title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse150

city: Philadelphia

first: Yeqing

last: Chen

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description: Library name: EP_150_bulkRNAseq

data_processing:
Raw bulk RNA-seq data were aligned to the hg38 human reference genome using STAR and gene-level counts were extracted. For normalization, transcript per million (TPM) values were calculated using transcript length information obtained from GTF annotation files. Pathway-level expression dynamics were further quantified via single-sample gene set enrichment analysis (ssGSEA), using the GSVA package64.
Assembly: hg38
Supplementary files format and content: table

source_name: In-vivo PDX

growth_protocol: Barcoded WM4237-1 cells are cultured in TU2% media consisting of 80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4 mM CaCl2, and passaged using 0.05% trypsin-EDTA.  Barcoded WM4237-1 cells (5 × 10⁵ in 100 μL of a 1:1 mixture of RPMI and Matrigel [Corning]) were subcutaneously injected into the right flanks of 6–8-week-old male NSG mice. Tumor growth was monitored using calipers, and volumes were calculated using the formula (W² × L)/2.

extract_protocol:
Post-treatment WM4237-1 cells were trypsinized, washed, and processed with Dead Cell Removal Kit (Miltenyi Biotec) following manufacturer’s instructions. Tumor chunks from replicates were harvested and snap-frozen for bulk RNA-seq. Samples were lysed and homogenized in TRIzol reagent to release RNA.
Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 700 ng of total RNA and 10 cycles of final PCR amplification. Library size was assessed using the 4200 Tapestation and the High-Sensitivity DNA assay (Agilent, Santa Clara, CA). Concentration was determined using the Qubit Fluorometer 2.0 (Thermofisher, Waltham, MA). Next Generation Sequencing with a paired-end 2x150bp run length was done on the NovaSeq X platform (Illumina, San Diego, CA). A minimum of 30 M reads per sample was acquired for each sample.

treatment_protocol: Barcoded WM4237-1 cells were treated for one week with media containing 0.3 µM dabrafenib and 30 nM trametinib refreshed every two days. Once tumors reached approximately 500 mm³, mice were treated with a rodent diet supplemented with 150 mg/kg dabrafenib and 1.5 mg/kg trametinib (Bio-Serv, S7581). Tumors were harvested on days 0, 21, and 57 (n = 3 per time point), and on day 91 (n = 6).

value: In-vivo PDX

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: 240326 siCtrl PE1h M1

status: Public on Feb 18 2026

type: SRA

city: San Diego

first: Yuliang

last: Tan

state: CA

address: 9500 Gilman Dr.

country: USA

institute: UCSD

description:
Library name: Sample 3
H4K20me1

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
The sequencing reads were aligned to rn7 using Bowtie2 using very sensitive parameters.
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data.
CUT&RUN enriched region identification, and quality control were performed using Samtools and HOMER, as described in our previously published methods.Briefly, we created tag directories for each individual sample, allowing no more than 2 tags per base pair and the combined replicates of each treatment, and then normalized each directory to the total number of mapped tags, ensuring each directory contained 10 million tags. We next made peak calls with a very low threshold, as required for IDR (findPeaks -style histone -o auto), for the individual samples, combined replicates, individual pseudo-replicates, and combined pseudo-replicates.
We then applied the HOMER-IDR program to format the data for the IDR R package, determined the IDR threshold and identified the top peaks above that threshold.
Assembly: rn7
Supplementary files format and content: Bedgraph
Library strategy: CUT&Run

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Heart

growth_protocol: Six-week-old male Sprague–Dawley rats were anesthetized with Ketamine (45–90 mg/kg i.p.) and Xylazine (5–13 mg/kg i.p.). Hearts were extracted and perfused using a Langendorff system with calcium depletion perfusion buffer (mmol/L: 120 NaCl, 5.4 KCl, 1.2 NaH2PO4·7H2O, 20 NaHCO3, 1.6 MgCl2·6H2O, 5 taurine, 5.6 glucose, and 10 2,3-butanedione monoxime [BDM]), followed by type II collagenase digestion at 37 °C. The ventricular tissue was cut using sterilized scissors, and the cells were disassociated by pipetting and then filtered using 250 µm pore-size mesh. Ventricular myocytes were collected by centrifugation at 50 xg for 1 min. Myocytes were then washed and purified using perfusion buffer containing 0.1% fatty acid-free bovine serum albumin (BSA), 1 mmol/L ATP (pH 7.2), and 1 mmol/L glutamine with CaCl2 added gradually until reaching a Ca2+ concentration of 1.8 mmol/L. The purified myocytes were then resuspended in a defined Minimal Medium [Medium 199 (11150059, ThermoFisher, United States) supplemented with (mmol/L) 5 creatine, 2 l-carnitine, 5 taurine, 25 HEPES, 0.2% fatty acid-free BSA, 10 BDM and 1x insulin-transferrin-selenium (ITS) supplement] and seeded onto square cover slips (22 mm × 22 mm) coated with mouse laminin (10 μg/mL diluted in phosphate-buffered saline [PBS]) in 6-well plates (100,000 cells per well).

extract_protocol:
Ventricular myocytes were cultured in six well plates at 100,000 per well. Myocytes were treated with control or KMT5A siRNA as indicated for 48 hours and/or treated with phenylephrine (20 µmol/L) for 1 h before harvest. CUT&RUN was performed using the CUTANA™ CUT&RUN Kit (EpiCypher, 14-1048) and K-MetStat Panel (EpiCypher, 19-1002) according to the manufacturer’s instructions with minor modification.55 Cells were immobilized on concanavalin A coated magnetic beads (EpiCypher catalog no. 21-1401) and incubated overnight (4 °C with gentle rocking) with 1 µg antibody per sample. CUTANA pAG-MNase was then added to samples to cleave DNA selectively at antibody-bound chromatin.
10 ng genomic DNA was used to prepare sequencing libraries with the KAPA HTP/LTP Library Preparation Kits (Roche catalog no. 07961880001). Libraries were sequenced with NovaSeq 6000 system according to the manufacturer’s instructions. Paired-end fastq files were aligned to the rn7 reference genome using the Bowtie v.2 algorithm.

treatment_protocol: One hour after isolation, myocytes were washed with 2 mL medium, infected with adenovirus (multiplicity of infection = 10-200) or transfected with 25 nmol/L each of 4 pooled target-plus siRNA (Smartpool siRNA) or 100 nmol/L individual siRNAs using Dharmafect1 (Dharmacon, T-2001-01) overnight, and then cultured for another 24 hrs in Minimal Medium with or without phenylephrine (20 µmol/L) as indicated.

tag: tissue

value: Heart

tag: cell line

value: Ventricular myocytes

tag: cell type

value: Primary Cells

tag: genotype

value: prague Dawley rats

tag: treatment

value: siCtrl PE1h

tag: batch


title: mesc_rad21_depletion_IAA-3h_139, Smart-seq3

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

library_source: transcriptomic single cell

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryonic stem cell

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, KO C1 SETa, alpha 4h addback experiement 0h rep1

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

library_source: transcriptomic

data_processing:
Sequenced reads were aligned with STAR (v2.5.4b) using default parameters to the mouse genome and transcriptome from ENSEMBL (GRCm38.97)
Gene counts were obtained using featureCounts (Subread package v2.0.0) with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each gene in every sample

source_name: KH2 SET-KO pBS31-HA-SETa

growth_protocol: Mouse ESCs were cultured on MEF coated plates, in DMEM (Sigma) supplemented with 15% FBS (Biological Industries), L‐glutamine, 1X MEM non‐essential amino acids, Sodium Pyruvate, 1x Penstrep, 0.2 mM β-ME and LIF.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
500ng of RNA was used to generate libraries with QuantSeq 3’ mRNASeq Kit (Lexogen) according to the manufacturer's instructions.

value: KH2 SET-KO pBS31-HA-SETa

value: Embryonic Stem Cells

value: SET KO clone 1

value: no dox


title: mesc_rad21_depletion_IAA-3h_143, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_138, Smart-seq3


title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse146

description: Library name: EP_146_bulkRNAseq

molecule: total RNA

organism: Homo sapiens


title: 240326 Ctrl M1

description:
Library name: Sample 1
H4K20me1

value: siCtrl


title: ESC, WT SETa, alpha 4h addback experiement 1h rep1

value: WT

value: 1ug/ml doxycycline, 1h


title: mesc_rad21_depletion_IAA-3h_137, Smart-seq3


title: 240326 siSet8 PE1h M1

description:
Library name: Sample 4
H4K20me1

value: siSet8 PE1h


title: ESC, WT SETa, alpha 4h addback experiement 0h rep2


title: L4_D_CTRL

city: Paris

first: Adrien

last: Dufour

address: 48, boulevard serurier

country: France

institute: INSERM

description:
Library name: D_L4_S16
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mRatBN7.2 genome to gene expression count using Space Ranger default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger’s default settings
Assembly: mRatBN7.2/ RefSeq 108
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene Ids
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Tissue samples were collected from both EG and CT rats at five (D5), ten (D10), twenty (D20), and forty (D40) days post-SE. The rats were anesthetised with Euthasol prior to decapitation. Brains were then dissected and separated into two hemispheres. Immediately after dissection, the hemispheres were frozen in isopentane cooled on dry ice and stored at -80°C. The right hemisphere was used for spatial transcriptomic analysis. It was embedded in Optimal Cutting Temperature (OCT) medium and cryosectioned coronally. Sections were cut until the hippocampus was fully visible. The tissue was then trimmed with a razor blade until it fit into a 6 mm wide square, with the hippocampus at its centre. A 10 µm tissue section was placed on one capture area of a Visium Gene Expression Slide (10x Genomics), while 6 sections before and 6 after were placed on regular glass slides (3 sections per slide). The Visium slide was stored at -80°C until further processing, and the regular glass slides were stored at -20°C. Each Visium Gene Expression slide consists of 4 capture areas,
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides v1 & Reagent kit according to manufacturer’s construction

treatment_protocol: One day prior to SE induction, all animals received a subcutaneous injection of lithium following light anesthesia with isoflurane. The next day (D0), all rats were administered an initial intraperitoneal (i.p.) injection of atropine sulfate. Fifteen minutes later, EG rats received a second i.p. injection of pilocarpine hydrochloride, while CT rats were given NaCl. The NaCl volume was calculated to match the mean pilocarpine injection volume. If the initial pilocarpine dose failed to induce SE (defined as a seizure lasting more than 2 minutes), additional half-doses were administered every 20 minutes until SE was induced. SE was stopped after 2 hours with i.p. injections of diazepam and phenytoin. CT rats also received i.p. injections of diazepam and phenytoin 2 hours after the NaCl injection.

tag: strain

value: Wistar Hanover

tag: slide

tag: capture area

value: D

value: brain

tag: Stage

value: CTRL


title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse138

description: Library name: EP_138_bulkRNAseq

value: In-vivo PDX

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse144

description: Library name: EP_144_bulkRNAseq


title: 240326 siSet8 M1

description:
Library name: Sample 2
H4K20me1

value: Heart

value: Ventricular myocytes

value: Primary Cells

value: prague Dawley rats


title: mesc_rad21_depletion_IAA-3h_136, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: L3_D_CTRL

description:
Library name: D2_L3_S12
Fresh frozen Spatial transcriptome sequencing


title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse129

description: Library name: EP_129_bulkRNAseq


title: ESC, KO SETb, beta 24h addback experiment rep2

source_name: KH2 SET-KO pBS31-HA-SETb

value: KH2 SET-KO pBS31-HA-SETb

value: Embryonic Stem Cells

value: SET KO + SETb

value: 1ug/ml doxycycline, 24h


title: In-vivo Bulk RNAseq Day92 Dabrafenib/Trametinib treated Mouse127

description: Library name: EP_127_bulkRNAseq


title: mesc_rad21_depletion_IAA-3h_134, Smart-seq3


title: In-vivo Bulk RNAseq Day57 Dabrafenib/Trametinib treated Mouse149

description: Library name: D57_149_bulkRNAseq


title: mesc_rad21_depletion_IAA-3h_135, Smart-seq3


title: L2_D_CTRL

description:
Library name: D2_L2_S8
Fresh frozen Spatial transcriptome sequencing

value: Wistar Hanover

value: D


title: ESC, KO SETb, beta 24h addback experiment rep1


title: ESC, KO, beta 24h addback experiment rep3

value: SET KO

value: no dox


title: L1_D_CTRL

description:
Library name: D_L1_S4
Fresh frozen Spatial transcriptome sequencing

value: brain

value: CTRL


title: mesc_rad21_depletion_IAA-3h_133, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_132, Smart-seq3


title: L4_C_SE

description:
Library name: C_L4_S15
Fresh frozen Spatial transcriptome sequencing

value: C

value: SE


title: ESC, WT SETa, alpha 4h addback experiement 0h rep1

value: WT


title: L3_C_SE

description:
Library name: C_L3_S11
Fresh frozen Spatial transcriptome sequencing


title: In-vivo Bulk RNAseq Day57 Dabrafenib/Trametinib treated Mouse137

description: Library name: D57_137_bulkRNAseq

value: In-vivo PDX

value: Melanoma

value: BRAF V600E

value: Dabrafenib/Trametinib


title: ESC, KO, beta 24h addback experiment rep2

value: KH2 SET-KO pBS31-HA-SETb


title: mesc_rad21_depletion_IAA-3h_131, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, KO, beta 24h addback experiment rep1

value: Embryonic Stem Cells


title: In-vivo Bulk RNAseq Day21 Dabrafenib/Trametinib treated Mouse142

description: Library name: D21_142_bulkRNAseq


title: In-vivo Bulk RNAseq Day57 Dabrafenib/Trametinib treated Mouse141

description: Library name: D57_141_bulkRNAseq


title: ESC, KO SETa,alpha 24h addback experiement rep3

value: KH2 SET-KO pBS31-HA-SETa

value: SET KO + SETa

value: 1ug/ml doxycycline, 24h


title: In-vivo Bulk RNAseq Day21 Dabrafenib/Trametinib treated Mouse140

description: Library name: D21_140_bulkRNAseq


title: mesc_rad21_depletion_IAA-3h_129, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_130, Smart-seq3


title: L4_B_CTRL

description:
Library name: B_L4_S14
Fresh frozen Spatial transcriptome sequencing

value: Wistar Hanover

value: B


title: L1_C_SE

description:
Library name: C_L1_S3
Fresh frozen Spatial transcriptome sequencing

value: brain


title: In-vivo Bulk RNAseq Day21 Dabrafenib/Trametinib treated Mouse139

description: Library name: D21_139_bulkRNAseq


title: mesc_rad21_depletion_IAA-3h_128, Smart-seq3


title: ESC, KO SETa, alpha 24h addback experiement rep2


title: L3_B_CTRL

description:
Library name: B_L3_S10
Fresh frozen Spatial transcriptome sequencing

value: CTRL


title: ESC, KO SETa, alpha 24h addback experiement rep1


title: L2_C_SE

description:
Library name: C_L2_S7
Fresh frozen Spatial transcriptome sequencing

value: C

value: SE


title: In-vivo Bulk RNAseq Day0 Treatment naïve Mouse134

description: Library name: D0_134_bulkRNAseq

value: In-vivo PDX

value: Treatment naïve


title: ESC, KO, alpha 24h addback experiement rep3

value: SET KO

value: no dox


title: mesc_rad21_depletion_IAA-3h_126, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_127, Smart-seq3


title: L2_B_CTRL

description:
Library name: B_L2_S6
Fresh frozen Spatial transcriptome sequencing


title: L1_B_CTRL

description:
Library name: B_L1_S2
Fresh frozen Spatial transcriptome sequencing


title: In-vivo Bulk RNAseq Day0 Treatment naïve Mouse126

description: Library name: D0_126_bulkRNAseq

value: Melanoma

value: BRAF V600E


title: mesc_rad21_depletion_IAA-3h_125, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, WT SETb, beta 24h addback experiment rep3

source_name: KH2 pBS31-HA-SETb

value: KH2 pBS31-HA-SETb

value: Embryonic Stem Cells

value: WT


title: In-vitro Bulk RNAseq Dabrafenib/Trametinib treated

description: Library name: DT_bulkRNAseq

source_name: In-vitro cell line

value: In-vitro cell line

value: Dabrafenib/Trametinib


title: In-vivo Bulk RNAseq Day0 Treatment naïve Mouse130

description: Library name: D0_130_bulkRNAseq


title: ESC, KO, alpha 24h addback experiement rep2

value: KH2 SET-KO pBS31-HA-SETa


title: In-vitro Bulk RNAseq Treatment naïve

description: Library name: CTRL_bulkRNAseq


title: L4_A_SE

description:
Library name: A_L4_S13
Fresh frozen Spatial transcriptome sequencing

value: Wistar Hanover

value: A

value: brain


title: L3_A_SE

description:
Library name: A_L3_S9
Fresh frozen Spatial transcriptome sequencing

value: SE


title: mesc_rad21_depletion_IAA-3h_123, Smart-seq3


title: L2_A_SE

description:
Library name: A_L2_S5
Fresh frozen Spatial transcriptome sequencing


title: mesc_rad21_depletion_IAA-3h_124, Smart-seq3


title: ESC, KO, alpha 24h addback experiement rep1


title: ESC, WT SETb, beta 24h addback experiment rep1


title: ESC, WT SETa, alpha 24h addback experiment rep3

source_name: KH2 pBS31-HA-SETa

value: KH2 pBS31-HA-SETa


title: L1_A_SE

description:
Library name: A_L1_S1
Fresh frozen Spatial transcriptome sequencing


title: Bulk RNAseq Carbon copy

description: Library name: CC_bulkRNAseq

value: Treatment naïve


title: GJB2-mo_3

city: Fuzhou

first: Yao

state: Fujian

address: Fujian Provincial Maternity and Children's Hospital, 18Daoshan Road, Gulou District

department: Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect

institute: Fujian Maternity and Child Hospital, Fujian Medical University

description: Library name: sample6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or lowquality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by SOAPnuke (version 0.18 0).The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
An index of the reference genome was built, and paired-end clean reads were mapped to thereference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in areference-based approach. For each transcription region, a FPKM(fragment per kilobase oftranscript per million mapped reads)value was calculated to quantify its expressionabundance and variations, using RSEM software.
Assembly: GRCz11
Supplementary files format and content: GeneExp_count_fpkm_tpm_geneinfo.txt:  tab-delimited text file includes raw count, FPKM, and TPM values for each Sample

organism: Danio rerio

source_name: Larval fish

growth_protocol: The larval fish were reared at a temperature of 28±0.5℃, with a pH value between 7 and 8, under a light cycle of 14 hours of light and 10 hours of darkness.

extract_protocol:
Total RNA was extracted from tissues or cells using a standard extraction method. Subsequently, the RNA samples were subjected to stringent quality control, with RNA integrity and total quantity serving as the primary reference indicators ①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Zebrafish GJB2 gene knockdown was performed using MO technology.Morpholino antisense oligonucleotide was designed on the https://www.gene-tools.com/oligo-design-form website and injected into 1-cell stage AB wild-type zebrafish embryos. The GJB2-MO sequence: TAAAGTGCTCCCCAACTCATCCTGT.

value: Larval fish

value: GJB2 knockdown


title: Line 13, Heat Shock by 22 hours plus three days of recovery, biol rep 1

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

description:
L1303D1
Methods: Four weeks old-L13 plants exposed to 45C for 22 hours and three days recovery at 22C.

data_processing:
Raw data and quality control. The original raw data from Illumina were transformed to Sequenced Reads by base calling. Raw data were recorded in a FASTQ files. GC content distribution was evaluated. Raw reads were filtered to remove reads containing adapters or reads of low quality.
Assembly: 10
Supplementary files format and content: Processed data files are in the txt format with two columns, 1 - "Gene.id" (the identifier of the gene or gene feature) and 2 - A column with the same name than the sample which contains the read count for the corresponding feature.

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis thaliana plants, ecotype Columbia, were used for the generation of transgenic plants. A. thaliana seeds were germinated and grown following standard methodologies. Briefly, seeds were sterilized by rinsing once with 70% ethanol, for 2min and then in a 20% hypochlorite solution for 5min. They were washed thrice with sterile distilled de-ionized (dd) water and kept under-water for 48 h at 4ºC. Vernalized seeds were germinated on 100 × 15mm Petri dishes containing 0.1 × Murashige and Skoog (MS) media (Murashige and Skoog, 1962) prepared with 0.43 g/ L MS salts (Caisson laboratories, North Logan, UT, USA), plus 0.5% sucrose, 100 mg/ L myo-inositol and 1% agar (Research Organics Inc., Cleveland, OH, USA). The dishes were transferred to growth chambers maintained under controlled conditions of light (PAR of 60–80 μmol m−2 s−1), photoperiod (16 h light/8 h dark) and temperature (22 ± 1ºC). Plants were grown for 10 d post germination before transferal to 125mL plastic pots filled with 60 g of a soil mixture composed of three parts Sunshine Mix 618 3TM (Sun-Gro Horticulture), one part loam, two parts mulch, one part vermiculite (SunGro Horticulture) and one part perlite (Termolita S.A.) and fertilized with a 20:10:20 (N: P: K) + micronutrients solution (Peters Professional). Plants were subsequently cultivated in growth rooms conditioned at 22ºC 16 h light/ 8 h dark photo-period. The WT, L12, and L13 lines were used to perform the heat shock experiments during 1, 5 and 11 hours. Heat shock for 22h and recovery 1 and 3 days.

extract_protocol:
Total RNA Sample QC. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280). (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination. (3) Agilent 2100: checks RNA integrity.
Library Construction. After the QC procedures, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
Library QC and sequencing. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina NovaSeq 6000 machines for sequencing.

treatment_protocol: Heat Shock. Samples of leaves were collected at the time (1, 5, 11) hours and recovery (1 and 3) days.

value: Leaf

tag: line

value: Transgenic; overexpressing AhHAB4-PAI-1

value: Heat shock

tag: time

value: 22 hours and three days recovery at 22C


title: GJB2-mo_2

description: Library name: sample5


title: ESC, WT SETa, alpha 4h addback experiement 1h rep2

value: Embryonic Stem Cells

value: 1ug/ml doxycycline, 1h


title: mesc_rad21_depletion_IAA-3h_121, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, WT SETa, alpha 24h addback experiment rep2

value: WT

value: no dox


title: ESC, WT SETb, beta 24h addback experiment rep2

value: KH2 pBS31-HA-SETb


title: Line 13, Heat Shock by 22 hours plus one day of recovery, biol rep 2

description:
L1301D2
Methods: Four weeks old-L13 plants exposed to 45C for 22 hours and one day recovery at 22C.

value: 22 hours and one day recovery at 22C


title: mesc_rad21_depletion_IAA-3h_122, Smart-seq3


title: GJB2-mo_1

description: Library name: sample4


title: ESC, WT SETa, alpha 24h addback experiment rep1


title: Line 13, Heat Shock by 22 hours plus three days of recovery, biol rep 2

description:
L1303D2
Methods: Four weeks old-L13 plants exposed to 45C for 22 hours and three days recovery at 22C.


title: Line 13, Heat Shock by 22 hours plus one day of recovery, biol rep 1

description:
L1301D1
Methods: Four weeks old-L13 plants exposed to 45C for 22 hours and one day recovery at 22C.


title: mesc_rad21_depletion_IAA-3h_118, Smart-seq3


title: control_3

description: Library name: sample3


title: mesc_rad21_depletion_IAA-3h_119, Smart-seq3


title: control_2

description: Library name: sample2


title: ESC, SETb-HA, CHIP rep2

data_processing:
ChIP-seq analysis was performed following alignment of reads with bowtie2 to the GRCm38 (mm10) genome under default settings
SET-HA peaks were called with MACS2 (with significance cut-off p-value <=0.005).
Bigwig files were generated from aligned and sorted BAM files using bamCoverage (deeptools) (with -e 250 --normalizeUsing RPKM --smoothLength RPGC)
Bed files containing reproducible peaks (idr-threshohld < 0.05) from 2 replicates were generated with the IDR tool. ENCODE blacklisted regions were filtered out of final bed files.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeaks (for SET-HA ChIP-seq except knockout control samples), bed (for IDR-filtered peaks)

extract_protocol:
Following MEF depletion, 10 million  ESCs were harvested and crosslinked with 1% formaldehyde for 10 min and reaction was quenched with glycine.  DSG was added at a final concentration of 2 mM for 45 min at RT prior to addition of formaldehyde. Cells were lysed at 4°C for 10 minutes in lysis buffer 1 (50 mM HEPES-KOH 1 mM EDTA, 140 mM NaCl, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol) 10 min in lysis buffer 2 (1 m mM Tris-HCl, 1 mM EDTA, 200 mM NaCl and 0.5 mM EGTA), and 30 min in lysis buffer 3 (10 mM Tris-HCl, 1 mM EDTA, 100 mM NaCl, 0.5mM EGTA and 0.1% Na-DOC). All lysis buffers were supplemented with protease inhibitors. Sonication was performed with Bioruptor® (Diagenode) for 27 cycles (30s on, 30s off), or until average DNA fragment size ranged from 300-500bp. Average sizes of libraries were determined by TapeStation (Agilent Technologies, USA). Samples were then incubated overnight at 4°C with Magna ChIP™ protein A beads (Sigma-Aldrich) coupled with 3 μg of HA (ab9110, Abcam) or SUZ12 (ab12073, Abcam) antibody. The beads were washed twice at 4°C with ice-cold RIPA buffer (10 mM Tris-HCl, 1mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, and 0.1% Na-DOC) and once with RIPA-500 buffer (10 mMTris-HCl, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, and 0.1% Na-DOC), LiCl wash buffer (10mM Tris-HCl, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, and 0.5% Na-DOC), TE buffer (10 mM Tris-HCl and 1 mM EDTA), and eluted from the beads in direct elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl, and 0.5% SDS). The supernatant was reverse-crosslinked with RNase and 1U Proteinase K per sample for at least 4 h at 65°C. Reverse-crosslinked DNA was purified with AMPure XP SPRI beads (Beckman). Quantification of DNA concentration was performed with Qubit fluorometric quantitation (Thermo Fisher Scientific).
Library preparation was carried out as previously published (Blecher-Gonen et al., 2013). Libraries were amplified with a thermocycler using 12-13 cycles. Library DNA was purified with AMPure XP SPRI beads (Beckman). Quantification of DNA concentration was performed with Qubit fluorometric quantitation (Thermo Fisher Scientific).

tag: chip antibody

value: HA (abcam, ab9110)

value: SETb overexpression

value: 1ug/ml doxycycline, 24h

tag: crosslinking

value: double crosslinked with DSG


title: mesc_rad21_depletion_IAA-3h_117, Smart-seq3


title: ESC, SETb-HA, CHIP rep1


title: mesc_rad21_depletion_IAA-3h_120, Smart-seq3


title: control_1

description: Library name: sample1

value: Larval fish


title: mesc_rad21_depletion_IAA-3h_116, Smart-seq3


title: Line 13, Heat Shock by 11 hours, biol rep 2

description:
L1311H2
Methods: Four weeks old-L13 plants exposed to 45C for 11 hours.

value: Leaf

value: 11 hours


title: Line 13, Heat Shock by 11 hours, biol rep 1

description:
L1311H1
Methods: Four weeks old-L13 plants exposed to 45C for 11 hours.

value: Transgenic; overexpressing AhHAB4-PAI-1

value: Heat shock


title: ESC, SETa-HA, CHIP rep2

value: KH2 pBS31-HA-SETa

value: Embryonic Stem Cells

value: SETa overexpression


title: Line 13, Heat Shock by 5.5 hours, biol rep 2

description:
L1305H2
Methods: Four weeks old-L13 plants exposed to 45C for 5.5 hours.

value: 5.5 hours


title: mesc_rad21_depletion_IAA-3h_115, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: KAE213_rep2_t2

city: Ithaca

first: Heather

last: Feaga

state: NY

address: 123 Wing Dr

institute: Cornell University

description:
Library name: 11
213_2_t2_S107

data_processing:
Mapped to genome (NC_000964.3) with Bowtie2 (2.5.1)
Read counts quantified with FeatureCounts.
Assembly: NC_000964.3
Supplementary files format and content: Count matrix for all samples.

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: S7 media

extract_protocol:
Cells harvested on frozen sodium azide. Washed with TE/NaCl. RNA extracted by treating with (1) acidic phenol, chloroform, SDS, (2) acid phenol, (3) acidic phenol, chloroform, (4) ethanol and LiCl. Precipitated RNA was resuspended in water.
Dnase treated (Invitrogen DNAse), Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp unique dual indices.

treatment_protocol: pre, 2 minutes post-, and 5 minutes post-rifampicin treatment (150 µg/mL).

value: bacterial

value: 168 trpC2 dsasBdsasA nahA(E49Q,E53Q) drel::kan

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 2, 2 minutes post-rifampicin treatment


title: Line 13, Heat Shock by 5.5 hours, biol rep 1

description:
L1305H1
Methods: Four weeks old-L13 plants exposed to 45C for 5.5 hours.


title: ESC, SET-KO, HA CHIP rep 2

value: HA (abcam, ab9110)

value: KH2 SET-KO pBS31-HA-SETb

value: SET KO

value: no dox


title: mesc_rad21_depletion_IAA-3h_114, Smart-seq3


title: ESC, SETa-HA, CHIP rep1

value: 1ug/ml doxycycline, 24h

value: double crosslinked with DSG


title: KAE213_rep1_t5

description:
Library name: 9
213_1_t5_S102

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 1, 5 minutes post-rifampicin treatment


title: mesc_rad21_depletion_IAA-3h_113, Smart-seq3


title: Line 13, Heat Shock by 1 hour, biol rep 2

description:
L1301H2
Methods: Four weeks old-L13 plants exposed to 45C for 1 hour.

value: Leaf

value: Transgenic; overexpressing AhHAB4-PAI-1

value: Heat shock

value: 1 hour


title: KAE213_rep2_t0

description:
Library name: 10
213_2_t0_S106

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 2, pre-rifampicin treatment


title: ESC, SET-KO SETb-HA, HA CHIP rep2

value: Embryonic Stem Cells

value: SET KO SETb addback


title: mesc_rad21_depletion_IAA-3h_112, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: ESC, SET-KO SETb-HA, HA CHIP rep1


title: KAE213_rep1_t2

description:
Library name: 8
213_1_t2_S101

value: bacterial

value: 168 trpC2 dsasBdsasA nahA(E49Q,E53Q) drel::kan

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 1, 2 minutes post-rifampicin treatment


title: Line 12, Heat Shock by 22 hours plus three days of recovery, biol rep 1

description:
L1203D1
Methods: Four weeks old-L12 plants exposed to 45C for 22 hours and three days recovery at 22C.

value: Transgenic; overexpressing Ah2880

value: 22 hours and three days recovery at 22C


title: mesc_rad21_depletion_IAA-3h_110, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_111, Smart-seq3


title: ESC, SET-KO, HA CHIP rep 1

value: HA (abcam, ab9110)

value: KH2 SET-KO pBS31-HA-SETa

value: SET KO

value: no dox


title: KAE55_rep2_t5

description:
Library name: 6
55_2_t5_S105

value: 168 trpC2 dsasBdsasAdrel::kan

value: (p)ppGpp0 mutant (KAE55), replicate 2, 5 minutes post-rifampicin treatment


title: Line 12, Heat Shock by 22 hours plus three days of recovery, biol rep 2

description:
L1203D2
Methods: Four weeks old-L12 plants exposed to 45C for 22 hours and three days recovery at 22C.

value: Leaf

value: Heat shock


title: ESC, SET-KO SETa-HA, HA CHIP rep2

value: Embryonic Stem Cells

value: SET KO SETa addback

value: 1ug/ml doxycycline, 24h

value: double crosslinked with DSG


title: Line 13, Heat Shock by 1 hour, biol rep 1

description:
L1301H1
Methods: Four weeks old-L13 plants exposed to 45C for 1 hour.

value: Transgenic; overexpressing AhHAB4-PAI-1

value: 1 hour


title: mesc_rad21_depletion_IAA-3h_109, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: Line WT, Heat Shock by 22 hours plus three days of recovery, biol rep 2

description:
WT03D2
Methods: Four weeks old-WT plants exposed to 45C for 22 hours and three days recovery at 22C.

value: WT

value: Wild Type

value: 22 hours and three days recovery at 22C


title: KAE213_rep1_t0

description:
Library name: 7
213_1_t0_S100

value: bacterial

value: 168 trpC2 dsasBdsasA nahA(E49Q,E53Q) drel::kan

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 1, pre-rifampicin treatment


title: ESC, SET-KO SETa-HA, HA CHIP rep1

value: HA (abcam, ab9110)

value: KH2 SET-KO pBS31-HA-SETa


title: KAE55_rep2_t2

description:
Library name: 5
55_2_t2_S104

value: 168 trpC2 dsasBdsasAdrel::kan

value: (p)ppGpp0 mutant (KAE55), replicate 2, 2 minutes post-rifampicin treatment


title: Line 12, Heat Shock by 22 hours plus one day of recovery, biol rep 2

description:
L1201D2
Methods: Four weeks old-L12 plants exposed to 45C for 22 hours and one day recovery at 22C.

value: Leaf

value: Transgenic; overexpressing Ah2880

value: Heat shock

value: 22 hours and one day recovery at 22C


title: mesc_rad21_depletion_IAA-3h_108, Smart-seq3


title: TRF2_HFLF_DOX_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Library name: Sample 6

data_processing:
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.10a with the GENCODE (release 36, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.2 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files incude count values and TPM for each sample.

source_name: HFLFs

growth_protocol: Lung progenitor cells were derived from iPSCs and CPM-high lung progenitor cells were cocultured with HFLFs in organoids to promote induction of alveolar organoids. The alveolar organoids were maintained in DCIK medium. DCIK medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin.

extract_protocol:
RNA was extracted using RNeasy micro (Qiagen).
Library preparation was performed using an Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Cat# 20040525, Illumina) according to the manufacturer’s instructions. The constructed libraries were sequenced on an Illumina NextSeq 2000 with the paired-end mode.

treatment_protocol: Alveolar organoids were treated with DOX from Day9 to Day17, with compounds added during the final 3 days of the treatment.

value: HFLFs

value: Human fetal lung fibroblasts

value: DOX


title: Line WT, Heat Shock by 22 hours plus three days of recovery, biol rep 1

description:
WT03D1
Methods: Four weeks old-WT plants exposed to 45C for 22 hours and three days recovery at 22C.

value: WT


title: KAE55_rep2_t0

description:
Library name: 4
55_2_t0_S103

value: (p)ppGpp0 mutant (KAE55), replicate 2, pre-rifampicin treatment


title: mesc_rad21_depletion_IAA-3h_107, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_106, Smart-seq3


title: TRF2_HFLF_DOX_1

description: Library name: Sample 4


title: KAE55_rep1_t2

description:
Library name: 2
55_1_t2_S98

value: bacterial

value: (p)ppGpp0 mutant (KAE55), replicate 1, 2 minutes post-rifampicin treatment


title: KAE55_rep1_t0

description:
Library name: 1
55_1_t0_S97

value: (p)ppGpp0 mutant (KAE55), replicate 1, pre-rifampicin treatment


title: TRF2_HFLF_3

description: Library name: Sample 3

value: PBS


title: Line 12, Heat Shock by 22 hours plus one day of recovery, biol rep 1

description:
L1201D1
Methods: Four weeks old-L12 plants exposed to 45C for 22 hours and one day recovery at 22C.


title: TRF2_HFLF_DOX_2

description: Library name: Sample 5


title: Line WT, Heat Shock by 22 hours plus one day of recovery, biol rep 2

description:
WT01D2
Methods: Four weeks old-WT plants exposed to 45C for 22 hours and one day recovery at 22C.

value: Wild Type


title: (p)ppGpp_rep2_t20

description:
Library name: 12
KAE74_rep2_20min_S88

extract_protocol:
Cell lysis, Trizol chloroform extraction of RNA, isopropoanol precipitation, ethanol wash, resuspension in water.
Dnase treated (Invitrogen DNAse), Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp unique dual indices.

treatment_protocol: genetic induction of pGpp or (p)ppGpp

value: 168 trpC2 dsasBdsasAdnahA amyE::Pxyl-sasA drel::kan

value: (p)ppGpp inducible strain (KAE74), replicate 2, 20 minutes post-induction


title: mesc_rad21_depletion_IAA-3h_104, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-3h_105, Smart-seq3


title: KAE55_rep1_t5

description:
Library name: 3
55_1_t5_S99

value: 168 trpC2 dsasBdsasAdrel::kan

value: (p)ppGpp0 mutant (KAE55), replicate 1, 5 minutes post-rifampicin treatment


title: Line WT, Heat Shock by 22 hours plus one day of recovery, biol rep 1

description:
WT01D1
Methods: Four weeks old-WT plants exposed to 45C for 22 hours and one day recovery at 22C.

value: Leaf

value: Heat shock

value: 22 hours and one day recovery at 22C


title: mesc_rad21_depletion_IAA-3h_103, Smart-seq3


title: Line 12, Heat Shock by 11 hours, biol rep 2

description:
L1211H2
Methods: Four weeks old-L12 plants exposed to 45C for 11 hours.

value: Transgenic; overexpressing Ah2880

value: 11 hours


title: TRF2_HFLF_1

description: Library name: Sample 1

value: HFLFs

value: Human fetal lung fibroblasts


title: (p)ppGpp_rep2_t10

description:
Library name: 11
KAE74_rep2_10min_S87

value: (p)ppGpp inducible strain (KAE74), replicate 2, 10 minutes post-induction


title: TRF2_Epithelial_DOX_CBP30_3

description: Library name: Sample 6

extract_protocol:
RNA was extracted using RNeasy micro (Qiagen).
Library preparation was performed using an Illumina Stranded mRNA Prep Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions. The constructed libraries were sequenced on an Illumina NextSeq 2000 with the paired-end mode.

value: iPSC-derived alveolar epithelial cells


title: (p)ppGpp_rep2_t0

description:
Library name: 10
KAE74_rep2_0min_S86

value: bacterial

value: (p)ppGpp inducible strain (KAE74), replicate 2, pre-induction


title: TRF2_HFLF_2

description: Library name: Sample 2

value: PBS


title: Line 12, Heat Shock by 11 hours, biol rep 1

description:
L1211H1
Methods: Four weeks old-L12 plants exposed to 45C for 11 hours.


title: mesc_rad21_depletion_IAA-3h_102, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_101, Smart-seq3


title: (p)ppGpp_rep1_t20

description:
Library name: 9
KAE74_rep1_20min_S85

value: 168 trpC2 dsasBdsasAdnahA amyE::Pxyl-sasA drel::kan

value: (p)ppGpp inducible strain (KAE74), replicate 1, 20 minutes post-induction


title: Line WT, Heat Shock by 11 hours, biol rep 2

description:
WT11H2
Methods: Four weeks old-WT plants exposed to 45C for 11 hours.

value: WT

value: Wild Type


title: TRF2_Epithelial_DOX_CBP30_2

description: Library name: Sample 5


title: Line WT, Heat Shock by 11 hours, biol rep 1

description:
WT11H1
Methods: Four weeks old-WT plants exposed to 45C for 11 hours.

value: Leaf

value: Heat shock


title: (p)ppGpp_rep1_t10

description:
Library name: 8
KAE74_rep1_10min_S84

value: (p)ppGpp inducible strain (KAE74), replicate 1, 10 minutes post-induction


title: Line 12, Heat Shock by 5.5 hours, biol rep 1

description:
L1205H1
Methods: Four weeks old-L12 plants exposed to 45C for 5.5 hours.

value: Transgenic; overexpressing Ah2880

value: 5.5 hours


title: TRF2_Epithelial_DOX_3

description: Library name: Sample 3

value: DOX


title: TRF2_Epithelial_DOX_CBP30_1

description: Library name: Sample 4


title: (p)ppGpp_rep1_t0

description:
Library name: 7
KAE74_rep1_0min_S83

value: (p)ppGpp inducible strain (KAE74), replicate 1, pre-induction


title: mesc_rad21_depletion_IAA-3h_099, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_100, Smart-seq3


title: KAE213_rep2_t5

description:
Library name: 12
213_2_t5_S108

value: 168 trpC2 dsasBdsasA nahA(E49Q,E53Q) drel::kan

value: (p)ppGpp0 nahA(E49Q,E53Q) mutant (KAE213), replicate 2, 5 minutes post-rifampicin treatment


title: Line 12, Heat Shock by 5.5 hours, biol rep 2

description:
L1205H2
Methods: Four weeks old-L12 plants exposed to 45C for 5.5 hours.


title: mesc_rad21_depletion_IAA-3h_098, Smart-seq3


title: TRF2_Epithelial_DOX_2

description: Library name: Sample 2

value: iPSC-derived alveolar epithelial cells


title: pGpp_rep2_t20

description:
Library name: 6
KAE60_rep2_20min_S82

value: bacterial

value: 168 trpC2 dsasBdsasA amyE::Pxyl-sasA drel::kan

value: pGpp inducible strain (KAE60), replicate 2, 20 minutes post-induction


title: mesc_rad21_depletion_IAA-3h_096, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: Line WT, Heat Shock by 5.5 hours, biol rep 2

description:
WT05H2
Methods: Four weeks old-WT plants exposed to 45C for 5.5 hours.

value: WT


title: TRF2_Epithelial_DOX_1

description: Library name: Sample 1


title: mesc_rad21_depletion_IAA-3h_097, Smart-seq3


title: pGpp_rep2_t0

description:
Library name: 4
KAE60_rep2_0min_S80

value: pGpp inducible strain (KAE60), replicate 2, pre-induction


title: pGpp_rep2_t10

description:
Library name: 5
KAE60_rep2_10min_S81

value: pGpp inducible strain (KAE60), replicate 2, 10 minutes post-induction


title: Line 12, Heat Shock by 1 hour, biol rep 2

description:
L1201H2
Methods: Four weeks old-L12 plants exposed to 45C for 1 hour.

value: Leaf

value: Heat shock

value: 1 hour


title: mesc_rad21_depletion_IAA-3h_095, Smart-seq3


title: HFLF_BLM_GNE781_2

description: Library name: Sample 8

data_processing:
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 32, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files incude count values and TPM for each sample.

growth_protocol: Lung progenitor cells were derived from iPSCs and CPM+ lung progenitor cells were cocultured with HFLFs in organoids to promote induction of alveolar organoids. Then, SPC+ alveolar type 2 cells were isolated and passaged in alveolar organoids cocultured with HFLFs. The alveolar organoids were maintained in DCIK medium. DCIK medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin.

treatment_protocol: Alveolar organoids were treated with DMSO or BLM from Day11 to Day14, followed by the removal of BLM and a 3-day incubation with or without compounds.

value: HFLFs

value: Human fetal lung fibroblasts


title: Line 12, Heat Shock by 1 hour, biol rep 1

description:
L1201H1
Methods: Four weeks old-L12 plants exposed to 45C for 1 hour.

value: Transgenic; overexpressing Ah2880


title: pGpp_rep1_t20

description:
Library name: 3
KAE60_rep1_20min_S79

value: pGpp inducible strain (KAE60), replicate 1, 20 minutes post-induction


title: Line WT, Heat Shock by 5.5 hours, biol rep 1

description:
WT05H1
Methods: Four weeks old-WT plants exposed to 45C for 5.5 hours.

value: Wild Type

value: 5.5 hours


title: mesc_rad21_depletion_IAA-3h_094, Smart-seq3


title: HFLF_BLM_GNE781_1

description: Library name: Sample 7


title: mesc_rad21_depletion_IAA-3h_093, Smart-seq3


title: HFLF_BLM_CBP30_3

description: Library name: Sample 6


title: rectus femoris, 12d after operation, patient 4, rep2

city: Puschino

first: Kirill

middle: S

last: Krasnov

state: Moscow region

address: institutskay 3

country: Russia

institute: ITEB RAS

description:
Library name: barcode71
column name in raw_counts_all_samples.csv: barcode71

data_processing:
The quality of raw sequencing data was assessed using NanoPlot software (v. 1.43.0; https://github.com/wdecoster/NanoPlot). Basecalling and adapter sequence removal were performed with dorado software (v. 0.8.3; https://github.com/nanoporetech/dorado). For alignment and annotation of sequencing data, we used the human reference genome assembly and annotation file from the Ensembl database (version 113, GRCh38.p14; https://www.ensembl.org/Homo_sapiens/Info/Index). The reference genome was indexed using minimap2 (v. 2.28; https://github.com/lh3/minimap2/?tab=readme-ov-file#map-long-splice), followed by read counting with featureCounts from the subread package (v. 2.0.8; https://github.com/ShiLab-Bioinformatics/subread). Differential gene expression analysis was conducted using DESeq2 software (v. 1.38.3) in the R programming language (v. 4.2.2).
Assembly: GRCh38.p14 (Ensembl v.113)
Supplementary files format and content: csv file includes raw counts for each sample

source_name: rectus femoris

extract_protocol:
RNA was extracted from frozen tissue samples (~30mg) using the HiPure Viral RNA Kit (Magen, China). RNA concentration was quantified using a fluorometer (Qubit 4.0; Thermo Fisher Scientific). Complementary DNA (cDNA) synthesis was performed using previously isolated mRNA and the Mint kit (Evrogen, Russia). The procedure fol-lowed the manufacturer’s protocol, including the addition of IP solution to enhance synthesis efficiency. Subsequently, the synthesized cDNA was amplified using the Encyclo Plus PCR Kit (Evrogen, Russia) with universal primers. To verify amplification success, the resulting products were visualized via horizontal agarose gel electrophoresis.
For library preparation, 200 ng of cDNA from each sample was used. Sequencing libraries were constructed from the obtained amplicons using the Ligation Sequencing Kit (SQK LSK109, Oxford Nanopore Technologies, UK), following the manufacturer’s pro-tocols. During the DNA end preparation step, End Prep Mix was added to the samples. The mixture was thoroughly mixed by pipetting, and droplets on the tube walls were removed via brief centrifugation. The reaction was carried out in a thermal cycler. After incubation, the mixture was purified using magnetic beads (VAHTS DNA Clean Beads, Vazyme, China). The DNA was eluted in 10 µL of Milli Q water, and its concentration was measured using a Qubit 4 fluorometer (Thermo Fisher Scientific, USA) with the QuDye HS Assay Kit (Lumiprobe, Russia). cDNA libraries were multiplexed for sequencing via native barcoding using the PCR Barcoding Expansion 1–96 kit (EXP PBC096, Oxford Nanopore Technologies, UK), according to the manufacturer’s protocol. Samples were purified with VAHTS DNA Clean Beads (Vazyme, China). The concentration of the pooled samples was measured on the Qubit 4. Following ligation, the mixture was cleaned with magnetic beads, washed with SFB (by removing from the magnet and resuspending the beads), and eluted in EB buffer. The final library concentration was verified using the Qubit 4, after which the library was loaded onto the sequencing flow cell.

value: rectus femoris

tag: condition

value: 12 days

value: experiment

tag: Sex

value: female

tag: patient no


title: HFLF_BLM_GNE781_3

description: Library name: Sample 9


title: pGpp_rep1_t0

description:
Library name: 1
KAE60_rep1_0min_S77

value: bacterial

value: 168 trpC2 dsasBdsasA amyE::Pxyl-sasA drel::kan

value: pGpp inducible strain (KAE60), replicate 1, pre-induction


title: rectus femoris, 12d after operation, patient 4, rep3

description:
Library name: barcode72
column name in raw_counts_all_samples.csv: barcode72

tag: tissue


title: rectus femoris, 12d after operation, patient 4, rep1

description:
Library name: barcode70
column name in raw_counts_all_samples.csv: barcode70


title: Psoriasis_3_LS_164

type: RNA

city: Aarhus N

first: Thomas

last: Emmanuel

state: Midtjylland

address: Palle Juul Jensens Boulevard 99

department: Dermatology

country: Denmark

institute: Aarhus University

hyb_protocol: Following RNA readout, tissues were incubated for 2 h with a cocktail of four fluorophore-conjugated antibodies (DNA, PanCK, CD45, CD68 and a general membrane stain) within the CosMx SMI instrument. After washing away unbound antibodies and DAPI with Reporter Wash Buffer, Imaging Buffer was added, and nine Z-stack images were acquired across the five channels (four antibodies plus DAPI).

scan_protocol: Image processing and feature extraction were performed using the Nanostring analysis pipeline, which first identifies the XYZ coordinates of individual transcripts. Following image registration, feature detection, and localisation, Z-stack images of nuclear and membrane markers were used to define cell boundaries through a machine-learning–based segmentation algorithm. These segmentation boundaries enabled assignment of transcripts to individual cells and subcellular compartments, resulting in the generation of a cell-by-gene count matrix. The pipeline outputs included the cell-by-gene matrix, cell segmentation polygons, and associated cell metadata.

data_processing: Processed files were combined into a seurat object; standard workflow for CosMx data, reflecting the output generated by the AtomX cloud. The processed files uploaded also allow for manual creation of the Seurat object in RStudio, if required.

source_name: skin

label_protocol: RNA target readout on the CosMx SMI instrument was performed according to the manufacturer’s workflow. Briefly, the assembled flow cell was loaded onto the instrument, and Reporter Wash Buffer was introduced to remove air bubbles. A preview scan of the full flow cell was acquired, and 9-12 fields of view (FOVs) were positioned on each TMA to correspond to regions of interest identified on an H&E-stained adjacent serial section. RNA readout commenced by introducing 100 μl of Reporter Pool 1 into the flow cell, followed by a 15-min incubation. Unbound reporter probes were removed by washing with 1 mL Reporter Wash Buffer, after which Imaging Buffer was added. For each FoV, nine Z-stack images (0.8 μm step size) were captured. Fluorophores were then photocleaved by UV exposure and removed with Strip Wash Buffer. This fluidic and imaging cycle was performed sequentially for all 16 reporter pools, and the complete 16-cycle hybridization–imaging process was repeated multiple times to enhance RNA detection sensitivity.

extract_protocol: Formalin fixed paraffin embedded tissue tissue microarray cores with a diameter of 1.5 mm were cut in 5 μm thick sections were using a microtome. Slides were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH),  deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes. In situ hybridization was performed according to the manufacturer’s instructions (User Manual: Slide Preparation for RNA Assays, NanoString).

value: skin

tag: lesional/nonlesional

value: LS

tag: characteristics

tag: patient id

tag: age

value: Male

tag: fields of view (fov)


title: Line WT, Heat Shock by 1 hour, biol rep 1

description:
WT01H1
Methods: Four weeks old-WT plants exposed to 45C for 1 hour.

value: Leaf

value: WT

tag: genotype

tag: treatment

value: Heat shock

value: 1 hour


title: HFLF_BLM_3

description: Library name: Sample 3

tag: cell line

value: HFLFs

tag: cell type

value: Human fetal lung fibroblasts

value: BLM


title: Psoriasis_3_LS_165


title: HFLF_BLM_CBP30_2

description: Library name: Sample 5


title: Psoriasis_3_LS_162


title: mesc_rad21_depletion_IAA-3h_092, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: rectus femoris, 1d after operation, patient 4, rep2

description:
Library name: barcode68
column name in raw_counts_all_samples.csv: barcode68

value: rectus femoris

value: 1 day

value: experiment


title: HFLF_BLM_CBP30_1

description: Library name: Sample 4


title: Line WT, Heat Shock by 1 hour, biol rep 2

description:
WT01H2
Methods: Four weeks old-WT plants exposed to 45C for 1 hour.

tag: line

value: Wild Type


title: mesc_rad21_depletion_IAA-3h_090, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-3h_091, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_089, Smart-seq3


title: Psoriasis_3_LS_166


title: HFLF_BLM_2

description: Library name: Sample 2


title: mesc_rad21_depletion_IAA-3h_086, Smart-seq3


title: Psoriasis_3_LS_163


title: Psoriasis_3_LS_160


title: mesc_rad21_depletion_IAA-3h_085, Smart-seq3


title: rectus femoris, 1d after operation, patient 6, rep3

description:
Library name: barcode66
column name in raw_counts_all_samples.csv: barcode66

value: control

value: female


title: rectus femoris, 1d after operation, patient 4, rep3

description:
Library name: barcode69
column name in raw_counts_all_samples.csv: barcode69


title: mesc_rad21_depletion_IAA-3h_088, Smart-seq3


title: HFLF_BLM_1

description: Library name: Sample 1


title: SPC_Epithelial_BLM_CBP30_3

description: Library name: Sample 6

growth_protocol: Lung progenitor cells were derived from iPSCs and subsequently cocultured with HFLFs to promote the generation of SPC+ cells. SPC+ cell-derived alveolar organoids were further passaged and maintained in DCIK medium. DCIK medium: Ham's F12 (Fujifilm Wako, 087-08335) containing 50 nM dexamethasone, 100 μM 8-Br-cAMP, 100 μM 3-isobutyl-1-methylxanthine, 10 ng/mL KGF, 1% B-27 supplement, 0.25% BSA (Thermo Fisher Scientific, 15260-037), 15 mM HEPES (Thermo Fisher Scientific, 17557-94), 0.8 mM CaCl2, 0.1% ITS premix (Corning), and 50 U/mL Penicillin/Streptomycin.

treatment_protocol: Alveolar organoids were treated with DMSO or BLM from day 11 to day14, followed by the removal of BLM and an additional 3-day incubation with or without compounds.

value: iPSC-derived alveolar epithelial cells


title: mesc_rad21_depletion_IAA-3h_087, Smart-seq3


title: SPC_Epithelial_BLM_GNE781_3

description: Library name: Sample 9


title: Psoriasis_3_LS_161

value: skin

value: LS

value: Male


title: Psoriasis_3_LS_159


title: SPC_Epithelial_BLM_GNE781_1

description: Library name: Sample 7


title: rectus femoris, before operation, patient 4, rep3

description:
Library name: barcode63
column name in raw_counts_all_samples.csv: barcode63

value: 0 day


title: Psoriasis_3_LS_158


title: mesc_rad21_depletion_IAA-3h_084, Smart-seq3


title: rectus femoris, 1d after operation, patient 6, rep1

description:
Library name: barcode64
column name in raw_counts_all_samples.csv: barcode64


title: mesc_rad21_depletion_IAA-3h_083, Smart-seq3


title: SPC_Epithelial_BLM_CBP30_2

description: Library name: Sample 5


title: SPC_Epithelial_BLM_GNE781_2

description: Library name: Sample 8


title: SPC_Epithelial_BLM_3

description: Library name: Sample 3


title: rectus femoris, before operation, patient 4, rep1

description:
Library name: barcode61
column name in raw_counts_all_samples.csv: barcode61


title: SPC_Epithelial_BLM_CBP30_1

description: Library name: Sample 4


title: mesc_rad21_depletion_IAA-3h_082, Smart-seq3


title: Psoriasis_3_NL_156

value: NL


title: rectus femoris, before operation, patient 4, rep2

description:
Library name: barcode62
column name in raw_counts_all_samples.csv: barcode62


title: SPC_Epithelial_BLM_1

description: Library name: Sample 1


title: mesc_rad21_depletion_IAA-3h_080, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_079, Smart-seq3


title: Psoriasis_3_NL_155


title: rectus femoris, 1d after operation, patient 6, rep2

description:
Library name: barcode65
column name in raw_counts_all_samples.csv: barcode65


title: Psoriasis_3_NL_153


title: Psoriasis_3_NL_157


title: Psoriasis_3_NL_151


title: mesc_rad21_depletion_IAA-3h_081, Smart-seq3


title: Psoriasis_3_NL_154


title: pGpp_rep1_t10

description:
Library name: 2
KAE60_rep1_10min_S78

value: bacterial

value: 168 trpC2 dsasBdsasA amyE::Pxyl-sasA drel::kan

value: pGpp inducible strain (KAE60), replicate 1, 10 minutes post-induction


title: SPC_Epithelial_BLM_2

description: Library name: Sample 2

value: BLM


title: rectus femoris, 12d after operation, patient 6, rep3

description:
Library name: barcode57
column name in raw_counts_all_samples.csv: barcode57

value: 12 days


title: rectus femoris, before operation, patient 6, rep3

description:
Library name: barcode60
column name in raw_counts_all_samples.csv: barcode60

value: rectus femoris


title: mesc_rad21_depletion_IAA-3h_076, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: rectus femoris, 12d after operation, patient 6, rep2

description:
Library name: barcode56
column name in raw_counts_all_samples.csv: barcode56


title: Psoriasis_3_NL_150


title: rectus femoris, before operation, patient 6, rep2

description:
Library name: barcode59
column name in raw_counts_all_samples.csv: barcode59


title: Kidney_K1_Norm ref_148

source_name: kidney

value: kidney

value: Norm ref


title: BA-MaPS_MDA-MB-231_ERK5-ko_Replicate 1

city: New Orleans

first: Van

last: Barnes

state: LA

address: 1430 Tulane Ave SL-78

institute: Tulane SOM

description: Library name: Sample 21

data_processing:
STAR was used to map short sequencing reads to the reference genome
Assembly: Reads were aligned to human_hg38 downloaded from GSEA
Supplementary files format and content: Data files represent relative gene abundance as TMPs. TPM values were determined by STAR

source_name: Breast Tissue + breast ASCs

growth_protocol: TNBC cell line MDA-MB-231 (ATCC, Manassas, VA, USA) was cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Waltham, MA, USA) supplemented with 10% HyClone Cosmic Calf Serum (Cytiva), 1% minimal essential amino acids (Gibco, Waltham, MA), 1% non-essential amino acids (Gibco, Waltham, MA, USA), 1% antibiotic/anti-mycotic (Gibco, Waltham, MA, USA) and insulin (Gibco, Waltham, MA, USA) under mycoplasma-free conditions at 37 °C and 5% v/v CO2.

extract_protocol:
For 2D and 3D cultures, total RNA was extracted from the cell lines using Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) and sent to Azenta (TU-BcX-4IC) (Burlington, MA, USA) for RNA sequencing. BA-MaPS (adipose tissue) samples were extracted using Qiazol and then Quick RNA Miniprep Kit from Zymo Research (Irvine, CA, USA) following tissue extraction protocol.
The RNA sequencing workflow after RNA isolation included initial PolyA selection: based mRNA enrichment, mRNA fragmentation, and random priming with subsequent first- and second-strand complementary DMA (cDNA) synthesis. Afterward, end-repair 5’ phosphorylation and nucleotide (dA)-tailing were performed. Last, adaptor ligation, polymerase chain reaction (PCR), and Illumina NovaSeq technology-based sequencing with 2 150-base pair (bp) read length were carried out.

treatment_protocol: No treatments were used in this study

value: Breast Tissue + breast ASCs

value: breast tissue + breast ASCs + MDA-MB-231

value: heterogenouse cell population (Cells native to breast tissue + stem cell+ breast cancer cell line)

value: WT


title: rectus femoris, 12d after operation, patient 8, rep3

description:
Library name: barcode54
column name in raw_counts_all_samples.csv: barcode54

value: control

value: female


title: BA-MaPS_MDA-MB-231_Replicate 4

description: Library name: Sample 20


title: mesc_rad21_depletion_IAA-3h_078, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_073, Smart-seq3


title: BA-MaPS_MDA-MB-231_ERK5-ko_Replicate 3

description: Library name: Sample 23


title: Psoriasis_3_NL_152

value: skin

value: NL

value: Male


title: mesc_rad21_depletion_IAA-3h_075, Smart-seq3


title: Kidney_K1_Norm ref_147


title: rectus femoris, before operation, patient 6, rep1

description:
Library name: barcode58
column name in raw_counts_all_samples.csv: barcode58

value: 0 day


title: BA-MaPS_MDA-MB-231_ERK5-ko_Replicate 4

description: Library name: Sample 24


title: mesc_rad21_depletion_IAA-3h_077, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_072, Smart-seq3


title: rectus femoris, 1d after operation, patient 4, rep1

description:
Library name: barcode67
column name in raw_counts_all_samples.csv: barcode67

value: 1 day

value: experiment


title: BA-MaPS_MDA-MB-231_ERK5-ko_Replicate 2

description: Library name: Sample 22


title: mesc_rad21_depletion_IAA-3h_074, Smart-seq3


title: Kidney_K1_Norm ref_145


title: rectus femoris, 12d after operation, patient 8, rep1

description:
Library name: barcode52
column name in raw_counts_all_samples.csv: barcode52

value: rectus femoris

value: 12 days


title: BA-MaPS_MDA-MB-231_Replicate 2

description: Library name: Sample 18


title: BA-MaPS_MDA-MB-231_Replicate 3

description: Library name: Sample 19


title: mesc_rad21_depletion_IAA-3h_070, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: Psoriasis_3_NL_149


title: rectus femoris, 12d after operation, patient 8, rep2

description:
Library name: barcode53
column name in raw_counts_all_samples.csv: barcode53


title: BA-MaPS_Breast_Tissue_Control_Replicate 3

description: Library name: Sample 15

value: breast tissue + breast ASCs

value: Cells native to breast tissue


title: Kidney_K1_Norm ref_144

value: kidney

value: Norm ref


title: rectus femoris, 12d after operation, patient 6, rep1

description:
Library name: barcode55
column name in raw_counts_all_samples.csv: barcode55


title: mesc_rad21_depletion_IAA-3h_067, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: BA-MaPS_MDA-MB-231_Replicate 1

description: Library name: Sample 17

value: Breast Tissue + breast ASCs

value: breast tissue + breast ASCs + MDA-MB-231

value: heterogenouse cell population (Cells native to breast tissue + stem cell+ breast cancer cell line)

value: WT


title: Kidney_K1_Norm ref_143


title: mesc_rad21_depletion_IAA-3h_066, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_069, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_071, Smart-seq3


title: rectus femoris, 1d after operation, patient 8, rep1

description:
Library name: barcode49
column name in raw_counts_all_samples.csv: barcode49

value: control

value: female


title: mesc_rad21_depletion_IAA-3h_065, Smart-seq3


title: rectus femoris, 12d after operation, patient 2, rep1

description:
Library name: barcode46
column name in raw_counts_all_samples.csv: barcode46


title: BA-MaPS_Breast_Tissue_Control_Replicate 2

description: Library name: Sample 14


title: Kidney_K1_Norm ref_146


title: rectus femoris, before operation, patient 8, rep3

description:
Library name: barcode45
column name in raw_counts_all_samples.csv: barcode45

value: 0 day


title: mesc_rad21_depletion_IAA-3h_068, Smart-seq3


title: Kidney_K1_Norm ref_142


title: 3D_MDA-MB-231_ERK5-ko_replicate 1

description: Library name: Sample 10

source_name: Cell line

value: Cell line

value: breast cancer cell line


title: BA-MaPS_Breast_Tissue_Control_Replicate 1

description: Library name: Sample 13

value: heterogenous cell popultaion (Cells native to breast tissue)


title: rectus femoris, 12d after operation, patient 2, rep3

description:
Library name: barcode48
column name in raw_counts_all_samples.csv: barcode48

value: rectus femoris

value: 12 days

value: experiment


title: BA-MaPS_Breast_Tissue_Control_Replicate 4

description: Library name: Sample 16

value: breast tissue + breast ASCs


title: Kidney_K1_Norm ref_141


title: Liver_L1_Norm ref_137

source_name: liver

value: liver


title: rectus femoris, 1d after operation, patient 8, rep2

description:
Library name: barcode50
column name in raw_counts_all_samples.csv: barcode50

value: 1 day


title: 3D_MDA-MB-231_replicate 3

description: Library name: Sample 9


title: 3D_MDA-MB-231_ERK5-ko_replicate 3

description: Library name: Sample 12


title: rectus femoris, 12d after operation, patient 2, rep2

description:
Library name: barcode47
column name in raw_counts_all_samples.csv: barcode47


title: mesc_rad21_depletion_IAA-3h_062, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: Liver_L1_Norm ref_135

value: Norm ref


title: Liver_L1_Norm ref_139


title: 3D_MDA-MB-231_ERK5-ko_replicate 2

description: Library name: Sample 11


title: 3D_MDA-MB-231_replicate 1

description: Library name: Sample 7


title: rectus femoris, 12d after operation, patient 7, rep2

description:
Library name: barcode41
column name in raw_counts_all_samples.csv: barcode41


title: Kidney_K1_Norm ref_140

value: kidney


title: mesc_rad21_depletion_IAA-3h_060, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_061, Smart-seq3


title: 2D_MDA-MB-231_ERK5-ko_replicate 3

description: Library name: Sample 6

value: WT


title: Liver_L1_Norm ref_134


title: rectus femoris, 12d after operation, patient 7, rep1

description:
Library name: barcode40
column name in raw_counts_all_samples.csv: barcode40


title: Liver_L1_Norm ref_138


title: mesc_rad21_depletion_IAA-3h_064, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_059, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_063, Smart-seq3


title: rectus femoris, before operation, patient 8, rep2

description:
Library name: barcode44
column name in raw_counts_all_samples.csv: barcode44

value: control


title: rectus femoris, before operation, patient 8, rep1

description:
Library name: barcode43
column name in raw_counts_all_samples.csv: barcode43

value: female


title: mesc_rad21_depletion_IAA-3h_058, Smart-seq3


title: Liver_L1_Norm ref_133


title: Liver_L1_Norm ref_132


title: Liver_L1_Norm ref_136


title: mesc_rad21_depletion_IAA-3h_057, Smart-seq3


title: rectus femoris, 1d after operation, patient 7, rep2

description:
Library name: barcode38
column name in raw_counts_all_samples.csv: barcode38


title: rectus femoris, 12d after operation, patient 7, rep3

description:
Library name: barcode42
column name in raw_counts_all_samples.csv: barcode42


title: 3D_MDA-MB-231_replicate 2

description: Library name: Sample 8


title: rectus femoris, before operation, patient 7, rep3

description:
Library name: barcode36
column name in raw_counts_all_samples.csv: barcode36

value: 0 day


title: 2D_MDA-MB-231_ERK5-ko_replcate 2

description: Library name: Sample 5

value: Cell line


title: 2D_MDA-MB-231_ERK5-ko_replicate 1

description: Library name: Sample 4

value: breast cancer cell line


title: Liver_L1_Norm ref_131


title: Psoriasis_11_LS_128

value: skin

value: LS

value: Male


title: 2D_MDA-MB-231_replicate 3

description: Library name: Sample 3


title: rectus femoris, 1d after operation, patient 7, rep3

description:
Library name: barcode39
column name in raw_counts_all_samples.csv: barcode39

value: rectus femoris

value: experiment


title: rectus femoris, 1d after operation, patient 7, rep1

description:
Library name: barcode37
column name in raw_counts_all_samples.csv: barcode37


title: mesc_rad21_depletion_IAA-3h_056, Smart-seq3


title: Psoriasis_11_LS_130


title: Psoriasis_11_LS_129


title: mesc_rad21_depletion_IAA-3h_055, Smart-seq3


title: 2D_MDA-MB-231_replicate 1

description: Library name: Sample 1


title: rectus femoris, 1d after operation, patient 8, rep3

description:
Library name: barcode51
column name in raw_counts_all_samples.csv: barcode51


title: rectus femoris, before operation, patient 7, rep2

description:
Library name: barcode35
column name in raw_counts_all_samples.csv: barcode35


title: mesc_rad21_depletion_IAA-3h_054, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-3h_053, Smart-seq3


title: 427 cells, control, RNaseH1 overexpression, irradiated

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Library name: DRIP_427_RH_OE_IR

data_processing:
Reads were alilgned to the human genome sequence (hg38) by Bowtie 2 v2.5.2 with default parameters
aligned reads were sorted by genomic coordinate using samtools v1.19.2
The genome was divided into 500bp bins and bins with read counts >20 in all replicates were kept for DESeq2 differential analysis. Peak calling was performed with MACS2 v2.2.9.1. Peak regions and differential bins were overlapped using bedtools intersect v2.31.1.
Assembly: UCSC Genome hg38
Supplementary files format and content: DESeq2 results

growth_protocol: Neuronal progenitor cells were maintained in STEMdiff™ Neural Progenitor Medium (STEMCELL Technologies) at 37°C and 5% CO2

extract_protocol:
Cells were washed once with phosphate-buffered saline (PBS; Thermo Fisher) and then pelleted and suspended in 1.6 mL of Tris-EDTA buffer (TE buffer, 10 mM Tris-HCl pH 8, and 1 mM EDTA). 50 µL of SDS 20% (wt./vol) (Santa Cruz) and 5 µL of Proteinase K (20 mg/mL; Invitrogen) were added. Samples were incubated at 37°C overnight. Samples were transferred to 15 mL high-density Maxtract phase lock gel tubes (Qiagen) and one volume (1.6 mL) of Phenol:Chloroform:Isoamyl alcohol (25:24:1; Sigma-Aldrich) was added to each sample. Samples were centrifuged at 1,500 g for 5 min and the supernatant was transferred to a new 15 mL tube. Nucleic acids were precipitated by adding 1/10 volume of 3 M NaOAc pH 5.2 (160 µL) and 2.5 volumes of 100% ethanol (4 mL). Tubes were gently inverted until DNA fully precipitated and became visible. Precipitate was then transferred to a 1.5 mL tube, washed twice with 80% ethanol, air-dried, and resolved in 100 µL of TE buffer. DNA was then fragmented with restriction enzymes (BsrG I, EcoR I, Hind III, Ssp I, Xba I, 30 units each) (NEB) at 37°C overnight. The digested nucleic acids were then recovered by phenol-chloroform extraction.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer's instructions. 10ng of DNA was used as starting material for input and ip. Libraries were size selected using AMPure XP beads from Beckman Coulter.

treatment_protocol: For ATM inhibition experiments, cells were treated with 100nM of AZD1390 for 12 hours within an incubator at 37°C and 5% CO2. For hydrogen peroxide experiments, cells were treated with 1mM of hydrogen peroxide for 6 horus within an incubator at 37°C and 5% CO2. For RNaseH1 overexpression experiments, cells were infected with a lentivirus containing FLAG-tagged RNaseH1. After 42 hours, cells were irradiated with and incubated for 6h at 37°C and 5% CO2

value: neuronal progenitor cells

value: RNaseH1 overexpression, irradiation, 6 hours in incubator

value: anti-RNA:DNA hybrid S9.6 (Millipore)


title: 426 cells, control, RNaseH1 overexpression, irradiated

description: Library name: DRIP_426_RH_OE_IR


title: 2D_MDA-MB-231_replicate 2

description: Library name: Sample 2


title: GM03487 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: DRIP_03487_RH_OE_IR

value: ATM null


title: Psoriasis_11_NL_123

value: NL


title: mesc_rad21_depletion_IAA-3h_052, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: Psoriasis_11_LS_126


title: mesc_rad21_depletion_IAA-3h_049, Smart-seq3


title: rectus femoris, 12d after operation, patient 5, rep2

description:
Library name: barcode32
column name in raw_counts_all_samples.csv: barcode32

value: 12 days

value: control


title: mesc_rad21_depletion_IAA-3h_051, Smart-seq3


title: GM01526 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: DRIP_01526_RH_OE_IR


title: 425 cells, control, RNaseH1 overexpression, irradiated

description: Library name: DRIP_425_RH_OE_IR

value: WT


title: Psoriasis_11_LS_125


title: 427 cells, control, hydrogen peroxide treatment

description: Library name: DRIP_427_H2O2

value: 1mM of hydrogen peroxide for 6 hours


title: rectus femoris, 12d after operation, patient 5, rep1

description:
Library name: barcode31
column name in raw_counts_all_samples.csv: barcode31

value: female


title: mesc_rad21_depletion_IAA-3h_047, Smart-seq3


title: Psoriasis_11_LS_127

value: skin


title: GM08436 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: DRIP_08436_RH_OE_IR


title: rectus femoris, 12d after operation, patient 5, rep3

description:
Library name: barcode33
column name in raw_counts_all_samples.csv: barcode33


title: Psoriasis_11_NL_121


title: Psoriasis_11_NL_124


title: mesc_rad21_depletion_IAA-3h_050, Smart-seq3


title: rectus femoris, 1d after operation, patient 5, rep1

description:
Library name: barcode28
column name in raw_counts_all_samples.csv: barcode28

value: 1 day


title: rectus femoris, before operation, patient 5, rep3

description:
Library name: barcode27
column name in raw_counts_all_samples.csv: barcode27

value: 0 day


title: rectus femoris, 1d after operation, patient 5, rep3

description:
Library name: barcode30
column name in raw_counts_all_samples.csv: barcode30

value: rectus femoris


title: Psoriasis_11_NL_119

value: Male


title: mesc_rad21_depletion_IAA-3h_048, Smart-seq3


title: 426 cells, control, hydrogen peroxide treatment

description: Library name: DRIP_426_H2O2

value: neuronal progenitor cells


title: rectus femoris, before operation, patient 5, rep2

description:
Library name: barcode26
column name in raw_counts_all_samples.csv: barcode26


title: mesc_rad21_depletion_IAA-3h_045, Smart-seq3


title: GM08436 cells, ATM null, hydrogen peroxide treatment

description: Library name: DRIP_08426_H2O2


title: rectus femoris, 1d after operation, patient 5, rep2

description:
Library name: barcode29
column name in raw_counts_all_samples.csv: barcode29


title: rectus femoris, 12d after operation, patient 3, rep3

description:
Library name: barcode24
column name in raw_counts_all_samples.csv: barcode24

value: experiment


title: Psoriasis_11_NL_122


title: rectus femoris, 12d after operation, patient 3, rep2

description:
Library name: barcode23
column name in raw_counts_all_samples.csv: barcode23


title: mesc_rad21_depletion_IAA-3h_046, Smart-seq3


title: Psoriasis_11_NL_120


title: GM01526 cells, ATM null, hydrogen peroxide treatment

description: Library name: DRIP_01526_H2O2

value: anti-RNA:DNA hybrid S9.6 (Millipore)


title: 425 cells, control, hydrogen peroxide treatment

description: Library name: DRIP_425_H2O2


title: mesc_rad21_depletion_IAA-3h_042, Smart-seq3


title: Psoriasis_4_LS_116

value: LS


title: rectus femoris, before operation, patient 5, rep1

description:
Library name: barcode25
column name in raw_counts_all_samples.csv: barcode25


title: GM03487 cells, ATM null, hydrogen peroxide treatment

description: Library name: DRIP_03487_H2O2

value: ATM null


title: 427 cells, control, ATM inhibition

description: Library name: DRIP_427_ATMi_UT

value: 100nM of AZD1390 for 12 hours


title: Psoriasis_11_NL_118

value: NL


title: Psoriasis_4_LS_115


title: rectus femoris, 12d after operation, patient 3, rep1

description:
Library name: barcode22
column name in raw_counts_all_samples.csv: barcode22

value: 12 days


title: mesc_rad21_depletion_IAA-3h_044, Smart-seq3

value: mouse embryonic stem cell

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_040, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_041, Smart-seq3


title: rectus femoris, 1d after operation, patient 3, rep3

description:
Library name: barcode21
column name in raw_counts_all_samples.csv: barcode21


title: Psoriasis_11_NL_117


title: 426 cells, control, ATM inhibition

description: Library name: DRIP_426_ATMi_UT

value: WT


title: Psoriasis_4_LS_113


title: mesc_rad21_depletion_IAA-3h_039, Smart-seq3


title: Psoriasis_4_LS_114


title: rectus femoris, 1d after operation, patient 3, rep2

description:
Library name: barcode20
column name in raw_counts_all_samples.csv: barcode20

value: female


title: 427 cells, control, ATM inhibition (input)

description: Library name: DRIP_Input


title: 427 cells, control, RNaseH1 overexpression, irradiated

description: Library name: RNA_427_RH_OE_IR

data_processing:
RNA-seq reads were aligned to the human genome (hg38) using TopHat v2.1.0 with default parameters
Aligned reads were sorted by genomic coordinate using samtools v1.19.2
Differential gene expression analysis was conducted using Cuffdiff v2.2.1
Assembly: UCSC Genome hg38
Supplementary files format and content: genes.fpkm
Supplementary files format and content: Differential gene expression file

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen). Approximately 1 million cells were lysed by repetitive pipetting in 1 mL of TRIzol. Phase separation was performed by adding 0.2 mL of chloroform (Sigma-Aldrich), followed by centrifugation at 20,000 g for 15 min at 4°C. The top aqueous layer (~500 µL) was transferred to a new tube and the RNA was precipitated overnight at -80°C with an equal volume (500 µL) of 100% isopropanol (Fisher Scientific), 1/10 volume (50 µL) of 3 M sodium acetate (Teknova), and 4 µL of 5 mg/mL glycogen (Thermo). Samples were then centrifuged at 15,000 g for 20 min at 4°C, washed twice with 1 mL of 75% ethanol, and dissolved in 50 µL of nuclease-free water.
RNA libraries for RNA-seq were prepared using the KAPA RNA Hyperprep Kit with RiboErase following the manufacturer's instructions

treatment_protocol: For RNaseH1 overexpression experiments, cells were infected with a lentivirus containing FLAG-tagged RNaseH1. After 42 hours, cells were irradiated with and incubated for 6h at 37°C and 5% CO2

value: RNaseH1 overexpression, irradiation, 6 hours in incubator


title: mesc_rad21_depletion_IAA-3h_043, Smart-seq3


title: 425 cells, control, ATM inhibition

description: Library name: DRIP_425_ATMi_UT


title: mesc_rad21_depletion_IAA-3h_037, Smart-seq3


title: rectus femoris, 1d after operation, patient 3, rep1

description:
Library name: barcode19
column name in raw_counts_all_samples.csv: barcode19

value: 1 day


title: mesc_rad21_depletion_IAA-3h_038, Smart-seq3


title: Psoriasis_4_LS_112

value: skin


title: 426 cellls, control, RNaseH1 overexpression, irradiated

description: Library name: RNA_426_RH_OE_IR


title: rectus femoris, before operation, patient 3, rep3

description:
Library name: barcode18
column name in raw_counts_all_samples.csv: barcode18

value: rectus femoris

value: 0 day


title: Psoriasis_4_LS_110

value: Male


title: Psoriasis_4_LS_111


title: rectus femoris, before operation, patient 7, rep1

description:
Library name: barcode34
column name in raw_counts_all_samples.csv: barcode34

value: experiment


title: rectus femoris, before operation, patient 3, rep1

description:
Library name: barcode16
column name in raw_counts_all_samples.csv: barcode16


title: rectus femoris, before operation, patient 3, rep2

description:
Library name: barcode17
column name in raw_counts_all_samples.csv: barcode17


title: rectus femoris, 1d after operation, patient 2, rep2

description:
Library name: barcode14
column name in raw_counts_all_samples.csv: barcode14


title: mesc_rad21_depletion_IAA-3h_036, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: mesc_rad21_depletion_IAA-3h_033, Smart-seq3


title: GM01526 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: RNA_01526_RH_OE_IR

value: neuronal progenitor cells


title: mesc_rad21_depletion_IAA-3h_035, Smart-seq3


title: Psoriasis_4_NL_107


title: GM08436 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: RNA_08426_RH_OE_IR


title: Psoriasis_4_LS_109

value: LS


title: rectus femoris, 1d after operation, patient 2, rep3

description:
Library name: barcode15
column name in raw_counts_all_samples.csv: barcode15


title: Psoriasis_4_LS_108


title: mesc_rad21_depletion_IAA-3h_034, Smart-seq3


title: Psoriasis_4_NL_104


title: rectus femoris, before operation, patient 2, rep2

description:
Library name: barcode11
column name in raw_counts_all_samples.csv: barcode11


title: 425 cells, control, RNaseH1 overexpression, irradiated

description: Library name: RNA_425_RH_OE_IR


title: rectus femoris, before operation, patient 2, rep1

description:
Library name: barcode10
column name in raw_counts_all_samples.csv: barcode10


title: rectus femoris, 1d after operation, patient 2, rep1

description:
Library name: barcode13
column name in raw_counts_all_samples.csv: barcode13


title: mesc_rad21_depletion_IAA-3h_032, Smart-seq3


title: GM03487 cells, ATM null, RNaseH1 overexpression, irradiated

description: Library name: RNA_03487_RH_OE_IR

value: ATM null


title: Psoriasis_4_NL_106


title: rectus femoris, 12d after operation, patient 1, rep3

description:
Library name: barcode09
column name in raw_counts_all_samples.csv: barcode09

value: control


title: rectus femoris, before operation, patient 2, rep3

description:
Library name: barcode12
column name in raw_counts_all_samples.csv: barcode12


title: UPN1177M

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

description:
Library name: 10X-Wu-UPN-1117-20230515-VisCyt-FFPEv2-hg
CytAssist FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to human GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz:  list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: neuroblastoma (lymph node metastasis)

extract_protocol:
Patient samples were formalin-fixed paraffin-embedded and 5 µm frozen sections were cut with vibratome on plain glass slides
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium (CytAssist FFPE Assays,  Visium V5 Slide - FFPE v2) Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: neuroblastoma (lymph node metastasis)

tag: tissue type

value: high-risk neuroblastoma from reticuloendothelial cervical lymph nodes


title: mesc_rad21_depletion_IAA-3h_031, Smart-seq3

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell


title: rectus femoris, 12d after operation, patient 1, rep2

description:
Library name: barcode08
column name in raw_counts_all_samples.csv: barcode08

value: 12 days


title: Control Spleen

city: Palo Alto

first: Roshani

last: Sinha

address: 240 Pasteur Drive BMI

department: Pediatrics

institute: Stanford University

description:
Library name: RS6
Column name in JMML_Gene_counts.txtt : Control Spleen

data_processing:
Trimmed sequence reads were aligned to whole genome of human hg38 using STAR aligner
Processing of raw sequencing data (fq.gz. files) including QA/QC steps, adapter trimming and alignment were conducted using the Partek™ Flow™ software, v12.3 21.
STAR alignment was performed to the whole human genome (hg38). Gene and feature annotation was performed using hg38_ensembl_release90_v2. Cells expressing fewer than 10 genes were excluded to minimize noise in downstream analyses.
Normalization of individual samples was performed using recommended median ratio for downstream DESeq2 package.
Assembly: hg38
Supplementary files format and content: tab delimited txt file includes normalized counts for each sample

source_name: Spleen

extract_protocol:
The protocol involved both mechanical and chemical disruption for tissue lysis and homogenization. Phase separation was subsequently performed via centrifugation to isolate RNA from DNA and proteins. The resulting RNA was further purified to yield the final total RNA samples used for library construction.
Following total RNA extraction, mRNA was enriched using poly(A) selection. The enriched mRNA was then used to construct cDNA libraries with an approximate insert size of 250-300 bp.

value: Spleen

value: hematopoietic cells

value: wt


title: Psoriasis_4_NL_105

value: NL


title: NF1 KO Spleen_1

description:
Library name: RS9
Column name in JMML_Gene_counts.txtt : NF1 KO Spleen_1

value: NF1 KO


title: UPN2855P

description:
Library name: 10X-Wu-UPN-2855P-20230515-VisCyt-FFPEv2-hg
CytAssist FFPE Spatial transcriptome sequencing

source_name: neuroblastoma (primary)

value: neuroblastoma (primary)

value: high-risk neuroblastoma from primary adrenal mass


title: rectus femoris, 12d after operation, patient 1, rep1

description:
Library name: barcode07
column name in raw_counts_all_samples.csv: barcode07

value: rectus femoris

value: female


title: Psoriasis_4_NL_103

value: skin

value: Male


title: NF1 KO BM_2

description:
Library name: RS8
Column name in JMML_Gene_counts.txtt : NF1 KO BM_2

source_name: bone marrow

value: bone marrow


title: mesc_rad21_depletion_IAA-3h_030, Smart-seq3

extract_protocol:
Isolated single cell was lysed wih gentle lysis buffer (containing 0.45% NP-40), and the supernant was collected for the construction of sequencing library.
Collected supernant was amplified with standard Smart-seq3 protocol, then perform library preparation with homemade Tn5 transposase.
Smart-seq3 & bulk RNA-seq

value: IAA (3h)


title: mesc_rad21_depletion_IAA-3h_029, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_025, Smart-seq3


title: Psoriasis_4_NL_102


title: GM01526 cels, ChIP-Seq, ATM null, irradiation

description: Library name: DRIP_AT3_IR_YH

data_processing:
Reads were alilgned to the human genome sequence (hg38) by Bowtie 2 v2.5.2 with default parameters
aligned reads were sorted by genomic coordinate using samtools v1.19.2
The genome was divided into 500bp bins and bins with read counts >20 in all replicates were kept for DESeq2 differential analysis. Peak calling was performed with MACS2 v2.2.9.1. Peak regions and differential bins were overlapped using bedtools intersect v2.31.1.
Assembly: UCSC Genome hg38
Supplementary files format and content: Peak files for each samples
Supplementary files format and content: Differential peak file

treatment_protocol: Cells were either left untreated or irradiated with 10Gy and incubated for 6h at 37°C and 5% CO2

value: neuronal progenitor cells

value: ATM null

value: irradiation, 6h recovery time

tag: chip antibody

value: anti-RNA:DNA hybrid S9.6 (Millipore)


title: NF1 KO BM_1

description:
Library name: RS7
Column name in JMML_Gene_counts.txtt : NF1 KO BM_1


title: mesc_rad21_depletion_IAA-3h_028, Smart-seq3

data_processing:
Smart-seq3 data were processed using zUMIs (https://github.com/sdparekh/zUMIs).
Bulk RNA-seq data were mapped to human reference genome using STAR and RSEM was used to calculate mRNA count for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA counts for each cell and sample
Supplementary files format and content: tab-delimited text files include cell barcode and sample information for Smart-seq3

value: mouse embryonic stem cell


title: Psoriasis_17_LS_99

value: LS


title: Psoriasis_4_NL_101


title: Psoriasis_4_NL_100


title: mesc_rad21_depletion_IAA-3h_027, Smart-seq3


title: Control BM

description:
Library name: RS5
Column name in JMML_Gene_counts.txtt : Control BM

value: hematopoietic cells

value: wt


title: mesc_rad21_depletion_IAA-3h_026, Smart-seq3


title: mesc_rad21_depletion_IAA-3h_023, Smart-seq3


title: rectus femoris, 1d after operation, patient 1, rep3

description:
Library name: barcode06
column name in raw_counts_all_samples.csv: barcode06

value: 1 day

value: control


title: Psoriasis_17_LS_98


title: rectus femoris, 1d after operation, patient 1, rep2

description:
Library name: barcode05
column name in raw_counts_all_samples.csv: barcode05


title: rectus femoris, 1d after operation, patient 1, rep1

description:
Library name: barcode04
column name in raw_counts_all_samples.csv: barcode04


title: mesc_rad21_depletion_IAA-3h_024, Smart-seq3

description:
Single-cell RNA-seq (Smart-seq3)
ss3_rad21_degron_readcount.matrix.tsv
ss3_rad21_degron_umicount.matrix.tsv


title: Psoriasis_17_LS_97


title: Psoriasis_17_LS_95


title: rectus femoris, before operation, patient 1, rep2

description:
Library name: barcode02
column name in raw_counts_all_samples.csv: barcode02

value: 0 day


title: GM03487 cels, ChIP-Seq, ATM null, irradiation

description: Library name: DRIP_AT1_IR_YH


title: rectus femoris, before operation, patient 1, rep3

description:
Library name: barcode03
column name in raw_counts_all_samples.csv: barcode03

value: rectus femoris


title: 426 cels, ChIP-Seq, control, irradiation

description: Library name: DRIP_C2_IR_YH

value: WT


title: mesc_rad21_depletion_IAA-3h_022, Smart-seq3


title: GM08436 cels, ChIP-Seq, ATM null, irradiation

description: Library name: DRIP_AT2_IR_YH


title: mesc_rad21_depletion_IAA-3h_021, Smart-seq3


title: Psoriasis_17_LS_96

value: skin


title: Psoriasis_17_LS_94

value: Male


title: Psoriasis_17_LS_93


title: 426 cels, ChIP-Seq, control, no treatment (Input)

description: Library name: DRIP_Input_YH

value: no treatment.


title: GM03487 cels, ChIP-Seq, ATM null, RNaseH treatment for 4h

description: Library name: DRIP_RH_YH

value: treated with RNaseH 4h


title: rectus femoris, before operation, patient 1, rep1

description:
Library name: barcode01
column name in raw_counts_all_samples.csv: barcode01

value: female


title: mesc_rad21_depletion_IAA-3h_019, Smart-seq3

value: IAA (3h)


title: 427 cels, ChIP-Seq, control, irradiation

description: Library name: DRIP_C3_IR_YH

value: neuronal progenitor cells

value: irradiation, 6h recovery time