title: Recombinant-Slurp1_3D_3

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

description:
Library name: Slurp1_3D_S12
Slurp1_3D_3

data_processing:
6 RNA-Seq samples were pooled and sequenced on Illumina HiSeq4000
Basecalling was performed by RTA (version 3.4.4).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered to retain reads with base quality Q30 and above (~92% retained)
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.5.2b) is run in twopass basic mode to align trimmed reads to mm10 genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the mm10 (Gencode M12)
differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains RSEM gene-level counts output.

source_name: In vitro cell culture

growth_protocol: 3D matrigel culture, DMEM with 10% FBS

extract_protocol:
Total RNA, treated with Dnase I (Qiagen; 79254), was extracted using RNeasy kit (Qiagen; 74106).
TruSeq mRNA prep kit

treatment_protocol: rGST (50nM) or rSLUPR1 (50nM)

value: In vitro cell culture

value: Mouse mammary tumor cell


title: Recombinant-Slurp1_3D_1

status: Public on Mar 12 2026

type: SRA

country: USA

description:
Library name: Slurp1_3D_S10
Slurp1_3D_1

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: Female_Brain_0.1PCB_YesFA_35_02

city: Davis

first: Janine

last: LaSalle

state: California

address: 1275 Med Science Dr

institute: University of California, Davis

description: Library name: 35_02_BRAIN

data_processing:
Raw RNA-seq fastq files were processed by trimming adapters using Trim Galore (v0.6.5)
Trimmed sequence reads were aligned to the mouse genome (mm10)
Gene count quantification was done using STAR (v2.7.3a)
QC metrics were generated with MultiQC (v1.9).
Assembly: mm10
Supplementary files format and content: .xlsx format; normalized counts

molecule: total RNA

extract_protocol:
Nucleic acids were extracted by homogenizing the same half of placenta and brain tissue using a TissueLyser II (Qiagen) followed by the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions.
Isolated RNA underwent quantification and QC using a Bioanalyzer Eukaryotic Total RNA Nano Assay (Agilent). Libraries were constructed using the KAPA mRNA HyperPrep kit (Roche) and NEXTFLEX Unique Dual Index Barcodes (PerkinElmer). Libraries were pooled and sequenced on a NovaSeq 6000 S4 flow cell (Illumina) for 150 bp paired end reads resulting in approximately 25 million uniquely mapped reads per sample.

value: Brain

tag: strain

tag: Sex

value: F

tag: pcb treatment

tag: folic acid_treatment

value: Yes


title: FKBP-SETDB1 A12A10 ES, dox, MPP8

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: Library name: xxC057_dTSETDB1A12A10_dox_MPP8

library_source: genomic

data_processing:
ChIP-sequencing analysis was performed using previously established pipelines45. For calibrated ChIP-seq experiments, raw fastq reads were mapped using Bowtie2 (v.2.3.5.1)67 to the 129S1xCast N-masked mm10 genome concatenated with the dm6 Drosophila genome using the following parameters: “--very-sensitive --no-discordant --no-mixed -X 2000”. Unmapped reads were then removed. PCR duplicates were identified and removed using picard-tools “MarkDuplicates” (Broad Institute) and remaining reads were then assigned to each allele using SNPsplit68. To calculate calibration factors, mm10 and dm6 mapped reads for each sample and input were counted using SAMtools (v.1.16)69. Calibration factors for cChIP-seq were then calculated according to the derived formula for occupancy ratio (ORi)70. In order to generate calibrated bigwig files for mouse chrX, bam files were initially filtered using the “intersect” function from BEDtools (v.2.30.0)71 to generate a bam file containing mouse chrX reads only. During the generation of the iXist-ChrXCast cell line using CRISPR-Cas9–facilitated homology-directed recombination, two SNPs (mm10, chrX:103482682 A/T and mm10, chrX:103482895 A/T) between the Cast and 129 alleles became uninformative, as both X alleles were converted to the 129 allele (T at both positions). Consequently, any reads spanning these two sites are no longer allele-specific as intended and were therefore removed from the allelic BAM files. BAM files were then sorted and indexed using SAMtools69 and bigWig files were finally generated using deepTools (v.3.5.1)72 bamCoverage per 10 million reads considering the calibration factors. For KAP1 and MPP8 (non-calibrated), ChIP signal was calculated from one million library size normalized values. BigWig files were then visualized using IGV (https://software.broadinstitute.org/software/igv/)73. To quantify the number of ChIP reads per kb over the Xist locus (chrX: 103460373-103483233), we used the function “bigWigAverageOverBed” from UCSCTools.
Assembly: mm10; dm6
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

growth_protocol: mESC were grown in ESC medium at 37oC in a 5% CO2 incubator and passaged onto 0.1% gelatin-coated plates in feeder-dependent conditions every 2-3 days using TrypLE Express (Life Technologies). Mitomycin C-inactivated SNLP (STO mouse fibroblasts expressing Neomycin and Puromycin resistance and Lif genes) were used as feeder cells. Cells were pre-plated and passaged at least twice to remove feeders prior to cell collection for genomic experiments. ESC medium consisted of Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS), 1x NEAA (Non-essential amino acids; Life Technologies), 2mM L-glutamine (Life Technologies), 1x Penicillin-Streptomycin (Life Technologies), 50µM b-mercaptoethanol (Life Technologies) and Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house.

extract_protocol:
For RNA polymerase II calibrated ChIP-seq (cChIP-seq), 5x107 mESCs were pooled with 1x107 Drosophila cells after collection, washed in PBS wash and counted using a Countess II FL Automated Cell Counter (Life Technologies). Cells were crosslinked for 10min with 1% formaldehyde. The reaction was quenched using glycine for additional 10min before recovering the cells by centrifugation at 1000g for 5min at 4oC. After a PBS wash, supernatant was removed and cells were snap frozen and stored at -80oC until use. Cell pellets were thawed on ice, resuspended in 1mL of FA-Lysis Buffer (50 mM HEPES pH7.9, 150 mM NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1%  Sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitors, 1 mM AEBSF, 10 mM NaF and incubated on ice for 10min prior to sonication using a Bioruptor Pico Sonicator (Diagenode) for 30 cycles (30sec on/off). Post-sonication chromatin was spun at maximum speed for 10min at 4oC and the supernatant was transferred to a new 1.5mL tube. For each IP, 300µg of chromatin were diluted to a total volume of 1mL in FA-Lysis Buffer and precleared by incubation with 40µL of pre-blocked rProtein A Sepharose™ Fast Flow bead slurry (Amersham) for 1h at 4oC with rotation. Pre-cleared chromatin was aliquoted in 1.5mL Protein lobind tubes and incubated overnight at 4oC with rotation with the corresponding antibody (15µL Anti-Rbp1 NTD, D8L4Y, Cell Signaling Technologies; 12.5µL Anti-Rbp1 Ser5P, D9N5I, Cell Signaling Technologies; 12.5µL Anti-Rbp1 Ser2P, E1Z3G, Cell Signaling Technologies). 10% of pre-cleared chromatin was kept as input. After incubation, 40µL of pre-blocked rProtein A Sepharose™ Fast Flow bead slurry (Amersham) were added to each sample and incubated for a minimum of 3h at 4oC followed by single 5min washes at 4oC with FA-Lysis, FA-Lysis 500 (same composition as FA-Lysis Buffer but with 500mM NaCl) and DOC (10 mM Tris pH8.0, 250 mM LiCl, 2 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate) buffers and two washes with TE pH8.0. The DNA was then eluted from the beads by incubation at 30oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. IP and input samples were reverse crosslinked overnight and RNAse- and Proteinase K-treated, and the DNA was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions. For KAP1 and MPP8 ChIP-seq, 5x107 mESC cells were collected in PBS and double crosslinked by incubating with 2mM DSG for 50min at room temperature followed by an additional 12min with 1% formaldehyde. The reaction was quenched by addition of glycine and further incubation with rotation for 10min. Cells were pelleted by centrifugation, washed once with PBS and the pellet was snap frozen and stored at -80oC. To prepare chromatin, the cell pellets were thawed on ice and lysed in 10mL of LB1 (50mM HEPES-KOH pH 7.9, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with protease inhibitors for 10min, rotating at 4oC. Nuclei were recovered by centrifugation and resuspended in 10mL LB2 (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) with protease inhibitors and incubated rotating for 10min. After centrifugation, the pellet was resuspended in 1mL of LB3 (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine) with protease inhibitors per 5x 107 cells and subjected to sonication using a Bioruptor Pico (Diagenode) for 30 cycles (30 sec on/off). After sonication, samples were spun for 2 min 2000rpm at 4oC and the supernatant was collected into a new tube to which 110µL of LB3 with 10% Triton X-100 were added and mixed by inversion. Chromatin was spun at maximum speed for 10 min and the supernatant was collected into a new tube, snap frozen and stored. For immunoprecipitation, chromatin was thawed on ice and 110µL were taken per reaction and diluted in 990µL ChIP dilution buffer (1% Triton X-100, 1mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl). Chromatin was precleared by incubation with pre-blocked rProtein A Sepharose™ Fast Flow beads (Amersham) for 1 hour (40μL bead slurry/mL of chromatin) at 4oC and 100μL set aside as input. Antibodies (KAP1, Abcam, ab22553, 5µg; MPP8, Proteintech, 16796-1-AP, 7µg) were added to 1mL of precleared chromatin each and incubated overnight at 4oC with rotation. Samples were then incubated for 4h with 40µL of pre-blocked rProtein A Sepharose™ Fast Flow beads (Amersham) followed by single 4min washes with Low Salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), High Salt (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl), LiCl (0.25M LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA, 10mM Tris pH 8.0) wash buffers and two washes with 1xTE. The DNA was then eluted from the beads by incubation at 25oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. IP and input samples were reverse crosslinked overnight and RNAse- and Proteinase K-treated, and the DNA was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions.
ChIP and input DNA was quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and submitted to library preparation using the the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and their length was estimated using the Bioanalyzer High Sensitivity DNA kit (Agilent) before pooling and subjected to paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

treatment_protocol: To induce Xist expression, medium was supplemented with 1µg/mL doxycycline. To induce protein degradation in lines expressing FKBP12F36V-tagged SETDB1, medium was supplemented with 100nM dTAG-13 (Tocris Bioscience).

tag: strain background

value: Cast x 129S

value: mESC

tag: treatment

value: doxycycline for 24hours

tag: chip antibody

value: anti-MPP8 (Proteintech, Cat# 16796-1-AP)

tag: spike-in


title: LUAD_1_TCR

city: Beijing

first: Yu

last: Wang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

department: Department of Neurosurgery

country: China

institute: Peking Union Medical College Hospital

description:
Library name: pt1556_TCR
TCR VDJ transcripts library enriched from total cDNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were madeusing the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-.gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human GRCh38
Supplementary files format and content: Cell Ranger multi output files: 5GEX_barcodes.tsv.gz, 5GEX_features.tsv.gz, 5GEX_matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi output files: clonetypes.csv, contig_annotations.csv.
Library strategy: TCR-Seq

organism: Homo sapiens

source_name: Brain Metastasis

extract_protocol:
Briefly, tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco), and enzymatically digested with gentleMACS (Miltenyi) using program 37C_m_TDK_2 on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% fetal bovine serum (FBS, Gibco)). Single cell suspensions were stained with antibodies against 7AAD for FACS sorting, performed on a BD Melody instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes and determine cell viability and cell concentration using a Countstar Automated Cell Counter.
Cells were loaded by using the 10x Chromium Single Cell V(D)J Reagent Kits v2. Cells were captured in droplets to generate nanoliter-scale Gel bead in EMulsion (GEMs). GEMs were then reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad programmed at 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific), followed by PCR amplification. Amplified cDNA was then used for both 5’ gene expression library construction and TCR/BCR V(D)J targeted enrichment performed with the Chromium Single Cell V(D)J Enrichment Kit (10x Genomics), followed by V(D)J library construction. For RNA-seq library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected. For TCR/BCR library construction, TCR/BCR transcripts were enriched from amplified cDNA by PCR. Subsequently, enriched PCR product was fragmented and end-repaired, size-selected, PCR-amplified with sample-indexing primers, and size-selected. Libraries prepared according to the manufacturer’s user guide were then purified and profiled for quality assessment. Single-cell RNA and TCR/BCR V(D)J libraries were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads (performed by Analytical Bioscience Limited, Beijing).

value: Brain Metastasis

tag: primary tumor

value: Lung adenocarcinoma

tag: group

value: Normal weighted

tag: library type

value: TCR


title: Female_Brain_0.1PCB_YesFA_36_01

description: Library name: 36_01_BRAIN


title: COAD_1_GEX

description:
Library name: pt4697_GEX
GEX (5' mRNA library)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were madeusing the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-.gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human GRCh38
Supplementary files format and content: Cell Ranger multi output files: 5GEX_barcodes.tsv.gz, 5GEX_features.tsv.gz, 5GEX_matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi output files: clonetypes.csv, contig_annotations.csv.

value: Colon adenocarcinoma

value: mRNA


title: FKBP-SETDB1 A12A10 ES, Control, KAP1

description: Library name: xxC059_dTSETDB1A12A10_ES_KAP1

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: anti-KAP1 (Abcam, Cat# ab22553)


title: Recombinant-Slurp1_3D_2

description:
Library name: Slurp1_3D_S11
Slurp1_3D_2

value: In vitro cell culture


title: COAD_1_TCR

description:
Library name: pt4697_TCR
TCR VDJ transcripts library enriched from total cDNA


title: FKBP-SETDB1 G6D2 ES, dTAG+dox, Input, single crosslinking

description: Library name: xC034_dTSETDB1_G6D2_dTAGdox_Input

value: dTAG-13 for 27hours and doxycycline for 24 hours

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Female_Brain_0.1PCB_YesFA_32_08

description: Library name: 32_08_BRAIN

value: Brain

value: F


title: GST-control_3D_3

description:
Library name: GST_3D_S15
GST_3D_3

value: Mouse mammary tumor cell

value: Control


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, MPP8

description: Library name: xxC058_dTSETDB1A12A10_dTAGdox_MPP8

value: Cast x 129S

value: mESC


title: GST-control_3D_1

description:
Library name: GST_3D_S13
GST_3D_1


title: Female_Brain_0.1PCB_YesFA_36_03

description: Library name: 36_03_BRAIN

value: Yes


title: Female_Brain_0.1PCB_YesFA_35_01

description: Library name: 35_01_BRAIN


title: FKBP-SETDB1 A12A10 ES, Control, MPP8

description: Library name: xxC056_dTSETDB1A12A10_ES_MPP8

value: anti-MPP8 (Proteintech, Cat# 16796-1-AP)


title: BRCA_2_TCR

description:
Library name: pt6284_TCR
TCR VDJ transcripts library enriched from total cDNA

value: Brain Metastasis

value: Breast Cancer

value: Obese


title: LUAD_1_GEX

description:
Library name: pt1556_GEX
GEX (5' mRNA library)

value: Lung adenocarcinoma

value: Normal weighted

value: mRNA


title: Female_Brain_0.1PCB_YesFA_32_06

description: Library name: 32_06_BRAIN


title: FKBP-SETDB1 G6D2 ES, dox, Input, single crosslinking

description: Library name: xC033_dTSETDB1_G6D2_dox_Input

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycycline for 24hours


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, Input, single crosslinking

description: Library name: xC032_dTSETDB1_P2F7_dTAGdox_Input

value: dTAG-13 for 27hours and doxycycline for 24 hours

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: BRCA_2_GEX

description:
Library name: pt6284_GEX
GEX (5' mRNA library)


title: BRCA_1_TCR

description:
Library name: pt6007_TCR
TCR VDJ transcripts library enriched from total cDNA

value: TCR


title: Female_Brain_0.1PCB_YesFA_32_03

description: Library name: 32_03_BRAIN

value: Brain

value: F


title: FKBP-SETDB1 P2F7 ES, dox, Input, single crosslinking

description: Library name: xC031_dTSETDB1_P2F7_dox_Input

value: Cast x 129S


title: Growing tumor cell in Tgfbr2 KO mice_3

description: Library name: GTS_Batch2_KO3_S57

data_processing:
12 RNA-Seq samples were pooled and sequenced on Illumina Nextera XT with HiSeq3000/4000 chemistry
Basecalling was performed by RTA (version 3.4.4).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.20) allowing 1 mismatch.
Reads were filtered to retain reads with base quality Q30 and above (~92% retained)
Trimming of adapters and low-quality bases was performed using CutAdapt (v1.18).
STAR (version 2.5.2b) is run in twopass basic mode to align trimmed reads to mm10 genome
Gene-level expression quantificiation  was performed using RSEM (version 1.3.3) and the mm10 (Gencode M12)
differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains RSEM gene-level counts output.

source_name: mouse lung

value: mouse lung

value: Mouse mammary tumor cell

value: Tgfbr2 KO


title: GST-control_3D_2

description:
Library name: GST_3D_S14
GST_3D_2

value: In vitro cell culture

value: Control


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, Input, single crosslinking

description: Library name: xC030_dTSETDB1_A12A10_dTAGdox_Input

value: mESC


title: Female_Brain_0.1PCB_YesFA_31_06

description: Library name: 31_06_BRAIN

value: Yes


title: BRCA_1_GEX

description:
Library name: pt6007_GEX
GEX (5' mRNA library)

value: Brain Metastasis

value: Breast Cancer

value: Normal weighted


title: Female_Brain_0.1PCB_YesFA_31_03

description: Library name: 31_03_BRAIN


title: Growing tumor cell in Tgfbr2 KO mice_1

description: Library name: GTS_Batch2_KO1_S55


title: Growing tumor cell in Tgfbr2 KO mice_2

description: Library name: GTS_Batch2_KO2_S56


title: Female_Brain_0.1PCB_YesFA_31_01

description: Library name: 31_01_BRAIN


title: Inhibitor_2

first: Wenfeng

last: Xie

state: Beijing

address: 49 North Garden Road

department: Department of Obstetrics and Gynecology

institute: Peking University Third Hospital

description:
Library name: T2
Human morula treatment with Concanamycin A

data_processing:
Differentially expressed genes (log2 fold change > 2, pvalue < 0.05) between two groups were analyzed using DESeq2 v1.28.1. Gene Ontology (GO) enrichment analysis of DEGs was performed by enrichGO function in the R package clusterProfiler v4.8.3. Gene set enrichment analysis (GSEA). GSEA was performed using GSEA v2.0.14 software (www.broadinstitute.org/gsea/index.jsp). Heatmap representation of gene expression was generated by the “pheatmap” package of R (https://CRAN.R-project.org/package=pheatmap).
Assembly: GRCh38
Supplementary files format and content: csv files include raw counts and FPKM values for each Sample

source_name: Human embryo

extract_protocol:
For the Concanamycin A-treated group, human morulae were cultured in G-2 medium (G2 plus, Vitrolife Sweden AB) supplemented with 1 nM Concanamycin A (MCE, HY-N1724) for at least 24 hours. On day 5 post in vitro fertilization, those Concanamycin A-treated embryos that remained at the morula stage without cavitation were identified as arrested morulae, while control embryos had progressed to the blastocyst stage with cavitation. Subsequently, human blastocysts from the control group and arrested morulae from the Concanamycin A-treated group were collected for Smart-seq2 sequencing and immunofluorescence analyses.
Human embryos were collected from control and Concanamycin A-treated groups. For each embryo, mRNA was isolated and reverse transcribed into cDNA using oligo-dT primers. Template switching was then employed to generate full-length cDNA. The cDNA was subsequently amplified by PCR. After amplification, the cDNA was processed for library construction and sequenced with a depth of 6G and paired-end reads (PE150) on the Illumina HiSeq platform by Annoroad Gene Technology (Beijing, P. R. China; www.annoroad.com).

value: Human embryo

value: WT

value: Concanamycin A

tag: batch

value: missing


title: FKBP-SETDB1 A12A10 ES, dox, Input, single crosslinking

description: Library name: xC029_dTSETDB1_A12A10_dox_Input

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: doxycycline for 24hours

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Male_Brain_0PCB_YesFA_20_01

description: Library name: 20_01_BRAIN

value: Brain

value: M


title: Growing tumor cell in WT mice_3

description: Library name: GTS_Batch1_WT3_S6

value: mouse lung

value: Mouse mammary tumor cell


title: FKBP-SETDB1 G6D2 ES, dTAG+dox, RNAPolII Ser2P

description: Library name: xC028_dTSETDB1_G6D2_dTAGdox_Ser2P

value: Cast x 129S

value: dTAG-13 for 27hours and doxycycline for 24 hours

value: anti-phospho-Rpb1 CTD (Ser2) (E1Z3G) (Cell Signaling, Cat# 13499)


title: Growing tumor cell in WT mice_2

description: Library name: GTS_Batch1_WT2_S5


title: Male_Brain_0PCB_YesFA_18_06

description: Library name: 18_06_BRAIN

value: Yes


title: FKBP-SETDB1 G6D2 ES, dTAG+dox, RNAPolII Ser5P

description: Library name: xC027_dTSETDB1_G6D2_dTAGdox_Ser5P

value: mESC

value: anti-phospho-RBP1 CTD (Ser5) (D9N5I) (Cell Signaling, Cat# 13523)


title: Ctrl_3

description:
Library name: C3
Human blastocyst

value: Human embryo


title: Dormant tumor cell_in Tgfbr2 KO mice_3

description: Library name: DTS_Batch2_KO3_S60

value: Tgfbr2 KO


title: Inhibitor_1

description:
Library name: T1
Human morula treatment with Concanamycin A

value: WT

value: Concanamycin A


title: Growing tumor cell in WT mice_1

description: Library name: GTS_Batch1_WT1_S4


title: Male_Brain_0PCB_YesFA_18_04

description: Library name: 18_04_BRAIN


title: Male_Brain_0PCB_YesFA_18_05

description: Library name: 18_05_BRAIN


title: Ctrl_4

description:
Library name: C4
Human blastocyst

value: missing


title: FKBP-SETDB1 G6D2 ES, dTAG+dox, RNAPolII

description: Library name: xC026_dTSETDB1_G6D2_dTAGdox_PolII

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: anti-RBP1 NTD (D8L4Y) (Cell Signaling, Cat# 14958)


title: Ctrl_1

description:
Library name: C1
Human blastocyst


title: FKBP-SETDB1 G6D2 ES, dox, RNAPolII Ser5P

description: Library name: xC024_dTSETDB1_G6D2_dox_Ser5P

value: doxycycline for 24hours

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Dormant tumor cell_in Tgfbr2 KO mice_1

description: Library name: DTS_Batch2_KO1_S58

value: mouse lung


title: FKBP-SETDB1 G6D2 ES, dox, RNAPolII Ser2P

description: Library name: xC025_dTSETDB1_G6D2_dox_Ser2P


title: Male_Brain_0PCB_YesFA_18_03

description: Library name: 18_03_BRAIN

value: Brain

value: M


title: Dormant tumor cell_in Tgfbr2 KO mice_2

description: Library name: DTS_Batch2_KO2_S59

value: Mouse mammary tumor cell


title: Ctrl_2

description:
Library name: C2
Human blastocyst


title: Inhibitor_3

description:
Library name: T3
Human morula treatment with Concanamycin A


title: FKBP-SETDB1 G6D2 ES, dox, RNAPolII

description: Library name: xC023_dTSETDB1_G6D2_dox_PolII

value: Cast x 129S


title: Dormant tumor cell_in WT mice_2

description: Library name: DTS_Batch1_WT2_S2


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, RNAPolII Ser2P

description: Library name: xC022_dTSETDB1_P2F7_dTAGdox_Ser2P

value: dTAG-13 for 27hours and doxycycline for 24 hours

value: anti-phospho-Rpb1 CTD (Ser2) (E1Z3G) (Cell Signaling, Cat# 13499)


title: BC5

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
PRINSEQ-lite (version 0.20.4) for quality filtering, trimming, and length filtering.
We utilized STAR (version 2.7.9a), for the alignment of the reads against the mouse (mm10) and human (GRCh38) reference genomes for the SMART-seq and RNA-seq datasets, respectively.
Post-processing of the aligned reads was performed using Samtools (version 1.13).
Normalization and differential expression analysis were conducted using DESeq2.
Assembly: mm10 and hg38
Supplementary files format and content: tab delimited text files contain the raw read counts per sample for mouse and human data
Supplementary files format and content: tab delimited text files contain the normalized counts per sample for mouse and human data

source_name: Peripheral blood

growth_protocol: C2, C6 and C15 cell lines were cultured in RPMI 1640 media containing 20% hi-FBS, 2 mM L-glutamine, 10 U/ml penicillin/streptomycin, 1x MEM Non-Essential Amino Acids, 20 mM HEPES buffer, 1 mM sodium pyruvate, 55 μM β-mercaptoethanol and 10 ng/ml IL-2. DERL-2 and DERL-7 cell lines were cultured in RPMI 1640 media containing 10% hi-FBS, 10 U/ml penicillin/streptomycin, 2 mM L-glutamine and 10 ng/ml IL-2. All cell lines were incubated at 37°C with 5% CO2 in a humidified environment

extract_protocol:
Mouse cells: 500 cells per well were collected by FACS sorting into a hard-shell, low-profile, thin-wall 96-well skirted PCR plate (Bio-Rad) containing 4 µl lysis buffer per well (2 U/μl RNase inhibitor (Clontech) in 0.2% (v/v) Triton X-100). Plates were kept at -80°C until further processing. For RNA extraction and preparation of NGS libraries, we followed the Smart-seq2 protocol (DOI: 10.1038/nprot.2014.006). Human cells: RNA extraction was performed with an RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
Mouse cells: library preparation from the amplified cDNA was performed using a Nextera XT DNA library prep kit (Illumina). Library concentrations were quantified with a Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using a 2100 Bioanalyzer instrument (Agilent). Human cells: RNA was subjected to library preparation and polyA-sequenced on a NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions.

value: Peripheral blood

value: Primary T cells


title: BC8


title: Male_Brain_0PCB_YesFA_13_04

description: Library name: 13_04_BRAIN

value: Yes


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, RNAPolII Ser5P

description: Library name: xC021_dTSETDB1_P2F7_dTAGdox_Ser5P

value: mESC

value: anti-phospho-RBP1 CTD (Ser5) (D9N5I) (Cell Signaling, Cat# 13523)


title: Dormant tumor cell_in WT mice_3

description: Library name: DTS_Batch1_WT3_S3

value: WT


title: Dormant tumor cell_in WT mice_1

description: Library name: DTS_Batch1_WT1_S1


title: Male_Brain_0PCB_YesFA_13_05

description: Library name: 13_05_BRAIN


title: BC37


title: Female_Brain_0PCB_YesFA_20_04

description: Library name: 20_04_BRAIN

value: F


title: WT_Ly5.2_gd_2

source_name: Lymph nodes

value: Lymph nodes

value: Primary Gamma-delta  T cells

tag: genetic modification

tag: mouse strain

value: Female


title: Male_Brain_0PCB_YesFA_13_03

description: Library name: 13_03_BRAIN

tag: tissue


title: FKBP-SETDB1 P2F7 ES, dox, RNAPolII Ser2P

description: Library name: xC019_dTSETDB1_P2F7_dox_Ser2P

tag: cell line

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

tag: cell type

value: doxycycline for 24hours

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, RNAPolII

description: Library name: xC020_dTSETDB1_P2F7_dTAGdox_PolII

value: anti-RBP1 NTD (D8L4Y) (Cell Signaling, Cat# 14958)


title: BC36


title: WT_Ly5.2_gd_3


title: Female_Brain_0PCB_YesFA_20_02

description: Library name: 20_02_BRAIN

value: Brain

tag: strain


title: Female_Brain_0PCB_YesFA_20_03

description: Library name: 20_03_BRAIN

tag: Sex


title: BC35


title: DERL7_3

source_name: DERL-7 cell line

value: DERL-7 cell line

value: Hepatosplenic T cell lymphoma


title: WT_Ly5.2_gd_1


title: FKBP-SETDB1 P2F7 ES, dox, RNAPolII

description: Library name: xC017_dTSETDB1_P2F7_dox_PolII

value: Cast x 129S


title: C6_3

value: C6 cell line

value: Gamma-delta  T cell lymphoma

value: STAT5B N642H transgene


title: FKBP-SETDB1 P2F7 ES, dox, RNAPolII Ser5P

description: Library name: xC018_dTSETDB1_P2F7_dox_Ser5P

value: mESC

value: anti-phospho-RBP1 CTD (Ser5) (D9N5I) (Cell Signaling, Cat# 13523)


title: DERL7_2


title: Female_Brain_0PCB_YesFA_18_02

description: Library name: 18_02_BRAIN

value: F

tag: pcb treatment

value: Yes


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, RNAPolII Ser2P

description: Library name: xC016_dTSETDB1_A12A10_dTAGdox_Ser2P

value: dTAG-13 for 27hours and doxycycline for 24 hours

value: anti-phospho-Rpb1 CTD (Ser2) (E1Z3G) (Cell Signaling, Cat# 13499)


title: Female_Brain_0PCB_YesFA_18_01

description: Library name: 18_01_BRAIN

tag: folic acid_treatment


title: C6_2

value: Lymph nodes

value: Female


title: DERL7_1


title: Female_Brain_0PCB_YesFA_13_02

description: Library name: 13_02_BRAIN


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, RNAPolII Ser5P

description: Library name: xC015_dTSETDB1_A12A10_dTAGdox_Ser5P

tag: strain background

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: Female_Brain_0PCB_YesFA_13_01

description: Library name: 13_01_BRAIN

value: Brain


title: C6_1


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, RNAPolII

description: Library name: xC014_dTSETDB1_A12A10_dTAGdox_PolII

tag: treatment

value: anti-RBP1 NTD (D8L4Y) (Cell Signaling, Cat# 14958)


title: DERL2_3

source_name: DERL-2 cell line

value: DERL-2 cell line

value: Hepatosplenic T cell lymphoma


title: C2_3

value: C2 cell line


title: Female_Brain_0PCB_YesFA_12_03

description: Library name: 12_03_BRAIN


title: DERL2_2


title: DERL2_1


title: C2_2

value: Gamma-delta  T cell lymphoma


title: Female_Brain_0PCB_YesFA_12_02

description: Library name: 12_02_BRAIN


title: FKBP-SETDB1 A12A10 ES, dox, RNAPolII Ser2P

description: Library name: xC013_dTSETDB1_A12A10_dox_Ser2P

value: Cast x 129S

value: doxycycline for 24hours

tag: chip antibody


title: C2_1

value: STAT5B N642H transgene


title: THUMPD2-His-Flag_B

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

country: Germany

institute: University Medical Centre Göttingen

data_processing:
Identical reads from forward sequencing reactions were collapsed using pyFastqDuplicateRemover.py (pyFastqDuplicateRemover.py -f -o) (version 1.5.2)
UMI at the 5' and poly(A) at the 3' end were removed using regular expressions with perl  (perl -pe 's/^[^>]{5}//gm' and perl -pe 's/A{5,}.*//g')  (version 5.32.1)
Trimmed reads were aligned to the U6 snRNA genomic sequence (Gene ID: 26827) extended with 10 extra “T’s” at the 3’ end. Alignment was performed using Bowtie2 (bowtie2 --local -x u6srna -f -S) (version 2.5.3)
Aligned reads were sorted and files were converted to bam and indexed using samtools (sort -O bam -o and index $input_file.bam) (version 1.19)
Assembly: U6 snRNA genomic sequence (Gene ID: 26827)
Supplementary files format and content: Aligned read counts per nucleotide in .csv format

source_name: Flp-In T-Rex HEK293

growth_protocol: HEK293 Flp-In T-Rex cell lines expressing THUMPD2-His-FLAG or the His-FLAG tag alone were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum .

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions, then proteins were degraded by Proteinase K treatment. Cyclic 2’,3’-phosphates were removed and RNAs were polyadenylated.
A cDNA library was prepared and amplifed by PCR using primers containing sequences complementary to the U6 snRNA and sequences of the Illumina Tru-Seq  adaptors.

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking. Cells were crosslinked (800 mJ/cm2) using UV light at 254 nm.

value: Flp-In T-Rex HEK293

tag: genotype

value: WT


title: C15_3

value: C15 cell line


title: Female_Brain_0PCB_YesFA_12_01

description: Library name: 12_01_BRAIN

value: F

value: Yes


title: FKBP-SETDB1 A12A10 ES, dox, RNAPolII

description: Library name: xC011_dTSETDB1_A12A10_dox_PolII

value: mESC

tag: spike-in


title: Male_Brain_6PCB_NoFA_57_08

description: Library name: 57_08_BRAIN

value: M

value: No


title: THUMPD2-His-Flag_A


title: Male_Brain_6PCB_NoFA_57_03

description: Library name: 57_03_BRAIN

value: Brain


title: FKBP-SETDB1 A12A10 ES, dox, RNAPolII Ser5P

description: Library name: xC012_dTSETDB1_A12A10_dox_Ser5P

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: anti-phospho-RBP1 CTD (Ser5) (D9N5I) (Cell Signaling, Cat# 13523)

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: THUMPD2-His-Flag_C


title: FKBP-SETDB1 P2F7 ES, dox, 4sU-seq

description:
Library name: 247_SETDB1P2F7_dox_ES_4sU
4sU labelled RNA

library_source: other

data_processing:
The data processing pipeline for 4sU-seq followed procedures similar to those described by Nesterova et al Nature Comm 2019. Briefly, raw FASTQ files containing paired-end reads were first aligned to a custom rRNA reference using Bowtie2 (v2.3.5.1) to remove rRNA contaminants. Reads mapping to rRNA were discarded, and the remaining unmapped read pairs were subsequently aligned to the mouse genome (mm10) using STAR (v2.7.9a). STAR was run with the following parameters: “--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 100 --alignEndsType EndToEnd –winAnchorMultimapNmax 100”. Alignments were sorted and strand split using Samtools (v1.16). Data were normalised to 10 million mapped reads. For data visualisation, Bedtools (v2.30) was used to generate bigWig coverage tracks, which were then visualized using IGV (https://software.broadinstitute.org/software/igv/). Metagene profiles and heatmaps were created using deepTools (v3.5.2), supplemented with custom Python scripts. Differential expression analysis of genes and transposable elements was performed using TEtranscripts (v2.2.1), applying an adjusted p-value threshold of 0.05 to define significance.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: other

extract_protocol:
4sU labelling of RNA, purification and sequencing was as previously described with a few modifications. For 4sU labelling of newly synthesized RNA, 4sU was added to the cell culture media at a final concentration of 500mM, and cells on a nearly confluent 10cm Petri dish were incubated for 20 minutes prior to quick removal of media and direct lysis using Trizol reagent (Life Technologies). Lysates were snap frozen and kept at -80oC until further processing. RNA isolation was performed using Trizol-chloroform phase separation, followed by isopropanol precipitation of the RNA and a 75% ethanol wash prior to dissolving the RNA pellet. Purified RNA was treated using TURBO DNAse as per manufacturer’s recommendation. RNA was then quantified using Nanodrop to prepare the Biotinylation reaction consisting of 7mg MTSEA biotin-XX linker (Biotium, cat. no. BT90066) dissolved in DMF at a concentration of 0.1 mg/mL, and 3.5μL of 10X Biotinylation buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA) per μg of purified RNA. This reaction was incubated at room temperature in the dark for 30 min, prior to two rounds of RNA purification using phenol:chloroform:isoamylalcohol (25:24:1) and Phase Lock Gel Heavy tubes and subsequent isopropanol precipitation with NaCl. RNA was then denatured at 65oC for 10min and immediately cooled on ice for 5 min.  Biotinylated 4sU-labelled RNA was captured using 200mL of μMACS streptavidin MicroBeads (from the μMACS Streptavidin Kit) and incubating for 15 minutes at room temperature prior to recovering using the μMacs Streptavidin Kit (Miltenyi). Samples were washed six times using Washing Buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1M NaCl, 0.1% Tween20), the first three at 65oC, before elution using fresh 100 mM DTT into RLT buffer from RNeasy minElute kit which was used for a final RNA cleanup.
Libraries were prepared for sequencing using the Illumina TruSeq stranded total RNA kit including the rRNA depletion. Libraries were quantified and verified using Qubit High Sensitivity DNA (Invitrogen) and the Bioanalyser High Sensitivity DNA (Agilent) kits before pooling and paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).


title: FKBP-SETDB1 P2F7 ES, dTAG+dox, 4sU-seq

description:
Library name: 248_SETDB1P2F7_dTAGdox_ES_4sU
4sU labelled RNA

value: dTAG-13 for 27hours and doxycycline for 24 hours


title: C15_2

value: Lymph nodes

value: Gamma-delta  T cell lymphoma

value: Female


title: C15_1

value: STAT5B N642H transgene


title: Male_Brain_6PCB_NoFA_57_01

description: Library name: 57_01_BRAIN


title: FKBP-SETDB1 G6D2 ES, dTAG+dox, 4sU-seq

description:
Library name: 246_SETDB1G6D2_dTAGdox_ES_4sU
4sU labelled RNA

value: Cast x 129S


title: HD7 IL-36 stimulated

city: London

first: Francesca

last: Capon

address: Great Maze Pond

institute: King's College London

description:
Library name: HD7pos
10X Genomics

data_processing:
Reads were processed with Cell Ranger v3.0.2 (10x Genomics)
Assembly: GRCh38 homo sapiens
Supplementary files format and content: Tab separated values for barcodes/features and matrix files

source_name: PBMC

extract_protocol:
PBMC were extracted from whole blood by density gradient centrifugation and cultured in 1640RPMI+1%P/S+10%FBS before stimulation with IL-36ɣ or PBS for 7 hours
Pooled libraries were sequenced on an Illumina HiSeq4000 instrument

treatment_protocol: IL-36ɣ stimulation for 7 hours at a concentration of 50ng/ml for stimulated samples only. Unstimulated samples were treated with PBS for 7 hours

tag: subject status

value: healthy donor

tag: subject id

value: PBMC

value: IL-36 stimulated

value: batch 1


title: Male_Brain_6PCB_NoFA_51_07

description: Library name: 51_07_BRAIN


title: FKBP-SETDB1 G6D2 ES, dox, 4sU-seq

description:
Library name: 245_SETDB1G6D2_dox_ES_4sU
4sU labelled RNA

value: mESC

value: doxycycline for 24hours


title: His-Flag_C

value: Flp-In T-Rex HEK293

value: WT


title: Male_Brain_6PCB_NoFA_51_06

description: Library name: 51_06_BRAIN

value: Brain

value: M

value: No


title: His-Flag_A


title: HD7 unstimulated

description:
Library name: HD7neg
10X Genomics

tag: batch


title: His-Flag_B


title: FKBP-SETDB1 A12A10 ES, dox, 4sU-seq

description:
Library name: 243_SETDB1A12A10_dox_ES_4sU
4sU labelled RNA

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: Male_Brain_6PCB_NoFA_51_05

description: Library name: 51_05_BRAIN


title: THUMPD2-His-Flag_B CRAC

data_processing:
1.Paired-end sequencing reads were merged using PEAR (v0.9.6) with the following arguments '-p 0.05 -n 4'
Merged (1) and paired-end (2) sequencing reads were demultiplexed based on their 5' barcode sequences NNNNNAGC using pyBarcode Filter (pyCRAC version 1.4.5).
3' adaptor sequences (TGGAATTCTCGGGTGCCAAGG) were removed using Flexbar (version 3.5.0) using the following settings '-q TAIL -qf i1.8 -qt 13 -u 0 -m 21 -n 6 -at RIGHT -o -ao 2 -ae 0.1 -as'
Duplicated reads containing the same UMI were collapsed using pyFastqDuplicateRemover (PyCRAC version 1.4.5).
1. Merged sequencing reads were aligned using STAR (v2.7.10a) using the following parameters: '--outReadsUnmapped Fastx   --outMultimapperOrder Random   --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS MD nM --outSAMmultNmax 1   --outSJfilterCountTotalMin -1 -1 -1 -1 --outSJfilterOverhangMin -1 -1 -1 -1 --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 4   --outFilterMismatchNoverReadLmax 0.04 --alignEndsType EndToEnd'. Peak calling was performed with PEAKachu (v0.2.0) in adaptive mode (default settings) and without normalization (-n none). Statistical analysis was done using DESeq2 package (v1.42.1) in R (version 4.3.2) accounting for batch differences. Peaks with adjusted p-value ≤ 0.1, baseMean > 100 and log₂FC ≥ 2 were considered significant. Significant peaks were exported as BED files and used to filter BAM files via samtools view (v1.21). Filtered reads were counted with featureCounts (v2.0.0) using the following arguments: -s 1 -0 -t exon -M --largestOverlap --fracOverlap 1 --fraction -g gene_type or gene_name. Bigwig files were generated using bamCoverage function from deeptools (v 3.5.6).
2. Paired-end sequencing reads were aligned using Bowtie2 (v2.3.5.1 ) using default settings. Unmapped, not primary alignment, and low quality reads were filtered using samotools (v1.10) using the following arguments 'view -F 1804 -f 2 -q 30'. Bedgraph files were generated using bedtools (version 2.27.1) with the following arguments 'genomecov -ibam -bg -scale RPM'
Assembly: 1. Homo sapiens GRCh38.29, 2. Homo sapiens U6 snRNA (NR_004394.1) with ten additional 'T' at 3'-end
Supplementary files format and content: 1. THUMPD2-His-Flag significant Peaks in BigWig format, 2. Aligned reads with RPM normalization in .bedgraph format

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-FLAG-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated, and a cDNA library was prepared by reverse transcription and amplified by PCR (Haag et al., 2017).


title: mitochondria_CSDE1 KD, eDRG cultured neuron_5

city: Daegu

first: Hoyong

last: Jin

address: E4-222, 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

country: South Korea

institute: DGIST

description: Library name: Sample 20

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

source_name: dorsal root ganglion

extract_protocol:
Total RNA was extracted and purified from freshly collected cultured dorsal root ganglion (DRG) neurons using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer's instructions. For mitochondrial RNA sequencing (mito-RNA-seq), mitochondria were first isolated from freshly collected cultured DRG neurons. RNA was then extracted and purified from the mitochondrial pellet using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer's instructions.
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: dorsal root ganglion

value: primary Dorsal root ganglion(DRG) neuron

value: Wild type


title: HD3 IL-36 stimulated

description:
Library name: HD3pos
10X Genomics


title: HD3 unstimulated

description:
Library name: HD3neg
10X Genomics


title: His-Flag_A CRAC


title: FKBP-SETDB1 A12A10 ES, dTAG+dox, 4sU-seq

description:
Library name: 244_SETDB1A12A10_dTAGdox_ES_4sU
4sU labelled RNA

value: dTAG-13 for 27hours and doxycycline for 24 hours


title: mitochondria_CSDE1 KD, eDRG cultured neuron_3

description: Library name: Sample 18


title: HD2 IL-36 stimulated

description:
Library name: HD2pos
10X Genomics


title: Male_Brain_6PCB_NoFA_51_02

description: Library name: 51_02_BRAIN


title: Male_Brain_6PCB_NoFA_51_01

description: Library name: 51_01_BRAIN


title: mitochondria_CSDE1 KD, eDRG cultured neuron_4

description: Library name: Sample 19


title: His-Flag_B CRAC


title: HD4 IL-36 stimulated

description:
Library name: HD4pos
10X Genomics


title: mitochondria_CSDE1 KD, eDRG cultured neuron_2

description: Library name: Sample 17


title: RPE1, NGS, rep2

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

data_processing:
The clean reads were generated by fastp (version 0.21.0) with default parameters.
Then, the clean reads were aligned by STAR v 2.7.8a against the human hg38 genome with parameters --outFilterMultimapNmax 1.
The transcript abundances were computed by kallisto quant (version 0.46.0, with default parameters).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 cells were purchased from ATCC (CRL-4000) and maintained in DMEM/F-12 (1:1) + GlutaMAXTM medium (GIBCO 31331-093) containing 10% fetal calf serum (FCS) (PAN-Biotech). Cells were grown and propagated at 37˚C with 5% CO2 in humidified atmosphere.

extract_protocol:
Total RNA was extracted by TRIzol Reagent (Life Technologies)
1 μg total RNA was used to prepare the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme)

value: hTERT RPE-1

value: hTERT-immortalized retinal pigment epithelial cells.


title: THUMPD2-His-Flag_A CRAC


title: Female_Brain_6PCB_NoFA_57_07

description: Library name: 57_07_BRAIN

value: F


title: HD2 unstimulated

description:
Library name: HD2neg
10X Genomics

value: healthy donor

value: PBMC


title: mitochondria_CSDE1 KD, eDRG cultured neuron_1

description: Library name: Sample 16


title: HD1 IL-36 stimulated

description:
Library name: HD1pos
10X Genomics

value: IL-36 stimulated

value: batch 1


title: HD4 unstimulated

description:
Library name: HD4neg
10X Genomics


title: HD1 unstimulated

description:
Library name: HD1neg
10X Genomics


title: RPE1, NGS, rep1


title: M.CviPI wild-type replicate 2, 480 min

first: David

middle: J.

last: Clark

address: 6 Center Drive

department: NICHD

institute: NIH

description: Library name: WT_MCviPI_R2_T5

data_processing:
Oxford Nanopore reads were base-called using Dorado v0.9.1 with the dna_r10.4.1_e8.2_400bps_sup v5.0.0 base-calling model and 5mCG_5hmCG v3 modification model (--min-qscore 8). Reads were aligned to sacCer3 or the YHP827 genome (Prajapati et al. 2025a) using the Dorado aligner. 5mCpG sites were predicted using modkit v0.4.3 (--cpg --combine-strands --ignore h).
Assembly: sacCer3/YHP827
Supplementary files format and content: BigWig files with the fraction of methylated CpGs

organism: Saccharomyces cerevisiae

growth_protocol: YHP827 and its derivatives YPE840, YPE841, YPE842 and YKW874 were inoculated in 250 mL 2% dextrose synthetic complete medium without isoleucine and valine (SC -ile -val) and grown at 30°C to OD600 of 0.6 – 0.8. For the first time point immediately before M.SssI induction (0 min), 50 mL culture was taken for the sample, of which 40 mL was reserved for DNA extraction and 10 mL for protein extraction. Cell pellets were stored at -80°C.

extract_protocol:
Cell pellets were permeabilized and flushed with two washes of 500 µL of 5× TE (50 mM Tris-HCl pH 8.0, 5 mM EDTA) + 2% SDS. Next, to remove the SDS, they were washed twice more with 500 µL 5× TE, then resuspended in 450 µL 5× TE + 15 mM 2-mercaptoethanol. To digest cell walls, 50 µL lyticase (Sigma-Aldrich L2524, 25,000 units/mL) was added, mixed gently by inversion, then incubated at 37°C for 10 min. To stop the reaction, 50 µL 20% SDS was added, mixed gently, and incubated at room temperature for 5 min. DNA was isolated by the addition of 110 µL 5 M potassium acetate, followed by two 1× volume chloroform extractions, precipitating and pelleting with 0.7× volume isopropanol, and washing with 70% ethanol. The resulting pellet was air-dried and dissolved in 100 µL 10 mM Tris-HCl pH 8.0, 0.1 mM Na-EDTA, 0.4 mg/mL RNase A and incubated at 37°C for 2 h. Further purification of DNA was performed with the PureLink Genomic DNA Mini Kit (Invitrogen K182002). 10 µL Proteinase K and 10 µL RNase A, supplied with the kit, were added to each sample and incubated at room temperature for 2 min. 100 µL PureLink Genomic Lysis/Binding Buffer was added to each sample, mixed gently by inversion, and incubated at 55°C for 10 min. Finally, 100 µL 100% ethanol was added to each sample and mixed gently by inversion before proceeding to the “Binding DNA” step of the manufacturer-provided protocol and completing the extraction as per instructions.
Genomic DNA samples were barcoded with the Native Barcoding Kit (SQK-NBD114.24) from Oxford Nanopore Technologies (ONT) as per manufacturer instructions and sequenced with R10.4.1 flow cells on a MinION Mk1C instrument running MinKNOW 24.11.8 (ONT).

treatment_protocol: To induce M.SssI expression, SC -ile -val was replenished to 225 mL and supplemented with SM (Sigma-Aldrich 324224, 2 mg/mL in DMSO) to a final concentration of 1 µg/mL. Cell pellets for time points after M.SssI induction (30, 60, 120 and 240 min) were obtained and stored as per the first time point. YHP853 cells expressing M.CviPI were cultured and processed as described above, except that an extra time point, at 480 min, was taken.

value: Haploid

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_NLS-degron-3HA-MCviPI_KanMX (p956)

value: SM induction of M.CviPI


title: Female_Brain_6PCB_NoFA_57_05

description: Library name: 57_05_BRAIN

value: Brain


title: Female_Brain_6PCB_NoFA_57_04

description: Library name: 57_04_BRAIN

value: No


title: Female_Brain_6PCB_NoFA_57_06

description: Library name: 57_06_BRAIN


title: mitochondria_control, eDRG cultured neuron_4

description: Library name: Sample 14

value: LV-control


title: mitochondria_control, eDRG cultured neuron_3

description: Library name: Sample 13

value: dorsal root ganglion


title: M.CviPI wild-type replicate 2, 120 min

description: Library name: WT_MCviPI_R2_T3


title: M.CviPI wild-type replicate 2, 240 min

description: Library name: WT_MCviPI_R2_T4


title: Female_Brain_6PCB_NoFA_57_02

description: Library name: 57_02_BRAIN


title: Female_Brain_6PCB_NoFA_51_04

description: Library name: 51_04_BRAIN


title: M.CviPI wild-type replicate 2, 60 min

description: Library name: WT_MCviPI_R2_T2


title: Adjacent Normal Skin Tissue Rep24 [76N]

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

data_processing:
Illumina HiSeq 4000 software was used for basecalling to generate paired-end reads of 200bp
Sequenced reads were trimmed for adaptor sequences using CutAdapt, quality trimmed at the 3′ ends, then mapped to the human genome (hg19/GRCh37) using STAR (v2.7.10a) with parameters --quantMode GeneCounts --chimSegmentMin 15 --chimJunctionOverhangMin 15 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --chimOutType Junctions SeparateSAMold
Transcript assembly of aligned reads was performed using StringTie (v1.3.3b).
The python script prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) was used to genearte raw read counts for all annotated genes in the human (hg19) genome.
Differential expression analysis was carried out using edgeR
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw read counts for all annotated genes for each sample.

source_name: Adjacent normal skin tissue

extract_protocol:
Skin biopsy tissues were snap frozen in liquid nitrogen and grinded using mortar and pestle. Total RNA extraction was performed using mirVana™ miRNA Isolation Kit (Thermo Fisher) following manufacturer’s protocol.
RNA Sequencing libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina) for Total RNA-Sequencing

value: Adjacent normal skin

tag: age of onset


title: Psoriatic Skin Tissue Rep23 [127D]

source_name: Lesional Psoriatic skin tissue

value: Lesional Psoriatic skin

tag: pasi score


title: mitochondria_control, eDRG cultured neuron_2

description: Library name: Sample 12

tag: tissue

value: primary Dorsal root ganglion(DRG) neuron

value: Wild type


title: Adjacent Normal Skin Tissue Rep23 [127N]


title: M.CviPI wild-type replicate 2, 0 min

description: Library name: WT_MCviPI_R2_T0

tag: cell line


title: total_CSDE1 KD, eDRG cultured neuron_5

description: Library name: Sample 10

tag: cell type


title: Male_Brain_1PCB_NoFA_49_07

description: Library name: 49_07_BRAIN

tag: strain

value: M


title: Male_Brain_1PCB_NoFA_49_03

description: Library name: 49_03_BRAIN

tag: Sex


title: mitochondria_control, eDRG cultured neuron_5

description: Library name: Sample 15


title: M.CviPI wild-type replicate 2, 30 min

description: Library name: WT_MCviPI_R2_T1


title: Psoriatic Skin Tissue Rep22 [159D]


title: M.CviPI wild-type replicate 1, 480 min

description: Library name: WT_MCviPI_R1_T5


title: Psoriatic Skin Tissue Rep24 [76D]


title: mitochondria_control, eDRG cultured neuron_1

description: Library name: Sample 11


title: total_CSDE1 KD, eDRG cultured neuron_4

description: Library name: Sample 9


title: total_CSDE1 KD, eDRG cultured neuron_3

description: Library name: Sample 8


title: Male_Brain_1PCB_NoFA_47_06

description: Library name: 47_06_BRAIN

tag: pcb treatment


title: M.CviPI wild-type replicate 1, 120 min

description: Library name: WT_MCviPI_R1_T3


title: Male_Brain_6PCB_NoFA_51_03

description: Library name: 51_03_BRAIN

tag: folic acid_treatment


title: M.CviPI wild-type replicate 1, 240 min

description: Library name: WT_MCviPI_R1_T4


title: Male_Brain_1PCB_NoFA_47_02

description: Library name: 47_02_BRAIN


title: total_CSDE1 KD, eDRG cultured neuron_2

description: Library name: Sample 7


title: M.CviPI wild-type replicate 1, 60 min

description: Library name: WT_MCviPI_R1_T2


title: Male_Brain_1PCB_NoFA_43_06

description: Library name: 43_06_BRAIN


title: Psoriatic Skin Tissue Rep21 [48D]


title: Male_Brain_1PCB_NoFA_49_02

description: Library name: 49_02_BRAIN


title: Psoriatic Skin Tissue Rep20 [59D]


title: Adjacent Normal Skin Tissue Rep21 [48N]


title: Female_Brain_1PCB_NoFA_49_05

description: Library name: 49_05_BRAIN

value: F


title: Adjacent Normal Skin Tissue Rep20 [59N]


title: total_control, eDRG cultured neuron_5

description: Library name: Sample 5


title: total_CSDE1 KD, eDRG cultured neuron_1

description: Library name: Sample 6


title: Adjacent Normal Skin Tissue Rep22 [159N]


title: sir4∆ replicate 2, 240 min

description: Library name: sir4D_MSssI_R2_T4

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1 -MSssI-degron-3HA-KanMX (p906) sir4_del::Hph (p925)

value: SM induction of M.SssI


title: Female_Brain_1PCB_NoFA_49_04

description: Library name: 49_04_BRAIN


title: M.CviPI wild-type replicate 1, 30 min

description: Library name: WT_MCviPI_R1_T1


title: M.CviPI wild-type replicate 1, 0 min

description: Library name: WT_MCviPI_R1_T0


title: Female_Brain_1PCB_NoFA_49_01

description: Library name: 49_01_BRAIN


title: total_control, eDRG cultured neuron_4

description: Library name: Sample 4


title: sir4∆ replicate 2, 120 min

description: Library name: sir4D_MSssI_R2_T3


title: Psoriatic Skin Tissue Rep19 [67D]


title: Psoriatic Skin Tissue Rep18 [58D]


title: total_control, eDRG cultured neuron_3

description: Library name: Sample 3


title: Female_Brain_1PCB_NoFA_47_07

description: Library name: 47_07_BRAIN


title: Adjacent Normal Skin Tissue Rep19 [67N]


title: sir4∆ replicate 2, 30 min

description: Library name: sir4D_MSssI_R2_T1


title: total_control, eDRG cultured neuron_1

description: Library name: Sample 1


title: Female_Brain_1PCB_NoFA_47_01

description: Library name: 47_01_BRAIN


title: Psoriatic Skin Tissue Rep17 [135D]


title: sir4∆ replicate 2, 0 min

description: Library name: sir4D_MSssI_R2_T0


title: Female_Brain_1PCB_NoFA_43_03

description: Library name: 43_03_BRAIN


title: Adjacent Normal Skin Tissue Rep17 [135N]


title: sir4∆ replicate 1, 240 min

description: Library name: sir4D_MSssI_R1_T4


title: Female_Brain_1PCB_NoFA_47_05

description: Library name: 47_05_BRAIN


title: human fetal testies, abortus at gestational week 19 rep 1 (GW19-1, 2014)

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description: Library name: Sample 8

data_processing:
The raw small RNA sequencing reads from human fetal gonads were obtained and underwent quality check using FastQC (v0.10.1). Adapter trimming was performed using cutadapt (v1.13). In oder to obtain only the reads that matched perfectly to the reference genome, we appied perfect match parameters on GRCh38 mapping with the Tophat2 (v2.0.12) commands "-g 1 -N 0 --read-gap-length 0 --read-edit-dist 0 --read-realign-edit-dist 0 --max-insertion-length 0 --max-deletion-length 0" in order to prevent irrelevant sequences from being included.
Bowtie (v1.1.1) was then used to filter out rRNA and tRNA sequences obtained from the Rfam database (v14.7). To identify both novel and known miRNAs, miRDeep2 mapper module was used for preprocessing by mapping to the hg38 reference genome, then the output was run through the main miRDeep2 module to obtain both known miRNA that perfectly mapped to miRbase (v22) and predicted miRNAs.
The remaining non-annotated reads with lengths between 24 to 34 nucleotides were taken as piRNA candidates. In order to estimate the confidence of piRNA candidates, we aligned them to the piRBase database (v3.0) and compared the number of mapped to unmapped sequences.
We applied nucleotide enrichment analysis for the 1U and 1U10A characteristic signature to validate piRNA candidacy and the presence of a ping-pong cycle, respectively.
Assembly: GRCh38
Supplementary files format and content: CSV files include piRPM values for each Sample.

source_name: fetal testis

extract_protocol:
Human fetal testes small RNAs from NTU cohort were extracted from abortus gonads using miRNeasy Tissue/Cells Advanced Kits (Cat.217684; Qiagen).
Library construction was performed using illumina Truseq Small RNA Sample Prep Kit, with the 2013 version composing all small RNAs, inculding microRNAs and larger small RNAs falling into piRNA criteria of 24-34 nt long. In the 2014 version of sequencing analysis, we enriched the proportion of piRNA sequencing reads by actively reducing a significant portion of inserting small RNAs below 22 nt via gel excision during sequencing library preparation.

treatment_protocol: Abortuses due to genetic or non-gonadal related phenotypic deficits.

value: fetal testis

value: germ cell

value: abortus


title: sir4∆ replicate 1, 120 min

description: Library name: sir4D_MSssI_R1_T3

value: Haploid


title: total_control, eDRG cultured neuron_2

description: Library name: Sample 2


title: human fetal testies, abortus at gestational week 22 rep 1 (GW22-1, 2014)

description: Library name: Sample 10


title: human fetal testies, abortus at gestational week 16 rep 2 (GW16-2, 2014)

description: Library name: Sample 7


title: human fetal testies, abortus at gestational week 19 rep 2 (GW19-2, 2014)

description: Library name: Sample 9


title: Adjacent Normal Skin Tissue Rep16 [134N]


title: Female_Brain_1PCB_NoFA_43_01

description: Library name: 43_01_BRAIN


title: sir4∆ replicate 1, 60 min

description: Library name: sir4D_MSssI_R1_T2


title: sir4∆ replicate 2, 60 min

description: Library name: sir4D_MSssI_R2_T2


title: Psoriatic Skin Tissue Rep15 [62D]


title: Male_Brain_0.1PCB_NoFA_30_04

description: Library name: 30_04_BRAIN


title: human fetal testies, abortus at gestational week 16 rep 1 (GW16-1, 2014)

description: Library name: Sample 6


title: Adjacent Normal Skin Tissue Rep15 [62N]


title: human fetal testies, abortus at gestational week 12 rep 1 (GW12-1, 2014)

description: Library name: Sample 5


title: sir4∆ replicate 1, 0 min

description: Library name: sir4D_MSssI_R1_T0


title: Adjacent Normal Skin Tissue Rep18 [58N]


title: sir4∆ replicate 1, 30 min

description: Library name: sir4D_MSssI_R1_T1


title: Male_Brain_0.1PCB_NoFA_30_05

description: Library name: 30_05_BRAIN


title: Male_Brain_0.1PCB_NoFA_30_01

description: Library name: 30_01_BRAIN


title: human fetal testies, abortus at gestational week 19 rep 1 (GW19-1, 2013)

description: Library name: Sample 4


title: Psoriatic Skin Tissue Rep14 [43D]


title: human fetal testies, abortus at gestational week 18 rep 1 (GW18-1, 2013)

description: Library name: Sample 3


title: sir3∆ replicate 2, 240 min

description: Library name: sir3D_MSssI_R2_T4

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1 -MSssI-degron-3HA-KanMX (p906) sir3_del::Hph (p924)


title: Psoriatic Skin Tissue Rep16 [134D]


title: Male_Brain_0.1PCB_NoFA_27_02

description: Library name: 27_02_BRAIN

value: Brain


title: Female_Brain_1PCB_NoFA_43_02

description: Library name: 43_02_BRAIN

value: No


title: Adjacent Normal Skin Tissue Rep14 [43N]


title: Psoriatic Skin Tissue Rep13 [56D]


title: sir3∆ replicate 2, 120 min

description: Library name: sir3D_MSssI_R2_T3


title: sir3∆ replicate 2, 30 min

description: Library name: sir3D_MSssI_R2_T1


title: Adjacent Normal Skin Tissue Rep13 [56N]


title: human fetal testies, abortus at gestational week 12 rep 1 (GW12-1, 2013)

description: Library name: Sample 1


title: Female_Brain_0.1PCB_NoFA_30_08

description: Library name: 30_08_BRAIN


title: Male_Brain_0.1PCB_NoFA_27_01

description: Library name: 27_01_BRAIN


title: sir3∆ replicate 2, 60 min

description: Library name: sir3D_MSssI_R2_T2


title: Female_Brain_0.1PCB_NoFA_30_07

description: Library name: 30_07_BRAIN


title: human fetal testies, abortus at gestational week 16 rep 2 (GW16-2, 2013)

description: Library name: Sample 2


title: Psoriatic Skin Tissue Rep12 [108D]


title: sir3∆ replicate 2, 0 min

description: Library name: sir3D_MSssI_R2_T0


title: Psoriatic Skin Tissue Rep11 [101D]


title: sir3∆ replicate 1, 120 min

description: Library name: sir3D_MSssI_R1_T3


title: X9dounce_PD_F_L_Both_rnaseq_PD_i_nap_L_F_74

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

institute: Van Andel Research Institute

description:
202308001_2sampsremoved_ruvr_cpmmoretthanthird_contrastmatrix_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_limma_printfit_coefficients_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_limma_RNA_DE_Results_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_ruvnormcounts.txt

data_processing:
RNA-seq: Following sequencing, fastq files were trimmed using Trimmomatic V0.36 and the settings: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
RNA-seq: Trimmed fastq files were aligned to HG19 using STAR v2.7 (Dobin and Gingeras, 2015).
RNA-seq: Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of HG19: Homo_sapiens.GRCh37.87.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse”.  This set included exon locations for 57,905 genomic entities including pseudogenes, lncRNAs, and 20,356 protein coding genes.
RNA-seq: Alignments (bam files) were converted to .tdf files using  igvtools (V2.3.60) count -z 5 -w 25 -e 250
RNA-seq: The resulting gene_id map counts included 2 technical replicates for each sample. The 2 replicates were combined to generate 8 total samples which were normalized using edgeR (TMM) and tested for significant differential expression (either between 2 WT MCF-7 batches generated here or compared to existing HMEC expression data) with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
Assembly: Hg19
Supplementary files format and content: .txt file, contrast matrix defining contrasts for statistical testing
Supplementary files format and content: .txt file, Limma determined coeficients for each variable
Supplementary files format and content: .txt, counts in log2cpm for each gene
Supplementary files format and content: .txt, expression counts in RUVseq normalized counts for each gene

source_name: prefrontal cortex, sorted for NEUN+

growth_protocol: Human prefrontal cortex tissue for this study was obtained NIH NeuroBioBank with approval from the ethics committee of the Van Andel Research Institute (IRB #15025)

extract_protocol:
Neuronal nuclei were isolated from the human prefrontal cortex using flow cytometry and filtering for an anti-NeuN antibody.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase. RNA was sheared to an average of 300 bp . Individually indexed libraries were pooled, and 75-bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer. Base calling was done by Illumina NextSeq Control Software (NCS; v2.0), and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0)

value: prefrontal cortex, sorted for NEUN+

tag: cod

value: Respiratory Failure; Pneumonia

tag: race

value: W

tag: rin

tag: pmi

value: Liz


title: Adjacent Normal Skin Tissue Rep12 [108N]

value: Adjacent normal skin


title: X99_Un_Cont_M_L_hcnt_rnaseq_W_d_hcnt_L_M_64

value: Idiopathic Pulmonary Fibrosis, Respiratory Failure

value: AA

value: JC


title: X97_Un_Cont_F_L_hcnt_rnaseq_W_a_hcnt_L_F_60

value: Hypertensive Heart Disease; Obesity


title: Adjacent Normal Skin Tissue Rep11 [101N]


title: sir3∆ replicate 1, 240 min

description: Library name: sir3D_MSssI_R1_T4

tag: genotype

tag: treatment

value: SM induction of M.SssI


title: sir3∆ replicate 1, 60 min

description: Library name: sir3D_MSssI_R1_T2


title: Female_Brain_0.1PCB_NoFA_30_03

description: Library name: 30_03_BRAIN

data_processing:
Raw RNA-seq fastq files were processed by trimming adapters using Trim Galore (v0.6.5)
Trimmed sequence reads were aligned to the mouse genome (mm10)
Gene count quantification was done using STAR (v2.7.3a)
QC metrics were generated with MultiQC (v1.9).
Assembly: mm10
Supplementary files format and content: .xlsx format; normalized counts

value: F


title: Female_Brain_0.1PCB_NoFA_30_02

description: Library name: 30_02_BRAIN


title: sir3∆ replicate 1, 30 min

description: Library name: sir3D_MSssI_R1_T1


title: Psoriatic Skin Tissue Rep10 [100D]

value: Lesional Psoriatic skin


title: X96_Un_Cont_F_RT_hcnt_rnaseq_W_h_hcnt_RT_F_87


title: Female_Brain_0.1PCB_NoFA_27_06

description: Library name: 27_06_BRAIN


title: Female_Brain_0.1PCB_NoFA_30_06

description: Library name: 30_06_BRAIN


title: X98_Un_Cont_F_RT_hcnt_rnaseq_W_a_hcnt_RT_F_60


title: sir2∆ replicate 2, 240 min

description: Library name: sir2D_MSssI_R2_T4

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1-MSssI-degron-3HA-KanMX (p906) sir2_del::Hph (p923)


title: Female_Brain_0.1PCB_NoFA_27_07

description: Library name: 27_07_BRAIN


title: Female_Brain_0.1PCB_NoFA_27_04

description: Library name: 27_04_BRAIN


title: Female_Brain_0.1PCB_NoFA_27_05

description: Library name: 27_05_BRAIN


title: sir3∆ replicate 1, 0 min

description: Library name: sir3D_MSssI_R1_T0

value: Haploid


title: X95_Un_Cont_F_L_hcnt_rnaseq_W_h_hcnt_L_F_87

value: Cardiopulmonary arrest; Generalized Atherosclerosis; Diabetes mellitus


title: X96rep_Un_Cont_F_RT_hcnt_rnaseq_W_h_hcnt_RT_F_87


title: X94_Un_Cont_F_RT_hcnt_rnaseq_W_g_hcnt_RT_F_82


title: Adjacent Normal Skin Tissue Rep9 [99N]


title: sir2∆ replicate 2, 120 min

description: Library name: sir2D_MSssI_R2_T3


title: Psoriatic Skin Tissue Rep9 [99D]


title: sir2∆ replicate 2, 30 min

description: Library name: sir2D_MSssI_R2_T1


title: Male_Brain_NoPCB_NoFA_6_02

description: Library name: 6_02_BRAIN

value: Brain

value: M


title: Adjacent Normal Skin Tissue Rep10 [100N]


title: Adjacent Normal Skin Tissue Rep8 [98N]


title: Psoriatic Skin Tissue Rep8 [98D]


title: X92rep_Un_Cont_F_RT_hcnt_rnaseq_W_f_hcnt_RT_F_72

value: prefrontal cortex, sorted for NEUN+


title: Female_Brain_0.1PCB_NoFA_27_03

description: Library name: 27_03_BRAIN

value: No


title: X92_Un_Cont_F_RT_hcnt_rnaseq_W_f_hcnt_RT_F_72

value: W


title: Psoriatic Skin Tissue Rep7 [97D]


title: sir2∆ replicate 2, 60 min

description: Library name: sir2D_MSssI_R2_T2


title: Male_Brain_NoPCB_NoFA_10_01

description: Library name: 10_01_BRAIN


title: sir2∆ replicate 2, 0 min

description: Library name: sir2D_MSssI_R2_T0


title: X93_Un_Cont_F_L_hcnt_rnaseq_W_g_hcnt_L_F_82

value: Metastatic Anal Cancer


title: Male_Brain_NoPCB_NoFA_1_06

description: Library name: 1_06_BRAIN


title: X91_Un_Cont_F_L_hcnt_rnaseq_W_f_hcnt_L_F_72

value: Liz


title: sir2∆ replicate 1, 240 min

description: Library name: sir2D_MSssI_R1_T4


title: Adjacent Normal Skin Tissue Rep7 [97N]

value: Adjacent normal skin


title: Psoriatic Skin Tissue Rep6 [91D]


title: Adjacent Normal Skin Tissue Rep6 [91N]


title: Male_Brain_NoPCB_NoFA_1_03

description: Library name: 1_03_BRAIN


title: X90_Un_Cont_M_RT_hcnt_rnaseq_W_b_hcnt_RT_M_61


title: sir2∆ replicate 1, 60 min

description: Library name: sir2D_MSssI_R1_T2


title: Male_Brain_NoPCB_NoFA_10_03

description: Library name: 10_03_BRAIN


title: Male_Brain_NoPCB_NoFA_1_05

description: Library name: 1_05_BRAIN


title: sir2∆ replicate 1, 120 min

description: Library name: sir2D_MSssI_R1_T3


title: X89_Un_Cont_M_L_hcnt_rnaseq_W_b_hcnt_L_M_61

value: Drowning


title: sir2∆ replicate 1, 30 min

description: Library name: sir2D_MSssI_R1_T1


title: Psoriatic Skin Tissue Rep5 [90D]


title: Female_Brain_NoPCB_NoFA_6_03

description: Library name: 6_03_BRAIN


title: Male_Brain_NoPCB_NoFA_1_02

description: Library name: 1_02_BRAIN


title: Adjacent Normal Skin Tissue Rep5 [90N]


title: Psoriatic Skin Tissue Rep4 [87D]


title: X88_Un_Cont_M_RT_hcnt_rnaseq_W_e_hcnt_RT_M_67

value: JC


title: sir1∆ replicate 2, 240 min

description: Library name: sir1D_MSssI_R2_T4

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_MSssI-degron-3HA_KanMX (p906) sir1_del::NatNT2 (p994)


title: X91rep_Un_Cont_F_L_hcnt_rnaseq_W_f_hcnt_L_F_72


title: Female_Brain_NoPCB_NoFA_6_01

description: Library name: 6_01_BRAIN


title: X87_Un_Cont_M_L_hcnt_rnaseq_W_e_hcnt_L_M_67

value: Coronary Artery Disease


title: sir1∆ replicate 2, 120 min

description: Library name: sir1D_MSssI_R2_T3

value: SM induction of M.SssI


title: Psoriatic Skin Tissue Rep3 [85D]

value: Lesional Psoriatic skin


title: Female_Brain_NoPCB_NoFA_10_02

description: Library name: 10_02_BRAIN

value: F


title: sir2∆ replicate 1, 0 min

description: Library name: sir2D_MSssI_R1_T0

value: Haploid

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1-MSssI-degron-3HA-KanMX (p906) sir2_del::Hph (p923)


title: Female_Brain_NoPCB_NoFA_1_07

description: Library name: 1_07_BRAIN

value: Brain


title: X86_Un_Cont_F_RT_hcnt_rnaseq_W_i_hcnt_RT_F_90


title: sir1∆ replicate 2, 60 min

description: Library name: sir1D_MSssI_R2_T2


title: X85_Un_Cont_F_L_hcnt_rnaseq_W_i_hcnt_L_F_90

value: Shock; Aortic Stenosis; Left Ventricle Injury; Cardiac Surgery


title: sir1∆ replicate 2, 30 min

description: Library name: sir1D_MSssI_R2_T1


title: Adjacent Normal Skin Tissue Rep3 [85N]


title: X9_PD_F_L_Both_rnaseq_PD_i_nap_L_F_74

value: prefrontal cortex, sorted for NEUN+

value: Respiratory Failure; Pneumonia


title: Adjacent Normal Skin Tissue Rep4 [87N]


title: Female_Brain_NoPCB_NoFA_1_04

description: Library name: 1_04_BRAIN

value: No


title: Female_Brain_NoPCB_NoFA_1_01

description: Library name: 1_01_BRAIN


title: X8_PD_M_RT_matched_rnaseq_PD_p_ma_RT_M_79

value: unknown

value: Respiratory Failure

value: W


title: X60_PD_M_RT_un_rnaseq_PD_u_u_RT_M_82

value: Pneumonia

value: Liz


title: sir1∆ replicate 2, 0 min

description: Library name: sir1D_MSssI_R2_T0

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_MSssI-degron-3HA_KanMX (p906) sir1_del::NatNT2 (p994)


title: Psoriatic Skin Tissue Rep2 [79D]


title: sir1∆ replicate 1, 240 min

description: Library name: sir1D_MSssI_R1_T4


title: E27 scRNA-seq of GAL mouse liver

city: Guilin

first: Honghao

last: Yu

state: Guangxi

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

description:
Library name: E27_Liver
PE150
Processed data:  See supplementary file.zip

data_processing:
Raw data was quality controlled using fastp to remove low-quality reads, adapters, and poly-A tails. Clean reads were aligned to the GRCm38 (mm10) mouse reference genome using STAR, generating a gene expression matrix for further bioinformatic analysis. Single-cell transcriptomics analysis was then performed using the Seurat package to identify differentially expressed genes and cell types.
Assembly: All sequencing data were aligned to the GRCm38 (mm10) mouse reference genome.
Supplementary files format and content: a gene expression matrix (CSV), metadata (CSV), and UMI counts (CSV)

source_name: liver

extract_protocol:
The entire liver tissues were harvested from euthanized mice, immediately placed in pre-chilled RPMI 1640 medium for initial washing to remove blood residues. The tissues were washed twice with PBS, cut into 1-2mm³ pieces, and enzymatically digested using SeekGene Tissue Dissociation Reagent A, Collagenase IV (0.1 mg/ml), and DNase I (0.01 mg/ml) in a 37°C water bath for 30 minutes to dissociate liver tissues into single-cell suspensions.
Single-cell RNA libraries were prepared using the SeekOne® Digital Droplet Single Cell Library Preparation Kit (SeekGene K00202). Cells were mixed with reverse transcription reagents and loaded into SeekOne® chips, followed by the addition of barcoded hydrogel beads and separation oil. After droplet generation, reverse transcription was performed at 42°C for 90 minutes, and PCR amplification was carried out to prepare the sequencing library.

treatment_protocol: Galt gene-edited mice (GAL mice) and wild-type (WT) mice were used in the experiments. All mice were euthanized before sample collection, and liver tissues were immediately dissected for further analysis.

value: liver

value: Galt gene-edited (GAL)


title: sir1∆ replicate 1, 120 min

description: Library name: sir1D_MSssI_R1_T3

value: SM induction of M.SssI


title: Adjacent Normal Skin Tissue Rep2 [79N]

value: Adjacent normal skin


title: Adjacent Normal Skin Tissue Rep1 [71N]


title: X6_PD_F_RT_matched_rnaseq_PD_d_ma_RT_F_66

value: Respiratory Failure; Parkinson's Disease


title: sir1∆ replicate 1, 60 min

description: Library name: sir1D_MSssI_R1_T2

value: Haploid


title: Psoriatic Skin Tissue Rep1 [71D]

value: Lesional Psoriatic skin


title: E19 scRNA-seq of GAL mouse liver

description:
Library name: E19_Liver
PE150
Processed data:  See supplementary file.zip


title: C80 scRNA-seq of GAL mouse liver

description:
Library name: C80_Liver
PE150
Processed data:  See supplementary file.zip

value: Wild-type (WT)


title: C73 scRNA-seq of GAL mouse liver

description:
Library name: C73_Liver
PE150
Processed data:  See supplementary file.zip


title: X59_PD_M_L_matched_rnaseq_PD_u_ma_L_M_82

value: prefrontal cortex, sorted for NEUN+


title: X58_PD_F_RT_un_rnaseq_PD_l_u_RT_F_75

value: Infection


title: X7_PD_M_L_un_rnaseq_PD_p_u_L_M_79


title: T3

city: shijiazhuang

first: jiaojiao

last: bai

address: huaizhong road No.286

institute: UCAS

description:
Library name: Sample 6
6-FPKM

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)(Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (ttree biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: arabidopsis_thaliana_gca_000001735_1_tair10
Supplementary files format and content: Excel file includes FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
RNA was harvested using traditional TRZOL method, 1.3μg of total RNA was used for construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: seedling

value: wild type

value: 200 nM CLE9


title: sir1∆ replicate 1, 0 min

description: Library name: sir1D_MSssI_R1_T0


title: T2

description:
Library name: Sample 5
5-FPKM


title: BMDM M2, Glu, S6

city: Lausanne

first: Cristina

last: Cosentino

address: Rue du Bugnon 9

department: Department of fundamental neurosciences

country: Switzerland

institute: Université de Lausanne

description: Library name: M2-Glu3

data_processing:
Fastq files were submitted to QIAGEN RNA-seq Analysis Portal v 5.1 for annotation to the mouse genome reference (GRCm38.101) and normalization of counts.
Assembly: GRCm38.101
Supplementary files format and content: txt file containing normalized counts (RPKM, TPM, CPM) per samples

source_name: Bone marrow

extract_protocol:
miRNeasy micro kit (Qiagen) was used to purified the total RNA
Illumina mRNA Stranded library kit was used following manifacturer instructions

value: Bone marrow

value: Bone marrow derived macrophages

value: Wild type


title: sir1∆ replicate 1, 30 min

description: Library name: sir1D_MSssI_R1_T1

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_MSssI-degron-3HA_KanMX (p906) sir1_del::NatNT2 (p994)


title: X57_PD_F_L_matched_rnaseq_PD_l_ma_L_F_75

value: W

value: Liz


title: Wild-type replicate 2, 240 min

description: Library name: WT_MSssI_R2_T4

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_MSssI-degron-3HA_KanMX (p906)

value: SM induction of M.SssI


title: T1

description:
Library name: Sample 4
4-FPKM


title: Wild-type replicate 2, 120 min

description: Library name: WT_MSssI_R2_T3


title: C3

description:
Library name: Sample 3
3-FPKM


title: BMDM M2, Glu, S5

description: Library name: M2-Glu2


title: X55_PD_M_L_matched_rnaseq_PD_o_ma_L_M_79

value: Cardiopulmonary Arrest, Myocardial Infarction


title: C1

description:
Library name: Sample 1
1-FPKM


title: C2

description:
Library name: Sample 2
2-FPKM


title: Wild-type replicate 2, 60 min

description: Library name: WT_MSssI_R2_T2

value: Haploid


title: X54_PD_F_RT_matched_rnaseq_PD_y_ma_RT_F_85

value: Blunt Head Trauma

value: JC


title: Wild-type replicate 2, 30 min

description: Library name: WT_MSssI_R2_T1


title: BMDM M2, Glu, S4

description: Library name: M2-Glu1


title: X53_PD_F_L_un_rnaseq_PD_y_u_L_F_85

value: prefrontal cortex, sorted for NEUN+


title: No Template Control

city: Houston

first: Ken

state: TX

address: 7007 Bertner Ave

institute: University of Texas MD Anderson Cancer Center

description: Library name: DSP-1001660035398-H-A01

data_processing:
Data was normalized with RUVg normalization with housekeeping genes (FCF1, DHX16, ABCF1, EDC3, ZNF143, HDAC3, CNOT10, SAP130, AGK, AMMECR1L, SF3A3, COG7, TMUB2, ZC3H14, DDX50, MRPS5, ZNF346, MTMR14, ERCC3, EIF2B4, TLK2, NUBP1, USP39, PRPF38A. NOL7, CNOT4).
Assembly: hg38
Supplementary files format and content: lab worksheet
Supplementary files format and content: dcc files
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: No Template Control

extract_protocol:
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail. The GeoMx Digital Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by pathologists. Probe barcodes were UV cleaved and collected.
Libraries were paired-end sequenced (2x50) on a NovoSeq 6000.

value: No Template Control

tag: segment

value: No template Control

tag: roi

tag: patient


title: BMDM M2, Ctr, S2

description: Library name: M2-Ctr2


title: Wild-type replicate 2, 0 min

description: Library name: WT_MSssI_R2_T0


title: Wild-type replicate 1, 240 min

description: Library name: WT_MSssI_R1_T4


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from db/db mice S24

description: Library name: iMACI.24

data_processing:
Following adapter sequences removal, identical reads longer than 16 nts were collapsed based on Unique Molecular Identifiers and aligned to the mouse genome (GRCm38.p6) Aligned reads were mapped to the dataset from http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Mmusc39/Mmusc39-summary.html. High confidence tRNA sequences and mature tRNA sequences were retained, and mtRNA seqences from http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/Search were added. Accesses done in February 2022.
Assembly: GRCm38.p6
Supplementary files format and content: txt file containing raw and normalized (cpm) counts per samples

source_name: Pancreatic islet

extract_protocol:
miRNeasy micro kit (Qiagen) was used to purified the total RNA
QiaSeq miRNA library kit was used following manifacturer instructions

value: Pancreatic islet

value: islet resident macrophages

value: db/db


title: Ileum, day 39, A144

city: Cerdanyola del Valles

first: Laia

last: Ferreres Serafini

state: Barcelona

address: Edifici V, Travessera dels Turons

country: Spain

institute: Autonomous University of Barcelona

description: Library name: A144

data_processing:
TrimGalore was used for quality filtering and adapter trimming; pseudo‑alignment and transcript quantification were performed using Kallisto against the Sus scrofa Sscrofa11.1 cDNA transcriptome; gene‑level counts were summarized and normalized using DESeq2 (median‑of‑ratios method).
Assembly: Sus scrofa reference genome Sscrofa11.1 (Ensembl).
Supplementary files format and content: Gene-level raw counts matrix, DESeq2 normalized counts, and sample metadata table (tab‑delimited or CSV).

organism: Sus scrofa

source_name: Ileum

extract_protocol:
RNA was extracted using Rneasy Mini Kit, Qiagen. RNA quantity and purity were assessed using NanoDrop spectrophotometry, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer to determine the RNA Integrity Number (RIN). The average RIN of samples used for library preparation was 7.8.
Libraries were prepared using poly‑A mRNA enrichment, RNA fragmentation, first‑ and second‑strand cDNA synthesis, end‑repair, A‑tailing, Illumina adapter ligation, size selection, and PCR amplification. Libraries were quality‑checked on an Agilent Bioanalyzer and sequenced as PE150 on an Illumina NovaSeq.

treatment_protocol: The two treatments were created based on growth, as average daily gain, from day 0 to 7 or  39.

value: Ileum

value: High growth


title: X56_PD_M_RT_un_rnaseq_PD_o_u_RT_M_79

value: w


title: X51_PD_M_L_un_rnaseq_PD_e_u_L_M_69

value: Aspiration Pneumonia

value: W


title: BMDM M2, Ctr, S1

description: Library name: M2-Ctr1

value: Bone marrow

value: Bone marrow derived macrophages

value: Wild type


title: BMDM M2, Ctr, S3

description: Library name: M2-Ctr3


title: X50_PD_F_RT_un_rnaseq_PD_k_u_RT_F_75

value: Parkinson's Disease

value: Liz


title: Wild-type replicate 1, 120 min

city: Bethesda

description: Library name: WT_MSssI_R1_T3

value: Haploid

value: MATa ade2-1 can1-100 HIS3 leu2-3,112 trp1-1 ura3-1 RAD5+ ho::TIR1_MSssI-degron-3HA_KanMX (p906)

value: SM induction of M.SssI


title: Ileum, day 39, A143

description: Library name: A143

value: Low growth


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from db/db mice S23

description: Library name: iMACH.23

value: Pancreatic islet


title: X5_PD_F_L_un_rnaseq_PD_d_u_L_F_66

value: prefrontal cortex, sorted for NEUN+

value: Respiratory Failure; Parkinson's Disease


title: Ileum, day 39, A142

description: Library name: A142

value: Ileum


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from wild type mice S22

description: Library name: iMACG.22

value: islet resident macrophages


title: Wild-type replicate 1, 60 min

description: Library name: WT_MSssI_R1_T2


title: Ileum, day 39, A141

description: Library name: A141


title: Wild-type replicate 1, 30 min

description: Library name: WT_MSssI_R1_T1


title: Ileum, day 39, A140

description: Library name: A140

value: High growth


title: Wild-type replicate 1, 0 min

description: Library name: WT_MSssI_R1_T0


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from wild type mice S21

description: Library name: iMACF.21


title: X48_PD_M_RT_Both_rnaseq_PD_j_nap_RT_M_75

value: Failure to Thrive


title: Ileum, day 39, A139

description: Library name: A139


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from db/db mice S19

description: Library name: iMACC.19

value: db/db


title: Ileum, day 39, A138

description: Library name: A138


title: P21TertCI_VASC_HFD_rep33

city: Marseille

first: Laura

last: BRAUD

address: 27 boulevard Leï Roure

country: France

institute: Institut Paoli Calmettes (IPC)

data_processing:
reads mapped to reference genome using Subread-align (v1.6.4)
reads filtered using samtools view -F4 (v1.9)
raw read counts at gene levels using featureCounts (v1.6.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Adipose tissue (AT)

extract_protocol:
Total RNA was harvested using RNeasy extraction kit (Qiagen 74104)
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase treatment. After adenylation of the 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments in the reange of 370-420 bp, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, using the Universal and Index (X) primers. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Adipose tissue (AT)

value: Primary cells

value: stromal cells

value: High Fat Diet (HFD)


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from db/db mice S20

description: Library name: iMACD.20


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from wild type mice S18

description: Library name: iMACB.18

value: Wild type


title: X44_PD_M_RT_un_rnaseq_PD_r_u_RT_M_81

value: Parkinson's Disease

value: W

value: Liz


title: X49_PD_F_L_matched_rnaseq_PD_k_ma_L_F_75


title: X47_PD_M_L_Both_rnaseq_PD_j_nap_L_M_75


title: P21TertCI_VASC_HFD_rep30


title: Ileum, day 39, A136

description: Library name: A136


title: P21TertCI_VASC_HFD_rep31


title: X43_PD_M_L_matched_rnaseq_PD_r_ma_L_M_81


title: FACS-isolated Cd45+, F4/80+, Cd11b+ and Cd11c+ islet macrophages from wild type mice S17

description: Library name: iMACA.17


title: X42_PD_M_RT_un_rnaseq_PD_f_u_RT_M_72

value: Cardiopulmonary arrest

value: JC


title: P21Tert_VASC_HFD_rep27


title: Ileum, day 39, A135

description: Library name: A135

value: Low growth


title: FACS-isolated pancreatic beta cells from db/db mice S24

description: Library name: bcell_I

value: Pancreatic islet

value: Beta cells


title: P21Tert_VASC_HFD_rep26


title: X52_PD_M_RT_matched_rnaseq_PD_e_ma_RT_M_69

value: prefrontal cortex, sorted for NEUN+

value: Aspiration Pneumonia


title: Ileum, day 39, A137

description: Library name: A137

value: Ileum


title: X41_PD_M_L_matched_rnaseq_PD_f_ma_L_M_72


title: FACS-isolated pancreatic beta cells from db/db mice S23

description: Library name: bcell_H

value: db/db


title: Ileum, day 39, A134

description: Library name: A134

value: High growth


title: Ileum, day 39, A133

description: Library name: A133


title: FACS-isolated pancreatic beta cells from wild type mice S22

description: Library name: bcell_G


title: P21Tert_VASC_HFD_rep25

value: Adipose tissue (AT)

value: Primary cells


title: P21het_VASC_HFD_rep20

value: stromal cells

value: High Fat Diet (HFD)


title: FACS-isolated pancreatic beta cells from wild type mice S21

description: Library name: bcell_F

value: Wild type


title: Ileum, day 7, A118

description: Library name: A118


title: Ileum, day 7, A119

description: Library name: A119


title: FACS-isolated pancreatic beta cells from db/db mice S19

description: Library name: bcell_C


title: X39rep_PD_M_L_matched_rnaseq_PD_ab_ma_L_M_91

value: Hypotension; Autonomic Dysfunction; Parkinson's Disease

value: W


title: X4_PD_M_RT_matched_rnaseq_PD_t_ma_RT_M_81

value: Cancer

value: Liz


title: P21het_VASC_HFD_rep17


title: FACS-isolated pancreatic beta cells from wild type mice S18

description: Library name: bcell_B


title: X39_PD_M_L_matched_rnaseq_PD_ab_ma_L_M_91


title: Ileum, day 7, A120

description: Library name: A120


title: X40rep_PD_M_RT_un_rnaseq_PD_ab_u_RT_M_91

value: JC


title: X38_PD_M_RT_matched_rnaseq_PD_a_ma_RT_M_62

value: Parkinson's Disease


title: P21het_VASC_SD_rep2

value: Standard Diet (SD)


title: X40_PD_M_RT_un_rnaseq_PD_ab_u_RT_M_91

value: prefrontal cortex, sorted for NEUN+


title: P21het_VASC_HFD_rep15


title: FACS-isolated pancreatic beta cells from wild type mice S17

description: Library name: bcell_A

value: Pancreatic islet

value: Beta cells


title: Ileum, day 7, A117

description: Library name: A117

value: Ileum

value: Low growth


title: FACS-isolated pancreatic beta cells from db/db mice S20

description: Library name: bcell_D

value: db/db


title: P21het_VASC_SD_rep1

value: Adipose tissue (AT)

value: Primary cells


title: Ileum, day 7, A116

description: Library name: A116

value: High growth


title: X37_PD_M_L_un_rnaseq_PD_a_u_L_M_62


title: Ileum, day 7, A115

description: Library name: A115


title: Mouse, skin, E18.5, scRNA, rep2

city: Seoul

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

institute: Seoul National University

description: Library name: E18.5_scRNA_Rep2

data_processing:
Raw reads were processed using the CellRanger ATAC pipeline (v2.1.0) for scATAC-seq datasets and the CellRanger pipeline (v7.1.0) for scRNA-seq datasets.
Assembly: mm10 (2020-A provided by 10x Genomics)
Supplementary files format and content: The filtered_peak_bc_matrices and filtered_feature_bc_matrices files in H5 format, along with the fragments.tsv.gz files (for scATAC data), that were generated using the default parameters of the CellRanger pipeline.

source_name: Skin

extract_protocol:
The entire back skin was harvested from sacrificed mice, and the epidermis was separated from the dermis by incubation with 1 mg/mL Dispase II (Roche) at 37°C for 30 minutes to 2 hours. The dermis was subsequently digested with 0.125 mg/mL Liberase TL (Roche) at 37°C for 30 minutes, while the epidermis was digested with 0.25% trypsin (Gibco) at 37°C for 15 minutes. Dissociated cells were filtered sequentially through 100-μm and 40-μm strainers, followed by a 1:1 matching of epidermal and dermal cells.
ScATAC-seq data were generated using 10x Chromium Single Cell ATAC Reagents Kits (v1 and v2), while scRNA-seq data were generated using the 10x Chromium Single Cell 3’ Kit (v3.1), following the manufacturer's instructions. Libraries were sequenced on a Novaseq system (Illumina), and two separate datasets, including replicates, were generated for each time point.

value: Skin


title: P21het_VASC_SD_rep3

value: stromal cells


title: Mouse, skin, E18.5, scRNA, rep1

description: Library name: E18.5_scRNA_Rep1


title: X36_PD_F_RT_un_rnaseq_PD_m_u_RT_F_76

value: W


title: Ileum, day 7, A114

description: Library name: A114


title: Mouse, skin, PD4, scATAC, rep2

description: Library name: PD4_scATAC_Rep2

library_source: genomic single cell


title: X31_PD_M_L_un_rnaseq_PD_g_u_L_M_73


title: Ileum, day 7, A111

description: Library name: A111


title: X34_PD_M_RT_matched_rnaseq_PD_h_ma_RT_M_74

value: Severe Aortic Stenosis; Left Ischial Tuberosity and Inferior Pubic Ramus Fractures; Advanced Stage Parkinson's Disease


title: Mouse, skin, PD2, scATAC, rep2

description: Library name: PD2_scATAC_Rep2


title: Ileum, day 7, A112

description: Library name: A112


title: YTK1644-2-Input

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

description: Library name: YTK1644-2-Input

data_processing:
Paired-end 101-bp sequencing reads were mapped to the reference S. cerevisiae (sacCer3) genome assemblies using Bowtie2 with default settings.
Duplicated mapped reads were removed using SAMtools.
Assembly: R64-1-1/sacCer3
Supplementary files format and content: bigWig files were generated using makeBigWig tool (in HOMER suite)

growth_protocol: Cells were grown in YPD media at 30℃ until O.D600nm was 0.5~0.6 and half of the cells were harvested.

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.

treatment_protocol: Half of the cells were subsequently shifted from YPD to 0.15x YP media for 4 hours at 30℃.

tag: chip antibody

value: Wild type (Dot1-FLAG)

value: YPD (Nutrient-rich, +N)


title: YTK1677-1-Input

description: Library name: YTK1677-1-Input

value: rad6del (Dot1-FLAG)


title: YTK1677-2-Input

description: Library name: YTK1677-2-Input