title: pADamID_CTCF_GSK_24h_Dam_r1

data_processing:
Library strategy: pA-DamID
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files of "raw" log2-normalized LaminB1 pADamID scores for 10kb genomic bins; tsv files with genomic coordinates and all z-scores per replicate / average scores per condition.

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 24h of IAA

growth_protocol: E14Tg2a mouse embryonic stem cells (mESCs) and derived cell lines were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), 104 U of leukemia inhibitory factor (LIF; Millipore), the MEK inhibitor PD0325901 (1 μM; Selleckchem), the GSK-3β inhibitor CHIR99021 (3 μM; Cayman Chemical) and 1-thioglycerol (1.5 × 10−4 M; Sigma-Aldrich) on 0.1% gelatin-coated plates. The cell lines were passaged every two days.

extract_protocol:
1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a LaminB1 antibody and for a Dam control condition, to specifically deposit m6A marks at peripherally positioned chromatin. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified with 15-19 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters.

treatment_protocol: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich). Protein degradation was induced at different time points and all samples were collected at the end of the time course.

tag: cell line

value: Embyonic stem cell

tag: library type

value: pA-DamID

value: OsTir1; CTCF-AID-eGFP


title: pADamID_CTCF_GSK_24h_Dam_r2

status: Public on Sep 16 2021

type: SRA

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genetic modification

tag: time point


title: PRE-R-030 [18R438_019]

city: Seoul

first: Tae Won

last: Kim

address: 88 Olympic-ro 43-gil

country: South Korea

institute: Asan Medical Center

library_source: transcriptomic

data_processing:
All fastq format reads were assessed for quality control using FASTQC software (v0.11.8).
The Illumina sequencing platform-specific adaptors and poor quality read bases were trimmed using Trim Galore (v0.4.5).
The trimmed reads were mapped to the reference genome  with STAR aligner (v2.6.0) and the output sam/bam files were obtained.
Gene expression was quantified using RSEM (v1.2.23)
normalized through DESeq2 BiocManager package (v1.20.0)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: comma-delimited text files include raw counts and FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer

extract_protocol:
macrodisssection of an unstained FFPE tissue section, followed by total RNA extraction using TRIzol reagent.
A cDNA library was constructed using TruSeq RNA Access Library Prep Kit (Illumina, Inc., San Diego, CA, USA) and paired-end sequencing was conducted using an HiSeq 2500 platform (Illumina Inc).

tag: tissue

value: primary tumor (colorectum)

value: pre-treatment

tag: treatment response

value: pre-Tx


title: PRE-R-033 [18R457_023]


title: mNPC_WAPLAID_ChIP_CTCF_24h

description: CTCF ChIP-seq in E14TG2a mNPCs (with OsTir1; WAPL-AID-eGFP), after 24h of IAA

data_processing:
DamID: The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. LADs were called using hidden Markov modeling (https://github.com/ gui11aume/HMMt). Additionally, individual replicates were averaged for create a combined data track and LAD model.
ChIP-seq: The full protocol is described in the corresponding manuscript. Reads were mapped to a concatenated reference genome (mm10 and hg19) using bowtie2 2.3.4.1. Reads were filtered for a mapping quality of at least 15 and optical PCR duplicates were removed with SAMtools 1.9. Deeptools 3.0 was used to create a normalized coverage track, scaled to 1 million HEK293T reads. Peak calling was performed with MACS2 2.1.1.20160309 at a q-value cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: DamID: BigWig files of log2-normalized LaminB1 pADamID scores for 10kb genomic bins, bed file with LAD coordinates; ChIP-seq: BigWig file of coverage, bed file with peak coordinates.

growth_protocol: Mouse neural precursor cells (mNPCs) were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), recombinant mouse EGF (10 ng/ml; PeproTech) and recombinant human FGF-basic (10 ng/ml; PeproTech) on 0.1% gelatin-coated plates. Cells were passaged every 3-4 days.

extract_protocol:
DamID: Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit. The DNA concentration was estimated with a Nanodrop; ChIP-seq: ChIP experiments were performed in the presence of 10% human HEK293T cells as internal reference. Cells were crosslinked (1% FA, 10 minutes) and quenced with glycine (2.0M). Chromatin was fragmented to ~300 bp fragments with a Bioruptor Plus sonication device (Diagenode). CTCF antibody (07-729, Merck Millipore; 5 μL per ChIP) was coupled with Protein G beads (Thermo Fisher Scientific) and incubated with fragmented chromatin overnight at 4 °C. Released DNA fragments were purified with the MinElute PCR Purification kit (Qiagen).
DamID: The full protocol is described in Leemans, 2019. 500 ng of genomic DNA was digested with DpnI at Dam-methylated GATC sequences, and ligated to adapters. Subsequent DpnII digestion destroyed DNA fragments containing unmethylated GATC sequences. DNA fragments were then amplified with 15-22 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; ChIP-seq: The purified DNA fragments were prepared with the KAPA HTP Library Preparation kit (Roche).

treatment_protocol: DamID: Cells were transduced with lentiviral particles containing either Dam-control or Dam-LaminB1 constructs and cultured for an additional 3 days; ChIP-seq: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich).

value: Neural precursor cell

tag: protocl

value: ChIP-seq

value: OsTir1; WAPL-AID-eGFP


title: mNPC_DamID_LaminB1_r1

description: LaminB1 DamID-seq in F121-9-CASTx129 mNPCs, replicate 1

data_processing:
Library strategy: DamID-seq
DamID: The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. LADs were called using hidden Markov modeling (https://github.com/ gui11aume/HMMt). Additionally, individual replicates were averaged for create a combined data track and LAD model.
ChIP-seq: The full protocol is described in the corresponding manuscript. Reads were mapped to a concatenated reference genome (mm10 and hg19) using bowtie2 2.3.4.1. Reads were filtered for a mapping quality of at least 15 and optical PCR duplicates were removed with SAMtools 1.9. Deeptools 3.0 was used to create a normalized coverage track, scaled to 1 million HEK293T reads. Peak calling was performed with MACS2 2.1.1.20160309 at a q-value cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: DamID: BigWig files of log2-normalized LaminB1 pADamID scores for 10kb genomic bins, bed file with LAD coordinates; ChIP-seq: BigWig file of coverage, bed file with peak coordinates.

value: DamID-seq


title: Case no 2, U2940, cell line

type: genomic

city: Leuven

first: Nicolas

last: Dierckxsens

address: ON I Herestraat 49

department: Human Genetics

country: Belgium

institute: KULeuven

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: Cytoscan (Illumina, San Diego, CA, USA)

data_processing: GenomeStudio  (Illumina, San Diego, CA, USA)

label: C-Bio and A-DNP

source_name: U2940, cell line

tag: diagnosis

value: primary mediastinal B cell lymphoma-derived

tag: gender

value: female origin

tag: age

value: not applicable

tag: stage (ann arbor)


title: Case no 6, tumor biopsy, mediastinum

source_name: tumor biopsy, mediastinum

label_protocol: According to the manufacturer's instructions.

value: tumor biopsy, mediastinum

value: primary mediastinal B cell lymphoma

value: female

value: II


title: Case no 4, tumor biopsy, mediastinum

extract_protocol: According to the manufacturer's instructions.

value: I


title: Case no 15, tumor biopsy, mediastinum

value: male

value: IV


title: pADamID_CTCF_GSK_0h_Dam_r1

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 0h of IAA

value: Embyonic stem cell

value: pA-DamID

value: OsTir1; CTCF-AID-eGFP


title: PRE-R-027 [18R435_015]

value: primary tumor (colorectum)

value: pre-treatment

value: pre-Tx


title: pADamID_CTCF_GSK_0h_Dam_r2


title: PRE-R-026 [18R433_013]


title: Case no 1, KARPAS-P, cell line

source_name: KARPAS-P, cell line

value: KARPAS-P

value: not available


title: mNPC_DamID_LaminB1_r2

description: LaminB1 DamID-seq in F121-9-CASTx129 mNPCs, replicate 2

value: Neural precursor cell

value: DamID-seq


title: pADamID_CTCF_EED_24h_Dam_r2


title: pADamID_CTCF_EED_0h_Dam_r2


title: PRE-R-023 [18R426_006]


title: PRE-R-021 [18R463_004]


title: pADamID_CTCF_DMSO_24h_Dam_r2


title: PRE-R-020 [18R421_001]


title: pADamID_CTCF_EED_0h_Dam_r1


title: PRE-R-022 [18R472_013]


title: PRE-15 [18R508_011]


title: PRE-R-019 [18R423_003]

value: lung metastases


title: Case no 3, tumor biopsy, mediastinum

value: tumor biopsy, mediastinum

value: primary mediastinal B cell lymphoma


title: PRE-R-024 [18R427_007]


title: pADamID_CTCF_EED_24h_Dam_r1


title: pADamID_CTCF_DMSO_24h_Dam_r1


title: RNAseq_∆mavR_aerobic_rep2

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Ave.

department: Microbiology

country: USA

institute: University of Virginia

data_processing:
After base-calling with Illumina casava, reads were trimmed/filtered to remove adapters or poor quality reads
Reads were mapped to the EHEC genome using Bowtie2.
Genome_build: NC_002695.2 (samples 7 and 8) or NZ_CP008957 (samples 1-6 and 9-12)
Supplementary_files_format_and_content: tables showing readcounts/FPKM

organism: Escherichia coli O157:H7

source_name: Enterohemorrhagic Escherichia coli O157:H7 86-24

growth_protocol: all samples were grown in low glucose DMEM (see SAMPLES section for more details)

extract_protocol:
Cells were pelleted and resuspended in Trizol. Purelink RNA mini kit (Invitrogen) was used to extract RNA.
RNAs were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: deltamavR

tag: growth condition

value: aerobic to mid-exponential phase


title: RNAseq_∆mavR_aerobic_rep1


title: RNAseq_∆mavR_aerobic_rep3


title: RNAseq_WT_aerobic_rep3

value: WT


title: pADamID_CTCF_DMSO_0h_Dam_r2


title: PRE-R-018 [18R466_007]


title: RNAseq_WT_aerobic_rep2


title: pADamID_CTCF_DMSO_0h_Dam_r1


title: RNAseq_WT_aerobic_rep1


title: MAPS_MS2_microaerobic

value: microaerobic to late-exponential phase (6 hrs)


title: MAPS_MS2-mavR_aerobic


title: PRE-R-016 [18R442_021]

value: liver metastases


title: pADamID_RAD21_24h_Dam_r1

source_name: Dam control in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 24h of IAA

value: Embyonic stem cell

value: pA-DamID

value: OsTir1; RAD21-AID-eGFP


title: PRE-R-015 [18R443_022]

value: primary tumor (colorectum)

value: pre-treatment


title: PRE-R-017 [18R436_016]

value: pre-Tx


title: pADamID_RAD21_24h_Dam_r2


title: PRE-R-014 [18R473_014]


title: Whole_CA_RNA_Control_5

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling and fastq.gz conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq the duplicates were removed by the command rmdup -s of samtools.
In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
In RNA-Seq reads were counted using FeaturesCount.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peaks.txt: Peak files.
Supplementary_files_format_and_content: geneCounts.txt: Count files.

source_name: Hippocampal CA whole tissue

extract_protocol:
RNA was isolated using TRIZOL from whole tissue. Chromatin immunoprecipitation was performed from fixed neuronal nuclei sorted by FACS.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

value: 4-6 month-old (adult)

tag: strain

value: Control

value: Hippocampal CA whole tissue


title: Whole_CA_RNA_Control_6


title: pADamID_RAD21_6h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 6h of IAA


title: pADamID_RAD21_6h_Dam_r1


title: MAPS_MS2_aerobic


title: PAIR-R-019 [18R696_04]

value: post-treatment

value: post-tx PD


title: Case no 11, tumor biopsy, mediastinum

value: tumor biopsy, mediastinum

value: primary mediastinal B cell lymphoma

value: male

value: IV


title: p40-/-IL-2Rα-/- mouse liver rep2

city: Guangzhou

first: Yafei

last: XU

address: Panyu Square, High Education Mega Center

country: China

institute: South China University of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and RNA was harvested using RNAiso Plus Reagent (TaKaRa). Illumina TruSeq RNA Sample Prep Kit v2 was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver


title: pADamID_RAD21_0h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 0h of IAA


title: p40-/-IL-2Rα-/- mouse liver rep3


title: Whole_CA_RNA_Control_3


title: PAIR-R-019 [18R695_03]


title: Whole_CA_RNA_Control_2


title: pADamID_RAD21_0h_Dam_r1


title: MAPS_MS2-mavR_microaerobic

value: deltamavR

value: microaerobic to late-exponential phase (6 hrs)


title: PRE-R-013 [18R460_001]


title: p40-/-IL-2Rα-/- mouse liver rep1


title: Whole_CA_RNA_Control_1


title: pADamID_PT_0h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1), after 0h of IAA

value: Embyonic stem cell

value: pA-DamID


title: Whole_CA_RNA_Control_4


title: Control mouse liver rep3


title: PAIR-R-018 [18R455_001]

value: liver metastases


title: Whole_CA_RNA_cKO_6

value: Setd1b cKO


title: pADamID_PT_0h_Dam_r1


title: Control mouse liver rep2


title: PAIR-R-018 [18R434_014]

value: primary tumor (colorectum)

value: pre-treatment

value: pre-Tx


title: Whole_CA_RNA_cKO_5

value: 4-6 month-old (adult)

value: Hippocampal CA whole tissue


title: pADamID_CTCF-WAPL_96h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 96h of IAA

value: OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry


title: Whole_CA_RNA_cKO_4


title: Control mouse liver rep1


title: pADamID_CTCF-WAPL_96h_Dam_r3


title: mNPC_DamID_Dam_r2

description: Dam-control DamID-seq in F121-9-CASTx129 mNPCs, replicate 2

value: Neural precursor cell

value: DamID-seq


title: pADamID_CTCF-WAPL_96h_Dam_r1


title: PRE-R-012 [18R432_012]


title: POST-R-013 [18R653_014]

value: post-treatment

value: post-tx PD


title: PRE-R-034 [18R458_025]


title: PRE-R-011 [18R645_006]


title: vasadrop_E9.5-8_i44

city: Leiden

first: Anna

last: Alemany

email: annalemany@gmail.com, a.alemany@lumc.nl

state: South Holland

address: ALBINUSDREEF 2

department: Anatomy and Embryology

institute: LUMC

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 99 for both mouse and human genomes
Supplementary_files_format_and_content: Tabular-separated file indicating number of UFIs per cell. In "total.UFICounts.tsv.gz" spliced and unspliced transcripts are reported together, and multi-annotations are indicated as "geneA_geneB". In "uniaggGenes_spliced.UFICounts.tsv.gz" and "uniaggGenes_unspliced.UFICounts.tsv.gz", count tables for spliced and unspliced transcripts are provided separatedy, and multi-annotations are aggregated.

extract_protocol:
vasaplate: Single cells were sorted by FACS into 384-well plates containing RT-primers and oil. Reagents were dispensed with a robot and plates incubated in a thermocycles after each dispensing. Briefly; 1) Lysis/fragmentation mix, 2) Poly(A)-tailing/end repair mix, 3) Reverse transcription mix, 4) Second strand synthesis mix. After second strand synthesis, wells were pooled and material was amplified with IVT. Amplified material was depleted of rRNA, second adapter was ligated and aRNA converted to cDNA. Full Illumina handles were added by PCR, and samples were sequenced.
vasadrop: Single-cells were co-encapsulated with barcoded inDrop v3 beads with with a lysis and RNA fragmentation buffer. The droplets were then incubated and further injected with a RNA repair and poly(A) tailing mix using a pico-injector. After incubation, the droplets were the injected with a reverse transcription mix and incubated. The. Droplets were then de-emulsified and processed similarly to the VASA-plate workflow.
cell dissociation: HEK293T were cultured in DMEM, dissociated with Trypsin-EDTA and washed with ice-cold PBS. Mouse ES cells were cultured in 2i/LIF conditions, dissociated with Accutase and washed with ice-cold PBS. Mouse embryos from E8.5 and E9.5 were cut into pieces under the microscope before collection in a tube, embryos from stage E6.5 and E7.5 were not cut. TrypLE Express was used for cell dissociation and washed with PBS supplemented with 0.4% BSA.
Illumina TruSeq adapaters

tag: protocol/barcodes

value: VASA-seq

tag: read format

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode

tag: plate format

tag: sample type

value: mouse embryo, E9.5


title: Whole_CA_RNA_cKO_3


title: vasadrop_E9.5-9_i45


title: Whole_CA_RNA_cKO_2


title: pADamID_CTCF-WAPL_24h_Dam_r4

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 24h of IAA

tag: cell line

tag: cell type

value: Embyonic stem cell

tag: library type


title: vasadrop_E9.5-7_i43


title: PRE-R-010 [18R642_003]

tag: tissue

tag: time point


title: Whole_CA_RNA_cKO_1


title: pADamID_CTCF-WAPL_24h_Dam_r3

value: pA-DamID

tag: genetic modification


title: PRE-R-009 [18R685_018]

tag: treatment response


title: pADamID_CTCF-WAPL_24h_Dam_r1


title: vasadrop_E9.5-5_i28


title: Neuron_H3K9ac_Control_3

source_name: Hippocampal CA neurons

value: Control

value: Hippocampal CA neurons

tag: chip antibody

value: H3K9ac (Millipore 07-352)


title: pADamID_CTCF-WAPL_6h_Dam_r4

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 6h of IAA


title: Neuron_H3K9ac_Control_4

tag: age


title: Neuron_H3K9ac_Control_1


title: Neuron_H3K9ac_Control_2


title: pADamID_CTCF-WAPL_6h_Dam_r2


title: PAIR-R-016 [18R307_0013]

value: primary tumor (colorectum)

value: pre-treatment


title: PAIR-R-016 [18R309_0015]

value: liver metastases


title: PAIR-61 [18R319_0014]

value: pre-Tx


title: vasadrop_E9.5-2_i11


title: vasadrop_E9.5-3_i41


title: Neuron_H3K9ac_cKO_2

value: 4-6 month-old (adult)

value: Setd1b cKO


title: PAIR-R-015 [18R665_02]

value: post-Tx non-PD


title: pADamID_CTCF-WAPL_0h_Dam_r4

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 0h of IAA

value: OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry


title: vasadrop_E9.5-4_i27


title: vasadrop_E9.5-1_i10


title: pADamID_CTCF-WAPL_6h_Dam_r1


title: vasadrop_E8.5-9_i33

value: mouse embryo, E8.5


title: vasadrop_E9.5-6_i42

value: VASA-seq


title: Neuron_H3K9ac_cKO_1


title: PAIR-R-015 [18R664_01]

source_name: colorectal cancer


title: pADamID_CTCF-WAPL_0h_Dam_r3


title: vasadrop_E8.5-8_i21

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode


title: PAIR-R-017 [18R311_0018]

value: post-treatment

value: post-tx PD


title: POST-R-012 [18R663_027]


title: pADamID_CTCF-WAPL_0h_Dam_r2

value: Embyonic stem cell

value: pA-DamID


title: Neuron_H3K27ac_Control_4

value: Control

value: Hippocampal CA neurons

value: H3K27ac (Abcam ab4729)


title: vasadrop_E8.5-7_i20


title: PAIR-R-014 [18R306_0012]


title: Neuron_H3K27ac_Control_3


title: pADamID_CTCF-WAPL_6h_Dam_r3


title: Neuron_H3K27ac_Control_1


title: PAIR-R-014 [18R302_0004]

value: primary tumor (colorectum)

value: pre-treatment


title: PRE-R-008 [18R301_0002]

value: pre-Tx


title: pADamID_WAPL_96h_Dam_r3

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 96h of IAA

value: OsTir1; WAPL-AID-eGFP


title: Neuron_H3K9ac_cKO_4

value: 4-6 month-old (adult)

value: Setd1b cKO

value: H3K9ac (Millipore 07-352)


title: vasadrop_E8.5-6_i19

value: mouse embryo, E8.5


title: vasadrop_E8.5-5_i18

value: VASA-seq


title: Neuron_H3K27ac_cKO_4


title: vasadrop_E8.5-4_i8

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode


title: POST-R-011 [18R661_021]

value: post-treatment

value: post-Tx non-PD


title: Neuron_H3K27ac_cKO_3


title: vasadrop_E8.5-3_i17


title: pADamID_WAPL_96h_Dam_r2

value: Embyonic stem cell


title: POST-R-010 [18R659_020]


title: Neuron_H3K27ac_cKO_2


title: pADamID_WAPL_24h_Dam_r3

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 24h of IAA

value: pA-DamID


title: pADamID_WAPL_24h_Dam_r2


title: PAIR-R-013 [18R310_0016]

value: liver metastases

value: post-tx PD


title: vasadrop_E8.5-2_i16


title: PAIR-R-013 [18R300_0027]


title: vasadrop_E8.5-23_i40


title: pADamID_CTCF-WAPL_0h_Dam_r1

value: OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry


title: pADamID_WAPL_24h_Dam_r1


title: vasadrop_E8.5-22_i39


title: PRE-R-032 [18R456_002]

value: primary tumor (colorectum)


title: Neuron_H3K4me3_Control_3

value: Control

value: Hippocampal CA neurons

value: H3K4me3 (Abcam ab8580)


title: Neuron_H3K4me3_Control_4

value: 4-6 month-old (adult)


title: pADamID_WAPL_6h_Dam_r3

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 6h of IAA

value: OsTir1; WAPL-AID-eGFP


title: vasadrop_E8.5-21_i38


title: pADamID_WAPL_96h_Dam_r1


title: Neuron_H3K4me3_Control_2


title: PAIR-R-012 [18R304_0006]


title: vasadrop_E8.5-20_i37


title: pADamID_WAPL_6h_Dam_r2


title: PRE-R-006 [18R178_0022]

value: pre-treatment

value: pre-Tx


title: pADamID_WAPL_6h_Dam_r1


title: PRE-R-007 [18R177_0021]


title: Neuron_H3K4me3_Control_1


title: pADamID_WAPL_0h_Dam_r3

source_name: Dam control in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 0h of IAA


title: Neuron_H3K4me3_cKO_4

value: Setd1b cKO


title: Neuron_H3K27ac_cKO_1

value: H3K27ac (Abcam ab4729)


title: vasadrop_E8.5-19_i36

value: VASA-seq

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode

value: mouse embryo, E8.5


title: Neuron_H3K4me3_cKO_3


title: PRE-R-005 [18R176_0020]


title: Neuron_H3K4me3_cKO_2


title: pADamID_WAPL_0h_Dam_r2

value: Embyonic stem cell

value: pA-DamID


title: vasadrop_E8.5-17_i26


title: PAIR-39 [18R318_0005]

value: lung metastases

value: post-treatment

value: post-tx PD


title: vasadrop_E8.5-16_i25


title: PAIR-R-011 [18R179_0023]

value: liver metastases


title: pADamID_WAPL_0h_Dam_r1


title: PAIR-R-012 [18R299_0025]

value: primary tumor (colorectum)


title: Neuron_H3K4me3_cKO_1

value: Hippocampal CA neurons

value: H3K4me3 (Abcam ab8580)


title: vasadrop_E8.5-1_i7


title: Neuron_H3K4me1_Control_4

value: 4-6 month-old (adult)

value: Control

value: H3K4me1 (Abcam ab8895)


title: vasadrop_E8.5-15_i35


title: pADamID_CTCF_96h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 96h of IAA

value: OsTir1; CTCF-AID-eGFP


title: pADamID_CTCF_96h_Dam_r1


title: Neuron_H3K4me1_Control_3


title: pADamID_CTCF_24h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 24h of IAA


title: vasadrop_E8.5-14_i24


title: vasadrop_E8.5-13_i34


title: PAIR-R-010 [18R175_0011]


title: Neuron_H3K4me1_Control_2


title: vasadrop_E8.5-12_i23


title: Neuron_H3K4me1_Control_1


title: pADamID_CTCF_6h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 6h of IAA


title: vasadrop_E8.5-11_i9


title: pADamID_CTCF_24h_Dam_r1


title: PAIR-28 [18R297_0009]


title: PAIR-28 [18R294_0001]

value: pre-treatment

value: pre-Tx


title: pADamID_CTCF_6h_Dam_r1


title: Neuron_H3K4me1_cKO_4

value: Setd1b cKO


title: PAIR-R-008 [18R648_09]

value: post-Tx non-PD


title: pADamID_CTCF_0h_Dam_r2

source_name: Dam control in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 0h of IAA

value: Embyonic stem cell


title: Neuron_H3K4me1_cKO_3


title: vasadrop_E8.5-10_i22

value: VASA-seq

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode

value: mouse embryo, E8.5


title: PAIR-R-008 [18R647_08]


title: PAIR-32 [18R296_0008]


title: vasadrop_E7.5-7_i32

value: mouse embryo, E7.5


title: pADamID_CTCF_0h_Dam_r1

value: pA-DamID


title: Neuron_H3K4me1_cKO_2


title: pADamID_CTCF_GSK_24h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 24h of IAA


title: vasadrop_E7.5-6_i31


title: vasadrop_E7.5-5_i15


title: 10 Gy - #4

type: RNA

city: Hirosaki

first: Satoru

last: Monzen

state: Aomori

address: Hon-cho 66-1

country: Japan

institute: Hirosaki University

hyb_protocol: A SurePrint G3 human miRNA microarray slide (8 × 60 K, Ver.21.0) was hybridised with the Cy3-labelled miRNA in a hybridisation solution prepared with a Gene Expression Hybridisation Kit (Agilent Technologies, Inc.), following the manufacturer’s instructions.

scan_protocol: Cy3 fluorescence signal images on the slide were obtained by a microarray scanner (Agilent SureScan Microarray Scanner G 2600 D; Agilent Technologies, Inc.) and processed using the Feature Extraction version 10.7 software based on the instructions from Agilent Technologies.

data_processing:
The expression data were processed using GeneSpring GX14.5 software (Agilent Technologies, Inc.) to make a normalisation to percentile shift 90% of all values on the respective microarrays, followed by normalisation of the median expression level of all samples.
The lower raw data signals (lower cut off 50) were removed, and miRNA expression was normalised using some internal controls. In addition, the coefficient of variation was also set to <50.0% to remove miRNAs with large variations between experiments in advance.

source_name: extracellular microRNAs in HCT116

label_protocol: Cy3-labelled miRNA was synthesised from 100 ng total RNA of X-irradiated and non-irradiated cell culture supernatant using an miRNA Complete Labelling Reagent and Hyb kit (Agilent Technologies, Inc.).

extract_protocol: The sample that is small RNAs were extracted from cell culture supernatant using ISOGEN kit (NIPPON Gene Inc.)..

treatment_protocol: HCT116 cell was exposed from higher dose rate of X-irradiation and the after samples were incubated for 72 h in the condition of RPMI1640 medium with 10%FBS.

tag: molecule subtype

value: extracellular miRNA

tag: radiation dose

value: 10 Gy


title: PAIR-29 [18R295_0003]

value: primary tumor (colorectum)


title: Neuron_H3K4me1_cKO_1

value: 4-6 month-old (adult)

tag: genotype

value: Hippocampal CA neurons


title: pADamID_CTCF_GSK_24h_r1


title: 10 Gy - #3


title: vasadrop_E7.5-4_i6


title: 10 Gy - #2


title: POST-R-008 [18R688_021]

value: liver metastases

value: post-treatment

value: post-tx PD


title: vasadrop_E7.5-2_i5


title: POST-R-007 [18R682_014]


title: pADamID_CTCF_GSK_0h_r1

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 0h of IAA

value: OsTir1; CTCF-AID-eGFP


title: pADamID_CTCF_EED_24h_r2


title: vasadrop_E7.5-1_i4


title: PAIR-R-007 [18R305_0007]


title: 10 Gy - #1


title: vasadrop_E6.5-7_i13

value: mouse embryo, E6.5


title: pADamID_CTCF_EED_24h_r1


title: PRE-R-003 [18R430_010]

value: pre-treatment

value: pre-Tx


title: PAIR-04 [18R298_0010]


title: POST-R-009 [18R646_007]


title: PRE-R-002 [18R429_009]


title: pADamID_CTCF_GSK_0h_r2

value: Embyonic stem cell


title: PAIR-R-006 [18R700_08]


title: POST-R-006 [18R651_012]

value: lung metastases


title: 6 Gy - #1

value: 6 Gy


title: vasadrop_E6.5-6_i12

value: VASA-seq

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode


title: pADamID_CTCF_EED_0h_r1

value: pA-DamID


title: pADamID_CTCF_DMSO_24h_r2


title: 6 Gy - #2

value: extracellular miRNA


title: vasadrop_E7.5-3_i14

value: mouse embryo, E7.5


title: PAIR-R-006 [18R699_07]

value: primary tumor (colorectum)


title: vasadrop_E6.5-4_i30


title: 2 Gy - #4

value: 2 Gy


title: 6 Gy - #4


title: 2 Gy - #3


title: pADamID_CTCF_DMSO_24h_r1


title: POST-R-005 [18R697_05]

value: post-Tx non-PD


title: pADamID_CTCF_DMSO_0h_r2


title: 6 Gy - #3


title: POST-R-004 [18R694_02]

value: post-treatment


title: pADamID_CTCF_EED_0h_r2


title: pADamID_CTCF_DMSO_0h_r1


title: vasadrop_E6.5-1_i1


title: vasadrop_E6.5-5_i3


title: 2 Gy - #1


title: PAIR-R-005 [18R689_022]


title: PAIR-R-005 [18R690_023]

value: post-tx PD


title: WT_2y_4

city: Madrid

first: Santiago

middle: García

last: Martín

state: Madrid

address: Calle de Melchor Fernández Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Spanish National Cancer Research Centre

data_processing:
RNA data quality assessment was performed using FastQC v0.11.9
Adaptors were removed using Cutadapt v2.10
Tanscript abundances were quantified with salmon v.1.2.0.0 (Kingsford, 2017) in mapping  mode with selective alignment enabled using a predefined set of sequences as decoys.
Transcripts abundances were annotated against Mus musculus reference transcriptome GRCm38/mm10 ENSEMBL version 97 and summarized to the gene-level with tximeta v1.4.3
Summarized gene level transcript abundances were imported into DESeq2 v1.26.0 and normalized by executing the DESeq function
Genome_build: mm10
Supplementary_files_format_and_content: The matrix of normalized gene level counts was generated by DESeq2 normalization after aggregating salmon transcript abundances to the gene level, importing them into DESeq2 and executing the DESeq function.

source_name: Wildtype mouse, 2 years old

extract_protocol:
The RNA extraction was performed following the protocol of ArcturusTM PicoPureTM RNA isolation kit (Applied Biosystems). 4000-5000 cells were sorted directly in the 100ul of extraction buffer of the kit. Quality and quantity of RNA was measured using Agilent 4200 TapeStation System.
The libraries were prepared following the Smart-seq2 protocol. Following reverse transcription, the quality of the cDNAs was evaluated using an Agilent 2100 Bioanalyzer. 0,5 ng of cDNA from each sample were tagmented and amplified using Illumina Nextera XT kit. The resulting libraries were pooled, double-sided size selected (0.5x followed by 0.8x ratio using Beckman Ampure XP beads) and quantified using an Agilent 4200 TapeStation System. The pool of libraries was sequenced in an Illumina NovaSeq6000 sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.

value: Wild-type

value: 2 year

value: haematopoietic stem cells

tag: replicate


title: pADamID_RAD21_24h_r1

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 24h of IAA

value: OsTir1; RAD21-AID-eGFP


title: PAIR-R-004 [18R684_016]

value: liver metastases


title: WT_2y_3


title: 0 Gy - #3

value: 0 Gy


title: pADamID_RAD21_24h_r2

value: Embyonic stem cell


title: 0 Gy - #4


title: pADamID_RAD21_6h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 6h of IAA


title: vasadrop_E6.5-3_i29

tag: protocol/barcodes

value: VASA-seq

value: mouse embryo, E6.5


title: pADamID_RAD21_6h_r1

value: pA-DamID


title: 0 Gy - #1

value: extracellular miRNA


title: 0 Gy - #2


title: pADamID_RAD21_0h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; RAD21-AID-eGFP), after 0h of IAA


title: PRE-R-001 [18R678_010]

value: pre-treatment

value: pre-Tx


title: PAIR-R-004 [18R683_015]

value: primary tumor (colorectum)


title: 2 Gy - #2

value: 2 Gy


title: vasadrop_E6.5-2_i2

tag: read format

value: Read 1 starts with a 6-nucleotide long UFI, followed by an 16 nucleotide long cell-specific barcode


title: WT_2y_1


title: WT_2mo_4

source_name: Wild type mouse, 2 months old

value: 2 month


title: POST-R-003 [18R677_09]

source_name: colorectal cancer

value: other site metastases

value: post-treatment

value: post-tx PD


title: Tonsil 7 scATAC-seq

city: Stanford

first: Zohar

last: Shipony

state: CA

address: Beckman Center B-279A  279 Campus Drive West

institute: Stanford University

data_processing:
BaseCall files were used to generate FASTQ files with either cellranger mkfastq (v3; 10X Genomics) or cellranger-atac (v1; 10X Genomics) prior to running cellranger count with the cellranger-GRCh38-3.0.0 reference or cellranger-atac count the cellranger-atac-GRCh38-1.1.0 reference for scRNA-seq and scATAC-seq libraries respectively.
Genome_build: hg38; GRCh38-3.0.0 reference
Supplementary_files_format_and_content: tsv

extract_protocol:
Tonsil samples were collected from children and adults undergoing routine tonsillectomy. All participants provided written informed consent and the protocols were approved by Stanford University’s Institutional Review Board. Whole tonsils were collected in saline and processed within four hours of receipt. Tissues were treated with penicillin, streptomycin, and normocin for 30 minutes on ice and heavily clotted or cauterized areas of the tissue were removed. Tonsils were then dissected into small pieces (roughly 5-8 pieces per tonsil) before mechanical dissociation through a 100um cell strainer using a syringe plunger. Mononuclear cells were isolated by ficoll density gradient centrifugation (GE Healthcare) and the buffy coats were collected. Cells were cryopreserved in 90% fetal bovine serum, 10% DMSO until use.
Libraries were contructed following the 10X scATAC and scRNA protocols

tag: subject status

value: tonsil


title: Tonsil 6 scATAC-seq

value: children and adults undergoing routine tonsillectomy


title: WT_2mo_3

value: Wild-type

value: haematopoietic stem cells


title: pADamID_PT_0h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1), after 0h of IAA

value: Embyonic stem cell


title: WT_2y_2

value: 2 year


title: Tonsil 5 scATAC-seq


title: WT_2mo_2


title: PAIR-R-003 [18R674_06]


title: WT_2mo_1


title: pADamID_PT_0h_r1

value: pA-DamID


title: PAIR-R-002 [18R671_03]

value: liver metastases

value: post-Tx non-PD


title: Tonsil_3b_scATC_seq


title: WT_1y_5

source_name: Wild type mouse, 1 year old

value: 1 year


title: Tonsil 4 scATAC-seq


title: PAIR-R-002 [18R670_02]

value: primary tumor (colorectum)

value: pre-Tx


title: pADamID_CTCF-WAPL_96h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 96h of IAA

value: OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry


title: Tonsil_3a_scATC_seq


title: pADamID_CTCF-WAPL_24h_r4

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 24h of IAA


title: WT_1y_3


title: pADamID_CTCF-WAPL_96h_r1


title: pADamID_RAD21_0h_r1

value: OsTir1; RAD21-AID-eGFP


title: PAIR-R-001-pre  [18R654_15]

value: pre-treatment


title: PAIR-R-003 [18R675_07]

value: peritoneal metastases

value: post-treatment


title: PAIR-R-001 [18R655_016]

value: post-tx PD


title: Tonsil_2b_scATC_seq

value: children and adults undergoing routine tonsillectomy

value: tonsil


title: Tonsil_2a_scATC_seq


title: pADamID_CTCF-WAPL_24h_r3


title: POST-R-001 [18R649_010]


title: WT_1y_1

value: Wild-type

value: haematopoietic stem cells


title: Tonsil_1b_scATC_seq


title: Tonsil_1a_scATC_seq


title: IL1RIKO_2y_5

source_name: IL1RIKO mouse, 2 years old

value: IL1R1 KO

value: 2 year


title: IL1RIKO_2y_4


title: pADamID_CTCF-WAPL_24h_r1

value: Embyonic stem cell

value: pA-DamID


title: pADamID_CTCF-WAPL_96h_r3


title: RNA_H1299_WT_Re2

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using RNA STAR (Galaxy website) with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq, and "-z 5 -w 10" for RNA-seq.
The gene expression profiling was analyzed by HOMER software
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) for ChIP-seq and RNA-seq samples.

growth_protocol: The human lung cancer H1299 cell lines were grown in DMEM (Gibco) medium supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Total RNAs were extrated using Quick-RNA  Miniprep kit (Zymo Research) and subjected to RNA-seq service provided by Genomic Core of University of North Carolina, USA . Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with indicated antibodies followed by purification with PCR purification kit (Qiagen). The  isolated genomic DNA were subjected to high throughput sequencing service provided by the genomic core facility of Nation Yang Ming Chiao Tung University, Taiwan.
Multiplexing libraries were prepared for sequencing using Illumina TruSeq Rapid SR Cluster Kit according to the standard protocol.

treatment_protocol: Cells were harvested at 80% confluency. For ChIP-seq, cell were fixed with 1% formaldehyde at room temp followed by quencing with 125 mM Glycine.

value: non-small cell lung cancer

value: WT


title: pADamID_CTCF-WAPL_6h_r4

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 6h of IAA


title: RNA_H1299_WT_Re1


title: pADamID_CTCF-WAPL_6h_r3


title: POST-R-002 [18R669_01]

value: primary tumor (colorectum)

value: post-Tx non-PD


title: WT_1y_4

value: 1 year


title: IL1RIKO_2y_3


title: Tonsil_3a_scRNA_seq


title: WT_1y_2


title: pADamID_CTCF-WAPL_6h_r1

value: OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry


title: pADamID_CTCF-WAPL_6h_r2


title: IL1RIKO_2y_1


title: Tonsil_2b_scRNA_seq


title: Tonsil_2a_scRNA_seq


title: pADamID_CTCF-WAPL_0h_r4

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP; CTCF-AID-mCherry), after 0h of IAA


title: IL1RIKO_2mo_3

source_name: IL1RIKO mouse, 2 months old

value: 2 month


title: Tonsil_1b_scRNA_seq


title: RNA_H1299_KO2_Re1


title: RNA_H1299_KO1_Re2


title: RNA_H1299_KO1_Re1


title: RNA_H1299_KO2_Re2


title: pADamID_CTCF-WAPL_0h_r3


title: IL1RIKO_2mo_2


title: IL1RIKO_2mo_1


title: DNA_H1299_WT_input


title: Tonsil_1a_scRNA_seq


title: Tonsil_3b_scRNA_seq


title: DNA_H1299_WT_IgG

value: normal rabit IgG


title: IL1RIKO_1y_4

source_name: IL1RIKO mouse, 1 year old


title: Human Donor Lung 86

city: San Francisco

first: Seoyeon

last: Lee

address: 513 Parnassus Ave HSE 1355B

department: Pulmonary and Critical Care Medicine

institute: University of California, San Francisco

data_processing:
Raw reads were aligned and gene counts generated with STAR v2.7.1a to the HG38 human genome and the Ensembl gene build v95 with the following parameters: --outSAMtype BAM   Unsorted      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC      --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJDBoverhangMin 1   --quantMode GeneCounts
Individual sample counts matrix were merged using custom python scripts and used as input to DESeq2 1.24.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with DESeq2 normalized gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Snap-frozen lungs were homogenized in Qiazol reagent. RNA was extracted using the miRNeasy Mini Kit (Qiagen).
First the mRNA was randomly fragmented; after cDNA first strand synthesis, second strand was generated by nick-translation, followed by purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment.

value: distal lung


title: pADamID_CTCF-WAPL_0h_r1


title: Human Donor Lung 85


title: DNA_H1299_WT2_H3K27Ac

value: anti-H3K27ac (ab4729, Abcam)


title: IL1RIKO_1y_3


title: pADamID_WAPL_96h_r3

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 96h of IAA

value: OsTir1; WAPL-AID-eGFP


title: DNA_H1299_WT1_H3K27Ac


title: IL1RIKO_1y_2


title: IL1RIKO_2y_2


title: Human Donor Lung 83


title: Human Donor Lung 84


title: pADamID_WAPL_96h_r2


title: pADamID_WAPL_96h_r1


title: IL1RIKO_1y_1


title: Human Donor Lung 82


title: Human Donor Lung 81


title: pADamID_CTCF-WAPL_0h_r2


title: GF_2mo_3

source_name: Bowel germ free mouse, 2 months old

value: Gerfm free


title: pADamID_WAPL_24h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 24h of IAA


title: pADamID_WAPL_24h_r3


title: mock_pub2pub4_rep3

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

data_processing:
TopHat 2.1.0 software (Trapnell, Pachter and Salzberg, 2009) was used to map the reads to the Arabidopsis genome (TAIR10). RSEM 2.1.30 (Anders, Pyl and Huber, 2015) was used for statistical analysis of the read counts for each gene.
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: files including all counts of samples

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: 16-h-light/8-h-dark cycle

extract_protocol: RNA was extracted using the Agilent Plant RNA Isolation Mini kit according to the manufacturer’s instructions. Bar-coded mRNA libraries were constructed by BGI (Shenzhen, China) using the Illumina’s reagents and protocols according to the manufacturer’s instruction. Samples were sequenced on Illumina HiSeq 2500 system.

value: leaf


title: mock_pub2pub4_rep2


title: Human Donor Lung 80


title: DNA_H1299_USP7KO1_H3K27Ac


title: GF_2mo_1

value: haematopoietic stem cells


title: pADamID_WAPL_24h_r1


title: Human Donor Lung 79


title: mock_pub2pub4_rep1


title: DNA_H1299_USP7KO2_H3K27Ac


title: pADamID_WAPL_6h_r3

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 6h of IAA


title: GF_1y_2

source_name: Bowel germ free mouse, 1 year old


title: Human Donor Lung 78


title: GF_2mo_2


title: GF_1y_1


title: Human Donor Lung 77


title: pADamID_WAPL_6h_r2


title: mock_wt_rep2


title: pADamID_WAPL_6h_r1


title: Day_6_ENR+CD+KPT-330 [D6_KPT_2]

city: Cambridge

first: Benjamin

middle: E

last: Mead

state: MA

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

description: UMI-collapsed DGE matrix

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
Alignment, barcode-, UMI-collapse to digital gene expression (DGE) matricies performed using DropSeqTools v2.1.0
DGEs were megred, cell barcodes were QC filtered and cell doublets removed using R script "Merge&QC_All_samples.R" and associated tables & QC R scripts referenced within & provided
Genome_build: mm11
Supplementary_files_format_and_content:
digital gene expression matricies (raw UMI-collapsed reads cell barcode x gene name) as .txt.gz files
All_merged_QC.txt.gz: Merged & QC-filtered UMI DGE Matrix from all samples

extract_protocol: Seq-Well Protocol: Samples were processed as described in Hughes T.K. et al.,  bioRxiv,  2019, full protocol available at http://shaleklab.com/resource/seq-well

value: small intestinal organoid

tag: exposure

tag: time point (day)


title: mock_wt_rep3


title: Human Donor Lung 76


title: mock_wt_rep1


title: Min6 cells, FoxOi_Loperamide_3

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Min6 cells, FoxOi_Loperamide

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen), including DNase treatment, following the manufacturer’s instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 4000 instrument using 50 bp single-read chemistry.

tag: cell line

tag: cell type

value: beta cell

tag: treatment

value: 48h 1µM FoxOi + 5µM Loperamide


title: Day_6_ENR+CD+KPT-330 [D6_KPT_1]

description: UMI-collapsed DGE matrix


title: pADamID_WAPL_0h_r3

data_processing:
Library strategy: pA-DamID
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 10kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts. Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files of "raw" log2-normalized LaminB1 pADamID scores for 10kb genomic bins; tsv files with genomic coordinates and all z-scores per replicate / average scores per condition.

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 0h of IAA

value: Embyonic stem cell

tag: library type

value: pA-DamID

tag: time point


title: Human Donor Lung 75

tag: tissue


title: Human Donor Lung 74


title: Min6 cells, FoxOi_Loperamide_2


title: pADamID_WAPL_0h_r2

tag: genetic modification


title: pADamID_WAPL_0h_r1


title: Day_6_ENR+CD [D6_CTRL_1]

description: UMI-collapsed DGE matrix

value: ENR+CD


title: Day_6_ENR+CD [D6_CTRL_2]

description: UMI-collapsed DGE matrix


title: Min6 cells, Loperamide_2

source_name: Min6 cells, Loperamide

value: 48h 5µM Loperamide


title: pADamID_CTCF_96h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 96h of IAA

value: OsTir1; CTCF-AID-eGFP


title: Human Donor Lung 73

tag: age


title: Min6 cells, Loperamide_3


title: Day_4_ENR+CD+KPT-330 [D4_KPT_2]

description: UMI-collapsed DGE matrix


title: pADamID_CTCF_96h_r1


title: Human Donor Lung 72


title: pADamID_CTCF_24h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 24h of IAA


title: Min6 cells, Loperamide_1


title: Day_4_ENR+CD [D4_CTRL_2]

description: UMI-collapsed DGE matrix


title: Min6 cells, FoxOi_Loperamide_1


title: Day_3_ENR+CD+KPT-330 [D3_KPT_1]

description: UMI-collapsed DGE matrix


title: Min6 cells, FoxOi_3

source_name: Min6 cells, FoxOi

value: 48h 1µM FoxOi


title: Day_3_ENR+CD+KPT-330 [D3_KPT_2]

description: UMI-collapsed DGE matrix


title: Human Donor Lung 70


title: Human Donor Lung 71


title: pADamID_CTCF_24h_r1


title: Human Donor Lung 69


title: Day_3_ENR+CD [D3_CTRL_2]

description: UMI-collapsed DGE matrix


title: Min6 cells, FoxOi_1


title: Human Donor Lung 68


title: Min6 cells, FoxOi_2


title: Min6 cells, DMSO_3

source_name: Min6 cells, DMSO

value: 48h DMSO


title: pADamID_CTCF_6h_r1

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 6h of IAA


title: Day_2_ENR+CD [D2_CTRL_2]

description: UMI-collapsed DGE matrix


title: Day_2_ENR+CD+KPT-330 [D2_KPT_2]

description: UMI-collapsed DGE matrix


title: pADamID_CTCF_0h_r2

source_name: LaminB1 pA-DamID in E14TG2a (with OsTir1; CTCF-AID-eGFP), after 0h of IAA


title: pADamID_CTCF_0h_r1


title: Human Donor Lung 65


title: Day_1_ENR+CD [D1_CTRL_1]

description: UMI-collapsed DGE matrix


title: Human Donor Lung 66


title: naïve B cells aPIK3CD rep4

city: Seattle

first: David

middle: J

last: Rawlings

address: 1900 9th Ave

institute: Seattle Children's Research Institute

data_processing:
Cells were sorted directly into reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed, followed by PCR amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads
Genome_build: The FASTQs were aligned to the mouse reference genome, using STAR v.2.4.2a
Supplementary_files_format_and_content: and gene counts were generated using htseq-count. QC and metrics analysis was performed using the Picard family of tools (v1.134).

source_name: Spleen

extract_protocol:
500 cells were sorted directly into reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were immunized with NP-CGG/alum i.p. and sorted 14 days post immunization for RNAseq

tag: strain

value: Spleen

value: AID-cre aPIK3CD

value: 12 weeks

value: 14 days post NP-CGG immun


title: Day_1_ENR+CD+KPT-330 [D1_KPT_1]

description: UMI-collapsed DGE matrix


title: Min6 cells, DMSO_1


title: pADamID_CTCF_6h_r2

extract_protocol:
1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a LaminB1 antibody and for a Dam control condition, to specifically deposit m6A marks at peripherally positioned chromatin. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified with 15-19 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters.


title: plasma cells aPIK3CD rep4


title: Day_0_ENR+CV [D0_ENRCV_2]

description: UMI-collapsed DGE matrix

value: ENR+CV


title: Human Donor Lung 64

source_name: Lung

value: distal lung


title: dark zone aPIK3CD rep4


title: Human Donor Lung 62


title: Human Donor Lung 63


title: Day_0_ENR+CV [D0_ENRCV_1]

description: UMI-collapsed DGE matrix


title: light zone aPIK3CD rep4


title: Human Donor Lung 67


title: Day_0.25_ENR+CD+KPT-330 [D025_KPT_1]

description: UMI-collapsed DGE matrix


title: Human Donor Lung 61


title: Min6 cells, DMSO_2


title: naïve B cells aPIK3CD rep3


title: PARP1 KO cortex rep 2

city: Ann Arbor

first: GABRIEL

last: CORFAS

state: MI

address: U of M Kresge Hearing Research Institute 1150 West Medical Center Drive Medical Sciences I Building, Rm. 5428

institute: The University of Michigan, Kresge Hearing Research Institute

data_processing:
Fastq reads were converted into sanger reads with FASTQ Groomer. Reads were mapped to the mouse genome (mm9) using HISAT. Read counts were obtained with Htseq-count.
Differential gene expression between genotypes was obtained with DeSeq2
Genome_build: mm9
Supplementary_files_format_and_content: raw gene counts for every gene per sample

molecule: polyA RNA

source_name: PARP1 KO cortex

extract_protocol:
Cortices were dissected and stored in RNAlater until lysis. RNA was extracted with Qiagen Rneasy kit with on-column DNase digestion, following the manufacturer's protocol.
cDNA library preparation was performed by the University of Michigan DNA sequencing core using standard Illumina protocols.

value: cortex

value: PARP1 -/-


title: Day_0.25_ENR+CD [D025_CTRL_1]

description: UMI-collapsed DGE matrix

value: small intestinal organoid


title: Human Donor Lung 60


title: PARP1 KO cortex rep 1


title: Human Donor Lung 59


title: plasma cells aPIK3CD rep3


title: WT cortex rep 4

source_name: WT cortex

value: WT


title: PARP1 KO cortex rep 4


title: QSC_sgMyc_rep1

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

institute: The Chinese University of Hong Kong

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Skeletal muscle

extract_protocol:
RNA from quiescent muscle stem cells was harvested using Trizol reagent.
Purified mRNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added. RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.

value: quiescent muscle stem cell

value: 6-8 weeks


title: QSC_sgMyc_rep2


title: Human Donor Lung 57


title: WT cortex rep 2


title: light zone aPIK3CD rep3


title: PARP1 KO cortex rep 3


title: QSC_Ct_rep2


title: dark zone aPIK3CD rep3


title: WT cortex rep 3


title: QSC_Ct_rep1


title: WT cortex rep 1


title: HiC_KO_Q_rep3

data_processing:
The in-situ Hi-C data was processed following a standard pipeline Hi-C-Pro. Briefly, the reads were aligned to reference genome (mm9) in two steps: global alignment was first performed for all pair-end reads; unaligned reads were then trimmed by restriction enzyme and aligned again.
All aligned reads were then merged together to assign to restriction fragment. In this step, invalid fragments (dangling end, self-cycle etc.) were discarded and PCR duplications were removed for each biological replicate separately.
At last, all validate pairs were merged for each condation and then normalized by read depth using HOMER followed by ICE matrix balancing to further get interaction matrix.
Genome_build: mm9

extract_protocol:
Genomic DNA was extracted by QuickExtract (Epicentre) solution.
DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification

value: Quiescent muscle stem cell

value: post natal day 38


title: Human Donor Lung 55


title: Human Donor Lung 56


title: plasma cells aPIK3CD rep2


title: naïve B cells aPIK3CD rep2


title: light zone aPIK3CD rep2


title: Neuron_RNA_Control_2

source_name: Hippocampal CA neurons

value: 4-6 month-old (adult)

value: Control

value: Hippocampal CA neurons


title: HiC_KO_Q_rep2


title: Human Donor Lung 54


title: Human Donor Lung 58


title: dark zone aPIK3CD rep2

value: Spleen


title: HiC_Ct_Q_rep2


title: Human Donor Lung 53


title: HiC_KO_Q_rep1


title: Neuron_RNA_cKO_3

value: Setd1b cKO


title: Neuron_RNA_Control_1


title: Neuron_RNA_Control_3


title: Human Donor Lung 52


title: Neuron_RNA_cKO_2


title: Neuron_RNA_cKO_1


title: HiC_Ct_Q_rep1


title: dark zone aPIK3CD rep1

value: AID-cre WT

value: 12 weeks


title: Human Donor Lung 51


title: plasma cells aPIK3CD rep1

value: 14 days post NP-CGG immun


title: Human Donor Lung 49

value: distal lung


title: DEEP_br3_myod

description: MyoD_deep seq_rep3

data_processing:
Library strategy: Deep-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and reads without primer(Fwd:5'-AGTTAAGACGACTCTCACGG-3' and Rev:AGGCCTCATTCACTTTGCTC) are removed,then mapped to mm9 and conduct editting pattern using CRISPResso2 with parameter -w 20 --max_paired_end_reads_overlap 150 --amplicon_min_alignment_score 40 --min_identity_score 40
Genome_build: mm9
Supplementary_files_format_and_content: folder(with all CRISPResso2 output files inside)

extract_protocol:
Genomic DNA was extracted by QuickExtract (Epicentre) solution.
Genomic DNAs from AAV9-sgRNA infected satellite cells were amplified using Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified through QIAQuick PCR purification kit (Qiagen) and subjected to library preparation using NEBNext® Ultra™ II DNA Library Preparation Kit (NEB).

value: Freshly isoalted muscle stem cell


title: plasma cells WT rep4


title: light zone aPIK3CD rep1


title: DEEP_br2_myod

description: MyoD_deep seq_rep2


title: DEEP_br1_myod

description: MyoD_deep seq_rep1


title: naïve B cells WT rep4


title: DEEP_br1_pknox2

description: Pknox2_deep seq_rep1


title: naïve B cells aPIK3CD rep1


title: DEEP_br1_myc

description: Myc_deep seq_rep1


title: DEEP_br1_bcl6

description: Bcl6_deep seq_rep1


title: Human Donor Lung 48


title: Human Donor Lung 47


title: light zone WT rep4


title: Human Donor Lung 50


title: Human Donor Lung 45


title: Human Donor Lung 46


title: dark zone WT rep4


title: plasma cells WT rep3


title: light zone WT rep3


title: Human Donor Lung 44


title: Human Donor Lung 42


title: Human Donor Lung 43


title: naïve B cells WT rep3


title: dark zone WT rep3


title: Human Donor Lung 41


title: S2-3

city: shanghai

first: Jianmin

last: Guo

state: Yangpu District

address: No 399 changhai street

institute: shanghai university of sport

hyb_protocol: Agilent one-color RNA Spike-in kit was used for hybridization according to the manufacturer's instruction.

scan_protocol: Agilent chip scanner (G2565CA) was used to scan the cleaned chip.

data_processing: Agilent Feature Extraction (v10.7) software was used to analyze hybridization images and extract data.  Agilent GeneSpring software was used to normalize and analyze the data.

source_name: Bone tissue of sham operation mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from Cy3-dCTP(GE Healthcare)according to the manufacturer's instructions, followed by RNAeasy column purification (Nucleospin® Extract II, MN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA of the bone was prepared using the Trizol reagent(Invitrogen)following the manufacturer's recommendations.

treatment_protocol: The speed was set at 6 m/min for 30 min for the 1st week (which comprised 5 days of exercise followed by 2 days of rest) to allow the mice to become familiarized with the exercise regime. From the 2nd week, all the mice performed a 5 min warm-up exercise at a speed of 6 m/min with a 25° slope, followed by a 55 min running exercise at a speed of 8 m/min with a 25° slope. Subsequently, the running exercise speed was increased by 1 m/min each week leading up to the completion of the treadmill running program after a total of 9 weeks (culminating in a running speed of 15 m/min with a 25° slope for the last training week)

value: bone tissue

tag: gender

value: female


title: naïve B cells WT rep2

tag: genotype


title: MyoD_single_low dose_deep seq_rep1

data_processing:
Library strategy: Deep-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and reads without primer or low-quality sequence are removed,then mapped to mm9 and conduct editting pattern using CRISPResso with parameter -w 15 -p 12 --save_also_png --keep_intermediate
Genome_build: mm9
Supplementary_files_format_and_content: folder(with all CRISPResso2 output files inside)


title: MyoD_single_mid dose_deep seq_rep2


title: MyoD_single_mid dose_deep seq_rep3


title: MyoD_single_low dose_deep seq_rep2


title: MyoD_single_mid dose_deep seq_rep1


title: MyoD_single_low dose_deep seq_rep3


title: light zone WT rep2


title: Human Donor Lung 39


title: Human Donor Lung 40


title: dark zone WT rep2


title: CD11c+Dcir-/- cells 3

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

institute: Tohoku Medicine and Pharmaceutical University

description: Sample 6

data_processing:
The raw sequenceing data were processed using TrimGalore v0.6.6 to remove adapter sequences and low-quality reads.
The processed reads were alined to the mouse genome reference mm10 using hisat2 v2.2.0.
Aligned read counts were caluculated by R package Rsubread v1.32.4.
Genome_build: mm10
Supplementary_files_format_and_content: An Excel file include differential gene values and p-value.

source_name: splenic DCs

extract_protocol:
CD11c+ cells were  separated with an autoMACS separator and total RNA was harvested using NucleoSpin (takara). The quality of RNA was determned by the TapeStation system. 25 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using a MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech).

value: spleen

value: 3-day culture

value: Dcir-/-


title: MyoD_single_high dose_deep seq_rep2


title: naïve B cells WT rep1


title: CD11c+Dcir-/- cells 2

description: Sample 5


title: MyoD_single_high dose_deep seq_rep1


title: Human Donor Lung 35


title: plasma cells WT rep1


title: MyoD_Ctrl_high dose_deep seq_rep3


title: Human Donor Lung 36


title: CD11c+Dcir-/- cells 1

description: Sample 4


title: CD11c+ WT cells 3

description: Sample 3

value: wild type


title: light zone WT rep1


title: plasma cells WT rep2


title: Human Donor Lung 38


title: Human Donor Lung 34


title: Human Donor Lung 37


title: Human Donor Lung 33


title: CD11c+ WT cells 2

description: Sample 2


title: MyoD_Ctrl_high dose_deep seq_rep1

value: post natal day 38


title: MyoD_Ctrl_high dose_deep seq_rep2


title: MyoD_dual_deep seq_rep3


title: TCR-Lung-MB-SIY

first: Amanda

middle: Margarita

last: Cruz

address: 500 Main Street, 76-431

department: Biology

description: SIY- CD8 V(D)J Sequences

data_processing:
Library strategy: VDJ
Demultiplexing, alignment to the mm10 genome (VDJ sequencing data was aligned to the prebuilt mouse GRCm38/mm10 VDJ reference supplied by 10X Genomics, version 3.1.0), and barcode/UMI counting were performed with 10X Genomics Cell Ranger v3.1.0. The resultant raw counts matrix was loaded into Seurat v3.2.2 for further processing. Cells expressing less than 100 genes or more than 4000 genes, as well as cells expressing more than 5% mitochondrial transcripts were excluded. Additionally, cell hashing data was utilized to remove cells called as doublets. RNA expression data was normalized using the Seurat LogNormalize function with the default scale factor of 10,000. Cell hashing counts were normalized by Centered Log Ratio (CLR) transformation at a positive quantile threshold of 0.98. All reported normalized counts were extracted from the data slot of the Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with normalized, log-transformed matrix from Seurat v3.2.2
Supplementary_files_format_and_content: mtx file with raw counts matrix from CellRanger v3.1.0

source_name: Sorted CD44+ CD8[alpha]+ SIYRYYGL+ cells from tumor-bearing lung of 5 week KP LucOS mice

extract_protocol:
Tumor-bearing lung tissue was collected 5 weeks post-tumor initiation from ten KP LucOS mice. Single cell suspensions were labeled with TotalSeq-C hashtag antibodies and FACS sorted for CD44+ CD8α+ SIINFEKL+ and CD44+ CD8α+ SIYRYGGL+ T cells.
10X Genomics Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1; 10X Genomics Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell. Gene expression libraries for SIINFEKL and SIYRYYGL were sequenced individually using HiSeq X (Illumina). VDJ and hashtag barcode libraries were sequenced with HiSeq 2500 (Illumina).

treatment_protocol: Lentiviruses expressing Cre recombinase and LucOS antigens were injected intratracheally into KrasLSL-G12D; p53fl/fl mice to initiate lung adenocarcinomas.

value: KrasLSLG12D; p53fl/fl


title: FBC-Lung-MB-SIY

description: SIY- CD8 T Cell Hashing

data_processing:
Library strategy: Hashtag barcode
Demultiplexing, alignment to the mm10 genome (VDJ sequencing data was aligned to the prebuilt mouse GRCm38/mm10 VDJ reference supplied by 10X Genomics, version 3.1.0), and barcode/UMI counting were performed with 10X Genomics Cell Ranger v3.1.0. The resultant raw counts matrix was loaded into Seurat v3.2.2 for further processing. Cells expressing less than 100 genes or more than 4000 genes, as well as cells expressing more than 5% mitochondrial transcripts were excluded. Additionally, cell hashing data was utilized to remove cells called as doublets. RNA expression data was normalized using the Seurat LogNormalize function with the default scale factor of 10,000. Cell hashing counts were normalized by Centered Log Ratio (CLR) transformation at a positive quantile threshold of 0.98. All reported normalized counts were extracted from the data slot of the Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with normalized, log-transformed matrix from Seurat v3.2.2
Supplementary_files_format_and_content: mtx file with raw counts matrix from CellRanger v3.1.0

value: Sorted CD44+ CD8[alpha]+ SIYRYYGL+ cells


title: CD11c+ WT cells 1

description: Sample 1


title: dark zone WT rep1


title: patient_NSC040_tumor

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: polyA RNA

data_processing:
Transcripts were mapped to the mouse transcriptome following an established bioinformatics pipeline (https://github.com/indrops/indrops) for inDrop experiments to create a raw gene-cell counts matrix (Klein et al, Cell, 2015) with the slight modification of adding an additional filtering step to remove lower quality base calls using Trimmomatic (v0.36, [45]) with the parameters “LEADING:28 SLIDINGWINDOW:4:26 MINLEN:15” after the “identifying abundant barcodes” step. Human and mouse samples were processed in a similar manner except mice samples were aligned to GRCm38.81 and human to GRCh38.91.
Genome_build: GRCm38.81(mouse), GRCh38.91(human)
Supplementary_files_format_and_content: Gene_vs_Cell raw counts matrix (single cell matrix)

source_name: non-small cell lung tumor

extract_protocol:
Human lung tumor tissue was dissociated for single cell RNA sequencing using the Tumor Dissociation kit by Miltenyi Biotec (cat. no. 130-095-929). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2-4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the gentleMACS Octo Dissociator and run using the “37_h-TDK2” program. After termination of the program, the cells were spun down at 300 x g for 10 min at 4°C, resuspended in RPMI-2% FBS, passed through a 70µm strainer and centrifugation was repeated. The cell pellet was treated with 1 ml ACK solution for 7 min at room temperature, the lysis stopped with 4 ml RPMI-2% FBS. After centrifugation, the cells were resuspended in 1 ml of RPMI-2 % FBS and passed through a cell strainer to obtain a single-cell suspension. Immediately before transcriptome barcoding using the inDrop platform, cells were pelleted at 300 x g for 5 min at 4°C in a swing-bucket rotor, gently resuspended in 1x PBS with 0.1% w/v BSA, manually counted on a hemocytometer and diluted to 100 k cells/ml. The final cell suspension included 15% v/v OptiPrep (Sigma-Aldrich, cat. no. D1556).
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols, with modifications summarized in Table S6 of Zilionis et al., 2019 (related to this GEO record).

tag: disease state

value: Non-small-cell lung carcinoma (NSCLC)

value: non-small cell lung tumor

value: F

tag: stage aj cc 8th ed

tag: purification

value: RBC-depletion


title: Human Donor Lung 32


title: TCR-Lung-MB-SIIN

description: SIIN- CD8 V(D)J Sequences

source_name: Sorted CD44+ CD8[alpha]+ SIINFEKL+ cells from tumor-bearing lung of 5 week KP LucOS mice


title: O1-2

source_name: Bone tissue of exercised ovariectomized mice


title: MyoD_dual_deep seq_rep2


title: S1-2

source_name: Bone tissue of exercised sham operation mice


title: MyoD_dual_deep seq_rep1


title: O1-1


title: patient_NSC037_tumor

description: polyA RNA


title: Human Donor Lung 29


title: patient_NSC036_tumor

description: polyA RNA


title: MyoD_single_deep seq_rep3


title: FBC-Lung-MB-SIIN

description: SIIN- CD8 T Cell Hashing

value: Sorted CD44+ CD8[alpha]+ SIINFEKL+ cells


title: S2-1


title: O2-3

source_name: Bone tissue of ovariectomized mice


title: S2-2


title: O2-1


title: O1-3


title: S1-3


title: Human Donor Lung 31


title: Human Donor Lung 28


title: Tom3

city: Portland

first: Mara

last: Sherman

state: OR

address: 2730 SW Moody Avenue CL6C

institute: Oregon Health & Science University

data_processing:
Reads trimmed using default paramters of Trim Galore! Version 0.4.3
Trimmed reads aligned to mouse reference genome GRCm38 release 87 using STAR 2.5.2b
Genes quantified using the STAR GeneCounts module
Unstranded gene counts used for downstream analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: gene expression read count file

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: FC1199 murine pancreatic cancer cells were injected into pancreas tissue of C57BL/6J Rosa-mTmG; Fabp4-Cre hosts at 8 weeks of age, and tumors developed without intervention for 4 weeks.

extract_protocol:
Tumors were removed, digested to yield a single-cell suspension, Podoplanin-positive cells were sorted into GFP-positive and Tomato-positive fractions, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 150 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rosa-mTmG; Fabp4-Cre in C57BL/6J background

value: Pancreas

value: Pancreatic ductal adenocarcinoma

value: Tomato+ (non-stellate cell-derived) CAFs

value: 12 weeks


title: GFP3

value: GFP+ (stellate cell-derived) CAFs


title: Human Donor Lung 27

data_processing:
Raw reads were aligned and gene counts generated with STAR v2.7.1a to the HG38 human genome and the Ensembl gene build v95 with the following parameters: --outSAMtype BAM   Unsorted      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC      --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJDBoverhangMin 1   --quantMode GeneCounts
Individual sample counts matrix were merged using custom python scripts and used as input to DESeq2 1.24.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with DESeq2 normalized gene counts for every gene and every sample

value: distal lung


title: O2-2

value: bone tissue

value: female


title: S1-1


title: MyoD_Ctrl_mid dose_deep seq_rep3

value: Freshly isoalted muscle stem cell

value: post natal day 38


title: Human Donor Lung 30


title: patient_NSC035_tumor

description: polyA RNA

value: M


title: patient_NSC021_tumor_nodule1

description: polyA RNA

value: Non-small-cell lung carcinoma (NSCLC)


title: MyoD_single_deep seq_rep1


title: GFP2


title: patient_NSC021_tumor_nodule2

description: polyA RNA

value: non-small cell lung tumor


title: Tom2


title: MyoD_single_high dose_deep seq_rep3


title: MyoD_Ctrl_mid dose_deep seq_rep2


title: Human Donor Lung 26


title: MyoD_single_deep seq_rep2


title: MyoD_Ctrl_mid dose_deep seq_rep1


title: Human Donor Lung 25


title: Human Donor Lung 24


title: patient_NSC020_tumor_nodule1

description: polyA RNA


title: GFP1


title: ASC_ChIP-seq_input

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, then mapped to mm9 whole genome using bowtie2 v2.2.3 with  default parameters
Duplication reads are removed by picard with default parameters,and then merged alignment files are used to call peaks by MACS2 with q-value equal to 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files are generateed by homer

growth_protocol: Freshly isolated muscle stem cells were cultured in growth medium containing F10, 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for 24h.

extract_protocol:
Chromatin from freshly isolated or activated muscle stem cells were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end or single-end ChIP-seq procedure. After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

value: Actiavetd muscle stem cells

value: 6-8 weeks


title: ASC_ChIP-seq_rep2


title: patient_NSC019_tumor_nodule2

description: polyA RNA

value: F

value: RBC-depletion


title: patient_NSC019_tumor_nodule1

description: polyA RNA


title: sEVs derived from senescent HDFs

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

institute: Korea Univ.

data_processing:
Sequence reads mapped by bowtie2 software to obtain alignment file.
Read counts mapped on mature miRNA sequence extracted from alignment file using bedtools (v2.25.0) and R (version 3.2.2).
Read counts used to determine miRNA expression levels.
Genome_build: Mature miRNA sequences available on miRBase was used as reference for mapping.
Supplementary_files_format_and_content: Excel files contain gene symbol, gold change, normalized data, raw data, mature id, sequence names, start, end, width, strand, type, alias, derives from, sequence, and target prediction based on miRBase search.

source_name: skin

growth_protocol: Human dermal fibroblasts were maintained in growth media (RPMI supplemented with 15% FBS and 1% penicilin/streptomycin).

extract_protocol:
Small extracellular vesicles were isolated using ExoSpin kit according to the manufacturer protocol. Total RNA from the small extracellular vesicles were extracted using Trizol reagent.
NEBNext Multiplex Small RNA Library Prep Kit

treatment_protocol: Human dermal fibroblasts were seeded in T75 flasks using serum free media supplemented with exosome-free FBS and incubated for 48 hours.

tag: cellular senescence

value: senescent

value: Human dermal fibroblasts (HDF)


title: Human Donor Lung 22

extract_protocol:
Snap-frozen lungs were homogenized in Qiazol reagent. RNA was extracted using the miRNeasy Mini Kit (Qiagen).
First the mRNA was randomly fragmented; after cDNA first strand synthesis, second strand was generated by nick-translation, followed by purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment.


title: Human Donor Lung 21


title: sEVs derived from nonsenescent HDFs

value: nonsenescent


title: Tom1

value: Rosa-mTmG; Fabp4-Cre in C57BL/6J background

value: Pancreas

value: Pancreatic ductal adenocarcinoma

value: Tomato+ (non-stellate cell-derived) CAFs

value: 12 weeks


title: ASC_ChIP-seq_rep1


title: FISC_ChIP-seq_rep3

value: Freshly isolated muscle stem cells


title: patient_NSC009_tumor_nodule2

description: polyA RNA

value: ypT4 N1Mx


title: FISC_ChIP-seq_rep1


title: FISC_ChIP-seq_rep2


title: Human Donor Lung 18

value: distal lung


title: Human Donor Lung 19


title: 37_3932Nantes_YAPS127A1_RNASeq_hs_i4

city: Nantes

first: Franck

last: Verrecchia

address: 1 Rue Gaston Veil

country: France

institute: University of Nantes

data_processing:
Bulk RNA sequencing was performed on an Illumina NextSeq 500 platform (Active Motif, Carlsbad, CA, USA).
Chastity-filtered FASTQ reads were mapped to the genome using the STAR algorithm (v2.5.2b). Read counts per gene were obtained using feature  Counts program in Subread software packages (v1.5.2).
Data analysis including differential expression analysis (DESeq2, v1.14.1) and Gene Set Enrichment Analysis (GSEA, v2-2.2.4) were performed
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: osteosarcoma KHOS cells

growth_protocol: Cells were cultured in DMEM (Dulbecco’s Modified Eagle’s Medium, Lonza, Basel, Switzerland) supplemented with 10% fetal calf serum (Hyclone Perbio, Bezons, France)

extract_protocol:
Qiagen RNeasy Mini/Midi kit
Libraries were prepared from purified RNA using the illumina TruSeq Stranded mRNA Sample Preparation kit

value: KHOS

value: Osteosarcoma cell line

tag: genotype/variation

value: YAP-S127A overexpression


title: 39_3932Nantes_YAPS127A3_RNASeq_hs_i6


title: 35_3932Nantes_YAPS94A2_RNASeq_hs_i2

value: YAP-S94A overexpression


title: Human Donor Lung 23


title: patient_NSC020_tumor_nodule2

description: polyA RNA

value: Non-small-cell lung carcinoma (NSCLC)

value: non-small cell lung tumor

value: M


title: 38_3932Nantes_YAPS127A2_RNASeq_hs_i5


title: sgBcl6_RNA-seq_rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

growth_protocol: Isolated muscle stem cells were cultured in growth medium containing F10, 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for 24h.

extract_protocol:
RNA from freshly isolated or culture muscle stem cells was harvested using Trizol reagent.
Purified mRNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added. RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.

value: muscle stem cells

value: post natal day 38


title: Human Donor Lung 17


title: sgBcl6_RNA-seq_rep2


title: patient_NSC010_tumor_nodule2

description: polyA RNA

value: RBC-depletion


title: patient_NSC010_tumor_nodule1

description: polyA RNA


title: 36_3932Nantes_YAPS94A3_RNASeq_hs_i3


title: Human Donor Lung 16


title: Human Donor Lung 20


title: 34_3932Nantes_YAPS94A1_RNASeq_hs_i1


title: patient_NSC004_tumor_nodule3

description: polyA RNA

value: pT2a N1Mx


title: patient_NSC004_tumor_nodule2

description: polyA RNA


title: Human Donor Lung 15


title: 33_3932Nantes_CT3_RNASeq_hs_i27


title: sgMyc_RNA-seq_rep1


title: patient_NSC004_tumor_nodule4

description: polyA RNA


title: Human Donor Lung 14


title: 32_3932Nantes_CT2_RNASeq_hs_i25


title: Human Donor Lung 13


title: Ctrl_RNA-seq_rep2


title: Human Donor Lung 12


title: Ctrl_RNA-seq_rep1


title: DSC_RNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Fresly isolated muscle stem cells were cultured in growth medium containing F10, 10% HIHS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for 24h(ASC) or 72h(DSC).

value: differentiated siolated muscle stem cell

value: 6-8 weeks


title: 31_3932Nantes_CT1_RNASeq_hs_i23


title: ASC_RNA-seq

value: activated siolated muscle stem cell


title: pEXO_monocyte_03

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

institute: The University of Hong Kong

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Human genome 38 (hg38) by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts or normalized gene counts for every gene and every sample

source_name: monocyte

growth_protocol: Primary monocytes were isolated by Ficoll-Paque density gradient centrifugation. Monocyte isolated by positive immunomagnetic separation. Culture in RPMI1640 + 10% FBS

extract_protocol:
Total RNA was extracted by Trizol
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

treatment_protocol: isolated monocytes were treated in the presence or absence of  20μg/ml pEXO

value: monocyte

tag: source

value: Buffy coat

value: Treated with pEXO


title: pEXO_monocyte_02


title: pEXO_monocyte_01


title: Human Donor Lung 10

source_name: Lung

value: distal lung


title: FISC_RNA-seq

value: freshly siolated muscle stem cell


title: Control_monocyte_04

value: untreated


title: ZNF333-FLAG Rep 1

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: ChIP-seq

data_processing:
Raw sequencing from ChIP-seq experiments were mapped using BWA. The mapped sequences were PCR-duplicate removed. The peak-calling tool Dfilter was used to identify significant peaks with the parameters of ks = 60, bs = 100, lpval = 6.
Genome_build: hg19
Supplementary_files_format_and_content: bed

extract_protocol:
Experiments were performed in two biological replicates for each tag (FLAG and Myc). In addition one GFP transfection was incubated with antibodies against each tag separately as control for IP specificity. Moreover, two input control experiments (ZNF333 transfected and GFP transfected) were performed. ZNF333 or GFP transfected HCT116 cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 mins. Cells were then washed in ice-cold PBS, scraped and pelleted down at 800g for 5 min at 4°C. The pellet was resuspended in FA lysis buffer to facilitate cell lysis. Nuclei were pelleted by centrifugation at 3,000 rpm for 5 min at 4°C and resuspended in 1% SDS lysis buffer (1% SDS, 1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH (pH 7.5), 0.1% sodium dodecyl sulfate, Roche 1X Complete protease inhibitor) to lyse nuclei. Chromatin was then isolated using ultracentrifugation at 20,000 rpm for 30 mins at 4°C, resuspended in 300 µl 0.1% SDS lysis buffer and fragmented via sonication to an average size of 200–500 bp (Bioruptor Next gen, Diagenode). Solubilised chromatin was immunoprecipitated using anti-Flag antibody (Sigma, #F3165) or anti-Myc (Abcam, #ab9106) overnight. Antibody-chromatin complexes were pulled-down using Protein G Dynabeads (Invitrogen), washed and eluted with elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8)). After cross-link reversal and Proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase. ChIP DNA was quantified using Qubit fluorometric quantification (Thermo Fisher Scientific).
Library Prep was performed using New England Biolabs Ultra II Kit according to the manufacturer’s specifications and sequenced on the Illumina NextSeq High platform with 76bp single end reads.

tag: antibody

value: ZNF333 FLAG


title: ZNF333-MYC Rep1

description: ChIP-seq

value: ZNF333 MYC


title: ZNF333-MYC Rep 2

description: ChIP-seq


title: patient_NSC004_tumor_nodule1

description: polyA RNA

value: Non-small-cell lung carcinoma (NSCLC)

value: non-small cell lung tumor


title: Human Donor Lung 9


title: Control_monocyte_03

tag: cell type


title: Tumor_PTC_nodule2

description: polyA RNA

source_name: lung tumor

extract_protocol:
Murine pulmonary tissue (healthy and tumor lung) were dissociated into single cell for further RNA sequencing downstream applications using the Tumor Dissociation kit by Miltenyi Biotec (# 130-096-730). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2-4 mm. The pieces were infused with RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI /enzyme mix, attached to the sleeve of the gentleMACS Octo Dissociator and run using a “37C_m_TDK_1” program. After termination of the program, the cells were spun down at 300 x g for 10 min at 4C, resuspended in RPMI-2% FBS, passed through a 70 μm strainer and centrifuge was repeated. The cell pellet was treated with 1 ml of ACK solution for 7 min at RT, and the lysis stopped with 4 ml of RPMI 2% FBS. After centrifugation, the cells were suspended in 1 ml RPMI-2% FBS and passed through a cell strainer (70 μm) to obtain a single-cell suspension. Immediately before transcriptome barcoding using the inDrop platform, cells were manually counted on a hemocytometer and diluted to 60k cells/ml. The final cell suspension included 15% v/v Optiprep (Sigma-Aldrich, Cat. No. D1556).
Single cell barcoding and library preparation were performed using the inDrops protocol as described in Zilionis et 2017, Nature Protocols, with modifications summarized in Table S6 of Zilionis et al., 2019 (related to this GEO record).

value: KP model of lung cancer

tag: treatment

value: K-Ras G12D/p53 null mice (Lox-stop-lox (LSL) K-RasG12D, p53 flox)

value: ~8 months at experiment end


title: Human Donor Lung 8


title: pEXO_monocyte_04


title: Human Donor Lung 7


title: GFP-MYC

description: ChIP-seq

value: GFP MYC


title: Control_monocyte_02


title: Human Donor Lung 11


title: Tumor_nodule3

description: polyA RNA

value: RBC-depletion


title: GFP-FLAG

description: ChIP-seq

value: GFP FLAG


title: Tumor_PTC_nodule1

description: polyA RNA


title: Tumor_nodule2

description: polyA RNA


title: patient_NSC009_tumor_nodule1

description: polyA RNA

value: F

value: ypT4 N1Mx


title: Control_monocyte_01

value: monocyte

value: Buffy coat


title: Human Donor Lung 5

value: distal lung


title: Human Donor Lung 4


title: Healthy_nodule2

description: polyA RNA


title: Human Donor Lung 3


title: Healthy_nodule1

description: polyA RNA


title: Tumor_nodule1

description: polyA RNA


title: CAFR-CM3

city: Guangzhou

first: xiang

last: zhang

state: Guangzhou

address: 58 Zhongshan Second Road, Yuexiu District

department: Department of General Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

description: pre-treated with CAFR-CM

data_processing:
The  data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4)
Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included,
Expression level of gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni
Genome_build: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13)
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

source_name: Panc1 cell

extract_protocol:
Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Cells were washed with PBS and the 1.5ml Trizol reagent was added into the 2ml tube containing the cell pellets. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3 ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mLtube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at12000×g for 20min at 4°C and then removed the supernatant. After washed with 1 ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water.
Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). According to the manufacturer’s instructions, the first step involves the removal of ribosomal RNA (rRNA) using target-specific oligos and RNase H reagents to deplete both cytoplasmic (5S rRNA,5.8S rRNA, 18S rRNA and 28S rRNA) and mitochodrial ribosomal RNA (12S rRNA and 16SrRNA) from total RNA preparations. Following SPRI beads purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. This process removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. After UDG treatment, the incorporation of dUTP quenches the second strand during amplification. The products are enriched with PCR to create the final cDNA library. The libraries were assessed quality and quantity in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The qualified libraries were sequenced pair end on the BGISEQ-500/ MGISEQ-2000 System (BGI-Shenzhen, China).

tag: cell line


title: GEX-Lung-MB-SIY

description: SIY- CD8 T Cell RNA Expression

data_processing:
Demultiplexing, alignment to the mm10 genome (VDJ sequencing data was aligned to the prebuilt mouse GRCm38/mm10 VDJ reference supplied by 10X Genomics, version 3.1.0), and barcode/UMI counting were performed with 10X Genomics Cell Ranger v3.1.0. The resultant raw counts matrix was loaded into Seurat v3.2.2 for further processing. Cells expressing less than 100 genes or more than 4000 genes, as well as cells expressing more than 5% mitochondrial transcripts were excluded. Additionally, cell hashing data was utilized to remove cells called as doublets. RNA expression data was normalized using the Seurat LogNormalize function with the default scale factor of 10,000. Cell hashing counts were normalized by Centered Log Ratio (CLR) transformation at a positive quantile threshold of 0.98. All reported normalized counts were extracted from the data slot of the Seurat object.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with normalized, log-transformed matrix from Seurat v3.2.2
Supplementary_files_format_and_content: mtx file with raw counts matrix from CellRanger v3.1.0

value: KrasLSLG12D; p53fl/fl

value: Sorted CD44+ CD8[alpha]+ SIYRYYGL+ cells


title: CAFS-CM3

description: pre-treated with CAFS-CM


title: CAFR-CM2

description: pre-treated with CAFR-CM


title: CAFS-CM2

description: pre-treated with CAFS-CM


title: CAFR-CM1

description: pre-treated with CAFR-CM


title: Human Donor Lung 2

first: Seoyeon

last: Lee

address: 513 Parnassus Ave HSE 1355B


title: CAFS-CM1

description: pre-treated with CAFS-CM


title: GEX-Lung-MB-SIIN

description: SIIN- CD8 T Cell RNA Expression

value: Sorted CD44+ CD8[alpha]+ SIINFEKL+ cells