title: Hypoxia

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

description: 1 timepoint x 3 replicates = 3 total files

data_processing:
Sequenced reads were calculated by Cellranger
Clustering and DEG was identified by Seurat
Pseudotime of cells was calculated by Monocle
Assembly: mm10
Supplementary files format and content: Normoxia_barcodes.tsv.gz
Supplementary files format and content: Normoxia_features.tsv.gz
Supplementary files format and content: Normoxia_matrix.mtx.gz
Supplementary files format and content: Hypoxia_barcodes.tsv.gz
Supplementary files format and content: Hypoxia_features.tsv.gz
Supplementary files format and content: Hypoxia_matrix.mtx.gz

source_name: tdT sorted from NG2tdT lungs

extract_protocol:
Explanted NG2tdT lungs were finely diced and digested for 30min in a mix of collagenase A/DNAse I. A single cell suspension was generated by filtering lungs through 70 micron and 40 micron filters and resuspending cells in PBS containing 0.04% BSA. Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to Chromium Next GEM Single Cell 3' Kit v 3.1 and performed by Stanford Functional Genomics Facility.

value: primary

value: 21 day FiO2 10% as Hypoxia treatment


title: Kidney_C24V1V2_pCREB_Veh_rep3

status: Public on Aug 25 2024

type: SRA

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

country: USA

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
Data was processed from NovaSeqX with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig files for display in the UCSC genome browser

molecule: genomic DNA

organism: Mus musculus

source_name: kidney

growth_protocol: C57BL/6 mice aged 8-9 wk (The Jackson Laboratory, Bar Harbor, ME) were housed in high density ventilated caging in the Animal Research Facility of University of Wisconsin-Madison under 12-hour light/dark cycles at 72°F and 45% humidity. All mice used in this study were maintained on a standard rodent chow diet (5008, Lab Diet, St. Louis, MO). All experiments and tissue collections were performed in the procedure rooms in the Research Animal Facility of University of Wisconsin-Madison. All animal studies were reviewed and approved by the Research Animal Care and Use Committee of University of Wisconsin-Madison under protocol A005478.

extract_protocol:
The kidneys were isolated, rinsed with cold 1× phosphate-buffered saline, and subjected to a cross-linking reaction for 10 min with 1.5% formaldehyde. After the fixative was neutralized for 5 min with glycine (0.125mfinal concentration), the kidney tissue was homogenized briefly in phosphate-buffered saline using a loose fitting Dounce pestle, and the cells were collected via 70-μm nylon cell strainers (BD Falcon). Cells were then subjected to ChIP analysis.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, #E7645S) with the NEBNext Multiplex Oligos for Illumina (NEB, #E6440S) according to the manufacturer’s protocols. Libraries were submitted to Azenta/Genewiz and sequenced on a NovaSeq X. Paired-end, 150 bp sequencing with a target of 30+ million reads was performed.

treatment_protocol: Animals were subjected to intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), or vehicle (EtOH, PBS). Animals were sacrificed and tissues collected at 30 min (PTH) or 60 min (all other treatments) and subjected to ChIP followed by ChIP-seq.

tag: tissue

value: kidney

tag: chip antibody

tag: genotype

tag: treatment

value: vehicle (EtOH, PBS)


title: Kidney_C24V1V2_pCREB_Veh_rep2


title: hPSC-hepatocytes, ARID2 knockout, rep2

city: Shanghai

first: Yijia

last: Chi

state: 上海

address: No. 555 Zuchongzhi Road, Pudong New District, Shanghai, China

country: China

institute: Shanghai Institute of Material Medica

library_source: transcriptomic

data_processing:
Sequencing reads from SMART-seq3 were processed using Umi-tools (version 1.1.4) to extract UMI-containing reads, which were subsequently aligned to the GRCh38 human reference genome (Gencode v43) using STAR (version 2.7.11a).
UMI reads were assigned to exon features using featureCounts (version 2.0.3). Normalization and differential expression analysis of counts were performed using the Deseq2 R package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: human pluripotent stem cells

growth_protocol: The H1 human embryonic stem cells were obtained from WiCell and grown in Pluripotency Growth Master 1 (PGM1) human pluripotent stem cell culture medium (Cellapy). Human pluripotent stem cell H1 were seeded at the density of 5 x 104 cells/cm2 in Matrigel-coated 48-well plates and cultured in complete PGM1 culture media for 1-2 days. To generate definitive endoderm, H1 were cultured in 1640 medium supplemented with 0.5 mg/ml albumin fraction V and 100 ng/ml Activin a for 1 day. On the following 2 days, 0.1% and 1% insulin-transferrin-selenium (ITS) was added to DAY1 medium. On the following steps, we sequentially differentiated definitive endoderm into posterior foregut, hepatic progenitors and hepatocytes stage according to the previous reports (Wang et al., Cell Res. 2020)

extract_protocol:
RNA-sequencing libraries were prepared based on the smart-seq3 and smart-seq3xpress methods, with direct lysed cells for library construction.
RNA-sequencing libraries were prepared based on the smart-seq3 and smart-seq3xpress method.

treatment_protocol: We conducted lentivirus-based gene modification on hPSC-derived hepatocytes at the hepatic progenitor stage

tag: cell type

value: human pluripotent stem cells

value: ARID2 knockout

value: hepatocytes differentiation


title: hPSC-hepatocytes, ARID2 knockout, rep1


title: Normoxia

state: CA

library_source: transcriptomic single cell

value: Non treatment


title: FlcnKD_i2CLC_Tfeb_2

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

data_processing:
The raw CUT&Tag reads were trimmed by trim-galore (v 0.6.7). The clean reads were mapped to mm10 genome by bowtie2 (v 2.3.5.1) with following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Samtools (v 1.9) was used to convert and sort the SAM files into BAM format.
SEACR (v 1.3) was used for peaks calling by selecting the top 1% regions of AUC.
Deeptools (v 3.5.1) was used to convert the bam file to the bigwig file via bamCoverage. ComputeMatrix was used to calculate the overall CUT&Tag signal, and plotProfile was used for signal distribution visualization.
Assembly: mm10
Supplementary files format and content: bed files include peaks region for each Sample
Library strategy: CUT&Tag

extract_protocol:
5×105 cells were washed once with PBS and resuspended in ice-cold NE1 buffer for 10 min. Cells were fixed in 0.1% formaldehyde and incubated for 2 min and 2.5 M glycine was used to stop cross-linking. Cells were incubated with activated ConA beads for 10 min. The bead-bound cells were resuspended in 100 µL antibody buffer containing appropriate primary antibody. Primary antibody incubation was performed on a rotator at 4 °C overnight. Secondary antibody was diluted in antibody buffer and incubation was performed on a rotator for 1 h. After washing by wash buffer, the cells were incubated with pA-Tn5 (~0.04 uM) on the rotator for 1 h. The cells were resuspended in Tagmentation buffer for 1 h. Tagmentation was stopped by adding 10µL of 0.5M EDTA, 3µL 10% SDS, and 5 µL 10 mg/ml Proteinase K and incubated at 56 °C for 30 min. The DNA was extracted by chloroform.
For library amplification, 21 µL DNA was mixed with 2 µL of a universal i5, 2 µL of a uniquely barcoded i7 primer, and 25 µL NEBNext HiFi 2× PCR Master mix. The library was amplified by following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 45 s; 14 cycles of 98 °C for 15 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 4 °C.

tag: cell line

value: embryonic stem cell

value: Flcn KO

value: DOX


title: hPSC-hepatocytes, APC knockout, rep2

value: APC knockout


title: 3F4 iPS replicate1

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

data_processing:
Paired-end read alignment to mouse genome (mm10 version) was performed with STAR aligner (version 2.7.10) with default setting. Samtools were used for filtering and sorting aligned reads before annotation to “mm10.GRCm38.95.gtf” gene version with featureCounts (subread 2.0.6 version). Only protein-coding and long-non-coding RNA transcripts were used for annotation and downstream differential expression analysis was performed with R package DESeq where we set a log2 fold change of 1.5 and P-adjusted of <0.05 as a cut off for calling deferentially expressed genes.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10 and mm10.GRCm38.95.gtf
Supplementary files format and content: raw counts for all samples are submitted in tab delimited format with official gene symbol and ensembl gene id

source_name: IPS 3F4

extract_protocol:
RNA-seq libraries were prepared and sequenced by Novogene Bioinformatics Technology Co. Ltd.
Sequencing libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s instructions. High-throughput sequencing was performed on an Illumina NovaSeq 6000 platform.

value: IPS 3F4

value: induced pluripotent cell


title: Intestine_C24V1V2_VDR_125_rep3

source_name: intestine (duodenum)

value: intestine (duodenum)

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: 3F2 XEN replicate2

source_name: XEN 3F2

value: XEN 3F2

value: extraembryonic endoderm stem cells


title: Intestine_C24V1V2_VDR_125_rep2


title: 3F2 XEN replicate1


title: 3F6 iPS replicate1

source_name: iPS 3F6

value: iPS 3F6


title: hPSC-hepatocytes, nontargeting control, rep2

value: WT


title: hPSC-hepatocytes, nontargeting control, rep1


title: Y2 [VDJ]

city: Fort Worth

first: Weikan

last: Wang

state: TX

address: 3500 Camp Bowie Blv

department: Dept. of Microbiology, Immunology and Genetics

institute: University of North Texas Health Science Center

description: 30 days after EAE induction

data_processing:
quality control, Cell Ranger Single Cell Software Suite
sample de-multiplexing, Cell Ranger Single Cell Software Suite
barcode processing, Cell Ranger Single Cell Software Suite
single-cell 5′ gene counting , Cell Ranger Single Cell Software Suite
alignment, Cell Ranger Single Cell Software Suite
Genome_build: mm10
Supplementary_files_format_and_content: h5 of matrix
Supplementary_files_format_and_content: zipped file of matrix
Supplementary_files_format_and_content: csv file
Supplementary_files_format_and_content: vloupe file

source_name: CNS infiltrated T cells

extract_protocol:
30 days after EAE induction, mononuclear cells were isolated from the CNS of three young and three aged EAE mice using the same method as described above. Cells were washed twice with RMPI 1640 (Corning, Cat# 10-040-CM) with 5% FBS (Corning, Cat#35-011-CV) and incubated with anti-CD3-APC (Biolegend, Cat#100236) and anti-CD11b-Brilliant Violet 711 (Biolegend, Cat#101242) on ice for 30min in dark. Cells were sorted on Sony SH800 Cell Sorter to collect CD3+CD11b-neg T cells. Cells were washed twice with 1xPBS containing 0.04% Bovine Albumin (Sigma, SRE0036) before loading onto the 10x Genomics Chromium Single Cell Controller.
cDNA was amplified using (the same kit as above, 10x Genomics, Cat#1000287) kit on the thermal cycler. Products were purified using Ampure XP beads and quality was controlled using Agilent Tapestation and Qubit 4 fluorometer. TCR target enrichment was performed from the same cDNA as above using Chromium Single Cell Mouse TCR Amplification kit (10x Genomics, Cat #1000254). TCR V(D)J and GEX libraries were constructed using the Library Construction Kit (10x Genomics, Cat #1000190) with Dual Index Kit TT Set A. TCR samples were sequenced on an Illumina NovaSeq 6000 according to 10x protocol sequencing recommendations.

tag: strain

tag: age

value: 2-3 months


title: Intestine_C24V1V2_VDR_Veh_rep2

value: vehicle (EtOH, PBS)


title: 3F2 iPS replicate1

source_name: iPS 3F2

value: iPS 3F2


title: O1 [VDJ]

description: 30 days after EAE induction

value: 18-20 months


title: O3 [VDJ]

description: 30 days after EAE induction


title: p12 neg control (Biol rep 5)

first: Elaine

last: Alarid

address: 111 Highland Avenue

institute: University of Wisconsin Madison

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality.
The trimmed reads were mapped to the reference Homo sapiens GRCh38 genome using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Batch effects were addressed using the ComBat_seq function in the R package "sva".
Differential expression testing was carried out with DESeq2, with log foldchange shrinkage (type="ashr"). Differentially expressed genes were identified with FDR < 0.05.
Gene set analysis was carried out the GSVA R package and the GO BP, C3 TFT and Hallmark sets downloaded from MsigDb. Differential analysis of GSVA results was performed with limma and FDR < 0.05.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Hit counts in txt files

source_name: Breast cancer

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium, supplemented with 10% VWR fetal bovine serum, 1% sodium pyruvate, and 1% penicillin streptomycin in 10% CO₂ at 37°C. Prior to treatment, cells were synchronized and stripped of any contaminates after being cultured for 3 days in phenol-red free DMEM, supplemented with 10% 6x charcoal stripped FBS, 1% sodium pyruvate, 1% Pen/Strep, and 2% L-glutamine.

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).The sequencing libraries were pooled and sequenced on 1 partial lane of NovaSeq (platform detailed above for the different orders). The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Cells were treated with 1 μg/mL doxycycline hyclate and 10 nM 17β-estradiol for 72 hours, changing the media every 24 hours.

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: vehicle

tag: sorting


title: Biol.repl.2 (oim/d21 cocultured with fetal liver MSCs)

city: London

first: Michelangelo

last: Corcelli

state: London

address: Zayed Centre for Research, 20 Guilford Street, London,

country: United Kingdom

institute: UCL

data_processing:
Genewiz bioinformatics analysis workflow. (Standard Package)
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: tab delimited text includes raw counts for each sample

source_name: neonatal calvarial bone

growth_protocol: Primary osteoblasts like cells (pre-osteoblasts) were isolated from the calvarial bone of neonatal WT and OIM mice. Cells were cultured in alpha modified Eagle’s medium (alpha-MEM) (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine, 50 IU/ml penicillin and 50 mg/ml streptomycin (Gibco), at 37 °C in a 5% CO2 incubator. Cells were expanded for about a week until there was a homogeneous population of ALP (alkaline phosphatase) positive cells at subconfluency. In vitro osteogenic differentiation. Cells were differentiated down the osteoblast lineage for up to 3 weeks (d21) in alpha-MEM supplemented with 2 mM β-glycerophosphate, 0.2 mM ascorbic acid and 10−8 M dexamethasone.

extract_protocol:
RNA TRIZOL extraction
Pre-made library -- no library preparation performed

treatment_protocol: OIM pre-osteoblasts samples F2Tand E2T cells were also additionally treated by coculturing with human fetal liver MSCs over 21 days.

value: neonatal calvarial bone

value: osteoblast

value: oim

value: osteogenic media+fetal liver MSCs (d21)


title: Y3 [VDJ]

description: 30 days after EAE induction


title: hPSC-hepatocytes, APC knockout, rep1

value: human pluripotent stem cells

value: APC knockout

value: hepatocytes differentiation


title: Y1 [VDJ]

description: 30 days after EAE induction


title: Intestine_C24V1V2_VDR_Veh_rep1

value: intestine (duodenum)

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: Intestine_C24V1V2_VDR_125_rep1


title: p12 GFP negative (Biol rep 5)

value: 1 μg/mL Dox for 72 hours

value: GFP negative


title: p12 GFP positive (Biol rep 5)

value: GFP positive


title: 3F2 iPS replicate2

value: iPS 3F2

value: induced pluripotent cell


title: Biol.repl.3 (oim/d21)

value: osteogenic induction media (d21)


title: p11 neg control (Biol rep 4)

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)


title: Biol.repl.2 (oim/d21)

value: neonatal calvarial bone


title: Intestine_C24V1V2_VDR_Veh_rep3

value: vehicle (EtOH, PBS)


title: Intestine_C24WT_VDR_125_rep3

value: wildtype


title: O2 [GEX]

description: 30 days after EAE induction

value: 18-20 months


title: Intestine_C24WT_VDR_125_rep1


title: Biol.repl.1 (oim/d21)

value: osteoblast

value: oim


title: p11 GFP positive (Biol rep 4)


title: O3 [GEX]

description: 30 days after EAE induction


title: Intestine_C24WT_VDR_Veh_rep3


title: p11 GFP negative (Biol rep 4)


title: Y2 [GEX]

description: 30 days after EAE induction

value: 2-3 months


title: O2 [VDJ]

description: 30 days after EAE induction


title: Biol.repl.3 (oim/d0)

value: pre-osteoblast

value: expansion  media (d0)


title: Intestine_C24WT_VDR_125_rep2

value: intestine (duodenum)

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: O1 [GEX]

description: 30 days after EAE induction


title: p10 GFP positive (Biol rep 3)

value: 1 μg/mL Dox for 72 hours

value: GFP positive


title: Biol.repl.1 (oim/d21 cocultured with fetal liver MSCs)

value: osteogenic media+fetal liver MSCs (d21)


title: pif1-m2 dna2, DSB, non aging, biol rep8, with new primers

city: Boston

first: Xin

state: MA

address: 300 Longwood Ave,

institute: Boston children's hospital

description:
The library has the forward index: CTC and reverse index: GGT. A total of  12000 colony number was in this library.
pif1m2dna2-newPrimer.One.bed
pif1m2dna2-newPrimer.MultipleClean.bed

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Reference: Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Reference: Methods of Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

source_name: No

growth_protocol: For amplicon sequencing analysis in normal conditions, cells were grown in YEPD (1% yeast extract, 2% peptone, 2% dextrose) o/n to saturation. Cells were washed twice in YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) media and inoculated in 10 ml of YEP-Raffinose and grown overnight. Once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For all analyses in stationary phase cells, we followed a previously established protocol for yeast growth (Hu et al., 2013). Yeasts were initially streaked out on YEPD plates and individual colonies were inoculated in 3 ml SC media (1.72g/L yeast nitrogen base without amino acids (USBiological, cat# Y2030), 2g/L amino acid mix (Bufferad, cat#S0051), 0.5% ammonium sulfate, 2% dextrose) and incubated overnight at 30 °C. The culture was diluted into fresh 50 mL SC media in 250 mL flasks to an OD600 of 0.1. Logarithmic growth phase control cells were plated when the culture reached 1x107 cells/ml. Cells were incubated on a shaker for 24 hrs (day 1), 3 days, 8 days, 16 days or as specified in individual experiments and plated on YEPGal plates for HO induction. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. Populations of old yeast mother cells were isolated as previously described (Tsuchiyama et al., 2013) with the following modifications. 3x10e8 yeast cells from a fresh log-phase culture in YEPD were treated with 3 mg of Sulfo-NHS-LC-Biotin (Thermo Scientific) and were used to seed a 1L culture in YEP-Raffinose. Seeded cultures were incubated with shaking at 30 °C for 15 hours to age biotin-labeled cells. The aged biotin-labeled cells were isolated using 1 mL Dynabeads Biotin Binder (Thermo Scientific). Three rounds of aging and sorting were conducted to obtain old mother cells with an average replicative age of around 20. Control young cells were obtained from last sorting and wash.

extract_protocol:
All colonies from YEP-Galactose plates were collected, pooled together and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl.
The construction of the sequencing library was adapted from Illumina’s amplicon sequencing protocol #15044223 Rev. B. Two rounds of PCR were performed to construct the sequencing library. For each sample, 3.2 μl genomic DNA, 0.5 μl 10 μM primers and 12.5 μl KAPA HiFi HotStart ReadyMix (Roche, 7958927001) was used for the first round of PCR for a total volume of 25 μl. The forward primers are 66-mers that contain (5’ to 3’): 33 bases Illumina adapter sequence, 3 bases unique home index, and 30 bases targeting the Mata locus which is located 11 bp upstream the HO cleavage site. The reverse primers are 66-mers that contain (5’ to 3’): 34 bases Illumina adapter sequence, 3 bases unique home index, and 29 bases targeting the MATa locus which is located 18 bp downstream the HO cleavage site. The following conditions were used for the first round of PCR: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 18μl PCR product was purified with 20μl AMPure XP beads (Beckman Coulter, A63880) and eluted with 52.5 μl 10 mM Tris pH 8.5. For the second round of PCR, 5 μl purified PCR product, 5 μl Nextera XT V2 Index (Illumina, FC-131-2001) primer N7xx, 5 μl index primer S5xx, and 25 μl KAPA HiFi HotStart ReadyMix were used. The total volume of PCR is 50 μl. The following conditions were used for PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 40 μl PCR product was purified with 48 μl AMPure XP beads and eluted with 27.5 μl 10 mM Tris pH 8.5. The DNA concentration of each sample was determined with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850) and the average size of the DNA was determined with TapeStation. The DNA was diluted to 4 nM using 10 mM Tris pH 8.5. An equal amount of DNA was pooled from ~20 samples into the library. The pooled library and PhiX library (Illumina, FC‐110‐3001) were denatured with 0.2 M NaOH separately and diluted with pre-chilled HT1 to 12 pM. 540μl pooled library and 60 μl PhiX were mixed, incubated at 96 °C for 2 min and immediately placed in an ice-water bath for 5 min.
The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003) for amplicon sequencing.

treatment_protocol: For growing cells once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For stationary phase cells, cells were plated after 1,2,3,8,16 days of incubation in SC media on YEPGalactose plates. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. For aged cells and control young cells, they were plated on YPE-Gal plates.

value: No

value: mutant isogenic to JKM139

value: dna2::kanMX pif1-m2 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pif1-m2 dna2 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus. Attention:we set up the new primer at DSBs


title: Biol.repl.1 (oim/d0)

value: neonatal calvarial bone


title: Y1 [GEX]

description: 30 days after EAE induction


title: p9 neg control (Biol rep 2)

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: vehicle


title: Biol.repl.2 (wt/d21)

value: osteoblast

value: wt

value: osteogenic induction media (d21)


title: pif1-m2 dna2, DSB, non aging, biol rep7, with new primers

description:
The library has the forward index: CAC and reverse index: CAT. A total of  40000 colony number was in this library.
pif1m2dna2-newPrimer.One.bed
pif1m2dna2-newPrimer.MultipleClean.bed

value: pif1-m2 dna2 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.  Attention:we set up the new primer at DSBs


title: Biol.repl.3 (wt/d21)


title: p9 GFP positive (Biol rep 2)


title: pol4, DSB, non aging, biol rep1

description:
The library has the forward index: AAG and reverse index: CGT. A total of  80160 colony number was in this library.
pol4.One.bed

value: pol4::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pol4 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Kidney_C24V1V2_VDR_125_rep1

value: kidney

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: Y3 [GEX]

description: 30 days after EAE induction

value: 2-3 months


title: p10 GFP negative (Biol rep 3)

value: 1 μg/mL Dox for 72 hours

value: GFP negative


title: Kidney_C24V1V2_VDR_125_rep2


title: Biol.repl.3 (wt/d0)

value: pre-osteoblast

value: expansion  media (d0)


title: nuc1 spt3, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: CAG and reverse index: GAG. A total of  16128 colony number was in this library.
nuc1spt3-8d.One.bed
nuc1spt3-8d.MultipleClean.bed

value: No

value: mutant isogenic to JKM139

value: spt3::klTRP1 nuc1::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 spt3 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Biol.repl.2 (oim/d0)

value: neonatal calvarial bone

value: oim


title: Kidney_C24V1V2_VDR_Veh_rep3

value: vehicle (EtOH, PBS)


title: Kidney_C24V1V2_VDR_Veh_rep2


title: p8 neg control (Biol rep 1)

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: vehicle


title: Kidney_C24V1V2_VDR_125_rep3

value: kidney


title: Intestine_C24WT_VDR_Veh_rep1

value: intestine (duodenum)

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)

value: wildtype


title: p9 GFP negative (Biol rep 2)

value: 1 μg/mL Dox for 72 hours

value: GFP negative


title: Intestine_C24WT_VDR_Veh_rep2


title: Biol.repl.1 (wt/d0)

value: pre-osteoblast

value: wt

value: expansion  media (d0)


title: Biol.repl.1 (wt/d21)

value: osteoblast

value: osteogenic induction media (d21)


title: Kidney_C24WT_VDR_125_rep3


title: pol4, DSB, non aging, biol rep2

description:
The library has the forward index: ACG and reverse index: GTG. A total of  93600 colony number was in this library.
pol4.One.bed

value: No

value: mutant isogenic to JKM139

value: pol4::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pol4 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: nuc1 spt3, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: CTC and reverse index: GGT. A total of  9504 colony number was in this library.
nuc1spt3-8d.One.bed
nuc1spt3-8d.MultipleClean.bed

value: spt3::klTRP1 nuc1::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 spt3 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: ID12167969, Ecoli, Cipro, 1h

city: South San Francisco

first: Yutian

last: Peng

address: 340 Point San Bruno

institute: Genentech Inc.

description:
ID12167969
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

data_processing:
Ribosomal RNA contamination was removed from the fastq sequence files and reads were filtered for quality, keeping only reads where at least 70% of the cycles had Q scores Ñ23.
Single-end 50 bp reads were aligned to the E. coli K12 MG1655 and A. baumannii ATCC19606 genome using GSNAP version 2013-11-01 with the following parameters: -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap.
Uniquely mapped reads were used to obtain read counts and RPKMs per gene.
Assembly: ASM73714v1 (Abaumannii) and ASM584v2 (Ecoli K-12)
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample, column metadata (samples), and row metadata (genes)

organism: Escherichia coli

source_name: bacterial cell

extract_protocol:
RNA was extracted using RNeasy spin columns (Qiagen) according to the manufacturer’s protocol.
RNA-seq library generation was continued using the Truseq RNA Library Prep Kit v2 (Illumina) starting at the “Elute, Prime, Fragment” step and was completed according to the manufacturer’s protocol.

value: bacterial cell

value: Cipro

tag: timepoint


title: Kidney_C24WT_VDR_125_rep2

value: kidney

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: p8 GFP positive (Biol rep 1)

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: 1 μg/mL Dox for 72 hours

value: GFP positive


title: Control2

city: Charlottesville

first: Harish

last: Narasimhan

state: Virginia

address: 345 Crispell Drive

institute: University of Virginia

description: Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing

data_processing:
The spatial transcriptome (ST, 10x Visium) data were preprocessed using the 10x Genomics pipeline (Space Ranger) v2.0.1 using the hg38/mm10 genome. Only high-quality spots with sufficient covered genes (>=2000) were retained for the downstream analysis.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5: Respective matrix files
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Library strategy: Spatial transcriptomics

source_name: Lungs

extract_protocol:
Formalin fixed paraffin embedded lung sections (5um) were mounted onto Visium slide
Spatial transcriptome sequecing libraries were prepared with 10X Genomics Visium spatial gene expression slides and reagent kit according to manufacturer's instructions.

value: Lungs

tag: disease state

value: control


title: spt3, DSB, Stationary 8day, biol rep5

description:
The library has the forward index: TCG and reverse index: GAT. A total of  31640 colony number was in this library.
spt3-8d.One.bed
spt3-8d.MultipleClean.bed

value: spt3::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary spt3 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: p8 GFP negative (Biol rep 1)

value: GFP negative


title: ID12167968, Ecoli, Cipro, 1h

description:
ID12167968
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: Biol.repl.2 (wt/d0)

value: neonatal calvarial bone

value: pre-osteoblast

value: wt

value: expansion  media (d0)


title: ID12167970, Ecoli, Cipro, 1h

description:
ID12167970
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

value: bacterial cell


title: spt3, DSB, Stationary 8day, biol rep4

description:
The library has the forward index: TCC and reverse index: CTT. A total of  26160 colony number was in this library.
spt3-8d.One.bed
spt3-8d.MultipleClean.bed

value: No

value: mutant isogenic to JKM139


title: Kidney_C24WT_VDR_125_rep1

value: kidney

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)

value: wildtype


title: Kidney_C24V1V2_VDR_Veh_rep1

value: vehicle (EtOH, PBS)


title: spt3, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: TTC and reverse index: GTC. A total of  24920 colony number was in this library.
spt3-8d.One.bed
spt3-8d.MultipleClean.bed


title: Kidney_C24WT_VDR_Veh_rep2


title: spt3, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: CTG and reverse index: CCA. A total of  23720 colony number was in this library.
spt3-8d.One.bed
spt3-8d.MultipleClean.bed


title: kap123 nuc1, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: TTC and reverse index: GTC. A total of  860 colony number was in this library.
kap123nuc1-8d.One.bed
kap123nuc1-8d.MultipleClean.bed

value: kap123::kanMX nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary karp123 nuc1 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: spt3, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: TCC and reverse index: CTT. A total of  24640 colony number was in this library.
spt3-8d.One.bed
spt3-8d.MultipleClean.bed

value: spt3::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: Kidney_C24WT_VDR_Veh_rep1


title: COVID2

value: Lungs

value: COVID


title: COVID1


title: ID12167966, Ecoli, GuaBi, 1h

description:
ID12167966
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

value: GuaBi


title: ID12167967, Ecoli, GuaBi, 1h

description:
ID12167967
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: Kidney_C24WT_VDR_Veh_rep3


title: COVID3


title: Rhino6_P

city: Escondido

first: Elena

last: Ruggeri

address: 15600 San Paqual Valley Rd.

institute: San Diego Zoo Wildlife Alliance

data_processing:
Galaxy Web Platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to  CerSimCot1.0 using HISAT2
Read count extraction was performed with StringTie
Assembly: CerSimCot 1.0
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Ceratotherium simum simum

source_name: In vivo cells

extract_protocol:
Total RNA was isoalted using the PicoPure RNA Isolation Kit (Thermo fisher Scientific)
Illumina TruSeq Stranded Total RNA Prep withRibo-Zero Plus

value: In vivo cells

tag: Stage

value: P

value: Granulosa Cell

value: WT

value: in vivo


title: ID12167965, Ecoli, GuaBi, 1h

description:
ID12167965
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

value: bacterial cell


title: nuc1 spt3, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: CAC and reverse index: CAT. A total of  10560 colony number was in this library.
nuc1spt3-8d.One.bed
nuc1spt3-8d.MultipleClean.bed

value: No

value: mutant isogenic to JKM139

value: spt3::klTRP1 nuc1::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary nuc1 spt3 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: ID12167964, Ecoli, No Drug, 1h

description:
ID12167964
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

value: No Drug


title: DMSO_Line951

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Raw read counts were counted by using FeatureCounts
Assembly: hg38
Supplementary files format and content: TPM Value.txt

source_name: iPSC-CM

growth_protocol: iPSCs were grown in E8 and differentiated using chemicaly defined protocol (Burridge et al., 2015; PMCID: PMC4597313)

extract_protocol:
RNA was extracted using the Qiagen RNEasy  Kit
Eukaryotic mRNA library (poly A enrichment)

treatment_protocol: iPSC-CMs were treated with vehicle of 50 uM BaP for 5 days

value: iPSC-CM

value: cell line

value: DMSO


title: kap123 nuc1, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: TGC and reverse index: GCA. A total of  1200 colony number was in this library.
kap123nuc1-8d.One.bed
kap123nuc1-8d.MultipleClean.bed

value: kap123::kanMX nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary karp123 nuc1 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Rhino5_P


title: DMSO_Line273


title: Rhino3_D

value: D


title: ID12167962, Ecoli, No Drug, 1h

description:
ID12167962
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: DMSO_Line100


title: ID12167963, Ecoli, No Drug, 1h

description:
ID12167963
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: Control1

description: Formalin Fixed Paraffin Embedded Spatial transcriptome sequencing

value: Lungs

value: control


title: Rhino1_G

value: In vivo cells

value: G

value: Granulosa Cell


title: kap123, DSB, Stationary 8day, biol rep2

description:
The library has the forward index: CTG and reverse index: CCA. A total of  4320 colony number was in this library.
kap123-8d.One.bed
kap123-8d.MultipleClean.bed

value: kap123::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary karp123 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Rhino2_G

value: WT

value: in vivo


title: BaP_Line100

value: 50 uM BaP


title: ID12167960, Ecoli, No Drug, 0h

description:
ID12167960
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt

value: bacterial cell

value: No Drug


title: BaP_Line273

value: iPSC-CM

value: cell line


title: ID12167961, Ecoli, No Drug, 0h

description:
ID12167961
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: Rhino4_D


title: kap123 nuc1, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: TCC and reverse index: CTT. A total of  5040 colony number was in this library.
kap123nuc1-8d.One.bed
kap123nuc1-8d.MultipleClean.bed

value: No

value: mutant isogenic to JKM139

value: kap123::kanMX nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: BaP_Line951


title: kap123, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: CAG and reverse index: GAG. A total of  3520 colony number was in this library.
kap123-8d.One.bed
kap123-8d.MultipleClean.bed


title: 222_DMSO_III

status: Public on Aug 24 2024

city: Copenhagen N

first: Morten

last: Scheibye-Knudsen

state: Copenhagen N

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

data_processing:
Mapping-based quantification of the GRCh38 transcriptome from RNA sequencing paired-end reads was performed with salmon using a pre-computed transcriptome index for salmon obtained from refgenie
Differential expression analysis was performed with DESeq2 1.38.2 on genes mapped from transcripts with the gencode annotation of the Ensembl gene set downloaded from refgenie http://refgenomes.databio.org/v3/assets/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index?tag=default
Genes with fewer than 10 reads across all samples were filtered prior to all downstream analyses
Assembly: hg38
Supplementary files format and content: DESEq2 counts

source_name: skin

extract_protocol:
RNA extraction with trizol-chloroform
libraries were prepared using the DNBseq protocol from BGI.

value: skin

value: primary dermal fibroblast

value: Ionizing radiation (IR) induced senescence, DMSO


title: kap123, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: TAC and reverse index: CGA. A total of  2380 colony number was in this library.
kap123-8d.One.bed
kap123-8d.MultipleClean.bed


title: 222_B10_III

value: Ionizing radiation (IR) induced senescence, 10 µM Nintedanib


title: ID12167959, Ecoli, No Drug, 0h

description:
ID12167959
Ecoli_counts.txt
Ecoli_metadata_samples.txt
Ecoli_metadata_genes.txt


title: 222_DMSO_IIII


title: 222_B1_IIIIII

value: Ionizing radiation (IR) induced senescence, 1 µM Nintedanib


title: 222_B1_IIII


title: 222_B1_III


title: 222_A1_IIII

value: Ionizing radiation (IR) induced senescence, 1 µM Axitinib


title: 222_A1_III


title: 222_B10_IIIIII


title: 222_DMSO_IIIIII


title: p10 neg control (Biol rep 3)

value: Breast cancer

value: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)

value: vehicle


title: SB870

first: Sydney

last: Blattman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

data_processing:
Barcode demultiplexing with cutadapt 1.18
UMIs extracted with UMI-tools version 0.5.5
Reads aligned with bwa version 0.7.17
Features called with featureCounts version 1.6.3
Final matrix generated by collapsing reads by UMI with a custom script in python 2.7.15
processed data files format and content: R objects to be loaded into Seurat, cell type names link barcodes to cell type (.rds; full - all counts; ds - downsampled to ~40 counts per cell); cell type overview (.csv)
Assembly: Genbank U00096

source_name: MG1655 or UPEC CFT073

extract_protocol:
in situ RT and ligations followed by cell lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit

value: MG1655 or UPEC CFT073

value: PETRI-seq; MG1655, metG* or UPEC CFT073 cells growing or after ampicillin treatment

value: after overnight growth, wildtype (MG1655 or CFT073) cells were diluted into fresh media and grown for 1 hour (wt_1hr_20231016, CFT073_1hr_20231016) or were diluted into fresh media + ampicillin (200 μg/mL) and incubated for 4 hours (wt_amp_20231016, CFT073_amp_20231016); for metG*, after overnight growth, cells were diluted into fresh media and growth for 3 hours (metG_pre_20231016) then incubated in ampicillin (200 μg/mL) for 4 hours (metG_amp_20231016)


title: SB866


title: 222_A10_IIIIII

value: Ionizing radiation (IR) induced senescence, 10 µM Axitinib


title: 222_A10_IIII


title: 222_A10_III


title: 222C_DMSO_III

value: DMSO


title: Wue N526/17

city: Tuebingen

first: Jonas

last: Scheid

state: Baden-Wuerttemberg

address: Auf der Morgenstelle 15

department: Peptide-based Immunotherapy

country: Germany

institute: University and Universityhospital Tuebingen

description:
QLVMB055A9
raw_gene_counts.tsv
tpm_gene_counts.tsv

data_processing:
Transcriptomic reads were quantified using the Nextflow-based nf-core pipelinernaseq v1.4.2 with the standard parameters
The quality of the FASTQ files was determined with FastQC, followed by adapter trimming with Trim Galore v0.6.4
Trimmed reads were used as input for the STAR v2.6.1 aligner to map reads to the reference genome GRCh37
RNA-seq data quality control was performed withRSeQC v3.0.1 and read counting of the features (e.g., genes) with featureCounts v1.6.4
Ultimately, an aggregation of the quality control for the RNAseq analysis was performed with MultiQC v1.7
The nf-core rnaseq pipeline contained the raw read count table resulting fromfeatureCounts.
This contentwas processed with the R packageDESeq2 v1.34.0 and used for the differential expression analysis.
Transcripts with an absolute log fold change > 2 and an FDR < 0.01 were differentially expressed.
Assembly: hg19
Supplementary files format and content: Tab-delimited file containing the raw counts for each Sample
Supplementary files format and content: Tab-delimited file containing the TPM values for each Sample

source_name: Medulloblastoma tumor

extract_protocol:
RNA was isolated from fresh frozen tumor tissue (≥ 20 mg) using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA sequencing was performed for all 28 tumors at CeGaT GmbH, Tübingen.
Following quality control for RNA integrity, sequencing libraries were prepared from 78 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR; Roche), whereby ribosomal RNA was depleted. Paired-end sequencing at 100 bp read length was performed on a NovaSeq 6000 sequencing system (Illumina).

value: Medulloblastoma tumor

tag: tumor grade

tag: tumor subgroup

value: Group 4

tag: age at_diagnosis

tag: treatment 1

value: Radiotherapy

tag: treatment 2

value: Chemotherapy

tag: Sex

value: Female


title: 222C_DMSO_IIII

tag: tissue

value: skin

value: primary dermal fibroblast


title: SB865d

tag: genotype


title: Wue N998/13

description:
QLVMB054A1
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Group 3

value: Male


title: Wue N391/17

description:
QLVMB056AH
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: WNT


title: 222C_DMSO_IIIIII

tag: treatment


title: HH04 2428/17

description:
QLVMB051AB
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: 222_B10_IIII

tag: cell type

value: Ionizing radiation (IR) induced senescence, 10 µM Nintedanib


title: 222_A1_IIIIII

tag: cell line

value: Ionizing radiation (IR) induced senescence, 1 µM Axitinib


title: HH03 1074/17

description:
QLVMB050A3
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: HH06 1559/18

description:
QLVMB053AR
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: 222C_B10_IIII

value: 10 µM Nintedanib


title: 222C_B10_IIIIII


title: ZH937

description:
QLVMB047AI
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: SHH


title: HH02 1662/15

description:
QLVMB049A0
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: 222C_B10_III


title: 222C_B1_IIIIII

value: 1 µM Nintedanib


title: 222C_B1_III


title: 222C_B1_IIII


title: HH05 2910/17

description:
QLVMB052AJ
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: ZH913

description:
QLVMB045A2
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: SB860d

value: MG1655 or UPEC CFT073

value: PETRI-seq; MG1655, metG* or UPEC CFT073 cells growing or after ampicillin treatment

value: after overnight growth, wildtype (MG1655 or CFT073) cells were diluted into fresh media and grown for 1 hour (wt_1hr_20231016, CFT073_1hr_20231016) or were diluted into fresh media + ampicillin (200 μg/mL) and incubated for 4 hours (wt_amp_20231016, CFT073_amp_20231016); for metG*, after overnight growth, cells were diluted into fresh media and growth for 3 hours (metG_pre_20231016) then incubated in ampicillin (200 μg/mL) for 4 hours (metG_amp_20231016)


title: 222C_A10_IIIIII

value: 10 µM Axitinib


title: ZH890

description:
QLVMB044AS
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Medulloblastoma tumor

value: Radiotherapy


title: HH01 491/12

description:
QLVMB048AQ
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Chemotherapy

value: Female


title: 222C_A1_IIII

value: skin

value: primary dermal fibroblast

value: 1 µM Axitinib


title: ZH919

description:
QLVMB046AA
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Group 4


title: 222C_A1_IIIIII


title: ZH868

description:
QLVMB041A4
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: 222C_A10_IIII


title: 222C_A1_III


title: ONT-DRS, ccr4a ccr4b ddm1 rdr2, seedlings

city: Onna-son, Kunigami-gun, Okinawa

first: ATSUSHI

last: SHIMADA

address: 1919-1 Tancha

department: Plant Epigenetics Unit

country: Japan

institute: Okinawa Institute of Science and Technology

data_processing:
Basecalling and poly(A) tail length estimation was performed with Dorado (v0.5.3).
fastq files were aligned to the Arabidopsis thaliana genome assembly using Minimap2 (v2.28-r1209).
Bigwig files normalized with CPM were generated using deepTools (v3.4.3)
Assembly: Col-CEN Arabidopsis thaliana genome assembly
Supplementary files format and content: text file for read ID and poly(A) tail length

organism: Arabidopsis thaliana

source_name: 12-day-old seedlings

growth_protocol: Plants were grown on MS plates at 22℃ under long-day conditions (light 16h, dark 8h).

extract_protocol:
Total RNA was extracted from the 12-day old plant seedlings using Direct-zol RNA Miniprep kit (Zymoresearch, R2050).
Library preparation was performed using Nanopore Direct RNA Sequencing Kit (SQK-RNA004)

value: 12-day-old seedlings

tag: ecotype

value: Columbia (Col-0)

value: Seedlings

value: ccr4a ccr4b ddm1 rdr2


title: ZH741

description:
QLVMB040AU
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: WNT


title: ONT-DRS, ddm1 rdr2, seedlings

value: ddm1 rdr2


title: 222C_A10_III


title: ZH872

description:
QLVMB042AC
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: SHH

value: Male


title: ZH859

description:
QLVMB043AK
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: ZBTB46DTR  treated with DT (Diphtheria toxin)_7Days hypoxia challenge_3

city: Aurora

first: Claudia

last: Mickael

state: Colorado

institute: University of Colorado

data_processing:
FASTQ files went to quality control using FastQC
adapters were removed using TrimmomaticÒ software
BAM files were analyzed using SeqMonkÒ software, where differentially expressed genes (DEG) were identified
Assembly: mm10
Supplementary files format and content: Excell sheet, raw read counts

source_name: Lung

growth_protocol: Lung tissue was dispersed by sonication

extract_protocol:
RNA was extracted from whole lungs using Qiagen RNA easy kit
Universal Plus™ mRNA-Seq library preparation kit with NuQuant®

treatment_protocol: diphtheria toxin 1 day prior to hypoxia challenge (40ng/g) and 8ng/g every 3 days to maintain depletion (total 3 doses)

value: Lung

value: ZBTB46 DTR

value: Diphtheria toxin (DT)


title: ONT-DRS, WT, seedlings

value: Wild type (Col-0)


title: ZBTB46DTR  treated with DT (Diphtheria toxin)_7Days hypoxia challenge_1


title: ZH718

description:
QLVMB038AJ
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Medulloblastoma tumor

value: Chemotherapy


title: ZH732

description:
QLVMB039AR
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Group 3

value: Radiotherapy


title: EM-seq, ccr4a ccr4b ddm1 rdr2, adult leaves

data_processing:
Sickle (v1.33) was used for filtering sequencing reads (quality score > 30)
Filtered reads were aligned to the Arabidopsis thaliana genome assembly with Bismark (v0.22.3)
CX report files were generated with Methylation Extractor (v0.22.3)
Assembly: Col-CEN Arabidopsis thaliana genome assembly
Supplementary files format and content: text file for the methylation count at each cytosine
Library strategy: EM-seq

source_name: 6-week-old adult plant leaves

growth_protocol: Plants were grown on soil at 22℃ under long-day conditions (light 16h, dark 8h).

extract_protocol:
Genomic DNA was extracted from 6-week-old plant leaves using Nucleon phytopure (Sigma-Aldrich, RPN8510)
Library preparation was performed with 100 ng of genomic DNA using NEBNext Enzymatic Methyl-seq Kit (NEB, E7120L) and Multiplex Oligos for Enzymatic Methyl-seq (E7140S). Library PCR was performed with 13 cycles and validation was performed with Takara Library Quantification kit (638324).

value: 6-week-old adult plant leaves

value: Adult plant leaves


title: EM-seq, ddm1 rdr2, adult leaves

value: Columbia (Col-0)


title: ZBTB46DTR  treated with DT (Diphtheria toxin)_7Days hypoxia challenge_2


title: ONT-DRS, ccr4a ccr4b, seedlings

value: 12-day-old seedlings

value: Seedlings

value: ccr4a ccr4b


title: EM-seq, WT, adult leaves


title: EM-seq, ccr4a ccr4b, adult leaves


title: smRNA-seq, rdr6, adult leaves, rep2

data_processing:
Cutadapt (v3.1) was used for trimming adapter sequences
FastXtoolkit (v0.0.13) was used for filtering sequencing reads (quality score > 30)
Filtered reads were aligned to the Arabidopsis thaliana genome assemblies with Bowtie2 (v2.4.2)
bedgraph files containing 24-nucleotide reads normalized with RPM (Reads Per Million) were generated using bedtools (v2.29.2)
Assembly: Col-CEN Arabidopsis thaliana genome assembly
Supplementary files format and content: text file for the read count of each gene

source_name: 5-week-old adult plant leaves

extract_protocol:
Total RNA was extracted from 5-week-old plant leaves using Direct-col RNA Miniprep kit (Zymoresearch, R2050).
Library preparation was performed using NEXTFLEX® Small RNA-Seq Kit v3 (Cosmobio, 5132–06) followed by validation with tapestation (Agilent).

value: 5-week-old adult plant leaves


title: ZH713

description:
QLVMB037AB
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: ZBTB46DTR  treated with PBS (vehicle)_7Days hypoxia challenge_2

value: PBS


title: smRNA-seq, rdr6, adult leaves, rep1


title: ZBTB46DTR  treated with PBS (vehicle)_7Days hypoxia challenge_3


title: ZH703

description:
QLVMB036A3
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Group 4

value: Male


title: smRNA-seq, ddm1 rdr2 rdr6, adult leaves, rep2

value: ddm1 rdr2 rdr6


title: ZBTB46DTR  treated with PBS (vehicle)_7Days hypoxia challenge_1

value: Lung

value: ZBTB46 DTR


title: ZH680

description:
QLVMB035AT
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Medulloblastoma tumor

value: Female


title: smRNA-seq, ddm1 rdr2 rdr6, adult leaves, rep1


title: smRNA-seq, ccr4a ccr4b ddm1 rdr2, adult leaves, rep1

value: ccr4a ccr4b ddm1 rdr2


title: smRNA-seq, ddm1 rdr2, adult leaves, rep2

value: ddm1 rdr2


title: ZH513

description:
QLVMB034AL
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Radiotherapy

value: Chemotherapy


title: smRNA-seq, ddm1 rdr2, adult leaves, rep1

value: Columbia (Col-0)

value: Adult plant leaves


title: smRNA-seq, ccr4a ccr4b ddm1 rdr2, adult leaves, rep2


title: smRNA-seq, ccr4a ccr4b, adult leaves, rep2


title: smRNA-seq, ccr4a ccr4b, adult leaves, rep1


title: Parental-HF 2

type: RNA

city: LA

first: Paul

middle: C

last: Boutros

address: UCLA

department: Human Genetics

institute: UCLA

description: NanoString

hyb_protocol: not provided

scan_protocol: not provided

data_processing: NanoString data was normalized and differential abundance analysis was performed as recommended by Bhattacharya et al with DEseq2

source_name: DU145 cell line

growth_protocol: Cells were cultured in tissue-culture flasks using Dulbecco's modified Eagle's medium containing 4.5 g/L D-glucose and GlutaMAX (DMEM; Gibco) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin. The cells were kept at 37°C in a humidified incubator with 5% CO2 and were passaged when they reached 80% confluency.

extract_protocol: RNeasy extraction kit (Qiagen)

treatment_protocol: An isogenic CF-radioresistant  cell line was created by pooling the surviving cells following a CF irradiation of 2 Gy x 59 fractions. An isogenic HF-radioresistant  cell line was created by pooling the surviving cells following a HF irradiation of 5 Gy x 10fractions.

value: Prostate

value: Mock


title: RNA-seq, ddm1 rdr2 rdr6, seedlings, rep3

data_processing:
Sickle (v1.33) was used for filtering sequencing reads (quality score > 30)
Filtered reads were aligned to the Arabidopsis thaliana genome assembly with STAR (2.7.9a)
Bigwig files normalized with CPM were generated using deepTools (v3.4.3)
Assembly: TAIR10 Arabidopsis thaliana genome assembly
Supplementary files format and content: text file for the read count of each gene

extract_protocol:
Total RNA was extracted from the 12-day old plant seedlings using Direct-zol RNA Miniprep kit (Zymoresearch, R2050).
Library preparation was performed with 500 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760). Library PCR was performed 9 cycles (IP) followed by validation with Takara Library Quantification kit (638324).

value: 12-day-old seedlings

value: Seedlings


title: SA3

description:
QLVMB031AV
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: SHH


title: Parental-HF 1

description: NanoString


title: SA5

description:
QLVMB033AD
raw_gene_counts.tsv
tpm_gene_counts.tsv


title: RNA-seq, ddm1 rdr2 rdr6, seedlings, rep2


title: smRNA-seq, WT, adult leaves, rep2

value: 5-week-old adult plant leaves

value: Wild type (Col-0)


title: SA2

description:
QLVMB030AN
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Group 3

value: Male


title: HF 2

description: NanoString

value: hypofractionated radiotherapy


title: SA4

description:
QLVMB032A5
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Medulloblastoma tumor

value: Group 4


title: SA1

description:
QLVMB029AK
raw_gene_counts.tsv
tpm_gene_counts.tsv

value: Female


title: HF 1

description: NanoString


title: Parental-CF 1

description: NanoString


title: RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep1

value: ccr4a ccr4b ddm1 rdr2


title: RNA-seq, ddm1 rdr2, seedlings, rep3

value: ddm1 rdr2


title: Parental-CF 2

description: NanoString


title: RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep2

value: Columbia (Col-0)


title: RNA-seq, ccr4a ccr4b ddm1 rdr2, seedlings, rep3


title: DDX17 KO MHCC97H 3

city: Chongqing

first: Hongzhong

last: Zhou

institute: ChongQing Medical University/.

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: DDX17 KO MHCC97H cell

growth_protocol: Cells were cultured with DMEM supplemented with 10% fetal bovine serum and penicillin-streptomycin at 37℃ in 5% CO2 and 95% air

extract_protocol:
Total RNA was extracted from MHCC97H cells with or without DDX17 knockout using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DDX17 knock out cell line (DDX17 KO) and non-target control cell line were constructed by using  the CRISPR/Cas9 system according to the manufacturer's instructions.

tag: genotype/variation

value: DDX17 KO


title: RNA-seq, ddm1 rdr2, seedlings, rep2


title: CF 2

description: NanoString

value: Prostate


title: RNA-seq, ddm1 rdr2, seedlings, rep1


title: RNA-seq, ccr4a ccr4b, seedlings, rep3

value: ccr4a ccr4b


title: DDX17 KO MHCC97H 2


title: DDX17 KO MHCC97H 1


title: RNA-seq, ccr4a ccr4b, seedlings, rep2

value: 12-day-old seedlings


title: SBC317

data_processing:
Barcode demultiplexing with custom python script
Remove flanking constant sequences with cutadapt 1.18
Reads aligned with bwa version 0.7.17
Features called with custom python scripts that check for PAM sequence
processed data files format and content: excel file with five tabs: sample overview, log2FC, p-value, significance (1=enriched, -1=depleted; FDR=0.1) and n_positions (number of crRNAs included per gene)
Assembly: Genbank U00096

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1455)

value: hipA7-pWJ445 (pTet-dCas9)

value: hipA7 lag outgrowth

value: after 4-hr lag abx; 2-day semisolid outgrowth


title: control MHCC97H 3

source_name: control MHCC97H cell

value: control


title: RNA-seq, WT, seedlings, rep3

value: Seedlings

value: Wild type (Col-0)


title: RNA-seq, ddm1 rdr2 rdr6, seedlings, rep1

value: ddm1 rdr2 rdr6


title: control MHCC97H 2


title: RNA-seq, WT, seedlings, rep2


title: RNA-seq, WT, seedlings, rep1


title: ChIP-seq, ddm1 rdr2 rdr6, Input, seedlings, rep2

description: AS20-13_ColCEN2024_ratio_normed_bs200_marked.bw

data_processing:
sickle (version 1.33) was used for filtering sequencing reads (quality score > 30)
Filtered reads were aligned to the Arabidopsis thaliana genome assembly with Bowtie2 (v2.4.2)
Duplicated reads were removed with samtools (v1.12)
bigwig files normalized with IP / Input and reads per million (RPM) were created with deeptools
Assembly: Col-CEN Arabidopsis thaliana genome assembly
Supplementary files format and content: Bigwig

source_name: 2-week-old seedlings

extract_protocol:
Plants were fixed with 1% FA followed by quencing with 0.125M Glycine. After cell lysis, nuclear chromatin was sheared with Branson 250 Digital Sonifier.
NEB UltraⅡLibrary Prep Kit was used for library preparation (NEB, E7645). Library PCR was performed with 8 (Input) and 11 cycles (IP) followed by validation with Takara Library Quantification kit (638324).

value: 2-week-old seedlings


title: SBC315

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1458)

value: delta-yqgE; pBbS6C-RFP; pWJ445 (pTet-dCas9)

value: MG1655-∆yqgE pBbS6A-RFP lag outgrowth

value: 4.25-hr liquid outgrowth after overnight (lag)


title: control MHCC97H 1


title: SBC314

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1457)

value: MG1655-∆yqgE pBbS6A-RFP after overnight (pre-outgrowth)

value: after overnight (with aTc, IPTG, and ampicillin)


title: CF 1

description: NanoString


title: ChIP-seq, ddm1 rdr2 rdr6, Input, seedlings, rep1

description: AS20-12_ColCEN2024_ratio_normed_bs200_marked.bw

value: Columbia (Col-0)


title: smRNA-seq, WT, adult leaves, rep1

value: 5-week-old adult plant leaves

value: Adult plant leaves


title: SBC313

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1455)

value: delta-yqgE; pBbS6C-yqgE; pWJ445 (pTet-dCas9)

value: MG1655-∆yqgE pBbS6A-yqgE lag outgrowth

value: 5.5-hr liquid outgrowth after overnight (lag)


title: Wü N391/17

type: genomic

description:
204088090155_R07C01
S1573Nr28

hyb_protocol: Genome-wide DNA methylation profiling was performed using the Infinium HumanMethylation450 and the Infinium HumanMethylation EPIC Kits

data_processing:
DNA methylation based-classification was performed using the Heidelberg Brain Tumor Methylation Classifier V12 (www.molecularneuropathology.org)
The Heidelberg Brain Tumor Methylation Classifier output contains confidence scores to which (super-) family class and brain tumor class the sample is predicted the best

label: Cy3 and Cy5

label_protocol: Illumina protocol

extract_protocol: Tumor DNA was extracted from fresh-frozen tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit.

value: Medulloblastoma tumor

value: WNT

tag: age at diagnosis

value: Radiotherapy

value: Chemotherapy

value: Male


title: SBC318

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1456)

value: hipA7-pWJ445 (pTet-dCas9)

value: hipA7 lag abx

value: 2-day semisolid outgrowth after overnight (lag)


title: Wü N526/17

description:
204088090155_R06C01
S1573Nr27

scan_protocol: Genome-wide DNA methylation profiling was performed using the Infinium HumanMethylation450 and the Infinium HumanMethylation EPIC Kits

value: Group 4

value: Female


title: ChIP-seq, ccr4a ccr4b ddm1 rdr2, Input, seedlings, rep1

description: AS17-15_ColCEN2024_ratio_normed_bs200_marked.bw

value: 2-week-old seedlings

value: Seedlings

value: ccr4a ccr4b ddm1 rdr2


title: ChIP-seq, ccr4a ccr4b, Input, seedlings, rep2

description: AS22-26_ColCEN2024_ratio_normed_bs200_marked.bw

value: Columbia (Col-0)

value: ccr4a ccr4b


title: Wü N998/13

description:
204088090155_R05C01
S1573Nr26

value: Group 3


title: ChIP-seq, ddm1 rdr2, Input, seedlings, rep2

description: AS17-14_ColCEN2024_ratio_normed_bs200_marked.bw

value: ddm1 rdr2


title: ChIP-seq, ddm1 rdr2, Input, seedlings, rep1

description: AS17-13_ColCEN2024_ratio_normed_bs200_marked.bw


title: SBC312

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1423, W1456)

value: delta-yqgE; pBbS6C-yqgE; pWJ445 (pTet-dCas9)

value: MG1655-∆yqgE pBbS6A-yqgE after overnight (pre-outgrowth)

value: after overnight (with aTc, IPTG, and ampicillin)


title: ChIP-seq, ccr4a ccr4b, Input, seedlings, rep1

description: AS17-11_ColCEN2024_ratio_normed_bs200_marked.bw


title: RNA-seq, ccr4a ccr4b, seedlings, rep1

value: 12-day-old seedlings


title: HH-Medullo 06

description:
204088090148_R08C01
S1573Nr25

value: Medulloblastoma tumor

value: Radiotherapy

value: Chemotherapy

value: Male


title: ChIP-seq, WT, Input, seedlings, rep2

description: AS22-25_ColCEN2024_ratio_normed_bs200_marked.bw

value: Wild type (Col-0)


title: ChIP-seq, WT, Input, seedlings, rep1

description: AS17-9_ColCEN2024_ratio_normed_bs200_marked.bw


title: ChIP-seq, ddm1 rdr2 rdr6,  H3K9me2 IP, seedlings, rep2

value: ddm1 rdr2 rdr6


title: HH-Medullo 05

description:
204088090148_R07C01
S1573Nr24

value: WNT

value: Female


title: SBC310

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1423, W1452)

value: wt; pBbS6C-RFP; pWJ445 (pTet-dCas9)

value: CRISPRi; MG1655 pBbS6A-RFP after overnight (pre-outgrowth)


title: ChIP-seq, ddm1 rdr2 rdr6,  H3K9me2 IP, seedlings, rep1

value: 2-week-old seedlings

value: Columbia (Col-0)

value: Seedlings


title: HH-Medullo 04

description:
204088090148_R06C01
S1573Nr23


title: SBC309

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1421, W1456)

value: wt; pBbS6C-yqgE; pWJ445 (pTet-dCas9)

value: CRISPRi; MG1655 pBbS6A-yqgE lag outgrowth

value: 5.5-hr liquid outgrowth after overnight (lag)


title: ChIP-seq, ccr4a ccr4b ddm1 rdr2,  Input, seedlings, rep2

description: AS17-16_ColCEN2024_ratio_normed_bs200_marked.bw

value: ccr4a ccr4b ddm1 rdr2


title: ChIP-seq, ccr4a ccr4b ddm1 rdr2,  H3K9me2 IP, seedlings, rep2


title: SBC308

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1421, W1455)

value: CRISPRi; MG1655 pBbS6A-yqgE after overnight (pre-outgrowth)

value: after overnight (with aTc, IPTG, and ampicillin)


title: ChIP-seq, ddm1 rdr2,  H3K9me2 IP, seedlings, rep2

value: ddm1 rdr2


title: HH-Medullo 02

description:
204088090148_R04C01
S1573Nr21

value: Medulloblastoma tumor

value: Group 3

value: Radiotherapy

value: Chemotherapy

value: Male


title: ChIP-seq, ccr4a ccr4b ddm1 rdr2,  H3K9me2 IP, seedlings, rep1


title: SBC125

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1412, W1455)

value: wt-pWJ445 (pTet-dCas9)

value: CRISPRi; MG1655 before overnight (before aTc induction)

value: before overnight (before aTc induction)


title: HH-Medullo 03

description:
204088090148_R05C01
S1573Nr22


title: SBC95

value: metG*-pWJ445 (pTet-dCas9)

value: CRISPRi; metG* before overnight (before aTc induction)


title: ChIP-seq, ddm1 rdr2, H3K9me2 IP, seedlings, rep1

value: 2-week-old seedlings

value: Columbia (Col-0)

value: Seedlings


title: ChIP-seq, WT, H3K9me2 IP, seedlings, rep2

value: Wild type (Col-0)


title: SB851d

extract_protocol:
in situ RT and ligations followed by cell lysis with detergent and proteinase K
Double-stranded cDNA was made by second strand synthesis. Libraries were tagmented and amplified using the Nextera XT kit

value: wildtype and metG*

value: PETRI-seq; metG* in ampicillin, MG1655 in rifampicin, MG1655 in tetracycline

value: after overnight growth (all), diluted into fresh media + ampicillin (200 μg/mL) and incubated for 4 hours (metG_imm_abx_20230919) or diluted into fresh media + rifampicin (200 μg/ml) or tetracycline (135 μg/ml) and incubated for 1 hour (rif1hr_20230919, tet1hr_20230919)


title: HH-Medullo 01

description:
204088090148_R03C01
S1573Nr20

value: Medulloblastoma tumor

value: SHH

value: Female


title: SBC311

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1423, W1455)

value: wt; pBbS6C-RFP; pWJ445 (pTet-dCas9)

value: CRISPRi; MG1655 pBbS6A-RFP lag outgrowth

value: 4.25-hr liquid outgrowth after overnight (lag)


title: ZH937

description:
204088090148_R02C01
S1573Nr19

value: Radiotherapy

value: Chemotherapy

value: Male


title: ChIP-seq, WT, H3K9me2 IP, seedlings, rep1


title: C_auris_WT_ISA-1.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: C. auris genome version gca002759435.2 ; https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002759435.2; accessed on 03/05/2024
Supplementary files format and content: Excel file includes raw and normalized data for each Samples

organism: Candidozyma auris

source_name: Isolate 2

growth_protocol: C. auris isolates, derived from the South Asian/Indian lineage, were used in this study. For C. auris isolates, the median planktonic MICs were >2.0 mg/L and 0.06 mg/L for ISA. Using the tentative epidemiological cutoff value (ECOFF) of ≤1 mg/L proposed by Arendrup et al (2017), these isolates were classified as non-wild-type (non-WT) and wild-type (WT) to ISA. Both strains were maintained on YPD agar plates [YPD broth (VWR, 1% yeast extract, 2% peptone, 2% glucose) and 2% agar (VWR), pH 5.8)] at 37 °C.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Strains were pre-cultured in YPD broth overnight at 37 °C, diluted to an OD640 of 0.1 in YPD broth (20 mL aliquots in 100 mL Erlenmeyer flasks). Cultures were incubated at 37 °C and 140 rpm for 8 h. ISA (0.015 mg/l final concentration) was added after 4 h of incubation to the exponentially growing phase cultures. Samples were collected after 4 h ISA exposure then were washed three times with physiological saline. Total RNA was isolated from lyophilized fungal cells in two biological replicates.

value: fungal cells

value: WT

value: 0.015 mg/l ISA treated


title: C_auris_WT_ISA-2.


title: SB848


title: C_auris_WT_Control-2.

value: untreated


title: ZH919

description:
204088090131_R08C01
S1573Nr18

value: Group 4


title: SB846d

value: wildtype and metG*


title: ZH913

description:
204088090131_R07C01
S1573Nr17


title: C_auris_non-WT_ISA-1.

source_name: Isolate 1

value: non-WT


title: C_auris_non-WT_ISA-2.


title: SBC192 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1449)

value: metG*-pBbS6C-dCas9 (pLlacO1-dCas9)

value: CRISPRi; metG* lag outgrowth

value: 6-hr liquid outgrowth after overnight (lag)


title: C_auris_non-WT_Control-1.


title: C_auris_non-WT_Control-2.


title: ChIP-seq, ccr4a ccr4b, H3K9me2 IP, seedlings, rep2

value: 2-week-old seedlings

value: Columbia (Col-0)

value: Seedlings

value: ccr4a ccr4b


title: ChIP-seq, ccr4a ccr4b, H3K9me2 IP, seedlings, rep1


title: SBC191 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1447)

value: CRISPRi; metG* after overnight

value: after overnight (with IPTG)


title: NovaST_coronal_section_plate12

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB-KU Leuven

description: Fresh frozen Nova-ST spatial transcriptome sequencing

data_processing:
Raw sequencing data was processed using bcl2fastq to generate fastq files
Nova-ST chip tiles were identified using a subset of data, and a witelist of barcodes was created from these tiles. Data was mapped and quantified against the mm10 using this whitelist and STARsolo
X/Y coordinates for barcodes with identified counts were normalised into a chip-based space and used alongside the expression data to create GEM files.
Assembly: galGal6
Supplementary files format and content: tif: H&E stained images
Supplementary files format and content: gem.gz: GEM formatted expression matrix including normalized X/Y coordinates of each cluster
Supplementary files format and content: BC_Coords.pickle: Python pickled dictionaries containing barcodes, tile information and X/Y coordinates used for whitelist creation.
Library strategy: Spatial Transcriptomics (Nova-ST)

molecule: polyA RNA

organism: Gallus gallus

source_name: Telencephalon

extract_protocol:
Telencephalons from 15 days old domestic chickens were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, the telencephalon was embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on Nova-ST chips
Pepsin was used to permeabilise the sectioned tissue and Maxima Rtase for the reverse transcription. Samples were treated with endonuclease and then tissue was cleared with Proteinase K. Klenow Fragment was used for second strand synthesis and the resulting cDNA was amplified and prepared for sequencing by addition of indexes and Illumina flow cell attachment sites.

value: Telencephalon

tag: breed

value: broiler


title: ZH859

description:
204088090122_R07C01
S1573Nr15

value: Medulloblastoma tumor

value: SHH

value: Radiotherapy

value: Chemotherapy

value: Male


title: ZH872

description:
204088090131_R04C01
S1573Nr14


title: SBC134 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1458)

value: wt-pWJ445 (pTet-dCas9)

value: CRISPRi; wildtype after exponential

value: 3.5-hr liquid outgrowth after dilution of SBC133


title: NovaST_coronal_section_plate5


title: Mouse Kidney Tumor 10

city: Bethesda

first: Christopher

middle: James

last: Ricketts

state: Maryland

address: Building 10

department: Urologic Oncology Branch

institute: National Cancer Institute

data_processing:
Data processing was performed by Novogene
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. So it's necessary to filter the raw reads and get the clean reads. The filtering process is as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Raw read count data  was provided by Novogene with the reads count being proportional to gene expression level, gene length and sequencing depth.
The gene count data provided by Novogene was analyzed by the NIH Integrated Data Analysis Portal (NIDAP) using the RNA sequencing data analysis pipeline to produce PCA plots, gene clustering heatmaps, and differential gene expression profiles, and perform pathway/gene set enrichment analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: kidney

extract_protocol:
Samples were cryo-pulverized in liquid nitrogen for RNA extraction for RNA sequencing.  The resultant powder was resuspended in 1 mL of Trizol Reagent (Invitrogen, CA, USA) and total RNA extraction was performed in accordance with the manufacturer’s protocol.
mRNA library preparation was performed by poly A enrichment by Novogene.

value: kidney

tag: group

value: Tumor


title: SBC132 version 2

value: CRISPRi; wildtype lag outgrowth

value: 4-hr liquid outgrowth after overnight (lag)


title: Mouse Kidney Tumor 8


title: ZH741

description:
204088090122_R07C01
S1573Nr12

value: WNT

value: Female


title: ZH868

description:
204088090131_R03C01
S1573Nr13


title: Mouse Kidney Tumor 6


title: Mouse Kidney Tumor 7


title: SBC131 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1455)

value: 2-day semi-solid outgrowth after overnight (lag)


title: ZH890

description:
204088090131_R06C01
S1573Nr16

value: Group 3


title: Mouse Kidney Tumor 4


title: Mouse Kidney Tumor 3


title: SBC130 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1452)

value: 4-hr semi-solid outgrowth after overnight (lag)


title: ZH718

description:
204088090138_R07C01
S1573Nr10

extract_protocol: Tumor DNA was extracted from fresh-frozen tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit.

value: Medulloblastoma tumor


title: C_auris_WT_Control-1.

value: fungal cells

value: WT

value: untreated


title: ZH713

description:
204088090138_R06C01
S1573Nr9

value: Radiotherapy

value: Chemotherapy

value: Male


title: Mouse Normal Kidney Sample 10

value: Normal kidney


title: Mouse Kidney Tumor 9

value: kidney


title: SBC133 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1457)

value: wt-pWJ445 (pTet-dCas9)

value: CRISPRi; wildtype pre-exponential

value: after exponential aTc induction


title: ZH703

description:
204088090129_R08C01
S1573Nr8

value: Group 4


title: Mouse Kidney Tumor 1

value: Tumor


title: Mouse Normal Kidney Sample 7


title: SBC126 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1455)

value: CRISPRi; wildtype after overnight

value: after overnight (with aTc)


title: Mouse Kidney Tumor 5


title: SBC102 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1423, W1456)

value: metG*-pWJ445 (pTet-dCas9)

value: CRISPRi; metG* lag outgrowth

value: 4-hr liquid outgrowth after overnight (lag)


title: ZH680

description:
204088090129_R07C01
S1573Nr7

value: Medulloblastoma tumor

value: Female


title: Mouse Normal Kidney Sample 6


title: UCLA1 naïve hESC, CD75-sorted PXGL d8, rep1 (ATAC-seq)

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

country: Canada

institute: McGill University

description: P39+2 (PXGL d8; sorted for CD75hi naïve hESCs)

data_processing:
Raw reads were trimmed to 50bp using TrimGalore!
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Mitochondrial reads were removed prior to making coverage files and differential analysis.
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Primed human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were lysis in 50 ul ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2) supplemented with 0.1% Tween-20, 0.1% NP-40 and 0.01% digitonin, and incubated on ice for three minutes. Lysis  buffer was then diluted with 1 ml ATAC resuspension buffer supplemented with 0.1% Tween-20 and tubes were inverted three times. Nuclei were pelleted by centrifugation at 500g for 10 minutes at  4°C. Transposition reaction was carried out in 50 ul volume for each sample by resuspending nuclei in 25 ul 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20 DMF), 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20 and 5 ul H2O. Reactions were incubated at 37°C  for 30 minutes in a thermomixer with 1000 RPM mixing. Reactions were quenched with 5x volume of buffer PB and DNA was purified using the MinElute PCR purification kit (Qiagen). Libraries were next amplified using Illumina-compatible primers.
Libraries were constructed as described in Corces et al (2017) Nature Methods.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate or DMSO of equivalent v/v concentration, where specified.

value: Primed human embryonic stem cells

value: UCLA1 naive hESCs

value: Human embryonic stem cells

value: WT


title: UCLA1 naïve hESC, CD75-sorted PXGL d8, rep2 (ATAC-seq)

description: P37+2 (PXGL d8; sorted for CD75hi naïve hESCs)


title: ZH513

description:
204088100026_R08C01
S1573Nr6

value: Radiotherapy

value: Chemotherapy

value: Male


title: ZH732

description:
204088090138_R08C01
S1573Nr11

value: Group 3


title: Mouse Kidney Tumor 2

value: kidney


title: SBC101 version 2

city: New York

value: 2-day semi-solid outgrowth after overnight (lag)


title: Mouse Normal Kidney Sample 5

value: Normal kidney


title: SBC100 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1423, W1452)

value: 4-hr semi-solid outgrowth after overnight (lag)


title: Input rep 1

city: shanghai

first: Jiaqiang

last: Luo

address: 85th Wujin Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The cells were cultured in MEM-α/StemPro-34 medium (12561, GIBCO) supplemented with 10 ng/ml GDNF and 10 ng/ml mouse fibroblast growth factor 2 (FGF2; 450-33, Peprotech).

extract_protocol:
The RNA immunoprecipitation assay was carried out with GenSeq RIP kit (GenSeq Inc.) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.). Library sequencing was sequenced with 150bp paired end reads.

value: mouse cultured germ stem cells

value: mouse germ stem cells


title: SBC128 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1457)

value: wt-pWJ445 (pTet-dCas9)

value: CRISPRi; wildtype lag abx

value: after 4-hr lag abx; 2-day semi-solid outgrowth


title: Input rep 2


title: SA4

description:
204088100026_R06C01
S1573Nr4

value: Medulloblastoma tumor

value: Group 4


title: Mouse Normal Kidney Sample 8


title: IgG rep 2


title: Mouse Normal Kidney Sample 9


title: SA3

description:
204088100026_R05C01
S1573Nr3

value: SHH

value: Female


title: SBC99 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1421, W1456)

value: metG*-pWJ445 (pTet-dCas9)

value: CRISPRi; metG* lag abx


title: IgG rep 1


title: Mouse Normal Kidney Sample 3


title: SBC98 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1421, W1455)


title: SBC129 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1434, W1458)

value: after 2-hr lag abx; 2-day semi-solid outgrowth


title: Mouse Normal Kidney Sample 1


title: Mouse Normal Kidney Sample 2


title: IGF2BP1 rep 2


title: SA1

description:
204088100026_R03C01
S1573Nr1

value: Radiotherapy

value: Chemotherapy


title: IGF2BP1 rep 1


title: TUG-4-SN

status: Public on Aug 23 2024

city: Incheon

first: TAEYOUNG

last: HA

address: 155 Gaetbeol-ro Yeonsu-gu Incheon, Korea

country: South Korea

institute: Lee Gil Ya Cancer And Diabetes Institute

data_processing:
RNA sequencing data were generated using an Illumina NovaSeq 6000 platform with paired-end reads
Quality control steps including FASTQC (version 0.11.7) and the low quality sequence reads with less than 30 PHRED score and adapter sequence reads were trimmed using a Trim Galore (version 0.38).
Alignment to the mouse genome reference (GRCm38) was performed using STAR (version 2.7.3a).
RNA abundance was estimated by as the FPKM values according to GENCODE database (version 25) using Cufflinks tool
Assembly: GRcm38
Supplementary files format and content: Excel file includes log2(FPKM+1) values for all sample
Supplementary files format and content: Excel file includes log2(FPKM+1) values for each sample

source_name: Substantianigra

extract_protocol:
Total RNA was extracted from each sample using the Qiagen Rneasy mini kit according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Kit).

value: Substantianigra

value: WT

tag: time

value: 6-OHDA intrastriatal inoculation and 10mg/kg/day TUG469 IP Injection


title: TUG-1-SN


title: Mouse Normal Kidney Sample 4

value: kidney

value: Normal kidney


title: 6OHDA-2-SN

value: 6-OHDA intrastriatal inoculation and PBS IP Injection


title: SA5

description:
204088100026_R07C01
S1573Nr5

tag: tumor grade


title: 6OHDA-3-SN

value: 6-OHDA intrastriatal inoculation and  PBS IP Injection


title: PBS3-SN

value: vehicle

value: 1x PBS intrastriatal inoculation and PBS IP Injection


title: PBS1-SN


title: TUG-2-SN


title: PBS2-SN


title: TUG-2-ST

source_name: Striatum

value: Striatum


title: 6OHDA-4-SN


title: TUG-4-ST


title: PBS2-ST


title: 6OHDA-3-ST


title: PBS1-ST


title: PBS3-ST


title: 6OHDA-2-ST


title: SBC96 version 2

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1412, W1455)

value: CRISPRi; metG* after overnight

value: after overnight (with aTc)


title: SA2

description:
204088100026_R04C01
S1573Nr2

value: Medulloblastoma tumor

tag: tumor subgroup

value: Group 3

value: Male


title: TUG-1-ST


title: Colon crypt,DSS,DSS-2

city: Foshan

first: Shaojie

last: Liang

address: No.3 Baojian road

institute: Shunde Maternal and Children’s Hospital, Guangdong Medical University

data_processing:
using fastp (v0.23.2) https://github.com/OpenGene/fastp processing fastq format of raw data, in order to obtain the clean data (the clean reads)
through the Bowtie2 (v2.4.5) https://github.com/BenLangmead/bowtie2 will clean the data than to NCBI database of ribosomes, removal of rRNA sequences.
Assembly: Reference genomes and annotated files are downloaded directly from the genome website. After removing the ribosome sequence through Hisat2 (v2.2.1) https://github.com/infphilo/hisat2 alignment to reference genome.
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel file include FPKM, values for each Sample

source_name: colon

growth_protocol: not applicable

extract_protocol:
NA extraction and purification from colonic crypts were carried out in accordance with the manufacturer’s instructions (Qiagen, Hilden, Germany)
Build the Library using the ALFA-SEQ RNA Library Prep Kit as recommended by the manufacturer and according to the accompanying instructions.

treatment_protocol: not applicable

value: colon

value: not applicable


title: Colon crypt,Control,CON-3

value: distilled water


title: Colon crypt,DSS,DSS-1

value: WT


title: Colon crypt,Control,CON-2


title: Colon crypt,Control,CON-1


title: 6OHDA-4-ST


title: M1 VLX 4

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Galaxy.
Reads were trimmed using trimmomatic. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel file with raw counts

source_name: bone marrow derived macrophages

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: M0 or M1 macrophages were treated with vehicle or VLX-1005

value: bone marrow derived macrophages

value: M1 Macrophages


title: M1 VLX 1


title: M1 Vehicle 4


title: cortex, control

city: SHANGHAI

first: MENGGE

last: SUN

address: FENGLIN ROAD

institute: FUDAN UNIVERSITY

description:
10x Genomics
scRNA sample1

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: cortex

extract_protocol:
FlashTag (CellTrace Yellow, Life Technologies, #C34567, 0.5 μl of 10 mM) was injected into the cortical lateral ventricle of control mice (Map2k1 and Map2k2 flox), Emx1-Cre; MAP2k1/2-dcko and hGFAP-Cre; MAP2k1/2-dcko mice at E18.0. P2 pups were sacrificed, and the brains were immediately removed and submerged in fresh ice-cold Hanks’ balanced salt solution (Gibco 14175-095). The dorsal cortices were cut into small pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction. The tdTomato+ (tdT+) cells were captured and harvested through fluorescence-activated cell sorting (FACS).
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Novaseq 6000.

value: cortex


title: M1 VLX 3


title: cortex, EMX-Cre_MAP2K1/2-dcko

description:
10x Genomics
scRNA sample2


title: SBC316

extract_protocol:
mini-prep
PCR to amplify crRNA sequence and add Illumina adapters (W1436, W1452)

value: hipA7-pWJ445 (pTet-dCas9)

value: hipA7 after overnight (pre-outgrowth)


title: cortex, hGFAP-Cre_MAP2K1/2-dcko

description:
10x Genomics
scRNA sample3


title: M1 Vehicle 3

value: vehicle


title: 4sU labeling, 250µM, rep1, SLAMseq

first: Jun

last: Lyu

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Raw sequencing data of SLAM-seq were first trimmed using cutadpt (v1.15) and then analyzed using SLAM-DUNK (v0.4.3) to map, filter and quantify reads containing T-to-C mutation.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files
Library strategy: SLAM-seq

source_name: lymph nodes

extract_protocol:
For single cell RNA sequencing, single cell suspension was prepared for 10X Genomics sample loading. For RNA-seq, RNA was extracted using RNeasy Mini Kit (Qiagen).
For NOTE-seq, Libraries were constructed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E) with serval additional steps detaied in the Method section. For regular 10xgenomics, libraries were constructed using  Chromium Next GEM Single Cell 3ʹ Kit v3.1 user guide (Rev E). For SLAM-seq, 2 µg RNA were combined with 10 mM iodoacetamide (Sigma-Aldrich, St. Louis, MO, USA), 50 mM sodium phosphate buffer (pH 8.0) and 50% DMSO, followed by 15 min of incubation at 50°C. The reaction was stopped by adding 20 mM DTT, followed by RNA purification using 1.8X RNA beads (Aline Bioscience) and RNA elution with 11 µl nuclease-free water. Then, 500 ng RNA was subject to library construction using Quant-seq 3′ mRNA-Seq Library Prep Kit (Lexogen)
scRNA-seq and RNA-seq

value: lymph nodes

value: T lymphocytes


title: 4sU labeling, 500µM, rep1, SLAMseq


title: 4sU labeling, 250µM, rep2, SLAMseq


title: Colon crypt,DSS,DSS-3


title: 4sU labeling, 1mM, rep2, SLAMseq


title: M1 Vehicle 2


title: 4sU labeling, 1mM, rep1, SLAMseq


title: M0 VLX 4

value: M0 macrophages


title: M0 VLX 3


title: 4sU labeling, control, rep2, SLAMseq


title: 4sU labeling, control, rep1, SLAMseq


title: M1 Vehicle 1


title: 4sU labeling, scRNA-seq, 8h

data_processing:
Raw sequencing data of scRNA-seq was subjected to fastq calling, reads alignment, and quantification using cellranger7.1.0  with default parameters and standard pipeline.
Raw sequencing data of SLAM-seq were first trimmed using cutadpt (v1.15) and then analyzed using SLAM-DUNK (v0.4.3) to map, filter and quantify reads containing T-to-C mutation.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-separate values files and matrix files


title: M0 Vehicle 4


title: 4sU labeling, scRNA-seq, 6h


title: 4sU labeling, scRNA-seq, 2h


title: M1 VLX 2


title: 4sU labeling, scRNA-seq, 4h


title: M0 VLX 1


title: 4sU labeling, scRNA-seq, 0h


title: no 4sU labeling, scRNA-seq, SNP background for mouse naïve T cell


title: M0 Vehicle 1


title: M0 VLX 2


title: VLX-1005 2

source_name: islet

treatment_protocol: Mice were treated with vehicle or 30 mg/kg VLX-1005 SDD

value: islet