title: Histone ChIP-seq from BLaER1 (ENCLB602HAF)

description:
https://www.encodeproject.org/experiments/ENCSR197KBA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 72 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR197KBA
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR841CWN
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB602HAF
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS912XQN at ENCODE; https://www.encodeproject.org/ENCBS912XQN/


title: Histone ChIP-seq from BLaER1 (ENCLB517LOX)

status: Public on Feb 27 2024

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR039AHR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 6 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR039AHR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR566AUD
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB517LOX
fragmentation methods: shearing (Covaris generic)

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens BLaER1 cell line 6 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

tag: geographic location

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: unknown

tag: age

tag: lab

value: Roderic Guigo, CRG

tag: source

value: Thomas Graf

tag: treatments

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

tag: link

value: ENCBS584ALJ at ENCODE; https://www.encodeproject.org/ENCBS584ALJ/


title: TF ChIP-seq from BLaER1 (ENCLB299OWN)

description:
https://www.encodeproject.org/experiments/ENCSR288MRA/
***************
biological replicate number: 2
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 168 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR288MRA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR354HOM
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB299OWN
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 168 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: Cebpa

value: ENCBS678NCP at ENCODE; https://www.encodeproject.org/ENCBS678NCP/


title: TF ChIP-seq from BLaER1 (ENCLB607KHV)

description:
https://www.encodeproject.org/experiments/ENCSR288MRA/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 168 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR288MRA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR354HOM
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB607KHV
fragmentation methods: shearing (Covaris generic)

value: ENCBS054NUM at ENCODE; https://www.encodeproject.org/ENCBS054NUM/


title: Histone ChIP-seq from BLaER1 (ENCLB115UAR)

description:
https://www.encodeproject.org/experiments/ENCSR011IBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR011IBZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB115UAR
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 48 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS766HUL at ENCODE; https://www.encodeproject.org/ENCBS766HUL/


title: Histone ChIP-seq from BLaER1 (ENCLB022VUM)

description:
https://www.encodeproject.org/experiments/ENCSR122IWP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR122IWP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB022VUM
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB047ZBH)

description:
https://www.encodeproject.org/experiments/ENCSR122IWP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR122IWP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB047ZBH
fragmentation methods: shearing (Covaris generic)

value: ENCBS777PXO at ENCODE; https://www.encodeproject.org/ENCBS777PXO/


title: TF ChIP-seq from BLaER1 (ENCLB078PFM)

description:
https://www.encodeproject.org/experiments/ENCSR195PUH/
***************
biological replicate number: 2
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR195PUH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB078PFM
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 12 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS768BYO at ENCODE; https://www.encodeproject.org/ENCBS768BYO/


title: Histone ChIP-seq from BLaER1 (ENCLB273MCZ)

description:
https://www.encodeproject.org/experiments/ENCSR029BVT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on BLaER1 cell line after 168 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR029BVT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR354HOM
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB273MCZ
fragmentation methods: shearing (Covaris generic)

value: ENCBS421XOH at ENCODE; https://www.encodeproject.org/ENCBS421XOH/


title: Histone ChIP-seq from BLaER1 (ENCLB015JCT)

description:
https://www.encodeproject.org/experiments/ENCSR285PDU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR285PDU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB015JCT
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 24 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS564GVM at ENCODE; https://www.encodeproject.org/ENCBS564GVM/


title: Histone ChIP-seq from BLaER1 (ENCLB261FZJ)

description:
https://www.encodeproject.org/experiments/ENCSR285PDU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-Seq on BLaER1 cell line after 24 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR285PDU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR954ZQC
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB261FZJ
fragmentation methods: shearing (Covaris generic)

value: not applicable

value: ENCBS528BRE at ENCODE; https://www.encodeproject.org/ENCBS528BRE/


title: Histone ChIP-seq from BLaER1 (ENCLB108MHC)

description:
https://www.encodeproject.org/experiments/ENCSR010OVI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 72 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR010OVI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR841CWN
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB108MHC
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 72 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: cell line

value: ENCBS912XQN at ENCODE; https://www.encodeproject.org/ENCBS912XQN/


title: Histone ChIP-seq from BLaER1 (ENCLB350RTD)

description:
https://www.encodeproject.org/experiments/ENCSR217SDT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR217SDT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB350RTD
fragmentation methods: shearing (Covaris generic)

value: female

value: unknown


title: Histone ChIP-seq from BLaER1 (ENCLB089BEY)

description:
https://www.encodeproject.org/experiments/ENCSR308PVP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-Seq on untreated BLaER1 cell line.
experiment encode accession: ENCSR308PVP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR455AFK
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB089BEY
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line

value: Roderic Guigo, CRG

value: Thomas Graf

value: ENCBS017NGB at ENCODE; https://www.encodeproject.org/ENCBS017NGB/


title: Histone ChIP-seq from BLaER1 (ENCLB981VPB)

description:
https://www.encodeproject.org/experiments/ENCSR010OVI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 72 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR010OVI
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR841CWN
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB981VPB
fragmentation methods: shearing (Covaris generic)

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;

value: ENCBS696TKD at ENCODE; https://www.encodeproject.org/ENCBS696TKD/


title: Histone ChIP-seq from BLaER1 (ENCLB964UNZ)

description:
https://www.encodeproject.org/experiments/ENCSR011IBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-Seq on BLaER1 cell line after 48 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR011IBZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR978XYH
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB964UNZ
fragmentation methods: shearing (Covaris generic)


title: Histone ChIP-seq from BLaER1 (ENCLB962AXK)

description:
https://www.encodeproject.org/experiments/ENCSR192IRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR192IRQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB962AXK
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 3 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS242WXP at ENCODE; https://www.encodeproject.org/ENCBS242WXP/


title: Histone ChIP-seq from BLaER1 (ENCLB726XCX)

description:
https://www.encodeproject.org/experiments/ENCSR285NFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 36 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR285NFQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR845IKY
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB726XCX
fragmentation methods: shearing (Covaris generic)

source_name: Homo sapiens BLaER1 cell line 36 hours after the sample was treated with 100 nM 17beta-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1

value: ENCBS769LHW at ENCODE; https://www.encodeproject.org/ENCBS769LHW/


title: Histone ChIP-seq from BLaER1 (ENCLB850HLH)

description:
https://www.encodeproject.org/experiments/ENCSR006ANF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR006ANF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB850HLH
fragmentation methods: shearing (Covaris generic)

value: ENCBS932XAE at ENCODE; https://www.encodeproject.org/ENCBS932XAE/


title: Histone ChIP-seq from BLaER1 (ENCLB295NDO)

description:
https://www.encodeproject.org/experiments/ENCSR006ANF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR006ANF
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB295NDO
fragmentation methods: shearing (Covaris generic)

value: ENCBS900NVU at ENCODE; https://www.encodeproject.org/ENCBS900NVU/


title: Crispr Mouse with ReDeeM, Batch2, Target Site, sample 15

status: Public on Feb 26 2024

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: Target Site library (Cell barcodes are matchable with ATAC and mtDNA and CellHash lib in sample 15): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains the indels generated by CRISPR Cas9 for lineage tracing. Use software Cassiopeia for analysis

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv
Library strategy: TargetSite

organism: Mus musculus

source_name: Lung cancer

extract_protocol:
Mouse experiments were approved by the Massachusetts Institute of Technology Institutional Animal Care and Use Committee (IACUC) (institutional animal welfare assurance no. A-3125-01). A male mouse embryonic stem cell (mESC) line harbouring the conditional alleles KrasLSL-G12D/+ and Trp53fl/fl (KP) was engineered with the lineage tracer cassettes. The detailed engineering process, including vector information, tumour harvest and single-cell suspension were prepared as described in Yang et al.  Two independent mESC lines were used for batch-1 and batch-2 experiments.
The single cells of batch-2 from multiple tumors were labelled with Cell Hash and were profiled using ReDeeM except the following modification. Additional Target Site libraries were needed. The amplified cDNA libraries were further amplified with Target Site-specific primers containing Illumina-compatible adapters and sample indices (oDYT023-oDYT038, forward:5′CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATCCAGCTAGCTGTGCAGC; reverse:5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCTTTCCCTACACGACGCTCTTCCGATCT; “N” denotes sample indices) using Kapa HiFi ReadyMix (Roche), as described.
For sequencing scRNA, scATAC, mtDNA libraries, the same strategy as described for ReDeeM were used, except that four sets of mouse specific probes were designed to enrich mitochondrial fragments. For sequencing Target Site libraries, 15,000 total reads per cell were expected, and the following read lengths were used: Read1: 26 cycles, i7: 8 cycles, Read2: 290 cycles).

tag: tissue

value: Lung cancer

tag: cell type

tag: library type

value: Target Site DNA


title: Crispr Mouse with ReDeeM, Batch2, RNA, sample 15

description: 3' mRNA library (Cell barcodes are matchable with ATAC, mtDNA,TargetSite and CellHash lib in sample 15): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

library_source: transcriptomic single cell

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv

molecule: polyA RNA

value: mRNA


title: Crispr Mouse with ReDeeM, Batch2, Cell Hash Site, sample 15

description: Cell Hash library (Cell barcodes are matchable with ATAC, mtDNA, mRNA, TargetSite lib in sample 15): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains Hashing barcode.

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv
Library strategy: Hash

value: Hash DNA


title: Histone ChIP-seq from BLaER1 (ENCLB739UTT)

description:
https://www.encodeproject.org/experiments/ENCSR285NFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-Seq on BLaER1 cell line after 36 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR285NFQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR845IKY
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB739UTT
fragmentation methods: shearing (Covaris generic)

value: cell line

value: not applicable

value: ENCBS943SUL at ENCODE; https://www.encodeproject.org/ENCBS943SUL/


title: WT4 20 wk

status: Public on Feb 24 2024

city: Albany

first: Ariel

last: Jaitovich

email: balnisj@amc.edu, jaitova@amc.edu

state: NY

address: 47 New Scotland Ave.

department: MCP

institute: Albany Medical College

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_107

library_source: transcriptomic

data_processing:
Automated RPM normalization by S5 Torrent software produced RPM normalized CHP files and normalized counts.
CHP file analysis using ThermoFisher Transcriptome Analysis Console (TAC) Software.
Assembly: AmpliSeq_Mouse_Transcriptome_v1
Supplementary files format and content: RPM normalized .CHP files
Supplementary files format and content: Normalized absolute counts for all samples in one .xls file.

molecule: total RNA

source_name: Skeletal muscle

growth_protocol: HSA-Cre/Lox-SDHC inducible skeletal muscle specific knockout C57/B6 mice were grown to 12 weeks of age then tamoxifen induced the collected 20 weeks post induction. HSA-Cre/No Lox littermates were induced similarly to control for effects of tamoxifen and considered WT samples.

extract_protocol:
Mouse TA muscle was collected and RNA was isolated with TriZol following standard techniques and DNA was digested.
Library construction was performed automatically by the Ion Chef robotic system following manufacturers protocols.

treatment_protocol: Mice at 12 weeks of age were all tamoxifen induced.

value: Skeletal muscle

tag: cell line

value: Primary skeletal muscle

value: Mature skeletal muscle

tag: genotype

value: Inducible HSA-Cre/No Lox C57BL/6

tag: treatment

value: Tamoxifen induction


title: Crispr Mouse with ReDeeM, Batch2, ATAC, (enriched mito included) sample 15

description: ATAC library (Cell barcodes are matchable with mRNA, mtDNA, TargetSite, and CellHash lib in sample 15): read1 file contains one end of accessible region; i5 file (1-24) contains cell barcodes, read2 file contains the other end of accessible region.

library_source: genomic single cell

value: ATAC


title: Histone ChIP-seq from BLaER1 (ENCLB459KXC)

description:
https://www.encodeproject.org/experiments/ENCSR105FGG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 36 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR105FGG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR845IKY
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB459KXC
fragmentation methods: shearing (Covaris generic)

tag: antibody

tag: line

tag: biosample encode accession

value: female

value: unknown

value: Roderic Guigo, CRG

value: Thomas Graf

value: treatment_term_id:CHEBI:16469; treatment_term_name:17beta-estradiol; treatment_type:chemical; treatment_term_id:UniProtKB:P08700; treatment_term_name:Interleukin-3; treatment_type:protein; treatment_term_id:UniProtKB:P09603; treatment_term_name:CSF1; treatment_type:protein;


title: TF ChIP-seq from BLaER1 (ENCLB668UCZ)

description:
https://www.encodeproject.org/experiments/ENCSR195PUH/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPA ChIP-Seq on BLaER1 cell line after 12 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR195PUH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR871SEB
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB668UCZ
fragmentation methods: shearing (Covaris generic)

value: Cebpa

tag: collection date

tag: geographic location

tag: encode accession

value: ENCBS271CDH at ENCODE; https://www.encodeproject.org/ENCBS271CDH/


title: Histone ChIP-seq from BLaER1 (ENCLB332FYO)

description:
https://www.encodeproject.org/experiments/ENCSR105FGG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-Seq on BLaER1 cell line after 36 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR105FGG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR845IKY
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB332FYO
fragmentation methods: shearing (Covaris generic)

tag: Sex

tag: dev stage

tag: age


title: KO1 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_102

value: Inducible HSA-Cre/Lox-SDHC C57BL/7


title: KO2 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_103

value: Inducible HSA-Cre/Lox-SDHC C57BL/8


title: KO4 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_108


title: WT4 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_124

growth_protocol: HSA-Cre/Lox-SDHC inducible skeletal muscle specific knockout C57/B6 mice were grown to 12 weeks of age then tamoxifen induced the collected 3 weeks post induction. HSA-Cre/No Lox littermates were induced similarly to control for effects of tamoxifen and considered WT samples.


title: WT3 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_106


title: KO3 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_105


title: WT2 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_104


title: KO3 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_122

value: Inducible HSA-Cre/Lox-SDHC C57BL/11


title: KO4 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_123

value: Inducible HSA-Cre/Lox-SDHC C57BL/12


title: WT3 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_121

value: Skeletal muscle


title: KO2 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_119

value: Primary skeletal muscle


title: Histone ChIP-seq from BLaER1 (ENCLB376GHG)

description:
https://www.encodeproject.org/experiments/ENCSR192IRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-Seq on BLaER1 cell line after 3 h treatment with 100 nM 17β-estradiol, 10 ng/mL Interleukin-3, 10 ng/mL CSF1.
experiment encode accession: ENCSR192IRQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR399JUL
encode release date: 2022-05-10
lab: Roderic Guigo, CRG
library encode accession: ENCLB376GHG
fragmentation methods: shearing (Covaris generic)

value: cell line

value: not applicable

tag: lab

tag: source

tag: treatments

value: ENCBS348QCD at ENCODE; https://www.encodeproject.org/ENCBS348QCD/


title: WT1 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_117

tag: tissue

tag: cell type

value: Mature skeletal muscle

value: Inducible HSA-Cre/No Lox C57BL/6

value: Tamoxifen induction


title: KO1 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_118

tag: cell line


title: WT2 3 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_120

tag: genotype


title: ESC_X_NANOG_LIF_2

status: Public on Feb 11 2024

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: RW.4 mESC, Serum/LIF

data_processing:
Sequencing was performed using 50:8:34 cycles (Read1:Index1:Read2) Illumina bcl2fastq was used to demultiplex paired-end sequencing reads by 8nt index1 read (PCR barcode). NextSeq lanes were merged into single fastq files, creating the primary fastq files. Read1 starts with 6nt UMI and 8nt barcode in the format NNNNNNABCDEFGH. A sample sheet was used with four columns corresponding to sample name, replicate name, barcode sequence, primary fastq name. For each line in the sample sheet, reads matching the barcode sequence were extracted from the primary fastq file, allowing up to two mismatches. Duplicate reads identified by identical first 24nt of read1 were discarded. Read pairs matching parts of the adaptor sequence (SBS3 or T7 promoter) in either read1 or read2 were removed. Demultiplexed and deduplicated reads were written into sample-specific fastq file used for subsequent mapping.
Sample-specific paired fastq files were mapped using botwie2 (v2.3.4.3) using --fast parameter to the mouse genome (mm9). Alignments were processed into sorted BAM files with samtools (v1.9). Blacklisted regions were removed from BAM file using BEDTools (v2.27.1). Reads were also mapped to a metagenome of RepBase murine repetitive sequences using botwie2.
Input coverage tracks with 1bp resolution in BigWig format were generated from BAM files using deepTools (v3.1.0) bamCoverage and scaled to a reads-per-genome-coverage of one (1xRPGC, also referred to as ‘1x normalization’) using mm9 genome size 2654895218. ChIP coverage tracks were generated from BAM files using deepTools (v3.1.0) bamCoverage. Quantitative scaling amongst samples within each pool was based on their total mapped read counts, as well as the total mapped read counts of the respective input data. One condition in the pool served as a reference (Serum condition, no treatment), which was scaled to 1xRPGC. All other samples were scaled relative to the reference using an explicit scaling factor. The RPGC was calculate by the following formula: ( #mapped[ChIP] / #mapped[Input] ) / ( #mapped[ChIP_Reference] / #mapped[Input_Reference] ).
Assembly: mm9
Supplementary files format and content: BigWig files are scaled according to MINUTE quantification with respect to the reference of each pool (Serum condition, 1xRPGC)

source_name: Embryonic Stem Cell

growth_protocol: Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes in Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore). For differentiated condition (RA), cells were washed with PBS and fresh medium lacking LIF was added. 24 hr after LIF withdrawal, 2µM of retonoic acid (Sigma R2625) was added and cells were harvested 48 hr after initiation of the treatment. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

extract_protocol:
For crosslinked MINUTE-ChIP, MINUTE-ChIP (PMID: 31533047) was adapted as follows: cells were harvested via trypsinization and fixed for 10 min at RT with 1 % Formaldehyde. Subsequently, the formaldehyde was quenched using 0.75 M Tris-HCl (ph 7.8) for 10 min at RT. The cell  were then pelleted by centrifugation at 800 g, 4 °C for 5 min, and washed twice using cold PBS. During the final PBS wash, 1e6 cells were pelleted per aliquot.  Pellets were flash frozen and stored at -80 °C. Flash frozen pellets of 2e6 cells were resuspended in 50uL of sonication buffer (50mM Tris HCl, 0.5% SDS, 1x PI), transferred to 0.5mL bioruptor tubes and lysed on ice for 10 mins. Samples were then sonicated for 40 mins, high power, 30 sec on/off  cycles on Biruptor sonicator ( 4 iterations of 10 mins each and between each  iteration, tubes were briefly vortexed and spun down).  The sheared cell suspension was spun down at 800g, 4 °C for 5 min and the supernatant was transferred to a fresh tube and topped up with 50uL of sonication dilution buffer (50mM Tris HCl, 1% Triton X-100).  Double-stranded DNA adaptors for barcoding and T7 amplification were generated by slow annealing of complementary single-stranded oligos (for sequences refer to Supplementary Table 1), where the UMI bases were randomized. While resulting dsDNA adaptors may contain mismatched bases within the UMI, only the bottom strand UMI is amplified and sequenced. For each sample, 40 μl of the whole cell lysate containing the digested chromatin was taken forward into an overnight blunt end ligation reaction (End-It DNA repair kit and Fast-Link DNA ligation kit, Epicentre) with double stranded DNA adapters at 16°C. Adaptors carried a partial SBS3 for Illumina sequencing flanked by a T7 RNA Polymerase for linear amplification. Between the SBS3 sequence and a 8bp sample barcode at the 3’ end, a 6bp randomized sequence was introduced, serving as a unique molecular identifier (UMI). UMI and sample barcode are ligated 5’ to the chromatin fragment and constitute the first 14 bases of read 1. The 4096 possible UMIs provide sufficient diversity to distinguish if two reads mapping to the exact same genomic location arose from a PCR amplification artifact or are indeed unique molecule. The adapter concentration was optimized to 2.5 μM / reaction to reduce adapter dimers. The ligation reaction was terminated with a lysis dilution buffer (50 mM Tris-HCl [pH 8.0], 150 mM NaCl, 1% Triton X-100, 50 mM EGTA, 50 mM EDTA, 0.1% sodium deoxycholate and 1x PIC) and barcoded samples were combined into a single pool, spun down at 24,000 r.p.m. for 10 min at 4°C. 50μl Protein A/G magnetic beads (BioRad) were washed twice with PBS-T (PBS+ 0.1% Tween 20) and coupled to 3 μl Nanog antibody (ab80892). Beads were then washed quickly with RIPA buffer. 200-400 μl of the cleared lysate pool was added to the pre-coupled magnetic beads and parallel ChIP assays were incubated further for 4 h at 4°C with rotation. 5% of the above volume was saved as the input pool and processed through the remaining protocol in a manner similar to the IPs. Next, the beads were washed (RIPA, RIPA high salt, LiCl and TE buffer) resuspended in ChIP elution buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.1% SDS, and 300 mM NaCl) containing 0.25 mg/mL Proteinase K and eluted at 63°C for 1 h.
The crosslinked ChIP DNA was treated with Protinase K at 65C for 4h and isolated using 1x SPRI beads (Beckman Coulter), retaining predominantly fragments > 100bp, and set up in an overnight in vitro transcription reaction (HiScribe T7 Quick High Yield RNA Synthesis kit, New England BioLabs).  The resulting RNA was purified using Silane beads (Life Technologies) and an RNA 3’ adapter was ligated onto it using T4 RNA ligase, truncated (New England BioLabs) for 1 h at 25°C. The mixture was subsequently supplemented with components of the reverse transcription reaction (SuperScript III First-Strand Synthesis SuperMix, Life Technologies) to produce cDNA, primed using the ligated 3’ adapter. Final libraries for each ChIP were produced using 150-200 ng of purified cDNA in a PCR reaction (High-Fidelity 2x master mix, New England BioLabs) for 8 cycles with 0.2 μM primers that carried a second 8bp barcode sequence. Quality assessment and concentration estimation of the purified DNA was done using the Qubit (Life Technologies) and BioAnalyzer (Agilent). Each library was then diluted to 4 nM and combined into a single pool before sequencing on the Illumina NextSeq500 platform.

treatment_protocol:
Optionally, medium without LIF was supplemented with 2µM of retonoic acid (Sigma R2625)
Murine embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin-coated dishes. "Serum" condition: Knockout DMEM (Life Technologies), 2 mM Glutamax (Gibco), 0.1 mM non-essential amino acids (Gibco), 15% ESC-grade fetal bovine serum (FBS) (Gibco), 0.1 mM β-mercaptoethanol, and leukemia inhibitory factor (LIF) (Millipore); "2i" condition: serum free ESGRO Complete Basal medium (Millipore) with 0.1mM LIF and 2i as described above. For differentiaed condition (RA), cells were washed with PBS and fresh medium lacking LIF was added. 24 hr after LIF withdrawal, 2µM of retonoic acid (Sigma R2625) was added and cells were harvested 48 hr after initiation of the treatment. For all conditions cells were passaged in 48 h intervals, using accutase (Sigma) for detachment. Cell line was tested for mycoplasma contamination.

value: Embryonic Stem Cell

tag: background

tag: condition

value: Serum

value: Nanog (ab80892)

tag: mixing ratio l

tag: processed data file scaling

value: relative to 100H


title: ESC_X_NANOG_LIF_1

description: RW.4 mESC, Serum/LIF

tag: antibody


title: ESC_X_NANOG_RA_2

description: RW.4 mESC, LIF withdrawn and treated with 2µM Retinoic Acid for 48h


title: ESC_X_IN_LIF_2

description: RW.4 mESC, Serum/LIF

value: Input

value: 1x genome coverage


title: ESC_X_IN_RA_2


title: ESC_X_NANOG_RA_1


title: ESC_X_IN_LIF_1

description: RW.4 mESC, Serum/LIF


title: BMDM KO +4h LPS rep 3

status: Public on Feb 09 2024

city: Bryan

first: Kristin

middle: L

last: Patrick

state: Texas

address: 8447 Riverside Pkwy, MREB 3102

department: Microbial Pathogenesis and Immunology

institute: Texas A&M University, College of Medicine

description: Neat1 KO vs. WT 4h LPS.xlsx

data_processing:
2x150 paired-end sequence reads
Illumina software used for basecalling
Read mapping using the STAR aligner
Quantification of reference genes and transcripts using salmon
Variant calling (SNVs and small indels) using the Strelka Variant caller
Optional fusion calling with Manta
QC metrics from picard and other sources
Assembly: Mus musculus UCSC mm10 (RefSeq gene annotation)
Supplementary files format and content: log2FoldChange

source_name: primary bone marrow derived macrophages

growth_protocol: Bone marrow–derived macrophages (BMDMs) were differentiated in DMEM containing 20% fetal bovine serum (FBS), 1 mM sodium pyruvate, and 10% myeloid colony stimulating factor (MCSF)-conditioned media

extract_protocol:
RNA was harvested using Trizol reagent. Zymo Research Direct-zol kits were used to isolate total RNA. 1 ug of total RNA per sample was sent for library construction and next generation sequencing.
Ribodepletion library preparation was carried out by the Baylor  College of Medicine Genomic and RNA Profiling Core (GARP) in biological triplicate. RNA sequencing (150 bp paired-end reads) was performed on an Illumina Novaseq 6000 with S4 flow cell
Total RNA-Seq with ribodepletion

treatment_protocol: 10 ng/ml LPS added to media for 2h and 4h

value: primary bone marrow derived macrophages

value: KO

tag: time

tag: treatment

value: LPS


title: BMDM KO +4h LPS rep 2

description: Neat1 KO vs. WT 4h LPS.xlsx


title: BMDM KO +4h LPS rep 1

description: Neat1 KO vs. WT 4h LPS.xlsx


title: ESC_X_IN_RA_1


title: WT1 20 wk

description:
Ion AmpliSeq™ Transcriptome Mouse
IonCode_101

value: Skeletal muscle


title: BMDM KO +2h LPS rep 2

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM KO +2h LPS rep 1

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM KO +2h LPS rep 3

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM WT +4h LPS rep 3

description: Neat1 KO vs. WT 4h LPS.xlsx

value: WT


title: BMDM KO UN rep 2

description: Neat1 KO vs. WT UN.xlsx

value: Untreated


title: BMDM KO UN rep 3

description: Neat1 KO vs. WT UN.xlsx


title: BMDM WT +4h LPS rep 1

description: Neat1 KO vs. WT 4h LPS.xlsx


title: BMDM WT +2h LPS rep 3

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM WT +2h LPS rep 2

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM KO UN rep 1

description: Neat1 KO vs. WT UN.xlsx


title: BMDM WT UN rep 2

description: Neat1 KO vs. WT UN.xlsx


title: BMDM WT +2h LPS rep 1

description: Neat1 KO vs. WT 2h LPS.xlsx


title: BMDM WT +4h LPS rep 2

description: Neat1 KO vs. WT 4h LPS.xlsx


title: BMDM WT UN rep 3

description: Neat1 KO vs. WT UN.xlsx


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_711_combined_61bp

status: Public on Feb 06 2024

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description:
Illumina NextSeq 500/550 and Illumina NextSeq 2000
Cell-free RNA was isolated from the plasma of 251 patients with a cough >= 2 weeks. We conducted RNA sequencing of the extracted cell-free RNA, quantified the gene transcripts, and normalized using VST normalization. We split these samples into validation (TBSQUARE), and discovery, (R2D2 and GHL). We further split the discovery into 70% training and 30% test. The data here is the training set. In the associated paper the cohorts have been renamed to cohort 1 (GHL), cohort 2 (R2D2) and cohort 3 (TBSQUARE) for clarity. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp). The file counts.val.tsv contains the gene counts for all samples listed here.

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, matched sequencing data from the Illumina NextSeq 500 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts30 (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts30 (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap31 (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 4, if a sample had less than 90,000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 4 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: tab-delimited .tsv file includes the gene counts for each sample.

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma samples were received on dry ice and stored at -80°C until processed. Prior to cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from plasma using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 µl of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

value: Plasma, extracted cell-free RNA

value: TB Positive

tag: hiv

value: Negative

tag: Sex

value: Male

tag: site

value: Uganda

tag: cohort

value: TBSQUARE

tag: volume

tag: bfcohort

value: tbs

tag: ftcount

tag: passqc

value: TRUE

tag: tb

value: positive

tag: semiquant

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_708_combined_61bp

tag: tissue

tag: age

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_702_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_703_combined_61bp

value: Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_699_combined_61bp


title: BMDM WT UN rep 1

description: Neat1 KO vs. WT UN.xlsx

tag: cell type

value: primary bone marrow derived macrophages

tag: genotype


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_698_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_697_combined_61bp

value: High


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_693_combined_61bp

value: Female


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_661_combined_61bp

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_636_combined_61bp

value: TB Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_695_combined_61bp

value: Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_638_combined_61bp

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_637_combined_61bp

value: Uganda


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_630_combined_61bp

value: TBSQUARE


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_640_combined_61bp

value: tbs


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_628_combined_61bp

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_696_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_694_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_648_combined_61bp

value: positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_634_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_620_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_623_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_635_combined_61bp

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_619_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_631_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_617_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_618_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_616_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_613_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_612_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_611_combined_61bp

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_609_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_649_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_608_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_589_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_564_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_596_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_569_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_601_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_591_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_602_combined_61bp

value: Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_597_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_584_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_568_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_572_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_570_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_599_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V273_combined_61bp

description:
Illumina NextSeq 500/550 and Illumina NextSeq 2000
Cell-free RNA was isolated from the plasma of 251 patients with a cough >= 2 weeks. We conducted RNA sequencing of the extracted cell-free RNA, quantified the gene transcripts, and normalized using VST normalization. We split these samples into validation (TBSQUARE), and discovery, (R2D2 and GHL). We further split the discovery into 70% training and 30% test. The data here is the training set. In the associated paper the cohorts have been renamed to cohort 1 (GHL), cohort 2 (R2D2) and cohort 3 (TBSQUARE) for clarity. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp). The file counts.test.tsv contains the gene transcript counts for all samples listed here.

value: Vietnam


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_557_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_555_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V242_combined_61bp

value: High


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_561_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_598_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_603_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_554_combined_61bp

value: Female


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_610_combined_61bp

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_614_combined_61bp

value: TB Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_583_combined_61bp

value: Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_573_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_577_combined_61bp

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V167_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_578_combined_61bp

value: Uganda


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V218_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V151_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V190_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V157_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V143_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: TBSQUARE_553_combined_61bp

value: TBSQUARE


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U315_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U312_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U323_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U329_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U133_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V130_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V139_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U269_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U114_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P33_combined_61bp

value: Philippines


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U132_combined_61bp

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P131_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U112_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U103_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P127_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P232_combined_61bp

value: positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P119_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U332_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P124_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P118_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL93_combined_61bp

value: Mulago

value: GHL

value: ghl


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U131_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL72_combined_61bp

value: Kisenyi

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL58_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL89_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P114_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U102_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL45_combined_61bp

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL56_combined_61bp

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL248_combined_61bp

value: TB Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL264_combined_61bp

value: Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL3_combined_61bp

value: Positive

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL27_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL229_combined_61bp

value: Female


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL34_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL210_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL269_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL208_combined_61bp

value: High


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL161_combined_61bp

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL144_combined_61bp

value: positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL188_combined_61bp

value: Mulago


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL172_combined_61bp

value: GHL


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL206_combined_61bp

value: ghl


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL166_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL138_combined_61bp

value: Kisenyi


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL132_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL123_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL128_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL119_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL109_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL114_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL235_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL131_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V159_combined_61bp

description:
Cell-free RNA was isolated from the plasma of 251 patients with a cough >= 2 weeks. We conducted RNA sequencing of the extracted cell-free RNA, quantified the gene transcripts, and normalized using VST normalization. We split these samples into validation (TBSQUARE), and discovery, (R2D2 and GHL). We further split the discovery into 70% training and 30% test. The data here is the training set. In the associated paper the cohorts have been renamed to cohort 1 (GHL), cohort 2 (R2D2) and cohort 3 (TBSQUARE) for clarity. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp). The file counts.train.tsv contains the gene transcript counts for all samples listed here.
Illumina NextSeq 500/550 and Illumina NextSeq 2000

value: Vietnam


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V166_combined_61bp

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V20_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V147_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V16_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V165_combined_61bp

value: Plasma, extracted cell-free RNA

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V286_combined_61bp

value: TB Positive

value: Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V153_combined_61bp

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V146_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V160_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V129_combined_61bp

value: Female


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V172_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V128_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V127_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V137_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V124_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V126_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V121_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V120_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V162_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V119_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V152_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V118_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V104_combined_61bp

value: High


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V108_combined_61bp

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U363_combined_61bp

value: Uganda

value: positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U371_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U357_combined_61bp

value: Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_V132_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U362_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U355_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U316_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U341_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U298_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U337_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U273_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U343_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U130_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U122_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U124_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U129_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U111_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U110_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U105_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U106_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U100_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P96_combined_61bp

value: Philippines


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P245_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P214_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P22_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P241_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P202_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P18_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P130_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P152_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P133_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U314_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U287_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P126_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P129_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P105_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P110_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_U118_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P108_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P104_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P1_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: R2D2_P113_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL94_combined_61bp

value: Mulago

value: GHL

value: ghl


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL9_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL99_combined_61bp

value: Plasma, extracted cell-free RNA

value: Kisenyi


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL88_combined_61bp

value: TB Positive

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL76_combined_61bp

value: Negative

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL84_combined_61bp

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL75_combined_61bp

value: Female

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL7_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL69_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL71_combined_61bp

value: positive

value: High


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL70_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL63_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL62_combined_61bp

value: Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL61_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL59_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL65_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL52_combined_61bp

value: negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL47_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL57_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL40_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL36_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL46_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL37_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL286_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL277_combined_61bp

value: Mulago


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL308_combined_61bp

value: GHL


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL35_combined_61bp

value: ghl


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL284_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL276_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL274_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL230_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL252_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL22_combined_61bp

value: TB Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL217_combined_61bp

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL204_combined_61bp

value: Kisenyi


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL199_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL201_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL53_combined_61bp

value: TB Positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL192_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL186_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL170_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL19_combined_61bp

value: Medium


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL169_combined_61bp

value: Negative


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL16_combined_61bp

value: Male


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL17_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL288_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL158_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL30_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL136_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL133_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL13_combined_61bp

value: Low


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL124_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL126_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL223_combined_61bp

value: Female


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL134_combined_61bp

value: TRUE


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL121_combined_61bp


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL108_combined_61bp

value: positive


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL112_combined_61bp


title: HOMO_CC_12

status: Public on Feb 02 2024

city: New York City

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
Trimming by TrimGalore
Alignment by STAR to mm10
Quantification by featureCounts
Assembly: mm10
Supplementary files format and content: bam file + gene counts

source_name: spleen

extract_protocol:
Trizol (Invitrogen)
Stranded mRNA Prep (Illumina)

treatment_protocol: SRBC immunization day 10

value: spleen

tag: cell line

value: primary cells

value: centrocytes

value: Arid1a HOM

value: SRBC immunization


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL1_combined_61bp

value: Mulago

value: GHL

value: ghl

value: negative


title: HOMO_CB_12

value: centroblasts


title: HOMO_CB_11


title: HOMO_CC_10


title: HOMO_CB_10


title: HET_CC_8

value: Arid1a HET


title: HOMO_CB_9


title: HOMO_CC_9


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL141_combined_61bp

value: Plasma, extracted cell-free RNA

value: TB Positive

value: Negative

value: High


title: HET_CB_8


title: HET_CB_7


title: HET_CB_6


title: HET_CC_7


title: WT_CC_5

value: Arid1a WT


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL107_combined_61bp

value: TB Negative

value: Female

value: Kisenyi

value: TRUE


title: WT_CB_5

value: spleen

value: primary cells


title: HET_CC_6

value: centrocytes

value: SRBC immunization


title: WT_CC_1


title: WT_CC_2


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL105_combined_61bp

value: Male

value: GHL

value: ghl

value: positive


title: WT_CB_4

value: centroblasts


title: WT_CC_3


title: WT_CC_4


title: Plasma cell-free RNA, RNA seq gene counts for patient: GHL103_combined_61bp

value: Plasma, extracted cell-free RNA

value: TB Positive

value: Mulago

value: Medium


title: CC_WT_R2

data_processing:
Trimming by TrimGalore, alignment by BWA, filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Please see nfcore atacseq pipeline for more details
Assembly: mm10
Supplementary files format and content: Peak counts

extract_protocol:
Zymo PCR Purification
Nextera Illumina

value: Arid1a WT


title: WT_CB_1


title: WT_CB_2


title: WT_CB_3


title: HOMO_CC_11

value: Arid1a HOM


title: CC_HOMO_R1

value: Arid1a HOMO


title: CC_HET_R2

value: Arid1a HET


title: CC_HET_R3

value: spleen


title: CC_HOMO_R5

value: primary cells


title: CC_WT_R4

value: centrocytes


title: CB_WT_R4


title: CC_HOMO_R2


title: CC_WT_R1


title: CC_HET_R1


title: CB_WT_R1


title: CC_HOMO_R4


title: CC_HOMO_R3


title: CB_WT_R3


title: CC_WT_R3


title: CB_HOMO_R4


title: CC_WT_R5


title: CB_WT_R5


title: CB_HOMO_R5


title: CB_WT_R2


title: HET_C43_12

data_processing:
Trimming by TrimGalore
Alignment by STAR to GRCh37
Quantification by featureCounts
Assembly: GRCh37
Supplementary files format and content: bam file + gene counts

source_name: cell line

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
Rneasy mini
Stranded mRNA Prep (Illumina)

value: cell line

value: RIVA

value: B-cell lymphoma ABC-DLBCL


title: CB_HOMO_R3


title: HET_C43_5


title: HET_C41_11


title: CB_HOMO_R1


title: CB_HOMO_R2


title: CB_HET_R3


title: CB_HET_R2


title: DQ2_FHD_24H_2_20221209

data_processing:
Trimming by TrimGalore, alignment by BWA, filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Please see nfcore atacseq pipeline for more details
Assembly: hg38
Supplementary files format and content: Peak counts

treatment_protocol: DMSO or 100nM FHD-286 (in DMSO) for 24h

value: YES


title: HET_RIVA_7


title: CB_HET_R1


title: WT_C10_10


title: DQ1_FHD_24H_1_20221209


title: WT_C10_3


title: DQ2_DMSO_24H_2_20221209

value: NO


title: WT_C4_9


title: DQ2_FHD_24H_1_20221209


title: WT_C4_2


title: HET_RIVA_14


title: Arid1a_WT_3U_R3

data_processing:
Data aligned and processed by nfcore mnaseseq pipeline.
Nucleosome positions recalled and normalized by Danpos3.
Assembly: hg38
Supplementary files format and content: Bigwig tracks for predicted nucleosome occupancy, quantile normalized

extract_protocol:
Qiagen Column Purification
NEB Ultra II

value: Mnase 3U


title: DQ1_DMSO_24H_2_20221209


title: Arid1a_HET_5U_R2

value: Mnase 5U


title: TQ2_FHD_24H_2_20221209


title: TQ1_FHD_24H_2_20221209


title: DQ1_FHD_24H_2_20221209


title: DQ1_DMSO_24H_1_20221209


title: TQ2_DMSO_24H_1_20221209


title: DQ2_DMSO_24H_1_20221209


title: TQ1_DMSO_24H_2_20221209


title: Arid1a_WT_3U_R2


title: Arid1a_WT_3U_R1


title: KO_sh2_R1

treatment_protocol: doxycycline for KD

value: Arid1a KD


title: HET_C41_4


title: KO_sh1_R1


title: ctrl_sh2_R1


title: TQ2_FHD_24H_1_20221209


title: ctrl_sh1_R2


title: Arid1a_HET_5U_R1


title: ctrl_sh1_R1


title: KO_sh1_R2


title: HET_R1


title: Arid1a_HET_3U_R3


title: TQ1_FHD_24H_1_20221209


title: Arid1a_HET_3U_R2


title: TQ2_DMSO_24H_2_20221209


title: Arid1a_HET_3U_R1


title: PROseq_Mac_90min_4

status: Public on Jan 25 2024

city: Saint Louis

first: Kodi

middle: S

last: Ravichandran

state: Missouri

address: 660 Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Read pairs trimmed with cutadapt. Paired-end reads were mapped to a combined genome index, including both the spike (dm6) and primary (mm39) genomes using bowtie2. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools, and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
Assembly: mm39
Supplementary files format and content: bw: BigWig genome browser track for PRO-seq data

source_name: bone marrow

extract_protocol:
Cells were gently resuspended in wash buffer (10mM Tris-Cl, pH 8.0; 10mM KCl; 250mM Sucrose; 5mM MgCl2; 1mM EGTA; 0.5mM DTT; 10% Glycerol; SUPERase-IN RNase inhibitor) to obtain a single-cell suspension. Subsequently, cells were permeabilized by adding permeabilization buffer (10mM Tris-Cl, pH 8.0; 10mM KCl; 250mM Sucrose; 5mM MgCl2; 1mM EGTA; 0.1% Igepal CA-630; 0.5mM DTT; 0.05% Tween-20; 10% Glycerol; SUPERase-IN RNase inhibitor) and incubating on ice for 5 minutes. After centrifugation, cells were resuspended in  wash buffer. Then, cells were resuspended in freezing buffer (50mM Tris-Cl, pH 8.0; 40% glycerol; 5mM MgCl2; 1.1mM EDTA; 0.5mM DTT; SUPERase-IN RNase inhibitor).
PRO-seq library preparation were conducted as previously described with slight modifications (PMID: 33440169).

value: bone marrow

value: Macrophages

value: +Apoptotic Jurkat cells (90min)


title: KO_sh2_R2


title: ctrl_sh2_R2


title: TQ1_DMSO_24H_1_20221209


title: HET_R3


title: PROseq_Mac_45min_4

value: +Apoptotic Jurkat cells (45min)


title: PROseq_Mac_90min_2


title: PROseq_Mac_90min_1


title: HET_R2


title: WT_R3

value: Arid1a WT


title: WT_R2


title: PROseq_Mac_45min_2


title: PROseq_Mac_Alone_1

value: Alone


title: WT_R1


title: PROseq_Mac_90min_3


title: RNAseq_Mac_90min_1

data_processing:
Reads were aligned with STAR-2.7.9a. The output BAM files were sorted with samtools and raw read counts were generated with Htseq.
Assembly: mm39
Supplementary files format and content: raw_counts.txt: raw gene expression table (genes x samples) for RNA-seq data

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen).
rRNAs were depleted using the NEBNext rRNA depletion kit, and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.


title: PROseq_Mac_45min_3


title: RNAseq_Mac_180min_2

value: +Apoptotic Jurkat cells (180min)


title: RNAseq_Mac_45min_1


title: PROseq_Mac_Alone_3


title: PROseq_Mac_45min_1


title: PROseq_Mac_Alone_4


title: RNAseq_Mac_90min_4


title: RNAseq_Mac_Alone_3


title: RNAseq_Mac_180min_4


title: RNAseq_Mac_90min_3


title: RNAseq_Mac_90min_2


title: ATACseq_Mac_45min_4

data_processing:
Trimmomatic v0.36 to cut NexteraPE adapter sequences. Bowtie v2.3.5 was used to align pair-end ATAC-seq read to the mm10 mouse reference genome. Bedtools package v2.30.089 was used to compute the consensus peak set for each condition.
Assembly: mm10
Supplementary files format and content: bw: BigWig genome browser track for ATAC-seq data

extract_protocol:
50,000 viable cells were resuspended in cold Lysis Buffer. Cells were resuspended in transposition mix containing TD buffer and Tn5 transposase.DNA purification was performed using Quagen MinElute Reaction Cleanup kit.
A modified version of the Omni-ATAC-seq protocol was used to preparae libraries (PMID: 28846090). Adapter ligation and amplification were carried out using Nextera Index Kit (Illumina).


title: RNAseq_Mac_180min_3


title: ATACseq_Mac_30min_4

value: +Apoptotic Jurkat cells (30min)


title: ATACseq_Mac_30min_3


title: ATACseq_Mac_30min_1


title: RNAseq_Mac_45min_3


title: RNAseq_Mac_45min_4


title: RNAseq_Mac_Alone_2


title: ATACseq_Mac_30min_2


title: ATACseq_Mac_45min_2


title: ATACseq_Mac_45min_3


title: PROseq_Mac_Alone_2


title: ATACseq_Mac_15min_4

value: +Apoptotic Jurkat cells (15min)


title: RNAseq_Mac_45min_2


title: ATACseq_Mac_Alone_3


title: RNAseq_Mac_Alone_1


title: ATACseq_Mac_Alone_4


title: ATACseq_Mac_45min_1


title: RNAseq_Mac_Alone_4


title: PFC, animal 2, vapor, snRNAseq

status: Public on Jan 10 2024

city: Austin

first: Dayne

last: Mayfield

state: TX

address: 2500 Speedway

institute: The University of Texas at Austin

description:
Sample14
10x Genomics

data_processing:
snRNA-seq Fastq files were processed using CellRanger-6.1.2 and the reference genome mm10-2020-A with introns included.
CellRanger outputs were imported to Seurat (4.3.0) , gene by feature count matrix was constructed, mitochondrial and ribosomal genes were eliminated, log normalization was performed and the log normalized values were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: The output of CellRanger Aggregate: features, barcodes, matrix files.  In barcodes.tsv, BC-1 corresponds to Sample1, BC-2 corresponds to Sample2, and so on.
Supplementary files format and content: csv file includes the sample name, cluster annotation, and treatment group corresponding to each barcode in barcodes.tsv.

molecule: nuclear RNA

source_name: Prefrontal Cortex

growth_protocol: C57/BL6J male mice underwent the two bottle choice-CIE vapor exposure (2BC-CIE) paradigm described in (Patel et al. 2021). Briefly, mice were placed in ethanol (n=6) or air vapor chambers (n=8) for four days (16 hours vapor on, 8 hours vapor off). Next, both treatment groups were given a bottle of water and a bottle of ethanol (15 % ethanol/water) for 2 hours. After four days of 2BC testing, CIE- and air-treated mice were subjected to a 72 hour abstinence period, and the paradigm was repeated for 5 cycles. Brains were harvested 3-5 hours after the last vapor exposure.

extract_protocol:
Micropunches were homogenized in 1.5 ml Nuclei EZ Lysis Buffer (Sigma # NUC101) supplemented with 0.2 U/ul RNAse inhibitor (NEB # ML314L) and 1X protease inhibitor (Sigma, 05892791001) in a pre-chilled 2mls KIMBLE Dounce tissue grinder (Sigma Aldrich D8938) until no tissue was visible. The lysate was filtered through a 35-µm cell strainer and centrifuged at 900 x g for 5 minutes at 4°C. The cell pellet was resuspended in wash/resuspension buffer (2% BSA in 1X PBS supplemented with 0.2 U/ul RNAse inhibitor) and mixed with Optiprep medium (60% iodixanol, Sigma-Aldrich # D1556) to a 25% final concentration. The suspension was carefully layered on to a 29% iodixanol cushion and centrifuged at 13,000 x g for 30 minutes at 4°C. The supernatant was carefully removed without disturbing the pellet and the pellet was resuspended in 100 μl wash and resuspension buffer. The nuclei were stained with DAPI and counted using a Countess Automated Cell Counter (Thermo Fisher Scientific).
Single nuclei libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics, PN-1000128) with a target cell count of 10,000 cells. Libraries were sequenced on a NovaSeq 6000 using a S4 flow cell.  NovaSeq PE100 S4.

value: single nuclei

value: Prefrontal Cortex

tag: strain

value: alcohol-vapor


title: ATACseq_Mac_15min_3

tag: treatment


title: ATACseq_Mac_15min_1


title: RNAseq_Mac_180min_1


title: PFC, animal 17, control, snRNAseq

description:
Sample10
10x Genomics

value: air-control


title: ATACseq_Mac_Alone_2


title: PFC, animal 5, control, snRNAseq

description:
Sample11
10x Genomics


title: ATACseq_Mac_Alone_1


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 12 [K4576]

status: Public on Jan 23 2024

city: New Brunswick

first: Jessie

middle: Yanxiang

last: Guo

state: NJ

address: 195 Little Albany Street, Room 3039, Lab 3029

department: Rutgers Cancer Institute of New Jersey

institute: Rutgers, The State University of New Jersey

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCm39/mm39
Read count extraction and nomalization were performed
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung tumor

extract_protocol:
Total RNA was harvasted using RNeasy Min Kit (QIAGEN). Total RNA was used for the construction of sequencing liabries.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: Lung tumor

tag: time

value: 12 weeks after tumor induction


title: PFC, animal 29, control, snRNAseq

description:
Sample9
10x Genomics


title: ATACseq_Mac_15min_2


title: PFC, animal 34, vapor, snRNAseq

description:
Sample8
10x Genomics


title: PFC, animal 24, control, snRNAseq

description:
Sample4
10x Genomics


title: PFC, animal 21, control, snRNAseq

description:
Sample13
10x Genomics


title: PFC, animal 33, vapor, snRNAseq

description:
Sample2
10x Genomics


title: PFC, animal 16, vapor, snRNAseq

description:
Sample7
10x Genomics


title: PFC, animal 9, vapor, snRNAseq

description:
Sample1
10x Genomics


title: A549-dcas9-RFP-Pool-CRISPR_S17

status: Public on Jan 01 2024

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Avenue

institute: NYU Langone

description: scRNA-seq of A540 dCas9-KRAB-MECP2 cells transfected with lentiviral barcoded sgRNA libraries

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger 7.0.0 software.
Samples were further demultiplexed based on HTOs using the hashedDrops function of the DropletUtils
Protospacer call thersholds were computed using Cell Ranger 7.0.0 software.
Assembly: GRChr38
Supplementary files format and content: Tab-separated values files and matrix file
Supplementary files format and content: Cell Ranger h5 file
Library strategy: Perturb-seq (scRNA-seq on pooled CRISPi perturbations)

source_name: shRNA counts (CRISPR guides)

growth_protocol: DMEM medium (Gibco/Invitrogen) + 10% FBS + 100 units/ml penicillin + 100 μg/ml streptomycin + 5% CO2 at 37℃

extract_protocol:
Fresh cells were harvested and hashtagged using 5 cell multiplexing oligos (10X Genomics) according to the manufacturer's protocol
The sequencing library was prepared using the Chromium Next GEM Single Cell 3ʹ Kit according to the manufacturer’s protocol

treatment_protocol: The lentiviral libraries were transduced into the A549-dCAS9-KRAB-MeCP2 cells according to Cellecta® protocols. Briefly, 105 cells/well were seeded into a 6 well-plate. The optimal MOI of viral particles (to reach ~30-40% of infected cells) were added. On day 3, 2 ug/ml of puromycin was added, resulting in >90% transduced cell selection as confirmed by cytofluorometry using RFP. Cells were expanded under puromycin selection until day 14

value: Lung

value: Alveolar Basal Epithelial

value: lentiviral sgRNA libraries


title: PFC, animal 22, control, snRNAseq

description:
Sample6
10x Genomics


title: A549-dcas9-RFP-Pool-HT

source_name: antibody oligo hashed-tagged counts


title: PFC, animal 26, vapor, snRNAseq

description:
Sample5
10x Genomics


title: AMS3.WGS

status: Public on Dec 21 2023

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing: Fastq reads were aligned against the EBV genome (accession NC_007605.1) using the BWA algorithm. Analysis of heterogeneous sites was performed following the procedure described by Čejková et al.. The consensus EBV genome for each sample was extracted using samtools59. Circus plots were generated using the R BioCircos package. Proteins were translated from nucleotide sequences using Geneious prime 2022.2 (https://www.geneious.com). Nucleotide and protein sequences were aligned using MAFFT  v7.407 and visualized using Geneious prime 2022.2. Reference EBNA1 regions, in addition to the sequence from NC_007605.1, were obtained by querying each SLCL-derived sequence against nr using tblastn and taking differentially occurring sequences between matches for the three groups of samples (HC, AMS, SMS). One representative for each of three groups of identical sequences was kept. A phylogenetic tree of the 13 resulting sequences (9 samples, 4 reference) was constructed using PhyML with default parameters and visualized using iTOL.

organism: human gammaherpesvirus 4

source_name: derived from human PBMC

extract_protocol: DNA was extracted from SLCLs using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). The Illumina DNA preparation kit was used for sequencing library preparation according to the manufacturer’s instructions. Sequencing was done with an Illumina NextSeq 500 system in high-output mode to generate a total of ∼4 × 108 paired-end 75-bp reads.

tag: host disease

value: MS

value: spontaneous lymphoblastoid cell lines

value: B cell

value: EBV


title: AMS4.WGS


title: AMS1.WGS


title: A549-dcas9-RFP-Pool_S9

source_name: RNA-seq


title: SMS3.WGS


title: SMS1.WGS


title: SMS2.WGS


title: Organoid scRNAseq OD6

status: Public on Dec 15 2023

city: London

first: Mattia

middle: Francesco Maria

last: Gerli

address: Rowland hill street

department: Department of Surgical Biotechnology

country: United Kingdom

institute: University College London

description:
Organoid scRNAseq
OD6

data_processing:
scRNAseq: v6.0.1 CellRanger for processing, with v4.2.0 Seurat was used for analysis. Bulk: Quality control was conducted on the FASTQ raw sequences using v0.11.9 FastQC (https://github.com/s-andrews/FastQC). v0.6.6 TrimGalore! (https://github.com/FelixKrueger/TrimGalore) was used to trim low quality reads (quality 20, length 70). v2.7.1a STAR (https://github.com/alexdobin/STAR) was applied to align the FASTQ sequences to the NCBI human reference genome GRCh38.p13 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39/). v1.6.3 featureCounts (https://doi.org/10.1093/bioinformatics/btt656) quantified the expression of individual genes to generate the raw count matrix, using the GRCh38.104 gene annotation (ensembl.org/Homo_sapiens/Info/Index). Default parameters used for both alignment and quantification. The generated count martrix was further processed with a custom R script. Genes will less than 10 reads across 3 samples were removed. Gene IDs were included using the added BioMart package (ensembl.org/info/data/biomart/biomart_r_package.html). Counts per million (CPM) normalisation was completed with the edgeR package (bioconductor.org/packages/release/bioc/html/edgeR.html). ComBat_seq batch correction (rdrr.io/bioc/sva/man/ComBat_seq.html) was applied between the 4 batches.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Differentiated Organoid Lane 6

growth_protocol: scRNAseq: None. Bulk: Viable amniotic fluid cells were resuspended in 30 μL of Matrigel (Corning) and plated 6x105 live cells/droplet onto a pre-warmed 24 well plate. Cells were cultured in an ad hoc defined generic medium (Supplementary Table 2) supplemented with Rho-kinase inhibitor (ROCKi; Tocris) and Primocin. To establish clonal organoid lines, single organoids formed were manually picked at passage 0 under the microscope to be clonally expanded. Each organoid was transferred in a 0.5 mL tube pre-coated with 1% BSA. After centrifugation the pellet was resuspended in 20 μL Matrigel (Corning). The plate was incubated for 20 min at 37°C and generic medium was added with ROCKi (Tocris) and Primocin for the first 3 days. Medium was replaced every 3-4 days. After approximately 10 days, grown organoids were passaged.

extract_protocol:
Bulk: RNA was harvested using Rneasy mini plus kit (Qiagen). scRNAseq: No extraction
Bulk: NEBNext Low Input RNA library preparation. scRNAseq: 10x Chromium 3' v3.1
Bulk: Single-end RNA-seq. scRNAseq: Single-end RNA-seq

value: Differentiated Organoid Lane 6

value: Fetal Fluid-derived Organoids

value: Mixed


title: HC2.WGS

value: healthy


title: HC1.WGS


title: AMS2.WGS


title: PFC, animal 20, control, snRNAseq

description:
Sample12
10x Genomics

value: single nuclei


title: Organoid scRNAseq OD5

description:
Organoid scRNAseq
OD5

source_name: Differentiated Organoid Lane 5

value: Differentiated Organoid Lane 5


title: Organoid scRNAseq OD4

description:
Organoid scRNAseq
OD4

source_name: Differentiated Organoid Lane 4

value: Differentiated Organoid Lane 4


title: AF scRNAseq H0758

description: AF scRNAseq

data_processing:
scRNAseq: Seurat. Bulk: Quality control was conducted on the FASTQ raw sequences using v0.11.9 FastQC (https://github.com/s-andrews/FastQC). v0.6.6 TrimGalore! (https://github.com/FelixKrueger/TrimGalore) was used to trim low quality reads (quality 20, length 70). v2.7.1a STAR (https://github.com/alexdobin/STAR) was applied to align the FASTQ sequences to the NCBI human reference genome GRCh38.p13 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39/). v1.6.3 featureCounts (https://doi.org/10.1093/bioinformatics/btt656) quantified the expression of individual genes to generate the raw count matrix, using the GRCh38.104 gene annotation (ensembl.org/Homo_sapiens/Info/Index). Default parameters used for both alignment and quantification. The generated count martrix was further processed with a custom R script. Genes will less than 10 reads across 3 samples were removed. Gene IDs were included using the added BioMart package (ensembl.org/info/data/biomart/biomart_r_package.html). Counts per million (CPM) normalisation was completed with the edgeR package (bioconductor.org/packages/release/bioc/html/edgeR.html). ComBat_seq batch correction (rdrr.io/bioc/sva/man/ComBat_seq.html) was applied between the 4 batches.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

value: Amniotic Fluid cells


title: AF scRNAseq H0744

description: AF scRNAseq


title: Organoid scRNAseq OU2

description:
Organoid scRNAseq
OU2

source_name: Undifferentiated Organoid Lane 2

value: Undifferentiated Organoid Lane 2


title: AF scRNAseq H0719

description: AF scRNAseq


title: AF scRNAseq H0725

description: AF scRNAseq


title: AF scRNAseq H0713

description: AF scRNAseq


title: Organoid scRNAseq OU1

description:
Organoid scRNAseq
OU1

source_name: Undifferentiated Organoid Lane 1

value: Undifferentiated Organoid Lane 1


title: AF scRNAseq H0774

description:
AF scRNAseq
20PCW_H0774


title: Organoid scRNAseq OD3

description:
Organoid scRNAseq
OD3

source_name: Differentiated Organoid Lane 3

value: Differentiated Organoid Lane 3


title: PFC, animal 19, control, snRNAseq

description:
Sample3
10x Genomics

value: Prefrontal Cortex

value: air-control


title: AF scRNAseq Combo

description: AF scRNAseq


title: AF scRNAseq H0689

description: AF scRNAseq


title: AF scRNAseq H0741

description: AF scRNAseq


title: AF scRNAseq H0687

description: AF scRNAseq


title: Organoid SI14w

description:
Small Intestine
5B2_S10

value: Fetal Tissue-derived Control Organoids


title: AF scRNAseq H0696

description: AF scRNAseq


title: Organoid K14w

description:
Kidney
5C2_S11


title: Organoid P14w

description:
Placenta
5H5_S40


title: Organoid 5F2

description:
Lung
5F2_S14

value: Amniotic Fluid-derived Organoids


title: Organoid 5H1

description:
Lung
5H1_S8


title: Organoid B14w

description:
Bladder
5G5_S39


title: Organoid 5G2

description:
Lung
5G2_S15


title: Organoid 5F1

description:
Small Intestine
5F1_S6


title: Organoid 5A2

description:
Kidney
5A2_S9


title: Organoid 5C1

description:
Lung
5C1_S3


title: Organoid 5G1

description:
Lung
5G1_S7


title: Organoid 5E2

description:
Lung
5E2_S13


title: Organoid 5A1

description:
Small Intestine
5A1_S1


title: Organoid 5D1

description:
Small Intestine
5D1_S4


title: Organoid 5E1

description:
Small Intestine
5E1_S5


title: Organoid 5F5

description:
Lung
5F5_S38

value: After-FETO


title: Organoid 5F6

description:
Lung
5F6_S46

value: Tracheal Fluid-derived Organoids

value: Before-FETO


title: Organoid 5H2

description:
Lung
5H2_S16


title: Organoid 5C5

description:
Kidney
5C5_S35


title: Organoid L23w

description:
Lung
5D5_S36


title: Organoid L14w

description:
Lung
5D2_S12


title: Organoid 5C6

description:
Lung
5C6_S43


title: Organoid 5A5

description:
Kidney
5A5_S33


title: Organoid 5B5

description:
Kidney
5B5_S34


title: Organoid 5G6

description:
Kidney
5G6_S47

value: Unknown-FETO


title: Organoid 5H6

description:
Lung
5H6_S48


title: Organoid 5D6

description:
Lung
5D6_S44


title: Organoid 5D3

description:
Kidney
5D3_S20


title: Organoid 5C3

description:
Removed
5C3_S19


title: Organoid 5B6

description:
Lung
5B6_S42


title: Organoid 5F3

description:
Lung
5F3_S22


title: Organoid 5G3

description:
Kidney
5G3_S23


title: Organoid 5B3

description:
Lung
5B3_S18


title: Organoid 5H4

description:
Kidney
5H4_S32


title: Organoid 5C4

description:
Lung
5C4_S27