title: THP-1-derived macrophages, sgKEAP1, 0h, rep2

value: without  LPS and IFN-γ stimulation


title: 1703796_mouse_spleen_HMOX-1_WT

status: Public on Aug 03 2023

type: SRA

city: Tarrytown

first: Wei Keat

last: Lim

state: NY

address: 777 Old Saw Mill River Rd

country: USA

institute: Regeneron

description:
10x 5prime NextGEM v2
10x Chromium

library_source: transcriptomic single cell

data_processing:
CellRanger (v.6.1.1, 10X Genomics) with GRCh38 reference was performed on the processed cells to compute gene expression levels and to generate analysis-ready data.
We checked the quality of the data (Number of cells, mean reads per cell, median genes per cell, median UMI counts per cell, etc.) to filter out artifacts, empty droplets, and multiplets. In each sample, cells with the total number of molecules detected within a cell higher than 30,000 and lower than 1,000 were filtered out.
Then Python module Scanpy (v1.7.1) was used to normalize the data. The normalization was done as following: 1. Transformation of total counts so each cell sums to 10,000. 2. Log1p of the transformed counts. 3.Unit Scaling of the gene expression counts across all cells to ensure a mean of zero and a max value of 10.
Lastly, R Seurat package (v4.3.0.1) was utilized to generate UMAP plots and to run clustering. In each cluster, we identified markers based on differentially expressed genes, and cell types were given to the clusters based on the top markers. Cell type percentages were calculated by [the number of cells for the cell type x 100 / the total number of cells in the condition].
Assembly: GRCh38 & GRCm38
Supplementary files format and content: Tab-separated matrix files

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
The generation of knock-in mice encoding human SIRPa, human M-CSF, human CD47, and Rag2/IL-2Rg deletions were created by Velocigene technology. Mice were maintained on a sulfa diet (LabDiet, St. Louis, MO) in a MPF facility, and were intra-bred for about 5-10 generations. Mouse and human CD45+ cell fractions were collected from the tissues of human HSC-engrafted HMOX-1+/+ and HMOX-1-/- hSIRPa/hM-CSF/hCD47/Rag2-/-/IL-2Ryc-/- mice. Cells were isolated by positive magnetic enrichment using either mouse CD45 or human CD45 microbeads (Miltenyi).
Library was performed according to the manufacter's insturction (10x 5prime NextGEM v2)

tag: tissue

value: spleen

tag: cell type

value: mCd45+ cells

tag: treatment


title: 1693166_mouse_bone marrow_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

source_name: bone marrow

value: bone marrow


title: THP-1-derived macrophages, sgKEAP1, 0h, rep1

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

library_source: transcriptomic

data_processing:
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36) and were further quality-filtered using fastq_quality_trimmer command in FASTX Toolkit (Version 0.0.13) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The high-quality reads were mapped to the mm10 genome by HISAT2, a fast and sensitive spliced alignment program for mapping RNA-seq reads, with -dta paramenter; PCR duplicate reads were removed using Picard tools
The expression levels of genes and repeat sequences were independently calculated by StringTie (Version v1.3.4d) with -e -B -G parameters using Release M18 (GRCm38.p6) gene annotations downloaded from GENCODE data portal and annotated repeats (RepeatMasker) downloaded from the UCSC genome browser, respectively.
Differential expression analysis of genes in different samples was performed by DESeq2 using the reads count matrix produced from a python script “prepDE.py” provided in StringTie website (http://ccb.jhu.edu/software/stringtie/).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

growth_protocol: THP-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme, NR612-02) according to the manufacturer’s protocol.

treatment_protocol: THP-1 cells were treated with PMA (50 ng/mL) for 48 h, then refreshed the medium or stimulated by LPS (50 ng/mL) plus IFN-γ (50 ng/mL) for 24 h.

tag: cell line

value: macrophage

tag: genotype

value: KEAP1 knockout


title: FL_MIC-MGI_48

city: Montreal

first: Heather

last: Melichar

state: Quebec

address: 5415 Boulevard de l'Assomption

department: Immunology-Oncology Unit

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center

data_processing:
Performed single-end RNA-seq using the Illumina NextSeq500 platform for 75 cycles
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression , either in TPM or FPKM values, for these stranded RNA libraries.
Assembly: GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88)
Supplementary files format and content: excel files with FPKM values

source_name: Fetal Liver

extract_protocol:
Cells were sorted directly into TRIZOL reagent. Total RNA was extracted and used to generate transcriptome libraries.
Library was prepared using the KAPA mRNA Hyper Prep (poly-A Capture)

value: Fetal Liver

value: WT

value: MIC-MGI


title: CTCF_10:1_2uM_ACF_15min_biolrep1_techrep1

city: San Francisco

first: Megan

last: Ostrowski

state: CA

address: 1700 Owens

institute: Gladstone Institutes

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

library_source: genomic

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular concensus sequences (CCS) using ccs
Aligning subreads to nonanucleosomal molecule reference
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Library strategy: SAMOSA

molecule: genomic DNA

organism: unidentified plasmid

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled

growth_protocol: N/A (in vitro samples)

extract_protocol:
CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
PacBio SMRTbell® library preparation

treatment_protocol:
N/A (in vitro samples)
N/A (in vitro samples)

tag: remodeler

value: ACF

tag: remodeler concentration

value: 2 uM

tag: remodeling turnover_conditions

value: single-turnover

tag: remodeling time

value: Standard

tag: remodeling atp/adp_conditions

value: plus ATP

tag: histone

value: dna ratio:10:1 ratio

tag: ecogii methylation

value: EcoGII Methylated

tag: sample type

value: in vitro (plasmid insert)


title: 1693165_mouse_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: FL_MIC_3

description:
DSP601
DSP601_genes_FPKM.annotated.xls
FL_MIC_Lin-Kit_S5

data_processing:
Performed paired-end RNA-seq using the Illumina NextSeq500 platform for 150 cycles
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression , either in TPM or FPKM values, for these stranded RNA libraries.
Assembly: GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88)
Supplementary files format and content: excel files with FPKM values

value: MIC


title: THP-1-derived macrophages, sgCtrl, 8h, rep3

value: LPS and IFN-γ stimulated for 8 h


title: 1693158_mouse_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

value: spleen

value: mCd45+ cells


title: FL_CG2_1

description:
DSP601
DSP601_genes_FPKM.annotated.xls
48h_CG2_n1_Lin-Kit_FL_S10


title: S2, array, 5:1, unrem, +M, rep2

data_processing:
Library strategy: SAMOSA
Demultiplexing BAM files using Lima
Generating circular concensus sequences (CCS) using ccs
Aligning CCS to mm10 using pbmm2 (in vivo samples only)
Aligning subreads to nonanucleosomal molecule reference (in vitro samples only)
Genome_build: mm10
Supplementary_files_format_and_content: pickle

molecule: other

source_name: CTCF site 2 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled  (in vitro)

growth_protocol: mESCs were thawed and grown for two passages onto CF-1 Irradiated mouse embryonic feeder cells. mESCs were MEF depleted at least two times prior to experimentation. mESCs were grown on 0.2% gelatin plates and maintained with 1X KnockOut DMEM supplemented with 10% Fetal Bovine Serum, 1% 100X GlutaMAX, 1% 100X MEM Non-Essential Amino Acids, 7.82 mM 2-Mercaptoethanol, and 1X Leukemia Inhibitory Factor.

extract_protocol:
Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.
Chromatin was purified with 10uL RNaseA at RT for 10 minutes (in vivo samples only), 10uL Proteinase K (20mg/mL) and 10uL 10% SDS at 65°C for a minimum of 2 hours up to overnight). DNA was extracted with Phenol-Chloroform and ethanol precipitation.
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
OTHER: PacBio SMRTbell® library preparation

treatment_protocol:
Isolated mESC nuclei were methylated (10uL EcoGII per 1e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 6.25mM (NEB) after 15 minutes.
Isolated nuclei (methylated or unmethylated) were digested with Micrococcal Nuclease (Sigma) at 1U per 50e6 nuclei at varying conditions (see characteristics above). MNase-digested nuclei were treated with 300ug/mL of Lysolethicin (L-α-Lysophosphatidylcholine from bovine brain, Sigma) for nuclear lysis and liberation of chromatin fibres.

tag: snf2h remodeling turnover conditions

value: unremodeled

tag: snf2h remodeling atp/adp conditions

value: dna ratio:5:1 ratio

tag: mnase digestion temperature

tag: mnase digestion duration

value: plasmid insert


title: THP-1-derived macrophages, sgCtrl, 8h, rep2

value: macrophage

value: WT


title: FL_MIC_4

description:
DSP601
DSP601_genes_FPKM.annotated.xls
FL_pMIC_48h_S4

tag: tissue

value: Fetal Liver


title: FL_MIC_2

description:
DSP601
DSP601_genes_FPKM.annotated.xls
pMIC_Lin-Kit_n2_FL_S7


title: 1693157_mouse_spleen_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium

tag: cell type


title: S2, array, 10:1, unrem, +M, rep2


title: S2, array, 15:1, unrem, +M, rep2


title: THP-1-derived macrophages, sgCtrl, 8h, rep1

tag: treatment


title: FL_MIC_1

description:
DSP601
DSP601_genes_FPKM.annotated.xls
MIC_n1_Lin-Kit_48h_FL_S6


title: 1686417_mouse_bone marrow_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

value: bone marrow


title: THP-1-derived macrophages, sgCtrl, 0h, rep2

tag: cell line

value: without  LPS and IFN-γ stimulation


title: THP-1-derived macrophages, sgKEAP1, 8h, rep1

tag: genotype

value: KEAP1 knockout


title: S2, array,  20:1, unrem, +M, rep2

value: dna ratio:20:1 ratio


title: S1, array 5:1, unrem, +M, rep2

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled  (in vitro)


title: FL_GLIS2-C265G_2

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_GLIS2_C265G_n2_S17


title: S1, array 10:1, unrem, +M, rep2

value: dna ratio:10:1 ratio


title: 1686416_mouse_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: THP-1-derived macrophages, sgCtrl, 0h, rep1


title: FL_GLIS2-C265G_1

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_GLIS2_C265G_n1_S16


title: FL_GLIS2_2

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_GLIS2_n2_S15


title: 1686408_mouse_spleen_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: 1686409_mouse_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium


title: S1, array 15:1, unrem, +M, rep2

value: EcoGII Methylated


title: S1, array, 5:1, +ADP, MT, rep2

value: multiple-turnover

value: plus ADP


title: FL_GLIS2_1

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_GLIS2_n1_S14


title: Endometrium_01-10_Epithelium_AS-Pre

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

address: Rda. de Narcís Monturiol, 11, Bloque C

country: Spain

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat

data_processing:
Processing of scRNA-seq data was conducted with the CellRanger software suite (version 3.1.0). Raw reads were demultiplexed using the mkfastq wrapper command of bcl2fastq (Illumina). The libraries were mapped using GRCh38-3.0.0 as a reference provided by 10x Genomics. The count gene expression matrices per cell were computed per sample using the counts pipeline (with --expect-cells parameter set to default), which performs the steps of read alignment (with STAR mapping tool), UMI counting, calling of cell barcodes, and filtering of empty droplets based on a simple. Processed samples were merged and saved into H5Seurat objects
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: H5Seurat single-cell object with barcode metadata

source_name: Endometrium

extract_protocol:
A two-stage dissociation protocol separated endometrial biopsies into stromal fibroblasts and epithelial enriched single-cell suspensions. Before dissociation, tissue was rinsed with PBS in a petri dish to remove blood and mucus, and excess PBS was removed after rinsing. The tissue was minced into small pieces and dissociated with 3 ml collagenase mix (Collagenase V, Sigma), RPMI+10% fetal bovine serum, and DNaseI (Sigma) at 37ºC under continuous shaking at 175 rpm for 25 min in a 15 mL Falcon tube in a horizontal position. This primary enzymatic step mostly dissociates stromal fibroblasts into single cells while leaving epithelial glands and lumen mostly undigested. The contents were transferred to a 50 mL tube in RPMI media and filtered with a 100 mm cell strainer. The tissue remaining on the filter was used for the epithelial enrichment cell isolation by resuspending and incubating in 10 ml Trypsin mix (Trypsin -EDTA (0.25%) phenol and DNaseI) for 10 min.    The resulting two contents were transferred to 50 mL tubes with 20 mL RPMI, filtered with a 100 mm cell strainer, centrifuged, and then resuspended in 1 mL RPMI. Dead cells were removed using the MACS dead cell removal kit (Miltenyi Biotec). Live-cell suspensions were loaded into a Chromium Next GEM Chip G (10X Genomics) to obtain cDNA from individual cells.    Mean cells obtained in stromal and epithelial enriched suspensions were 2.38x106 (5x105-6.4x106) and 1.25x106 (2x105-5.3x106), respectively. Viability of stromal cells was 67.44% (31-87%) and 39.5% (20-80%) for epithelial cells.
Total RNA was extracted using the RNeasy Micro Kit with on-column DNase treatment (Qiagen) following the manufacturer's instructions. RNA was resuspended in 14 μl of RNase-free water, and purity and concentration determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher). For cDNA synthesis, 500-1000 ng of total RNA was reverse transcribed following the manufacturer's instructions(Thermo Fisher).    10x-Genomics v3 libraries were prepared as per the manufacturer's instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell, on an Illumina NovaSeq 6000 S2v1.5 300 cycles at a mean 40x coverage (paired-end; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles)

treatment_protocol: BMDSC mobilization was performed using granulocyte-CSF (G-CSF) injection at 10 mcgr/kg. CD133+ cells were collected through peripheral blood apheresis and subsequently isolated. Patients were excluded if they did not reach the minimal requirements for mobilized cells (at least 30 million cells with a purity above 70% and viability >50%), presented an unstable medical condition, or refused a central venous catheter when required. Finally, isolated CD133+ cells were delivered into the spiral arterioles of the patient using a minimal invasive radiology intervention through the left brachial artery, reaching each uterine artery using a microcatheter

tag: biospy origin

value: Epithelium

tag: seurat id

value: Endometrium

tag: treatment stage

value: AS-Pre


title: Endometrium_01-12_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: FL_CBFA2T3_2

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_CBFA2T3_n2_S13


title: S1, array, 10:1, +ADP, MT, rep2


title: FL_CBFA2T3_1

description:
DSP649
DSP649_genes_FPKM.annotated.xls
FL_CBFA2T3_n1_S12


title: Endometrium_01-12_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat

value: Stroma


title: FL_MIC_7

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_MIC_DSP601-4_S6

value: MIC


title: Endometrium_01-09_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: Endometrium_01-09_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: Endometrium_01-10_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: S2, array, 5:1, +ADP, MT, rep2

value: dna ratio:5:1 ratio

value: plasmid insert


title: FL_MIC_6

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_MIC_DSP601-3_S5

value: WT


title: S1, array, 15:1, +ADP, MT, rep2


title: S1, array, 20:1, +ADP, MT, rep2


title: FL_MIC_5

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_MIC_DSP601-2_S10

value: Fetal Liver


title: Hepa1-6 cell_3

city: Shanghai

first: Ji-hang

last: Yuan

address: 800 Xiangyin Road

department: Department of Medical  Genetics

country: China

institute: Naval medical university

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the sequencing instrument.
Assembly: CRISPR screen sequenced reads were mapped to Mouse Genome-Scale CRISPR Knock-Out Pooled Library.
Supplementary files format and content: tab-delimited text file includes counts for each Sample

source_name: in vitro

extract_protocol:
The genomic DNA was extracted with a DNeasy Blood & Tissue Kit (Qiagene).
The extracted genomic DNA was subjected to the initial round of 24 cycles of PCR to amplify sgRNA sequences. Amplicons from the first PCR were used in a second PCR of 8 cycles to add index and adapter sequences for Illumina sequencing. The final sequencing libraries were quantified using the Qubit 3 Fluorometer (Thermo Fisher) and assessed for size using the 2200 TapeStation System (Agilent).

value: in vitro

value: hepatocellular carcinoma cell


title: liver metastatic tissue_3

source_name: liver metastatic tissue

value: liver metastatic tissue


title: S2, array, 10:1, +ADP, MT, rep2


title: Endometrium_01-08_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: liver metastatic tissue_1


title: FL_MIC_21

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_MIC_no21_S4


title: S2, array, 15:1, +ADP, MT, rep2


title: S1, array, 20:1, unrem, +M, rep2

value: unremodeled

value: dna ratio:20:1 ratio


title: Hepa1-6 cell_2


title: Endometrium_01-07_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: FL_GLIS2-C265G_20

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_GLIS2_C265G_no20_S3


title: Hepa1-6 cell_1


title: liver metastatic tissue_2


title: S2, array, 20:1, +ADP, MT, rep2

value: EcoGII Methylated


title: S1, array, 5:1, +ATP, MT, rep2

value: multiple-turnover

value: plus ATP


title: Endometrium_01-07_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: colonic epithelial cells, Tvp23b_KO3

city: Dallas

first: Jin Huk

last: Choi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4
Trimmed fastq.gz were aligned to the mm10 reference genome using tophat-2.0.10
BAM files resulting from alignments were run through cuffdiff (cufflinks v2.1.1) for differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw gene counts for each sample
Supplementary files format and content: tab-delimited text file include FPKM values for each sample
Supplementary files format and content: excel file include differential gene expression between WT and KO

source_name: colon

growth_protocol: No

extract_protocol:
Colons were isolated from mice and stool removed from the lumen. Colons were then cut to 5-10 mm pieces and incubated at room temperature for 30 minutes in PBS containing 5 mM EDTA with rotation on a platform shaker. The epithelial cells were collected by passing through a 100-μm cell strainer. RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s protocol.

treatment_protocol: No

value: colon

value: colonic epithelial cells

value: Tvp23b homozygous mutant

value: No


title: Endometrium_01-05_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat

value: Stroma

value: Endometrium

value: AS-Pre


title: S1, array, 10:1, +ATP, MT, rep2

value: dna ratio:10:1 ratio

value: plasmid insert


title: FL_GLIS2_18

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_GLIS2_no18_S1

value: Fetal Liver

value: WT


title: FL_GLIS2_17

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_GLIS2_no17_S9


title: colonic epithelial cells, Tvp23b_KO2


title: Endometrium_01-08_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat

value: Epithelium


title: Endometrium_01-15_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: colonic epithelial cells, WT3

value: wild type


title: S1, array, 20:1, +ATP, MT, rep2

value: dna ratio:20:1 ratio


title: S2, array, 5:1, +ATP, MT, rep2

value: dna ratio:5:1 ratio

value: EcoGII Methylated


title: colonic epithelial cells, WT2


title: Endometrium_01-14_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: Endometrium_01-14_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: FL_CBFA2T3_16

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_CBFA2T3_no16_S8


title: FL_CBFA2T3_15

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_CBFA2T3_no15_S7


title: BM_2

source_name: Bone Marrow

value: Bone Marrow


title: colonic epithelial cells, WT1

value: colon


title: Endometrium_01-13_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: Endometrium_01-15_Epithelium_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat


title: BM_1


title: WT5 month, skeletal muscle [W5S5299]

city: pittsburgh

first: Huabo

last: Wang

state: PA

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

data_processing:
CLC Genomics Workbench v 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Mus musculus (GRCm38.p6) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include CPM(TMM-adjusted) values for each Sample

source_name: skeletal muscle

growth_protocol: Animal work was conducted in compliance with the Public Health Service Policy on Humane Care and Use of Laboratory Animal Research (ILAR) Guide for Care and Use of Laboratory Animals. All experimental procedures, diets and tests were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Pittsburgh. All mice were housed in a specific pathogen-free facility, maintained under standard conditions at UPMC Children’s Hospital of Pittsburgh.

extract_protocol:
RNAs were isolated from mouse tissues using RNeasy kit,according to the directions of the supplier (Qiagen, Inc. Germantown, MD). Exceptions to this were made in the case of adipose tissue and skeletal muscle for which we utilized an RNeasy Lipid Tissue extraction Kit(Qiagen, Inc., Germantown, MD).
Sequencing libraries were generated using a NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, Beverly, MA).Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms.

treatment_protocol: CreER activation and Myc excision were initiated at the time of weaning in mice that had attained a weight of 15 g or greater.  Each mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil.

value: skeletal muscle

tag: strain

tag: age

value: 5 month

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: S2, array, 10:1, +ATP, MT, rep2

value: multiple-turnover

value: plus ATP

tag: histone


title: WT5 month, skeletal muscle [W5S5277]


title: S1, array, 15:1, +ATP, MT, rep2

tag: ecogii methylation


title: WT5 month, skeletal muscle [W5S5042]


title: OSA11, replicate 11, scRNAseq

city: Columbia

first: Rene

last: Cortese

state: MO

address: 1 Hospital Dr. Room MA104E

department: Department of Child Health, School of Medicine

institute: Child Health Research Institute

data_processing:
Data were processed using CellRanger (version 3.0.2). Raw reads were assessed by FastQC, followed by trimming of adapters using TrimGalore, and mapping using STAR. All data analysis was conducted in R (version 4.1.0). Cluster analysis was performed using the R package Seurat (version 4.0.5)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
PBMCs from subjects' blood samples were isolated by gradient centrifugation using Ficoll-PAQUE (GE Healthcare Pharmacia, Chicago IL), cell viability was verified, and samples were cryopreserved in liquid nitrogen until use.
After thawing, quality control of the isolated single-cells was conducted thoroughly to monitor the suitability of each sample before undergoing single-cell sorting and library preparation, as detailed in the Supplemental Material. scRNA-seq libraries were generated from isolated PBMCs using Chromium 3’ v3.1 (10X Genomics, Pleasanton, CA), with a targeted output of 10,000 cells per sample.
Libraries were sequenced using an NextSeq (Illumina, San Diego, CA) instrument, targeting over 50,000 reads per cell.

value: PBMC

tag: status

value: OSA

tag: Sex

value: Female

tag: bmi

tag: ahi


title: BM_CG2_RAS_28

value: MIC-RAS


title: BM_CG2_RAS_76

value: WT


title: Endometrium_01-13_Stroma_AS-Pre

description:
10x Genomics
sc_AS_pre_vs_post.h5seurat

value: Stroma

value: Endometrium

value: AS-Pre


title: FL_GLIS2-C265G_19

description:
DSP749
DSP749_genes_FPKM.annotated.xls
FL_GLIS2_C265G_no19_S2

value: Fetal Liver


title: S2, array, 15:1, +ATP, MT, rep2

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

value: dna ratio:5:1 ratio

tag: mnase digestion temperature

tag: mnase digestion duration

value: EcoGII Methylated

tag: sample type

value: plasmid insert


title: OSA10, replicate 10, scRNAseq

tag: tissue

value: Male


title: S2, array, 20:1, +ATP, MT, rep2

value: dna ratio:20:1 ratio


title: BM_CG2_RAS_22

value: Bone Marrow

tag: cell type

tag: genotype

tag: treatment


title: S1, array, 5:1, +ADP, MT, rep1

value: multiple-turnover

value: plus ADP


title: WT5 month, skeletal muscle [W5S5041]

value: skeletal muscle

tag: strain

value: 5 month

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: OSA09, replicate 9, scRNAseq

value: PBMC

value: OSA

value: Female

tag: age


title: colonic epithelial cells, Tvp23b_KO1

value: colon

value: colonic epithelial cells

value: Tvp23b homozygous mutant

value: No


title: BM_CG2_LUC_97

value: WT


title: WT5 month, skeletal muscle [W5S5004]


title: WT5 month, skeletal muscle [W5S5007]


title: OSA08, replicate 8, scRNAseq


title: S1, array, 15:1, +ADP, MT, rep1

tag: histone

value: dna ratio:5:1 ratio

value: EcoGII Methylated

value: plasmid insert


title: S1, array, 20:1, +ADP, MT, rep1

value: dna ratio:20:1 ratio

tag: ecogii methylation


title: WT 20 month, skeletal muscle [W18S72]

value: 20 month


title: BM_CG2_LUC_41

value: Bone Marrow


title: OSA07, replicate 7, scRNAseq

tag: status


title: OSA06, replicate 6, scRNAseq

tag: Sex

value: Male


title: WT 20 month, skeletal muscle [W18S66]

value: skeletal muscle


title: S2, array, 5:1, +ADP, MT, rep1

value: multiple-turnover

value: plus ADP


title: S1, array, 10:1, +ADP, MT, rep1

value: dna ratio:10:1 ratio


title: S2, array, 15:1, +ADP, MT, rep1


title: OSA05, replicate 5, scRNAseq

value: PBMC

value: OSA

value: Female

tag: bmi


title: WT 20 month, skeletal muscle [W18S45]

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: OSA04, replicate 4, scRNAseq

tag: ahi


title: WT 20 month, skeletal muscle [W18S42]


title: S2, array, 10:1, +ADP, MT, rep1

tag: snf2h remodeling turnover conditions


title: OSA03, replicate 3, scRNAseq


title: BM_CG2_LUC_74


title: S2, array, 20:1, +ADP, MT, rep1

tag: snf2h remodeling atp/adp conditions


title: WT 20 month, skeletal muscle [W18S41]


title: OSA02, replicate 2, scRNAseq


title: S1, array, 5:1, +ATP, MT, rep1

value: plus ATP

tag: mnase digestion temperature


title: OSA01, replicate 1, scRNAseq


title: S1, array, 10:1, +ATP, MT, rep1

tag: mnase digestion duration


title: MycKO 5 month, skeletal muscle [K5S5116]

value: 5 month

value: MycKO


title: MycKO 5 month, skeletal muscle [K5S5118]


title: S1, array, 15:1, +ATP, MT, rep1

value: dna ratio:5:1 ratio

value: EcoGII Methylated

tag: sample type


title: Liver - Diet Ref - Rep7

type: RNA

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

country: France

institute: INRAe

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 64 out of 79 microarrays or with a minimal weight of 8 per group from at least one experimental group. At this step, 35538 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32897 rows each corresponding to a unique ProbeName.

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All mice were housed at 21–23°C on a 12-h light (ZT0–ZT12)/ 12-h dark (ZT12–ZT24) cycle and allowed free access to the diets for 9 weeks.

extract_protocol: Following euthanasia, liver tissue was weighed, snap-frozen in liquid nitrogen and stored at -80°C until used. Total RNA was extracted using TRI Reagent® (Molecular Research Center, Cincinnati, Ohio, USA). RNAs were quantified using Nanodrop (NanoDropTM 1000; Thermo Scientific).

treatment_protocol: Mce were fed ad libitum the different diet for 9 weeks. The mice were fasted for 4 h before they were killed. Liver tissue was harvested for transcriptomic profiling.

tag: diet

value: Ref

tag: washbatch


title: MycKO 5 month, skeletal muscle [K5S4285]

tag: tissue

tag: genotype


title: Liver - Diet A - Rep8

tag: strain

value: A


title: Liver - Diet D - Rep8

value: D


title: Liver - Diet B - Rep7

value: Male

value: B


title: Control10, replicate 10, scRNAseq

value: NoOSA

tag: age


title: S2, array, 5:1, +ATP, MT, rep1

value: multiple-turnover

tag: histone

value: plasmid insert


title: MycKO 20 month, skeletal muscle [K18S64]

value: skeletal muscle

value: 20 month

tag: treatment


title: MycKO 5 month, skeletal muscle [K5S4284]


title: Control11, replicate 11, scRNAseq

value: PBMC

tag: status


title: S2, array, 10:1, +ATP, MT, rep1

value: dna ratio:10:1 ratio

tag: ecogii methylation


title: S1, array, 20:1, +ATP, MT, rep1

value: plus ATP

value: dna ratio:20:1 ratio


title: Control07, replicate 7, scRNAseq

tag: Sex

value: Female

tag: bmi


title: Liver - Diet C - Rep9

value: C


title: MycKO 20 month, skeletal muscle [K18S63]

value: MycKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: S2, array, 20:1, +ATP, MT, rep1

tag: snf2h remodeling turnover conditions

value: EcoGII Methylated


title: Control09, replicate 9, scRNAseq

tag: ahi


title: S2, array, 15:1, +ATP, MT, rep1

tag: snf2h remodeling atp/adp conditions

value: dna ratio:5:1 ratio

tag: mnase digestion temperature


title: Control06, replicate 6, scRNAseq


title: MycKO 20 month, skeletal muscle [K18S62]


title: MycKO 20 month, skeletal muscle [K18S61]


title: Liver - Diet G - Rep8

value: Male

value: G


title: Liver - Diet C - Rep5


title: Liver - Diet D - Rep7

value: D


title: S1, array, 5:1, +ADP, ST, rep2

value: single-turnover

value: plus ADP

tag: mnase digestion duration

tag: sample type


title: Liver - Diet E - Rep5

tag: diet

value: E

tag: washbatch


title: Liver - Diet F - Rep7

value: F


title: Liver - Diet Ref - Rep6

value: Ref


title: MycKO 20 month, skeletal muscle [K18S48]

tag: tissue

value: skeletal muscle

value: 20 month

tag: genotype


title: Control04, replicate 4, scRNAseq

value: PBMC

value: NoOSA

tag: age


title: S1, array, 10:1, +ADP, ST, rep2

tag: histone

value: dna ratio:10:1 ratio

value: plasmid insert


title: Control05, replicate 5, scRNAseq


title: WT 5 month, Liver [W5L5299]

value: Liver

tag: strain

value: 5 month

value: WT

tag: treatment

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: Control03, replicate 3, scRNAseq

tag: status

value: Female


title: Control02, replicate 2, scRNAseq

tag: Sex

value: Male


title: WT 5 month, Liver [W5L5277]


title: WT 5 month, Liver [W5L5042]


title: S2, array, 5:1, +ADP, ST, rep2

value: single-turnover

value: dna ratio:5:1 ratio

tag: ecogii methylation

value: EcoGII Methylated


title: WT 5 month, Liver [W5L5041]


title: S1, array, 20:1, +ADP, ST, rep2

tag: snf2h remodeling turnover conditions

value: plus ADP

value: dna ratio:20:1 ratio


title: S2, array, 10:1, +ADP, ST, rep2


title: HCC827.OR.WES

city: New Haven

first: Fernando

middle: J.

last: de Miguel

state: Connecticut

address: 333 Cedar Street

department: Yale Cancer Center

institute: Yale University

description:
HCC827.SNV.txt
HCC827.CNV.txt

data_processing:
Sequencing reads were aligned to human genome build 38 (GRCh38/hg38) using the BWA-MEM
Aggregated into a BAM file, and further processed to produce somatic variants with GATK v3.4 and MuTect
Identified variants were further filtered based on their presence in repositories of common variations
CNV analysis was based on the read depth ratio differences between osimertinib resistant and sensitive cells using custom scripts.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes the annotated SNVs/indels and annotated CNVs
Library strategy: WES

source_name: Lung tumor

extract_protocol:
Genomic DNA for whole-exome sequencing (WES) or Sanger sequencing of the sensitive and the osimertinib resistant cells was extracted from cells in culture using the DNeasy Blood & Tissue kit (Qiagen, #69504).
WES libraries for WES were prepared using TruSeq V3 SBS-Kit -HS Library Prep Kit following manufacturer's protocols.

value: Lung tumor

tag: cell line

tag: cell type

value: lung adenocarcinoma cells

tag: phenotype

value: Osimertinib resistant

value: osimertinib 1 uM


title: WT 5 month, Liver [W5L5005]


title: Liver - Diet G - Rep7

value: G


title: HCC827.WES

description:
HCC827.SNV.txt
HCC827.CNV.txt

value: Parental

value: untreated


title: H1975.OR.WES

description:
H1975.SNV.txt
H1975.CNV.txt

value: osimertinib 2 uM


title: WT 20 month, Liver [W18L05]

value: Liver

value: 20 month

value: WT


title: WT 5 month, Liver [W5L5004]

value: 5 month

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: S1, array, 5:1, +ATP, ST, rep2

value: single-turnover

tag: snf2h remodeling atp/adp conditions

value: plus ATP

value: dna ratio:5:1 ratio

tag: mnase digestion temperature

tag: mnase digestion duration

value: plasmid insert


title: S2, array, 15:1, +ADP, ST, rep2

value: plus ADP

value: EcoGII Methylated

tag: sample type


title: S1, array, 15:1, +ADP, ST, rep2


title: Liver - Diet E - Rep6

value: Male

tag: diet

value: E

tag: washbatch


title: Liver - Diet B - Rep6

value: B


title: Liver - Diet A - Rep7

value: A


title: Liver - Diet Ref - Rep5

value: Ref


title: Liver - Diet E - Rep4


title: Liver - Diet G - Rep6

value: G


title: Liver - Diet B - Rep5


title: Control01, replicate 1, scRNAseq

tag: tissue

value: PBMC

value: NoOSA

tag: age

tag: bmi

tag: ahi


title: WT 20 month, Liver [W18L04]

value: Liver

tag: strain

value: 20 month

tag: genotype

value: WT

tag: treatment


title: Control08, replicate 8, scRNAseq

tag: status

tag: Sex

value: Female


title: S1, array, 10:1, +ATP, ST, rep2

tag: snf2h remodeling turnover conditions

value: single-turnover

value: plus ATP

tag: histone

value: dna ratio:10:1 ratio

tag: ecogii methylation


title: PC9.OR.WES

description:
PC9.SNV.txt
PC9.CNV.txt

value: Lung tumor

tag: cell line

tag: cell type

value: lung adenocarcinoma cells

tag: phenotype

value: Osimertinib resistant

value: osimertinib 1 uM


title: WT 20 month, Liver [W18L03]

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: Liver - Diet A - Rep6

value: Male

tag: diet

value: A


title: S1, array, 20:1, +ATP, ST, rep2

tag: snf2h remodeling atp/adp conditions

value: dna ratio:20:1 ratio

tag: mnase digestion temperature

tag: mnase digestion duration

value: EcoGII Methylated

tag: sample type

value: plasmid insert


title: S1, array, 15:1, +ATP, ST, rep2

value: dna ratio:5:1 ratio


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 3 (RNA-seq)

data_processing:
Quality control of the reads with FastQC (v0.11.8)
Adapter removal of the reads with Flexbar (3.0.3)
Alignment to human genome build 38 (GRCh38/hg38) reference genome with STAR (2.7.3)
Obtaining of read counts, TPMs, FPKMs and annotation with RSEM (1.3.3)
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes TPM values for al the samples

extract_protocol:
RNA was extracted at the specified times and conditions. For sensitive and osimertinib resistant cells, RNA was extracted from cells in culture. All extractions were performed with the RNeasy extraction kit (Qiagen, #74004) and concentrations were measured by nanodrop technology.
RNA libraries for RNA-seq were prepared using TruSeq V3 SBS-Kit -HS Library Prep Kit following manufacturer's protocols.

tag: tissue

value: SMARCA4 KD

value: osimertinib 250 nM


title: PC9.WES

description:
PC9.SNV.txt
PC9.CNV.txt

value: Parental

value: untreated


title: Liver - Diet D - Rep6

tag: strain

value: D

tag: washbatch


title: S2, array, 20:1, +ADP, ST, rep2

value: single-turnover

value: plus ADP


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 2 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

tag: genotype

tag: treatment


title: H1975.WES

description:
H1975.SNV.txt
H1975.CNV.txt


title: WT 20 month, Liver [W18L01]

value: Liver

tag: age

value: 20 month

value: WT


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 1 (RNA-seq)


title: MycKO 5 month, Liver [K5L5248]

value: 5 month

value: MycKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: S2, array, 15:1, +ATP, ST, rep2

tag: snf2h remodeling turnover conditions

value: plus ATP

value: EcoGII Methylated

value: plasmid insert


title: MycKO 5 month, Liver [K5L5218]


title: S2, array, 10:1, +ATP, ST, rep2

tag: histone

value: dna ratio:10:1 ratio


title: S2, array, 5:1, +ATP, ST, rep2

value: dna ratio:5:1 ratio

tag: ecogii methylation


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 3 (RNA-seq)

tag: cell line

value: SMARCA4 KD

value: untreated


title: Liver - Diet F - Rep6

tag: Sex

value: Male

value: F


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 2 (RNA-seq)

value: Lung tumor

tag: cell type


title: MycKO 5 month, Liver [K5L5118]


title: WT 20 month, Liver [W18L02]


title: MycKO 5 month, Liver [K5L5116]


title: Liver - Diet F - Rep5

tag: diet


title: S2, array 10:1 +ADP, ST, rep1

value: single-turnover

tag: snf2h remodeling atp/adp conditions

value: plus ADP


title: Liver - Diet G - Rep5

value: G


title: MycKO 5 month, Liver [K5L4284]

value: Liver


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 1 (RNA-seq)

value: lung adenocarcinoma cells


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 3 (RNA-seq)

value: osimertinib 250 nM


title: S2, array 5:1 +ADP, ST, rep1

tag: mnase digestion temperature


title: Liver - Diet C - Rep4

value: C


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 2 (RNA-seq)


title: S2, array 15:1 +ADP, ST, rep1

tag: mnase digestion duration


title: S2, array 20:1 +ADP, ST, rep1

value: dna ratio:20:1 ratio

tag: sample type


title: Liver - Diet B - Rep4

value: B


title: S2, array, 20:1, +ATP, ST, rep2

value: plus ATP

value: EcoGII Methylated

value: plasmid insert


title: S1, array 5:1 +ATP, ST, rep1

value: dna ratio:5:1 ratio


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 1 (RNA-seq)

tag: tissue

value: SMARCA4 KD


title: Liver - Diet E - Rep3

tag: strain

value: Male

value: E


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 3 (RNA-seq)

value: Lung tumor

value: untreated


title: Liver - Diet C - Rep6

tag: washbatch


title: Liver - Diet D - Rep4

value: D


title: MycKO 20 month, Liver [K18L09]

value: 20 month

tag: genotype

value: MycKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: MycKO 20 month, Liver [K18L08]

value: Liver

tag: treatment


title: Liver - Diet A - Rep5

value: A


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 2 (RNA-seq)

value: lung adenocarcinoma cells


title: MycKO 5 month, Liver [K5L4285]

tag: age

value: 5 month


title: Liver - Diet Ref - Rep4

value: Ref


title: S1, array 10:1 +ATP, ST, rep1

tag: snf2h remodeling turnover conditions

value: single-turnover

value: plus ATP

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: MycKO 20 month, Liver [K18L07]


title: S1, array 15:1 +ATP, ST, rep1

tag: histone

value: dna ratio:5:1 ratio

value: plasmid insert


title: YU-005C cells osimertinib scramble shRNA rep 3 (RNA-seq)

value: Lung tumor

value: WT

value: osimertinib 250 nM


title: MycKO 20 month, Liver [K18L10]

value: 20 month


title: WT 5 month, omental adipose tissue [W5F5299]

source_name: omental adipose tissue

value: omental adipose tissue


title: MycKO 20 month, Liver [K18L06]

value: MycKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: YU-005C cells osimertinib scramble shRNA rep 2 (RNA-seq)


title: WT 5 month, omental adipose tissue [W5F5277]


title: YU-005C cells osimertinib scramble shRNA rep 1 (RNA-seq)


title: YU-005C cells untreated scramble shRNA rep 3 (RNA-seq)

value: untreated


title: WT 5 month, omental adipose tissue [W5F5042]


title: S2, array, 15:1, unrem, +M, rep1

value: unremodeled

tag: ecogii methylation


title: YU-005C cells untreated scramble shRNA rep 2 (RNA-seq)

tag: cell line

value: lung adenocarcinoma cells


title: Liver - Diet A - Rep9

tag: Sex

value: Male

value: A


title: S2, array,  20:1, unrem, +M, rep1

value: dna ratio:20:1 ratio


title: S1, array 5:1, unrem, +M, rep1


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 1 (RNA-seq)

tag: cell type

value: SMARCA4 KD


title: WT 5 month, omental adipose tissue [W5F5006]

value: 5 month


title: Liver - Diet G - Rep9

tag: diet

value: G


title: S1, array 20:1, +ATP, ST, rep1

value: single-turnover

tag: snf2h remodeling atp/adp conditions

value: plus ATP

value: EcoGII Methylated

value: plasmid insert


title: Liver - Diet D - Rep5

value: D


title: Liver - Diet Ref - Rep3

value: Ref


title: Liver - Diet B - Rep8

value: B


title: WT 5 month, omental adipose tissue [W5F5041]

value: omental adipose tissue

value: WT

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: S2, array, 5:1, unrem, +M, rep1

value: unremodeled

value: dna ratio:5:1 ratio

tag: mnase digestion temperature


title: YU-005C cells untreated scramble shRNA rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: untreated


title: S1, array 10:1, unrem, +M, rep1

value: dna ratio:10:1 ratio

tag: mnase digestion duration


title: PC9-OR cells osimertinib SMARCA4 #2 shRNA rep 2 (RNA-seq)

value: SMARCA4 KD

value: osimertinib 250 nM


title: Liver - Diet E - Rep7

value: Male

value: E


title: WT 20 month, omental adipose tissue [W18F25]

value: 20 month


title: Liver - Diet F - Rep8

value: F


title: S2, array, 10:1, unrem, +M, rep1

value: EcoGII Methylated

tag: sample type

value: plasmid insert


title: Liver - Diet C - Rep8

value: C


title: S1, array 15:1, unrem, +M, rep1


title: Liver - Diet D - Rep9

value: D


title: S1, array, 20:1, unrem, +M, rep1

value: dna ratio:20:1 ratio


title: PC9-OR cells osimertinib SMARCA4 #2 shRNA rep 1 (RNA-seq)

tag: tissue


title: PC9-OR cells untreated SMARCA4 #2 shRNA rep 2 (RNA-seq)


title: WT 20 month, omental adipose tissue [W18F24]

value: omental adipose tissue

tag: strain

value: WT

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: WT 20 month, omental adipose tissue [W18F23]


title: Liver - Diet Ref - Rep8

value: Ref

tag: washbatch


title: S2, DNA, -m

source_name: CTCF site 2 DNA from Mus Musculus amplified, gibson cloned and isolated (in vitro)

value: unremodeled

value: dna ratio:N/A

value: Unmethylated


title: WT 20 month, omental adipose tissue [W18F22]

tag: genotype


title: WT 5 month, omental adipose tissue [W5F5005]

value: 5 month

tag: treatment


title: PC9-OR cells untreated SMARCA4 #2 shRNA rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: SMARCA4 KD

value: untreated


title: S2, DNA, +m

value: EcoGII Methylated


title: PC9-OR cells osimertinib SMARCA4 #1 shRNA rep 1 (RNA-seq)

value: osimertinib 250 nM


title: S1, DNA, -m

source_name: CTCF site 1 DNA from Mus Musculus amplified, gibson cloned and isolated (in vitro)

value: plasmid insert


title: PC9-OR cells osimertinib SMARCA4 #1 shRNA rep 2 (RNA-seq)


title: S1, DNA, +m


title: WT 20 month, omental adipose tissue [W18F21]

tag: age

value: 20 month


title: MycKO 5 month, omental adipose tissue [K5F5248]

value: MycKO


title: PC9-OR cells untreated SMARCA4 #1 shRNA rep 2 (RNA-seq)


title: MycKO 5 month, omental adipose tissue [K5F5218]

value: omental adipose tissue


title: S1, array, 5:1 +ADP,  ST, rep1

tag: snf2h remodeling turnover conditions

value: single-turnover

value: plus ADP

value: dna ratio:5:1 ratio


title: PC9-OR cells untreated SMARCA4 #1 shRNA rep 1 (RNA-seq)


title: Liver - Diet G - Rep4

value: Male

value: G


title: MycKO 5 month, omental adipose tissue [K5F5118]

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: Liver - Diet F - Rep4

value: F


title: S1, array, 10:1 +ADP,  ST, rep1

tag: histone

value: dna ratio:10:1 ratio


title: PC9-OR cells osimertinib scramble shRNA rep 2 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: WT


title: Liver - Diet C - Rep3

value: C


title: S1, array, 15:1 +ADP,  ST, rep1

tag: ecogii methylation

value: EcoGII Methylated


title: PC9-OR cells osimertinib scramble shRNA rep 1 (RNA-seq)

tag: cell line

value: osimertinib 250 nM


title: Liver - Diet B - Rep3

tag: Sex

value: B


title: Liver - Diet E - Rep8

value: E


title: PC9-OR cells untreated scramble shRNA rep 2 (RNA-seq)

tag: cell type

value: untreated


title: S1, array, 20:1 +ADP,  ST, rep1

value: single-turnover

value: dna ratio:20:1 ratio

value: plasmid insert


title: Liver - Diet A - Rep4

value: Male

tag: diet

value: A


title: S2, array, 5:1 +ATP,  ST, rep1

tag: snf2h remodeling atp/adp conditions

value: plus ATP

value: dna ratio:5:1 ratio


title: Liver - Diet C - Rep7


title: MycKO 5 month, omental adipose tissue [K5F4285]

value: omental adipose tissue

value: 5 month

value: MycKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: MycKO 5 month, omental adipose tissue [K5F4284]


title: PC9-OR cells untreated scramble shRNA rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: WT


title: S2, array, 10:1 +ATP,  ST, rep1

value: dna ratio:10:1 ratio

tag: mnase digestion temperature

value: EcoGII Methylated


title: Liver - Diet D - Rep3

value: D


title: Liver - Diet A - Rep3


title: MycKO 20 month, omental adipose tissue [K18F30]

value: 20 month


title: PC9 cells osimertinib rep 2 (RNA-seq)

value: osimertinib 250 nM


title: MycKO 20 month, omental adipose tissue [K18F29]


title: PC9 cells osimertinib rep 1 (RNA-seq)


title: MycKO 20 month, omental adipose tissue [K18F28]


title: S2, array, 15:1 +ATP,  ST, rep1

value: single-turnover

tag: mnase digestion duration

value: plasmid insert


title: MycKO 5 month, omental adipose tissue [K5F5116]


title: S2, array, 20:1 +ATP,  ST, rep1

value: dna ratio:20:1 ratio

tag: sample type


title: Liver - Diet F - Rep3

value: Male

value: F


title: Liver - Diet E - Rep9

value: E


title: Liver - Diet G - Rep3

value: G


title: MycKO 20 month, omental adipose tissue [K18F27]

tag: tissue

value: omental adipose tissue

value: MycKO


title: S1, array, 5:1 +M -ATP,  ST

value: minus ATP

value: dna ratio:5:1 ratio


title: MycKO 20 month, omental adipose tissue [K18F26]

tag: strain

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: Liver - Diet Ref - Rep9

value: Ref

tag: washbatch


title: S1, array, 10:1 +M -ATP,  ST

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: PC9 cells untreated rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

tag: genotype

value: WT

value: untreated


title: HCC827-OR cells rep 3 (RNA-seq)

value: Osimertinib resistant

tag: treatment

value: osimertinib 1 uM


title: Liver - Diet B - Rep9

value: Male

value: B


title: HCC827-OR cells rep 2 (RNA-seq)


title: S1, array, 15:1 +M -ATP,  ST

value: single-turnover

value: plasmid insert


title: S1, array, 20:1 +M -ATP,  ST

value: dna ratio:20:1 ratio


title: HCC827-OR cells rep 1 (RNA-seq)


title: S2, array 5:1 +M -ATP,  ST

value: minus ATP


title: PC9 cells untreated rep 2 (RNA-seq)


title: S2, array 10:1 +M -ATP,  ST


title: HCC827 cells rep 3 (RNA-seq)

value: Parental


title: T9_undiff_ana_72

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Base calling was done with Illumina NovaSeq software.
We used the SLAMdunk pipeline to map the reads and calculate the conversion rate due to the incorporation of 4sU.
The decay or synthesis half-life for each transcript was estimated by fitting a first-order exponential.
Assembly: mm10 assembly annotated with GENCODE vM17 genes
Supplementary files format and content: SlamDunk output as a tab-separated value table with conversion rates.
Library strategy: SLAM-seq

source_name: P19 cells

growth_protocol: Mouse embryonal carcinoma P19 cells (ATCC) were maintained in Dulbecco's modified Eagle's medium with 4,500 mg/L of glucose supplemented with 100 units/mL penicillin/streptomycin (Life Technologies) and 10% fetal bovine serum (FBS, Gemini Bio-Products).

extract_protocol:
Total RNA was extracted with TRIzol.
Libraries were constructed following the SLAM-seq catabolic and anabolic protocols using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: To induce neuronal differentiation, 3x105 cells were seeded in poly-L-lysine-coated 6-well plates in the presence TaKaRa NDiff® 227 Medium and 500 nM retinoic acid. Media was changed daily up to 6 days after induction.

value: P19 cells

value: Embryonal carcinoma

value: Undifferentiated

tag: treatment assay

value: anabolic

tag: treatment time


title: T9_undiff_ana_70


title: T3_undiff_ana_62


title: T3_undiff_ana_63


title: S2, array 15:1 +M -ATP, ST

tag: snf2h remodeling turnover conditions

tag: histone

value: dna ratio:5:1 ratio

value: EcoGII Methylated


title: Liver - Diet B - Rep2


title: T9_undiff_ana_71

tag: cell line

value: WT


title: HCC827 cells rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: untreated


title: Liver - Diet F - Rep2

tag: Sex

value: Male

value: F


title: Liver - Diet E - Rep2

value: E


title: Liver - Diet D - Rep2

value: D


title: H1975-OR cells rep 3 (RNA-seq)

tag: cell type

value: Osimertinib resistant

value: osimertinib 2 uM


title: S2, array, 20:1, +M, -ATP, ST

value: single-turnover

value: minus ATP

value: dna ratio:20:1 ratio

tag: ecogii methylation

value: plasmid insert


title: T3_undiff_ana_61

value: P19 cells

value: Embryonal carcinoma

value: Undifferentiated

value: anabolic


title: T1_undiff_ana_60

value: WT


title: H1975-OR cells rep 2 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells


title: HCC827 cells rep 2 (RNA-seq)

value: Parental

value: untreated


title: Ts12Ls-3

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
The clean miRNA reads were obtained from raw reads after discarding sequences, adaptor-ligated contaminants, and reads shorter than 18 nt.
Clean reads were compared against small RNAs in Rfam database to identify and remove rRNA, scRNA, sonRNA, snRNA, and tRNA.
Known miRNAs were identified by aligning against the miRbase database (v.22), and unannotated reads were considered as novel miRNAs according to their genome positions and hairpin structures using Mireap_v0.2.
Assembly: miRbase database (v.22)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: liver tissues

value: acute hypoxia

value: wild-type


title: T1_undiff_ana_59


title: Ts12Ls-2


title: H1975-OR cells rep 1 (RNA-seq)

value: Osimertinib resistant

value: osimertinib 2 uM


title: Liver - Diet G - Rep2

value: Male

tag: diet

value: G


title: Ts12Ls-1


title: T1_undiff_ana_58


title: Liver - Diet Ref - Rep2

value: Ref


title: Liver - Diet A - Rep10

value: A


title: Liver - Diet Ref - Rep10


title: Liver - Diet C - Rep2

value: C


title: H1975 cells rep 3 (RNA-seq)


title: T0_undiff_ana_57

value: P19 cells

value: Embryonal carcinoma

value: Undifferentiated


title: Liver - Diet A - Rep2


title: T0_undiff_ana_56

value: WT

value: anabolic


title: H1975 cells rep 1 (RNA-seq)

value: Lung tumor

value: lung adenocarcinoma cells

value: Parental


title: Tm12Ls-3

value: liver tissues

value: moderate hypoxia


title: Tm12Ls-2

value: wild-type


title: Liver - Diet B - Rep10

value: B


title: PC9-OR cells rep 3 (RNA-seq)

value: Osimertinib resistant

value: osimertinib 1 uM


title: T9_diff_ana_54

value: Neuronal differentiation


title: CLs-3

value: control


title: Tm12Ls-1


title: PC9-OR cells rep 2 (RNA-seq)


title: T0_undiff_ana_55


title: T9_diff_ana_53


title: Liver - Diet F - Rep9

value: Male

value: F


title: PC9 cells rep 3 (RNA-seq)

value: untreated


title: T9_diff_ana_52

value: P19 cells

value: Embryonal carcinoma


title: CLs-2


title: Liver - Diet C - Rep10

value: C


title: PC9-OR cells rep 1 (RNA-seq)

value: Lung tumor


title: Liver - Diet E - Rep10

value: E


title: CLs-1


title: Liver - Diet D - Rep10

value: D


title: H1975 cells rep 2 (RNA-seq)

value: lung adenocarcinoma cells

value: Parental


title: T3_diff_ana_45

value: WT

value: anabolic


title: Liver - Diet G - Rep10

value: G


title: Mp, B48hr3

city: Singapore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Lifescience Laboratory

data_processing:
STAR (v.2.5.3a) with default settings
Genome_build: Marchantia polymorpha MpTak1_V5.1 reference genome. Arabidopsis thaliana (TAIR10) reference genome. Lettuce Lsat_Salinas_v7_genomic
Supplementary_files_format_and_content: Raw read counts
Lists_of_DEGs.xlsx: lists of differentially expressed genes (DEGs) obtained from the following types of comparisons. 1) Comparisons between genotypes and treatments in the experiment involving M. polymorpha gemmalings of wild type Tak-1 and the knockout mutant gpb1-2 under two conditions (2 mM Ca and 0 mM Ca); 2) Comparisons between treatments in the experiment with Arabidopsis Col-0 seedlings under two conditions (2 mM Ca and 0 mM Ca); 3) Comparisons between treatments in the experiment with Lettuce wildtype under two conditions (2 mM Ca and 0.15 mM Ca).

organism: Marchantia polymorpha

source_name: Whole plant

growth_protocol: M. polymorpha Tak-1 and gpb1-2 gemma was grown in liquid Yamagami media with 1% sucrose for 6 days under continuous light (50 – 60 µmol m-2s-1) at 22°C. Arabidopsis thaliana Col-0 were grown on 1/2 MS media with 1% sucrose, 0.05% MES, 1% plant agar pH5.8 for six days under long-day condition (16 hr light / 8 hr darkness, 100 µmol/m2/sec and 22°C). Lettuce var. Little Gem were grown on water agar (1%) for 4 days under continuous light (50 – 60 µmol m-2s-1) at 22°C.

extract_protocol:
M. polymorpha gemmalings were collected through filtering through Miracloth. Arabidopsis and lettuce shoots were excised. All plant samples were immediately frozen in liquid nitrogen and followed by RNA extraction using Rneasy Plant Mini Kit. (Qiagen)
RNA libraries were prepared for sequencing using standard novaseq protocols

treatment_protocol: M. polymorpha 6-day old gemmalings were transferred to liquid Yamagami media with 1% sucrose, and with 0 mM of calcium chloride and treated for 48 hours. Arabidopsis 6-day old seedlings were transferred to Yamagami media with 1% sucrose, 1% plant agar, pH 5.8, with 2 mM CaCl2 or 0 mM CaCl2. Lettuce 4-day old seedlings were transferred to Yamagami media with 1% sucrose, 1% plant agar, pH 5.8 with 2 mM CaCl2 or 0.15mM CaCl2.

value: Thallus

tag: age

value: 6-day old

value: gpb1-2, k/o

tag: stress

value: calcium deficient condition


title: PC9 cells rep 2 (RNA-seq)


title: Mp, B48hr4


title: Mp, B48hr2


title: Liver - Diet G - Rep1

value: Male


title: T3_diff_ana_44

value: Neuronal differentiation


title: PC9 cells rep 1 (RNA-seq)

value: untreated


title: T1_diff_ana_42

value: P19 cells

value: Embryonal carcinoma


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 3 (ATAC-seq)

data_processing:
Quality control of the reads with FastQC (v0.11.8)
Trimming and adapter removal of the reads with Trimmomatic (0.39)
Alignment to human genome build 37 (GRCh37/hg19) reference genome with Bowtie2 (2.2.9)
Marking and removal of duplicates with Picard (2.9.0)
Samtools (1.9) was used to manage SAM & BAM files. Coverage of BAM files was obtained using deepTools bamCoverage (3.4.3)
Kent tools from UCSC were used to generate the visualization of bigwig files, which were managed in IGV (2.8.2)
BAM files from replicates were merged using Samtools and the peaks were called using Macs2 (2.1.1)
Peaks were counted using featureCounts (Subread package 2.0.0)
Assembly: GRCh37/hg19
Supplementary files format and content: BigWig files for the merge replicate samples are provided

extract_protocol:
For ATAC-sequencing sample preparation the Omni-ATAC Supplementary Protocol 1 was followed step by step as instructed by the authors (Corces et al., 2017). Nanodrop and Qubit methodologies were used to assess the concentration of the final amplified libraries.
Library was constructed using the Omni-ATAC-Seq protocol (Corces et al., 2017). Library quality control and Illumina sequencing was performed at the YCGA following their standard protocols (https://medicine.yale.edu/keck/ycga/)

value: Lung tumor

value: SMARCA4 KD

value: osimertinib 250 nM


title: Mp, B48hr1


title: T1_diff_ana_41


title: Liver - Diet E - Rep1

value: E


title: Liver - Diet Ref - Rep1

value: Ref


title: Liver - Diet F - Rep1

value: F


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 2 (ATAC-seq)

value: lung adenocarcinoma cells


title: YU-005C cells osimertinib SMARCA4 #2 shRNA rep 1 (ATAC-seq)


title: T1_diff_ana_40

value: WT

value: anabolic


title: T0_diff_ana_39


title: Liver - Diet B - Rep1

value: B


title: T3_diff_ana_43


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 3 (ATAC-seq)


title: Liver - Diet C - Rep1

value: C


title: Mp, B0hr3

value: Thallus

value: 6-day old

value: gpb1-2, k/o

value: control condition


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 2 (ATAC-seq)

value: untreated


title: Mp, B0hr2


title: Mp, B0hr1


title: T0_diff_ana_38

value: P19 cells

value: Embryonal carcinoma

value: Neuronal differentiation


title: YU-005C cells untreated SMARCA4 #2 shRNA rep 1 (ATAC-seq)

value: Lung tumor

value: SMARCA4 KD


title: T0_diff_ana_37


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 3 (ATAC-seq)

value: osimertinib 250 nM


title: Liver - Diet D - Rep1

value: Male

value: D


title: Mp, C48hr4

value: Tak-1, WT

value: calcium deficient condition


title: T9_undiff_cata_36

value: WT

value: Undifferentiated

value: catabolic


title: Mp, B0hr4

value: Thallus

value: 6-day old


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 2 (ATAC-seq)

value: lung adenocarcinoma cells


title: Mp, C48hr3


title: YU-005C cells osimertinib SMARCA4 #1 shRNA rep 1 (ATAC-seq)


title: Liver - Diet A - Rep1

value: A


title: Mp, C48hr2


title: T9_undiff_cata_35

value: P19 cells


title: Mp, C48hr1


title: T9_undiff_cata_34

value: Embryonal carcinoma


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 3 (ATAC-seq)

value: untreated


title: Mp, C0hr4

value: control condition


title: T3_undiff_cata_33


title: T3_undiff_cata_32


title: Mp, C0hr3


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 1 (ATAC-seq)

value: Lung tumor

value: SMARCA4 KD


title: Mp, C0hr2


title: T3_undiff_cata_31


title: YU-005C cells osimertinib scramble shRNA rep 3 (ATAC-seq)

value: osimertinib 250 nM


title: Sca1mAIDpln

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned at 3 µm resolution using an Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1.Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: Naïve CD8+ T cell of AID KO C57BL/6

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: CD8+ T cells or naïve (CD44low) CD8+ T cells were purified by autoMACS (Miltenyi Biotec; 130-096-543) and/or Mojosort system (MojoSort; 480008, 480044) according to the manufacturer’s instructions. We further isolated the interested population (e.g., Sca-1+ P1 CD8+ T cells) by FACSAria (BD Biosciences). The RNA of purified cells were extracted using the RNeasy Micro kit (QIAGEN) according to the manufacturer’s protocols.

value: Naive CD8+ T cells

value: AID KO

tag: gender

value: Female

value: Peripheral Lymph node


title: T1_undiff_cata_30

value: WT

value: Undifferentiated


title: Sca1pAIDpln

source_name: Naïve CD8+ T cell of  AID KO C57BL/6

tag: tissue


title: T1_undiff_cata_29

value: catabolic


title: AID_MLN

source_name: Total CD8+ T cell of AID KO C57BL/6

value: Total CD8+ T cells

value: Mesenteric lymph node

tag: strain


title: Sca1muMTpln

source_name: Naïve CD8+ T cell of  uMT C57BL/6

value: uMT


title: YU-005C cells osimertinib scramble shRNA rep 2 (ATAC-seq)

value: lung adenocarcinoma cells


title: Mp, C0hr1

value: Thallus

value: 6-day old

value: Tak-1, WT


title: Sca1puMTpln


title: YU-005C cells osimertinib scramble shRNA rep 1 (ATAC-seq)

value: Lung tumor


title: YU-005C cells untreated SMARCA4 #1 shRNA rep 2 (ATAC-seq)

value: SMARCA4 KD

value: untreated


title: T1_undiff_cata_28

value: P19 cells

value: Embryonal carcinoma


title: WT_MLN

source_name: Total CD8+ T cell of C57BL/6

value: Female


title: MMT_PLN

source_name: Total CD8+ T cell of uMT C57BL/6

value: Peripheral Lymph node


title: YU-005C cells untreated scramble shRNA rep 3 (ATAC-seq)

value: WT


title: T0_undiff_cata_27

value: Undifferentiated


title: CD8_MLN_MMT


title: YU-005C cells untreated scramble shRNA rep 2 (ATAC-seq)


title: CD8_MLN_WT


title: WT_PLN_(corresponding control for MMT_PLN)


title: P19 cells, D6, rep 3

description:
Direct RNA-seq
DESeq2_annotated_all.csv
master.polya.tsv

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10 assembly annotated with GENCODE vM17 genes and repetitive elements.
Supplementary files format and content: Comma-separated value file with polyA tail length, mapping transcript, and replicate information for each read.
Supplementary files format and content: DESeq results comparing Day 0 expression levels to Day 2, Day 4, and Day 6 expression levels.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted with TRIzol. Poly(A) RNAs were purified using Dynabeads™ Oligo(dT)25 (ThermoFisher).
Total RNA libraries were prepared with the Nanopore direct RNA-seq kit.
Libraries were run on a Nanopore R9 chip on a MinIon instrument.

value: Day 6


title: T0_undiff_cata_26

value: catabolic


title: PC9-OR cells osimertinib SMARCA4 #2 shRNA rep 2 (ATAC-seq)

value: osimertinib 250 nM


title: P19 cells, D6, rep 2


title: T9_diff_cata_18

value: Neuronal differentiation


title: AID_PLN

value: Total CD8+ T cells

value: AID KO


title: Hutu82_siCOL6A1#1_4

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 ug were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using TAC software using RMA and Repated Measure for patients were applied

label: biotin

source_name: primary GBM cells transfected with siRNA#1 against COL6A1

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Primary GBM cells were cultured DMEM/F12 supplemented with 10% BIT9500, 20 ng/ml basic Fibroblast Growth Factor (bFGF) and 20 ng/ml Epidermal Growth Factor (EGF) and maintained in an atmosphere of 2% oxygen, 5% carbon dioxide and balanced nitrogen in a H35 hypoxic cabinet.

extract_protocol: RNA was extracted using QIAzol and miRNeasy Micro Kit from Qiagen.

treatment_protocol: Transient transfection with 50pmol of siNEG, siCOL6A1#1, or siCOL6A1#2 and total RNA extraction after 72h

value: primary GBM cells

tag: sirna type

tag: sample


title: PC9-OR cells osimertinib SMARCA4 #2 shRNA rep 1 (ATAC-seq)

value: lung adenocarcinoma cells

tag: genotype

tag: treatment


title: P19 cells, D4, rep 3

value: Day 4


title: WT_PLN_(corresponding control for AID_PLN)


title: T9_diff_cata_17

tag: treatment assay

tag: treatment time


title: Hutu82_siCOL6A1#2_3

source_name: primary GBM cells transfected with siRNA#2 against COL6A1


title: P19 cells, D4, rep 2


title: PC9-OR cells untreated SMARCA4 #2 shRNA rep 2 (ATAC-seq)

value: Lung tumor

value: SMARCA4 KD


title: Hutu82_siCOL6A1#2_4


title: T9_diff_cata_16

value: P19 cells


title: Hutu82_siNeg_4

source_name: primary GBM cells transfected with negative control

value: siNEG


title: T3_diff_cata_15

value: Embryonal carcinoma


title: P19 cells, D4, rep 1


title: YU-005C cells untreated scramble shRNA rep 1 (ATAC-seq)

value: untreated


title: Hutu82_siCOL6A1#1_3


title: PC9-OR cells osimertinib SMARCA4 #1 shRNA rep 2 (ATAC-seq)


title: T0_undiff_cata_25

value: WT


title: P19 cells, D2, rep 3

value: Day 2


title: T3_diff_cata_14


title: P19 cells, D6, rep 1

value: Day 6


title: PC9-OR cells osimertinib SMARCA4 #1 shRNA rep 1 (ATAC-seq)


title: Hutu82_siNeg_3


title: Hutu82_siNeg_2


title: P19 cells, D2, rep 2


title: Hutu82_siCOL6A1#2_2


title: T1_diff_cata_12

value: catabolic


title: P19 cells, D2, rep 1


title: PC9-OR cells untreated SMARCA4 #1 shRNA rep 1 (ATAC-seq)


title: PC9-OR cells untreated SMARCA4 #2 shRNA rep 1 (ATAC-seq)


title: T1_diff_cata_11


title: PC9-OR cells osimertinib scramble shRNA rep 2 (ATAC-seq)

value: osimertinib 250 nM


title: Ls, NoCa3

organism: Lactuca sativa

source_name: Shoot

value: Shoot

value: 4-day old

value: calcium deficient condition


title: T1_diff_cata_10

value: Neuronal differentiation


title: Hutu82_siCOL6A1#2_1

value: primary GBM cells


title: P19 cells, D0, rep 2

value: Day 0


title: T0_diff_cata_09


title: P19 cells, D0, rep 3


title: Hutu82_siCOL6A1#1_2


title: PC9-OR cells osimertinib scramble shRNA rep 1 (ATAC-seq)

source_name: Lung tumor

value: Lung tumor

value: lung adenocarcinoma cells


title: Ls, NoCa2


title: T0_diff_cata_08

value: P19 cells


title: Ls, NoCa1


title: PC9-OR cells untreated scramble shRNA rep 2 (ATAC-seq)


title: T0_diff_cata_07


title: 77Bm1_1_flipped_out

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: small RNAs from cluster_77Bm1-1_cassette_removed

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) and then trimming 4nt from the 5' and the 3' end to remove random nucleotides contained in the adaptors.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries

organism: Drosophila melanogaster

source_name: ovary

growth_protocol:
25˚C, 12h dark/light, ovary dissection into 1x PBS on ice, snap frozen
OSC culture according to Niki et al., PNAS, 2006

extract_protocol:
Libraries were prepared by ligation of 3' and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)

value: ovary

value: 4-6 days old


title: P19 cells, D0, rep 1

value: Embryonal carcinoma


title: Hutu82_siNeg_1

value: siNEG


title: Ls, Ca3

value: WT

value: control condition


title: PC9-OR cells untreated SMARCA4 #1 shRNA rep 2 (ATAC-seq)

value: SMARCA4 KD

value: untreated


title: PC9 cells untreated rep 2 (ATAC-seq)


title: Embryoid body, Day 4, C2 ceramide treated

city: Bunkyo-ku

first: Satoshi

last: Kofuji

state: Tokyo

address: 1-5-45 Yushima

institute: Institute of Science Tokyo

description:
EB_ceramide_gene_expression.txt
EB_ceramide_transcript_expression.txt

data_processing:
DRAGEN
Adaptor sequence was not removed. Sequence reads were mapped to GGRCm39 (mm39RC) using DRAGEN.
Read count extraction and normalization were performed using DRAGEN
Assembly: mm39RC
Supplementary files format and content: Tab-delimited text files for both gene expression and transcript expression include TPM values and read counts in each sample.

source_name: Embryoid body

growth_protocol: mES cells (3×10^3) were cultured in 25 µl hanging drops in medium without LIF (Dulbecco’s modified Eagle’s medium (26400044; Gibco, Massachusetts, USA) supplemented with 15% bovine calf serum (SFBM30-2362; Equitech-bio, Texas, USA), 0.1 mM 2-mercaptoethanol (M3148; Sigma, Burlington, USA)) to form embryoid bodies. After 2 days, embryoid bodies were transferred into a non-coated bacterial Petri dish for suspension culture.

extract_protocol:
RNeasy Mini Kits (74104; QIAGEN, Hilden, German) were used for total RNA extraction according to the manufacturer’s instructions. Extracted RNA was incubated with DNase I (2270B; Takara, Shiga, Japan) to degrade the genomic DNA. The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and subsequently by absorption spectrophotometry.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input Kit following manufacturer's protocols.

treatment_protocol: Embryoid bodies were treated with 30 μM C2 ceramide (860502P; Avanti Polar Lipids, Alabama, USA) from the beginning of day 3

value: embryonic stem cells

value: formed embryiod body in LIF free medium and treated with 30 μM C2 ceramide from the begining of day 3

value: Embryoid body

tag: time

value: Day 4


title: Ls, Ca2

value: Shoot

value: 4-day old


title: wt_w1118

description: small RNAs from w1118 ovaries

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GTCAGAGATCGGAAGAGCACACGTCT) and then trimming 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries

extract_protocol:
Libraries were prepared by ligation of 3' barcoded adaptors containing 6 random nucleotides and a 5 nt in-line barcode and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)

value: w1118 strain homozygous


title: 7B_minos_insertion_44898

description: small RNAs from cluster77B_Mi(MIC)MI07908

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GTCAGAGATCGGAAGAGCACACGTCT ) and then trimming 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries


title: Embryoid body, Day 4, control

tag: cell line

value: formed embryiod body in LIF free medium


title: Ls, Ca1


title: PC9 cells untreated rep 1 (ATAC-seq)

value: Lung tumor

value: lung adenocarcinoma cells


title: Hutu82_siCOL6A1#1_1

value: primary GBM cells


title: ACC59  (Agilent)

status: Public on Aug 02 2023

type: genomic

city: Gothenburg

first: Mattias

last: Andersson

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent SurePrint G3 Human CGH Microarray 4X180K and Human Genome CGH Microarray 244K) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent Microarray Confocal Scanner (G2506B) and the images were quantified with Agilent Feature Extraction Software (v.12.0.1.1) using the intensity-dependent linear normalization method.

data_processing:
Data analysis was carried out using Nexus Copy Number software v.8.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the FASST2 segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to P=1.0E-8 for FFPE and P=10E-6 for FF and the Log2 ratio thresholds for gain/loss were set to 0.25/−0.2 for FF and 0.3/-0.3 for FFPE; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.
*TMA.txt processed data files report normalized log10 ratio (Cy5/Cy3) representing tumor DNA/normal DNA

source_name: adenoid cystic carcinoma

label_protocol: Genomic tumor DNA and sex-matched reference normal DNA (pooled peripheral blood cells from 5 normal female and male genomes) were labeled with Cy5-dUTP and Cy3-dUTP (Agilent).

extract_protocol: Genomic DNA was isolated from FF and FFPE tumor specimens using the Qiagen DNeasy Blood & Tissue Kit and QIAamp DNA FFPE Tissue Kit respectively (Qiagen GmbH, Hilden, Germany).

treatment_protocol: Fresh frozen (FF) tumor material from 58 ACCs and formalin-fixed paraffin-embedded (FFPE) tumor material from 42 ACCs were obtained  from Sahlgrenska university hospital, Gothenburg university, Sweden; MD Anderson Cancer Center, University of Texas, US; the University of Virginia Hospital, Virginia, US; Hamburg University Medical Centre, Hamburg, Deutschland, the Portuguese Institute of Oncology, Lisboa, Portugal; and Icahn School of Medicine at Mount Sinai, New York, US. Tumors were classified according to the WHO histological classification of salivary gland tumors and graded as tumors with no solid component (grade 1), <30% solid component (grade 2), and ≥30% solid component (grade 3).

value: adenoid cystic carcinoma

tag: obtained from

value: The University of Texas MD Anderson Cancer Center

tag: tumor grade

value: male

tag: tumor material

value: FF

source_name: normal tissue

value: normal tissue


title: ACC60  (Agilent)

value: female


title: PC9-OR cells untreated scramble shRNA rep 1 (ATAC-seq)

tag: cell type

value: WT

value: untreated


title: ACC56  (Agilent)

tag: age


title: ACC57  (Agilent)


title: ACC49  (Agilent)


title: ACC47  (Agilent)


title: ACC50  (Agilent)


title: ACC54  (Agilent)


title: ACC52  (Agilent)


title: ACC55  (Agilent)


title: ACC46  (Agilent)


title: ACC45  (Agilent)


title: ACC44  (Agilent)


title: ACC51  (Agilent)


title: ACC39  (Agilent)

value: Icahn School of Medicine at Mount Sinai

value: FFPE


title: ACC43  (Agilent)


title: ACC41  (Agilent)


title: wt_iso1

description: small RNAs from iso1 ovaries

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TGACTAGATCGGAAGAGCACACGTCT) and then trimming 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries

value: ovary

value: 4-6 days old

value: iso-1 strain homozygous


title: ACC38  (Agilent)


title: ACC40  (Agilent)


title: ACC42  (Agilent)


title: Embryoid body, Day 3, control

value: embryonic stem cells

value: formed embryiod body in LIF free medium

value: Embryoid body

value: Day 3


title: ACC34  (Agilent)

value: adenoid cystic carcinoma


title: ACC58  (Agilent)

value: The University of Texas MD Anderson Cancer Center


title: ACC37  (Agilent)


title: ACC35  (Agilent)

value: male


title: ACC36  (Agilent)


title: ACC53  (Agilent)

value: FF


title: ACC32  (Agilent)

value: normal tissue


title: ACC28  (Agilent)


title: ACC30  (Agilent)


title: ACC23  (Agilent)

value: female


title: ACC25  (Agilent)


title: ACC22  (Agilent)


title: ACC21  (Agilent)


title: ACC20  (Agilent)


title: ACC19  (Agilent)


title: ACC29  (Agilent)


title: ACC18  (Agilent)


title: ACC48  (Agilent)


title: ACC15  (Agilent)


title: ACC14  (Agilent)


title: ACC13  (Agilent)


title: ACC33  (Agilent)


title: ACC12  (Agilent)


title: ACC11  (Agilent)


title: ACC10  (Agilent)


title: ACC16  (Agilent)


title: ACC31  (Agilent)


title: ACC17  (Agilent)


title: ACC27  (Agilent)


title: ACC26  (Agilent)


title: ACC24  (Agilent)


title: Z309T

city: Prague

first: Petr

last: Holý

address: Šrobárova 48/49

country: Czech Republic

institute: National Institute of Public Health

hyb_protocol: Hybridized and washed using the default manufacturer’s protocol v4.0.

scan_protocol: Scanned using the Agilent Microarray Scanner instrument with SureScan v9 software (Agilent Technologies Inc., CA, USA). All settings were as recommended by the manufacturer and default for the platform.

data_processing: Data were extracted using the Feature Extraction software 11.5 (both Agilent Technologies Inc., CA, USA). All settings were as recommended by the manufacturer and default for the platform.

source_name: breast tumor

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and Hyb Kit and the SurePrint G3 Unrestricted miRNA 8x60K v19.0 microarray slides (both Agilent Technologies Inc., CA, USA) were used according to the manufacturer’s protocol v4.0. 100 ng of total RNA per sample was dephosphorylated, labeled with Cyanine 3-pCp according to the default manufacturer’s protocol v4.0.

growth_protocol: Primary tumor tissue resected from patients

extract_protocol: Total RNA was extracted from tumor tissue using the TRIZOL reagent (Thermofisher) following the manufacturer’s protocol. The tissue was first pulverized with mortar and pestle under liquid nitrogen.

tag: disease

value: early-stage luminal breast cancer

tag: Sex


title: Z303T


title: Z315T


title: Z297T


title: Z267T


title: Z320T


title: Z229T


title: Z265T


title: Z256T


title: Z206T


title: Z194T


title: Z183T


title: Z188T


title: Z160T


title: Z182T


title: Z161T


title: Z168T


title: Z163T


title: Z159T


title: Z223T


title: Z148T


title: Z145T


title: Z139T


title: Z138T


title: Z103T


title: Z107T


title: Z084T


title: Z187T


title: Z078T


title: Z074T


title: Z076T


title: Z069T


title: Z042T


title: Z065T


title: Z157T


title: Z007T


title: Z022T


title: Z039T


title: P611T


title: P534T


title: P494T


title: P525T


title: P424T


title: P477T


title: P489T


title: P433T


title: P422T


title: P332T


title: P377T


title: P539T


title: P400T


title: P370T


title: P368T


title: P267T


title: P535T


title: P220T


title: P268T


title: P271T


title: P287T


title: P227T


title: P421T


title: P420T


title: P408T


title: P272T


title: P290T


title: P215T


title: P210T


title: P190T


title: P188T


title: P189T


title: P179T


title: P207T


title: P176T


title: P217T


title: P174T


title: P049T


title: P195T


title: P054T


title: P044T


title: P125T


title: P158T


title: P151T


title: P026T


title: P115T


title: P061T


title: M366T


title: P196T


title: P596T


title: M389T


title: M396T


title: M406T


title: M415T


title: M420T


title: M408T


title: M330T


title: P021T


title: M325T


title: M358T


title: M326T


title: M318T


title: M305T


title: M294T


title: M315T


title: M255T


title: M235T


title: M250T


title: M291T


title: M202T


title: M226T


title: M218T


title: M234T


title: M259T


title: M284T


title: M199T


title: M266T


title: M290T


title: M251T


title: M172T


title: M277T


title: M154T


title: siLINC01534-2 cells_rep2

city: Suita

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: LINC01534-2 knockdown HCT116 cells_rep2

data_processing:
Sequencing was performed on an Illumina Hiseq2500 platform in a 75-base single-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: LINC01534-2 knockdown HCT116 cells_rep2

extract_protocol:
An RNeasy Mini Kit (Qiagen) was used to isolate total RNA.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.


title: siLINC01534-1 cells_rep2

description: LINC01534-1 knockdown HCT116 cells_rep2

source_name: LINC01534-1 knockdown HCT116 cells_rep2


title: siLINC01534-1 cells_rep1

description: LINC01534-1 knockdown HCT116 cells_rep1

source_name: LINC01534-1 knockdown HCT116 cells_rep1


title: Parent_cells_rep1

description: Parent_HCT116 cells_rep1

source_name: Parent_HCT116 cells_rep1


title: Parent_cells_rep2

description: Parent_HCT116 cells_rep2

source_name: Parent_HCT116 cells_rep2


title: M152T


title: siLINC01534-2 cells_rep1

description: LINC01534-2 knockdown HCT116 cells_rep1

source_name: LINC01534-2 knockdown HCT116 cells_rep1


title: M111T


title: M097T


title: M098T


title: M169T


title: sample_3943

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 7

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: Tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation.

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

value: yeast

value: deletion CKF44_07470

tag: medium

value: YPD

tag: atmosphere

value: room air

tag: temperature

value: cAMP none

value: 90 min


title: sample_3941

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 6

value: deletion CKF44_05081


title: sample_3591

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-09-07, biol rep: 4


title: sample_3937

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-11-08, biol rep: 5

value: WT


title: sample_3484

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 2


title: sample_3482

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 1


title: sample_3935

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 9

value: 30 min


title: sample_3488

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 90 min, librarydate: 2021-07-19, biol rep: 3


title: sample_3933

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-11-08, biol rep: 8


title: sample_3476

description: medium: YPD, atmosphere: room air, temperature: 30C, cAMP: none, time: 30 min, librarydate: 2021-07-19, biol rep: 2