title: snRNA-Seq NCH1098

description: Library name: exp_snRNA_NCH1098

tag: patient


title: BMDM Snx5 knockout, infected with MTB Erdman,  24H, biol rep 2

status: Public on Mar 10 2026

type: SRA

city: Dallas

first: Michael

last: Shiloh

state: TX

address: 5323 Harry Hines Blvd. Y9.308

department: Internal Medicine

country: USA

institute: University of Texas Southwestern Medical Center - UTSW

description:
Library name: KO_2_Infected_24h
612__KO_plus_MTB_2

library_source: transcriptomic

data_processing:
Single-end 100 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads from fastq files for each library was mapped to human reference genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes corresponding to  igenomes gtf file
Normalized read counts were  generated using edgeR
Assembly: mm10
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells from Snx5-/- or wild-type mice femurs and tibia were flushed and used to generate bone marrow-derived macrophages (BMDMs) and bone marrow dendritic cells (BMDCs). To obtain BMDMs, bone marrow cells were cultivated in DMEM (Gibco, 11965-092) containing 20% heat-inactivated endotoxin-free FBS (Gibco, 1600-044), 30% L929 cell-conditioned media, Glutamax (Gibco, 35050-061), 1 mM sodium pyruvate (Gibco, 11360-070), 1 mM HEPES (Cytiva, SH30237.01), and 50 mM b-mercaptoethanol (Gibco, 21985-023). Media was replaced after 3 days of culture. After 7 days, adherent BMDMs were detached from Petri dishes (100x15mm) with 1 mM EDTA in PBS and cultured in DMEM supplemented with 10% FBS and 5% L929 cell-conditioned media.

extract_protocol:
After 4 or 24 h of infection, samples were lysed using TRIzol (Invitrogen, 15596018) for 5 min, incubated with chloroform, and centrifuged at 12,000 x g for 5 min at 4 °C. Then, the aqueous phase was subject to RNA extraction using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol.
Samples were analyzed on an Agilent Tapestation 4200 to determine level of degradation to ensure that only high quality RNA was used (RIN Score 8 or higher). We used a Qubit® 4.0 Fluorimeter (ThermoFisher) to determine RNA concentration prior to starting library prep. One microgram of total DNAse treated RNA was then prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Poly-A RNA was purified and fragmented before strand-specific cDNA synthesis. cDNA was then A-tailed and indexed adapters ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200. Before being normalized and pooled, samples were quantified by Qubit then sequenced on the Illumina NextSeq 2000 using a P2-100 flowcell.

treatment_protocol: WT and Snx5-/- BMDMs from 3 different animals were plated in 6-well plates (106) and infected or not with Mtb (MOI of 5).

tag: cell line

value: Bone marrow derived macrophages

tag: cell type

value: Primary

tag: genotype

value: KO

tag: treatment

value: Infected with Mtb Erdman 24h


title: PP_CAMHB_rep1

city: La Jolla

first: Heera

last: Bajpe

state: CA

address: 9500 Gilman Dr.

institute: UC San Diego

description: Library name: PP_CAMHB_1

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts were generated using featureCounts
Assembly: AE015451.2
Supplementary files format and content: Supplementary files format and content: Comma-delimited text file containing logTPM values for each sample.

organism: Pseudomonas putida KT2440

source_name: bacterial cell

growth_protocol: Cells were grown overnight at 30 °C with shaking in 4 mL of the base medium (M9 or CAMHB). The following day, fresh cultures were inoculated in duplicate to an initial OD600 of 0.05. For iron starvation (2,2' dipyridyl treatment) and nitrogen starvation (nitrogen-free M9 media with addition of eighteen amino acids, with the exception of cysteine and methionine) conditions, cultures were grown in medium supplemented as specified. Cultures were harvested at mid-log phase (OD₆₀₀ ≈ 0.5) and 3 mL of culture was immediately mixed with 6 mL of RNAprotect reagent for the following conditions: growth in M9 glucose media (with and without trace element solution), CAMHB media, mixed carbon source (succinate, fructose, and toluene treatment), iron starvation, and nitrogen starvation. Cells were pelleted and stored at −80 °C until RNA extraction and RNA-seq library preparation.

extract_protocol:
Total RNA was isolated and prepared from cell pellets using reagents from Zymo Research and silica-coated magnetic beads (Luna Nanotech) accroding to the vendor's manual. Concentrations and quality of the RNA were assessed using an Agilent TapeStation and Nanodrop, respectively. For each sample, 1 ug was used as input for the standard RiboRid procedure.
RNA-seq libraries were prepared from 5 uL of the rRNA-subtracted RNA using KAPA RNA HyperPrep Kit (Roche) according to the manufacturer’s protocol with volumes reduced by half. The final PCR amplification step was modified by incorporating SYBR and using a qPCR instrument. Samples were removed from the thermal cycler just before entering the plateau phase of amplification to avoid biases being potentially introduced by reagent depletion. The quality and concentrations of the libraries were checked with an Agilent TapeStation and Qubit instrument, respectively. Pooled libraries were then run on an AVITI instrument (Element Biosciences).

treatment_protocol: For ceftazidime treatment conditions, ceftazidime (¼ of minimum inhibitory concentration) was added at OD₆₀₀ ≈ 0.2, and cultures were incubated for 1 h prior to collection. For osmotic stress (NaCl treatment), oxidative stress (H2O2 treatment), and metal ion stress (CuSO4 and ZnSO4 treatment) conditions, cultures were grown to OD₆₀₀ ≈ 0.5 before addition of the corresponding supplement to the final concentration indicated. This was followed by incubation for an additional 30 min (osmotic and oxidative stress conditions) or 1 h (metal ion stress conditions) before mixing 3 mL of culture with 6 mL of RNAprotect reagent.

tag: strain

value: bacterial cell

value: wild-type

tag: medium

value: CAMHB media


title: PP_CAMHB_ceftazidime_rep1

description: Library name: PP_CAMHB_ceftazidime_1

value: ceftazidime (1 ug/mL)


title: BMDM Snx5 knockout, infected with MTB Erdman,  24H, biol rep 1

description:
Library name: KO_1_Infected_24h
604_KO_plus_MTB_24


title: BMDM WT, infected with MTB Erdman,  24H, biol rep 3

description:
Library name: WT_3_Infected_24h
611_WT_plus_MTB_24

value: WT


title: PP_M9gluc_H2O2_rep1

description: Library name: PP_M9gluc_H2O2_1

value: glucose (2 g/L) and H2O2 (5 mM)

value: M9 media


title: snRNA-Seq NCH5119

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

country: Germany

institute: University Hospital Heidelberg

description: Library name: exp_snRNA_NCH5119

library_source: transcriptomic single cell

data_processing:
FASTQ files for each sequencing batch were processed with Cell Ranger (v 7.1.0) using the human reference (GRCh38) with intronic reads enabled (--include-introns) to accommodate nuclear-localized transcripts. For the sequencing batch with multiplexed samples, cell barcodes were demultiplexed using an in-house developed genotype-based pipeline, scSNPdemux. In brief, scSNPdemux took aligned reads (BAM file) and gene expression count matrix of the batch from Cell Ranger, population SNP information from 1000 genomes phase 3 dataset and SNPs genotyped using Infinium OncoArray-500K (Illumina) from the multiplexed samples in VCF format, which are mapped to the human genome reference GRCh38, as inputs, incorporated Cellsnp-lite for single cell SNP calling and selection, followed by SNP-based demultiplexing step based on Vireo. The output per-nuclei sample identity and its likelihood, as well as cross-sample doublets were added as metadata to the Seurat object.
Assembly: GRCh38
Supplementary files format and content: Seurat object in a RDS file

organism: Homo sapiens

source_name: BCBM

extract_protocol:
Nuclei were isolated from cryo-preserved 100 µm BCBM tissue slices, which had been prepared under tissue quality control as described above, immediately before further downstream analysis by single nuclei RNA sequencing using an optimized protocol in part adapted from published sources. All reagents and materials were pre-cooled to 4°C. Tissue slices were stored at -80°C and transported on dry ice. For a combined chemical and mechanical lysis, five tissue slices were chopped with scissors for 5 min in 3 ml TST buffer (Tween with salts and tris buffer, 146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2, 0.03 % Tween-20, 0.01 % BSA), followed by addition of 2 ml TST buffer, transfer to a douncer, and application of 12 hits with the pestle of size A, then 15 hits with the pestle of size B. Finally, cell debris and free RNA were removed by filtering through a 40 µm strainer and washing by addition of 40 ml ST buffer (salts and tris buffer, 146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2) and centrifugation for 5 min at 1000xg at 4 °C. The pellet was resuspended in ST buffer, nuclei were counted and further processed immediately.
Single nuclei RNA-sequencing was performed using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index, 10x Genomics) according to the manufacturer´s instructions, and 5´gene expression dual index libraries were constructed from the generated full-length cDNA. 10,000 - 30,000 nuclei were loaded per sample, and 28 samples were pooled using 1-3 samples per run, resulting in 12 runs in total. Samples were sequenced in batches using a NovaSeq 6000 SP, NovaSeq 6000 S1, or NovaSeq 6000 S4 (all Illumina). To allow for in silico demultiplexing of pooled samples and patient assignment using single-nucleotide polymorphisms (SNPs), genotyping arrays via Infinium OncoArray-500K BeadChip (Illumina) were performed with patient-individual DNA from blood or, if not available, tumor tissue as a reference.

tag: ghga accession

tag: tissue

value: BCBM

tag: age

tag: gender

value: FEMALE

tag: batch

value: Exp. 4, pool A

tag: bcbm location

value: Cerebellum

tag: nuclei loaded

tag: snp array

value: yes

tag: snp array_dna_source

value: blood


title: snRNA-Seq NCH2972

description: Library name: exp_snRNA_NCH2972

value: Exp. 3, pool B

value: Cerebrum


title: snRNA-Seq NCH4160

description: Library name: exp_snRNA_NCH4160


title: PP_CAMHB_rep2

description: Library name: PP_CAMHB_2


title: BMDM WT, infected with MTB Erdman,  24H, biol rep 2

description:
Library name: WT_2_Infected_24h
607_WT_plus_MTB_24

value: Bone marrow derived macrophages

value: Primary


title: snRNA-Seq NCH7023

description: Library name: exp_snRNA_NCH7023

value: Exp. 3, pool A


title: snRNA-Seq NCH4464

description: Library name: exp_snRNA_NCH4464


title: PP_M9gluc_rep2

description: Library name: PP_M9gluc_2

value: bacterial cell

value: wild-type

value: glucose (2 g/L) and trace element solution


title: PP_M9_mixed_carbon_rep1

description: Library name: PP_M9_mixed_carbon_1

value: succinate (2g/L), fructose(2g/L), toluene (2g/L), and trace element solution


title: PP_M9gluc_rep1

description: Library name: PP_M9gluc_1


title: Patient 31, TBM, CSF, D7

city: London

first: James

middle: Royce

last: Barnacle

state: London

address: Francis Crick Institute, 1 Midland Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description: Library name: BAR6802A86

data_processing:
Raw data were processed using nf-core/rnaseq (v3.10.1) of the nf-core collection of workflows. This workflow used FASTQ files as input, performed quality control (QC), trimming and (pseudo-)alignment to the GRCh38 release 95 human reference genome, and produced a gene expression matrix and QC report. The pipeline was executed with Nextflow (v22.10.3). The output matrix was read into R (v4.2.0) in which subsequent analysis was done.
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: nfcore output .genes.results files

source_name: CSF

extract_protocol:
CSF was collected directly into PAXgene RNA tubes (QIAGEN/BD Biosciences) at the bedside from patients enrolled in the LASER-TBM and INTENSE-TBM trials. Lumbar puncture was done at day 3 (LASER-TBM) and day 7 (INTENSE-TBM) and week 4 (both trials) per the study protocols. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN, Venlo, Netherlands). RNA extraction of samples from the two trials was done at separate timepoints but DNA libraries were prepared at the same time. Samples were stored at -80˚C before and after RNA extraction. The quantity and quality of RNA was assessed using a Qubit fluorimeter (ThermoFisher) and Agilent 2100 Bioanalyzer.
The Watchmaker DNA library prep kit (Watchmaker Genomics, Boulder, USA, CAT# 7K0102) with ribosomal depletion was used to construct libraries. CSF samples were divided into three batches of different input concentrations (2 ng, 1 ng, 0.5 ng) so that RNA loading could be maximised for samples with higher RNA concentrations. Following library preparation, DNA library size distribution was assessed using the D1000 TapeStation kit processed on the 4200 TapeStation (Agilent Technologies). Concentration was measured using the QuantiFluor dsDNA System (Promega Corporation). Libraries were sequenced on an Illumina NovaSeq 6000 with a paired-end 100 cycle read configuration with a target sequencing depth of 30 million reads/sample. Five rounds of re-pooling and sequencing were done, which achieved a median read depth of 41 million reads/sample (range 16.2-149 million).

value: CSF


title: BHC_3, treated

city: 青岛 Qingdao

first: Warren

last: Chanda

state: Shandong Province

address: No. 72 Beihai road, Jimo District

department: State Key Laboratory of Microbial Technology

country: China

institute: Shandong University

description:
Library name: Sample 6
Column name in all_comare.txt: BHC_3_count

data_processing:
Raw sequencing reads in FASTQ format were quality-checked and filtered to remove adapter sequences, reads containing poly-N regions, and low-quality reads. Clean reads were evaluated for quality metrics (Q20, Q30, and GC content) and used for downstream analyses. Reads were aligned to the Blautia producta reference genome (Blautia producta NCBI accession: GCF_002270465.1_ASM227046v1) using Bowtie2 v2.2.3 . Gene-level read counts were obtained with HTSeq v0.6.1, and gene expression levels were normalized as fragments per kilobase of transcript per million mapped reads (FPKM), accounting for gene length and sequencing depth to minimize technical bias
Assembly: Reference genome use was Blautia producta NCBI accession: GCF_002270465.1_ASM227046v1
Supplementary files format and content: tab-delimited text file consisting of raw counts and FPKM for each sample

organism: Blautia hominis

source_name: Strain

growth_protocol: Blautia hominis strain HA2291 cells were cultured anaerobically at 37C in modified Gifu Anaerobic Medium (mGAM) media supplemented with 0.5 g/L each of various carbohydrates (D-mannose, D-fructose, D-galactose, D-trehalose, D-cellobiose, inulin, palatinose, L-rhamnose), amino acids (L-arginine, L-cysteine, 0.3 g/L L-tryptophan), 5% clarified rumen fluid, 2.4 g/L sodium acetate, 2 g/L sodium hydrogen carbonate, 0.5% hemin, and 0.1% resazurin

extract_protocol:
Total RNA was extracted and assessed for integrity and purity. RNA degradation and contamination were evaluated on 1% agarose gels, and RNA integrity was determined using the RNA Nano 6000 Assay Kit on the Bioanalyzer 2100 system (Agilent Technologies, USA).
For library preparation, mRNA was purified from total RNA using oligo-dT probes to remove rRNA. Fragmentation was performed with divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5×). First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase, followed by RNase H digestion to remove RNA. Second-strand cDNA synthesis was performed using DNA polymerase I with dUTP substituted for dTTP. Overhangs were converted to blunt ends by exonuclease/polymerase treatment, followed by 3′-end adenylation and ligation of adaptors containing hairpin loop structures. USER enzyme treatment was applied to degrade the uracil-containing second strand. cDNA fragments of approximately 370-420 bp were size-selected using the AMPure XP system (Beckman Coulter, USA). The resulting libraries were amplified using Phusion High-Fidelity DNA polymerase with universal and index primers, purified again with AMPure XP, and assessed for quality on the Agilent Bioanalyzer 2100 system. Cluster generation was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) following the manufacturer’s protocol.

treatment_protocol: A 1% inoculum from a 24 h culture was transferred into 5 mL mGAM and incubated for 6-7 h at 37 °C until OD₆₀₀ = 0.6. From this, a 1% suspension was inoculated into 100 mL mGAM with or without 100 µg/mL cholesterol and incubated anaerobically at 37 °C for 48 h. Cells were harvested by centrifugation (5,000 × g, 10 min, 4 °C) and snap-frozen in liquid nitrogen. Samples were shipped on dry ice to Novogene Co., Ltd (Beijing, China) for RNA sequencing and bioinformatic analysis.

value: Strain

value: culture cells

value: wild type

value: mGAM+cholesterol

tag: time


title: Patient 4, TBM, CSF, D3

description: Library name: BAR6802A9


title: BMDM KO, uninfected,  24H, biol rep 3

description:
Library name: KO_3_Uninfected_24h
614_KO_24H_S18_R1_

value: KO

value: Uninfected 24h


title: Patient 30, TBM, CSF, D7

description: Library name: BAR6802A85


title: snRNA-Seq NCH1475

description: Library name: exp_snRNA_NCH1475

value: BCBM

value: FEMALE

tag: patient

value: yes

value: blood


title: snRNA-Seq NCH6239

description: Library name: exp_snRNA_NCH6239

value: Exp. 4, pool A

value: Cerebellum


title: PP_M9_mixed_carbon_rep2

description: Library name: PP_M9_mixed_carbon_2

value: bacterial cell

value: M9 media


title: BMDM KO, uninfected,  24H, biol rep 2

description:
Library name: KO_2_Uninfected_24h
612_KO_24H_S17_R1_

tag: cell line

value: Bone marrow derived macrophages

value: Primary


title: BMDM WT, infected with MTB Erdman,  24H, biol rep 1

description:
Library name: WT_1_Infected_24h
606_WT_plus_MTB_24

tag: cell type

value: WT

value: Infected with Mtb Erdman 24h


title: BMDM WT, uninfected,  24H, biol rep 3

description:
Library name: WT_3_Uninfected_24h
611_WT_24H

tag: genotype


title: Patient 27, TBM, CSF, D7

description: Library name: BAR6802A82

value: CSF


title: BHC_2, treated

description:
Library name: Sample 5
Column name in all_comare.txt: BHC_2_count

value: Strain

value: culture cells

value: wild type

tag: treatment


title: Patient 2, TBM, CSF, D0

description: Library name: BAR6802A87


title: Patient 28, TBM, CSF, D7

description: Library name: BAR6802A83


title: snRNA-Seq NCH698g

description: Library name: exp_snRNA_NCH698g

value: Exp. 3, pool A

value: Cerebrum


title: BHC_1, treated

description:
Library name: Sample 4
Column name in all_comare.txt: BHC_1_count

value: mGAM+cholesterol


title: Patient 3, TBM, CSF, D28

description: Library name: BAR6802A8


title: BH_3, control

description:
Library name: Sample 3
Column name in all_comare.txt: BH_3_count

value: mGAM


title: BMDM WT, uninfected,  24H, biol rep 2

description:
Library name: WT_2_Uninfected_24h
607_WT_24H

value: Uninfected 24h


title: BMDM KO, uninfected, 24H, biol rep 1

description:
Library name: KO_1_Uninfected_24h
604_KO_24H

value: KO


title: Patient 25, TBM, CSF, D7

description: Library name: BAR6802A78


title: BH_2, control

description:
Library name: Sample 2
Column name in all_comare.txt: BH_2_count


title: BMDM Snx5 knockout, infected with MTB Erdman,  4H, biol rep 3

description:
Library name: KO_3_Infected_4h
614_KO_plus_MTB_4H

value: Infected with Mtb Erdman 4h


title: BMDM WT, uninfected,  24H, biol rep 1

description:
Library name: WT_1_Uninfected_24h
606_WT_24H


title: Patient 23, TBM, CSF, D7

description: Library name: BAR6802A76


title: Patient 26, TBM, CSF, D7

description: Library name: BAR6802A80


title: BMDM Snx5 knockout, infected with MTB Erdman,  4H, biol rep 2

description:
Library name: KO_2_Infected_4h
612_KO_plus_MTB_4H


title: Patient 29, TBM, CSF, D7

description: Library name: BAR6802A84


title: Patient 22, TBM, CSF, D7

description: Library name: BAR6802A75


title: PA_M9gluc_wo_TE_rep2

description: Library name: PA_M9gluc_wo_TE_2

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts were generated using featureCounts
Assembly: NC_002516.2
Supplementary files format and content: Supplementary files format and content: Comma-delimited text file containing logTPM values for each sample.

organism: Pseudomonas aeruginosa PAO1

treatment_protocol: For ceftazidime treatment conditions, ceftazidime (¼ of minimum inhibitory concentration) was added at OD₆₀₀ ≈ 0.2, and cultures were incubated for 1 h prior to collection. For osmotic stress (NaCl treatment), oxidative stress (H2O2 treatment), and metal ion stress (CuSO4 treatment) conditions, cultures were grown to OD₆₀₀ ≈ 0.5 before addition of the corresponding supplement to the final concentration indicated. This was followed by incubation for an additional 30 min (osmotic and oxidative stress conditions) or 1 h (metal ion stress conditions) before mixing 3 mL of culture with 6 mL of RNAprotect reagent.

value: bacterial cell

tag: strain

value: wild-type

value: glucose (2 g/L)


title: Patient 37, TBM, CSF, D7

description: Library name: BAR6802A72


title: PA_M9gluc_wo_TE_rep1

description: Library name: PA_M9gluc_wo_TE_1

tag: medium

value: M9 media


title: BH_1, control

description:
Library name: Sample 1
Column name in all_comare.txt: BH_1_count


title: BMDM Snx5 knockout, infected with MTB Erdman,  4H, biol rep 1

description:
Library name: KO_1_Infected_4h
604_KO_plus_MTB_4H

value: Bone marrow derived macrophages

value: Primary


title: Patient 36, TBM, CSF, D28

description: Library name: BAR6802A71

value: CSF


title: Patient 35, TBM, CSF, D28

description: Library name: BAR6802A67


title: Patient 34, TBM, CSF, D7

description: Library name: BAR6802A65


title: Patient 36, TBM, CSF, D7

description: Library name: BAR6802A70


title: BMDM WT, infected with MTB Erdman,  4H, biol rep 3

description:
Library name: WT_3_Infected_4h
611_WT_plus_MTB_4H

value: WT


title: BMDM WT, infected with MTB Erdman,  4H, biol rep 2

description:
Library name: WT_2_Infected_4h
607_WT_plus_MTB_4H


title: PA_NFM9gluc_rep2

description: Library name: PA_NFM9gluc_2

value: glucose (2 g/L) and amino acids (0.05g/L) (all except methionine and cysteine)

value: M9 media without NH4Cl


title: Patient 24, TBM, CSF, D7

description: Library name: BAR6802A77


title: Patient 35, TBM, CSF, D7

description: Library name: BAR6802A66


title: Patient 38, TBM, CSF, D28

description: Library name: BAR6802A64


title: BMDM WT, infected with MTB Erdman,  4H, biol rep 1

description:
Library name: WT_1_Infected_4h
606_WT_plus_MTB_4H


title: Patient 33, TBM, CSF, D7

description: Library name: BAR6802A63


title: Patient 25, TBM, CSF, D28

description: Library name: BAR6802A79


title: PA_M9gluc_DPD_rep2

description: Library name: PA_M9gluc_DPD_2

value: glucose (2 g/L), trace element solution (Without FeCl3), and 2,2' dipyridyl (0.2 mM)


title: Patient 53, TBM, CSF, D28

description: Library name: BAR6802A61


title: BMDM KO, uninfected,  4H, biol rep 3

description:
Library name: KO_3_Uninfected_4h
614_KO_4H

value: Uninfected 4h


title: PA_M9gluc_DPD_rep1

description: Library name: PA_M9gluc_DPD_1


title: Patient 52, TBM, CSF, D7

description: Library name: BAR6802A60


title: PA_NFM9gluc_rep1

description: Library name: PA_NFM9gluc_1


title: Patient 1, TBM, CSF, D3

description: Library name: BAR6802A6


title: Patient 51, TBM, CSF, D7

description: Library name: BAR6802A59


title: BMDM KO, uninfected,  4H, biol rep 2

description:
Library name: KO_2_Uninfected_4h
612_KO_4H


title: Patient 50, TBM, CSF, D28

description: Library name: BAR6802A58


title: BMDM WT, uninfected,  4H, biol rep 3

description:
Library name: WT_3_Uninfected_4h
611_WT_4H


title: Patient 49, TBM, CSF, D28

description: Library name: BAR6802A56


title: BMDM KO, uninfected,  4H, biol rep 1

description:
Library name: KO_1_Uninfected_4h
604_KO_4H


title: PA_M9gluc_Cu_rep1

description: Library name: PA_M9gluc_Cu_1

value: glucose (2 g/L), trace element solution, and CuSO4 ( 0.2 mM)


title: PA_M9gluc_Cu_rep2

description: Library name: PA_M9gluc_Cu_2


title: Patient 48, TBM, CSF, D7

description: Library name: BAR6802A55


title: Patient 47, TBM, CSF, D7

description: Library name: BAR6802A54


title: Patient 50, TBM, CSF, D7

description: Library name: BAR6802A57


title: PA_M9gluc_H2O2_rep2

description: Library name: PA_M9gluc_H2O2_2

value: glucose (2 g/L) and H2O2 (5 mM)


title: PA_M9gluc_H2O2_rep1

description: Library name: PA_M9gluc_H2O2_1


title: BMDM WT, uninfected,  4H, biol rep 1

description:
Library name: WT_1_Uninfected_4h
606_WT_4H


title: Patient 46, TBM, CSF, D7

description: Library name: BAR6802A53


title: Patient 44, TBM, CSF, D7

description: Library name: BAR6802A50


title: Patient 32, TBM, CSF, D28

description: Library name: BAR6802A62


title: Patient 43, TBM, CSF, D7

description: Library name: BAR6802A46


title: Patient 43, TBM, CSF, D28

description: Library name: BAR6802A47


title: PA_M9gluc_NaCl_rep2

description: Library name: PA_M9gluc_NaCl_2

value: glucose (2 g/L) and NaCl (0.35 M)


title: Mll4-AID_MyoD-ER_BRM_4OHT_ATAC

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 72

library_source: genomic

data_processing:
Basecalls performed using Bcl2fastq.
CUT&RUN and ATAC-Seq reads were aligned to the mm10 genome assembly using bowtie2.
CUT&RUN peaks were called using SICER (v2) with following configuration: For transcription factors and co-factors, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For histone modifications, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all CUT&RUN data.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM

molecule: genomic DNA

source_name: Kmt2c-/-;Kmt2dAID/AID preadipocytes

growth_protocol: Preadipocytes were maintained in growth media (DMEM plus 10% Foundation FBS).

extract_protocol:
50,000 fresh preadipocytes were subjected to cell lysis and tagmentation reaction using the ATAC-Seq Kit (#53150, Active Motif) according to the manufacturer’s instructions.
Tagmented DNA was PCR-amplified the ATAC-Seq Kit (#53150, Active Motif) according to the manufacturer’s instructions.

treatment_protocol: MyoD-ER-T7 preadipocytes were grown in growth media (DMEM plus 10% Foundation FBS) for 2 days. On the day of experiments, growth medium was replaced with differentiation medium (DMEM plus 2% horse serum), and cells were rested for 3h. Cells were then pretreated with 1 µM BRM014 or 3 µM A-485 for 1h; 1 µM 5Ph-IAA for 2h; or 250 nM dCBP-1 for 3h, before 400 nM 4-OHT was added for 1h to induced MyoD nuclear translocation.

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Preadipocyte


title: Patient 41, TBM, CSF, D7

description: Library name: BAR6802A44


title: Patient 42, TBM, CSF, D7

description: Library name: BAR6802A45


title: Patient 45, TBM, CSF, D7

description: Library name: BAR6802A51


title: Mll4-AID_MyoD-ER_A485_4OHT_ATAC

description: Library name: Sample 73

data_processing:
Basecalls performed using Bcl2fastq.
ATAC-Seq reads were aligned to the mm10 genome assembly using bowtie2.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM


title: BMDM WT, uninfected,  4H, biol rep 2

description:
Library name: WT_2_Uninfected_4h
607_WT_4H


title: PA_CAMHB_ceftazidime_rep1

description: Library name: PA_CAMHB_ceftazidime_1

value: bacterial cell

value: ceftazidime (16 ug/mL)

value: CAMHB meda


title: PA_M9gluc_NaCl_rep1

description: Library name: PA_M9gluc_NaCl_1

value: wild-type

value: M9 media


title: Patient 40, TBM, CSF, D7

description: Library name: BAR6802A42


title: Mll4-AID_MyoD-ER_4OHT_ATAC

description: Library name: Sample 71

value: 4OHT (1h)


title: Mll4-AID_MyoD-ER_unt_ATAC

description: Library name: Sample 70

value: untreated


title: PA_CAMHB_rep2

description: Library name: PA_CAMHB_2


title: Patient 39, TBM, CSF, D28

description: Library name: BAR6802A41

value: CSF


title: Patient 20, TBM, CSF, D28

description: Library name: BAR6802A38


title: Patient 40, TBM, CSF, D28

description: Library name: BAR6802A43


title: Patient 19, TBM, CSF, D3

description: Library name: BAR6802A36


title: Huh7 cells, CDK16;18 dKO , Day 6, Replicate 3

city: Barcelona

first: Agustín

middle: Sánchez

last: Belmonte

state: Barcelona

address: Nazaret 115 -117

department: Systems Oncology Program

country: Spain

institute: Vall d ́Hebron Institute of Oncology (VHIO)

description: Cells infected, and cultured for 6 days before RNA extraction

data_processing:
The alignment to the GRCh38/hg38 transcriptome, generating metrics, files and matrices required for secondary analysis were performed in "BluBee"
Reads were aligned to the human genome (GRCh38) with TopHat-2.0.10 (https://ccb.jhu.edu/software/tophat/index.shtml) using Bowtie 2.0.10 (Langmead et al., 2009) and Samtools 0.1.19 (Li et al., 2009), allowing two mismatches and five multihits. Transcript quantification was calculated with htseq (Anders et al., 2015), and differential expression was calculated with DEseq2 (Love et al., 2014), using the human GRCh38 transcript annotations from The GENCODE project version 28 (http://gencodegenes.org). Enrichr (Kuleshov et al., 2016) and DAVID (Huang et al., 2007) were used for enrichment analysis of transcription factor sites or gene ontology. GSEA Preranked was used to perform gene set enrichment analysis for several gene signatures on a preranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q < 0.25) were considered.
Assembly: hg38
Supplementary files format and content: counts data, txt file

molecule: polyA RNA

growth_protocol: Cells were grown in DMEM 10% FBS medium

extract_protocol:
Cells were extracted using miRVana commercial kit, following manufacturer's instructions for total RNA isolation.
Total RNA samples (250ng) were used as provided by the user. Sample RNA Integrity numbers were 8.8 on average (range 5.0-9.8) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were infected with virus-containing medium (produced in HEK293T) and  4 µg/mL polybrene. Fresh medium was added 4 hours later. Puromycin for selection was added 24h post-infection.

value: hepatocellular carcinoma cell line

value: CDK16;18 dKO

value: Day 6


title: Patient 21, TBM, CSF, D3

description: Library name: BAR6802A39


title: PA_M9_mixed_carbon_rep2

description: Library name: PA_M9_mixed_carbon_2

value: succinate (2g/L), fructose(2g/L), toluene (2g/L), and trace element solution


title: Patient 19, TBM, CSF, D28

description: Library name: BAR6802A37


title: PA_CAMHB_ceftazidime_rep2

description: Library name: PA_CAMHB_ceftazidime_2


title: Patient 18, TBM, CSF, D3

description: Library name: BAR6802A35


title: Huh7 cells, CDK16;18 dKO , Day 6, Replicate 2


title: Patient 17, TBM, CSF, D3

description: Library name: BAR6802A34


title: Huh7 cells, CDK16;18 dKO , Day 6, Replicate 1


title: Huh7 cells, CDK18 KO, Day 6, Replicate 2

value: CDK18 KO


title: Patient 16, TBM, CSF, D3

description: Library name: BAR6802A31


title: PA_M9gluc_rep2

description: Library name: PA_M9gluc_2

value: glucose (2 g/L) and trace element solution


title: Patient 15, TBM, CSF, D3

description: Library name: BAR6802A30


title: Patient 12, TBM, CSF, D28

description: Library name: BAR6802A25


title: Huh7 cells, CDK18 KO, Day 6, Replicate 1


title: PA_CAMHB_rep1

description: Library name: PA_CAMHB_1


title: Patient 13, TBM, CSF, D3

description: Library name: BAR6802A28


title: Patient 12, TBM, CSF, D3

description: Library name: BAR6802A24


title: Patient 10, TBM, CSF, D28

description: Library name: BAR6802A22


title: Huh7 cells, CDK16 KO, Day 6, Replicate 2

value: CDK16 KO


title: Patient 11, TBM, CSF, D28

description: Library name: BAR6802A23


title: Patient 10, TBM, CSF, D3

description: Library name: BAR6802A21


title: 48h aged wildtyoe cells

city: South San Francisco

first: Nathaniel

middle: H

last: Thayer

address: 1130 Veteran's Blvd

institute: Calico Life Sciences LLC

description: Library name: timecourse_48_hour

data_processing:
scRNA-seq reads were aligned to the genome using kallisto bustools (kb count with default arguments; kb_python v0.27.1; kallisto: v0.48.0; bustools: v0.41.0). Reference was created from the sacCer3 R64-3-1 genome build  obtained from UCSC. The GTF used to generate the reference was created by selecting the largest mRNA feature in the R64-3-1 GFF for each gene. Additional features were added for rDNA NTS regions.
Assembly: sacCer3 - R64-3-1
Supplementary files format and content: .h5ad -- hdf5 formatted AnnData object containing a count matrix for each condition. All barcodes are included without filtering.
Supplementary files format and content: _barcodes.tsv.gz -- gzip compressed tab-separated list of cell barcodes (rows of the matrix)
Supplementary files format and content: _features.tsv.gz -- gzip compressed tab-separated list of gene identifiers (columns of the matrix).
Supplementary files format and content: _matrix.mtx.gz -- gzip compressed sparse matrix of raw counts. Rows correspond to cells; columns correspond to genes. All barcodes are included without filtering.

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: ScRNA-Seq experiments were performed on either young (exponentially growing) cells or cells aged in MADs that had been purified on magnets as described here (doi: 10.1073/pnas.2119593119). After harvesting, cells were washed in TAF buffer (1 M Sorbitol, 100 mM Tris base, 20 mM sodium azide, 20 mM sodium fluoride, 0.1 mg/µL BSA at pH 8.5) with 1 U/µL Protector RNase Inhibitor (Sigma-Aldrich) and adjusted to a concentration of 500 cells/µL. The TAF buffer ensures that mRNA is stable, while retaining functional proteins in the cell to allow for fluorophore-based assays such as FACS. For experiments that combined FACS with scRNA-Seq, cells were aged in MADs, purified as above and stained with Dylight (viability) and Wheat Germ Agglutinin (WGA; bud scars) for 10 min while kept in TAF buffer on ice. For both the Srp40-mNeon and MMP sorts, Dylight-680 and WGA-405 (Thermo Fisher) were used. Only Dylight-negative and WGA-high cells were included. For binning, cells were sorted into “low” and “high” subpopulations as defined by the top or bottom 25% of Srp40 fluorescence or the MMP ratio, respectively. Cells were in the presence of 1 U/µL Protector RNase Inhibitor from harvest until chip loading and kept on ice whenever possible. Loading into the Chromium chip and processing for scRNA-Seq was done as above.

extract_protocol:
ScRNA-Seq was performed using the Chromium GEM-X Single Cell 3’ Kit v4 or the Chromium Next GEM Single Cell 3’ LT kit v3.1 (10x Genomics) with two modifications: 5 Units of Zymolyase (Zymo Research) were added to the RT Master Mix immediately before cells were loaded into the Chromium GEM-X chip and an extra step of 10 min at 37 C was added at the beginning of the reverse transcription protocol.
Post GEM-RT cleanup and cDNA amplification (15 cycles) was performed as per manufacturer’s instructions and 10 µL of purified cDNA was used for sequencing library construction. The final library was quality checked using the High Sensitivity DNA Kit and a Biolanalyzer (Agilent) and sequencing was performed using a NovaSeq 6000 (Illumina).

value: Cell culture

value: yeast cell

value: pre-grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5, aged in MADs


title: PA_M9gluc_rep1

description: Library name: PA_M9gluc_1

value: bacterial cell


title: 24h aged wildtype cells

description: Library name: timecourse_24_hour


title: Huh7 cells, CDK16 KO, Day 6, Replicate 3


title: PA_M9_mixed_carbon_rep1

description: Library name: PA_M9_mixed_carbon_1


title: Patient 8, TBM, CSF, D3

description: Library name: BAR6802A18


title: Patient 8, TBM, CSF, D28

description: Library name: BAR6802A19


title: Patient 7, TBM, CSF, D3

description: Library name: BAR6802A17


title: Huh7 cells, CDK16 KO, Day 6, Replicate 1


title: Huh7 cells, Control, Day 6, Replicate 3

value: WT


title: Young wildtype cells

description: Library name: timecourse_0_hour_log

value: grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5


title: 48h aged cells with low SRP40

description: Library name: low_SRP40_48_hour


title: Patient 6, TBM, CSF, D28

description: Library name: BAR6802A15


title: 24h aged cells with low MMP

description: Library name: low_MMP_24_hour

value: MATa Chr1-199447..199460::pTPI-preCOX4-SL17-mNeonGreen-URA3 TIM50-yEmCherry-NatMX ura3d0


title: Patient 14, TBM, CSF, D3

description: Library name: BAR6802A29


title: Huh7 cells, Control, Day 6, Replicate 2


title: Huh7 cells, Control, Day 6, Replicate 1


title: Patient 9, TBM, CSF, D3

description: Library name: BAR6802A20


title: HCT116 cells transduced with GeCKO-v2 knockout pooled library, Day14

city: Shanghai

first: Xiaoai

last: Lyu

address: 567 West Yangsi Road

institute: New York University Shanghai

description: Library name: Sample2

data_processing:
MAGeCK pipeline (W. Li et al., 2014)
Assembly: GeCKO-v2 Human Library (A and B pools)
Supplementary files format and content: csv file includes raw counts for each sample, csv files for GeCKO-v2 Human Library (A and B pools)
Library strategy: CRISPR Screen

source_name: colon

extract_protocol:
To extract gDNA from the CRISPR/Cas9 screen cells, every 100 million cells were resuspended in 12 ml of NK lysis buffer (50 mM Tris-HCl pH 8.0, 50 mM EDTA, 1% SDS) and mixed with 120 µl of 10 mg/ml Proteinase K (Mesgen, MG0324). Cell lysis proceeded overnight at 55oC. Then, incubation with 60 µl of 20 µg/ml RNase A (ThermoScientific, #EN0531) was maintained for 30 minutes at 37oC, followed by precipitation with 4 ml of 7.5 M ammonium acetate (Sigma, #A1542). After centrifugation at 4000 x g for 30 minutes, the supernatant was collected and mixed with 12 ml of isopropanol before proceeding to centrifugation at 4000 x g for 10 minutes. The final DNA pellet was washed twice with 70% ethanol, air dried, and resuspended in 0.2X TE buffer. To ensure complete dissolution of genomic DNA, the solution was incubated at 65oC for 1 hour, followed by overnight incubation at room temperature prior to PCR amplification.
The GeCKOv2 Human CRISPR Knockout Pooled Library was processed according to the manufacturer's protocols

value: colon

value: human colorectal carcinoma


title: Patient 5, TBM, CSF, D28

description: Library name: BAR6802A12

value: CSF


title: Patient 6, TBM, CSF, D3

description: Library name: BAR6802A14


title: GeCKO library

description: Library name: Sample3

library_source: other

molecule: other

value: knockout library

value: PCR amplification


title: 48h aged cells with high SRP40

description: Library name: high_SRP40_48_hour


title: Huh7 cells, CDK16;18 dKO , Day 4, Replicate 2

description: Cells infected, and cultured for 4 days before RNA extraction

value: hepatocellular carcinoma cell line

value: CDK16;18 dKO

value: Day 4


title: HCT116 cells transduced with GeCKO-v2 knockout pooled library, noAZ, Day14

description: Library name: Sample1

value: mock


title: PC9 cells, Osimertinib, 36 hours, replicate 2

city: Worcester

last: Lee

state: MA

address: 55 N Lake Ave

institute: Umass Chan Medical School

description: Library name: S15

data_processing:
Sequencing results were processed using the UMass Medical School Biocore’s DolphinNext pipeline.
DESeq2 in R computed log2(fold change) from the generated counts table (treated vs. T0) and computed FDR-adjusted P values.
Assembly: GRCh38
Supplementary files format and content: CSV file of read depth normalized counts

growth_protocol: PC9 an H1650 cells were grown in RPMI supplemented with 10% fetal bovine serum and penicillin/streptomycin in a humidified incubator at 5% CO2 and 37C

extract_protocol:
At assay endpoint cells were trypsinized, counted using a hemacytometer, pelleted, washed with PBS, and moved immediately to RNA extraction. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) according to manufacturer protocol.
Extracted total RNA was sent on dry ice to Novogene for sequencing.

treatment_protocol: Cells were seeded at 200,000 cells per well on 6 wells and left to adhere overnight. Cells were drugged the following day with either .1% DMSO, 10  µM erlotinib, or .1  µM osimertinib.

value: non-small cell lung cancer

value: Wild-type

value: Osimertinib 0.1  µM

value: 36 hours


title: 24h aged cells with high MMP

description: Library name: high_MMP_24_hour

value: Cell culture

value: yeast cell

value: pre-grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5, aged in MADs


title: H1650 cells, Erlotinib, 36 hours, replicate 2

description: Library name: S14

value: Erlotinib 10  µM


title: 24h aged msn2∆msn4∆ cells replicate 3

description: Library name: msn24_24_rep3

data_processing:
Raw sequencing reads were demultiplexed with bcl2fastq.
Reads were trimmed with cutadapt v2.6 with parameters -j 8 -e 0.1 -q 20 -O 1 and aligned to build R64-1-1 of the Saccharomyces cerevisiae genome using STAR v2.7.6a with extra parameters --twopassMode Basic --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif.
Alignments were assigned to features in the Ensembl R64-1-1 GTF using featureCounts (Subread v1.6.2). Quantification was performed in paired-end mode, utilizing the -O --fraction options to account for overlapping features.
Assembly: sacCer3 R64-1-1
Supplementary files format and content: Tab-separated table of gene counts

growth_protocol: Cells were pre-grown in biotin-free medium for 24 hours at OD <0.05 and 5 ODs were harvested from each Ministat Aging Device (MAD) as previously described (doi: 10.7554/eLife.39911; 10.1073/pnas.2119593119). Cells were washed three times with PBS and then incubated with 0.5 mg Sulfo-NHS-LC-LC-Biotin (Sigma-Aldrich) per OD for 30 min at room temperature. Biotinylated cells were then washed extensively with medium and grown in flasks at 30 C for 4-5 hours. Cells were then incubated with 20 µL of Dynabeads MyOne Streptavidin C1 magnetic beads (Thermo Fisher) in medium and incubated for 10 min at room temperature. Cells were harvested on a 0.22-µm filter (Corning) and bead-labeled mother cells were extracted from the culture by repeated washing on a DynaMag-2 magnet (Invitrogen). Finally, cells were loaded into a MAD prefilled with medium and let bind to the magnet for 5 min before the media pumps were turned on. Cells were harvested after 24 hours. Exponentially growing cells were used as non-aged control (young cells).

extract_protocol:
Exponentially growing (young) or aged (24 h) cells were harvested and washed in RNA-Later (Sigma-Aldrich) and frozen at -80C. Bulk RNA-seq was performed by Admera Health. Total RNA was extracted and purified using the RNeasy Plant Mini Kit for RNA Extraction (Qiagen). RNA was quality-controlled and quantified using a TapeStation (Agilent) and only high quality samples (RNA integrity number >6) were used.
The NEB Ultra II Directional RNA Library Prep Kit (New England BioLabs Inc.) was used to generate cDNA and sequencing libraries. Libraries were indexed using Admera's in-house index primers and cleaned with AFTMag NGS DNA Clean Beads (Abclonal). The indexed libraries were pooled and sequenced on the Illumina NovaSeq X plus platform with a read length of 2x 150bp.

value: MAT@ msn2::HphNT1 msn4::NatNT2

value: pre-grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5, aged in MADs for 24h


title: PC9 cells, Erlotinib, 36 hours, replicate 2

description: Library name: S13


title: Huh7 cells, CDK16;18 dKO , Day 4, Replicate 1


title: 24h aged msn2∆msn4∆ cells replicate 2

description: Library name: msn24_24_rep2


title: H1650 cells, DMSO, 0 hour, replicate 2

description: Library name: S12

value: DMSO

value: 0 hours


title: Huh7 cells, CDK18 KO, Day 4, Replicate 2

value: CDK18 KO


title: Huh7 cells, CDK16;18 dKO , Day 4, Replicate 3

value: hepatocellular carcinoma cell line


title: 24h aged msn2∆msn4∆ cells replicate 1

description: Library name: msn24_24_rep1


title: H1650 cells, Osimertinib, 36 hours, replicate 1

description: Library name: S6


title: PC9 cells, DMSO, 0 hour, replicate 2

description: Library name: S11


title: PC9 cells, Osimertinib, 36 hours, replicate 1

description: Library name: S5


title: H1650 cells, Osimertinib, 36 hours, replicate 2

description: Library name: S16


title: 24h aged msn2∆ cells replicate 3

description: Library name: msn2_24_rep3

value: MAT@ msn2::HphNT1


title: 24h aged msn2∆ cells replicate 1

description: Library name: msn2_24_rep1


title: Huh7 cells, CDK16 KO, Day 4, Replicate 3

value: CDK16 KO

value: Day 4


title: Huh7 cells, CDK18 KO, Day 4, Replicate 1


title: PC9 cells, Erlotinib, 36 hours, replicate 1

description: Library name: S3

value: non-small cell lung cancer


title: H1650 cells, Erlotinib, 36 hours, replicate 1

description: Library name: S4

value: Wild-type


title: H1650 cells, DMSO, 0 hour, replicate 1

description: Library name: S2


title: PC9 cells, DMSO, 0 hour, replicate 1

description: Library name: S1


title: 24h aged msn2∆ cells replicate 2

description: Library name: msn2_24_rep2


title: Participant 051, Nasal mucosa, scRNAseq

city: Chicago

first: Manu

last: Jain

state: IL

address: 303 E Superio

institute: Northwestern University

description:
Library name: CFHV_sc_subj_051
Raw sequence data not distributed per IRB approval

data_processing:
Single-cell data were processed using the Cell Ranger 7.0.0 pipeline with exon-only processing mode (10x Genomics) and aligned to GRCh38.98.
Bulk RNAseq data were demultiplexed with bclconvert (Illumina, v4.0.3) and processed using the nf-core/rnaseq pipeline (v3.10.1) with sequence alignment to GRCh38 using STAR (v2.7.9a) and transcript quantitation using Salmon (v1.9.0)
Assembly: scRNAseq: GRCh38.98
Assembly: bulk RNAseq: GRCh38.113
Supplementary files format and content: scRNAseq: tab-separated and matrix files
Supplementary files format and content: bulk RNAseq: tab-separated count file

source_name: Nasal mucosa

extract_protocol:
Samples for scRNAseq were placed immediately in 2mL HypoThermosol buffer (BioLife Solutions) and stored at 4°C until prompt processing. Samples for bulk RNAseq were placed immediately in RLT (Qiagen) buffer and cryopreserved at -80°C until processing.
A single-cell suspension was generated using the cold-active dispase protocol reported by Deprez et al. and Zaragosi and Barbry with slight modification. Specifically, EDTA was omitted and cells were dispersed by pipetting 20 every 5 min using a 1-ml tip instead of trituration using a 21G or 23G needle. Single-cell libraries were generated from the resulting single-cell suspension following the protocol for 5′ v1 (10x Genomics, protocol no. CG000086 Rev M) or v2 chemistry (10x Genomics, protocol no. CG000331 Rev A). Excess cells from two of the samples from healthy volunteers were pooled to generate one additional single-cell library. Libraries were prepared according to the manufacturer’s protocol.

value: Nasal mucosa

tag: Sex

value: M

tag: disease state

value: HV


title: Participant 049, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_049
Raw sequence data not distributed per IRB approval

tag: tissue


title: Huh7 cells, CDK16 KO, Day 4, Replicate 1


title: 24h aged wildtype cells replicate 3

description: Library name: WT_24_rep3

value: Cell culture

value: yeast cell


title: Huh7 cells, Control, Day 4, Replicate 3

value: WT


title: Participant 050, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_050
Raw sequence data not distributed per IRB approval

value: F


title: Participant 046, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_046
Raw sequence data not distributed per IRB approval


title: Huh7 cells, CDK16 KO, Day 4, Replicate 2


title: Huh7 cells, Control, Day 4, Replicate 2


title: Participant 045, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_045
Raw sequence data not distributed per IRB approval


title: 24h aged wildtype cells replicate 2

description: Library name: WT_24_rep2

value: pre-grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5, aged in MADs for 24h


title: Participant 047, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_047
Raw sequence data not distributed per IRB approval


title: Participant 021, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_021
Raw sequence data not distributed per IRB approval

value: CF


title: 24h aged wildtype cells replicate 1

description: Library name: WT_24_rep1


title: Participant 045 and 051 combined sample, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_045+CFHV_sc_subj_051
Raw sequence data not distributed per IRB approval


title: Young msn2∆msn4∆ cells replicate 3

description: Library name: msn24_log_rep3

value: MAT@ msn2::HphNT1 msn4::NatNT2

value: grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5


title: Participant 021, Nasal mucosa, scRNAseq, resequenced

description:
Library name: CFHV_sc_subj_021_deep
Raw sequence data not distributed per IRB approval


title: Participant 016, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_016
Raw sequence data not distributed per IRB approval


title: Young msn2∆msn4∆ cells replicate 2

description: Library name: msn24_log_rep2


title: Young msn2∆msn4∆ cells replicate 1

description: Library name: msn24_log_rep1


title: Huh7 cells, CDK16;18 dKO , Day 2, Replicate 3

description: Cells infected, and cultured for 2 days before RNA extraction

value: hepatocellular carcinoma cell line

value: CDK16;18 dKO

value: Day 2


title: Participant 015, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_015
Raw sequence data not distributed per IRB approval


title: Participant 011, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_011
Raw sequence data not distributed per IRB approval


title: Huh7 cells, CDK16;18 dKO , Day 2, Replicate 2


title: Young msn2∆ cells replicate 3

description: Library name: msn2_log_rep3

value: MAT@ msn2::HphNT1


title: Participant 008, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_008
Raw sequence data not distributed per IRB approval


title: Huh7 cells, CDK16;18 dKO , Day 2, Replicate 1


title: Participant 048, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_048
Raw sequence data not distributed per IRB approval


title: Participant 003, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_003
Raw sequence data not distributed per IRB approval


title: NCH5557

description: Library name: Exp_NCH5557

data_processing:
The reads were mapped to the human reference genome GRCh38.p7 and quantified using STAR (version 2.6.0c).
PIPELINE_VERSION 1.4.62
bcl-convert 4.1.5
RTA 3.4.4
Phred+33
Assembly: GRCh38.p7
Supplementary files format and content: Excel file of count matrix

extract_protocol:
QIAcube Sample Preparator and the QIAgen AllPrep DNA/RNA Kit (Qiagen)
RNA libraries for transcriptome analyses (Illumina TruSeq Stranded RNA) were prepared according to the manufacturer's protocol and sequenced using an Illumina NovaSeq6000 S4 v1.5 kit

value: BCBM

tag: age

tag: gender

value: female

tag: location

value: cerebrum

tag: ghgax raw_data_accession


title: Participant 004, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_004
Raw sequence data not distributed per IRB approval

value: Nasal mucosa


title: Young msn2∆ cells replicate 2

description: Library name: msn2_log_rep2


title: Huh7 cells, CDK18 KO, Day 2, Replicate 1

value: CDK18 KO


title: Huh7 cells, Control, Day 4, Replicate 1

description: Cells infected, and cultured for 4 days before RNA extraction

value: Day 4


title: Young msn2∆ cells replicate 1

description: Library name: msn2_log_rep1

value: Cell culture

value: yeast cell


title: Participant 013, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_013
Raw sequence data not distributed per IRB approval

value: F


title: Young wildtype cells replicate 3

description: Library name: WT_log_rep3


title: Huh7 cells, CDK16 KO, Day 2, Replicate 3

value: CDK16 KO


title: NCH4562

description: Library name: Exp_NCH4562

value: cerebellum

tag: batch


title: Participant 001, Nasal mucosa, scRNAseq

description:
Library name: CFHV_sc_subj_001
Raw sequence data not distributed per IRB approval

value: CF


title: NCH3762

description: Library name: Exp_NCH3762


title: NCH4921

description: Library name: Exp_NCH4921


title: Young wildtype cells replicate 2

description: Library name: WT_log_rep2

value: grown in SC YNB (no Biotin) 2% Glucose 2% MMP DAPA pH4.5


title: Huh7 cells, CDK18 KO, Day 2, Replicate 2

value: hepatocellular carcinoma cell line


title: NCH748y

description: Library name: Exp_NCH748y

value: male


title: Huh7 cells, CDK16 KO, Day 2, Replicate 2

value: Day 2


title: Huh7 cells, CDK16 KO, Day 2, Replicate 1


title: NCH2006

description: Library name: Exp_NCH2006


title: NCH572j

description: Library name: Exp_NCH572j


title: NCH7629

description: Library name: Exp_NCH7629


title: Young wildtype cells replicate 1

description: Library name: WT_log_rep1


title: Huh7 cells, Control, Day 2, Replicate 3

value: WT


title: NCH7126

description: Library name: Exp_NCH7126

value: BCBM


title: NCH724y

description: Library name: Exp_NCH724y

value: female


title: Mll4-AID_par_p300i-Dex_p300

description: Library name: Sample 118

data_processing:
Basecalls performed using Bcl2fastq.
CUT&RUN and ChIP-Seq reads were aligned to the mm10 genome assembly using bowtie2.
CUT&RUN and ChIP-Seq peaks were called using SICER (v2) with following configuration: For Arid1a, GR, and KMT2D, a window size of 50 bp, gap size of 50 bp , and a false discovery rate of 1E-10 were used. For MyoD and p300, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all CUT&RUN or ChIP-Seq data.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (#14-1048, Epicypher), following the manufacturer’s instructions with the following modifications. 0.5 million cells were used for each CUT&RUN reaction. Cells were gently fixed with 0.1% formaldehyde for 1 min. Cells were resuspended in cold Nuclei Extract Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MgCl2 supplemented with protease inhibitor and 0.5 mM Spermidine), lysed on ice for 10 mins, and centrifuged at 600 g for 3 min 4°C. Nuclei were resuspended in 100 uL cold Nuclei Extract Buffer and incubated with activated 10 uL/reaction Concanavalin A beads for 10 min at RT. The following steps are performed according to the manufacturer’s instructions.
Libraries were prepared following the instruction of CUTANA™ CUT&RUN Library Prep Kit for Illumina sequencing. CUT&RUN enriched DNA were used to construct libraries, using NEBNext® Ultra™ II DNA Library Prep kit (#E7645L, NEB) with AMPure XP magnetic beads (Beckman Coulter).
Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Preadipocyte

value: A-485 (1h) Dexamethasone (1h)

tag: chip antibody


title: Huh7 cells, Control, Day 2, Replicate 2

tag: time


title: NCH6795

description: Library name: Exp_NCH6795

value: cerebrum


title: NCH7592

description: Library name: Exp_NCH7592


title: Mll4-AID_par_p300i-Dex_input

description: Library name: Sample 117


title: Huh7 cells, Control, Day 2, Replicate 1


title: Mll4-AID_par_p300i-Dex_KMT2D

description: Library name: Sample 116

value: Anti-MLL4 #3 (home-made, Kai Ge Lab)


title: TNBC_48_FF

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

data_processing:
Sequenced reads were trimmed with fastp v0.20.1 and mapped to GRCh38 using HISAT2 v2.1.0 both with default parameters.
Reads overlapping genomic features were counted with featureCounts v2.0.031 from the Subread package and Ensembl v99.
Only uniquely mapped and not duplicated reads were counted.  Multiple overlaps of unique genomic feature were not counted.
Assembly: GRCh38
Supplementary files format and content: tabular file representing counts

source_name: breast tumor, fresh frozen sample

extract_protocol:
RNA extraction was performed with COVARIS ME220 Focused-ultrasonicator, to allow a high quantity and high quality of RNA extracted.
RNA libraries were prepared with the SureSelect XT RNA Direct Reagent kit and the SureSelectXT Human All Exon V6 +UTR probes from Agilent.   All libraries were sequenced on an Illumina NextSeq 550 in paired-end mode (2 x 75bp) with a target depth of 20 million fragments per sample.

value: breast tumor, fresh frozen sample

value: triple-negative breast cancer

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

value: IDC

tag: tumor size (in mm)

tag: event

tag: event time (in days)


title: NCH6937

description: Library name: Exp_NCH6937

tag: tissue

tag: age

value: cerebellum


title: NCH6784

description: Library name: Exp_NCH6784

tag: gender

tag: location


title: Mll4-AID_par_p300i-Dex_GR_M20

description: Library name: Sample 115

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Anti-GR (M-20) (sc-100041, Santa Cruz)


title: NCH6758

description: Library name: Exp_NCH6758

tag: ghgax raw_data_accession

tag: batch


title: NCH6409

description: Library name: Exp_NCH6409


title: TNBC_46_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: Mll4-AID_par_p300i-Dex_ARID1A

description: Library name: Sample 114

tag: chip antibody

value: Anti-ARID1A/BAF250A (D2A8U) (12354, CST)


title: NCH7024

description: Library name: Exp_NCH7024


title: TNBC_45_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)

tag: event

tag: event time (in days)


title: NCH6239

description: Library name: Exp_NCH6239

tag: tissue

tag: age

tag: gender

tag: location


title: Mll4-AID_par_BRG1i-Dex_p300

description: Library name: Sample 113

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: BRM014 (1h) Dexamethasone (1h)


title: NCH5800

description: Library name: Exp_NCH5800

tag: ghgax raw_data_accession

tag: batch


title: NCH5781

description: Library name: Exp_NCH5781


title: TNBC_44_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: Mll4-AID_par_BRG1i-Dex_input

description: Library name: Sample 112


title: TNBC_43_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)

tag: event


title: NCH5535

description: Library name: Exp_NCH5535

tag: tissue

tag: age

tag: gender

tag: location


title: Mll4-AID_par_BRG1i-Dex_KMT2D

description: Library name: Sample 111

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody


title: NCH5521

description: Library name: Exp_NCH5521

tag: ghgax raw_data_accession

tag: batch


title: Mll4-AID_par_BRG1i-Dex_GR_M20

description: Library name: Sample 110


title: NCH5474

description: Library name: Exp_NCH5474


title: TNBC_47_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)

tag: event time (in days)


title: NCH5119

description: Library name: Exp_NCH5119

tag: tissue


title: NCH5080

description: Library name: Exp_NCH5080

tag: age


title: NCH6077

description: Library name: Exp_NCH6077

tag: gender


title: NCH5396

description: Library name: Exp_NCH5396

tag: location


title: NCH5067

description: Library name: Exp_NCH5067


title: TNBC_42_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)

tag: event


title: Mll4-AID_par_BRG1i-Dex_ARID1A

description: Library name: Sample 109

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: chip antibody


title: NCH4960

description: Library name: Exp_NCH4960

tag: ghgax raw_data_accession

tag: batch


title: TNBC_41_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)

tag: event time (in days)


title: TNBC_40_FF

tag: tissue

tag: erbb2 (by ihc)

tag: ki67 (in pct)


title: Mll4-AID_par_dMLL4-Dex_p300

description: Library name: Sample 108

value: 5-Ph-IAA (2h) Dexamethasone (1h)


title: TNBC_39_FF

tag: histological type

tag: tumor size (in mm)

tag: event


title: Mll4-AID_par_dMLL4-Dex_KMT2D

description: Library name: Sample 106

tag: cell line

tag: cell type

tag: genotype


title: NCH4454

description: Library name: Exp_NCH4454

tag: age

tag: gender

tag: location

tag: ghgax raw_data_accession


title: Mll4-AID_par_dMLL4-Dex_input

description: Library name: Sample 107

tag: treatment


title: NCH4475

description: Library name: Exp_NCH4475

tag: batch


title: NCH4641

description: Library name: Exp_NCH4641


title: TNBC_38_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: Mll4-AID_par_dMLL4-Dex_GR_M20

description: Library name: Sample 105

tag: chip antibody


title: NCH4359

description: Library name: Exp_NCH4359

tag: tissue


title: NCH4033

description: Library name: Exp_NCH4033


title: NCH4838

description: Library name: Exp_NCH4838


title: NCH4211

description: Library name: Exp_NCH4211


title: NCH3745

description: Library name: Exp_NCH3745


title: NCH3826

description: Library name: Exp_NCH3826


title: TNBC_36_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)

tag: event

tag: event time (in days)


title: Mll4-AID_par_Dex_p300

description: Library name: Sample 103

tag: cell line

tag: cell type

tag: genotype

value: Dexamethasone (1h)


title: Mll4-AID_par_dMLL4-Dex_ARID1A

description: Library name: Sample 104

tag: treatment


title: NCH3714

description: Library name: Exp_NCH3714

tag: age

tag: gender

tag: location

tag: ghgax raw_data_accession

tag: batch


title: Mll4-AID_par_Dex_input

description: Library name: Sample 102


title: NCH4464

description: Library name: Exp_NCH4464


title: TNBC_33_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: TNBC_35_FF

tag: tissue

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)


title: NCH3216

description: Library name: Exp_NCH3216


title: NCH3218

description: Library name: Exp_NCH3218


title: NCH3466

description: Library name: Exp_NCH3466


title: Mll4-AID_par_Dex_KMT2D

description: Library name: Sample 101

tag: cell line

tag: cell type

tag: genotype

tag: chip antibody


title: Mll4-AID_par_Dex_GR_M20

description: Library name: Sample 100

tag: treatment


title: TNBC_37_FF

tag: event

tag: event time (in days)


title: NCH3551

description: Library name: Exp_NCH3551

tag: age

tag: gender

tag: location

tag: ghgax raw_data_accession

tag: batch


title: TNBC_31_FF

tag: tissue

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: NCH3206

description: Library name: Exp_NCH3206


title: Mll4-AID_par_Dex_ARID1A

description: Library name: Sample 99

tag: cell line

tag: cell type


title: NCH3369

description: Library name: Exp_NCH3369


title: NCH3161

description: Library name: Exp_NCH3161


title: TNBC_30_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)


title: NCH3074

description: Library name: Exp_NCH3074

tag: age


title: Mll4-AID_par_unt_p300

description: Library name: Sample 98

tag: genotype

tag: chip antibody


title: TNBC_34_FF

tag: event

tag: event time (in days)


title: NCH2932

description: Library name: Exp_NCH2932

tag: tissue

tag: gender

tag: location

tag: ghgax raw_data_accession

tag: batch


title: TNBC_32_FF

tag: disease state

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: pr (by ihc)


title: NCH3195

description: Library name: Exp_NCH3195


title: NCH3494

description: Library name: Exp_NCH3494


title: NCH946

description: Library name: Exp_NCH946


title: NCH2860

description: Library name: Exp_NCH2860


title: Mll4-AID_par_unt_KMT2D

description: Library name: Sample 96

tag: cell line

tag: cell type


title: Mll4-AID_par_unt_input

description: Library name: Sample 97


title: NCH739q

description: Library name: Exp_NCH739q

tag: age


title: NCH715b

description: Library name: Exp_NCH715b


title: TNBC_26_FF

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

value: others

tag: tumor size (in mm)


title: NCH1011

description: Library name: Exp_NCH1011

tag: tissue

value: BCBM


title: TNBC_27_FF

tag: event

tag: event time (in days)


title: C2C12_D1_A485-2h_input

description: Library name: Sample 93

value: Myoblast

tag: treatment

value: A-485 (2h) + myogenic differentiation

tag: time


title: TNBC_28_FF

tag: disease state


title: Mll4-AID_par_unt_ARID1A

description: Library name: Sample 94

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Preadipocyte

tag: genotype

tag: chip antibody


title: TNBC_29_FF

tag: age (in years)

tag: nodal status

tag: er (by ihc)


title: TNBC_25_FF

tag: pr (by ihc)


title: NCH1007

description: Library name: Exp_NCH1007

tag: age

tag: gender

value: female

tag: location

value: cerebrum

tag: ghgax raw_data_accession

tag: batch


title: Mll4-AID_par_unt_GR_M20

description: Library name: Sample 95

tag: cell line

tag: cell type


title: NCH728k

description: Library name: Exp_NCH728k

tag: tissue


title: NCH574g

description: Library name: Exp_NCH574g


title: NCH576b

description: Library name: Exp_NCH576b


title: C2C12_D1_A485-2h_p300

description: Library name: Sample 92

tag: treatment


title: NCH740m

description: Library name: Exp_NCH740m


title: NCH1837

description: Library name: Exp_NCH1837


title: TNBC_24_FF

value: breast tumor, fresh frozen sample

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

value: ILC

tag: tumor size (in mm)

tag: event

tag: event time (in days)


title: NCH1894

description: Library name: Exp_NCH1894


title: TNBC_23_FF

tag: disease state

value: triple-negative breast cancer

tag: age (in years)

tag: nodal status

tag: er (by ihc)

value: IDC


title: NCH942

description: Library name: Exp_NCH942

tag: age

tag: gender

tag: location


title: NCH2340

description: Library name: Exp_NCH2340

tag: ghgax raw_data_accession

tag: batch


title: NCH998

description: Library name: Exp_NCH998

tag: tissue


title: NCH693b

description: Library name: Exp_NCH693b

value: cerebellum


title: TNBC_21_FF

tag: pr (by ihc)


title: TNBC_22_FF

tag: erbb2 (by ihc)


title: C2C12_A485-2h_input

description: Library name: Sample 89

tag: cell line

tag: cell type

tag: treatment

tag: time


title: C2C12_D1_DMSO-2h_p300

description: Library name: Sample 90

value: myogenic differentiation

tag: chip antibody


title: NCH724m

description: Library name: Exp_NCH724m


title: NCH723r

description: Library name: Exp_NCH723r


title: NCH1281

description: Library name: Exp_NCH1281


title: NCH749b

description: Library name: Exp_NCH749b


title: C2C12_DMSO-2h_p300

description: Library name: Sample 86


title: NCH631b

description: Library name: Exp_NCH631b


title: TNBC_18_FF

tag: disease state

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)

tag: event

tag: event time (in days)


title: NCH2940

description: Library name: Exp_NCH2940

tag: age

tag: gender

tag: location


title: TNBC_17_FF

tag: tissue

tag: age (in years)

tag: nodal status

tag: er (by ihc)


title: NCH747q

description: Library name: Exp_NCH747q

tag: ghgax raw_data_accession

tag: batch


title: NCH2710

description: Library name: Exp_NCH2710


title: C2C12_D1_DMSO-2h_input

description: Library name: Sample 91

tag: cell line

tag: cell type

tag: treatment

tag: time


title: C2C12_A485-2h_p300

description: Library name: Sample 88

tag: chip antibody


title: C2C12_unt_p300

description: Library name: Sample 84


title: TNBC_16_FF

tag: disease state

tag: pr (by ihc)

tag: erbb2 (by ihc)

tag: ki67 (in pct)

tag: histological type

tag: tumor size (in mm)


title: NCH730b

description: Library name: Exp_NCH730b

tag: tissue

tag: age

tag: gender

tag: location


title: NCH735u

description: Library name: Exp_NCH735u

tag: ghgax raw_data_accession


title: TNBC_20_FF

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: event

tag: event time (in days)


title: TNBC_19_FF


title: C2C12_unt_input

description: Library name: Sample 85

tag: cell line

tag: cell type


title: NCH1941

description: Library name: Exp_NCH1941

tag: batch


title: HCC, WT, R5

description: Library name: HCC-WT-5

data_processing:
Sequencing quality control was performed using fastqc preprocessing(v0.11.9), UMIs were extracted and deduplicated using umi_tools (v1.1.2) and adapters were removed with BBDuk (bbtools v37.62)
We performed read alignment to the mm10 version of GRCh38 mouse reference genome using STAR (v2.7.11a) and quantification using htseq-count  (v1.99.2) and count matrices were used for downstream analysis in DESeq2 R Bioconductor package (v1.32.0, Love et al., 2014).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample, txt file

source_name: liver tumor

growth_protocol: Liver tumors were induced in mice via hydrodynamic injection of plasmids encoding mice c-Myc and β-catenin. Tumor development was monitored weekly using high-resolution ultrasound imaging. Tumors were harvested upon reaching the predefined endpoint criteria (tumor diameter ≥ 15 mm, signs of distress, or 8 weeks post-injection). All procedures followed IACUC-approved protocols.

extract_protocol:
Total RNA was extracted from snap-frozen liver tumor tissue using the QIAGEN RNeasy Mini Kit. Briefly, tumors were mechanically disrupted by chopping in liquid nitrogen, followed by homogenization in RLT buffer (supplemented with β-mercaptoethanol) using a rotor-stator homogenizer. Lysates were processed according to the manufacturer’s protocol, including on-column DNase I digestion (QIAGEN RNase-Free DNase). RNA integrity was verified via Agilent Bioanalyzer (RIN ≥ 8.0)
Provided total RNA samples (300ng, with average RIN/RQS 8.3, range 7.5-8.8) were converted into sequencing libraries using the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier tag are used {to be addressed for bias correction at data analysis}. Directional cDNA libraries, stranded in the sense orientation {--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq, Reverse for HISAT}, were completed by PCR and sequenced in a single read format on an Illumina NovaSeq X (with NovaSeq X Series Reagent Kits) and siingle read 151 bases

treatment_protocol: To conditionally knockout Cdk16 in established tumors, mice carrying floxed Cdk16 alleles (*Cdk16fl/fl*) and expressing Cre-ERT2 and CRE-ERT2 controls were administered tamoxifen (20 mg/mL in corn oil) via intraperitoneal injection (75 mg/kg body weight, 5 consecutive days). Tumors were collected 10 days post-treatment completion for RNA extraction.

value: liver tumor

tag: genotype

value: WT


title: TNBC_14_FF

tag: disease state

tag: pr (by ihc)

tag: erbb2 (by ihc)

tag: ki67 (in pct)


title: NCH714k

description: Library name: Exp_NCH714k

tag: tissue

tag: age


title: NCH640f

description: Library name: Exp_NCH640f

tag: gender

tag: location


title: HCC, WT, R4

description: Library name: HCC-WT-4


title: C2C12_DMSO-2h_input

description: Library name: Sample 87

tag: treatment

tag: time


title: TNBC_13_FF

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: histological type

tag: tumor size (in mm)


title: HCC, WT, R2

description: Library name: HCC-WT-2


title: NCH1098

description: Library name: Exp_NCH1098

tag: ghgax raw_data_accession

tag: batch


title: HCC, WT, R3

description: Library name: HCC-WT-3

tag: genotype


title: NCH741o

description: Library name: Exp_NCH741o


title: NCH708c

description: Library name: Exp_NCH708c


title: TNBC_12_FF

tag: disease state

tag: pr (by ihc)

tag: event

tag: event time (in days)


title: TNBC_11_FF

tag: tissue

tag: erbb2 (by ihc)

tag: ki67 (in pct)


title: NCH718e

description: Library name: Exp_NCH718e

tag: age

tag: gender

tag: location


title: NCH1367

description: Library name: Exp_NCH1367


title: HCC, WT, R1

description: Library name: HCC-WT-1


title: HCC, CDK16KO CDK18KO, R4

description: Library name: HCC-DKO-4

value: CDK18KO, CDK16KO


title: TNBC_15_FF

tag: age (in years)

tag: nodal status


title: NCH1849

description: Library name: Exp_NCH1849


title: TNBC_10_FF

tag: er (by ihc)

tag: histological type


title: NCH767

description: Library name: Exp_NCH767

tag: ghgax raw_data_accession


title: NCH1648

description: Library name: Exp_NCH1648

tag: batch


title: TNBC_09_FF

tag: tumor size (in mm)


title: NCH637c

description: Library name: Exp_NCH637c


title: NCH2183

description: Library name: Exp_NCH2183


title: NCH1151

description: Library name: Exp_NCH1151


title: NCH2494

description: Library name: Exp_NCH2494


title: TNBC_08_FF

tag: disease state


title: HCC, CDK16KO CDK18KO, R2

description: Library name: HCC-DKO-2

tag: genotype


title: TNBC_07_FF

tag: pr (by ihc)

tag: event


title: NCH1645

description: Library name: Exp_NCH1645

tag: tissue


title: NCH2646

description: Library name: Exp_NCH2646


title: HCC, CDK16KO CDK18KO, R1

description: Library name: HCC-DKO-1


title: HCC, CDK18KO, R5

description: Library name: HCC-18KO-5


title: NCH2760

description: Library name: Exp_NCH2760


title: NCH2280

description: Library name: Exp_NCH2280


title: NCH721o

description: Library name: Exp_NCH721o


title: NCH710e

description: Library name: Exp_NCH710e


title: NCH1865

description: Library name: Exp_NCH1865


title: HCC, CDK18KO, R3

description: Library name: HCC-18KO-3


title: HCC, CDK18KO, R4

description: Library name: HCC-18KO-4


title: TNBC_05_FF

tag: erbb2 (by ihc)

tag: event time (in days)


first: Fabien

last: Dachet

address: 1200 W Harrison St

institute: University of Illinois Chicago

description:
Library name: UIC1_batchB_Lumbar_Arm
Tissue from Lumbar sampled from Patient UIC-ALS1 with Onset: Arm (batchB)

data_processing:
FASTQ files obtained from Illumina BaseSpace were processed using Trim Galore (v0.6.10) for adapter trimming and quality filtering, then aligned to the human reference genome GRCh38.p14 using the STAR aligner (v2.7.11b) with GENCODE v47 annotation. Gene-level read counts were generated with featureCounts from the Subread package (v2.0.4). Differential expression analysis was performed in R (v4.4.1) using DESeq2 (v1.44.0), with comparisons conducted in the medulla (bulbar vs non-bulbar onset) and cervical spinal cord (arm vs non-arm onset). Gene ontology enrichment analysis was carried out using the DAVID database, considering pathways with a gene count ≥5 and a Benjamini–Hochberg false discovery rate <0.01
Assembly: Sequencing reads were aligned to the human reference genome assembly GRCh38.p14 using gene annotations from GENCODE release 47
Supplementary files format and content: Raw count from FeatureCount using same strand counting

source_name: spinal cord

extract_protocol:
Human postmortem tissues were collected through a rapid autopsy protocol performed within 3 hours of death, with samples obtained from the medulla, cervical spinal cord (C4–6), and lumbar spinal cord (L3–5); tissues were rapidly frozen and stored at −80 °C. For RNA extraction, multiple thin frozen sections from each region were pooled, and total RNA was isolated using the Qiagen RNeasy Lipid Tissue Kit (Cat#74804, Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol, yielding approximately 3 µg of RNA per sample. RNA samples were treated with DNase (RCC-5, Zymo Research, Irvine, CA) to remove genomic DNA, and RNA quality was assessed using a Qubit 4.0 instrument, with only samples having a RNA integrity number (RIN) ≥ 7 included for downstream analyses
RNA library construction was performed by the UIC Genome Research Core facility using total RNA extracted from postmortem human tissues. Following quality control, samples meeting inclusion criteria were used for library preparation, after which sequencing was carried out on an Illumina NovaSeq 6000 platform at the UIC-Urbana Core Facility. Sequencing was performed in paired-end mode, generating an average depth of approximately 30–40 million paired reads per sample, and resulting FASTQ files were retrieved from Illumina BaseSpace for downstream analyses.

value: spinal cord

tag: cell type

value: Multiple type of cells present in human spinal cord

value: Batch B


title: TNBC_04_FF

tag: ki67 (in pct)


title: HCC, CDK18KO, R2

description: Library name: HCC-18KO-2


title: TNBC_03_FF


title: MP075, MP078, NS031, NS035

description:
Library name: Multiplex 1
4-plex

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger v9.0.1 aligned to the human GRCh38 genome. Multiplex 1 used a 4-plex kit (BC001-004) and Multiplex 2 and 3 used a 16-plex kit (BC001-016). The barcode used for each sample can be found in the demultiplexing_barcodes.txt file.
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: CellRanger-generated HDF5 format with expression values and associated gene and cell annotations

source_name: Cerebrospinal fluid

extract_protocol:
CSF was obtained from an LP performed at day 7 following enrolment as part of the INTENSE-TBM trial (47). Up to 6 ml CSF was collected in a 15 ml falcon tube at the bedside after prioritising necessary clinical investigations. Samples were transferred to the biosafety level 3 laboratory at 4˚C and processed within two hours of collection. Fresh CSF was centrifuged at 400 RCF for 10 minutes at 4˚C and supernatant removed.
Cells were fixed in a 4% formaldehyde fixative solution, as described in the Demonstrated Protocols CG000478 and CG000553 and using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics PN-1000414), then stored at -80˚C for up to 12 months. Fixed samples were processed following the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples Protocol (10x Genomics CG000527, Revision A) using the Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 4 BC  (10x Genomics PN-1000475) and 4 rxns x 16 BC (PN-1000476). Gene expression was measured using barcoded probe pairs designed to hybridise to mRNA specifically. Using a microfluidic chip, the fixed and probe-hybridised single cell suspensions were partitioned into nanolitre-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes was sampled separately to index the contents of each partition. Inside the GEMs, probes were ligated and the 10x GEM Barcode was added, and all ligated probes within a GEM share a common 10x GEM Barcode. Barcoded and ligated probes were then pre-amplified in bulk, after which gene expression libraries were generated (User Guide: CG000527, Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples) and sequenced (NovaSeq 6000, NovaSeq X. Sequencing read configuration: 28-10-10-90). Samples were processed and sequenced in three batches. All samples in the same batch were multiplexed using sample-specific probe sets and sequenced together. Two samples in batch 3 were double barcoded to maximise use of the 16-plex kit. These samples therefore had twice the number of cells sequenced.

value: Cerebrospinal fluid


title: HCC, CDK18KO, R1

description: Library name: HCC-18KO-1


title: HCC, CDK16KO CDK18KO, R3

description: Library name: HCC-DKO-3


title: NCH798

description: Library name: Exp_NCH798

value: BCBM

tag: age

tag: gender

tag: location


title: third instar larval wing disc, Mef2>Argk-RNAi, rep 2

first: Maria

middle: Paula

last: Zappia

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

description:
Library name: Wing_Mef2ArgkKD_2
10x Genomics

data_processing:
After demultiplexing sequence reads were processed through IndexHopping (v1.1.0)
The alignment, filtering, barcode counting and UMI counting was done using Cell Ranger (v7.1.0) with the command count and default settings
Assembly: Dmel 6.32 (Ensembl 109)
Supplementary files format and content: Tab-separeted values files and matrix files
Supplementary files format and content: List of cell barcodes used for the analysis of the myoblasts. Includes cell type annotation.
Supplementary files format and content: Processed Seurat object generated from the analysis of the myoblasts. Includes cell type annotation.

organism: Drosophila melanogaster

source_name: Wing discs

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.

extract_protocol:
Wing discs from wandering third instar larvae were dissected for 30-60 min. Discs were harvested in chilled HBSS + 0.1 % BSA. Tissue was dissociated for 15 min in 100-200 μl dissociation buffer (2 mg/ml collagenase A (Roche 11088793001), 0.8U/ml Dispase II (Roche 04942078001), 2 mM CaCl2 in HBSS) in an Eppendorf Thermo mixer C set at 30°C, 500 rpm. Cells were washed two times with 0.5 % BSA in PBS 1x  by centrifugating at 800 g for 5 min at 4°C, and filtered with two consecutive cell strainers: a Bel-Art Flowmi 40 μm and a mini-strainer 10 μm (43-10010-40). Cell viability and concentration was assessed by staining cells with Trypan blue and counting cells using a hemocytometer. Only samples showing cell viability over 90% were used for scRNA-seq.
Chromium Single-Cell 3’ Reagent kits v3 for experiment 1 and Chromium Next GEM Single-Cell 3’ Reagent kits v3.1 for experiment 2 were used according to the manufacturer’s protocol (10x Genomics, CG000183RevA and CG000315 Rev C, respectively). Around 10,000 cells were loaded per sample in the Chromium Controller for experiment 1 and around 20,000 cells in the Chromium X for experiment 2. The pooled barcoded cDNA was cleaned up with Dynabeads, amplified by PCR. The fragments were size selected with SPRIselect reagent during library construction. Libraries were single-indexed for experiment 1 while dual indexed for experiment 2. The qualities of both amplified cDNA and libraries were assessed using Agilent TapeStation 4200 instrument. The libraries were pooled and diluted for paired-end equencing onto HiSeq 4000, NovaSeq 6000, NovaSeq X Plus instruments (PE 150, Illumina).

value: Wing discs

tag: developmental stage

value: wandering third instar larva (25 deg C)

value: Exp 2


title: Mll4_AID_MyoD_ER_p300_deg_4OHT_p300_CST

description: Library name: Sample 69

data_processing:
Basecalls performed using Bcl2fastq.
CUT&RUN and ATAC-Seq reads were aligned to the mm10 genome assembly using bowtie2.
CUT&RUN peaks were called using SICER (v2) with following configuration: For transcription factors and co-factors, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For histone modifications, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all CUT&RUN data.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (#14-1048, Epicypher), following the manufacturer’s instructions with the following modifications. 0.5 million cells were used for each CUT&RUN reaction. Cells were gently fixed with 0.1% formaldehyde for 1 min. Cells were resuspended in cold Nuclei Extract Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MgCl2 supplemented with protease inhibitor and 0.5 mM Spermidine), lysed on ice for 10 mins, and centrifuged at 600 g for 3 min 4°C. Nuclei were resuspended in 100 uL cold Nuclei Extract Buffer and incubated with activated 10 uL/reaction Concanavalin A beads for 10 min at RT. The following steps are performed according to the manufacturer’s instructions.
Libraries were prepared following the instruction of CUTANA™ CUT&RUN Library Prep Kit for Illumina sequencing. CUT&RUN enriched DNA were used to construct libraries, using NEBNext® Ultra™ II DNA Library Prep kit (#E7645L, NEB) with AMPure XP magnetic beads (Beckman Coulter).

tag: cell line

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Preadipocyte

tag: treatment

value: dCBP-1 (3h) 4OHT (1h)

tag: chip antibody


title: TNBC_01_FF

value: breast tumor, fresh frozen sample

value: triple-negative breast cancer

tag: age (in years)

tag: nodal status

tag: er (by ihc)

tag: histological type

value: IDC

tag: tumor size (in mm)


description:
Library name: M18_batchA_Lumbar_Bulbar
Tissue from Lumbar sampled from Patient MALS1018 with Onset: Bulbar (batchA)

tag: tissue

tag: batch

value: Batch A


description:
Library name: UIC1_batchB_Medulla_Arm
Tissue from Medulla sampled from Patient UIC-ALS1 with Onset: Arm (batchB)

source_name: medulla

value: medulla

value: Multiple type of cells present in human medulla


description:
Library name: UIC1_batchB_Cervical_Arm
Tissue from Cervical sampled from Patient UIC-ALS1 with Onset: Arm (batchB)

value: spinal cord


title: TNBC_06_FF

tag: disease state

tag: pr (by ihc)

tag: erbb2 (by ihc)

tag: event

tag: event time (in days)


title: TNBC_02_FF

tag: ki67 (in pct)


title: third instar larval wing disc, control, rep 2

description:
Library name: Wing_Mef2mcherryKD_3
10x Genomics

tag: developmental stage

tag: genotype


title: third instar larval wing disc, control, rep 1

description:
Library name: Wing_Mef2mcherryKD_1
10x Genomics

source_name: Wing discs (pouch was removed)

value: Wing discs (pouch was removed)

value: Exp 1


title: PS_M9gluc_wo_TE_rep2

description: Library name: PS_M9gluc_wo_TE_2

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts were generated using featureCounts
Assembly: NC_004578.1, NC_004633.1, NC_004632.1
Supplementary files format and content: Supplementary files format and content: Comma-delimited text file containing logTPM values for each sample.

organism: Pseudomonas syringae pv. tomato str. DC3000

growth_protocol: Cells were grown overnight at 30 °C with shaking in 4 mL of the base medium (M9 or CAMHB). The following day, fresh cultures were inoculated in duplicate to an initial OD600 of 0.05. For nitrogen starvation (nitrogen-free M9 media with addition of eighteen amino acids, with the exception of cysteine and methionine) conditions, cultures were grown in medium supplemented as specified. Cultures were harvested at mid-log phase (OD₆₀₀ ≈ 0.5) and 3 mL of culture was immediately mixed with 6 mL of RNAprotect reagent for the following conditions: growth in M9 glucose media (with and without trace element solution), CAMHB media, and nitrogen starvation. Cells were pelleted and stored at −80 °C until RNA extraction and RNA-seq library preparation.

extract_protocol:
Total RNA was isolated and prepared from cell pellets using reagents from Zymo Research and silica-coated magnetic beads (Luna Nanotech) accroding to the vendor's manual. Concentrations and quality of the RNA were assessed using an Agilent TapeStation and Nanodrop, respectively. For each sample, 1 ug was used as input for the standard RiboRid procedure.
RNA-seq libraries were prepared from 5 uL of the rRNA-subtracted RNA using KAPA RNA HyperPrep Kit (Roche) according to the manufacturer’s protocol with volumes reduced by half. The final PCR amplification step was modified by incorporating SYBR and using a qPCR instrument. Samples were removed from the thermal cycler just before entering the plateau phase of amplification to avoid biases being potentially introduced by reagent depletion. The quality and concentrations of the libraries were checked with an Agilent TapeStation and Qubit instrument, respectively. Pooled libraries were then run on an AVITI instrument (Element Biosciences).

tag: strain

tag: cell type

value: bacterial cell

value: wild-type

tag: treatment

value: glucose (2 g/L)

tag: medium

value: M9 media


title: Mll4_AID_MyoD_ER_p300_deg_4OHT_MLL4

description: Library name: Sample 67

tag: cell line

tag: chip antibody

value: Anti-MLL4 #3 (home-made, Kai Ge Lab)


description:
Library name: M18_batchA_Cervical_Bulbar
Tissue from Cervical sampled from Patient MALS1018 with Onset: Bulbar (batchA)

value: Multiple type of cells present in human spinal cord


title: BSHRI_2015-1401 WT Middle Frontal Gyrus MFG_10

city: New York

first: Joshua

last: Orrick

state: NY

address: 194 E 2nd St

department: Genetics & Genomics

institute: Mount Sinai School of Medicine

description:
Library name: BSHRI-2015-1401-MFG
European Female Control

data_processing:
Processed matrix of unfiltered MAPT isoform read counts was generated by (1) isoform exon coordinate and read count extraction from BED files for each sample, then (2) cross-sample consolidation of listed isoforms if there are exact coordinate pair matches between extracted isoforms while keeping individual samples' read counts of each isoform unaltered upon merge.
Assembly: Hg38
Supplementary files format and content: Comma separated value file of raw per-sample read counts of sequenced MAPT isoform exon coordinates extracted from BED files. Column titles are exact matches of each sample library name.

source_name: Middle Frontal Gyrus

growth_protocol: Donor brain tissue was kept frozen prior to extraction.

extract_protocol:
Qiagen RNAeasy Mini extraction of total RNA using manufacturer's protocol.
PacBio Iso-Seq full-length cDNA libraries were generated from brain tissue total RNA by oligo(dT)-primed cDNA synthesis with template switching, PCR amplification, bead cleanup, and SMRTbell library construction.

value: Middle Frontal Gyrus

value: WT

value: D


title: BSHRI_2015-735 WT Middle Frontal Gyrus MFG_8

description:
Library name: BSHRI-2015-735-MFG
European Male Control


description:
Library name: M8_batchA_Lumbar_Bulbar
Tissue from Lumbar sampled from Patient MALS1008 with Onset: Bulbar (batchA)


title: Mll4_AID_MyoD_ER_p300_deg_4OHT_T7

description: Library name: Sample 68

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Preadipocyte

value: dCBP-1 (3h) 4OHT (1h)


title: Mll4_AID_MyoD_ER_p300_deg_4OHT_IgG

description: Library name: Sample 66

value: Anti-IgG (13-0042K, Epicypher)


title: PS_M9gluc_wo_TE_rep1

description: Library name: PS_M9gluc_wo_TE_1


description:
Library name: M18_batchA_Medulla_Bulbar
Tissue from Medulla sampled from Patient MALS1018 with Onset: Bulbar (batchA)

value: medulla

value: Multiple type of cells present in human medulla

value: Batch A


title: BSHRI_2015-1431 WT Middle Frontal Gyrus MFG_9

description:
Library name: BSHRI-2015-1431-MFG
European Female Control


title: Mll4_AID_MyoD_ER_p300_deg_4OHT_ARID1A

description: Library name: Sample 65

value: Anti-ARID1A/BAF250A (D2A8U) (12354, CST)


title: BSHRI_2015-280 WT Middle Frontal Gyrus MFG_7

description:
Library name: BSHRI-2015-280-MFG
European Female Control


title: Mll4_AID_MyoD_ER_p300_inh_4OHT_p300_CST

description: Library name: Sample 64


title: BSHRI_2015-1433 WT Middle Frontal Gyrus MFG_6

description:
Library name: BSHRI-2015-1433-MFG
European Male Control


title: third instar larval wing disc, Mef2>Argk-RNAi, rep 1

description:
Library name: Wing_Mef2ArgkKD_1
10x Genomics

value: Wing discs (pouch was removed)

value: wandering third instar larva (25 deg C)

value: Exp 1


title: PS_M9gluc_Zn_rep2

description: Library name: PS_M9gluc_Zn_2

value: bacterial cell

value: wild-type

value: glucose (2 g/L), trace element solution, and ZnSO4 ( 0.7 mM)

value: M9 media


title: Mll4_AID_MyoD_ER_p300_inh_4OHT_T7

description: Library name: Sample 63


description:
Library name: M8_batchA_Medulla_Bulbar
Tissue from Medulla sampled from Patient MALS1008 with Onset: Bulbar (batchA)


title: PS_NFM9gluc_rep1

description: Library name: PS_NFM9gluc_1

value: glucose (2 g/L) and amino acids (0.05g/L) (all except methionine and cysteine)

value: M9 media without NH4Cl


title: Mll4_AID_MyoD_ER_p300_inh_4OHT_MLL4

description: Library name: Sample 62

value: Kmt2c-/-;Kmt2dAID/AID preadipocytes

value: Anti-MLL4 #3 (home-made, Kai Ge Lab)


title: PS_NFM9gluc_rep2

description: Library name: PS_NFM9gluc_2


title: NBB_2019-116 WT Caudate CAU_5

description:
Library name: NBB-2019-116-cau
European Male Control

source_name: Caudate

value: Caudate

value: WT

value: D


description:
Library name: UIC9_batchA_Lumbar_Arm
Tissue from Lumbar sampled from Patient UIC-ALS9 with Onset: Arm (batchA)

value: spinal cord

value: Multiple type of cells present in human spinal cord


title: PS_M9gluc_Zn_rep1

description: Library name: PS_M9gluc_Zn_1

source_name: bacterial cell


title: HBCC_2871 WT Caudate CAU_4

description:
Library name: HBCC-2871-cau
European Male Control

value: C


title: Mll4_AID_MyoD_ER_p300_inh_4OHT_IgG

description: Library name: Sample 61

value: Preadipocyte

value: Anti-IgG (13-0042K, Epicypher)


title: HBCC_1987 WT Caudate CAU_3

description:
Library name: HBCC-1987-cau
European Male Control


title: PS_M9gluc_Cu_rep1

description: Library name: PS_M9gluc_Cu_1

value: glucose (2 g/L), trace element solution, and CuSO4 (0.05 mM)


title: Mll4_AID_MyoD_ER_p300_inh_4OHT_ARID1A

description: Library name: Sample 60

value: Anti-ARID1A/BAF250A (D2A8U) (12354, CST)


description:
Library name: UIC9_batchA_Medulla_Arm
Tissue from Medulla sampled from Patient UIC-ALS9 with Onset: Arm (batchA)

value: medulla

value: Multiple type of cells present in human medulla

value: Batch A


title: PS_M9gluc_Cu_rep2

description: Library name: PS_M9gluc_Cu_2

value: bacterial cell

value: wild-type

value: glucose (2 g/L), trace element solution, and CuSO4 ( 0.05 mM)

value: M9 media


description:
Library name: UIC9_batchA_Cervical_Arm
Tissue from Cervical sampled from Patient UIC-ALS9 with Onset: Arm (batchA)


description:
Library name: UIC8_batchA_Cervical_Arm
Tissue from Cervical sampled from Patient UIC-ALS8 with Onset: Arm (batchA)


description:
Library name: UIC8_batchA_Lumbar_Arm
Tissue from Lumbar sampled from Patient UIC-ALS8 with Onset: Arm (batchA)


title: UWA_6904 WT Caudate CAU_1

description:
Library name: 6904-cau
European Female Control

value: Caudate


title: NBB_2020-054 WT Caudate CAU_2

description:
Library name: 2020-054-2-cau-put
European Female Control

value: WT


title: PS_M9gluc_H2O2_rep2

description: Library name: PS_M9gluc_H2O2_2

value: glucose (2 g/L) and H2O2 (5 mM)