title: Kras_513_LJE28

city: La Jolla

first: Reuben

last: Shaw

state: California

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology Laboratory

institute: Salk Institute for Biological Studies

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_513_LJE28_S76

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: primary_tumors_fpkm tab delimited text file Columns: (A) Transcript (B) chr (C) start (D) end (E) strand (F) length (G) Copies (H) Annotation (I-AW) FPKM for each experiment.

source_name: Primary Kras-mutant NSCLC tumor

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.  Strand-specific polyA+ RNA-seq

value: primary NSCLC tumor

value: Kras-mutant

tag: guide rna


title: Kras_511_LJE26

status: Public on Jul 14 2023

type: SRA

middle: J

country: USA

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_511_LJE26_S75

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: Kras_514_LJE29

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_514_LJE29_S77


title: Inhbe KO, chow diet, epididymal adipose, biol rep7

city: Tarrytown

first: Yuanqi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: Sample 85

data_processing:
OmicSoft Aligner Version 4 (OSA4) Benchmark
sequence reads were trimmed for adaptor sequence/low-quality sequence using OSA benchmark (parameter-trim by quality score is 2)
trimmed sequence reads were mapped to GenomeReference Mouse.mm10.regn, genemodel regn20150724 using OSA4 benchwork(parameters - Fixed penalty is 3, Indel penalty is 2)
read count extraction and normalization were performed using OSA4 benchmark
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

molecule: total RNA

extract_protocol: mRNA-seq libraries were generated using KAPA® mRNA HyperPrep Kit (Roche Sequencing.) Starting material was 500 ng RNA and fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM xGen Dual Index UMI Adapters (Integrated DNA Technologies) and amplified using 14 PCR cycles. In addition to the vendor-indicated post-library amplification clean up step, another 0.65X SPRI bead clean up was performed to enrich for larger sized fragments for optimized sequencing. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 76 cycle, paired-end sequencing recipe targeting 25 million paired reads per library.

tag: strain

tag: Sex

value: male

tag: diet

value: chow

value: KO


title: Healthy.Control_67

type: RNA

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘simpleaffy’ package). Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package.

label: biotin

organism: Macaca mulatta

source_name: CD3 Transcripts

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of NHP received either an allogeneic or autologous HCT. Allogeneic HCT recipients received various immunoprophylactic treatments for prevention of GVHD. CD3 T cells were sorted by FACS from peripheral blood at various timepoints in the post transplant period and from healthy controls.

tag: tag

tag: hct

value: NO

tag: batch

tag: survival

tag: dayposthct

tag: sample group


title: ChIPseq_48hDox_3hAux_CCNT1_BRD4G3-MS6

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
ChIP-seq: Reads were aligned with bowtie 1.2.50. Genes (N=6,481) with pausing site and TES annotation were obtained from a previously published study. FeatureCounts 2.0.1.52 was used to calculate the total mapped reads from Pol II ChIP-seq. BamCoverage in deeptools 3.1.1.53 was used to extend ChIP-seq reads to 150bp. Log2FC of ChIP-seq was calculated using bigwigCompare in deeptools with the following nondefault options: binSize 10, pseudocount 0.1.
RNA-seq:  Reads were aligned using STAR v.2.5.2 and quantified with HTSeq v.2.0.2. Read counts were corrected for technical differences and normalized between samples with R package RUVseq.  Differential gene expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: counts table

molecule: genomic DNA

organism: Homo sapiens

source_name: colon

growth_protocol: DLD1 human cells were purchased from ATCC (CCL-221) and cultured in DMEM (Corning, #10013CV) supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
ChIP-seq: DLD1 cells were crosslinked with 15ml 1% PFA (ThermoFisher, #28908) in PBS on 15cm plates for 10 minutes at RT and quenched by the addition of 2ml 2.5M glycine followed by shaking for 5 minutes. Crosslinked cells were collected by scraping. Chromatin sonication was performed for 10 minutes using a Covaris E200 set to 10% duty factor, 200 cycles per burst, and 140 peak intensity power.
ChIP-seq: Eluted DNA was purified with the QIAquick PCR Purification Kit (Qiagen, #28106), and libraries were prepared using the KAPA HTP library preparation kit (Roche, #07961901001) for sequencing on the NovaSeq 6000
RNA-seq: Total RNAs from 6-well plate were extracted using the RNeasy mini kit from Qiagen (Qiagen, #74106).
RNA-seq: mRNAs were enriched using a NEBNext poly(A) mRNA magnetic isolation module (NEB, #E7490L). RNA libraries were prepared using NEBNext Ultra II Directional RNA library preparation kit (NEB, #E7760L) and sequenced on the Illumina NovaSeq 6000.

value: colon

tag: cell line

tag: cell type

value: colorectal carcinoma

value: Dox,Aux

tag: chip antibody


title: Healthy.Control_63


title: WT, HFD diet, epididymal adipose, biol rep4

description: Sample 89

value: HFD

value: WT


title: ChIPseq_48hDox_3hAux_CCNT1_BRD4G3-MS0


title: ChIPseq_48hDox_2hAux_3hDMSO_DSHBGFP_BRD4G3-MS2

value: Dox,Aux,DMSO

value: DSHBGFP


title: ChIPseq_48hDox_2hAux_3hDMSO_DSHBGFP_BRD4G3-MS4


title: Inhbe KO, chow diet, epididymal adipose, biol rep6

description: Sample 84


title: Kras_502_LJE23

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_502_LJE23_S73


title: ChIPseq_48hDox_2hAux_3hDMSO_DSHBGFP_BRD4G3-MS1


title: Inhbe KO, chow diet, epididymal adipose, biol rep5

description: Sample 83


title: Kras_500_LJE22

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_500_LJE22_S72


title: ChIPseq_48hDox_2hAux_3hDMSO_DSHBGFP_BRD4G3-MS0


title: WT, HFD diet, epididymal adipose, biol rep2

description: Sample 87


title: ChIPseq_48hDox_2hAux_3hDMSO_DSHBGFP_BRD4G3-MS3


title: Healthy.Control_62


title: Healthy.Control_60


title: Healthy.Control_61


title: Healthy.Control_58


title: Healthy.Control_57


title: Inhbe KO, chow diet, epididymal adipose, biol rep4

description: Sample 82


title: Healthy.Control_59


title: Healthy.Control_55


title: Kras_496_LJE21

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_496_LJE21_S71


title: Kras_504_LJE24

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_504_LJE24_S74


title: Healthy.Control_56


title: Kras_494_LJE20

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_494_LJE20_S70


title: Inhbe KO, chow diet, epididymal adipose, biol rep3

description: Sample 81


title: KPL_LJE44

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE44_S37

source_name: Primary Kras-mutant, Lkb1-/-, p53-/- NSCLC tumor

value: Kras-mutant, Lkb1-/-, p53-/-


title: Inhbe KO, chow diet, epididymal adipose, biol rep2

description: Sample 80


title: Inhbe KO, chow diet, epididymal adipose, biol rep1

description: Sample 79


title: Kras_493_LJE19

description:
RNA-seq on cells isolated from a Kras primary NSCLC tumor
Kras_493_LJE19_S69


title: Healthy.Control_54


title: WT, chow diet, epididymal adipose, biol rep8

description: Sample 78


title: ChIPseq_3hJQ1_5uM_Ser2P_BRD4G3


title: ChIPseq_3hJQ1_Pol2CST_BRD4IAA7G3


title: Healthy.Control_53


title: KPL_LJE43

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE43_S34


title: ChIPseq_3hJQ1_5uM_CCNT1CST_BRD4G3


title: ChIPseq_48hDox_2hAux_3hdCDK9_DSHBGFP_BRD4G3-MS0


title: ChIPseq_3hJQ1_1uM_Ser2P_BRD4G3


title: WT, chow diet, epididymal adipose, biol rep6

description: Sample 76


title: ChIPseq_3hJQ1_10uM_Ser2P_BRD4G3


title: ChIPseq_3hJQ1_1uM_CCNT1CST_BRD4G3


title: WT, chow diet, epididymal adipose, biol rep7

description: Sample 77


title: KPL_LJE42

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE42_S33


title: KPL_LJE39

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE39_S31


title: KPL_LJE41

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE41_S32


title: ChIPseq_3hJQ1_10uM_CCNT1CST_BRD4G3


title: WT, chow diet, epididymal adipose, biol rep5

description: Sample 75


title: Healthy.Control_52


title: WT, chow diet, epididymal adipose, biol rep4

description: Sample 74


title: Healthy.Control_50


title: KPL_LJE38

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE38_S30


title: ChIPseq_3hJQ1_025uM_Ser2P_BRD4G3


title: Healthy.Control_49


title: KPL_LJE37

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE37_S29


title: WT, chow diet, epididymal adipose, biol rep3

description: Sample 73


title: ChIPseq_3hJQ1_025uM_CCNT1CST_BRD4G3


title: WT, chow diet, epididymal adipose, biol rep2

description: Sample 72


title: KPL_LJE12

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE12_S8


title: ChIPseq_3hDMSO_Ser2P_BRD4G3

value: DMSO


title: KPL_LJE9

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE9_S7


title: KPL_LJE8

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE8_S6


title: ChIPseq_3hDMSO_Pol2CST_BRD4IAA7G3


title: ChIPseq_3hDMSO_Pol2CST_BRD4G3


title: Healthy.Control_51


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep8

description: Sample 70


title: Healthy.Control_48


title: Healthy.Control_46


title: Healthy.Control_47


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep7

description: Sample 69


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep6

description: Sample 68


title: WT, chow diet, epididymal adipose, biol rep1

description: Sample 71


title: KPL_LJE6

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE6_S4


title: ChIPseq_3hDMSO_CCNT1CST_BRD4G3


title: ChIPseq_3hDMSO_CDK9SC_BRD4G3


title: KPL_LJE7

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE7_S5


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep5

description: Sample 67


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep4

description: Sample 66


title: Healthy.Control_44


title: Healthy.Control_43


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep3

description: Sample 65


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep2

description: Sample 64


title: Inhbe KO, HFD diet, subcutaneous adipose, biol rep1

description: Sample 63


title: WT, HFD diet, subcutaneous adipose, biol rep7

description: Sample 62


title: ChIPseq_3hDMSO_CCNT1CST_BRD4G3_bis


title: ChIPseq_3hdBET6_250nM_Ser2P_BRD4G3


title: ChIPseq_3hdBET6_Pol2CST_BRD4IAA7G3


title: ChIPseq_3hAux_Pol2CST_BRD4IAA7G3

value: Aux


title: ChIPseq_3hAux_Pol2CST_BRD4G3


title: KPL_LJE1

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE1_S1


title: KP_138_LJE8

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_138_LJE8_S58

source_name: Primary Kras-mutant, p53-/- NSCLC tumor

value: Kras-mutant, p53-/-


title: KP_137_LJE7

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_137_LJE7_S57

value: primary NSCLC tumor


title: KP_119_LJE6

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_119_LJE6_S56


title: Healthy.Control_42


title: KP_116_LJE5

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_116_LJE5_S55


title: Healthy.Control_45


title: WT, HFD diet, subcutaneous adipose, biol rep6

description: Sample 61


title: ChIPseq_3hAux_CDK9SC_BRD4G3


title: KPL_LJE2

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE2_S2


title: KPL_LJE5

description:
RNA-seq on cells isolated from a KPL primary NSCLC tumor
KPL_LJE5_S3


title: Healthy.Control_41


title: ChIPseq_3hdBET6_250nM_CCNT1CST_BRD4G3


title: Healthy.Control_39


title: WT, HFD diet, subcutaneous adipose, biol rep5

description: Sample 60


title: KP_115_LJE4

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_115_LJE4_S54


title: Healthy.Control_40


title: Healthy.Control_37


title: KP_109_LJE3

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_109_LJE3_S53


title: WT, HFD diet, subcutaneous adipose, biol rep4

description: Sample 59


title: ChIPseq_3hAux_CCNT1CST_BRD4G3


title: ChIPseq_2hH2O_K27AcCST_BRD4AID


title: Healthy.Control_36


title: Healthy.Control_38


title: Healthy.Control_35


title: Healthy.Control_34


title: Healthy.Control_33


title: KP_97_LJE2

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_97_LJE2_S52


title: ChIPseq_2hDMSO_2hNVP2_Pol2CST_WT

value: DMSO, NVP2


title: ChIPseq_2hDMSO_2hDMSO_Pol2CST_WT


title: WT, HFD diet, subcutaneous adipose, biol rep1

description: Sample 56

value: male


title: KP_96_LJE1

description:
RNA-seq on cells isolated from a KP primary NSCLC tumor
KP_96_LJE1_S51


title: WT, HFD diet, subcutaneous adipose, biol rep2

description: Sample 57


title: WT, HFD diet, subcutaneous adipose, biol rep3

description: Sample 58


title: Healthy.Control_64


title: KL_LJE34

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE34_S27

source_name: Primary Kras-mutant, Lkb1-/- NSCLC tumor

value: Kras-mutant, Lkb1-/-


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep7

description: Sample 55

value: chow

value: KO


title: KL_LJE32

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE32_S26


title: KL_LJE30

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE30_S25


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep6

description: Sample 54


title: KL_LJE29

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE29_S24


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep4

description: Sample 52


title: KL_LJE28

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE28_S23


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep3

description: Sample 51


title: KL_LJE35

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE35_S28


title: ChIPseq_0hAux_Pol2CST_BRD4IAA7G3

value: colon


title: KL_LJE26

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE26_S21


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep2

description: Sample 50


title: Healthy.Control_31

value: NO


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep1

description: Sample 49


title: KL_LJE27

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE27_S22


title: WT, chow diet, subcutaneous adipose, biol rep8

description: Sample 48


title: Healthy.Control_28


title: Healthy.Control_32


title: Healthy.Control_29


title: Inhbe KO, chow diet, subcutaneous adipose, biol rep5

description: Sample 53


title: Healthy.Control_23


title: Healthy.Control_27


title: WT, chow diet, subcutaneous adipose, biol rep6

description: Sample 46


title: Healthy.Control_25


title: WT, chow diet, subcutaneous adipose, biol rep7

description: Sample 47


title: Healthy.Control_26


title: WT, chow diet, subcutaneous adipose, biol rep5

description: Sample 45


title: Healthy.Control_24


title: KL1_Veh13d_R3

description: RNA-seq in KL LJE1 cells treated with DMSO 13 days, replicate 3

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: KLLJE1_Tram_Ent_fpkm tab delimited text file Columns: (A) Transcript (B) chr (C) start (D) end (E) strand (F) length (G) Copies (H) Annotation (I-W) FPKM for each experiment.

source_name: Immortalized cell line derived from Kras-mutant, Lkb1-/- NSCLC lung tumor

value: NSCLC lung tumor


title: KL1_Veh13d_R2

description: RNA-seq in KL LJE1 cells treated with DMSO 13 days, replicate 2


title: KL1_Veh13d_R1

description: RNA-seq in KL LJE1 cells treated with DMSO 13 days, replicate 1


title: Healthy.Control_30


title: KL_LJE25

description:
RNA-seq on cells isolated from a KL primary NSCLC tumor
KL_LJE25_S20


title: KL1_Veh3d_R1

description: RNA-seq in KL LJE1 cells treated with DMSO 3 days, replicate 1


title: KL1_Veh3d_R3

description: RNA-seq in KL LJE1 cells treated with DMSO 3 days, replicate 3


title: WT, chow diet, subcutaneous adipose, biol rep3

description: Sample 43


title: WT, chow diet, subcutaneous adipose, biol rep4

description: Sample 44


title: WT, chow diet, subcutaneous adipose, biol rep2

description: Sample 42


title: WT, chow diet, subcutaneous adipose, biol rep1

description: Sample 41


title: Healthy.Control_22


title: KL1_TramEnt13d_R3

description: RNA-seq in KL LJE1 cells treated with Trametinib+Entinostat 13 days, replicate 3

value: 10nM Trametinib + 1uM Entinostat


title: Healthy.Control_21


title: Healthy.Control_20


title: KL1_TramEnt13d_R2

description: RNA-seq in KL LJE1 cells treated with Trametinib+Entinostat 13 days, replicate 2


title: mInhbe AAV, epididymal adipose, biol rep9

description: Sample 39

value: WT

value: mInhbe AAV


title: KL1_TramEnt13d_R1

description: RNA-seq in KL LJE1 cells treated with Trametinib+Entinostat 13 days, replicate 1


title: mInhbe AAV, epididymal adipose, biol rep8

description: Sample 38


title: KL1_Veh3d_R2

description: RNA-seq in KL LJE1 cells treated with DMSO 3 days, replicate 2


title: 2169150_SB1_dBRD9_n1  [RNA-seq]

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas pl.

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
~100M, 100-bp, paired-end reads were generated by using NovaSeq 6000 for 3 biological replicates of each sample.  The RNA-seq reads were mapped to the human GRCh37-lite (HG19) reference genome via STAR (Dobin et al., 2013).  Gene-level counts were quantified by RSEM (v1.3.1) with GENCODE version 19 Ensembl 74 annotation. The read counts were further normalized by using the R package DESeq2. Differential gene expression was called by using the R package DESeq2. Gene ontology enrichment analyses of up- or downregulated gene lists were performed by using the GO Enrichment Analysis by Enrichr (https://maayanlab.cloud/Enrichr/).
Assembly: HG19
Supplementary files format and content: RSEM counts for each n=3 comparison made in the paper.

extract_protocol:
Qiagen RNeasy plus mini kit (74034) according to the manufacturer’s instructions
TruSeq Stranded mRNA Library Prep kit according to the manufacturer’s instructions

value: Rhabdoid Tumor

tag: dox induction


title: 2169158_SB1_dBRD9_n3  [RNA-seq]


title: 2169154_SB1_dBRD9_n2  [RNA-seq]


title: Healthy.Control_19


title: Healthy.Control_16


title: KL1_Tram13d_R3

description: RNA-seq in KL LJE1 cells treated with Trametinib 13 days, replicate 3

value: 10nM Trametinib

tag: guide rna


title: 2169157_GFP_dBRD9_n3  [RNA-seq]

value: GFP


title: mInhbe AAV, epididymal adipose, biol rep7

description: Sample 37

tag: tissue


title: KL1_Tram13d_R2

description: RNA-seq in KL LJE1 cells treated with Trametinib 13 days, replicate 2

tag: genotype


title: Healthy.Control_17


title: 2169153_GFP_dBRD9_n2  [RNA-seq]

tag: treatment


title: mInhbe AAV, epididymal adipose, biol rep10

description: Sample 40

tag: strain


title: mInhbe AAV, epididymal adipose, biol rep6

description: Sample 36

tag: Sex


title: Healthy.Control_18


title: 2169149_GFP_dBRD9_n1  [RNA-seq]


title: Healthy.Control_15


title: KL1_Tram13d_R1

description: RNA-seq in KL LJE1 cells treated with Trametinib 13 days, replicate 1


title: mInhbe AAV, epididymal adipose, biol rep5

description: Sample 35

tag: diet


title: 2169156_SB1_n3  [RNA-seq]

value: DMSO


title: Healthy.Control_12

tag: tag


title: Healthy.Control_11

tag: hct


title: mInhbe AAV, epididymal adipose, biol rep4

description: Sample 34


title: 2169152_SB1_n2  [RNA-seq]


title: Healthy.Control_13

tag: batch


title: KL1_Tram3d_R1

description: RNA-seq in KL LJE1 cells treated with Trametinib 3 days, replicate 1


title: 2169148_SB1_n1  [RNA-seq]


title: mInhbe AAV, epididymal adipose, biol rep2

description: Sample 32


title: mInhbe AAV, epididymal adipose, biol rep3

description: Sample 33


title: KL1_NT_NT_R3

description:
RNA-seq in KL LJE1 cells transduced with sgNT + sgNT, replicate 3
KL1_NT_NT_R3_LJE27_S72

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: KLLJE1_HDAC3KO_p65KO_tpm tab delimited text file Columns: (A) Transcript (B) chr (C) start (D) end (E) strand (F) length (G) Copies (H) Annotation (I-T) TPM for each experiment.

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions. Strand-specific polyA+ RNA-seq

value: sgNT + sgNT


title: Healthy.Control_9

tag: survival


title: 2169155_GFP_n3  [RNA-seq]


title: Healthy.Control_10

tag: dayposthct


title: KL1_NT_NT_R2

description:
RNA-seq in KL LJE1 cells transduced with sgNT + sgNT, replicate 2
KL1_NT_NT_R2_LJE26_S71


title: mInhbe AAV, epididymal adipose, biol rep1

description: Sample 31


title: 2169151_GFP_n2  [RNA-seq]


title: Healthy.Control_14

tag: sample group


title: KL1_NT_NT_R1

description:
RNA-seq in KL LJE1 cells transduced with sgNT + sgNT, replicate 1
KL1_NT_NT_R1_LJE25_S70


title: KL1_Tram3d_R2

description: RNA-seq in KL LJE1 cells treated with Trametinib 3 days, replicate 2


title: control GFP AAV, epididymal adipose, biol rep10

description: Sample 30

value: Control GFP AAV


title: KL1_Tram3d_R3

description: RNA-seq in KL LJE1 cells treated with Trametinib 3 days, replicate 3


title: 2169147_GFP_n1  [RNA-seq]

tag: cell line


title: control GFP AAV, epididymal adipose, biol rep9

description: Sample 29


title: Healthy.Control_8


title: Healthy.Control_7


title: 2286490_G401_IgGepi_SB1_NA_1_RJM  [CUT&RUN]

data_processing:
library strategy: CUT & RUN
Paired-end reads of 75 bp were mapped to the human genome hg19 (GRCh37-lite) and the Escherichia coli genome r46 (Ensembl r46 ASM584v2) hybrid by BWA (version 0.7.12-r1039, default parameter) (Li and Durbin, 2009). The duplicated reads were then marked by biobambam2 (version 2.0.87) (Tischler and Leonard, 2014). After the duplicated reads were marked, bam files were split by either the human bam file or the Escherichia coli spike-in bam file. For the spike-in bam files, we counted the nonduplicated reads with SAMtools. For the human bam files only, the uniquely, properly paired reads were extracted by SAMtools, (version 1.2, parameter -q 1 -F 1804) (Li et al., 2009) sorted based on read name, (biobambam2) and convert to BEDPE format by using bedtools. Fragment sizes <2000 bp were extracted, and the center 80 bp of each fragment were used to generate normalized (to 10 million fragments) bigwig tracks for visualization. Peaks were called against Igg control for BRD9 and GFP-induced cells assayed with the same antibody for SMARCB1. Peaks were identified by using Easeq (Adaptive Local Thresholding) with a p-value and FDR cutoff of 1×10-4 and a log2(fold-change) over control cutoff of 0.5. SMARCB1 peaks are peaks called in both biological replicates. For BRD9 peaks, differential binding analysis was accomplished using only peaks occurring in at least 2 of the 3 biological replicates for a given sample by using R packages diffbind and edger. Differential binding was determined using FDR and Log2(fold-change) cutoffs of 0.05 and 0.5, respectively. Averaged bedgraphs were generated for CUT & RUN by (1) combining replicates UCSC-bigWigMerge, (2) sorting combined bedgraphs (LC_COLLATE=C sort -k1,1 -k2,2n), and (3) averaging the 4th bedgraph column based on number of input replicates using awk.
Assembly: HG19
Supplementary files format and content: easeq peak .txt files
Supplementary files format and content: bigwig coverage

extract_protocol:
Epicypher CUTANA™ ChIC/CUT&RUN Kit 14-1048 according to manufacturer's instructions
Kapa Hyper Library prep kit (# 7962363001) according to the manufacturer’s specifications

tag: cell type

tag: antibody target

value: Rabbit IgG

tag: antibody manufacturer

value: Epicypher

tag: antibody identifiers


title: H3KO_p65g2_R2

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#2, replicate 2
H3KO_p65g3_R2_LJE35_S80

value: Kras-mutant, Lkb1-/-

tag: guide rna

value: sgHdac3 #1 + sgp65 #2


title: H3KO_p65g2_R3

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#2, replicate 3
H3KO_p65g3_R3_LJE36_S81

tag: genotype


title: control GFP AAV, epididymal adipose, biol rep8

description: Sample 28

tag: tissue

value: male

value: chow

tag: treatment


title: Healthy.Control_5

value: NO


title: Healthy.Control_4


title: Healthy.Control_6


title: H3KO_p65g2_R1

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#2, replicate 1
H3KO_p65g3_R1_LJE34_S79

value: NSCLC lung tumor


title: control GFP AAV, epididymal adipose, biol rep7

description: Sample 27

tag: strain

tag: Sex


title: 2295882_G401_BRD9abcam137245_SB1_NA_3_RJM  [CUT&RUN]

tag: dox induction

value: BRD9, Rabit Polyclonal

value: ABCAM


title: control GFP AAV, epididymal adipose, biol rep6

description: Sample 26

tag: diet

value: WT


title: 2295881_G401_BRD9abcam137245_GFP_NA_3_RJM  [CUT&RUN]

value: Rhabdoid Tumor


title: H3KO_p65g1_R3

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#1, replicate 3
H3KO_p65g2_R3_LJE33_S78

value: sgHdac3 #1 + sgp65 #1


title: 2295880_G401_BRD9abcam137245_SB1_NA_2_RJM  [CUT&RUN]


title: Healthy.Control_2

tag: tag

tag: hct

tag: batch


title: 2295879_G401_BRD9abcam137245_GFP_NA_2_RJM  [CUT&RUN]

value: GFP


title: H3KO_p65g1_R2

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#1, replicate 2
H3KO_p65g2_R2_LJE32_S77


title: control GFP AAV, epididymal adipose, biol rep5

description: Sample 25


title: H3KO_NT_R3

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgNT, replicate 3
H3KO_NT_R3_LJE30_S75

value: sgHdac3 #1 + sgNT


title: control GFP AAV, epididymal adipose, biol rep3

description: Sample 23


title: H3KO_p65g1_R1

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgp65#1, replicate 1
H3KO_p65g2_R1_LJE31_S76


title: 2295877_G401_BRD9abcam137245_GFP_NA_1_RJM  [CUT&RUN]


title: control GFP AAV, epididymal adipose, biol rep4

description: Sample 24


title: Healthy.Control_1

tag: survival

tag: dayposthct

tag: sample group


title: 2295878_G401_BRD9abcam137245_SB1_NA_1_RJM  [CUT&RUN]

tag: cell line

tag: cell type

tag: antibody target


title: control GFP AAV, epididymal adipose, biol rep2

description: Sample 22


title: 2271157_G401_SMARCB1cst91735_SB1_NA_1_RJM  [CUT&RUN]

value: SMARCB1, Rabbit Monoclonal

tag: antibody manufacturer

value: Cell Signaling Technologies

tag: antibody identifiers


title: 2271158_G401_SMARCB1cst91735_SB1_NA_2_RJM  [CUT&RUN]

tag: genotype


title: control GFP AAV, epididymal adipose, biol rep1

description: Sample 21

tag: tissue

tag: treatment

value: Control GFP AAV


title: H3KO_NT_R1

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgNT, replicate 1
H3KO_NT_R1_LJE28_S73

tag: guide rna


title: H3KO_NT_R2

description:
RNA-seq in KL LJE1 cells transduced with sgHdac3 #1 + sgNT, replicate 2
H3KO_NT_R2_LJE29_S74


title: Healthy.Control_0


title: Healthy.Control_3


title: 634_NT_R3

description: RNA-seq in 634T cells transduced with sgNT, replicate 3

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: HDAC3KO_NKX2KO_diff2 Excel file with Columns: (A) Transcript (B) chr (C) start (D) end (E) strand (F) length (G) Annotation (H-AC) Log2 Fold change and adj. p-value for each comparison indicated in row 1.

source_name: Immortalized cell line derived from Kras-mutant, p53-/- NSCLC lung tumor

value: sgNT

value: Kras-mutant, p53-/-


title: 2271156_G401_SMARCB1cst91735_GFP_NA_2_RJM  [CUT&RUN]

tag: dox induction


title: mInhbe AAV, subcutaneous adipose, biol rep10

description: Sample 20

tag: strain

tag: Sex

tag: diet

value: mInhbe AAV


title: FR104.D15_1

tag: tag

tag: hct

value: YES

tag: batch


title: mInhbe AAV, subcutaneous adipose, biol rep9

description: Sample 19

value: male

value: chow


title: aDLL4.Nx_6

tag: survival

tag: dayposthct

tag: sample group


title: 634_NT_R2

description: RNA-seq in 634T cells transduced with sgNT, replicate 2

tag: cell type

value: NSCLC lung tumor


title: FR104.D15_2


title: aDLL4.Nx_7


title: 1937855G401 WT N_2 [ChIP-seq]

data_processing:
Single-end reads of 50 bp were mapped to the human genome hg19 (GRCh37-lite)  by BWA (version 0.7.12-r1039, default parameter) (Li and Durbin, 2009).
Unique reads were extracted by samtools, (version 1.2, parameter -q 1 -F 1804) (Li et al., 2009) sorted based on read name, (biobambam2) and bedtools was used to convert to BEDPE format.
 Fragments were used to generate normalized (to 10 million fragments) bigwig tracks for visualization.
H3K27Ac peaks were called against the input sample using Easeq (Adaptive Local Thresholding) with a p-value and FDR cutoff of 1x10-4 and a log2(fold-change) over control cutoff of 0.5.
Averaged bigwigs were generated for ChIP or RNA-Seq by (1) combining replicates UCSC-bigWigMerge, (2) sorting combined bedgraphs (LC_COLLATE=C sort -k1,1 -k2,2n), and (3) averaging the 4th bedgraph column based on number of input replicates using awk.
Assembly: HG19
Supplementary files format and content: narrowpeak (peaks);  (ROSE enhancers)
Supplementary files format and content: bigwig coverage

extract_protocol:
Cell Signaling Enzymatic ChIP kit #9003
Kapa Hyper Library prep kit (# 7962363001) according to the manufacturer’s specifications

tag: cell line

tag: chip antibody_target

value: input


title: aDLL4.Nx_4


title: FR104.D15_0


title: mInhbe AAV, subcutaneous adipose, biol rep8

description: Sample 18

tag: genotype


title: aDLL4.Nx_3


title: 634_NT_R1

description: RNA-seq in 634T cells transduced with sgNT, replicate 1


title: 1937854G401 WT N_1 [ChIP-seq]


title: aDLL4.Nx_5


title: 634_H3KOg2_R3

description: RNA-seq in 634T cells transduced with sgHdac3 #2, replicate 3

value: sgHdac3 #2


title: 1937852G401 GFP N_1 [ChIP-seq]


title: 634_H3KOg2_R2

description: RNA-seq in 634T cells transduced with sgHdac3 #2, replicate 2


title: 1937853G401 GFP N_2 [ChIP-seq]


title: mInhbe AAV, subcutaneous adipose, biol rep6

description: Sample 16

tag: tissue

value: WT


title: 1933222G401 WT_BRG1_2 [ChIP-seq]

value: Rhabdoid Tumor

value: SMARCA4, Rabbit monoclonal

tag: chip antibody_vendor

value: ABCAM

tag: chip antibody_identifiers


title: 634_H3KOg1_R3

description: RNA-seq in 634T cells transduced with sgHdac3 #1, replicate 3

tag: treatment

tag: guide rna

value: sgHdac3 #1


title: mInhbe AAV, subcutaneous adipose, biol rep4

description: Sample 14

tag: strain

tag: Sex


title: mInhbe AAV, subcutaneous adipose, biol rep5

description: Sample 15

tag: diet


title: 634_H3KOg2_R1

description: RNA-seq in 634T cells transduced with sgHdac3 #2, replicate 1


title: aDLL4.Nx_1

tag: tag

tag: hct


title: aDLL4.Nx_2

tag: batch

tag: survival


title: 1933221G401 GFP_BRG1_2 [ChIP-seq]

tag: dox induction

value: GFP


title: 634_H3KOg1_R2

description: RNA-seq in 634T cells transduced with sgHdac3 #1, replicate 2

tag: cell type


title: mInhbe AAV, subcutaneous adipose, biol rep7

description: Sample 17


title: 634_H3KOg1_R1

description: RNA-seq in 634T cells transduced with sgHdac3 #1, replicate 1


title: 1933209G401 GFP_BRG1_1 [ChIP-seq]

tag: cell line


title: mInhbe AAV, subcutaneous adipose, biol rep2

description: Sample 12


title: KL7_H3KOg1_R3

description: RNA-seq in KL LJE7 cells transduced with sgHdac3 #1, replicate 3

value: Kras-mutant, Lkb1-/-


title: aDLL4.D15_7

tag: dayposthct

tag: sample group


title: control GFP AAV, subcutaneous adipose, biol rep10

description: Sample 10

tag: tissue

tag: genotype

value: Control GFP AAV


title: aDLL4.D15_8


title: aDLL4.D15_6


title: 1937870G401 SMARCB1 H3K4me1_1 [ChIP-seq]

tag: chip antibody_target

value: H3K4me1 Rabbit Monoclonal

tag: chip antibody_vendor

value: Cell Signaling Technologies

tag: chip antibody_identifiers


title: aDLL4.D15_5


title: aDLL4.Nx_0


title: 1933210G401 WT_BRG1_1 [ChIP-seq]


title: aDLL4.D15_4


title: mInhbe AAV, subcutaneous adipose, biol rep3

description: Sample 13

tag: strain

tag: treatment

value: mInhbe AAV


title: aDLL4.D15_3

value: YES


title: KL7_H3KOg1_R1

description: RNA-seq in KL LJE7 cells transduced with sgHdac3 #1, replicate 1

tag: guide rna


title: control GFP AAV, subcutaneous adipose, biol rep8

description: Sample 8

tag: Sex

value: male

tag: diet


title: KL7_NT_R3

description: RNA-seq in KL LJE7 cells transduced with sgNT, replicate 3

value: sgNT


title: mInhbe AAV, subcutaneous adipose, biol rep1

description: Sample 11

value: chow


title: control GFP AAV, subcutaneous adipose, biol rep7

description: Sample 7


title: mESC_F15_96_rep3

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

description: scNanoHi-C

data_processing:
Sequencing data were first demultiplexed to single cells by Nanoplexer using default parameters. Adapter sequences were trimmed by Cutadapt and reads shorter than 500bp were also removed. These cleaned reads of each cell were then fed into the Pore-C snakemake pipeline to align to reference genome using the bwasw algorithm, tag haplotype by whatshap using known phased SNV sites, assign to restriction fragments and identify high-order concatemers. The resulting single cells concatemer sets were further filtered to remove single-cell artifacts according to previous single-cell Hi-C methods, which included duplicated, promiscuous and isolated contacts. The final single-cell concatemer sets then could be decomposed into virtual pair-wise contacts (VPCs) to store in a parquet format and assigned to genomic bins for contacts map visualization with cooler in mcool format.
Assembly: GRh38 or mm10
Supplementary files format and content: .parquet: filtered pair-wise contacts file of scNanoHi-C single cells with metadata
Supplementary files format and content: .mcool scNanoHi-C pair-wise multi-resolution cooler contacts matrcies
Library strategy: scNanoHi-C

source_name: mESC F15

growth_protocol: GM12878 (HG001) cell line and GM24385 (HG002) cell line were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 15%fetal bovine serum (FBS,Gibco,cat#26140079) and Penicillin/Streptomycin (PS; Gibco, cat#15140122). K562 cell line was cultured in RPMI-1640 supplemented with 10% FBS and 1% PS. COLO320DM cell line was cultured RPMI-1640 supplemented with 10% FBS and 1% PS. Wild-type V6.5 murine embryonic stem cells (mESCs) were cultured on 0.25% gelatin-coated 6-well plate in Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco, cat#11320033) containing 15%FBS,1%Glutamax(Gibco, cat#35050061),0.1mM 2-mercaptoethanol (Gibco, cat#21985023),1%MEM nonessential amino acids(Gibco, cat#11140050),1%nuleoside (Millipore, cat#ES-008-D), 1%PS and 10000× 107 units/ml Leukemia Inhibitory Factor (LIF; Millipore, cat#ESG1107). The other male mouse ES cell line (named F15) was cultured in serum-free 2i/LIF medium, with in equal volume of DMEM (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 131 21103049) maintained in 2i (3 μM CHIR99021 and 1 μM PD0325901), LIF (1 000 U/ml), as previously described. These cell lines were all cultured at 37 ˚C with 5% CO2.

extract_protocol:
Resuspended ligated nuclei pellets in 200μL 0.25%BSA in PBS each tube and added 0.2μL 1000×DAPI for sorting nuclei. Single nucleus was flow sorted into each well of 96-well plate containing 2 μL lysis buffer(0.04 μL 1M Tris-HCl (pH 8.0),0.08μL 500 mM NaCl,0.03μL10% Triton X-100 (Sigma), 0.0004μL 0.5 M EDTA,0.05μL 20mg/mL QIAGEN protease). And then to decrosslinking and digest, incubated at 50°C, 3h; 70°C, 20 min; 68°C, 45 min; 4°C pause. After digesting, 96-well plates were stored at −80 ˚C.
A total amount of 1 g DNA per sample was used as input material for the DNA library preparations. SQK-LSK109 Kit (Nanopore, UK) was used to construct 1D library. The DNA library was constructed by standard ligation method without DNA fragmentation, after end repaired, added the sequencing adaptor, motor protein and tether protein were connected to prepare the DNA library. After that, each amplicon fragment library was loaded into 1 R9 flow cell and sequenced on PromethION HAC (high accuracy) model.

value: mESC F15

value: mouse embryonic stem cell


title: 1937871G401 SMARCB1 H3K4me1_2 [ChIP-seq]


title: KL7_NT_R2

description: RNA-seq in KL LJE7 cells transduced with sgNT, replicate 2

value: NSCLC lung tumor


title: control GFP AAV, subcutaneous adipose, biol rep6

description: Sample 6

value: WT


title: aDLL4.D15_0

tag: tag

tag: hct

tag: batch


title: KL7_NT_R1

description: RNA-seq in KL LJE7 cells transduced with sgNT, replicate 1

tag: cell type


title: KL7_H3KOg1_R2

description: RNA-seq in KL LJE7 cells transduced with sgHdac3 #1, replicate 2


title: control GFP AAV, subcutaneous adipose, biol rep9

description: Sample 9


title: 1937866G401 SMARCB1 H3K4me3_1 [ChIP-seq]

tag: cell line

value: Rhabdoid Tumor

tag: dox induction

value: H3K4me3 Rabbit Monoclonal


title: KL1_H3KOg2_R3

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #2, replicate 3

value: sgHdac3 #2


title: 1937869G401 GFP H3K4me1_2 [ChIP-seq]

value: GFP


title: control GFP AAV, subcutaneous adipose, biol rep5

description: Sample 5


title: mESC_F15_300_rep1

description: scNanoHi-C


title: control GFP AAV, subcutaneous adipose, biol rep4

description: Sample 4


title: KL1_H3KOg2_R2

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #2, replicate 2

value: Kras-mutant, Lkb1-/-


title: 1937868G401 GFP H3K4me1_1 [ChIP-seq]


title: aDLL4.D15_1

tag: survival

tag: dayposthct

tag: sample group


title: control GFP AAV, subcutaneous adipose, biol rep3

description: Sample 3

tag: tissue

tag: genotype

value: Control GFP AAV


title: 1937864G401 GFP H3K4me3_1 [ChIP-seq]

tag: chip antibody_target

tag: chip antibody_vendor

tag: chip antibody_identifiers


title: aDLL4.D15_2


title: 1937859G401 SMARCB1 H3K27Ac_2 [ChIP-seq]

value: H3K27Ac Rabbit Monoclonal


title: NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 0:100

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were basecalled with Guppy 6.2.1 in `sup’ accuracy (dna_r9.4.1_450bps_sup_prom.cfg), disabling trimming and enabling read splitting.
Passed reads were aligned to the Gencode V33 reference transcriptome and RNA sequin annotation 2.4 with minimap2 version 2.24.
Transcript-level counts were obtained using salmon version 1.9.0.
Assembly: GrCh38 and RNA sequin annotation 2.4
Supplementary files format and content: Tab-separated files with transcript IDs, lengths and read counts

source_name: Lung adenocarcinoma

growth_protocol: The cell lines were retrieved from the ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. The cells were grown independently at 37°C with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).
The NCI-H1975+sequins mixA replicate 1 RNA was mixed with the HCC827+sequins mixB replicate 1 RNA in the 5 following mass ratios: 100:0, 75:25, 50:50, 25:75 and 0:100. 1 ng of each mix was then used for library preparation. The cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit was used with the supplied ONT protocol. Amplication for purified mRNA spiked with sequins was done with 16 PCR cycles with a 2 minutes and 30 seconds extension step and a 0.8X final bead clean up. Size selection was performed for the standard ~2kb target. 65 ng of the final library were loaded onto 1 FLO-PRO002 PromethION flow cell (R9.4.1).

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Lung adenocarcinoma


title: NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 25:75


title: control GFP AAV, subcutaneous adipose, biol rep2

description: Sample 2

tag: strain

tag: treatment


title: 1937867G401 SMARCB1 H3K4me3_2 [ChIP-seq]

value: Cell Signaling Technologies


title: KL1_NT(H3g2)_R3

description: RNA-seq in KL LJE1 cells transduced with sgNT, replicate 3

tag: guide rna


title: mESC_F15_96_rep2

description: scNanoHi-C


title: NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 50:50


title: 1937858G401 SMARCB1 H3K27Ac_1 [ChIP-seq]


title: control GFP AAV, subcutaneous adipose, biol rep1

description: Sample 1

tag: Sex

tag: diet


title: KL1_NT(H3g2)_R2

description: RNA-seq in KL LJE1 cells transduced with sgNT, replicate 2


title: 1937857G401 GFP H3K27Ac_2 [ChIP-seq]


title: NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 75:25


title: KL1_NT(H3g2)_R1

description: RNA-seq in KL LJE1 cells transduced with sgNT, replicate 1


title: 1937865G401 GFP H3K4me3_2 [ChIP-seq]


title: mESC_F15_96_rep1

description: scNanoHi-C


title: 1937856G401 GFP H3K27Ac_1 [ChIP-seq]


title: KL1_H3KOg2_R1

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #2, replicate 1


title: KPT3_TTFKOgS_R1

description: RNA-seq in KP T3 cells transduced with sgTTF1 SR, replicate 1

value: sgTtf1(Nkx2-1) SR

value: Kras-mutant, p53-/-


title: 2112969_SMARCB1_dBRD9_ATAC_n1

description: free = nucleosome free, nuc = nulceosomal

data_processing:
Quality trimmed reads are mapped to the HG19 reference genome by bwa(v0.7.12-r1039, PMID: 19451168)
converted to bam file by samtools (v1.2, PMID: 19505943)
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads.
Nucleosome free fragments and nucleosomal fragments were extracted by bedtools (v2.24.0, PMID: 20110278).
Narrow peaks were called by MACS2 (v2.1.1.20160309, PMID: 18798982) on nucleosome free reads (fragment size < 100bp, find out why @2.2) using False Positive Rate corrected p-value 0.05 (find out more @2.3).
Differential accessibility was called on nucleosome free regions identified from three biological replicates of each sample using R packages diffbind and deseq2. Background normalization was utilized, and nucleosome free regions were only considered if identified in two of the three replicates.
Averaged bedgraphs were generated for ATAC-seq nucleosomal and nucleosome free regions by (1) combining replicates UCSC-bigWigMerge, (2) sorting combined bedgraphs (LC_COLLATE=C sort -k1,1 -k2,2n), and (3) averaging the 4th bedgraph column based on number of input replicates using awk.
Assembly: HG19
Supplementary files format and content: bigwig containing nucleosome free reads
Supplementary files format and content: bigwig containing nucleosomal reads
Supplementary files format and content: peak file containing peaks called from nucleosome free regions

extract_protocol: Active Motif ATAC-seq kit and library prep protocol

treatment_protocol: 24hrs dox and DMSO or dBRD9-A


title: KPT3_TTFKOgS_R3

description: RNA-seq in KP T3 cells transduced with sgTTF1 SR, replicate 3


title: 2161070_SMARCB1_dBRD9_ATAC_n3


title: KPT3_TTFKOgG_R3

description: RNA-seq in KP T3 cells transduced with sgTTF1 #2, replicate 3

value: sgTtf1(Nkx2-1) #2


title: 2118892_SMARCB1_dBRD9_ATAC_n2


title: K562

description: scNanoHi-C

growth_protocol: GM12878 (HG001) cell line and GM24385 (HG002) cell line were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 15%fetal bovine serum (FBS,Gibco,cat#26140079) and Penicillin/Streptomycin (PS; Gibco, cat#15140122). K562 cell line was cultured in RPMI-1640 supplemented with 10% FBS and 1% PS. COLO320DM cell line was cultured RPMI-1640 supplemented with 10% FBS and 1% PS. Wild-type V6.5 murine embryonic stem cells (mESCs) were cultured on 0.25% gelatin-coated 6-well plate in Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco, cat#11320033) containing 15%FBS,1%Glutamax(Gibco, cat#35050061),0.1mM 2-mercaptoethanol (Gibco, cat#21985023),1%MEM nonessential amino acids(Gibco, cat#11140050),1%nuleoside (Millipore, cat#ES-008-D), 1%PS and 10000× 107 units/ml Leukemia Inhibitory Factor (LIF; Millipore, cat#ESG1107). The other male mouse ES cell line (named F15) was cultured in serum-free 2i/LIF medium, with in equal volume of DMEM (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 131 21103049) maintained in 2i (3 uM CHIR99021 and 1 uM PD0325901), LIF (1 000 U/ml), as previously described. These cell lines were all cultured at 37 ˚C with 5% CO2.

value: chronic myelogenous leukemia


title: 2118890_GFP_dBRD9_ATAC_n2


title: HG002_48cell

description: scNanoHi-C

value: lymphoblast cell


title: KPT3_TTFKOgS_R2

description: RNA-seq in KP T3 cells transduced with sgTTF1 SR, replicate 2


title: KPT3_TTFKOgG_R2

description: RNA-seq in KP T3 cells transduced with sgTTF1 #2, replicate 2


title: 2112967_GFP_dBRD9_ATAC_n1


title: KPT3_TTFKOgG_R1

description: RNA-seq in KP T3 cells transduced with sgTTF1 #2, replicate 1


title: COLO320DM

description: scNanoHi-C

value: colorectal adenocarcinoma


title: GM12878_high

description: scNanoHi-C


title: GM12878_medium

description: scNanoHi-C


title: 2161068_SMARCB1_ATAC_n3

value: DMSO


title: 2161069_GFP_dBRD9_ATAC_n3


title: P3_hom2, replicate 2, scRNAseq

city: Solna

first: Emma

middle: R

last: Andersson

state: Not required for this country

address: Solnav. 9, BioMedicum

country: Sweden

institute: Karolinska Institutet

description:
10x Genomics
Instrument models: Illumina NextSeq 550, Illumina NovaSeq

library_source: transcriptomic single cell

data_processing:
Demultiplexing, quality control, raw data, gene expression data counts were performed using CellRanger v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), by the BEA and SciLife core facilities. Matrices were further processed and analyzed with R (version 4.1.2) in R Studio. Prior to transformation into Seurat Objects, matrices were precleared using SoupX (https://github.com/constantAmateur/SoupX) with default settings of setContaminationFraction parameter (sc) for the P3, and (sc, 0.13) for the E16.5 stages. All bioinformatic analyses was performed using Seurat pipeline, doublet removal with scDblFinder (https://github.com/plger/scDblFinder), QC cutoffs for E16.5 datasets were nFeature_RNA > 500 & nFeature_RNA < 7000 & percent.mt < 10, for P3 a range of nFeature_RNA > 300-500 & nFeature_RNA < 4500-6000 & percent.mt < 10 were used, followed by SCT based integration of the E16.5 and P3 Jag1+/+, Jag1Ndr/+, and Jag1Ndr/ Ndr datasets 13. In total, 183,542 cells passed through the cross-contamination adjustment, quality control filtering and doublet removal in each of the duplicates per genotype and stage, analyzed in Seurat (https://satijalab.org/seurat/). A mean of 1520 genes, 6703 reads, and 3.0% of mitochondrial mRNA content were detected per cell.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Embryo stage was determined based on the presence of vaginal plug, the morning after breeding initiation, noon of day of plug was considered as E0.5. All embryos at E16.5 and P3 pups from the Jag1Ndr/+ x Jag1Ndr/+ breeding were sacrificed by decapitation, their livers (and spleens at P3) dissected out and placed in 12- or 24-well plates with ice-cold DPBS on ice unless stated otherwise. In case of P3 pups we further determined the sex based on pigmentation of the scrotum. Material for genotyping was collected (tail or limb tissue) and processed for genotyping using TaqMan probe (Thermo Fisher) yielding results in 3 hours (P3 Jag1Ndr/Ndr pups were identified based on the presence of jaundice and random Jag1Ndr/+ and Jag1+/+ controls genotypes were confirmed afterwards). The tissue was kept in ice-cold DPBS for 30min before being transferred into 5ml FACS tubes with 1.5 ml LDM + 0.5 ml of TrypLE Express (E16.5) or 2ml LDM (P3 stage), pipetted 5x through sterile wide-bore blue tip (E16.5) or transfer pipettes (P3) and incubated at 37°C/5min in a water bath (inverting each tube after 2-3 minutes). After the 5 min incubation, we disrupted the tissue further by gentle pipetting of the tissue 10x using a filtered 1 ml tip, followed by an additional round of incubation at 37°C/5min in a water bath (inverting each tube after 2-3 minutes). The enzymatic digestion was terminated by addition of 1.5 ml of WB16-E/ WBP3-E and additional mechanical disruption of the remaining tissue by pipetting each sample 20x using filtered 1 ml wide-bore blue pipette tip. We immediately poured the suspension through 70 µm filters into FACS tubes, rinsed the filter once with 0.5 ml WB16/WBP3, and passed the filtered suspension through a 40 µm strainer, each sample into two 2 ml Eppi tubes.  The duplicates of E16.5/P3 samples were centrifuged at 100g for 5mins at 5°C. Each supernatant was transferred to two new tubes, while the pellets were resuspended in 200 μl of Dead Cell Removal MicroBead suspension in Binding buffer and the resuspended pellets were further incubated for 5min at RT. In the meantime, the supernatant from the previous step was centrifuged at 250g for 5min at 5°C. The new supernatant was discarded, and the corresponding pellets were mixed with 200 μl of Dead Cell Removal MicroBeads with the previous cell suspension in Binding buffer. The mixture was incubated for 10min at RT. After the incubation 300 μl 1× Binding Buffer was added to the cell suspension to obtain a final volume of 500 μl, suitable for magnetic separation with MS columns. The separation was done based on the manufacturer’s recommendations. Briefly, we rinsed the columns with 500 μl of 1× Binding Buffer, applied the cell suspension onto the column, and collected the flowthrough containing unlabeled cells (living cells). Columns were further washed three more times with 500μl of 1× Binding Buffer, flowthrough collected and 20 μl filter sterile 10% BSA was added to the purified cells. Resulting samples were divided in two, whereof 250 μl was used for scRNAseq, following the 10x Genomics® Single Cell Protocol, and the remainder was used for the FACS as described below.  The duplicate P3 samples were centrifuged at 100g for 5min at 5°C, and supernatants were transferred to new tubes. The pelleted cells from each duplicate were pooled and resuspended in 1.5 ml of the WBP3-E buffer and transferred to a new 2 ml tube. In the meantime, the supernatants from the previous step were centrifuged at 250g for 5min at 5°C. The supernatants were discarded, and the corresponding pelleted cells were resuspended in 0.5 ml of the WBP3-E buffer and added to the resuspended cells obtained from the first centrifugation. The full sample cell suspensions (now in 2 ml of WBP3-E buffer) were then transferred into a new protein lo-bind tube through 40 μl cell strainer to remove any remaining cell debris or large clumps. We then determined the cell concentration using a Countess® II Quantification to calculate the appropriate volume for the subsequent resuspension to obtain the target concentrations of ~1200cells/μl as recommended by the 10x Genomics® Single Cell Protocol. Buffers: E16.5 - Wash Buffer (WB16-E) 1% BSA in HBSS, filter sterile (0.22 µm), Wash Buffer (WB16) 1% BSA, 1mM EDTA, HBSS, filter sterile (0.22 µm).P3 - Wash Buffer (WBP3-E) 1% FCS in HBSS, filter sterile (0.22 µm), Wash Buffer (WBP3) 1% FCS, 1mM EDTA, HBSS, filter sterile (0.22 µm).
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriated-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: multiple

value: liver

tag: age

value: postnatal day 3


title: KPT3_NT_R2

description: RNA-seq in KP T3 cells transduced with sgNT, replicate 2

tag: cell type

value: NSCLC lung tumor

value: sgNT


title: KPT3_NT_R3

description: RNA-seq in KP T3 cells transduced with sgNT, replicate 3


title: GM12878_low

description: scNanoHi-C

tag: cell line


title: NCI-H1975 + sequins mixA mixed with HCC827 + sequins mixB in ratio 100:0


title: 2118891_SMARCB1_ATAC_n2

value: Rhabdoid Tumor

tag: dox induction


title: KPT3_NT_R1

description: RNA-seq in KP T3 cells transduced with sgNT, replicate 1


title: 2112968_SMARCB1_ATAC_n1


title: P3_hom1, replicate 1, scRNAseq


title: P3_het2, replicate 2, scRNAseq

description: 10x Genomics


title: KPT3_H3KOg2_R3

description: RNA-seq in KP T3 cells transduced with sgHdac3 #2, replicate 3

value: sgHdac3 #2


title: 2161067_GFP_ATAC_n3

value: GFP


title: P3_het1, replicate 1, scRNAseq

description: 10x Genomics


title: 2118889_GFP_ATAC_n2


title: PBMC Aged+GA, scRNAseq

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Single Cell Software Suite (v3.1.0)  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of mice. Cell viability was examined under a microscope with 0.4% trypan blue staining. When the survival rate of cells reached 80% or more, library construction experiments were performed.
Single-cell libraries were constructed using Chromium™ Controller and Chromium™ Single Cell 3ʹ Reagent Version 3 Kit (10× Genomics, Pleasanton, CA). Single cells, reagents, and gel beads were enclosed in “gel beads in emulsion” (GEMs). Lysis and barcoded reverse transcription of single-cell polyadenylate mRNA was performed within each GEM. RT-GEMs were cleaned up to amplify cDNA, which was subsequently fragmented. Fragmented ends were repaired and A-tailing was added at the 3' end. Aptamers were ligated to fragments that were screened by two-sided solid-phase reversible immobilization (SPRI). After sample index PCR, another two-sided SPRI screen was performed. The final library was checked for fragment size distribution using an Agilent 2100 Bioanalyzer (Santa Clara, CA) and the library was quantified using real-time quantitative PCR (qPCR) with TaqMan probes. Finally, sequencing was performed using the DNBseq platform (BGI Group, Shenzhen, China).

value: PBMC

value: 16 months old

value: Glycyrrhizic acid (GA) for 1 month


title: KPT3_H3KOg2_R1

description: RNA-seq in KP T3 cells transduced with sgHdac3 #2, replicate 1

value: Kras-mutant, p53-/-


title: KPT3_H3KOg2_R2

description: RNA-seq in KP T3 cells transduced with sgHdac3 #2, replicate 2


title: 2112966_GFP_ATAC_n1


title: PBMC Aged, scRNAseq

description: 10x Genomics


title: Legionella WT 8hr 1

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

data_processing:
Release 94 of the human reference transcriptome GRCh38 was downloaded from ENSEMBL on 7/20/2019.  Relative abundances (reported as TPM values [Li and Dewey PMID: 21816040]) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the preprocessed reads and the transcriptome using KALLISTO version 0.43.0 [Bray et al PMID:27043002]. Further analysis was restricted to transcripts with TPM >= 10 in at least one sample.  Raw KALLISTO output is included in the processed data files.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.30.8 [Ritchie et al PMID:25605792,Smyth PMID:16646809]. Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 2x (absolute log2 fold change >= 1) for a given contrast.  Mean normalized log2(CPM) values and LIMMA fit contrasts and adjusted p-values are included in the supplementary file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM and estimated count values for each sample

growth_protocol: HEK293T and HEK-293 FcγR, were cultured at 37°C in DMEM-high glutamine media supplemented with 10% FCS.

extract_protocol:
RNA isolation was performed using the Direct-zol™ RNA Miniprep Plus kit (Zymo Research) according to the manufacturers protocols. The yield and the integrity of RNA were determined by spectrophotometer NanoDrop 2000c.
After RNA extraction, mRNA was enriched by using Oligo dT beads from the KAPA mRNA Capture Kit (KK8581). Subsequent library preparation steps of fragmentation, adapter ligation and cDNA synthesis were done on the enriched mRNA using the KAPA RNA HyperPrep kit (KK8540). Truncated universal stub adapters were used for ligation, and indexed primers were used during PCR amplification to complete the adapters and to enrich the libraries for adapter-ligated fragments. Samples were checked for quality on an AATI (now Agilent) Fragment Analyzer.
Samples were transferred to the Vincent J. Coates Genomics Sequencing Laboratory (GSL), a QB3-Berkeley Core Research Facility at UC Berkeley, where Illumina sequencing library molarity was measured with quantitative PCR with the Kapa Biosystems Illumina Quant qPCR Kits on a BioRad CFX Connect thermal cycler. Libraries were then pooled evenly by molarity and sequenced on an Illumina NovaSeq6000 150PE S4 flowcell, generating 25M read pairs per sample. Raw sequencing data was converted into fastq format, sample specific files using the Illumina bcl2fastq2 software on the sequencing centers local linux server.

treatment_protocol: For infection experiments, primary patches of L.p. were grown for 2 days at 37°C on CYE plates. Single colonies of bacteria were picked and grown as heavy patches for 2 further days on CYE plates at 37°C. Heavy patches were then harvested, diluted in AYE broth supplemented with the required chemicals (as appropriate) and grown overnight at 37°C with shaking (220rpm) until the OD600 = ~3. HEK293 FcγR cells were infected at a multiplicity of infection (MOI) of 50. For opsonization, L.p. bacteria were diluted in complete media and mixed with a Legionella polyclonal antibody (Invitrogen, Cat #PA1-7227) at 1:1,000 dilution. The mixtures were then incubated for 20 minutes at room temperature in a rotary mixer. Immediately after addition of the opsonized L.p. mixtures, cells were centrifuged for 5 min at 1,000 rpm to facilitate spin-fection. Cells were then incubated at 37 °C for 60 minutes to allow bacterial uptake via the FcγR. After 60 minutes, the cells were washed with 1x PBS to remove extracellular bacteria and replenished with DMEM supplemented with 10% FBS. Infected cells were then cultured at 37 °C and harvested at 1 hour, 2 hours, 4 hours and 8 hours post infection. For elongation inhibitor treatments, HEK293T cells were treated with anisomycin (0.1µM) or didemnin-B  (0.1µM) for 4 hours before harvest.

value: Legionella WT

tag: time

tag: replicate

tag: batch


title: KPT3_H3KOg1_R3

description: RNA-seq in KP T3 cells transduced with sgHdac3 #1, replicate 3

value: sgHdac3 #1


title: KPT3_H3KOg1_R1

description: RNA-seq in KP T3 cells transduced with sgHdac3 #1, replicate 1


title: PBMC Young, scRNAseq

description: 10x Genomics

value: 8 weeks old


title: Type_L_Diaphysis

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Sequenced reads were aligned to the reference genome (mm10) using Cell Ranger v3.0.2 software (10×Genomics).
Sequenced reads with low quality and PCR duplicates were removed.
Data analysis was performed using Loupe Cell Browser (10× Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cell barcode
Supplementary_files_format_and_content: tab-delimited text files include gene features
Supplementary_files_format_and_content: tab-delimited matrix files

source_name: CD31+CD45- cells from diaphysis

extract_protocol:
Femurs from wild-type mice were collected in PBS. Epiphysis, metaphysis and diaphysis were crushed separately with pestle in DMEM (+ Collagenase IV 10μl/ml, + Dispase 4μ/ml, + DNase 0.2μ/ml), and incubated 30min at 37°. The cells were dissociated to a single-cell suspension by filtering thorough 40μm nylon mesh. To eliminate red blood cells, we used RBC Lysis Buffer (pluriSelect 60-00050-11). Cells are FC-blocked and stained with FITC anti-mouse CD31 antibody (Biolegend 102506; 1:200), and APC anti mouse CD45 antibody (Biolegend 103112;1:200) for 40 min. Cell sorting was performed with Cell Sorter SH800S (SONY, Tokyo,Japan).
Libraries were constructed using a Chromium Single Cell 3’ v3.1 (10×Genomics, Pleasanton, CA) according to the manufacturer’s instructions.
single cell RNA-Seq


title: Type_H_Metaphysis

source_name: CD31+CD45- cells from metaphysis


title: KL1_TTF1_SR_R2

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 SR, replicate 2

value: sgTtf1(Nkx2-1) SR

value: Kras-mutant, Lkb1-/-


title: KL1_TTF1_SR_R1

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 SR, replicate 1


title: KL1_TTF1_SR_R3

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 SR, replicate 3


title: HG002_mESC_BeforeFix

description: scNanoHi-C

organism:
Homo sapiens
Mus musculus

value: lymphoblast cell / mouse embryonic stem cell


title: Type_S_Epiphysis

source_name: CD31+CD45- cells from epiphysis


title: Legionella WT 4hr 1


title: HG002_mESC_AfterFix

description: scNanoHi-C


title: KL1_TTF1_GPP1_R3

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 #2, replicate 3

value: sgTtf1(Nkx2-1) #2


title: Legionella WT 2hr 1


title: Legionella WT 4hr 2


title: KL1_TTF1_GPP1_R2

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 #2, replicate 2


title: Legionella WT 2hr 2


title: Legionella WT 1hr 1


title: NY-17 Leaf tissue, RD

city: Wuhan

first: Wei

last: Wang

address: No.2 Xudong Road

department: Ministry of Agriculture and Rural Affairs Oil Crops Research Institute

institute: Chinese Academy of Agricultural Science

data_processing:
remove the low quality reads and cut the adapters with fastp with default parameters
high-quality reads were mapped to the Lusitatissimum reference genome version (BGIv1.0) using BISMARK(v0.23.0)
The mapped reads were used to identify differentially methylated cytosines in each of 16 samples separately using the methylKit package
Cytosines were considered only if they were covered by at least 5 high-quality reads . Three methylation call files corresponding to the CG, CHG, and CHH sequence contexts were generated for each treatment
the Lusitatissimum genome was divided into 200-bp non-overlapping windows and used to identify differentially hyper- and hypomethylated regions (200-bp bins) in drought stress samples compared to the corresponding control samples using the methylKit package with a minimum methylation difference of 50% in the CG, 20% in the CHG and 10% in the CHH sequence contexts using a FDR of less than 5%.
Assembly: Lusitatissimum reference genome version (BGIv1.0)
Supplementary files format and content: each site methylation level in bedgraph format

organism: Linum usitatissimum

source_name: leaf

extract_protocol:
DNA extracted using CTAB method, the specific experimental steps are as described by Clarke(Clarke, 2009).
The Bisulfite-treated linseed DNA samples were used to prepare methylC-seq libraries. A total of 16 DNA samples (one control and three different drought treatments × two biological × two linseed varieties ) were sent to BioMarker Biotechnology Co., Ltd. (Beijing) for sequencing library construction and MethylC-sequencing. Sequencing libraries were prepared using a NEXTflex™ Bisulfite Sequencing Kit (PerkinElmer, USA) following the manufacturer’s recommendations, followed by MethylC-sequencing using the Illumina NovaSeq 6000 platform (San Diego, USA)

tag: tissue

value: leaf

value: RD rep3


title: KL1_TTF1_GPP1_R1

description: RNA-seq in KL LJE1 cells transduced with sgTTF1 #2, replicate 1

value: NSCLC lung tumor

tag: genotype


title: NY-17 Leaf tissue, RW

value: RW rep3


title: Legionella WT 1hr 2


title: Uninfected  1

value: Uninfected


title: KL1_NT(TTF)_R3

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgTTF1), replicate 3

value: sgNT


title: Legionella WT 8hr 2


title: NY-17 Leaf tissue, DS

value: DS rep3


title: NY-17 Leaf tissue, CK

value: CK rep3


title: Uninfected  2


title: GenX, Water concetration 1 mg/L, 28 Day timepoint 3

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
STAR Alignment using default arguments.
Reads were aligned to the human genome GRCh38
Counts were taken using the argument within the STAR software.
Read count extraction and normalization were performed using DESeq2 in Rstudio.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2 normalzied values for each Sample

source_name: whole liver lysate

extract_protocol:
Total RNA was isolated using the TRIzol method from ~ 40mg of liver tissue.
mRNA libraries were prepared for sequencing using Tecan universal plus mRNA-seq following manufacturer's protocols.

treatment_protocol:
FRG humanized mice were exposed to PFOA, PFOS, or GenX through spiked water ad libitum for 28 days.
Water concentrations: PFOA 0.067 mg/L; PFOS: 0.145 mg/L; and GenX: 1 mg/L

value: whole liver lysate

tag: type of_mice

value: Yecuris FRG Humanzied Mice

tag: background

value: NOD Background

value: 29 year old male

value: GenX

value: Day 28


title: KL1_NT(TTF)_R2

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgTTF1), replicate 2

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.  Strand-specific polyA+ RNA-seq

value: Kras-mutant, Lkb1-/-


title: Z141 Leaf tissue,RD


title: GenX, Water concetration 1 mg/L, 28 Day timepoint 2

value: 28 year old male


title: KL1_NT(TTF)_R1

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgTTF1), replicate 1


title: Legionella dotA 8hr 1

value: Legionella delta-dotA


title: Z141 Leaf tissue,RW

value: leaf


title: PFOS, Water concetration 0.145 mg/L, 28 Day timepoint 3

value: 26 year old male

value: PFOS


title: Legionella dotA 8hr 2


title: Z141 Leaf tissue, CK


title: KL1_NT(H3)_R3

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgHdac3 #1), replicate 3

value: NSCLC lung tumor


title: Z141 Leaf tissue,DS


title: Legionella dotA 4hr 1


title: Legionella dotA 4hr 2


title: KL1_NT(H3)_R2

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgHdac3 #1), replicate 2


title: PFOS, Water concetration 0.145 mg/L, 28 Day timepoint 2

value: 25 year old male


title: NY_RD_3

source_name: NY-17 Leaf tissue, RD

tag: cultivar

value: RD


title: KL1_NT(H3)_R1

description: RNA-seq in KL LJE1 cells transduced with sgNT (control for sgHdac3 #1), replicate 1

value: sgNT


title: PFOS, Water concetration 0.145 mg/L, 28 Day timepoint 1

value: 24 year old male


title: PFOA, Water concetration 0.067 mg/L, 28 Day timepoint 3

value: whole liver lysate

value: 23 year old male

value: PFOA


title: KL1_H3KO_R3

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #1, replicate 3

value: sgHdac3 #1


title: KL1_H3KO_R2

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #1, replicate 2


title: NY_RD_1


title: Legionella dotA 2hr 2


title: Legionella dotA 1hr 1


title: PFOA, Water concetration 0.067 mg/L, 28 Day timepoint 2

value: Yecuris FRG Humanzied Mice

value: NOD Background

value: 22 year old male


title: NY_RW_3

source_name: NY-17 Leaf tissue, RW

value: RW


title: KL1_H3KO_R1

description: RNA-seq in KL LJE1 cells transduced with sgHdac3 #1, replicate 1

value: Kras-mutant, Lkb1-/-


title: GenX, Water concetration 1 mg/L, 28 Day timepoint 1

value: 27 year old male

value: GenX

value: Day 28


title: Legionella dotA 1hr 2

value: Legionella delta-dotA


title: NY_RW_2

value: leaf


title: PFOA, Water concetration 0.067 mg/L, 28 Day timepoint 1

value: 21 year old male


title: Didemnin B  1

value: Didemnin B


title: Input_KP_R2

description: Input for Hdac3 ChIP-seq in primary KP tumors

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bedGraphs. For primary tumor ChIP-seq data, peaks were called for each replicate individually using the findPeaks command with parameters -style factor -F 3, using HDAC3 ChIP-seq as target and Input sequencing data as Input (-i).  Peaks were merged using the mergePeaks command to generate a consolidated file containing all HDAC3 ChIP-seq peaks identified in KL and KP tumors.  The getDifferentialPeaks command with -F 3 -same was used to identify peaks bound in both KL and KP tumors.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
For ChIP-Seq, cells were collected and cross-linked in 1% formaldehyde.  After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, nuclei were isolated and then sheared in a Covaris E229 sonicator for 8 minutes to generate DNA fragments between ~ 200-1000 bp.  After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Hdac3 or H3K27ac then bound to Protein A Dynabeads (Invitrogen). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.

value: primary NSCLC tumor

value: Kras-mutant, p53-/-

tag: antibody source


title: Legionella dotA 2hr 1

tag: treatment


title: Control, 28 Day timepoint 3

value: whole liver lysate

value: 20 year old male

value: No Treatment


title: NY_DS_3

source_name: NY-17 Leaf tissue, DS

value: DS


title: Input_KP_R1

tag: guide rna


title: Control, 28 Day timepoint 2

value: Yecuris FRG Humanzied Mice

value: NOD Background

value: 19 year old male


title: NY_DS_2


title: Input_KL_R2

description: Input for Hdac3 ChIP-seq in primary KL tumors

value: Kras-mutant, Lkb1-/-


title: Didemnin B  2


title: Control, 28 Day timepoint 1

value: 18 year old male


title: Control  1

value: Control


title: NY_CK_2

source_name: NY-17 Leaf tissue, CK

value: CK


title: Input_KL_R1


title: NY_CK_1


title: Hdac3_x4_KP_R2

description: ChIP-seq for Hdac3 in primary KP tumors

source_name: Primary Kras-mutant, p53-/- NSCLC tumor

tag: chip antibody


title: Anisomycin  1

value: Anisomycin


title: DSS-treated colon mucosa, experimental day 23

first: Cambrian

middle: Yangshao

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina software was used for basecalling.
Transcript abundances were obtained from cellranger 3.0.0 using default options.
Downstream analyses were primarily performed using monocle3. Count matrices were loaded from the cellranger quantification. Cells from a separate experiment (GSE168033) profiling the anorectal junction were added in as a separate batch (Batch B). Cells with fewer than 100 UMI counts were filtered out. All samples were merged into a CellDataSet object. Batch correction was performed with a nearest-neighbors technique. Squamous cells were filtered out of the dataset.
The count matrix was normalized by the per-cell count total and subsequently log-transformed (preprocess_cds() and reduce_dimension() function defaults). The top 50 principal components were used for dimensional reduction and uniform manifold approximation and projection (UMAP). Clustering of cells was performed using the leiden algorithm with automatic detection of the resolution (cluster_cells() function defaults). Trajectories were computed using the defaults of the learn_graph() function.
Analysis scripts are available at: https://github.com/stalepig/2021-stem-cell-clonality
Assembly: mm10
Supplementary files format and content: Sparse Matrix (mtx) file of merged UMI counts with each row representing a gene and each column a cell barcode, can be read into R with readMM function in the Matrix package
Supplementary files format and content: Tab-delimited text (txt) files providing gene names (row data) or cell clustering and sample information (column data), matched to the sparse Matrix file

source_name: colonic mucosa

growth_protocol: Each sample is derived from mucosal tissue pooled from colons of 3-8 mice. Mice were ordered from Jackson Laboratory. At 8 wks-old, they were either dissected (for the no-injury or "day 0" control sample) or treated with 3% DSS for 6 days (for DSS samples). Mice treated with DSS were dissected at either 6, 7, 9, 11, 12, 16, 18, 19, or 23 days after their first day of exposure to DSS. Il10-/- mice were purchased from Jackson Laboratory and maintained in a specific pathogen-free animal facility for approximately 8 months; these mice were dissected at approximately 10 months-old. Colitis in Il10-/- mice was confirmed with measurements of fecal lipocalin levels that were found to be elevated.

extract_protocol:
Colons were dissected, manually stripped of myenteric layers, and enzymatically digested in Liberase TM/DNAse I. Dissociated tissue was strained through 70 and 40-micron filters, and the resulting single-cell suspension was treated with a red blood cell lysis buffer. Dead cells were removed using a magnetic separation kit with antibodies targeted against annexin V. The purified suspension was either frozen in 90% fetal bovine serum supplemented with 10% dimethyl sulfoxide (Batch A), or directly submitted (Batch C) for single-cell analysis and library prep via the 10X Genomics Chromium platform.
Samples in Batch A were thawed and processed on the same day, representing a single batch run. Samples in Batch C were directly processed after cell isolation, representing a separate batch run. Cells were washed with PBS and pre-loading viability was confirmed to exceed 75%. Cells were run on the Chromium (10X Genomics) platform for single-cell lysis, reverse transcription, barcoding, and library preparation. Paired-end sequencing of 3' transcript ends was performed on a novaSeq machine (Illumina).

tag: injury

value: 3percent DSS (treated for 6 days)

value: WT

tag: inflammation

value: Inflamed

value: ~2 months


title: Z141_RD_3

source_name: Z141 Leaf tissue, RD

value: leaf

value: RD


title: Anisomycin  2


title: DSS-treated colon mucosa, experimental day 19

tag: age


title: DSS-treated colon mucosa, experimental day 16


title: Hdac3_x4_KL_R2

description: ChIP-seq for Hdac3 in primary KL tumors

source_name: Primary Kras-mutant, Lkb1-/- NSCLC tumor

value: primary NSCLC tumor


title: Z141_RW_3

source_name: Z141 Leaf tissue, RW

value: RW


title: Hdac3_x4_KL_R1

description: ChIP-seq for Hdac3 in primary KL tumors


title: Z141_RW_2


title: Control  2

tag: cell line


title: DSS-treated colon mucosa, experimental day 9


title: Z141_DS_2

source_name: Z141 Leaf tissue, DS

value: DS


title: Colon mucosa from Il10-/- mice, approximately 10 months-old

value: Il10-/-, ~10 months-old

value: ~10 months


title: InputF_NT_R2

description: Input for H3K27ac ChIP-seq in KL LJE1 cells transduced with sgNT

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate ChIP-seq bedGraphs. ChIP-seq peaks for Hdac3 and H3K27ac were found by using the findPeaks program in HOMER with the parameter "-style factor" or "-style histone", respectively.  Peaks were called by using the appropriate ChIP input experiments as input, and for Hdac3 ChIP-seq in KL LJE1 cells Hdac3 ChIP-seq data from Hdac3 KO cells was used as background.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Immortalized cell line derived from Kras-mutant, Lkb1-/- NSCLC lung tumor

extract_protocol:
For ChIP-Seq, cells were collected and either cross-linked first in 2mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde (for Hdac3 CST-85057 ChIP-seq) or only in 1% formaldehyde (for H3K27ac and Hdac3 ab7030 ChIP-seq).  After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, nuclei were isolated and then sheared in a Covaris E229 sonicator for 8 minutes to generate DNA fragments between ~ 200-1000 bp.  After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against Hdac3 or H3K27ac then bound to Protein A Dynabeads (Invitrogen). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.

tag: cell type

value: NSCLC lung tumor

value: none (input)

value: sgNT


title: Z141_DS_1


title: DSS-treated colon mucosa, experimental day 12


title: DE_UAS_STARR-seq, GFP, rep1

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

description:
36bp
normalized_counts_BAC_screens.tsv

data_processing:
Paired-end sequencing reads were demultiplexed using the standard illumina i5 and i7  indexes and mapped Drosophila Melanogaster (dm3) genome and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in), using Bowtie v.1.2.2. PE 36bp reads with a maximal insert size of 2 kb and up to three mismatches were kept. The olig screens were demultiplexed and mapped to a synthetic reference genome containing the 249bp sequences with both wildtype and mutant enhancers, only exact matches were kept and subsequently to the artificial Drosophila Pseudoobscura BAC genome (spike-in).
For the genome-wide screen enhancers were detected macs25 callpeak using –nomodel and –fe-cutoff 4 as additional parameters. Enhancers were called on all 12 samples separately, and their genomic coordinates were merged into one enhancer backbone file. Rep-STARR-seq reads falling into these enhancers were quantified for every sample, obtaining a raw counts matrix. The raw counts matrix was then normalized using the spike-in normalization factors and the normalized matrix was used to perform differential enhancer activity analysis.
We quantified the differences in enhancer activites between the Gal4-GFP (control) samples and our Gal4-CoRs using EdgeR with two biological replicates.
Assembly: For the genome-wide screens: BDGP R5/dm3 For the disigned oligo library we generated a custom assembly
Supplementary files format and content: Spike-in normalized reads matrix for all samples
Supplementary files format and content: genomic coverage of rep-STARR-seq for every sample in bigWig format

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Schneider’s Medium (Gibco; cat. no. 21720-024) supplemented with 10% heat inactivated FBS (Sigma; cat. no. F7524)

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Mini Prep Kit.
mRNAs were enriched with Dynabeads Oligo-dT25 (Invitrogen), followed by a DNA digest with Turbo DNase (Ambion).
mRNAs were cleaned up with AMPure XP DNA beads (Agencourt; ratio sample/beads 1:1.8) and then reverse transcribed with Superscript III (50°C for 60 min, 70°C for 15 min; Invitrogen 18080085) and a primer binding within the poly-A site of candidate mRNAs (reverse_transcription_rv: CTCATCAATGTATCTTATCATGTCTG).
Next, RNA was digested with Rnase A (Thermo) for 1 h at 37°C, followed by bead cleanup of the remaining DNA (ratio sample/beads 1:1.4).
All subsequent PCR reactions were prepared using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2602). A junction PCR was performed with a primer binding only in correctly spliced candidate mRNAs junction_primer_fw: AAGCCACCATGGAAAAG*G*C*C*A*T, junction_primer_rv: TATCATGTCTGCTCGAAG*C*G*G (98°C for 45s, (98°C for 15s,  65°C for 30 s, 72°C for 45 s)X15, followed by bead cleanup (ratio sample/beads 1:0.9).
Sequencing ready PCR: candidate fragments were amplified (98°C 45 s, followed by 6-15 cycles, 98°C 15 s, 65°C 30 s, 72°C 30s) with the following primers: i5: aatgatacggcgaccaccgagatctacacXXXXXXXXacactctttccctacacgacgctcttccgatct (XXXXXXXX indicates the position of the index sequence for NGS) and the reverse primer TruSeq IDX with approptiate barcode for demultiplexing individual samples. PCR products were purified by Agencourt AMPure XP DNA beads (ratio sample/beads 1:0.8), pooled, and subjected to NGS.
After another beads cleanup we measured each sample and made and equimolar mixture that was subjected to sequencing

treatment_protocol:
per OC-400, 200million Drosophila S2 cell lines were transfected with a pre-mixed rep-STARR-seq library (20ug) + Gal4-CoR expression vector (20ug) + spike-in (0.2ug).  2 OC 400 were used per gw rep-STARR-seq sample and one OC 400 was used for the BAC and designed oligonucleotide libraries.
24h after transfection, the cells were havested and the same samples pooled to then be processed like regular STARR-seq (Arnold et al., 2013)

tag: enhancer library

value: 32 BAC sheared ~750bp

tag: core-promoter

value: Mixed DSCP and Rps12

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: DSS-treated colon mucosa, experimental day 6

value: 3percent DSS (treated for 6 days)

value: WT


title: InputF_NT_R1


title: Hdac3_x4_KP_R1

description: ChIP-seq for Hdac3 in primary KP tumors

value: Kras-mutant, p53-/-


title: input, enhancers, repSTARR-seq, gw,Rps12

treatment_protocol:
per OC-400, 200million Drosophila S2 cell lines were transfected with a pre-mixed rep-STARR-seq library (20ug) + Gal4-CoR expression vector (20ug) + spike-in (0.2ug). 2 OC 400 were used per gw rep-STARR-seq sample and one OC 400 was used for the BAC and designed oligonucleotide libraries.
24h after transfection, the cells were havested and the same samples pooled to then be processed like regular STARR-seq (Arnold et al., 2013)

value: genome-wide sheared ~750bp

value: PCR amplyfied the enhancers from the cloned rep-STARR-seq oligo library (used for performing the screens


title: Z141_RD_2

value: leaf

value: RD


title: Uninjured colon mucosa

value: Normal

value: ~2 months


title: InputF_HKO_R1

description: Input for H3K27ac ChIP-seq in KL LJE1 cells transduced with sgHdac3 #1


title: InputF_HKO_R2


title: input, enhancers, repSTARR-seq, gw,DSCP

value: DSCP


title: Z141_CK_1

source_name: Z141 Leaf tissue, CK

value: CK


title: DE_UAS_STARR-seq, Rbf, rep1

description:
36bp
normalized_counts_BAC_screens.tsv


title: SiO2-56d TCR

city: Nanjing

first: Chao

last: Jie

state: Jiangsu

address: 87 Dingjiaqiao Rd

institute: Southeast University

data_processing:
Library strategy: TCR-seq
bcl2fastq tools for base calling
CellRanger software for single cell identifying
PCA and UMAP/TSNE for dimensionality reduction
Cellranger software and Seurat for finding clusters
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression text files with tab-delimited

source_name: lung cells

growth_protocol: Male C57BL/6 were raised in a cage at a stable temperature (22 °C ± 2 °C) and humidity (40% ± 10%) with a 12-h light–dark cycle.

extract_protocol:
The totla cDNA was extracted  for libraries construction by Chromium  Single Cell A Chip Kits according the standard protocol
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male C57BL/6J mice (6 weeks of age, 22±1 g weight) were anaesthetized with pentobarbital sodium (1%, 50 mg/kg in ddH2O) administered by intraperitoneal injection. After the fur on the neck was shaved, the skin was disinfected with 75% alcohol, and an incision (1 cm) was made on the skin along the midline. We bluntly separated the soft tissue in front of the neck to expose the trachea. For the mice in the SiO2-7d and SiO2-56d groups, we administered 100 µl of silica suspension (50 mg/ml) to the lungs via intratracheal instillation. For the mice in the NS-7d and NS-56d groups, we administered NS via the same method. For the model group (mice instilled with SiO2 suspension), mouse with obviously high density shadow  on CT were included. Lung samples  for single-cell sequencing were collected from four mice, namely the NS-7d, SiO2-7d, NS-56d, and SiO2-56d samples. Whole lung of each mouse was removed as fast as possible after euthanasia  and quickly washed in precooled PBS 3 times.

value: whole lung cells

tag: strain

tag: Sex

value: male

value: instilllation of SiO2 suspension for 56d


title: repSTARR-seq, Sin3A, rep2

description:
36bp
spike-in.normalized.reads.over.gw.enhancers.txt

value: Mixed DSCP and Rps12


title: DE_UAS_STARR-seq, CtBP, rep1

description:
36bp
normalized_counts_BAC_screens.tsv

value: 32 BAC sheared ~750bp

value: Schneider S2


title: DE_UAS_STARR-seq, GFP, rep2

description:
36bp
normalized_counts_BAC_screens.tsv

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: InputDF_NT_R2

description: Input for Hdac3 ChIP-seq in KL LJE1 cells transduced with sgNT

value: NSCLC lung tumor

value: none (input)

value: sgNT


title: InputDF_NT_R1


title: repSTARR-seq, Sin3A, rep1

value: genome-wide sheared ~750bp


title: Z141_CK_3

tag: tissue

value: leaf


title: repSTARR-seq, Rbf2, rep2


title: InputDF_HKO_R1

description: Input for Hdac3 ChIP-seq in KL LJE1 cells transduced with sgHdac3 #1


title: SiO2-7d TCR

value: instilllation of SiO2 suspension for 7d


title: InputDF_HKO_R2


title: NS-7d TCR

value: instilllation of NS for 7d


title: HDAC3DF_NT_R2

description: ChIP-seq for Hdac3 in KL LJE1 cells transduced with sgNT


title: repSTARR-seq, Rbf2, rep1


title: SiO2-56d BCR

data_processing:
Library strategy: BCR-seq
bcl2fastq tools for base calling
CellRanger software for single cell identifying
PCA and UMAP/TSNE for dimensionality reduction
Cellranger software and Seurat for finding clusters
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression text files with tab-delimited


title: ES24-3 day 151

city: Baltimore

first: Kellie

last: Smith

address: 1550 Orleans St

institute: Johns Hopkins University

data_processing:
raw sequences were aligned using MIXCR 3.0.13
Non-productive TCR sequences were filtered out using immunoR in R
Assembly: hg38
Supplementary files format and content: tab delimited table (.txt files) with information about all productive clonotypes assembled by CDR3 sequence (clone abundance, CDR3 sequence, V, D, J genes, etc.).

source_name: CD8 T cell depleted PBMCs

growth_protocol: MANAFEST assay

extract_protocol:
Qiagen DNeasy Blood and Tissue kit
AmpliSeq for Illumina TCR beta-sr panel
DNA sequencing for TCR V-beta region

treatment_protocol: IL-2, IL-7, and IL-15 every 3 days

value: Peripheral CD4+ T cells 151 days after chemoradiation

value: CD8 T cell depleted PBMCs


title: ES24-4 day 151


title: ES24-4 day -6

value: Peripheral CD4+ T cells 6 days before chemoradiation


title: repSTARR-seq, Rbf, rep2


title: ES24-2 day 151


title: ES24-1 day 151


title: NS-56d TCR

value: whole lung cells

value: instilllation of NS for 56d


title: SiO2-7d BCR

value: male


title: ES24-3 day-6


title: HDAC3DF_HKO_R2

first: Reuben

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: ChIP-seq for Hdac3 in KL LJE1 cells transduced with sgHdac3 #1


title: HDAC3DF_NT_R1


title: NS-56d BCR


title: repSTARR-seq, Rbf, rep1

value: Mixed DSCP and Rps12


title: repSTARR-seq, CtBP, rep2


title: ES24-2 day -6


title: NS-7d BCR


title: HDAC3DF_HKO_R1


title: repSTARR-seq, CtBP, rep1


title: ES24-1 day -6


title: SiO2-56d single cell

data_processing:
bcl2fastq tools for base calling
CellRanger software for single cell identifying
PCA and UMAP/TSNE for dimensionality reduction
Cellranger software and Seurat for finding clusters
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression text files with tab-delimited

value: instilllation of SiO2 suspension for 56d


title: H3K27F_NT_R2

description: ChIP-seq for H3K27ac in KL LJE1 cells transduced with sgNT


title: ES24 unstimulated

value: Unstimulated CD4+ T cells


title: repSTARR-seq, CoRest, rep2

value: Schneider S2

value: cells transfected (electroporation) with pre-mixed rep-STARR-seq library + Gal4-CoR expression vector + spike-in


title: ES24 peptide 61 expansion 3

value: CD4+ T cells stimulated with cognate peptide


title: repSTARR-seq, CoRest, rep1


title: H3K27F_NT_R1

value: NSCLC lung tumor

value: sgNT


title: H3K27F_HKO_R2

description: ChIP-seq for H3K27ac in KL LJE1 cells transduced with sgHdac3 #1


title: repSTARR-seq, GFP, rep2

value: genome-wide sheared ~750bp


title: NS-56d single cell


title: ES24 peptide 61 expansion 1


title: SiO2-7d single cell

value: instilllation of SiO2 suspension for 7d


title: repSTARR-seq, GFP, rep1


title: ES24 peptide 61 expansion 2


title: H3K27F_HKO_R1


title: NS-7d single cell

value: instilllation of NS for 7d


title: KPT3_H3KOg1_R2

description: RNA-seq in KP T3 cells transduced with sgHdac3 #1, replicate 2

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: HDAC3KO_NKX2KO_diff2 Excel file with Columns: (A) Transcript (B) chr (C) start (D) end (E) strand (F) length (G) Annotation (H-AC) Log2 Fold change and adj. p-value for each comparison indicated in row 1.

source_name: Immortalized cell line derived from Kras-mutant, p53-/- NSCLC lung tumor

value: sgHdac3 #1

tag: genotype

value: Kras-mutant, p53-/-