled-environment cabinets with 16 h of light at 22°C and 8 h of dark at 15°C. Plant-prod 20-20-20 soluble fertilizer (Master Plant Products Brampton Ontario, Canada) was applied in the water at a rate of 0.75 g/L and 2 g of slow release fertilizer (14-14-14) was added 40 days after planting. At the three-leaf stage, the plants were thinned to one plant per pot.

extract_protocol:
RNA extraction was performed from sectioned rachis node and rachilla samples using the Trizol Reagent (Ambion), according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: At 50% of anthers extrusion, single floret inoculation was performed with 10 µL of Fg inoculum at a concentration of 5 x 104 macroconidia /mL,  and water (control) between the lemma and palea at the midpoint of the spike

value: wheat spikelet

value: AC Emerson

value: F. graminearum infected


title: AC Emerson spikeletes 7 days post inoculation with F. graminearum 3


title: BMMC_LPS_Ly6C-high_rep2

description: FACS sorted for Ly6C-high monocytes


title: BMMC_PBS_Ly6C-low_rep2

description: FACS sorted for Ly6C-low monocytes


title: AC Morley spikeletes 7 days post inoculation with F. graminearum 2

value: AC Morley


title: AC Morley spikeletes 7 days post inoculation with F. graminearum 3


title: BMMC_LPS_Ly6C-int_rep2

description: FACS sorted for Ly6C-int monocytes


title: BMMC_LPS_Ly6C-int_rep1

description: FACS sorted for Ly6C-int monocytes


title: AC Emerson spikeletes 7 days post inoculation with F. graminearum 1


title: AC Morley spikeletes 7 days post inoculation with F. graminearum 1


title: CDC Falcon spikeletes 7 days post inoculation with F. graminearum 2

value: CDC Falcon


title: CDC Falcon spikeletes 7 days post inoculation with F. graminearum 3


title: CDC Falcon spikeletes 7 days post inoculation with F. graminearum 1


title: water inoculated spikelet in AC Emerson 3

value: uninfected


title: water inoculated spikelet in AC Morley 3


title: water inoculated spikelet in AC Emerson 2


title: water inoculated spikelet in AC Emerson 1


title: water inoculated spikelet in AC Morley 2


title: water inoculated spikelet in CDC Falcon 1


title: water inoculated spikelet in AC Morley 1


title: water inoculated spikelet in CDC Falcon 2