title: MSU, 22 hours, replicate 5 [HSA-000022242]

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (6 for WT only studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use. Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

treatment_protocol: Cells were treated with DMSO, 25nM BafA1, 6uM U18666A, 2uM VPS34IN1, 50uM E64 + 50uM leupeptin + 50uM pepstatin (E/LP), or 200ug/mL monosodium urate (MSU) for 1, 7, or 22h to RNA extraction. Total DMSO concentration was equal across all different treatments.

value: MSU

value: 200 ug/ml


title: MSU, 22 hours, replicate 4 [HSA-000022241]

status: Public on Jul 17 2026

type: SRA

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

library_source: transcriptomic

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewelset al., 2020) using Gencode M31 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a Microsoft Excel file with four worksheets: 1. sample information, 2. gene information, 3. raw count table, 4. normalized count table (log2 counts per million).

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

extract_protocol:
RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent). Libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWB for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 Screen Tape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593). Libraries were pooled in equimolar ratios and sent to SeqMatic for sequencing on a NovaSeq S1 (75bp, single-end reads).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 ScreenTape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593).

tag: replicate

tag: cell type

value: BMDM

tag: genotype

value: WT

tag: treatment

tag: treatment dose

tag: treatment duration

value: 22 hours

tag: rin


title: MSU, 22 hours, replicate 2 [HSA-000022239]


title: MSU, 22 hours, replicate 1 [HSA-000022238]


title: E/L/P, 22 hours, replicate 5 [HSA-000022237]

value: E/L/P

value: 50 uM


title: E/L/P, 22 hours, replicate 4 [HSA-000022236]


title: E/L/P, 22 hours, replicate 3 [HSA-000022235]


title: E/L/P, 22 hours, replicate 2 [HSA-000022234]


title: VPS34IN-1, 22 hours, replicate 5 [HSA-000022232]

value: 2 uM


title: VPS34IN-1, 22 hours, replicate 3 [HSA-000022230]


title: VPS34IN-1, 22 hours, replicate 2 [HSA-000022229]


title: E/L/P, 22 hours, replicate 1 [HSA-000022233]


title: VPS34IN-1, 22 hours, replicate 1 [HSA-000022228]


title: P4 Derived MSC Low Serum VEGF Bevacizumab

status: Public on Jul 18 2026

city: Boston

first: Ian

last: Dryg

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: P4MSLSVB

data_processing:
Raw paired-end FASTQ files were quantified using Salmon (v1.2.1), reads were quasi-mapped against the human GENCODE v34 reference annotation.
tximeta was used to read in the data and export counts matrix.
Assembly: GENCODE v34 (GRCh38.p13)
Supplementary files format and content: pseudocounts

organism: Homo sapiens

extract_protocol:
RNA was extracted using the commercially available RNeasy Mini Kit (Qiagen; 74104). RNA concentration was evaluated via NanoDrop spectrophotometer. Samples were diluted to the final concentration of 20ng/ul prior shipment to Novogene Corporation Inc. 2921 Stockton Blvd. Suite 1810 Sacramento CA 95817.
Human mRNA Sequencing (WOBI): 80 total RNA samples were subjected to Eukaryotic mRNA-seq on the NovaSeq 6000 (PE150) with poly-A capture and non-directional library.

tag: cell line

value: Mesenchymal Stem Cell

tag: serum

value: Low Serum

value: VEGF + Bevacizumab


title: U18666A, 22 hours, replicate 4 [HSA-000022226]

value: 6 uM


title: U18666A, 22 hours, replicate 5 [HSA-000022227]


title: U18666A, 22 hours, replicate 3 [HSA-000022225]


title: U18666A, 22 hours, replicate 2 [HSA-000022224]


title: BafA1, 22 hours, replicate 5 [HSA-000022222]

value: 25 nM


title: BafA1, 22 hours, replicate 4 [HSA-000022221]


title: BafA1, 22 hours, replicate 3 [HSA-000022220]


title: BafA1, 22 hours, replicate 2 [HSA-000022219]


title: DMSO, 22 hours, replicate 4 [HSA-000022216]

value: DMSO

value: 0 nM


title: DMSO, 22 hours, replicate 5 [HSA-000022217]


title: DMSO, 22 hours, replicate 1 [HSA-000022213]


title: MSU, 7 hours, replicate 4 [HSA-000022211]

value: 7 hours


title: MSU, 7 hours, replicate 1 [HSA-000022208]


title: E/L/P, 7 hours, replicate 5 [HSA-000022207]


title: E/L/P, 7 hours, replicate 4 [HSA-000022206]


title: E/L/P, 7 hours, replicate 3 [HSA-000022205]


title: E/L/P, 7 hours, replicate 1 [HSA-000022203]


title: VPS34IN-1, 7 hours, replicate 5 [HSA-000022202]


title: VPS34IN-1, 7 hours, replicate 4 [HSA-000022201]


title: VPS34IN-1, 7 hours, replicate 3 [HSA-000022200]


title: Grn KO, 4 hours, replicate 2, Regular protocol [HSA-000027351]

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (6 for WT only studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use.

treatment_protocol: Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

value: Grn KO

tag: timepoint

value: 4 hours

tag: protocol

value: Regular


title: Grn KO, 4 hours, replicate 4, Regular protocol [HSA-000027353]

value: BMDM


title: Trem2 KO, 4 hours, replicate 2, Regular protocol [HSA-000027356]

value: Trem2 KO


title: Ctsd KO, 4 hours, replicate 4, Regular protocol [HSA-000027343]

value: Ctsd KO


title: Grn KO, 4 hours, replicate 1, Regular protocol [HSA-000027350]


title: VPS34IN-1, 7 hours, replicate 2 [HSA-000022199]

value: WT


title: Ctsd KO, 4 hours, replicate 2, Regular protocol [HSA-000027341]


title: VPS34IN-1, 7 hours, replicate 1 [HSA-000022198]


title: Npc1 KO, 4 hours, replicate 3, Regular protocol [HSA-000027332]

value: Npc1 KO


title: U18666A, 7 hours, replicate 5 [HSA-000022197]


title: U18666A, 7 hours, replicate 3 [HSA-000022195]


title: U18666A, 7 hours, replicate 4 [HSA-000022196]


title: U18666A, 7 hours, replicate 2 [HSA-000022194]


title: U18666A, 7 hours, replicate 1 [HSA-000022193]


title: BafA1, 7 hours, replicate 5 [HSA-000022192]


title: Atp6v1a KO, 4 hours, replicate 1, Regular protocol [HSA-000027325]

value: Atp6v1a KO


title: Atp6v1a KO, 4 hours, replicate 3, Regular protocol [HSA-000027327]


title: BafA1, 7 hours, replicate 4 [HSA-000022191]


title: Atp6v1a KO, 4 hours, replicate 2, Regular protocol [HSA-000027326]


title: BafA1, 7 hours, replicate 3 [HSA-000022190]


title: BafA1, 7 hours, replicate 2 [HSA-000022189]


title: DMSO, 7 hours, replicate 5 [HSA-000022187]


title: DMSO, 7 hours, replicate 4 [HSA-000022186]


title: BafA1, 7 hours, replicate 1 [HSA-000022188]


title: DMSO, 7 hours, replicate 3 [HSA-000022185]


title: DMSO, 7 hours, replicate 1 [HSA-000022183]


title: MSU, 1 hour, replicate 5 [HSA-000022182]

value: MSU

value: 200 ug/ml

value: 1 hour


title: MSU, 1 hour, replicate 4 [HSA-000022181]


title: E/L/P, 1 hour, replicate 5 [HSA-000022177]

value: E/L/P

value: 50 uM


title: E/L/P, 1 hour, replicate 4 [HSA-000022176]


title: E/L/P, 1 hour, replicate 2 [HSA-000022174]


title: E/L/P, 1 hour, replicate 1 [HSA-000022173]


title: VPS34IN-1, 1 hour, replicate 5 [HSA-000022172]

value: 2 uM


title: VPS34IN-1, 1 hour, replicate 4 [HSA-000022171]


title: VPS34IN-1, 1 hour, replicate 3 [HSA-000022170]


title: VPS34IN-1, 1 hour, replicate 1 [HSA-000022168]


title: VPS34IN-1, 1 hour, replicate 2 [HSA-000022169]


title: U18666A, 1 hour, replicate 5 [HSA-000022167]

value: 6 uM


title: U18666A, 1 hour, replicate 4 [HSA-000022166]


title: U18666A, 1 hour, replicate 3 [HSA-000022165]


title: U18666A, 1 hour, replicate 2 [HSA-000022164]


title: BafA1, 1 hour, replicate 5 [HSA-000022162]

value: 25 nM


title: BafA1, 1 hour, replicate 4 [HSA-000022161]


title: BafA1, 1 hour, replicate 3 [HSA-000022160]


title: BafA1, 1 hour, replicate 2 [HSA-000022159]


title: BafA1, 1 hour, replicate 1 [HSA-000022158]


title: DMSO, 1 hour, replicate 5 [HSA-000022157]

value: DMSO

value: 0 nM


title: DMSO, 1 hour, replicate 3 [HSA-000022155]


title: DMSO, 1 hour, replicate 2 [HSA-000022154]


title: DMSO, 1 hour, replicate 4 [HSA-000022156]


title: BafA1, 22 hours, replicate 3 [HSA-000022266]

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewelset al., 2020) using Gencode M31 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a Microsoft Excel file with four worksheets: 1. sample information, 2. gene information, 3. raw count table,  4. normalized count table (log2 counts per million).

source_name: brain

growth_protocol: For isolation of primary microglia, brains of neonatal mice (P1-P3) were removed and the cerebral cortices and hippocampus were harvested. Isolated tissues were diced into a fine slurry, suspended in 50mL cold HBSS, and centrifuged at 200xg for 3 minutes. Then, the pelleted tissue was resuspended in warm 0.25% Trypsin-EDTA (Gibco; Cat# 25200056), mixed by inversion, and incubated at 37C for 20 minutes with agitation (100rpm). After 20 minutes, the enzymatic digestion was stopped by adding primary microglia culture medium [DMEM/F12 (Gibco; Cat# 11-330-057), 10% HyClone FBS (Cytiva; Cat# SH30080.03), 1X GlutaMax (Gibco; Cat# 35050061), and penicillin-streptomycin (Gibco; Cat# 15140122)] supplemented with DNase-I (Sigma-Aldrich; Cat# 5025) at 625U/mL culture medium. Dissociated tissue was mixed by inversion 10-12 times and triturated until a homogenous, single-cell suspension was observed. Cells were pelleted by centrifugation at 200xg for 7 minutes, supernatant was removed, and the cells were resuspended in primary microglia culture medium. Cells were filtered through a 70mm strainer to create a single-cell suspension and counted. Poly-D-lysine (Sigma-Aldrich; Cat# P6407)-coated T-75 vented culture flasks were washed twice with PBS and primary microglia were seeded at a density of 6 million cells/flask. After 3 days, the medium was replaced with fresh primary microglia culture medium. Subsequently, half-media changes were performed every other day until the mixed glial culture reached a confluency of 90% (10-14 days). Microglia were then detached from the mixed glial flask using a heated orbital shaker for 2 hours at 240rpm at 37C and 5% CO2. The microglial suspension was centrifuged at 200xg for 8 minutes, resuspended in conditioned medium, counted, and seeded for experiments in 50% conditioned medium with 50% fresh medium. The original mixed glial culture flasks were replenished with fresh medium and maintained in culture with half-media changes every other day. Primary microglia were similarly harvested every 6-8 days for a total duration of 3 weeks. Isolated primary microglia were seeded at assay-dependent concentrations onto poly-D-lysine-coated plates in 50% conditioned medium from the mixed glial culture flask with 50% fresh primary microglia culture medium [DMEM/F12 (Gibco; Cat# 11-330-057), 10% HyClone FBS (Cytiva; Cat# SH30080.03), 1X GlutaMax (Gibco; Cat# 35050061), and penicillin-streptomycin (Gibco; Cat# 15140122)]. After 24 hours, seeded microglia were washed twice with PBS to remove debris, cultured in 50% fresh medium and 50% conditioned medium (collected from mixed glial culture flasks and centrifuged at 1000xg for 3 minutes to remove cellular debris), and used for experiments.

treatment_protocol: Cells were treated with 50nM BafA1 or equal percentage of DMSO (vehicle) for 1, 7, 14, 22h prior to RNA extraction.

tag: tissue

value: brain

value: primary microglia

value: 22 hours

value: 50 nM


title: BafA1, 22 hours, replicate 2 [HSA-000022265]

value: WT


title: PBMC_operator2_draw1_fresh

city: Carlsbad

first: Tom

last: Chen

state: CA

address: 6155 Corte Del Cedro

department: R&D

institute: Universal Sequencing Technology Corp.

description:
AmpliDrop
221118_05_IM1116s1_PBMC_operator2_draw1_fresh

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed with AmpliDrop software v1.0. Cell calling and data processing was generated with Cell Ranger v5.1
Within AmpliDrop software analysis, after bcl files been converted to fastq files, the pipeline generated three types of fastq files: cDNA reads, been called as "R1"; sample index reads, with 8 nucleotides, been called as "I1"; and barcode reads, with 20 nucleotides, been called as "I2", in which six nucleotides at positions of 4, 5, 10, 11, 16, and 17 were used as code. The pipeline was then demultiplexing the samples based on the sample index combined with the code used. However, the sample index and code sequences were not saved after demultiplexing. To evaluate the fastq quality, the pipeline ran the fastqc tool on each set of fastq files for the demultiplexed sample. After the barcodes were error collected and the cDNA reads were trimmed with the potential adapter sequences and poly-A nucleotides, the pipeline ran a merging algorithm to merge the barcodes that were located in the same droplet. At the end of the pipeline, the fastq files were converted into 10X Genomic cellranger compatible format.
Assembly: hg38 and mm10
Supplementary files format and content: _barcodes.tsv.gz contains all cellular barcodes, tab separated text file, gzipped; _features.tsv.gz contains feature annotations, tab separated text file, gzipped, column1: feature id, column2: feature name, and column3: type of feature, i.e., "Gene Expression"; _matrix.mtx.gz contains UMI counts in each gene and in each cellular barcode, with mtx format, gzipped.

source_name: blood

growth_protocol: All cell lines were grown in an incubator at 37C and 5% CO2 with media conditions as suggested by ATCC (293T, NIH-3T3, MCF7, HCT-116, and Jurkat) or Sigma (A2780 and A2780cis) supplemented with pen/strep antibiotics. Cells were generally grown close to confluency at the moment of collecting the cells. The WT83 clone6 of human induced-pluripotent stem cells (hiPSCs), derived from a typically developing Caucasian male 29,72, were grown on growth factor-reduced Matrigel, coated 6-cm dishes in mTeSR Plus without antibiotics. For propagation, cells were dissociated with Versene, EDTA, or Relers. To generate forebrain organoids, we followed a semi-guided protocol with a few modifications. Human iPSCs were grown in mTeSR Plus to a confluency of approximately 70% in a 6-cm plate and dissociated with a 1:1 mix of accutase/DPBS. Approximately, three million hiPSCs with a viability >95% were transferred into ultra-low attachment 6-well plates with mTeSR plus media supplemented with the SMAD inhibitors SB-431542 and Dorsomorphin, and the Rho-associated proteinase kinase (ROCK) inhibitor (RI) Y-27632. Plates were placed on orbital shaker. Alternatively, 2 million hiPSCs were transferred to a well of AggreWell-800 plate, pre-coated with Anti-Adherent Solution in mTeSR plus supplemented with RI. The AggreWell plate was centrifugated and transferred to incubator overnight. The following day, embryoid bodies (EB) were transferred to a well of 6-well plate changing the media to fresh mTsERplus supplemented with SB and Dorsomorphin as described above. Regular media and factors changes to complete generation of forebrain organoids were performed in M2 medium composed of Neurobasal supplemented with 1% Glutamax, 1% MEM non-essential amino acids solution, NEAA, and 1x B27 performing half/medium changes every two days for the first month or twice a week after.

extract_protocol:
Peripheral venous blood was drawn from voluntary donor using EDTA-treated tubes and LymphoprepTM and stored at 4°C. Cells were resuspended in 1x phosphate-buffered saline buffer solution (1xPBS) supplemented with 2% bovine serum albumin, BSA, and layered over 1.5 mL Lymphoprep Density Gradient Medium in a 15 mL conical tube, according to the manufacturer’s protocol.  The solution was centrifuged at 800xg for 20 min at room temperature without brake.  The mononuclear cell layer at the gradient interface was collected in a new tube and washed in PBS/2% FBS (10 mL total volume) and centrifuged at 120xg for 10 min at room temperature without brake.  The wash step was repeated two more times, and the cells were resuspended in PBS for sequencing library preparation.  The cells not used immediately were cryopreserved in 90% FBS/10% DMSO.
3' scRNA-seq (AmpliDrop technology); Dissociated cells (typically, >90-95% viable) in 0.1% BSA-supplemented 1x DPBS buffer were processed with AmpliDrop 3’ scRNA-seq kits following the manufacturer’s recommendations. Briefly, more than 200,000 cells were typically fixed at room temperature for 45 minutes and permeabilized for 10 minutes. For the RT and tagmentation reactions, we used 60,000 fixed and permeabilized cells. RT was conducted at 50°C for 10 minutes, and 10 cycles at 60°C for 30 sec and 50°C for 3 min, and tagmentation was conducted at 37°C for 15 minutes. Cell encapsulation was based on the following mixing protocol: 50 mixes of 170 µL at Speed 2 followed by 10 mixes of 170 µL at Speed 3. The emulsions were then moved to a thermocycler to run the following PCR/barcoding program: 72°C for 5 min, 98°C for 1 min, 26 cycles with 98°C for 15 sec, 61°C for 40 sec, and 72°C for 30 sec, and 5 cycles with 98°C for 15 sec, 50°C for 2 min, and 72°C for 40 sec, ending with 72°C for 2 min. After PCR/barcoding, the emulsions were dissolved, and the DNA was recovered from the solution  with the same volume of SPRI beads from MagBio genomics. The libraries were cleaned up with 80% ethanol for three times and finally eluted in 38 µL of 0.1x TE buffer, and half of this volume was used for indexing using Illumina adapters. Typically, we amplified the library with 9 to 12 cycles depending on the expected number of cell output (12 cycles for 1,000-2,000 cells and 9 cycles for 7,000-10,000 cells). The PCR indexing program is the following: 98°C for 30 sec, and 9-12 cycles with 98°C for 20 sec, 61°C for 30 sec, and 72°C for 30 sec, ending with 72°C for 2 min. After PCR, the library (40 µL) was diluted to 100 µL with TE buffer and cleaned up with 90 µL of SPRI beads. After washing with 80% ethanol twice, the library was eluted in 30 µL of 0.1x TE buffer. Libraries were then subject to quality control, sizing, and quantification using Agilent 4150 TapeStation system with High Sensitivity D1000 ScreenTape and Reagents.

treatment_protocol: No treatments were performed on cell lines. For seven-month-old organoids (Exp 1), mildly-perturbed conditions refer to a regimen of pipette aspiration with a wide-origfice 1mL tip and transfer of the organoids to a metal platform to mimic a mild physical manipulation of these multicellular structures. Severely-perturbed conditions refer to smashing the organoids to generate deformative compression to mimic a highly damaging physicial manipulation. Both treatments required maintaining the organoids for approximately 90 minutes outside the incubator. In the incubator, both sets of organoids were maintained withouth motion for 3 days. Non-perturbed organoids were maintained under orbital shaking all the time. For six-month-old organoids (Exp 2), everything was as in Exp1 but the non-perturbed group of organoids was also maintained 90 minutes outside the incubator. For two-month-old organoids (Exp3), one set was grown under orbital shaking always, while the other set was kept withouth motion for three days before library preparation.

value: blood

value: PBMC

value: Human peripheral blood mononuclear cell


title: BafA1, 22 hours, replicate 1 [HSA-000022264]


title: Jurkat_deep

description:
AmpliDrop
211208_01_Jurkat_deep

source_name: acute T cell leukemia cell line

value: acute T cell leukemia cell line

value: Jurkat

value: T lymphoblast


title: DMSO, 22 hours, replicate 3 [HSA-000022263]


title: DMSO, 22 hours, replicate 2 [HSA-000022262]


title: BafA1, 14 hours, replicate 3 [HSA-000022260]

value: 14 hours


title: DMSO, 22 hours, replicate 1 [HSA-000022261]


title: BafA1, 14 hours, replicate 2 [HSA-000022259]


title: DMSO, 14 hours, replicate 3 [HSA-000022257]


title: DMSO, 14 hours, replicate 2 [HSA-000022256]


title: BafA1, 7 hours, replicate 3 [HSA-000022254]

value: 7 hours


title: BafA1, 7 hours, replicate 2 [HSA-000022253]


title: BafA1, 7 hours, replicate 1 [HSA-000022252]


title: DMSO, 7 hours, replicate 2 [HSA-000022250]


title: Control_Col_WT_2

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

description:
Library name: Sample2
Wild-type Col-0 control, biological replicate 2

data_processing:
Reads trimmed with Trimmomatic (v0.38) with options "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true", "LEADING:3", "TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:36"
Reads aligned with STAR (v2.7.6a) with options "--alignIntronMin 60", "--alignIntronMax 6000"
Counts gathered for features using HTSeq-count (v0.13.5) with options "--mode=union". The strandedness parameter was set to --stranded=reverse for Ler_Cvi_RIL samples, and to --stranded=no for overexpression (OX), mutant, and control samples.
Assembly: TAIR10 genome and Araport11 annotation
Supplementary files format and content: HTSeq count files (.txt) with the following columns: <locus> <read count>

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Transgenic overexpression lines and mutant plants were grown under long-day conditions (16h light/8h dark) at 22C on soil. T1 plants were selected in the presence of 50 ug/ml kanamycin. RIL plants were grown on half-strength MS plates under long-day conditions (16h light/8h dark) at 25C for 7-9 days.

extract_protocol:
For VIM overexpression and mutant lines, total RNA was extracted from leaves of 4 to 12-week-old T1 plants with the Monarch Total RNA Miniprep Kit (N2010, NEB) and tested with Qubit RNA BR Assay (Q33223, Thermo Fisher). For Ler x Cvi RILs, total RNA was extracted from bulk seedlings following the TRIzol extraction method.
For VIM overexpression and mutant lines, library preparation and 150 bp paired-end sequencing were performed by Novogene on an Illumina NovaSeq X Plus platform. For Ler x Cvi RILs, libraries were constructed using the TruSeq Stranded mRNA Library Kit (No.20020594, Illumina) with a custom dual index workflow. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq 6000 platform.

value: leaf tissue


title: DMSO, 7 hours, replicate 1 [HSA-000022249]


title: BafA1, 1 hour, replicate 3 [HSA-000022248]

value: 1 hour


title: BafA1, 1 hour, replicate 1 [HSA-000022246]


title: DMSO, 1 hour, replicate 1 [HSA-000022243]

value: DMSO


title: DMSO, 1 hour, replicate 2 [HSA-000022244]

value: 0 nM


title: Pancreas, CT, rep7

city: Ya'an

first: Songqi

last: Duan

state: Sichuan

address: No.46, Xinkang Road, Yucheng District

department: College of Food Science

country: China

institute: Sichuan Agricultural University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (v0.23.4) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using STAR (2.7.11b).
The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files generated by STAR.
Assembly: mm39
Supplementary files format and content: tab-delimited text files contain raw counts values for each sample

source_name: Pancreas

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: Pancreas

tag: diet

value: chow diet with Tibetan tea


title: Liver, HT, rep6

source_name: Liver

value: Liver

value: high fat diet with Tibetan tea


title: Bone marrow, HT, rep5

source_name: Bone marrow

value: Bone marrow


title: Bone marrow, HT, rep4


title: Bone marrow, HT, rep3


title: Bone marrow, HT, rep2


title: BafA1, 14 hours, replicate 1 [HSA-000022258]

value: brain

value: primary microglia

value: WT

value: 50 nM


title: DMSO, 14 hours, replicate 1 [HSA-000022255]


title: Bone marrow, HW, rep4

value: high fat diet with water


title: Bone marrow, HW, rep5


title: Bone marrow, HW, rep3


title: DMSO, 7 hours, replicate 3 [HSA-000022251]


title: Bone marrow, HW, rep2


title: Bone marrow, HW, rep1


title: Bone marrow, CW, rep4

value: chow diet with water


title: Bone marrow, CT, rep4


title: Bone marrow, CT, rep2


title: BafA1, 1 hour, replicate 2 [HSA-000022247]


title: Bone marrow, CW, rep1


title: Sketch muscle, HT, rep5

source_name: Sketch muscle

value: Sketch muscle


title: Bone marrow, CW, rep2


title: DMSO, 1 hour, replicate 3 [HSA-000022245]


title: Sketch muscle, HT, rep3


title: Sketch muscle, HT, rep2


title: Sketch muscle, HT, rep4


title: Sketch muscle, HT, rep1


title: Sketch muscle, HW, rep5


title: Sketch muscle, HW, rep4


title: Sketch muscle, HW, rep3


title: Sketch muscle, HW, rep2


title: Sketch muscle, HW, rep1


title: Sketch muscle, CT, rep5


title: Sketch muscle, CT, rep4


title: Sketch muscle, CT, rep3


title: Sketch muscle, CT, rep1


title: Sketch muscle, CT, rep2


title: Sketch muscle, CW, rep5


title: Sketch muscle, CW, rep4


title: Sketch muscle, CW, rep3


title: MSU, 1 hour, replicate 3 [HSA-000022180]

value: BMDM

value: MSU

value: 200 ug/ml


title: RIL168_G02_L02_4

description: Library name: Sample307

library_source: genomic

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute (Taudt et al. 2018)

molecule: genomic DNA

growth_protocol: The MAMP was grown in climate-controlled chambers for nine selfing generations (Long day conditions, 16-h-day lengths, 18 C).

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end 150bp format.

value: leaf tissue

value: Ler X Cvi RIL

tag: ril line

tag: generation

tag: lineage

tag: sublineage


title: Sketch muscle, CW, rep2


title: DMSO, 7 hours, replicate 2 [HSA-000022184]

tag: replicate

value: DMSO

value: 0 nM

value: 7 hours


title: Sketch muscle, CW, rep1


title: MSU, 1 hour, replicate 1 [HSA-000022178]

tag: cell type

value: 1 hour


title: MSU, 1 hour, replicate 2 [HSA-000022179]

tag: genotype


title: Colon, HT, rep4

source_name: Colon

value: Colon

value: high fat diet with Tibetan tea


title: E/L/P, 1 hour, replicate 3 [HSA-000022175]

tag: treatment

value: E/L/P

value: 50 uM


title: Colon, HT, rep5


title: Colon, HT, rep2


title: Colon, HT, rep3


title: Colon, HW, rep5


title: Colon, HT, rep1


title: Colon, HW, rep4


title: Colon, HW, rep1


title: Colon, HW, rep2


title: Colon, HW, rep3


title: Colon, CT, rep5

value: chow diet with Tibetan tea


title: Colon, CT, rep4


title: Colon, CT, rep3


title: Colon, CT, rep2


title: Colon, CT, rep1


title: Colon, CW, rep5


title: Colon, CW, rep4


title: Colon, CW, rep3


title: Colon, CW, rep1


title: Colon, CW, rep2


title: Pancreas, HT, rep4

value: Pancreas


title: Pancreas, HT, rep3


title: Pancreas, HT, rep2


title: Pancreas, HT, rep1


title: Pancreas, HW, rep5

value: high fat diet with water


title: U18666A, 1 hour, replicate 1 [HSA-000022163]

value: WT

tag: treatment dose

value: 6 uM


title: Pancreas, HW, rep3


title: Pancreas, HW, rep4


title: Pancreas, HW, rep2


title: Pancreas, HW, rep1


title: Pancreas, CT, rep5


title: Pancreas, CT, rep4


title: Pancreas, CT, rep2


title: Pancreas, CT, rep1


title: Pancreas, CW, rep5

value: chow diet with water


title: Pancreas, CW, rep4


title: Pancreas, CW, rep2


title: Pancreas, CW, rep3


title: Liver, HT, rep5

value: Liver


title: Liver, HT, rep4


title: Liver, HT, rep3


title: Liver, HT, rep1


title: Liver, HW, rep5


title: Liver, HW, rep4


title: Liver, HW, rep3


title: Liver, HW, rep2


title: DMSO, 1 hour, replicate 1 [HSA-000022153]

value: BMDM

tag: treatment duration


title: Liver, CT, rep5


title: RIL163_G02_L02_4

description: Library name: Sample283

value: leaf tissue

value: Ler X Cvi RIL


title: Liver, CT, rep4


title: Liver, HW, rep1


title: Liver, CT, rep2


title: Liver, CT, rep1


title: Liver, CT, rep3


title: Liver, CW, rep5


title: Liver, CW, rep4


title: Liver, CW, rep3


title: Liver, CW, rep2


title: Kidney, HT, rep5

source_name: Kidney

value: Kidney


title: Liver, CW, rep1


title: Kidney, HT, rep4


title: Kidney, HT, rep3


title: Kidney, HT, rep2


title: Kidney, HT, rep1


title: Kidney, HW, rep5


title: Kidney, HW, rep4


title: Kidney, HW, rep3


title: Kidney, HW, rep2


title: Kidney, HW, rep1


title: Kidney, CT, rep4


title: Kidney, CT, rep2


title: Kidney, CT, rep3


title: Kidney, CT, rep5


title: Kidney, CW, rep5


title: Kidney, CT, rep1


title: Kidney, CW, rep4


title: Kidney, CW, rep2


title: Kidney, CW, rep1


title: Kidney, CW, rep3


title: Heart, HT, rep5

source_name: Heart

value: Heart


title: Heart, HT, rep4


title: Heart, HT, rep3


title: Heart, HT, rep1


title: Heart, HW, rep5


title: Heart, HT, rep2


title: Heart, HW, rep4


title: Heart, HW, rep3


title: Heart, HW, rep1


title: Heart, CT, rep5


title: Heart, HW, rep2


title: Heart, CT, rep4


title: Heart, CT, rep3


title: Heart, CT, rep2


title: Heart, CT, rep1


title: Heart, CW, rep5


title: Heart, CW, rep3


title: Heart, CW, rep4


title: Heart, CW, rep1


title: Heart, CW, rep2


title: Brown adipose tissue, HT, rep5

source_name: Brown adipose tissue

value: Brown adipose tissue


title: Brown adipose tissue, HT, rep4


title: Brown adipose tissue, HT, rep3


title: Brown adipose tissue, HT, rep2


title: Brown adipose tissue, HW, rep5


title: Brown adipose tissue, HT, rep1


title: Brown adipose tissue, HW, rep3


title: Brown adipose tissue, HW, rep4


title: Brown adipose tissue, HW, rep1


title: Brown adipose tissue, HW, rep2


title: Brown adipose tissue, CT, rep5


title: Brown adipose tissue, CT, rep4


title: Brown adipose tissue, CT, rep3


title: Brown adipose tissue, CT, rep2


title: Brown adipose tissue, CT, rep1


title: Brown adipose tissue, CW, rep4


title: Brown adipose tissue, CW, rep5


title: Brown adipose tissue, CW, rep3


title: Brown adipose tissue, CW, rep2


title: DMSO, 22 hours, replicate 3 [HSA-000022215]

value: DMSO

value: 0 nM

value: 22 hours

tag: rin


title: Brain, HT, rep5

source_name: Brain

value: Brain

value: high fat diet with Tibetan tea


title: Brown adipose tissue, CW, rep1


title: Brain, HT, rep3


title: Brain, HT, rep2


title: Brain, HT, rep4


title: Brain, HT, rep1


title: Brain, HW, rep3


title: Brain, HW, rep5


title: Brain, HW, rep4


title: Brain, HW, rep2


title: Brain, HW, rep1


title: Brain, CT, rep4

value: chow diet with Tibetan tea


title: Brain, CT, rep5


title: Brain, CT, rep3


title: Brain, CT, rep1


title: Brain, CT, rep2


title: Brain, CW, rep5


title: Brain, CW, rep4


title: Brain, CW, rep3


title: Brain, CW, rep2


title: Brain, CW, rep1


title: U118MGR-2

city: Hefei

first: Yanru

last: Gao

address: 81 Meishan Road

institute: Anhui Medical University

description:
Library name: U118MGR-2_lib
TPM expression values for U118MGR-2 in mRNA-12.TPM.genes.tsv

data_processing:
Raw sequencing reads were processed using fastp (v0.23.2) to remove adapter sequences and low-quality bases.
Clean reads were aligned to the Homo sapiens genome (GRCh38/hg38) using STAR (v2.7.10a).
Gene-level read counts were quantified using featureCounts (v2.0.3) from the Subread package.
TPM (Transcripts Per Million) values were calculated for each gene based on the featureCounts output.
Assembly: GRCh38
Supplementary files format and content: mRNA-12.TPM.genes.tsv: Tab-separated text file containing TPM expression values for all genes across all 12 samples.
Supplementary files format and content: Rows represent genes, and columns represent individual samples.

growth_protocol: SF126, SF126R, U118 MG, and U118 MG-R cells were cultured in MEM (Minimum Essential Medium) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from each cell line using TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
mRNA was enriched from total RNA using oligo-dT magnetic beads. The enriched mRNA was fragmented and reverse transcribed into cDNA. The cDNA library was prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB, #E7770) according to the manufacturer's protocol. The final library was amplified and purified.

treatment_protocol: SF126 and U118 MG cells were left untreated as controls. SF126R and U118 MG-R cells were continuously exposed to temozolomide (TMZ) for at least 6 months to establish acquired resistance.

tag: cell line

value: Glioblastoma

value: Resistant

value: Treated with temozolomide (TMZ) for 6 months to induce resistance

tag: batch


title: U118MGR-3

description:
Library name: U118MGR-3_lib
TPM expression values for U118MGR-3 in mRNA-12.TPM.genes.tsv


title: U118MGR-1

description:
Library name: U118MGR-1_lib
TPM expression values for U118MGR-1 in mRNA-12.TPM.genes.tsv


title: U118MG-3

description:
Library name: U118MG-3_lib
TPM expression values for U118MG-3 in mRNA-12.TPM.genes.tsv

value: Sensitive

value: untreated


title: U118MG-2

description:
Library name: U118MG-2_lib
TPM expression values for U118MG-2 in mRNA-12.TPM.genes.tsv


title: U118MG-1

description:
Library name: U118MG-1_lib
TPM expression values for U118MG-1 in mRNA-12.TPM.genes.tsv


title: SF126R-3

description:
Library name: SF126R-3_lib
TPM expression values for SF126R-3 in mRNA-12.TPM.genes.tsv

value: Astrocytoma


title: SF126R-2

description:
Library name: SF126R-2_lib
TPM expression values for SF126R-2 in mRNA-12.TPM.genes.tsv


title: SF126R-1

description:
Library name: SF126R-1_lib
TPM expression values for SF126R-1 in mRNA-12.TPM.genes.tsv


title: SF126-2

description:
Library name: SF126-2_lib
TPM expression values for SF126-2 in mRNA-12.TPM.genes.tsv


title: SF126-1

description:
Library name: SF126-1_lib
TPM expression values for SF126-1 in mRNA-12.TPM.genes.tsv


title: daf-7daf-16_38h_1mM_replicate3

city: Baltimore

first: John

middle: K

last: Kim

state: MD

address: 3400 North Charles St

department: Biology

institute: Johns Hopkins University

description:
Library name: daf-7daf-16_38h_1mM_rep3
QK215 on 1mM auxin at 38h replicate 3

data_processing:
Pooled libraries were sequenced on an Illumina® NovaSeq6000 instrument using standard protocols for SP 2x150bp Paired end sequencing. The resulting fastq files were concatenated for further analysis.
Read quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trim Galore! v0.6.6 with parameters –length 36
Trimmed reads were aligned to the C. elegans WBCel235 reference genome using STAR with default parameters
Final BAM files were sorted and indexed using samtools for downstream analyses
Assembly: WBCel235
Supplementary files format and content: csv files including FPKM values for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were developmentally semi-synchronized by sodium hypochlorite treatment. Briefly, eggs were isolated by lysing gravid hermaphrodites in sodium hypochlorite, suspended in M9 buffer, and plated on nematode growth medium (NGM) plates seeded with E. coli strain HB101. 4,000–8,000 embryos on 10 cm NGM plates seeded with 10x concentrated bacteria at 24°C.

extract_protocol:
Animals were collected in TRI Reagent (ThermoFisher Scientific AM9738). Following five freeze-thaw cycles, 1-bromo-3-chloropropane was added and RNA in the aqueous phase was precipitated with isopropanol for 2 h at -30°C. Samples were centrifuged at 21,000 x g for 30 min at 4°C to pellet RNA. Pellets were washed three times with 75% ethanol and resuspended in nuclease-free water.
Samples were checked for quality/quantity on Fragment Analyzer and Qubit prior to library prep. NEBNext rRNA Depletion Kit v2 (NEB # E7400) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat# E7765) were used to generate libraries. The resulting library insert size was 200bp-500bp with a median size around 300bp. Libraries were barcoded using unique dual indexing (E6440S) and pooled for sequencing.

treatment_protocol: Worms were transferred to NGM plates with 1mM auxin (3-indole acetic acid; Sigma-Aldrich I2886) after 30 h and collected every 2 hrs.

value: whole worm

tag: time point

tag: strain name

value: daf-16(mgDf50) nhr-23(xk40[nhr-23::aid::3xflag]) I; ieSi57[eft-3p::tir1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; daf-7(e1372) III; maIs105[col-19p::gfp] V

value: 0mM Auxin


title: daf-7daf-16_36h_1mM_replicate3

description:
Library name: daf-7daf-16_36h_1mM_rep3
QK215 on 1mM auxin at 36h replicate 3

tag: tissue


title: daf-7daf-16_38h_0mM_replicate3

description:
Library name: daf-7daf-16_38h_0mM_rep3
QK215 on 0mM auxin at 38h replicate 3


title: daf-7daf-16_36h_0mM_replicate3

description:
Library name: daf-7daf-16_36h_0mM_rep3
QK215 on 0mM auxin at 36h replicate 3


title: daf-7daf-16_32h_0mM_replicate3

description:
Library name: daf-7daf-16_32h_0mM_rep3
QK215 on 0mM auxin at 32h replicate 3


title: daf-7daf-16_30h_0mM_replicate3

description:
Library name: daf-7daf-16_30h_0mM_rep3
QK215 on 0mM auxin at 30h replicate 3


title: daf-7daf-16_34h_0mM_replicate3

description:
Library name: daf-7daf-16_34h_0mM_rep3
QK215 on 0mM auxin at 34h replicate 3


title: daf-7_38h_0mM_replicate3

description:
Library name: daf-7_38h_0mM_rep3
QK216 on 0mM auxin at 38h replicate 3

value: nhr-23(xk40[nhr-23::aid::3xflag]) I; ieSi57[eft-3p::tir1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; daf-7(e1372) III; maIs105[col-19p::gfp] V


title: daf-7_36h_0mM_replicate3

description:
Library name: daf-7_36h_0mM_rep3
QK216 on 0mM auxin at 36h replicate 3


title: daf-7_34h_0mM_replicate3

description:
Library name: daf-7_34h_0mM_rep3
QK216 on 0mM auxin at 34h replicate 3


title: daf-7_32h_0mM_replicate3

description:
Library name: daf-7_32h_0mM_rep3
QK216 on 0mM auxin at 32h replicate 3


title: daf-7daf-16_38h_1mM_replicate2

description:
Library name: daf-7daf-16_38h_1mM_rep2
QK215 on 1mM auxin at 38h replicate 2


title: daf-7daf-16_36h_1mM_replicate2

description:
Library name: daf-7daf-16_36h_1mM_rep2
QK215 on 1mM auxin at 36h replicate 2


title: daf-7daf-16_38h_0mM_replicate2

description:
Library name: daf-7daf-16_38h_0mM_rep2
QK215 on 0mM auxin at 38h replicate 2


title: daf-7daf-16_32h_1mM_replicate2

description:
Library name: daf-7daf-16_32h_1mM_rep2
QK215 on 1mM auxin at 32h replicate 2


title: daf-7daf-16_36h_0mM_replicate2

description:
Library name: daf-7daf-16_36h_0mM_rep2
QK215 on 0mM auxin at 36h replicate 2


title: daf-7daf-16_34h_0mM_replicate2

description:
Library name: daf-7daf-16_34h_0mM_rep2
QK215 on 0mM auxin at 34h replicate 2


title: daf-7daf-16_32h_0mM_replicate2

description:
Library name: daf-7daf-16_32h_0mM_rep2
QK215 on 0mM auxin at 32h replicate 2


title: daf-7daf-16_30h_0mM_replicate2

description:
Library name: daf-7daf-16_30h_0mM_rep2
QK215 on 0mM auxin at 30h replicate 2


title: daf-7_38h_0mM_replicate2

description:
Library name: daf-7_38h_0mM_rep2
QK216 on 0mM auxin at 38h replicate 2


title: daf-7_36h_0mM_replicate2

description:
Library name: daf-7_36h_0mM_rep2
QK216 on 0mM auxin at 36h replicate 2


title: daf-7_34h_0mM_replicate2

description:
Library name: daf-7_34h_0mM_rep2
QK216 on 0mM auxin at 34h replicate 2


title: daf-7_32h_0mM_replicate2

description:
Library name: daf-7_32h_0mM_rep2
QK216 on 0mM auxin at 32h replicate 2


title: daf-7_30h_0mM_replicate2

description:
Library name: daf-7_30h_0mM_rep2
QK216 on 0mM auxin at 30h replicate 2


title: daf-7daf-16_38h_1mM_replicate1

description:
Library name: daf-7daf-16_38h_1mM_rep1
QK215 on 1mM auxin at 38h replicate 1


title: daf-7daf-16_36h_1mM_replicate1

description:
Library name: daf-7daf-16_36h_1mM_rep1
QK215 on 1mM auxin at 36h replicate 1


title: daf-7daf-16_34h_1mM_replicate1

description:
Library name: daf-7daf-16_34h_1mM_rep1
QK215 on 1mM auxin at 34h replicate 1


title: daf-7daf-16_32h_1mM_replicate1

description:
Library name: daf-7daf-16_32h_1mM_rep1
QK215 on 1mM auxin at 32h replicate 1


title: daf-7daf-16_36h_0mM_replicate1

description:
Library name: daf-7daf-16_36h_0mM_rep1
QK215 on 0mM auxin at 36h replicate 1


title: daf-7daf-16_38h_0mM_replicate1

description:
Library name: daf-7daf-16_38h_0mM_rep1
QK215 on 0mM auxin at 38h replicate 1


title: daf-7daf-16_34h_0mM_replicate1

description:
Library name: daf-7daf-16_34h_0mM_rep1
QK215 on 0mM auxin at 34h replicate 1


title: daf-7daf-16_32h_0mM_replicate1

description:
Library name: daf-7daf-16_32h_0mM_rep1
QK215 on 0mM auxin at 32h replicate 1


title: daf-7_38h_0mM_replicate1

description:
Library name: daf-7_38h_0mM_rep1
QK216 on 0mM auxin at 38h replicate 1


title: daf-7daf-16_30h_0mM_replicate1

description:
Library name: daf-7daf-16_30h_0mM_rep1
QK215 on 0mM auxin at 30h replicate 1


title: daf-7_36h_0mM_replicate1

description:
Library name: daf-7_36h_0mM_rep1
QK216 on 0mM auxin at 36h replicate 1


title: daf-7_34h_0mM_replicate1

description:
Library name: daf-7_34h_0mM_rep1
QK216 on 0mM auxin at 34h replicate 1


title: daf-7_30h_0mM_replicate1

description:
Library name: daf-7_30h_0mM_rep1
QK216 on 0mM auxin at 30h replicate 1


title: DSF_IP_replicate2

address: 3400 Charles Street

department: Department of Biology

description:
Library name: ChIP2021-026-N2-concatenated
daf-16::3xflag DAF-16 ChIP-seq IP replicate 2

data_processing:
All samples were sequenced across two lanes, and resulting FASTQ files were merged prior to downstream processing.
Adapter sequences and low-quality bases were trimmed using Trim Galore! v0.5.0.
Trimmed reads were aligned to the C. elegans WBCel235 reference genome using Bowtie2 with default parameters.
Alignments were filtered using samtools to remove unmapped, secondary, and low-quality alignments. PCR duplicates were identified with Picard MarkDuplicates 2.22.1 and subsequently removed.
Binding profiles for DAF-16 were identified using MACS2 at a p-value threshold of 0.05. Fold-enrichment tracks were generated with MACS2, with blacklisted regions removed, and converted into bigWig format using the bedGraphToBigWig command-line utility from the UCSC Genome Browser kentUtils package.
Peaks from biological replicates for each genotype were intersected using BEDTools, required at least 10% reciprocal overlap, and overlapping regions were retained as consensus summit regions. From these consensus regions, those showing at least 2-fold higher signal in starved dauers expressing daf-16::mScarlet::3xflag  compared to wild-type starved dauers were retained for further analysis. Retained summit regions were annotated to the nearest gene using HOMER.
Assembly: WBcel235
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: For collection of starved dauers used for DAF-16 ChIP-seq, wild-type and daf-16(ar620[daf-16::zf1-wrmScarlet-3xFLAG]) animals were grown at 20°C. Worms were developmentally synchronized by sodium hypochlorite treatment. Briefly, eggs were isolated by lysing gravid hermaphrodites in sodium hypochlorite, suspended in M9 buffer, and incubated for 24 h with aeration at room temperature to allow L1 arrest. Starved L1d larvae were plated on NGM plates seeded with HB101. Approximately 15,000 L1d hatchlings were plated on 15 cm NGM plates seeded with 10x concentrated bacteria and maintained at 25°C on Day 1. Animals were re-fed on Day 3, and starved worms were subject to SDS isolation on Day 5. Starved worms were incubated with 1% SDS in water for 30 min with aeration, washed with water, and plated on 15 cm NGM plates to allow viable worms to move out. The surviving worms were collected for ChIP-seq.

extract_protocol:
Animals starved at 25°C were collected as ~500L packed pellets in M9. Worms were crosslinked in 12mL of 2.6% (v/v) formaldehyde for 30 min at room temperature. Crosslinking was quenched by addition of 600 µL 2.5 M glycine for 5 min. Samples were then washed three times in water and flash-frozen in liquid nitrogen. Frozen pellets were ground using a Retsch MM400 CryoMill for two 1-min cycles at 30 Hz in liquid nitrogen-cooled stainless steel cryomill chambers. The resulting powder was resuspended and further lysed in 2 mL of RIPA buffer (1x PBS, 1% (v/v) NP40, 0.5% sodium deoxycholate, and 0.1% SDS), supplemented with HALT protease and phosphatase inhibitor cocktail (ThermoFisher Scientific) for 10 min at 4°C.  To shear the chromatin, samples were sonicated in a Bioruptor Pico (Diagenode) for three cycles of 3 min each (30 s ON/30 s OFF cycles) at 4°C. A 20 µL aliquot of the sample was treated with Proteinase K for 10 min and then subjected to phenol chloroform extraction, as described below. The concentration of the aliquot was determined using a Qubit Fluorometer 3.0 (Invitrogen). Based on the initial concentration of the aliquot, the chromatin sample was diluted to 20–30 ng/µL. To check the extent of shearing, the same aliquot was run on an agarose gel. The sample was processed further only if the DNA smear was centered around 200 bp.  Of the total amount of chromatin that remained, 10% was used as the input sample (stored at 4°C) and 90% was subjected to immunoprecipitation. Every 10 µg of chromatin was incubated with 2 µg of mouse M2 anti-Flag monoclonal antibodies (Sigma-Aldrich) overnight at 4°C on a nutator. Samples were then incubated with 1.5 mg of affinity-purified sheep anti-mouse IgG antibodies covalently attached to superparamagnetic Dynabeads M-280 (Invitrogen) for 2 h at 4°C. Thereafter, complexes bound to the beads were separated three times from the supernatant and washed in 800 µL LiCl buffer (100 mM Tris HCL pH 7.5, 500 mM LiCl, 1% (v/v) NP40, and 1% sodium deoxycholate). The resulting immunoprecipitates were de-crosslinked by incubation with 80 µg of proteinase K in 400 µL of worm lysis buffer (100 mM Tris-HCL pH 7.5, 100 mM NaCl, 50 mM EDTA, and 1% SDS) at 65°C for 4 h; input samples underwent the same treatment in parallel. Residual proteins were removed from both IP and input samples by phenol-chloroform extraction. Briefly, 400 µL of phenol-chloroform-isoamyl alcohol pH 8.0 (Sigma-Aldrich) was added to each sample. Samples were vortexed vigorously and centrifuged at 15,000 x g for 5 min at 4°C. The aqueous phase top layer was transferred to a new tube and DNA was precipitated by incubation with 1 mL of 0.3 M ammonium acetate (Sigma-Aldrich) in ethanol for 1 h at -30°C. The resulting DNA pellet was washed twice with 100% ethanol and resuspended in Tris-EDTA, pH 8.0. Prior to use as a template for qPCR, the entire DNA sample was treated with RNase A for 1 h at 37°C.
ChIP-seq libraries were prepared using the Ovation Ultralow System V2 kit (NuGEN, 0344NB-A01) according to the manufacturer’s protocol, with 15 PCR amplification cycles. Libraries were sequenced on an Illumina NovaSeq 6000 instrument using paired-end 50 bp reads.

tag: age

value: starved dauer

value: IP


title: N2_input_replicate2

description:
Library name: ChIP2021-023-N2-concatenated
N2 DAF-16 ChIP-seq input replicate 2

value: input


title: DSF_IP_replicate1

description:
Library name: ChIP2021-022-N2-concatenated
daf-16::3xflag DAF-16 ChIP-seq IP replicate 1


title: DSF_input_replicate2

description:
Library name: ChIP2021-024-N2-concatenated
daf-16::3xflag DAF-16 ChIP-seq input replicate 2


title: DSF_input_replicate1

description:
Library name: ChIP2021-020-N2-concatenated
daf-16::3xflag DAF-16 ChIP-seq input replicate 1


title: N2_input_replicate1

description:
Library name: ChIP2021-019-N2-concatenated
N2 DAF-16 ChIP-seq input replicate 1


title: Burn 72 hpb Replicate 3

city: Madison

first: Anna

last: Huttenlocher

state: WI

address: 1550 Linden Drive

department: Pediatrics

institute: University of Wisconsin School of Medicine and Public Health

description: Library name: Sample24

data_processing:
Raw sequencing data were aligned to zebrafish genome GRCz11 with an improved gene annotation, published in "improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes” using RSEM v1.3.3 with parameters “-p 16 --paired-end --star --estimate-rspd --append-names --output-genome-bam” and STAR version 2.7.11b.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files

organism: Danio rerio

source_name: tail half of the larvae

growth_protocol: Adult fish were maintained on a 14-hour light, 10-hour dark cycle. Following breeding, embryos were transferred to E3 medium (5 mM NaCl, 0.17 mM KCl, 0.44 mM CaCl2, 0.33 mM MgSO4, 0.025 mM NaOH, and 0.0003% methylene blue) and maintained at 28.5°C until sample collection.  For all experiments, larval zebrafish were anesthetized in 0.2 mg/mL tricaine (ethyl 3-aminobnzoate) in E3 medium prior to use.

extract_protocol:
RNA extraction was performed on collected tail fin tissues using TRIzol reagent and RNAqueous Micro Kit (Invitrogen) following manufacturer's instructions
Sequencing libraries were constructed by GENEWIZ

treatment_protocol: To perform burn injury, zebrafish larvae were transferred to a 60 mm tissue-culture treated dish containing 0.2 mg/mL tricaine in E3 medium. A fine tip cautery pen (Geiger Medical Instruments) was used to burn the caudal fin of larval zebrafish. Burn wounds were applied until the wounded region bordered but did not touch the posterior notochord boundary. In all cases, larvae were washed to remove tricaine immediately following injury until ready for use.

value: tail half of the larvae


title: Burn 72 hpb Replicate 2

description: Library name: Sample23


title: Burn 48 hpb Replicate 3

description: Library name: Sample21


title: Burn 48 hpb Replicate 2

description: Library name: Sample20


title: Burn 24 hpb Replicate 2

description: Library name: Sample17


title: Burn 24 hpb Replicate 3

description: Library name: Sample18


title: Burn 24 hpb Replicate 1

description: Library name: Sample16


title: Burn 6 hpb Replicate 1

description: Library name: Sample13


title: Unwounded 6 dpf Replicate 3

description: Library name: Sample12


title: Unwounded 6 dpf Replicate 2

description: Library name: Sample11


title: Unwounded 5 dpf Replicate 2

description: Library name: Sample8


title: Unwounded 5 dpf Replicate 1

description: Library name: Sample7


title: Unwounded 4 dpf Replicate 3

description: Library name: Sample6


title: Unwounded 4 dpf Replicate 2

description: Library name: Sample5


title: Unwounded 4 dpf Replicate 1

description: Library name: Sample4


title: Unwounded 3 dpf Replicate 2

description: Library name: Sample2


title: Unwounded 3 dpf Replicate 1

description: Library name: Sample1


title: Wildtype_Roots_TuYV-WT

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: Col-0_Roots

data_processing:
Raw reads were quality filtered using fastp (default parameters, --length_required 15, --trim_poly_x, --poly_x_min_len 10) to remove low-quality reads, polyX tails, and reads shorter than 15 nt. Filtered reads were aligned to viral reference genomes (TuYV-wt and TuYV-GFP) or plasmid sequence (pG7_pWER_H2B_eGFP_LB-RB) using Bowtie2 (default parameters, --no-unal) in end-to-end mode. Aligned reads were filtered by read length (21 nt, 22 nt, 24 nt representing DCL4, DCL2, and DCL3 activities respectively) and visualised as strand-specific coverage plots normalised to reads per million (RPM).
Assembly: Custom viral and plasmid reference sequences: TuYV-wt (Turnip yellow mosaic virus wild type), TuYV-GFP (TuYV with GFP insertion), and pG7_pWER_H2B_eGFP_LB-RB (pWER::H2B:GFP transgene plasmid). Reference sequences available upon request.
Supplementary files format and content: Processed data files are tab-delimited text files containing raw counts for small RNA classes (miRNA, snoRNA, snRNA, tRNA, rRNA, ncRNA, Transposon, Pseudogene, ProteinCoding, Intergenic) mapped to the Arabidopsis thaliana TAIR10 genome and TuYV virus, followed by read size distributions (18-30nt) and first nucleotide statistics.

source_name: Roots

extract_protocol:
Small RNA were purified using the TraPR Small RNA Isolation Kit (Lexogen)
Small RNA-seq Library Preparation Kit (Lexogen)

value: Roots

value: Wildtype

value: TuYV-WT


title: FLASH_03

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

description: Library name: FLASH_03

data_processing:
Element Biosciences Bases2Fastq v1.6 was used to demultiplex sequencing data and convert base calls to fastq.
Cells were called and read counts were summarized per gene per cell using the 10x cellranger pipeline (v9.0.0) against the Mus musculus genome (mm10, refdata-gex-GRCm39-2024-A, built from GENCODE vM33 and Ensembl release 110).
filtered_feature_bc_matrix matrices per library were imported into R version 4.4.1 (2024-06-14). The count matrices of the cells of each library were combined into a single dataset for further downstream analysis using the Seurat package for R (v5.1.0).
Assembly: mm10, refdata-gex-GRCm39-2024-A, built from GENCODE vM33 and Ensembl release 110
Supplementary files format and content: For each library of single cells, we provide the 3 files generated by the Cell Ranger count pipeline within the filtered_feature_bc_matrix folder (i.e the cells called by Cell Ranger): barcodes.tsv.gz (tab-separated file, contains the cell barcodes), features.tsv.gz (tab-separated file, contains the genes included in the mm10 transcriptome) and matrix.mtx.gz (sparse matrix format, contains the raw counts per gene (in the rows), per cell (in the columns)). The prefix of the three files per library corresponds to the sample name.
Supplementary files format and content: We provide raw counts of the cells retained after QC filtering (mtx files), the first column contains gene symbols of genes. Along with the raw counts of the retained cells, we provide metadata information per cell such as cluster ID and UMAP coordinates (comma-separated values files). The mtx and metadata files contain cells merged from all libraries.

source_name: Small intestine (jejunum)

growth_protocol: C57BL/6 mice were maintained under specific pathogen-free conditions with ad libitum access to food and water on a 12 h light/dark cycle. Mice were used at 8–12 weeks of age. Animals received either FLASH or conventional (CONV) whole-abdominal irradiation at a dose of 15 Gy, or were left untreated as controls.

extract_protocol:
Cell lysis and RNA capture was performed according to the 10x Genomics protocol (Single Cell 3' v4 chemistry). The cells of each condition were processed as a single-library.
10x Genomics Dual Single Cell 3' v4 chemistry

treatment_protocol: Mice were subjected to a single fraction of 15 Gy whole-abdominal irradiation delivered either at ultra-high dose rate (FLASH) or conventional dose rate (CONV). Unirradiated mice served as controls. Small intestinal tissue was harvested 24 h after irradiation. Blood endothelial cells were isolated by fluorescence-activated cell sorting (FACS) for single-cell RNA sequencing analysis.

value: Small intestine (jejunum)

value: Blood endothelial cells

value: Flash radiotherapy


title: Unwounded 3 dpf Replicate 3

description: Library name: Sample3


title: FLASH_02

description: Library name: FLASH_02


title: FLASH_01

description: Library name: FLASH_01


title: CONV_03

description: Library name: CONV_03

value: Conventional radiotherapy


title: CONV_01

description: Library name: CONV_01


title: Ctrol_03

description: Library name: Ctrol_03

value: No treatment


title: Ctrol_01

description: Library name: Ctrol_01


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl,  Ground state, BiolRep2

first: Chulan

last: Kwon

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

description:
Library name: d0_siControl_2_ATAC_iMGT-MEF
50 M read

data_processing:
Bowtie2 was used to map reads.
MACS3 was used to call peaks.
Assembly: mm10, hg38
Supplementary files format and content: narrowPeak bed files containing peak locations.

growth_protocol: iMGT-MEF were cultured in plates precoated with 0.1% gelatin (Stem Cell Technologies, #7903) and maintained in Fibroblast Culture Medium (FCM) consisting of DMEM (Corning, #10-013-CV), 10% fetal bovine serum (FBS; VWR, #89510-186), and 1% antibiotic-antimycotic solution (Gibco, #15240062) at 37°C in a 5% CO2 atmosphere. IMR90 cells (Coriell) were grown in growth media (GM) consisting of EMEM (ATCC) supplemented with 10% FBS (Omega Scientific), and 1% antibiotic-antimycotic solution (Gibco, #15240062) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
At Day 1 post-MGT or MYOD overexpression, cells were harvested and frozen in 90% FBS with 10% DMSO using a controlled-rate freezing container (Mr. Frosty) at –80C. Approximately 250,000 cells were used per condition.
ATAC-seq DNA samples prepared with Active Motif ATAC-seq Kit (#53150) following the manufacturer’s protocol. DNA cleanup, library preparation, and indexing were performed with kit reagents.

treatment_protocol: On siRNA transfection day (day −1), cells were detached using 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, neutralized with fibroblast culture medium (FCM), centrifuged, and resuspended in induction cardiac reprogramming medium (iCRM), consisting of DMEM, 20% Medium 199 (Gibco, #11150-059), 10% FBS, and 1% A/A. Cells were plated in 6-well plates at a density of 300,000 cells per well and transfected with siJunb, siH1f0, or siControl. The following day (day 0), 1 μg/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in iCRM was added to induce MGT expression. For IMR90 human cells, on siRNA transfection day (day −1), cells were detached using 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, neutralized with GM, centrifuged, and resuspended in GM. Cells were plated in 6-well plates at a density of 300,000 cells per well and transfected with siJunb, siH1f0, or siControl. The following day (day 0), 100 ng/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in GM was added to induce MYOD expression.

value: mouse embryonic fibroblasts

tag: treatment 1

value: siCtrl

tag: treatment 2

value: Doxy induced (MGT) cardiac reprogramming

tag: time

value: Ground state


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl, Ground state, BiolRep1

description:
Library name: d0_siControl_1_ATAC_iMGT-MEF
50 M read


title: U251 recurrent (post-LITT) [NL71B]

city: Detroit

first: Tavarekere

last: Nagaraja

state: MI

address: 2799 W. Grand Blvd.

department: Neurosurgery

institute: Henry Ford Health

description:
Library name: NL71B
DE cohort; xengsort graft fraction 33.05%

data_processing:
Raw paired-end reads were sorted into human (graft) and rat (host) streams with xengsort 2.1.0 using GRCh38 and Rattus norvegicus reference k-mer indices.
The human (graft) read stream was quantified with nf-core/rnaseq v3.22.2 (Nextflow 25.10.2; STAR alignment and Salmon 1.10.3 quantification, reverse-stranded) against GRCh38, GENCODE release 44.
Gene-level counts were merged across samples into salmon.merged.gene_counts.tsv.
Differential expression between recurrent (post-LITT) and primary (pre-LITT) tumors was computed with nf-core/differentialabundance v1.5.0 (DESeq2; design ~ Classification).
Assembly: GRCh38 (human graft transcriptome), GENCODE release 44 (GRCh38.primary_assembly.annotation).
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited matrix; rows = Ensembl gene IDs (column gene_id) with gene symbols (gene_name), columns = samples, values = Salmon-estimated gene-level counts for the human/graft transcriptome.

organism:
Homo sapiens
Rattus norvegicus

source_name: brain (orthotopic xenograft)

growth_protocol: Adult female immune-compromised RNU/RNU rats (Charles River Laboratories) were stereotactically implanted intracerebrally with log-growth-phase U251N human glioblastoma cells (5 x 10^4 cells in 10 uL PBS) under isoflurane anesthesia. A burr hole was drilled 3.50 mm right of bregma (anterio-posterior 0.0); cells were injected at a depth of 2.5 mm at 0.5 uL/10 s and the needle held in place 5 min before withdrawal. IACUC #1509. Tumor establishment was confirmed by MRI/DCE-MRI ~2 weeks after implantation.

extract_protocol:
Tumor-bearing brains were sliced (2 mm), flash-frozen in 2-methylbutane chilled to -40 C on dry ice, and stored at -80 C; tumor tissue was dissected from the frozen slices. Total RNA was extracted by the originating laboratory using the Qiagen RNeasy Total RNA Purification Kit with QIAzol Lysis Reagent for tissue lysis; no separate DNase digestion was performed, as the RNeasy silica-membrane purification efficiently removes most genomic DNA. RNA was provided to the sequencing core already extracted. RNA integrity number (RIN) per sample: C2B 9.2, IL64B 8.7, IL66B 8.8, IL67B 8.9, IL68B 7.8, IL69B 8.9, NL70B 8.6, NL71B 8.1, N168B 6.1, N269B 8.9.
RNA libraries were prepared at the USC Molecular Genomics Core, University of Southern California, using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio, cat# 634411), an rRNA/total-RNA depletion (ribodepletion) based, strand-specific chemistry that preserves the reverse (antisense) strand. Library yield was quantified on a Qubit fluorometer and validated by qPCR (Thermo Fisher QuantStudio 7). Libraries were sequenced on an Illumina NextSeq 2000 in 2x100 bp paired-end configuration; the resulting data are reverse-stranded (Salmon auto-detected library type ISR).

treatment_protocol: Recurrent-arm tumors underwent diffusion-weighted-imaging-guided laser interstitial thermal therapy (DWI-LITT) using the Visualase system under real-time DWI-MRI guidance, performed ~24 h after a localizing MRI; ablation was stopped when it reached the tumor margins and animals were monitored longitudinally for recurrence. Primary-arm tumors were not ablated.

value: brain (orthotopic xenograft)

value: glioblastoma

value: post-LITT (laser interstitial thermal therapy)


title: dcl234_Roots_TuYV-WT

description: Library name: dcl234_Roots


title: ATAC-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, BiolRep2

description:
Library name: d1_siH1f0_2_ATAC_iMGT-MEF
50 M read

value: Day 1 post-MGT


title: U251 recurrent (post-LITT) [NL70B]

description:
Library name: NL70B
DE cohort; xengsort graft fraction 42.67%


title: Ctrol_02

description: Library name: Ctrol_02


title: ATAC-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, BiolRep1

description:
Library name: d1_siH1f0_1_ATAC_iMGT-MEF
50 M read


title: U251 recurrent (post-LITT) [IL66B]

description:
Library name: IL66B
DE cohort; xengsort graft fraction 29.44%


title: ATAC-iMGT-Myh6-eGFP-MEFs, siJunb, D1, BiolRep2

description:
Library name: d1_siJunb_2_ATAC_iMGT-MEF
50 M read

value: siJunb


title: SF126-3

description:
Library name: SF126-3_lib
TPM expression values for SF126-3 in mRNA-12.TPM.genes.tsv

value: Brain

value: Astrocytoma

value: Sensitive

value: untreated


title: U251 primary (pre-LITT) [IL69B]

description:
Library name: IL69B
DE cohort; xengsort graft fraction 64.40%

value: pre-LITT


title: ATAC-iMGT-Myh6-eGFP-MEFs, siJunb, D1, BiolRep1

description:
Library name: d1_siJunb_1_ATAC_iMGT-MEF
50 M read


title: daf-7daf-16_32h_1mM_replicate3

description:
Library name: daf-7daf-16_32h_1mM_rep3
QK215 on 1mM auxin at 32h replicate 3

value: whole worm

value: daf-16(mgDf50) nhr-23(xk40[nhr-23::aid::3xflag]) I; ieSi57[eft-3p::tir1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; daf-7(e1372) III; maIs105[col-19p::gfp] V

value: 0mM Auxin


title: daf-7daf-16_34h_1mM_replicate3

description:
Library name: daf-7daf-16_34h_1mM_rep3
QK215 on 1mM auxin at 34h replicate 3


title: U251 primary (pre-LITT) [IL68B]

description:
Library name: IL68B
DE cohort; xengsort graft fraction 45.38%


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep2

description:
Library name: d1_siControl_2_ATAC_iMGT-MEF
50 M read

value: mouse embryonic fibroblasts


title: daf-7_30h_0mM_replicate3

description:
Library name: daf-7_30h_0mM_rep3
QK216 on 0mM auxin at 30h replicate 3

value: nhr-23(xk40[nhr-23::aid::3xflag]) I; ieSi57[eft-3p::tir1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; daf-7(e1372) III; maIs105[col-19p::gfp] V


title: U251 primary (pre-LITT) [IL67B]

description:
Library name: IL67B
DE cohort; xengsort graft fraction 42.52%


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep1

description:
Library name: d1_siControl_1_ATAC_iMGT-MEF
50 M read

value: siCtrl

value: Doxy induced (MGT) cardiac reprogramming


title: U251 in vivo control [N269B]

description:
Library name: N269B
RUVSeq contamination anchor (excluded from DE); xengsort graft fraction 4.90%

value: brain (orthotopic xenograft)

value: procedural / failed-graft control


title: U251 in vivo control [N168B]

description:
Library name: N168B
RUVSeq contamination anchor (excluded from DE); xengsort graft fraction 0.55%

value: glioblastoma


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, IgG, BiolRep1

description:
Library name: d0_siControl_1_C_R_IgG
30 M read
A8_d0_h1f0.relaxed.bed

data_processing:
Reads were mapped with Bowtie2.
Peaks were called with SEACR.
Assembly: mm10
Supplementary files format and content: Bed files contain peak start and end points.
Library strategy: CUT&Run

growth_protocol: The cells were cultured in plates precoated with 0.1% gelatin (Stem Cell Technologies, #7903) and maintained in Fibroblast Culture Medium (FCM) consisting of DMEM (Corning, #10-013-CV), 10% fetal bovine serum (FBS; VWR, #89510-186), and 1% antibiotic-antimycotic solution (Gibco, #15240062) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
At Day 1 post-MGT overexpression, cells were harvested and frozen in 90% FBS with 10% DMSO using a controlled-rate freezing container (Mr. Frosty) at –80C. Approximately 250,000 cells were used per condition.
CUT&RUN DNA samples sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) along with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, NEB #E7600S). DNA libraries were cleaned up using AMPure XP reagent, Bechman Coulter, A63881).

treatment_protocol: On siRNA transfection day (day −1), cells were detached using 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, neutralized with fibroblast culture medium (FCM), centrifuged, and resuspended in induction cardiac reprogramming medium (iCRM), consisting of DMEM, 20% Medium 199 (Gibco, #11150-059), 10% FBS, and 1% A/A. Cells were plated in 6-well plates at a density of 300,000 cells per well and transfected with siJunb, siH1f0, or siControl. The following day (day 0), 1 μg/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in iCRM was added to induce MGT expression.

tag: cut&run antibody

value: IgG

value: Ground state


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, IgG, BiolRep2

description:
Library name: d0_siControl_2_C_R_IgG
30 M read
A8_d0_h1f0.relaxed.bed


title: daf-7daf-16_34h_1mM_replicate2

description:
Library name: daf-7daf-16_34h_1mM_rep2
QK215 on 1mM auxin at 34h replicate 2

tag: replicate


title: U251 in vivo control [IL64B]

description:
Library name: IL64B
RUVSeq contamination anchor (excluded from DE); xengsort graft fraction 0.33%

tag: cell type


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, H3k9me3, BiolRep2

description:
Library name: d0_siControl_2_C_R_H3K9me3
30 M read


title: LN, replicate 1, stereo-seq

city: Singapore

first: Zexi

last: Guo

address: 90 Tanglin Halt Road

country: Singapore

institute: National Cancer Centre Singapore

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Stereo-seq Analysis Workflow (SAW) v7 workflow was  utilized to map sequenced reads to their spatial location on the tissue section, quantify the corresponding gene expression levels and visually present spatial gene expression distribution.
Assembly: GRCh38
Supplementary files format and content: GEF (Geotechnical Exchange Format)
Library strategy: Spatial transcriptomics

source_name: Lymph node

extract_protocol:
The fresh frozen lymph node tissue was OCT embedded and 10 uM frozen sections were cut with a cryostat for the assay.
Spatial transcriptome sequencing libraries were prepared with the BGI STOmics kits as instructed by the manufacturer's protocol. The final library was sequenced on the DNBSEQ-G400 as per manufacturer's protocol.

value: Lymph node


title: ATAC-iMYOD-IMR90, siH1F0, D1, BiolRep2

description:
Library name: d1_siH1f0_2_ATAC_iMYOD-IMR90
50 M read

value: human fetal lung fibroblast

value: Doxy induced (MYOD) Skeletal muscles reprogramming

value: Day 1 post-MYOD


title: MMTV_Pymt_Blood_Rep1

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

description:
Library name: W18
10x Genomics

data_processing:
CellRanger (v6.0.2; 10x Genomics) was used to map the scRNAseq data. In brief, CellRanger’s mkfastq module was used to preprocess/demultiplex the raw sequences in the FASTQ files and also convert the BCL files to FASTQ files. Then, CellRanger’s align module (using STAR aligner v2.7.10b) was used to align the reads to the murine reference genome (GRCm38/mm10). The feature-barcode matrices, which contain the quantified expression of each gene in each cell, was generated using CellRanger’s count module. This module identifies the cell barcodes and UMIs (unique molecular identifiers) within each BAM files and creates a new filtered BAM file, which only contains cell-associated reads. The filtered BAM file is used to generate a digital expression matrix (DEMs), which quantifies the number of UMIs that correspond to genes in each individual cell. Finally, CellRanger’s agger module was used to perform quality control of the mapped data. This involves combining the DEMS from multiple scRNAseq libraries to generates a normalized expression matrix, which is used for downstream analyses. Since neutrophils are poor in RNA and, therefore, have less UMIs per barcode, we ran CellRanger with the "force-cells" option to capture cells with lower UMIs and gene counts. We also included introns using the "include-introns" option since neutrophils are known to retain more introns during differntiation (10x Genomics; Technical Note CG000444).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated files and matrix files

source_name: Blood

growth_protocol: All animals will be housed in a pathogen-free animal facility at the University of Illinois at Chicago and fed a standard autoclaved diet ad libitum on a 12 hour light/dark schedule with two to five companions per cage.

extract_protocol:
Bone marrow cells were collected by flushing tibia and femur with complete RPMI media with 2mM EDTA, followed by RBC lysis and 3 washes with complete RPMI. Blood was collected via the vena cava, followed by RBC lysis and three washes with complete RPMI. Lungs and tumor cells were collected after digestion with the tissue dissociation kit from Miltenyi Biotec following manufacturer's recommended protocol and then treated with RBC lysis buffer followed by three washes with complete RPMI. Spleen was collected and minced in a dish with complete RPMI, treated with RBC lysis buffer, and washed three times with complete RPMI. Cells were strained with a 70uM filter.
Samples were processed for scRNAseq using the Chromium Single Cell Library and Gel bead kit v3; the manufacturer’s recommended protocol was followed (10x Genomics, CG000183_ChromiumSingleCell3__v3_UG_RevB).  Chromium’s Controller was used to make nanoliter-sized droplets that harbor uniquely barcoded beads called Gel Bead-InEMulsions or GEMs. After GEM generation, the mRNA was reverse-transcribed, and the resulting cDNA was amplified with 11 PCR cycles. The Chromium i7 Samples Index plate (10x Genomics) was utilized to PCR amplify the final library for 11 to 14 cycles. QC of the libraries was assessed using the High Sensitivity D5000 ScreenTape (TapeStation, Agilent Technologies). Finally, the libraries were sequenced using a NovaSeq 6000 SP flowcell (Illumina). The facilities at Illinois Urbana-Champaign conducted the sequencing.

value: Blood

value: Unsorted single cells

tag: genotype

value: Ert2Cre; MMTV-Pymt


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, H3K9me3, BiolRep1

description:
Library name: d0_siControl_1_C_R_H3K9me3
30 M read


title: MMTV_Pymt_Pri_Tumor_Rep1

description:
Library name: W21
10x Genomics

source_name: Tumor

value: Tumor


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, H1.0, BiolRep2

description:
Library name: d0_siControl_2_C_R_H1.0
30 M read

value: mouse embryonic fibroblasts


title: C&R-iMGT-Myh6-eGFP-MEFs, Ground state, H1.0, BiolRep1

description:
Library name: d0_siControl_1_C_R_H1.0
30 M read


title: ATAC-iMYOD-IMR90, siH1F0, D1, BiolRep1

description:
Library name: d1_siH1f0_1_ATAC_iMYOD-IMR90
50 M read


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, H3k9me3, BiolRep2

description:
Library name: d1_siControl_2_C_R_H3K9me3
30 M read

value: Day 1 post-MGT


title: ATAC-iMYOD-IMR90, siJUNB, D1, BiolRep2

description:
Library name: d1_siJunb_2_ATAC_iMYOD-IMR90
50 M read

value: siJUNB


title: daf-7_32h_0mM_replicate1

description:
Library name: daf-7_32h_0mM_rep1
QK216 on 0mM auxin at 32h replicate 1

value: whole worm

value: nhr-23(xk40[nhr-23::aid::3xflag]) I; ieSi57[eft-3p::tir1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II; daf-7(e1372) III; maIs105[col-19p::gfp] V

tag: treatment

value: 0mM Auxin


title: ATAC-iMYOD-IMR90, siJUNB, D1, BiolRep1

description:
Library name: d1_siJunb_1_ATAC_iMYOD-IMR90
50 M read


title: N2_IP_replicate2

description:
Library name: ChIP2021-025-N2-concatenated
N2 DAF-16 ChIP-seq IP replicate 2

value: starved dauer

value: IP


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, H3K9me3, BiolRep1

description:
Library name: d1_siControl_1_C_R_H3K9me3
30 M read

value: siCtrl

value: Doxy induced (MGT) cardiac reprogramming


title: ATAC-iMYOD-IMR90, siCTRL, D1, BiolRep2

description:
Library name: d1_siControl_2_ATAC_iMYOD-IMR90
50 M read

value: human fetal lung fibroblast


title: ATAC-iMYOD-IMR90, siCTRL, D1, BiolRep1

description:
Library name: d1_siControl_1_ATAC_iMYOD-IMR90
50 M read

value: Doxy induced (MYOD) Skeletal muscles reprogramming


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, H1.0, BiolRep1

description:
Library name: d1_siControl_1_C_R_H1.0
30 M read


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, H1.0, BiolRep2

description:
Library name: d1_siControl_2_C_R_H1.0
30 M read


title: N2_IP_replicate1

description:
Library name: ChIP2021-021-N2-concatenated
N2 DAF-16 ChIP-seq IP replicate 1


title: MiaPaCa-2,sgMETTL1,input,rep2

city: Monrovia

first: Ajay

last: Goel

address: 1218 south 5th avenue

department: Molecular Diagnostics and Experimental Therapeutics

institute: City of Hope National Medical Center

description:
Library name: MSM_I_rep2
2_all sample.xlsx

data_processing:
Paired-end raw sequencing reads were initially assessed for quality using FastQC. Adapter trimming and quality filtering were performed with Trim Galore. Processed reads were first aligned to a custom reference index containing human rRNA and tRNA sequences (GENCODE v26) using STAR. Unmapped reads were then aligned to the human reference genome (GRCh38/hg38) using STAR with the same alignment parameters. Count tables were generated by extracting the relevant columns from featureCounts output.
Assembly: hg38
Supplementary files format and content: xlsx file include raw counts for each sample from BxPC-3 cells.
Supplementary files format and content: xlsx file include raw counts for each sample from MiaPaCa-2 cells.

extract_protocol:
RNA was extracted from polysome fractions and input using QIAzol Lysis Reagent (Qiagen).
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB).

value: Pancreatic Ductal Adenocarcinoma cell

value: METTL1 knockout

value: input


title: C&R-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, IgG, BiolRep2

description:
Library name: d1_siH1f0_2_C_R_IgG
30 M read
D3_d1sih1f0_mef2c.relaxed.bed

value: IgG


title: MiaPaCa-2,sgMETTL1,input,rep1

description:
Library name: MSM_I_rep1
2_all sample.xlsx


title: MiaPaCa-2,sgNC,input,rep2

description:
Library name: MSN_I_rep2
2_all sample.xlsx

value: WT


title: C&R-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, IgG, BiolRep1

description:
Library name: d1_siH1f0_1_C_R_IgG
30 M read
D2_d1sih1f0_mef2c.relaxed.bed

value: mouse embryonic fibroblasts


title: Burn 72 hpb Replicate 1

description: Library name: Sample22

value: tail half of the larvae


title: C&R-iMGT-Myh6-eGFP-MEFs, siJunb, D1, IgG, BiolRep2

description:
Library name: d1_siJunb_2_C_R_IgG
30 M read
C3_d1sijunb_mef2c.relaxed.bed

value: siJunb

value: Day 1 post-MGT


title: MiaPaCa-2,sgNC,input,rep1

description:
Library name: MSN_I_rep1
2_all sample.xlsx


title: C&R-iMGT-Myh6-eGFP-MEFs, siJunb, D1, IgG, BiolRep1

description:
Library name: d1_siJunb_1_C_R_IgG
30 M read
C4_d1sijunb_mef2c.relaxed.bed


title: BxPC-3,sgMETTL1,input,rep2

description:
Library name: BSM_I_rep2
1_all sample.xlsx


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, IgG, BiolRep2

description:
Library name: d1_siControl_2_C_R_IgG
30 M read
B6_d1ctrl_mef2c.relaxed.bed


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, IgG, BiolRep1

description:
Library name: d1_siControl_1_C_R_IgG
30 M read
B9_d1ctrl_h1f0.relaxed.bed


title: BxPC-3,sgNC,input,rep2

description:
Library name: BSN_I_rep2
1_all sample.xlsx


title: C&R-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, MEF2C, BiolRep2

description:
Library name: d1_siH1f0_2_C_R_MEF2C
30 M read


title: BxPC-3,sgNC,input,rep1

description:
Library name: BSN_I_rep1
1_all sample.xlsx


title: C&R-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, MEF2C, BiolRep1

description:
Library name: d1_siH1f0_1_C_R_MEF2C
30 M read


title: MiaPaCa-2,sgMETTL1,polysome,rep2

description:
Library name: MSM_P_rep2
2_all sample.xlsx

value: polysome


title: C&R-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, MEF2C, BiolRep3

description:
Library name: d1_siH1f0_3_C_R_MEF2C
30 M read


title: C&R-iMGT-Myh6-eGFP-MEFs, siJunb, D1, MEF2C, BiolRep3

description:
Library name: d1_siJunb_3_C_R_MEF2C
30 M read


title: C&R-iMGT-Myh6-eGFP-MEFs, siJunb, D1, MEF2C, BiolRep2

description:
Library name: d1_siJunb_2_C_R_MEF2C
30 M read


title: C&R-iMGT-Myh6-eGFP-MEFs, siJunb, D1, MEF2C, BiolRep1

description:
Library name: d1_siJunb_1_C_R_MEF2C
30 M read


title: BxPC-3,sgMETTL1,polysome,rep2

description:
Library name: BSM_P_rep2
1_all sample.xlsx


title: BxPC-3,sgMETTL1,polysome,rep1

description:
Library name: BSM_P_rep1
1_all sample.xlsx


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, MEF2C, BiolRep1

description:
Library name: d1_siControl_1_C_R_MEF2C
30 M read


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, BiolRep1

description: Library name: d1_siH1f0_1_RNA-seq_iMGT-MEF

data_processing:
HISAT2 was used to map reads from fastq files
Subread featurecounts was used to create a counts table
Assembly: mm10
Supplementary files format and content: A txt file containing a raw counts matrix with gene names as rows and samples as columns

extract_protocol:
At Day 1 post-MGT or MYOD overexpression, cells were harvested and frozen in 90% FBS with 10% DMSO using a controlled-rate freezing container (Mr. Frosty) at –80C. Approximately 250,000 cells were used per condition.
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436).


title: BxPC-3,sgNC,polysome,rep2

description:
Library name: BSN_P_rep2
1_all sample.xlsx


title: 3350909_2B10_IgG_2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description: Library name: 3350909_2B10_IgG_2

data_processing:
Raw sequencing reads were adapter-trimmed and quality-filtered using Trim Galore (v0.4.4), which utilizes cutadapt with a quality cutoff of Q20.
Trimmed reads were aligned to the human reference genome (hg38/GRCh38.p12) using BWA-MEM (v0.7.17-r1198). Aligned reads were converted to BAM format and filtered using samtools (v1.2).
Duplicate reads were marked using biobambam2 bamsormadup (v2.0.87). Uniquely mapped, non-duplicate reads with MAPQ ≥1 were retained for downstream analyses using samtools.
Quality control and fragment length estimation were performed using strand cross-correlation analysis with SPP (v1.11). Reads were converted to BED format and extended to the estimated fragment length using bedtools (v2.17.0).
Genome-wide coverage was calculated using bedtools genomecov in bedGraph mode, scaled to a sequencing depth of 15 million reads, and converted to bigWig format using UCSC bedGraphToBigWig (v4). Peak calling was performed using MACS2 (v2.1.1.20160309) with matched IgG controls, using parameters “–nomodel –extsize <fragment_size>”. High-confidence peaks were defined at q ≤ 0.05 and peaks overlapping ENCODE blacklist regions were removed using bedtools.
Assembly: hg38
Supplementary files format and content: Processed files include normalized genome-wide signal tracks in bigWig format and peak calls in BED format

source_name: CMY

growth_protocol: CMY cells and isogenic clones  were cultured in RPMI medium (Gibco) supplemented with heat-inactivated fetal bovine serum (10%) and 1× penicillin/streptomycin. CMY and derived clones were passaged every 2–3 days. Cell identity was confirmed by STR profiling and all cultures tested negative for mycoplasma.

extract_protocol:
ChIP-seq chromatin preparation was performed using formaldehyde crosslinking. Ten million cells per replicate were crosslinked with 1% formaldehyde for 10 minutes at 37 °C and quenched with glycine. Cells were lysed in SDS lysis buffer, and chromatin was sheared to ~200–500 bp fragments using a Bioruptor sonicator. Immunoprecipitation was performed using target-specific antibodies or IgG control, followed by protein A/G magnetic bead capture, sequential washes, elution, reverse crosslinking, proteinase K digestion, and DNA purification by phenol–chloroform extraction and ethanol precipitation.
ChIP and corresponding input DNA libraries were prepared using a KAPA Biosciences paired-end library preparation kit compatible with Illumina sequencing platforms, following the manufacturer’s protocol. Library fragment size (~350–450 bp) was verified by Agilent TapeStation. Libraries were normalized, pooled, and sequenced on an Illumina NovaSeq platform using paired-end 50 bp reads.

treatment_protocol: For ChIP-seq experiments, cells were harvested under basal culture conditions without additional chemical treatment. Genome-edited cell lines were generated using CRISPR/Cas9 technology as described, and validated clones were expanded prior to chromatin immunoprecipitation.

value: CMY

value: Myeloid leukemia of Down syndrome (ML-DS) cell line

value: RAD21 WT

tag: antibody

value: CST 2729S


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siJunb, D1, BiolRep2

description: Library name: d1_siJunb_2_RNA-seq_iMGT-MEF

value: Doxy induced (MGT) cardiac reprogramming


title: 3350907_3D11_IgG_2

description: Library name: 3350907_3D11_IgG_2


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siJunb, D1, BiolRep1

description: Library name: d1_siJunb_1_RNA-seq_iMGT-MEF


title: 3350906_3D11_IgG_1

description: Library name: 3350906_3D11_IgG_1


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep1

description: Library name: d1_siControl_1_RNA-seq_iMGT-MEF

value: siCtrl


title: 3350905_3D11_CIITA_3

description: Library name: 3350905_3D11_CIITA_3


title: 3350904_3D11_CIITA_2

description: Library name: 3350904_3D11_CIITA_2


title: 30-day_cultured_EPCR_High_HSC_8

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description:
Library name: Sample24
R162-30d-8

data_processing:
Trimming, alignment (to mouse genome mm10), and Read counts were performed by Trimmomatic, Hisat2, and featureCounts, respectively. The normalization and comparison between groups were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Comma-separated values (CSV) file containing DESeq2-normalized gene expression values

growth_protocol: Sorted HSCs were cultured for 5 or 30 days.

extract_protocol:
One hundred cells were directly sorted into lysis buffer.
We performed RNA sequence as previously reported (Hayashi et al., 2018) with minor modification. Briefly, using one hundred sorted cells, the first strand of cDNA was synthesized by using PrimeScript RT reagent Kit (TAKARA Bio Inc., Kusatsu, Japan) and not-so random primers. Following the synthesis of the 1st strand, the 2nd strand was synthesized by using Klenow Fragment (3’-5’ exo-) (New England Biolabs Inc., Ipswich, MA) and complement chains of not-so random primers. Using purified double-strand cDNA, the library for RNA-Seq was prepared and amplified using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA).

treatment_protocol: R162 was added during the culture.

value: Bone marrow

value: Primary cells

value: Hematopoietic stem cells


title: 3350903_3D11_CIITA_1

description: Library name: 3350903_3D11_CIITA_1


title: 3350901_2B10_IgG_1

description: Library name: 3350901_2B10_IgG_1


title: 30-day_cultured_EPCR_High_HSC_6

description:
Library name: Sample22
R162-30d-6


title: 30-day_cultured_EPCR_High_HSC_5

description:
Library name: Sample21
R162-30d-5


title: 3350900_2B10_CIITA_3

description: Library name: 3350900_2B10_CIITA_3


title: 3350899_2B10_CIITA_2

description: Library name: 3350899_2B10_CIITA_2


title: 30-day_cultured_EPCR_High_HSC_4

description:
Library name: Sample20
R162-30d-4


title: 3350898_2B10_CIITA_1

description: Library name: 3350898_2B10_CIITA_1


title: 30-day_cultured_EPCR_High_HSC_3

description:
Library name: Sample19
R162-30d-3


title: 30-day_cultured_EPCR_High_HSC_2

description:
Library name: Sample18
R162-30d-2


title: 3350896_CMY_IgG_2

description: Library name: 3350896_CMY_IgG_2

value: RAD21 Y3*


title: 3350895_CMY_IgG_1

description: Library name: 3350895_CMY_IgG_1


title: 30-day_cultured_EPCR_High_HSC_1

description:
Library name: Sample17
R162-30d-1


title: 3350894_CMY_CIITA_3

description: Library name: 3350894_CMY_CIITA_3


title: 5-day_cultured_EPCR_Low_HSC_4

description:
Library name: Sample16
Culture_Low-4

value: Hematopoietic progenitor cells


title: C240221006 - Healthy control 3

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

description: Library name: C240221006

data_processing:
Raw sequencing reads were processed using CeleScope (Singleron Biotechnologies; www.github.com/singleron-RD/CeleScope). The dataset was processed with CeleScope v1.15.0. Barcode recognition, correction, and chemistry assignment were performed automatically. Reads were aligned using STARsolo (STAR v2.7.11a) against the GRCh38 human reference genome (Ensembl 92) to generate nucleus-by-gene expression matrices. Downstream quality control, normalization, clustering, and cell-type annotation were performed using standard single-nucleus RNA-sequencing workflows.
Assembly: GRCh38 human reference genome (Ensembl 92)
Supplementary files format and content: The processed data are split in 3 files (barcodes.tsv, genes.tsv, matrix.mtx) for each sample.

source_name: brain

extract_protocol:
Microtome-cut human midbrain tissue sections mounted on glass slides. All samples were handled on dry ice upon arrival. Nuclei were isolated following the manufacturer’s instructions using the GEXSCOPE® Single Nucleus RNA Library Kit V2 (Singleron Biotechnologies; cat. nos. 1185011/2) and the included Nucleus Separation Solution V2. Briefly, tissue was minced on ice, incubated in Nucleus Separation Mix, mechanically dissociated, and filtered through a 40-µm strainer. The nuclei-containing flow-through was washed in PBS supplemented with EGTA, pelleted at low speed, and gently resuspended. Nuclear integrity and concentration were assessed microscopically using exclusion dyes such as DAPI or Trypan Blue.
Sequencing libraries were generated using the GEXSCOPE® Single Nucleus RNA Library Kit V2 (cat. nos. 1185011/2). For all samples, 50 ng of amplified cDNA was used as input. cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to truncated Illumina adapters. Adapter-ligated fragments were indexed by PCR using Unique Dual Indexes Set A (UDI Set A, included in the kit) and purified by dual size selection with AMPure XP beads. Library concentrations were quantified using a Qubit™ 4 Fluorometer (Thermo Fisher Scientific; cat. Q33238), and library fragment size distributions were evaluated using an Agilent TapeStation system (Agilent Technologies). Final libraries showed an average insert size of approximately 400–700 bp, with <5% of fragments below 300 bp, consistent with expectations for SCOPE-chip SD–derived single-nucleus RNA-seq libraries.

value: brain

value: Healthy

tag: Sex

value: Male


title: 3350893_CMY_CIITA_2

description: Library name: 3350893_CMY_CIITA_2


title: C240221005 - Healthy control 2

description: Library name: C240221005


title: 5-day_cultured_EPCR_Low_HSC_2

description:
Library name: Sample14
Culture_Low-2

source_name: Bone marrow


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siH1f0, D1, BiolRep2

description: Library name: d1_siH1f0_2_RNA-seq_iMGT-MEF

value: mouse embryonic fibroblasts


title: C&R-iMGT-Myh6-eGFP-MEFs, siControl, D1, MEF2C, BiolRep2

description:
Library name: d1_siControl_2_C_R_MEF2C
30 M read

value: Day 1 post-MGT


title: BxPC-3,sgNC,polysome,rep1

description:
Library name: BSN_P_rep1
1_all sample.xlsx

value: Pancreatic Ductal Adenocarcinoma cell

value: WT

value: polysome


title: 5-day_cultured_EPCR_Low_HSC_1

description:
Library name: Sample13
Culture_Low-1


title: 5-day_cultured_EPCR_High_HSC_4

description:
Library name: Sample12
Culture_High-4


title: C240221004 - PD LRRK2-G2019S 2

description: Library name: C240221004

value: PD LRRK2-G2019S

value: Female


title: 5-day_cultured_EPCR_High_HSC_3

description:
Library name: Sample11
Culture_High-3


title: C240221003 - PD LRRK2-G2019S 1

description: Library name: C240221003


title: RNA-seq-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep2

description: Library name: d1_siControl_2_RNA-seq_iMGT-MEF

value: Doxy induced (MGT) cardiac reprogramming