title: DRGneurons_Vehicle_sample04

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

data_processing:
Sequence alignment was done with SeqMan NGen 17 (Lasergene) and with Qiagen's CLC genomic workbench (v. 22). Processed data are the CLC result
Sample quality was assessed with demultiplexed fastq.gz files and subsequently the alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Each biological sample consisted in 4 technical replicates which were aligned as a group.
For comparison, sequence reads were processed using Qiagen's software CLC Genomics workbench (v22) with CLC's default settings for RNA-Seq analysis. The CLC alignment result was used as processed data file
Sequence reads were trimmed for adaptor sequences and low quality sequences using CLC genomic workbench (Quality limit 0.05)
Sequence reads were aligned to GRCm38 genome. Read counts extraction and normalization (TMM) were done using CLC genomc workbench. The parameters were: mismatch cost 2; insertion cost 3; deletion cost 3; length fraction 0.8, similarity fraction 0.8. The expression value unit is TMM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files of TMM normalized feature counts for each DRG culture (each from one mouse), target length, coordinates and gene IDs
Supplementary files format and content: tab-delimited text files of TMM normalized feature counts and gene IDs of filtered valid genes, columns N-U are linear TMM counts, columns V-AC are TMM counts with imputation of missing values, columns AD-AK are LOG2 transformed TMM counts

source_name: DRGs

growth_protocol: Primary sensory neurons were prepared from mouse dorsal root ganglia (DRGs) and seeded on PLL and laminin coated cover slips (9-12 cover slips per mouse). Cells were cultured in  serum-free Neurobasal medium containing 1x B27 supplement , 1x Pen/Strep, 200 ng/ml nerve growth factor nd 2 mM L-glutamine at 37 °C and 5% CO2 and 95% humidity.

extract_protocol:
Total RNA was isolated using a single cell RNA extraction kit (PicoPure, Thermo Fisher). Quantity of total RNA was determined using Invitrogen’s Qubit HS assay and quality was checked using Agilent's bioanalyzer
First strand cDNA was prepared and amplified from 1 ng total RNA using SMART Seq v4 Ultra Low Input RNA Kit for sequencing (TaKaRa) according to the manual compatible with Illumina NGS. Barcoded sequencind libraries were subsequently prepared using the low input library preparation kit (TaKaRa). The Sv4 PLUS kit includes first stand cDNA synthesis kit using SMART technology and library preparation kit that incorporates enzymatic fragmentation and stem-loop adapters to construct high-quality, Illumina-compatible libraries from the cDNA synthesized with the core kit. Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

treatment_protocol: The day after cell seeding, GlcCer 24:1 was added to the medium at a final concentration of 1 µM. Control cells received the same volume of vehicle which was a 1:10000 solution of a 2:1 mixture of chloroform and methanol. Cells were collected two days after adding treatments.

value: DRGs

value: primary neurons

value: Primary DRG neurons

tag: mouse strain

value: male

value: Grnflfl

tag: treatment compound

value: Vehicle

tag: treatment concentration

value: 0 uM

tag: treatment duration

value: 2 days


title: DRGneurons_Vehicle_sample03

status: Public on Sep 03 2025

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: Sex

tag: genotype


title: 45

city: New York

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ files were aligned to the Rat Genome (mRatBN7.2) using STAR.
Aligned BAM files were counted against the Ensembly Rnor_6.0_ GTF reference file using featureCounts and assigned gene names using BioMart.
Differential expression analysis was completed with DESeq2
Assembly: mRatBN7.2
Supplementary files format and content: Comma-delimited file containing raw counts per sample.

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA was extracted using the Zymo Clean and Concentrator Kit. Purified RNA was sent to Azenta Biosciences for quality control checking, library preparation, and sequencing.
Ilumina RNA with PolyA selection

value: Brain

value: WT

tag: treatment


title: Patient 0001, Baseline

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Library name: patient_0001_BL

data_processing:
The raw sequencing reads were first trimmed with cutadapt (v2.1.0) to remove adapter sequences, short sequences, and low quality bases (-m20, -q10).
Trimmed reads were quantitated using Salmon (1.4.0) with a gencode v36 reference and -numBootstraps 50.
These Salmon assignments were imported into R and summarized by gene using tximport (v1.30.0).
Assembly: GRCh38
Supplementary files format and content: tsv file with gene-level counts from salmon/tximport

molecule: polyA RNA

organism: Homo sapiens

source_name: Nasal brush biopsy

extract_protocol:
Nasal brush biopsies were obtained serially from the same participant at baseline and at approximately 6 months and 2 years after initiating ETI therapy. Brushes from the right nostril were collected in Qiagen RLT Plus lysis buffer supplement with 40 mM DTT and stored at -80C. Total RNA and DNA were isolated simultaneously using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Nasal brush biopsy

tag: individual

value: Patient 0001

tag: treatment timepoint

value: Baseline


title: Patient 0001, 6 Months

description: Library name: patient_0001_6M

value: 6 Months


title: DRGneurons_Vehicle_sample01


title: 44


title: DRGneurons_Vehicle_sample02


title: 40


title: 39


title: DRGneurons_GlcCer24:1_sample03

value: 1 uM


title: Patient 0001, 2 Years

description: Library name: patient_0001_2Y

value: 2 Years


title: DRGneurons_GlcCer24:1_sample01


title: DRGneurons_GlcCer24:1_sample04


title: 37


title: 4C-rDNA, Mel Z, matrigel, rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description:
Library name: 4C-Sample2M
Replicate 2 matrigel

library_source: genomic

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from adaptor sequences and low quality sequences by cutadapt v. 4.9 using the following options: 1. 4C full length adapters (both direct and reverse complement (RC)) were: >A1D TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT >A1RC AAGTCCAGAAATCAACTCGCCAGTTCTGTACAGCATTCTGTAGGGAGATCAAATCTGGGATGTCAGAAGTGAA >A2D TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT >A2RC AGGATCCTGGGCAGGAAAGTTCTCAGCAGGCTTAGGCCTCCTAGCCAAAAAGCCAAAACCACTTCTGGGATTTTTTTCAAAGA were removed at 5' ends by the options -O 10 (minimal overlap adapter with the read) --trim-n (omit N’s at the ends of reads) --times=4 (search for the adapter up to 4 times in the read consequently) --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality). All untrimmed reads were collected to the separate file.
2. Illumina 3' adapters array from AGATCGGAAGAGC to AGATCGGAAGAGCNNNNNNNNNN and from GATCGGAAGAGC to GATCGGAAGAGCNNNNNNNNNN anchored to 3' end of reads were removed by cutadapt with the following options: -a -O 10 (minimal overlap adapter with the read) --times=4 (search for the adapter up to 4 times in the read consequently) --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality).
3. Incomplete from 5' 4C full length adapters arrays: from TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT to TTCACTTCTGACATCCCAGA (minimal length = 20) and from TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT to TCTTTGAAAAAAATCCCAGA (minimal length = 20) both direct and reverse complement, anchored to 5' end of reads were removed by cutadapt with the same options as above.
4. Illumina Adapter GATCGGAAGAGC and IlluminaPE adapter AGATCGGAAGAGC were remove by cutadapt from 3' ends of reads with the following options: -a -O 5 (minimal overlap adapter with the read) --times=4 --minimum-length 20 (minimum acceptable read length after trimming) -q 24 (minimal acceptable quality)
5. Incomplete from 3' 4C full length adapters arrays: from TTCACTTCTGACATCCCAGATTTGATCTCCCTACAGAATGCTGTACAGAACTGGCGAGTTGATTTCTGGACTT to GCGAGTTGATTTCTGGACTT (minimal length = 20) and from TCTTTGAAAAAAATCCCAGAAGTGGTTTTGGCTTTTTGGCTAGGAGGCCTAAGCCTGCTGAGAACTTTCCTGCCCAGGATCCT to ACTTTCCTGCCCAGGATCCT (minimal length = 20) both direct and reverse complement were removed by cutadapt from the 3' end of reads with the same options as in points 2 and 3 of this protocol.
6. All untrimmed reads collected at the first step of the described procedure (i.e., the reads without at least 10 nucleotides overlap of adapter and the read) were trimmed again by the described procedure (points 1-5) with the only difference: at the first step the changed set of cudatapt options was applied: -O 15 (instead of -O 10 thus requiring more adapter nucleotides to overlap with the read), -e 0.2 (this option fixes error rate to 0.2 thus enabling to find adapters that were read with a lesser quality).
Trimmed reads were re-paired by BBTools 39.01 repair.sh script with the option “repair” and mapped to hg38p12 by bwa 0.7.17-r1188 using the mem algorithm. Post-alignment processing of BAM files was performed using SAMtools v1.17, with unaligned reads and supplementary alignments filtered out using the -F 2052 flag. Alignments to chromosomes chrMT, chrGL000220, and chrY were completely excluded from further analysis. In addition, to eliminate alignments to the 4C anchor (i.e., rDNA sequences) from the further condsideration, reads mapped to the region chr21:8202045–8472360 were also removed.
Alignments entirely overlapping low-complexity genomic regions from DFAM v3.8 database were removed using BEDTools 2.31.0 (intersect -wa -v -f 1.0), ensuring that only alignments that are mapped completely into low complexity regions are filtered out
Aligned 4C-rDNA-associated BAM files were intersected across replicates using an in-house R script employing data.table 1.15.2 and dplyr 1.1.4 libraries, with only intersecting alignments retained for further analysis. Intersected alignments were converted to resulting tables using SAMtools 1.17, BioPerl and in-house Perl scripts.
deepTools v3.5.5 was used to generate genome-wide 4C-rDNA–associated profiles with RPKM normalization and a bin size of 10 bp for each replicate (rep1, rep2) and condition (plastic, matrigel). The following options were used with the bamCoverage tool: -bs 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM --exactScaling --ignoreForNormalization chrGL000220 chr21 --skipNAs. Genome-wide profiles of replicates were merged using a custom Bash script that employed bedtools v2.31.0 and bedops v2.4.41.
Assembly: Homo Sapiens hg38/GRCh38.p12 genome
Supplementary files format and content: Tab-delimited text file include the following features of each 4C-rDNA–associated mapping: chromosome, begin, end, length, coverage, number of reads, sequence.
Supplementary files format and content: bedGraph genome-wide profiles of the each replicate and merged profile: chromosome, begin, end, RPKM-normalized number of 4C-rDNA contacts.
Library strategy: Capture-C

molecule: genomic DNA

source_name: skin

growth_protocol: Mel Z cells were drown in RPMI 1640 media (PanEco, Russia) supplemented with heat-inactivated fetal calf serum (HyClone, USA), 2 mM glutamine, 250 u/ml penicillin and 250 microg/ml streptomycin (PanEco, Russia) at 37 °C in a humidified atmosphere containing 5% CO2. The cells were initially propagated on a plastic surface in RPMI-1640 medium supplemented with 10% fetal calf serum, 2 mM glutamine, and 0.1% gentamicin sulfate at 37 °C in a humidified atmosphere containing 5% CO2 and, up to 10 million cells with 70–75% confluency. Then, the cells were divided into two equal samples and seeded either on plastic, or on Matrigel. Growth took place under identical conditions for 15 h; then, the cells were used for 4C experiments. Petri dishes coated with Matrigel (BD Bioscience, USA) were prepared as follows: the Matrigel (8.7 mg/mL) was thawed at 4 °C, and 6 mL was quickly added to each 10 cm dish and allowed to solidify for 30 min at room temperature; then, it was placed in a humidified 5% CO2 incubator for one hour at 37 °C.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978). Cross-linking To suspension containing about 6x106 of  Mel Z melanoma cells in 40 ml of DMEM formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C. Lysis The pellet of cells was resuspended at 0°C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C. Digestion with EcoRI The nuclei pellet was resuspended in 756 ul of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C. Ligation To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.  DNA purification For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40 l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE. Digestion with FaeI About 15 g of DNA was digested in 250 ul solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100 l of 0.1xTE. Ligation For circularization 15 g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 l of 0.1xTE. PCR and library preparation For preparation of 4C-rDNA libraries about 30 ng of 4C DNA preparations were used for 35 cycles of PCR with primers 5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ for each biological replicate. Deep sequencing of libraries were performed using NextSeq 2000 (Illumina) using 150-nt long paired-end reads.
For preparation of 4C-rDNA libraries about 30 ng of 4C DNA preparations were used for 35 cycles of PCR with primers 5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ for each biological replicate. Deep sequencing of libraries were performed using NextSeq 2000 (Illumina) using 150-nt long paired-end reads.

treatment_protocol: The cells were initially propagated on a plastic surface in RPMI-1640 medium supplemented with 10% fetal calf serum, 2 mM glutamine, and 0.1% gentamicin sulfate at 37 °C in a humidified atmosphere containing 5% CO2 and, up to 10 million cells with 70–75% confluency. Then, the cells were divided into two equal samples and seeded either on plastic, or on Matrigel. Growth took place under identical conditions for 15 h; then, the cells were used for 4C experiments and for RNA isolation. Petri dishes coated with Matrigel (BD Bioscience, USA) were prepared as follows: the Matrigel (8.7 mg/mL) was thawed at 4 °C, and 6 mL was quickly added to each 10 cm dish and allowed to solidify for 30 min at room temperature; then, it was placed in a humidified 5% CO2 incubator for one hour at 37 °C.

value: skin

value: Mel Z

value: melanocyte

value: melanoma

tag: medium

value: matrigel

tag: batch


title: siMLK4+M2_3

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Library name: siMLK4+M2_3

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20
hisat2
Genome Analysis Toolkit, version 4.2.3.0, MarkDuplicates --REMOVE_DUPLICATES false --OPTICAL_DUPLICATE_PIXEL_DISTANCE 12000 --REMOVE_SEQUENCING_DUPLICATES true
htseq-count, version 2.0.1, parameters: --type=exon --idattr=gene_id --additional-attr=gene_name --additional-attr=gene_biotype --stranded=reverse --secondary-alignments=ignore
Assembly: Genome_build: grch38
Supplementary files format and content: htseq-count matrix, separate files for paired and unpaired reads

source_name: breast

growth_protocol: SUM149PT cells were cultured in Ham’s F12 medium with 25 mM HEPES supplemented with 5% FCS, 1% penicillin/streptomycin, 1 µg/ml hydrocortisone and 10 µg/ml insulin. THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, 2 mM L-glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated using the RNAeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 S4 Reagent Kit following manufacturer's protocols.

treatment_protocol: SUM149PT cells were transfected in triplicates with non-targeting control siRNA or MLK4-targeting siRNA. 24 hours after transfection, cells were either left untreated or co-cultured with THP-1-derived M2 macrophages for additional 48 hours.

value: breast

value: TNBC

value: MLK4 KD

value: co-culture with M2 macrophages


title: 36

value: Brain


title: 47

value: WT


title: D24 Uhrf1+/+ iTreg 1

city: Chicago

first: Qianli

last: Liu

state: IL

address: 303 E. Superior St. Simpson Querrey

institute: Northwestern Univesity

description:
Library name: Sample 1
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: EM-seq

source_name: iTreg cells (Foxp3-GFP+tdTomato+)

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument.  gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then enzymatically converted using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) per manufecture's instruction. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the Pico Methyl-Seq Library Prep Kit (Zymo Research). Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and 4-6 pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 100 cycles NextSeq 2000 P2 reagent kit.

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: siMLK4+M2_4

description: Library name: siMLK4+M2_4


title: 4C-rDNA, Mel Z, plastic, rep2

description:
Library name: 4C-Sample2P
Replicate 2 plastic

value: plastic


title: 4C-rDNA, Mel Z, plastic, rep1

description:
Library name: 4C-Sample1P
Replicate 1 plastic


title: 35


title: 34


title: White blood cells (CapSeq with and without hairpin ligation)

city: Vilnius

first: Denis

last: Baronas

address: Saulėtekio al. 7

country: Lithuania

institute: Vilnius University

description:
Library name: wbc
CapSeq with and without hairpin ligation on white blood cells

library_source: transcriptomic single cell

data_processing:
The STARsolo wrapper pipeline (https://github.com/jsimonas/solo-in-drops) was used to process the sequencing data and to obtain cell ⨉ gene count matrices. Shortly, barcode ligation linker sequences were removed from the read1 the and read1 was reassembled to have a structure of BC3[8nt]BC2[10nt]BC1[8nt] UMI[8nt]. Next, STAR(https://doi.org/10.1101/2021.05.05.442755) (version 2.7.10a) was run with the following parameters: --soloUMIdedup Exact, --soloFeatures GeneFull, --soloType CB_UMI_Complex, --soloCBposition 0_0_0_7 0_8_0_17 0_18_0_25, --soloUMIposition 0_26_0_33, --soloCBmatchWLtype EditDist_2. The reads were aligned to either the human GRCh38 genome (GENCODE v41).
Assembly: GRCh38
Supplementary files format and content: Matrix files of gene expression raw count data in _matrix.mtx
Supplementary files format and content: Tab separated files of barcodes in _barcodes.tsv
Supplementary files format and content: Tab separated files of genes in _features.tsv
Supplementary files format and content: AnnData files in _adata.h5ad
Supplementary files format and content: Excel files of metadata containing barcode information linked to patient code or condition in _metadata.xlsx

source_name: Blood (white blood cells)

extract_protocol:
White blood cells were prepared by removing red blood cells (RBC) in the following manner. Peripheral blood was collected within the last 2 hours into a K2EDTA vacutainer and stored on wet ice. Subsequently, 10 µL of 0.5 M EDTA (Invitrogen, cat. no. 15575-038) was added per 1 mL of peripheral blood. In 2 mL Protein LoBind tube (Eppendorf, cat. no. 0030108132) 1800 µL of RBC lysis buffer (R7757, Sigma-Aldrich) was combined with 200 µL of peripheral blood. Cells with RBC lysis buffer were incubated for 5 min at room temperature and the tube was gently inverted every 5 s. Next, cells were centrifuged for 10 min at 300g and 4 °C using a swinging-bucket rotor. After discarding the supernatant, the pellet was gently resuspended with 2 mL RBC lysis buffer. The tube was incubated for 3 min at room temperature and gently inverted every 5 s. Then the cells were centrifuged for 5 min at 300g and 4 °C using a swinging-bucket rotor, and supernatant was discarded. Additional wash in RBC lysis buffer was performed if very bright red color was still visible on the pellet. Finally, the pellet was resuspended to the final volume of 100 µL with ice cold 1X DPBS. Cells were fixed by slowly adding 900 µL of ice-cold methanol into the 100 µL of cell suspension in 2 mL Protein LoBind tube. To avoid cell clumping the first 500 µL of the methanol was added drop by drop (3-5 drops per 1 s) and the remaining volume was added more quickly (in 1-2 s). After methanol was added, the tube was gently inverted 10-times. Next, the tube with methanol-fixed cells was incubated on ice for 15-30 min and transferred at -20 °C (for short period <6 months) or at -80 °C (for longer period >6 months). The fixed cells from the freezer were initially incubated on ice for 15-30 min followed by centrifugation for 5 min at 1000g and 4 °C using a swinging-bucket rotor. Next, the methanol was removed, and the cell pellet was resuspended in 1 mL of rehydration buffer (RB; 1X SSC, 2 M NaCl, 0.1% BSA) and transferred to a new 1.5 mL tube. The resuspended cells were then subjected to an additional centrifugation step for 5 min at 1000g and 4 °C. Subsequently, the supernatant was discarded, and the cells were subjected to an identical wash procedure using 1 mL of RB. A 10 µL aliquot of the cell suspension was utilized to determine the cell concentration using a hemocytometer. Following removal of the supernatant, the cell pellet was resuspended to achieve a final volume corresponding to 3 million cells per milliliter.
Illumina sequencing libraries were prepared for each amplified cDNA aliquot with NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat. no. E7805S) according to the instructions in the manual, with minor changes. In particular, 5-10 ng of amplified cDNA was used for cDNA fragmentation and transferred to a PCR tube. Nuclease-free water was added to reach the final volume on 13 µL. Fragmentation reaction was assembled on ice by adding 3.5 µL of NEBNext® Ultra™ II FS Reaction Buffer followed by 1 µL of NEBNext® Ultra™ II FS Enzyme Mix. Reaction mix was vortexed and spun-down for 3-5 seconds. The fragmentation was performed for 8 minutes at 37 °C, followed by end-repair and dA tailing for 30 min at 65 °C (lid was set at 75 °C). Fragmented cDNA was purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 17.5 µL with nuclease-free water. Then, 1.5 µM ligation adapter was prepared in advance by mixing 1.5 µL of forward ligation primer (100 µM, /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC; HPLC purification, IDT) and 1.5 µL of reverse ligation primer (/5AmMC6/GCTCTTCCGATCT; HPLC purification, IDT) with 97 µL of water. To anneal oligos, the solution was heated to 95 °C for 2 min (lid at 100 °C) and cooled at room temperature for 5 min. Next, purified fragmented cDNA was mixed with 15 µL of NEBNext® Ultra™ II Ligation Master Mix, 1.25 µL of ligation adapter and 0.5 µL of NEBNext® Ligation Enhancer. Reaction solution was well mixed by pipetting and incubated for 15 min at 20 °C (lid set at 37 °C). The ligation product was diluted to 100 µL with nuclease-free water, followed by a 0.8X SPRI size selection procedure and eluted in 40 µL with nuclease-free water. Finally, the ligation product was amplified by 12-cyles of PCR: 95 ºC for 3 min, 12-cycles [98 ºC for 20 s, 54 ºC for 30 s, 72 ºC for 20 s], and 72 ºC for 60 s. PCR mix was prepared by mixing 20 µL of ligation product, 2.5 µL of forward indexing primer (Table  S25), 2.5 µL of reverse indexing primer (Table S25) and 25 µL of 2X KAPA HiFi HotStart ReadyMix. Amplified sequencing libraries were purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 20 µL with nuclease-free water.

value: Blood (white blood cells)


title: siMLK4+M2_1

description: Library name: siMLK4+M2_1


title: 4C-rDNA, Mel Z, matrigel, rep1

description:
Library name: 4C-Sample1M
Replicate 1 matrigel


title: White blood cells from 4 AML patients (FACS-sorted capsules)

description:
Library name: facs
CapSeq of FACS-sorted transcriptomes of white blood cells from AML patients

data_processing:
The STARsolo wrapper pipeline (https://github.com/jsimonas/solo-in-drops) was used to process the sequencing data and to obtain cell ⨉ gene count matrices. Shortly, barcode ligation linker sequences were removed from the read1 the and read1 was reassembled to have a structure of BC3[8nt]BC2[10nt]BC1[8nt] UMI[8nt]. Next, STAR(https://doi.org/10.1101/2021.05.05.442755) (version 2.7.10a) was run with the following parameters: --soloUMIdedup Exact, --soloFeatures GeneFull, --soloType CB_UMI_Complex, --soloCBposition 0_0_0_7 0_8_0_17 0_18_0_25, --soloUMIposition 0_26_0_33, --soloCBmatchWLtype EditDist_2. The reads were aligned to either the human GRCh38 genome (GENCODE v41) or the mouse GRCm39 genome (GENCODE M30).
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Matrix files of gene expression raw count data in _matrix.mtx
Supplementary files format and content: Tab separated files of barcodes in _barcodes.tsv
Supplementary files format and content: Tab separated files of genes in _features.tsv
Supplementary files format and content: AnnData files in _adata.h5ad
Supplementary files format and content: Excel files of metadata containing barcode information linked to patient code or condition in _metadata.xlsx


title: siMLK4_4

description: Library name: siMLK4_4


title: NX-siCTRL_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Lung

growth_protocol: PASMCs were cultured in Smooth Muscle Cell Growth Medium 2 (Promocell)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) using manufactures protocols. Sequencing was performed on the NextSeq2000 instrument (Illumina) using v3 chemistry, 1x72bp single end setup.

treatment_protocol: PASMCs were transfected with non-targeting control siRNA (25 nM) or siADAR1 (25 nM) for 48 hours according to DharmaFECT Transfection protocol (Dharmacon)

value: Lung

value: primary pulmonary artery smooth muscle cells (PASMCs)

value: non-targeting siRNA control

value: siRNA transfection (48 hours)


title: White blood cells (different lysis conditions and CapSeq with and without hairpin ligation)

description:
Library name: lysis_hairpin
Comparison of CapSeq under mild vs harsh lysis conditions on white blood cells and comparison of CapSeq with and without hairpin ligation on white blood cells


title: NX-siCTRL_1


title: DRGneurons_GlcCer24:1_sample02

value: DRGs

value: primary neurons

value: Primary DRG neurons

value: male

value: Grnflfl

value: 1 uM

value: 2 days


title: NX-siCTRL_2


title: NX-siADAR_3

value: ADAR1 knockdown


title: 31

value: Brain


title: siMLK4_3

description: Library name: siMLK4_3

value: breast

value: TNBC

value: MLK4 KD


title: siMLK4_2

description: Library name: siMLK4_2


title: NX-siADAR_2


title: siMLK4_1

description: Library name: siMLK4_1


title: siCTRL_3

treatment_protocol: PASMCs were transfected with non-targeting control siRNA (25 nM), siADAR1 (25 nM), siADAR2 (25 nM) or siADAR1+siADAR2 (12.5+12.5 nM) for 48 hours according to DharmaFECT Transfection protocol (Dharmacon)

value: siRNA transfection (48h)


title: 29

value: WT


title: White blood cells from 8 AML patients, 8 neutropenia patients, 5 G-CSF treated donors, and 4 healthy donors

description:
Library name: global
CapSeq of white blood cells from AML patients, neutropenia patients, G-CSF treated donors, and healthy donors

value: Blood (white blood cells)


title: siMLK4+M2_2

description: Library name: siMLK4+M2_2

value: co-culture with M2 macrophages


title: siCTRL_2

value: Lung

value: primary pulmonary artery smooth muscle cells (PASMCs)

value: non-targeting siRNA control


title: siCTRL_1


title: siNT+M2_4

description: Library name: siNT+M2_4


title: 27


title: NX-siADAR_1

value: siRNA transfection (48 hours)


title: siADAR2_3

value: ADAR2 knockdown


title: siNT+M2_3

description: Library name: siNT+M2_3


title: siADAR2_2


title: 32


title: siADAR2_1


title: 25


title: 24


title: siNT+M2_2

description: Library name: siNT+M2_2


title: siADAR1-2_3

value: ADAR1/2 knockdown


title: siADAR1-2_2


title: siNT+M2_1

description: Library name: siNT+M2_1


title: siADAR1-2_1


title: 23


title: 30


title: siADAR1_3


title: siNT_4

description: Library name: siNT_4


title: siADAR1_2


title: 22


title: HL60, HTO-derived cDNA

city: New Orleans

first: Guoshun

last: Wang

state: LA

address: CSRB 607, 533 Bolivar Street

institute: Louisiana State University Health Sciences Center

description:
HL60_GW2_HTO
10x Genomics

library_source: other

data_processing:
10x Cellranger V.6.0.0 were used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting and aggregation.
Seurat v4.2.1 for scRNA QC and further analysis.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

molecule: protein

extract_protocol:
mRNA was extracted from HL-60 single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. mRNA derived cDNA and antibody-derived tagged DNA were constructed to libraries according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics). mRNA derived cDNA library and antibody-derived tagged library were pooled and sequenced at 4:1 ratio.

value: WT and CF

tag: condition

value: Parental and differentiated

value: With LPS and without LPS

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD298 + Anti beta2 microglobulin:WT_Parental -- TotalSeq-B0251; WT_Differentiated -- TotalSeq-B0252; WT_Differentiated&Stimulated -- TotalSeq-B0253; CF_Parental -- TotalSeq-B0254; CF_Differentiated -- TotalSeq-B0255; CF_Differentiated&Stimulated -- TotalSeq-B0256


title: 19

value: Brain


title: siNT_2

description: Library name: siNT_2

value: breast

value: TNBC


title: 501mel_Torin_2

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
Basecalling, demultiplexing were carried out by the Wellcome Trust Genomic Service, Oxford
Raw fastq reads for each samples were stitched using UNIX, quality controlled using fastqc (v0.11.9)
adaptor-, poly-A-, and 2 colour-trimmed using cutadapt 2.10 with Python 3.6.10
Trimmed reads were mapped to the Human reference genome (hg38) with STAR (version 2.7.8a)
Normalisation and differential gene expression analyses were performed as previously described (PMID: 31207090, 31733993, 31595650) using edgeR glmQLFTest.
Assembly: hg38
Supplementary files format and content: .txt (normalised gene expression)

growth_protocol: All cell lines were maintained in DMEM with 10% FBS in humidified incubator with 10% CO2

extract_protocol:
Total RNA samplewere prepared using RNeasy Mini Kit (QIAGEN #74106)  according to manufacturer protocol
500ng Total RNA was used to generate sequencing library using QuantSeq Forward kit (LEXOGEN #0.15.96) according to the supplier protocol

value: melanoma

value: WT

value: 12h 250nM Torin1


title: 18


title: 501mel_Torin_1


title: siNT_1

description: Library name: siNT_1


title: 15


title: 501mel_TFE_dKO_Torin_2

extract_protocol:
Total RNA samplewere prepared using RNeasy Mini Kit (QIAGEN #74106)  according to manufacturer protocol
3' end RNA-seq; 500ng Total RNA was used to generate sequencing library using QuantSeq Forward kit (LEXOGEN #0.15.96) according to the supplier protocol

value: TFE3 and TFEB double KO


title: 501mel_TFE_dKO_Torin_3


title: 14


title: 501mel_TFE_dKO_CTRL_3

value: 12h CTRL


title: M2_DMEM_KO_4

city: Padua

first: Marco

last: Fantuz

state: Veneto

address: Via Orus, 2

country: Italy

institute: Veneto Institute of Molecular Medicine

description:
Library name: C49
C49_S7_R1_001.fastq.gz

data_processing:
Raw reads were preprocessed using Trimmomatic, removing adapter sequences using the Illuminaclip step and employing a sliding window approach averaged on 4 bases and keeping only sequences with average quality evaluated with phred value>20.
Optimal quality was checked employing the FastQC tool.
Passing filtered reads were mapped to the mouse reference (mm39) using HISAT2 with default parameters.
Mapped reads were filtered excluding unpaired mate/pair reads and reads with a MAPQ quality score <20 using Samtools.
Raw counts were obtained from filtered reads using featureCounts.
Subsequently, differential expression analysis was performed using DESe2, retaining only genes with a corrected p-value <0.05. F
Assembly: mm39
Supplementary files format and content: raw_counts_matrix_mm39.txt - DESeq derived non-normalized raw counts matrix

growth_protocol: Age-matched female C57BL/6 mice, both wild-type (WT) and TRAP1-deficient, approximately 4 months old were used to perform macrophage extraction. Briefly, bone marrow cells were collected by flushing the femurs and tibias of WT and TRAP1 KO C57BL/6 female age-matched mice (3-4 months) with complete RPMI using a 25 g needle. The suspension was filtered (cell strainer 40 µm) and centrifuged at 400 g for 5 min. After treatment with red blood cell lysis buffer (Sigma-Aldrich) for 10 min at RT, the suspension was neutralized with complete RPMI, centrifuged at 400 g for 5 min and cells were resuspended in 10 mL macrophage DM, seeded at an 8 × 10⁵ cell density in a 100 mm low adhesion Petri dish with 10 mL macrophage DM, and incubated at 37°C in a humidified atmosphere containing 5% CO₂. After 4 days, 5 mL of fresh macrophage DM were added to each Petri dish and cells were kept in culture for 3 additional days when the M0 macrophage phenotype was assessed. For the subsequent M2 polarization, M0 macrophages were treated with 10 ng/mL of IL-4 (ImmunoTools) for 24 h in complete RPMI, and incubated at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction by oligodT priming.
The primer already contained Illumina-compatible linker sequences. After first strand synthesis the RNA was removed and second strand synthesis was initiated by random priming and a DNA polymerase. The random primer also contained Illumina-compatible linker sequences. Second strand synthesis was followed by a magnetic bead-based purification step. The library was then amplified, introducing the sequences required for cluster generation. External barcodes were introduced during the PCR amplification step. Library quantification was performed by fluorometer (Qubit) and Bioanalyzer (Agilent). Sequencing was performed on NextSeq500 ILLUMINA instrument to produce at least 10 million of reads (75bp SE) for sample.  QuantSeq Forward contained the Read 1 linker sequence in the second strand synthesis primer, hence NGS reads were generated towards the poly(A) tail and directly corresponded to the mRNA sequence. QuantSeq FWD maintained strand-specificity and allowed mapping of reads to their corresponding strand on the genome, enabling the discovery and quantification of antisense transcripts and overlapping genes.

treatment_protocol: M0 and M2 macrophages were exposed to DMEM (control medium) 10 mL of MPNST cells-derived conditioned medium (CM) for 48 h. After the initial 24 h, the media were replaced with fresh MPNST-CM.

value: TRAP1 KO

value: control medium (DMEM)


title: Sorted hCD34+cells, Uncultured CB, scRNAseq

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description: Library name: sc-RNAseq_Uncultured_CB_CD34-lib1

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.

source_name: Sorted GFP+CD34+, shJARID2, 20 weeks post-transplantation in the bone marrow of NSG mice.

growth_protocol: Enriched human cord blood CD34+ cells were cultured in SFEM II medium (StemCell Technologies, #09605) supplemented with Penicillin-Streptomycin (50 U/mL), human SCF (100 ng/mL), human TPO (100 ng/mL), and human FLT3L (100 ng/mL). Media were refreshed every other day.

extract_protocol:
All cell sorting was performed using a BD Aria Ilu SORP cell sorter. For scRNA-seq, 10,000 sorted CD34⁺ cells were used to prepare gene expression (GEX) libraries according to the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3 User Guide. For CITE-seq, 10,000 sorted CD34⁺ cells were processed to generate GEX libraries using the 10x Chromium Single Cell 3' Reagent Kits User Guide, v3.1 Chemistry Dual Index, with Feature Barcoding Technology for Cell Surface Protein, User Guide CG000317. For RNA sequencing, approximately 5,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells were sorted, followed by RNA isolation using the NucleoSpin RNA XS kit (Macherey-Nagel #740902.250) and library preparation with the SMARTer Ultra Low RNA Kit (Clontech), according to the manufacturer's instructions. For CUT&Tag, 10,000–20,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells or enriched human cord blood CD34⁺ cells were sorted and processed following the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff's lab (DOI: dx.doi.org/10.17504/protocols.io.bcuhiwt6). For CUT&RUN, libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher #14-1001).
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 (PN-1000075), following the manufacturer's user guide. CITE-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index Chemistry) along with Feature Barcoding Technology for Cell Surface Protein, according to the Feature Barcoding User Guide (CG000317). Bulk RNA-seq libraries were generated using the SMARTer Ultra Low RNA Kit (Clontech), following the manufacturer's instructions. CUT&Tag libraries were prepared using the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff’s laboratory (DOI: 10.17504/protocols.io.bcuhiwt6). CUT&RUN libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher, #14-1001), according to the manufacturer’s protocols.

treatment_protocol: We used an optimized microRNA lentiviral backbone to carry our shRNAs, as recommended by Fellmann et al. (2013). Lentiviral particles were produced by co-transfecting 293T cells with the packaging plasmids pMD.G, psPAX2, and pSFFV-eGFP-miR-E, in which the miR-E cassette was engineered to target Renilla, JARID2, EZH2, or STAT1. All plasmids were mixed at a 1:1:1 molar ratio. Enriched human cord blood CD34+ cells were transduced with constitutive lentiviral vectors carrying shRNAs, using LentiBOOST (1:100, SIRION Biotech, Cat No. SB-P-LV-101-12) and protamine sulfate (1:1000) to enhance transduction efficiency, as described by Schott et al. (2019).

value: hCD34+ HSPC


title: 501mel_TFE_dKO_Torin_1


title: Sorted hCD34+GFP+ cells, shJARID2#2, scRNAseq

description: Library name: sc-RNAseq_shJARID2#2_CD34-lib1

value: Lentivirus


title: siADAR1_1

value: Lung

value: primary pulmonary artery smooth muscle cells (PASMCs)

value: ADAR1 knockdown

value: siRNA transfection (48h)


title: 11


title: M0_DMEM_wt_4

description:
Library name: C43
C43_S1_R1_001.fastq.gz

value: wild-type


title: 501mel_TFE_dKO_CTRL_1


title: M2_CM_KO_4

description:
Library name: C48
C48_S6_R1_001.fastq.gz

value: MPNST cells-derived conditioned medium


title: 501mel_TFE_dKO_CTRL_2


title: Sorted hCD34+GFP+ cells, shJARID2#1, scRNAseq

description: Library name: sc-RNAseq_shJARID2#1_CD34-lib1


title: Sorted GFP+CD34+ cells, shRen, Day 8, GEX, rep2

description: Library name: CITEseq_shREN-CB2_mRNA

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CITE-seq

source_name: Sorted GFP+CD34+, shRen, Day8 ex vivo culture


title: HL60, mRNA-derived cDNA

description:
HL60_GW1_GEX
10x Genomics
single cell gene expression RNA-seq

value: WT and CF

value: Parental and differentiated

value: With LPS and without LPS

value: mRNA


title: siNT_3

description: Library name: siNT_3

value: breast

value: TNBC

value: WT


title: 10

value: Brain


title: 501mel_TFEB_KO_Torin_2

value: melanoma

value: TFEB KO

value: 12h 250nM Torin1


title: 9


title: M2_DMEM_wt_4

description:
Library name: A53
A53_S24_R1_001.fastq.gz

value: control medium (DMEM)


title: 501mel_TFEB_KO_Torin_3


title: 13


title: Sorted hCD34+GFP+ cells, shRen, scRNAseq

description: Library name: sc-RNAseq_shREN_CD34-lib1

value: hCD34+ HSPC

value: Lentivirus


title: 8


title: 501mel_TFEB_KO_Torin_1


title: 12


title: Sorted GFP+CD34+ cells, shRen, Day 8, GEX, rep1

description: Library name: CITEseq_shREN-CB1_mRNA


title: 501mel_TFEB_KO_CTRL_3

value: 12h CTRL


title: 501mel_Torin_3


title: M2_DMEM_KO_3

description:
Library name: A52
A52_S23_R1_001.fastq.gz

value: TRAP1 KO


title: Sorted GFP+CD34+ cells, shJARID2#2, Day 8, GEX, rep2

description: Library name: CITEseq_shJARID2#2-CB2_mRNA

source_name: Sorted GFP+CD34+, shJARID2, Day8 ex vivo culture


title: 6


title: Sorted GFP+CD34+ cells, shRen, Day 8, ADT, rep1

description: Library name: CITEseq_shREN-CB1_adt


title: M2_CM_wt_3

description:
Library name: A50
A50_S21_R1_001.fastq.gz

value: wild-type

value: MPNST cells-derived conditioned medium


title: 501mel_TFEB_KO_CTRL_2


title: 4


title: 5


title: Sorted GFP+CD34+ cells, shJARID2#2, Day 8, ADT, rep2

description: Library name: CITEseq_shJARID2#2-CB2_adt


title: M0_CM_wt_3

description:
Library name: A48
A48_S19_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shJARID2#2, Day 8, GEX, rep1

description: Library name: CITEseq_shJARID2#2-CB1_mRNA


title: 501mel_TFE3_KO_Torin_3

value: TFE3 KO


title: 501mel_TFEB_KO_CTRL_1


title: M0_CM_KO_3

description:
Library name: A49
A49_S20_R1_001.fastq.gz


title: M2_CM_KO_3

description:
Library name: A51
A51_S22_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shRen, Day 8, ADT, rep2

description: Library name: CITEseq_shREN-CB2_adt


title: M0_DMEM_KO_3

description:
Library name: A47
A47_S18_R1_001.fastq.gz


title: 501mel_TFE3_KO_Torin_2


title: Male explanded blastocyst, rep4

city: Ithaca

first: Guangsheng

last: Li

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

description:
Library name: M3_1
M3_1

data_processing:
The adaptor removal and QC of the raw sequencing reads were performed using fastp (v 0.20.0) . Reads with a percentage of low-quality base (quality score <20) >40% were removed. Reads with length < 30 bp or with high N content (>5%) were also removed in this study. The cow reference genome (ARS-UCD 2.0) was downloaded from NCBI database, and clean reads were aligned to the reference genome using STAR (v 2.7.10b)  allowing no more than 3 mismatches. The raw read counts for each gene were extracted using featureCounts. Iso-seq long-read data was processed following the official protocol.
Assembly: ARS-UCD 2.0
Supplementary files format and content: tab-delimited text files include raw read count for each Sample

organism: Bos taurus

source_name: Expanded blastocyst

extract_protocol:
For RNA-seq samples, there was no separate extration step. For Iso-seq sample, RNA was extracted using PicoPure™ RNA isolation kit (KIT0204, Applied Biosytems™) with Dnase treatment (RNase-Free DNase Set, Qiagen).
For RNA-seq, libraries were constructed using SMART-Seq® HT PLUS Kit (R400748, Taraka), and 15 PCR cycle were applied  for cDNA synthesis and 13 PCR cycles for library amplification. For Iso-seq, ISO-Seq® express 2.0 kit for cDNA synthesis, SMRTbell® prep kit 3.0 for library preparation.

value: Expanded blastocyst

value: Male


title: Sorted GFP+CD34+ cells, shJARID2#2, Day 8, ADT, rep1

description: Library name: CITEseq_shJARID2#2-CB1_adt


title: Male explanded blastocyst, rep5

description:
Library name: M3_2
M3_2


title: M0_DMEM_wt_3

description:
Library name: A46
A46_S17_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shJARID2#1, Day 8, ADT, rep2

description: Library name: CITEseq_shJARID2#1-CB2_adt


title: Male explanded blastocyst, rep3

description:
Library name: M2_1
M2_1


title: Male explanded blastocyst, rep2

description:
Library name: M1_2
M1_2


title: M2_DMEM_KO_2

description:
Library name: A44
A44_S15_R1_001.fastq.gz


title: 501mel_TFE3_KO_Torin_1


title: 501mel_TFE3_KO_CTRL_2


title: M2_CM_KO_2

description:
Library name: A43
A43_S14_R1_001.fastq.gz


title: M2_DMEM_wt_3

description:
Library name: A45
A45_S16_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shJARID2#1, Day 8, ADT, rep1

description: Library name: CITEseq_shJARID2#1-CB1_adt


title: Sorted GFP+CD34+ cells, shJARID2#1, Day 8, GEX, rep2

description: Library name: CITEseq_shJARID2#1-CB2_mRNA


title: 501mel_TFE3_KO_CTRL_3


title: M2_CM_wt_2

description:
Library name: A42
A42_S13_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shEZH2#2, Day 8, GEX, rep2

description: Library name: CITEseq_shEZH2#2-CB2_mRNA

source_name: Sorted GFP+CD34+, shEZH2, Day8 ex vivo culture


title: Sorted GFP+CD34+ cells, shJARID2#1, Day 8, GEX, rep1

description: Library name: CITEseq_shJARID2#1-CB1_mRNA


title: 501mel_HBSS_3

value: 12h HBSS


title: M0_CM_KO_2

description:
Library name: A41
A41_S12_R1_001.fastq.gz


title: Female explanded blastocyst, rep5

description:
Library name: F3_1
F3_1

value: Female


title: 501mel_TFE3_KO_CTRL_1


title: Sorted GFP+CD34+ cells, shEZH2#2, Day 8, ADT, rep2

description: Library name: CITEseq_shEZH2#2-CB2_adt


title: Female explanded blastocyst, rep4

description:
Library name: F2_2
F2_2


title: M0_CM_wt_2

description:
Library name: A40
A40_S11_R1_001.fastq.gz


title: Female explanded blastocyst, rep6

description:
Library name: F3_2
F3_2


title: Sorted GFP+CD34+ cells, shEZH2#2, Day 8, GEX, rep1

description: Library name: CITEseq_shEZH2#2-CB1_mRNA


title: 501mel_HBSS_1

value: WT


title: Female explanded blastocyst, rep3

description:
Library name: F2_1
F2_1


title: M0_DMEM_KO_2

description:
Library name: A39
A39_S10_R1_001.fastq.gz


title: Sorted GFP+CD34+ cells, shEZH2#2, Day 8, ADT, rep1

description: Library name: CITEseq_shEZH2#2-CB1_adt


title: Male explanded blastocyst, rep1

description:
Library name: M1_1
M1_1


title: M2_DMEM_wt_2

description:
Library name: A37
A37_S8_R1_001.fastq.gz


title: Female explanded blastocyst, rep1

description:
Library name: F1_1
F1_1


title: 501mel_CTRL_2

value: Non-treated


title: Female explanded blastocyst, rep2

description:
Library name: F1_2
F1_2


title: 501mel_CTRL_1

value: melanoma


title: Sorted GFP+CD34+ cells, shEZH2#1, Day 8, GEX, rep2

description: Library name: CITEseq_shEZH2#1-CB2_mRNA


title: BR_shSPANXB1_3

city: beijing

first: qi

last: wang

address: No. 10 Xitoutiao, Youanmenwai Street, Fengtai District

country: China

institute: capital medical university

data_processing:
RNA-Seq library preparation and sequencing were conducted in BGI Tech via BGISEQ-500 sequencer
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, and removing reads whose unknown base ('N' base) ratio is more than 5%.
Clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set.
The expression level of gene was measured in the normalized read count (FPKM).
Assembly: GRCh38.p12
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample.

growth_protocol: The BR-shCON cells and BR-shSPANXB1 cells was maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA from 231-BR and MDA-MB-231 cells was extracted using TRIzol reagent according to the manufacturer’s instructions.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB). DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform.

value: human breast cancer brain metastasis cells SPANXB1 knockdown


title: M2_DMEM_KO_1

description:
Library name: A36
A36_S7_R1_001.fastq.gz


title: BR_shSPANXB1_2


title: Sorted GFP+CD34+ cells, shEZH2#1, Day 8, ADT, rep1

description: Library name: CITEseq_shEZH2#1-CB1_adt


title: 501mel_HBSS_2


title: Sorted GFP+CD34+ cells, shEZH2#1, Day 8, GEX, rep1

description: Library name: CITEseq_shEZH2#1-CB1_mRNA


title: M2_CM_wt_1

description:
Library name: A34
A34_S5_R1_001.fastq.gz


title: M2_CM_KO_1

description:
Library name: A35
A35_S6_R1_001.fastq.gz


title: D_6_7, TP53 WT

city: Shanghai

first: Yiying

last: Xue

address: Siping road 1239

institute: Tongji University School of Life Sciences and Technology

description:
Library name: Sample 60
D_6_7

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: Text file includes gene TPM for each Sample

source_name: peripheral blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: peripheral blood

value: TP53 WT


title: BR_shCON_3

value: human breast cancer brain metastasis cells control knockdown


title: BR_shSPANXB1_1


title: LNCAP Prom + -9.5 kb CRISPRa

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 genome using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: HG19
Supplementary files format and content: hg19 aligned merged ATAC-seq of biological replicates

source_name: prostate cancer

growth_protocol: Cells were grown in CMRL1066 + 10% FBS using standard protocols

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion

value: prostate cancer

value: LNCAP

value: epithelial cell line

value: promoter + -9.5 kb CRISPRa


title: LNCAP Prom CRISPRa

value: promoter CRISPRa


title: D_6_5, TP53 WT

description:
Library name: Sample 59
D_6_5


title: LNCAP VPR NC

value: VPR (NC) CRISPRa


title: M0_CM_KO_1

description:
Library name: A33
A33_S4_R1_001.fastq.gz

value: TRAP1 KO

value: MPNST cells-derived conditioned medium


title: M0_CM_wt_1

description:
Library name: A32
A32_S3_R1_001.fastq.gz

value: wild-type


title: HEP Prom +-9.5 CRISPRa Rep2

source_name: epididymis

value: epididymis

value: HEP

value: promoter + -9.5kb CRISPRa


title: D_5_5, TP53 WT

description:
Library name: Sample 58
D_5_5


title: 501mel_CTRL_3

value: melanoma

value: WT

value: Non-treated


title: M0_DMEM_wt_2

description:
Library name: A38
A38_S9_R1_001.fastq.gz

value: control medium (DMEM)


title: Sorted GFP+CD34+ cells, shEZH2#1, Day 8, ADT, rep2

description: Library name: CITEseq_shEZH2#1-CB2_adt

value: hCD34+ HSPC

value: Lentivirus


title: HEP Prom +-9.5 CRISPRa Rep1


title: BR_shCON_1

value: human breast cancer brain metastasis cells control knockdown


title: HEP Prom CRISPRa Rep2

value: epithelial cell line


title: M0_DMEM_KO_1

description:
Library name: A31
A31_S2_R1_001.fastq.gz


title: IDBN-Blood channel, γ-ray, 16 Gy, rep3

city: Hefei

first: Jianhua

last: Qin

state: Anhui

address: No.96 JinZhai Road Baohe District

department: School of Biomedical engineering

institute: University of Science and Technology of China

data_processing:
STAR software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCh38_release110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: The endothelium of the brain

extract_protocol:
Total RNA was extracted from HBMECs and brain cells separately using TRizol reagent (Invitrogen)
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Brain

value: Human brain microvascular endothelial cell

value: Exposed to 16 Gy γ-rays


title: C_8_1, TP53 WT

description:
Library name: Sample 56
C_8_1

value: peripheral blood

value: TP53 WT


title: C_8_6, TP53 WT

description:
Library name: Sample 57
C_8_6


title: HEP Prom CRISPRa Rep1

value: promoter CRISPRa


title: C_7_6, TP53 WT

description:
Library name: Sample 55
C_7_6


title: KO NK cells, rep 3

city: Brisbane

first: Vikas

last: Duhan

state: QLD

address: 300 Herston Rd, Herston

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: tumorNK7

data_processing:
CutAdapt version 1.9, STAR version 2.5.2a, RSEM version 1.2.30
Assembly: Mus musculus GRCm38 assembly
Supplementary files format and content: Expected gene counts output by RSEM

source_name: Tumour bearing lung derived

extract_protocol:
Qiagen RNeasy Plus Micro Kit
NEB NEBNext Ultra II Directional RNA Library Prep Kit with poly(A) mRNA enrichment and RNA single indexes

value: Tumour bearing lung derived

value: NK cell

value: KO

value: Naive


title: KO NK cells, rep 4

description: Library name: tumorNK8


title: HEP VPR NC Rep2

value: epididymis

value: HEP

value: negative control VPR (NC)


title: HEP VPR NC Rep1


title: C_6_5, TP53 WT

description:
Library name: Sample 53
C_6_5


title: IDBN-Blood channel, γ-ray, 16 Gy, rep1

value: WT


title: KO NK cells, rep 2

description: Library name: tumorNK6


title: C_6_8, TP53 WT

description:
Library name: Sample 54
C_6_8


title: Abr-Blood channel, γ-ray, 16 Gy, rep2


title: HEP WT untransfected Rep2

value: WT untransfected


title: BR_shCON_2

value: human breast cancer brain metastasis cells control knockdown


title: HEP WT untransfected Rep1

value: epithelial cell line


title: C_4_1, TP53 WT

description:
Library name: Sample 52
C_4_1


title: KO NK cells, rep 1

description: Library name: tumorNK5


title: Abr-Blood channel, γ-ray, 16 Gy, rep1

value: Brain


title: WT NK cells, rep 4

description: Library name: tumorNK4


title: D-6

city: Hohhot

first: Xiaolin

last: Yang

address: No. 29, Erdosdong Road, Saihan District

institute: Inner Mongolia Agricultural University

description: replicate sample 6

data_processing:
Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.
Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs)
R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw_gene_counts_matrix
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Macrophage

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Macrophage

value: Bone marrow derived macrophages

value: Macrophage were pretreated with HQL-79 for 24 h and then infected with E. coli for 4 h


title: M0_DMEM_wt_1

description:
Library name: A30
A30_S1_R1_001.fastq.gz

value: wild-type

value: control medium (DMEM)


title: Blood channel, γ-ray, 16 Gy, rep3

value: Human brain microvascular endothelial cell

value: Exposed to 16 Gy γ-rays


title: C_1_5, TP53 WT

description:
Library name: Sample 51
C_1_5

value: peripheral blood

value: TP53 WT


title: IDBN-Blood channel, γ-ray, 16 Gy, rep2


title: B_9_4, TP53 WT

description:
Library name: Sample 50
B_9_4


title: B_8_4, TP53 WT

description:
Library name: Sample 49
B_8_4


title: Blood channel, γ-ray, 16 Gy, rep2


title: D-4

description: replicate sample 4


title: D-5

description: replicate sample 5


title: WT NK cells, rep 2

description: Library name: tumorNK2

value: Tumour bearing lung derived

value: NK cell

value: Naive


title: Abr-Blood channel, γ-ray, 16 Gy, rep3

value: WT


title: Blood channel, γ-ray, 16 Gy, rep1


title: B_7_5, TP53 WT

description:
Library name: Sample 48
B_7_5


title: D-3

description: replicate sample 3


title: Blood channel, Ctrl 0 Gy, rep3


title: KO NK cells, IL-15 treated, rep 4

description: Library name: IL15NK10

source_name: Spleen derived

value: Spleen derived

value: KO

value: IL-15 treated


title: Blood channel, Ctrl 0 Gy, rep2

value: Brain


title: B_6_5, TP53 WT

description:
Library name: Sample 47
B_6_5


title: WT NK cells, rep 1

description: Library name: tumorNK1


title: KO NK cells, IL-15 treated, rep 3

description: Library name: IL15NK8


title: D-1

description: replicate sample 1

value: Macrophage


title: Blood channel, Ctrl 0 Gy, rep1


title: KO NK cells, IL-15 treated, rep 2

description: Library name: IL15NK7


title: C-6

description: replicate sample 6

value: Bone marrow derived macrophages

value: Macrophage were pretreated with H-PGDS inhibitor 1 for 24 h and then infected with E. coli for 4 h


title: Brain channel, γ-ray, 16 Gy, rep3

source_name: Human Microglial Clone 3, Human Astrocytes, iPSCs-derived Pericytes

value: Glial cells, stem cells


title: WT NK cells, rep 3

description: Library name: tumorNK3


title: C-5

description: replicate sample 5


title: B_4_1, TP53 WT

description:
Library name: Sample 44
B_4_1


title: KO NK cells, IL-15 treated, rep 1

description: Library name: IL15NK6


title: Brain channel, γ-ray, 16 Gy, rep2


title: B_3_4, TP53 WT

description:
Library name: Sample 43
B_3_4


title: KO NK cells, naïve, rep 4

description: Library name: naiveNK9


title: KO NK cells, naïve, rep 3

description: Library name: naiveNK8


title: B_12_5, TP53 WT

description:
Library name: Sample 42
B_12_5


title: C-3

description: replicate sample 3


title: Brain channel, X-ray, 16 Gy, rep3


title: C-4

description: replicate sample 4


title: B_12_1, TP53 WT

description:
Library name: Sample 41
B_12_1


title: Brain channel, X-ray, 16 Gy, rep2


title: KO NK cells, naïve, rep 2

description: Library name: naiveNK7


title: B_10_7, TP53 WT

description:
Library name: Sample 40
B_10_7


title: C-2

description: replicate sample 2


title: C-1

description: replicate sample 1


title: KO NK cells, naïve, rep 1

description: Library name: naiveNK6


title: B_5_4, TP53 WT

description:
Library name: Sample 46
B_5_4


title: Brain channel, X-ray, 16 Gy, rep1


title: WT NK cells, IL-15 treated, rep 4

description: Library name: IL15NK4


title: B_4_6, TP53 WT

description:
Library name: Sample 45
B_4_6


title: D-2

description: replicate sample 2

value: Macrophage were pretreated with HQL-79 for 24 h and then infected with E. coli for 4 h


title: Brain channel, Ctrl 0 Gy, rep3

value: Recived no radiation exposure


title: A_9_5, TP53 WT

description:
Library name: Sample 39
A_9_5


title: WT NK cells, IL-15 treated, rep 3

description: Library name: IL15NK3


title: A_9_4, TP53 WT

description:
Library name: Sample 38
A_9_4


title: B-5

description: replicate sample 5

value: E. coli infection treatment


title: WT NK cells, IL-15 treated, rep 2

description: Library name: IL15NK2


title: B-4

description: replicate sample 4


title: A_8_4, TP53 WT

description:
Library name: Sample 37
A_8_4

value: peripheral blood


title: Brain channel, Ctrl 0 Gy, rep2


title: Brain channel, γ-ray, 16 Gy, rep1

value: Exposed to 16 Gy γ-rays


title: A_7_5, TP53 WT

description:
Library name: Sample 36
A_7_5

value: TP53 WT


title: Brain channel, Ctrl 0 Gy, rep1


title: WT NK cells, IL-15 treated, rep 1

description: Library name: IL15NK1

value: NK cell


title: B-3

description: replicate sample 3


title: B-2

description: replicate sample 2


title: A_7_1, TP53 WT

description:
Library name: Sample 35
A_7_1


title: WT NK cells, naïve, rep 4

description: Library name: naiveNK5

value: Naive


title: Blood channel, γ-ray, 16 Gy, rep2

value: Human brain microvascular endothelial cell

value: WT

value: Exposed to 16 Gy X-rays


title: A_6_8, TP53 WT

description:
Library name: Sample 34
A_6_8


title: B-6

description: replicate sample 6


title: B-1

description: replicate sample 1


title: A_6_1, TP53 WT

description:
Library name: Sample 33
A_6_1


title: Blood channel, γ-ray, 16 Gy, rep1


title: Blood channel, X-ray, 16 Gy, rep3


title: A_3_5, TP53 WT

description:
Library name: Sample 32
A_3_5


title: WT NK cells, naïve, rep 1

description: Library name: naiveNK1

value: Spleen derived


title: A-6

description: replicate sample 6

value: Uninfected


title: A-5

description: replicate sample 5

value: Macrophage


title: A_12_8, TP53 WT

description:
Library name: Sample 31
A_12_8


title: V_3_2

city: nanjing

first: qiu

last: zhong

address: No. 1 Weigang, Xuanwu District

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
Library name: sample 4
PEDV group, replicate biosample 2

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-separated values files and matrix files

organism: Sus scrofa

source_name: Jejunal mucosa

extract_protocol:
An appropriate number of cells were loaded into the flow channel of the SeekOne MM chip and allowed to settle into microwells by gravity. Unsettled cells were removed, and cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle into microwells under a magnetic field. Excess CBBs were rinsed away, and cells on the MM chip were lysed to release and capture RNA.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

treatment_protocol: To isolate intestinal mucosal cells, fresh intestinal mucosa was minced into small fragments. Tissue slices were then dissociated using a Multi-Tissue Dissociation Kit 2 (Miltenyi Biotec, Germany) according to the manufacturer’s instructions. After DNase treatment, fresh cells were washed twice in RPMI 1640 and resuspended at 1 × 10⁶ cells/mL in 1× phosphate-buffered saline (PBS) containing 0.04 % bovine serum albumin. Cell concentration and viability were assessed with trypan blue and a Countess automated cell counter (Thermo Fisher Scientific, Waltham, USA); only cells meeting viability criteria were used for downstream experiments.

value: Jejunal mucosa


title: A_11_8, TP53 WT

description:
Library name: Sample 30
A_11_8


title: WT NK cells, naïve, rep 2

description: Library name: naiveNK2


title: Blood channel, Ctrl 0 Gy, rep3

value: Brain


title: Blood channel, γ-ray, 16 Gy, rep3


title: A-3

description: replicate sample 3

value: Bone marrow derived macrophages


title: M_3_2

description:
Library name: sample 2
MOCK group, replicate biosample 2


title: Blood channel, X-ray, 16 Gy, rep1


title: A-4

description: replicate sample 4


title: A_10_8, TP53 WT

description:
Library name: Sample 29
A_10_8


title: WT NK cells, naïve, rep 3

description: Library name: naiveNK3


title: A-2

description: replicate sample 2


title: Blood channel, Ctrl 0 Gy, rep2


title: M_3_1

description:
Library name: sample 1
MOCK group, replicate biosample 1


title: C_6_4, TP53 MUT

description:
Library name: Sample 28
C_6_4

value: TP53 MUT


title: V_3_1

description:
Library name: sample 3
PEDV group, replicate biosample 1


title: A-1

description: replicate sample 1


title: Blood channel, Ctrl 0 Gy, rep1

value: Recived no radiation exposure


title: ChIP-Seq endometrial GD15_Input rep3

city: wuhan

first: yan

last: sun

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
ChIP-seq reads were alignedwere first aligned to the susScr11 genome using Bowtie2 version 2.3.5.1. The filtered BAM files were generated by removing low MAPQ reads (<25), unmapped reads, mate unmapped reads, not primary alignments, reads failing platform, and duplicates using SAMTools (version 1.9)
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks in both replicates were detected with MACS2 (version 2.1.2) with the following settings (macs2 callpeak -g genome.size -q 0.01 --nomodel --shift 0 --extsize n -B --SPMR)
Assembly: susScr11
Supplementary files format and content: summits_bed (except for Input sample)

source_name: endometrial tissues

extract_protocol:
Tissues were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using Sonics VCX130.
ChIP-seq libraries were prepared using the Next Ultra II DNA Library Prep Kit for Illumina. <10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 300-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: endometrial tissues

tag: time point

value: day 15

tag: chip antibody


title: C_5_4, TP53 MUT

description:
Library name: Sample 27
C_5_4

value: peripheral blood


title: Blood channel, X-ray, 16 Gy, rep2


title: Rapamycin treated and isolated ATMs_sample4

city: Leipzig

first: Raphaela

last: Wehr

state: Saxony

address: Liebigstraße

department: Institute of Anatomy

institute: Leipzig University

description:
Library name: RW_3R
Rapamycin treated sample

data_processing:
Results were then analyzed using the DESeq2 package on Galaxy2. Normalized counts were calculated and are presented vs. control (DMSO)
Assembly: DESeq2 package on Galaxy
Supplementary files format and content: processed data was savged as tabular format for each group

molecule: cytoplasmic RNA

source_name: adipose tissue macrophages

growth_protocol: Adipose tissue explants were cultivated for seven days. At day 7 SVF, which contains macrophages were isolated

extract_protocol:
RNA Isolation and purification was performed using the RNAeasy micro Kit by Qiagen
RNA sequencing and analysis was performed at Leipzig University’s Core Unit ‘DNA Technologien’. RNA extraction and library preparation was performed with a sequencing depth of 10 million reads/sample.

treatment_protocol: Adipose tissue was treated with Rapamycin 0.5 µM or Apilimod 0.5 µM or Lalistat 10 µM or DMSO-control 0.5%

value: adipose tissue macrophages

value: Csf1r-eGFP reporter mice  on a C57BL/6J background


title: C_2_5, TP53 MUT

description:
Library name: Sample 26
C_2_5


title: ChIP-Seq endometrial GD15_CEBP-β rep2

value: C/EBP-beta (Abcam, #ab32358)


title: B_8_5, TP53 MUT

description:
Library name: Sample 24
B_8_5


title: Liver - Male - CTRL_TN - Rep6

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 23 out of 28 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 38776 spots out of 62976 were selected.  The mean signal of the 13 first samples and 15 last ones were substracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33110 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All mice were housed on a 12 h light (ZT0-ZT12)/12 h dark (ZT12-ZT24) cycle.

extract_protocol: Total cellular RNA from liver was extracted with Trizol Reagent® (Molecular Research Center, Inc., Cincinnati, OH, USA).

treatment_protocol: Ctrl: Ctrl diet for 13 weeks; WD: Western diet for 13 weeks; RT = room temperature (22°C); TN= thermoneutrality (30°C).

value: Male

tag: age

value: 23 weeks

tag: diet

value: CTRL

tag: temperature

value: TN

tag: washbatch


title: Rapamycin treated and isolated ATMs_sample3

description:
Library name: RW_2R
Rapamycin treated sample

tag: cell type


title: B_5_8, TP53 MUT

description:
Library name: Sample 23
B_5_8

tag: tissue


title: DMSO treated and isolated ATMs_sample4

description:
Library name: RW_3D
DMSO control

tag: genotype


title: Apilimod treated and isolated ATMs_sample4

description:
Library name: RW_3A
Apilimod treated sample


title: ChIP-Seq endometrial GD15_CEBP-β rep3


title: ChIP-Seq endometrial GD15_CEBP-β rep1


title: Lalistat treated and isolated ATMs_sample3

description:
Library name: RW_2L
Lalistat treated sample


title: ChIP-Seq endometrial GD15_Input rep1


title: ChIP-Seq endometrial GD15_Input rep2


title: B_2_8, TP53 MUT

description:
Library name: Sample 21
B_2_8


title: C_1_1, TP53 MUT

description:
Library name: Sample 25
C_1_1


title: Lalistat treated and isolated ATMs_sample4

description:
Library name: RW_3L
Lalistat treated sample


title: ChIP-Seq endometrial GD12_CEBP-β rep3

value: day 12


title: B_3_5, TP53 MUT

description:
Library name: Sample 22
B_3_5


title: Apilimod treated and isolated ATMs_sample3

description:
Library name: RW_2A
Apilimod treated sample


title: ChIP-Seq endometrial GD12_Input  rep3


title: DMSO treated and isolated ATMs_sample3

description:
Library name: RW_2D
DMSO control


title: Liver - Male - WD_RT - Rep6

tag: Sex

value: WD

value: RT


title: Liver - Male - WD_TN - Rep3


title: Liver - Male - CTRL_RT - Rep3


title: Liver - Male - WD_TN - Rep1


title: Liver - Male - CTRL_RT - Rep1


title: B_1_5, TP53 MUT

description:
Library name: Sample 20
B_1_5


title: ChIP-Seq endometrial GD12_CEBP-β rep2


title: A_2_4, TP53 MUT

description:
Library name: Sample 18
A_2_4


title: Rapamycin treated and isolated ATMs_sample

description:
Library name: RW_1R
Rapamycin treated sample


title: Liver - Male - WD_RT - Rep1


title: A_12_1, TP53 MUT

description:
Library name: Sample 17
A_12_1


title: Lalistat treated and isolated ATMs_sample2

description:
Library name: RW_1L
Lalistat treated sample


title: ChIP-Seq endometrial GD12_Input  rep2


title: Apilimod treated and isolated ATMs_sample2

description:
Library name: RW_1A
Apilimod treated sample


title: B_11_8, TP53 MISS+MUT

description:
Library name: Sample 15
B_11_8

value: TP53 MISS+MUT


title: ChIP-Seq endometrial GD12_Input  rep1


title: Liver - Male - CTRL_TN - Rep2


title: A_2_7, TP53 MUT

description:
Library name: Sample 19
A_2_7


title: ChIP-Seq endometrial GD12_CEBP-β rep1


title: A_4_5, TP53 MISS+MUT

description:
Library name: Sample 14
A_4_5


title: Rapamycin treated and isolated ATMs_sample1

description:
Library name: RW_133R
Rapamycin treated sample


title: HCT116, Infection, Repeat 4

city: Xi'an

first: Hai

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

description: Library name: Infection_4

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12. Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: Colon

growth_protocol: HCT116 cells were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin–streptomycin. The cells were maintained at 37°C, 5% CO2 in a humidified atmosphere.

extract_protocol:
RNA was isolated from cells using RNeasy Plus mini kit (QIAGEN).
Library construction was performed using the Illumina platform according to the manufacturer’s instruction.

treatment_protocol: HCT116 cells are infected with oncolytic NDV Lasota strain at a MOI of 5.

value: Colon

tag: cell line

value: Colonic Carcinoma

tag: treatment


title: Lalistat treated and isolated ATMs_sample1

description:
Library name: RW_133L
Lalistat treated sample


title: Liver - Male - WD_TN - Rep7


title: Liver - Male - WD_TN - Rep6


title: Liver - Male - WD_RT - Rep3


title: Liver - Male - CTRL_TN - Rep4


title: Liver - Male - CTRL_RT - Rep5


title: B_2_1, TP53 MISS+MUT

description:
Library name: Sample 16
B_2_1


title: A_2_8, TP53 MISS+MUT

description:
Library name: Sample 13
A_2_8


title: Liver - Male - WD_RT - Rep5


title: HCT116, Infection, Repeat 2

description: Library name: Infection_2

value: infected with oncolytic NDV Lasota strain at a MOI of 5


title: A_10_4, TP53 MISS+MUT

description:
Library name: Sample 12
A_10_4


title: HCT116, Infection, Repeat 3

description: Library name: Infection_3


title: DMSO treated and isolated ATMs_sample1

description:
Library name: RW_133D
DMSO control


title: A_1_8, TP53 MISS+MUT

description:
Library name: Sample 11
A_1_8


title: HCT116, Control, Repeat 3

description: Library name: Control_3


title: HCT116, Control, Repeat 2

description: Library name: Control_2


title: HCT116, Infection, Repeat 1

description: Library name: Infection_1


title: Apilimod treated and isolated ATMs_sample1

description:
Library name: RW_133A
Apilimod treated sample


title: C_7_3, TP53 MISS

description:
Library name: Sample 10
C_7_3

value: TP53 MISS


title: C_5_5, TP53 MISS

description:
Library name: Sample 9
C_5_5


title: MuSCs, Aged, ISR-a, 2

city: San Francisco

first: Andrew

last: Brack

state: CA

address: 35 Medical Center Way

department: Orthopaedic Surgery

institute: UCSF

description:
Library name: Sample AGS2
10x Genomics

data_processing:
Fastq files were processed using the count function from CellRanger (version 5.0.1) .
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values and matrix files

source_name: hindlimb and forelimb

extract_protocol:
RNA seq profiling of murine muscle stem cells of adult (4 months) and aged (22 months) were isolated by Fluorescence-activated cell sorting (FACS). And plated on extracellular coated plates (ECM) in growth media ((F10 (Gibco), 20% fetal bovine serum (FBS) (Gibco), (5 ng/ml) FGF2 (R&D Systems)) for 18 hours in DMSO or in 10 µM of the the ISR activator (ISR-a Sal003 (activated). The activated cells were dissociated using cell dissociation buffer (Gibco), stained with propidium iodide and FACS sorted to remove dead cells and debris.
Live activated cells were transferred to the 10x Chromium System for library preparation and sequencing using Illumina NovaSeq.

value: hindlimb and forelimb

value: Muscle Stem Cells

value: 22 months


title: MuSCs, Aged, ISR-a 4

description:
Library name: Sample AGS4
10x Genomics


title: Liver - Male - CTRL_TN - Rep7


title: HCT116, Control, Repeat 4

description: Library name: Control_4


title: Liver - Male - CTRL_RT - Rep7


title: HCT116, Control, Repeat 1

description: Library name: Control_1


title: C_4_5, TP53 MISS

description:
Library name: Sample 8
C_4_5

value: peripheral blood


title: Liver - Male - CTRL_TN - Rep3


title: Liver - Male - CTRL_TN - Rep1