title: AG_UnpT_nRNA_1

description:
Neuroplasticity_RPKM
Nascent RNA capture

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
BioProject for the genome:PRJNA13635
Reference Genome: AASC00000000.3 Aplysia californica
Reference assembly: GCA_000002075.2, (assembly AplCal3.0)
RefSeq assembly accession: GCF_000002075.1 (latest)
Supplementary_files_format_and_content: TPMs for all single neurons samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all developmental stage samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all tissue samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all neuroplasticity samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE

source_name: Isolated Ganglion

extract_protocol:
Tissue were dissected and RNA isolated with QIAGEN Rneasy. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEB NEXT Ultra Library Construction for Illumina.

value: Isolated Ganglion


title: AG_C_RNA-seq_1

status: Public on Oct 11 2022

type: SRA

city: St Augustine

first: Leonid

middle: L

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

country: USA

institute: University of Florida

library_source: transcriptomic

molecule: total RNA

organism: Aplysia californica

tag: tissue type


title: AG_UnpT_nRNA_2


title: AG_UnpT_nRNA_3


title: AG_C_nRNA_3


title: AG_PT_RNA-seq_1


title: AG_C_nRNA_2


title: AG_PT_nRNA_3


title: lymphnode_aPD1_e29d2G4_L1

city: Candiolo

first: Luigia

last: Pace

address: Strada Provinciale, 142 -KM 3.95

country: Italy

institute: Italian Institute for Genomic Medicine

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing files (base calls) were demultiplexed with bcl2fastq2 v.2.20.0.422 with default parameters for paired-end sequencing
FASTQ files were aligned to GRCm38 mouse (mm10) genome using STAR v.2.7.3a
Transcript-per-million (TMP) counts were obtained by processing the alignment results with RSEM v.1.3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files of transcript expression quantification obtained via RSEM

organism: Mus musculus

source_name: lymph node

extract_protocol:
Dextramer-Adpgk+ CD8+ T cells were FACS sorted from draining lymph nodes and tumors, harvested from non-treated tumor bearing mice, treated with αPD-1, and αPD-1 combined with GAd. Neoepitope specific- CD8+ T cells were sorted into 384-well plates, containing lyses buffer and immediately frozen.
Single cell library preparation was done as previously described (Picelli et al., 2014).

tag: cell type

value: Adpgk+ CD8+ T cell

tag: tissue

value: lymph node

tag: strain

tag: age

value: 6-10 weeks old


title: lymphnode_aPD1_e29d2G13_L1


title: AG_UnpT_RNA-seq_3


title: lymphnode_aPD1_e29d2G16_L1


title: AG_PT_nRNA_2


title: AG_PT_RNA-seq_3


title: SN_Cont_nRNA_2


title: SN_Cont_nRNA_3


title: SN_FMRF_nRNA_3


title: lymphnode_aPD1_e29d2G12_L1


title: AG_C_nRNA_1


title: SN_5HT_nRNA_2


title: lymphnode_aPD1_e29d2G10_L1


title: lymphnode_aPD1_e29d2F9_L1


title: SN-Cont_nRNA_1


title: lymphnode_aPD1_e29d2F8_L1


title: Mantle

source_name: Isolated Tissue

value: Mantle


title: SN_5HT_nRNA_1


title: Ink_gland


title: lymphnode_aPD1_e29d2F4_L1


title: lymphnode_aPD1_e29d2F6_L1


title: AG_PT_nRNA_1


title: Eye

value: Eye


title: Foot

value: Foot


title: lymphnode_aPD1_e29d2F5_L1


title: lymphnode_aPD1_e29d2F7_L1


title: lymphnode_aPD1_e29d2G14_L1


title: St8_46hr_10-animals

source_name: Developmental Stages

value: St 8_46hr_10-animals


title: lymphnode_aPD1_e29d2F3_L1


title: lymphnode_aPD1_e29d2F2_L1


title: lymphnode_aPD1_e29d2G11_L1


title: St8_46hr_eyebrows


title: lymphnode_aPD1_e29d2G15_L1


title: St7_24hr_heart_beating


title: lymphnode_aPD1_e29d2F24_L1


title: St7_23hr_5-larvae


title: lymphnode_aPD1_e29d2F22_L1


title: lymphnode_aPD1_e29d2F20_L1


title: lymphnode_aPD1_e29d2F21_L1


title: St7_24 hr

value: St7_24 hr


title: St6B_20hr_7-larvae


title: lymphnode_aPD1_e29d2F1_L1


title: St6B_6hr_3-larvae


title: lymphnode_aPD1_e29d2F19_L1


title: St6B_5hr_attached

value: St6B_5 hr_attached


title: lymphnode_aPD1_e29d2F18_L1


title: St6B_4.5hr_losing_cilia


title: lymphnode_aPD1_e29d2F15_L1


title: St6AB_2hr_4-larvae


title: lymphnode_aPD1_e29d2F17_L1


title: St6A_Controls_8-larvae


title: St6B_2hr


title: lymphnode_aPD1_e29d2F14_L1


title: lymphnode_aPD1_e29d2F12_L1


title: lymphnode_aPD1_e29d2F13_L1


title: Bag_cells_1

source_name: Single Neurons Isolated from CNS

value: Single Neuron Isolated from CNS


title: R15_1


title: BL1_1


title: lymphnode_aPD1_e29d2F10_L1


title: lymphnode_aPD1_e29d2F11_L1


title: Abd_5HT_3


title: lymphnode_aPD1_e29d2E8_L1


title: Abd_5HT_2


title: lymphnode_aPD1_e29d2E7_L1


title: L29_2


title: lymphnode_aPD1_e29d2E6_L1


title: Abd_5HT_1


title: lymphnode_aPD1_e29d2E5_L1


title: L29_1


title: LFs_7


title: St6B_5hr_swimmer

value: St6B_5 hr_swimmer


title: lymphnode_aPD1_e29d2E4_L1


title: lymphnode_aPD1_e29d2E24_L1


title: lymphnode_aPD1_e29d2E2_L1


title: LFs_4


title: LFs_6


title: LFs_2


title: LFs_1


title: LFs_5


title: lymphnode_aPD1_e29d2E20_L1


title: Buccal_SC_1


title: LE_2


title: lymphnode_aPD1_e29d2E21_L1


title: LFs_3


title: LE_1


title: lymphnode_aPD1_e29d2E9_L1


title: VC_3


title: lymphnode_aPD1_e29d2E17_L1


title: VC_2


title: lymphnode_aPD1_e29d2E15_L1


title: lymphnode_aPD1_e29d2E3_L1


title: VC_1


title: lymphnode_aPD1_e29d2E19_L1


title: L7_L2


title: lymphnode_aPD1_e29d2E13_L1


title: lymphnode_aPD1_e29d2E22_L1


title: lymphnode_aPD1_e29d2E23_L1


title: Abd_7


title: lymphnode_aPD1_e29d2E11_L1


title: Abd_6


title: lymphnode_aPD1_e29d2E12_L1


title: lymphnode_aPD1_e29d2E18_L1


title: Abd_4


title: lymphnode_aPD1_e29d2E10_L1


title: lymphnode_aPD1_e29d2D9_L1


title: L11_2


title: lymphnode_aPD1_e29d2D7_L1


title: LPL1_mutant


title: Abd_5


title: LPL1_4


title: lymphnode_aPD1_e29d2D4_L1


title: lymphnode_aPD1_e29d2D6_L1


title: lymphnode_aPD1_e29d2E14_L1


title: LPL1_1


title: lymphnode_aPD1_e29d2D3_L1


title: lymphnode_aPD1_e29d2D8_L1


title: lymphnode_aPD1_e29d2D2_L1


title: R2_mutant


title: Abd_8


title: lymphnode_aPD1_e29d2D23_L1


title: lymphnode_aPD1_e29d2D22_L1


title: lymphnode_aPD1_e29d2D5_L1


title: LPL1_2


title: R2_3


title: R2_2


title: lMCC_4


title: lymphnode_aPD1_e29d2D1_L1


title: lymphnode_aPD1_e29d2D18_L1


title: lMCC_3


title: rMCC_4


title: lymphnode_aPD1_e29d2D13_L1


title: lMCC_2


title: lymphnode_aPD1_e29d2D14_L1


title: LPL1_3


title: rMCC_3


title: rMCC_2


title: lymphnode_aPD1_e29d2D11_L1


title: lymphnode_aPD1_e29d2D12_L1


title: lymphnode_aPD1_e29d2C9_L1


title: lymphnode_aPD1_e29d2D10_L1


title: PC-WT-597-4-PC

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Star
Feature counts
DESeq2
Genome_build: GRCm38.p6

source_name: Perichondrium from WT mouse

extract_protocol:
RNA was extracted using the Rneasy micro kit from Qiagen
cDNA libraries were prepared using Smart-seqV4 low input NexteraXT

value: Limb bone perichondrium

tag: genotype

value: WT mice


title: PC-mut-795-11-PC-Koscx

source_name: Perichondrium from Fbn1Scx-/- mouse

value: Fbn1Scx-/- mouse


title: lymphnode_aPD1_e29d2C8_L1


title: PC-mut-597-12-PC-Koscx


title: lymphnode_aPD1_e29d2D20_L1


title: PC-mut-596-6-ScxCRE


title: lymphnode_aPD1_e29d2C6_L1


title: lymphnode_aPD1_e29d2C7_L1


title: lymphnode_aPD1_e29d2C4_L1


title: lymphnode_aPD1_e29d2D15_L1


title: Wildtype-caffeine50mM-2

city: Seoul

first: Woo-Hyun

last: Chung

address: Samyangro 144-gil 33, Dobonggu

country: South Korea

institute: Duksung Women's University

description: WT caffeine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to sacCer3 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: sacCer3
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cell cultures and treatments with caffeine were performed in YEPD (1% yeast extract, 2% peptone, and 2% dextrose) or minimal SD media supplemented with the required amino acids.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Cells were untreated or treated with 50 mM caffeine for 1h

tag: cell line

value: WT

tag: treatment

value: 51mM Caffeine


title: Wildtype-control-1

description: WT no treatment

value: no


title: lymphnode_aPD1_e29d2C2_L1

value: Adpgk+ CD8+ T cell


title: PC-WT-795-2-PC


title: lymphnode_aPD1_e29d2C3_L1

value: lymph node


title: yap1ADH2

description: yap1 deletion mutant

value: yap1 pRS426ADH


title: Wildtype-control-2

description: WT no treatment


title: lymphnode_aPD1_e29d2C24_L1

value: 6-10 weeks old


title: Wildtype-caffeine50mM-1

description: WT caffeine

value: 50mM Caffeine


title: lymphnode_aPD1_e29d2C22_L1


title: yap1ADH3

description: yap1 deletion mutant


title: PC-WT-596-3-PC


title: yap1ADH1

description: yap1 deletion mutant


title: YAP1_2

description: Yap1 overexpression

value: WT pRS426ADH-YAP1


title: YAP1_3

description: Yap1 overexpression


title: YAP1_1

description: Yap1 overexpression


title: lymphnode_aPD1_e29d2C20_L1


title: lymphnode_aPD1_e29d2C21_L1


title: lymphnode_aPD1_e29d2C19_L1


title: WT2

description: WT

value: WT pRS426ADH


title: WT3

description: WT


title: lymphnode_aPD1_e29d2C5_L1


title: tumor_aPD1.GAd_e29d3K11_L1

source_name: tumor

value: tumor


title: WT1

description: WT


title: lymphnode_aPD1_e29d2C17_L1


title: lymphnode_aPD1_e29d2C18_L1


title: lymphnode_aPD1_e29d2C1_L1


title: lymphnode_aPD1_e29d2C16_L1


title: lymphnode_aPD1_e29d2C15_L1


title: lymphnode_aPD1_e29d2C14_L1


title: lymphnode_aPD1_e29d2C13_L1


title: 172_SN_

city: Boston

first: Yinglu

last: Zhou

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
fastq files were aligned to version 97 of human reference genome GRCm38 using the Salmon.
Low read counts gene and sample filtering
Expression data was normalized using the VOOM with LOESS fit, and Combat-seq function in the Limma package in R
Assembly: version 97 of human reference genome GRCm38
Supplementary files format and content: Normalized RNA-seq

organism: Homo sapiens

source_name: Prostate Stroma from RP

extract_protocol:
For each case, FFPE blocks with stroma-enriched (>60%) areas adjacent to tumor and benign areas distant from the tumor (another prostate quadrant or lobe in a separate FFPE block) were selected. Besides the identification of tumor- and benign-adjacent stroma areas for sampling, pathologists (G.N.F., M.L.) determined the Gleason score in the nearby tumor and annotated cribriform patterns and other histologic features. Stroma-enriched regions of interest (ROIs) adjacent to the tumor or benign glands were manually circled on slides. Tissue edges and ROIs were outlined on a parafilm strip and transferred onto the corresponding FFPE block.
Libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

tag: gleason score

tag: lethal

value: No

tag: cribriform

tag: used in analysis

value: Yes


title: 178_ST_GS3

value: Non-Cribriform


title: 174_ST_


title: lymphnode_aPD1_e29d2B8_L1


title: lymphnode_aPD1_e29d2C12_L1


title: lymphnode_aPD1_e29d2C11_L1


title: 170_ST_


title: 171_ST_


title: 169_SN_


title: 168_SN_


title: 170_SN_


title: 168_ST_


title: 169_ST_


title: lymphnode_aPD1_e29d2C10_L1


title: lymphnode_aPD1_e29d2B4_L1


title: 166_SN_


title: 167_ST_


title: lymphnode_aPD1_e29d2B5_L1


title: 166_ST_


title: lymphnode_aPD1_e29d2B2_L1


title: lymphnode_aPD1.GAd_e29d2B24_L1


title: 167_SN_


title: lymphnode_aPD1_e29d2B6_L1


title: lymphnode_aPD1_e29d2B3_L1


title: lymphnode_aPD1.GAd_e29d2B22_L1


title: 163_ST_


title: 163_SN_


title: lymphnode_aPD1.GAd_e29d2B20_L1


title: lymphnode_aPD1_e29d2B1_L1


title: lymphnode_aPD1_e29d2B7_L1


title: lymphnode_aPD1.GAd_e29d2B19_L1


title: lymphnode_aPD1.GAd_e29d2B18_L1


title: 162_SN_


title: 172_ST_


title: 162_ST_


title: 160_ST_

value: Cribriform


title: 160_SN_


title: lymphnode_aPD1.GAd_e29d2B16_L1


title: lymphnode_aPD1.GAd_e29d2B17_L1


title: 159_ST_


title: lymphnode_aPD1.GAd_e29d2B15_L1


title: 159_SN_


title: lymphnode_aPD1.GAd_e29d2B14_L1


title: lymphnode_aPD1.GAd_e29d2B13_L1


title: 158_ST_


title: 156_SN_


title: lymphnode_aPD1.GAd_e29d2B12_L1


title: 158_SN_


title: lymphnode_aPD1.GAd_e29d2B11_L1


title: 156_ST_


title: lymphnode_controltumorfree_e29d2A9_L1

value: CD8+ T cell


title: lymphnode_aPD1.GAd_e29d2B10_L1


title: 165_ST_


title: 155_ST_


title: 155_SN_


title: lymphnode_controltumorfree_e29d2A8_L1


title: 152_SN_


title: lymphnode_aPD1.GAd_e29d2A24_L1


title: lymphnode_aPD1.GAd_e29d2A23_L1


title: 151_ST_


title: 147_ST_


title: 144_ST_GS3


title: lymphnode_aPD1.GAd_e29d2A20_L1


title: 144_SN_


title: lymphnode_aPD1.GAd_e29d2A17_L1


title: lymphnode_controltumorfree_e29d2A15_L1


title: lymphnode_controltumorfree_e29d2A14_L1


title: 141_ST_


title: 140_ST_


title: 140_SN_

value: DUCTAL ADENOCARCINOMA


title: lymphnode_controltumorfree_e29d2A13_L1


title: 139_SN_


title: lymphnode_controltumorfree_e29d2A11_L1


title: lymphnode_controltumorfree_e29d2A10_L1


title: 139_ST_


title: 138_ST_


title: lymphnode_aPD1.GAd_e29d1P9_L1


title: 138_SN_


title: lymphnode_aPD1.GAd_e29d1P8_L1


title: 137_ST_


title: lymphnode_aPD1.GAd_e29d1P7_L1


title: lymphnode_aPD1.GAd_e29d2A21_L1


title: 136_SN_


title: lymphnode_aPD1.GAd_e29d1P6_L1


title: lymphnode_aPD1.GAd_e29d1P5_L1


title: 136_ST_


title: 135_SN_


title: lymphnode_aPD1.GAd_e29d2A18_L1


title: 143_ST_


title: 142_ST_


title: 134_ST_


title: lymphnode_aPD1.GAd_e29d1P2_L1


title: 133_ST_


title: lymphnode_aPD1.GAd_e29d1P3_L1


title: 132_ST_


title: lymphnode_controltumorfree_e29d2A12_L1


title: lymphnode_aPD1.GAd_e29d1P22_L1


title: lymphnode_aPD1.GAd_e29d1P20_L1


title: 130_ST_GS3


title: 131_ST_


title: 130_ST_GS4


title: lymphnode_aPD1.GAd_e29d1P21_L1


title: lymphnode_aPD1.GAd_e29d1P18_L1


title: 128_ST_


title: 129_ST_


title: 127_ST_


title: lymphnode_aPD1.GAd_e29d1P1_L1


title: lymphnode_aPD1.GAd_e29d1P15_L1


title: lymphnode_aPD1.GAd_e29d1P16_L1


title: lymphnode_aPD1.GAd_e29d1P4_L1


title: lymphnode_aPD1.GAd_e29d1P13_L1


title: lymphnode_aPD1.GAd_e29d1P12_L1


title: 125_ST_


title: 124_SN_


title: lymphnode_aPD1.GAd_e29d1P11_L1


title: 126_ST_


title: lymphnode_aPD1.GAd_e29d1P10_L1


title: 124_ST_


title: 123_ST_


title: lymphnode_aPD1.GAd_e29d1O8_L1


title: 123_SN_


title: lymphnode_aPD1.GAd_e29d1O9_L1


title: 122_ST_


title: lymphnode_aPD1.GAd_e29d1O7_L1


title: 121_ST_GS3


title: lymphnode_aPD1.GAd_e29d1P17_L1


title: lymphnode_aPD1.GAd_e29d1O4_L1


title: lymphnode_aPD1.GAd_e29d1O5_L1


title: 120_ST_


title: lymphnode_aPD1.GAd_e29d1O3_L1


title: 119_ST_


title: 126_SN_


title: lymphnode_aPD1.GAd_e29d1O2_L1


title: 117_ST_


title: 116_ST_


title: 117_SN_


title: lymphnode_aPD1.GAd_e29d1O24_L1


title: lymphnode_aPD1.GAd_e29d1O23_L1


title: 116_SN_


title: 115_SN_


title: lymphnode_aPD1.GAd_e29d1O22_L1


title: lymphnode_aPD1.GAd_e29d1O21_L1


title: lymphnode_aPD1.GAd_e29d1O18_L1


title: lymphnode_aPD1.GAd_e29d1O1_L1


title: 114_SN_


title: lymphnode_aPD1.GAd_e29d1O17_L1


title: 114_ST_


title: lymphnode_aPD1.GAd_e29d1O6_L1


title: lymphnode_aPD1.GAd_e29d1O14_L1


title: lymphnode_aPD1.GAd_e29d1O15_L1


title: 112_ST_


title: 121_ST_GS4


title: 112_SN_


title: lymphnode_aPD1.GAd_e29d1O13_L1


title: 118_ST_


title: lymphnode_aPD1.GAd_e29d1O12_L1


title: 111_ST_


title: 111_SN_


title: lymphnode_aPD1.GAd_e29d1O11_L1


title: 110_SN_


title: lymphnode_aPD1.GAd_e29d1N8_L1


title: 110_ST_GS4


title: 109_ST_


title: lymphnode_aPD1.GAd_e29d1N9_L1


title: 113_ST_


title: 108_ST_


title: lymphnode_aPD1.GAd_e29d1N6_L1


title: lymphnode_aPD1.GAd_e29d1N7_L1


title: 107_ST_


title: lymphnode_aPD1.GAd_e29d1N3_L1


title: lymphnode_aPD1.GAd_e29d1N4_L1


title: 108_SN_


title: 106_SN_


title: lymphnode_aPD1.GAd_e29d1N24_L1


title: lymphnode_aPD1.GAd_e29d1N23_L1


title: lymphnode_aPD1.GAd_e29d1N2_L1


title: 105_ST_


title: lymphnode_aPD1.GAd_e29d1N22_L1


title: lymphnode_aPD1.GAd_e29d1N20_L1


title: 104_ST_


title: 100_ST_


title: 98_ST_


title: lymphnode_aPD1.GAd_e29d1N1_L1


title: lymphnode_aPD1.GAd_e29d1N19_L1


title: lymphnode_aPD1.GAd_e29d1N15_L1


title: 102_ST_


title: lymphnode_aPD1.GAd_e29d1N16_L1


title: 97_ST_


title: 106_ST_


title: 97_SN_


title: 96_ST_


title: lymphnode_aPD1.GAd_e29d1N14_L1


title: lymphnode_aPD1.GAd_e29d1N13_L1


title: 96_SN_


title: 95_ST_


title: lymphnode_aPD1.GAd_e29d1N11_L1


title: lymphnode_aPD1.GAd_e29d1M8_L1


title: 92_ST_


title: lymphnode_aPD1.GAd_e29d1N12_L1


title: 93_ST_


title: lymphnode_aPD1.GAd_e29d1M9_L1


title: 92_SN_


title: 94_SN_


title: 91_ST_


title: lymphnode_aPD1.GAd_e29d1M7_L1


title: 90_ST_


title: 90_SN_


title: 89_ST_


title: 88_ST_


title: lymphnode_aPD1.GAd_e29d1M4_L1


title: lymphnode_aPD1.GAd_e29d1M2_L1


title: lymphnode_aPD1.GAd_e29d1M3_L1


title: 85_ST_


title: 86_ST_


title: lymphnode_aPD1.GAd_e29d1M24_L1


title: lymphnode_aPD1.GAd_e29d1M20_L1


title: 84_ST_


title: lymphnode_aPD1.GAd_e29d1M19_L1


title: 82_ST_


title: 81_ST_


title: lymphnode_aPD1.GAd_e29d1M15_L1


title: lymphnode_aPD1.GAd_e29d1M14_L1


title: 77_ST_


title: lymphnode_aPD1.GAd_e29d1M13_L1


title: lymphnode_aPD1.GAd_e29d1M6_L1


title: 80_ST_


title: lymphnode_aPD1.GAd_e29d1M16_L1


title: lymphnode_aPD1.GAd_e29d1M5_L1


title: 87_ST_


title: lymphnode_aPD1.GAd_e29d1M1_L1


title: lymphnode_aPD1.GAd_e29d1M22_L1


title: 78_ST_


title: 75_ST_


title: 76_ST_


title: 73_ST_


title: lymphnode_aPD1.GAd_e29d1M11_L1


title: lymphnode_aPD1.GAd_e29d1M10_L1


title: lymphnode_aPD1.GAd_e29d1M12_L1


title: 72_ST_


title: lymphnode_aPD1.GAd_e29d1L2_L1


title: lymphnode_aPD1.GAd_e29d1L4_L1


title: lymphnode_aPD1.GAd_e29d1M18_L1


title: 78_SN_


title: lymphnode_aPD1.GAd_e29d1L3_L1


title: 71_SN_


title: 71_ST_


title: lymphnode_aPD1.GAd_e29d1L24_L1


title: lymphnode_aPD1.GAd_e29d1L23_L1


title: 70_ST_


title: 69_ST_


title: lymphnode_aPD1.GAd_e29d1L21_L1


title: 70_SN_


title: 68_ST_


title: lymphnode_aPD1.GAd_e29d1L22_L1


title: 67_ST_


title: lymphnode_aPD1.GAd_e29d1L20_L1


title: lymphnode_aPD1.GAd_e29d1L1_L1


title: lymphnode_aPD1.GAd_e29d1L18_L1


title: 66_SN_


title: lymphnode_aPD1.GAd_e29d1L19_L1


title: 72_SN_


title: lymphnode_aPD1.GAd_e29d1L17_L1


title: 64_ST_


title: lymphnode_aPD1.GAd_e29d1L16_L1


title: 63_ST_


title: 62_ST_


title: 62_SN_


title: lymphnode_aPD1.GAd_e29d1L11_L1


title: 61_ST_


title: 61_SN_


title: lymphnode_aPD1.GAd_e29d1K6_L1


title: 60_ST_


title: lymphnode_aPD1.GAd_e29d1K7_L1


title: 59_ST_


title: lymphnode_aPD1.GAd_e29d1K4_L1


title: lymphnode_aPD1.GAd_e29d1K2_L1


title: 57_ST_


title: 56_ST_


title: 65_SN_


title: 65_ST_


title: lymphnode_aPD1.GAd_e29d1K24_L1


title: lymphnode_aPD1.GAd_e29d1K23_L1


title: 55_ST_


title: lymphnode_aPD1.GAd_e29d1L15_L1


title: 54_ST_


title: 52_ST_


title: lymphnode_aPD1.GAd_e29d1L12_L1


title: lymphnode_aPD1.GAd_e29d1K22_L1


title: lymphnode_aPD1.GAd_e29d1K21_L1


title: 52_SN_


title: lymphnode_aPD1.GAd_e29d1K5_L1


title: 51_ST_


title: lymphnode_aPD1.GAd_e29d1K20_L1


title: 50_ST_


title: 50_SN_


title: 58_ST_


title: lymphnode_aPD1.GAd_e29d1K1_L1


title: lymphnode_aPD1.GAd_e29d1K17_L1


title: lymphnode_aPD1.GAd_e29d1K18_L1


title: lymphnode_aPD1.GAd_e29d1K3_L1


title: lymphnode_aPD1.GAd_e29d1K19_L1


title: lymphnode_aPD1.GAd_e29d1K16_L1


title: 49_ST_


title: 48_ST_


title: lymphnode_aPD1.GAd_e29d1K15_L1


title: 47_SN_


title: 53_ST_


title: 46_SN_


title: 46_ST_


title: lymphnode_aPD1.GAd_e29d1K13_L1


title: lymphnode_aPD1.GAd_e29d1K11_L1


title: 44_ST_


title: lymphnode_aPD1.GAd_e29d1J7_L1


title: 43_ST_


title: 42_ST_


title: lymphnode_aPD1.GAd_e29d1J9_L1


title: 41_ST_


title: 41_SN_


title: lymphnode_aPD1.GAd_e29d1J6_L1


title: lymphnode_aPD1.GAd_e29d1J5_L1


title: lymphnode_aPD1.GAd_e29d1J3_L1


title: lymphnode_aPD1.GAd_e29d1J4_L1


title: lymphnode_aPD1.GAd_e29d1J23_L1


title: 40_ST_


title: lymphnode_aPD1.GAd_e29d1J2_L1


title: lymphnode_aPD1.GAd_e29d1J21_L1


title: 39_ST_


title: 39_SN_


title: 38_SN_


title: lymphnode_aPD1.GAd_e29d1J20_L1


title: 38_ST_


title: 37_ST_


title: lymphnode_aPD1.GAd_e29d1J19_L1


title: lymphnode_aPD1.GAd_e29d1J1_L1


title: lymphnode_aPD1.GAd_e29d1J18_L1


title: lymphnode_aPD1.GAd_e29d1J13_L1


title: 36_SN_


title: lymphnode_aPD1.GAd_e29d1J12_L1


title: lymphnode_aPD1.GAd_e29d1J17_L1


title: lymphnode_aPD1.GAd_e29d1J11_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4WT.SMARCC1

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Cut & Tag, ATAC-Seq, and human RNA-seq samples were sequenced with the Illumina NextSeq 500 technology, and VERO RNA-seq samples were sequenced with Illumina NovaSeq 6000 technology.
RNAseq reads were aligned to the reference genomes hg19 and chlSab2 (NCBI annotation release 100), using STAR aligner v2.7.3a [1] with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts, and bigWig files were generated using the deeptools v3.1.3 bamCoverage function [2] with the normalizeUsingRPKM parameter.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: chlSab2, NCBI annotation release 100, hg19
Supplementary files format and content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes.

molecule: genomic DNA

organism: Chlorocebus sabaeus

source_name: VERO E6

growth_protocol: Vero E6 cells were grown in DMEM (Gibco, 11960-44), supplemented with 10% FBS (Gibco), 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
Omni-ATAC protocol was used to probe DNA accessibility with slight modifications covered below 54. 100,000 cells per sample were trypsinized and washed with cold PBS to remove trypsin. Cell pellets were lysed in 50μl cold resuspension buffer (RSB) supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v) (RSB recipe: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and nuclei were pelleted at 500g for 10 min at 4°C after incubating on ice for 3 minutes. Nuclei were resuspended in 50μl transposition reaction mix containing 25 μl 2X Tagment DNA buffer (Illumina), 2.5μl Tn5 transposase, 16.5μl 1X PBS, 0.5μl 1% digitonin (final 0.01% v/v), 0.5μl 10% Tween-20 (final 0.1% v/v), and 5μl nuclease-free water. Transposition reaction was incubated at 37°C for 30 min with constant shaking (1000 rpm) on a thermomixer. Tagmented DNA was purified using the Qiagen MinElute Reaction Cleanup Kit. Standard ATAC-seq amplification protocol with 7 cycles of amplification was used to amplify tagmented libraries. Libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
RNAs were extracted using Direct-zol RNA MiniPrep Kit and submitted to the Yale Center for Genome Analysis for library preparation. RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 instrument with the goal of at least 25 × 106 reads per sample. Reads were aligned to reference genome chlSab2, NCBI annotation release 100, using STAR aligner v2.7.3a(Dobin et al., 2013) with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts. Differential expression was obtained using the R package DESeq2 v1.32(Dobin et al., 2013; Love et al., 2014). Bigwig files were generated using deeptools v3.1.3(Ramírez et al., 2016) with parameter --normalizeUsing RPKM
CUT&Tag was carried out using a protocol developed by Epicypher in 8-strip PCR tubes with slight modifications as described below. Briefly, Concanavalin A (ConA) coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 300,000 cells/sample were trypsinized and pelleted by centrifugation at room temperature (600g for 3 min). Cells were lysed using cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche) for 2 min. Nuclei were pelleted by centrifugation (600g for 3 min), resuspended in 100ul/sample Resuspension buffer (20 mM HEPES–KOH, pH 7.9, 150mM NaCl supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor) and incubated with activated ConA beads at room temperature for 15 min. The nuclei-ConA bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 0.5ug primary antibody/sample. Following overnight incubation at 4°C on a nutator, supernatant was discarded, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. The ConA-nuclei complexes were then incubated with Digitonin 150 buffer supplemented with 0.5ug/sample Secondary antibody for 1hr at room temperature on a nutator. They were then washed with Digitonin 150 Buffer twice before resuspension in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, protease inhibitor, and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample and incubated on a nutator for 1hr at room temperature. Following incubation, beads were washed twice with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out according to Epicypher’s protocol.
RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were packaged in 293TX cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Vero E6 cells were lentivirally infected with either Empty vector, SMARCA4 WT or SMARCA4 K785R for 24h and then selected with 5ug/ml Puromycin for 4 days. Cells were harvested for genomics experiments using standard protocols. For Huh7.5 and Calu3 Compound 12 (C12) treatment studies, cells were treated with DMSO vehicle or 1.25uM C12 for 3 days.

value: VERO E6

value: SMARCA4 knockout + SMARCA4 WT

tag: cut&tag antibody

value: Rabbit anti-SMARCC1 (D7F8S);  11956S


title: lymphnode_aPD1.GAd_e29d1I9_L1

value: Adpgk+ CD8+ T cell


title: CutAndTag.VERO.SMARCA4KO.SMARCA4WT.H3K4me1

value: Rabbit anti-H3K4me1 (ab176877)


title: CutAndTag.VERO.SMARCA4KO.SMARCA4WT.SMARCA4

value: Rabbit anti-SMARCA4 (D1Q7F);  49360S


title: 35_ST_


title: 34_ST_


title: lymphnode_aPD1.GAd_e29d1I7_L1

value: lymph node

value: 6-10 weeks old


title: lymphnode_aPD1.GAd_e29d1I6_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4WT.H3K27ac

value: Rabbit anti-H3K27ac (D5E4); 8173S


title: lymphnode_aPD1.GAd_e29d1I5_L1


title: 34_SN_


title: lymphnode_aPD1.GAd_e29d1I3_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4WT.ARID1A

value: Rabbit anti-ARID1A (D2A8U);  12354S


title: lymphnode_aPD1.GAd_e29d1I4_L1


title: 36_ST_


title: lymphnode_aPD1.GAd_e29d1I2_L1


title: lymphnode_aPD1.GAd_e29d1I23_L1


title: lymphnode_aPD1.GAd_e29d1I22_L1


title: lymphnode_aPD1.GAd_e29d1I21_L1


title: 33_ST_


title: 32_ST_


title: 31_ST_


title: CutAndTag.VERO.SMARCA4KO.SMARCA4K785R.SMARCA4

value: SMARCA4 knockout + SMARCA4 K785R


title: lymphnode_aPD1.GAd_e29d1I20_L1


title: lymphnode_aPD1.GAd_e29d1I1_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4K785R.H3K4me1


title: 30_ST_

value: No


title: lymphnode_aPD1.GAd_e29d1I19_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4K785R.H3K27ac


title: lymphnode_aPD1.GAd_e29d1I18_L1


title: 29_ST_

value: Yes


title: CutAndTag.VERO.SMARCA4KO.SMARCA4K785R.ARID1A


title: lymphnode_aPD1.GAd_e29d1I17_L1


title: CutAndTag.VERO.SMARCA4KO.SMARCA4K785R.SMARCC1


title: lymphnode_aPD1.GAd_e29d1I16_L1


title: lymphnode_aPD1.GAd_e29d1I15_L1


title: lymphnode_aPD1.GAd_e29d1I14_L1


title: 28_SN_


title: lymphnode_aPD1.GAd_e29d1I12_L1


title: 27_ST_


title: lymphnode_aPD1.GAd_e29d1I11_L1


title: lymphnode_aPD1.GAd_e29d1I10_L1


title: 27_SN_


title: CutAndTag.VERO.SMARCA4KO.EmptyVector.SMARCC1

value: SMARCA4 knockout + Empty Vector Control


title: lymphnode_aPD1.GAd_e29d1H7_L1


title: lymphnode_aPD1.GAd_e29d1H9_L1


title: 26_ST_

value: Non-Cribriform


title: CutAndTag.VERO.SMARCA4KO.EmptyVector.H3K4me1


title: CutAndTag.VERO.SMARCA4KO.EmptyVector.ARID1A


title: lymphnode_aPD1.GAd_e29d1H8_L1


title: CutAndTag.VERO.SMARCA4KO.EmptyVector.SMARCA4


title: 26_SN_


title: lymphnode_aPD1.GAd_e29d1H6_L1


title: CutAndTag.VERO.LentiCRISPRv2.Control.SMARCC1

value: LentiCRISPRv2 control


title: lymphnode_aPD1.GAd_e29d1H5_L1


title: 28_ST_


title: CutAndTag.VERO.LentiCRISPRv2.Control.SMARCA4


title: 25_ST_


title: 24_ST_


title: lymphnode_aPD1.GAd_e29d1H2_L1


title: lymphnode_aPD1.GAd_e29d1H3_L1


title: lymphnode_aPD1.GAd_e29d1I13_L1


title: 24_SN_


title: CutAndTag.VERO.LentiCRISPRv2.Control.H3K27ac


title: lymphnode_aPD1.GAd_e29d1H21_L1


title: CutAndTag.VERO.SMARCA4KO.EmptyVector.H3K27ac


title: lymphnode_aPD1.GAd_e29d1H22_L1


title: lymphnode_aPD1.GAd_e29d1H20_L1


title: 21_ST_


title: lymphnode_aPD1.GAd_e29d1H19_L1


title: lymphnode_aPD1.GAd_e29d1H1_L1


title: 23_ST_


title: lymphnode_aPD1.GAd_e29d1H17_L1


title: CutAndTag.VERO.HNF1AKO.SMARCC1

value: HNF1A knock-out


title: lymphnode_aPD1.GAd_e29d1H18_L1


title: lymphnode_aPD1.GAd_e29d1H4_L1


title: 20_ST_

value: Cribriform


title: CutAndTag.VERO.HNF1AKO.SMARCA4

value: VERO E6


title: lymphnode_aPD1.GAd_e29d1H16_L1


title: CutAndTag.VERO.LentiCRISPRv2.Control.H3K4me1


title: lymphnode_aPD1.GAd_e29d1H23_L1


title: lymphnode_aPD1.GAd_e29d1H15_L1


title: 20_SN_


title: lymphnode_aPD1.GAd_e29d1H14_L1


title: CutAndTag.VERO.HNF1AKO.H3K4me1


title: CutAndTag.VERO.HNF1AKO.H3K27ac


title: 19_ST_


title: lymphnode_aPD1.GAd_e29d1H11_L1


title: lymphnode_aPD1.GAd_e29d1H12_L1


title: ATACseq.VERO.SMARCA4KO.SMARCA4WT.Rep2

value: SMARCA4 knockout + SMARCA4 WT


title: lymphnode_aPD1.GAd_e29d1H10_L1

value: Adpgk+ CD8+ T cell


title: 18_ST_


title: lymphnode_aPD1.GAd_e29d1G9_L1


title: lymphnode_aPD1.GAd_e29d1G8_L1


title: 17_ST_


title: ATACseq.VERO.SMARCA4KO.SMARCA4WT.Rep1


title: lymphnode_aPD1.GAd_e29d1G5_L1


title: ATACseq.VERO.SMARCA4KO.SMARCA4K785R.Rep2


title: ATACseq.VERO.SMARCA4KO.EmptyVector.Rep2


title: 14_ST_


title: lymphnode_aPD1.GAd_e29d1G2_L1


title: lymphnode_aPD1.GAd_e29d1G3_L1


title: 16_ST_


title: ATACseq.VERO.SMARCA4KO.EmptyVector.Rep1


title: lymphnode_aPD1.GAd_e29d1G22_L1


title: ATACseq.VERO.LentiCRISPRv2.Control.Rep2


title: lymphnode_aPD1.GAd_e29d1G19_L1


title: lymphnode_aPD1.GAd_e29d1G4_L1


title: 12_ST_


title: 15_ST_


title: lymphnode_aPD1.GAd_e29d1G18_L1


title: lymphnode_aPD1.GAd_e29d1G6_L1


title: lymphnode_aPD1.GAd_e29d1G1_L1


title: ATACseq.VERO.HNF1AKO.Rep2


title: lymphnode_aPD1.GAd_e29d1G23_L1


title: lymphnode_aPD1.GAd_e29d1G17_L1


title: lymphnode_aPD1.GAd_e29d1G7_L1


title: lymphnode_aPD1.GAd_e29d1G16_L1


title: 12_SN_


title: ATACseq.VERO.SMARCA4KO.SMARCA4K785R.Rep1


title: lymphnode_aPD1.GAd_e29d1G15_L1


title: 11_SN_


title: ATACseq.VERO.HNF1AKO.Rep1


title: 13_SN_


title: lymphnode_aPD1.GAd_e29d1G13_L1


title: ATACseq - cultured murine RUNX1/EVI1 leukemia cells - shEVI1.2658

city: Vienna

first: Florian

last: Andersch

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

description: ATAC-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shEVI1.2568 (Day5 ON DOX)

data_processing:
Paired-end reads were processed with the Nextflow based nf-core/atacseq pipeline (Ewels et al., 2020), using default parameter and “GRCm38”  as reference genome.
To filter for nucleosome-free regions and account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase, the filtered and aligned reads were further processed with deeptools’s (v3.3.1) alignmentSieve with the option –ATACshift and –maxFragmentLength set to 120.
Bigwig tracks were produced with deeptools’s (v3.3.1) bamCoverage using a bin size of 100 and RPGC as normalization method.
genome build: GRCm38
processed data files format and content: Bigwig files were generated using deeptools’s (v3.3.1) bamCoverage
For standard murine RNA-seq data, reads were processed using the Nextflow based nf-core/rna-seq pipeline (Ewels et al., 2020) using Illumina’s mouse iGenome (GRCm38) as reference and “reverse” as input parameter for strandedness. Default parameters were kept for each processing step.
Read trimming with trimgalore (v0.6.6)
Alignment and quantification with STAR (v2.6.1d) (Dobin et al., 2013) and salmon (v1.4.0) (Patro et al., 2017)
Differential expression analysis with DESeq2 (v1.28.0) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...

source_name: Bone marrow

growth_protocol: Cell culture was maintained at 37ºC with 5% CO2, cells cultivated in RPMI 1640 (Gibco) supplemented with l-glutamine (4 mM, Gibco), sodium pyruvate (1 mM, Sigma-Aldrich), penicillin-streptomycin (100 U/ml & 100 µg/ml, Sigma-Aldrich) and 10% FBS (Gibco)

extract_protocol:
sorted IRFP670+/shRNA expressing cells
Facility (ATAC-seq/Nextera)

treatment_protocol: cells treated with Dox (0.5 ug/ml) for 5 days to induce shRNA expression

tag: source

value: in vitro cultured leukemia cells

value: DOX-induced induction of shEVI1.2568 (5 days)


title: lymphnode_aPD1.GAd_e29d1G11_L1

value: lymph node


title: 10_ST_


title: lymphnode_aPD1.GAd_e29d1G10_L1

value: 6-10 weeks old


title: cardiomyocytes treated, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: treated, replicate 3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

molecule: polyA RNA

source_name: cardiomyocytes

extract_protocol:
RNA was extracted using translating ribosome affinity purification (TRAP) method as described in: https://doi.org/10.1038/nprot.2014.085
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

value: Tamoxifen

tag: replicate


title: ATACseq.VERO.LentiCRISPRv2.Control.Rep1


title: 9_ST_


title: 8_ST_


title: lymphnode_aPD1.GAd_e29d1F8_L1


title: cardiomyocytes treated, replicate 2

description: treated, replicate 2


title: 6_ST_


title: lymphnode_aPD1.GAd_e29d1F9_L1


title: lymphnode_aPD1.GAd_e29d1F6_L1


title: lymphnode_aPD1.GAd_e29d1F7_L1


title: cardiomyocytes treated, replicate 1

description: treated, replicate 1


title: 6_SN_


title: lymphnode_aPD1.GAd_e29d1F5_L1


title: lymphnode_aPD1.GAd_e29d1F4_L1


title: lymphnode_aPD1.GAd_e29d1F3_L1


title: 5_ST_


title: lymphnode_aPD1.GAd_e29d1F2_L1


title: lymphnode_aPD1.GAd_e29d1G14_L1


title: cardiomyocytes control, replicate 2

description: control, replicate 2

value: vehicle


title: lymphnode_aPD1.GAd_e29d1F24_L1


title: ATACseq - cultured murine RUNX1/EVI1 leukemia cells - shRen.713

description: ATAC-seq: in-vitro-cultured BM-derived leukemia cells - TET-ON for shRNA - constitutive RUNX1/EVI1, NRAS(G12D) - shRen.713 (Day5 ON DOX)

value: DOX-induced induction of shRen713 (5 days)


title: lymphnode_aPD1.GAd_e29d1F23_L1


title: 4_ST_


title: 3_ST_

value: No


title: cardiomyocytes control, replicate 1

description: control, replicate 1


title: lymphnode_aPD1.GAd_e29d1F21_L1


title: lymphnode_aPD1.GAd_e29d1F1_L1


title: 2_ST_

value: Yes


title: lymphnode_aPD1.GAd_e29d1F17_L1


title: lymphnode_aPD1.GAd_e29d1F18_L1


title: 2_SN_


title: lymphnode_aPD1.GAd_e29d1F19_L1


title: ESC_LMNA_KO_HIC_seq_Rep2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description:
processed data file:
ESC_LMNA_KO_merge.allValidPairs.gz
ESC_LMNA_KO_merge_mm10.PC1.bedGraph
ESC_LMNA_KO_MergeNearContacts_WashU_epigenome.bed.gz.tbi

data_processing:
Hi-C paired-end reads were aligned to the mm10 genome, duplicate reads were removed, reads were assigned to MboI restriction fragments, filtered into valid interactions, and the interaction matrices were generated using the HiC-Pro pipeline default settings (Servant et al., 2015).
HiC-Pro valid interaction reads were then used to detect significant loops and generate Washu epigenome browser file using FitHiChIP. Significant loops were detected using the following settings: FDR 0.01, All to All loop detection without providing peak file (Hi-C mode), binsize 10 kb, LowDistThre 20000 and UppDistThr 2000000.
The PE alignment output of HiC-Pro was used to build a h5 multi matrix of 10K, 100Kb and 1000Kb using hicBuildMatrix command with default settings from HiCExplorer. The .h5 matrixes were normalized (hiNormalize command), corrected (HicCorrectMatrix command) and matrix bins were merged (hicMergeMatrixbins -nb 50). The merged bins matrix was then used to generate heatmaps.
Validpairs HiC-Pro output were used to generate HOMER TagDirectories (Heinz et al., 2010) which were used to do the principal component analysis with a resolution of 25 kb. DNA segments with a positive principal component 1 (PC1) value in at least two biological replicates were defined as compartment A, while those with a negative value were defined as compartment B. DNA compartment switches from A to B or B to A was considered if changes were observed in at least two biological replicates in both control and knockout. A DNA segment was defined as static if it stayed in compartment A or B in at least two biological replicates from the control and Lamin A knockout mESCs.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, bed and vlidpairs files

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were dissociated by 0.05% trypsin-EDTA , preplated for 45 min to remove the feeders and collected for RNA-seq.

extract_protocol: Hi-C libraries were generated according to (Rao et al., 2014) with modifications. Five million mESC were crosslinked with 1% formaldehyde for 10 min at RT and quenched with 120µM Gylcine for 5 min at RT on a rotator. Cells were pelleted at 4 °C for 5 min at 2,500 relative centrifugal force (RCF) and washed twice with ice cold PBS. Cells were lysed om 500 μL of ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1× protease inhibitors) with rotation at 4 °C for 30 min. Nuclei were then pelleted and resuspended in 100 μL of 0.5% SDS and incubated at 62 °C for 10 min. The SDS reaction were stopped by adding 285 μL of water and 50 μL of 10% Triton X-100 to each sample at 37 °C for 15 min. 200 U of MboI restriction enzyme (NEB, R0147) and 50µl of NEB Buffer 2 were used to digest the chromatin. Samples were then incubated at 37 °C for 3 h with rotation. The restriction enzyme was then heat inactivated at 62 °C for 20 min. To fill-in the MboI overhang and mark the ends, 52 μL of incorporation master mix ( 37.5 μL of 0.4 mM biotin–dATP (Thermo Fisher, 19524016); 4.5 μL of a dCTP, dGTP, and dTTP mix at 10 mM each; and 10 μL of 5 U/μL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210)) were added to the nuclei and incubated at 37 °C  for 1 h with rotation. 948 μL of ligation master mix (150 μL of 10× NEB T4 DNA ligase buffer with 10 mM ATP (NEB, B0202), 125 μL of 10% Triton X-100, 3 μL of 50 mg/mL BSA (Thermo Fisher, AM2616), 10 μL of 400 U/μL T4 DNA Ligase (NEB, M0202), and 660 μL of water ) were then added to each samples and incubated overnight at 16 °C. After proximity ligation, the nuclei were pelleted at 2,500 RCF for 5 min at room temperature and the supernatant was used further. Reverse crosslinking were done by overnight incubation at 65°C. DNA was purified using ChIP DNA Clean & Concentrator Kit (Zymo Researhc, D5205) and then sheared to a length of ∼400 bp. 50 ng of the sheared DNA was used for pull down of biotinylated proteins with 5 μL of Streptavidin C-1 beads (Thermo Fisher, Cat. N) in biotin binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) at room temperature for 15 min while shaking. Beads were then captured on the magnet, washed twice with 500 μL of Tween Wash Buffer at 55 °C for 2 min with shaking followed by one washing step using 100 μL of 1× TD Buffer (10 mM Tris-HCl pH 7.5, 5 mM magnesium chloride, 10% dimethylformamide). The beads were then resuspended in 25 μL of 2× TD Buffer, 2.5 μL Tn5 and water to 50 μL and incubated at 55 °C for 10 min while shaking. The beads were captured with a magnet and incubated in 50 mM EDTA at 50 °C for 30 min while shaking. Beads were further washed two times with 50 mM EDTA followed by a wash with Tween Wash Buffer at 55 °C for 2 min and with 10 mM Tris before PCR amplification. Beads were then resuspended in 25 μL of Phusion HF 2× (New England Biosciences), 1.25 μL of illumine Index 1 (i7) adapters and Index 2 (i5) Adapters (from Nextera kit, Cat N) and 22.5 μL of water and amplification was carried out using the following PCR program: 72 °C for 5 min, 98 °C for 1 min, then cycle at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min. Cycle numbers needed for amplification (beginning of exponential amplification) was determined for each sample. Afterwards, Ampure beads were used for double size selection to purify DNA with size range of 300- 700 bp. After size selection, libraries were quantified on Bioanalyzer and sequenced paired end with read length of 75.

tag: cell line background

value: E14 Tg(Nkx2-5-EmGFP)

value: ES

value: Lmna KO


title: ESC_LMNA_KO_HIC_seq_Rep3

description:
processed data file:
ESC_LMNA_KO_merge.allValidPairs.gz
ESC_LMNA_KO_merge_mm10.PC1.bedGraph


title: lymphnode_aPD1.GAd_e29d1F16_L1


title: cardiomyocytes control, replicate 3

description: control, replicate 3


title: ESC_LMNA_KO_HIC_seq_Rep1

description:
processed data file:
ESC_LMNA_KO_merge.allValidPairs.gz
ESC_LMNA_KO_merge_mm10.PC1.bedGraph
ESC_LMNA_KO_MergeNearContacts_WashU_epigenome.bed.gz


title: 1_ST_


title: lymphnode_aPD1.GAd_e29d1F15_L1


title: lymphnode_aPD1.GAd_e29d1F14_L1


title: lymphnode_aPD1.GAd_e29d1G12_L1


title: lymphnode_aPD1_e29d2E1_L1


title: ESC_LMNA_ctr_HIC_seq_Rep3

description:
processed data file:
ESC_LMNA_ctr_merge.allValidPairs.gz
ESC_LMNA_ctr_merge_mm10.PC1.bedGraph

value: WT


title: lymphnode_aPD1.GAd_e29d1F13_L1


title: lymphnode_aPD1.GAd_e29d1F11_L1


title: ESC_LMNA_ctr_HIC_seq_Rep2

description:
processed data file:
ESC_LMNA_ctr_merge.allValidPairs.gz
ESC_LMNA_ctr_merge_mm10.PC1.bedGraph
ESC_LMNA_ctr_MergeNearContacts_WashU_epigenome.bed.gz.tbi


title: lymphnode_aPD1.GAd_e29d1F12_L1


title: lymphnode_aPD1.GAd_e29d1F10_L1


title: lymphnode_aPD1.GAd_e29d1E9_L1


title: lymphnode_aPD1.GAd_e29d1E8_L1


title: lymphnode_aPD1.GAd_e29d1E7_L1


title: ESC_LMNA_ctr_HIC_seq_Rep1

description:
processed data file:
ESC_LMNA_ctr_merge.allValidPairs.gz
ESC_LMNA_ctr_merge_mm10.PC1.bedGraph
ESC_LMNA_ctr_MergeNearContacts_WashU_epigenome.bed.gz


title: lymphnode_aPD1.GAd_e29d1E6_L1


title: lymphnode_aPD1.GAd_e29d1E4_L1


title: RNA-Seq Dual-specificity Aptamer_Wnt+_Rep3

city: Baltimore

first: Yi

last: Zhu

address: 511 WBSB, 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins University, School of Medicine

description: Dual-specificity Aptamer_Wnt+_Rep3

data_processing:
Analysis of the RNA-Seq data was performed following the protocols by (Doyle et al., 2021). Sequencing adaptors were trimmed from the raw reads using Trim Galore. Trimmed reads were mapped to the human reference genome (GRCh38.p13) using HISAT2. Mapped reads were counted to each genes by featureCounts. Differential expression of genes was analyzed with DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: A csv file generated by DESeq2 that contains the results of differential analysis on every gene, comparing Dual-specificity Aptamer vs. Individual Aptamers in Wnt - samples
Supplementary files format and content: A csv file generated by DESeq2 that contains the results of differential analysis on every gene, comparing Dual-specificity Aptamer vs. Individual Aptamers in Wnt + samples

source_name: Cultured Cells

growth_protocol: Cells were cultured in DMEM with 1 g/L glucose, pyruvate and GlutaMAX (Gibco), supplemented with 10% heat-inactivated Fetal bovine serum, 200 U/mL penicillin and 200 µg/mL streptomycin.

extract_protocol:
At 24 hr post-transfection, medium was discarded, and cells were lysed using 1 mL of TRIzol Reagent per culture dish. Lysates were mixed by pipetting, transferred into a Phasemaker tube (Invitrogen A33248) and incubated at room temperature for 5 min. The aqueous phase was separated by adding 200 μL chloroform, thoroughly vertexing and spinning at 12,000 rcf for 15 min at 4 °C. The upper aqueous layer was carefully collected without toughing the other layers. RNA was precipitated with isopropanol, washed with 70% ethanol, dissolved in nuclease-free water, and submitted to GENEWIZ (South Plainfield, NJ, USA) for sequencing.
Library construction was performed by GENEWIZ.

treatment_protocol: 2E6 HEK293T cells that stably express a shRNA targeting EZH2 were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+).

value: Cultured Cells

value: EZH2 was knocked-down with a shRNA. Cells were cultured in 50% Wnt3A-conditioned DMEM for 4 hr (Wnt+).


title: lymphnode_aPD1.GAd_e29d1E3_L1


title: lymphnode_aPD1.GAd_e29d1E2_L1


title: CM_LMNA_KO_ATAC_seq_Rep1

description: Number on the Epi to sequence: CM_LMNA_KO_ATAC_seq_Rep1

data_processing:
ATAC-seq reads were trimmed of adapters using Trimmomatic-0.39 and then mapped to mm10 mouse genome with Bowtie2.
Following removal of unmapped reads by SAMtools (-F 1804 -f 2), PCR artefacts were excluded by the MarkDuplicates.jar from Picard-tools-1.119.
BamCoverage function of deepTools with normalization to RPKM was used to generate the bigwig files for visualization of ATAC-seq reads in the genome browser IGV (-bs 20 --smoothLength 40 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 -e). Afterwards, fastq.gz files of each 3 replicates were merged and processing was performed like described.
Peak calling was applied from merged bam-files with MACS2 (-q 0.01 --nomodel --shift -75 --extsize150) 51, whereas peaks overlapping blacklist defined by ENCODE were discarded by the help of Bedtools v2.28.0 (intersect -wa).
Called peaks from merged files and individual bam files were further used to quantify and normalize counts as well as to calculate differentially accessible chromatin regions upon LMNA deletion using the R package DiffBind 53 with normalizing to RPKM and using DESeq2 method to perform differential analysis. Peaks were annotated by a custom R script combining ChIPseeker 54 and rtracklayer packages. Promoter regions were defined as ±3 kb around the mm10 gene transcription start site unless otherwise stated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file and BigWig files

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were differentiated into cardiomyocytes by hanging droplets method . Briefly, differentiation through the hanging drop method was initiated following mESCs dissociation by 0.05% trypsin-EDTA and suspension at 33000 cells/ml in mESC growth medium without LIF in 15 μl drops. After two day the resulting embryoid bodies (EBs) were transferred to low attachment culture dishes . At day10, EBs were dissociated and  CMs were FACS sorted by Nkx2-5-GFP expression and performed RNA-seq.

extract_protocol: Nuclei of sorted NKX2.5 CM control and LMNA KO lines were isolated and permeabilised for tagmentation to receive nucleosomes. DNA fragments were detached from nucleosomes, amplified and size selected by bead purification to yield fragment size ranging from 150-1000bp. Fragment distribution was checked by bioanalyzer.

value: cardiomyocyte

tag: passages

tag: antibody


title: RNA-Seq Individual Aptamers_Wnt+_Rep1

description: Individual Aptamers_Wnt+_Rep1


title: RNA-Seq Individual Aptamers_Wnt+_Rep3

description: Individual Aptamers_Wnt+_Rep3


title: CM_LMNA_KO_ATAC_seq_Rep3

description: Number on the Epi to sequence: CM_LMNA_KO_ATAC_seq_Rep3

tag: cell type


title: lymphnode_aPD1.GAd_e29d1E23_L1

value: Adpgk+ CD8+ T cell

tag: tissue


title: RNA-Seq Individual Aptamers_Wnt+_Rep2

description: Individual Aptamers_Wnt+_Rep2


title: RNA-Seq Dual-specificity Aptamer_Wnt-_Rep3

description: Dual-specificity Aptamer_Wnt-_Rep3

value: EZH2 was knocked-down with a shRNA. Cells were cultured in regular DMEM (Wnt-).


title: CM_LMNA_KO_ATAC_seq_Rep2

description: Number on the Epi to sequence: CM_LMNA_KO_ATAC_seq_Rep2


title: CM_LMNA_ctr_ATAC_seq_Rep2

description: Number on the Epi to sequence: CM_LMNA_ctr_ATAC_seq_Rep2


title: CM_LMNA_ctr_ATAC_seq_Rep3

description: Number on the Epi to sequence: CM_LMNA_ctr_ATAC_seq_Rep3


title: lymphnode_aPD1.GAd_e29d1E1_L1

tag: strain


title: RNA-Seq Dual-specificity Aptamer_Wnt+_Rep2

description: Dual-specificity Aptamer_Wnt+_Rep2


title: CM_LMNA_ctr_ATAC_seq_Rep1

description: Number on the Epi to sequence: CM_LMNA_ctr_ATAC_seq_Rep1


title: RNA-Seq Dual-specificity Aptamer_Wnt-_Rep2

description: Dual-specificity Aptamer_Wnt-_Rep2


title: lymphnode_aPD1.GAd_e29d1E16_L1

tag: age


title: lymphnode_aPD1.GAd_e29d1E17_L1


title: RNA-Seq Dual-specificity Aptamer_Wnt+_Rep1

description: Dual-specificity Aptamer_Wnt+_Rep1


title: lymphnode_aPD1.GAd_e29d1E14_L1


title: lymphnode_aPD1.GAd_e29d1E12_L1


title: lymphnode_aPD1.GAd_e29d1E5_L1


title: ESC_LMNA_KO_ATAC_seq_Rep3

description: Number on the Epi to sequence: DNA12

extract_protocol: Nuclei of ESC control and LMNA KO lines were isolated and permeabilised for tagmentation to receive nucleosomes. DNA fragments were detached from nucleosomes, amplified and size selected by bead purification to yield fragment size ranging from 150-1000bp. Fragment distribution was checked by bioanalyzer.

tag: genotype


title: RNA-Seq Individual Aptamers_Wnt-_Rep3

description: Individual Aptamers_Wnt-_Rep3

tag: cell line


title: lymphnode_aPD1.GAd_e29d1E21_L1


title: RNA-Seq Individual Aptamers_Wnt-_Rep2

description: Individual Aptamers_Wnt-_Rep2

tag: treatment


title: ESC_LMNA_KO_ATAC_seq_Rep2

description: Number on the Epi to sequence: DNA11


title: ESC_LMNA_KO_ATAC_seq_Rep1

description: Number on the Epi to sequence: DNA10


title: lymphnode_aPD1.GAd_e29d1D7_L1


title: lymphnode_aPD1.GAd_e29d1D8_L1


title: lymphnode_aPD1.GAd_e29d1E18_L1


title: lymphnode_aPD1.GAd_e29d1D9_L1


title: ESC_LMNA_ctr_ATAC_seq_Rep3

description: Number on the Epi to sequence: DNA09


title: lymphnode_aPD1.GAd_e29d1E10_L1


title: RNA-Seq Individual Aptamers_Wnt-_Rep1

description: Individual Aptamers_Wnt-_Rep1


title: lymphnode_aPD1.GAd_e29d1D5_L1


title: ESC_LMNA_ctr_ATAC_seq_Rep2

description: Number on the Epi to sequence: DNA08


title: CUT&RUN II Control - IgG, in beta-catenin knockdown cells

data_processing:
Analysis of the sequencing data followed the protocol of (Zheng et al., 2020). Sequencing adaptors were trimmed from the raw reads using Trim Galore. Trimmed reads were mapped to the human reference genome (GRCh38.p13) using Bowtie2. For spike-in calibration, the trimmed reads were additionally mapped to the E.coli reference genome (ASM584v2). Mapped BAM files were filtered by samtools view and converted to BED format using bedtools bamtobed. The BED files were spike-in calibrated and converted to genomic coverage bedgraph files using the bedtools genomecov function. Peak calling was performed with SEACR under the stringent mode, using the bedgraph file of IgG as control. Differential binding analysis was performed using Diffbind, using the mapped BAM reads (to human and E.coli reference genomes) from Bowtie2 and the called peaks from SEACR as input. The differential binding sites were annotated with ChIPSeeker.
Assembly: GRCh38.p13
Assembly: ASM584v2 (for spike-in calibration)
Supplementary files format and content: bigwig files were generated using the mapped BAM reads.

extract_protocol:
At 24 hr post-transfection, cells were monodispersed by scrapping and pipetting. Nuclei from 5E5 cells were isolated for each reaction. CUT&RUN was performed using the CUTANA CUT&RUN kit (EpiCypher 14-1048), following the kit manual. 500 ng of EZH2 antibody (CST 5246) or Rabbit IgG (EpiCypher 13-0042k) was used in each 50 μL of binding reaction. After chromatin digestion, 0.12 ng of E.coli genomic DNA (kit included) was spiked-in to each reaction with the Stop Buffer. After chromatin release, DNA fragments were purified by Phenol:Chloroform extraction and isopropanol precipitation. Concentrations of DNA were measured using the Qubit 1X dsDNA HS Assay Kit (Invitrogen Q33230).
Preparation of Sequencing Library was performed using the NEBNext Ultra II DNA Library Prep Kit (NEB E7103L), and NEBNext Multiplex Oligos for Illumina (NEB E6440S). 6 ng DNA from each CUT&RUN reaction was used as the starting material. Prepared DNA library was dissolved in nuclease-free water, and submitted to GENEWIZ (South Plainfield, NJ, USA) for sequencing. Sequencing was performed on an Illumina HiSeq 4000 sequencer in 2x150 bp mode.
Other: CUT&RUN-Seq

treatment_protocol: 2E6 HEK293T cells that stably express a shRNA targeting beta-catenin were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+).

value: beta-catenin was knocked-down with a shRNA.

tag: cut&run antibody

value: Normal Rabbit IgG (EpiCypher 13-0042k)


title: lymphnode_aPD1.GAd_e29d1D6_L1

value: lymph node

value: 6-10 weeks old


title: RNA-Seq Dual-specificity Aptamer_Wnt-_Rep1

description: Dual-specificity Aptamer_Wnt-_Rep1


title: CUT&RUN II Dual-specificity Aptamer_Wnt+_Rep3

description: Dual-specificity Aptamer_Wnt+_Rep3

value: beta-catenin was knocked-down with a shRNA. Cells were cultured in 50% Wnt3A-conditioned DMEM for 4 hr (Wnt+).

value: EZH2 (Cell Signaling, 5246S)


title: lymphnode_aPD1.GAd_e29d1D3_L1


title: lymphnode_aPD1.GAd_e29d1D4_L1


title: ESC_LMNA_ctr_ATAC_seq_Rep1

description: Number on the Epi to sequence: DNA07


title: lymphnode_aPD1.GAd_e29d1D2_L1


title: lymphnode_aPD1.GAd_e29d1D24_L1


title: CUT&RUN II Dual-specificity Aptamer_Wnt+_Rep2

description: Dual-specificity Aptamer_Wnt+_Rep2


title: lymphnode_aPD1.GAd_e29d1D22_L1


title: lymphnode_aPD1.GAd_e29d1E11_L1


title: lymphnode_aPD1.GAd_e29d1D20_L1


title: CUT&RUN II Dual-specificity Aptamer_Wnt+_Rep1

description: Dual-specificity Aptamer_Wnt+_Rep1


title: lymphnode_aPD1.GAd_e29d1D1_L1


title: MCF-7 LTED cells, PTBsi2

city: Guangzhou

first: Xueman

last: Chen

state: Guangdong

address: 107 Yanjiang West Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were processed through in-house Perl scripts.
Index of the reference genome was built using Bowtie2 v2.2.3.
Paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample.
Assembly: hg38
Supplementary files format and content: Matrix files include FPKM values for each Sample

source_name: MCF-7 cells

growth_protocol: MCF-7 LTED cells were maintained in  steroid-deprived phenol red-free RPMI 1640 medium supplemented with 10% dextran charcoal-stripped fetal bovine serum in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol (Invitrogen) according to the manufacturer’s instructions. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations.

treatment_protocol: MCF-7 cells underwent long-term estrogen deprivation (LTED) by being cultured in steroid-deprived phenol red-free RPMI 1640 medium with 10% dextran charcoal-stripped fetal bovine serum for at least 10 months.

value: MCF-7 cells

value: breast cancer cells

value: PTBP1 knockdown

value: long term estrogen deprivation


title: MCF-7 LTED cells, PTBsi1


title: lymphnode_aPD1.GAd_e29d1D19_L1


title: CUT&RUN II Individual Aptamers_Wnt+_Rep3

description: Individual Aptamers_Wnt+_Rep3


title: lymphnode_aPD1.GAd_e29d1D18_L1


title: MCF-7 LTED cells, LTlna2

value: DIO3OS knockdown


title: CUT&RUN II Individual Aptamers_Wnt+_Rep2

description: Individual Aptamers_Wnt+_Rep2


title: lymphnode_aPD1.GAd_e29d1D17_L1


title: lymphnode_aPD1.GAd_e29d1D15_L1


title: lymphnode_aPD1.GAd_e29d1D16_L1


title: lymphnode_aPD1.GAd_e29d1D13_L1


title: lymphnode_aPD1.GAd_e29d1D14_L1


title: lymphnode_aPD1.GAd_e29d1D12_L1


title: CUT&RUN II Dual-specificity Aptamer_Wnt-_Rep3

description: Dual-specificity Aptamer_Wnt-_Rep3

value: beta-catenin was knocked-down with a shRNA. Cells were cultured in regular DMEM (Wnt-).


title: CUT&RUN II Dual-specificity Aptamer_Wnt-_Rep2

description: Dual-specificity Aptamer_Wnt-_Rep2

value: Cultured Cells


title: lymphnode_aPD1.GAd_e29d1D10_L1


title: PeG_NO_nRNA_1

tag: tissue type

value: Isolated Ganglion


title: CUT&RUN II Dual-specificity Aptamer_Wnt-_Rep1

description: Dual-specificity Aptamer_Wnt-_Rep1


title: lymphnode_aPD1.GAd_e29d1D11_L1


title: lymphnode_aPD1.GAd_e29d1C9_L1


title: lymphnode_aPD1.GAd_e29d1C8_L1


title: CUT&RUN II Individual Aptamers_Wnt-_Rep3

description: Individual Aptamers_Wnt-_Rep3


title: lymphnode_aPD1.GAd_e29d1C7_L1


title: PeG_5HT_nRNA_1


title: lymphnode_aPD1.GAd_e29d1C6_L1


title: MCF-7 LTED cells, PTBnc

value: WT


title: CUT&RUN II Individual Aptamers_Wnt-_Rep2

description: Individual Aptamers_Wnt-_Rep2


title: CUT&RUN II Individual Aptamers_Wnt+_Rep1

description: Individual Aptamers_Wnt+_Rep1


title: MCF-7 LTED cells, LTlna1


title: MCF-7 LTED cells, LTnc


title: lymphnode_aPD1.GAd_e29d1C4_L1

value: Adpgk+ CD8+ T cell


title: lymphnode_aPD1.GAd_e29d1C2_L1


title: lymphnode_aPD1.GAd_e29d1C3_L1


title: CUT&RUN I Control - IgG, in Ac5S treated cells

description: Control - IgG, in Ac5S treated cells

treatment_protocol: 2E6 HEK293T cells were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+). Ac5S, the OGT inbititor, was added into culture media at 50 μM at 4 hr post-transrection and present in all fresh media since then.

value: Cells were treated with 50 μM Ac5S for 20 hr.


title: lymphnode_aPD1.GAd_e29d1C24_L1


title: lymphnode_aPD1.GAd_e29d1C23_L1


title: CUT&RUN I Dual-specificity Aptamer_Wnt+_Rep3

description: Dual-specificity Aptamer_Wnt+_Rep3

value: Cells were treated with 50 μM Ac5S for 20 hr. Cells were cultured in 50% Wnt3A-conditioned DMEM for 4 hr (Wnt+).


title: lymphnode_aPD1.GAd_e29d1C18_L1


title: CUT&RUN II Individual Aptamers_Wnt-_Rep1

description: Individual Aptamers_Wnt-_Rep1


title: CUT&RUN I Dual-specificity Aptamer_Wnt+_Rep2

description: Dual-specificity Aptamer_Wnt+_Rep2


title: lymphnode_aPD1.GAd_e29d1C17_L1


title: PeG_5HT_nRNA_2


title: lymphnode_aPD1.GAd_e29d1C16_L1


title: CUT&RUN I Dual-specificity Aptamer_Wnt+_Rep1

description: Dual-specificity Aptamer_Wnt+_Rep1


title: lymphnode_aPD1.GAd_e29d1C15_L1


title: lymphnode_aPD1.GAd_e29d1C1_L1


title: lymphnode_aPD1.GAd_e29d1C12_L1


title: lymphnode_aPD1.GAd_e29d1C13_L1


title: lymphnode_aPD1.GAd_e29d1C5_L1


title: lymphnode_aPD1.GAd_e29d1C10_L1


title: lymphnode_aPD1.GAd_e29d1C11_L1


title: CUT&RUN I Individual Aptamers_Wnt+_Rep2

description: Individual Aptamers_Wnt+_Rep2


title: lymphnode_aPD1.GAd_e29d1B9_L1


title: lymphnode_aPD1.GAd_e29d1B7_L1


title: CUT&RUN I Individual Aptamers_Wnt+_Rep3

description: Individual Aptamers_Wnt+_Rep3


title: lymphnode_aPD1.GAd_e29d1B6_L1


title: CUT&RUN I Dual-specificity Aptamer_Wnt-_Rep3

description: Dual-specificity Aptamer_Wnt-_Rep3

value: Cells were treated with 50 μM Ac5S for 20 hr. Cells were cultured in regular DMEM (Wnt-).


title: lymphnode_aPD1.GAd_e29d1B3_L1

value: lymph node


title: CUT&RUN I Dual-specificity Aptamer_Wnt-_Rep1

description: Dual-specificity Aptamer_Wnt-_Rep1


title: lymphnode_aPD1.GAd_e29d1B4_L1

value: 6-10 weeks old


title: CUT&RUN I Individual Aptamers_Wnt+_Rep1

description: Individual Aptamers_Wnt+_Rep1


title: lymphnode_aPD1.GAd_e29d1C19_L1


title: lymphnode_aPD1.GAd_e29d1B5_L1


title: lymphnode_aPD1.GAd_e29d1B2_L1


title: lymphnode_aPD1.GAd_e29d1B24_L1


title: lymphnode_aPD1.GAd_e29d1B14_L1


title: lymphnode_aPD1.GAd_e29d1B13_L1


title: lymphnode_aPD1.GAd_e29d1B18_L1


title: lymphnode_aPD1.GAd_e29d1B1_L1


title: lymphnode_aPD1.GAd_e29d1B12_L1


title: CUT&RUN I Individual Aptamers_Wnt-_Rep3

description: Individual Aptamers_Wnt-_Rep3


title: lymphnode_aPD1.GAd_e29d1B15_L1


title: CUT&RUN I Individual Aptamers_Wnt-_Rep2

description: Individual Aptamers_Wnt-_Rep2


title: CUT&RUN I Dual-specificity Aptamer_Wnt-_Rep2

description: Dual-specificity Aptamer_Wnt-_Rep2


title: HNT-34 - shEVI1.2658

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shEVI1.2658 (Day 5 ON DOX)

data_processing:
For human Quant-seq (3’ mRNA-Seq) data, the six nucleotide long 5’ UMIs were attached to each read name with umi-tools (v1.0.0) (Smith et al., 2017), before trimming away the UMIs plus the next four nucleotides (UMI spacer), as well as 3’ adapters (stringency of 3) and bases with low quality (threshold of 25), using cutadapt (v1.18) (MARIN, 2011) and its wrapper tool trimgalore (v0.6.2).
Read quality control was performed with FastQC (v0.11.8) (Andrews, 2010).
The remaining reads were sample-wise aligned to the human (GRCh38.p13; GCA_000001405.28) reference genome.
Mapping and subsequent filtering of 3’ UTR mapped reads was performed with slamdunk (v0.4.3) (Neumann et al., 2019). 3’ UTR regions were assembled as described previously (Muhar et al., 2018).
Aligned and filtered reads were deduplicated with umi-tools (v1.0.0) (Smith et al., 2017), based on the mapping coordinate and the UMI attached to the read name, prior to quantifying read abundances within 3’ UTR regions using featureCounts (v2.0.1) (Liao et al., 2014).
Differential expression analysis was performed with DESeq2 (v1.30.1) (Love et al., 2014).
genome build: GRCh38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...
For standard murine RNA-seq data, reads were processed using the Nextflow based nf-core/rna-seq pipeline (Ewels et al., 2020) using Illumina’s mouse iGenome (GRCm38) as reference and “reverse” as input parameter for strandedness. Default parameters were kept for each processing step.
Read trimming with trimgalore (v0.6.6)
Alignment and quantification with STAR (v2.6.1d) (Dobin et al., 2013) and salmon (v1.4.0) (Patro et al., 2017)
Differential expression analysis with DESeq2 (v1.28.0) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...

source_name: DSMZ

growth_protocol: Cell culture was maintained at 37ºC with 5% CO2, cells cultivated in RPMI 1640 (Gibco) supplemented with l-glutamine (4 mM, Gibco), sodium pyruvate (1 mM, Sigma-Aldrich), penicillin-streptomycin (100 U/ml & 100 µg/ml, Sigma-Aldrich) and 20% FBS (Gibco)

extract_protocol:
sorrted GFP+/shRNA expressing cells
Facility (RNA/Lexogen, Quant-seq), stranded

value: in vitro cultured leukemia cells

value: DOX-induced induction of  shEVI1.2658 (5 days)


title: HNT-34 - shEVI1.1470

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shEVI1.1470 (Day 5 ON DOX)

value: DOX-induced induction of  shEVI1.1470 (5 days)


title: CUT&RUN I Individual Aptamers_Wnt-_Rep1

description: Individual Aptamers_Wnt-_Rep1

value: EZH2 (Cell Signaling, 5246S)


title: lymphnode_aPD1.GAd_e29d1B11_L1


title: lymphnode_aPD1.GAd_e29d1B10_L1


title: lymphnode_controltumorfree_e29d1A9_L1

value: CD8+ T cell


title: lymphnode_controltumorfree_e29d1A8_L1


title: lymphnode_aPD1.GAd_e29d1A23_L1


title: CDPC16-23051

city: Los Angeles

first: Rivkah

last: Gonsky

state: California

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

description: NEXTSEQ 500 SBS SEQUENCING v2

data_processing:
Expression analysis of CD3+ T cells was performed using Nugen human FFPE RNA-seq library system.
The data were log2-transformed and normalized using robust spline normalization.
Reads were mapped to the UCSC transcript set using Bowtie2 version 2.1.0.
Gene expression level was estimated using RSEM v1.2.15 and normalized using FPKM.
Assembly: hg19
Supplementary files format and content: FPKM

source_name: Blood

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit
total RNA

treatment_protocol: CD3+ T cells were isolated using CD3-immunomagnetic beads (Miltenyi Biotech, Auburn, CA) and were at least 95% pure.

value: Blood

tag: disease

value: Crohn Disease


title: HNT-34 - shEVI1.118

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shEVI1.118 (Day 5 ON DOX)

value: DOX-induced induction of  shEVI1.118 (5 days)


title: HNT-34 - shRen.713

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shRen.713 (Day 5 ON DOX)

value: DOX-induced induction of  shRen.713 ctrl (5 days)


title: lymphnode_aPD1.GAd_e29d1A24_L1


title: CDPC16-22936

description: NEXTSEQ 500 SBS SEQUENCING v2


title: lymphnode_aPD1.GAd_e29d1A16_L1


title: lymphnode_aPD1.GAd_e29d1A22_L1


title: lymphnode_controltumorfree_e29d1A15_L1


title: HNT-34 - shRen.660

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shRen.660 (Day 5 ON DOX)

value: DOX-induced induction of  shRen.660 ctrl (5 days)


title: CDPC15-22315

description: NEXTSEQ 500 SBS SEQUENCING v2


title: lymphnode_controltumorfree_e29d1A14_L1


title: lymphnode_controltumorfree_e29d1A13_L1


title: HNT-34 - shEmpty

description: Quant-seq: HNT-34 AML cells, constitutive rtTA3, TET-ON for shRNA - shEmpty (Day 5 ON DOX)

value: DOX-induced induction of empty vector (5 days)


title: CDPC15-21597

description: NEXTSEQ 500 SBS SEQUENCING v2


title: lymphnode_controltumorfree_e29d1A12_L1


title: lymphnode_controltumorfree_e29d1A11_L1


title: CDPC15-20261

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDPC15-20973

description: NEXTSEQ 500 SBS SEQUENCING v2


title: DKO [BP53-6]

city: Chicago

first: Young

last: Yoo

state: IL

address: 303 E Superior St

institute: Northwestern University Feinberg School of Medicine

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw gene counts

source_name: Prostate

extract_protocol:
Total RNA was extracted from mice prostate grafts using RNAeasy Plus mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Total RNA-Seq Library Prep Kit following manufacturer's protocols.

value: Prostate

value: Bmi1-CreER; Ptenf/f; Tp53f/f

value: Castration


title: lymphnode_controltumorfree_e29d1A10_L1


title: DKO [BP53-5]


title: tumor_aPD1.GAd_P8_L2

value: Adpgk+ CD8+ T cell

value: tumor


title: DKO [BP53-4]


title: tumor_aPD1.GAd_P7_L2

value: 6-10 weeks old


title: CDPC14-20199

description: NEXTSEQ 500 SBS SEQUENCING v2


title: PTEN KO [BP-7]

value: Bmi1-CreER; Ptenf/f


title: CDPC15-22412

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_P6_L2


title: CDPC14-20107

description: NEXTSEQ 500 SBS SEQUENCING v2


title: PTEN KO [BP-6]


title: tumor_aPD1.GAd_P4_L2


title: tumor_aPD1.GAd_P3_L2


title: tumor_aPD1.GAd_P2_L2


title: CDPC14-19903

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_P5_L2


title: PTEN KO [BP-5]


title: CDPC14-19256

description: NEXTSEQ 500 SBS SEQUENCING v2


title: PTEN KO [BP-4]


title: tumor_aPD1.GAd_P23_L2


title: tumor_aPD1.GAd_P9_L2


title: tumor_aPD1.GAd_P24_L2


title: tumor_aPD1.GAd_P21_L2


title: tumor_aPD1.GAd_P22_L2


title: Spleen cells, CIA mice, Day 40

city: Nanjing

first: Pan

last: Yuting

address: Guangzhou Road

institute: Children’s Hospital of Nanjing Medical University

data_processing:
First, transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded.
Then, we utilized the CPC and CNCI scores to predict transcripts with coding potential. All transcripts with CPC scores < –1 and CNCI scores < 0 were removed, and the remaining transcripts were considered as lncRNAs.
The mRNA and lncRNA expression levels in the spleen tissues were determined using StringTie by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) .
Differential expression analysis for mRNAs and lncRNAs was performed using the R package ballgown, and mRNAs and lncRNAs with log2 (fold change) > 1 or log2 (fold change) < -1 were considered significantly expressed.
Assembly: Genome v96,
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol: Total RNA was extracted from cell samples using TRIzol reagent according to the manufacturer’s instructions. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit.

value: spleen

value: A CIA (type II) mouse model was established as previously described. All mice were sacrificed at 42 days after first immunization.


title: Spleen cells, Healthy Control, Day 40

value: without any treatment


title: CDPC14-19079

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_P18_L2

extract_protocol:
Dextramer-Adpgk+ CD8+ T cells were FACS sorted from draining lymph nodes and tumors, harvested from non-treated tumor bearing mice, treated with αPD-1, and αPD-1 combined with GAd. Neoepitope specific- CD8+ T cells were sorted into 384-well plates, containing lyses buffer and immediately frozen.
Single cell library preparation was done as previously described (Picelli et al., 2014).


title: tumor_aPD1.GAd_P19_L2


title: CDPC14-19231

description: NEXTSEQ 500 SBS SEQUENCING v2


title: TET-OFF mouse model - ON DOX - Replicate 3

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - ON DOX (3 days) - Replicate 3

data_processing:
For standard murine RNA-seq data, reads were processed using the Nextflow based nf-core/rna-seq pipeline (Ewels et al., 2020) using Illumina’s mouse iGenome (GRCm38) as reference and “reverse” as input parameter for strandedness. Default parameters were kept for each processing step.
Read trimming with trimgalore (v0.6.6)
Alignment and quantification with STAR (v2.6.1d) (Dobin et al., 2013) and salmon (v1.4.0) (Patro et al., 2017)
Differential expression analysis with DESeq2 (v1.28.0) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...
For standard murine RNA-seq data, reads were processed using the Nextflow based nf-core/rna-seq pipeline (Ewels et al., 2020) using Illumina’s mouse iGenome (GRCm38) as reference and “reverse” as input parameter for strandedness. Default parameters were kept for each processing step.
Read trimming with trimgalore (v0.6.6)
Alignment and quantification with STAR (v2.6.1d) (Dobin et al., 2013) and salmon (v1.4.0) (Patro et al., 2017)
Differential expression analysis with DESeq2 (v1.28.0) (Love et al., 2014).
genome build: GRCm38
processed data files format and content: tab-delimited text files include abundance measurements as normalized count values for each Sample ...

growth_protocol: in vivo

extract_protocol:
sorted ex-vivo BM-derived CD45.2/GFP/cKit+ Mac1- leukemia cells
Facility (RNA/Lexogen, poly-A), stranded

treatment_protocol: Transplanted mouse treated with Doxycycline (DOX) (4 mg/ml) for 3 days

value: DOX-induced repression of RUNX1/EVI1 (3days)


title: tumor_aPD1.GAd_P17_L2

data_processing:
Single-cell sequencing files (base calls) were demultiplexed with bcl2fastq2 v.2.20.0.422 with default parameters for paired-end sequencing
FASTQ files were aligned to GRCm38 mouse (mm10) genome using STAR v.2.7.3a
Transcript-per-million (TMP) counts were obtained by processing the alignment results with RSEM v.1.3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files of transcript expression quantification obtained via RSEM


title: CDPC14-19088

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Blood


title: TET-OFF mouse model - ON DOX - Replicate 2

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - ON DOX (3 days) - Replicate 2

value: ex-vivo BM-derived CD45.2/GFP/cKit+ Mac1- leukemia cells


title: CDPC14-18733

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Crohn Disease


title: tumor_aPD1.GAd_P16_L2


title: CDPC14-18551

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_P14_L2


title: TET-OFF mouse model - ON DOX - Replicate 1

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - ON DOX (3 days) - Replicate 1


title: CDPC14-18380

description: NEXTSEQ 500 SBS SEQUENCING v2


title: TET-OFF mouse model - OFF DOX - Replicate 3

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - OFF DOX - Replicate 3

treatment_protocol: Transplanted mouse untreated

value: untreated


title: tumor_aPD1.GAd_P11_L2


title: tumor_aPD1.GAd_P13_L2


title: tumor_aPD1.GAd_P12_L2


title: tumor_aPD1.GAd_P10_L2


title: CDPC14-18287

description: NEXTSEQ 500 SBS SEQUENCING v2


title: TET-OFF mouse model - OFF DOX - Replicate 2

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - OFF DOX - Replicate 2


title: tumor_aPD1.GAd_P20_L2


title: tumor_aPD1.GAd_P1_L2


title: tumor_aPD1_O8_L2


title: tumor_aPD1_O9_L2


title: CDPC14-18148

description: NEXTSEQ 500 SBS SEQUENCING v2


title: TET-OFF mouse model - OFF DOX - Replicate 1

description: RNA-seq: murine BM-derived leukemia cells - TET-OFF model - regulatable RUNX1/EVI1, constitutive NRAS(G12D) - OFF DOX - Replicate 1


title: tumor_aPD1_O7_L2


title: tumor_aPD1_O6_L2


title: CDPC14-18047

description: NEXTSEQ 500 SBS SEQUENCING v2


title: DOX ctrl mouse model - ON DOX - Replicate 3

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - ON DOX (3 days) - Replicate 3

value: DOX (3days)


title: tumor_aPD1_O5_L2


title: tumor_aPD1.GAd_P15_L2


title: tumor_aPD1_O4_L2


title: DOX ctrl mouse model - ON DOX - Replicate 2

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - ON DOX (3 days) - Replicate 2


title: tumor_aPD1.GAd_O24_L2


title: DOX ctrl mouse model - ON DOX - Replicate 1

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - ON DOX (3 days) - Replicate 1


title: CDPC13-17832

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_O2_L2


title: CDPC13-17791

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_O23_L2


title: tumor_aPD1_O22_L2


title: CDPC13-17752

description: NEXTSEQ 500 SBS SEQUENCING v2


title: DOX ctrl mouse model - OFF DOX - Replicate 3

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - OFF DOX - Replicate 3


title: tumor_aPD1_O1_L2


title: DOX ctrl mouse model - OFF DOX - Replicate 2

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - OFF DOX - Replicate 2


title: tumor_aPD1_O21_L2


title: tumor_aPD1_O20_L2


title: DOX ctrl mouse model - OFF DOX - Replicate 1

description: RNA-seq: murine BM-derived leukemia cells - DOX ctrl model - constitutive RUNX1/EVI1, NRAS(G12D) - OFF DOX - Replicate 1


title: CDPC13-17378

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_O18_L2


title: CDPC13-16955

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 359_SN_

tag: gleason score

tag: lethal

value: No

tag: cribriform

tag: used in analysis

value: Yes


title: tumor_aPD1_O17_L2


title: tumor_aPD1_O19_L2


title: CDPC13-5387

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 353_ST_

value: Non-Cribriform


title: tumor_aPD1_O15_L2


title: CDPC13-17188

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_O16_L2


title: tumor_aPD1_O14_L2


title: tumor_aPD1_O3_L2


title: tumor_aPD1_O13_L2


title: CDPC13-16485

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 351_ST_


title: tumor_aPD1_O12_L2


title: CDPC13-16483

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_O11_L2


title: 350_ST_


title: CDPC12-5176

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 351_SN_


title: tumor_aPD1_N9_L2


title: WT_JZL184_3

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Transcript abundances in Transcripts Per Million (TPM) were quantified with Salmon 0.7.2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ventricle

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.

value: heart


title: CDPC12-4592

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_O10_L2

value: Adpgk+ CD8+ T cell


title: WT_JZL184_2


title: 348_ST_

extract_protocol:
For each case, FFPE blocks with stroma-enriched (>60%) areas adjacent to tumor and benign areas distant from the tumor (another prostate quadrant or lobe in a separate FFPE block) were selected. Besides the identification of tumor- and benign-adjacent stroma areas for sampling, pathologists (G.N.F., M.L.) determined the Gleason score in the nearby tumor and annotated cribriform patterns and other histologic features. Stroma-enriched regions of interest (ROIs) adjacent to the tumor or benign glands were manually circled on slides. Tissue edges and ROIs were outlined on a parafilm strip and transferred onto the corresponding FFPE block.
Libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.


title: 347_ST_


title: tumor_aPD1_N8_L2

value: tumor


title: CDPC12-3064

description: NEXTSEQ 500 SBS SEQUENCING v2


title: WT_JZL184_1


title: CDPC13-16676

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDPC12-3017

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDPC12-3414

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 353_SN_


title: tumor_aPD1_N6_L2

value: 6-10 weeks old


title: tumor_aPD1_N7_L2


title: 346_ST_


title: WT_veh_2


title: 346_SN_


title: tumor_aPD1_N5_L2


title: CD_veh_1

value: WBS-CD


title: WT_veh_1


title: CDPC12-2936

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_N4_L2


title: 345_ST_


title: CD_JZL184_3


title: CDPC12-2593

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDPC12-2592

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CD_JZL184_2


title: 349_ST_


title: tumor_aPD1_N3_L2


title: CD_veh_3


title: 335_ST_


title: 338_ST_


title: CDPC12-2333

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_N2_L2


title: tumor_aPD1_N24_L2


title: CDPC11-959

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CD_JZL184_1


title: 333_ST_


title: CD_veh_2


title: tumor_aPD1_N23_L2


title: Hermaphroditic

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
BioProject for the genome:PRJNA13635
Reference Genome: AASC00000000.3 Aplysia californica
Reference assembly: GCA_000002075.2, (assembly AplCal3.0)
RefSeq assembly accession: GCF_000002075.1 (latest)
Supplementary_files_format_and_content: TPMs for all single neurons samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all developmental stage samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all tissue samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all neuroplasticity samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE

source_name: Isolated Tissue

extract_protocol:
Tissue were dissected and RNA isolated with QIAGEN Rneasy. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEB NEXT Ultra Library Construction for Illumina.

value: Hermaphroditic


title: tumor_aPD1_N22_L2


title: CDPC11-1188

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 329_ST_

data_processing:
fastq files were aligned to version 97 of human reference genome GRCm38 using the Salmon.
Low read counts gene and sample filtering
Expression data was normalized using the VOOM with LOESS fit, and Combat-seq function in the Limma package in R
Assembly: version 97 of human reference genome GRCm38
Supplementary files format and content: Normalized RNA-seq


title: Hepatopancreas

value: Hepatopancreas


title: Ovotestis

value: Ovotestis


title: CDP11-1263

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 329_SN_


title: 340_SN_


title: tumor_aPD1_N21_L2


title: Digestive

value: Digestive


title: tumor_aPD1_N20_L2


title: tumor_aPD1_N1_L2


title: Muscle

value: Muscle


title: CDPC11-491

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Blood


title: CDP11-1220

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Crohn Disease


title: tumor_aPD1_N19_L2


title: 327_ST_GS4


title: CDP11-1258

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 328_SN_


title: CDP11-1195

description: NEXTSEQ 500 SBS SEQUENCING v2


title: Gills

value: Gills


title: Heart

value: Heart


title: tumor_aPD1_N18_L2


title: 328_ST_

value: No


title: CDP11-1184

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 327_SN_

value: Yes


title: Salivary_glands

value: Salivary Glands


title: tumor_aPD1_N17_L2


title: CDP11-1182

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 326_SN_


title: Statocyst

value: Statocyst


title: CDP11-1181

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 324_ST_GS4

value: Non-Cribriform


title: Chemoreceptive_tissue

value: Chemoreceptive tissue


title: tumor_aPD1_N16_L2

value: Adpgk+ CD8+ T cell

value: tumor

value: 6-10 weeks old


title: CDP11-1180

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 324_SN_


title: CNS

value: CNS


title: 322_ST_GS4

value: Cribriform


title: tumor_aPD1_N14_L2


title: 320_ST_GS4


title: 321_ST_GS4


title: 12th_day_hatchling_veliger

source_name: Developmental Stages

value: 12 Day hatching veliger


title: 4th_day_early_trochophora

value: 4 Day early trochophora


title: CDP10-1145

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Blood


title: 9th_day_veliger

value: 9 Day veliger


title: tumor_aPD1_N13_L2


title: 319_ST_GS4


title: CDP11-1166

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Crohn Disease


title: tumor_aPD1_N10_L2


title: 317_ST_GS4


title: tumor_aPD1_N11_L2


title: 3rd_day

value: 3 Day


title: Gastrulation

value: Gastrulation


title: CDP10-1144

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 316_ST_

value: No

value: Yes


title: lymphnode_controltumorfree_M9_L2

source_name: lymph node

value: CD8+ T cell

value: lymph node


title: Early_cleavage

value: Early Cleavage


title: tumor_aPD1_N15_L2

value: Adpgk+ CD8+ T cell


title: 311_ST_

value: Non-Cribriform


title: SC-2

source_name: Single Neurons Isolated from CNS

value: Single Neuron Isolated from CNS


title: CDP11-1179

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDP10-1113

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 310_ST_


title: CDP11-1164

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_N12_L2

value: tumor

value: 6-10 weeks old


title: lymphnode_controltumorfree_M7_L2


title: CDP10-1108

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 309_ST_


title: R2_1


title: tumor_aPD1.GAd_M4_L2


title: 308_ST_


title: CDP10-1102

description: NEXTSEQ 500 SBS SEQUENCING v2


title: rMCC_1


title: tumor_aPD1.GAd_M3_L2


title: lMCC_1


title: CDP10-1136

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 308_SN_


title: CDP10-1098

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1.GAd_M2_L2


title: 307_ST_

value: Cribriform


title: CDP10-1120

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDP10-1083

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_M24_L2


title: Kdm6b-cKO, H3K27me3, ChIP-seq, Rep 3

city: Durham

first: Anne

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

description: SE 50bp

data_processing:
ChIP-seq raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Genome coverage was calculated using bedtools v2.25.0 genomecov.
Peak calling was performed using Macs2, with definitions for broad peaks and FDR cut-off of 0.01
DESeq2 1.36.0 was used to obtain differentially bound peaks between timepoints, using an adjusted p value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: bed

source_name: Cerebellum

extract_protocol:
Cerebellum samples were dounced in a glass homogenizer containing 2 ml of 1% formaldehyde (w/v) PBS buffer per sample and kept at 25 °C for 15 min, washed twice with cold PBS, lysed in 600 μl lysis buffer (1% SDS (w/v), 10 mM EDTA, and 50 mM Tris, pH 8.1). The cross-linked material was sonicated with a Bioruptor (Diagenode), with output set to “high” with 30 s on/off cycles to an average size range of 150–350 bp which was then determined by agarose gel electrophoresis.
ChIP-seq libraries were made using the MicroPlex Library Preparation kit V2 (C05010012, Diagenode); and 50 bp single-end sequencing was performed at the Duke Sequencing and Analysis Core Resource on a Hi-Seq 2000 machine.

value: Cerebellum

value: H3K27me3 Active Motif 39166


title: Kdm6b-cKO, H3K27me3, ChIP-seq, Rep 2

description: SE 50bp


title: lymphnode_controltumorfree_M8_L2


title: CDP09-973

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Blood


title: tumor_aPD1_M23_L2

source_name: tumor


title: CDP09-967

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Crohn Disease


title: Kdm6b-cKO, H3K27me3, ChIP-seq, Rep 1

description: SE 50bp


title: tumor_aPD1_M22_L2


title: Kdm6b-WT, H3K27me3, ChIP-seq, Rep 2

description: SE 50bp

value: H3K27me3 Active Motif 39165


title: tumor_aPD1_M21_L2


title: CDP09-959

description: NEXTSEQ 500 SBS SEQUENCING v2


title: Kdm6b-WT, H3K27me3, ChIP-seq, Rep 1

description: SE 50bp

value: H3K27me3 Active Motif 39164


title: CDP09-956

description: NEXTSEQ 500 SBS SEQUENCING v2


title: tumor_aPD1_M20_L2


title: CDP09-1057

description: NEXTSEQ 500 SBS SEQUENCING v2


title: P60, H3K27me3, ChIP-seq, Rep 3

description: SE 50bp

value: H3K27me3 Active Motif 39163


title: tumor_aPD1_M18_L2


title: CDP09-1016

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 307_SN_

source_name: Prostate Stroma from RP

value: No

value: Yes


title: tumor_aPD1_M17_L2


title: CDP09-1055

description: NEXTSEQ 500 SBS SEQUENCING v2


title: 303_SN_


title: 303_ST_


title: P60, H3K27me3, ChIP-seq, Rep 1

description: SE 50bp

value: H3K27me3 Active Motif 39161


title: P60, H3K27me3, ChIP-seq, Rep 2

description: SE 50bp

value: H3K27me3 Active Motif 39162


title: P14, H3K27me3, ChIP-seq, Rep 3

description: SE 50bp

value: H3K27me3 Active Motif 39160


title: 302_ST_

value: Non-Cribriform


title: CDP09-1015

description: NEXTSEQ 500 SBS SEQUENCING v2


title: CDP09-1012

description: NEXTSEQ 500 SBS SEQUENCING v2


title: lymphnode_controltumorfree_M15_L2

value: CD8+ T cell

value: lymph node


title: P14, H3K27me3, ChIP-seq, Rep 2

description: SE 50bp

value: H3K27me3 Active Motif 39159


title: tumor_aPD1_M16_L2

value: Adpgk+ CD8+ T cell

value: tumor

value: 6-10 weeks old


title: 301_ST_


title: 306_ST_


title: 306_SN_


title: 305_ST_


title: 300_ST_


title: 305_SN_


title: lymphnode_controltumorfree_M14_L2


title: CDP09-1002

description: NEXTSEQ 500 SBS SEQUENCING v2

value: Blood


title: Blood cells from CLL patient 79

city: Montpellier

first: Jerome

last: Moreaux

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS-UM

description: RNA-seq expression data from blood cells of CLL patient

data_processing:
Assembly: RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner
The expression level of each gene was summarized and normalized using the DESeq2 R/Bioconductor package. Differential expression analysis was performed using the DESeq2 pipeline. p-values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package.

extract_protocol:
Total RNAs, including small RNAs, were extracted using the PAXgene Blood miRNA Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instruction.
The RNA-seq library preparation was completed with 150 ng of input RNA using the Illumina TrueSeq Stranded mRNA Library Prep Kit.
Paired-end RNA-seq was performed with an Illumina NextSeq sequencing instrument

treatment_protocol: Blood was collected befor treatment in PAXgene blood RNA tubes

value: Blood cells from CLL patient


title: P14, H3K27me3, ChIP-seq, Rep 1

description: SE 50bp

value: Cerebellum

value: H3K27me3 Active Motif 39158


title: lymphnode_controltumorfree_M13_L2


title: P7, H3K27me3, ChIP-seq, Rep 2

description: SE 50bp

value: H3K27me3 Active Motif 39156


title: Blood cells from CLL patient 78


title: tumor_aPD1_M19_L2


title: lymphnode_controltumorfree_M12_L2


title: P7, H3K27me3, ChIP-seq, Rep 3

description: SE 50bp

value: H3K27me3 Active Motif 39157


title: lymphnode_controltumorfree_M11_L2


title: 298_ST_

value: No

value: Yes


title: 299_ST_


title: P7, H3K27me3, ChIP-seq, Rep 1

description: SE 50bp

value: H3K27me3 Active Motif 39155


title: 297_ST_


title: lymphnode_controltumorfree_M10_L2


title: 297_SN_