title: gp49B-LLC-plasma exo pool-1

status: Public on Apr 13 2022

city: Miyagi

first: Me-Tzu

last: Su

address: 4-1 Seiryo-machi, Aoba-ku, Sendai

department: Department of Experimental Immunology

country: Japan

institute: Institute of Development, Aging and Cancer

description: A pool of 4 plasma samples from gp49BKO-tumor-bearing mice

data_processing:
RNA-seq raw reads were quality checked by FastQC (version 0.11.9), and were then pre-processed by filtering out sequencing adapters, short-fragment reads (<10 nt) and other low-quality reads.
Unique Molecular Identifier (UMI) analysis was performed on GeneGlobe data analysis center (Qiagen)
Phe processed reads was mapped to the mouse [Mus musculus, GRCm38 (mm10) assembly] reference genome.
The mapped reads were normalized using Strand NGS with the Trimmed Mean of M value (TMM) method.
Normalized reads containing miRNA sequences were annotated compliant with existing sequences in the miRBase database ( http://www.mirbase.org/).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized data for every gene and every sample

source_name: plasma exosome

extract_protocol:
Murine whole blood samples from tumor-bearing mice were collected with 4 mM EDTA, pH 8.0 (Invitrogen Inc., Carlsbad, CA, USA) and subjected to plasma separation by centrifugation at 3500 ×g for 5 min at room temperature. Plasma exosomes were isolated using the ExoQuick exosome precipitation solution (SBI, System Biosciences, CA, USA) according to the manufacturer’s protocol. The extracted exosomes were resuspended in 1 × PBS and sterilized by Ultrafree-MC Centrifugal Filter Devices (0.22 μm, Millipore Co.), and exosomal RNA was isolated using the miRNAeasy Mini kit (Qiagen Company, Hilden, Germany) according to the manufacturer’s instruction.
Libraries were prepared for sequencing using QIAseq miRNA Library Kit (Qiagen Company, Hilden, Germany).

treatment_protocol: WT and gp49B deficiency mice were inoculated with Lewis Lung Cancer (LLC) cells by intravenous injection. After inoculation, LLC--bearing mice were sacrificed on day 21, and plasma samples were harvested for exosome isolation.

value: i.v. injected with LLC cells


title: Ctrl_2

type: SRA

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: transcriptomic

data_processing:
RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41 was used for basecalling.
Reads were aligned to Ensemble mouse genome (GRCm38) using STAR (2.7.7a) with argument “----quantMode TranscriptomeSAM GeneCounts".
Gene-based read counts were performed by STAR as well.
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were removed and flash frozen in liquid nitrogen RNA was harvested using TRIzol and the Qiagen RNAeasy kit with Dnase treatment. RNA was quanified by Agilent 2100 bioanalsyer.
PolyA enrichment was performed using NEBNext Poly(A) mRNA magnetic Isolation and libraries prepared using NEBNext Ultra II RNA Library Prep kit for Illumina

tag: tissue

value: Liver

tag: genotype

value: WT

tag: strain


title: gp49B-LLC-plasma exo pool-2

tag: treatment


title: WT-LLC-plasma exo pool-1

description: A pool of 3 plasma samples from WT-tumor-bearing mice

value: wild type


title: Ctrl_1


title: srsf10_KD_4


title: Ctrl_3


title: srsf10_KD_1


title: srsf10_KD_3


title: WT-LLC-plasma exo pool-2


title: srsf10_KD_2


title: Ctrl_4


title: 504_HC

type: RNA

city: Bialystok

first: Agnieszka

last: Bielska

address: Marii Sklodowskiej-Curie 24a

country: Poland

institute: Medical University of Bialytsok

hyb_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer’s recommendations (NanoString Technologies, USA). Briefly, 3 ng miRNA samples were prepared by ligating a specific miR-tag onto 3′ end of each mature miRNA followed by an overnight hybridization (65 °C) to nCounter Reporter and Capture probes. Subsequently, samples were placed into the nCounter Prep Station for automated sample purification and subsequent reporter capture.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the ligation positive controls. The threshold count value was set to 20. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

label: oligonucleotide probe

organism: Homo sapiens

source_name: serum

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (nanostring technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: miRNeasy Serum/Plasma Kit (Qiagen, Germany) according to the manufacturer’s instructions

treatment_protocol: not applicable

tag: type 2 diabetes mellitus (t2dm)

tag: ischemic heart disease status

tag: age

tag: bmi


title: 321_HC


title: 423_HC


title: 315_HC


title: 467_HC


title: 431_HC


title: 440_HC


title: 367_HC


title: 243_HC


title: 274_HC


title: 247_HC


title: WT_T5_H33_CR_rep2

city: New York

first: Zhiguo

last: Zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the mouse genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density. Read counts on plus strand, minus strand were also calculated seperately.

molecule: genomic DNA

source_name: mESC+HeLa

growth_protocol: Mouse E14 ES cells (a gift from Dr. Tom Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere.

extract_protocol:
eSPAN in mESC was performed exactly as previously described (Li et al., 2020).Total RNA samples were purified the same as for RT-PCR.
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For CUT&TAG and eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.
CUT&TAG, eSPAN, RNA-seq, CUT&RUN

tag: experiments

tag: chip antibody

value: biotin antibody


title: WT_T11_H33_CR_rep2


title: WT_T0_H33_CR_rep2


title: 146_HC


title: WT_T11_H33_CR_rep1


title: WT_T0_H33_CR_rep1


title: 604_IHD_T2DM


title: 602_T2DM


title: 141_HC


title: 590_T2DM


title: 470_HC


title: 112_HC


title: 88_T2DM


title: MCM22APOLE4KO_H3K36me3_eSPAN_rep1

source_name: mESC

value: Mcm2-2A and Pole4 KO

value: H3K36me3 antibody


title: 454_HC


title: 589_T2DM


title: POLA12A_H3K36me3_eSPAN_rep1


title: 566_IHD_T2DM


title: WT_T5_H33_CR_rep1


title: MCM22APOLE4KO_BrdU_rep1

value: BrdU antibody


title: 560_IHD_T2DM


title: POLA12A_H33_eSPAN_rep2


title: MCM22APOLE4KO_H33_eSPAN_rep2


title: POLA12A_BrdU_rep2


title: POLA12A_H33_eSPAN_rep1


title: 549_T2DM


title: MCM22APOLE4KO_H33_eSPAN_rep1


title: 555_T2DM


title: 556_T2DM


title: POLA12A_H33_CUT_rep1


title: MCM22APOLE4KO_H33_CUT_rep2


title: POLA12A_BrdU_rep1


title: POLA12A_H33_CUT_rep2


title: 522_T2DM


title: 510_T2DM


title: 509_T2DM


title: 502_T2DM


title: MCM22APOLE4KO_H33_CUT_rep1


title: 456_T2DM


title: 532_IHD_T2DM


title: 492_IHD_T2DM


title: Sertoli-KO1_RNA-seq

city: Xi'an

first: Bo

last: Liu

address: No.169 Changle West Road

country: China

institute: the Fourth Military Medical University

data_processing:
Sequencing was carried  out with Illumina HiSeq 2000
Raw paired-end clean sequencing reads were aligned to Mus_musculus.GRCm38.90.chr reference genome by HISAT2 v2.1.0
FPKMs (fragments per kilobase of  transcript per million mapped reads) were calculated using HTSeq v0.6.0
Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs)
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: text files

source_name: Sertoli cells

growth_protocol: Purified Sertoli cells were cultured at 34˚C in a shumidified atmosphere with 5% CO2.

extract_protocol:
Total RNA of  Pa1-/-  and Pa1F/F Sertoli cells purified from 20d-old mice testes  was harvested using Trizol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

tag: cell type

value: mouse Sertoli cell

value: untreated


title: Sertoli-WT3_RNA-seq


title: 447_IHD_T2DM


title: Sertoli-WT2_RNA-seq


title: 4_IHD_T2DM


title: MCM22APOLE4KO_BrdU_rep2


title: Sertoli-KO3_RNA-seq


title: 434_T2DM


title: Pole4KO_RNAseq_rep2

extract_protocol:
eSPAN in mESC was performed exactly as previously described (Li et al., 2020).Total RNA samples were purified the same as for RT-PCR.
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For CUT&TAG and eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

value: mESC

value: Pole4 KO


title: Sertoli-WT1_RNA-seq


title: 530_IHD_T2DM


title: Pole3KO_RNAseq_rep2

value: Pole3 KO


title: Sertoli-KO2_RNA-seq


title: Mcm22A_BrdU_rep1

data_processing:
Library strategy: CUT&TAG
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the mouse genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density. Read counts on plus strand, minus strand were also calculated seperately.


title: 357_IHD_T2DM


title: 349_IHD_T2DM


title: Pole4KO_RNAseq_rep1


title: WT_H3K36me3_eSPAN_rep2

data_processing:
Library strategy: eSPAN
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. RNA-Seq reads were mapped using STAR.
Coverage for each base pair of the mouse genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes and log fold change were calculated by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores represent the normalization reads density. Read counts on plus strand, minus strand were also calculated seperately.


title: 386_IHD_T2DM


title: 378_T2DM


title: 383_IHD_T2DM


title: 322_T2DM


title: Pole3KO_RNAseq_rep1


title: 376_IHD_T2DM


title: 365_IHD_T2DM


title: 490_IHD_T2DM


title: Pole4KO_H3K36me3_eSPAN_rep1


title: Mcm22A_H3K36me3_eSPAN_rep1


title: 306_IHD_T2DM


title: 326_T2DM


title: 336_IHD_T2DM


title: WT_BrdU_rep1


title: Mcm22A_H3K36me3_eSPAN_rep2


title: 356_IHD_T2DM


title: Pole4KO_H3K36me3_eSPAN_rep2


title: 337_IHD_T2DM


title: 268_T2DM


title: 292_T2DM


title: 295_IHD_T2DM


title: WT_H3K36me3_eSPAN_rep1


title: Pole4KO_BrdU_rep1


title: Pole4KO_H3K36me3_CUT_rep1


title: WT_H3K36me3_CUT_rep2


title: Mcm22A_H3K36me3_CUT_rep1


title: WT_H3K36me3_CUT_rep1


title: 264_IHD_T2DM


title: 271_IHD_T2DM


title: 266_T2DM


title: 197_IHD_T2DM


title: Pole4KO_newTN5_BrdU_rep2


title: Pole3KO_newTN5_BrdU_rep2


title: WT_newTN5_BrdU_rep2


title: Pole3KO_newTN5_BrdU_rep1


title: Mcm22A_newTN5_BrdU_rep2


title: Pole4KO_newTN5_BrdU_rep1


title: 283_T2DM


title: Mcm22A_newTN5_BrdU_rep1


title: Endometrium, r-101

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Assembly: Bovine genome assembly: (ARS-UCD1.2)
Supplementary files format and content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: Endometrium

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration and quality were determined using spectrophotometry (NanoDrop 2000 Spectrophotometer, Thermo Fisher Scientific, Waltham, MA, USA) by absorbance at 260 nm and the 260/280 nm ratios, respectively. Absorbance ratios ranged from 1.8 to 2.1.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: Endometrium

value: luminal epithelial cell

tag: cow id

tag: time

value: day 4

value: H


title: Endometrium, r-104

value: L


title: Endometrium, r-112


title: Endometrium, r-105

value: day 7


title: Endometrium, r-108


title: Endometrium, r-99


title: Endometrium, r-100

value: day 14


title: Endometrium, r-102


title: WT_H33_eSPAN_rep2

value: WT


title: Pole4KO_H33_eSPAN_rep2

value: biotin antibody


title: Pole3KO_H33_eSPAN_rep2


title: WT_newTN5_BrdU_rep1


title: Endometrium, r-98


title: Endometrium, r-96


title: Endometrium, r-113


title: Pole4KO_H33_eSPAN_rep1


title: 535_IHD_T2DM


title: Pole3KO_H33_eSPAN_rep1


title: Endometrium, r-95


title: Mcm22A_H33_eSPAN_rep1


title: Endometrium, r-93


title: Mcm22A_H33_eSPAN_rep2


title: Endometrium, r-90


title: Endometrium, r-87


title: Pole4KO_H33_CUT_rep2


title: Endometrium, r-86


title: WT_H33_eSPAN_rep1


title: Pole3KO_H33_CUT_rep2


title: Mcm22A_H33_CUT_rep2


title: Spermatheca_R3

city: Darlington

first: Owen

last: Watson

state: NSW

address: 2 Butlin Ave, G08 - Molecular Bioscience Building The University of Sydney

department: School of Life and Environmental Sciences

country: Australia

institute: Sydney University

data_processing:
Adaptor sequences were trimmed, then mapped to Amel4.5 genome using bowtie v1.2.3 with parameters --wrapper basic-0 --sam -n 1 -l 18 -e 70 --best
Individual sample BAM files were merged by tissue type
Merged BAM sequences were annotated to small RNAs from OGSv3.2
For piRNA analysis, sequences annotated as other small RNAs or sequences <26nt or >31nt were removed
Genome_build: Amel4.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for piRNA analysis

organism: Apis mellifera

source_name: Spermatheca

extract_protocol:
Trizol- Illumina TruSeq Small RNA Library Prep Kit
small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult laying queens

tag: caste

value: Queen

value: Spermatheca

tag: molecule type

value: small RNAs


title: Spermatheca_R2

description: spermatheca_4queens_C9KF6ANXX_GATCAG_L001


title: Pole4KO_H33_CUT_rep1


title: Spermatheca_R1

description: spermatheca_160316_10_CA5W5ANXX_CTTGTA_L006


title: WT_H33_CUT_rep1


title: Endometrium, r-83


title: Pole3KO_H33_CUT_rep1


title: Endometrium, r-74


title: Endometrium, r-73


title: Endometrium, r-75


title: Endometrium, r-82


title: WT_H33_CUT_rep2


title: Endometrium, r-77


title: Endometrium, r-76


title: Semen_R2

source_name: Semen

value: Adult drones

value: Drone

value: Semen


title: Semen_R1


title: Endometrium, r-80


title: Mcm22A_H33_CUT_rep1

value: mESC


title: Endometrium, r-72

value: Endometrium


title: Testes_R7

source_name: Testes

value: 72 hrs after pupation

value: Testes


title: Endometrium, r-71

value: luminal epithelial cell

value: day 4

value: H


title: Testes_R8


title: Testes_R5

value: 24 hrs after pupation


title: Testes_R6


title: Endometrium, r-84

value: day 7

value: L


title: Endometrium, r-70

value: day 14


title: Endometrium, r-68


title: Endometrium, r-78


title: Testes_R4


title: Endometrium, r-64


title: Testes_R1

value: 144 hrs after pupation


title: Testes_R3


title: Testes_R2


title: Endometrium, r-65


title: Eggs_R7

source_name: Eggs

tag: eggs specifics

value: Virgin queen Worker cell

value: <24 hrs after laying

value: Queen

value: Eggs


title: Endometrium, r-62


title: Eggs_R6

value: Virgin queen Drone cell

value: small RNAs


title: Eggs_R3

value: Mated queen Fertilised


title: Endometrium, r-58

value: Endometrium


title: Endometrium, r-69


title: Eggs_R4

value: Mated queen Unfertilised


title: Endometrium, r-60

value: luminal epithelial cell


title: Eggs_R5


title: Endometrium, r-59

value: day 4


title: Endometrium, r-57


title: Eggs_R2


title: Eggs_R1


title: Endometrium, r-63

value: H


title: Endometrium, r-53


title: Endometrium, r-55


title: Endometrium, r-50


title: Ovaries_R3

source_name: Ovaries

value: Adult laying queens

value: Ovaries


title: Endometrium, r-52

value: day 7

value: L


title: Endometrium, r-49


title: Ovaries_R2


title: Ovaries_R1


title: Endometrium, r-67

value: day 14


title: Endometrium, r-48


title: Eggs_R8


title: Endometrium, r-44


title: PBAT_bulk_untreated [PBAT-Untreated_S52_L001]

city: Newcastle

first: Heather

last: Lee

address: University Drive, Callaghan

institute: The University of Newcastle

data_processing:
Post-bisulfite adaptor tagging (PBAT) reads were trimmed using Trim Galore (v0.6.5) to remove 9bp from the 5’ end of all reads.
Reads were mapped non-directionally and as paired end using Bismark (v0.22.3)
Unmapped reads were re-aligned in single-end mode to account for chimeric reads seen in PBAT libraries [Krueger, F. PBAT and single-cell (scBS-Seq) libraries may generate chimeric read pairs. 2016.].
After producing coverage files with Bismark methylation extraction module, paried and single end alignments for each sample were merged into a single file using the cat (concatenate) command.
Downstream analysis was performed using Seqmonk. Global DNA methylation levels was defined using 3000bp windows across the genome with a minimum of 5 observations per window.
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: The genome-wide CpG methylation reports (.cov files) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>

growth_protocol: KG1a cells were resuspended in binding buffer before staining with annexin V and 7-AAD. Live cells (Annexin V - /7-AAD -) were sorted into individual wells of a 96 well plate containing lysis buffer 2.5μL RLT Plus Lysis Buffer (QIAGEN, catalog # 1053393) containing 1U/μL SUPERase-In (ThermoFisher, catalog # AM2696) in 96 well plates. Before sorting, bulk samples of 1000000 cells were collected from both the untreated and treated populations.

extract_protocol:
We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015.]. Genomic DNA from each cell was purified and bisulphite conversion was performed as described [Angermueller, C., et al., Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nature methods, 2016], with minor modifications.
A post-bisulphite adaptor tagging (PBAT) approach protocol [Miura, F., et al., Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Research, 2012] was used to prepare genome-wide sequencing libraries from bulk samples. Libraries were prepared as described [Rulands, S., et al., Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency. Cell Systems, 2018]. The only alteration from this protocol is the use of a new 6NR adaptor 2 oligo (5’-CAGACGTGTGCTCTTCCGATCTNNNNNN-3’) that is suitable for use with NEBNext dual index oligo kits.

treatment_protocol: Cell lines were treated with 100nM decitabine every 24 hours (0, 24 and 48 hours) and harvested at 72 hours

tag: cell line

value: untreated

tag: cancer type

value: Acute myeloid leukemia

tag: sample type

value: genomic DNA, bisulfate treated


title: Endometrium, r-46

tag: tissue


title: Endometrium, r-40

tag: treatment


title: Endometrium, r-42


title: Endometrium, r-43


title: AML01_Alu_pool_cell_93 [i508_H9_i709_201027_AML01_Alu_pool_S4_L001]

data_processing:
library strategy: single-cell transposable element methylation sequencing (scTEM-seq)
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis. We excluded cells with coverage of less than 1000 annotated TE sites.
Downstream analysis was performed using Seqmonk and custom R scripts
Genome_build: GRCh38
Supplementary_files_format_and_content: The genome-wide CpG methylation reports (.cov files) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>

source_name: patient sample

growth_protocol: Enriched mononuclear cells were purified from peripheral blood using Lymphoprep density gradient medium (StemCell, catalog # 7851) and SepMate tubes (StemCell, catalog # 85450), and cryopreserved. Cryopreserved primary human cells were resuspended in thawing media (IMDM, 20% FBS), washed twice and resuspended in thawing media. The cells were then rested for 1h at 37°C before preparation for flow cytometry. Cells (1x106/100ul) were stained with 1.5μg/mL propidium iodide (PI, Sigma-Aldrich), 1:20 CD45-PECy7 (2D1, Invitrogen), 1:20 CD33-FITC (WM-53, Invitrogen) and 1:20 CD19-BV711 (SJ25C1, BD Biosciences). Single blasts (PI-CD45dim) were collected in 2.5μL RLT Plus Lysis Buffer containing 1U/μL SUPERase-In (Invitrogen) in 96 well plates.

extract_protocol:
We utilised the G&T-seq protocol to separate genomic DNA and RNA from the single-cell samples [Macaulay, I.C., et al., G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 2015.]. Genomic DNA from each cell was purified and bisulphite conversion was performed as described [Angermueller, C., et al., Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nature methods, 2016], with minor modifications.
Bisulphite conversion was carried out using the EZ-96 DNA Methylation-Direct MagPrep Kit (Integrated Sciences, catalog # D5054) with half volumes of the manufacturer’s instructions. Bisulphite converted DNA was eluted directly from MagBeads into PCR-mix, and amplification of TEs was performed with MagBeads still in the well. PCR cycling conditions used were 95°C for 5 min (1 cycle), 98°C for 20 sec, 53°C for 15 sec, 72°C for 1 min (35 cycles), and 72°C for 10min (1 cycle). PCR mix used 7.5µl 1x KAPA HiFi hotStart Uracil + ReadyMix (Millennium, catalog # ROC-07959079001) and 0.3µM primer mix. Primers were designed against SINE Alu and LINE-1 consensus sequences (Supplementary Figure S2A) and are contained in Supplementary Tables S1 and S2. After amplification, plates of 96 single cell libraries purified using a 1.2x volume of AMPure XP beads (Beckman Coulter, catalog # A63881). All libraries were then quantified using the Qubit dsDNA HS kit (Life Technologies), normalised and pooled to a single tube. Pools where then added to 0.8µM NEBNext dual index oligo sets (Genesearch, catalog # E7780S) and 14.5µl 1x KAPA HiFi HotStart ReadyMix (Millennium, catalog # ROC-07958935001) for indexing and adaptor addition. PCR cycling conditions used were 98°C for 45 sec (1 cycle), 98°C for 15 sec, 65°C for 30 sec, 72°C for 30 sec (5 cycles), and 72°C for 5 min (1 cycle). Pools were then purified using 0.9x volume of Ampure XP beads, normalised and combined for sequencing.

tag: Sex

value: M


title: AML01_Alu_pool_cell_91 [i508_H7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_92 [i508_H8_i708_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_88 [i508_H4_i704_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_89 [i508_H5_i705_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_95 [i508_H11_i711_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_90 [i508_H6_i706_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-41


title: Endometrium, r-38


title: Endometrium, r-39


title: AML01_Alu_pool_cell_87 [i508_H3_i703_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_86 [i508_H2_i702_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-36


title: Endometrium, r-37


title: Endometrium, r-35


title: AML01_Alu_pool_cell_84 [i507_G12_i712_201027_AML01_Alu_pool_S4_L001]


title: PBAT_bulk_DAC_treated [PBAT-DAC_S51_L001]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: Endometrium, r-34


title: AML01_Alu_pool_cell_94 [i508_H10_i710_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-47


title: AML01_Alu_pool_cell_83 [i507_G11_i711_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-45


title: Endometrium, r-33


title: AML01_Alu_pool_cell_81 [i507_G9_i709_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_80 [i507_G8_i708_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-32


title: Endometrium, r-31


title: Endometrium, r-29


title: AML01_Alu_pool_cell_78 [i507_G6_i706_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-23


title: Endometrium, r-24


title: AML01_Alu_pool_cell_79 [i507_G7_i707_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-25


title: AML01_Alu_pool_cell_77 [i507_G5_i705_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_75 [i507_G3_i703_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_73 [i507_G1_i701_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_72 [i506_F12_i712_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-21


title: AML01_Alu_pool_cell_74 [i507_G2_i702_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-28


title: AML01_Alu_pool_cell_71 [i506_F11_i711_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-20


title: AML01_Alu_pool_cell_82 [i507_G10_i710_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_70 [i506_F10_i710_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-18


title: Endometrium, r-19


title: AML01_Alu_pool_cell_66 [i506_F6_i706_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_67 [i506_F7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_69 [i506_F9_i709_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_68 [i506_F8_i708_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-17


title: AML01_Alu_pool_cell_76 [i507_G4_i704_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-16


title: Endometrium, r-13


title: Endometrium, r-15


title: AML01_Alu_pool_cell_62 [i506_F2_i702_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-27


title: AML01_Alu_pool_cell_63 [i506_F3_i703_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-11


title: AML01_Alu_pool_cell_61 [i506_F1_i701_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_65 [i506_F5_i705_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-10


title: AML01_Alu_pool_cell_64 [i506_F4_i704_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-9


title: Endometrium, r-12


title: AML01_Alu_pool_cell_60 [i505_E12_i712_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_59 [i505_E11_i711_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-14


title: AML01_Alu_pool_cell_58 [i505_E10_i710_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-7


title: Endometrium, r-8


title: Endometrium, r-6


title: AML01_Alu_pool_cell_57 [i505_E9_i709_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-3


title: Endometrium, r-5


title: Endometrium, r-2


title: AML01_Alu_pool_cell_56 [i505_E8_i708_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_54 [i505_E6_i706_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_55 [i505_E7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_53 [i505_E5_i705_201027_AML01_Alu_pool_S4_L001]


title: Endometrium, r-1


title: AML01_Alu_pool_cell_52 [i505_E4_i704_201027_AML01_Alu_pool_S4_L001]


title: P3 cystitis glandularis

city: Shenzhen

first: Yongxiang

last: Luo

state: Guangdong

address: 47 Youyi Road, Luohu District, Shenzhen

institute: The Third Affiliated Hospital of Shenzhen  University

data_processing:
Using fastqc (version 0.11.7) and cutadapt (version 1.17) to quality control and filter the data.
Reads were compared to the reference genome GRCh38 with ensemble version 93 gene annotation using STAR (version 2.6.1b)
Finally, featureCounts (version 1.6.2) was used to output the gene counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix file with raw gene counts for every gene and every cell.

source_name: cystitis glandularis

extract_protocol:
The fresh tissue samples were washed by using Hanks Balanced Salt Solution (HBSS), and then cut them into 1~2 mm pieces. The small tissue pieces were transferred to a 15 ml centrifuge tube, and digested using XSCOPETM Tissue Dissociation Solution (Singleron) under shaking conditions at 37°C for 15 minutes. After the digestion, the samples were filtered with 40um sterile strainers, and then centrifuged at 1000 rpm at 4°C for 5 minutes. The supernatant was removed, and the cells were resuspended with 1ml PBS, then added 2 mL GEXSCOPETM red blood cell lysis buffer (Singleron) and incubated for 10 minutes to lyse the red blood cells.
After single-cell suspensions with 1×10^5 cells/mL in concentration in PBS (HyClone) were prepared. Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).

tag: disease state

value: cystitis glandularis

tag: patient id

tag: grade


title: P2 bladder cancer

source_name: primary bladder cancer

value: primary bladder cancer

value: Low

value: bladder cancer


title: AML01_Alu_pool_cell_51 [i505_E3_i703_201027_AML01_Alu_pool_S4_L001]

tag: age


title: P1 relapsed bladder cancer

source_name: recurrent bladder cancer

value: recurrent bladder cancer

value: High


title: AML01_Alu_pool_cell_50 [i505_E2_i702_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_49 [i505_E1_i701_201027_AML01_Alu_pool_S4_L001]


title: P1 bladder cancer


title: AML01_Alu_pool_cell_47 [i504_D11_i711_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_48 [i504_D12_i712_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_44 [i504_D8_i708_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_45 [i504_D9_i709_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_43 [i504_D7_i707_201027_AML01_Alu_pool_S4_L001]


title: AKT-shNF1-2

city: Melbourne

first: Jian

last: Kang

state: Victoria

address: 9 Princes street, Fitzroy

department: research division

institute: St Vincent's institute of medical research

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against NF1. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#2.

data_processing:
The quality of the 3' end reads was assessed with FastQC 0.11.2.
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg19/GRCh37) using HISAT2 (v2.0.4)
Picard 1.125 was used to generate BAM indices and to calculate insert size.
Samtools 1.1.0 was used to sort and merge.
featureCounts (v1.6.2) was used to count the number of reads per gene with ENSEMBL GTF v87
Assembly: hg19
Supplementary files format and content: csv file includes normalized counts for each sample

molecule: polyA RNA

source_name: BJ-TERT fibroblasts

growth_protocol: BJ-TERT cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) + 20 mM HEPES, 17% Medium 199, 15% fetal bovine serum (FBS), and 1% GlutaMAXTM L-alanyl-L-glutamine dipeptide at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Mini Kit as per the manufacturer's instructions.
RNA libraries were prepared for sequencing according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen).

treatment_protocol: BJ-TERT cells were transduced with retrovirus containing pBabe-puro empty vector or pBabe-puro-myrAKT1. On day 6 post-transduction myrAKT1 cells were transduced with either pGIPZ-shRNA against CBS, Tp53 and NF1, or the control vector pGIPZ-NTC, pBabe-EV cells transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq.

tag: replicate

value: replicate 2

value: expressing pBabe-puro-myrAKT1 and pGIPZ-shNF1

tag: harvest time point

value: 14 days


title: AML01_Alu_pool_cell_42 [i504_D6_i706_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_41 [i504_D5_i705_201027_AML01_Alu_pool_S4_L001]


title: AKT-shTp53-3

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against Tp53. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#3.

value: replicate 3

value: expressing pBabe-puro-myrAKT1 and pGIPZ-shTp53


title: AKT-shTp53-2

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against Tp53. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#2.


title: AKT-shNF1-1

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against NF1. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#1.

value: replicate 1


title: AKT-shNF1-3

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against NF1. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#3.


title: AKT-shTp53-1

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against Tp53. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#1.


title: AKT-shCBS-3

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against CBS. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#3.

value: expressing pBabe-puro-myrAKT1 and pGIPZ-shCBS


title: AML01_Alu_pool_cell_39 [i504_D3_i703_201027_AML01_Alu_pool_S4_L001]

value: untreated

value: Acute myeloid leukemia


title: AKT-shCBS-2

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against CBS. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#2.


title: AML01_Alu_pool_cell_37 [i504_D1_i701_201027_AML01_Alu_pool_S4_L001]

value: M

value: genomic DNA, bisulfate treated


title: AML01_Alu_pool_cell_38 [i504_D2_i702_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_46 [i504_D10_i710_201027_AML01_Alu_pool_S4_L001]


title: BM-MSC AD+Chidamide

city: Jining

first: Mingtai

last: Chen

state: China

institute: Affiliated Hospital of Jining Medical University

description: Gene expression after adipogenic induction and chidamide treatment of BM-MSC for 8 days

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BM-MSC adipogenic induction+Chidamide

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BM-MSCs were isolated from the bone marrow and cultured in DMEM supplemented with 10%FBS.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BM-MSCs were seeded into 6-well plates. Upon reaching confluence, the cells were changed into adipogenic medium composed of DMEM with 10% FBS, 1 mM dexamethasone, 0.01 mg/mL insulin, 100 mg/mL indomethacin, and 0.5 mM 3-isobutyl-1-methyl-xanthine for 8 days. Chidamide was used to treat BM-MSCs at final concentration of 2 μM.

value: Bone marrow

tag: cell type

value: BM-MSC


title: AKT-NTC-3

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#3.

value: expressing pBabe-puro-myrAKT1 and pGIPZ-shNTC


title: BM-MSC AD+DMSO

description: Gene expression after adipogenic induction and DMSO treatment of BM-MSC for 8 days

source_name: BM-MSC adipogenic induction+DMSO


title: AKT-shCBS-1

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA against CBS. Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#1.


title: AKT-NTC-2

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#2.


title: AKT-NTC-1

description: BJ-TERT cells were transduced with pBabe-puro-myrAKT1 to induce senescence. On day 6 post-transduction myrAKT1 cells were transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#1.


title: AML01_Alu_pool_cell_33 [i503_C9_i709_201027_AML01_Alu_pool_S4_L001]


title: BM-MSC AD

description: Gene expression after adipogenic induction of BM-MSC for 8 days

source_name: BM-MSC adipogenic induction


title: AML01_Alu_pool_cell_35 [i503_C11_i711_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_32 [i503_C8_i708_201027_AML01_Alu_pool_S4_L001]


title: pBabe-NTC-2

description: BJ-TERT cells were transduced with pBabe-puro empty vector (EV). On day 6 post-transduction, pBabe-EV cells transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#2.

value: expressing pBabe-puro and pGIPZ-NTC


title: BM-MSC UN

description: Gene expression in untreated BM-MSC

source_name: BM-MSC untreated


title: AML01_Alu_pool_cell_28 [i503_C4_i704_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_29 [i503_C5_i705_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_36 [i503_C12_i712_201027_AML01_Alu_pool_S4_L001]


title: pBabe-NTC-1

description: BJ-TERT cells were transduced with pBabe-puro empty vector (EV). On day 6 post-transduction, pBabe-EV cells transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#1.


title: AML01_Alu_pool_cell_31 [i503_C7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_30 [i503_C6_i706_201027_AML01_Alu_pool_S4_L001]


title: Sample_337

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: RNAseq counts from the glomerular compartment from kidney biopsies.

data_processing:
fastQC 0.11.5
fastqScreen 0.11.4
cutadapt 1.14 -m 50 -A CTGTCTCTTATA -a CTGTCTCTTATA
STAR 2.5.2.a --bamRemoveDuplicatesType UniqueIdentical --twopassMode Basic --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
htseq-count --stranded=no --order=pos --mode=union
Genome_build: GRCh 38.86

source_name: Glomeruli from kidney biopsy

extract_protocol:
Qiagen Allprep DNA/RNA Micro Kit (cat# 80284)
Takara SMART-Seq v4 Ultra Low Input RNA Kit (cat# 634891)
oligo(dT)

value: Glomeruli from kidney biopsy

tag: disease

value: Focal Segmental Glomerulosclerosis


title: Sample_319


title: Sample_282

value: Minimal Change Disease


title: AML01_Alu_pool_cell_27 [i503_C3_i703_201027_AML01_Alu_pool_S4_L001]


title: Sample_111


title: Sample_20

value: Other Nephrotic Syndrome


title: Sample_339

value: Membranous Nephropathy


title: AML01_Alu_pool_cell_26 [i503_C2_i702_201027_AML01_Alu_pool_S4_L001]


title: Sample_210


title: AML01_Alu_pool_cell_34 [i503_C10_i710_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_23 [i502_B11_i711_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_24 [i502_B12_i712_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_25 [i503_C1_i701_201027_AML01_Alu_pool_S4_L001]


title: Sample_50


title: Sample_72


title: pBabe-NTC-3

description: BJ-TERT cells were transduced with pBabe-puro empty vector (EV). On day 6 post-transduction, pBabe-EV cells transduced with pGIPZ-shRNA non-targeting control (NTC).  Total RNA was extracted on day 14 post-transduction for RNA-seq. This is the replicate#3.

value: replicate 3

value: 14 days


title: AML01_Alu_pool_cell_40 [i504_D4_i704_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_22 [i502_B10_i710_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_21 [i502_B9_i709_201027_AML01_Alu_pool_S4_L001]


title: Sample_226


title: AML01_Alu_pool_cell_19 [i502_B7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_20 [i502_B8_i708_201027_AML01_Alu_pool_S4_L001]


title: Sample_215


title: AML01_Alu_pool_cell_18 [i502_B6_i706_201027_AML01_Alu_pool_S4_L001]


title: Sample_198


title: AML01_Alu_pool_cell_17 [i502_B5_i705_201027_AML01_Alu_pool_S4_L001]


title: Sample_65


title: Sample_183


title: AML01_Alu_pool_cell_15 [i502_B3_i703_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_14 [i502_B2_i702_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_11 [i501_A11_i711_201027_AML01_Alu_pool_S4_L001]


title: Sample_230


title: Sample_68


title: AML01_Alu_pool_cell_10 [i501_A10_i710_201027_AML01_Alu_pool_S4_L001]


title: Sample_94


title: AML01_Alu_pool_cell_16 [i502_B4_i704_201027_AML01_Alu_pool_S4_L001]


title: Sample_332


title: Sample_145


title: AML01_Alu_pool_cell_13 [i502_B1_i701_201027_AML01_Alu_pool_S4_L001]


title: Sample_203


title: AML01_Alu_pool_cell_9 [i501_A9_i709_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_5 [i501_A5_i705_201027_AML01_Alu_pool_S4_L001]


title: Sample_168


title: AML01_Alu_pool_cell_6 [i501_A6_i706_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_7 [i501_A7_i707_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_8 [i501_A8_i708_201027_AML01_Alu_pool_S4_L001]


title: AML01_Alu_pool_cell_3 [i501_A3_i703_201027_AML01_Alu_pool_S4_L001]


title: Sample_34


title: Sample_312


title: Sample_197


title: Sample_308


title: Sample_266


title: Sample_272


title: Sample_190


title: KG1a_Alu_pool_cell_95 [i508_H11_i711_KG1a_Alu]

tag: molecule subtype


title: KG1a_Alu_pool_cell_96 [i508_H12_i712_KG1a_Alu]


title: Sample_338


title: Sample_302


title: AML01_Alu_pool_cell_2 [i501_A2_i702_201027_AML01_Alu_pool_S4_L001]


title: Sample_238


title: Sample_277


title: KG1a_Alu_pool_cell_93 [i508_H9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_92 [i508_H8_i708_KG1a_Alu]


title: Sample_260


title: KG1a_Alu_pool_cell_89 [i508_H5_i705_KG1a_Alu]

value: decitabine treated:at 0, 24 and 48 hours, harvested at 72 hours


title: KG1a_Alu_pool_cell_90 [i508_H6_i706_KG1a_Alu]


title: Sample_142


title: AML01_Alu_pool_cell_4 [i501_A4_i704_201027_AML01_Alu_pool_S4_L001]


title: KG1a_Alu_pool_cell_88 [i508_H4_i704_KG1a_Alu]


title: Sample_164


title: Sample_320


title: Sample_193


title: Sample_251


title: KG1a_Alu_pool_cell_85 [i508_H1_i701_KG1a_Alu]


title: KG1a_Alu_pool_cell_86 [i508_H2_i702_KG1a_Alu]


title: KG1a_Alu_pool_cell_94 [i508_H10_i710_KG1a_Alu]


title: KG1a_Alu_pool_cell_84 [i507_G12_i712_KG1a_Alu]


title: KG1a_Alu_pool_cell_87 [i508_H3_i703_KG1a_Alu]


title: Sample_42


title: Sample_120


title: Sample_156


title: Sample_316


title: KG1a_Alu_pool_cell_91 [i508_H7_i707_KG1a_Alu]


title: Sample_55


title: KG1a_Alu_pool_cell_81 [i507_G9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_80 [i507_G8_i708_KG1a_Alu]


title: KG1a_Alu_pool_cell_82 [i507_G10_i710_KG1a_Alu]


title: Sample_133


title: KG1a_Alu_pool_cell_83 [i507_G11_i711_KG1a_Alu]


title: Sample_305


title: KG1a_Alu_pool_cell_79 [i507_G7_i707_KG1a_Alu]


title: Sample_194


title: KG1a_Alu_pool_cell_78 [i507_G6_i706_KG1a_Alu]


title: KG1a_Alu_pool_cell_77 [i507_G5_i705_KG1a_Alu]


title: KG1a_Alu_pool_cell_76 [i507_G4_i704_KG1a_Alu]


title: Sample_25


title: Sample_280


title: Sample_88


title: KG1a_Alu_pool_cell_75 [i507_G3_i703_KG1a_Alu]


title: Sample_241


title: Sample_147


title: KG1a_Alu_pool_cell_74 [i507_G2_i702_KG1a_Alu]


title: Sample_71


title: Sample_179


title: KG1a_Alu_pool_cell_73 [i507_G1_i701_KG1a_Alu]


title: KG1a_Alu_pool_cell_72 [i506_F12_i712_KG1a_Alu]


title: KG1a_Alu_pool_cell_71 [i506_F11_i711_KG1a_Alu]


title: Sample_74


title: KG1a_Alu_pool_cell_70 [i506_F10_i710_KG1a_Alu]


title: Sample_295


title: KG1a_Alu_pool_cell_69 [i506_F9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_68 [i506_F8_i708_KG1a_Alu]


title: Sample_35


title: Sample_1


title: KG1a_Alu_pool_cell_66 [i506_F6_i706_KG1a_Alu]


title: KG1a_Alu_pool_cell_64 [i506_F4_i704_KG1a_Alu]


title: Sample_54


title: KG1a_Alu_pool_cell_67 [i506_F7_i707_KG1a_Alu]


title: KG1a_Alu_pool_cell_65 [i506_F5_i705_KG1a_Alu]


title: Sample_49


title: KG1a_Alu_pool_cell_63 [i506_F3_i703_KG1a_Alu]


title: Sample_27


title: KG1a_Alu_pool_cell_61 [i506_F1_i701_KG1a_Alu]


title: Sample_130


title: Sample_196


title: Sample_186


title: KG1a_Alu_pool_cell_62 [i506_F2_i702_KG1a_Alu]


title: KG1a_Alu_pool_cell_59 [i505_E11_i711_KG1a_Alu]


title: Sample_329


title: Sample_278


title: Sample_279


title: Sample_53


title: KG1a_Alu_pool_cell_60 [i505_E12_i712_KG1a_Alu]


title: KG1a_Alu_pool_cell_57 [i505_E9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_58 [i505_E10_i710_KG1a_Alu]


title: KG1a_Alu_pool_cell_56 [i505_E8_i708_KG1a_Alu]


title: KG1a_Alu_pool_cell_53 [i505_E5_i705_KG1a_Alu]


title: Sample_195


title: KG1a_Alu_pool_cell_52 [i505_E4_i704_KG1a_Alu]


title: Sample_192


title: KG1a_Alu_pool_cell_51 [i505_E3_i703_KG1a_Alu]


title: Sample_256


title: KG1a_Alu_pool_cell_49 [i505_E1_i701_KG1a_Alu]


title: Sample_235


title: Sample_205


title: KG1a_Alu_pool_cell_48 [i504_D12_i712_KG1a_Alu]


title: Sample_87


title: Sample_69


title: KG1a_Alu_pool_cell_47 [i504_D11_i711_KG1a_Alu]


title: Sample_246

value: Nephrotic Syndrome, unspecified


title: Sample_150


title: KG1a_Alu_pool_cell_46 [i504_D10_i710_KG1a_Alu]


title: KG1a_Alu_pool_cell_44 [i504_D8_i708_KG1a_Alu]


title: Sample_229


title: Sample_77


title: Sample_333


title: KG1a_Alu_pool_cell_40 [i504_D4_i704_KG1a_Alu]

value: untreated


title: Sample_271


title: Sample_218


title: KG1a_Alu_pool_cell_39 [i504_D3_i703_KG1a_Alu]

value: Acute myeloid leukemia


title: Sample_299


title: KG1a_Alu_pool_cell_41 [i504_D5_i705_KG1a_Alu]

value: M


title: KG1a_Alu_pool_cell_38 [i504_D2_i702_KG1a_Alu]

value: genomic DNA, bisulfate treated


title: KG1a_Alu_pool_cell_50 [i505_E2_i702_KG1a_Alu]


title: KG1a_Alu_pool_cell_36 [i503_C12_i712_KG1a_Alu]


title: KG1a_Alu_pool_cell_37 [i504_D1_i701_KG1a_Alu]


title: Sample_171


title: Sample_334


title: Sample_100


title: Sample_204


title: KG1a_Alu_pool_cell_35 [i503_C11_i711_KG1a_Alu]


title: KG1a_Alu_pool_cell_45 [i504_D9_i709_KG1a_Alu]


title: Sample_248


title: Sample_12


title: Sample_213


title: KG1a_Alu_pool_cell_33 [i503_C9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_32 [i503_C8_i708_KG1a_Alu]


title: Sample_206


title: KG1a_Alu_pool_cell_31 [i503_C7_i707_KG1a_Alu]


title: KG1a_Alu_pool_cell_30 [i503_C6_i706_KG1a_Alu]


title: Sample_237


title: Sample_326


title: KG1a_Alu_pool_cell_29 [i503_C5_i705_KG1a_Alu]


title: Sample_284


title: Sample_209


title: KG1a_Alu_pool_cell_28 [i503_C4_i704_KG1a_Alu]


title: IgG

city: Nanjing

first: Xing

last: Ma

address: No.1 Weigang, Nanjing, Jiangsu 210095, P. R. China

institute: Nanjing Agricultural University

data_processing:
All clean reads in three biological replicates were aligned to the MSU v7.0 reference genome using BWA
SAMtools was used to exclude reads with mapping quality below 10
PCR duplicates were removed by using Picard
Aligned reads with at least length 50 were used for iM-IP peak calling by using MACS2 (version 2.1.1) (42)with parameters as below: callpeak -g 3.8e+8 -p 1e-4 -nomodel -f BAMPE
Supplementary_files_format_and_content: a bed file containing information of regular PiMFSs

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: Nipponbare (Japonica) rice seeds (Oryza. sativa L.) were pre-germinated at room temperature (RT) for three days. Germinated seeds were grown in a greenhouse at 28-30°C and a 14h/10h light-dark cycle. Two-week-old rice seedlings were cut into1-1.5 cm slices and cross-linked in HEPES buffer pH=8.0 (20mM HEPES, 1mM EDTA, 100mM NaCl and 1mM PMSF) with a final 1% of formaldehyde under vacuum for 10 min at RT. A final concentration of 0.125 M glycine was added for an additional 5min vacuum for quenching excess of formaldehyde. The cross-linked seedlings were ground to a fine powder using liquid nitrogen.

extract_protocol:
The fine powder was used for nuclei preparation and genomic DNA extraction following the procedures as described previously
The genomic DNA was fragmented into sizes, ranging from 100-500 bp, using the water-based Biorupter (Diagnode), followed by DNA extraction and purification. Total 5μg fragmented genomic DNA was diluted in iM stabilization buffer (50mM Tris-AcOH, pH=5.5) for denaturing and re-association treatment using a PCR program as below: 95°C for 8 min，95°C for 30s (-0.5 °C /cycles, 129 cycles)，35°C hold on. The re-associated DNA was diluted with iM-IP incubation buffer (50mM Tris-AcOH, 1mM MgCl2, 130nM CaCl2, 1%BSA and Complete mini, pH=5.5), then incubated with 3μg iMab antibody (Ab01462-23.0, Kappa) for 4 h at 4℃. The antibody incubation reaction was incubated with 30 μl of washed protein G Dynalbeads (10004D, Invitrogen) for another 4 h at 4°C. The iMab-bound DNA was finally eluted with 200 μl elution buffer (0.1M NaHCO3 and 1% SDS) at 65°C for two times with 15 min each. Three biologically replicated iM-IPed DNA or Input/IgG-IPed control DNA was used for library preparation. All libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S). Libraries were finally quality controlled and sequenced using paired-end mode on Illumina NovaSeq platform.

tag: chip antibody

value: IgG


title: KG1a_Alu_pool_cell_27 [i503_C3_i703_KG1a_Alu]


title: Input


title: KG1a_Alu_pool_cell_25 [i503_C1_i701_KG1a_Alu]


title: KG1a_Alu_pool_cell_26 [i503_C2_i702_KG1a_Alu]


title: KG1a_Alu_pool_cell_24 [i502_B12_i712_KG1a_Alu]


title: Sample_185


title: KG1a_Alu_pool_cell_34 [i503_C10_i710_KG1a_Alu]


title: iMIP_rep3

value: iMab


title: KG1a_Alu_pool_cell_23 [i502_B11_i711_KG1a_Alu]


title: Sample_51


title: iMIP_rep2


title: KG1a_Alu_pool_cell_20 [i502_B8_i708_KG1a_Alu]


title: Sample_22


title: Sample_47


title: iMIP_rep1


title: KG1a_Alu_pool_cell_19 [i502_B7_i707_KG1a_Alu]


title: KG1a_Alu_pool_cell_17 [i502_B5_i705_KG1a_Alu]


title: KG1a_Alu_pool_cell_18 [i502_B6_i706_KG1a_Alu]


title: Sample_290


title: KG1a_Alu_pool_cell_15 [i502_B3_i703_KG1a_Alu]


title: KG1a_Alu_pool_cell_14 [i502_B2_i702_KG1a_Alu]


title: Sample_118


title: MSU_rep5_mDM

city: La Jolla

first: Isidoro

last: Cobo

state: CA

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

data_processing:
FASTQ sequencing files were mapped to the mm10 or hg38 reference genomes for mouse samples or human samples, respectively using STAR with default parameters. Biological replicates were used in all experiments.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: Raw expression (TPM) files

source_name: mDM

growth_protocol: Flushed bone marrow from both femurs and tibias of C57BL/6 mice were cultured in DMEM medium supplemented with 10% de-complemented FBS, 100 units/ml penicillin and 100 ug/ml streptomycin, 2mM L-glutamine, and 20% of L929 conditioned media for for six days at 37ºC and 5% CO2. On day six, BMDM were trypsinized and plated in DMEM medium supplemented with 10% de-complemented FBS, 2mM L-glutamine, 100 units/ml penicillin and 100 ug/ml streptomycin, and 10 ng/mL recombinant murine M-CSF (Peprotech, #315-02) for one day prior being stimulated for five hours with 100ng/mL of LPS or 250 μg/mL of MSUc

extract_protocol:
BMDM or mDM were lysed in TRIzol (ThermoFisher, #15596026). RNA isolation and DNase treatment was carried out using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB)
500ng-1 μg total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94ºC in 2X Superscript III first-strand buffer containing 10mM DTT (Invitrogen, #P2325). The 10 μl of fragmented RNA was added to 0.5 μl of Random primers (Invitrogen, #48190011), 0.5 μl of Oligo d(T) primer (Invitrogen, #18418020), 0.5 μl of SUPERase inhibitor (Ambion, #AM2696), 1 μl of 10mM dNTPs and incubated at 50ºC for three minutes. Then, 5.8 μl of water, 1 μl of 10mM DTT, 0.1 μl of 2 μg/μl Actinomycin D (Sigma, #A1410), 0.2 μl of 1% Tween-20 (Sigma) and 0.5 μl of SuperScript III (Invitrogen, #ThermoFisher 18080044) was added to the mix. Reverse-transcription (RT) reaction was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and eluted in 10 μl in 0.01% Tween-20. The RNA-cDNA complex was then added to 1.5 μl of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μl of 5U/μl RNAseH (Enzymatics, #Y9220L), 1 μl of 10U/μl DNA polymerase I (Enzymatics, #P7050L), 0.15 μl of 1% Tween-20 and 1.05 μl of nuclease free water; and incubated at 16ºC for 2.5h or overnight. The resulting dsDNA product was purified using 28 μl of SpeedbBead Magnetic Carboxylate (GE Healthcare, #651521050 50250) diluted in 20%PEG8000:2.5M NaCl to a final 13% PEG concentration, washed twice with 80% etOH, air dry and eluted in 40 μl of 0.05% Tween-20. The purified 40 μl of dsDNA was end-repaired by blunting followed by A-tailing and adapter ligation as described elsewhere (69) using BIOO Barcodes (BIOO Scientific, #514104), IDT TruSeq Unique Dual Indexes or Kapa Unique Dual-Indexed Adapters using 15 μl Rapid Ligation Buffer (Enzymatics, #L603-LC-L), 0.33 μl 1% Tween-20 and 0.5 μl T4 DNA ligase HC (Enzymatics, #L6030-HC-L). Libraries were amplified by PCR for 11-15 cycles using Solexa IGA and Solexa IGB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), purified using 1 μl of SpeedbBead Magnetic Carboxylate in 15.2 μl of 20%PEG8000:2.5M NaCl, washed with 80% etOH and eluted in 0.05% Tween-20. Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on a NextSeq 500 or Hi-Seq 4000 (Illumina, San Diego, California).

treatment_protocol: 20 μM of JNK inhibitor SP600125 (Tocris, #1496), 10 μM of BHA (Sigma, B1253), 20nM of BAY-876 (Selleckchem,#S8452), 3 μM of p38 MAPK inhibitor SB203580 (Tocris, #1202) or NLRP3 inflammasome inhibitor MCC950 (1uM, Selleckchem, #S7809) were added to the media one hour prior to stimulation with LPS or MSUc.

tag: agent

value: MSU

tag: time point


title: KG1a_Alu_pool_cell_22 [i502_B10_i710_KG1a_Alu]

tag: cancer type


title: MSU_rep3_mDM


title: MSU_rep4_mDM


title: KG1a_Alu_pool_cell_13 [i502_B1_i701_KG1a_Alu]


title: KG1a_Alu_pool_cell_12 [i501_A12_i712_KG1a_Alu]


title: KG1a_Alu_pool_cell_11 [i501_A11_i711_KG1a_Alu]


title: KG1a_Alu_pool_cell_21 [i502_B9_i709_KG1a_Alu]


title: KG1a_Alu_pool_cell_10 [i501_A10_i710_KG1a_Alu]


title: KG1a_Alu_pool_cell_9 [i501_A9_i709_KG1a_Alu]


title: Sample_253


title: Sample_315


title: MSU_rep2_mDM


title: Sample_239


title: KG1a_Alu_pool_cell_7 [i501_A7_i707_KG1a_Alu]


title: KG1a_Alu_pool_cell_16 [i502_B4_i704_KG1a_Alu]


title: Sample_265


title: LPS_rep7_mDM

value: LPS


title: KG1a_Alu_pool_cell_5 [i501_A5_i705_KG1a_Alu]


title: KG1a_Alu_pool_cell_3 [i501_A3_i703_KG1a_Alu]


title: KG1a_Alu_pool_cell_6 [i501_A6_i706_KG1a_Alu]


title: KG1a_Alu_pool_cell_4 [i501_A4_i704_KG1a_Alu]


title: LPS_rep6_mDM


title: Sample_39

value: Glomeruli from kidney biopsy


title: Sample_127

value: Focal Segmental Glomerulosclerosis


title: KG1a_Alu_pool_cell_2 [i501_A2_i702_KG1a_Alu]


title: KG1a_Alu_pool_cell_1 [i501_A1_i701_KG1a_Alu]


title: LPS_rep5_mDM


title: LPS_rep4_mDM


title: Sample_262


title: Gastric benign sample 4GB-036

type: genomic

city: Ciudad de México

first: Martha

middle: Eugenia

last: Ruiz-Tachiquín

state: CIudad de México

address: Av. Cuauhtémoc No.330, Col. Doctores, Deleg. Cuauhtémoc.

department: Tercer piso. UMAE-Hospital de Oncología

country: Mexico

institute: Centro Médico Nacional Siglo XXI-IMSS

description: Hybridized to Cytoscan HD Affymetrix

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the GeneChip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (version v3.2.2). Copy number values were extracted and converted from CEL files into CYCHP files using Chromosome Analysis Suite software (v.3.2.0.1252). Reference file was CytoScan HD Array.na33.r3, ChAS Browser was NefAffx Build hg19 (20170803).

label: Biotin

source_name: Gastric benign sample 4GB-036

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA extraction was done with a QIAamp® micro kit (QIAGEN) according to the manufacturer’s instructions. The extractions were modified to include an initial incubation at 95°C for 15 min followed by 5 min at room temperature as described previously, before being digested with proteinase K for 3 days at 56°C in a water-bath with addition of fresh enzyme at 24 h intervals.

value: Gastric benign


title: Sample_62


title: LPS_rep3_mDM


title: Gastric benign sample 4GB-042

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-042


title: Gastric benign sample 4GB-015

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-015


title: KG1a_Alu_pool_cell_8 [i501_A8_i708_KG1a_Alu]


title: LPS_rep2_mDM


title: Gastric benign sample 4GB-025

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-025


title: Gastric benign sample 4GB-031

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-031


title: MSU_rep1_mDM


title: Sample_167

value: Minimal Change Disease


title: Gastric benign sample 4GB-001

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-001


title: Adjacent tissue diffuse sample 3AT-064

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 3AT-064

value: Adjacent tissue diffuse


title: LPS_rep1_mDM


title: Sample_220


title: PBS_rep5_mDM

value: PBS


title: Adjacent tissue diffuse sample 3AT-035

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 3AT-035


title: Adjacent tissue diffuse sample 8AT-004

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 8AT-004


title: Adjacent tissue diffuse sample 3AT-042

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 3AT-042


title: Sample_201


title: Adjacent tissue diffuse sample 1AT-001

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 1AT-001


title: PBS_rep4_mDM


title: Sample_255


title: Gastric benign sample 4GB-033

description: Hybridized to Cytoscan HD Affymetrix

source_name: Gastric benign sample 4GB-033


title: Sample_288

value: Other Nephrotic Syndrome


title: Sample_208


title: Adjacent tissue diffuse sample 3AT-173

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 3AT-173


title: PBS_rep3_mDM


title: Adjacent tissue diffuse sample 3AT-047

description: Hybridized to Cytoscan HD Affymetrix

source_name: Adjacent tissue diffuse sample 3AT-047


title: Adjacent tissue intestinal sample 3AT-099

description: Hybridized to Cytoscan HD Affymetrix

value: Adjacent tissue intestinal


title: Sample_212

source_name: Glomeruli from kidney biopsy


title: Adjacent tissue intestinal sample 3AT-046

description: Hybridized to Cytoscan HD Affymetrix


title: Adjacent tissue intestinal sample 3AT-126

description: Hybridized to Cytoscan HD Affymetrix


title: Sample_56

value: Membranous Nephropathy


title: Sample_152


title: Adjacent tissue intestinal sample 3AT-146

description: Hybridized to Cytoscan HD Affymetrix


title: Adjacent tissue intestinal sample 3AT-128

description: Hybridized to Cytoscan HD Affymetrix


title: PBS_rep2_mDM


title: Adjacent tissue intestinal sample 3AT-008

description: Hybridized to Cytoscan HD Affymetrix


title: Cancer gastric diffuse sample 3CG-064

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 3CG-064

value: Cancer gastric diffuse


title: si-ALKBH5 rep 2

city: Shanghai

first: Hailong

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix table include FPKM values for every sample.

source_name: oral squamous cell carcinoma

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions.

treatment_protocol: cells were transfected with ALKBH5-specific siRNA using RNAiMax reagent.

tag: transfection


title: si-ALKBH5 rep 1


title: si-scramble rep 2

value: siScramble


title: Sample_2

tag: tissue


title: Cancer gastric diffuse sample 3CG-035

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 3CG-035


title: Cancer gastric diffuse sample 3CG-042

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 3CG-042


title: Sample_154


title: Cancer gastric diffuse sample 8CG-004

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 8CG-004


title: Cancer gastric diffuse sample 1CG-001

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 1CG-001


title: si-ALKBH5 rep 2 Input

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix table with peaks calling results for every peak and every sample

extract_protocol:
m6A RNA immunoprecipitation was performed with the GenSeq™ m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

tag: antibody


title: Cancer gastric diffuse sample 3CG-173

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 3CG-173


title: si-ALKBH5 rep 2 IP


title: Cancer gastric intestinal sample 3CG-146

description: Hybridized to Cytoscan HD Affymetrix

value: Cancer gastric intestinal


title: Cancer gastric intestinal sample 3CG-104

description: Hybridized to Cytoscan HD Affymetrix.. No adjacent normal tissue for this sample.


title: Sample_232


title: si-ALKBH5 rep 1 Input


title: Sample_99


title: Cancer gastric diffuse sample 3CG-047

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric diffuse sample 3CG-047


title: Sample_245


title: Cancer gastric intestinal sample 3CG-128

description: Hybridized to Cytoscan HD Affymetrix


title: si-scramble rep 2 Input

value: siSramble


title: Cancer gastric intestinal sample 3CG-046

description: Hybridized to Cytoscan HD Affymetrix


title: Cancer gastric intestinal sample 3CG-099

description: Hybridized to Cytoscan HD Affymetrix


title: si-scramble rep 2 IP


title: Cancer gastric intestinal sample 3CG-008

description: Hybridized to Cytoscan HD Affymetrix


title: si-ALKBH5 rep 1 IP


title: si-scramble rep 1


title: Sample_73


title: Sample_257


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S135_rep2

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
For BrdU-IP-ssSeq and eSPAN strand bias calculations, consistent paired-end reads mapped to Watson (W) and Crick (C) strands of the reference genome were separated with the bamtobed function from BEDTools and in-house Perl programs. Genome-wide reads coverage was calculated by deepTools. Strand bias was calculated in 10bp bins from these separated Watson and Crick reads using the formula Bias = (W − C)/(W + C) across the whole genome.
MACS2 was used to perform BrdU peak calling (--broad-cutoff 0.001) in the BrdU-IP-ssSeq samples relative to the corresponding control samples (input).
For spike-in normalization, we first followed the same procedure as above to align FASTQ files to the S. pombe reference genome. S. cerevisiae genome coverage at each base pair was multiplied by scaling factor based on S. pombe reads as described previously (Jeronimo et al., 2019).
Genome_build: S. cerevisiae (UCSC sacCer3) and S. pombe (Downloaded from https://www.pombase.org/ on March 10th 2018)
Supplementary_files_format_and_content: bigwig files were generated for plus strand, minus strand and both strands, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae W303

source_name: whole cell

growth_protocol: Yeast cells were grown in rich medium (1% yeast extract, 2% peptone) supplemented with 2% glucose (YPD) or, for galactose-induction experiments, with 2% raffinose (YPRaff). Exponentially growing cells were arrested at G1 phase with 5 ug/ml alpha-factor (EZBiolab) for 3 hours (YPD) or 3.5 hours (YPRaff). Degradation of AID-tagged proteins was achieved with the addition of 1 mM 3-indolacetic acid (IAA, I2886 Sigma) into the media. Induction of proteins under the GAL1 promoter was achieved with the addition of 2% galactose into YPRaff.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously (Yu et al., 2014). For H3K4me3 and H3K56ac ChIP, chromatin was pelleted, washed twice with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM b-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine), resuspended in the same buffer, and digested with MNase (9013-53-0, Worthington Biochemical) for 20 min at 37C yielding a majority of mono- and di-nucleosome fragments. Digestion was stopped with the addition of 5 l 0.5 M EDTA, 1/5 volume of 5xChIP lysis buffer, and incubating 10 min on ice. For RNA Pol II CTD-Ser5p ChIP, chromatin was sheared by sonication using a Bioruptor Pico (15 seconds ON, 30 seconds OFF, 10 cycles)(Diagenode) to yield fragments of an average size of 300 bp.   Sonicated and MNase-digested chromatin was cleared by centrifugation and immunoprecipitated with the appropriate antibody (anti-H3K4me3 (ab8580, Abcam), anti-H3K56ac (38), or anti-RPB1 CTD-Ser5p (04-1572, Millipore)) and protein G Sepharose beads (17-0618-02, GE Healthcare). After washing the beads extensively, DNA from both input and ChIP was recovered with the Chelex-100 protocol (39) and used for BrdU IP/eSPAN or purified with MinElute PCR Purification kit (28004, Qiagen). Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA library kit (10096, Swift Biosciences). Input and ChIP DNA was used for BrdU immunoprecipitation to prepare BrdU IP and eSPAN samples, respectively. Recovered DNA from the Chelex-100 extraction was incubated at 100C for 5 min and immediately chilled on ice for 5 min. BrdU immunoprecipitation was performed by diluting DNA 10-fold with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v), 6.7 g/ml Escherichia coli tRNA, 0.17 g/ml BrdU antibody (555627, BD Bioscience)) and incubated for 2 hours at 4C. Protein G Sepharose beads were added to each sample for 1 additional hour at 4C. Beads were washed extensively and DNA was recovered with TE + 1% SDS at 65C  for 15 min and purified with MinElute PCR Purification kit (28004, Qiagen). Single-stranded DNA sequencing libraries were prepared using the Accel-NGS 1S Plus DNA library kit (10096, Swift Biosciences).
ChIP-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center.

tag: treatment

value: MNase

tag: strains genetic background

tag: genotype

value: complementation spp1-W45A

value: anti-H3K4me3 (ab8580, Abcam)

tag: spike-in

value: Schizosaccharomyces pombe

value: whole cell


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S105_rep2


title: Sample_307

value: Glomeruli from kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S075_rep2


title: si-scramble rep 1 Input


title: si-scramble rep 1 IP


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S045_rep2


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_G1_rep2


title: Sample_310

value: Minimal Change Disease


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S135_rep2

value: complementation Spp1


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S105_rep2


title: Cancer gastric intestinal sample3CG-126

description: Hybridized to Cytoscan HD Affymetrix

source_name: Cancer gastric intestinal sample 3CG-126

tag: patient id


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S075_rep2


title: WI38_NFKB1/p52_Day7_ChIPSeq

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were trimmed with Trimmomatic (version 0.39) to remove low quality reads.
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie version 2.4.4 with default configurations.
Peaks were called using Homer pipeline version 4.11 with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file

growth_protocol: WI-38 cell line was maintained in DMEM supplemented with 10% FBS and 1%PS.

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor/DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina (Part# E7103). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (reduced exo enzyme activity) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer HiSeq4000 following the manufacturer's protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min, and neuralized with Glycine for 5 min at room temperature.

tag: cell line

value: Human fibroblast cell Line

value: Tissue culture Day 7

value: NF-κB2 p100/p52 (D7A9K) Rabbit mAb #37359 (Cell Signaling)


title: Sample_269


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S045_rep2


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_G1_rep2


title: Sample_231


title: WI38_NFKB1/p52_Day0_ChIPSeq

value: Tissue culture Day 0


title: Sample_268


title: Spp1AID_mcm23A_Spp1W45A_Input_S105_rep2


title: WI38_Input


title: Spp1AID_mcm23A_Spp1W45A_Input_S135_rep2


title: Spp1AID_mcm23A_Spp1W45A_Input_S045_rep2


title: Sample_234


title: Sample_207


title: Subject  102.100.035 , day 92

first: Yan

last: Che

state: Illinois

address: 303 E Superior St

institute: Northwestern University

description: healthy adults after vaccination with a replication-competent tetravalent dengue vaccine

data_processing:
Sequencer-generated base call (BCL) files were converted to FASTQ files and the multiplexed samples were separated using bcl2fastq
Demultiplexed fastq were assessed for sequencing quality using FastQC (version 0.11.4, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The fastq files were quality filtered by using FASTAX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with the invocation fastq_quality_filter -q 30 -p 50 -v -Q 33
Sequencing reads that met all quality control requirements were aligned to the latest human reference genome (GRCh38) using HISAT2 (version 2.0.4)
Gene expression in units of overlapping read counts per million were obtained by using the script from ballgown on gtf files of preprocessed RNA-seq alignments.
expression profiling was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: TDV_gene_count_matrix.csv

source_name: Whole blood

extract_protocol:
Total RNA was extracted from PAXgene RNA blood tubes  with Roche MagNAPure96 PaxGeneRNA isolation
Following ribosomal RNA (rRNA) and globin mRNA depletion with Globin-Zero® Gold rRNA Removal kit, the enriched RNA was fragmented and primed for cDNA synthesis using TruSeq Total Stranded RNA HT kit  on a Microlab STAR automated liquid handling system
TruSeq HT indices used for multiplexing. The 2nM libraries were clustered on a patterned flow cell using a cBot  and sequenced on the HiSeq 4000 sequencing platform

value: Whole blood

tag: timepoint

value: Day 92

tag: Sex

value: M


title: Spp1AID_mcm23A_Spp1W45A_Input_S075_rep2


title: Spp1AID_mcm23A_Spp1W45A_Input_G1_rep2


title: Subject  102.100.038 , day 92


title: Sample_221

tag: disease

value: Other Nephrotic Syndrome


title: Spp1AID_mcm23A_Spp1_Input_S105_rep2

value: MNase


title: Subject  102.100.029 , day 92


title: Subject  102.100.002 , day 92


title: Sample_317


title: Sample_259


title: Spp1AID_mcm23A_Spp1_Input_S135_rep2


title: Spp1AID_mcm23A_Spp1_Input_S045_rep2


title: Spp1AID_mcm23A_Spp1_Input_G1_rep2


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S135_rep1

value: complementation spp1-W45A


title: Subject  102.100.041 , day 92

value: F


title: Sample_199


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S075_rep1

value: anti-H3K4me3 (ab8580, Abcam)

value: Schizosaccharomyces pombe


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S105_rep1

value: whole cell


title: Sample_141

value: Glomeruli from kidney biopsy

value: Focal Segmental Glomerulosclerosis


title: Sample_117


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_S045_rep1


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S135_rep1

value: complementation Spp1


title: Spp1AID_mcm23A_Spp1W45A_H3K4me3_ChIP_G1_rep1


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S105_rep1


title: Spp1AID_mcm23A_Spp1_Input_S075_rep2


title: Sample_66


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_G1_rep1


title: Subject  102.100.006 , day 92


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S045_rep1


title: Spp1AID_mcm23A_Spp1_H3K4me3_ChIP_S075_rep1


title: Subject  102.100.014 , day 92


title: Spp1AID_mcm23A_Spp1W45A_Input_S135_rep1


title: Sample_80

value: Membranous Nephropathy


title: Sample_182


title: Subject  102.100.038 , day 7

value: Day 7


title: Subject  102.100.017 , day 92


title: Subject  102.100.035 , day 7


title: Spp1AID_mcm23A_Spp1W45A_Input_S045_rep1


title: Spp1AID_mcm23A_Spp1W45A_Input_G1_rep1


title: Subject  102.100.002 , day 7


title: Sample_286


title: Spp1AID_mcm23A_Spp1_Input_S135_rep1


title: Subject  102.100.016 , day 92


title: Subject  102.100.029 , day 7


title: Sample_181


title: Subject  102.100.041 , day 7


title: Sample_13

value: Minimal Change Disease


title: Spp1AID_mcm23A_Spp1_Input_G1_rep1


title: Spp1AID_mcm23A_Spp1_Input_S045_rep1


title: Subject  102.100.017 , day 7


title: spp1W45A_H3K4me3_ChIP_S150_rep2

value: spp1-W45A mutant


title: Spp1AID_mcm23A_Spp1W45A_Input_S105_rep1


title: Sample_191


title: Subject  102.100.016 , day 7

value: Whole blood


title: spp1W45A_H3K4me3_ChIP_S120_rep2


title: Sample_313


title: Spp1AID_mcm23A_Spp1W45A_Input_S075_rep1


title: Sample_309


title: Subject  102.100.014 , day 7


title: spp1W45A_H3K4me3_ChIP_S090_rep2


title: Spp1AID_mcm23A_Spp1_Input_S105_rep1


title: Sample_223


title: Spp1AID_mcm23A_Spp1_Input_S075_rep1


title: spp1W45A_H3K4me3_ChIP_S060_rep2


title: spp1W45A_H3K4me3_ChIP_G1_rep2


title: WT_H3K4me3_ChIP_S150_rep2

value: WT


title: Subject  102.100.006 , day 7


title: Sample_155


title: WT_H3K4me3_ChIP_S120_rep2


title: WT_H3K4me3_ChIP_S060_rep2


title: Subject  102.100.038 , day 4

value: Day 4

value: M


title: Sample_293


title: WT_H3K4me3_ChIP_S090_rep2

value: MNase


title: WT_H3K4me3_ChIP_G1_rep2


title: WT_H3K4me3_ChIP_S030_rep2


title: Subject  102.100.035 , day 4


title: spp1W45A_H3K4me3_ChIP_S030_rep2


title: spp1W45A_Input_S150_rep2


title: Sample_281


title: spp1W45A_Input_S120_rep2


title: spp1W45A_Input_S090_rep2


title: Subject  102.100.029 , day 4


title: spp1W45A_Input_S060_rep2


title: Subject  102.100.002 , day 4


title: Sample_124

value: Other Nephrotic Syndrome


title: spp1W45A_Input_S030_rep2


title: Subject  102.100.041 , day 4

value: F


title: Sample_189


title: Sample_112


title: Subject  102.100.016 , day 4


title: WT_Input_S150_rep2


title: WT_Input_S120_rep2


title: spp1W45A_Input_G1_rep2


title: Subject  102.100.017 , day 4


title: WT_Input_S060_rep2


title: spp1W45A_H3K4me3_ChIP_S150_rep1

value: anti-H3K4me3 (ab8580, Abcam)


title: WT_Input_S090_rep2

value: Schizosaccharomyces pombe


title: Sample_318


title: spp1W45A_H3K4me3_ChIP_S120_rep1

value: whole cell


title: WT_Input_G1_rep2


title: Subject  102.100.006 , day 4


title: Subject  102.100.014 , day 4


title: Sample_289

value: Glomeruli from kidney biopsy


title: WT_Input_S030_rep2


title: spp1W45A_H3K4me3_ChIP_S60_rep1


title: Sample_24

value: Focal Segmental Glomerulosclerosis


title: Subject  102.100.038 , day 2

value: Day 2


title: Subject  102.100.035 , day 2


title: spp1W45A_H3K4me3_ChIP_S90_rep1


title: Sample_33


title: Sample_324


title: Sample_165


title: spp1W45A_H3K4me3_ChIP_G1_rep1


title: spp1W45A_Input_S90_rep1


title: spp1W45A_Input_S150_rep1


title: Sample_291


title: spp1W45A_Input_S120_rep1


title: spp1W45A_Input_S60_rep1


title: Subject  102.100.029 , day 2


title: spp1W45A_Input_G1_rep1


title: Subject  102.100.041 , day 2


title: Sample_188


title: WT_H3K4me3_ChIP_S150_rep1


title: Sample_64


title: Subject  102.100.002 , day 2


title: spp1W45A_H3K4me3_ChIP_S30_rep1


title: Subject  102.100.014 , day 2


title: WT_H3K4me3_ChIP_G1_rep1


title: Sample_306


title: WT_H3K4me3_ChIP_S30_rep1


title: WT_H3K4me3_ChIP_S120_rep1


title: Sample_250

value: Membranous Nephropathy


title: Subject  102.100.017 , day 2


title: spp1W45A_Input_S30_rep1


title: Subject  102.100.016 , day 2


title: WT_Input_S60_rep1


title: WT_Input_S90_rep1


title: Subject  102.100.035 , day 0

value: Day 0


title: WT_H3K4me3_ChIP_S90_rep1


title: WT_Input_G1_rep1


title: WT_H3K4me3_ChIP_S60_rep1


title: Spp1AID_mcm23A_+IAA_S90_H3K4me3_eSPAN_rep2

value: mcm2-3A mutant and Spp1 KO


title: Sample_23


title: Sample_276


title: Subject  102.100.006 , day 2


title: WT_Input_S150_rep1


title: WT_Input_S120_rep1


title: Subject  102.100.002 , day 0


title: Subject  102.100.038 , day 0


title: Sample_287


title: WT_Input_S30_rep1


title: Sample_202

value: Minimal Change Disease


title: Subject  102.100.029 , day 0

value: Whole blood


title: Spp1AID_mcm23A_-IAA_S90_BrdU_rep2

value: mcm2-3A mutant

value: anti-BrdU (555627, BD Bioscience)


title: Spp1AID_mcm23A_-IAA_S90_H3K4me3_eSPAN_rep2


title: Spp1AID_mcm23A_-IAA_S30_BrdU_rep2


title: Sample_129


title: Spp1AID_mcm23A_+IAA_S90_H3K4me3_ChIP_rep2


title: Spp1AID_mcm23A_+IAA_S30_H3K4me3_eSPAN_rep2


title: Spp1AID_mcm23A_+IAA_S30_H3K4me3_ChIP_rep2


title: Spp1AID_mcm23A_-IAA_S90_H3K4me3_ChIP_rep2


title: Sample_304


title: Sample_148


title: Subject  102.100.014 , day 0


title: Spp1AID_mcm23A_-IAA_S30_H3K4me3_eSPAN_rep2


title: Spp1AID_mcm23A_-IAA_S30_H3K4me3_ChIP_rep2


title: Sample_303


title: Subject  102.100.016 , day 0


title: Sample_114


title: Subject  102.100.006 , day 0


title: Subject  102.100.017 , day 0


title: Spp1AID_mcm23A_-IAA_S90_Input_rep2


title: Spp1AID_mcm23A_+IAA_S30_BrdU_rep2


title: Subject  102.100.041 , day 0


title: Spp1AID_mcm23A_+IAA_S90_BrdU_rep1


title: Sample_275


title: Sample_81


title: Spp1AID_mcm23A_+IAA_S90_H3K4me3_ChIP_rep1


title: Subject  102.100.031 , day 92

value: Day 92

value: M


title: Spp1AID_mcm23A_+IAA_S90_Input_rep1

value: MNase


title: Sample_258

value: Other Nephrotic Syndrome


title: Sample_46


title: Spp1AID_mcm23A_+IAA_S30_BrdU_rep1


title: Subject  102.100.049 , day 92


title: Spp1AID_mcm23A_-IAA_S90_BrdU_rep1


title: Spp1AID_mcm23A_-IAA_S30_Input_rep2


title: Spp1AID_mcm23A_+IAA_S30_Input_rep2


title: Sample_211


title: Spp1AID_mcm23A_+IAA_S90_Input_rep2


title: Subject  102.100.034 , day 92


title: Sample_270


title: Spp1AID_mcm23A_+IAA_S90_BrdU_rep2


title: Spp1AID_mcm23A_+IAA_S30_H3K4me3_ChIP_rep1

value: anti-H3K4me3 (ab8580, Abcam)


title: Sample_296


title: Subject  102.100.046 , day 92


title: Sample_31


title: Sample_187


title: Subject  102.100.008 , day 92


title: Subject  102.100.019 , day 92

value: F


title: Spp1AID_mcm23A_+IAA_S30_H3K4me3_eSPAN_rep1

value: whole cell


title: Sample_102

value: Glomeruli from kidney biopsy


title: Swd1AID_mcm23A_+IAA_S90_RNApolII_ChIP

value: Sonication

value: mcm2-3A mutant and Swd1 KO

value: anti-RPB1 CTD-Ser5p (04-1572, Millipore)


title: Spp1AID_mcm23A_-IAA_S30_Input_rep1


title: Spp1AID_mcm23A_-IAA_S90_H3K4me3_eSPAN_rep1


title: Swd1AID_mcm23A_+IAA_S90_RNApolII_ChIP_Input


title: Spp1AID_mcm23A_+IAA_S90_H3K4me3_eSPAN_rep1


title: Subject  102.100.010 , day 92


title: Subject  102.100.015 , day 92


title: Subject  102.100.003 , day 92


title: Swd1AID_mcm23A_+IAA_S90_H3K4me3_eSPAN_rep2


title: Spp1AID_mcm23A_-IAA_S90_H3K4me3_ChIP_rep1


title: Subject  102.100.048 , day 92


title: Sample_6

value: Membranous Nephropathy


title: Spp1AID_mcm23A_-IAA_S30_H3K4me3_eSPAN_rep1


title: Sample_41


title: Sample_110

value: Focal Segmental Glomerulosclerosis


title: Swd1AID_mcm23A_+IAA_S90_Input_rep2


title: Subject  102.100.032 , day 92


title: Spp1AID_mcm23A_-IAA_S30_BrdU_rep1


title: Sample_233

value: Minimal Change Disease


title: Spp1AID_mcm23A_-IAA_S90_Input_rep1


title: Spp1AID_mcm23A_-IAA_S30_H3K4me3_ChIP_rep1


title: Sample_323


title: Swd1AID_mcm23A_+IAA_S90_BrdU_rep2


title: Swd1AID_mcm23A_+IAA_S60_H3K4me3_eSPAN_rep2


title: Swd1AID_mcm23A_+IAA_S60_RNApolII_ChIP_Input


title: Swd1AID_mcm23A_+IAA_S60_H3K4me3_ChIP_rep2


title: Swd1AID_mcm23A_+IAA_S90_H3K4me3_ChIP_rep2


title: Subject  102.100.049 , day 7

value: Whole blood

value: Day 7


title: Sample_336


title: Subject  102.100.046 , day 7


title: Sample_101


title: Subject  102.100.031 , day 7


title: Subject  102.100.008 , day 7


title: Subject  102.100.034 , day 7


title: Swd1AID_mcm23A_+IAA_S30_RNApolII_ChIP


title: Swd1AID_mcm23A_+IAA_S60_Input_rep2


title: Swd1AID_mcm23A_+IAA_S30_H3K4me3_eSPAN_rep2


title: Swd1AID_mcm23A_+IAA_S60_RNApolII_ChIP


title: Subject  102.100.003 , day 7


title: Sample_264


title: Subject  102.100.048 , day 7


title: Sample_301


title: Swd1AID_mcm23A_+IAA_S30_BrdU_rep2

value: anti-BrdU (555627, BD Bioscience)


title: Subject  102.100.032 , day 7


title: Swd1AID_mcm23A_+IAA_S60_BrdU_rep2


title: Sample_103


title: Swd1AID_mcm23A_+IAA_S30_Input_rep2


title: Swd1AID_mcm23A_+IAA_G1_RNApolII_ChIP


title: Swd1AID_mcm23A_+IAA_G1_RNApolII_ChIP_Input


title: Subject  102.100.019 , day 7


title: Swd1AID_mcm23A_+IAA_S30_RNApolII_ChIP_Input


title: Swd1AID_mcm23A_+IAA_G1_H3K4me3_ChIP_rep2


title: Sample_216


title: Sample_48


title: Swd1AID_mcm23A_-IAA_S90_H3K4me3_eSPAN_rep2

value: mcm2-3A mutant


title: Swd1AID_mcm23A_-IAA_S90_BrdU_rep2


title: Subject  102.100.015 , day 7


title: Sample_169


title: Sample_227


title: Swd1AID_mcm23A_+IAA_S30_H3K4me3_ChIP_rep2


title: Swd1AID_mcm23A_-IAA_S90_H3K4me3_ChIP_rep2


title: Swd1AID_mcm23A_+IAA_G1_Input_rep2


title: Sample_106


title: Swd1AID_mcm23A_-IAA_S60_H3K4me3_eSPAN_rep2


title: Swd1AID_mcm23A_-IAA_S60_BrdU_rep2


title: Swd1AID_mcm23A_-IAA_S90_Input_rep2


title: Swd1AID_mcm23A_-IAA_S60_Input_rep2


title: Subject  102.100.010 , day 7


title: Subject  102.100.049 , day 4

value: Day 4

value: M


title: Sample_335

value: Other Nephrotic Syndrome


title: Subject  102.100.034 , day 4


title: Swd1AID_mcm23A_-IAA_S30_H3K4me3_eSPAN_rep2

value: MNase

value: anti-H3K4me3 (ab8580, Abcam)


title: Sample_116


title: Swd1AID_mcm23A_-IAA_S60_H3K4me3_ChIP_rep2

value: whole cell


title: Swd1AID_mcm23A_-IAA_S30_BrdU_rep2


title: Subject  102.100.046 , day 4


title: Swd1AID_mcm23A_-IAA_S30_H3K4me3_ChIP_rep2


title: Subject  102.100.031 , day 4


title: Swd1AID_mcm23A_-IAA_S30_Input_rep2


title: Sample_158

value: Glomeruli from kidney biopsy


title: Subject  102.100.008 , day 4


title: Swd1AID_mcm23A_-IAA_G1_H3K4me3_ChIP_rep2


title: Swd1AID_mcm23A_-IAA_G1_Input_rep2


title: Sample_85


title: Swd1AID_mcm23A_+IAA_S90_H3K4me3_eSPAN_rep1


title: Swd1AID_mcm23A_+IAA_S90_BrdU_rep1


title: Swd1AID_mcm23A_+IAA_S90_H3K4me3_ChIP_rep1


title: Subject  102.100.048 , day 4

value: F


title: Swd1AID_mcm23A_+IAA_S60_H3K4me3_eSPAN_rep1

value: mcm2-3A mutant and Swd1 KO


title: Subject  102.100.003 , day 4


title: Sample_283


title: Sample_236


title: Sample_294


title: Swd1AID_mcm23A_+IAA_S90_Input_rep1


title: Sample_200


title: Subject  102.100.015 , day 4


title: Swd1AID_mcm23A_+IAA_S60_BrdU_rep1


title: Swd1AID_mcm23A_+IAA_S60_H3K4me3_ChIP_rep1


title: Sample_136


title: Subject  102.100.019 , day 4


title: Swd1AID_mcm23A_+IAA_S30_H3K4me3_eSPAN_rep1


title: Swd1AID_mcm23A_+IAA_S30_H3K4me3_ChIP_rep1


title: Swd1AID_mcm23A_+IAA_S30_BrdU_rep1


title: Subject  102.100.032 , day 4


title: Subject  102.100.010 , day 4


title: Sample_159


title: Sample_86


title: Swd1AID_mcm23A_+IAA_S60_Input_rep1


title: Swd1AID_mcm23A_+IAA_G1_H3K4me3_ChIP_rep1


title: Swd1AID_mcm23A_+IAA_S30_Input_rep1


title: Swd1AID_mcm23A_+IAA_G1_Input_rep1


title: Swd1AID_mcm23A_-IAA_S90_H3K4me3_eSPAN_rep1


title: Sample_328


title: Sample_115


title: Sample_149


title: Subject  102.100.034 , day 2

value: Day 2


title: Swd1AID_mcm23A_-IAA_S90_BrdU_rep1


title: Swd1AID_mcm23A_-IAA_S90_H3K4me3_ChIP_rep1


title: Swd1AID_mcm23A_-IAA_S60_H3K4me3_eSPAN_rep1


title: Swd1AID_mcm23A_-IAA_S60_H3K4me3_ChIP_rep1


title: Subject  102.100.031 , day 2


title: Subject  102.100.049 , day 2


title: Subject  102.100.008 , day 2


title: Swd1AID_mcm23A_-IAA_S60_BrdU_rep1


title: Subject  102.100.003 , day 2


title: Sample_90


title: Swd1AID_mcm23A_-IAA_S60_Input_rep1


title: Sample_67


title: Swd1AID_mcm23A_-IAA_S30_H3K4me3_ChIP_rep1


title: Sample_261


title: Subject  102.100.048 , day 2


title: Swd1AID_mcm23A_-IAA_S30_BrdU_rep1


title: Swd1AID_mcm23A_-IAA_S30_H3K4me3_eSPAN_rep1


title: Swd1AID_mcm23A_-IAA_S30_Input_rep1


title: Subject  102.100.046 , day 2


title: Swd1AID_mcm23A_-IAA_G1_H3K4me3_ChIP_rep1


title: Subject  102.100.032 , day 2


title: Swd1AID_mcm23A_-IAA_G1_Input_rep1


title: Subject  102.100.019 , day 2


title: Swd1AID_mcm23A_-IAA_S90_Input_rep1


title: mcm23A_H3K56ac_eSPAN_S90_rep2

value: Sonication


title: Sample_285

value: Focal Segmental Glomerulosclerosis


title: Subject  102.100.015 , day 2


title: Sample_327

value: Minimal Change Disease


title: mcm23A_RNApolII_ChIP_S90_rep2

value: anti-RPB1 CTD-Ser5p (04-1572, Millipore)


title: mcm23A_BrdU_S90_S_rep2


title: mcm23A_H3K56ac_ChIP_S90_rep2


title: Subject  102.100.010 , day 2

value: Whole blood


title: Sample_225


title: mcm23A_BrdU_S60_S_rep2

value: anti-BrdU (555627, BD Bioscience)


title: mcm23A_RNApolII_ChIP_S60_rep2

value: mcm2-3A mutant


title: mcm23A_H3K56ac_ChIP_S60_rep2


title: mcm23A_H3K56ac_eSPAN_S60_rep2


title: Sample_123

value: Membranous Nephropathy


title: mcm23A_H3K56ac_eSPAN_S30_rep2


title: Sample_244


title: Subject  102.100.034 , day 0

value: Day 0

value: M


title: Sample_109

value: Other Nephrotic Syndrome


title: mcm23A_Input_S60_S_rep2


title: mcm23A_RNApolII_ChIP_S30_rep2


title: Subject  102.100.031 , day 0


title: mcm23A_BrdU_S30_S_rep2


title: mcm23A_Input_S90_S_rep2


title: Sample_8


title: mcm23A_H3K56ac_ChIP_S30_rep2


title: Subject  102.100.008 , day 0


title: mcm23A_Input_S30_S_rep2


title: Sample_325


title: Subject  102.100.049 , day 0


title: Sample_135


title: Subject  102.100.046 , day 0


title: mcm23A_Input_G1_S_rep2


title: Sample_249


title: mcm23A_BrdU_S90_rep2

value: MNase


title: Sample_14


title: Subject  102.100.003 , day 0


title: Subject  102.100.048 , day 0


title: Sample_3


title: mcm23A_H3K4me3_ChIP_S90_rep2

value: anti-H3K4me3 (ab8580, Abcam)

value: whole cell


title: Subject  102.100.032 , day 0

value: F


title: mcm23A_Input_S90_rep2


title: mcm23A_H3K4me3_eSPAN_S60_rep2


title: mcm23A_BrdU_S60_rep2


title: Subject  102.100.019 , day 0


title: mcm23A_H3K4me3_ChIP_S60_rep2


title: mcm23A_RNApolII_ChIP_G1_rep2


title: Sample_224

value: Glomeruli from kidney biopsy


title: Subject  102.100.010 , day 0


title: mcm23A_BrdU_S30_rep2


title: Sample_252


title: mcm23A_H3K4me3_ChIP_S30_rep2


title: mcm23A_Input_S60_rep2


title: Subject  102.100.015 , day 0


title: mcm23A_Input_S30_rep2