title: AKP, Medulloblastoma, KO, RNA-seq, rep3

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Library name: Sd10

data_processing:
Paired-end FASTQ files were processed using the nf-core-rnaseq pipeline (v3.17.0) (auto strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR to GRCm38 (NCBI, p.6, release 108) and quantified to gene counts using RSEM.
Downsteam analysis was performed using Pluto (https://pluto.bio).
Assembly: GRCm38 (NCBI, p.6, release 108)
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: Medulloblastoma

extract_protocol:
Cerebellum or medulloblastoma tumor tissue from mouse were homogenised and total RNAs were extracted using RNeasy kits (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Library Prep Kit v2).

value: Medulloblastoma

value: AtohI-Cre Kmt2dfl/+ Ptch+/-

value: AKP

tag: Sex

value: Female

tag: condition

value: KO

tag: age


title: pre-treatment tumor RNA from individual with NSCLC_S093

status: Public on Jun 02 2025

type: SRA

city: Thousand Oaks

first: Abraham

last: Anderson

state: California

address: 1 amgen center drive

country: USA

institute: Amgen Inc.

description: Library name: S093

library_source: transcriptomic

data_processing:
Transcript level pseudo-alignment and quantification to the Ensembl GRCh37 Release 97 (July 2019) reference was performed using Kallisto (version 0.44). Raw counts or transcripts per million (TPM) were calculated for 180,253 transcripts in the Ensembl reference. 134,160 transcripts were covered by the Tempus|RS panel.
Assembly: Ensembl GRCh37 Release 97 (July 2019)
Supplementary files format and content: tab-delimited text file with columns for ensembl_gene, hgnc_symbol, <sampleID>. TPM values are in the <sampleID> column.

molecule: total RNA

organism: Homo sapiens

source_name: tumor biopsy

extract_protocol:
Total nucleic acid (TNA) was extracted from tissue specimens using a Chemagic 360 or similar instrumentation, and the recovered TNA was quantified and qualified, and may have been concentrated if necessary. Extracted TNA that was intended for processing by Tempus|RS was treated with Invitrogen TURBO DNase to degrade DNA. The minimum amount of input total RNA required to perform the test was 50 ng. RNA was fragmented using heat and magnesium, with variable parameters, to yield similar sized fragments from RNA inputs with different starting size distributions.
Strand-specific library preparation was performed using the KAPA RNA HyperPrep Kit for Illumina with KAPA single indexed 6 base pair adapters. The libraries were amplified with high fidelity, low-bias PCR using primers complementary to adapter sequences. After library preparation and amplification, targets were captured by hybridization, clean-up of captured targets was performed, and unbound fragments were washed away. Library capture is conducted using the xGen Exome Research Panel v1 probe set, along with the xGen Hybridization and Wash Kit and xGen Universal Blockers. The enriched targets are amplified using the KAPA HiFi HotStart ReadyMix and primers supplied in the KAPA Library amplification kit, followed by a magnetic bead-based clean-up. The amplified target-captured libraries were sequenced with a 2x76 read length to an average of 50 million total reads on an Illumina HiSeq4000 System using patterned flowcells.

tag: tissue

value: tumor biopsy

tag: study

tag: atm

tag: kpclsignature

value: KL

value: low


title: AKP, Medulloblastoma, KO, RNA-seq, rep2

description: Library name: Sd9

molecule: polyA RNA

organism: Mus musculus

tag: genotype

tag: group

value: Male


title: 12M_Utricle

city: Shanghai

first: Jiaoyao

last: Ma

state: Shanghai

address: No. 130, Dong'an Road, Xuhui District

country: China

institute: Fudan University

description: one sample from 12M murine utricle

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: utricle

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: utricle


title: ESC_ChIP-H3K27me3_WT_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: Library name: ESC_ChIP-H3K27me3_WT_rep1

library_source: genomic

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 34 for R1 and 34 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)) on gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Chromatin was isolated and used for ChIP according to standard procedures.
ChIP-seq. Libraries were constructed according to the Illumina Nextera protocol.

tag: cell line

value: Embryonic stem cells

tag: treatment

value: Cell Signaling 9733


title: 38_H524_REST_dox

city: Bethesda

first: Nitin

last: Roper

state: MD

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

data_processing:
Samples were pooled and sequenced on NovaSeq 6000 SP.
Samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome and the annotated transcripts using STAR.
Gene expression quantification analysis was performed using STAR/RSEM tools.
RSEM generated read counts for each gene between samples were normalized using TMM method implemented in edgeR and then transformed to RPKM.
Assembly: hg19 and mm10
Supplementary files format and content: csv files contains RSEM RPKM (log2+1) values for each sample

extract_protocol:
RNA was extracted using an AllPrep DNA/RNA extraction kit according to the manufacturer’s protocol (Qiagen #80204).
RNA libraries for bulk RNA-seq were prepared using Illumina Stranded mRNA Prep

tag: cell type

value: small cell lung cancer


title: pre-treatment tumor RNA from individual with NSCLC_S092

description: Library name: S092

value: KC


title: NKP, Medulloblastoma, KO, RNA-seq, rep3

description: Library name: Sd7

value: Nestin-Cre Kmt2dfl/+ Ptch+/-

value: NKP


title: pre-treatment tumor RNA from individual with NSCLC_S091

description: Library name: S091


title: 24M_Cochlea_BU

description: one sample from 24M murine cochlea epithliem

source_name: cochlea epithliem

value: cochlea epithliem


title: ESC_ChIP-H3K9ac_WT_rep1

description: Library name: ESC_ChIP-H3K9ac_WT_rep1

value: Abcam 4441


title: 36_H524_REST_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S090

description: Library name: S090


title: NKP, Medulloblastoma, KO, RNA-seq, rep2

description: Library name: Sd6

value: Medulloblastoma


title: 35_H524_REST_no_dox


title: 24M_Utricle

description: one sample from 24M murine utricle


title: 39_H524_REST_dox


title: 12M_Cochlea

description: one sample from 12M murine cochlea epithliem


title: NKP, Medulloblastoma, KO, RNA-seq, rep1

description: Library name: Sd5


title: pre-treatment tumor RNA from individual with NSCLC_S088

description: Library name: S088

value: KP


title: 3M_Cochlea

description: one sample from 3M murine cochlea epithliem


title: AKP, Medulloblastoma, KO, RNA-seq, rep1

description: Library name: Sd8

value: AtohI-Cre Kmt2dfl/+ Ptch+/-

value: AKP


title: 37_H524_REST_dox


title: pre-treatment tumor RNA from individual with NSCLC_S129

description: Library name: S129

value: tumor biopsy


title: Ptch, Cerebellum, Control, RNA-seq, rep4

description: Library name: Sd4

source_name: Cerebellum

value: Cerebellum

value: Ptch+/-

value: Ptch

value: Control


title: Ptch, Cerebellum, Control, RNA-seq, rep3

description: Library name: Sd3

value: Female


title: 3M_Utricle

description: one sample from 3M murine utricle

value: utricle


title: pre-treatment tumor RNA from individual with NSCLC_S087

description: Library name: S087

value: low


title: 31_H82_NOTCH1_REST_KO_dox

value: small cell lung cancer


title: pre-treatment tumor RNA from individual with NSCLC_S089

description: Library name: S089

value: KC


title: 30_H82_NOTCH1_REST_KO_no_dox


title: 32_H82_NOTCH1_REST_KO_dox


title: 33_H82_NOTCH1_REST_KO_dox


title: Rbm-KO2.IP

first: Mingyu

last: Xia

address: No. 83, Fenyang Road, Xuhui District

department: ENT Institute and Otorhinolaryngology Department of the Affiliated Eye and ENT Hospital, Sta

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Genes were identified by MACS software with every pair.
Differentially sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: mm8
Supplementary files format and content: Collected peaks in xlsx.

source_name: Inner ear

growth_protocol: The cochlear epithelia from postnatal day (P) 1–2 mice were dissected and collected in ice-cold PBS. Then tissues were incubated in 0.125% trypsin for 15 min at 37°C, and a trypsin neutralizer was used to terminate the digestion process. After gentle trituration repeatedly with a 1 ml syringe, the cell suspension was passed through a 40 μm cell strainer. Single cells were collected after washing with PBS two times and centrifuging at 1,500 rpm for 6 min. Collected cells were resuspended in 5% Matrigel dissolved in the expansion culture medium. During the first 8–10 days, Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 supplemented with 1% N2 , 2% B27 , and 100 μg/ml penicillin/streptomycin, 50 ng/mL EGF, 50 ng/mL bFGF, 50 ng/mL IGF, 3.5 μM CHIR99021 was used as expansion medium. The formed organoids were released from Matrigel with cell recovery solution and then attached to the slides for differentiation. During the differentiation stage, the growth factors were removed, and small molecules containing 3 μM CHIR99021 and 5 μM LY411575  were added for 7-8 days. Subsequently, small molecules were replaced by a low dose of EGF (10 ng/mL) and bFGF (10 ng/mL) for 9-10 days.

extract_protocol:
Control organoids  were collected in ice-cold PBS solution and then incubated in RIP buffer (150 mM KCl, 0.5 mM DTT, 25 mM Tris, pH 7.4, 1 mM PMSF, 0.5% NP40 and protease Inhibitor) after centrifugation. Organoids in RIP buffer were then rocked on a nutator at 4°C for 30 min, then cell membrane and debris were discarded by centrifugation at 4°C for 15 min. The collected supernatant was then added to either antibody anti-IgG or anti-RBM25 and incubated at 4°C overnight. Protein A/G Dynabeads was added and incubated at room temperature for 2 h. Dynabeads were then washed 5 times each for 10 min with washing buffer (1 M NaCl, 1% NP-40, 1 mM EDTA, 50 mM Tris, pH 7.4, 0.1% SDS, and 0.5% sodium deoxycholate) and then subjected to RNA extraction. RNAs were extracted from the Dynabeads using Trizol.
Extracted RNAs from RIP samples and then underwent library construction on the Illumina NovaSeq 6000 sequence.

treatment_protocol: Organoid were treated with control or RBM25 KD lentivirus.

value: Inner ear

value: Inner ear organoid cell

value: Rbm-KO

value: RBM25 antibody+Rbm25 knockdown


title: pre-treatment tumor RNA from individual with NSCLC_S086

description: Library name: S086

value: KP


title: pre-treatment tumor RNA from individual with NSCLC_S084

description: Library name: S084


title: 29_H82_NOTCH1_REST_KO_no_dox


title: Rbm-KO2.Input

value: None+Rbm25 knockdown


title: 34_H524_REST_no_dox


title: 24M_Cochlea

value: cochlea epithliem


title: Rbm-KO2.IgG

value: IgG  antibody+Rbm25 knockdown


title: pre-treatment tumor RNA from individual with NSCLC_S085

description: Library name: S085

value: tumor biopsy


title: pre-treatment tumor RNA from individual with NSCLC_S082

description: Library name: S082


title: pre-treatment tumor RNA from individual with NSCLC_S083

description: Library name: S083


title: Ptch, Cerebellum, Control, RNA-seq, rep1

description: Library name: Sd1

value: Cerebellum

value: Ptch+/-

value: Male


title: Rbm-KO1.IP


title: Rbm-KO1.Input


title: Ptch, Cerebellum, Control, RNA-seq, rep2

description: Library name: Sd2

value: Ptch

value: Female

value: Control


title: 27_H524_NOTCH1_dox

value: small cell lung cancer


title: pre-treatment tumor RNA from individual with NSCLC_S080

description: Library name: S080

value: KC

value: high


title: Control2.IP

value: Inner ear

value: Inner ear organoid cell

value: WT

value: RBM25 antibody


title: Rbm-KO1.IgG

value: Rbm-KO


title: 26_H524_NOTCH1_dox


title: pre-treatment tumor RNA from individual with NSCLC_S081

description: Library name: S081

value: KL

value: low


title: Sting_scRNA

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description: 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1 (1000020). B Cell V(D)J enrichment was performed in these samples according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit

data_processing:
The count models in Cell Ranger (v 7.2.0) were used to align the raw sequencing reads to the mm10 reference genome, generating a counts table for the transcriptomic data. Additionally, the VDJ model in Cell Ranger was employed to detect the BCR clonotype using single-cell barcodes, utilizing the GRCm38 version of the reference genome files
To filter out low-quality single-cell data, the Seurat (v 4.4.0) pipeline was employed along with miQC (v 1.10.0) spline models. In the Ad5XBB.1.5+RBDXBB.1.5-HR group, 544 of 16,284 cells, in the WT group, 446 of 18,646 cells, and in the Sting-/- Ad5XBB.1.5+RBDXBB.1.5-HR group, 487 of 16,286 cells were removed.
Assembly: refdata-gex-GRCh38-2020-Arefdata-gex-mm10-2020-A
Supplementary files format and content: MTX
Supplementary files format and content: RDS

source_name: lung

extract_protocol:
Single-cell RNA sequencing (scRNA-seq) was performed on female C57BL/6 mice treated with PBS, as well as on Ad5XBB.1.5+RBDXBB.1.5-HR groups, including Sting-/- mice that also received Ad5XBB.1.5+RBDXBB.1.5-HR immunization as previously described. Forty-eight hours after the final vaccination, the mice were euthanized, and lung tissues were collected. The lungs were minced with scissors and treated with a tissue dissociation solution to generate a single-cell suspension. After treatment with a red blood cell lysis reagent, the suspension was filtered through 40-µm strainers and resuspended in PBS.
Single-cell suspensions from four mice per group were pooled and loaded onto a 10x Chromium Single Cell and VDJ library construction system (10x Genomics, 5’scRNA+BCR). The concentration of single-cell suspensions was adjusted to 500–1200 cells/µl. Between 10,000 and 18,000 cells were loaded, with subsequent steps performed following the standard protocols provided by the manufacturer.
10X 5' scRNA+TCR

value: lung

value: Sting

tag: library type


title: Control2.Input


title: Control2.IgG

value: IgG  antibody


title: pre-treatment tumor RNA from individual with NSCLC_S079

description: Library name: S079

value: tumor biopsy


title: 24_H524_NOTCH1_no_dox


title: Control1.IP


title: 23_H524_NOTCH1_no_dox


title: 25_H524_NOTCH1_dox


title: pre-treatment tumor RNA from individual with NSCLC_S077

description: Library name: S077


title: pre-treatment tumor RNA from individual with NSCLC_S078

description: Library name: S078


title: Control1.IgG


title: 22_H524_NOTCH1_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S075

description: Library name: S075

value: KP


title: pre-treatment tumor RNA from individual with NSCLC_S076

description: Library name: S076


title: Control1.Input


title: Brain, WT Control, rep4

first: Richard

middle: L

last: Proia

address: 10 Center Drive Room 9D11

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

description:
ABEvsWT_deg_all.txt
N272WT

data_processing:
Raw reads in FASTQ format were first processed to remove adapters, reads containing poly-N, and low-quality reads using fastp.
high-quality clean reads were mapped to reference genome mm10 (GRCm38) using hisat2 2.0.5.
Gene-expression quantification was performed using featureCounts 1.5.0-p3  and differential analysis performed using DESeq2 1.20.0
Pathway enrichment Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed using clusterProfiler 3.8.1 with corrected p-value set to <0.05 for significant enrichment.
Gene Set Enrichment Analysis (GSEQ) was performed using the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp
Assembly: mm10
Supplementary files format and content: FPKM values and gene count in tab-delimited text files

source_name: Brain

growth_protocol: Healthy mice were obtained from The Jackson Laboratory. HEXA mouse lines were generated by CRISPR/Cas9 genome editing using two sgRNAs targeting intron sequences flanking exon 7 of the mouse Hexa gene and a donor template oligonucleotides containing the HEXA exon 7, (flanking introns, and mouse homology arms) were injected into 1-cell mouse C57BL/6J embryos. Neu3 KO mice were generated by CRISPR/Cas9-targeted gene disruption. HEXA c.805A mice were crossed with Neu3 KO mice to generate the HEXA c.805A/Neu3 KO LOTS mice. C57BL/6J mice (Jackson Labs) were used as controls.

extract_protocol:
Total RNA from one brain hemisphere each was isolated using miRNeasy Mini Kit(Qiagen).
3 ug of total RNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA with PolyA Selection Kit (New England Biolab).

treatment_protocol: Vascular delivery of AAV--PHP-ABE.eB or AAV-PHP.eB-GFP (a total dose of 2.4 x 1012 vg/mouse) was performed by retro-orbital injection on HEXA c.805A/Neu3 KO LOTS mice. Mice at 6–7 weeks old were anesthetized using isoflurane and virus injected into the retrobulbar sinus of the right eye using a 29-gauge, 0.5 mL tuberculin syringe and brain was harvested at 21 weeks.

value: Brain

value: No Treatment


title: 21_H524_parental

value: small cell lung cancer

value: parental


title: 19_H524_parental


title: Brain, WT Control, rep3

description:
ABEvsWT_deg_all.txt
N271WT


title: pre-treatment tumor RNA from individual with NSCLC_S074

description: Library name: S074


title: 20_H524_parental


title: pre-treatment tumor RNA from individual with NSCLC_S073

description: Library name: S073

value: high


title: Brain, WT Control, rep1

description:
ABEvsWT_deg_all.txt
WT1586


title: 18_CORL88_TAS1440_GSI


title: pre-treatment tumor RNA from individual with NSCLC_S072

description: Library name: S072

value: KC


title: Brain, WT Control, rep2

description:
ABEvsWT_deg_all.txt
W623WT


title: 43_CORL88_STING_KO_TAS1440


title: 17_CORL88_TAS1440_GSI


title: pre-treatment tumor RNA from individual with NSCLC_S071

description: Library name: S071


title: 28_H82_NOTCH1_REST_KO_no_dox


title: pre-treatment tumor RNA from individual with NSCLC_S069

description: Library name: S069


title: Brain, AAV GFP, rep3

description:
ABEvsGFP_deg_all.txt
M409G

value: HEXA c.805A/Neu3 KO

value: AAV GFP


title: 15_CORL88_TAS1440


title: pre-treatment tumor RNA from individual with NSCLC_S070

description: Library name: S070


title: 16_CORL88_TAS1440_GSI


title: Brain, AAV GFP, rep2

description:
ABEvsGFP_deg_all.txt
M326G


title: Brain, AAV GFP, rep4

description:
ABEvsGFP_deg_all.txt
F777G


title: pre-treatment tumor RNA from individual with NSCLC_S068

description: Library name: S068


title: 14_CORL88_TAS1440


title: Brain, AAV GFP, rep1

description:
ABEvsGFP_deg_all.txt
F772G


title: 13_CORL88_TAS1440


title: Brain, AAV ABE, rep4

description:
ABEvsWT_deg_all.txt
ABEvsGFP_deg_all.txt
M575A

value: AAV ABE


title: pre-treatment tumor RNA from individual with NSCLC_S067

description: Library name: S067


title: 12_CORL88_DMSO

value: DMSO


title: Brain, AAV ABE, rep3

description:
ABEvsWT_deg_all.txt
ABEvsGFP_deg_all.txt
M574A


title: pre-treatment tumor RNA from individual with NSCLC_S066

description: Library name: S066

value: KL


title: 11_CORL88_DMSO


title: pre-treatment tumor RNA from individual with NSCLC_S065

description: Library name: S065

value: low


title: 9_H82_NOTCH1_dox


title: 10_CORL88_DMSO


title: Brain, AAV ABE, rep1

description:
ABEvsWT_deg_all.txt
ABEvsGFP_deg_all.txt
F780A


title: pre-treatment tumor RNA from individual with NSCLC_S063

description: Library name: S063


title: pre-treatment tumor RNA from individual with NSCLC_S064

description: Library name: S064


title: pre-treatment tumor RNA from individual with NSCLC_S061

description: Library name: S061


title: pre-treatment tumor RNA from individual with NSCLC_S062

description: Library name: S062


title: 6_H82_NOTCH1_no_dox


title: ESC_CnT-H3K27ac_KAP1cKO_rep1

data_processing:
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 10-bp windows across the genome using deepTools for presentation as genome browser tracks (Ramirez et al, 2014).
The seqeunce length was 150 for R1 and 150 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Samples were prepared according to the Epicypher CUT&Tag protocol with some adjustments made for crosslinking. Briefly, nuclei from 106 cells were made using NE1 buffer (20mM HEPES (pH 8), 10% Glycerol, 0.34 M Sucrose, 10mM KCl, 2mM EDTA, 10mM Sodium butyrate, 1 Roche Complete Protease Inhibitor, 0.5mM Spermidine). 2.5x105 nuclei per replicate was resuspended in Wash125 buffer (20mM HEPES pH 7.5, 125mM NaCl, 10mM Sodium butyrate, 0.025% Digitonin, 1 Roche Complete Protease Inhibitor, 0.5 mM Spermidine) and bound to CUTANA Concanavalin A Beads (Epicypher 21-1401) for 15 minutes at 4C. Bound nuclei were then incubated with 50 μL Wash125 + 0.1% BSA, 2mM EDTA, and 1 μL Primary antibody (H3K9me3: Abcam 8898, H3K27ac: Active Motif 39133) overnight at 4C. Nuclei were washed once with Wash125 and resuspended in 100 μL Wash125 + 1 μL Secondary antibody at room temperature for 60 minutes at 4C. Nuclei were washed twice in 1mL Wash125 then resuspended in 200 μL Wash125 + 0.2% formaldehyde for 2 minutes at RT. After 2 minutes, formaldehyde was quenched with 50 μL 2.5M Glycine. Nuclei were washed once in 1mL Wash350 (20mM HEPES pH 7.5, 350mM NaCl, 10mM Sodium butyrate, 0.025% Digitonin, 1 Roche Complete Protease Inhibitor, 0.5 mM Spermidine) then incubated in 47.5 μL Wash350 + 2.5 μL pAG-Tn5 (Epicypher 15-1017) for 60 minutes at RT. Nuclei were washed twice in 1mL Wash350, then resuspended in 300 μL Wash350 + 10mM MgCl2 and incubated for either 120 minutes (H3K9me3) or 60 minutes (H3K27ac) at 37C. Tn5 reaction was stopped with 10 µL 0.5M EDTA, 3 µL 10% SDS, and 3 µL 18 mg/mL Proteinase K, briefly vortexed, then incubated at 55C for 120 minutes to reverse crosslinks and release fragments. The fragments were then purified with phenol-chloroform and resuspended in 22 µL 1mM Tris-HCl (pH 8), 0.1mM EDTA.
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: ESCs were treated with either EtOH or 2 μM 4-OHT (Sigma) for 48hrs before harvesting for CUT&Tag.

value: Embryonic stem cells

value: C57Bl/6 KAP1 KO

value: H3K27ac:Active Motif 39133


title: 8_H82_NOTCH1_dox


title: 5_H82_NOTCH1_no_dox


title: 7_H82_NOTCH1_dox


title: ESC_CnT-H3K27ac_WT_rep2

value: C57Bl/6 KAP1 loxP/loxP


title: pre-treatment tumor RNA from individual with NSCLC_S059

description: Library name: S059

value: tumor biopsy


title: ESC_CnT-H3K9me3_KAP1cKO_rep2

value: H3K9me3:Abcam 8898


title: pre-treatment tumor RNA from individual with NSCLC_S058

description: Library name: S058


title: ESC_CnT-H3K27ac_WT_rep1


title: 3_H82_parental


title: ESC_CnT-H3K27ac_KAP1cKO_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S057

description: Library name: S057


title: ESC_CnT-H3K9me3_WT_rep2


title: 2_H82_parental


title: ESC_CnT-H3K9me3_WT_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S056

description: Library name: S056


title: Brain, AAV ABE, rep2

description:
ABEvsWT_deg_all.txt
ABEvsGFP_deg_all.txt
M422A

value: Brain


title: ESC_ATAC_KAP1cKO_V488E-AB_rep3

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

value: KAP1 V488E cDNA


title: pre-treatment tumor RNA from individual with NSCLC_S060

description: Library name: S060

value: KP


title: 1_H82_parental

value: small cell lung cancer

value: parental


title: ESC_ATAC_KAP1cKO_V488E-AB_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S054

description: Library name: S054


title: 4_H82_NOTCH1_no_dox


title: HSC,young,replicate 2, scATACseq

city: New York

first: Harold

middle: Kunal

last: Elias

state: New York

address: 417E 68th Street

department: Pathology

institute: Memorial Sloan Kettering Cancer Center

description:
3649_HA-1570_Young_mice_2_11_multiome_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.01).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: bone marrow

extract_protocol:
Femurs, tibias, pelvises, and the spine were dissected from euthanized mice and cleaned of muscles and connective tissue on ice in 1X PBS. Bone marrow cells were collected by crushing all the bones with a sterile mortar and pestle in FACS buffer: 1X PBS containing 2% Fetal Bovine Serum (Hyclone) and 2 mM EDTA.  BM cells were enriched for c-Kit+ cells using mouse CD117 magnetic microbeads (Miltenyi Biotec) per manufacturer’s protocol. Cells were FACS sorted using a FACS Aria II cell sorter (BD Biosciences).
Single Cell Multiome ATAC + Gene Expression was performed with the 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol - Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing. Briefly, cells (viability 95%) were lysed for 4min and resuspended in Diluted Nuclei Buffer (10x Genomics, PN- 2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue staining.  Nuclei were loaded per transposition reaction, with a targeting recovery between 1,000 and 10,000 nuclei after encapsulation. After transposition reaction nuclei were encapsulated and barcoded. Next-generation sequencing libraries were constructed following User Guide

value: bone marrow

value: hematopoeitic stem cells


title: pre-treatment tumor RNA from individual with NSCLC_S053

description: Library name: S053


title: HSC,old,replicate 2, scATACseq

description:
3650_HA-1570_Old_mice_2_11_multiome_ATAC
10x Genomics


title: HSC,young,replicate 1, scATACseq

description:
3575_HA-1536_Young_mice_multiome_ATAC
10x Genomics


title: pre-treatment tumor RNA from individual with NSCLC_S052

description: Library name: S052


title: ESC_ATAC_KAP1cKO_WT-AB_rep2

value: KAP1 cDNA


title: ESC_ATAC_KAP1cKO_V488E-AB_rep1


title: HSC,old,replicate 1, scATACseq

description:
3576_HA-1536_Old_mice_multiome_ATAC
10x Genomics


title: ESC_ATAC_KAP1cKO_WT-AB_rep3


title: HSC,old,replicate 2, scRNAseq

description:
3648_HA-1570_Old_mice_2_11_multiome
10x Genomics


title: ESC_ATAC_KAP1cKO_WT-AB_rep1


title: pre-treatment tumor RNA from individual with NSCLC_S050

description: Library name: S050


title: pre-treatment tumor RNA from individual with NSCLC_S049

description: Library name: S049


title: ESC_ATAC_KAP1cKO_rep3


title: HSC,old,replicate 1, scRNAseq

description:
3574_HA-1536_Old_mice_multiome
10x Genomics


title: ESC_ATAC_KAP1cKO_rep2


title: pre-treatment tumor RNA from individual with NSCLC_S048

description: Library name: S048

value: high


title: ESC_ATAC_KAP1cKO_rep1


title: HSC,young,replicate 1, scRNAseq

description:
3573_HA-1536_Young_mice_multiome
10x Genomics


title: 9_KP1_TAS1440_GSI


title: pre-treatment tumor RNA from individual with NSCLC_S047

description: Library name: S047

value: KL


title: pre-treatment tumor RNA from individual with NSCLC_S046

description: Library name: S046

value: low


title: ESC_ATAC_KAP1WT_rep3

value: Embryonic stem cells


title: pre-treatment tumor RNA from individual with NSCLC_S051

description: Library name: S051


title: ESC_ATAC_KAP1WT_rep2


title: 8_KP1_TAS1440_GSI


title: pre-treatment tumor RNA from individual with NSCLC_S045

description: Library name: S045

value: KC


title: ESC_ATAC_KAP1WT_rep1


title: HSC,young,replicate 2, scRNAseq

description:
3647_HA-1570_Young_mice_2_11_multiome
10x Genomics


title: pre-treatment tumor RNA from individual with NSCLC_S043

description: Library name: S043


title: pre-treatment tumor RNA from individual with NSCLC_S042

description: Library name: S042


title: vostok RNA-seq repeat3

city: Princeton

first: Michael

last: Levine

state: New Jersey

address: Icahn lab, Princeton University

institute: Princeton University

description: Library name: vostok-r-3

data_processing:
RNA-seq sample was processed by nf-core RNA-seq pipeline. Micro-C sample was aligned with bwa, sorted and filtered with pairtools, and multi-resolution contact matrices was generated with cooler.
Assembly: dm6
Supplementary files format and content: RNA-seq count table/tsv, contact matrix/cool

organism: Drosophila melanogaster

source_name: 3rd instar larval brain

extract_protocol:
Whole larval brains were dissected from 3rd instar larvae
For bulk RNA-seq, the total RNA was extracted in Trizol, following standard protocol and the library was prepared by NEBNext Ultra II Directional RNA Library Prep Kit. For MicroC, the whole brains were fixed in 1% formaldehyde and then DSG and EGS. After MNase digestion, biotin end labeling and proximal ligation, the ligated genomic DNA was extracted by PCI and enriched by streptavidin beads, and finally the libraries were prepared by NEBNext Ultra II DNA Library Prep Kit

value: 3rd instar larval brain

value: vostok


title: 5_KP1_TAS1440


title: vostok RNA-seq repeat4

description: Library name: vostok-r-4


title: 4_KP1_TAS1440


title: pre-treatment tumor RNA from individual with NSCLC_S044

description: Library name: S044

value: tumor biopsy


title: vostok RNA-seq repeat2

description: Library name: vostok-r-2


title: pre-treatment tumor RNA from individual with NSCLC_S041

description: Library name: S041


title: vostok RNA-seq repeat1

description: Library name: vostok-r-1


title: pre-treatment tumor RNA from individual with NSCLC_S040

description: Library name: S040


title: pre-treatment tumor RNA from individual with NSCLC_S039

description: Library name: S039


title: 7_KP1_TAS1440_GSI


title: 1_KP1_DMSO

value: DMSO


title: control RNA-seq repeat 3

description: Library name: yw-r-3

value: control


title: 6_KP1_TAS1440


title: WT_PBS_Oil_4

city: New

first: Sean

last: Houghton

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
TRB WT + PBS + Oil
TRB.707

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Trim Galore cutadapt wrapper (v0.6.7)
STAR (v2.7.9a) for alignment and gene count quantification using --quantMode GeneCounts
Assembly: ensembl 90 GRCm38
Supplementary files format and content: raw gene count matrix

source_name: WT on olive oil and hypothyroid

growth_protocol: RNA was purified from mouse liver 24 hours after the last injection of Carbon tetrachloride

extract_protocol:
liver RNA was extracted using RNA-STAT following a standar protocol
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with fed a PTU/LID diet and treated with carbon tetrachloride at a concentration of 0.4ul/g twice a week for four weeks, 9 injections total. Mice were replaced with T3 at 1 ug/ml in the drinking water during the last week of the carbon tetrachloride treatment.

value: Liver

value: WT

value: PBS and oil


title: pre-treatment tumor RNA from individual with NSCLC_S038

description: Library name: S038


title: control RNA-seq repeat 2

description: Library name: yw-r-2


title: WT_PBS_Oil_3

description:
TRB WT + PBS + Oil
TRB.709


title: pre-treatment tumor RNA from individual with NSCLC_S037

description: Library name: S037


title: control RNA-seq repeat 1

description: Library name: yw-r-1


title: WT_PBS_Oil_2

description:
TRB WT + PBS + Oil
TRB.639


title: 3_KP1_DMSO

value: small cell lung cancer


title: vostok Micro-C repeat 2

description: Library name: vostok-c-2


title: KO_PBS_Oil_4

description:
TRB KO + PBS + Oil
TRB.727

source_name: KO on olive oil and hypothyroid

value: Thyroid hormone receptor beta KO


title: vostok Micro-C repeat 1

description: Library name: vostok-c-1


title: pre-treatment tumor RNA from individual with NSCLC_S036

description: Library name: S036


title: 2_KP1_DMSO


title: WT_PBS_Oil_1

description:
TRB WT + PBS + Oil
TRB.726


title: GBM8205,TMZ,Olaparib2

city: 丰台区

first: xiaowei

last: Sha

state: 北京市

address: 北京市丰台区首都医科大学

institute: Capital Medical University

description: Library name: Sample 4

data_processing:
Preprocess the raw data using Cutadapt (version 1.9.1), filter out low-quality data, and remove contamination and adapter sequences.
The trimmed sequence reads were aligned using HISAT2 (v2.0.1) with the reference genome version hg38. The mismatch penalty  was set to 6,2; the insertion penalty  was set to 1,1; and the deletion penalties were set to 5,3. The minimum alignment score was set to L,0,-0.2.
HTSeq (v0.91) extracts gene read counts from aligned data. The DESeq2 tool is used for normalization.
Assembly: hg38
Supplementary files format and content: raw counts for each sasmple
Supplementary files format and content: FPKM values for each sample

growth_protocol: The GBM8205 cells were cultured at 37°C in a humidified incubator maintaining 5% CO₂, in high-glucose Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco, Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco, 15140-122, NY, USA).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (15596-026, Invitrogen, USA) and purified using an RNA-Quick Purification Kit (Yishan Biotechnology Co., Ltd., Shanghai, China).
The transcriptome library was constructed following the standard protocol for VAHTS Universal V5 RNA-seq Library Preparation Kit (NR616-01/02, Vazyme, Nanjing, China).

treatment_protocol: Cells treated with a combination of 20 μM Olaparib and 50 μM TMZ were compared to those treated with TMZ alone over a 24-hour period.

value: patient-derived glioblastoma cell line

value: TMZ and bevacizumab resistance


title: pre-treatment tumor RNA from individual with NSCLC_S034

description: Library name: S034


title: control RNA-seq repeat 4

description: Library name: yw-r-4


title: KO_PBS_Oil_3

description:
TRB KO + PBS + Oil
TRB.728


title: pre-treatment tumor RNA from individual with NSCLC_S032

description: Library name: S032

value: high


title: KO_PBS_Oil_2

description:
TRB KO + PBS + Oil
TRB.720


title: pre-treatment tumor RNA from individual with NSCLC_S031

description: Library name: S031


title: KO_PBS_Oil_1

description:
TRB KO + PBS + Oil
TRB.729


title: GBM8205,TMZ1

address: 北京市丰台区首都医科大学

description: Library name: Sample 1


title: pre-treatment tumor RNA from individual with NSCLC_S035

description: Library name: S035

value: KL


title: WT_PBS_CCL4_4

description:
TRB WT + PBS + CCL4
TRB.759

source_name: WT on CCL4 and hypothyroid

value: PBS and CCL4


title: pre-treatment tumor RNA from individual with NSCLC_S030

description: Library name: S030

value: KP

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S029

description: Library name: S029


title: WT_PBS_CCL4_3

description:
TRB WT + PBS + CCL4
TRB.645


title: pre-treatment tumor RNA from individual with NSCLC_S033

description: Library name: S033

value: KC


title: pre-treatment tumor RNA from individual with NSCLC_S028

description: Library name: S028


title: C1_rep2

city: Lexington

first: Jessica

middle: S

last: Blackburn

state: Kentucky

address: 741 S. Limestone

institute: University of Kentucky

description:
Library name: 1-6
second column is sum of raw read counts labelled : SCC126_C1_1-6

data_processing:
Cutadapt was used to trim adapters on Galaxy
Transcript read counts were generated using Htseq
mirDeep2 was used to map reads to hairpin and mature sequences and qunatify mapped reads on galaxy
R was used to sum read count files.
Assembly: gencode v44
Supplementary files format and content: csv file for each sample with a list of summed raw read counts

growth_protocol: SF8628 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM glutamine, and antibiotics in a hunmidifed atmosphere with 5% CO2 at 37C. SF7761 cells were maintained in ReNCell media supplemetned with 20ng/ul of hEGF, hFGF, antibiotics, and 1mM glutamine.

extract_protocol:
Total RNA was harvested using Trizol extraction.
Libraries were generated using the SMARTer smRNA-Seq kit. 5ng of RNA input was used.

treatment_protocol: Cells were grown to confluence either in 100mm dishes (SF8628) or in T75 flasks when neuroshperes reach ~50-200um in diameter (SF7761). For SF8628 cells, conditioned media for sEV isolation was harvested under FBS depleted media conditions. sEVs were isolated via differntial ultracentrifugation followed by 100 kDa ultrafiltration

value: pDMG


title: 127

description:
Library name: 1-9
second column is sum of raw read counts labelled : SCC127


title: C1_rep1

description:
Library name: 1-5
second column is sum of raw read counts labelled : SCC126_C1_1-5


title: KO_PBS_CCL4_4

description:
TRB KO + PBS + CCL4
TRB.760

source_name: KO on CCL4 and hypothyroid


title: Organoid,RBM25 KO+Tnfa,3

description:
one sample from inner ear organoid with TNF-α treatment and RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204T_3

data_processing:
Fastq files were trimmed with Trimmomatic. Clean reads were mapped to the mouse reference genome (mm10) using HISAT2, followed by transcript assembly using HTSeq and differential gene expression analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

growth_protocol: For inner ear tissues, Male C57BL6/J mice were used in this study. 2-month-old male mice were purchased from Jihui Experimental Animal Breeding Co., Ltd (Shanghai) and then raised in a certificated SPF-grade facility (Fudan University Animal Facility) with individually ventilated cages. For snRNA-seq, young mice (3-month-old, n=20 mice), medium mice (12-month-old, n=20 mice), and old mice (24-month-old, n=20 mice) were sacrificed. For bulk RNA-seq, young mice (3-month-old, n=4 mice), medium mice (11-month-old, n=4 mice), and old mice (20-month-old, n=4 mice) were sacrificed. For organoids cculture, the cochlear epithelia from postnatal day (P) 1–2 mice were dissected and collected in ice-cold PBS. Then tissues were incubated in 0.125% trypsin for 15 min at 37°C, and a trypsin neutralizer was used to terminate the digestion process. After gentle trituration repeatedly with a 1 ml syringe, the cell suspension was passed through a 40 μm cell strainer. Single cells were collected after washing with PBS two times and centrifuging at 1,500 rpm for 6 min. Collected cells were resuspended in 5% Matrigel dissolved in the expansion culture medium. During the first 8–10 days, Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 supplemented with 1% N2 , 2% B27 , and 100 μg/ml penicillin/streptomycin, 50 ng/mL EGF, 50 ng/mL bFGF, 50 ng/mL IGF, 3.5 μM CHIR99021 was used as expansion medium. The formed organoids were released from Matrigel with cell recovery solution and then attached to the slides for differentiation. During the differentiation stage, the growth factors were removed, and small molecules containing 3 μM CHIR99021 and 5 μM LY411575  were added for 7-8 days. Subsequently, small molecules were replaced by a low dose of EGF (10 ng/mL) and bFGF (10 ng/mL) for 9-10 days.

extract_protocol:
Total mRNA was extracted using Trizol (Life Technologies) and purified with an RNeasy Mini Kit (QIAGEN).
TruSeq RNA Library Prep Kit v2 (Illumina) was used for preparing libraries and samples were sequenced on an Illumina HiSeq 2500 platform.

treatment_protocol: Mice were without treatment. Inner ear organoids were treated with TNF-α, RBM25 knock down (lentivirus transfected), and  TNF-α+RBM25 knock down (lentivirus transfected).

value: Inner ear

value: Inner ear organoid cell

value: TNF-α+ RBM25 knock down


title: pre-treatment tumor RNA from individual with NSCLC_S027

description: Library name: S027

value: tumor biopsy


title: 126Par

description:
Library name: 1-3
second column is sum of raw read counts labelled : SCC126Par

value: WT


title: pre-treatment tumor RNA from individual with NSCLC_S026

description: Library name: S026


title: WT_PBS_CCL4_1

description:
TRB WT + PBS + CCL4
TRB.746

value: Liver


title: Organoid,RBM25 KO+Tnfa,2

description:
one sample from inner ear organoid with TNF-α treatment and RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204T_2


title: GBM8205,TMZ,Olaparib1

address: 北京市丰台区首都医科大学

description: Library name: Sample 3


title: GBM8205,TMZ2

address: 北京市丰台区首都医科大学

description: Library name: Sample 2


title: pre-treatment tumor RNA from individual with NSCLC_S024

description: Library name: S024


title: Organoid,RBM25 KO+Tnfa,1

description:
one sample from inner ear organoid with TNF-α treatment and RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204T_1


title: KO_PBS_CCL4_2

description:
TRB KO + PBS + CCL4
TRB.718


title: pre-treatment tumor RNA from individual with NSCLC_S023

description: Library name: S023


title: Organoid,RBM25 KO,3

description:
one sample from inner ear organoid with RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204_3

value: RBM25 knock down


title: KO_PBS_CCL4_3

description:
TRB KO + PBS + CCL4
TRB.688

value: Thyroid hormone receptor beta KO


title: WT_PBS_CCL4_2

description:
TRB WT + PBS + CCL4
TRB.708


title: pre-treatment tumor RNA from individual with NSCLC_S022

description: Library name: S022


title: Organoid,RBM25 KO,2

description:
one sample from inner ear organoid with RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204_2


title: pre-treatment tumor RNA from individual with NSCLC_S025

description: Library name: S025


title: pre-treatment tumor RNA from individual with NSCLC_S021

description: Library name: S021


title: FiNs, Day5

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
The clean scRNA-seq reads were mapped to the human reference genome hg38 using Cell Ranger v.4.0.0 for all of the samples.
Assembly: GRCh38

source_name: FiN cells

growth_protocol: BJ  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Each sample dissociated cells (~10,000 cells per sample) were loaded into a 10× Genomics Chromium Single Cell system using Chromium Single Cell 3’ Reagent Kits v3.1 (10× Genomics, Pleasanton, CA).
Library was performed according to the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1manufacter’s instructions.

treatment_protocol: BJ cells were seeded on Poly-D-Lysine (PDL) (Gibco, Cat. #A38904-01) coated dishes, cultured with DMEM+10% FBS to a cell density of 80%, then replaced with neuronal induction medium (including 10μM Forskolin) (IM) supplemented with 10μM Forskolin, replace this medium every 2 days. On day 2, induction mediumIM+F  was replaced with neuronal maturation medium (MM) supplemented with 10μM Forskolin, and replace this medium every 2 days. On day 5, 10μM Forskolin was removed and the medium was replaced with neuronal cell culture medium (NM), which was replaced every 2 days.

value: FiN cells

value: induced neuron cells

value: reprogramming


title: WT_T3_Oil_3

description:
TRB WT + T3 + Oil
TRB.664

source_name: WT on olive oil and T3

value: T3 and oil


title: WT_T3_Oil_4

description:
TRB WT + T3 + Oil
TRB.648


title: Organoid,RBM25 KO,1

description:
one sample from inner ear organoid with RBM25 knock down
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
R204_1


title: SJE2A025 primary leukemic blasts

city: Memphis

first: Mondira

last: Kundu

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Hospital

data_processing:
Single-cell RNA sequencing data were processed by the CellRanger pipeline (v1.2.0).
Assembly: hg19
Supplementary files format and content: Barcode sequences, feature IDs in txt format and gene level count in Market Exchange Format
Supplementary files format and content: Filtered barcode sequences containing only detected cell-associated barcodes
Supplementary files format and content: Feature ID and name
Supplementary files format and content: Filtered sparese count matrix in the Market Exchange Format (MEX), where feature and barcode sequences corresponding to row and column indices respectively
Supplementary files format and content: Raw barcode sequence with at least one UMI
Supplementary files format and content: Feature ID and name
Supplementary files format and content: Sparese count matrix in the Market Exchange Format (MEX), where feature and barcode sequences corresponding to row and column indices respectively

source_name: primary leukemic blasts

extract_protocol:
Cryopreserved bone marrow samples were thawed and sorted for viable cells.  Viable single-cell suspensions were processed using the Chromium v.2 Single Cell 3′ Library and Gel Bead Kit protocol, for sequencing on a 10X Genomics Chromium single-cell platform
Libraries were constructed according to the Chromium v.2 Single Cell 3′ Library and Gel Bead Kit protocol
Libraries were paired-end sequenced (26-bp read 1, 8-bp I7 index, and 98-bp read 2 configuration) on an Illumina NovaSeq 6000 genome analyzer

value: Bone marrow

value: pediatric

tag: disease state

value: B-lineage acute lymphoblastic leukemia


title: SJE2A037 primary leukemic blasts


title: WT_T3_Oil_2

description:
TRB WT + T3 + Oil
TRB.742


title: pre-treatment tumor RNA from individual with NSCLC_S020

description: Library name: S020

data_processing:
Transcript level pseudo-alignment and quantification to the Ensembl GRCh37 Release 97 (July 2019) reference was performed using Kallisto (version 0.44). Raw counts or transcripts per million (TPM) were calculated for 180,253 transcripts in the Ensembl reference. 134,160 transcripts were covered by the Tempus|RS panel.
Assembly: Ensembl GRCh37 Release 97 (July 2019)
Supplementary files format and content: tab-delimited text file with columns for ensembl_gene, hgnc_symbol, <sampleID>. TPM values are in the <sampleID> column.

source_name: tumor biopsy

extract_protocol:
Total nucleic acid (TNA) was extracted from tissue specimens using a Chemagic 360 or similar instrumentation, and the recovered TNA was quantified and qualified, and may have been concentrated if necessary. Extracted TNA that was intended for processing by Tempus|RS was treated with Invitrogen TURBO DNase to degrade DNA. The minimum amount of input total RNA required to perform the test was 50 ng. RNA was fragmented using heat and magnesium, with variable parameters, to yield similar sized fragments from RNA inputs with different starting size distributions.
Strand-specific library preparation was performed using the KAPA RNA HyperPrep Kit for Illumina with KAPA single indexed 6 base pair adapters. The libraries were amplified with high fidelity, low-bias PCR using primers complementary to adapter sequences. After library preparation and amplification, targets were captured by hybridization, clean-up of captured targets was performed, and unbound fragments were washed away. Library capture is conducted using the xGen Exome Research Panel v1 probe set, along with the xGen Hybridization and Wash Kit and xGen Universal Blockers. The enriched targets are amplified using the KAPA HiFi HotStart ReadyMix and primers supplied in the KAPA Library amplification kit, followed by a magnetic bead-based clean-up. The amplified target-captured libraries were sequenced with a 2x76 read length to an average of 50 million total reads on an Illumina HiSeq4000 System using patterned flowcells.

value: KP

value: low


title: pre-treatment tumor RNA from individual with NSCLC_S019

description: Library name: S019


title: Organoid,Con+Tnfa,2

description:
one sample from inner ear organoid with TNF-α treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
CT_2

value: Inner ear

value: TNF-α


title: SJE2A015 primary leukemic blasts


title: pre-treatment tumor RNA from individual with NSCLC_S018

description: Library name: S018

value: KC


title: pre-treatment tumor RNA from individual with NSCLC_S017

description: Library name: S017

value: tumor biopsy


title: BJs, Day0 [scATAC-Seq]

data_processing:
Expression profiling by high throughput sequencing
Sequencing data were processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) using default parameters and mapped to the human reference genome hg38.
Assembly: GRCh38

source_name: BJ cells

extract_protocol:
Use Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 to preparation Nuclei suspensions.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell ATAC Reagent Kits v1.1).

value: BJ cells

value: Fibroblast cells

value: WT


title: KO_T3_Oil_3

description:
TRB KO + T3 + Oil
TRB.684

source_name: KO on olive oil and T3

value: Liver

value: Thyroid hormone receptor beta KO


title: Organoid,Con,3

description:
one sample from inner ear organoid without treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
C_3

value: Inner ear organoid cell


title: WT_T3_Oil_1

description:
TRB WT + T3 + Oil
TRB.747


title: FiNs, Day3

data_processing:
Expression profiling by high throughput sequencing
The clean scRNA-seq reads were mapped to the human reference genome hg38 using Cell Ranger v.4.0.0 for all of the samples.
Assembly: GRCh38

value: FiN cells

value: induced neuron cells

value: reprogramming


title: Organoid,Con+Tnfa,3

description:
one sample from inner ear organoid with TNF-α treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
CT_3


title: KO_PBS_CCL4_1

description:
TRB KO + PBS + CCL4
TRB.689

value: PBS and CCL4


title: pre-treatment tumor RNA from individual with NSCLC_S016

description: Library name: S016

value: high


title: KO_T3_Oil_2

description:
TRB KO + T3 + Oil
TRB.651

value: T3 and oil


title: FiNs, Day3 [scATAC-Seq]


title: pre-treatment tumor RNA from individual with NSCLC_S015

description: Library name: S015

value: KL

value: low


title: KO_T3_Oil_1

description:
TRB KO + T3 + Oil
TRB.676


title: BJs, Day0


title: WT_T3_CCL4_4

description:
TRB WT + T3 + CCL4
TRB.667

source_name: WT on CCL4 and T3

value: T3 and CCL4


title: pre-treatment tumor RNA from individual with NSCLC_S014

description: Library name: S014

value: KP


title: FiNs, Day5, 2

data_processing:
Expression profiling by high throughput sequencing
Assembly: GRCh38
Supplementary files format and content: gene.count

extract_protocol:
Total RNA was extracted from the treated BJ cells with F from day 0 , day 2 and day 5 using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina using 1μg of total RNA.

tag: time point


title: WT_T3_CCL4_3

description:
TRB WT + T3 + CCL4
TRB.683


title: pre-treatment tumor RNA from individual with NSCLC_S013

description: Library name: S013

value: tumor biopsy


title: Organoid,Con,1

description:
one sample from inner ear organoid without treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
C_1

value: Inner ear


title: Organoid,Con,2

description:
one sample from inner ear organoid without treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
C_2


title: FiNs, Day5, 1


title: Cochlea,20M,3

description:
one sample from 20M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Twe_M3

value: Inner ear cell


title: pre-treatment tumor RNA from individual with NSCLC_S012

description: Library name: S012


title: FiNs, Day2, 2

value: WT


title: Organoid,Con+Tnfa,1

description:
one sample from inner ear organoid with TNF-α treatment
RBM25 FPKM_anno.txt
RBM25 counts_anno.txt
CT_1

value: TNF-α


title: WT_T3_CCL4_2

description:
TRB WT + T3 + CCL4
TRB.675

value: Liver


title: Cochlea,20M,2

description:
one sample from 20M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Twe_M2


title: Cochlea,20M,4

description:
one sample from 20M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Twe_M4


title: FiNs, Day2, 1


title: ESC_CnT-H3K9me3_KAP1cKO_rep1

source_name: Embryonic stem cells

value: Embryonic stem cells

value: C57Bl/6 KAP1 KO

value: H3K9me3:Abcam 8898


title: pre-treatment tumor RNA from individual with NSCLC_S055

description: Library name: S055


title: KO_T3_CCL4_4

description:
TRB KO + T3 + CCL4
TRB.761

source_name: KO on CCL4 and T3

value: Thyroid hormone receptor beta KO


title: WT_T3_CCL4_1

description:
TRB WT + T3 + CCL4
TRB.763


title: Cochlea,20M,1

description:
one sample from 20M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Twe_M1

source_name: Inner ear


title: BJs, Day0, 2

value: BJ cells

value: Fibroblast cells

value: reprogramming


title: Cochlea,11M,4

description:
one sample from 11M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Ele_M4


title: pre-treatment tumor RNA from individual with NSCLC_S010

description: Library name: S010


title: pre-treatment tumor RNA from individual with NSCLC_S009

description: Library name: S009

value: KC

value: high


title: BJs, Day0, 1


title: KO_T3_Oil_4

description:
TRB KO + T3 + Oil
TRB.749

value: T3 and oil


title: Cochlea,11M,2

description:
one sample from 11M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Ele_M2


title: KO_T3_CCL4_2

description:
TRB KO + T3 + CCL4
TRB.743

value: T3 and CCL4


title: pre-treatment tumor RNA from individual with NSCLC_S007

description: Library name: S007

value: tumor biopsy

value: KP

value: low


title: GM23338_Microglia_screen, mTeSR1 + DOX

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

description: Amplified barcode region from Tfome screens of 16+ TFs for each target cell type

data_processing:
homer v4.9 read trimming (Transcriptome sequencing)
Bowtie2 v2.2.9 to align reads to hg38 (Transcriptome sequencing)
homer v4.9 peak calling and read count extraction (Transcriptome sequencing)
Custom script for barcode tallying in amplicon sequencing (TFome screening)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample and barcode counts for amplicon sequencing

growth_protocol: All iPSCs maintained in mTeSR1 until differentiation

extract_protocol:
RNA was harvested using Directzol RNA miniprep kit (Transcriptome sequencing) (Zymo) or Directzol RNA microprep kit (amplicon sequencing of TFome screens) (Zymo)
RNA libraries for RNA-seq were prepared using either SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TFome screening) or NEBNext Ultra II RNA Kit (Transcriptome sequencing) following manufacturer's protocols.

treatment_protocol: Differentiation for 6 days in mTeSR1 and a variety of target cell type-specific media conditions with 1ug/mL DOX

value: iPSC-derived microglia

value: Overexpression of screening TFs:[16+ TFs]

value: Induction with 1ug/mL DOX in mTeSR1 Medium

tag: time

value: Day 6


title: pre-treatment tumor RNA from individual with NSCLC_S008

description: Library name: S008


title: Cochlea,11M,3

description:
one sample from 11M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Ele_M3

value: Inner ear

value: Inner ear cell

value: WT


title: pre-treatment tumor RNA from individual with NSCLC_S006

description: Library name: S006


title: KO_T3_CCL4_3

description:
TRB KO + T3 + CCL4
TRB.748

value: Liver

value: Thyroid hormone receptor beta KO


title: GM23338_Hepatocyte_screen, mTeSR1 + DOX

value: iPSC-derived hepatocytes


title: GM23338_regulatory_TCell_screen, mTeSR1 + DOX

value: iPSC-derived regulatory T-cells


title: Cochlea,11M,1

description:
one sample from 11M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Ele_M1


title: Cochlea,3M,4

description:
one sample from 3M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Thr_M4


title: Cochlea,3M,3

description:
one sample from 3M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Thr_M3


title: genomic DNA from peripheral blood [9992576025_R06C01]

type: genomic

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
The Bioconductor R package minfi was used for the quality control of DNAm data. Failed probes based on a detection P-value larger than 0.01 in >50% of the samples as well and non-specific binding probes a nd probes on X and Y chromosome were removed.
We also excluded probes if single nucleotide polymorphisms (SNPs) were documented in the interval for which the Illumina probe is designed to hybridize. Probes located close (10 bp from query site) to a SNP which had a minor allele frequency of ≥0.05, as reported in the 1,000 Genomes Project, were also removed
The data were then normalized with functional normalization. Batch effects were identified using the Empirical Bayes’ method ComBat . Batch corrected M-values after ComBat were used for all further statistical analyses

label: cy3, cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood

tag: genetic sex (male=1, female=2)

tag: weighted life events


title: genomic DNA from peripheral blood [9992576025_R06C02]


title: pre-treatment tumor RNA from individual with NSCLC_S004

description: Library name: S004

value: KC

value: high


title: genomic DNA from peripheral blood [9992576025_R05C02]


title: Cochlea,3M,2

description:
one sample from 3M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Thr_M2


title: KO_T3_CCL4_1

description:
TRB KO + T3 + CCL4
TRB.649

value: T3 and CCL4


title: Cochlea,3M,1

description:
one sample from 3M murine cochlea
Aging FPKM_anno.txt
Aging counts_anno.txt
Thr_M1


title: pre-treatment tumor RNA from individual with NSCLC_S002

description: Library name: S002

value: tumor biopsy


title: delta_pbpp6, KO 3

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

data_processing:
Reads counts were obtained with HTSeq v0.9.1. Differential expression analysis of genes between the WT and Δpbpp6 parasites were determined using the DESeq R package (1.18.0). The p-values were adjusted using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR). Genes with an adjusted P value <0.05 found by DESeq were assigned as differentially expressed.
Assembly: PbANKA01 of the P. berghei ANKA reference genome
Supplementary files format and content: tab-delimited text files include readsount values for each Sample

organism: Plasmodium berghei ANKA

source_name: gamete

growth_protocol: activated gametocytes from WT and Δpbpp6 parasite were maintained in gametocyte activation buffer

extract_protocol:
activated gametocytes from WT and Δpbpp6 parasite were purified with 48% Nycodenz and activated in gametocyte activation buffer at 25℃ for 15 min
mRNA was enriched using poly-T oligo-attached magnetic beads. Reverse transcription was performed with SuperScript II (Invitrogen) using random primers. The reaction was then treated with RNaseH to remove the RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced using the Illumina platform.
RNA-seq raw data were initially filtered by fastq to obtain high-quality, clean data. Adapter trimming was performed using cutadapt version 1.13 (http://cutadapt.readthedocs.io/en/stable/guide.html). Processed reads were aligned to the P. berghei ANA genome (assembly PlasmoDB-67) with Hisat2 v2.0.4 [108] and deduplicated according to UMI using UMI-tools (v1.0.0)

value: gamete

tag: strain

value: ANKA

value: pbpp6 gene deleton


title: genomic DNA from peripheral blood [9992576018_R03C02]

tag: age


title: delta_pbpp6, KO 2

tag: tissue


title: genomic DNA from peripheral blood [9992576025_R02C01]


title: pre-treatment tumor RNA from individual with NSCLC_S011

first: Abraham

last: Anderson

description: Library name: S011

tag: study

value: KP

value: low


title: delta_pbpp6, KO 1


title: GM23338_BCell_screen, mTeSR1 + DOX

value: iPSC-derived B-cells

value: Overexpression of screening TFs:[16+ TFs]

value: Induction with 1ug/mL DOX in mTeSR1 Medium

value: Day 6


title: pre-treatment tumor RNA from individual with NSCLC_S001

description: Library name: S001

tag: atm


title: GM23338_Cytotoxic_TCell_screen, mTeSR1 + DOX

value: iPSC-derived cytotoxic T-cells


title: genomic DNA from peripheral blood [9992576018_R03C01]


title: pre-treatment tumor RNA from individual with NSCLC_S005

description: Library name: S005

tag: kpclsignature


title: CD45 positive immune cells isolated from plasma of the rGBM patient

city: Chicago

first: Derek

middle: A

last: Wainwright

state: IL

address: 2160 South First Avenue

department: Cancer Biology

institute: Loyola University Chicago Stritch School of Medicine

description:
Library name: NU03118_PBMC_S2_L001
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software.
Assembly: hg38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: blood

extract_protocol:
Single cell suspension was prepared from fresh surgically resected tumor tissue using the Adult Brain Dissociation Kit (Miltenyi Biotec) according to manufacturer’s protocol. Tumor infiltrating leukocytes and peripheral immune cells were further isolated using biotinylated CD45 antibodies coupled with magnetic streptavidin microbeads (Miltenyi Biotec) form the tumor single cell suspension and PBLs, respectively. Cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method.
Sixteen thousand cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with 2 × 50 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

value: blood

value: CD45+ immune cell


title: genomic DNA from peripheral blood [9992576018_R01C01]


title: CD45 positive immune cells isolated from rGBM signle cell suspension

description:
Library name: NU03118_CD45_S3_L001
10x Genomics

source_name: GBM tumor

value: GBM tumor


title: PbANKA wild type strain, control 3

tag: genotype

value: WT


title: GM23338_TypeII_astrocyte_screen, mTeSR1 + DOX

value: iPSC-derived typeII astrocytes


title: C2C12_DM_pLXSN_rep1

city: Ottawa

first: Nadine

last: Wiper-Bergeron

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
HISAT2 (v 2.0.4) was used to map the reads to the GRCm38 (mm10) genome, using the Gencode M12 transcript annotations to guide alignment to spliced transcripts and mapping parameters appropriate for a stranded RNA-seq library
featureCounts (v 1.4.6) used to count the mapped reads associated with each GENCODE transcript
The differential analysis is run using the DESeq2 package, which uses the read count tables generated by featureCounts
All data processing were performed by the Ottawa Bioinformatics Core Facility (OBCF) by Christopher Porter
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts gene quantification: tab-delimited text file of raw read counts per gene.
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text table extracted from DESeqResults object

source_name: differentiating myoblasts

growth_protocol: Myoblast cell line (C2C12) were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and at 90% confluency, cells were differentiated for 2 days in DMEM supplemented with 2% hourse serum (HS) at 37ºC with 5% CO2

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) sent to the McGill University Genome Quebec Innovation Centre for sequencing using Illumina HiSeq 2500 platform.
mRNASeq stranded library (NEB) by McGill University Genome Quebec Innovation Centre

treatment_protocol: C2C12s were retrovirally transduced with empty vector or to overexpress C/EBPβ. After 7 days of 1200 μg/ml G418 selection, pooled stable cells were allowed to proliferate for 2 days then differentiated for 2 days.

tag: differentiation  status

value: differentiating myoblasts


title: C2C12_DM_C/EBPβ_rep1

tag: cell line

value: retrovirally transduced to overexpress C/EBPBeta


title: Single cell suspension isolated from recurrent GBM (rGBM) tumor

description:
Library name: NU03118_Tumor_S1_L001
10x Genomics

value: rGBM tumor cell


title: genomic DNA from peripheral blood [9992576025_R02C02]


title: pre-treatment tumor RNA from individual with NSCLC_S003

city: Thousand Oaks

address: 1 amgen center drive

institute: Amgen Inc.

description: Library name: S003

value: tumor biopsy

value: KL


title: genomic DNA from peripheral blood [9992571104_R06C02]


title: SF8628_Biol_rep_3

description:
Library name: 1F
Row name in processed data file : SF8628-R1

data_processing:
Fastq files were aligned with the human reference sequence using STAR aligner.
Transcript read counts were generated using Htseq
Assembly: GRCh38 was used
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was harvested by spinning down 1E6 cells and using the pellet with the Zymo Research Quick-RNA kit. 250ng of RNA was used for library prepartion after using the NEBNext Poly (A) mRNA Magnetic Isolation Module
Libraries were generated using the NEBNext Ultra II Express Library Preparation kit for Illumina

treatment_protocol: Cells were grown to confluence either in 100mm dishes (SF8628) or in T75 flasks when neuroshperes reach ~50-200um in diameter (SF7761).

value: pDMG


title: PbANKA wild type strain, control 1

value: gamete

value: ANKA

tag: treatment


title: C2C12_DM_C/EBPβ_rep2


title: genomic DNA from peripheral blood [9992571104_R06C01]


title: Pateint 112 PBLs sample collected at C1D1

description: Library name: s112-1-5_S22_R1

data_processing:
For RNA-seq data analysis, the quality of reads, in FASTQ format, was evaluated using FastQC.  Reads were trimmed to remove Illumina adapters from the 3’ ends using CUTADAPT1.  Trimmed reads were aligned to the human genome (hg38) using STAR2.  Read counts for each gene were calculated using HTseq-count3 in conjunction with a gene annotation file for mm10 obtained from Ensembl (http://useast.ensembl.org/index.html).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted and purified from frozen PBL cell pellets using Invitrogen PureLink RNA Mini kit (ThermoFisher Scientific, #12183018A). RNA sample quantity and quality were measured by Qubit RNA HS assay kit and Agilent Bioanalyzer RNA Nano chip to confirm RNA integrity, respectively.
Three hundred nanogram of total RNA was used to construct RNA-seq library using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB #E7765L) according to manufacturer’s protocol.

value: Blood

tag: cell type

value: Peripheral blood leukocytes

tag: patient diagnosis

value: glioblastoma (GBM)


title: genomic DNA from peripheral blood [9992571104_R04C02]


title: Patient C oligodendroglioma tumor resection

city: Melbourne

first: Saskia

last: Freytag

address: 1G Royal Parade, Parkville

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
Library name: O-C
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the multi command from the Cell Ranger software (v7.1.0) and BAM files created using the CellRanger software (v9.0.0). Further processing was performed using R (v4.4.1).
Assembly: Human GRCh38 (hg38)
Supplementary files format and content: BAM files and Tab-seperated value (TSV) files

molecule: nuclear RNA

source_name: Brain tumour resection

extract_protocol:
Tumor resection tissue was frozen on dry ice and stored at -80°C until nuclei isolation. All steps involved in isolation of nuclei were conducted using pre-chilled buffers and a centrifuge pre-set to 4°C. Tissue was transferred to a Dounce homogeniser containing homogenisation buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris pH 8.0, 1 mM dithiothreitol (DTT), 0.2 U/μl RNasin ribonuclease inhibitor, and 0.1% Triton X-100) and incubated for one minute before homogenization. Tissue was homogenized using a combination of loose and/or tight pestles and a 1 ml pipette tip, depending on the individual piece of tissue. The resulting homogenates were filtered through a 30 μm strainer and centrifuged at 500 × g for 5 minutes. Supernatant was discarded and the pellet was resuspended in wash and resuspension buffer (Dulbecco’s PBS containing 1% bovine serum albumin (BSA), 1 mM DTT, and 0.2 U/μl RNasin ribonuclease inhibitor). A further 1-2 washes were conducted, depending on pellet size. Nuclei were counted using trypan blue and a haemocytometer. Nuclei were then fixed using the Chromium Next GEM single cell fixed RNA sample preparation kit (10x Genomics) and stored at -80°C according to the manufacturer’s instructions.
Fixed nuclei were barcoded using the human transcriptome Chromium Fixed RNA kit, human transcriptome (4 reactions x 4-3 barcodes) (10x Genomics) with probe hybridisation conducted according to the manufacturer’s instructions. Nuclei were targeted on the Chromium controller, after which library preparation was conducted. Library preparation was performed using the Chromium Single Cell Gene Expression Flex Kit (10X Genomics) according to the manufacturer's instructions. Briefly, single nuclei were encapsulated into Gel Bead-In-Emulsions (GEMs), where poly-A RNA was reverse transcribed to cDNA incorporating a Unique Molecular Identifier (UMI) and a 10X Barcode. Adapter ligation was performed to generate paired-end libraries with P5 and P7 adapters and multiplexed for Illumina sequencing. Final libraries were quality checked and sequenced on an Illumina platform.

value: Brain tumour resection

tag: number of_cells_detected


title: SF7761_Clone_1_Biol_rep_3

description:
Library name: 1B
Row name in processed data file : SF7761-Clone #1-R1


title: Patient 112 PBLs sample collected at baseline

description: Library name: s112-01_S12_R1


title: C2C12_DM_pLXSN_rep2

value: retrovirally transduced with empty vector


title: genomic DNA from peripheral blood [9992571104_R04C01]


title: Patient 111 PBLs sample collected at baseline

description: Library name: s111-01_S11_R1


title: Patient A oligodendroglioma tumor resection

description:
Library name: O-A
10x Genomics


title: PbANKA wild type strain, control 2


title: Patient H astrocytoma tumor resection

description:
Library name: A-H
10x Genomics


title: Patient B oligodendroglioma tumor resection

description:
Library name: O-B
10x Genomics


title: Patient 110 PBLs sample collected at baseline

description: Library name: s110-01_S10_R1


title: SF8628_Biol_rep_2

description:
Library name: 127-R2
Row name in processed data file : SF8628-R3


title: SF7761_Biol_rep_3

description:
Library name: 1A
Row name in processed data file : SF7761-Parent Line-R1


title: SF7761_Clone_1_Biol_rep_1

description:
Library name: C1-R1
Row name in processed data file : SF7761-Clone #1-R2


title: SF8628_Biol_rep_1

description:
Library name: 127-R1
Row name in processed data file : SF8628-R2


title: Patient F astrocytoma tumor resection

description:
Library name: A-F
10x Genomics


title: Patient 109 PBLs sample collected at baseline

description: Library name: s109-01_S9_R1


title: Patient 108 PBLs sample collected at C1D1

description: Library name: s108-02_S20_R1


title: Patient G astrocytoma tumor resection

description:
Library name: A-G
10x Genomics


title: genomic DNA from peripheral blood [9761749038_R04C01]


title: SF7761_Biol_rep_2

description:
Library name: 126-R2
Row name in processed data file : SF7761-R3


title: genomic DNA from peripheral blood [9761749038_R03C02]


title: Patient 109 PBLs sample collected at C1D1

description: Library name: s109-02_S21_R1


title: Patient E astrocytoma tumor resection

description:
Library name: A-E
10x Genomics


title: genomic DNA from peripheral blood [9761749038_R02C02]


title: SF7761_Clone_1_Biol_rep_2

description:
Library name: C1-R2
Row name in processed data file : SF7761-Clone #1-R3


title: SF7761_Biol_rep_1

description:
Library name: 126-R1
Row name in processed data file : SF7761-R2


title: Patient 107 PBLs sample collected at C1D1

description: Library name: s107-02_S19_R1


title: Patient D astrocytoma tumor resection

description:
Library name: A-D
10x Genomics


title: genomic DNA from peripheral blood [9761749033_R06C02]


title: Patient C astrocytoma tumor resection

description:
Library name: A-C
10x Genomics


title: RS-Clone#1-sEV-Biol_rep_3

description:
Library name: 9_DIPG_SF7761_Library
Column name in processed data file : 126_EV-3

data_processing:
UMI adapters were trimmed using the Trim adapters package, duplicated reads were removed using the UMI deduplication package. Alignment was done using STAR aligner. Raw counts were generated using HTseq.  All packages were run on the Partek Illumina Pipeline
Assembly: GRCh38 was used
Supplementary files format and content: xlsx file inlcudes raw counts for each Sample

growth_protocol: SF7761 cells were maintained in ReNCell media supplemented with 20ng/ul of hEGF, hFGF, 1mM glutamine, and antibiotics.

extract_protocol:
Total RNA was extracted using Trizol
Libraries were generated using the SMART-Seq mRNA LP Kit (with UMIS). 10ng of RNA was used as input for each sample

treatment_protocol: SF7761 cells were plated at 40,000 cells/mL in a 100ul volume and left to adhere for 1-2 hours. Cells were than treated with either sEVs or 100 kDa flow through solution of the EV ultrafiltration at 5000 sEVs/cell based on Nano particle tracking partcile counts. Treatment duration time was 18 hours before total RNA was harvested

value: RS-Clone#1-sEV (18 hour)


title: Patient 107 PBLs sample collected at baseline

description: Library name: s107-01_S7_R1


title: genomic DNA from peripheral blood [9992571104_R01C01]


title: genomic DNA from peripheral blood [9761749033_R05C01]


title: genomic DNA from peripheral blood [9992571104_R03C01]


title: Patient 106 PBLs sample collected at C1D1

description: Library name: s106-02_S18_R1


title: Patient B astrocytoma tumor resection

description:
Library name: A-B
10x Genomics


title: genomic DNA from peripheral blood [9761749033_R01C01]


title: RS-Clone#1-sEV-Biol_rep_2

description:
Library name: 8_DIPG_SF7761_Library
Column name in processed data file : 126_EV-2


title: Patient A astrocytoma tumor resection

description:
Library name: A-A
10x Genomics


title: Patient 106 PBLs sample collected at baseline

description: Library name: s106-01_S6_R1


title: genomic DNA from peripheral blood [9761749029_R06C01]


title: RS-Clone#1-sEV-Biol_rep_1

description:
Library name: 7_DIPG_SF7761_Library
Column name in processed data file : 126_EV-1


title: Patient 105 PBLs sample collected at C1D1

description: Library name: s105-02_S17_R1


title: genomic DNA from peripheral blood [9761749029_R04C01]


title: RR-sEV_Biol_rep_3

description:
Library name: 6_DIPG_SF7761_Library
Column name in processed data file : 127_EV-3

value: RR-sEV (18 hour)


title: Patient 108 PBLs sample collected at baseline

description: Library name: s108-01_S8_R1


title: genomic DNA from peripheral blood [9761749029_R01C02]


title: Patient 105 PBLs sample collected at baseline

description: Library name: s105-01_S5_R1


title: RR-sEV_Biol_rep_2

description:
Library name: 5_DIPG_SF7761_Library
Column name in processed data file : 127_EV-2

value: WT


title: Control_Biol_rep_3

description:
Library name: 3_DIPG_SF7761_Library
Column name in processed data file : NT-3

value: Control (18 hour)


title: genomic DNA from peripheral blood [9761749020_R06C01]


title: Patient 104 PBLs sample collected at C1D1

description: Library name: s104-02_S16_R1


title: RR-sEV_Biol_rep_1

description:
Library name: 4_DIPG_SF7761_Library
Column name in processed data file : 127_EV-1


title: genomic DNA from peripheral blood [9761749020_R04C02]


title: AD-C9_08

type: RNA

city: Baltimore

first: Shawn

last: Kwatra MD

address: 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins School of Medicine

data_processing: Gene expression analysis was conducted for 770 neuroinflammatory-related genes using nCounter’s Human Neuroinflammation Panel and a panel of 30 genes focused on Mrgpr genes and cytokines. Nsolver Analysis Software 4.0 was used to complete quality control, background thresholding, and normalization of the raw expression data. 1 sample was flagged for mRNA content; thus, 119/120 samples were used for subsequent statistical analysis. Background thresholding to the geometric mean of the average counts for eight negative control samples was completed. Positive control normalization was calculated using the geometric mean of the average counts for six synthetic ssDNA control samples; housekeeping normalization was calculated using the geometric mean of the average counts for 9 selected housekeeping genes.

source_name: skin punch biopsy

extract_protocol: RNA was extracted from lesional and non-lesional samples using the RNAeasy FFPE Kit (Qiagen) as per the manufacturer's instructions

tag: race

value: C

tag: Sex

value: M


title: Patient 103 PBLs sample collected at C1D1

description: Library name: s103-02_S15_R1


title: Patient 104 PBLs sample collected at baseline

description: Library name: s104-01_S4_R1


title: genomic DNA from peripheral blood [9761749020_R05C02]

tag: genetic sex (male=1, female=2)


title: Control_Biol_rep_1

description:
Library name: 1_DIPG_SF7761_Library
Column name in processed data file : NT-1


title: 177PN02L_03

value: Other

value: F


title: 177PN02NL_04


title: Control_Biol_rep_2

description:
Library name: 2_DIPG_SF7761_Library
Column name in processed data file : NT-2


title: genomic DNA from peripheral blood [9761749020_R02C02]

tag: weighted life events


title: 156-4AD10NL_06

value: AA


title: 156-4AD10L_05


title: 156-3PN20NL_10


title: Patient 102 PBLs sample collected at C1D1

description: Library name: s102-02_S14_R1


title: 156-3PN20L_09


title: Patient 102 PBLs sample collected at baseline

description: Library name: s102-01_S2_R1


title: genomic DNA from peripheral blood [9761749001_R06C01]


title: genomic DNA from peripheral blood [9761749001_R05C02]


title: Patient 101 PBLs sample collected at  baseline

description: Library name: s101-01_S1_R1


title: genomic DNA from peripheral blood [9761749020_R03C01]


title: 156-3PN15NL_02


title: genomic DNA from peripheral blood [9761749001_R05C01]


title: Patient 101 PBLs sample collected at C1D1

description: Library name: s101-02_S13_R1


title: 156-3HC11_07


title: 156-3PN15L_01


title: genomic DNA from peripheral blood [9761749001_R02C02]


title: minus, scRNAseq

city: Utrecht

first: Cristoforo

last: Grasso

address: Heidelberglaan 25, 3584 CS Utrecht

country: Netherlands

institute: Prinses Maxima Centrum

description: 10X Genomics

data_processing:
Demultiplexing of raw base call (BCL) files and conversion to FASTQ files was performed with the Cell Ranger pipeline (10x Genomics, version 3.0.2) using ‘cellranger mkfastq’. Alignment to the human reference genome (10x Genomics; GRCh38 version 3.1.0), read filtering, barcode correction, UMI counting and filtering of empty barcodes was performed using ‘cellranger count’ to generate feature counts for every single cell.
Assembly: GRCh38 version 3.1.0
Supplementary files format and content: tab-delimited tekst file includes raw counts for each sample

source_name: Lymph node

extract_protocol:
LNs were collected from kidney transplantation recipients during living donor kidney transplantation. We have noticed that HLA-DR+ stromal cells represent only a small population within the stromal compartment of the lymph node. To ensure that sufficient HLA-DR+ stromal cells were included in the sorted cells used for sequencing, we included HLA-DR in the gating strategy of the sorting. We first gated on the HLA-DR+ (plus) and HLA-DR- (minus) stromal cells, subsequently we sorted DN, FRC, BEC and LEC based on PDPN and CD31 expression, resulting in two sorted cell suspensions. To assess the presence of a possible batch effect between these two samples, we added spike-in B cells in each sample.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10X Genomics). Briefly LNSCs were resuspended in the master mix and loaded together with partitioning oil   and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, whcih contains an Illumoiina R1 primer sequenc, Unique Molecular Identifier (UMI) and the 10X barcode. The pooled barcoded cDNA was then cleaned up with Dyna beads, amplified by PCR and the apropriate sizxed fragment were selected with SPRI select reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index were added.
Single-cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions (CG000204 Rev D) using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) and Chromium Next GEM Chip G Single Cell Kit (10X Genomics, PN-1000120)

value: Lymph node

value: Lymph node stroma cells


title: plus, scRNAseq

description: 10X Genomics


title: genomic DNA from peripheral blood [9761749001_R01C02]


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #3

city: Austin

first: Anna

last: Battenhouse

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description:
Library name: Library-7DCtrl-3
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

data_processing:
The cellranger count pipeline (version 6.1.2) was used for alignment, using default arguments, producing a filtered matrix containing UMI counts.
The Seurat package was used to preprocess and integrate the samples, following the preprocessing workflow outlined by Kölsch et al. Briefly, for each sample, filtered matrices were log-normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next, integrated data is re-scaled and PCA, TSNE, and UMAP embeddings are computed using Seurat’s RunPCA, RunUMAP, and RunTSNE functions. Lastly, an initial clustering was computed of the integrated data using FindNeighbors (dims=1:40) and FindClusters.
To focus on retinal ganglion cell populations, clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically, clusters were removed that had high expression of at least two of the following genes: opn1lw2, opn1mw2, opn1mw1, opn1sw2, opn1lw1, gngt2b, gngt2a, rho, crx, pde6c, pde6ga, opn6a, vsx1, glula, cabp5a, cabp2a, gng13b, gad1b, cd82a, gad2, pax6b, pax6a, cd74a, fcer1gl, and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters.
Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl, version 106
Supplementary files format and content: Tab-delimited files from cellranger outs/raw_feature_bc_matrix

organism: Danio rerio

source_name: retina

growth_protocol: isl2b:GFP transgenic zebrafish (Danio rerio) used in this study were 3-6 maintained on a 14:10 hour light:dark cycle at 28C.

extract_protocol:
1 and 7 days post injury (dpi), the retina were harvested, cells dissociated using papain digestion, and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit (10X genomics)
Single cell libraries were prepared using the single-cell gene expression 3’ v2 kit on the Chromium platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel beads in EMulsion (GEMs) in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA, amplification, enzymatic fragmentation, 50 adaptor attachment and sample indexing. On average, approximately 7,000 single cells were loaded on each channel and approximately 2,000- 4,000 cells were recovered. Libraries were sequenced on NovaSeq S2-100 platform (Paired end reads: Read 1: 26 bases, Read 2: 98 bases).

treatment_protocol: Optic nerve transection (ONT) was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured (sham) control.

value: retina

value: adult retinal ganglion cells from isl2b:eGFP transgenic fish line

value: retinal ganglion cells

value: isl2b:eGFP transgenic fish line

value: uninjured

tag: time

value: day 7


title: genomic DNA from peripheral blood [9741779108_R06C02]

tag: age


title: 156-10AD04NL_12


title: genomic DNA from peripheral blood [9741779108_R03C02]


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #2

description:
Library name: Library-7DCtrl-2
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

tag: tissue


title: 156-10AD04L_11


title: genomic DNA from peripheral blood [9741779108_R03C01]


title: 177PN01NL_08


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #3

description:
Library name: Library-7DPI-3
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: optic nerve transection

value: day 7 post-injury


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #1

description:
Library name: Library-7DCtrl-1
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix


title: Patient 103 PBLs sample collected at baseline

description: Library name: s103-01_S3_R1

value: Blood

value: Peripheral blood leukocytes

value: glioblastoma (GBM)


title: 177PN01L_07


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #2

description:
Library name: Library-7DPI-2
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix


title: genomic DNA from peripheral blood [9702496103_R05C01]


title: genomic DNA from peripheral blood [9761749001_R01C01]


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #1

description:
Library name: Library-7DPI-1
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix


title: 156-3PN23L_01


title: 156-4HC04_06


title: genomic DNA from peripheral blood [9702496103_R04C01]


title: BPA-3-BRG1-Cut&TAG

city: Durham

first: Christopher

middle: R

last: Day

state: NC

address: 111 TW Alexander Dr.

department: ERBL

institute: NIH/NIEHS

data_processing:
Adaptors were trimmed using Cutadapt and reads were aligned to the hg38 genome assembly using Bowtie2. Samtools was used to sort the reads and deduplication was performed using Picard Tools (http://broadinstitute.github.io/picard). Coverage files were generated using bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

growth_protocol: MCF-7 cells (ATCC) were grown in MEM supplemented with 10% FBS (Sigma), 2mM Glutamine and 1X Pen/strep (Gibco).

extract_protocol:
CUT&Tag was performed following the Bench top CUT&Tag V.3 protocol (Kaya-Okur, Wu et al. 2019). Briefly, we used 100K nuclei isolated from E2, BPA, or vehicle treated MCF7 cells. 10 µL BioMag-Plus Concanavalin (Bangs Laboratories) were used per reaction to immobilize the nuclei. Then we added 1:50 mouse ERα (sc-8005, Santa Cruz), 1:25 rabbit FOXA1 (#53528, Cell Signaling Technology), 1:50 mouse H3K27ac (#MA5-23516, Invitrogen), 1:40 Rabbit BRG1 (#NB100-2594, Novus Biologicals) or 1:25 rabbit MED1 (#51613, Cell Signaling Technology) antibody and incubated for 2 hours. After one hour of secondary antibody incubation 1.25μL of CUTANA pAG-Tn5 adapter complex was used to load the enzyme to the antibody bound regions. One hour of tagmentation at 37°C was followed by DNA extraction using MinElute PCR Purification Kit (Qiagen).
Extracted DNA was subjected to PCR amplification using unique primers sets (Nextera XT v2 Full set (N7-S5)). Number of PCR cycles were determined specifically to prevent overamplification. We amplified ERα, FOXA1, H3K27ac, or MED1 with 14, 15, 15 or 17 PCR cycles, respectively. Libraries were size selected using AMPure XP Beads (Beckman Coulter) with 1.3X ratio. We quantified and assessed the quality of the libraries with Qubit Flex and Tapestation and then sequenced the libraries with 50 bp paired-end reads on Illumina high output NovaSeq SP.

treatment_protocol: MCF7 cells were hormone depleted for 2d prior to treatment. Cells were then treated with 1nM E2, 10uM BPA or vehicle for 8hs.

value: ER+ Breast Cancer

value: 8h BPA


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #3

description:
Library name: Library-1DCtrl-3
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: day 1


title: BPA-2-BRG1-Cut&TAG


title: genomic DNA from peripheral blood [9702496103_R03C02]


title: BPA-1-BRG1-Cut&TAG


title: 156-3PN23NL_02

value: AA

value: F


title: 156-10PN16NL_10


title: genomic DNA from peripheral blood [9702496103_R01C01]


title: 156-10HC07_05


title: 156-10PN16L_09


title: genomic DNA from peripheral blood [9702496103_R06C02]


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #4

description:
Library name: Library-1DPI-4
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: day 1 post-injury


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #2

description:
Library name: Library-1DCtrl-2
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: retina


title: 156-10AD15NL_12


title: genomic DNA from peripheral blood [9702496102_R03C02]


title: E2-2-BRG1-Cut&TAG

value: 8h E2


title: 156-10AD15L_11


title: genomic DNA from peripheral blood [9702496102_R01C01]


title: E2-3-BRG1-Cut&TAG


title: 156-10AD05NL_04


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #3

description:
Library name: Library-1DPI-3
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: adult retinal ganglion cells from isl2b:eGFP transgenic fish line

value: retinal ganglion cells


title: E2-1-BRG1-Cut&TAG


title: genomic DNA from peripheral blood [9702496101_R06C02]


title: genomic DNA from peripheral blood [9702496101_R04C01]


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #2

description:
Library name: Library-1DPI-2
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: isl2b:eGFP transgenic fish line


title: EtOH-3-BRG1-Cut&TAG

value: 8h EtOH


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #1

description:
Library name: Library-1DPI-1
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: optic nerve transection


title: EtOH-2-BRG1-Cut&TAG


title: 156-10AD05L_03


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #1

description:
Library name: Library-1DCtrl-1
10x Genomics; processed files from cellranger outs/raw_feature_bc_matrix

value: uninjured


title: PS-C8_09

value: C


title: genomic DNA from peripheral blood [9702496101_R01C02]