title: HEK293T,MULTI,AC,H3K4ME1,BS,rep3


title: littermate control Tx-755, male, 102 days old

status: Public on Jan 10 2026

type: SRA

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

country: USA

institute: University of Iowa

description:
Library name: Control-5
Ctrl-5_755

library_source: transcriptomic

data_processing:
Data analysis was performed using Partek Flow interface (Partek, Illumina, CA)
Assembly: mm39
Supplementary files format and content: csv files include raw count for each sample

molecule: total RNA

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice were maintained on a 12h light/12h dark cycle at 22-25 C. Food and water were available ad libitum.

extract_protocol:
Total RNA was prepared using Invitrogen miRVana miRNA Isolation Kit with phenol (Thermo Fisher Scientific, #AM1560) according to manufacturer’s instructions.
Illumina Stranded mRNA Prep, Ligation.

tag: tissue

value: hippocampus

tag: genotype

value: WT

tag: batch


title: GBA IVS/+-clone1-astrocytes-R2

city: Seattle

first: Colby

last: Samstag

state: WA

address: 300 Ninth Ave

institute: University of Washington

description: Library name: Sample 17

data_processing:
Raw data was processed by Azenta’s standard bioinformatics analysis workflow.
Reads were checked for quality control and adapter sequences were trimmed using Trimmomatic v.0.36.
The resulting BAMs were used to generate hit counts using Subread v.1.5.2, with only exonic regions included for downstream RNA-seq analyses.
Assembly: Sequence data was aligned to the GRCh38 Homo Sapiens reference genome using STAR aligner v.2.5.2b.
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Homo sapiens

source_name: iPSC-astrocytes

growth_protocol: iPSC-neurons and -astrocytes were cultured 10-14 days before being pelleted and frozen prior to RNA extraction

extract_protocol:
cDNA libraries were preparation using polyA capture, and sequencing was performed on an Illumina NovaSeq X Plus using 2x150bp paired-end reads at a final read depth of ~20 million reads per sample.
RNA libraries for RNAseq were prepared by Azenta

treatment_protocol: 3 replicates (R1-3) of cell pellets of 1x10^6 of the following clones differentiated into astrocytes and neurons were submitted to Azenta RNA extraction and sequencing: GBA1IVS/+ clones #1,2,6, control GBA1+/+ clones #1,2,4, GBA1+/+ Rev isogenic control clone generated by CRISPR Cas9 editing of GBA1IVS/+ clone #1, and a matched control GBA1IVS/+ A4 clone unedited by the CRISPR Cas9 process.

tag: Sex

value: Male

value: iPSC-astrocytes

tag: cell line

value: H4997 clone 1

tag: cell type

value: astrocytes

value: GBA1 IVS/+


title: GBA IVS/+-clone1-neurons-R3

description: Library name: Sample 21

source_name: iPSC-neurons

value: iPSC-neurons

value: midbrain dopaminergic neurons


title: HEK293T,MULTI,AC,H3K4ME1,IN,rep1

city: guagnzhou

first: tang

last: guorun

address: xingang

country: China

institute: Sun Yat-sen University

library_source: genomic

data_processing:
Adapter sequences were removed using trim-galore
fastp was used to trim 10 bp from both the 5' and 3' ends
For the bisulfite-treated DNA fragments, alignment, deduplicate and  Single-base resolution methylation information extraction was performed using bismark . bismark_methylation_extractor function.
For control samples that were not subjected to BS treatment, the same workflow was preformed to obtain clean data. These data were then aligned to the reference genome using Bowtie2,dupliate reads were removed using Picard
We use MACS2 to call peak
Assembly: hg38,mm39
Supplementary files format and content: bed,cov.gz

molecule: genomic DNA

extract_protocol:
After the cells were treated according to the Cut-tag protocol, the DNA was extracted using DNA clean beads.
For 5mC-CUT&Tag, pA/G-Tn5 assembled with Tn5-P5-mC was utilized to profile various histone modifications in K562, HEK-293T, and L1210 cells. This protocol was executed using the Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903), following the manufacturer’s instructions. For 5mC-Multi-CUT&Tag, we employed anti-rabbit and anti-mouse nb-Tn5 assembled with Multi-P5-mC-1/2 to simultaneously profile multiple histone modifications in K562, HEK-293T, and L1210 cells. This process was performed using the Multi-CUT&Tag Library Prep Kit for Illumina (YEASEN, 12592ES), adhering to the provided guidelines. The 5mC-ATAC protocol was conducted in HEK-293T cells using Tn5 assembled with Tn5-P5-mC, facilitated by the ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).  In each of the methods described above, the procedures were halted prior to library PCR amplification. At this stage, 10% of the library templates were reserved for direct 3’ adaptor ligation (Vazyme, NE103) as the IN group (without bisulfite treatment). The remaining 90% of the library templates underwent bisulfite conversion (Zymo, D5030), followed by 3’ adaptor ligation, constituting the BS group (with bisulfite treatment). Additionally, 1 ng of fragmented λDNA with methylated adaptors, prepared using the NEBNext Ultra II DNA Library Prep Kit (E7645S), was spiked in with the library templates before bisulfite conversion to monitor C-to-U conversion rates.
Library PCR amplification was carried out using KAPA HiFi HotStart Uracil+ ReadyMix (KAPA, KK2801) with N5/D7 primers for 5mC-CUT&Tag and 5mC-ATAC, or Multi-P5/D7 primers for 5mC-Multi-CUT&Tag. DNA clean beads (Vazyme, N411) were employed for purification and size selection of the final library products.

tag: treatment


title: WT and KO

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: sample 1

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
For each tissue section and corresponding library, the whole slide brightfield image and CytAssist image were aligned manually using the Loupe Browser (v6.4.1) via landmark registration. Each whole slide image was uploaded to a local OMERO server where a rectangular region of interest (ROI) containing just the tissue was drawn via OMERO.web and OMETIFF images of each ROI were programmatically generated using the OMERO Python API.
FASTQ files, the image registration JSON file, and associated OMETIFF corresponding to high resolution bright field image were used for further processing, including alignment to the GRCm38-specific filtered probe set (10x Genomics Mouse Probeset v1.0.0) using the version 2.1.0 Space Ranger count pipeline (10x Genomics).
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz: cell barcode
Supplementary files format and content: features.tsv.gz: gene list
Supplementary files format and content: matrix.mtx.gz: gene by cell expression matrix file
Supplementary files format and content: tissue_hires_image.png: imaging files with high resolution
Supplementary files format and content: tissue_lowres_image.png: imaging files with low resolution
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: kidney

extract_protocol:
MFAP2+/+ and MFAP2-/- mice ischemic kidneys were quickly collected and embed in OCT. Then, immersing the OCT-embedded block in isopentane precooled with liquid nitrogen.  Four 25um sections from each tissue block were used for total RNA extraction (Qiagen), and the percentage of RNA fragments larger than 200bp as determined by Agilent TapeStation 4200 High Sensitivity DNA ScreenTape (DV200 score) was used as a measure of RNA quality.  Tissue blocks with DV200 scores above 30% were used for downstream processing; selected tissues had DV200 scores above 97%.
Briefly, 10um sections from each tissue block were placed on microscopy slides (ColorFrost Plus, Fisher) fixed with MeOH, H&E stained, then imaged in brightfield using a NanoZoomer SQ (Hamamatsu) slide scanner at 40x equivalent magnification (Protocol CG000614, 10x Genomics).  Each slide was incubated with mouse-specific probe sets provided by the manufacturer for subsequent mRNA labeling, probe transfer using the CytAssist (10x Genomics) onto one capture area of a 6.5mm x 6.5mm Visium CytAssist Slide, and subsequent library generation per the manufacturer's protocol (10x Genomics, CG000495, Rev C).  Library concentration was quantified using a Tapestation High Sensitivity DNA ScreenTape (Agilent) and fluorometry (Thermofisher Qubit) and verified via KAPA qPCR.  Libraries were pooled for sequencing on an Illumina NovaSeq X Plus 100 cycle 10B flow cell using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue (approximately 300M per tissue).

value: kidney

value: WT and KO


title: Parse combined conditions sublibrary 7

city: Ann Arbor

first: Kurt

last: Hankenson

state: MI

address: 109 Zina Pitcher Pl.

department: Department of Orthopaedic Surgery

institute: University of Michigan

description:
Library name: Sample 7
Split-pool combinatorial barcoding of all conditions

library_source: transcriptomic single cell

data_processing:
Demultiplexing and fastq generation was done via BclConvert, this generated a fastq file for each sub-library (8 sub-libraries generated).
Due to the Parse Biosciences Split Barcode Pipeline, 8 fastq files make up the entire dataset.
The Parse pipeline was run for sample/cell demultiplexing, cell assignment, gene counting.
All sample analysis was performed using the all conditions unfiltered matrix (all_unfiltered_DGE.mtx).
Assembly: Mouse mm10
Supplementary files format and content: comma separated values files (.csv)
Supplementary files format and content: matrix files (.mtx)

source_name: Fracture Callus, Periosteum

extract_protocol:
For single cell RNA sequencing, tibiae were harvested at 4 and 7 days post fracture. Fracture calluses were manually harvested via stereomicroscope dissection from mice at 4 and 7 days post fracture and digested using a shaking waterbath at 37 degrees Celsius for 30 minutes in 10 mL PBS (+Ca/+Mg) supplemented with 2 mg/mL Collagenase P, 2 mg/mL Hyaluronidase, and 200 µg/mL DNase. Periosteum was scraped prior to a 1 hour digestion. scRNAseq (Parse Biosciences pipeline) was used to characterize the transcriptomic differences in early response of Intact and Ischemic WT fracture calluses and CD47-null calluses at 4 and 7 days post fracture and baseline periosteum. For each fracture condition, we sequenced a single biological replicate made up of 8 pooled calluses (equal male/female). Periosteum consisted of 8 pooled limbs (equal male/female). Following enzymatic callus digestion, single cell suspensions were fixed using the Parse fixation kit, frozen down to -80 °C in media containing 1.6% DMSO, and subsequently submitted to the University of Michigan Advanced Genomics Core for sequencing using the Parse Biosciences pipeline.
Samples were counted using AO/PI and the LunaFx7 (Logos Bio).Samples were prepped according to manufacturer's instructions (Parse Biosciences Evercode V1). In short, individual transcriptomes are uniquely labeled by passing fixed cells or nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Round 1 does reverse transcription of the RNA and adds the first barcode. Rounds 2 and 3 ligate additional barcodes. Round 4 adds the library index, as well as the complete Illumina adapter sequences. cDNA was quantified by Qubit and assessed on TapeStation 2200 (Agilent). Final libraries were quantified by Qubit and assessed on LabChip GX Touch (Revvity).

value: Fracture Callus, Periosteum

value: WT, CD47-KO

tag: sample names

value: WT_Day_4_Bi-lateral_tibia_fracture, WT_Day_4_Ischemic_tibia_fracture, CD47_KO_Day_4_Bi-lateral_tibia_fracture, WT_Day_7_Bi-lateral_tibia_fracture, WT_Day_7_Ischemic_tibia_fracture, CD47_KO_Day_7_Bi-lateral_tibia_fracture, WT_Periosteum, CD47_KO_Periosteum


title: Control-clone3-neurons-R2

description: Library name: Sample 14

value: H1112 clone 3


title: Control-clone3-astrocytes-R1

description: Library name: Sample 10


title: Control-clone2-astrocytes-R3

description: Library name: Sample 9

value: H1112 clone 2


title: Control-clone3-astrocytes-R3

description: Library name: Sample 12


title: Control-clone2-astrocytes-R2

description: Library name: Sample 8


title: GBA IVS/+-clone1-astrocytes-R3

description: Library name: Sample 18


title: Control-clone3-astrocytes-R2

description: Library name: Sample 11


title: HEK293T,MULTI,AC,H3K4ME1,IN,rep2


title: Control-clone3-neurons-R1

description: Library name: Sample 13


title: HEK293T,MULTI,AC,H3K4ME1,BS,rep2


title: Control-clone1-neurons-R2

description: Library name: Sample 5

value: H1112 clone 1


title: K562,EX,H3K9AC,5W,IN,rep2


title: K562,EX,H3K9AC,5W,BS,spike,rep2


title: Parse combined conditions sublibrary 6

description:
Library name: Sample 6
Split-pool combinatorial barcoding of all conditions


title: Control-clone1-neurons-R1

description: Library name: Sample 4


title: Parse combined conditions sublibrary 3

description:
Library name: Sample 3
Split-pool combinatorial barcoding of all conditions


title: K562,EX,H3K9AC,5W,BS,spike,rep1


title: HEK293T,MULTI,AC,H3K4ME1,BS,rep1


title: Parse combined conditions sublibrary 2

description:
Library name: Sample 2
Split-pool combinatorial barcoding of all conditions


title: Control-clone1-neurons-R3

description: Library name: Sample 6


title: Parse combined conditions sublibrary 5

description:
Library name: Sample 5
Split-pool combinatorial barcoding of all conditions


title: male, high fat diet, sample 3

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

data_processing:
Sequenced reads were aligned to the mouse genome mm9 (NCBIv37/mm9) using Bowtie2. Duplicated reads or those that mapped to the mitochondrial genome or aligned to unmapped contiguous regions were removed. MACS2 was applied for peak calling using the option: –nomodel –keep-dup all -q 0.01 –llocal 10000. Bedgraph files were generated by HOMER. Gene annotation was performed by Homer annotation function using the genome location of peaks.
Assembly: mm9
Supplementary files format and content: bedgraph files are provided for peak visualization.
Supplementary files format and content: Bedgraph

source_name: Liver

extract_protocol:
ATAC-seq using frozen liver samples were performed using our previous optimized protocol (Zhang, Z. et al. Nat Commun, 2020). The number of nuclei in each sample was counted using Trypan Blue (Thermo Fisher) and a hemocytometer, and 75,000 nuclei were extracted and centrifuged at 500 g for 5 min at 4°C and used for the transposition reaction.
ATAC-Seq libraries were constructed using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described (Buenrostro et al., Curr Protoc Mol Biol, 2015). We performed size selection usign AMPure XP magnetic beads.

value: Liver

value: High fat diet


title: K562,EX,H3K9AC,5W,BS,rep1


title: Parse combined conditions sublibrary 1

description:
Library name: Sample 1
Split-pool combinatorial barcoding of all conditions


title: K562,EX,H3K9AC,5W,IN,rep1


title: Post15

city: Chicago

first: Lavanya

last: Visvabharathy

state: IL

address: 5812 S. Ellis Ave.

department: Surgery

institute: University of Chicago

description: Library name: Post15

data_processing:
Counts were estimated from raw reads using the nf-core rnaseq pipeline (v3.12.0) with human reference GRCh38 with GENCODE release 34.
Assembly: GRCh38 with GENCODE release 34
Supplementary files format and content: CSV files with raw counts

source_name: Blood

extract_protocol:
RNA extracted using RNEasy Mini Kit.
Stranded Total RNA-Seq Library Prep

treatment_protocol: Overnight stimulation with VZV-Orf4 peptides

value: Blood

value: CD4 memory T cells


title: Post13

description: Library name: Post13


title: Control-clone1-astrocytes-R3

description: Library name: Sample 3

value: Male

value: iPSC-astrocytes


title: Control-clone1-astrocytes-R2

description: Library name: Sample 2

value: astrocytes


title: Post16

description: Library name: Post16


title: K562,EX,H3K9AC,5W,BS,rep2


title: Post14

description: Library name: Post14


title: male, high fat diet, sample 2

value: WT


title: male, high fat diet, sample 1


title: littermate control Tx-728, male, 118 days old

description:
Library name: Control-3
Ctrl-3_728

value: hippocampus


title: male, western diet, sample 3

value: Western diet


title: Parse combined conditions sublibrary 4

description:
Library name: Sample 4
Split-pool combinatorial barcoding of all conditions


title: Post11

description: Library name: Post11


title: Post9

description: Library name: Post9


title: Post7

description: Library name: Post7


title: male, western diet, sample 2


title: K562,EX,H3K4ME1,5W,BS,spike,rep1


title: male, western diet, sample 1


title: Post10

description: Library name: Post10


title: Post8

description: Library name: Post8


title: K562,EX,H3K4ME1,5W,IN,rep1


title: K562,EX,H3K4ME1,5W,BS,spike,rep2


title: Post5

description: Library name: Post5


title: Post6

description: Library name: Post6


title: male, chow diet, sample 2

value: Chow diet


title: Post3

description: Library name: Post3


title: Post4

description: Library name: Post4


title: Post12

description: Library name: Post12


title: K562,EX,H3K4ME1,5W,IN,rep2


title: Post1

description: Library name: Post1


title: Pre16

description: Library name: Pre16


title: male, chow diet, sample 1


title: K562,EX,H3K4ME1,5W,BS,rep1


title: male, chow diet, sample 3


title: Post2

description: Library name: Post2


title: Control-clone2-astrocytes-R1

description: Library name: Sample 7


title: female, high fat diet, sample 3


title: Control-clone1-astrocytes-R1

description: Library name: Sample 1


title: K562,EX,H3K4ME3,5W,BS,spike,rep2


title: K562,EX,H3K4ME1,5W,BS,rep2


title: Pre15

description: Library name: Pre15


title: K562,EX,H3K4ME3,5W,BS,spike,rep1


title: Pre13

description: Library name: Pre13


title: Pre12

description: Library name: Pre12


title: female, high fat diet, sample 2


title: K562,EX,H3K4ME3,5W,IN,rep1


title: Pre7

description: Library name: Pre7


title: HEK293T,EX,H3K9AC,5W,BS,spike,rep3


title: female, western diet, sample 2


title: Pre6

description: Library name: Pre6


title: K562,EX,H3K4ME3,5W,IN,rep2


title: K562,EX,H3K4ME3,5W,BS,rep2


title: Pre4

description: Library name: Pre4


title: female, western diet, sample 3


title: Pre5

description: Library name: Pre5


title: Pre9

description: Library name: Pre9


title: Pre10

description: Library name: Pre10


title: Pre2

description: Library name: Pre2


title: female, chow diet, sample 3


title: Pre3

description: Library name: Pre3


title: Pre14

description: Library name: Pre14


title: Pre1

description: Library name: Pre1


title: MMOAseq_Roottip_BR3

city: Tallahassee

first: Hank

last: Bass

state: FL

address: 222 S Copeland St

department: Biological Sciences

institute: Florida State University

description:
Library name: Sample 10
MMOA-seq

data_processing:
Hi-C paired-end reads Fastq files were processed using Hi-C pro pipeline with default parameters, MMOA paired-end reads were aligned by bwa mem and resulting alignment converted into bam files.
Assembly: Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: .validPairs from Hi-C pro ; .hic for visualization with juicebox ; MMOA bigwig file for genome browser view

organism: Zea mays

source_name: 1 mm root tip (1 primary and 2 seminal roots per seedling)

growth_protocol: Hi-C: For rootip samples, seeds were imbibed overnight in sterile water at room temperature in constantly stirring, and aerated with an aquarium air pump. After imbibition, seeds were surface-sterilized with 0.5% sodium hypochlorite, 0.05% Tween-20 solution, and then rinsed 4X with water. Seeds were placed in boxes with paper towels moistened with sterile water and germinated at 28 °C for 3 days under continuous light. For Earshoot samples, field-grown maize plants were harvested in the morning, and earshoots ranging in size from 0.5-1cm were harvested. MMOA-seq: Equal numbers of seeds were planted in six such trays  with daily watering. At 2:30 PM on the 5th day after planting seedling rotttips were harvested for all replicates.

extract_protocol:
For Hi-C, approximately 1.25 million nuceli were sorted and used for library preparation. For MMOA 100,000 sorted G1 nuclei per replicate were used.
Hi-C custom protocol, using NEBNext kits, MMOA-seq library prep using NEBNext Ultra II DNA library prep Kits

treatment_protocol: Primary and seminal roots were harvested from 3 days old seedlings and fixed in 1% paraformaldehyde. Similarly, earshoot were harvested and fixed with 1% paraformaldehyde.

value: mixed population, G1

value: inbred cultivar B73


title: female, western diet, sample 1


title: female, chow diet, sample 1


title: Pre8

description: Library name: Pre8


title: HEK293T,EX,H3K9AC,5W,BS,spike,rep2


title: Pre11

description: Library name: Pre11


title: MMOAseq_Roottip_BR2

description:
Library name: Sample 9
MMOA-seq

value: 1 mm root tip (1 primary and 2 seminal roots per seedling)


title: female, high fat diet, sample 1


title: HEK293T,EX,H3K9AC,5W,BS,spike,rep1


title: HEK293T,EX,H3K9AC,5W,IN,rep3


title: Hi-C_Earshoot_BR3

description:
Library name: Sample 7
In situ Hi-C

source_name: 0.5-1 cm field-grown top most earshoot

value: 0.5-1 cm field-grown top most earshoot

value: mixed population


title: MMOAseq_Roottip_BR1

description:
Library name: Sample 8
MMOA-seq


title: l1210,MULTI,BE,BS,spike,rep2

source_name: Leukemia L1210

value: Leukemia L1210


title: female, chow diet, sample 2

value: Liver


title: K562,EX,H3K4ME3,5W,BS,rep1


title: Hi-C_Earshoot_BR1

description:
Library name: Sample 5
In situ Hi-C


title: HEK293T,EX,H3K9AC,5W,IN,rep1


title: l1210,MULTI,BE,H3K27ME3,IN,rep2


title: l1210,MULTI,BE,BS,spike,rep1


title: Hi-C_Roottip_BR2

description:
Library name: Sample 2
In situ Hi-C


title: Hi-C_Roottip_BR3

description:
Library name: Sample 3
In situ Hi-C


title: HEK293T,EX,H3K9AC,5W,IN,rep2


title: l1210,MULTI,BE,H3K27ME3,IN,rep1


title: Hi-C_Roottip_BR1

description:
Library name: Sample 1
In situ Hi-C


title: GSC08_KDM1A_KO_1

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: GSCs transduced with KDM1A gRNA

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the genes using htseq-count

source_name: patient derived glioma stem cell line

growth_protocol: Patient-derived primary GSCs were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).

extract_protocol:
Patient derived GSCs  were transduced with scramble  and KDM1A-specific gRNA.  RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from control and KDM1A knockout GSCs.

value: knockout


title: HEK293T,EX,H3K9AC,5W,BS,rep2


title: HEK293T,EX,H3K9AC,5W,BS,rep3


title: GSC08_control_1

description: GSCs transduced with scramble gRNA

value: control


title: Hi-C_Roottip_BR4

description:
Library name: Sample 4
In situ Hi-C


title: GSC08_KDM1A_KO_2

description: GSCs transduced with KDM1A gRNA


title: Hi-C_Earshoot_BR2

description:
Library name: Sample 6
In situ Hi-C


title: GSC08_control_2

description: GSCs transduced with scramble gRNA


title: l1210,MULTI,BE,H3K9ME3,IN,rep2


title: l1210,MULTI,BE,H3K27ME3,BS,rep1


title: HEK293T,EX,H3K4ME1,5W,BS,spike,rep2


title: HEK293T,EX,H3K4ME1,5W,BS,spike,rep3


title: HEK293T,EX,H3K9AC,5W,BS,rep1


title: Quiescence_8hr_ctrl_rep2

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Base calling - bcl2fastq 2
Reads were processed using slam dunk pipeline using slamdunk all with default parameters (version 0.3.3)
Genome_build: GRCh38
Supplementary_files_format_and_content: Collapsed Tcount file as described by https://t-neumann.github.io/slamdunk/docs.html#tcount-file

source_name: BJ-5Ta cells

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1% pen/step and 2 mM L-glutamine (hereafter called complete medium). All cell lines were incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted under reducing conditions in the isopropanol precipitation and RNA resuspension. RNA was then split into two, one of which was subject to thiol modification treatment with iodoacetamide.
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD was used for library preparations, with addition of UMI Second Strand Synthesis Module

treatment_protocol: For serum starvation growth conditions cells were seed one day prior to serum starvation. Cells were washed twice with PBS and the media replaced with either 10% or 0% FBS containing DMEM for 72 hours. proliferating and quiescent cells were incubated for nine hours in complete medium containing 100 µM s4U. This medium was exchanged every three hours. The chase consisted of two PBS washes and replacement of complete media supplemented with 1 mM uridine. Cells were harvested with direct application of Trizol reagent at hours 0, 2, 4 and 8 post-removal of s4U.

value: FBS -; 9 hours s4U treatment; 8 hours chase

value: quiescent fibroblast


title: l1210,MULTI,BE,H3K27ME3,BS,rep2


title: HEK293T,EX,H3K4ME1,5W,BS,spike,rep1


title: Quiescence_8hr_s4U-IAA_rep3

value: FBS -; 9 hours s4U treatment; 8 hours chase; IAA treated


title: Quiescence_8hr_s4U-IAA_rep2


title: Quiescence_4hr_s4U-IAA_rep3

value: FBS -; 9 hours s4U treatment; 4 hours chase; IAA treated


title: l1210,MULTI,BE,H3K9ME3,BS,rep2


title: Quiescence_4hr_s4U-IAA_rep2


title: Quiescence_8hr_s4U-IAA_rep1


title: Quiescence_8hr_ctrl_rep1


title: HEK293T,EX,H3K4ME1,5W,IN,rep2


title: Quiescence_4hr_ctrl_rep3

value: FBS -; 9 hours s4U treatment; 4 hours chase


title: HEK293T,EX,H3K4ME1,5W,IN,rep3


title: Quiescence_4hr_s4U-IAA_rep1


title: HEK293T,EX,H3K4ME1,5W,IN,rep1


title: Quiescence_8hr_ctrl_rep3


title: Quiescence_2hr_s4U-IAA_rep3

value: FBS -; 9 hours s4U treatment; 2 hours chase; IAA treated


title: Quiescence_2hr_s4U-IAA_rep2


title: l1210,MULTI,AE,BS,spike,rep2


title: l1210,MULTI,AE,H3K27ME3,IN,rep2


title: Quiescence_2hr_ctrl_rep3

value: FBS -; 9 hours s4U treatment; 2 hours chase


title: Quiescence_2hr_ctrl_rep1


title: HEK293T,EX,H3K4ME1,5W,BS,rep3


title: l1210,MULTI,BE,H3K9ME3,IN,rep1


title: HEK293T,EX,H3K4ME1,5W,BS,rep2


title: Quiescence_4hr_ctrl_rep1


title: Quiescence_2hr_ctrl_rep2


title: HEK293T,EX,H3K4ME1,5W,BS,rep1


title: Quiescence_0hr_s4U-IAA_rep2

value: FBS -; 9 hours s4U treatment; 0 hours chase; IAA treated


title: Quiescence_2hr_s4U-IAA_rep1


title: l1210,MULTI,AE,H3K27ME3,IN,rep1


title: l1210,MULTI,BE,H3K9ME3,BS,rep1


title: Quiescence_4hr_ctrl_rep2


title: HEK293T,EX,H3K4ME3,5W,BS,spike,rep1


title: l1210,MULTI,AE,BS,spike,rep1


title: Quiescence_0hr_ctrl_rep2

value: FBS -; 9 hours s4U treatment; 0 hours chase


title: Quiescence_0hr_s4U-IAA_rep3


title: HEK293T,EX,H3K4ME3,5W,BS,spike,rep2


title: Quiescence_0hr_ctrl_rep1


title: Quiescence_0hr_s4U-IAA_rep1


title: l1210,MULTI,AE,H3K27ME3,BS,rep1


title: Quiescence_0hr_ctrl_rep3


title: l1210,MULTI,AE,H3K4ME3,IN,rep1


title: l1210,MULTI,AE,H3K27ME3,BS,rep2


title: HEK293T,EX,H3K4ME3,2W,BS,spike,rep3


title: Proliferation_8hr_ctrl_rep3

value: FBS +; 9 hours s4U treatment; 8 hours chase

value: proliferating fibroblast


title: l1210,MULTI,AE,H3K4ME3,BS,rep1


title: l1210,MULTI,AE,H3K4ME3,IN,rep2


title: HEK293T,EX,H3K4ME3,2W,BS,spike,rep2


title: Proliferation_8hr_s4U-IAA_rep2

value: FBS +; 9 hours s4U treatment; 8 hours chase; IAA treated


title: Proliferation_8hr_s4U-IAA_rep3


title: Proliferation_4hr_s4U-IAA_rep2

value: FBS +; 9 hours s4U treatment; 4 hours chase; IAA treated


title: Proliferation_4hr_s4U-IAA_rep3


title: HEK293T,EX,H3K4ME3,2W,BS,spike,rep1


title: Proliferation_8hr_ctrl_rep1


title: Proliferation_4hr_s4U-IAA_rep1


title: l1210,EX,H3K9ME3,5W,BS,spike,rep2

value: Leukemia L1210


title: l1210,EX,H3K9ME3,5W,BS,spike,rep1


title: l1210,MULTI,AE,H3K4ME3,BS,rep2


title: HEK293T,EX,H3K4ME3,5K,BS,spike,rep3


title: l1210,EX,H3K9ME3,5W,IN,rep2


title: Proliferation_4hr_ctrl_rep1

value: FBS +; 9 hours s4U treatment; 4 hours chase


title: Proliferation_4hr_ctrl_rep2


title: HEK293T,EX,H3K4ME3,5K,BS,spike,rep2


title: HEK293T,EX,H3K4ME3,5W,IN,rep2


title: Proliferation_2hr_s4U-IAA_rep1

value: FBS +; 9 hours s4U treatment; 2 hours chase; IAA treated


title: Proliferation_2hr_ctrl_rep3

value: FBS +; 9 hours s4U treatment; 2 hours chase


title: Proliferation_2hr_s4U-IAA_rep2


title: l1210,EX,H3K9ME3,5W,BS,rep2


title: l1210,EX,H3K9ME3,5W,BS,rep1


title: Proliferation_2hr_s4U-IAA_rep3


title: HEK293T,EX,H3K4ME3,5W,BS,spike,rep3


title: Proliferation_8hr_s4U-IAA_rep1


title: Proliferation_2hr_ctrl_rep2


title: l1210,EX,H3K9ME3,5W,IN,rep1


title: Proliferation_8hr_ctrl_rep2


title: Proliferation_0hr_ctrl_rep2

value: FBS +; 9 hours s4U treatment; 0 hours chase


title: Proliferation_0hr_ctrl_rep3


title: Proliferation_0hr_s4U-IAA_rep3

value: FBS +; 9 hours s4U treatment; 0 hours chase; IAA treated


title: HEK293T,EX,H3K4ME3,5W,IN,rep1


title: HEK293T,EX,H3K4ME3,2W,IN,rep1


title: Proliferation_2hr_ctrl_rep1


title: Proliferation_0hr_s4U-IAA_rep2


title: l1210,EX,H3K27ME3,5W,IN,rep2


title: HEK293T,EX,H3K4ME3,5K,IN,rep2


title: l1210,EX,H3K27ME3,5W,BS,spike,rep1


title: l1210,EX,H3K27ME3,5W,BS,rep2


title: Quiescence_rep2

data_processing:
Base calling - bcl2fastq 2
Alignment - hisat2 genocode v28
Samtools
Counts obtained - featureCounts
Expression data was normalized using the VOOM function in the Limma package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM

extract_protocol:
Cells were lysed directly in Trizol followed by acid-phenol extraction
rRNA was depleted using NEXTFLEX® Poly(A) Beads. Biooscientific’s NEXTflex Rapid Directional qRNAseq kit was used to generate libraries according to manufacturer’s instructions

treatment_protocol: For serum starvation growth conditions cells were seed one day prior to serum starvation. Cells were washed twice with PBS and the media replaced with either 10% or 0% FBS containing DMEM for 72 hours.

value: fibroblast

value: 72 hours FBS-


title: l1210,EX,H3K27ME3,5W,BS,rep1


title: l1210,EX,H3K27ME3,5W,IN,rep1


title: Proliferation_0hr_ctrl_rep1


title: Proliferation_0hr_s4U-IAA_rep1


title: HEK293T,EX,H3K4ME3,2W,IN,rep2


title: HEK293T,EX,H3K4ME3,5K,IN,rep3


title: HEK293T,EX,H3K4ME3,2W,IN,rep3


title: Quiescence_rep1


title: Quiescence_rep3


title: PLC/PFR/5_siRNA-NC_2

type: RNA

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

institute: Tongji Hospital

description: Control Group

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: PLC/PRF/5 cells were cultured in six well plates and incubated in a 37 °C, 5% CO2 humidified incubator.

extract_protocol: 48h after transient introduction of si-PPT1 or siRNA-NC, total RNA was extracted and purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Each well of PLC/PRF/5 cells in six well plates was transfected by 7 nmol si-PPT1 or the control siRNA-NC using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer’s instructions.

value: hepatoma cell line

value: transfected with siRNA-NC


title: Proliferation_rep3

value: 72 hours FBS+


title: l1210,EX,H3K4ME3,5W,BS,spike,rep2


title: HEK293T,EX,H3K4ME3,5W,BS,rep3


title: Proliferation_rep2


title: PLC/PFR/5_siRNA-NC_3

description: Control Group


title: HEK293T,EX,H3K4ME3,5K,IN,rep1


title: HEK293T,EX,H3K4ME3,5W,BS,rep2


title: HEK293T,EX,H3K4ME3,2W,BS,rep3


title: PLC/PFR/5_si-PPT1-1_2

description: Experimental Group

value: transfected with si-PPT1 -1


title: l1210,EX,H3K4ME3,5W,BS,spike,rep1


title: PLC/PFR/5_si-PPT1-1_3

description: Experimental Group


title: PLC/PFR/5_siRNA-NC_1

description: Control Group


title: Proliferation_rep1


title: l1210,EX,H3K4ME3,5W,IN,rep2


title: Maze_CocSA_TRAP_Q

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Differential expression was conducted using the DESeq2 package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files
Library strategy: TRAP-seq

source_name: Brain

extract_protocol:
TRAP was conducted as previously described (Eagle et al., 2020). Polyribosome-associated RNA was affinity purified by homogenizing vHPC tissue in ice-cold tissue-lysis buffer (20mM HEPES [pH 7.4], 150mM KCl, 10mM MgCl2, 0.5mM dithiothreitol, 100 μg/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors) using a motor-driven Teflon glass homogenizer. Homogenates were centrifuged for 10 min at 2000×g (4 °C), supernatant was supplemented with 1% NP-40 (AG Scientific, #P1505) and 30mM DHPC (Avanti Polar Lipids, #850306P), and centrifuged again for 10 min at 20,000 × g (4 °C). Supernatant was collected and incubated with Streptavidin MyOne T1 Dynabeads (Invitrogen, #65601) that were coated with anti-GFP antibodies (Memorial Sloan-Kettering Monoclonal Antibody Facility; clone names: Htz-GFP-19F7 and Htz-GFP-19C8, 50 μg per antibody per sample) using recombinant biotinylated Protein L (Thermo Fisher Scientific, #29997) for 16–18 h on a rotator (4 °C) in low salt buffer (20mM HEPES [pH 7.4], 350mM KCl, 1% NP-40, 0.5mM dithiothreitol, 100 μg/ml cycloheximide). Beads were isolated and washed with high-salt buffer (20mM HEPES [pH 7.4], 350mM KCl, 1% NP-40, 0.5mM dithiothreitol, 100 μg/ml cycloheximide) and RNA was purified using the RNeasy MicroKit (Qiagen, #74004). In order to increase yield, each RNA sample was initially passed through the Qiagen MinElute™ column three times. Following purification, RNA was quantified using a Qubit fluorometer (Invitrogen) and RNA quality was analyzed using a 4200 Agilent Tapestation (Agilent Technologies).
cDNA libraries from 5 ng total RNA were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Takara Bio USA, #635005), according to manufacturer’s instructions. cDNA libraries were pooled following Qubit measurement and TapeStation analysis, with a final concentration of 4 nM.

value: Brain

tag: region

value: Ventral hippocampus

value: Coc


title: HEK293T,EX,H3K4ME3,2W,BS,rep2


title: Maze_CocSA_TRAP_P

value: Sal


title: Maze_CocSA_TRAP_R

value: CocFlox


title: l1210,EX,H3K4ME3,5W,BS,rep2

value: Leukemia L1210


title: RNA seq of normal-3 Rattus norvegicus

city: Nanjing

first: Mengchi

last: Yu

address: No. 300 Guangzhou Road, Gulou District

institute: The First Affiliated Hospital of Nanjing Medical University

description: Library name: normal-3 Rattus norvegicus

data_processing:
Raw sequencing data were first filtered using Trimmomatic (v0.39) to remove adapter sequences, low-quality reads (Phred quality score < 20), and reads with length < 50 bp to obtain clean reads. The clean reads were then aligned to the reference genome using Hisat2 (v2.2.1) with default parameters. After alignment, featureCounts (v2.0.3) was used to quantify the gene expression levels as raw read counts. The raw counts were normalized to fragments per kilobase of transcript per million mapped reads (FPKM) using DESeq2 (v1.36.0) for subsequent differential expression analysis. Principal component analysis (PCA) and quality control of mapped reads (mapping rate, uniquely mapped rate) were performed to ensure the reliability of the sequencing data.
Assembly: The rat reference genome used for read alignment and annotation was Rnor_6.0 (GCA_000001895.4), which was downloaded from the Ensembl database (https://www.ensembl.org/Rattus_norvegicus/Info/Index).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: brain tissues

extract_protocol:
Total RNA was extracted from rat brain tissues using the TRIzol® Reagent (Invitrogen, USA) following the manufacturer's standard protocol. The purity, integrity, and concentration of the extracted RNA were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Only RNA samples with an RNA Integrity Number (RIN) ≥ 8.0 and A260/A280 ratio between 1.8 and 2.1 were selected for subsequent experiments.
RNA-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the kit instructions. Briefly, poly(A)-tailed mRNA was enriched from total RNA using oligo(dT) magnetic beads, then fragmented into short segments (approximately 200 bp) under elevated temperature. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis with DNA polymerase I and RNase H. The cDNA fragments were then subjected to end repair, adenylation of 3' ends, and ligation of Illumina sequencing adapters. Finally, the ligation products were purified and amplified by PCR to generate the final cDNA libraries.

value: brain tissues


title: HEK293T,EX,H3K4ME3,5W,BS,rep1


title: RNA seq of normal-2 Rattus norvegicus

description: Library name: normal-2 Rattus norvegicus


title: Proliferation_4hr_ctrl_rep3

value: FBS +; 9 hours s4U treatment; 4 hours chase

value: proliferating fibroblast


title: l1210,EX,H3K4ME3,5W,BS,rep1


title: HEK293T,EX,H3K4ME3,5K,BS,spike,rep1


title: GSC08_NCD38+TMZ_2

description: GSCs treated with NCD38 and TMZ combination

extract_protocol:
Patient derived GSCs  were treated with vehicle or NCD38 (3 µM) or TMZ (50 µM) or NCD38+TMZ for 24 hours. RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from GSCs treated with vehicle or NCD38 (3 µM) or TMZ (50 µM) or NCD38+TMZ for 24 hours.

value: NCD38 and TMZ combination


title: PLC/PFR/5_si-PPT1-1_1

description: Experimental Group


title: l1210,EX,H3K4ME3,5W,IN,rep1


title: RNA seq of EAP-2 Rattus norvegicus

description: Library name: EAP-2 Rattus norvegicus


title: Maze_CocSA_TRAP_O


title: RNA seq of normal-1 Rattus norvegicus

description: Library name: normal-1 Rattus norvegicus


title: HEK293T,EX,H3K4ME3,5K,BS,rep1


title: GSC_082209

description: glioma stem cells established from glioblastoma tumor tissue

source_name: patient derived glioma stem cells

extract_protocol:
RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from GSC082209 cells.

value: tumor


title: Lung cells from Sting-deficient mice treated with HCQ

city: Tokyo

first: Hideo

last: Negishi

address: 4-6-1 Shirokanedai, Minato-ku

department: Vaccine Science

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Library name: Lung_StingKO_HCQ

data_processing:
The resulting scRNA-seq reads underwent processing via the CellRanger pipeline (ver. 7.2.0) against the refdata-gex-mm10-2020-A reference genome in 3’ v3 chemistry mode (10x Genomics, Pleasanton, CA, USA).
Assembly: mm10
Supplementary files format and content: Run summary metrics files of the "cellranger count" command in CSV format
Supplementary files format and content: HDF5 files containing matrix files of UMI counts per feature-barcode pair for all cells, including those that did not pass the filter
Supplementary files format and content: HDF5 files containing matrix files of UMI counts per feature-barcode pair for cells that passed the filter

source_name: Lung

extract_protocol:
Lungs were harvested on day 3, lung cells were isolated using the gentleMACS Dissociator (Miltenyi Biotec) according to the manufacturer’s standard protocol.
Sequencing was performed in paired-end mode (read1: 28 bp; read2: 90 bp) using a DNBSEQ-G400 sequencer (MGI Tech, Shenzhen, China).

value: Lung

value: Sting-/-

value: HCQ

tag: strain

tag: time

value: day 3


title: HEK293T,EX,H3K4ME3,2W,BS,rep1


title: Maze_CocSA_TRAP_L


title: HEK293T,EX,H3K4ME3,5K,BS,rep3


title: Maze_CocSA_TRAP_M


title: HEK293T,EX,H3K4ME3,1W,BS,spike,rep2


title: GSC08_TMZ_1

description: GSCs treated with Temozolomide

value: Temozolomide


title: HEK293T,EX,H3K4ME3,1W,BS,spike,rep1


title: RNA seq of EAP-1 Rattus norvegicus

description: Library name: EAP-1 Rattus norvegicus


title: HEK293T,EX,H3K4ME3,1W,IN,rep2


title: RNA seq of EAP-3 Rattus norvegicus

description: Library name: EAP-3 Rattus norvegicus


title: Maze_CocSA_TRAP_N


title: HEK293T,EX,H3K4ME3,5K,BS,rep2


title: Lung cells from WT mice treated with HCQ

description: Library name: Lung_WT_HCQ

value: WT


title: Maze_CocSA_TRAP_I

value: Brain


title: GSC08_TMZ_2

description: GSCs treated with Temozolomide


title: Maze_CocSA_TRAP_J

value: Ventral hippocampus


title: GSC08_NCD38_1

description: GSCs treated with KDM1A inhibitor NCD38

value: KDM1A inhibitor NCD38


title: GSC08_NCD38_2

description: GSCs treated with KDM1A inhibitor NCD38


title: HEK293T,EX,H3K4ME3,1W,IN,rep1


title: Maze_CocSA_TRAP_K

value: Coc


title: GSC08_NCD38+TMZ_1


title: Maze_CocSA_TRAP_H


title: Lung cells from WT mice treated with water (control)

description: Library name: Lung_WT_control

value: water


title: HEK293T,EX,H3K4ME3,1W,BS,rep2


title: GSC08_Vehicle_2

description: GSCs treated with vehicle

value: Vehicle


title: GM-BMCs treated with cGAMP (5 μg/ml)

description: Library name: GMBMC_cGAMP_5ugml

source_name: GM-CSF cultured bone marrow cells

extract_protocol:
Bone marrow cells were isolated from the legs of mice and cultured in RPMI 1640 (Nacalai Tesque, Kyoto, Japan) containing 10% foetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA) and 10 ng/ml of GM-CSF (PeproTech, Cranbury, NJ, USA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA) before culture. After 4 days, additional GM-CSF (10 ng/ml) was added and used for the experiment on days 6–7. GM-BMCs were treated with HCQ (100 μM) or cGAMP (5 μg/ml) for 6 h.
Sequencing was performed in paired-end mode (read1: 28 bp; read2: 100 bp) using a DNBSEQ-G400 sequencer (MGI Tech, Shenzhen, China).

value: GM-CSF cultured bone marrow cells

value: cGAMP


title: GM-BMCs treated with HCQ (100 μM)

description: Library name: GMBMC_HCQ_100uM


title: Maze_CocSA_TRAP_G

value: Sal


title: HEK293T,EX,H3K4ME3,1W,BS,rep1


title: GSC08_Vehicle_1

description: GSCs treated with vehicle


title: ALDH4A1 S352L 802-30F Homozygous knock-in iPSCs Replicate 3

status: Public on Jan 09 2026

city: Stanford

first: Benjamin

middle: R

last: Kraemer

address: 736 Serra Street

institute: Stanford University

description:
Library name: B3
Column name in raw_counts_all and normalized_counts: B3

data_processing:
Genewiz Azenta performed the data analysis using their standard operating procedures and assessed quality with their FastQC protocol. Quality scores for two reads were calculated for each base and the GC content was assessed for each read.  Read count extraction and normalization were performed by Azenta.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: normalized_counts includes normalized counts for each sample
Supplementary files format and content: raw_counts_all includes raw counts for each sample

growth_protocol: Cells were maintained in mTeSR Plus media (Stemcell Technologies, catalogue number 100-0276) and passaged using accutase (Stemcell Technologies, catalogue number 07920). When passaged, wells were coated with 0.25 µg/cm2 iMatrix-511 (Reprocell, catalogue number NP892-011) and 10 µM Y27632 ROCK inhibitor (Reprocell, catalogue number 04-0012).

extract_protocol:
Cell pellets snap frozen and transferred to Genewiz Azenta and RNA was extracted following their standard operating procedures.
RNA libraries for RNA-seq were prepared Azenta following their established protocols.

treatment_protocol: No treatments used.

value: Induced pluripotent stem cell

value: ALDH4A1 S352L homozygote

value: Basal conditions


title: ALDH4A1 S352L 802-30F Homozygous knock-in iPSCs Replicate 1

description:
Library name: B1
Column name in raw_counts_all and normalized_counts: B1


title: ALDH4A1 S352L 802-30F Homozygous knock-in iPSCs Replicate 2

description:
Library name: B2
Column name in raw_counts_all and normalized_counts: B2


title: HEK293T,NLS,ribominus,C1

city: Houston

first: Surbhi

last: Sharma

address: 1840, Dynamic way

institute: Baylor College of Medicine

description: Library name: NLS Ribominus Control 1

data_processing:
The RNA-seq reads were first trimmed using trimmomatic to remove the barcode and primer sequences using the following commnad:perl trimming.pl -1 "${R1_fastq}" -2 "${R2_fastq}" -p "${R1_trim_fastq}" -q "${R2_trim_fastq}" -a adapter.fa -l 0 -t 0 -m 36
The trimmed reads were mapped to GRCh38 using STAR (Dobin et al. 2013) with GRCh38.p13 from the Ensembl release 104 genome annotations. The following command was used for mapping:STAR --genomeDir "${GENOMEDIR}/star" --runThreadN 8 --readFilesIn "${R1_trim_fastq}" "${R2_trim_fastq}" --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 1 --outFileNamePrefix "${bam_prefix}"
The mapped reads were counted using HTSeq (Anders, Pyl, and Huber 2015):python -m HTSeq.scripts.count --stranded=reverse --nonunique=all --format=bam --order=pos --idattr=gene_id "${bam}" "${hg38_gtf}" > "${counts_txt}"
The mapped data were visualized using the UCSC Genome Browser (Karolchik, Hinrichs, and Kent 2009). To generate genome tracks, samtools was used to convert each SAM file into stranded BAM files. These BAM files were subsequently used to produce bedGraph files using BEDTools: bedtools genomecov -bg -split -ibam "${bam}" > "${bedGraph}"
Assembly: hg38
Supplementary files format and content: The text files contain DESeq2 (Love, Huber, and Anders 2014) log2fold changes and P adjusted values or count data derived from STAR and HTSeq.

source_name: Cell line

growth_protocol: HEK293T cells expressing APEX2 were maintained in DMEM media supplemented with 10% (v/v) FBS, 1% (v/v) penicillin-streptomycin at 37oC in humidified chamber with 5%CO2.

extract_protocol:
Total RNA from cells was extracted using RNeasy Plus Mini Kit (Qiagen), replacing RW1 buffer with RWT for the column wash.
RNA-seq libraries were prepared using Smarter® Stranded Total RNA-Seq Kit v2 for NLS and TruSeq Stranded mRNA Library Prep for OMM derived samples.

value: Cell line

value: Human embryonic kidney


title: WT 802-30F iPSCs Replicate 1

description:
Library name: A1
Column name in raw_counts_all and normalized_counts: A1


title: HEK293T,NLS,ribominus,C2

description: Library name: NLS Ribominus Control 2


title: WT 802-30F iPSCs Replicate 3

description:
Library name: A3
Column name in raw_counts_all and normalized_counts: A3


title: WT 802-30F iPSCs Replicate 2

description:
Library name: A2
Column name in raw_counts_all and normalized_counts: A2


title: HEK293T,NLS,ribominus,T1

description: Library name: NLS Ribominus Target 1


title: 8814

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
raw mRNA sequencing data were processed using MAP-Rse2 configured to use the hg38 genome and Ensemble version 78 transcriptome to produce gene-level raw read count data.  For unsupervised differential expression analysis, data were input into edgeR and log2-transformed, and normalized read count data were extracted for analysis.
Assembly: hg38
Supplementary files format and content: Tab-delimited file of raw count data

source_name: ALCL tumors

extract_protocol:
RNA was extracted using Qiagen AllPrep per manufacturer instructions from formalin-fixed, paraffin-embedded (FFPE) tissue sections, using macrodissection when needed to enrich for tumor content.  RNA was analyzed on an Agilent Bioanalyzer.
Libraries were constructed from 400 ng RNA and sequenced as 150 bp paired-end reads on an Illumina 4000.  Cases meeting the following 5 criteria were included in the sequenced cohort: (1) adequate tissue for extraction; (2) tumor content ≥50%; (3) adequate extracted RNA; (4) RNA DV200 ≥20%; and (5) adequate sequencing data quality.

value: ALCL tumors

tag: who classification

value: ALCLNEG

tag: alcl genetics

value: TN

tag: pstat3 status

value: positive


title: 8822

value: negative


title: 8813


title: 8817

value: BIAALCL


title: 8818


title: 8793

value: ALCLPOS

value: ALK


title: 8810


title: 8824


title: 8812


title: 8735

value: CUTALCL

value: DH


title: 8734


title: 8828


title: 8809


title: 8833


title: 8733


title: HEK293T,NLS,ribominus,T2

description: Library name: NLS Ribominus Target 2


title: 8736


title: 8815


title: 8792


title: 8723


title: 8726


title: l1210,EX,H3K27ME3,5W,BS,spike,rep2

extract_protocol:
After the cells were treated according to the Cut-tag protocol, the DNA was extracted using DNA clean beads.
For 5mC-CUT&Tag, pA/G-Tn5 assembled with Tn5-P5-mC was utilized to profile various histone modifications in K562, HEK-293T, and L1210 cells. This protocol was executed using the Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903), following the manufacturer’s instructions. For 5mC-Multi-CUT&Tag, we employed anti-rabbit and anti-mouse nb-Tn5 assembled with Multi-P5-mC-1/2 to simultaneously profile multiple histone modifications in K562, HEK-293T, and L1210 cells. This process was performed using the Multi-CUT&Tag Library Prep Kit for Illumina (YEASEN, 12592ES), adhering to the provided guidelines. The 5mC-ATAC protocol was conducted in HEK-293T cells using Tn5 assembled with Tn5-P5-mC, facilitated by the ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).  In each of the methods described above, the procedures were halted prior to library PCR amplification. At this stage, 10% of the library templates were reserved for direct 3’ adaptor ligation (Vazyme, NE103) as the IN group (without bisulfite treatment). The remaining 90% of the library templates underwent bisulfite conversion (Zymo, D5030), followed by 3’ adaptor ligation, constituting the BS group (with bisulfite treatment). Additionally, 1 ng of fragmented λDNA with methylated adaptors, prepared using the NEBNext Ultra II DNA Library Prep Kit (E7645S), was spiked in with the library templates before bisulfite conversion to monitor C-to-U conversion rates.
Library PCR amplification was carried out using KAPA HiFi HotStart Uracil+ ReadyMix (KAPA, KK2801) with N5/D7 primers for 5mC-CUT&Tag and 5mC-ATAC, or Multi-P5/D7 primers for 5mC-Multi-CUT&Tag. DNA clean beads (Vazyme, N411) were employed for purification and size selection of the final library products.

value: Leukemia L1210


title: 8718


title: 8698


title: 8788


title: 8586


title: 8571


title: 8576


title: 8502


title: 8520


title: 8493


title: 8499


title: 8644


title: 8719


title: 8668


title: 8639


title: 8497


title: 8490


title: 8503


title: 8495


title: 8501


title: 8645


title: 8500


title: 8481


title: 8488


title: 8480


title: 8186


title: 8492


title: 8479


title: 8183


title: 8583


title: 8099


title: 8184


title: 8004


title: 8147


title: 8112


title: 8504


title: 8129


title: 7970


title: 8470


title: 8100


title: 8143


title: 8355


title: 8458


title: 8142


title: 7955


title: 7936


title: 8044


title: 7940


title: 7927


title: 7910


title: 7929


title: 7900


title: 7905


title: 7886


title: 7890


title: 7966


title: 7874


title: 7797


title: 7794


title: 7791


title: 7773


title: 7796


title: 7756


title: 7749


title: 7752


title: 7792


title: 7793


title: 7774


title: 7755


title: 7877


title: 7781


title: 7875


title: 7748


title: 7750


title: 7746


title: 7747


title: 7790


title: HEK293T,EX,H3K4ME3,5W,IN,rep3


title: 7696


title: 7684


title: 7682


title: 7676


title: 7680


title: 7672


title: 7675


title: 7667


title: 7666


title: 7665


title: 7697


title: 7602


title: 7622


title: 7566


title: 7579


title: 7594


title: 7590


title: 7598


title: 7593


title: 7592


title: 7552


title: 7576


title: 7560


title: 7549


title: 7547


title: 7545


title: 7554


title: 7548


title: 7575


title: 7551


title: 7628


title: 7604


title: 7543


title: 7524


title: 7527


title: 7636


title: 7521


title: 7523


title: 7522


title: 7534


title: 7515


title: 7559


title: 7519


title: 7505


title: 7501


title: 7491


title: 7508


title: 7518


title: 7494


title: 7493


title: 7487


title: 7096


title: 7496


title: 7517


title: 7178


title: 7506


title: 7488


title: 6749


title: 7492


title: 7095


title: 6696


title: 6746


title: 6981


title: 7075


title: 7512


title: 7249


title: 7014


title: 6577


title: 6547


title: 6511


title: 6807


title: 6778


title: 7207


title: 6434


title: 5131


title: 6362


title: 6941


title: 6347


title: 6192


title: 6766


title: 6728


title: 6172


title: 6142


title: 6167


title: 6146


title: 6420


title: 6016


title: 6389


title: 6351


title: 6754


title: 6484


title: 5770


title: 5773


title: 5816


title: 5827


title: 5766


title: 5996


title: 6049


title: 5769


title: 5767


title: 5764


title: 6115


title: 6549


title: 6002


title: 5947


title: 5763


title: 6087


title: 5838


title: 6133


title: 5744


title: 6017


title: 5946


title: 5865


title: 5749


title: 6102


title: 5752


title: 5741


title: 6015


title: 5756


title: 5739


title: 5746


title: 5757


title: 5730


title: 5737


title: 5714


title: 5669


title: 5659


title: 5657


title: 5667


title: 5728


title: 5656


title: 5709


title: 5653


title: 5651


title: 5701


title: 5655


title: 5638


title: 5710


title: 5700


title: 5649


title: 5650


title: 5640


title: 5637


title: 5566


title: 5648


title: 5624


title: 5606


title: 5428


title: 5447


title: 5459


title: 5552


title: 5423


title: 5627


title: 5479


title: 5427


title: 5422


title: 5429


title: 5499


title: 5645


title: 5290


title: 5269


title: 5272


title: 5504


title: 5082


title: 5270


title: 5420


title: 5416


title: 5418


title: 5299


title: 4839


title: 4891


title: 4773


title: 5407


title: 4342


title: 4861


title: 4640


title: 4404


title: 5268


title: 5283


title: 4876


title: 5023


title: 4157


title: 5421


title: 4992


title: 5619


title: 4144


title: 4192


title: 4809


title: 4154


title: 4197


title: 3941


title: 3950


title: 3900


title: 4828


title: 3909


title: 4297


title: 4367


title: 3808


title: 3552


title: 3551


title: 3535


title: Induced cortical neurons, TDP-43 CRISPRi, replicate 2

first: Oliver

middle: H

last: Tam

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

description: Library name: i3N_noAza_TDP43KD_rep2

data_processing:
Reads were aligned to the hg38 human genome using STAR v2.7.6, allowing up to 100 alignments per read to capture transposon sequences. Abundance of gene and transposon reads was calculated with TEtranscripts v2.2.3.
Assembly: hg38
Supplementary files format and content: Count table with features (gene/TE) as rows, and samples as columns

source_name: KOLF2.1J -derived

growth_protocol: A previously engineered CRISPRi-i3N-KOLF2.J1 iPSC line, obtained from The Jackson Laboratory (a gift from the NIH/INDi Consortium), was used for cortical neuron differentiation with minor modifications. This line expresses human NGN2 under a doxycycline-inducible promoter (2 µg/mL) and constitutively expresses a dCas9-BFP-KRAB CRISPRi construct. Prior to differentiation, iPSCs received lentiviral particles encoding either non-targeting (NT) or TDP-43-targeting sgRNAs. The Lentiblast™ transduction enhancer (1:1000; OZ Biosciences, Cat. no. LBPX1500) was added to improve transduction efficiency. Forty-eight hours post-transduction, transduced cells were selected with 2 µg/mL puromycin (InvivoGen, Cat. no. ant-pr-1) for five days. The resulting stable cell pools were expanded before initiating differentiation. To initiate differentiation, 7 × 10⁶ cells from the stable pools were dissociated using accutase (Innovative Cell Technologies, Inc., Cat. no. AT104), and seeded into AggreWell™800 plates (STEMCELL Technologies, Cat. no. 34815) using differentiation medium consisting of Neurobasal™ Plus Medium (Thermo Fisher Scientific, cat. no. A3582901), GlutaMAX™ (Thermo Fisher Scientific, cat. no. 35050061), BDNF (10 ng/mL; Thermo Fisher Scientific, cat. no. 450-02), NT-3 (10 ng/mL; Thermo Fisher Scientific, Cat. no. 450-03), doxycycline (2 µg/mL; Thermo Fisher Scientific, Cat.no.J67043.AD), and Gem21 NeuroPlex™ (without Vitamin A; Gemini Bio, Cat. no. 400-161-010), supplemented with 1X RevitaCell™ (Thermo Fisher Scientific, Cat. no. A2644501), to form spheroids98. After 24 hours, cell media was switched to fresh medium lacking RevitaCell, and changed daily. On day 8, neuronal spheroids were transferred and plated onto culture plates pre-coated with Geltrex™ (1:100; Thermo Fisher Scientific, Cat. no. A1413302) and Cultrex™ Stem Cell Qualified Laminin I (5 µg/mL; Bio-Techne, Cat. no. 3400-010-03).

extract_protocol:
RNA was extracted and purified from cultured cells using the Direct-zol™ RNA Miniprep Plus (R2071, Zymo Research, Irvine, CA, USA). RNA concentration was determined with the Qubit RNA BR Assay Kit (Q10210, ThermoFisher Scientific, Waltham, MA, USA) and Qubit 4 Fluorometer (Q33226, ThermoFisher Scientific, Waltham, MA, USA). RNA quality was assessed using the RNA 6000 Nano (5067-1511, Agilent, Santa Clara, CA, USA) on the Agilent 2100 Bioanalyzer (G2939BA, Agilent, Santa Clara, CA, USA).
RNA-seq libraries were prepared from 1000 ng of total RNA subjected to rRNA depletion with the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (E7405L, New England Biosciences, Ipswich, MA, USA). Strand specific library preparation was performed using the NEBNext II Ultra Directional Library Prep Kit (E7760S, New England Biosciences, Ipswich, MA, USA)

treatment_protocol: After overnight attachment, fresh medium was added, supplemented with 5 µM 5-Azacytidine, and the cells were incubated for 72 hours. Neuronal cultures were maintained in differentiation medium ± 5-azacytidine and harvested for analysis on either day 12 or day 15, depending on the specific downstream application.

value: KOLF2.1J -derived

value: induced cortical neurons (i3N)

value: TDP-43 CRISPRi


title: 3531


title: 3642


title: 3558


title: 3570


title: 3439


title: 3444


title: 3599


title: 3458


title: 3879


title: Induced cortical neurons, control, replicate 1

description: Library name: i3N_noAza_Ctrl_rep1

value: Control


title: 3374


title: Induced cortical neurons, 5-Azacytidine + TDP-43 CRISPRi, replicate 1

description: Library name: i3N_5Aza_TDP43KD_rep1

value: 5-Azacytidine & TDP-43 CRISPRi


title: 3366


title: 3556


title: Induced cortical neurons, control, replicate 2

description: Library name: i3N_noAza_Ctrl_rep2


title: Induced cortical neurons, TDP-43 CRISPRi, replicate 1

description: Library name: i3N_noAza_TDP43KD_rep1


title: 3453


title: Induced cortical neurons, 5-Azacytidine + TDP-43 CRISPRi, replicate 2

description: Library name: i3N_5Aza_TDP43KD_rep2


title: Induced cortical neurons, 5-Azacytidine, replicate 2

description: Library name: i3N_5Aza_Ctrl_rep2


title: 3363


title: 3560


title: 3644


title: CGND-HRA-03662 Ctrl Isoseq

description:
Library name: NYGC_Control_03662
CTL_03662_clustered_hg38_minimap2

data_processing:
Circular consensus sequencing reads were generated from PacBio sequencing output using the CCS algorithm (version 8, Pacific Biosciences). Libraries were demultiplexed, refined and clustered using IsoSeq toolkit (version 4.0.0). FASTA files were generated and aligned to the hg38 genome using minimap2104 (version 2.24) with splice:hq preset (-x splice:hq) and GT-AG search on the transcript strand (-u f). Transcript discovery and quantification was performed using bambu105 (version 3.2.6), with the GENCODE106 gene annotation (version 47) as reference.
Assembly: hg38
Supplementary files format and content: Count table of detected genes in isoseq library
Supplementary files format and content: Count table of detected transcripts in isoseq library
Supplementary files format and content: Count table of "full length" transcripts in isoseq library
Supplementary files format and content: Count table of uniquely aligned transcripts in isoseq library
Supplementary files format and content: Counts per million reads of detected transcripts in isoseq library
Supplementary files format and content: GTF of detected transcripts

extract_protocol:
RNA was extracted and purified from cultured cells using the Direct-zol™ RNA Miniprep Plus (R2071, Zymo Research, Irvine, CA, USA). RNA concentration was determined with the Qubit RNA BR Assay Kit (Q10210, ThermoFisher Scientific, Waltham, MA, USA) and Qubit 4 Fluorometer (Q33226, ThermoFisher Scientific, Waltham, MA, USA). RNA quality was assessed using the RNA 6000 Nano (5067-1511, Agilent, Santa Clara, CA, USA) on the Agilent 2100 Bioanalyzer (G2939BA, Agilent, Santa Clara, CA, USA).
CrypTE-seq read libraries were prepared from ~300ng total RNA per sample following a modified PacBio Iso-Seq v2 library protocol (103-071-500, PacBio, Menlo Park, CA, USA) and pooled using the SMRTbell Prep Kit 3.0 (102-182-700, PacBio, Menlo Park, CA, USA). Modifications include the use of post-primer annealing with first strand cDNA synthesis performed with MarathonRT (200035, RNAConnect, Branford, CT, USA) followed by Iso-seq RT and then addition of the template switch oligo. All other steps followed the Iso-seq v2 library protocol (103-071-500, PacBio, Menlo Park, CA, USA).

tag: diagnosis


title: 5031


title: CGND-HRA-03374 Ctrl isoseq

description:
Library name: NYGC_Control_03374
CTL_03374_clustered_hg38_minimap2


title: Induced cortical neurons, 5-Azacytidine, replicate 1

description: Library name: i3N_5Aza_Ctrl_rep1


title: 3342


title: 3346


title: 3343


title: 3332


title: 3359


title: CGND-HRA-02988 ALS-CI isoseq

description:
Library name: NYGC_ALS-ci_02988
ALS-ci_02988_clustered_hg38_minimap2

value: ALS + cognitive impairment


title: 3351

value: ALCL tumors


title: 3348


title: 3129

value: ALCLNEG


title: WT [BEC1]

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: BEC1

data_processing:
Raw sequencing data were aligned to the Drosophila melanogaster reference genome (BDGP6.32, Ensembl release 104) using 10x Genomics Cell Ranger v7.0.0.
The count matrices were imported into Seurat (v4.3.0) and cells with less than 1300 or greater than 60,000 UMIs were filtered out, and low abundance genes with less than 10 counts were removed from further analysis.
Cell types were manually annotated using the top marker genes from each cluster, using Gal4 expression patterns to validate marker gene expression patterns.
Assembly: BDGP6.32
Supplementary files format and content: "FC_08073.mat.csv": csv file, expression matrix of raw counts
Supplementary files format and content: "FC_08073.meta.csv": csv file, metadata file about cell type and sample

organism: Drosophila melanogaster

source_name: proventriculus

growth_protocol: Flies were raised at 18ºC on standard lab food and conditions until 2-3 days post eclosion, then temperature shifted to 29ºC for 8-9 days to activate Gal4 expression prior to dissection. All samples are mated females.

extract_protocol:
Single-nucleus suspension was conducted as described by Li et 2022. Briefly 600 proventriculi (300 per genotype) were dissected in cold Schneider’s medium, flash-frozen and stored at -80°C. Nuclei were released by via dounce, while keeping samples on ice and avoiding foam. Nuclei were filtered through 5 ml cell strainer (40 μm) and via 40 μm Flowmi. Nuclei were centrifuged,  resuspended in PBS/BSA with 0.5% RNase inhibitor and filtered again with 40 μm Flowmi. Single nuclei DAPI stained and sorted using Sony SH800Z Cell Sorter and 100k nuclei per sample were collected in PBS/BSA buffer.
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

treatment_protocol: Samples include control flies (genotype  BEC1: esg-Gal4, tubGal80ts, UAS:GFP / +) and cachectic flies with midgut tumors (genotype BEC2: esg-Gal4, tubGal80ts, UAS:GFP ; UAS-yki3SA)

value: proventriculus

value: esg-Gal4, tubGal80ts, UAS:GFP / +


title: 3137

value: negative


title: HEK293T_RNA_G10

city: Charlottesville

first: Brett

middle: P

last: Ransegnola

state: VA

address: 755 Walker Square, Apt 2D

institute: UVA SOM

description:
Library name: RNA_G10
RNA_G10Aligned.sortedByCoord.out.bam

data_processing:
Base calling and quality control performed by Novogene Inc. Each sequencing read file had > 96% of reads clean. Adapters and base correction using paired read information was performed using Fastp. Reads were aligned to the human genome GENCODE v49 GCh38 primary assembly using STAR.
Assembly: GENCODE v49 GCh38 primary assembly
Supplementary files format and content: Raw read counts output from STAR.

growth_protocol: Cells were sterum starved in DMEM low glucose without serum for 24 hrs, then media replaced with complete Media and grown for 48 hr.

extract_protocol:
Cells were lysed in cell culture plates with Trizol LS and homogenized by 10x passage through an 18G needle. RNA isolated by Novogene Inc.
Unstranded mRNAseq standard Illumina polyA enrichment library prep kit

value: Cell line

value: Embryonic kidney immortalized

value: MAJOR

value: 48hr post 24hr serum starvation


title: CGND-HRA-03634 ALS-nonCI isoseq

description:
Library name: NYGC_ALS_03634
ALS_03634_clustered_hg38_minimap2

value: ALS


title: 3124

value: ALCLPOS

value: ALK

value: positive


title: 3175


title: CGND-HRA-04118 ALS-CI isoseq

description:
Library name: NYGC_ALS-ci_04118
ALS-ci_04118_clustered_hg38_minimap2


title: HEK293T_RNA_C8

description:
Library name: RNA_C8
RNA_C8Aligned.sortedByCoord.out.bam

value: MINOR


title: CGND-HRA-02759 ALS-nonCI isoseq

description:
Library name: NYGC_ALS-C9_02759
ALS-C9_02759_clustered_hg38_minimap2


title: 3105

value: CUTALCL


title: 3110


title: CGND-HRA-03363 ALS-CI isoseq

description:
Library name: NYGC_ALS-C9_03363
ALS-C9_03363_clustered_hg38_minimap2


title: HEK293T_RNA_C12

description:
Library name: RNA_C12
RNA_C12Aligned.sortedByCoord.out.bam


title: CGND-HRA-02763 ALS-nonCI isoseq

description:
Library name: NYGC_ALS_02763
ALS_02763_clustered_hg38_minimap2


title: yki

description: Library name: BEC2

value: esg-Gal4, tubGal80ts, UAS:GFP ; UAS-yki3SA


title: 3108

value: TN


title: HEK293T_RNA_A6

description:
Library name: RNA_A6
RNA_A6Aligned.sortedByCoord.out.bam


title: HEK293T_RNA_9F

description:
Library name: RNA_9F
RNA_9FAligned.sortedByCoord.out.bam


title: HEK293T_RNA_9C

description:
Library name: RNA_9C
RNA_9CAligned.sortedByCoord.out.bam

value: HET


title: 3104

value: ALCL tumors


title: 3103

value: ALCLNEG


title: 3100


title: HEK293T_RNA_8E

description:
Library name: RNA_8E
RNA_8EAligned.sortedByCoord.out.bam


title: HEK293T_RNA_12G

description:
Library name: RNA_12G
RNA_12GAlRNAigned.sortedByCoord.out.bam


title: 3101


title: HEK293T_RNA_7D

description:
Library name: RNA_7D
RNA_7DAligned.sortedByCoord.out.bam


title: 3054


title: 3096


title: ELI_1

city: Guangzhou

first: hui

last: zeng

address: 106 Zhongshan 2nd Rd

institute: Guangdong Provincial People's Hospital

description: Library name: Sample2

data_processing:
Personalbio Technologies
Assembly: The cells were then sent to Personalbio Technologies for RNA isolation and sequencing.
Supplementary files format and content: Approximately 1×106 MV4-11 cells (both including DMSO, 48 h ELI and ABT at the indicated concentrations alone or in combination treatment groups) were collected and suspended in TRIzol reagent. The cells were then sent to Personalbio Technologies for RNA isolation and sequencing.

source_name: bone marrow

growth_protocol: All the media contained 10% fetal bovine serum (BI) plus 1% penicillin/streptomycin (Gibco). Cells were maintained in a 37 ℃ humidified atmosphere containing 5% CO2.

extract_protocol:
Eliglustat (HY-14885) and Venetoclax (HY-15531) were purchased from MedChemExpress.
Personalbio Technologies

value: bone marrow

value: AML

value: WT

value: Different drugs


title: 3078

value: negative


title: DMSO_3

description: Library name: Sample9


title: 4444


title: ELI_3

description: Library name: Sample10


title: Comb_2

description: Library name: Sample8


title: 3018

value: BIAALCL


title: 2742


title: 2806


title: ELI_2

description: Library name: Sample6


title: DMSO_2

description: Library name: Sample5


title: ABT_3

description: Library name: Sample11


title: 2704


title: DMSO_1

description: Library name: Sample1


title: 2862


title: ABT_2

description: Library name: Sample7


title: 2698


title: 2675


title: Comb_1

description: Library name: Sample4


title: COL_5FU_3

first: Shiro

last: Yui

address: 1-5-45, Yushima, Bunkyo-ku

department: Center for stem cell and Regenerative medicine

institute: Institute of Science Tokyo

description: Library name: Sample 12

data_processing:
Raw sequencing data were converted to FASTQ files using bcl2fastq2 v2.20. Reads were aligned to the human reference genome (GRCh38; GENCODE release 39) using the DRAGEN Bio-IT Platform v4.3.6, and gene-level read counts and TPM values were quantified.
Assembly: GRCh38; GENCODE release 39
Supplementary files format and content: Tab-separated values files (Read count and TPM velues)

source_name: Small intestine

growth_protocol: Surgical specimens of human proximal small intestine were obtained from the Institute of Science Tokyo Hospital with approval from the Medical Research Ethics Committee of Institute of Science Tokyo (approval number: M2023-195). Crypts were isolated from the epithelial layer of the proximal small intestine. The epithelial tissue was dissected and cut into small fragments, which were washed twice in 30 mL of PBS and once in 2% Mucofilin (Eisai). The tissue was then incubated in 15 mM EDTA at 4 °C for 20 minutes. After an additional wash with 30 mL of PBS, the fragments were digested in 10 mL of collagenase solution (0.5 mg/mL in PBS; Sigma-Aldrich, #C7657) at 37 °C for 20 minutes. Following digestion, the supernatant was passed through a 70 μm mesh filter and transferred to a fresh 50 mL conical tube. The volume was adjusted to 10 mL with 0.1% (v/v) BSA/PBS, transferred to a 15 mL conical tube, and centrifuged at 500 × g for 3 minutes. The resulting pellet was resuspended in Matrigel and plated into 24-well plates. Organoids were cultured in 20% cWRNE medium consisting of Advanced DMEM/F12 supplemented with 1% (v/v) penicillin/streptomycin, 1% (v/v) GlutaMAX, 20% (v/v) L-WRN conditioned medium, recombinant murine EGF (50 ng/mL), nicotinamide (10 mM), 1× N2 supplement, 1× B27 supplement, N-acetyl-L-cysteine (1 mM; Sigma-Aldrich #A9165), gastrin I (10 nM; Sigma-Aldrich #G9145), and A83-01 (500 nM; Tocris #2939). Matrigel-grown organoids were subsequently passaged into either collagen matrices (COL) or Matrigel (MG) and maintained in 20% cWRNE medium.

extract_protocol:
On day 6, organoids were released from the ECM, and total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
Whole-transcriptome libraries were generated using the SMART-Seq mRNA kit (Takara Bio) based on the SMART (Switching Mechanism at the 5′ End of RNA Template) method. cDNA libraries were purified using AMPure XP beads (Beckman Coulter). Tagmentation and adapter ligation were performed using the Nextera XT DNA Library Prep Kit (Illumina) together with Illumina DNA-RNA UD Indexes. Pooled libraries were sequenced on an Illumina NovaSeq X Plus system.

treatment_protocol: For 5-FU treatment, 40 µM 5-fluorouracil (Selleck Chemicals, #S-1209) was added to the culture medium of MG- or COL-embedded organoids on days 5–6 of culture.

value: Small intestine

value: intestinal epithelial cells


title: 3087


title: 3540

value: ALCLPOS

value: ALK


title: COL_5FU_2

description: Library name: Sample 11


title: ABT_1

description: Library name: Sample3


title: 2620

value: positive


title: Comb_3

description: Library name: Sample12


title: 2614

value: CUTALCL


title: 2897


title: 2624


title: COL_5FU_1

description: Library name: Sample 10


title: 2460


title: COL_Control_1

description: Library name: Sample 7

value: non-treat


title: COL_Control_3

description: Library name: Sample 9


title: MG_5FU_1

description: Library name: Sample 4


title: 2539

value: TN


title: 2509


title: MG_5FU_2

description: Library name: Sample 5


title: COL_Control_2

description: Library name: Sample 8


title: MG_5FU_3

description: Library name: Sample 6


title: HEK293T,OMM,trizol,C1

description: Library name: OMM Trizol Control 1

value: Cell line

value: Human embryonic kidney


title: 1047

value: ALCL tumors

value: ALCLNEG


title: 1033


title: HEK293T,OMM,trizol,C2

description: Library name: OMM Trizol Control 2


title: 1457


title: MG_Control_2

description: Library name: Sample 2


title: 1264


title: MG_Control_1

description: Library name: Sample 1


title: MG_Control_3

description: Library name: Sample 3


title: 757


title: 1007


title: 1616


title: HEK293T,OMM,trizol,T2

description: Library name: OMM Trizol Target 2


title: 731


title: HEK293T, RNA-seq, ND5 silencing, 48h, r4

city: Sherbrooke

first: Luis

middle: Daniel

last: Cruz-Zaragoza

state: Quebec

address: 2500 boul. de l'Université

department: Biology

country: Canada

institute: Université de Sherbrooke

description: Library name: ND5_4

data_processing:
Analysis was performed in RStudio (R version 4.3.0) using packages from the Bioconductor repository {Gentleman:2004tt, Huber:2015wt} and the Tidyverse suite. Differential gene expression analysis was conducted using DESeq2 (version 1.40.2) {Love:2014vr}. Batch correction was applied using limma (version 3.56.2) {Ritchie:2015tm} to account for variability between replicates performed on different days to improve clustering and reliability of differential expression results.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: txt file containing raw counts (not normalized)

growth_protocol: HEK293T cells were cultured in DMEM/glucose+10%FCS+glutamine+pyruvate at 37°C. 400 000 cells were transfered to each T25 flask and incubated for 48 hours

extract_protocol:
After the treatment, the media was removed and 1mL of Trizol reagent added, and the cells lysed and resuuspended. The Trizol samples were stored at -80°C until processing. Total RNA was extracted from the aqueous phase and isolated with ZymoResearch RNA isolation kit 25.
mRNA library preparation (poly A enrichment) performed at Novogene

treatment_protocol: The media was removed and fresh media was added containing EndoPorter. Next, the corresponding chimeras (pCox4-MO), targeting the cognate mt-mRNA, were added to the media at a final concentration of 2 micromolar. The cells were incubated for 48 hours.

value: epithelial-like cell

value: ND5 chimera, 48h


title: HEK293T, RNA-seq, ND5 silencing, 48h, r3

description: Library name: ND5_3

value: WT


title: 514


title: 1790


title: 660


title: HEK293T,OMM,trizol,T1

description: Library name: OMM Trizol Target 1


title: HEK293T, RNA-seq, ND5 silencing, 48h, r2

description: Library name: ND5_2


title: HEK293T, RNA-seq, ND4L silencing, 48h, r3

description: Library name: ND4L_3

value: ND4L chimera, 48h


title: 5197

value: DH

value: negative


title: HEK293T, RNA-seq, ND3 silencing, 48h, r4

description: Library name: ND3_4

value: ND3 chimera, 48h


title: HEK293T, RNA-seq, ND4L silencing, 48h, r2

description: Library name: ND4L_2


title: HEK293T, RNA-seq, ND3 silencing, 48h, r3

description: Library name: ND3_3


title: 378


title: HEK293T, RNA-seq, ND5 silencing, 48h, r1

description: Library name: ND5_1


title: 285


title: 451

value: ALCLPOS


title: 832


title: 317

value: ALK


title: 280

value: positive


title: HEK293T, RNA-seq, ND4L silencing, 48h, r1

description: Library name: ND4L_1


title: HEK293T, RNA-seq, ND3 silencing, 48h, r1

description: Library name: ND3_1


title: HEK293T, RNA-seq, ND3 silencing, 48h, r2

description: Library name: ND3_2


title: 277


title: HEK293T, RNA-seq, ND2 silencing, 48h, r3

description: Library name: ND2_3

value: ND2 chimera, 48h


title: HEK293T, RNA-seq, ND4L silencing, 48h, r4

description: Library name: ND4L_4


title: 256


title: HEK293T, RNA-seq, ND2 silencing, 48h, r1

description: Library name: ND2_1


title: 257


title: HEK293T, RNA-seq, ND1 silencing, 48h, r4

description: Library name: ND1_4

value: ND1 chimera, 48h


title: 413

value: CUTALCL


title: 253


title: 255


title: HEK293T, RNA-seq, ND2 silencing, 48h, r4

description: Library name: ND2_4


title: 298

value: TN


title: 238


title: 250


title: HEK293T, RNA-seq, ND1 silencing, 48h, r3

description: Library name: ND1_3


title: 251


title: 316


title: HEK293T, RNA-seq, negative control, 48h, r2

description: Library name: Cneg_2

value: pCox4 presequence, 48h


title: 248

value: ALCL tumors


title: HEK293T, RNA-seq, negative control, 48h, r3

description: Library name: Cneg_3


title: 254

value: ALCLNEG


title: HEK293T, RNA-seq, CYTB silencing, 48h, r3

description: Library name: CYTB_3

value: epithelial-like cell

value: CYTB chimera, 48h


title: HEK293T, RNA-seq, CYTB silencing, 48h, r4

description: Library name: CYTB_4

value: WT


title: HEK293T, RNA-seq, ND1 silencing, 48h, r1

description: Library name: ND1_1


title: HEK293T, RNA-seq, ND1 silencing, 48h, r2

description: Library name: ND1_2


title: HEK293T, RNA-seq, COX3 silencing, 48h, r3

description: Library name: COX3_3

value: COX3 chimera, 48h


title: 249


title: 91


title: 133


title: 237


title: HEK293T, RNA-seq, COX3 silencing, 48h, r4

description: Library name: COX3_4


title: HEK293T, RNA-seq, CYTB silencing, 48h, r1

description: Library name: CYTB_1


title: HEK293T, RNA-seq, negative control, 48h, r4

description: Library name: Cneg_4


title: 190


title: HEK293T, RNA-seq, negative control, 48h, r1

description: Library name: Cneg_1


title: 240


title: HEK293T, RNA-seq, COX3 silencing, 48h, r2

description: Library name: COX3_2


title: 88


title: 178


title: HEK293T, RNA-seq, CYTB silencing, 48h, r2

description: Library name: CYTB_2


title: HEK293T, RNA-seq, COX3 silencing, 48h, r1

description: Library name: COX3_1


title: 53


title: 59


title: HEK293T, RNA-seq, COX1 silencing, 48h, r4

description: Library name: COX1_4

value: COX1 chimera, 48h


title: HEK293T, RNA-seq, COX1 silencing, 48h, r2

description: Library name: COX1_2


title: 24.SGs_WDM_tet_R3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Sequence reads were trimmed from 3’ end to a final length of 100 nt using Trimmomatic (CROP:100)
Trimmed reads were mapped to Homo sapiens genome (GRCh38) using RNA-STAR with default parameters for paired-ends (--alignIntronMax 1000000 –alignMAtesGapMax 1000000)
Duplicated aligned reads were labeled using MarkDuplicates from picard package
Raw counts were generated by featureCounts function of Rsubread package (strandSpecific=2, ignoreDup=TRUE, primaryOnly=TRUE, requireBothEndsMapped=TRUE, GTF.featureType=”gene”). GTF file used from ENSEMBL: Homo_sapiens.GRCh38.104.gtf
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Human embryonic kidney

growth_protocol: The maternal Flp-InTM T-RexTM-HEK293 cell line (Invitrogen), and the derivative FT293-GFP-TIA1aWT and FT293-GFP-TIA1aWDM cell lines were generated and maintained as described (Sánchez-Jiménez et al. (2015) Cell Death Dis., 6, e1669; Carrascoso et al. (2017) Mol. Cell. Biol., 37, e0017417; Carrascoso et al. (2019) Mol. Cell. Biol., 39, e0029918).

extract_protocol:
Total RNAs were purified from cellular extracts and immunopurified TIA1-stress granules using TRIzol Reagent (Ambion by Life Technologies).
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Human/Mouse/Rat.

treatment_protocol: The above HEK293 cell lines were treated in the presence and the absence of 0.5 mM NaAsO2 for 60 minutes.

value: Human embryonic kidney

value: Epithelial

value: WDM

value: Tetracyclie


title: HEK293T, RNA-seq, ATP8 silencing, 48h, r4

description: Library name: ATP8_4

value: ATP8 chimera, 48h


title: 30.SGs_WDM_tet_ars_R3

value: Tet plus sodium arsenite


title: 25.SGs_WT_tet_ars_R1


title: HEK293T, RNA-seq, COX2 silencing, 48h, r3

description: Library name: COX2_3

value: COX2 chimera, 48h


title: 27.SGs_WT_tet_ars_R3


title: HEK293T, RNA-seq, COX2 silencing, 48h, r4

description: Library name: COX2_4


title: 28.SGs_WDM_tet_ars_R1


title: 23.SGs_WDM_tet_R2


title: 26.SGs_WT_tet_ars_R2


title: HEK293T, RNA-seq, COX1 silencing, 48h, r3

description: Library name: COX1_3


title: HEK293T, RNA-seq, ATP8 silencing, 48h, r2

description: Library name: ATP8_2


title: 22.SGs_WDM_tet_R1


title: HEK293T, RNA-seq, COX2 silencing, 48h, r2

description: Library name: COX2_2


title: 29.SGs_WDM_tet_ars_R2


title: HEK293T, RNA-seq, ATP6 silencing, 48h, r3

description: Library name: ATP6_3

value: ATP6 chimera, 48h


title: HEK293T, RNA-seq, ATP8 silencing, 48h, r1

description: Library name: ATP8_1


title: HEK293T, RNA-seq, ATP8 silencing, 48h, r3

description: Library name: ATP8_3


title: HEK293T, RNA-seq, ATP6 silencing, 48h, r2

description: Library name: ATP6_2


title: 20.SGs_WT_tet_R2


title: 19.SGs_WT_tet_R1


title: HEK293T, RNA-seq, ATP6 silencing, 48h, r4

description: Library name: ATP6_4


title: HEK293T, RNA-seq, COX1 silencing, 48h, r1

description: Library name: COX1_1


title: HEK293T, RNA-seq, ATP6 silencing, 48h, r1

description: Library name: ATP6_1


title: Healthy control 6

city: Ann Arbor

first: Phillip

middle: John

last: McCown

address: 1500 E. Medical Center Drive

department: Internal Medicine - Nephrology

institute: University of Michigan Medicine

description:
Library name: HC6
10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v6.0. SoupX (v.1.5.0) was conducted on all samples at default parameters to remove ambient RNA from all samples. Mitochondrial transcript threshold, which was to retain cells that had 50% or less, was a filtration step. Integration consisted of harmony-based integration. Default scaling and PCA analysis was then used on the integrated object. Clusters were cell typed manually by examining for cell type markers that are specific to a specific kidney cell type.
Assembly: hg38
Supplementary files format and content: MTX and TSV from 10x Genomics kits

source_name: Kidney

extract_protocol:
Cortical human kidney biopsies that were CryoStor and were subjected to a cellular extraction protocol from the Kidney Precision Medicine Project.
Library construction was performed according to manufacturer's protocols or instructions for 10x Genomics, specifically the Chromium Next GEM Single Cell 3' v3.1 kit and protocol.

treatment_protocol: Healthy control patients were subjected to a kidney biopsy at time of clinical donation visit. All vertical sleeve gastrectomy patients were subjected to a kidney biopsy at time of vertical sleeve gastrectomy and were subjected to an additional kidney biopsy approximately 12 months post vertical sleeve gastrectomy.

value: Kidney

value: Kidney and immune cells


title: 21.SGs_WT_tet_R3


title: 17.Cytosol_WDM_tet_ars_R2


title: Healthy control 5

description:
Library name: HC5
10x Genomics


title: 15.Cytosol_WT_tet_ars_R3


title: 14.Cytosol_WT_tet_ars_R2


title: 16.Cytosol_WDM_tet_ars_R1


title: 12.Cytosol_WDM_tet_R3

value: Tetracycline


title: 18.Cytosol_WDM_tet_ars_R3


title: Healthy control 4

description:
Library name: HC4
10x Genomics


title: 13.Cytosol_WT_tet_ars_R1


title: 11.Cytosol_WDM_tet_R2


title: Biol rep 2 Patient 4

description:
Library name: Patient4_Post
10x Genomics

value: 12 months post vertical sleeve gastrectomy


title: 9.Cytosol_WT_tet_R3


title: Healthy control 1

description:
Library name: HC1
10x Genomics


title: Healthy control 2

description:
Library name: HC2
10x Genomics


title: 10.Cytosol_WDM_tet_R1


title: 5.Cytosol_WDM_R2


title: Biol rep 2 Patient 1

description:
Library name: Patient1_Post
10x Genomics


title: Healthy control 3

description:
Library name: HC3
10x Genomics


title: Biol rep 2 Patient 5

description:
Library name: Patient5_Post
10x Genomics


title: 8.Cytosol_WT_tet_R2


title: Biol rep 2 Patient 3

description:
Library name: Patient3_Post
10x Genomics


title: 3.Cytosol_WT_R3


title: Biol rep 2 Patient 2

description:
Library name: Patient2_Post
10x Genomics


title: Biol rep 1 Patient 5

description:
Library name: Patient5_Pre
10x Genomics


title: 1.Cytosol_WT_R1


title: Biol rep 1 Patient 3

description:
Library name: Patient3_Pre
10x Genomics


title: 7.Cytosol_WT_tet_R1


title: Biol rep 1 Patient 2

description:
Library name: Patient2_Pre
10x Genomics


title: 4.Cytosol_WDM_R1


title: Multiplexed, human PBMC, naive CD4+ T cells, HTO

city: Lebanon

first: J. Louise

last: Lines

state: NH

address: DHMC

institute: Dartmouth College

description:
Library name: naive_CD4_HTO
Hashtag-derived oligonucleotide (HTO) and Antibody-Derived Tags (ADT)

library_source: other

data_processing:
The CellRanger Single-Cell Software Suite (10x Genomics) versions v2.1.1 to v7.1.0 were used to perform barcode processing and transcript counting after alignment to the mm10 reference genome with default parameters. Sample barcode hashtags were matched to cells using the HTODemux function of the Seurat package. Droplets containing reads from multiple hashtags were deemed doublets or triplets and filtered out. Hashtags associated with low numbers of reads, likely suggestive of free-floating RNA, were also removed from consideration.
Assembly: GRCh38-2020-A
Supplementary files format and content: Matrix files
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
PBMCs were collected from healthy adult female donors [IRB protocol, STUDY02000116: VISTA in Autoimmune Disease to Christopher Burns]. Human PBMC were pre-enriched directly from total blood with BioLegend EasySep™ Direct Human CD4+ T Cell Isolation Kits. Human cells were sorted as singlet, viability dye-, CD4+, CD8-, CD45RA+, CD45RO-, CD127hi, CD25-, CD95-.
Droplet-based 5′ end scRNA-seq was performed using the 10x Genomics platform and libraries were prepared and sequenced on a NextSeq2000 using 28×90bp reads for GEX libraries using the Chromium Single Cell NextGEM 5' v2 chemistry Reagent kit.

value: PBMC

value: naive CD4+ T cells

value: untreated

tag: library type

value: ADT

tag: adt

value: TotalSeq™-C0251 anti-human Hashtag 1 Antibody, TotalSeq™-C0252 anti-human Hashtag 2 Antibody, TotalSeq™-C0253 anti-human Hashtag 3 Antibody, anti-human CD86, anti-human CD274 (B7-H1, PD-L1), anti-human CD270 (HVEM, TR2), anti-human CD155 (PVR), anti-human CD112 (Nectin-2), anti-human CD47, anti-human CD48, anti-human CD40, anti-human CD154, anti-human CD52, anti-human CD3, anti-human CD8, anti-human CD56, anti-human CD19, anti-human CD33, anti-human CD11c, anti-human HLA-A,B,C, anti-human CD45RA, anti-human CD123, anti-human CD7, anti-human CD105, anti-human/mouse CD49f, anti-human CD194 (CCR4), anti-human CD4, anti-mouse/human CD44, anti-human CD14, anti-human CD16, anti-human CD25, anti-human CD45RO, anti-human CD279 (PD-1), anti-human TIGIT (VSTM3), Mouse IgG1, κ isotype Ctrl, Mouse IgG2a, κ isotype Ctrl, Mouse IgG2b, κ isotype Ctrl, Rat IgG2b, κ Isotype Ctrl, anti-human CD20, anti-human CD335 (NKp46), anti-human CD31, anti-human CD146, anti-human IgM, anti-human CD5, anti-human CD183 (CXCR3), anti-human CD195 (CCR5), anti-human CD32, anti-human CD196 (CCR6), anti-human CD185 (CXCR5), anti-human CD103 (Integrin αE), anti-human CD69, anti-human CD62L, anti-human CD161, anti-human CD152 (CTLA-4), anti-human CD223 (LAG-3), anti-human KLRG1 (MAFA), anti-human CD27, anti-human CD107a (LAMP-1), anti-human CD95 (Fas), anti-human CD134 (OX40), anti-human HLA-DR, anti-human CD1c, anti-human CD11b, anti-human CD64, anti-human CD141 (Thrombomodulin), anti-human CD1d, anti-human CD314 (NKG2D), anti-human CD35, anti-human CD57 Recombinant, anti-human CD272 (BTLA), anti-human/mouse/rat CD278 (ICOS), anti-human CD58 (LFA-3), anti-human CD39, anti-human CX3CR1, anti-human CD24, anti-human CD21, anti-human CD11a, anti-human CD79b (Igβ), anti-human CD244 (2B4), anti-human CD169 (Sialoadhesin, Siglec-1), anti-human/mouse integrin β7, anti-human CD268 (BAFF-R), anti-human CD42b, anti-human CD54, anti-human CD62P (P-Selectin), anti-human CD119 (IFN-γ R α chain), anti-human TCR α/β, Rat IgG1, κ isotype Ctrl, Rat IgG2a, κ Isotype Ctrl, Armenian Hamster IgG Isotype Ctrl, anti-human CD122 (IL-2Rβ), anti-human CD267 (TACI), anti-human FcεRIα, anti-human CD41, anti-human CD137 (4-1BB), anti-human CD163, anti-human CD83, anti-human CD124 (IL-4Rα), anti-human CD13, anti-human CD2, anti-human CD226 (DNAM-1), anti-human CD29, anti-human CD303 (BDCA-2), anti-human CD49b, anti-human CD81 (TAPA-1), anti-human IgD, anti-human CD18, anti-human CD28, anti-human CD38, anti-human CD127 (IL-7Rα), anti-human CD45, anti-human CD22, anti-human CD71, anti-human CD26, anti-human CD36, anti-human CD158 (KIR2DL1/S1/S3/S5), anti-human CD49a, anti-human CD49d, anti-human CD73 (Ecto-5'-nucleotidase), anti-human TCR Vα7.2, anti-human TCR Vδ2, anti-human LOX-1, anti-human CD158b (KIR2DL2/L3, NKAT2), anti-human CD158e1 (KIR3DL1, NKB1), anti-human CD319 (CRACC), anti-human CD99, anti-human CLEC12A, anti-human CD352 (NTB-A), anti-human CD94, anti-human Ig light chain κ, anti-human CD85j (ILT2), anti-human CD23, anti-human Ig light chain λ, anti-human CD328 (Siglec-7), anti-human GPR56, anti-human HLA-E, anti-human CD82, anti-human CD101 (BB27), anti-human CD88 (C5aR), anti-human CD224


title: Biol rep 1 Patient 4

description:
Library name: Patient4_Pre
10x Genomics

tag: tissue


title: Multiplexed, human PBMC, naive CD4+ T cells, GEX

description:
Library name: naive_CD4_mRNA
polyA RNA

value: mRNA


title: 2.Cytosol_WT_R2

value: Human embryonic kidney

value: Epithelial

tag: genotype

value: WT


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 24hr, rep5

city: Evanston

first: Yue

last: Yang

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description:
Library name: RNA-seq_chromatin_Adult_30m-24hr_5
Adult_opto30m-24hr.bigwig

data_processing:
Sequenced reads were aligned to the mm10 reference genome with HISAT2 using the public server at https://usegalaxy.org/, normalized by library size, and visualized using bigwig files. Gene annotations were derived using GENCODE version M11. Differential gene expression analyses were performed using pair-wise negative binomial tests with edgeR and the false discovery rate (FDR) was calculated for all genes. Gene ontology analyses of differentially expressed genes were performed using DAVID (Dennis et al., 2003) Knowledgebase v2025_1 with a background of all H3K4me3-marked genes in the adult mouse cerebellum.
Assembly: mm10
Supplementary files format and content: bigwig files

molecule: nuclear RNA

source_name: anterior dorsal cerebellar vermis

extract_protocol:
For NEUROD1/2 knockout mice, cerebella were removed, microdissected, and total RNA from ADCV was extracted with Trizol. For optostimulation, the medial part of the ADCV was homogenized and spun down. The supernatant was removed and the RNA in the pellet representing the chromatin fraction was extracted with Trizol. Purified RNA was treated with NEBNext rRNA depletion kit  (#E6310).
RNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (#E7760).

treatment_protocol: For AAV injection, 0.5 µl of AAV9-gRNA-mCherry (titer 1x10^13vg/ml) was delivered to the ADCV using a fine glass pipette connected to a microinjector system (Nanoinject II, Drummond) and mounted in the stereotaxic frame (Stoelting). Optogenetic stimulation of ADCV granule neurons was performed using a 450nm diode blue laser (Opto Engine, 200mW) coupled to a multimode fiber cable (Oz Optics) with 68 mW of power at the tip of the fiber delivered through a fiber optic cannula. Each 100 ms optogenetic stimulus was composed of a 50 Hz train of 10 ms pulses and was delivered at 30 second intervals. Animals were stimulated over a 10 minute period, or over a 30 minute period and returned to their homecage.

value: anterior dorsal cerebellar vermis

value: cerebellar cells

value: Math1-Cre; ChR2YFP-GN

value: optostimulation 30 minutes, return to homecage 1 day


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 24hr, rep4

description:
Library name: RNA-seq_chromatin_Adult_30m-24hr_4
Adult_opto30m-24hr.bigwig


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 24hr, rep1

description:
Library name: RNA-seq_chromatin_Adult_30m-24hr_1
Adult_opto30m-24hr.bigwig


title: Biol rep 1 Patient 1

description:
Library name: Patient1_Pre
10x Genomics

value: Kidney


title: 6.Cytosol_WDM_R3

value: WDM


title: Human iPSC derived neurons, HSV-1 infected, MOI 1

city: Bostin

first: Don

middle: M

last: Coen

address: 25 Shattuck St

description: Library name: LIB059710_TRA00263386

data_processing:
Sequence reads were mapped to hg38 using STAR
Gene counts were next quantified using salmon
Gene counts were then scaled to TPM counts
Assembly: hg38
Supplementary files format and content: csv files include TPM counts for each sample

source_name: iNGN3 iPSC

growth_protocol: iNGN3 iPSC-derived neurons were maintained at 37 °C using an incubator with a humidified atmosphere of 5% CO2.

extract_protocol:
RNAse Plus Mini Kit (Qiagen #74134) was used to extract RNA, with DNA eliminated by treatment with the gDNA Eliminator Spin Columns, as per manufacturer's instructions.
NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs #E7760S) was used to construct the library as per manufacturer’s instructions.

treatment_protocol: Cells were mock infected or infected with HSV-1 (strain KOS) using an MOI of 10 or 1 at 21 days post-seeding.

value: iNGN3 iPSC

value: Neurons

tag: batch

value: MOI 1


title: Human iPSC derived neurons, mock infected, MOI 10

description: Library name: LIB058443_TRA00254138

value: Mock

value: MOI 10


title: RNA-seq ADCV, chromatin fraction, Adult 30m opto to 24hr, rep2

description:
Library name: RNA-seq_chromatin_Adult_30m-24hr_2
Adult_opto30m-24hr.bigwig


title: Human iPSC derived neurons, mock infected, MOI 1

description: Library name: LIB059710_TRA00263384


title: Human iPSC derived neurons, HSV-1 infected, MOI 10

description: Library name: LIB058443_TRA00254139