title: control muscle with EET treatment 3dpi

city: Hangzhou

first: Di

last: Wang

address: Yuhangtang Road.866

institute: Zhejiang University

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (v2.20). Sample demultiplexing, barcode processing, and single-cell 3’ gene counting was performed with Cell Ranger (version 3.1.0), and scRNA-seq data were aligned to the Ensembl genome GRCm38 reference genome. The pipelines were run with the assistance of LC-Bio Technology Co., Ltd (Hangzhou, China).  Downstream analysis was performed with the Seurat package (v4.0.1)85. Low-quality cells with <200 or >1000 genes detected and cells with mitochondrial encoded transcripts representing >20% were excluded from analysis. The raw gene expression matrix after quality control was cell-normalized over total expression, and 2000 variable features were selected for the integration of 6 samples (WT_CON, WT_Day2, WT_Day10, KO_CON, KO_Day2, and KO_Day10) in Gsdmdf/f vs GsdmdCKO analysis; while using 3000 variable features for the integration of 5 samples (WT_CON, Mock_Day3, Mock_Day10, EET_Day3, and EET_Day10) in EET treatment analysis.
Assembly: Ensembl genome GRCm38 reference genome
Supplementary files format and content: matrix.mtx.gz; features.tsv.gz; barcodes.tsv.gz

source_name: TA muscle tissue

extract_protocol:
TA muscle tissue was collected from mice with the indicated treatment or genotype. After washing with ice-cold PBS, the tissue was minced into 2-3 mm pieces and washed twice with ice-cold PBS. Digestion was performed with digestion buffer [0.5 mg/mL Collagenase I (Sigma), 0.5 mg/mL Collagenase V (Sigma), and 0.5 mg/mL Dispase (Worthington)] at 37℃ with 100 rpm for 10 min, and stopped with an equal volume of ice-cold PBS containing 10% FBS. Cell suspensions were passed through a 70-30 µm filter twice, counted with a cell counter (Countstar), and centrifuged at 400 g for 6 min at 12℃. Cells were resuspended with RPMI 1640 (Gibco) on ice. The remaining muscle tissue was digested with 6 ml 0.25% Trypsin-EDTA at 37℃ with 100 rpm for 10 min, and stopped with an equal volume of ice-cold PBS containing 10% FBS, followed by 2 PBS washes and passage through 70-30 µm filters. The two cell portions were collected and red blood cells were removed using 4 ml Red Blood Cell Lysis Solution. Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged twice at 300 g for 3 min at 4℃. The cell pellet was resuspended in 50 μL of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which was required to be >85%, single cell suspensions were counted using a cell counter, and the final concentration was adjusted to 700-1200 cells/μL. The single-cell suspensions were loaded to 10x Chromium to capture 8,000-10,000 single cells according to the manufacturer’s instructions with the 10X Genomics Chromium Single-Cell 3’ kit (V3).
Library construction was performed according to 10X Genomics Chromium Single-Cell 3’ kit (V3)
The subsequent cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150 bp) at a 800 minimum depth of 20,000 reads per cell.

value: TA muscle tissue

value: wildtype

value: CTX intramuscluar injection 3dpi with EET treatment


title: GCA045-Mild-TI-Endoscopy

status: Public on Jul 29 2024

type: SRA

city: nashville

first: Qi

last: Liu

state: TN

address: 2525 West End Ave

country: USA

institute: Vanderbilt univeristy medical center

description:
5314-YX-12_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

library_source: transcriptomic single cell

data_processing:
Single-cell RNAseq reads were filtered, demultiplexed, and quantified by dropEst to generate cell-by-gene count matrices. Specifically, reads with expected structure were kept, and cell barcodes and UMI were extracted by dropTag.
Assembly: Demultiplexed reads were aligned to the human reference transcriptome GRCh38 using STAR
Supplementary files format and content: Processed data includes raw count and meta data with annotation for each cell.

molecule: total RNA

organism: Homo sapiens

source_name: Terminal Ileum

extract_protocol:
Tissues were incubated in a chelating buffer (0.5M EDTA, 0.1M DTT in DPBS) for 1.25hrs, and then transferred to cold active protease (5 mg/ml Protease from Bacillus licheniformis, 2.5 mg/mL DNase in PBS) for 25 minutes at 4˚c. Tissues were then pipetted 10-20 times to yield single cells. Cell suspensions were filtered, washed, and inspected for count and quality before loading onto inDrops for microfluidic capture.
TruDrop libraries, at a 2 nM standard loading concentration, were pooled with other Illumina compatible libraries, and sequenced to various target depths (50–500 million reads)

tag: tissue

value: Terminal Ileum

tag: patient

value: Mild


title: ssHi-C WT, DSB 4 hr replicate 3

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

library_source: genomic

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb
Library strategy: ssHi-C

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT, DSB 4 hr

growth_protocol: Cells were grown to exponential phase in YP-lactate media and synchronized in G1 with alpha-factor for 3 hours. Cells were washed 3 times in pre-warmed YP-lactate and released in S-phase in YP-lactate supplemented with 2% galactose. For Scc1-AID depletion experiment, 2 mM IAA were added at the time of release. For Pol3/Rfc1-AID depletion, 50 ug/mL doxycycline and  2 mM IAA were added 1 hour post-release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: S. cerevisiae culture


title: GCA039-Normal_CD-AC-Endoscopy

description:
5222-YX-24_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

source_name: Ascending Colon

value: Ascending Colon


title: OSN_ac1pCBSdel_rep2_Bisulfite_oxo

city: SAN FRANCISCO

first: Lea

last: Kiefer

state: CA

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

description: WGBS

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
10x scRNAseq data were analyzed using 10x Genomics Cell Ranger 6.0.1 with a recovery of 4000-8000 cells per experiment. Data analysis was performed using Seurat and custom scripts.
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

organism: Mus musculus

source_name: Olfactory epithilium

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.  For in situ HiC was carried out according to Rao et al. 2014 and according to the manufacturer's instructions of the Arima HiC kit. For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments: Libraries were made following the SMARTer Stranded Total RNA-Seq. Raw FASTQ files were aligned with either Tophat or STAR using  mm10 reference genomes. The initial 4 bases of both paired reads were trimmed prior to alignment.  For single cell RNA-seq: Libraries were generated using 10x Genomics 5' kits according to manufacturer's instructions. Raw FASTQ files were analyzed using cellranger.  For in situ Hi-C experiments: Libraries were generated according to Rao et al. 2014 and the manufacturer's instructions of the Arima HiC kit. Raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015). For WGBS: Libraries were constructed according to the Ultralow Methyl-Seq with TrueMethyl oxBS according to manufacturer's instructions. Analysis was performed using the instructions outlined in https://github.com/nugentechnologies/NuMetWG .

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For  HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: Olfactory epithilium

tag: genotype


title: IMQ+N_rep3

type: RNA

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Clariom D mouse arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console Software v4.0 (AGCC 4.0, Affymetrix®) and Transcriptome Analysis Console (TAC) Software v4.0.1 were used with default analysis settings, and expression values were processed with the signal space transformation and robust multichip average methods, which included log2 transformation and quantile normalization.

label: biotin

source_name: Skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After hair was removed from the back skin of C57BL/6J mice (8 weeks old), a traction device (Figure 1) was adhered to by quick-drying glue.

extract_protocol: Total RNAs extracted from the mouse skin were isolated by using RNeasy mini kit

treatment_protocol: Traction force was induced by elongating plastic device on the skin for a total 10 mm at first day. Thereafter, IMQ cream (5%) was topically applied on the stretched or non-stretched skin every day for total 7 days as previous experiments

tag: strain

tag: treatment

value: IMQ-treated mouse without full-stretch (Non-stretch)


title: control muscle with EET treatment 10dpi

country: China

description: 10X Genomics Chromium Single-Cell 3’ kit

library_source: transcriptomic

value: CTX intramuscluar injection 10dpi with EET treatment


title: IMQ+F_rep5

value: IMQ-treated mouse with full-stretch


title: GCA043-Normal_CD-TI-Endoscopy

description:
5222-YX-9_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: IMQ+F_rep3


title: ssHi-C WT, DSB 2 hr replicate 2

source_name: WT, DSB 2 hr


title: control muscle with control treatment 10dpi

value: CTX intramuscluar injection 10dpi with control treatment


title: IMQ+F_rep4


title: GCA037-Normal_CD-TI-Endoscopy

description:
5222-YX-20_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: IMQ+F_rep1


title: control muscle with control treatment 3dpi

value: CTX intramuscluar injection 3dpi with control treatment


title: IMQ+F_rep2


title: OSN_ac1pCBSdel_rep1_Bisulfite_oxo

description: WGBS


title: Hi-C exo1D DSB 4 hr

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb

source_name: exo1D DSB 4 hr


title: OSN_3xCBS_rep2_Bisulfite_oxo

description: WGBS


title: GCA037-Quiescent-AC-Endoscopy

description:
5222-YX-19_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Quiescent


title: Hi-C exo1D DSB 2 hr

source_name: exo1D DSB 2 hr


title: ssHi-C WT, DSB 2 hr + Noco

source_name: WT, DSB 2 hr + Noco


title: Gsdmd WT muscle 10dpi

value: Gsdmdf/f

value: CTX intramuscluar injection 10dpi


title: Hi-C WT, DSB 4 hr + Noco

source_name: WT, DSB 4 hr + Noco


title: GCA036-Moderate-AC-Endoscopy

description:
5177-YX-3_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Moderate


title: Gsdmd WT muscle 2dpi

value: TA muscle tissue

value: CTX intramuscluar injection 2dpi


title: Hi-C WT, DSB 2 hr + Noco


title: GCA035-Moderate-TI-Endoscopy

description:
5222-YX-17_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: OSN_HS5del_rep2_Bisulfite_oxo

description: WGBS


title: Gsdmd WT control muscle

value: no


title: GCA035-Mild-AC-Endoscopy

description:
5222-YX-18_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: GCA033-Mild-TI-Endoscopy

description:
5222-YX-16_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

value: Terminal Ileum


title: Hi-C WT, DSB 4 hr replicate 3


title: OSN_WT_rep2_Bisulfite_oxo

description: WGBS


title: Gsdmd cKO muscle 10dpi


title: Gsdmd cKO muscle 2dpi


title: Hi-C WT, DSB 2 hr replicate 2


title: GCA033-Mild-AC-Endoscopy

description:
5222-YX-15_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Mild


title: Gsdmd cKO muscle


title: GCA031-Normal_CD-AC-Endoscopy

description:
5222-YX-2_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Hi-C metaphase-arrested (cdc20) replicate 2

source_name: metaphase-arrested (cdc20)

value: S. cerevisiae culture


title: OSN_WT_rep1_Bisulfite_oxo

description: WGBS


title: OSN_ac1pCBSdel_rep2_Bisulfite

description: WGBS


title: OSN_HS5inv_scRNA

description: 10x scRNA-seq


title: OSN_ac1pCBSdel_rep1_Bisulfite

description: WGBS


title: Hi-C metaphase-arrested (cdc20) replicate 1


title: GCA031-Normal_CD-TI-Endoscopy

description:
5222-YX-1_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: ssHi-C Cdc45-AID +IAA DSB 4 hr (after G1 release) replicate 2


title: OSN_3xCBS_rep2_Bisulfite

description: WGBS


title: OSN_3xCBS_rep1_Bisulfite_oxo

description: WGBS


title: OSN_HS5del_rep1_Bisulfite_oxo

description: WGBS


title: ssHi-C Cdc45-AID +IAA DSB 4 hr (after G1 release) replicate 1


title: GCA028-Normal_CD-AC-Endoscopy

description:
5222-YX-14_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Ascending Colon


title: OE_ac1pCBSdel_scRNA

description: 10x scRNA-seq

value: Olfactory epithilium


title: OE_HS5del_scRNA

description: 10x scRNA-seq


title: OSN_HS5del_rep2_Bisulfite

description: WGBS


title: GCA028-Mild-TI-Endoscopy

description:
5222-YX-13_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA024-Control-AC-Endoscopy-Rep2

description:
5314-YX-16_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

value: Control


title: ssHi-C Cdc45-AID +DMSO DSB 4 hr (after G1 release) replicate 1


title: ssHi-C rad51D DSB 4 hr replicate 1

source_name: rad51D DSB 4 hr


title: OT-1 cells, wildtype, NOH (HTO)

city: Freiburg

first: Frederic

last: Arnold

address: Hugstetterstr. 55

department: Internal Medicine IV

country: Germany

institute: University of Freiburg Medical Center

description:
wildtype, biological replicate 1 (Hashtag-Ab_1: ACCCACCAGTAAGAC)
wildtype, biological replicate 2 (Hashtag-Ab_2: GGTCGAGAGCATTCA)
NOH, biological replicate 1 (Hashtag-Ab_3: CTTGCCGCATGTCAT)
NOH, biological replicate 2 (Hashtag-Ab_4: AAAGCATTCTTCACG)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
Demultiplexing, alignment, barcode processing, and gene counting was performed using Cell Ranger Software (Version 6.0.0, 10x Genomics); cellranger count ( --expect-cells = 50000)
Assembly: mm10-2020-A based on GRCm38/mm10
Supplementary files format and content: TSV and matrix files
Supplementary files format and content: feature_reference.csv (used Hashtag-Antibodies: 1-4)

molecule: protein

source_name: mixed sample (Spleen/Lymphnode)

extract_protocol:
Single-cell suspensions of spleen and lymph nodes of 2 wt and 2 NOH mice at day 7 after infection were pre-enriched for CD8+ cells applying negative selection immunomagnetic cell separation. CD8α+CD90.1+DAPI- OT-1 cells were isolated from pre-enriched cell suspensions by flow cytometry-assisted cell sorting using a FACSAria III cytometer. Sorted OT-1 cells of each sample were labelled with different oligonucleotide-tagged TotalSeq anti-CD45/anti-MHC-I hashing antibodies. Hashed cells were multiplexed and loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsion (GEMs).
Gene expression and feature barcode libraries were generated as described in the User’s Guide for 10x Chromium Single Cell Reagent Kits with Feature Barcoding technology for Cell Surface Protein. The library pool was commercially sequenced on an Illumina NovaSeq6000 platform (PE150bp) at Novogene Europe (Cambridge, UK).
scRNA-seq (10X platform)

treatment_protocol: Transfer of 2*10^6 OT-1 cells (d-1), infection with 5000 cfu LM-OVA (d0)

value: mixed sample (wildtype/NOH)

value: mixed sample (Spleen/Lymphnode)

tag: cell type

value: CD8 T cells

tag: age

value: OT-1 transfer + LM-OVA infection


title: OSN_WT_mus_cas_scRNA

description: 10x scRNA-seq


title: OSN_HS5del_rep1_Bisulfite

description: WGBS


title: OT-1 cells, wildtype, NOH (GEX)


title: OSN_3xCBS_scRNA

description: 10x scRNA-seq


title: OSN_WT_rep1_Bisulfite

description: WGBS


title: ssHi-C rad51D DSB 2 hr replicate 1

source_name: rad51D DSB 2 hr


title: GCA022-Control-TI-Endoscopy

description:
5314-YX-3_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: ssHi-C WT, DSB 4 hr replicate 2


title: CN_WT_rep2_HiC

description: Hi-C

source_name: Cortex

value: Cortex


title: GCA020-Control-TI-Endoscopy

description:
5222-YX-5_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: ssHi-C WT, DSB 2 hr replicate 1


title: OSN_3xCBS_rep1_Bisulfite

description: WGBS


title: ssHi-C Cdc45-AID +DMSO DSB 4 hr (after G1 release) replicate 2


title: CN_WT_rep1_HiC

description: Hi-C


title: ssHi-C exo1-cd DSB 4 hr

source_name: exo1-cd DSB 4 hr


title: OSN_3xCBS_rep2_HiC

description: Hi-C


title: GCA019-Normal_CD-TI-Endoscopy

description:
5222-YX-11_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: GCA020-Control-AC-Endoscopy

description:
5222-YX-6_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: 11,12-EET treated muring MuSCs [EET1]

data_processing:
In downstream analysis, FastQC was used for quality control with default parameters. After adaptor trimming with Cutadapt, read pairs with length >30 bp were kept, and aligned to the mouse reference genome GRCm38.102 using star. Differentially-expressed genes were called using DESeq2. GSEA enrichment analysis was applied with ClusterProfiler according to the default pipeline. Volcano plots and other visualizations were based on ggplot2.
Assembly: GRCm38.102
Supplementary files format and content: count.csv, count matrix of each sample

source_name: 11,12-EET treated muring MuSCs

extract_protocol:
Primary MuSCs were isolated and cultured with/without 11,12-EET for 2 days. Total RNA was isolated and purified using TRIzol reagent (Invitrogen) following the manufacturer's procedure. The amount and purity of each RNA sample was quantified with NanoDrop ND-1000 (NanoDrop) and RNA integrity was assessed by Bioanalyzer 2100 (Agilent) with RNA Integrity Number >7.0, and further confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA was purified from 1 μg total RNA using Dynabeads Oligo (dT) (25-61005, Thermo Fisher) using two rounds of purification, followed by fragmentation using the Magnesium RNA Fragmentation Module (cat.e6150, NEB) at 94℃ for 5-7min. Cleaved RNA fragments were reverse-transcribed to create the cDNA with SuperScript™ II Reverse Transcriptase (cat.1896649, Invitrogen), which were next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (cat.m0209, NEB), RNase H (cat.m0297, NEB) and dUTP Solution (cat.R0133, Thermo Fisher).
After PCR amplification, the average insert size for the final cDNA library was 300 ± 50 bp. Finally, 2 × 150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 was performed following the vendor's recommended protocol.

value: mice primary MuSCs

value: Muslce stem cell

value: wildtype

value: 11,12-EET for 2 days


title: 11,12-EET treated muring MuSCs [EET2]


title: control murine MuSCs [CON3]

source_name: control murine MuSCs


title: GCA024-Control-AC-Endoscopy-Rep1

description:
5314-YX-17_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: OSN_3xCBS_rep1_HiC

description: Hi-C


title: ssHi-C exo1-cd DSB 2 hr

source_name: exo1-cd DSB 2 hr


title: GCA019-Moderate-AC-Endoscopy

description:
5222-YX-12_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz

source_name: Ascending Colon

value: Moderate


title: GCA022-Control-AC-Endoscopy

description:
5314-YX-4_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: Hi-C exo1-cd DSB 4 hr


title: OSN_WT_rep2_Bisulfite

description: WGBS

source_name: Olfactory epithilium


title: control murine MuSCs [CON2]


title: OSN_ac1pCBSdel_rep2_HiC

description: Hi-C


title: GCA018-Control-TI-Endoscopy

description:
5314-YX-2_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz

source_name: Terminal Ileum


title: 11,12-EET treated muring MuSCs [EET3]


title: Hi-C exo1-cd DSB 2 hr


title: OSN_ac1pCBSdel_rep1_HiC

description: Hi-C


title: GCA017-Control-TI-Endoscopy

description:
5314-YX-23_S1_L005
Raw_counts_TI_Endoscopy.txt.gz
Annotation_TI_Endoscopy.txt.gz


title: control murine MuSCs [CON1]


title: Hi-C rad51D DSB 4 hr replicate 1


title: OSN_HS8del_rep2_HiC

description: Hi-C


title: GCA017-Control-AC-Endoscopy

description:
5314-YX-24_S1_L005
Raw_counts_AC_Endoscopy.txt.gz
Annotation_AC_Endoscopy.txt.gz


title: RAW 264.7, 3xFL-SRSF7, input

city: Bryan

first: Kristin

last: Patrick

state: Texas

address: 8441 Riverside Parkway

department: MPIM

institute: Texas A&M

description: SR7 I (57806)

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2.
Reads were aligned to the Mus musculus genome build mm10 using bowtie23. Per-sample quality assessment plots were generated with HOMER4and Mosaics5.
Peaks were called using MACS26(with input/IgG controls background subtracted, if provided). Peak overlaps and differential binding were calculated using the DiffBind R library7.
Differential binding was calculated at gene promoter sites. Read distribution percentages, identity heatmaps, and FRiP plots were generated as part of the QC step using ChIPQC R library8and HOMER.
Assembly: Mus musculus genome build mm10
Supplementary files format and content: bigwig

growth_protocol: DMEM supplemented with 10% FBS and 2% Hepes. Cells cultured at 37C and 5% CO2.

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min. After quenching and lysis chromatin was sonicated with Bioruptor UCD-200 (Diagenode).

treatment_protocol: 100 ng/ml LPS added to CM for 4h

tag: cell line

value: macrophage-like

value: 3xFL-SRSF7 overexpressing

value: 4h LPS


title: Hi-C rad51D DSB 2 hr replicate 1

value: S. cerevisiae culture


title: RAW 264.7, 3xFL-SRSF7, IP

description: SR7 E (57809)


title: OSN_HS8del_rep1_HiC

description: Hi-C


title: Hi-C WT, DSB 4 hr replicate 2

source_name: WT, DSB 4 hr


title: RAW 264.7, 3xFL-GFP, input

description: GFP I (57801)

value: 3xFL-GFP overexpressing


title: OSN_HS5inv_rep2_HiC

description: Hi-C

value: Olfactory epithilium


title: ssHi-C No DSB

source_name: No DSB


title: HDF-3 shAR-1_Lamin A/C

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Data analysis involved alignment, peak calling, and differential binding analysis using bioinformatics tools, with BWA-MEM for the alignment step and Macs2 for peak calling, with pv=0.001
Assembly: GRCh38
Supplementary files format and content: bigwig files
Library strategy: Cut & Run

growth_protocol: Cells were cultured, harvested, and processed following the kit protocol.

extract_protocol:
Three different HDF strains were infected either with lentiviruses expressing shAR-1 or shCtrl, selected with puromycin and harvested for Cut & Run experiments 7th day post infection.
Briefly, 500,000 cells were incubated with Protein A-MNase fusion protein, digested with Micrococcal Nuclease, and nuclei were washed and incubated with Protein A-G-MNase beads for elution.
Cut & Run assays were performed using the CUTANA™ ChIC / CUT&RUN Kit ( EpiCypher; Cat. No. # SKU: 14-1048) to investigate chromatin interactions of pSer301 and total Lamin A/C in parallel to H3K27Ac in HDF cells with and without AR silencing. DNA purification and library preparation were performed, followed by Illumina sequencing

value: human dermal fibroblasts (HDFs)

value: Lamin A/C


title: HDF-3 shAR-1_pSer301


title: HDF-3 shAR-1_H3K27Ac


title: Hi-C WT, DSB 2 hr replicate 1

source_name: WT, DSB 2 hr


title: OSN_HS5del_rep2_HiC

description: Hi-C


title: OSN_HS5inv_rep1_HiC

description: Hi-C


title: ssHi-C WT, DSB 4 hr, left DSB-distal annealing oligos


title: HDF-3 shCtrl_Lamin A/C


title: RAW 264.7, 3xFL-GFP, IP

description: GFP IP (57804)


title: OSN_HS5del_rep1_HiC

description: Hi-C


title: ssHi-C WT, DSB 4 hr, left staggered 2 annealing oligos


title: OSN_HS8del_rep2_captureHiC

description: capture Hi-C


title: HDF-3 shCtrl_pSer301


title: ssHi-C WT, DSB 4 hr, left DSB-proximal annealing oligos


title: ssHi-C WT, DSB 4 hr, left staggered 1 annealing oligos


title: OSN_HS8del_rep1_captureHiC

description: capture Hi-C


title: 5_chir_cdh_ko_8_10_22

city: Los Angeles

first: Helena

last: Bugacov

address: 1425 San Pablo St.

department: Development, Stem Cell and Regenerative Medicine

institute: USC STEM CELL

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.  RNA-seq reads were then aligned to the combined mouse GRCm38 and human GRCh38 Ensembl release 76 primary assemblies with STAR version 2.5.1a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
Normalized counts tables were ran through DeSEQ2 (Love, 2014 #412) to create differential gene expression tables with Log2Fc cut offs no less than 1 and p-adjusted values no greater than 0.05. Significance of Cre and Cas9 intersected gene lists was calculated with hypergeometric function in R. Differential expression tables were passed through Gene Ontology package clusterProfiler (Yu, 2012). Data was visualized using ggplot and Complex heatmap functions in R (Gu, 2016). Benjamini-Hochberg correction (False Discovery Rate) applied as well as significance associated with intersections compared to all genes expressed with gene normalized counts greater than or equal to 10 using hypergeometric test.
Assembly: mm10, mouse GRCm38

source_name: kidney

extract_protocol:
RNA was isolated using Qiagen RNeasy Micro Kit (74004).
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends
Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: kidney

value: Primary

value: nephron progenitor

value: 5uM CHIR-CdhsgRNA


title: HDF-3 shAR-1_IgG

value: IgG control


title: HDF-3 shCtrl_H3K27Ac


title: HDF-3 shCtrl_IgG


title: SCD3_UT

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova

data_processing:
Read quality was verified using FastQC (v. 0.11.9). Raw reads were trimmed for adapters and low-quality tails (quality < Q20) with BBDuk (v. 38.92); moreover, the first 15 nucleotides were force-trimmed for low quality. Reads shorter than 35 bp after trimming were removed.
Reads were subsequently aligned to the human reference genome (hg38) using STAR (v. 2.7.9a). Raw gene counts were obtained in R-4.1.1 using the featureCounts function of the Rsubread R package (v. 2.6.4) and the GENCODE 38 basic gene annotation for hg38 reference genome.
Gene counts were normalized to counts per million mapped reads (CPM) and to fragments per kilobase of exon per million mapped reads (FPKM) using the edgeR R package (v. 3.34.1); only genes with a CPM greater than 1 in at least 3 samples were retained for differential analysis.
Assembly: hg38
Supplementary files format and content: FPKM obtained using edgeR

source_name: SCD CD34+ HSPCs

extract_protocol:
Total RNA was isolated from untreated or RNP-transfected plerixafor-mobilized HD and SCD HSPCs (n=3 for each group) using the RNeasy Kit (QIAGEN)
RNA-seq libraries were prepared starting from 30 ng of total RNA using the Universal Plus mRNA-Seq kit (Nugen) as recommended by the manufacturer.

value: SCD CD34+ HSPCs

value: SCD

value: untreated


title: OSN_WT_captureHiC

description: capture Hi-C


title: 1.25_chir_cdh_ko_8_10_22

value: 1.25uM CHIR-CdhsgRNA


title: SCD3_AAVS1

value: treated with the Cas9 RNP containing the AAVS1 gRNA


title: 1.25_chir_cdh_ko_8_5_22


title: ssHi-C WT, DSB 4 hr replicate 1


title: SCD3_196

value: treated with the Cas9 RNP containing the -196 gRNA


title: Hi-C No DSB


title: 5_chir_ctnna1_ko_8_10_22

value: 5uM CHIR-Ctnna1sgRNA


title: SCD3_197

value: treated with the Cas9 RNP containing the -197 gRNA


title: Wild Type 2

city: Exeter

first: Paul

middle: Andrew

last: O'Neill

state: --- Select a state ---

address: Stocker Road

country: United Kingdom

institute: University of Exeter

data_processing:
merge paired reads into single .fasta file
run kissplice (https://kissplice.prabi.fr/tools/kiss2refgenome/) against all samples
extract snps which match the pattern wt: homozygous_1, mutant: homozygous_2, sibling, heterozygous
blast candidate snps vs nt
Assembly: n/a

molecule: polyA RNA

organism: Kryptolebias marmoratus

source_name: embryo

extract_protocol:
RNeasy
Illumina Drirections -> cDNA

value: embryo


title: Wild Type 1


title: 5_chir_ctnna1_ko_7_15_22


title: Wild Type 3


title: SCD2_UT


title: 1.25_chir_ctnna1_ko_8_10_22

value: 1.25uM CHIR-Ctnna1sgRNA


title: Hi-C WT, DSB 4 hr, left staggered 2 annealing oligos

value: S. cerevisiae culture


title: Sibling M

value: Sibling


title: SCD2_AAVS1


title: Sibling 3


title: ssHi-C WT, DSB 4 hr, right annealing oligos only


title: 5_chir_cdh_ko_8_5_22

value: kidney


title: Hi-C WT, DSB 4 hr, left DSB-proximal annealing oligos


title: Hi-C WT, DSB 4 hr, left staggered 1 annealing oligos


title: OSN_HS5del_captureHiC

description: capture Hi-C

value: Olfactory epithilium


title: 1.25_chir_ctnna1_ko_7_15_22

value: Primary

value: nephron progenitor


title: 5_chir_ctnnb1_ko_8_10_22

value: 5uM CHIR-Ctnnb1sgRNA


title: Wild Type M


title: SCD2_197

value: SCD CD34+ HSPCs


title: ssHi-C WT, DSB 4 hr, left annealing oligos only


title: Hi-C WT, DSB 4 hr, right annealing oligos only


title: 5_chir_ctnnb1_ko_8_5_22


title: SCD1_UT

value: SCD


title: Sibling 1


title: Hi-C WT, DSB 4 hr, left DSB-distal annealing oligos


title: Hi-C WT, DSB 4 hr, left annealing oligos only


title: NFR Mutant M

value: Nfr mutant


title: 5_chir_ctnnb1_ko_7_15_22


title: SCD1_AAVS1


title: Hi-C WT, DSB 4 hr replicate 1


title: 1.25_chir_ctnnb1_ko_8_10_22

value: 1.25uM CHIR-Ctnnb1sgRNA


title: SCD2_196


title: NFR Mutant 3


title: NFR Mutant 2


title: OE_3xCBS_Rad21_rep2_ChIP

description: ChIP


title: OE_3xCBS_Rad21_rep1_ChIP

description: ChIP


title: NFR Mutant 1


title: 1.25_chir_ctnnb1_ko_7_15_22


title: SCD1_196


title: OE_3xCBS_CTCF_rep2_ChIP

description: ChIP


title: SCD1_197


title: Sibling 2


title: HD3_AAVS1

source_name: HD CD34+ HSPCs

value: HD CD34+ HSPCs

value: HD

value: treated with the Cas9 RNP containing the AAVS1 gRNA


title: 5_chir_gfp_8_10_22

value: 5uM CHIR-GFPsgRNA


title: LN229, replicates 3-4, 2 time points, 20 drugs, multiplexed

city: Zurich

first: Berend

last: Snijder

address: Otto-Stern-Weg 3, HPM building

country: Switzerland

institute: ETH Zurich

description: column names of processed data file corresponds to sample metadata

data_processing:
Code for de-multiplexing of DRUG-Seq data can be found on GitHub: https://github.com/RebekkaWegmann/drugseq_toolbox
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include DESeq2 vsd-normalized count values and raw counts for each sample. Separate sample metadata sheet corresponding to column names is also additionally provided.

growth_protocol: LN-229 glioblastoma cells were maintained in DMEM supplemented with 2% fetal bovine serum (FBS), 1% Pen-strep, and 25mM HEPES in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
LN-229 cells in drug-treated 96-wells were lysed with TRIzol and RNA was isolated using the Zymo Direct-zol-96 RNA isolation kit.
Subsequent cDNA and library prep was performed as described  in Ye et al., 2018 with a few modifications including the change of reverse transcription primers to be compatible with standard Illumina sequencing primers.

treatment_protocol: Drugs were manually added (final concentration, 20uM) to LN-229 cells that were plated in 96-well plates one day prior to the experiment.

value: Glioblastoma

value: Brain; Right frontal parieto-occipital cortex

value: 20 different drug treatment conditions described in the sample metadata sheet

tag: time

value: 6 hours, 22 hours


title: OE_3xCBS_CTCF_rep1_ChIP

description: ChIP


title: 5_chir_gfp_8_5_22

value: kidney


title: HD3_196

value: treated with the Cas9 RNP containing the -196 gRNA


title: LN229, replicates 1-2, 2 time points, 20 drugs, multiplexed


title: OE_ac1pCBSdel_Rad21_rep2_ChIP

description: ChIP

value: Olfactory epithilium


title: 5_chir_gfp_7_15_22

value: Primary

value: nephron progenitor


title: HD3_197

value: treated with the Cas9 RNP containing the -197 gRNA


title: STm-SPC+45

city: Bhubaneswar

first: Suraj

middle: Kumar

last: Tripathy

state: Odisha

address: Campus 11

department: Biotechnology

country: India

institute: KIIT-DU

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.9 and MultiQC v1.9 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.1 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Salmonella enterica subsp. enterica serovar Typhimurium SL1344 reference genome using Bowtie2 v2.1.0 aligner.
Gene expression values were obtained as read counts using ensembl annotation file (Salmonella enterica subsp. enterica serovar Typhimurium SL1344 and featureCounts v2.0.1 software.
Genome_build: assembly (GCF_000210855.2; ASM21085v2)
Supplementary_files_format_and_content: Raw reads counts in excel format

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Bacteria

growth_protocol: The bacteria were grown in nutrient broth at 37℃, 150 rpm.

extract_protocol:
The RNA extraction was performed using TRIzol method.
Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

treatment_protocol: Required amount of bacteria in its log phase was washed using normal saline. This was spiked into the sonophotocatalytic setup and was treated for 45 minutes. The treatment exposed bacteria was recovered by providing it with fresh nutrient source and subsequently grown till log phase for further extraction.

value: Exposed to sonophotocatalysis


title: 1.25_chir_gfp_8_10_22

value: 1.25uM CHIR-GFPsgRNA


title: STm

value: Untreated


title: HD2_UT

value: HD CD34+ HSPCs

value: untreated


title: HD3_UT

value: HD


title: RChIP_siNC_rep2

city: La Jolla

first: Alon

last: Goren

address: 9500 Gilman Drive

institute: University of California San Diego

description:
RChIP_siNC.fwd.bed
RChIP_siNC.rev.bed

data_processing:
FASTQ reads were quality-checked and adaptor-trimmed with trim galore, and then mapped to the human hg38 reference genomes with bwa mem. ChIP peak calling were performed with MACS2 as described in methods.
Assembly: hg38
Supplementary files format and content: RChIP narrowPeak file of both forward and reverse strand.
Library strategy: R-ChIP

extract_protocol:
Refer to the published protocol, Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP)
R-ChIP library was prepared based on published R-ChIP protocols.

value: cell line

value: siNC


title: HD2_AAVS1

value: treated with the Cas9 RNP containing the AAVS1 gRNA


title: RChIP_siNC_rep1

description:
RChIP_siNC.fwd.bed
RChIP_siNC.rev.bed


title: 1.25_chir_gfp_8_5_22


title: OE_ac1pCBSdel_CTCF_rep1_ChIP

description: ChIP


title: 1.25_chir_gfp_7_15_22


title: 5um_chir_cre_pos_Rep2B

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cre_pos_rep2

value: 5uM CHIR-Cre-pos


title: OSN_WT_Rad21_rep1_ChIP

description: ChIP


title: OSN_WT_CTCF_rep1_ChIP

description: ChIP


title: HD2_196


title: 5um_chir_cre_pos_Rep1A

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cre_pos_rep1


title: HD2_197


title: HD1_UT


title: OSN_WT_H3K4me3_rep2_ChIP

description: ChIP


title: RChIP_siCSB_rep1

description:
RChIP_siCSB.fwd.bed
RChIP_siCSB.rev.bed

value: siCSB


title: 1.25um_chir_cre_pos_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cre_pos_rep2

value: kidney

value: 1.25uM CHIR-Cre-pos


title: NPC_wildtype_Rep3

city: Ann Arbor

first: Charles

middle: William

last: Ryan

state: Michigan

address: 1241 Catherine St, 4909 Buhl Building

department: Human Genetics

institute: University of Michigan

description: Sequencing performed by Azenta life sciences

data_processing:
FASTQ files were sligned to hg38 and hg38.refgene.gtf with STAR aligner.
Assembly: hg38
Supplementary files format and content: Reads per gene matrix output of STAR alignment to hg38.refgene.gtf

source_name: Neural progenitor cell monolayer

growth_protocol: N2/B27/FGF growth media at 37C 5%CO2

extract_protocol:
a PureLinkTM RNA Mini Kit (Invitrogen, #12183018A).
polyA transcripts were sequenced on an illumina HiSeq platform

treatment_protocol: CRISPR-cas9 genome editing was used to generate a RING1/RNF2 allelic series. Otherwise, NPCs were grown under normal growth conditions.

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell

value: wild type

value: Normal growth conditions


title: OE_ac1pCBSdel_Rad21_rep1_ChIP

description: ChIP

value: Olfactory epithilium


title: OSN_WT_H3K4me3_rep1_ChIP

description: ChIP


title: NPC_wildtype_Rep2


title: HD1_AAVS1


title: 1.25um_chir_cre_pos_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cre_pos_rep1

value: Primary

value: nephron progenitor


title: HD1_196

value: HD CD34+ HSPCs

value: treated with the Cas9 RNP containing the -196 gRNA


title: OE_ac1pCBSdel_CTCF_rep2_ChIP

description: ChIP


title: OSN_WT_H3K27ac_rep3_ChIP

description: ChIP


title: 5um_chir_cre_neg_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cre_neg_rep2

value: 5uM CHIR-Cre-neg


title: NPC_wildtype_Rep1


title: HD1_197

value: HD

value: treated with the Cas9 RNP containing the -197 gRNA


title: RChIP_siCSB_rep2

description:
RChIP_siCSB.fwd.bed
RChIP_siCSB.rev.bed

value: cell line


title: OSN_WT_H3K27ac_rep1_ChIP

description: ChIP


title: NPC_RNF2ms/ms_Rep3

value: Homozygous RNF2 R98Q missense (RNF2 c.292_293AG > CA;p.R98Q)


title: PN4

city: Guangzhou

first: Lu

last: peng

address: No.106, Zhongshan 2nd Road

department: Dermatology

institute: Guangdong Provincial People's Hospital

data_processing:
The sequencing data were subjected to quality control and statistical analysis, including the evaluation of exon ratios and barcode information, using the Cell Ranger (Version 5.1.0).
Cell Ranger was also used to transform the sequencing raw data into a cell expression matrix. The single-cell sequencing results from different samples were merged and normalized based on the sample with the lowest sequencing depth.
Multiple cells were filtered out using the R package “DoubletFinder”.
Cells with with fewer than 500 genes and and more than 25% mitochondrial expression  were filtered out using the R package “Seurat”.
Assembly: GRCh38

source_name: previously resolved region tissues of patient 4

extract_protocol:
The MACS whole-skin dissociation kit (130-101-540, Miltenyi, USA) was utilized to digest the biopsy skin tissues. The single-cell sequencing was formed through the 10x Genomics.
Gene expression cDNA libraries were prepared according to the manufacturer's instructions with 13 cycles of PCR amplification in the water-in-oil emulsion system. The concentration of the library was measured using the Qubit system (Thermo Fisher), and the fragment size was determined using the 2100 Bioanalyzer instrument (Agilent). Libraries with an effective concentration above 10nM were selected for paired-end sequencing (Illumina 6000).

value: Skin cells

tag: medical history

value: 5 years

tag: race

value: Asian

tag: gender

value: male

tag: biopsy site

value: lower back


title: 1.25um_chir_cre_neg_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cre_neg_rep2

value: kidney

value: 1.25uM CHIR-Cre-neg


title: NPC_RNF2ms/ms_Rep2

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell

value: Normal growth conditions


title: 5um_chir_cre_neg_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cre_neg_rep1

value: Primary

value: nephron progenitor


title: PP4

source_name: the autologous on-site recurrence with psoriatic plaque tissues of patient 4


title: 1.25_chir_ctnnb1_ko_8_5_22

value: 1.25uM CHIR-Ctnnb1sgRNA


title: 1.25um_chir_cre_neg_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cre_neg_rep1


title: CN4

source_name: the autologous appearing-normal control tissues of patient 4


title: OSN_WT_H3K9me3_rep1_ChIP

description: ChIP

value: Olfactory epithilium


title: OSN_WT_H3K9me3_rep2_ChIP

description: ChIP


title: NPC_RNF2ms/ms_Rep1


title: 5um_chir_tcf_ko_Rep3

description:
Tcf_Lef_normalized_counts.csv
Rep3_5um_chir_tcf_ko

value: 5uM CHIR-TcfsgRNA


title: PN3

source_name: the previously resolved region tissues of patient 3

value: 4 years


title: 5um_chir_tcf_ko_Rep2

description:
Tcf_Lef_normalized_counts.csv
Rep2_5um_chir_tcf_ko


title: CN_ac1pCBSdel_rep2_RNA

description: RNA-seq

source_name: Cortex

value: Cortex


title: PP3

source_name: the autologous on-site recurrence with psoriatic plaque tissues of patient 3

value: Skin cells


title: NPC_RING1ms/ms_Rep2

value: Homozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: CN_ac1pCBSdel_rep1_RNA

description: RNA-seq


title: 5um_chir_tcf_ko_Rep1

description:
Tcf_Lef_normalized_counts.csv
Rep1_5um_chir_tcf_ko


title: NPC_RING1ms/ms_Rep1


title: CN_HS5inv_rep4_RNA

description: RNA-seq


title: NPC_RING1ms/ms_Rep3


title: 1.25um_chir_tcf_ko_Rep3

description:
Tcf_Lef_normalized_counts.csv
Rep3_1.25um_chir_tcf_ko

value: 1.25uM CHIR-TcfsgRNA


title: CN3

source_name: the autologous appearing-normal control tissues of patient 3

value: Asian

value: male

value: lower back


title: NPC_RING1+/ms_Rep3

value: Neural progenitor cell monolayer

value: Heterozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: PN2

source_name: the previously resolved region tissues of patient 2

value: 22 years


title: CN_HS5inv_rep3_RNA

description: RNA-seq


title: 1.25um_chir_tcf_ko_Rep1

description:
Tcf_Lef_normalized_counts.csv
Rep1_1.25um_chir_tcf_ko

value: kidney


title: NPC_RING1+/ms_Rep2

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell

value: Normal growth conditions


title: CN_HS5inv_rep2_RNA

description: RNA-seq


title: 5um_chir_gfp_Rep3

description:
Tcf_Lef_normalized_counts.csv
Rep3_5um_chir_gfp

value: Primary

value: nephron progenitor

value: 5uM CHIR-GFPsgRNA


title: NPC_RING1+/ms_Rep1


title: PP2

source_name: the autologous on-site recurrence with psoriatic plaque tissues of patient 2

value: 21 years


title: PN1

source_name: the previously resolved region tissues of patient 1

value: Skin cells

value: 31 years


title: CN_HS5inv_rep1_RNA

description: RNA-seq

value: Cortex


title: 5um_chir_gfp_Rep2

description:
Tcf_Lef_normalized_counts.csv
Rep2_5um_chir_gfp


title: PP1

source_name: the autologous on-site recurrence with psoriatic plaque tissues of patient 1

value: 30 years

value: Asian


title: CN_HS5del_rep3_RNA

description: RNA-seq


title: 5um_chir_gfp_Rep1

description:
Tcf_Lef_normalized_counts.csv
Rep1_5um_chir_gfp

source_name: kidney


title: NPC_RING1-/-_Rep2

value: Homozygous RING1 Knockout (RING1 c.280delG; p.S96SFS10*)


title: CN

source_name: the autologous appearing-normal control tissues of patient 1 and patient 2

value: 30 years \ 21 years

value: male

value: lower back


title: patient J1798_P25 at time point C2D1

city: Baltimore

first: Ludmila

last: Danilova

address: 550 N Broadway St 1103E

institute: Johns Hopkins School of Medicine

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files. Default parameters were used
trimgalore v0.6.3 was used to trim the reads. Default parameters were used
rsem-1.3.0 was used for running the alignments as well as generating gene and transcript expression levels
RSEM expected counts were used as gene expression
Assembly: hg38
Supplementary files format and content: tab-delimited file with RSEM expected counts for each samples

source_name: tumor cells

extract_protocol: RNA libraries were generated using the TruSeq Stranded Total RNA Library kit according to manufacturer instructions (Illumina; San Diego, CA)

value: tumor cells

tag: patient id

tag: time point

tag: recist

value: NonResponder


title: CN_HS5del_rep2_RNA

description: RNA-seq


title: NPC_RING1-/-_Rep1

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: neural progenitor cell


title: CN_HS5del_rep1_RNA

description: RNA-seq


title: patient J1798_P25 at time point C1D1


title: 1.25um_chir_gfp_Rep2

description:
Tcf_Lef_normalized_counts.csv
Rep2_1.25um_chir_gfp

value: kidney

value: Primary

value: nephron progenitor

value: 1.25uM CHIR-GFPsgRNA


title: CN_HS5wt_rep2_RNA

description: RNA-seq


title: 1.25um_chir_gfp_Rep1

description:
Tcf_Lef_normalized_counts.csv
Rep1_1.25um_chir_gfp


title: OSN_WT_H3K27ac_rep2_ChIP

description: ChIP

source_name: Olfactory epithilium

value: Olfactory epithilium


title: N_SH_ref6-1_1

city: Shanghai

first: Qican

last: Cheng

state: Shanghai

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to TAIR10 using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Assembly: TAIR10
Supplementary files format and content: Supplementary_files_format_and_content: The expression levels (TPM) of differentially expressed genes after shade treatment.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: seedlings were grown under N (4-day-old seedlings + 8 h white light + 40 h recovering white light + 1 h triggering shade) and P (4-day-old seedlings + 8 h priming shade + 40 h recovering white light + 1 h triggering shade) conditions.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shade treatment (R/FR≈0.5)

value: whole seedling

value: 1 hr shade


title: CN_HS5wt_rep1_RNA

description: RNA-seq

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
10x scRNAseq data were analyzed using 10x Genomics Cell Ranger 6.0.1 with a recovery of 4000-8000 cells per experiment. Data analysis was performed using Seurat and custom scripts.
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

value: Cortex


title: 5um_chir_cas9_ctnnb1sgrna_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cas9_ctnnb1sgrna_rep2

value: 5uM CHIR-Ctnnb1sgRNA


title: NPC_RING1-/-_Rep3

description: Sequencing performed by Azenta life sciences

source_name: Neural progenitor cell monolayer

value: Homozygous RING1 Knockout (RING1 c.280delG; p.S96SFS10*)

value: Normal growth conditions


title: patient J1798_P21 at time point Baseline

value: Baseline


title: CN_ac1pCBSwt_rep1_RNA

description: RNA-seq


title: N_WL_ref6-1_1

value: control


title: 5um_chir_cas9_ctnnb1sgrna_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cas9_ctnnb1sgrna_rep1


title: OSN_ac1pCBSdel_rep2_RNA

description: RNA-seq


title: 1.25um_chir_cas9_ctnnb1sgrna_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cas9_ctnnb1sgrna_rep2

value: 1.25uM CHIR-Ctnnb1sgRNA


title: patient J1798_P12 at time point Baseline

value: tumor cells

value: NonResponder


title: OSN_ac1pCBSdel_rep1_RNA

description: RNA-seq


title: 1.25um_chir_gfp_Rep3

description:
Tcf_Lef_normalized_counts.csv
Rep3_1.25um_chir_gfp


title: 1.25um_chir_cas9_ctnnb1sgrna_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cas9_ctnnb1sgrna_rep1


title: N_SH_pif7-1_1


title: N_SH_ref6-1_2


title: N_WL_ref6-1_2


title: OSN_3xCBS_rep2_RNA

description: RNA-seq


title: N_WL_pif7-1_2


title: 5um_chir_cas9_gfpsgrna_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cas9_gfpsgrna_rep2

value: 5uM CHIR-GFPsgRNA


title: patient J1798_P15 at time point C1D1


title: OSN_3xCBS_rep1_RNA

description: RNA-seq


title: 5um_chir_cas9_gfpsgrna_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
5umchir_cas9_gfpsgrna_rep1

value: kidney


title: patient J1798_P25 at time point Baseline


title: N_WL_pif7-1_1


title: OSN_HS5delRad21cKO_rep2_RNA

description: RNA-seq


title: 1.25um_chir_cas9_gfpsgrna_Rep2

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cas9_gfpsgrna_rep2

value: Primary


title: patient J1798_P21 at time point C1D1


title: P_SH_ref6-1_2

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT.
Quality filtered reads were then mapped to TAIR10 using STAR.
Read counts were calculated by using htseq-count.
Differential gene expression analysis was done using R package DESeq2.
Assembly: TAIR10
Supplementary files format and content: all_genes_expression_TPM.txt: The expression levels (TPM) of differentially expressed genes after shade treatment.

growth_protocol: Seedlings were grown under N (4-day-old seedlings + 8 h white light + 40 h recovering white light + 1 h triggering shade) and P (4-day-old seedlings + 8 h priming shade + 40 h recovering white light + 1 h triggering shade) conditions.

extract_protocol:
Total RNA was extracted from the snap-frozen tissues using TRIzol® Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Shade treatment (R/FR≈0.5).

tag: condition

value: primed


title: patient J1798_P26 at time point C1D1


title: patient J1798_P26 at time point Baseline


title: P_SH_ref6-1_1

tag: tissue


title: P_WL_ref6-1_2


title: OSN_HS5delRad21cKO_rep1_RNA

description: RNA-seq

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.  For in situ HiC was carried out according to Rao et al. 2014 and according to the manufacturer's instructions of the Arima HiC kit. For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments: Libraries were made following the SMARTer Stranded Total RNA-Seq. Raw FASTQ files were aligned with either Tophat or STAR using  mm10 reference genomes. The initial 4 bases of both paired reads were trimmed prior to alignment.  For single cell RNA-seq: Libraries were generated using 10x Genomics 5' kits according to manufacturer's instructions. Raw FASTQ files were analyzed using cellranger.  For in situ Hi-C experiments: Libraries were generated according to Rao et al. 2014 and the manufacturer's instructions of the Arima HiC kit. Raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015). For WGBS: Libraries were constructed according to the Ultralow Methyl-Seq with TrueMethyl oxBS according to manufacturer's instructions. Analysis was performed using the instructions outlined in https://github.com/nugentechnologies/NuMetWG .


title: 1.25um_chir_cas9_gfpsgrna_Rep1

description:
Ctnnb1_KO_All_datasets_normalized_counts_121722.csv
1_25umchir_cas9_gfpsgrna_rep1

value: nephron progenitor

value: 1.25uM CHIR-GFPsgRNA


title: 5um_chir_wt_Rep3

description:
WT_counts.csv
5um_chir_rep3

value: Wild Type

value: 5uM CHIR


title: OSN_HS5inv_rep2_RNA

description: RNA-seq

value: Olfactory epithilium


title: N_SH_pif7-1_2

value: whole seedling

value: 1 hr shade


title: patient J1798_P14 at time point C1D1


title: OSN_HS5inv_rep1_RNA

description: RNA-seq


title: patient J1798_P15 at time point C2D1


title: P_WL_ref6-1_1


title: 5um_chir_wt_Rep2

description:
WT_counts.csv
5um_chir_rep2


title: patient J1798_P14 at time point Baseline


title: patient J1798_P6 at time point C1D1


title: OSN_HS5del_rep2_RNA

description: RNA-seq


title: P_SH_pif7-1_2


title: patient J1798_P44 at time point C2D1


title: P_SH_pif7-1_1


title: OSN_HS5del_rep1_RNA

description: RNA-seq


title: patient J1798_P15 at time point Baseline


title: P_WL_pif7-1_2


title: 1.25um_chir_wt_Rep3

description:
WT_counts.csv
1.25um_chir_rep3

value: 1.25uM CHIR


title: 1.25um_chir_wt_Rep2

description:
WT_counts.csv
1.25um_chir_rep2


title: patient J1798_P44 at time point C1D1


title: OSN_HS8del_rep2_RNA

description: RNA-seq


title: OSN_HS8del_rep1_RNA

description: RNA-seq


title: P_WL_pif7-1_1


title: 1.25um_chir_wt_Rep1

description:
WT_counts.csv
1.25um_chir_rep1


title: patient J1798_P44 at time point Baseline

value: Baseline


title: OSN_WT_rep2_RNA

description: RNA-seq


title: P_SH_WT_2


title: OSN_WT_rep1_RNA

description: RNA-seq


title: patient J1798_P33 at time point C1D1


title: 0um_chir_wt_Rep3

description:
WT_counts.csv
0um_chir_rep3

value: 0uM CHIR


title: P_SH_WT_1


title: 0um_chir_wt_Rep2

description:
WT_counts.csv
0um_chir_rep2


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample SW1783-6-3-6

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.Human astrocytoma cell line, SW1783 (HTB-13) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz’s L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, without CO2 incubator. The cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco’s modified Eagle medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin–streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Leibovitz’s L-15 medium was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO) and wortmannin were purchased from Sigma-Aldrich (St. Louis, MO, USA), and QIAzol Lysis Reagent was purchased from Qiagen (Germany). The EZ-Cytox Cell Viability Assay Kit was purchased from DoGen Bio (Seoul, Republic of Korea). Dried ACD was supplied by Kwangmyungdang Medicinal Herbs Co. (Ulsan, Re-public of Korea) and its morphology was carefully validated by Dr. Goya Choi from the Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine (KIOM), Republic of Korea. A voucher specimen (2-23-0011) was deposited in the Ko-rean Herbarium of Standard Herbal Resources of KIOM (Naju, Republic of Korea). The crushed material was extracted at 100 ± 3 °C for 3 h using a water reflux system (MS-DM609, Misung Scientific, Yangu, Republic of Korea) and filtered through a 5 µm cartridge filter (KOC Biotech, Daejeon, Republic of Korea). The filtrates were concen-trated at 40 °C using a rotary evaporator (Ev-1020t, SciLab, Seoul, Republic of Korea) and freeze-dried (LP20, ilShin Biobase, Dongducheon, Republic of Korea). The yield of water extract of ACD was 25.4%, and the final extracts were homogenized and stored in an airtight container in a cold room at 4 °C. For the in vitro investigation, homoge-nous ACD extract was vigorously vortexed for 30 min at room temperature in PBS (Thermo Fisher Scientific) containing 2% DMSO and then sterilized by filtering through a 0.22-µm membrane. The stock solution of ACD extracts (10 mg/mL) was al-iquoted in a 1.5 mL tube and stored at −80 °C until use.

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: P_WL_WT_2

value: control


title: 5um_chir_wt_Rep1

description:
WT_counts.csv
5um_chir_rep1


title: patient J1798_P33 at time point Baseline

value: tumor cells

value: NonResponder


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

description: sample SW1783-6-3-5

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: ventricular cells, myd88-/-, 24 hpci

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: 10x Genomics

data_processing:
Raw reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo (Dobin et al., doi: 10.1093/bioinformatics/bts635) followed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy (Wolf et al., doi: 10.1186/s13059-017-1382-0). Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration.
We removed 32 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 10%. Furthermore, we filtered 7823 genes if they were detected in less than 30 cells (<0.01%). Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance
We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection (Traag et al., https://arxiv.org/abs/1810.08473), were based on the initial PCA.
Final data visualization was done by CellxGene package (DOI 10.5281/zenodo.3235020).
Assembly: DanRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: cardiac ventricles

extract_protocol:
Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88-/- ventricles for the myd88+/+ and myd88-/- sample, respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) following the manufacturer’s instructions and with the following modifications: Incubation was performed at 30°C for 20 min, followed by resuspension in 1× Hanks’ balanced salt solution (Gibco) with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter (BD) to exclude dead cells using DAPI (Sigma).
Library preparation was conducted according to the manufacturer indications (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121).

treatment_protocol: cardiac cryoinjury 24 hours prior to heart extraction

value: cardiac ventricles

value: ventricular cells

value: cardiac cryoinjury


title: 0um_chir_wt_Rep1

description:
WT_counts.csv
0um_chir_rep1

value: kidney

value: Primary

value: nephron progenitor


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

description: sample SW1783-6-3-4

value: Aconiti Lateralis Radix Preparata water extract 500 ug/mL


title: P_WL_WT_1

value: whole seedling

value: primed


title: ventricular cells, myd88+/+, 24 hpci

description: 10x Genomics


title: N_SH_WT_2

value: naive

value: 1 hr shade


title: patient J1798_P38 at time point Baseline

value: Baseline

value: Responder


title: patient J1798_P18 at time point C1D1


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

description: sample SW1783-6-2-5


title: injured tissue, myd88+/+, 24 hpci-2

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 99) with STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: DanRer11
Supplementary files format and content: library normilzed counts

extract_protocol:
RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-free DNase set, Qiagen) to avoid contamination by genomic DNA.
400ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation V6 following manufacture’s protocol (Vazyme).

treatment_protocol: untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2

description: sample SW1783-6-2-6

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: N_SH_WT_1


title: patient J1798_P18 at time point Baseline

value: tumor cells


title: N_WL_WT_2

value: control


title: injured tissue, myd88+/+, 1 hpci-2


title: patient J1798_P3 at time point C1D1

value: NonResponder


title: patient J1798_P3 at time point Baseline


title: patient J1798_P33 at time point C2D1


title: patient J1798_P38 at time point C1D1


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

description: sample SW1783-6-1-5

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: ventricle, myd88+/+, untouched-2

value: cardiac ventricles

value: ventricular cells


title: N_WL_WT_1


title: patient J1798_P34 at time point C1D1


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

description: sample SW1783-6-1-4


title: NB1643, Vehicle, rep2

city: Philadelphia

first: Steven

last: Pastor

state: PA

address: 3401 Civic Center Blvd.

institute: Children's Hospital of Philadelphia

data_processing:
The NFCORE RNA-seq Nextflow workflow (https://nf-co.re/rnaseq/3.14.0) was used for quality control of fastq files and for the ultimate production of raw counts. Any version of specified packages below were handled with the nfcore/rnaseq version specified on this line
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic
Trimmed reads were simultaneously mapped to GRCh38 and GRCm38 using BBTools to deconvolve mouse and human reads
Human-specific reads were aligned to GRCh38 with STAR
Raw counts were produced with RSEM (*.genes used in downstream analyses)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts per Sample at the gene level (raw_counts.txt)

source_name: cell line

growth_protocol: Patient-Derived Xenografts, Felix-PDX and COG-N-453x, COG-N-424x and cell line-derived xenograft NB-1643 and NB-1 were implanted subcutaneously into the right flank of female CB17 SCID mice (Taconic Biosciences, Inc.). PDX tumors were established in the laboratory of Dr. C. Patrick Reynolds and obtained through the Children’s Oncology Group Cell Culture and Xenograft Repository.

extract_protocol:
Tumors were harvested (3 per group) and homogenized in Trizol (Invtrogen) using Quiagen TissueRuptor. RNA was extracted using Quiagen mini elute kit according to manufacturer’s instructions.
library preparation was done using 1mg of RNA using the Truseq total mRNA kit and ribosomal RNA was removed with Gold rRNA removal mix.

treatment_protocol: Mice were randomized and balanced into three different treatment groups according to their tumor sizes and weight: Crizotinib (100 mg/kg QD), lorlatinib (10 mg/kg/day, 5 mg/kg BID), and vehicle control (0.5% methylcellulose and 0.5% Tween-80 in water, and hydrochloric acid in water equimolar to the lorlatinib solvent). Mice were treated at a median starting tumor volume of 200–300 mm3with three mice per group. Each drug was administered by oral gavage at 100 μl/10 g of body weight for 2.5 days. On day 2.5 or 6.5 the mice received a half dose of Crizotinib, lorlatinib, or vehicle, the tumors were collected 4 hours after treatment,

value: cell line

value: Vehicle


title: injured tissue, myd88+/+, 24 hpci-1

value: cardiac cryoinjury


title: NB1643, Vehicle, rep3


title: ventricle, myd88+/+, untouched-1


title: NB1643, Vehicle, rep1


title: patient J1798_P24 at time point Baseline


title: SW1783_BatchB_Vehicle(DMSO)_rep2

description: sample SW1783-B1-2-1

value: 0.1% DMSO


title: injured tissue, myd88-/-, 1 hpci-2


title: NB1643, Lorlatinib, rep4

value: Lorlatinib


title: SW1783_BatchB_Vehicle(DMSO)_rep1

description: sample SW1783-B1-1-1


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

description: sample SW1783-6-2-4

value: Aconiti Lateralis Radix Preparata water extract 500 ug/mL


title: patient J1798_P40 at time point Baseline


title: ventricle, myd88-/-, untouched-2


title: NB1643, Lorlatinib, rep2


title: SW1783_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

description: sample SW1783-6-1-6


title: SW1783_BatchA_Wortmannin_rep3

description: sample SW1783-1-3-4

value: wortmannin 10 uM


title: NB1643, Lorlatinib, rep3


title: patient J1798_P30 at time point Baseline


title: injured tissue, myd88+/+, 1 hpci-1


title: NB1643, Lorlatinib, rep1


title: patient J1798_P9 at time point Baseline


title: patient J1798_P24 at time point C1D1


title: SW1783_BatchA_Wortmannin_rep2

description: sample SW1783-1-2-4


title: injured tissue, myd88-/-, 24 hpci-2


title: NB1643, Crizotinib, rep3

value: Crizotinib


title: SW1783_BatchB_Vehicle(DMSO)_rep3

description: sample SW1783-B1-3-1


title: SW1783_BatchA_Wortmannin_rep1

description: sample SW1783-1-1-4


title: NB1643, Crizotinib, rep2


title: patient J1798_P27 at time point Baseline

value: Baseline


title: patient J1798_P1 at time point C1D1


title: D8_Ctr_rep2

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University

data_processing:
Sequence were trimmed by Trimmomatic-0.39.
Trimmed sequence reads were mapped to mm10 by hista2.
Read count extraction were performed using featureCounts.
Analysis by R.
Assembly: mm10
Supplementary files format and content: A Comma Separated Values (CSV) file include TPM values for each Sample

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from 13.5-dpc male homozygous 4F2A embryos.4F2A MEFs were cultured in KnockOut DMEM with 15% KnockOut Serum Replacement, 1% NEAA, 1% L-Glutamine, 1% Penicillin-Streptomycin, 1% Sodium Pyruvate,1000 U/mL LIF, 0.1% 2-Mercaptoethanol and 2 μg/mL doxycycline. The medium was changed every day.

extract_protocol:
DOX was added in D0, the total RNA of 4F2A MEFs was harvested by using TRIzol reagent (Invitrogen). Each group was prepared with two parallel replicates.
All the samples were sent to BGI Corporation (China) for further RNA-seq analysis via BGISEQ-500 sequencer.

treatment_protocol: Dox were added in D0.

value: Mouse embryonic fibroblasts (MEFs)

value: Dox in D0


title: ventricle, myd88-/-, untouched-1


title: patient J1798_P1 at time point Baseline

value: tumor cells


title: SW1783_BatchA_Vehicle(DMSO)_rep3

description: sample SW1783-A1-3-1


title: D8_Ctr_rep1


title: patient J1798_P5 at time point C1D1


title: COG-N-453, Vehicle, rep3


title: SW1783_BatchA_Vehicle(DMSO)_rep1

description: sample SW1783-A1-1-1


title: SW1783_BatchA_Vehicle(DMSO)_rep2

description: sample SW1783-A1-2-1


title: COG-N-453, Vehicle, rep2


title: D6_Ctr_rep2


title: injured tissue, myd88-/-, 24 hpci-1


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep3

description: sample HT29-6-3-6

value: Aconiti Lateralis Radix Preparata water extract 20 ug/mL


title: patient J1798_P8 at time point C1D1

value: NonResponder


title: COG-N-453, Vehicle, rep1


title: injured tissue, myd88-/-, 1 hpci-1


title: patient J1798_P5 at time point Baseline


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep3

description: sample HT29-6-3-5

value: Aconiti Lateralis Radix Preparata water extract 100 ug/mL


title: D4_Ctr_rep2


title: patient J1798_P8 at time point Baseline


title: COG-N-453, Lorlatinib, rep4


title: NB1643, Crizotinib, rep1


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep3

description: sample HT29-6-3-4


title: D4_Ctr_rep1


title: patient J1798_P42 at time point Baseline


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep2

description: sample HT29-6-2-6


title: COG-N-453, Lorlatinib, rep3


title: patient J1798_P19 at time point C1D1


title: COG-N-453, Lorlatinib, rep2


title: D2_Ctr_rep2


title: D2_Ctr_rep1


title: patient J1798_P19 at time point Baseline


title: COG-N-453, Lorlatinib, rep1


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep2

description: sample HT29-6-2-5


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep2

description: sample HT29-6-2-4


title: obesity_3

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

data_processing:
The sequencing data was filtered with trim-galore (v0.6.6) by removing reads containing sequencing adapter and reads with low-quality base, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome (Macaca_fascicularis_5.0) using STAR (v2.7.8a). Then expression level of gene was calculated by RSEM (v1.3.3).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: obesity

extract_protocol:
Total RNA was extracted from the skeletal muscle tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces using fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The double stranded PCR products were heated denatured and circularized by the splint oligo sequence to get the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 150) bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Skeletal muscle tissue near knee joint

tag: Sex

value: male

value: obesity

tag: height (cm)

tag: weight (kg)

tag: bmi (kg/m2)


title: COG-N-453, Crizotinib, rep3

tag: cell type

value: cell line

tag: treatment


title: patient J1798_P41 at time point C1D1


title: D6_Ctr_rep1

tag: strain


title: COG-N-453, Crizotinib, rep2


title: obesity_2

tag: age


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Low dose)_rep1

description: sample HT29-6-1-6

tag: cell line

tag: time


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (Medium dose)_rep1

description: sample HT29-6-1-5


title: obesity_1


title: COG-N-453, Crizotinib, rep1


title: patient J1798_P28 at time point Baseline

value: Responder


title: HT29_BatchB_water extract of Aconiti Lateralis Radix Preparata (High dose)_rep1

description: sample HT29-6-1-4


title: lean_3

source_name: lean

value: lean


title: Myeloma_patient_01_nonBnonT_cells, Gene expression (M2_GEX)

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave N

department: Immunotherapy Integrated Research Center, Translational Science and Therapeutics Division

institute: Fred Hutch Cancer Center

description: 10x Genomics

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.
CellRanger version 5 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
Doublet detection scoring was performed on the filtered gene expression matrices from Cell Ranger using DoubletDetection with default parameters, and then the combined gene expression matrix were analyzed by Scanpy pipeline. The following filters were set to retain high-quality cells: 1) cells with less than 10% mitochondrial transcripts, 2) number of detected genes per cell was above 100 but below 2,500 genes, 3) genes expressed in at least 3 cells were kept, 4) platelets (PF4 UMI>0), red blood cells (HBB UMI>1), and doublets were removed. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used Combat and Harmony for batch correction prior to Leiden clustering and UMAP visualization
Assembly: GRCh38 3.0.0
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files

source_name: PBMC

extract_protocol:
Bone marrow aspirates were diluted 1:1 in FACS buffer (PBS without magnesium or calcium, with 0.1% BSA and 2 mM EDTA). Peripheral blood samples were diluted 1:2 in FACS buffer. Mononuclear cell separation was performed by density centrifugation (Ficollpauqe, GE) with diluted bone marrow cells. Cells were manually aspirated and washed with FACS buffer. Red blood cells were lysed using RBC lysis buffer (Invitrogen) for 5 min at 4C. Within 1 hour of processing, cells were stained and sorted (Aria Fusion, BD) based on forward and side scatter, gated on CD45+ CD19- CD3+ (T cells) and CD45+ CD19- CD3- (nonB nonT cells).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5ʹ Reagent Kits version 1, according to manufacturer instructions. 10X 5’ kits for TCR amplification were used to generate libraries per manufacturer instructions.

tag: individual

tag: cell subtype

value: Immune and tumor cells

value: PBMC

tag: timepoint

tag: library type

value: Gene expression


title: ForebrainOrganoid_WildType_Rep3

description:
Illumina NextSeq 75 cycle instrument
Sequencing performed by University of Michigan Advanced Genomics Core

data_processing:
FASTQ files were aligned to hg38 and processed to single cell gene expression matrices using the Drop-seq_tools-1.13 pipeline.
Assembly: hg38
Supplementary files format and content: Single cell reads per gene matrix output

growth_protocol: Dual SMAD inhibition neural differentiation protocol. After day 14, , maintained in N2/B27/FGF growth media at 37C 5%CO2 shaking in suspension at 95 rpm.

extract_protocol:
SEQWell Protocol
Prepped libraries with Nextera XT kit (illumina) and sequenced on  Illumina NextSeq 75 cycle instrument

treatment_protocol: CRISPR-cas9 genome editing was used to generate a RING1/RNF2 allelic series. Otherwise, organoids were cultivated to dat 42 of differentiation as described in the associated manuscript

value: Neural progenitor cell monolayer

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: Forebrain organoid at day 42 of differentiation

tag: genotype

value: wild type

value: Normal growth conditions


title: HT29_BatchB_Vehicle(DMSO)_rep3

description: sample HT29-B1-3-1

value: 0.1% DMSO


title: lean_2

tag: condition


title: lean_1

tag: tissue


title: ForebrainOrganoid_RING1ms/ms_Rep4

value: Homozygous RING1 R95Q missense (RING1 c.284G > A;p.R95Q)


title: HT29_BatchB_Vehicle(DMSO)_rep2

description: sample HT29-B1-2-1


title: HT29_BatchB_Vehicle(DMSO)_rep1

description: sample HT29-B1-1-1


title: ForebrainOrganoid_RING1ms/ms_Rep3


title: Clostridium perfringens ATCC 13124 cultured in Poor + medium supplemented with mucin

city: Uji

first: Sayoko

last: Oiki

address: Gokasho

country: Japan

institute: Kyoto University

data_processing:
Illumina NovaSeq 6000 System User Guide Document # 1000000019358 v02
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Subsequently, the reads were mapped to the reference of Clostridium perfringens ATCC 13124 whole genome using bowtie v1.1.2
Assembly: Clostridium perfringens ATCC 13124
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample …

organism: Clostridium perfringens ATCC 13124

source_name: cell

growth_protocol: Clostridium perfringens ATCC 13124 cells were grown in Poor + medium, Poor + hyaluronic acid medium, or Poor + mucin medium. Minimum medium-like condition Poor + was prepared by adding 0.1% potassium dihydrogenphosphate, 0.1% disodium hydrogenphosphate, 0.01% magnesium sulfate heptahydrate to 20-fold diluted GAM medium. To the host polysaccharide-containing medium, hyaluronic acid or mucin was added by 0.2%, respectively. C. perfringens ATCC 13124 was anaerobically preincubated in GAM medium at 37 ° C. for 1 day. Cells were harvested and resuspended in 0.85% NaCl. 100 μl of a suspension with OD 600 = 1 was inoculated into 10 ml of Poor + medium, Poor + hyaluronic acid medium or Poor + mucin medium. After inoculation, each cell was grown to log phase growth.

extract_protocol:
Bacterial cells were centrifuged and suspended in 0.85% NaCl, and total RNAs were extracted by following Hot phenol method (Damm et al. 2015). Illumina (NovaSeq 6000)  was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Washing with 0.85% NaCl and harvesting by the centrifuge.

value: cell

value: Poor + medium supplemented with mucin


title: ForebrainOrganoid_RING1ms/ms_Rep2


title: HT29_BatchA_Wortmannin_rep3

description: sample HT29-1-3-4

value: wortmannin 10 uM


title: Healthy_donor_01_T_cells, T cell receptor (T43_TCR)

description: 10x Genomics

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.
CellRanger version 5 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
Doublet detection scoring was performed on the filtered gene expression matrices from Cell Ranger using DoubletDetection with default parameters, and then the combined gene expression matrix were analyzed by Scanpy pipeline. The following filters were set to retain high-quality cells: 1) cells with less than 10% mitochondrial transcripts, 2) number of detected genes per cell was above 100 but below 2,500 genes, 3) genes expressed in at least 3 cells were kept, 4) platelets (PF4 UMI>0), red blood cells (HBB UMI>1), and doublets were removed. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used Combat and Harmony for batch correction prior to Leiden clustering and UMAP visualization
Assembly: GRCh38 3.0.0
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files
Library strategy: scTCR-seq

value: T cells

value: Healthy control

value: VDJ


title: Clostridium perfringens ATCC 13124 cultured in Poor + medium supplemented with hyaluronic acid


title: patient J1798_P41 at time point Baseline

value: tumor cells

tag: patient id

tag: time point

value: Baseline

tag: recist

value: NonResponder


title: HT29_BatchA_Wortmannin_rep2

description: sample HT29-1-2-4


title: Clostridium perfringens ATCC 13124 cultured in Poor + medium

value: Poor + medium


title: ForebrainOrganoid_WildType_Rep1

value: Neural progenitor cell monolayer


title: Healthy_donor_01_T_cells, T cell receptor (T42_TCR)

description: 10x Genomics

source_name: Bone Marrow

value: Immune and tumor cells

value: Bone Marrow


title: Myeloma_patient_04_T_cells, T cell receptor (T5_TCR)

description: 10x Genomics

value: 30d post treatment


title: ForebrainOrganoid_RING1ms/ms_Rep1

value: H9 Human Embryonic Stem Cel (WiCell Lot#WB0090)

value: Forebrain organoid at day 42 of differentiation

value: Normal growth conditions


title: 100vertRBNS input

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

data_processing:
Reads were trimmed using fastx_toolkit before mapping with STAR to generate counts
Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: Custom genome (see supplementary files)
Supplementary files format and content: tab-delimited text file includes enrichment values for each sample

organism:
Pan troglodytes
Homo sapiens

source_name: in vitro large scale binding experiment, input

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 4 mM biotin (nsRBNS) or 0.1% SDS with 0.3 mg/mL proteinase K (100vertRBNS). RNA was concentrated via phenol-chloroform extraction
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified

value: 100vertRBNS input


title: HT29_BatchA_Vehicle(DMSO)_rep3

description: sample HT29-A1-3-1

value: 0.1% DMSO


title: Healthy_donor_01_T_cells, Gene expression (T42_GEX)

description: 10x Genomics

value: Gene expression


title: HT29_BatchA_Wortmannin_rep1

description: sample HT29-1-1-4

value: wortmannin 10 uM


title: UNK 100vertRBNS, 100nM, rep3

source_name: in vitro large scale binding experiment

value: UNK 100vertRBNS


title: 77y bone marrow scRNA-seq (GR93)

city: Cambridge

first: Hojun

last: Li

state: MA

address: 500 Main St

department: David H. Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

data_processing:
inDrop Pipeline:
Count normalization - Default parameters:  Seurat v3.0 NormalizeData function, normalization to 10^4 counts per cell, along with log transformation on each sample individually (default parameters).
Find variable features - Default parameters:  Seurat v3.0 FindVariableGenes function, vst method based on top 2000 features (default parameters).
Sample integration - Default parameters:  Seurat v3.0 IntegrateData function using 2000 anchors and 30 dimensions.
Filtering - Default parameters:  Iterative visualizations and plotting of QC metrics led to the exclusion of cells with low transcript and high mitochondrial content, as well as cells displaying endothelial and liver markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed count matrix, compressed MM and TXTs - Sparse matrix with normalized counts, feature names and cell identifiers in compressed TXTs
Supplementary_files_format_and_content: Cell metadata, compressed CSV -  Contains cell identifiers, sample of origin, cluster assignments, and cluster labels for all cells retained for downstream analysis.

source_name: 77y bone marrow

growth_protocol: N/A, cells analyzed without being cultured

extract_protocol:
Cryopreserved bone marrow CD34-enriched cells were thawed and FACS-sorted for CD34+ cells. Sorted CD34+ cells were submitted for scRNA-seq analysis.
InDrop
InDrop protocol
InDrop scRNA-seq library prep (Illumina NextSeq500)

treatment_protocol: N/A, cells were not treated prior to analysis

value: 77y bone marrow

value: CD34+ Cells


title: Myeloma_patient_01_nonBnonT_cells, Gene expression (M1_GEX)

description: 10x Genomics

value: Baseline


title: Myeloma_patient_04_T_cells, Gene expression (T5_GEX)

description: 10x Genomics

value: T cells


title: 76y bone marrow scRNA-seq (GR92)

source_name: 76y bone marrow

value: 76y bone marrow


title: UNK 100vertRBNS, 100nM, rep2