title: Snx5_3

city: shanghai

first: xue

last: jiang

state: shanghai

address: No. 399, Yanchang Middle Road, Jing 'an District

institute: Tongji University

description:
Snx5-/-, replicate biosample 3
A3_4

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: BMSCs were extracted from 3-week-old mice.

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

value: bone marrow stromal cells

value: Snx5-/- mouse BMSCs


title: E3_47A_DOXPOT1A_POT1B_KO

status: Public on Feb 25 2026

type: SRA

city: Bethesda

first: Eros

last: Lazzerini Denchi

address: 9000 Rockville Pike

country: USA

institute: NCI

description: Library name: Library 11

library_source: genomic

data_processing:
Telomeric reads were isolated from the fastq files using the following command: zcat XXX.fastq.gz | grep -E "CTAACCCTAACC|CAAACCCAAACC|GTTAGGGTTAGG|GTTTGGGTTGG">XXX.txt The resulting txt files were analyzed in RStudio to quantify number of reads containing mutants repeats and number of consecutive mutant repeats. In the manuscript associated with this file we report the quantifications.
Assembly: mm10
Supplementary files format and content: The .txt files contain reads corresponding to the telomeric reads

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESCs (E14) were grown on 0.1% gelatin-coated plates in DMEM medium containing LIF (1,000 U/ml) and 2i (1 μM PD03259010 and 3 μM CHIR99021). Cell lines were tested for mycoplasma contamination.

extract_protocol:
Cells were washed with PBS, treated with Trypsin/EDTA, and neutralized with growth media. Genomic DNA was isolated, digested, and telomere sequences were enriched following the same protocol described for the dot blot assay. A total of 100-150 ng of enriched telomeric DNA was then sonicated using a Covaris S220 Ultrasonicator to generate DNA fragments ranging from 300-500 bp.
Library preparation for Illumina sequencing was performed using the NEBNext Ultra II kit, following the manufacturer’s instructions.

tag: cell line

value: mESC

tag: genotype

value: POT1a dTAG_POT1b knockout

tag: treatment

value: 1 μg/ml of doxycycline for 72 hours


title: liver_2dpi_non-infection_rep2

city: Nanjing

first: Tailong

last: Wang

state: Jiangsu

address: Xuanwu

department: College of Veterinary Medicine

country: China

institute: Nanjing Agricultural University

description: Library name: Sample2

library_source: transcriptomic

data_processing:
The raw data in ASTQ format were filtered by fastp (v0.20.1).The clean reads of each sample were then aligned to the reference genome GRCg7b using HISAT2 (v2.2.1) software to obtain the raw counts of the reads aligned to each gene.
Assembly: Genome assembly bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited tex file includes raw counts for each Sample

molecule: total RNA

organism: Gallus gallus

source_name: liver

extract_protocol:
Total RNA was extracted with TRIzol reagent.RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the total RNA samples were tested to be qualified, the MGIEasy RNA library preparation kit was used for library construction. Magnetic beads with oligo (DT) were used for enrichment and purification; Fragment buffer was added to the purified mRNA to make its fragment into a short fragment; the fragment mRNA was used as a template for reverse transcription into double stranded cDNA with six base random primers, and then the product was purified. The purified double stranded cDNA was subjected to end repair, addition of dA tail, linker connection and PCR amplification. After the amplified product was qualified, it was denatured and single stranded cyclized, and the cyclized product was inspected.

treatment_protocol: infection and non-infection

tag: tissue

value: liver

tag: time point

value: non-infection


title: CD11b+CON2

city: Jinan

first: Xiaofei

last: Li

address: Duanxing Road 4

institute: Shandong Provincial ENT Hospital, Shandong University

description:
tpm_HC2_11b_po
read_count_HC2_11b_po

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Structure variation detection The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Homo sapiens

source_name: healthy control, female, 62 yrs old

extract_protocol:
1. Introduction This procedure is suitable for Total RNA extraction of animal tissues, cells and other samples to provide high quality RNA for library preparation. 2. Experimental Procedures 2.1 Tissue Sample Fragmentation and Lysis 2.1.1 Grinding Machine 2.1.1.1 Transfer appropriate sample to corresponding grinding tube, 2.1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 2.1.2 Liquid Nitrogen Grinding and Crushing 2.1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 2.1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.  Stand flat for 5 min for the fully lysis of tissue cells. 2.1.3 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2.2 Sample Purification 2.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.  Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: blood cell

tag: cell type

value: CD11b+Myeloid cell

tag: gender

value: female

tag: age

value: 62 yrs old

value: Control


title: E3_47A_DOXPOT1A_dTAG_POT1B_KO

description: Library name: Library 12

value: 1 μg/ml of doxycycline for 72 hours /0.5 µM dTAG-13  for 72 hrs


title: Snx5_2

description:
Snx5-/-, replicate biosample 2
A3_2


title: SKOV3 Vehicle, rep1

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: SKOV3_C1

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 algorithm (v2.0.8b)
gene count measurements were obtained using HTSeq algorithm using refseq annotation
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count

molecule: polyA RNA

growth_protocol: SKOV3 cells were cultured in RPMI medium supplented with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen, Cat#74004) and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: SKOV3 cells treated with vehicle, and ERX-208 (1000 nM) for 48 hours

tag: strain

value: Human

value: Ovarian cancer

value: Vehicle control


title: Snx5_1

description:
Snx5-/-, replicate biosample 1
A3_1


title: CD11b+CON3

description:
tpm_HC3_11b_po
read_count_HC3_11b_po

source_name: healthy control, male, 65 yrs old

value: male

value: 65 yrs old


title: liver_2dpi_non-infection_rep3

description: Library name: Sample3


title: WT_2

description:
control group, replicate biosample 2
A2_2

value: bone marrow stromal cells

value: wild-type(WT) BMSCs


title: CON7

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification  Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: healthy control, male, 42 yrs old

extract_protocol:
1. Introduction This protocol applies to the isolation and purification of RNA from whole blood that are stabilized on PAXgene Blood RNA Tubes to provide high-quality RNA for library preparation. 2. Experimental Procedures 2.1 Remove the blood sample from the refrigerator and balance at room temperature for 2 h. 2.2 Centrifuge at 3000~5000×g for 10 min, discard the supernatant. 2.3 Add 4 mL RNase-free water, vortex shaking until the cells are dispersed, centrifugation at 3000-5000×g for 10 min and removal of the supernatant. 2.4 Add 350 μL BR1, vortex and shake well, add 300 μL BR2 and 40 μL proteinase K, vortex and shake well for 5 s and incubate at 55℃, 400~1400 rpm for 10 min.  2.5 Let the mixture pass through the PAXgene Shredder spin column, centrifuge at full speed for 3 min, and then transfer the supernatant to a 1.5 mL centrifuge tube, add 350 μL ethanol absolute and mix thoroughly by vortexing. 2.6 Transfer the supernatant to PAXgene RNA spin column, centrifuge at 8000~20000×g for 1 min. 2.7 Add 350 μL BR3, centrifuge at 8000~20000×g for 1 min. 2.8 Add 70 μL DNA digestion buffer and 10μL DNase I, stay at 20-30℃ for 15 min. 2.9 Add 350 μL BR3, centrifuge at 8000~20000×g for 1 min, discard the filtrate. 2.10 Add 500 μL BR4, centrifuge at 8000~20000×g for 1 min, discard the filtrate. 2.11 Add 500 μL BR4, centrifuge at 8000~20000×g for 3 min, discard the filtrate. 2.12 Transfer the column into a new 1.5 mL tube, add 20-50 μL BR5, centrifuge at 8000~20000×g for 1min to elute the DNA.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.  Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: whole blood

value: 42 yrs old


title: CON6

source_name: healthy control, male, 31 yrs old

value: 31 yrs old


title: Transcriptome of MB_Myr_3 midbrain

city: Gwangju

first: Eunkyung

last: Lee

address: 123 Cheomdan-gwagiro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

description: Library name: MB_Myr_3

data_processing:
Sequencing reads were first quality-controlled using fastp. Cleaned paired-end reads were aligned to the Mus musculus reference genome (GRCm39) using STAR (v2.7.3a) with GENCODE M32 gene annotation. The genome index was generated with sjdbOverhang set to 150. Aligned reads were sorted by coordinate. Gene-level read counts were quantified using featureCounts (Subread v2.0.1) with the same GENCODE M32 annotation. Only uniquely mapped fragments were counted. No further normalization was applied.
Assembly: GRCm39 (GENCODE M32)
Supplementary files format and content: Tab-delimited plain text file containing gene-level raw read counts. Rows: Ensembl gene IDs; Columns: samples.

source_name: Midbrain

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher Scientific). 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, #20020599), which includes ribosomal RNA depletion.

value: Midbrain

value: Myriocin


title: liver_2dpi_non-infection_rep1

description: Library name: Sample1

value: liver

value: non-infection


title: E3_47A_DOXPOT1A_dTAG

description: Library name: Library 10

value: mESC

value: POT1a dTAG


title: E3_47APOT1A

description: Library name: Library 8

value: 1 μg/ml of doxycycline for 72 hours


title: CON5

source_name: healthy control, male, 55 yrs old

value: 55 yrs old

value: Control


title: E3_47A_DOXPOT1A

description: Library name: Library 9


title: Transcriptome of MB_Myr_2 midbrain

description: Library name: MB_Myr_2


title: WT_3

description:
control group, replicate biosample 3
A2_4


title: WT_1

description:
control group, replicate biosample 1
A2_1


title: CON4

source_name: healthy control, male, 37 yrs old

value: 37 yrs old


title: E2_47APOT1adTAG_47A_DOX

description: Library name: Library 7

value: POT1a dTAG_POT1b knockout

value: 1 μg/ml of doxycycline for 72 hours /0.5 µM dTAG-13  for 72 hrs


title: mouse lymphatic endothelial cells，MI，day3-3

city: Shanghai

first: yunhao

last: duan

address: 150 Jimo Rd, Pudong New District

institute: Shanghai East Hospital

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: fpkm, tpm, read count

source_name: heart

growth_protocol: mouse lymphatic endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum（FBS）and antibiotics

extract_protocol:
1 ug of total RNA was used for the construction of sequencing  libraries
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: The heart tissues or primary heart endothelial cells were obtained . Isolated RNA was subsequently used for RNA-sequencing analysis

value: heart

value: lymphatic endothelial cells

value: WT

value: MI


title: Transcriptome of MB_Myr_1 midbrain

description: Library name: MB_Myr_1


title: E2_47APOT1a_47A_DOX

description: Library name: Library 6

value: wild-type


title: Transcriptome of MB_PD_3 midbrain

description: Library name: MB_PD_3

value: Midbrain

value: Vehicle


title: Transcriptome of MB_PD_2 midbrain

description: Library name: MB_PD_2


title: E2_47A

description: Library name: Library 4


title: MD5

source_name: MD, female, 31 yrs old

value: whole blood

value: female

value: 31 yrs old

value: MD


title: E2_47A_DOX

description: Library name: Library 5

value: mESC

value: 1 μg/ml of doxycycline for 72 hours


title: Transcriptome of MB_WT_3 midbrain

description: Library name: MB_WT_3


title: mouse lymphatic endothelial cells，sham，day3-2

value: sham


title: CON1

source_name: healthy control, female, 35 yrs old

value: 35 yrs old

value: Control


title: mouse lymphatic endothelial cells，sham，day3-1


title: CON3

source_name: healthy control, female, 38 yrs old

value: 38 yrs old


title: mouse lymphatic endothelial cells，MI，day3-1

value: heart


title: MD2

source_name: MD, male, 60 yrs old

value: male

value: 60 yrs old


title: ctrli_rep2

status: Public on Feb 24 2026

city: Daejeon

first: Seung-Jae

middle: V

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

description: Library name: Sample 2

data_processing:
The processed reads were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 98) by using STAR (v.2.7.0e) with parameters of --alignSoftClipAtReferenceEnds Yes --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Read start coordinates in the reads were collated. The read starts were visualized by using Integrative Genomics Viewer (IGV) (v.2.14.1) and by adjusting the total number of reads to 1,000,000.
Assembly: WBcel235 (ce11)
Supplementary files format and content: BigWig files representing PARE-seq 5′ end tag density for each sample after pooling technical replicates.
Library strategy: PARE-seq

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Synchronized L4-prefertile wild-type worms under control or rnk-1 rnk-2 RNAi conditions were maintained on HT115 at 20°C.

extract_protocol:
Total RNAs were extracted from synchronized L4 stage animals by using TRIzol Reagent (Life Technologies, California, USA). The purified total RNAs were subjected to dephosphorylation by alkaline phosphatase (New England Biolabs, Ipswich, USA), phosphorylation by polynucleotide kinase (New England Biolabs, Ipswich, USA), and polyadenylation by E. coli Poly(A) Polymerase (New England Biolabs, Ipswich, USA), sequentially. Polyadenylated RNAs were purified by using DynabeadTM Oligo(dT)25 (Invitrogen, Waltham, MA, USA) and ligated to an RNA oligonucleotide adaptor by using T4 RNA ligase (New England Biolabs, Ipswich, USA). The ligated products were purified with DynabeadsTM Oligo(dT)25 (Thermo Scientific, Waltham, MA, USA) and used as a template in an RT reaction for the synthesis of first-strand cDNAs. The cDNAs were then amplified with SolgTM pfu DNA polymerase (Solgent, Daejeon, South Korea). The PCR products were cleaved with MmeI (New England Biolabs, Ipswich, USA), and the cleaved products with the length of 42 nucleotides (nt) were excised from 12% Tris-Borate-EDTA (TBE) gel. The fragments were ligated to a double-stranded DNA adaptor by using T4 DNA ligase (F. Hoffmann–La Roche, Basel, Switzerland). The ligated products (63 nt) were isolated by using gel extraction and PCR amplified with P5 primer and P7 index primer.
Synchronized L4-prefertile wild-type worms under control or rnk-1 rnk-2 RNAi conditons were maintained on OP50 at 20°C, and harvested after washing three times independently using M9 buffer.For rnk-1 rnk-2 double RNAi experiments, the two double-stranded RNA (dsRNA)-expressing bacteria were separately cultured using liquid LB media containing 100 μg/mL ampicillin (USB, Santa Clara, CA, USA) at 37°C overnight until the optical density (OD) value at 600 nm reached 0.9. The bacteria were then mixed to 1:1 ratio. Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions. The PCR products (126 nt in length) were purified and subjected to high-throughput sequencing on Illumina HiSeq 2500 platform (Macrogen, Seoul, South Korea). Adaptors were removed from sequencing reads by using Trim Galore (v.0.6.6) (https://www.bioinformatics.babraham.ac.uk /projects/trim_galore).

value: whole body

tag: Sex

value: hermaphrodite

tag: developmental stage

value: L4-Prefertile adults


title: rnk1irnk2i_rep2

description: Library name: Sample 4


title: Transcriptome of MB_WT_2 midbrain

description: Library name: MB_WT_2

value: Midbrain

value: Vehicle


title: mouse lymphatic endothelial cells，sham，day3-3

value: lymphatic endothelial cells

value: WT


title: MD4

value: whole blood

value: female

value: 31 yrs old

value: MD


title: rnk1irnk2i_2

description: Library name: Sample 5

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) by using TopHat (v.2.1.0) and Bowtie (v.0.12.9) with parameters of --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search. Back splice junctions were extracted and circRNAs were annotated based on known exon-intron junctions (Ensembl gene annotations registered in UCSC Table Browser in 2019-02-10) by using CIRCexplorer2 (v.2.3.8). Specifically, circRNAs that contained only annotated exon boundaries were detected. The levels of annotated circRNAs were calculated and normalized relative to linear RNA counterparts as fragments per billion mapped bases (FPB) by using CIRCexplorer3-CLEAR (v.1.0). The FPB was interpreted as the junction ratio. circRNAs with FPB larger than 1 in at least 50% of total samples were defined as confidently detected ones. circRNAs with significant level changes (fold change > 2 and adjusted p value < 0.05) were identified by using DESeq2 (v.1.28.1), after combining with linear RNAs whose total count was at least 10. Wald test p values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

extract_protocol:
Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions.
Synchronized L4-prefertile wild-type worms under control or rnk-1 rnk-2 RNAi conditons were maintained on OP50 at 20°C, and harvested after washing three times independently using M9 buffer.For rnk-1 rnk-2 double RNAi experiments, the two double-stranded RNA (dsRNA)-expressing bacteria were separately cultured using liquid LB media containing 100 μg/mL ampicillin (USB, Santa Clara, CA, USA) at 37°C overnight until the optical density (OD) value at 600 nm reached 0.9. The bacteria were then mixed to 1:1 ratio. Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions. A sequencing library was constructed and paired-end RNA sequencing using Illumina NovaSeq 6000 platform was performed (Macrogen, South Korea).


title: Transcriptome of MB_PD_1 midbrain

description: Library name: MB_PD_1


title: E2_Ctrl

description: Library name: Library 3

value: mESC

value: wild-type


title: liver_2dpi_infection_rep1

description: Library name: Sample6

value: liver

value: infection


title: rnk1irnk2i_1

description: Library name: Sample 4


title: E1_Ctrl

description: Library name: Library 1


title: E1_47A_DOX

description: Library name: Library 2

value: 1 μg/ml of doxycycline for 72 hours


title: ctrli_3

description: Library name: Sample 3


title: MD3

source_name: MD, female, 39 yrs old

value: 39 yrs old


title: ctrli_2

description: Library name: Sample 2

value: whole body


title: ctrli_rep1

description: Library name: Sample 1

value: hermaphrodite


title: rnk1_RNAi_4

description: Library name: Sample 6

growth_protocol: Synchronized L4-prefertile wild-type worms under control or rnk-1 RNAi conditions were maintained on HT115 at 20°C.

extract_protocol:
Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions.
Synchronized L4-prefertile wild-type worms under control or rnk-1 RNAi conditons were maintained on OP50 at 20°C, and harvested after washing three times independently using M9 buffer. Total RNA was isolated using RNAiso plus (Takara, Japan) in accordance with the manufacturer’s instructions. A sequencing library was constructed and paired-end RNA sequencing using Illumina NovaSeq 6000 platform was performed (Macrogen, South Korea).

value: L4-Prefertile adults


title: rnk1irnk2i_rep1

description: Library name: Sample 3


title: rnk1irnk2i_3

description: Library name: Sample 6


title: Transcriptome of MB_WT_1 midbrain

description: Library name: MB_WT_1

value: Midbrain


title: ctrli_1

description: Library name: Sample 1


title: H2A-TerminaTOR cells, cycloheximide and PDGF treatment, replicate 2

city: La Jolla

first: Jin

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pharmacology

institute: University of California San Diego

description: Library name: Sample14

data_processing:
Raw data were analyzed using the web-based platform Galaxy (https://usegalaxy.org) and open-source R software (version 4.1.0, https://www.r-project.org). Briefly, high-quality raw reads were mapped to the reference human genome hg38 using HISAT2 (version 2.2.1), and aligned reads were counted using htseq-count (version 0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes total raw counts of reads mapped to known genome for each sample.

extract_protocol:
Total RNA was extracted using RNA extraction kit (Zymol).1 µg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: mouse fibroblast

value: Cycloheximide + PDGF


title: H2A-mCherry cells, cycloheximide and PDGF treatment, replicate 3

description: Library name: Sample12


title: H2A-mCherry cells, Rapamycin and PDGF treatment, replicate 2

description: Library name: Sample8

value: Rapamycin + PDGF


title: rnk1_RNAi_1

description: Library name: Sample 2


title: H2A-mCherry cells, cycloheximide and PDGF treatment, replicate 2

description: Library name: Sample11


title: CD45+ cell, Ctrl

city: Haidian District

first: Wenbo

last: Hu

state: Beijing

address: 30 Shuangqing Road

institute: Tsinghua University

description:
Library name: Sample1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files of gene expression were aligned to the reference genome using Cellranger counting (Cellranger v7.1.0 ), performing simultaneous filtering, barcode counting, and UMI counting
Assembly: GRCm39
Supplementary files format and content: barcodes, features and matrix files generated by CellRanger

source_name: tumor

extract_protocol:
Tumor tissues were collected, cut into small pieces, and digested with 100μg/ml DNase I (Roche) and 1 mg/ml collagenase IV (Roche) at 37 °C for 40 min. The digested tumors were then passed through a 70 μm cell strainer to make single-cell suspensions. Single cells were blocked with anti-CD16/32 Ab (clone 93) for 30 min and then stained with specific antibodies for 30 min on ice. Live CD45+ cells were sorted by FACS, and five biological replicates were amalgamated for library construction. The sorted cells were loaded onto a Chromium single-cell chip to generate barcoded nucleic acid fragments.
Single-cell transcriptomic libraries were generated using the commercial workflow specified by 10x Genomics (https://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf).

treatment_protocol: MC38 tumor inoculation, BiDT treatment

value: tumor

value: CD45+ cells

value: Ctrl

tag: batch


title: H2A-mCherry cells, PDGF treatment, replicate 2

description: Library name: Sample5

value: PDGF


title: rnk1_RNAi_2

description: Library name: Sample 4


title: ctrl_RNAi_4

description: Library name: Sample 5


title: ctrl_RNAi_2

description: Library name: Sample 3


title: H2A-mCherry cells, no PDGF treatment, replicate 1

description: Library name: Sample1

value: no


title: CD45+ cell, BiDT

description:
Library name: Sample2
10X Genomics

value: BiDT


title: Pparg-/-epi

city: Indianapolis

first: Raymond

middle: Lloyd

last: Konger

state: IN

address: 1481 West Tenth Street

department: Pathology & Laboratory Medicine

institute: Richard L. Roudebush VA Medical Center

description:
Library name: Sample1
10X Genomics

data_processing:
Sequence data were first processed with cellranger-6.1.1
cells derived from male and female animals were separated based on the expression of female and male specific genes
Seurat V4 was used for the ata normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis.  A QC metrics of the library size, number of features/genes, and mitochondrial reads (based on median absolute deviation (MAD); MAD of 3 used here) was calculated with Scater. This, together with the QC analysis in Seurat, were used to determine the parameters used for excluding low-quality cells.  Low-quality cells were excluded with the following criteria: cells with unique feature/gene counts over 7000 or less than 300 or >10% reads mapped to mitochondrial genome.
Unsupervised clustering was performed using Loupe Browser software (v6.5.0; 10x Genomics, Pleasanton, CA, USA) by uniform manifold approximation and projection (UMAP). Using Loupe Browser, DEGs for each individual cell cluster were obtained. The cell type within each cluster was identified by uploading the top differentially expressed genes for each cluster into the Enrichr online analysis application  and then cross-referencing with the PanglaoDB database.
Assembly: mouse reference geneome refdata-gex-mm10-2020-A (10x Genomics)
Supplementary files format and content: 10x HDF5 Output

source_name: Skin

extract_protocol:
Two mice (one male and one female) were euthanized for each genotype (wildtype and Pparg-/-epi). Dermal and epidermal cells were isolated from areas of telogen phase hair cycling for each mouse. For dermal cell preparation, the tissues were minced and digested in 2.5 mg Liberase TM, 16.7 mg DNase I, penicillin, and streptomycin in RPMI media (all reagents from Sigma-Aldrich, St. Louis, MO, USA) for 90 min at 37 °C. The digest was filtered through a 40 μm filter. After adding 5 mL of ice-cold dialyzed FBS, the samples were centrifuged at 300× g for 10 min. RBC lysis (RBC Lysis Buffer, Cat #00-4333-57, ThermoFisher Scientific, Waltham, MA, USA) followed by dead cell removal (dead cell removal kit #130-090-101, Miltenyi Biotec, Auburn, CA, USA) with centrifugation were performed after each step. The cell prep was washed twice with cell suspension buffer [PBS (calcium, magnesium, DNase, and RNase free) (Catolog # 40120706, bioWORLD, Dublin, OH, USA) containing 1% BSA] followed by centrifugation. RNA sequencing was then performed on a final cell prep resuspended in cell suspension buffer containing 0.5 U/µL SUPERaseIn™ RNase Inhibitor (Catalog #AM2694, ThermoFisher Scientific, Waltham, MA, USA) and 0.5 U/µL Protector RNase Inhibitor (Catalog #3335399001, Sigma-Aldrich, St. Louis, MO, USA). For epidermal cell preps, the dermal fat and dermis were removed using a scalpel, and the epidermal sheet was suspended in dispase II solution Sigma-Aldrich, St. Louis, MO, USA) for 2 hrs at 37 °C. After suctioning the dispase and scraping the epidermis from the dermis, the tissue was rinsed with PBS, centrifuged, and incubated in 5 mL Accutase solution (Cat# CnT-Accutase-100, CELLnTEC Advanced Cell Systems, Bern, Switzerland) for 20 min at room temp. After filtering through a 70 µm filter, 5 mL of dialyzed FBS was added, and the cells were pelleted by centrifugation. Dead cell removal and further processing were then performed as described for the dermal cell prep. The epidermal cells and dermal cells were then recombined at a 1:10 ratio (dermal vs. epidermal), and the male and female cells were pooled together.
single cell RNA-seq libraries were prepared using the 10X Genomics Chromium NextGEM Single Cell 3' V3.1 kit.

treatment_protocol: No treatment, the studies utilizes skin cells from epidermal Pparg knockout mouse skin relative to wildtype mouse skin

value: Skin

value: Homozygous floxed Pparg x K14-Cre cross


title: H2A-TerminaTOR cells, cycloheximide and PDGF treatment, replicate 3

description: Library name: Sample15


title: H2A-mCherry cells, no PDGF treatment, replicate 2

description: Library name: Sample2


title: WT

description:
Library name: Sample2
10X Genomics

value: Homozygous floxed Pparg


title: H2A-TerminaTOR cells, cycloheximide and PDGF treatment, replicate 1

description: Library name: Sample13


title: ctrl_RNAi_1

description: Library name: Sample 1


title: mouse lymphatic endothelial cells，MI，day3-2

value: heart

value: lymphatic endothelial cells

value: WT

value: MI


title: H2A-mCherry cells, PDGF treatment, replicate 1

description: Library name: Sample4


title: Cl13_STAT3CA_P14, Vehicle, spleen, D21

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

description: Library name: Sample 9

data_processing:
scRNA-seq: The scRNA-seq reads were aligned to the mm10 reference genome and quantified using the cellranger count (10X Genomics, version 3.0.0). The filtered gene-barcode matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the quality control were used for downstream analyses.
Assembly: Mouse mm10
Supplementary files format and content: the filtered matrix output folder from the 10X pipeline of each sample is provided as a tar archive.

source_name: spleen

extract_protocol:
By using fluorescence-activated cell sorting, CD8+ T cells were obtained from the livers or lungs of chronic virus-infected mice and from metastatic lungs/livers of tumor-engrafted mice. Then, the CD8+ T cells were performed with single-cell RNA-seq library construction.
For single-cell RNA-seq library construction, the libraries were prepared using Chromium Next GEM Single Cell 3’ reagent Kits (10x Genomics) according to the manufacturer’s instructions. Briefly, sorted CD8 T cells were suspended in DPBS containing 0.04% BSA and captured in droplets using a Chromium Single Cell Controller instrument (10x Genomics). After reverse transcription and cell barcoding in droplets, cDNA was purified and PCR amplified, followed by fragmentation, end-repair, double-size selection and PCR amplification with sample-indexing primers.

value: spleen


title: H2A-mCherry cells, cycloheximide and PDGF treatment, replicate 1

description: Library name: Sample10

value: mouse fibroblast


title: H2A-mCherry cells, PDGF treatment, replicate 3

description: Library name: Sample6


title: H2A-mCherry cells, Rapamycin and PDGF treatment, replicate 3

description: Library name: Sample9


title: H2A-mCherry cells, Rapamycin and PDGF treatment, replicate 1

description: Library name: Sample7


title: B16gp_P14. Vehicle, lung metastasis, D21

description: Library name: Sample 5

source_name: lung

value: lung


title: B16gp_P14, aPDL1, liver metastasis, D21

description: Library name: Sample 4

source_name: liver

value: liver


title: Cl13_MigR1_P14, Vehicle, spleen, D21

description: Library name: Sample 7


title: B16gp_P14. Vehicle, liver metastasis, D21

description: Library name: Sample 3


title: Cl13_P14, aPDL1, liver , D21

description: Library name: Sample 2


title: TRMs - HTO

city: Pittsburgh

first: Taylor

last: Eddens

state: PA

address: 4401 Penn Avenue, Rangos Research Building 9128

institute: University of Pittsburgh

description: Library name: HTO

data_processing:
CellRanger7.0
Assembly: NY Genome Assembly
Supplementary files format and content: Processed data will be provided in the form of demultiplexed .rds file.

source_name: Lung

extract_protocol: 10x genomics

value: Lung

value: B6 mice

value: HMPV infection


title: TRMs - TCR

description: Library name: TCR


title: H2A-mCherry cells, no PDGF treatment, replicate 3

description: Library name: Sample3


title: Cl13_STAT3CA_P14, aPD-L1, spleen, D21

description: Library name: Sample 10


title: Spinal cord from contusion-injured mouse treated with Syringin (SCI+Syr group, replicate 2)

city: Dongying

first: Dejing

state: Shandong

address: NO.31 Jinan Road

institute: Shengli Oilfield Central Hospital

description:
Library name: SCI+Syr_2_library
Spinal cord tissue from contusion-injured mouse treated with Syringin for 3 days, harvested at day 3 post-injury for RNA-seq.

data_processing:
The sequencing data underwent quality control using Fastp software to remove low-quality sequences.
The processed data were then aligned with the mouse reference genome utilizing HISAT2.
Gene assembly was performed using StringTie, and gene expression was quantified using FPKM
Assembly: GRCm38 (mm10)
Supplementary files format and content: Gene count matrix (raw counts) for all samples.

source_name: Spinal cord

growth_protocol: Mice were housed in SPF facilities with a 12-hour light/dark cycle, free access to food and water.

extract_protocol:
Total RNA was extracted from spinal cord tissue using TRIzol reagent according to manufacturer's instructions.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Spinal cord contusion injury was performed at T10 level using an impactor device. Mice received daily intraperitoneal injections of PBS (SCI group) or Syringin at 50 mg/kg (SCI+Syr group) for 3 days post-injury.

value: Spinal cord

value: wild type

value: spinal cord contusion injury, treated with Syringin


title: Cl13_P14, Vehicle, liver, D21

description: Library name: Sample 1


title: B16gp_P14. FTY720, lung metastasis, D21

description: Library name: Sample 6


title: Cl13_MigR1_P14, aPD-L1, spleen, D21

description: Library name: Sample 8


title: Spinal cord from contusion-injured mouse treated with PBS (SCI group, replicate 2)

description:
Library name: SCI_2_library
Spinal cord tissue from contusion-injured mouse treated with PBS for 3 days, harvested at day 3 post-injury for RNA-seq.

value: spinal cord contusion injury, treated with PBS


title: BRD2 Degron mESCs: DMSO_NascentRNA_Rep2_for_TTSeq

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Library name: B1_IP_Control_Rep2

library_source: other

data_processing:
TT-Seq: TT-Seq data analysis was performed as previously described. The data were processed through the snakePipes mRNA-seq pipeline (modified version of v.2.1.2), similar to RNA-seq analysis. Adapters and low-quality bases (<Q20) were removed using Cutadapt (v.2.8; https://github.com/marcelm/cutadapt). For all of the samples, reads were then mapped to the reference genome with STAR (v.2.7.4a). Then, reads per gene were counted using featureCounts (v.2.0.0). The gene-level counts obtained from featureCounts were then used for differential expression analysis using DESeq2 (v.1.26.0), similar to the RNA-seq analysis. For transcriptional rate calculations, read counts for all genes were obtained from each corresponding labeled and unlabelled TT-seq sample. To estimate the rates of RNA degradation and synthesis, we used a statistical model that was described previously.
ChIP-Seq: ChIP-Seq data was processed using the default parameters of SnakePipes v. 2.5.1 DNA-mapping and ChIP-Seq pipelines with "--trim --dedup --mapq 3 --properPairs" options.
Micro-C: Micro-C data was processed using snakePipes (v. 3.2.0) using makePairs function.
Pro-Seq: Dual, 6-nucleotide UMIs were extracted from read pairs using UMI-tools (v. 1.1.2) and adapter sequences were removed using cutadapt (v. 3.5). After trimming, reads shorter than 26 nucleotides were discarded. Then, the paired-end reads were mapped to a hybrid genome, which includes the spike-in genome build, dm6 and the primary genome build, mm10, using bwa-mem2 (v. 2.3-0) with ‘-k 19’ setting. Alignments were coordinate-sorted and indexed using samtools (v. 1.22.1) and only properly-paired reads with a mapping quality greater than 20 were retained. The bam files were splitted by the genome using sambamba (v. 0.8.1), independently deduplicated using UMI-tools and coordinate-sorted. Then, the bam files were converted into BEDPE format using bedtools and strand-aware, single-nucleotide positions corresponding to 3’ and 5’ ends of nascent RNA were extracted from the first mapped position of R1 and R2 reads, respectively.
Assembly: mm10
Supplementary files format and content: Tab-limited text files include raw counts for total and nascent RNA samples. Narrowpeak files were generated using default settings of MACS2. Cool files include micro-C genomic interaction data.
Supplementary files format and content: bigwig files:Spike-in, input or sequencing-depth normalized files for genome-wide data

molecule: other

source_name: Embryo

growth_protocol: ESCs were cultured at 37°C and 5 % CO2 on 0.1% gelatin (Merck #G1393)-coated dishes and were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco #37966-021) supplemented with 15% heat- inactivated ES-cell specific fetal calf serum (FCS), 100 U/mL penicillin and 100 U/mL streptomycin (Gibco #15140-122), 1mM glutamine (GlutaMax, Gibco #35050061), 1mM sodium pyruvate (Gibco #11360-70), non-essential amino acids (NEAA, Gibco #11140050), ß-Mercaptoethanol (Gibco #31350-010), and in-house purified LIF.

extract_protocol:
ChIP-Seq: ESCs were crosslinked with 1 % Formaldehyde in 1X PBS for 10 minutes at RT followed by quenching with 125 mM Glycine at 4 °C. After washing the ESCs twice with PBS, ESCs were lysed in LB1 buffer (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton X-100) for 20 minutes at 4 °C. Then, samples were washed in LB2 buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 minutes at 4 °C. Chromatin was extracted by incubation in LB3 buffer (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 % DoC-Na, 0.5 % Na-Sarcosinate, 1 % Triton X-100) for 10 minutes on ice followed by sonication for 12 minutes on a Covaris sonicator. The sonicated chromatin was spun down at 16,000g for 10 minutes at 4 °C and the supernatant was incubated with the appropriate antibody overnight at 4 °C. Antibody-bound chromatin fragments were collected by incubation with Protein A or G DynaBeads for 3 h at 4 °C. The beads were washed for 5 minutes at 4 °C with the following buffers: RIPA-150 (50 mM Tris- HCl, pH 8.0, 150 mM NaCl, 0.1 % SDS, 0.5 % DoC-Na, 1 % NP-40), RIPA-500 (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 0.1 % SDS, 1 % NP-40), Li-Buffer (50 mM Tris- HCl, pH 8.0, 250 mM LiCl, 0.5 % DoC-Na, 1 % NP-40), TE Buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA). After an additional wash with TE Buffer, beads were resuspended in 100 μL of elution buffer (50 mM Tris-HCl, pH 7.4, 1 % SDS, 1 mM EDTA) and crosslinks were reversed by incubation at 65 °C for at least 4 h. Proteins and RNA were degraded by further incubations with RNase A and Proteinase K, respectively. Resulting DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo) according to the manufacturer's protocol.                                                                                Native Histone ChIP-Seq: 3 x 106 ESCs per replicate were harvested using accutase, washed once in 1X PBS and flash-frozen. The cell pellet was thawn on ice and resuspended in 150 μL of 1X PBS and mixed with 150 μL of 2X Lysis buffer (100 mM Tris-HCl, pH 8.0, 0.2 % Triton X-100, 0.1 % DOC-Na, 10 mM CaCl2, 10 mM Na-Butyrate) containing 0.9 μL of MNase. The cell lysate was incubated first for 20 minutes at 4 °C and then for 10 minutes at 37 °C. The MNase digestion was quenched by addition of 30 μL of 25 mM EGTA. Afterwards, the sample was immediately placed on ice and mixed ocassionally by inverting the tube for 2 minutes. The soluble chromatin was collected by spinning down the sample at 16000g for 5 minutes at 4 °C and mixed with the dilution buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% DOC-Na, 2.2% Triton X-100, 50 mM EDTA, 50 mM EGTA, 5 mM Na-Butyrate). 2 % of the soluble fraction was taken as input and the rest was incubated overnight with the histone PTM antibody at 4 °C. The next day, magnetic Protein A or G Dynabeads were washed in PBS thrice and 20 μl per sample were added to collect the antibody-chromatin conjugates. Then, they were washed in the following buffers, each for 5 minutes at 4 °C: Low salt buffer (0.1 % SDS, 1 % Triton X-100, 0.1 % DOC-Na, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl)[twice], high salt buffer (0.1 % SDS, 1 % Triton X-100, 0.1 % DOC-Na, 20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 360 mM NaCl), LiCl buffer (0.25 M LiCl, 1 % NP- 40, 1 % DOC-Na. 1 mM EDTA, 10 mM Tris-HCl, pH 8.0) [twice]. Finally, the samples were rinsed once in TE buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA) and resuspended in 100 μL of elution buffer (50 mM Tris-HCl, pH 7.4, 1 % SDS, 1 mM EDTA) and incubated first for 1 h at 55 °C with Proteinase K and then for 30 minutes at 37 °C with RNAse A. Resulting DNA was purified using ChIP DNA Clean and Concentrator kit according to manufacturer’s protocol.                                                                                TT-Seq: TT-Seq was performed as previously described with minor modifications 28: ESCs were treated with 500 μM 4-sU for 5 minutes under regular growth conditions and lysed using Trizol (Invitrogen) immediately afterwards. Total RNA was purified using chloroform and isopropanol precipitation and resuspended in TE buffer. 300 μg of total RNA for each sample was spiked with spike-in mix (appendix) and fragmented using Bioruptor Plus (30 seconds ON, 30 seconds OFF, 1 cycle, HIGH setting) and an aliquot was taken as Total RNA sample. The rest of the fragmented total RNA was biotinylated using Biotin-HPDP (Thermo Fisher) at room temperature for 2 hours. To remove excess Biotin-HPDP, RNA was precipitated using phenol:chloroform-isoamyl alcohol (Sigma) and ethanol and resuspended in ddH2O. Biotinylated RNA fragments were purified using μMACS streptavidin beads and μMACS columns (Miltenyi Biotec) according to the recommendations of the manufacturer. Labeled RNA was eluted twice using 100 mM DTT and purified using Oligo Clean and Concentrator Kit (Zymo Research). Both total and labeled RNA samples were treated with Turbo DNAse (Invitrogen) for 30 minutes at 37 °C and purified again Oligo Clean and Concentrator Kit (Zymo Research). PRO-Seq: Cells were harvested using accutase and washed with 10 ml of ice-cold PBS. Then, the cell pellet was resuspended in 250 µl of buffer W (10 mM Tris-HCl, pH 8.0, 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2, 1 mM EGTA, 10 % (v/v) glycerol, 0.5 mM DTT, SUPERase In 0.2 µl/ml) and mixed with 10 ml of buffer P (buffer W supplemented with 0.1 % (v/v) NP-40, 0.05 % (v/v) Tween-20). Upon incubation for 5 minutes on ice, the permeabilized cells were spun down and washed with 10 ml of buffer W. The pellet was resuspended in 400 µl of buffer F (50 mM Tris-HCl, pH 8.0, 40 % (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, SUPERase In 1 µl/ml) and number of cells in each sample were counted upon diluting a 10 µl aliquot in PBS. The samples were aliquoted in DNA low-bind tubes to a cell density of 1 × 106 cells per 45 µl buffer F and snap-frozen. After thawing, the samples were mixed with permeabilized Drosophila S2 cells as spike-in. The mixed permeabilized cells were used for the run-on reactions containing biotin-dNTPs and sarkosyl. Purified biotinylated RNA was subjected to chemical fragmentation at 95 °C for 5 minutes. Enrichment of nascent RNA and library preparation were performed as previously described. Micro-C: MicroC was performed as previously described with some modifications (Goel, Huseyin & Hansen, 2023).
RNA libraries for total RNA and TT-Seq samples were prepared using Illumina Stranded Total RNA Prep Kit with RiboZero Plus. ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina. PRO-Seq libraries were prepared according to Mimoso and Goldman (2023, Current Protocols). Micro-C libraries were prepared using NEBNext Ultra II DNA Library Prep kit.

treatment_protocol: PROTAC reagents were prepared in DMSO and diluted in cell culture medium to the indicated concentrations at 37°C. Auxin was dissolved in water and diluted in cell culture medium to 500 µM.

value: Embryo

value: WT26 mESC

value: Mouse embryonic stem cells

value: DMSO


title: Spinal cord from contusion-injured mouse treated with Syringin (SCI+Syr group, replicate 3)

description:
Library name: SCI+Syr_3_library
Spinal cord tissue from contusion-injured mouse treated with Syringin for 3 days, harvested at day 3 post-injury for RNA-seq.


title: Spinal cord from contusion-injured mouse treated with Syringin (SCI+Syr group, replicate 1)

description:
Library name: SCI+Syr_1_library
Spinal cord tissue from contusion-injured mouse treated with Syringin for 3 days, harvested at day 3 post-injury for RNA-seq.


title: Spinal cord from contusion-injured mouse treated with PBS (SCI group, replicate 3)

description:
Library name: SCI_3_library
Spinal cord tissue from contusion-injured mouse treated with PBS for 3 days, harvested at day 3 post-injury for RNA-seq.


title: BRD2 Degron mESCs: Auxin_TotalRNA_Rep1_for_TTSeq

description: Library name: B1_Total_3h_Rep1

value: Auxin


title: BRD2 Degron mESCs: Auxin_TotalRNA_Rep2_for_TTSeq

description: Library name: B1_Total_3h_Rep2


title: BRD2 Degron mESCs: DMSO_NascentRNA_Rep1_for_TTSeq

description: Library name: B1_IP_Control_Rep1


title: BRD2 Degron mESCs: DMSO_TotalRNA_Rep2_for_TTSeq

description: Library name: B1_Total_Control_Rep2


title: Spinal cord from contusion-injured mouse treated with PBS (SCI group, replicate 1)

description:
Library name: SCI_1_library
Spinal cord tissue from contusion-injured mouse treated with PBS for 3 days, harvested at day 3 post-injury for RNA-seq.


title: BRD2 Degron mESCs: Control_IP_Rep2_for_V5_ChIP

description: Library name: B1_Untreated_V5_Rep2


title: BRD2 Degron mESCs: Auxin_IP_Rep1_for_V5_ChIP

description: Library name: B1_Auxin_V5_Rep1


title: BRD2 Degron mESCs: DMSO_TotalRNA_Rep1_for_TTSeq

description: Library name: B1_Total_Control_Rep1


title: BRD2 Degron mESCs: Flavopiridol_IP_Rep2_for_V5_ChIP

description: Library name: B1_FP_V5_Rep2

value: Flavopiridol


title: BRD2 Degron mESCs: Auxin_NascentRNA_Rep2_for_TTSeq

description: Library name: B1_IP_3h_Rep2


title: BRD2 Degron mESCs: Auxin_IP_Rep2_for_V5_ChIP

description: Library name: B1_Auxin_V5_Rep2


title: BRD2 Degron mESCs: Control_Input_Rep2_for_V5_ChIP

description: Library name: B1_Untreated_Input_Rep2


title: BRD2 Degron mESCs: Control_IP_Rep1_for_V5_ChIP

description: Library name: B1_Untreated_V5_Rep1


title: BRD2 Degron mESCs: Auxin_NascentRNA_Rep1_for_TTSeq

description: Library name: B1_IP_3h_Rep1


title: BRD2 Degron mESCs: Flavopiridol_Input_Rep2_for_V5_ChIP

description: Library name: B1_FP_Input_Rep2


title: BRD2 Degron mESCs: Auxin_IP_Rep2_for_TAF1_ChIP

description: Library name: B1F_KO2_TAF1_merged


title: BRD2 Degron mESCs: Flavopiridol_IP_Rep1_for_V5_ChIP

description: Library name: B1_FP_V5_Rep1


title: BRD2 Degron mESCs: Auxin_Input_Rep1_for_TAF1_ChIP

description: Library name: B1F_KO1_Input_merged


title: BRD2 Degron mESCs: Control_Input_Rep1_for_V5_ChIP

description: Library name: B1_Untreated_Input_Rep1


title: BRD2 Degron mESCs: Flavopiridol_Input_Rep1_for_V5_ChIP

description: Library name: B1_FP_Input_Rep1


title: BRD2 Degron mESCs: Auxin_IP_Rep1_for_TAF1_ChIP

description: Library name: B1F_KO1_TAF1_merged


title: BRD2 Degron mESCs: Control_Input_Rep2_for_TAF1_ChIP

description: Library name: B1F_WT2_Input_merged

value: Water


title: BRD2 Degron mESCs: Auxin_Input_Rep2_for_TAF1_ChIP

description: Library name: B1F_KO2_Input_merged


title: BRD2 Degron mESCs: Control_IP_Rep1_for_TAF1_ChIP

description: Library name: B1F_WT1_TAF1_merged


title: BRD2 Degron mESCs: ZXH-3-26_PROSeq_Rep2

description: Library name: B1_Proseq_ZXH_Rep2

data_processing:
TT-Seq: TT-Seq data analysis was performed as previously described. The data were processed through the snakePipes mRNA-seq pipeline (modified version of v.2.1.2), similar to RNA-seq analysis. Adapters and low-quality bases (<Q20) were removed using Cutadapt (v.2.8; https://github.com/marcelm/cutadapt). For all of the samples, reads were then mapped to the reference genome with STAR (v.2.7.4a). Then, reads per gene were counted using featureCounts (v.2.0.0). The gene-level counts obtained from featureCounts were then used for differential expression analysis using DESeq2 (v.1.26.0), similar to the RNA-seq analysis. For transcriptional rate calculations, read counts for all genes were obtained from each corresponding labeled and unlabelled TT-seq sample. To estimate the rates of RNA degradation and synthesis, we used a statistical model that was described previously.
ChIP-Seq: ChIP-Seq data was processed using the default parameters of SnakePipes v. 2.5.1 DNA-mapping and ChIP-Seq pipelines with "--trim --dedup --mapq 3 --properPairs" options.
Micro-C: Micro-C data was processed using snakePipes (v. 3.2.0) using makePairs function.
Pro-Seq: Dual, 6-nucleotide UMIs were extracted from read pairs using UMI-tools (v. 1.1.2) and adapter sequences were removed using cutadapt (v. 3.5). After trimming, reads shorter than 26 nucleotides were discarded. Then, the paired-end reads were mapped to a hybrid genome, which includes the spike-in genome build, dm6 and the primary genome build, mm10, using bwa-mem2 (v. 2.3-0) with ‘-k 19’ setting. Alignments were coordinate-sorted and indexed using samtools (v. 1.22.1) and only properly-paired reads with a mapping quality greater than 20 were retained. The bam files were splitted by the genome using sambamba (v. 0.8.1), independently deduplicated using UMI-tools and coordinate-sorted. Then, the bam files were converted into BEDPE format using bedtools and strand-aware, single-nucleotide positions corresponding to 3’ and 5’ ends of nascent RNA were extracted from the first mapped position of R1 and R2 reads, respectively.
Assembly: mm10
Supplementary files format and content: Tab-limited text files include raw counts for total and nascent RNA samples. Narrowpeak files were generated using default settings of MACS2. Cool files include micro-C genomic interaction data.
Supplementary files format and content: bigwig files:Spike-in, input or sequencing-depth normalized files for genome-wide data
Library strategy: PRO-Seq


title: BRD2 Degron mESCs: Control_IP_Rep2_for_TAF1_ChIP

description: Library name: B1F_WT2_TAF1_merged


title: BRD2 Degron mESCs: Auxin_Input_Rep2_for_V5_ChIP

description: Library name: B1_Auxin_Input_Rep2


title: BRD2 Degron mESCs: Control_Input_Rep1_for_TAF1_ChIP

description: Library name: B1F_WT1_Input_merged


title: BRD2 Degron mESCs: Auxin_Input_Rep1_for_V5_ChIP

description: Library name: B1_Auxin_Input_Rep1


title: BRD2 Degron mESCs: DMSO_PROSeq_Rep2

description: Library name: B1_Proseq_DMSO_Rep2


title: BRD2 Degron mESCs: AuxinZXH-3-26_PROSeq_Rep1

description: Library name: B1_Proseq_AuxinZXH_Rep1

value: Auxin and ZXH-3-26


title: BRD2 Degron mESCs: Auxin_PROSeq_Rep2

description: Library name: B1_Proseq_Auxin_Rep2


title: BRD2 Degron mESCs: Auxin_PROSeq_Rep1

description: Library name: B1_Proseq_Auxin_Rep1


title: BRD2 Degron mESCs: DMSO_PROSeq_Rep1

description: Library name: B1_Proseq_DMSO_Rep1


title: MOF Degron mESCs: Auxin90min_timecourse_totalRNA_Rep4

description: Library name: MOF_A3_90min_4


title: MOF Degron mESCs: Auxin90min_timecourse_totalRNA_Rep2

description: Library name: MOF_A3_90min_2


title: MOF Degron mESCs: Auxin90min_timecourse_totalRNA_Rep3

description: Library name: MOF_A3_90min_3


title: MOF Degron mESCs: Auxin90min_timecourse_totalRNA_Rep1

description: Library name: MOF_A3_90min_1


title: MOF Degron mESCs: Auxin45min_timecourse_totalRNA_Rep3

description: Library name: MOF_A3_45min_3


title: BRD2 Degron mESCs: ZXH-3-26_PROSeq_Rep1

description: Library name: B1_Proseq_ZXH_Rep1


title: BRD2 Degron mESCs: AuxinZXH-3-26_PROSeq_Rep2

description: Library name: B1_Proseq_AuxinZXH_Rep2


title: MOF Degron mESCs: Control_timecourse_totalRNA_Rep4

description: Library name: MOF_A3_0h_4


title: MOF Degron mESCs: Auxin3h_timecourse_totalRNA_Rep1

description: Library name: MOF_A3_3h_1


title: MOF Degron mESCs: Auxin45min_timecourse_totalRNA_Rep1

description: Library name: MOF_A3_45min_1


title: MOF Degron mESCs: Auxin45min_timecourse_totalRNA_Rep2

description: Library name: MOF_A3_45min_2


title: MOF Degron mESCs: Control_timecourse_totalRNA_Rep3

description: Library name: MOF_A3_0h_3


title: MOF Degron mESCs: Auxin45min_timecourse_totalRNA_Rep4

description: Library name: MOF_A3_45min_4


title: MOF Degron mESCs: Auxin3h_timecourse_totalRNA_Rep4

description: Library name: MOF_A3_3h_4


title: MOF Degron mESCs: Control_timecourse_totalRNA_Rep2

description: Library name: MOF_A3_0h_2


title: BRD2 Degron mESCs: Auxin_microC_Rep2

description: Library name: B1_MicroC_Auxin3h_Rep2


title: MOF Degron mESCs: Auxin3h_timecourse_totalRNA_Rep3

description: Library name: MOF_A3_3h_3


title: MOF Degron mESCs: Auxin3h_timecourse_totalRNA_Rep2

description: Library name: MOF_A3_3h_2


title: BRD2 Degron mESCs: Auxin_microC_Rep1

description: Library name: B1_MicroC_Auxin3h_Rep1


title: BRD2 Degron mESCs: DMSO_microC_Rep3

description: Library name: B1_MicroC_DMSO_Rep3


title: Expt3_Hom_RFP

city: New York City

first: Joo-Hyeon

state: NY

address: 430 East 67th Street

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Sample 4
10x Genomics

data_processing:
Alignment performed using 10x cellranger (v7.2.0).
Assembly: GRCm38
Supplementary files format and content: mtx, tsv, csv files: raw count, barcodes and genes

source_name: Distal lung

extract_protocol:
For isolation of lung cell, mice were culled by cervical dislocation and lungs cleared of blood via perfusion with 10ml of PBS. Lungs were inflated with 2-3ml of a Dispase solution via intratracheal injection. When isolating mesenchymal cells, Collagenase I was added to the Dispase solution at 350U/ml before inflation. Lungs were carefully dissected out of the thoracic cavity and placed on a petri dish on ice. Individual lobes were separated from each lung, placed in a 50ml falcon and minced into small pieces. Cells were washes down with 3ml of PBS to the bottom of the falcon tube. When isolating epithelial cells only, 60ul of 100mg/ml Collagenase/Dispase solution was added per tube. Samples were places in a shaking incubator at 37ºC, 190 rpm, for 45 min. 7.5ul of 1% DNase I was added to each sample in the final 10 min of incubation. The resulting cell suspensions were filtered sequentially through 100 µm and 40 µm cell strainers and washed with 2 ml of 10% foetal bovine serum (FBS) in PBS (PF10) to collect remaining cells. Samples were centrifuged at 800 rpm for 5 min at 4ºC. Supernatant was removed and pellets were resuspended in 1 ml of red blood cell lysis buffer (RBC buffer, made inhouse: 150 mM NH4Cl and 10 mM KHCO3 in distilled H2O) for 60 seconds at RT. After lysis, 6 ml of Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 820 (DMEM/F-12) was added to the tube to neutralize the RBC buffer. 500µL of filtered FBS was added slowly to the bottom of each tube to collect live cells. Tubes were centrifuged again at 800rpm for 5 min at 4ºC. Cell pellets were resuspended in PF10 and placed into separate 1.5 ml tubes for antibody staining. Lineage-labelled epithelial cells (EpCAM+RFP+) and a mixed population of mesenchymal and immune cells (1:1 ratio of mesenchymal cells (CD45–CD31–EpCAM–) and immune cells (CD45+CD31–EpCAM–)) were then sorted and submitted for sequencing.
Cell suspensions were spun down, counted, and resuspended in 0.04% bovine serum albumin (BSA) in PBS to achieve a cell concentration of ~345 cells/µL. Single-cell 3′ RNA-seq libraries were generated according to manufacturer’s instructions (Chromium Single Cell 3′ Reagent v3 Chemistry Kit, 10X Genomics) and cDNA quality was assessed.

value: Distal lung

value: RFP+ lineaged-traced AT2 cells

value: Sftpc-CreERT2; Red2Kras; Areg-flox/flox


title: BRD2 Degron mESCs: DMSO_microC_Rep2

description: Library name: B1_MicroC_DMSO_Rep2


title: Expt3_Het_niche

description:
Library name: Sample 1
10x Genomics

value: Mesenchymal and immune cells

value: Sftpc-CreERT2; Red2Kras; Areg-flox/+


title: BRD2 Degron mESCs: DMSO_microC_Rep1

description: Library name: B1_MicroC_DMSO_Rep1


title: NPC3

city: Xiamen

first: Boxin

address: 良渚实验室1369号

institute: 良渚实验室

description:
Library name: Sample48
NPC_gene_fpkm

data_processing:
FASTQ files was filtered using the Trim_Galore (v.0.6.5)
Filtered Sequences were aligned with STAR (v.2.5.3a) to the mm10 assembly
Gene expression and TE expression were quantified from uniquely aligned reads using Featurecounts (v.2.0.4) with -f parameters and their annotations from the UCSC
For repeat analysis, alignment positions were mapped with repeats annotated in UCSC with RepeatMasker (rmsk table from mm10)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cortex

extract_protocol:
RNA was extracted with the TRIzol method, and used for the construction of sequencing libraries.
RNA-seq libraries were prepared using NEB Next Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: RNA-seq

value: cortex

value: Ctrl


title: MOF Degron mESCs: Control_timecourse_totalRNA_Rep1

description: Library name: MOF_A3_0h_1


title: NPC1

description:
Library name: Sample46
NPC_gene_fpkm


title: P1_VPA1

description:
Library name: Sample43
P1_CT_VPA_gene_fpkm

value: VPA


title: P1_CT3

description:
Library name: Sample42
P1_CT_VPA_gene_fpkm


title: P1_VPA3

description:
Library name: Sample45
P1_CT_VPA_gene_fpkm


title: BRD2 Degron mESCs: Auxin_microC_Rep3

description: Library name: B1_MicroC_Auxin3h_Rep3


title: P1_CT2

description:
Library name: Sample41
P1_CT_VPA_gene_fpkm


title: P1_CT1

description:
Library name: Sample40
P1_CT_VPA_gene_fpkm


title: P21_WT3_Ctrl

description:
Library name: Sample39
P21_CTRL_RTI_gene_fpkm


title: P21_MT3_Ctrl

description:
Library name: Sample35
P21_CTRL_RTI_gene_fpkm

value: mG-cKO-ctrl


title: Expt3_Hom_niche

description:
Library name: Sample 2
10x Genomics


title: Expt2_Confetti_niche

description:
Library name: Sample 1
10x Genomics

data_processing:
Alignment was performed using 10x cellranger v3.1.0
Assembly: GRCm38
Supplementary files format and content: mtx, tsv, csv files: raw count, barcodes and genes

extract_protocol:
For isolation of lung cell, mice were culled by cervical dislocation and lungs cleared of blood via perfusion with 10ml of PBS. Lungs were inflated with 2-3ml of a Dispase solution via intratracheal injection. When isolating mesenchymal cells, Collagenase I was added to the Dispase solution at 350U/ml before inflation. Lungs were carefully dissected out of the thoracic cavity and placed on a petri dish on ice. Individual lobes were separated from each lung, placed in a 50ml falcon and minced into small pieces. Cells were washes down with 3ml of PBS to the bottom of the falcon tube. When isolating epithelial cells only, 60ul of 100mg/ml Collagenase/Dispase solution was added per tube. Samples were places in a shaking incubator at 37ºC, 190 rpm, for 45 min. 7.5ul of 1% DNase I was added to each sample in the final 10 min of incubation. The resulting cell suspensions were filtered sequentially through 100 µm and 40 µm cell strainers and washed with 2 ml of 10% foetal bovine serum (FBS) in PBS (PF10) to collect remaining cells. Samples were centrifuged at 800 rpm for 5 min at 4ºC. Supernatant was removed and pellets were resuspended in 1 ml of red blood cell lysis buffer (RBC buffer, made inhouse: 150 mM NH4Cl and 10 mM KHCO3 in distilled H2O) for 60 seconds at RT. After lysis, 6 ml of Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 820 (DMEM/F-12) was added to the tube to neutralize the RBC buffer. 500µL of filtered FBS was added slowly to the bottom of each tube to collect live cells. Tubes were centrifuged again at 800rpm for 5 min at 4ºC. Cell pellets were resuspended in PF10 and placed into separate 1.5 ml tubes for antibody staining. 1:1 mixture of immune cells (CD45+) and both endothelial and mesenchyme cells (CD45–EpCAM–) were submitted for sequencing.
Library construction was performed according to manufacturers instructions (single cell 3' v2 chemstry, 10x Genomics)

value: Mesenchymal, immune and endothelial cells


title: NPC2

description:
Library name: Sample47
NPC_gene_fpkm


title: P1_VPA2

description:
Library name: Sample44
P1_CT_VPA_gene_fpkm


title: P21_MT2_Ctrl

description:
Library name: Sample33
P21_CTRL_RTI_gene_fpkm


title: Expt2_Red2Kras_niche

description:
Library name: Sample 2
10x Genomics


title: Expt3_Het_RFP

description:
Library name: Sample 3
10x Genomics


title: P21_MT3_RTI

description:
Library name: Sample36
P21_CTRL_RTI_gene_fpkm

value: mG-cKO-rti


title: P21_MT1_Ctrl

description:
Library name: Sample31
P21_CTRL_RTI_gene_fpkm


title: P21_MT2_RTI

description:
Library name: Sample34
P21_CTRL_RTI_gene_fpkm


title: P21_Het3_RTI

description:
Library name: Sample30
P21_CTRL_RTI_gene_fpkm

value: mG-cKD-rti


title: P21_Het3_Ctrl

description:
Library name: Sample29
P21_CTRL_RTI_gene_fpkm

value: mG-cKD-ctrl


title: P21_Het2_RTI

description:
Library name: Sample28
P21_CTRL_RTI_gene_fpkm


title: P21_WT1_Ctrl

description:
Library name: Sample37
P21_CTRL_RTI_gene_fpkm


title: P21_WT2_Ctrl

description:
Library name: Sample38
P21_CTRL_RTI_gene_fpkm


title: P45M2ctx

description:
Library name: Sample23
P1_P7_P14_P45_gene_fpkm

value: mG-cKO


title: P45M3ctx

description:
Library name: Sample24
P1_P7_P14_P45_gene_fpkm


title: P21_Het1_RTI

description:
Library name: Sample26
P21_CTRL_RTI_gene_fpkm


title: P45W2ctx

description:
Library name: Sample20
P1_P7_P14_P45_gene_fpkm


title: P21_MT1_RTI

description:
Library name: Sample32
P21_CTRL_RTI_gene_fpkm


title: P21_Het2_Ctrl

description:
Library name: Sample27
P21_CTRL_RTI_gene_fpkm


title: P45W3ctx

description:
Library name: Sample21
P1_P7_P14_P45_gene_fpkm


title: P45M1ctx

description:
Library name: Sample22
P1_P7_P14_P45_gene_fpkm


title: P45W1ctx

description:
Library name: Sample19
P1_P7_P14_P45_gene_fpkm


title: P14M1ctx

description:
Library name: Sample16
P1_P7_P14_P45_gene_fpkm


title: P14M3ctx

description:
Library name: Sample18
no proc data


title: P14W1ctx

description:
Library name: Sample13
P1_P7_P14_P45_gene_fpkm


title: P14M2ctx

description:
Library name: Sample17
P1_P7_P14_P45_gene_fpkm


title: P14W2ctx

description:
Library name: Sample14
P1_P7_P14_P45_gene_fpkm


title: P14W3ctx

description:
Library name: Sample15
no proc data


title: P7M3ctx

description:
Library name: Sample12
no proc data


title: P7W3ctx

description:
Library name: Sample9
no proc data


title: P7M1ctx

description:
Library name: Sample10
P1_P7_P14_P45_gene_fpkm


title: P7W1ctx

description:
Library name: Sample7
P1_P7_P14_P45_gene_fpkm


title: P21_Het1_Ctrl

description:
Library name: Sample25
P21_CTRL_RTI_gene_fpkm


title: P1M3ctx

description:
Library name: Sample6
P1_P7_P14_P45_gene_fpkm


title: P7W2ctx

description:
Library name: Sample8
P1_P7_P14_P45_gene_fpkm


title: P1M2ctx

description:
Library name: Sample5
P1_P7_P14_P45_gene_fpkm


title: P1M1ctx

description:
Library name: Sample4
P1_P7_P14_P45_gene_fpkm


title: P1W2ctx

description:
Library name: Sample2
P1_P7_P14_P45_gene_fpkm


title: P1W3ctx

description:
Library name: Sample3
P1_P7_P14_P45_gene_fpkm


title: P7M2ctx

description:
Library name: Sample11
P1_P7_P14_P45_gene_fpkm


title: P1W1ctx

description:
Library name: Sample1
P1_P7_P14_P45_gene_fpkm


title: Wild type_Rep2_Organ of Corti P21

city: Paris

first: Sedigheh

last: Delmaghani

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

description: Library name: WT-2

data_processing:
Gene expression was quantified using Integragen’s Galileo software. STAR was used to obtain the number of reads associated to each gene in the Gencode vM24 annotation (restricted to protein-coding genes, antisense and lincRNAs). Raw counts for each sample were imported into R statistical software using the Bioconductor DESeq2 package.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Cochlea - Organ of Corti

extract_protocol:
RNA extraction and purification was performed using the NucleoSpin RNA, Mini kit for RNA purification (Macherey-Nagel, 740955.50)
RNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations. Briefly, the key stages of the protocol are successively: the purification of Poly-A containing mRNA molecules using poly-T oligo attached magnetic beads from 100ng total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing.

value: Cochlea - Organ of Corti

value: Wild-type


title: Wild type_Rep3_Organ of Corti P21

description: Library name: WT-3


title: Wild type_Rep1_Organ of Corti P21

description: Library name: WT-1


title: Clrn1-/-Clrn2-/-_Rep3_Organ of Corti P21

description: Library name: MUT3-3


title: Clrn2-/-_Rep3_Organ of Corti P21

description: Library name: MUT2-3


title: Clrn2-/-_Rep2_Organ of Corti P21

description: Library name: MUT2-2


title: Clrn1-/-Clrn2-/-_Rep1_Organ of Corti P21

description: Library name: MUT3-1


title: Clrn1-/-_Rep3_Organ of Corti P21

description: Library name: MUT1-3


title: Clrn2-/-_Rep1_Organ of Corti P21

description: Library name: MUT2-1


title: Clrn1-/-Clrn2-/-_Rep2_Organ of Corti P21

description: Library name: MUT3-2


title: MT_K9_S25C0152_rep1

description: Library name: Sample8

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
clean reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.2.8).
Enriched peaks of H3K9me3 were identified by HOMER v4.10.1 with histone style (http://homer.ucsd.edu/homer).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Approximately 1× 10^7 cells from cortex as above was fixed in 1% formaldehyde for 10 min at room temperature (RT), followed by quenching in 125 nM glycine for 5 min. Cell nuclei were collected and lysed in lysing buffer (50 mM HEPES/KOH pH 7.6, 1 mM EDTA, 140 nM NaCl, 10% v/v Glycerol, 0.5% NP-40, 0.25% v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with 1.5 μg H3K9me3 antibody (Abcam, #ab232324) or 3 μg H3K27ac antibody (Abcam, #ab4729) overnight at 4°C, followed with collection using 30 μl protein A/G plus agarose beads (Millipore). After elute and purify the chromatin, the ChIP-seq library was constructed using a KAPA HyperPrep Kits (Roche, 07962347001) according to the manufacturer’s instructions，and then run on the Illumina sequencer Hiseq-Xten PE150.
ChIP-Seq libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

tag: antibody

value: H3K9me3 antibody (Abcam, #ab232324)


title: Clrn1-/-_Rep2_Organ of Corti P21

description: Library name: MUT1-2


title: WT_K27_S25C0153_rep1

description: Library name: Sample2

value: H3K27ac antibody (abcam , #ab4729)


title: MT_K27_S25C0154_rep1

description: Library name: Sample4


title: INPUT_WT_K27_S25C0155_rep2

description: Library name: Sample1


title: INPUT_MT_K9_S25C0156_rep1

description: Library name: Sample7


title: INPUT_MT_K27_S25C0156_rep2

description: Library name: Sample3


title: Rec1

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: F303

data_processing:
This WGS dataset originates from the exome-based CNVkit analysis, in which CNVkit was run using exome target regions rather than whole-genome coverage
Assembly: mouse mm10, for WGS, FVB_NJ (provided by NoVo gene)
Supplementary files format and content: table-delimited text files includes raw counts, for WGS, cnr and cns

source_name: uterine tumor

extract_protocol:
For RNA-seq:Total RNA was extracted from tissue samples using a standard column-based purification method following the manufacturer’s instructions. RNA quality and integrity were assessed using the Agilent 2100 Bioanalyzer and only high-quality RNA was used for library construction. All RNA extractions were performed prior to submission to Novogene for RNA-seq library preparation and sequencing. For WGS:Genomic DNA was extracted from tumor tissues using a standard column-based DNA purification kit following the manufacturer’s protocol. DNA purity and concentration were assessed using Nanodrop. High-quality genomic DNA was used for subsequent whole-genome sequencing (WGS), and the processed CNV data uploaded here were generated from the WGS results.
RNA-seq libraries were prepared using Novogene’s standard Illumina TruSeq-compatible mRNA-seq library construction workflow. Briefly, poly(A)+ mRNA was enriched using oligo(dT) magnetic beads, followed by fragmentation and synthesis of first- and second-strand cDNA. After end repair, A-tailing, and adaptor ligation, the cDNA products were PCR-amplified to generate sequencing-ready libraries. Whole-genome sequencing (WGS) libraries were prepared using a standard Illumina DNA library construction protocol. Genomic DNA was sheared to the desired fragment size, followed by end repair, A-tailing, adaptor ligation, and PCR amplification. Libraries passing quality control were sequenced on an Illumina platform, and the resulting WGS data were used for downstream CNV analysis.

value: uterine tumor

value: mouse tumor cell


title: Clrn1-/-_Rep1_Organ of Corti P21

description: Library name: MUT1-1


title: INPUT_WT_K9_S25C0155_rep1

description: Library name: Sample5


title: KrasG12D; PTEN-/-_1

description:
Library name: CX2a
Colume names: Geneid, CX2a, CX2b

value: KrasG12D; PTEN-/-_1


title: KrasG12D; PTEN-/-_2

description:
Library name: CX2b
Colume names: Geneid, CX2a, CX2b

value: KrasG12D; PTEN-/-_2


title: WT_K9_S25C0151_rep1

description: Library name: Sample6

value: cortex


title: FF 50% 24h rep3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

description: Library name: FF50_24h_3

data_processing:
Libraries  were sequenced on a NovaSeq 6000 (Illumina; 151 bases, paired-end) and basecall demultiplexing was performed with bcl2fastq 2 (Illlumina).
Read pairs (151bp) were trimmed using cutadapt 2.3 (Martin, 2011).
Trimmed reads were aligned to the mm10 mouse reference genome using STAR 2.7.8a (Dobin et al., 2013) and gene-level quantification was performed using RSEM 1.3.3 (Li and Dewey, 2011).
Assembly: GRCm38
Supplementary files format and content: For each sample, a gene quantification file is provided (tab-delimited text with header).  Each quantification file contains Ensembl, Entrez, and symbol IDs along with counts (RSEM pseudocounts), FPKM, and TPM.
Supplementary files format and content: A supplementary quantification matrix is provided for count, FPKM, and TPM, containing gene annotations and values for all samples in the experiment.

source_name: oviductal epithelium

growth_protocol: Organoids were generated from mouse oviductal epithelium from wild type B6 mice aged 8-12 weeks.

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen).
Strand-specific, polyA-selected libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760).

treatment_protocol: Organoids were exposed to human follicular fluid (or PBS) at a 1:1 ratio with organoid media and then harvested after 24 hours. Follicular fluid was gathered from patients from Michigan Medicine (IRBMED # HUM0133335) under IRB consented protocol.

value: oviductal epithelium

value: organoids

value: human follicular fluid (50% of media)


title: FF 50% 24h rep2

description: Library name: FF50_24h_2


title: Rec9

description: Library name: A568


title: FF 50% 24h rep4

description: Library name: FF50_24h_4


title: FF 50% 24h rep1

description: Library name: FF50_24h_1


title: FF 0% 24h rep2

description: Library name: FF0_24h_2

value: PBS


title: FF 0% 24h rep4

description: Library name: FF0_24h_4


title: FF 0% 24h rep1

description: Library name: FF0_24h_1


title: Mouse_RNA-seq:APP-LPS5

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

institute: Institut Pasteur de Lille

description: Library name: 60_S36

data_processing:
Raw reads were quality-checked using FastQC.
Adapter sequences and low-quality bases were trimmed with Trimmomatic.
Pseudoalignment was performed with Kallisto against the Ensembl Mus musculus transcriptome (release-111).
Transcript abundance estimates were imported into R using tximport.
Differential expression analysis was performed using DESeq2. Genes with |log2FC| > 1 and FDR < 0.05 were considered differentially expressed.
Assembly: Mus musculus, Ensembl transcriptome release-111
Supplementary files format and content: Normalized read counts per gene (tab-delimited text file).
Supplementary files format and content: Differential expression tables including log2 fold change, p-values, and FDR (CSV or TSV).

source_name: microglia

growth_protocol: Adult microglia were isolated from the cortices of 10–11-month-old wild-type and APP-transgenic (hAPPJ20, PDGFAPPSw,Ind) mice. Cells were maintained for 4 weeks in DMEM/F12 medium supplemented with 10% fetal bovine serum, 1% GlutaMAX, non-essential amino acids, sodium pyruvate, HEPES, and macrophage colony-stimulating factor (5 ng/mL), with half-media changes twice weekly.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit (#74136) following the manufacturer’s instructions. RNA integrity was assessed, and only samples with RIN > 8.5 were used for sequencing.
Libraries were prepared using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD, incorporating ERCC RNA spike-in mixes and Unique Molecular Identifiers (UMIs) before PCR amplification.

treatment_protocol: Microglia were treated with either vehicle (medium only) or lipopolysaccharide (LPS, 100 ng/mL) for 6 h, followed by a 16 h recovery in fresh medium.

value: microglia

value: APP

value: LPS


title: Mouse_RNA-seq:APP-Veh5

description: Library name: 59_S35

value: Veh


title: FF 0% 24h rep3

description: Library name: FF0_24h_3


title: Mouse_RNA-seq:APP-LPS4

description: Library name: 52_S30


title: Mouse_RNA-seq:WT-LPS5

description: Library name: 58_S32

value: WT


title: APM

description: Library name: M406

value: APM


title: Mouse_RNA-seq:WT-LPS4

description: Library name: 42_S26


title: Mouse_RNA-seq:WT-Veh4

description: Library name: 57_S31


title: Mouse_RNA-seq:APP-Veh4

description: Library name: 51_S29


title: Mouse_RNA-seq:WT-Veh3

description: Library name: 41_S25


title: Mouse_RNA-seq:WT-Veh2

description: Library name: 21_S39


title: Mouse_RNA-seq:WT-LPS3

description: Library name: 22_S40


title: Mouse_RNA-seq:APP-LPS3

description: Library name: 12_S22


title: Mouse_RNA-seq:APP-Veh3

description: Library name: 11_S21


title: Mouse_RNA-seq:APP-LPS2

description: Library name: 8_S14


title: Mouse_RNA-seq:WT-LPS2

description: Library name: 10_S18


title: Mouse_RNA-seq:APP-Veh2

description: Library name: 7_S13


title: Mouse_RNA-seq:WT-LPS1

description: Library name: 5_S9


title: Mettl3_shRNA-1

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: Library name: Mettl3-shRNA-1

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: read counts for each genes were given in the processed data files

source_name: mouse embryonic fibroblasts

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

value: mouse embryonic fibroblasts

value: overexpress Ascl1/Brn3b/Isl1


title: Mouse_RNA-seq:APP-LPS1

description: Library name: 4_S2


title: Mettl3_shRNA-2

description: Library name: Mettl3-shRNA-2


title: Mouse_RNA-seq:APP-Veh1

description: Library name: 3_S1


title: Ctrl_shRNA-2

description: Library name: Ctrl_shRNA-2


title: Mettl3_shRNA-3

description: Library name: Mettl3-shRNA-3


title: Ctrl_shRNA-3

description: Library name: Ctrl_shRNA-3


title: Ctrl_shRNA-1

description: Library name: Ctrl_shRNA-1


title: Mettl3_OE-3

description: Library name: Mettl3-OE-3


title: Mettl3_OE-1

description: Library name: Mettl3-OE-1


title: Mettl3_OE-2

description: Library name: Mettl3-OE-2


title: Ctrl_OE-3

description: Library name: Ctrl_OE-3


title: Ctrl_OE-1

description: Library name: Ctrl_OE-1


title: Ctrl_OE-2

description: Library name: Ctrl_OE-2


title: DAI13_m6Aseq_IP

description: Library name: DAI13_IP

data_processing:
raw data was processed to remove adaptor and low quanlity reads using trimmomatic and get clean reads
clean reads were aligned to the mouse reference genome (mm10) using Bowtie2
peak calling was performed using MACS2  peak finding algorithm.
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: MeRIP-seq

source_name: MEF

extract_protocol:
RNAs were extracted using TRIzol reagent
poly(A)-RNA was purified using Dynabeads mRNA DIRECT purification kit (Thermo Fisher), and was then immunoprecipitated against an m6A antibody (Synaptic Systems) bound to Protein G Dynabeads (Thermo Fisher), eluted by competition with free m6A (Sigma). The precipitated RNAs were reverse transcribed, amplified, tagmented and indexed using Smart-Seq2 protocol.

value: MEF

value: MEFs overexpressing Ascl1/Brn3b/Isl1


title: DAI5_m6Aseq_IP

description: Library name: DAI5_IP


title: DAI13_m6Aseq_input

description: Library name: DAI13_input


title: Mouse_RNA-seq:WT-Veh1

description: Library name: 9_S17


title: DC2, INP, rep3

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: DC2_INP_rep3
input_rep2_DC2

data_processing:
51-bp paired-end reads were mapped to a hybrid genome made from concatenating the mouse mm10 genome (Ensembl GRCm38) with the yeast sacCer3 genome.
Mapping was performed using BWA-MEM (version 0.7.18-r1243) with the option ‘-M’ and filtered for a mapping quality of 10. Duplicate alignments were removed using MarkDuplicates from the Picard toolset (version 3.3.0) with the option ‘-REMOVE_DUPLICATES true’.
Paired-end reads were converted to fragments by reading in mapped, properly paired reads using the GenomicAlignments R/Bioconductor package (release 3.20). Peaks were called using MACS2 version 2.2.9.1 using samples pooled by treatment and pooled input samples as the ‘control’ argument using the options ‘-f BEDPE -g mm --keep-dup all --broad’. Peaks detected on yeast chromosomes were removed.
Genomic bigwig tracks were generated for both individual samples and samples pooled by treatment from fragments mapping to the mouse genome using a custom R script using the ‘coverage’ function from the GenomicRanges R/Bioconductor package. The track heights were multiplied by a factor ‘1x10e6 / number of yeast reads’ for values to represent ‘coverage per million yeast reads’ to allow quantitative comparisons. Signal values per peak were obtained by using the BigWigFile-method of the ‘summary’ function in the rtracklayer R/Bioconductor package.
For aggregate visualization of coverage data the tornadoplot R/GitHub package was used and TSS/exons were determined using the EnsDb.Mmusculus.v75 R/Bioconductor package. To calculate distances to the first internal exon, exons within a gene were first collapsed to disjoint ranges using the ‘reduce’ function from the GenomicRanges R/Bioconductor package. The distance was then taken as the number of basepairs between the 3’ end of the most 5’ exon and the 5’ end of the subsequent exon for genes that have at least 2 distinct exons.
Assembly: mm10, sacCer3
Supplementary files format and content: bigwig (per sample)
Supplementary files format and content: broadpeak (per cell type)
Supplementary files format and content: Excel workbook (normalized peak counts of all samples)

source_name: Isolated and sorted DC2

extract_protocol:
Bone marrow was isolated from femur and tibia. pDC, DC1 and DC2 populations (N=3 biological replicates) were sorted by FACS. Cells from 5 (WT or KO) mice were pooled per replicate. N=2 pools with the highest cell count for each cell type were fixed with 1% methanol free formaldehyde for 10 minutes & quenched with 125 mM glycine for 5 minutes. Quenced cells were lysed in 50 mM Tris-HCl pH8, 10 mM EDTA pH8, 1 % SDS + protease inhibitor cocktail, and sonicated for 3 minutes (30sec on, 30 sec off) on the Bioruptor PICO. Yeast chromatin was spiked in (1:1000) based on DNA concentration) prior to immunoprecipitation to allow for downstream normalization.
The library was prepped using the KAPA genomic DNA prep Hyper, purified and quantified using the Bioanalyzer DNA 7500.

tag: spike-in organism

value: Saccharomyces cerevisiae

value: Isolated and sorted DC2

tag: chip antibody


title: DC1, INP, rep3

description:
Library name: DC1_INP_rep3
input_rep2_DC1

source_name: Isolated and sorted DC1

value: Isolated and sorted DC1


title: MEF_m6Aseq_input

description: Library name: MEF_input

value: MEFs


title: DC2, INP, rep2

description:
Library name: DC2_INP_rep2
input_rep1_DC2


title: MEF_m6Aseq_IP

description: Library name: MEF_IP


title: DAI5_m6Aseq_input

description: Library name: DAI5_input


title: pDC, INP, rep3

description:
Library name: pDC_INP_rep3
input_rep2_pDC

source_name: Isolated and sorted pDC

value: Isolated and sorted pDC


title: pDC, INP, rep1

description:
Library name: pDC_INP_rep1
input_rep1_pDC


title: DC2, IP, rep2

description:
Library name: DC2_IP_rep2
H3K79me2_rep1_DC2

value: anti-H3K79me2 (04-835 Sigma), anti-HA-12CA5 (17 03 2019 NKI; in-house)


title: DC2, IP, rep3

description:
Library name: DC2_IP_rep3
H3K79me2_rep2_DC2


title: DC1, IP, rep3

description:
Library name: DC1_IP_rep3
H3K79me2_rep2_DC1


title: DC1, INP, rep1

description:
Library name: DC1_INP_rep1
input_rep1_DC1


title: pDC, IP, rep3

description:
Library name: pDC_IP_rep3
H3K79me2_rep2_pDC


title: DC1, KO, day12

description:
Library name: DC1_Dot1l_KO
4_DC1_DOT1L_KO

data_processing:
51-bp paired-end reads were aligned against the mouse reference genome (Ensembl build 38) using Tophat (version 2.1, bowtie version 1.1).
Tophat was supplied with a Gene Transfer File (GTF, Ensembl version 77) and was supplied with the following parameters: “prefilter-multihits –no-coverage-search – bowtie1 –library-type fr-firststrand”.
To count the number of reads per gene, a custom script which is based on the same ideas as HTSeq-count has been used.
A list of the total number of uniquely mapped reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Assembly: mm10
Supplementary files format and content: Tab delineated text file with raw counts for each sample

extract_protocol:
Bone marrow was isolated from femur and tibia. pDC, DC1 and DC2 populations were sorted by FACS. Cells from 5 (WT or KO) mice were pooled per sample. Cells were resuspended in RLT supplemented with 2-mercapthoethanol. Total RNA was isolated with the RNAeasy mini kit (Qiagen).
cDNA libraries were generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) as per manufacturers protocol.

treatment_protocol: Mice received intraperitoneal injections of 4-hydroxytamoxifen (4-OHT), 75 mg/kg on three consecutive days. Mice were sacrificed ten days after the final injection (day 12).

value: het; hom

tag: time

value: day 12


title: DC1, WT, day12

description:
Library name: DC1_Dot1l_WT
3_DC1_DOT1L_WT

value: het; wt


title: DC2, WT, day12

description:
Library name: DC2_Dot1l_WT
5_DC2_DOT1L_WT


title: pDC, IP, rep1

description:
Library name: pDC_IP_rep1
H3K79me2_rep1_pDC


title: pDC, KO, day12

description:
Library name: pDC_Dot1l_KO
2_pDC_DOT1L_KO

source_name: pDC

value: pDC


title: DC2, KO, day12

description:
Library name: DC2_Dot1l_KO
6_DC2_DOT1L_KO