title: Mouse 4, CSF-cNs enriched by FACS

city: San Francisco

first: David

last: Julius

state: CA

address: Genentech Hall Room N-276, 600 16th Street

department: Physiology

institute: UCSF

data_processing:
Sequencing quality was examined by using FASTQC.
Adapters and low-quality reads were trimmed or removed by TrimGalore.
Reads were then aligned to the annotated mouse reference genome (mm10) containing an additional exogenous sequence for AAV-CAG-tdT by using STAR through RSEM.
Gene counts were imported into RStudio (v4.2.0) for analysis by using the DESeq2 module (v1.36.0, Bioconductor v3.16).
Assembly: mm10 containing an additional exogenous sequence for AAV-CAG-tdT
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized abundance values for each sample

source_name: Spinal cord

extract_protocol:
Sagittal slices of the spinal cord containing the ependymal region were prepared by using a vibratome. Slices were cut into smaller pieces and transferred into Enzyme Mix 1 (955 μl of Buffer Z, 25 μl of Enzyme P from Miltenyi Biotec) for 15-min incubation at 37°C, followed by addition of Enzyme Mix 2 (15 μl of Buffer Y, 7.5 μl of Enzyme A from Miltenyi Biotec) and another 5-min, 37°C incubation. The digested tissues were transferred to 1 ml HABG (97.75% Hibernate A Low Fluorescence, 2% B27 supplement, 0.25% GlutaMAX) and were mechanically dissociated. After centrifugation over 4-ml 20% Percoll (in HABG) at 300 rcf for 15 min in a cold room, supernatant was removed, and cells were resuspended in 0.8 ml HABG containing 0.4 U/μl Ribolock RNase inhibitor and a far-red LIVE/DEAD dye (1:1000). The cell suspension was sorted based on forward and side scatters, as well as tdTomato and LIVE/DEAD fluorescence in a BD Biosciences FACSAria II Cell Sorter by using a C57BL6 preparation as negative control. Fifty cells were collected in ice-cold lysis buffer  from Takara Bio.
cDNA synthesis was done according to the Smart-Seq v4 manual (Takara Bio) with a PCR cycle number of 11. cDNA library was prepared by using Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: CSF-cNs were labelled by intracerebroventricular injection of AAV2-CAG-tdT

value: Spinal cord

value: Enriched in CSF-cNs

value: AAV2-CAG-tdT injected


title: Mouse 3, CSF-cNs enriched by FACS

status: Public on Jun 29 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: LOS_H3_S260_Aligned.quant

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

library_source: transcriptomic single cell

data_processing:
raw sequencing reads were aligned to the mouse reference genome (UCSC release mm39) using STAR (v2.6)
The expression values of each gene were quantified as both raw counts and transcripts per million (TPM) using Salmon (v.1.4.0), and compiled in R (v.3.6.1) using RStudio (v.3.4.2) by Tximport (v.1.12.3)
Raw count and metadata matrices for HFSCs across the hair cycle were loaded in SCANPY as an AnnData object. Single cell data was preprocessed to remove lowly detected genes (expressed in <75 cells) and cells with low complexity libraries (<2,000 genes detected).
SCANPY was used to normalize counts per cell, and highly variable genes were detected. Prior to dimensionality reduction by principal component analysis (PCA), data was centered and scaled. PCA was performed on highly variable genes, with 100 components and the svd_solver using ‘arpack’ (SCANPY default setting). To construct a k-nearest neighbours graph on Euclidean distance, 41 principal components were used (which captured 25% of the variance in the data). Data was visualized using uniform manifiold projection (UMAP) in SCANPY, and clustering was done using the Leiden algorithm (with a resolution setting of 0.5). Cluster resolution was chosen after iterating through resolution parameters from 0.1 to 0.75, as best capturing both hair follicle cycle stages and anatomic location (upper bulge region/upper ORS versus hair germ/upper-middle ORS versus lower ORS).
Assembly: mm39
Supplementary files format and content: raw count matrix as txt
Supplementary files format and content: metadata for samples as txt

source_name: skin

extract_protocol:
Cells from 3-6 animals were pooled prior to FACS-isolation. In brief, cells were sorted into hypotonic lysis buffer, snap frozen in liquid nitrogen and stored at -80oC until all samples were collected. Cells were lysed by heating at 72oC for 3 min, followed by reverse transcription of mRNA using dT30 oligos, template switching oligos and Maxima H- reverse transcriptase. The whole transcriptome was amplified (15 cycles) by KAPA HiFi DNA polymerase (Roche), and then size-selected using 0.6X AmpPure XP beads (Beckman Coulter). To exclude cells with poor amplification, and wells containing multiple cells, qPCR for Gapdh was performed.
Illumina sequencing libraries were indexed with unique 5’ and 3’ barcode combinations (up to 384 cells) using the Nextera XT DNA library preparation kit (Illumina). Libraries were pooled and size-selected with 0.9X AmpPure XP beads. Prior to sequencing on Illumina NextSeq500 using a 75 bp paired-end read mid-output setting, library quality was assessed by TapeStation (Agilent).

value: skin

value: hair follicle epithelial cell

value: wild type

tag: hair follicle_epithelia_region

value: lower outer root sheath

tag: hair cycle_stage

value: AnaVI


title: Mouse 2, CSF-cNs enriched by FACS


title: LOS_H2_S259_Aligned.quant


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_Rep3

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 3

library_source: genomic

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for deletion rate around the gRNA target sites.
Supplementary files format and content: txt file for indel rate for gRNA taget sites.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF7 cells were maintained inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
Two round PCR were performed, the forward and reverse primers were used to amplify the target site of the first round of PCR, and then an equal amount of the first PCR product was mixed with primers containing P5 and p7 for a second round of PCR to generate the library.

treatment_protocol: In 24-well plates, MCF7 cells were transfected with 490ng gRNA plasmids and 10ng CasMINI or hpCasMINI or SpCas9 or LbCas12a plasmids.

tag: cell line

value: epithelial cell


title: LOS_H11_S268_Aligned.quant


title: LOS_H1_S258_Aligned.quant


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 2


title: MOS_A1_S91_Aligned.quant

value: upper-middle outer root sheath


title: LOS_H10_S267_Aligned.quant


title: CasMINI_SM7_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 7 repeat 1


title: Mouse 1, CSF-cNs enriched by FACS


title: LOS_G9_S254_Aligned.quant


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 3


title: LOS_G6_S251_Aligned.quant


title: LOS_G7_S252_Aligned.quant


title: LOS_G8_S253_Aligned.quant


title: LOS_G5_S250_Aligned.quant


title: sh_2_tumor

city: Shanghai

first: Hu

last: Cegui

address: 160 Pujian Road, Pudong New Area, Shanghai

institute: Ren Ji Hospital

data_processing:
Isolation of mRNA
Fragmentation of mRNA
First strand cDNA synthesis
Second strand cDNA synthesis
End of chain repair
Add A to the end of the 3 '
Add connection connector
Chain enrichment
The sequencing sample library was constructed
Assembly: mm10
Supplementary files format and content: excel spreadsheet file includes counts and FPKM for each sample

molecule: total RNA

source_name: Tumor

extract_protocol:
Tianmo#TR205-200 kit was used for RNA extraction of samples in this project. The extraction strictly followed the standard operating process manual provided by the kit manufacturer, and the extracted total RNA of samples was obtained.
The library was constructed according to the attached library construction experimental procedure. See the attached operation manual for the library construction procedure

value: Tumor

value: mesenchymal cell

value: FGF21 Knockdown


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 1


title: CasMINI_SM6_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 6 repeat 2


title: LOS_G3_S248_Aligned.quant


title: LOS_G2_S247_Aligned.quant


title: sh_1_tumor


title: microvascular endothelial cells, Wild type, Unstimulated, rep 4

city: Bethesda

first: Kirk

middle: M.

last: Druey

state: MD

address: 10 Center Drive Room 11N238A

department: NIAID

institute: National Institutes of Health

data_processing:
Adapter and quality trimmed using CutAdapt v1.18
Trimmed reads were mapped to GRCh38 reference and GENCODE v39 using STAR v2.7.6a in 2pass mode
Gene-level expression quantification was performed using RSEM v.1.3.0
Assembly: GRCh38, GENCODE v39

source_name: Dermal microvascular endothelial cell line

extract_protocol:
Direct-zol RNA Miniprep Kit
Illumina TruSeq RNA Library Kit v2

treatment_protocol: Stimulated cells were stimulated with CM-M (5% vol/vol) for 16 hours

value: PARP15 G628R

value: Unstimulated


title: LOS_G12_S257_Aligned.quant


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 3


title: microvascular endothelial cells, Wild type, Unstimulated, rep 2

value: Dermal microvascular endothelial cell line


title: NC_1_tumor

value: WT


title: LOS_G10_S255_Aligned.quant


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 1


title: microvascular endothelial cells, Wild type, Unstimulated, rep 3


title: sh_3_tumor


title: sh2sh4_Tcell

value: T cell

value: Immune cell

value: FGF22 Knockdown


title: CasMINI_SM4_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 3


title: LOS_G1_S246_Aligned.quant

value: skin


title: CasMINI_SM4_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 2


title: LOS_G4_S249_Aligned.quant

value: hair follicle epithelial cell


title: microvascular endothelial cells, Wild type, Unstimulated, rep 1


title: LOS_F8_S241_Aligned.quant

value: wild type


title: NC124_Tcell


title: CasMINI_SM4_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 4 repeat 1


title: microvascular endothelial cells, Wild type, 16 hour stimulation, rep 4

value: CM-Mf (5% vol/vol) stimulated


title: LOS_F9_S242_Aligned.quant

value: lower outer root sheath

value: AnaVI


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 3

value: epithelial cell


title: NC_6_tumor

value: Tumor


title: NC_2_tumor

value: mesenchymal cell


title: N2N3N5_Tcell


title: LOS_G11_S256_Aligned.quant


title: microvascular endothelial cells, Wild type, 16 hour stimulation, rep 3


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 2


title: N6N7N8_Tcell


title: microvascular endothelial cells, Wild type, 16 hour stimulation, rep 2


title: CasMINI_SM5_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 5 repeat 2


title: LOS_F7_S240_Aligned.quant


title: LOS_F6_S239_Aligned.quant


title: testis HSCF-3 [THSCF3]

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

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

source_name: testis

extract_protocol:
Testis were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

value: testis

tag: age

value: 10 weeks

value: High fat diet & STZ+control-FMT


title: testis HSCF-2 [THSCF2]


title: LOS_F4_S237_Aligned.quant


title: microvascular endothelial cells, Wild type, 16 hour stimulation, rep 1

value: Dermal microvascular endothelial cell line

value: PARP15 G628R


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 3


title: LOS_F5_S238_Aligned.quant


title: microvascular endothelial cells, PARP15 mutant, Unstimulated, rep 3

value: Unstimulated


title: CasMINI_SM3_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 3 repeat 1


title: sh1sh3_Tcell

value: T cell

value: Immune cell

value: FGF21 Knockdown


title: LOS_F3_S236_Aligned.quant

value: skin

value: hair follicle epithelial cell

value: wild type


title: testis HSCF-1 [THSCF1]


title: microvascular endothelial cells, PARP15 mutant, Unstimulated, rep 2


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 2


title: CasMINI_SM2_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 2 repeat 1


title: testis HSAF-3 [THSAF3]

value: High fat diet & STZ+AOS10mg/kg-FMT


title: LOS_F2_S235_Aligned.quant

value: lower outer root sheath

value: AnaVI


title: LOS_F12_S245_Aligned.quant


title: microvascular endothelial cells, PARP15 mutant, Unstimulated, rep 1


title: testis HSAF-2 [THSAF2]


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 3

value: epithelial cell


title: testis HSAF-1 [THSAF1]

value: ICR


title: microvascular endothelial cells, PARP15 mutant, 16 hour stimulation, rep 4

value: CM-Mf (5% vol/vol) stimulated


title: testis HSA10-3 [THSA3]

value: testis

value: 10 weeks

value: High fat diet & STZ+AOS10mg/kg


title: microvascular endothelial cells, PARP15 mutant, 16 hour stimulation, rep 3

value: Dermal microvascular endothelial cell line

value: PARP15 G628R


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 1


title: CasMINI_SM1_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, single mismatch gRNA site 1 repeat 2


title: LOS_F10_S243_Aligned.quant


title: testis HSA10-2 [THSA2]


title: microvascular endothelial cells, PARP15 mutant, 16 hour stimulation, rep 2


title: LOS_F1_S234_Aligned.quant


title: microvascular endothelial cells, PARP15 mutant, 16 hour stimulation, rep 1


title: LOS_E9_S231_Aligned.quant


title: testis HSA10-1 [THSA1]


title: blood_P3

city: Poznań

first: Katarzyna

last: Rolle

address: Noskowskiego 12/14

department: Department of Molecular Neurooncology

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

description: patient blood 3

data_processing:
Quality control of raw sequencing reads was done with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were removed using Trimmomatic (doi: 10.1093/bioinformatics/btu170), version 0.38 with the following parameters ILLUMINACLIP:2:30:10 SLIDINGWINDOW:10:25 MINLEN:35.
Genomic index was created using Burrows-Wheeler aligner (doi: 10.1093/bioinformatics/btu356), version 0.7.17 (bwa –bwtsw).
Reads were mapped to the human genome with the following parameters: bwa-mem –T 19.
CircRNAs were detected from alignment files with CIRI (doi: 10.1186/s13059-014-0571-3), version 2.0.6 using default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tabular text file with raw circRNA counts

source_name: glioblastoma patient blood

extract_protocol:
Total RNA extraction from GBM patient tissue was performed with TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA samples have been subjected to DNase I treatment using a ready-to-use DNA-free™ DNA Removal Kit reagents following the manufacturer’s instructions (Ambion). The quality of purified RNA was measured utilizing NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) followed by agarose gel electrophoresis. RNA integrity was verified on an Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA extraction from blood was performed with TRI LS Reagent® Solution (Thermo Fisher Scientific). Blood was stored in EDTA bloods in 4°C and RNA was extracted within 4 hours from collection. First, blood was diluted with PBS in 1:2 ratio, then adequate TRI LS Reagent® Solution was added. After incubation with chloroform, centrifugation and supernatant collection isopropanol was added and incubation was performed in –20 °C through the night. Finally, after centrifugation and ethanol precipitation depc-treated water was added and the quality of purified RNA was measured utilizing NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) followed by agarose gel electrophoresis. RNA integrity was verified on an Agilent Bioanalyzer 2100 (Agilent Technologies).
300 ng of total RNA were rRNA depleted using RNase H according to the protocol (http://dx.doi.org/10.1126/science.aam8526). Ribosomal depleted libraries were constructed using Illumina’s TruSeq Total RNA Library Prep Kit. Adaptor ligation were performed according to manufacturer’s instructions and the cDNA fragments were amplified with qPCR for 8-15 cycles. After the purification with AMPure XP beads the DNA concentration was measured with Qubit and the fragments length were defined with Screen Tape Assay Agilent D1000, 4200 Tape Station System.

value: blood

tag: disease

value: primary glioblastoma


title: testis HS-3 [THS3]

value: High fat diet & STZ


title: CasMINI_Full_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, complete gRNA repeat 3


title: LOS_E8_S230_Aligned.quant

value: skin


title: CasMINI_Full_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, complete gRNA repeat 1


title: LOS_F11_S244_Aligned.quant

value: hair follicle epithelial cell


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting two different genomic sites, repeat 3


title: testis HS-1 [THS1]


title: blood_P1

description: patient blood 1


title: blood_P2

description: patient blood 2


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting two different genomic sites, repeat 2


title: testis con-3 [Tcon3]

value: control


title: microvascular endothelial cells, PARP15 mutant, Unstimulated, rep 4

value: Unstimulated


title: LOS_E4_S226_Aligned.quant

value: wild type

value: lower outer root sheath


title: blood_H4

description: healthy donor blood 4

source_name: healthy donor blood


title: testis con-2 [Tcon2]


title: blood_H3

description: healthy donor blood 3


title: LOS_E5_S227_Aligned.quant

value: AnaVI


title: Ctrl_Deep-seq_OsCas12f1_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected without the enOsCas12f1 or hpOsCas12f1 system targeting seven different genomic sites, repeat 3

value: epithelial cell


title: testis con-1 [Tcon1]

value: ICR


title: CasMINI_Full_Deep-seq_gRNA-mismatch_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting two different genomic sites, complete gRNA repeat 2


title: blood_H2

description: healthy donor blood 2


title: testis A10-3 [TA3]

value: testis

value: AOS 10mg/kg


title: blood_H1

description: healthy donor blood 1


title: LOS_E3_S225_Aligned.quant


title: testis HS-2 [THS2]

value: 10 weeks


title: Ctrl_Deep-seq_OsCas12f1_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected without the enOsCas12f1 or hpOsCas12f1 system targeting seven different genomic sites, repeat 2


title: LOS_E7_S229_Aligned.quant


title: testis A10-2 [TA2]


title: R3

description: GBM recurrent patient 29

source_name: recurrent glioblastoma

value: brain

value: recurrent glioblastoma


title: LOS_E6_S228_Aligned.quant


title: LOS_E11_S233_Aligned.quant


title: hpOsCas12f1_Deep-seq_OsCas12f1_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpOsCas12f1 system targeting seven different genomic sites, repeat 3


title: Ctrl_Deep-seq_OsCas12f1_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected without the enOsCas12f1 or hpOsCas12f1 system targeting seven different genomic sites, repeat 1


title: R2

description: GBM recurrent patient 28


title: hpOsCas12f1_Deep-seq_OsCas12f1_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpOsCas12f1 system targeting seven different genomic sites, repeat 2


title: CasMINI_Ctrl_Deep-seq_gRNA-mismatch_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI system targeting two different genomic sites, repeat 1


title: R1

description: GBM recurrent patient 27


title: LOS_E1_S223_Aligned.quant


title: spleen HSCF-3 [SHSCF3]

source_name: spleen

extract_protocol:
Spleen were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: High fat diet & STZ+control-FMT


title: hpOsCas12f1_Deep-seq_OsCas12f1_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpOsCas12f1 system targeting seven different genomic sites, repeat 1


title: P26

description: GBM primary patient 26

source_name: primary glioblastoma

value: primary glioblastoma


title: spleen HSCF-2 [SHSCF2]


title: P25

description: GBM primary patient 25


title: LOS_D9_S219_Aligned.quant

value: skin


title: LOS_E2_S224_Aligned.quant

value: hair follicle epithelial cell


title: LOS_D8_S218_Aligned.quant


title: spleen HSAF-3 [SHSAF3]

value: High fat diet & STZ+AOS10mg/kg-FMT


title: spleen HSCF-1 [SHSCF1]


title: LOS_D7_S217_Aligned.quant


title: enOsCas12f1_Deep-seq_OsCas12f1_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the enOsCas12f1 system targeting seven different genomic sites, repeat 3


title: P23

description: GBM primary patient 23


title: enOsCas12f1_Deep-seq_OsCas12f1_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the enOsCas12f1 system targeting seven different genomic sites, repeat 1


title: SpCas9_Deep-seq_compare_Rep3

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat3


title: enOsCas12f1_Deep-seq_OsCas12f1_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the enOsCas12f1 system targeting seven different genomic sites, repeat 2


title: LOS_E10_S232_Aligned.quant


title: LOS_D5_S215_Aligned.quant


title: spleen HSAF-2 [SHSAF2]


title: LOS_D6_S216_Aligned.quant


title: SpCas9_Deep-seq_compare_Rep2

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat2


title: P22

description: GBM primary patient 22


title: P21

description: GBM primary patient 21


title: spleen HSA10-3 [SHSA3]

value: High fat diet & STZ+AOS10mg/kg


title: LOS_D4_S214_Aligned.quant

value: wild type


title: P20

description: GBM primary patient 20


title: testis A10-1 [TA1]


title: spleen HSA10-2 [SHSA2]


title: LOS_D3_S213_Aligned.quant

value: lower outer root sheath


title: spleen HSA10-1 [SHSA1]


title: LOS_D2_S212_Aligned.quant

value: AnaVI


title: LbCas12a_Deep-seq_compare_Rep3

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat3

value: epithelial cell


title: LbCas12a_Deep-seq_compare_Rep2

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat2


title: P19

description: GBM primary patient 19


title: P24

description: GBM primary patient 24


title: P18

description: GBM primary patient 18


title: LOS_D11_S221_Aligned.quant


title: LbCas12a_Deep-seq_compare_Rep1

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, LbCas12a repeat1


title: spleen HSAF-1 [SHSAF1]

value: ICR


title: P17

description: GBM primary patient 17


title: spleen HS-2 [SHS2]

value: High fat diet & STZ


title: P16

description: GBM primary patient 16


title: LOS_D10_S220_Aligned.quant


title: spleen HS-1 [SHS1]


title: hpCasMINI_Deep-seq_compare_Rep3

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, hpCasMINI repeat3


title: P15

description: GBM primary patient 15


title: spleen con-3 [Scon3]

value: control


title: hpCasMINI_Deep-seq_compare_Rep1

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, hpCasMINI repeat1


title: hpCasMINI_Deep-seq_compare_Rep2

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, hpCasMINI repeat2


title: LOS_D1_S211_Aligned.quant


title: SpCas9_Deep-seq_compare_Rep1

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, SpCas9 repeat1


title: P14

description: GBM primary patient 14


title: LOS_C9_S207_Aligned.quant


title: Ctrl_Deep-seq_compare_Rep3

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat3


title: P13

description: GBM primary patient 13


title: LOS_C8_S206_Aligned.quant


title: Ctrl_Deep-seq_compare_Rep2

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat2


title: spleen HS-3 [SHS3]

value: 10 weeks


title: Ctrl_Deep-seq_compare_Rep1

description: Evaluation of the editing efficiency of hpCasMINI in parallel with Cas9 and Cas12a in the MCF7 cells, Ctrl repeat1


title: spleen con-2 [Scon2]


title: P12

description: GBM primary patient 12

value: brain


title: spleen A10-3 [SA3]

value: AOS 10mg/kg


title: LOS_C7_S205_Aligned.quant


title: LOS_D12_S222_Aligned.quant


title: spleen A10-2 [SA2]

value: spleen


title: LOS_C6_S204_Aligned.quant


title: Ctrl_Deep-seq_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting ten different genomic sites, repeat 3


title: spleen A10-1 [SA1]


title: P11

description: GBM primary patient 11


title: LOS_C5_S203_Aligned.quant


title: kidney HSCF-3 [KHSCF3]

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

source_name: kidney

extract_protocol:
Kidney were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: High fat diet & STZ+control-FMT


title: Ctrl_Deep-seq_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting ten different genomic sites, repeat 2


title: P9

description: GBM primary patient 9

value: primary glioblastoma


title: Ctrl_Deep-seq_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected without the CasMINI or hpCasMINI system targeting ten different genomic sites, repeat 1


title: hpCasMINI_Deep-seq_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting ten different genomic sites, repeat 3


title: P8

description: GBM primary patient 8


title: kidney HSCF-2 [KHSCF2]


title: LOS_C4_S202_Aligned.quant

value: skin

value: hair follicle epithelial cell


title: LOS_C3_S201_Aligned.quant


title: P7

description: GBM primary patient 7


title: spleen con-1 [Scon1]


title: kidney HSCF-1 [KHSCF1]


title: hpCasMINI_Deep-seq_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting ten different genomic sites, repeat 2


title: hpCasMINI_Deep-seq_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the hpCasMINI system targeting ten different genomic sites, repeat 1


title: kidney HSAF-2 [KHSAF2]

value: High fat diet & STZ+AOS10mg/kg-FMT


title: LOS_C12_S210_Aligned.quant

value: wild type


title: LOS_C2_S200_Aligned.quant

value: lower outer root sheath


title: CasMINI_Deep-seq_Rep3

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 3


title: P4

description: GBM primary patient 4


title: P6

description: GBM primary patient 6


title: P5

description: GBM primary patient 5


title: LOS_C11_S209_Aligned.quant

value: AnaVI


title: LOS_C10_S208_Aligned.quant


title: CasMINI_Deep-seq_Rep2

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 2

value: epithelial cell


title: P10

description: GBM primary patient 10


title: kidney HSAF-1 [KHSAF1]

value: ICR


title: kidney HSA10-3 [KHSA3]

value: High fat diet & STZ+AOS10mg/kg


title: P3

description: GBM primary patient 3


title: CasMINI_Deep-seq_Rep1

description: The DNA cleavage efficiency in the MCF7 cells transfected with the CasMINI system targeting ten different genomic sites, repeat 1


title: kidney HSA10-2 [KHSA2]


title: P2

description: GBM primary patient 2


title: LOS_B9_S195_Aligned.quant


title: P1

description: GBM primary patient 1


title: kidney HSA10-1 [KHSA1]


title: hb18

description: brain RNA library

source_name: Clontech Healthy brain RNA


title: dhpCasMINI_IL1RN_Activation_Rep2

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dhpCasMINI-VPR targeting IL1RN, repeat 2.

data_processing:
The raw paired-end reads were preprocessed to remove the adapters with cutadapt
Subsequently, the reads were mapped to the human genome (hg38) using HISAT2 aligner
The uniquely mapped reads that passed the "markdup –r" filter by sambamba
The generation of gene counts (reads aligned to each gene of each sample) was performed using gencode.v43.primary_assembly.basic.annotation GTF file (available at https://www.gencodegenes.org/human/) and FeatureCounts
Assembly: hg38
Supplementary files format and content: Gene counts for each library

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested.
RNA was isolated using Trizol Reagent according to the manufacturer’s protocol. The constructed sequencing libraries were sequenced on the Illumina HiSeq Platform with 150 bp paired-end reads.

treatment_protocol: In 24-well plates, HEK293T cells were transfected with 490ng gRNA plasmids and 10ng dCasMINI or dhpCasMINI plasmids.

value: Human embryonic Kidney


title: LOS_B8_S194_Aligned.quant


title: dhpCasMINI_IL1RN_Activation_Rep3

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dhpCasMINI-VPR targeting IL1RN, repeat 3.


title: kidney HS-3 [KHS3]

value: 10 weeks

value: High fat diet & STZ


title: kidney HSAF-3 [KHSAF3]


title: LOS_B7_S193_Aligned.quant


title: dhpCasMINI_IL1RN_Activation_Rep1

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dhpCasMINI-VPR targeting IL1RN, repeat 1.


title: kidney HS-1 [KHS1]


title: hb16

description: brain RNA library

value: brain


title: kidney HS-2 [KHS2]


title: hb17

description: brain RNA library


title: dCasMINI_IL1RN_Activation_Rep2

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dCasMINI-VPR targeting IL1RN, repeat 2.


title: dCasMINI_IL1RN_Activation_Rep3

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dCasMINI-VPR targeting IL1RN, repeat 3.


title: LOS_B5_S191_Aligned.quant


title: kidney con-3 [Kcon3]

value: control


title: LOS_B6_S192_Aligned.quant


title: LOS_C1_S199_Aligned.quant


title: kidney con-2 [Kcon2]

value: kidney


title: hb15

description: brain RNA library


title: dCasMINI_IL1RN_Activation_Rep1

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dCasMINI-VPR targeting IL1RN, repeat 1.


title: LOS_B4_S190_Aligned.quant


title: Ctrl_IL1RN_Activation_Rep3

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected without dCasMINI-VPR or dhpCasMINI-VPR, repeat 3.


title: hb13

description: brain RNA library

source_name: AM6050 Healthy brain RNA


title: kidney con-1 [Kcon1]


title: LOS_B2_S188_Aligned.quant


title: hb14

description: brain RNA library


title: hb12

description: brain RNA library


title: LOS_B3_S189_Aligned.quant


title: Ctrl_IL1RN_Activation_Rep1

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected without dCasMINI-VPR or dhpCasMINI-VPR, repeat 1.


title: LOS_B12_S198_Aligned.quant


title: kidney A10-2 [KA2]

value: AOS 10mg/kg


title: hb11

description: brain RNA library


title: hb10

description: brain RNA library

source_name: TAKARA HB total RNA


title: kidney A10-1 [KA1]


title: LOS_B11_S197_Aligned.quant


title: hb9

description: brain RNA library


title: LOS_B1_S187_Aligned.quant


title: WI38-3

city: Singapore

first: Koji

last: Itahana

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
cleaned/trimmed and demultiplex followed by mapping to PA genome (annotation 102, 2018) using cufflinks/Tophat. DEG analysis performed using DESeq2 and GeTMM/EdgeR
Assembly: hg19 and P.alecto reference genome (NCBI genome database: ASM32557v1, 1.02)
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each sample

source_name: lung

growth_protocol: All the cells were cultured in DMEM with 10% fetal bovine serum and penicillin/streptomycin in a 37 °C incubator with 5% CO2.

extract_protocol:
RNeasy Plus Mini Kit (QIAGEN).
TruSeq Stranded Total RNA Library Prep Gold

treatment_protocol: No treatment

value: lung

value: Lung Fibroblast

value: wild-type


title: hb8

description: brain RNA library


title: WI38-2


title: hb7

description: brain RNA library


title: LOS_A9_S184_Aligned.quant

value: skin

value: hair follicle epithelial cell


title: A549 cells,QD_1

city: hefei

first: Liu

last: Kaiyue

state: anhui

institute: University of Science and Technology of China

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with raw counts for every gene and every sample.
Supplementary files format and content: Matrix table include FPKM values for every gene and log2(fold change) values between two groups.

growth_protocol: A549 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco)  supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For glutamine deprivation, A549 cells were washed by PBS 3 times, and then cells were maintained for 24 hours in glutamine-free DMEM medium supplemented with 10% FBS.

value: Alveolar basal epithelial cells

value: glutamine deprivation for 24 hours


title: A549 cells,ctrl_2


title: WI38-1


title: A549 cells,QD_2

value: glutamine deprivation for 25 hours


title: HepG2 cell, shEPDR1

first: Xiaoyu

last: Qian

state: Guangzhou

address: Guangzhou Panyu University City

institute: South China University of Technology

data_processing:
Reads were aligned to the human genome hg38. TopHat2 v.2.1.0 and cufflinks v.2.2.1 were used to analyze RNA-seq data. Gene differential expression analysis was carried out with the DEGSeq R package (1.26.0).
Assembly: hg38
Supplementary files format and content: fpkm_tracking

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin‒streptomycin. Cells were grown at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cell lines using TRIzol Reagent (Life Technologies). RNA integrity was assessed by RNA integrity number and determined using an Agilent 2100 Bioanalyzer.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes  were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic  beads. Fragmentation was carried out using divalent cations under elevated temperature  in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was  synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’  ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to  prepare for hybridization. In order to select cDNA fragments of preferentially 250~300  bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with sizeselected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100  system.

treatment_protocol: HepG2 cells were were infected with lentivirus expressing shEPDR1  and selected with 0.5 µg.ml–1 puromycin to establish stable cells, with a NTC as control

value: hepatocarcinoma cell


title: hb6

description: brain RNA library

source_name: First choice Healthy brain RNA


title: LOS_A8_S183_Aligned.quant

value: wild type

value: lower outer root sheath

value: AnaVI


title: A549 cells,ctrl_1


title: kidney A10-3 [KA3]

value: ICR

value: 10 weeks


title: Ctrl_IL1RN_Activation_Rep2

description: The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected without dCasMINI-VPR or dhpCasMINI-VPR, repeat 2.

value: Human embryonic Kidney


title: HepG2 cell, shNTC

value: wt


title: LOS_A7_S182_Aligned.quant


title: LOS_A6_S181_Aligned.quant


title: SG replicate 3 48 hours

city: Palo Alto

first: Fan

last: Yang

state: California

address: Orthopedic Surgery, 240 Pasteur Drive, Biomedical Innovation Building 1200

institute: Stanford University

data_processing:
ATAC-seq reads were trimmed using NGSUtils. Trimmed reads were aligned to GRCh38.p5 assembly of the human genome using Bowtie2 with ‘--very-sensitive’ parameter.
Duplicates and mitochondrial reads were removed using NGSUtils and reads with high mapping quality (>q30) were retained using Samtools. Peak calling was performed with MACS2. All default options were used, with the following flags explicitly set: ‘-nomodel –keep-dup all’.
Peaks overlapping blacklisted features as defined by the ENCODE project were discarded. Only peaks with FDR q < 0.01 were retained. Differential analysis was performed using DESeq2
Differential analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Mesenchymal Stem Cells

extract_protocol:
The transposition reaction was conducted while the cells were inside the hydrogels at 37C for 1 hour. The samples were then crushed and homogenized and the supernatant was collected and processed for library prep.
Omni-ATAC-seq libraries were prepared using Nextera DNA CD Indexes (24 Indexes, 24 Samples) - Catalog # 20018707 and 20034197 ILMN Tag DNA Enzyme & Buffer Small Kit. Libraries were amplified using 5 cycles for amplification. Post-amplication libraries were size selected at 150-500 bp in length using SPRIselect beads. The libraries were validated using Agilent D5000 high sensitivity DNA kit in the Tapestation (Agilent).

tag: condition

value: SG

tag: time

value: 48 hours

value: Mesenchymal Stem Cells

value: WT

value: Chondrogenic differentiation


title: hb4

description: brain RNA library

value: brain


title: hb5

description: brain RNA library


title: LOS_B10_S196_Aligned.quant

value: skin

value: hair follicle epithelial cell


title: LOS_A5_S180_Aligned.quant


title: SG replicate 2 48 hours


title: N2 HS biol rep 3

city: Budapest

first: Janos

last: Barna

state: Budapest

address: ELTE Egyetem tér 1-3.

department: Genetics

country: Hungary

institute: Eotvos Lorand University

data_processing:
The Galaxy Server, running version23.0.5.dev0
Raw reads were examined for quality issues using FastQC to ensure library generation and sequencing data were suitable for further analysis.
Reads were aligned to the WBcel235 of the C. elegans genome using HISAT2
The number of reads mapped to each gene was counted using HTSeq
Differential expression analysis was performed using edgeR package
Assembly: WBCel235 was used as a reference genome.
Supplementary files format and content: readcount.xlsx: Matrix table with normalized gene counts for every gene and every sample.

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Nematodes were maintained  at 20°C on nematode growth medium (NGM)-containing plates and fed with Escherichia coli OP50 bacteria.

extract_protocol:
Total RNA was prepared, using RNAzol® RT (MRC, RN 190) standard protocols, and then cleaned up on RNeasy columns (QIAgen, cat# 74104). Gel electrophoresis using a 1% agarose gel was performed for a visual determination of sample quality. RNA integrity analysis, sample preparation, and RNA sequencing was performed by Novogene
mRNA library preparation (poly A enrichment) was performed by Novogene

treatment_protocol: Wild-type and hsf-1(sy441) mutant nematodes were synchronized and stored at 20ºC until they have reached the young adult stage. Worms were than heat shocked at 35ºC for 30 minutes, and after a 1-hour long recovery at 20ºC, RNA was isolated from heat treated vs. untreated worms.

value: whole animals

value: Day 1 of adulthood

value: WT (N2)

value: heat shock at 35C for 30 min


title: sy441 HS biol rep 1


title: hb3

description: brain RNA library


title: LOS_A4_S179_Aligned.quant

source_name: skin

value: wild type

value: lower outer root sheath

value: AnaVI


title: SG replicate 1 48 hours


title: sy441 HS biol rep 3


title: hb2

description: brain RNA library


title: N2 HS biol rep 2


title: N2 HS biol rep 1


title: hb1

description: brain RNA library


title: CG replicate 3 48 hours

value: CG


title: LOS_A2_S270_Aligned.quant


title: LOS_A3_S178_Aligned.quant


title: CG replicate 2 48 hours


title: sMCAO_contra

city: Vienna

first: Daniel

last: Bormann

state: Vienna

address: Waehringer Guertel 18-20

department: Department of Thoracic Surgery

country: Austria

institute: Medical University of Vienna

description: Single-cell RNAseq data

data_processing:
Raw sequencing data were demultiplexed, aligned to the rattus norvegicus reference genome mRatBN7.2  and counted using Cell Ranger (version 7.0.0; 10x Genomics).
Assembly: mRatBN7.2
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files contain filtered count gene UMI counts for each sample (=Filtered feature-barcode matrix). Files represent standard barcodes, features and matrix outputs from Cell Ranger  (version 7.0.0; 10x Genomics).

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Nuclei extraction buffer (Miltenyi) and discontinuous iodixanol gradient separation were used to generate single nuclei suspensions, in accordance with manufacturers' protocols.
Libraries were prepared using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Next GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA), as per standard manufacturers' protocols.

value: 12 weeks old

tag: Sex

value: male


title: SG replicate 2 16 hours

value: SG

value: 16 hours


title: sy441 HS biol rep 2


title: LOS_A11_S186_Aligned.quant


title: mMCAO_contra

description: Single-cell RNAseq data

value: WT


title: CG replicate 1 48 hours

value: 48 hours

value: Mesenchymal Stem Cells

value: Chondrogenic differentiation


title: SG replicate 1 16 hours


title: sy441 K biol rep 2

value: no treatment


title: sy441 K biol rep 3

value: whole animals


title: LOS_A1_S269_Aligned.quant

value: skin

value: hair follicle epithelial cell


title: N2 K biol rep 2

value: Day 1 of adulthood

value: WT (N2)


title: Sham_R

description: Single-cell RNAseq data

value: brain


title: CG replicate 2 16 hours


title: sy441 K biol rep 1


title: mMCAO_ipsi

description: Single-cell RNAseq data


title: PaLung-2

organism: Pteropus alecto

value: lung

value: PaLung

value: Lung Fibroblast

value: wild-type


title: N2 K biol rep 3


title: LOS_A10_S185_Aligned.quant

value: wild type

value: lower outer root sheath

value: AnaVI


title: PaLung-3


title: CG replicate 1 16 hours

value: CG

value: 16 hours

value: WT


title: Sham_L

description: Single-cell RNAseq data

value: 12 weeks old

value: male


title: sMCAO_ipsi

description: Single-cell RNAseq data


title: PaLung-1


title: samp26

status: Public on Jun 28 2024

city: San Francsico

first: Neel

middle: S

last: Singhal

address: 1700 Owens St., Receiving Room 349

department: Neurology

description: small RNA-seq

library_source: other

data_processing:
1) Remove low quality tags, tags with primer contaminants, without insertions, with poly A, and <18nts
Alignment, mapping, and counts with MANATEE (Handzlik et al., 2020)
Assembly: Hg v38
Supplementary files format and content: tab-delimited text of raw counts for each sample

molecule: other

source_name: L1EVs, plasma

extract_protocol:
250 ul of plasma was incubated with 100 ul of thromboplastin-D (Fisher Scientific) followed by the addition of 150 ul of calcium- and magnesium-free Dulbecco’s balanced salt solution with protease and phosphatase inhibitor cocktail (Roche Applied Science). ExoQuick (System Biosciences) was added to precipitate total EVs, that were re-suspended for immunochemical enrichment of EVs from neural sources. L1EVs were obtained by sequential immunoprecipitation with biotinylated monoclonal antibody to L1 cell adhesion molecule (L1CAM; eBioscience). Nanosight NS300 instrument (Malvern Instruments) in combination with an EV membrane label, ExoGlow (System Biosciences) confirmed that the particle sizes of total EV extracts were within range for exosomes (30–220 nm). To determine EV purity per total protein of sample, plasma protein concentration was measured by spectrophotometer at 562 nm after Pierce Bicinchoninic Acid Protein Assay (ThermoFisher). Small RNA enriched total RNA was isolated from each sample using Acid-Phenol:Chloroform extraction (mirVana PARIS Kit, Invitrogen).
75 ng of extracted RNA was used for the library synthesis. Small RNA was enriched, purified, and cDNA libraries synthesized by a commercial vendor (BGI America, San Jose, CA). 3' end adaptor ligation was performed to ligate the 5-adenylated and 3-blocked adaptor to the 3' end of the small RNA fragment. A unique molecular identifier sequences was added along with a 5' end adaptor. The libraries were quantified and quality control measured using a Bioanalyzer (Agilent). Barcoded libraries were pooled together and sequenced. After eliminating low-quality reads and adaptors, each sample generated over 20 million clean reads

value: L1EVs, plasma

value: Female

value: Acute ischemic stroke


title: samp25

description: small RNA-seq


title: samp28

description: small RNA-seq


title: samp29

description: small RNA-seq

value: Control


title: samp27

description: small RNA-seq


title: samp22

description: small RNA-seq


title: samp23

description: small RNA-seq


title: samp21

description: small RNA-seq


title: samp20

description: small RNA-seq

value: Male


title: samp17

description: small RNA-seq


title: samp14

description: small RNA-seq


title: samp18

description: small RNA-seq


title: samp19

description: small RNA-seq


title: samp16

description: small RNA-seq


title: samp15

description: small RNA-seq


title: samp09

description: small RNA-seq


title: samp12

description: small RNA-seq


title: samp13

description: small RNA-seq


title: N2 K biol rep 1

value: whole animals

value: Day 1 of adulthood

value: WT (N2)

value: no treatment


title: samp05

description: small RNA-seq


title: samp10

description: small RNA-seq


title: samp04

description: small RNA-seq


title: samp07

description: small RNA-seq


title: samp01

description: small RNA-seq


title: samp03

description: small RNA-seq


title: samp02

description: small RNA-seq


title: samp24

description: small RNA-seq


title: samp08

description: small RNA-seq


title: samp06

description: small RNA-seq


title: TH165, COPD, Tissue, scRNA

city: Seoul

first: Jihwan

last: Moon

address: gangnam-gu irwon-ro 81

department: Department of Digital Health

country: South Korea

institute: Sungkyunkwan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
The samples used in this study were obtained from patients with lung cancer at the Samsung Medical Center between 2019 and 2022. The collected tissue was immediately placed in advanced DMEM/F12 containing 1X glutamax, 10 mM HEPES, penicillin/streptomycin, and primocin (adDF + + +) and transferred to the laboratory for organoid culture. The samples were minced and then digested in 1 mL collagenase I (Stemcell-07902) at 37 °C for 1 h. The digested tissue suspension went through a sterile 70 μm filter, and adDF+++ with 10% FBS was added. After centrifuging at 1,300 rpm for 3 min, the pellet was resuspended in 40 μL ice-cold cultrex growth factor reduced BME type 2 (Trevigen-3533-010-02) and allowed to solidify on pre-warmed 24-well suspension culture plates (Greiner M9312) at 37 °C for 20 min. Then, 400 μL organoid culture medium were added to each well, and the plates were transferred to humidified 37 °C/5% CO2 incubators. Organoids were passaged every two weeks or at a diameter of 200 µm.
The library preparation was performed using the Chromium Next GEM Single cell 5’kit v2 (10x Genomics) with a cell recovery target of 5,000 per patient, following the manufacturer’s instruction. Following the manufacturer’s instructions, barcoded sequencing libraries were generated, and sequencing libraries were sequenced on an Illumina HiSeq 2500 system using 100 bp paired-end sequencing.

value: Lung

value: COPD

tag: gold grade

tag: smoking status

value: current

tag: pack years

value: M


title: TH154, COPD, Tissue, scRNA

description: 10x Genomics

value: Ex


title: TH165, COPD, Organoid, scRNA

description: 10x Genomics


title: TH153, Control, Tissue, scRNA

description: 10x Genomics

value: Never

value: F


title: TH153, Control, Organoid, scRNA

description: 10x Genomics


title: TH154, COPD, Organid, scRNA

description: 10x Genomics


title: TH147, COPD, Tissue, scRNA

description: 10x Genomics


title: TH147, COPD, Organoid, scRNA

description: 10x Genomics


title: TH137, Control, Tissue, scRNA

description: 10x Genomics


title: TH137, Control, Organoid, scRNA

description: 10x Genomics


title: TH122, Control, Tissue, scRNA

description: 10x Genomics


title: TH122, Control, Organoid, scRNA

description: 10x Genomics


title: PDDM16

type: genomic

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

institute: Pusan National University

hyb_protocol: The genomic DNA underwent bisulfite conversion utilizing the EZ DNA methylation kit from Zymo Research. Subsequently, it was examined using the Illumina Infinium MethylationEPIC BeadChip

scan_protocol: Arrays were imaged on the iScan system by Illumina at Queensland University of Technology

data_processing: ChAMP package within R software

label: Cy3 and Cy5

source_name: gigival tissue

label_protocol: Standard Illumina protocol

extract_protocol: The DNA from gingival tissue were extracted following the guidelines provided by the manufacturer's MGI FS DNA library prep set (cat No. 1,000,005,256).

value: gigival tissue

tag: subject status

value: PDDM

value: gingival


title: PD22

description: Illumina Infinium MethylationEPIC BeadChip

tag: tissue

value: PD


title: PD6

tag: cell type


title: PD7


title: PDDM3


title: PDDM19


title: PDDM4


title: PD14


title: 40TR

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecall performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference with corresponding GENCODE annotation p7 using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Assembly: hg38
Supplementary files format and content: raw read counts for each sample in comma-separated format. First column contains ENSembl gene ids and second column gene symbols.

source_name: Breast tumor

extract_protocol:
Qiagen miRNAeasy kit
Illumina TruSeq Stranded Total RNA kit
Whole transcriptome (ribo-depletion)

treatment_protocol: Women with stage I-III newly diagnosed breast luminal breast cancer (ESR1+/HER-) diagnosed by core needle biopsy were randomized to Arm A: standard of care without intervention or Arm B: Tam 20 mg PO daily for 28 days immediately preceding primary surgery

value: Breast tumor

tag: disease state

value: ESR1+ breast cancer

value: With tamoxifen


title: PD2


title: PDDM12


title: PDDM15


title: PD19


title: PD18


title: PD21


title: PDDM14


title: 41TR

tag: treatment


title: PD13


title: PDDM7


title: 37TR


title: 28TR


title: Healthy10

value: Healthy


title: 31TR

value: Without tamoxifen


title: PD20


title: PD4


title: 26TR


title: 34TR


title: 38TR


title: Liver_Normal_55

city: Bath

first: Adele

last: Murrell

address: Claverton Down

department: Life Sciences Department

country: United Kingdom

institute: University of Bath

description: Instrument model: Illumina Genome Analyzer IIx. Narrow peak output from MACS2. Raw fastq data was first aligned to the hg38 reference genome, filtered to remove greylist regions, and then peaks were called relative to a tissue-matched input sequence dataset.

data_processing:
Sequence reads were aligned to the hg38 human reference genome build.
Aligned files were sorted using samtools.
Overrepresented regions (greylisted) were filtered out prior to peak calling.
Peak calling was performed using MACS2.
Assembly: hg38 (GRCh38)
Supplementary files format and content: narrowPeak (BED6+4) file format, incl: signalValue, pValue, qValue, peak.

source_name: hMeDIP-seq of colorectal cancer metastases to liver 55: normal liver adjacent to tumour (bound)

extract_protocol:
High molecular weight DNA was isolated using a proteinase K/phenol extraction method. See: Ibrahim et al. (2011).  Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression. Gut 60: 499-508. https://doi.org/10.1136/gut.2010.223602
Illumina libraries were prepared before the pull-down using 1 to 3 micrograms of sonicated genomic DNA (Bioruptor). Libraries were prepared using a ‘with-bead’ procedure or with the TruSeq DNA sample preparation kit (Illumina) following manufacturer’s instructions. Adaptor modified genomic DNA was then immunoprecipitated following. Input and pull-down material was whole genome amplified with 10 PCR cycles, ran on 2% EX agarose gels (LifeTechnologies), size selection of 300 to 500 bp fragments with the MinElute gel extraction kit (Qiagen), further amplified with seven PCR cycles and purified with AMPURE XP beads. This procedure was also done for amplification with TruSeq reagents. Libraries were qualified and quantified by Bioanalyzer and submitted for sequencing by the CI Genomics core facility. See: Urribe-Lewis et al. (2014). 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol 16, 69 (2015). https://doi.org/10.1186/s13059-015-0605-5

value: Liver

value: Normal


title: Liver_Tumour_55

description: Instrument model: Illumina Genome Analyzer IIx. Narrow peak output from MACS2. Raw fastq data was first aligned to the hg38 reference genome, filtered to remove greylist regions, and then peaks were called relative to a paired input sequence dataset.

source_name: hMeDIP-seq of colorectal cancer metastases to liver 55: secondary liver tumour (input)

value: Metastasis


title: PD3


title: 27TR


title: Colon_Tumour_53

source_name: hMeDIP-seq of colorectal cancer metastases to liver 53: primary colon tumour (bound)

value: Colon

value: Primary tumour


title: 25TR


title: 14TR


title: Liver_Tumour_53

source_name: hMeDIP-seq of colorectal cancer metastases to liver 53: secondary liver tumour (input)


title: Liver_Normal_53

source_name: hMeDIP-seq of colorectal cancer metastases to liver 53: normal liver adjacent to tumour (bound)


title: 19TR


title: Liver_Tumour_52

source_name: hMeDIP-seq of colorectal cancer metastases to liver 52: secondary liver tumour (input)


title: PDDM6


title: PD5


title: 36TR


title: Liver_Normal_52

source_name: hMeDIP-seq of colorectal cancer metastases to liver 52: normal liver adjacent to tumour (bound)


title: PD11


title: PDDM1


title: Colon_Normal_53

source_name: hMeDIP-seq of colorectal cancer metastases to liver 53: normal colon adjacent to tumour (input)


title: 39TR


title: PD10


title: 20TR


title: PDDM13


title: 32TR


title: 30TR


title: Healthy9


title: 33TR


title: Colon_Tumour_52

source_name: hMeDIP-seq of colorectal cancer metastases to liver 52: primary colon tumour (bound)


title: Liver_Tumour_51

source_name: hMeDIP-seq of colorectal cancer metastases to liver 51: secondary liver tumour (input)


title: 29TR


title: Liver_Normal_51

source_name: hMeDIP-seq of colorectal cancer metastases to liver 51: normal liver adjacent to tumour (bound)


title: Colon_Tumour_51

source_name: hMeDIP-seq of colorectal cancer metastases to liver 51: primary colon tumour (bound)


title: 23TR


title: 24TR


title: Colon_Normal_52

source_name: hMeDIP-seq of colorectal cancer metastases to liver 52: normal colon adjacent to tumour (input)


title: S d60 6 [S60-6]

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
STAR (version 2.7.9a) was used to align sequence reads to golden hamster genome build MesAur1.0 (NCBI accession GCF_000349665.1).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 105 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.32.0).
Assembly: MesAur1.0
Supplementary files format and content: counts.txt: 22246 x 21 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 22246 x 21 matrix of variance-stabilizing-transformed (VST) expression values

organism: Mesocricetus auratus

source_name: skeletal muscle

growth_protocol: Six to eight week-old male Golden Syrian hamsters (Mesocricetus auratus) were obtained from Charles River Laboratories. Hamsters were acclimated to the CDC/USDA-approved Biosafety Level 3 (BSL-3) facility at the Center for Comparative Medicine and Surgery (CCMS) at Icahn School of Medicine at Mount Sinai (New York, NY, USA) for at least 14 days.

extract_protocol:
After perfusion, quadriceps muscle (ventral thigh) was exposed and harvested. Samples for RNA extraction were placed into "lysing matrix A" homogenization tubes (MP Biomedicals) filled with TRIzol and homogenized before being frozen at -80oC.  RNA was later isolated from homogenized muscle samples by TRIzol/phenol-chloroform extraction.
100 nanograms of total RNA from each sample was enriched for polyadenylated RNA and prepared for next-generation sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) according to the manufacturer’s instructions.

treatment_protocol: When the hamsters reached 10 weeks of age, they were divided into three cohorts: 1) mock treatment group: intranasally infected with PBS; 2) SARS-CoV-2-infected group: intranasally infected with 1000 pfu (total volume 100 μL) of SARS-CoV-2 (USA-WA1/2020); and 3) IAV-infected group: intranasally infected with 100,000 pfu (total volume 100 μL) of H1N1 IAV (A/California/04/2009).  Intranasal administration was performed under ketamine/xylazine anesthesia. Hamsters were housed for 3, 30, and 60 days post-infection before being euthanized via sodium pentobarbital and intracardiac perfusion with PBS (with severed inferior vena cava).

value: skeletal muscle

tag: infection

value: SARS-CoV-2 (USA-WA1/2020)

tag: timepoint


title: 21TR

value: Without tamoxifn


title: 18TR


title: Liver_Tumour_49

source_name: hMeDIP-seq of colorectal cancer metastases to liver 49: secondary liver tumour (bound)


title: S d60 5 [S60-5]


title: 16TR


title: S d60 4 [S60-4]


title: Liver_Normal_49

source_name: hMeDIP-seq of colorectal cancer metastases to liver 49: normal liver adjacent to tumour (bound)


title: 22TR

source_name: Breast tumor


title: 15TR


title: Colon_Normal_51

source_name: hMeDIP-seq of colorectal cancer metastases to liver 51: normal colon adjacent to tumour (input)


title: Healthy8

source_name: gigival tissue

value: gigival tissue


title: S d30 6 [S30-6]


title: Colon_Tumour_49

source_name: hMeDIP-seq of colorectal cancer metastases to liver 49: primary colon tumour (bound)


title: 09TR


title: S d30 4 [S30-4]


title: 07TR


title: 08TR


title: Colon_Normal_49

source_name: hMeDIP-seq of colorectal cancer metastases to liver 49: normal colon adjacent to tumour (input)


title: S d3 3 [S-3-3]


title: 03TR


title: 05TR


title: S d3 2 [S-3-2]


title: RNA, MSK165, NUP98-NSD1-CFSEnega-2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Table_RNA_MSK165_CFSE_NUP98NSD1_rawcounts.txt

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: human patient AML cells

growth_protocol: Human patient AML cells were labeled with CFSE and transplanted into pre-irradiated NSG mice. Two weeks later, bone marrow cells were harvested, and LRCs and non-LRCs of human leukemia cells were separately isolated using FACS cell sorting.

extract_protocol:
Total RNA was extracted using the Quick-RNA MicroPrep kit (Zymo Research).
Libraries were constructed using QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) with ERCC RNA spike-in Mix (Thermo Fisher).

tag: cell origin

value: human patient AML cell xenograft

tag: cell id

tag: classification

value: Non-label retaining cells (non-LRCs)

tag: oncogene fusion


title: RNA, MSK165, NUP98-NSD1-CFSEnega-3


title: RNA, MSK165, NUP98-NSD1-CFSEnega-1


title: S d3 1 [S3-1]


title: #251-UT

city: Munich

first: Julia

last: Jellusova

department: Klinikum rechts der Isar

country: Germany

institute: Technical University Munich

data_processing:
Quality ccontrol In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Novel gene prediction: The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. Cufflinks includes a utility program called ‘Cuffcompare’ that can compare Cufflinks assemblies to reference annotation files and help sort out new genes from known ones. The Cuffcompare class codes underlying transcript classification were: "u" for "Potentially novel gene"; the set of "j", "u", "i", "o" and "x" for "Potentially novel isoform".
Quantification: HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: xls, FPKM annotated

source_name: B cell precursors

growth_protocol: Iscoves medium with supplements and IL7

extract_protocol:
Quick-RNA MicroPrep (ZYMO RESEARCH)
Novogene company:

treatment_protocol: untreated or treated over night with the GSK3 inhibitor LY2090314

tag: genotype

value: control

value: untreated


title: Injured_RGC_Itga5_Itgav_loci

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

data_processing:
Sequence reads were mapped to the mm10 genome and transcriptome by Hisat2 and transcripts quantified using the Cufflinks/cuffdiff pipeline
Reads mapping to the loci for Itga5 and Itgav were extracted in BAM file format using SamTool 1.9 and then converted to fastq format
Fastq files submitted to SRA contain reads for only two genes.
Assembly: mm10
Supplementary files format and content: csv file includes FPKM values for Itga5 and Itgav genes expressed in adult uninjured and injured RGCs based on Cufflinks/Cuffdiff analysis

source_name: RGCs

extract_protocol:
Adult uninjured or ONC-injured RGCs transduced with AAV2 expressing mCherry were Thy1-immunopanned from single cell retinal suspension (from 10 retinas per condition) and FACS’ed for mCherry+ cells. Approximately, 5,000 RGCs (per condition) were collected by FACS. RNA was isolated immediately using the Zymo QuickRNA microprep kit. Total RNA with RNA Integrity Number (RIN) ≥ 9 (by Bioanalyzer 2100 using the Nano 6000 kit, Agilent) was extracted using Direct-zol RNA MiniPrep kit (R2050, Zymo Research).
cDNA libraries were prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), and paired reads were sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

tag: strains

value: RGCs

value: WT

value: Injured ONC


title: RNA, MSK165, NUP98-NSD1-CFSEposi-3

value: Label retaining cells (LRCs)


title: 06TR

value: Breast tumor

value: ESR1+ breast cancer

value: With tamoxifen


title: Uninjured_RGC_Itga5_Itgav_loci

description: Fastq files submitted to SRA contain reads for only two genes.

value: Uninjured


title: Healthy7

value: Healthy

value: gingival


title: #251-GSK3

value: Treated with a GSK3 inhibitor


title: 10TR

value: Without tamoxifen


title: S d30 5 [S30-5]

value: skeletal muscle

value: SARS-CoV-2 (USA-WA1/2020)


title: Healthy1

value: gigival tissue


title: #249-GSK3

value: control


title: F d60 5 [F60-5]

value: H1N1 influenza A virus (A/California/04/2009, IAV)


title: RNA, MSK165, NUP98-NSD1-CFSEposi-2

value: human patient AML cell xenograft


title: RNA, MSK011, MLL-ENL, CFSEnega-3

description: Table_RNA_MSK011_CFSE_MLLENL_rawcounts.txt

value: Non-label retaining cells (non-LRCs)

value: MLL-ENL


title: RNA, MSK011, MLL-ENL, CFSEnega-2


title: RNA, MSK011, MLL-ENL, CFSEnega-1


title: #242-GSK3


title: RNA, MSK011, MLL-ENL, CFSEposi-3

value: Label retaining cells (LRCs)


title: #249-UT

value: untreated


title: RNA, MSK011, MLL-ENL, CFSEposi-2


title: F d30 6 [F30-6]


title: #242-UT


title: F d60 4 [F60-4]


title: F d30 5 [F30-5]


title: RNA, MSK162, MOZ-CBP, CFSEneg-3

description: Table_RNA_MSK162_CFSE_MOZCBP_rawcounts.txt

value: MOZ-CBP


title: 35TR

value: Breast tumor

value: ESR1+ breast cancer


title: Healthy2

value: Healthy


title: F d60 6 [F60-6]


title: RNA, MSK011, MLL-ENL, CFSEposi-1


title: RNA, MSK165, NUP98-NSD1-CFSEposi-1


title: #249 (WT)


title: F d30 4 [F30-4]


title: Healthy3

value: gingival


title: RNA, MSK162, MOZ-CBP, CFSEneg-2


title: RNA, MSK162, MOZ-CBP, CFSEneg-1


title: 13TR


title: #242 (WT)


title: RNA, MSK162, MOZ-CBP, CFSEpos-3


title: F d3 6 [F3-6]


title: RNA, MSK162, MOZ-CBP, CFSEpos-2


title: Healthy6


title: Healthy5


title: RNA, MSK162, MOZ-CBP, CFSEpos-1


title: F d3 5 [F3-5]


title: #262 (ko)


title: F d3 4 [F3-4]


title: #251 (WT)


title: ATAC, MSK165, NUP98-NSD1, CFSE-nega2

description: genomic DNA fragments

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 (v2.2.2) with default parameters and duplicates were collapsed using Picard (v2.16).
To create density files, read counts were normalized to 10 million mapped reads and converted to BigWig format using BEDTools.
Assembly: hg19
Supplementary files format and content: BigWig files containing read densities normalized to sequencing depth.

extract_protocol:
Isolated nuclei were tagmented using Nextera DNA sample prep kit (Illumina). Tagmented DNA was purified using Agencourt AMPure XP beads (Beckman Coulter).
Libraries were generated using the NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) and Nextera index primers (Illumina).

value: human patient AML cells


title: ATAC, MSK165, NUP98-NSD1, CFSE-nega1

description: genomic DNA fragments


title: ATAC, MSK165, NUP98-NSD1, CFSE-posi3

description: genomic DNA fragments


title: M d3 6 [M3-6]

value: mock (PBS)


title: #244 (KO)


title: ATAC, MSK165, NUP98-NSD1, CFSE-posi2

description: genomic DNA fragments


title: ATAC, MSK165, NUP98-NSD1, CFSE-posi1

description: genomic DNA fragments


title: M d3 5 [M3-5]

value: skeletal muscle


title: #255 (ko)


title: ATAC, MSK011, MLL-ENL, CFSE-nega3

description: genomic DNA fragments


title: ATAC, MSK011, MLL-ENL, CFSE-nega2

description: genomic DNA fragments


title: ATAC, MSK011, MLL-ENL, CFSE-nega1

description: genomic DNA fragments


title: V_N_3

city: Chongqing

first: Hongsheng

last: Zhang

state: Chongqing

address: No.1, Yixuanyuan Road, Chongqing

institute: Chongqing Medical University

data_processing:
Sample quality was assessed by using FastQC. Samples were aligned to the mouse reference genome GRCm38 by using HISAT2. Mapped sequencing reads were assigned to genomic features by using the featureCounts function
Normalized by DESeq2 with rlogTransformed.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: hippocampus

growth_protocol: Primary neurons were maintained in Neurobasal supplemented with 10%B27 and 1%GlutaMAX in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
Primary neuron cultured with fresh neural substrates containing B27 and penicillin-streptomycin were harvested. Isolated RNA was subsequently used for RNA-seq analysis. cDNA library construction and sequencing were performed by the BGI using BGI platform.
RNA libraries were prepared by BGI for sequencing using standard DNBSEQ protocols

treatment_protocol: Primary neurons were cultured with fresh neural substrates containing B27 and penicillin-streptomycin.

value: hippocampus

value: Primary neuron

value: WT

value: Fresh neural substrates containing B27 and penicillin-streptomycin


title: M d3 4 [M3-4]


title: ATAC, MSK011, MLL-ENL, CFSE-posi3

description: genomic DNA fragments

value: human patient AML cell xenograft


title: ATAC, MSK165, NUP98-NSD1, CFSE-nega3

description: genomic DNA fragments

value: Non-label retaining cells (non-LRCs)


title: SNU-719/tet-MUC1shRNA_DOX+ Rep2

city: Brookline

first: Hiroki

last: Ozawa

address: 450 Brookline

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: stomach

growth_protocol: YCCEL1 AND SNU-719 cells were maintained in Gibco RPMI 1640 Media containing 10% heat inactivated FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: stomach

tag: cell line

value: gastric cancer

value: DOX


title: V_N_2


title: SNU-719/tet-MUC1shRNA_DOX+ Rep3


title: ATAC, MSK011, MLL-ENL, CFSE-posi2

description: genomic DNA fragments

value: Label retaining cells (LRCs)

value: MLL-ENL


title: SNU-719/tet-MUC1shRNA_DOX+ Rep1


title: ATAC, MSK162, MOZ-CBP, CFSEneg-3

description: genomic DNA fragments

value: MOZ-CBP


title: SNU-719/tet-MUC1shRNA_DOX- Rep3

value: DMSO


title: ATAC, MSK011, MLL-ENL, CFSE-posi1

description: genomic DNA fragments


title: ATAC, MSK162, MOZ-CBP, CFSEneg-2

description: genomic DNA fragments


title: V_N_1


title: ATAC, MSK162, MOZ-CBP, CFSEneg-1

description: genomic DNA fragments


title: SNU-719/tet-MUC1shRNA_DOX- Rep2


title: ATAC, MSK162, MOZ-CBP, CFSEpos-3

description: genomic DNA fragments


title: SNU-719/tet-MUC1shRNA_DOX- Rep1


title: ATAC, MSK162, MOZ-CBP, CFSEpos-2

description: genomic DNA fragments


title: ATAC, MSK162, MOZ-CBP, CFSEpos-1

description: genomic DNA fragments


title: ADVTa1-3

city: Nanjing

first: kua

last: liu

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

description:
ADVT_1-3_fpkm
ADVTa1 group, replicate 3

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool
The clean reads obtained were then aligned to the mm10/hg19 mouse/human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie
Differentially expressed genes (DEGs) were identified by DEseq2(for sample with replications) or edgeR (for sample with no replication) with a cut-off value of log2|fold-change|>1 and p-value <0.05.
Assembly: mm10
Supplementary files format and content: readcount, TPM, FPKM for each sample

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12310ES, China) following manufacturer’s recommendations. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA).

value: breast cancer cell

value: Adenovirus combined with Ta1


title: YCCEL1/tet-MUC1shRNA_DOX+ Rep3


title: ADVTa1-1

description:
ADVT_1-1_fpkm
ADVTa1 group, replicate 1


title: ADVTa1-2

description:
ADVT_1-2_fpkm
ADVTa1 group, replicate 2


title: IEC-6 cells, Liph_sh2, rep3

city: Shanghai

first: ying

last: sun

address: 2005 Songhu road

institute: Fudan University

data_processing:
Raw data reads quality was checked by Fastp. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. Differential gene expression analysis was performed using DESeq2.
Assembly: Drosophila melanogaster reference genome sequence (UCSC dm6 assembly) or rat genome (UCSC rn6 assembly)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: Eclosed flies were raised on standard cornmeal fly food at 29 °C with 60% relative humidity in a 12 hours light/dark cycle; Rat small intestinal epithelial cell line (IEC-6) were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin-streptomycin) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from fly guts or IEC-6 cells with Trizol reagent (15596018CN, Invitrogen, Massachusetts, USA), and treated with DNase I (EN401, Vazyme, Nanjing, China) to eliminate genomic DNA. 1 μg of total RNA was used for the construction of sequencing libraries.
The RNA-seq libraries were then generated using VAHTS Universal V6 RNA-seq Library Prep Kit (NR604, Vazyme, Nanjing, China).

value: rat intestinal epithelial cells

value: Liph knockdown


title: IEC-6 cells, Liph_sh2, rep2


title: IEC-6 cells, Liph_sh2, rep1


title: YCCEL1/tet-MUC1shRNA_DOX+ Rep2


title: Healthy4

value: gigival tissue

value: Healthy

value: gingival


title: IEC-6 cells, Liph_sh1, rep2


title: IEC-6 cells, Liph_sh1, rep1


title: IEC-6 cells, control, rep3

value: WT


title: IEC-6 cells, Liph_sh1, rep3


title: YCCEL1/tet-MUC1shRNA_DOX+ Rep1


title: YCCEL1/tet-MUC1shRNA_DOX- Rep3


title: ADV-3

description:
ADV-3_fpkm
ADV group, replicate 3

value: Adenovirus infection


title: IEC-6 cells, control, rep1


title: ADV-1

description:
ADV-1_fpkm
ADV group, replicate 1


title: IEC-6 cells, control, rep2


title: Ctrl-3

description:
Ctrl-3_fpkm
CTRL group, replicate 3

value: No stimulation, control group


title: hplm_gmcsf_3

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

institute: Imperial College London

data_processing:
adaptor and quality trimmed using Trimmomatic (v0.40)
STAR (v2.7.4a) for alignmen to human genome (GRCh38 build 88)
RSEM (v1.3.1) for gene counting
DESeq2 (v1.42.0) for differential expression analysis
Assembly: GRCh38 build 88
Supplementary files format and content: txt file on raw gene count of all 18 samples

source_name: iPSc-derived macrophage

growth_protocol: iPSc-derived macrophages were grown in three separate types of cell culture media: XVIVO, OXM or HLPM and were stimulated with either GM-CSF or M-CSF. RNAseq was performed to compare the influence of cell culture media and activation chemokine in the overall cellular phenotype and response to Mycobacterium tuberculosis infection

extract_protocol:
Cells were lysed in Trizol and extracted using Zymo's Direct-zol RNA extraction kit
polyA selection using NEB Ultra II Directional RNA Library Prep kit

value: iPSc-derived macrophage

value: Macrophage


title: ADV-2

description:
ADV-2_fpkm
ADV group, replicate 2


title: YCCEL1/tet-MUC1shRNA_DOX- Rep2

value: stomach

value: gastric cancer


title: YCCEL1/tet-MUC1shRNA_DOX- Rep1


title: hplm_gmcsf_1


title: hplm_gmcsf_2


title: Ctrl-2

description:
Ctrl-2_fpkm
CTRL group, replicate 2


title: hplm_mcsf_3


title: hplm_mcsf_2


title: oxm_gmcsf_2


title: hplm_mcsf_1


title: oxm_gmcsf_3


title: Ctrl-1

description:
Ctrl-1_fpkm
CTRL group, replicate 1


title: HK2_OEKDM5C, input, ChIP

city: Wuhan

first: Jie

last: Xiong

address: 185, Donghu road

institute: Wuhan University

data_processing:
Basecalls were performed using fastq Novaseq output.
ChIP-seq reads were trimmed with fastp.
ChIP-seq reads were aligned to the hg38 and mm10 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Assembly: Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10min and then quenched with 0.125M glycine for 10min at room temperature with rotation. Cell pellet was lysed with cell lysis buffer (10mM Tris, pH8.0; 10mM NaCl; 0.2% NP-40; protease inhibitor) on ice for 10min and chromatin DNA was sonicated to 200-500bp average in size. Chromatin fragments lysates were immune-precipitated with primary antibodies at 4°C overnight and then conjugated with protein A/G Beads 4FF (Smart-lifesciences, SA032500). Bound fractions were washed and eluted from agarose beads. ChIP and input samples were de-crosslinked at 55°C overnight.
ChIP-seq libraries were prepared using the NEBNext ultra II DNA library prep kit for Illumina.

value: Human Kidney

tag: chip antibody

value: input


title: HK2_OEKDM5C_H514A, input, ChIP


title: oxm_mcsf_3


title: WT3_plus_corpsesBEL

city: New York City

first: Katherine

last: Stewart

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm39) using Salmon (v 1.4.0)
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts with Tximport (v 1.12.3) in R (v 3.6.1)(Salmon aligned data)
Assembly: mm39 (UCSC release)
Supplementary files format and content: text files contain raw counts
Supplementary files format and content: text files contain calculated TPM

source_name: cultured hair follicle stem cells

extract_protocol:
Cells were isolated by FACS, and collected into trizol. RNA was extracted using the Direct-zol RNA extraction kit (Zymo) following manufacturer's instructions.
RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit. Libraries were sequenced on an Illumina HiSeq 4000 or NovaSeq instrument as indicated.

value: cultured hair follicle stem cells

tag: sort strategy

value: plus BEL plus corpses


title: oxm_gmcsf_1


title: HK2_Parental, input, ChIP


title: WT4_plus_corpsesBEL


title: WT2_plus_corpsesBEL


title: HK2_OEKDM5C_H514A, YY1, ChIP


title: xvivo_gmcsf_3


title: WT1_plus_corpsesBEL


title: HK2_shKDM5C, YY1, ChIP


title: oxm_mcsf_2


title: oxm_mcsf_1


title: xvivo_mcsf_3


title: xvivo_gmcsf_1


title: xvivo_gmcsf_2


title: WT3_plus_corpses

value: plus corpses


title: HK2_shKDM5C, input, ChIP


title: HK2_Parental, YY1, ChIP


title: xvivo_mcsf_2


title: Liver from patient with benign pancreatic lesion, #36 [36MP_IGO_06756_D_5]

first: Linda

last: Bojmar

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

institute: Weill Cornell Medicine

description:
AR
36MP_IGO_06756_D_5

data_processing:
The output data (FASTQ files) are mapped to the target genome using the STAR aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used).
After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: Normalized count matrix

source_name: liver

extract_protocol:
total RNA from 5 mg of fresh-frozen liver tissue was extracted using the RNeasy Mini Kit (QIAGEN catalog # 74104)
Samples underwent ribosomal RNA depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202)

treatment_protocol: fresh liver tissue was snap frozen in liquid nitrogen and stored in -80C until RNA extraction

value: liver

tag: tissue type

value: whole liver tissue


title: WT2_plus_corpses


title: WT1_plus_corpses


title: Liver from patient with benign pancreatic lesion, #33 [33DF_IGO_06756_D_4]

description:
AQ
33DF_IGO_06756_D_4


title: Liver from patient with benign pancreatic lesion, #28 [28PF_IGO_06756_D_2]

description:
AP
28PF_IGO_06756_D_2


title: pre-metastatic liver, pancreatic cancer, patient #24 [24RF-2_IGO_06756_D_12]

description:
AO
24RF-2_IGO_06756_D_12

value: pre-metastatic liver


title: ACHN_OEKDM5C_H514A, input, ChIP

source_name: ACHN

value: ACHN

value: ccRCC


title: ACHN_shKDM5C, input, ChIP


title: cKO4_plus_corpses


title: ACHN_OEKDM5C, input, ChIP


title: xvivo_mcsf_1


title: WT4_plus_corpses


title: cKO3_plus_corpses


title: pre-metastatic liver, pancreatic cancer, patient #21 [21CS_23SS_IGO_06756_D_8]

description:
AL
21CS_23SS_IGO_06756_D_8


title: HK2_OEKDM5C, YY1, ChIP


title: ACHN_Parental, input, ChIP


title: Liver from patient with benign pancreatic lesion, #5 [5VS_IGO_06756_D_1]

description:
AK
5VS_IGO_06756_D_1


title: pre-metastatic liver, pancreatic cancer, patient #3 [3JD_21CS_IGO_06756_D_7]

description:
AJ
3JD_21CS_IGO_06756_D_7


title: cKO1_plus_corpses


title: ACHN_shKDM5C, H3K4me3, ChIP

value: H3K4me3(Abclonal #A2357)


title: pre-metastatic liver, pancreatic cancer, patient #6 [6PW_IGO_06756_G_3]

description:
AG
6PW_Liver_IGO_06756_G_3


title: pre-metastatic liver, pancreatic cancer, patient #7 [7KA_IGO_06756_G_4]

description:
AH
7KA_Liver_IGO_06756_G_4


title: cKO2_plus_corpses


title: pre-metastatic liver, pancreatic cancer, patient #50 [50SO_IGO_06756_G_27]

description:
AF
50SO_Liver_IGO_06756_G_27


title: ACHN_Parental, H3K4me3, ChIP


title: pre-metastatic liver, pancreatic cancer, patient #48 [48MS_IGO_06756_G_26]

description:
AE
48MS_Liver_IGO_06756_G_26


title: ACHN_shKDM5C, YY1, ChIP


title: pre-metastatic liver, pancreatic cancer, patient #46 [46FM_IGO_06756_G_25]

description:
AD
46FM_Liver_IGO_06756_G_25


title: pre-metastatic liver, pancreatic cancer, patient #23 [23SS-2_IGO_06756_D_10]

description:
AN
23SS-2_IGO_06756_D_10


title: ACHN_OEKDM5C_H514A, YY1, ChIP


title: Untreated_Rxr_1

description:
Untreated_Rxr_1
un_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm39) using Burrows-Wheeler Aligner (BWA, v.0.7.18)
The output .sam files were name-sorted and duplicate reads were marked and removed using SAMtools (v.1.17)
Reads were filtered to less than 121 bp using SAMtools (v.1.3.1).
BAM files for each replicate were combined using Samtools.
Bigwig files were generated using Deeptools (v.3.1.2) with reads per kilobase of transcript per million mapped reads (RPKM) normalization
CNR peaks were called using SEACR (v.1.3) 91 from bedGraph files generated from RPKM-normalized Bigwig files (bigWigToBedGraph, UCSC Tools) using stringent setting and a numeric threshold of 0.01
Assembly: mm39 (UCSC release)
Supplementary files format and content: bedgraph files of peaks called from SEACR
Supplementary files format and content: bigwig files of processed data
Library strategy: CUT&RUN

source_name: cultured wild type hair follicle stem cells

extract_protocol:
Cells were isolated by 0.25% trypsin/EDTA, pelleted and washed with PBS. Cells were pelleted and were cross-linked. Cut-&-Run libraries were prepared on these cross-linked nuclei, according to Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6 (2017).
CNR sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1X ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen). All CNR libraries were sequenced on Illumina NextSeq using 40 bp paired-end reads.

value: Media only


title: Mlcl_Rxr_2

description:
Mlcl_Rxr_2
mlcl_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph

value: cultured wild type hair follicle stem cells

value: Recombinant AA+LPC+RA


title: Liver from patient with benign pancreatic lesion, #22 [22EB_IGO_06756_D_3]

description:
AM
22EB_IGO_06756_D_3


title: Liver from patient with benign pancreatic lesion, #45 [45ID_IGO_06756_G_24]

description:
AC
45ID_Liver_IGO_06756_G_24


title: Untreated_Rxr_2

description:
Untreated_Rxr_2
un_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph


title: pre-metastatic liver, pancreatic cancer, patient #43 [43JW_IGO_06756_G_22]

description:
AA
43JW_Liver_IGO_06756_G_22


title: Mlcl_Rxr_1

description:
Mlcl_Rxr_1
mlcl_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph


title: ACHN_OEKDM5C, YY1, ChIP


title: pre-metastatic liver, pancreatic cancer, patient #42 [42BS_IGO_06756_G_21]

description:
Z
42BS_Liver_IGO_06756_G_21


title: pre-metastatic liver, pancreatic cancer, patient #9 [9CF_IGO_06756_G_5]

description:
AI
9CF_Liver_IGO_06756_G_5


title: Liver from patient with benign pancreatic lesion, #40 [40BM_IGO_06756_G_19]

description:
X
40BM_Liver_IGO_06756_G_19


title: Corpse_Rxr_2

description:
Corpse_Rxr_2
corpse_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph

value: Corpses


title: pre-metastatic liver, pancreatic cancer, patient #37 [37IL_IGO_06756_G_17]

description:
V
37IL_Liver_IGO_06756_G_17