title: 4_1025-4_cd14pluscd16plus

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
raw_counts_p199.txt
lib23606

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: Homo sapiens GRCh38.77 (version 77)
Supplementary_files_format_and_content: raw_counts_p199.txt is a tab-delimited matrix. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library. Outlier samples have been removed but data have not been gene filtered or normalized.

extract_protocol:
200-1000 cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

tag: timepoint

value: cd14+cd16+ monocytes

tag: severity

value: severe II

value: male

tag: cell number


title: SY5Y input 2

status: Public on Feb 01 2024

type: SRA

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

country: USA

institute: University of Chicago

library_source: genomic

data_processing:
raw read quality was assessed using fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to filter raw reads with a minimum Phred score of 33
Reads were aligned to GRCh38 using Bowtie2 (version 2.3.0) with default settings
Duplicate reads were eliminated using picard (version 2.18.29) with default settings.
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were grown at 5% CO2 in RPMI1640 medium (Life Technologies) supplemented with 10% heat-inactivated FBS, 2 mmol/L l-glutamine, and 1% penicillin/streptomycin

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. After cell lysis, chromatin was sonicated using a Diagenode Bioruptor (30 seconds on and 30 seconds off) for 10 minutes in precooled conditions. Lysates were pelleted at 4˚C and the supernatant was collected.
DNA was purified using Qiagen PCR kit (Qiagen 28104). ChIP DNA libraries were made using Ovation® Ultralow System V2 kit (Tecan Genomics 0344NB-32).

treatment_protocol: Cells were treated with tazemetostat 600nM for 72 hours.

tag: cell line

tag: cell type

value: neuroblastoma cell line, MYCN-non-amplified

tag: chip antibody


title: 3_1025-4_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23605

library_source: transcriptomic

molecule: total RNA

value: cd14+cd16- monocytes

tag: Sex


title: 5S, KAS-Seq, biol rep2

data_processing:
reads were trimmed using the trim-galore package in single-end mode.
Trimmed reads were aligned to hg38 using bowtie2 (v2.3.0) with standard parameters and sorted to bam files using samtools sort (v1.9)
samtools rmdup (v1.9) was utilized to get unique mapped reads, which were then extended to 150 bp
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: KAS-Seq

extract_protocol:
cells were incubated for 5–10 min at 37 °C, 5% CO2  in complete culture medium containing 5 mM N3-kethoxal. Using the PureLink genomic DNA mini kit (Thermo, K182002), genomic DNA (gDNA) was isolated from collected cells.
Accel-NGS Methyl-seq DNA library kit (Swift, 30024) was used for library construction on eluted DNA and corresponding input.

value: neuroblastoma cell line, MYCN-amplified


title: CD3+ cells, PMA Ionomycin, 6 hours, NFAT1 antibody [PMA_Iono_NFAT1_primary_2]

city: Cleveland

first: Yi Fan

last: Chen

state: OH

address: 2109 Adelbert Road Biomedical Research Building 747A

institute: Case Western Reserve University School of Medicine

data_processing:
Reads were trimmed using Trim Galore version 0.6.7 followed by alignment to hg38 genome build using bowtie2 version 2.4.5.
Reads were de-duplicated using Picard MarkDuplicates version 2.18.2.3
RPGC-normalized bigwig files and bedgraph files were generated using deeptools version 3.4.3
Peaks were called using SEACR version 1.3 under stringent conditions normalized to respective IgG controls
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files
Library strategy: CUT&RUN

growth_protocol: Jurkat cells were cultured in RPMI-1640 supplemented with glutamine, 10% FBS, penicillin/streptomycin, and 10 mM HEPES

extract_protocol:
Cells were fixed with 1% formaldehyde for 1 minute. After quenching and permeabilization, cells were treated with respective antibodies
Samples were treated with pA/G-Mnase to cleave target DNA sequences following antibody incubation
CUT&RUN libraries were prepared using NEBNext DNA Ultra II  Library Prep kit according to manufacturer instructions.
Libraries were amplified for 15 cycles in the thermo cycler and samples purified with magnetic purification beads (NEB  E7104S)

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM SP100030 treatments were co-administered at the same time and cells were incubated for 6 hours prior ot harvest

tag: antibody

tag: tissue

value: Peripheral blood mononuclear cells

value: T cells

tag: genotype

value: WT

tag: treatment

value: PMA Ionomycin


title: WN input 2

source_name: NBL-W-N

value: NBL-W-N


title: 1_1025-4_Epithelial

description:
raw_counts_p199.txt
lib23604

value: epithelial


title: CD3+ cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1_primary_2]

value: PMA Ionomycin + SP100030


title: CD3+ cells, DMSO, 6 hours, NFAT1 antibody [DMSO_NFAT1_primary_2]

value: DMSO


title: Akata Ctl anti-H3K4Me3

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: anti H3K4Me3; CST (9751S)

data_processing:
Reads were aligned to hg38 and EBV genomes using bowtie2.
Duplicates were marked and removed using Picard
Assembly: hg38 and chrEBV_Akata_inverted
Supplementary files format and content: bigWig

source_name: Akata

extract_protocol:
DNA was sheared using Covaris 220 sonication device to an average length of 150-300bp, then immunoprecipitated using an anti-H3K4Me3 antibody (CST)
Libraries were constructed by BGI

value: Akata


title: SHEP input 2

source_name: SHEP

value: SHEP


title: 3_1027-1-cd14cdplus16negative

description:
raw_counts_p199.txt
lib23602

value: mild

value: female


title: DG75-R-C1

description:
Stranded
dg75_cntl_rta_zta_gene_expression.tpm.tsv

data_processing:
Kallisto
Assembly: hg38 + chrEBV_Akata_inverted
Supplementary files format and content: transcripts per million matrix

source_name: B cell lymphoma

extract_protocol:
RNA was extracted from cell pellets using TRIzol Reagent (ThermoFisher Scientific, cat no. 15596018) according to the manufacturer's protocol
Libraries were prepared by the Beijing Genomics Institute. Briefly, RNA fragmentation followed by reverse transcription, end repair and adaptor ligation, PCR, single strand separation and cyclization, then DNA nanoball synthesis and sequencing

value: B cell lymphoma

value: cell line

value: 24h Ctl


title: 4_1027-1-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23603

value: cd14+cd16+ monocytes


title: 5S, KAS-Seq, biol rep1

value: neuroblastoma cell line, MYCN-amplified


title: WS input 2

source_name: NBL-W-S

value: NBL-W-S


title: M6Z3

description:
Not stranded
mutu_zta_timecourse_gene_expression.tpm.tsv

molecule: polyA RNA

value: Mutu

value: 6h Zta


title: 55N input 2


title: CD3+ cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1_primary_2]

value: Peripheral blood mononuclear cells

value: T cells

value: WT

value: PMA Ionomycin


title: Scramble, IgG

city: Philadelphia

first: Israel

last: Canadas

state: PA

address: 333 Cottman Ave.

department: Nuclear Dynamics and Cancer Program

institute: Fox Chase Cancer Center

data_processing:
For analysis of RE expression from RIP-seq data, FASTQ reads were trimmed by TrimGalore (version 0.6.4).
The trimmed FASTQ reads were mapped against H. sapiens UCSC hg19 using the Bowtie 2 (version 2.3.5) alignment software.
The counts of RE were calculated by RepEnrich2 using default settings, and were normalized by one million reads as CPM (counts per million).
Assembly: hg19
Supplementary files format and content: Expression data in excel format

extract_protocol:
Scramble or sgDHX9 H446 cells were harvested, and RNA immunoprecipitation (RIP) was conducted with J2 or isotype control antibody using a Magna RIP RNA-Binding Protein Immunoprecipitation kit, according to the manufacturer’s instructions.
Illumina sequencing libraries were prepared by Novogene, with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB). Libraries were quantified using the Qubit 2.0 Fluorometer (Life Technologies).

treatment_protocol: H446 cells were infected with lentivirus containing Scramble or sgDHX9 vector.

value: Small Cell Lung Cancer

value: Scramble

value: IgG-IP


title: M6Z2


title: BE2 input 2


title: CD3+ cells, DMSO, 6 hours, H3K27Ac antibody [H3K27Ac_primary_2]

value: DMSO


title: 1_1027-1-epithelial

description:
raw_counts_p199.txt
lib23601

value: epithelial

value: mild

value: female


title: 5S, H3K4me3, Cell Signaling, contro2

value: H3K4me3 (Cell Signaling 9751)


title: CD3+ cells, DMSO, 6 hours, XPO1 antibody [DMSO_XPO1_primary_2]


title: M6Z1

value: B cell lymphoma

value: cell line


title: M6C4

value: 6h Ctl


title: 3_1025-2-Epithelial

description:
raw_counts_p199.txt
lib23598

value: severe II

value: male


title: 1_1025-3-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23599

value: cd14+cd16- monocytes


title: M6C3

value: Mutu


title: CD3+ cells, PMA Ionomycin + SP100030, 6 hours, NFAT1 antibody [PMA_Iono_SP_NFAT1_primary]

value: Peripheral blood mononuclear cells

value: T cells

value: WT

value: PMA Ionomycin + SP100030


title: CD3+ cells, PMA Ionomycin, 6 hours, NFAT1 antibody [PMA_Iono_NFAT1_primary]

value: PMA Ionomycin


title: 5S, H3K4me3, Cell Signaling, control1

value: neuroblastoma cell line, MYCN-amplified


title: NBLS input 2

source_name: NBL-S

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing


title: CD3+ cells, DMSO, 6 hours, NFAT1 antibody [DMSO_NFAT1_primary]

value: DMSO


title: SY5Y, H3K4me3, Cell Signaling, control2

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K4me3 (Cell Signaling 9751)


title: M6C1

value: B cell lymphoma

value: cell line


title: 1_1025-2-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23596

value: severe II


title: M6Z4

value: 6h Zta


title: CD3+ cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1_primary]


title: 2_1025-2-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23597

value: cd14+cd16+ monocytes

value: male


title: 2_1025-1_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23595


title: CD3+ cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1_primary]

value: Peripheral blood mononuclear cells


title: WN, H3K4me3, Cell Signaling, control2

value: NBL-W-N


title: WN, H3K4me3, Cell Signaling, control1


title: 2_1024-2_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23593

value: severe I


title: M24Z1

value: Mutu

value: 24h Zta


title: CD3+ cells, DMSO, 6 hours, H3K27Ac antibody [H3K27Ac_primary]

value: T cells

value: WT


title: SHEP, H3K4me3, Cell Signaling, control2

value: SHEP


title: 1_1025-1_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23594

value: cd14+cd16- monocytes


title: M24Z2


title: M24C4

value: 24h Ctl


title: CD3+ cells, DMSO, 6 hours, XPO1 antibody [DMSO_XPO1_primary]

value: DMSO


title: U-2 OS cells, DMSO, 6 hours, XPO1 antibody [XPO1 U-2 OS]

description: XPO1 U-2 OS

value: Bone

value: U-2 OS

value: Epithelial


title: CD3+ cells, DMSO, 6 hours, IgG control antibody [IgG_10]

value: IgG


title: 3_1023-4-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23590

value: female


title: SHEP, H3K4me3, Cell Signaling, control1

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K4me3 (Cell Signaling 9751)


title: SY5Y, H3K4me3, Cell Signaling, control1


title: WS, H3K4me3, Cell Signaling, control2

value: NBL-W-S

value: neuroblastoma cell line, MYCN-amplified


title: CD3+ cells, DMSO, 6 hours, IgG control antibody [IgG_11]

value: Peripheral blood mononuclear cells


title: 2_1025-3-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23600

value: cd14+cd16+ monocytes

value: severe II

value: male


title: 24hrUninduced-1

description:
Stranded
akata_24h_bcr_induction_gene_expression.tpm.tsv

value: B cell lymphoma

value: Akata

value: cell line


title: U-2 OS cells, DMSO, 6 hours, IgG antibody [IgG U-2 OS]

description: IgG U-2 OS

value: WT

value: DMSO


title: M24Z4

value: Mutu

value: 24h Zta


title: WS, H3K4me3, Cell Signaling, control1


title: 1_1023-4-Epithelial

description:
raw_counts_p199.txt
lib23589

value: epithelial

value: severe I


title: M24C3

value: 24h Ctl


title: M24C2


title: THP-1 cells, DMSO, 6 hours, XPO1 antibody [XPO1 THP-1]

description: XPO1 THP-1

value: Peripheral blood

value: Monocyte


title: M6C2

value: 6h Ctl


title: M24Z3


title: 1_1024-2_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23592

value: cd14+cd16- monocytes


title: M24C1


title: 4_1022-4-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23588

value: cd14+cd16+ monocytes

value: female


title: 55N, H3K4me3, Cell Signaling, control2

value: neuroblastoma cell line, MYCN-amplified

value: H3K4me3 (Cell Signaling 9751)


title: M12Z4

value: B cell lymphoma

value: 12h Zta


title: THP-1 cells, DMSO, 6 hours, IgG antibody [IgG THP-1]

description: IgG THP-1

value: IgG

value: WT


title: 3_1022-4-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23587


title: Loucy cells, DMSO, 6 hours, XPO1 antibody [XPO1 Loucy]

description: XPO1 Loucy

value: Lymphoid

value: Loucy

value: T lymphoblast

value: DMSO


title: M12Z3

value: Mutu

value: cell line


title: NBLS, H3K4me3, Cell Signaling, control2

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing


title: M12Z2


title: NBLS, H3K4me3, Cell Signaling, control1


title: BE2, H3K4me3, Cell Signaling, control2


title: 1_1022-4-Epithelial

description:
raw_counts_p199.txt
lib23586

value: epithelial

value: severe I


title: Loucy cells, DMSO, 6 hours, IgG antibody [IgG Loucy]

description: IgG Loucy


title: 55N, H3K4me3, Cell Signaling, control1


title: 1022-3_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23584

value: cd14+cd16- monocytes

value: female


title: BE2, H3K4me3, Cell Signaling, control1

value: neuroblastoma cell line, MYCN-amplified

value: H3K4me3 (Cell Signaling 9751)


title: M12C4

value: B cell lymphoma

value: 12h Ctl


title: M12Z1

value: 12h Zta


title: 1022-3_Epithelial

description:
raw_counts_p199.txt
lib23583


title: WS, H3K27me3, ABCAM, taz2

value: NBL-W-S

value: H3K27me3 (Abcam ab6002)


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1_3]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: WT

value: PMA Ionomycin + SP100030


title: 1019-4-Epithelial

description:
raw_counts_p199.txt
lib23582


title: WS, H3K27me3, ABCAM, taz1


title: Jurkat cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1_3]

value: PMA Ionomycin


title: M12C2

value: Mutu

value: cell line


title: HeLa cells, DMSO, 6 hours, XPO1 antibody [XPO1 HeLa]

description: XPO1 HeLa

value: Cervix

value: HeLa

value: Epithelial

value: DMSO


title: 1022-3_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23585

value: cd14+cd16+ monocytes

value: severe I

value: female


title: HeLa cells, DMSO, 6 hours, IgG control antibody [IgG HeLa]

description: IgG HeLa

value: IgG


title: M12C1

value: B cell lymphoma

value: 12h Ctl


title: WS, H3K27me3, ABCAM, control2

value: NBL-W-S

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: Jurkat cells, DMSO, 6 hours, FLAG antibody [DMSO_FLAG_XPO1]

value: FLAG

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: WT


title: WS, H3K27me3, ABCAM, control1


title: 4_1021-1-Epithelial

description:
raw_counts_p199.txt
lib23579

value: epithelial

value: moderate

value: male


title: ASC Treat2

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

data_processing:
Reads were trimmed using Trimmomatic v0.39
mapped to hg38/GRCh38  use STAR
Gene counts were generated using featureCounts
DESeq2 Bioconductor package was used on the RNA-Seq data to conduct differential expression analyse
Assembly: hg38/GRCh38
Supplementary files format and content: tab-delimited text file include raw count for each Sample

source_name: kidney

growth_protocol: HEK 293T cells were cultured in DMEM high glucose (GIBCO) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin and 100 μg/mL of streptomycin. Cells were kept under standard 37 ℃ and 5% CO2 conditions

extract_protocol:
Total RNA was extracted by Trizol in accordance with the manufacturer’s protocol. mRNA were purified by VAHTS mRNA capture beads (Vazyme)
Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

treatment_protocol: For ascorbic acid treatment, cells were seeded for 24 hours, and subsequently were treated with ascorbic acid (Sigma-Aldrich) for another 24 hours (for DNA methylation test) or 36 hours (for RNA methylation test). Media were changed every 6 h to avoid the accumulation of unabsorbed ascorbate

value: kidney

value: Human embryonic kidney

value: Ascorbic acid treatment


title: 3_1021-1-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23578

value: cd14+cd16+ monocytes


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_9]

value: IgG

value: DMSO


title: ASC Treat1


title: WN, H3K27me3, ABCAM, taz1

value: NBL-W-N


title: 2_1021-1-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23577

value: cd14+cd16- monocytes


title: Ctrl3


title: M12C3

value: B cell lymphoma

value: Mutu

value: cell line

value: 12h Ctl


title: Jurkat cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1_2]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: PMA Ionomycin


title: WN, H3K27me3, ABCAM, control2

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: WN, H3K27me3, ABCAM, taz2


title: 1020-2-Epithelial

description:
raw_counts_p199.txt
lib23576

value: epithelial

value: severe II

value: male


title: Ctrl2

value: kidney

value: Human embryonic kidney

value: WT


title: 1019-4-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23581

value: cd14+cd16+ monocytes

value: severe I

value: female


title: WN, H3K27me3, ABCAM, control1

value: NBL-W-N


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1_2]

value: PMA Ionomycin + SP100030


title: 1020-2-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23575


title: Ctrl1


title: Jurkat cells, DMSO, 6 hours, XPO1 antibody [DMSO_XPO1_2]

value: Peripheral blood mononuclear cells

value: DMSO


title: Jurkat cells, DMSO, 6 hours, XPO1 antibody [DMSO_XPO1_3]

value: Jurkat E6-1

value: T cells


title: 1019-4-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23580

value: cd14+cd16- monocytes


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, H3K27Ac antibody [PMA_Iono_SP_H3K27Ac_2]


title: 1020-2-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23574


title: SY5Y, H3K27me3, ABCAM, taz2

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K27me3 (Abcam ab6002)


title: 4_1023-4-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23591


title: SY5Y, H3K27me3, ABCAM, taz1


title: 1019-3-Epithelial

description:
raw_counts_p199.txt
lib23573

value: epithelial


title: Jurkat cells, PMA Ionomycin, 6 hours, H3K27Ac antibody [PMA_Iono_H3K27Ac_2]

value: PMA Ionomycin


title: 293T, ASC Treat2

data_processing:
Reads were trimmed using Trimmomatic v0.39
mapped to hg38/GRCh38  use STAR
Assembly: hg38/GRCh38
Supplementary files format and content: tab-delimited text file include m6A level for each Sample

extract_protocol:
total RNA was extracted by Trizol in accordance with the manufacturer’s protocol. mRNA were purified by VAHTS mRNA capture beads (Vazyme). 300 ng mRNA were applied GLORI step.In brief, RNA was fragmented by incubation at 70 °C for 5 min with Zinc Fragmentation Buffer. RNA was added into 40 μl reaction buffer containing 6 μl glyoxal solution (Sigma-Aldrich, 50649), 20 μl DMSO and nuclease-free water. The mixture was incubated for 30 min at 50 °C. Then 10 μl saturated H3BO3 (Sigma-Aldrich, B0394) solution was added and the incubation continued at 50 °C for 30 min following cooled on ice for next use. The 50-μl sample was added to premixed deamination buffer and gently mixed. The tubes were incubated for 8 h at 16 °C. RNA was purified by Dynabeads™ MyOne™ Silane (Thermo Fisher Scientific, cat. no. 37002D). The silane beads were dissolved by 50 μl deprotection buffer as before(文献XXX). The mixture was incubated at 95 °C for 10 min. RNA was purified by silane beads. RNA samples were then treated by PNK (NEB, M0201S) to achieve dephosphorylation of 3′ ends. The RNA was purified by silane beads and then 3′ adapter (sequence:/5rApp/AGATCGGAAGAGCGTCGTG/3Bio/) ligation was performed using T4 RNA ligase2, truncated KQ (NEB, M0373S). The excess adapter was digested by 5′ deadenylase (NEB, M0331S) and RecJf (NEB, M024S). The RNA was purified by silane beads and then subjected to reverse transcription by SuperScript™ III (Thermo Fisher Scientific, cat. no.18080051). The cDNA was purified by silane beads and then cDNA adapter (sequence:    /5Phos/NNNNNNAGATCGGAAGAGCACACGTCTG/3SpC3/) ligation was performed using T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (New England BioLabs, cat. no. M0437M). Library were constructed by PCR with index primers.
Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

value: kidney

value: Ascorbic acid treatment


title: 293T, ASC Treat1

value: Human embryonic kidney


title: Jurkat cells, DMSO, 6 hours, H3K27Ac antibody [DMSO_H3K27Ac_2]

value: WT


title: SY5Y, H3K27me3, ABCAM, control2


title: 293T, con2


title: SY5Y, H3K27me3, ABCAM, control1


title: SHEP, H3K27me3, ABCAM, taz2

value: SHEP


title: 4_1020-1_Epithelial

description:
raw_counts_p199.txt
lib23570

value: severe II

value: male


title: 1019-3-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23571

value: severe I

value: female


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, XPO1 antibody [PMA_Iono_SP_XPO1]

value: Peripheral blood mononuclear cells

value: PMA Ionomycin + SP100030


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_8]

value: IgG

value: Jurkat E6-1

value: T cells

value: DMSO


title: SHEP, H3K27me3, ABCAM, taz1

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K27me3 (Abcam ab6002)


title: 293T, con1

value: kidney


title: Jurkat cells, PMA Ionomycin, 6 hours, XPO1 antibody [PMA_Iono_XPO1]

value: PMA Ionomycin


title: 3_1020-1_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23569

value: cd14+cd16+ monocytes


title: HOS,shNC,rnc,rep1

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

institute: the First affiliated hospital of Sun Yat-sen University

description:
Polyribosome-bound-RNA-seq
mRNA expression for polyribosome-bound-mRNA-seq

data_processing:
For the RNA-seq, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Assembly: hg19,hg38
Supplementary files format and content: xlsx

source_name: HOS

growth_protocol: HOS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted by TRIZol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HOS cells were  transfected with shRNA for stable knockdown of METTL1. HOS cells expressing normal METTL1 level were used as control.

value: HOS

value: mesenchymal stem cells

value: Wild type

value: Polysome associated RNA


title: SHEP, H3K27me3, ABCAM, control2

value: SHEP


title: HOS,shNC,rnc,rep2


title: Jurkat cells, DMSO, 6 hours, XPO1 antibody [DMSO_XPO1]

value: WT


title: SHEP, H3K27me3, ABCAM, control1


title: Jurkat cells, DMSO, 6 hours, H3K27Ac antibody [DMSO_H3K27Ac]

value: Peripheral blood mononuclear cells


title: 4_1019-2_Epithelial

description:
raw_counts_p199.txt
lib23567

value: epithelial

value: severe I

value: female


title: 2_1020-1_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23568

value: cd14+cd16- monocytes

value: severe II

value: male


title: 3_1019-2_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23566


title: HOS,shNC,input,rep2

value: Total RNA


title: Jurkat cells, DMSO, 6 hours, H3K4Me3 antibody [DMSO_H3K4Me3]

value: Jurkat E6-1

value: T cells

value: DMSO


title: 5S, H3K27me3, ABCAM, taz2

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: 1019-3-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23572

value: cd14+cd16+ monocytes


title: HOS,shM1-2,rnc,rep2

value: HOS

value: mesenchymal stem cells

value: METTL1 knockdown

value: Polysome associated RNA


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_7]

value: IgG

value: Peripheral blood mononuclear cells

value: WT


title: HOS,shM1-2,rnc,rep1


title: 5S, H3K27me3, ABCAM, control2


title: 2_1019-2_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23565

value: cd14+cd16- monocytes

value: severe I

value: female


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, NFAT4 antibody [PMA_Iono_SP_NFAT4]

value: PMA Ionomycin + SP100030


title: 4_1018-4_Epithelial

description:
raw_counts_p199.txt
lib23564

value: epithelial

value: severe II

value: male


title: HOS,shM1-2,input,rep2

value: Total RNA


title: 5S, H3K27me3, ABCAM, control1

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: HOS,shM1-2,input,rep1

value: HOS


title: 3_1018-4_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23563

value: cd14+cd16+ monocytes


title: Jurkat cells, PMA Ionomycin, 6 hours, NFAT4 antibody [PMA_Iono_NFAT4]

value: Jurkat E6-1

value: T cells

value: PMA Ionomycin


title: 55N, H3K27me3, ABCAM, taz2


title: HOS,shNC,input,rep1

value: mesenchymal stem cells

value: Wild type


title: 55N, H3K27me3, ABCAM, taz1


title: Jurkat cells, DMSO, 6 hours, NFAT4 antibody [DMSO_NFAT4]

value: Peripheral blood mononuclear cells

value: WT

value: DMSO


title: 4_1018-2_Epithelial

description:
raw_counts_p199.txt
lib23561


title: 5S, H3K27me3, ABCAM, taz1


title: HOS,shM1-1,rnc,rep1

value: METTL1 knockdown

value: Polysome associated RNA


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, NFAT2 antibody [PMA_Iono_SP_NFAT2]

value: PMA Ionomycin + SP100030


title: 55N, H3K27me3, ABCAM, control2


title: 2_1018-4_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23562

value: cd14+cd16- monocytes

value: severe II

value: male


title: 55N, H3K27me3, ABCAM, control1

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: Jurkat cells, PMA Ionomycin, 6 hours, NFAT2 antibody [PMA_Iono_NFAT2]


title: HOS,shM1-1,input,rep2

value: HOS

value: Total RNA


title: 3_1018-2_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23560

value: cd14+cd16+ monocytes


title: Jurkat cells, DMSO, 6 hours, NFAT2 antibody [DMSO_NFAT2]

value: Jurkat E6-1

value: T cells


title: BE2, H3K27me3, ABCAM, taz2


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, NFAT1 antibody [PMA_Iono_SP_NFAT1]


title: BE2, H3K27me3, ABCAM, taz1


title: 4_1017-4-Epithelial

description:
raw_counts_p199.txt
lib23558

value: epithelial

value: severe I

value: female


title: HOS,shM1-1,input,rep1

value: mesenchymal stem cells


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_6]

value: IgG

value: Peripheral blood mononuclear cells

value: WT

value: DMSO


title: HOS,shM1-1,rnc,rep2

value: METTL1 knockdown

value: Polysome associated RNA


title: 2_1017-4-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23556

value: cd14+cd16- monocytes


title: BE2, H3K27me3, ABCAM, control1

value: neuroblastoma cell line, MYCN-amplified

value: H3K27me3 (Abcam ab6002)


title: Jurkat cells, PMA Ionomycin, 6 hours, NFAT1 antibody [PMA_Iono_NFAT1]

value: PMA Ionomycin


title: 4_1017-3-Epithelial

description:
raw_counts_p199.txt
lib23555


title: NBLS, H3K27me3, ABCAM, taz2

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing


title: BE2, H3K27me3, ABCAM, control2


title: 2_1018-2_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23559

value: severe II

value: male


title: 3_1017-3-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23554

value: cd14+cd16+ monocytes

value: severe I


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_5]

value: Jurkat E6-1

value: T cells


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, JUN antibody [PMA_Iono_SP_JUN]

value: JUN

value: Peripheral blood mononuclear cells

value: PMA Ionomycin + SP100030


title: 2_1017-3-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23553

value: female


title: NBLS, H3K27me3, ABCAM, control2


title: NBLS, H3K27me3, ABCAM, control1


title: Jurkat cells, DMSO, 6 hours, JUN antibody [DMSO_JUN]

value: WT

value: DMSO


title: 4_1016-4-Epithelial

description:
raw_counts_p199.txt
lib23552

value: epithelial


title: 3_1016-4-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23551


title: 3_1017-4-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23557


title: 2_1016-4-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23550

value: cd14+cd16- monocytes


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_4]

value: IgG


title: 3_1016-2-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23549


title: WS input

value: NBL-W-S

value: neuroblastoma cell line, MYCN-amplified


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, FOS antibody [PMA_Iono_SP_FOS_2]

value: FOS


title: SY5Y input

value: neuroblastoma cell line, MYCN-non-amplified


title: Jurkat cells, DMSO, 6 hours, NFAT1 antibody [DMSO_NFAT1]


title: Jurkat cells, PMA Ionomycin, 6 hours, FOS antibody [PMA_Iono_FOS_2]

value: PMA Ionomycin


title: 1_1016-2-Epithelial

description:
raw_counts_p199.txt
lib23547

value: severe II


title: WS, H3K27ac, ABCAM, taz2

value: H3K27ac (Abcam ab4729)


title: NBLS, H3K27me3, ABCAM, taz1

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing

value: H3K27me3 (Abcam ab6002)


title: SHEP input

value: SHEP


title: WS, H3K27ac, ABCAM, taz1


title: Jurkat cells, PMA Ionomycin, 6 hours, JUN antibody [PMA_Iono_JUN]

value: JUN

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells


title: Jurkat cells, PMA Ionomycin, 6 hours, NFAT1 antibody [PMA_Iono_NFAT1_2]

value: WT


title: WS, H3K27ac, ABCAM, control2


title: Jurkat cells, DMSO, 6 hours, NFAT1 antibody [DMSO_NFAT1_2]

value: DMSO


title: 2_1016_1_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23545

value: cd14+cd16- monocytes

value: female


title: 3_1016_1_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23546

value: cd14+cd16+ monocytes


title: 1_1016_1_Epithelial

description:
raw_counts_p199.txt
lib23544

value: epithelial


title: Jurkat cells, PMA Ionomycin, 6 hours, FOS antibody [PMA_Iono_FOS]

value: FOS

value: PMA Ionomycin


title: WS, H3K27ac, ABCAM, control1

value: NBL-W-S

value: neuroblastoma cell line, MYCN-amplified

value: H3K27ac (Abcam ab4729)


title: 1_1015_2_Epithelial

description:
raw_counts_p199.txt
lib23541

value: moderate

value: male


title: WN, H3K27ac, ABCAM, taz2

value: NBL-W-N


title: 6_1013-2-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23540

value: severe I


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, FOS antibody [PMA_Iono_SP_FOS]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: PMA Ionomycin + SP100030


title: WN input


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_3]

value: IgG

value: T cells

value: WT

value: DMSO


title: 3_1015_2_cd14pluscd16plus

description:
raw_counts_p199.txt
lib23543

value: cd14+cd16+ monocytes


title: 2_1015_2_cd14pluscd16negative

description:
raw_counts_p199.txt
lib23542

value: cd14+cd16- monocytes


title: WN, H3K27ac, ABCAM, control1


title: WN, H3K27ac, ABCAM, taz1


title: Jurkat cells, DMSO, 6 hours, FOS antibody [DMSO_FOS]

value: FOS


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, RelA antibody [PMA_Iono_SP_RelA]

value: RelA


title: 4_1012-3-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23538

value: severe II


title: SY5Y, H3K27ac, ABCAM, taz1

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K27ac (Abcam ab4729)


title: Jurkat cells, DMSO, 6 hours, RelA antibody [DMSO_RelA]


title: Jurkat cells, DMSO, 6 hours, FOS antibody [DMSO_FOS_2]


title: Jurkat cells, PMA Ionomycin, 6 hours, RelA antibody [PMA_Iono_RelA]

value: PMA Ionomycin


title: 3_1012-3-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23537

value: male


title: SY5Y, H3K27ac, ABCAM, control2


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, NFAT1 antibody [PMA_Iono_SP_NFAT1_2]


title: Jurkat cells, DMSO, 6 hours, H3K4Me3 antibody [H3K4Me3_1]


title: 2_1005-3-cd14pluscd16plus

description:
raw_counts_p199.txt
lib23536

value: severe I


title: SY5Y, H3K27ac, ABCAM, control1


title: 2_1016-2-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23548

value: female


title: WN, H3K27ac, ABCAM, control2

value: NBL-W-N

value: neuroblastoma cell line, MYCN-amplified


title: 5_1013-2-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23539


title: SY5Y, H3K27ac, ABCAM, taz2


title: SHEP, H3K27ac, ABCAM, taz2

value: SHEP


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, ATF2 antibody [PMA_Iono_SP_ATF2]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells

value: PMA Ionomycin + SP100030


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_2]

value: IgG

value: WT

value: DMSO


title: IP_RORγ_Mycotoxin_ChIPSeq

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

data_processing:
Sequencing tags were mapped against the SUS Scrofa (Pig) reference genome (Sscrofa11.1) using Bowtie 2.
Uniquely mapped tags were used for peak calling by MACS(2.1.0) to identify regions of ChIP-Seq enrichment over background.
A q value threshold of enrichment of 5 x 10^-2 was used for all data sets. by using ngs.plot (https://github.com/shenlab-sinai/ngsplot)
Normalized genome-wide signal coverage tracks from raw read alignment files were built by MACS2, fold-enrichment normalized wiggle files were generated by MACS, UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig/bedClip) and bedTools (http://code.google.com/p/bedtools/).
Visualization of ChIP-seq singnal at enriched genomic regions(avgprof and heatmap) was achieved
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: bigwig files were generated using MACS2 and UCSC tools

organism: Sus scrofa

source_name: Liver

extract_protocol:
Liver were collected and fresh frozen in liquid nitrogen.Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's paired-end DNA sample Prep kit.

value: Liver

tag: strain

value: three-breed cross Duroc x (Landrace x Yorkshire)

value: anti-RORgamma rabbit serum was generated by Covance, using purified GST-human RORgamma fragment (amino acids 79-301) expressed in Escherichia coli.

tag: agent

value: Mycotoxin


title: SHEP, H3K27ac, ABCAM, taz1

value: neuroblastoma cell line, MYCN-non-amplified

value: H3K27ac (Abcam ab4729)


title: IP_RORγ_Vehicle_ChIPSeq


title: 1_1005-3-cd14pluscd16negative

description:
raw_counts_p199.txt
lib23535

value: cd14+cd16- monocytes

value: severe I

value: male


title: Th2 cells-Klrg1Cre Gata3(fl/fl) 2

city: Bethesda

first: Jinfag

last: Zhu

state: MD

address: 10 Center Drive

department: Laboratory of Immune System Biology

institute: NIAID/NIH

data_processing:
PartekFlow was used for transcriptome comparison and expression analysis
Sequenced reads were trimmed for low-quality reads then mapped to mouse mm9 whole genome using STAR method.
The allined reads were quantified using "Quantify to annotated model(Partek E/M)
counts per million (CPM) method was used for data normalization. GSA method was used for differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with fold change and GS mean for every gene and every sample

organism: Mus musculus

source_name: Lung

extract_protocol:
Single cell suspension was prepared from erfused lungs digested with Collagenase (1 mg/ml) + Dnase (100 U/ml) for 30 min. Th2 cells (live CD4+ T1ST/2+) were isolated by FACS sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Chronic papain

value: Klrg1Cre Gata3(fl/fl)


title: 5S input

value: neuroblastoma cell line, MYCN-amplified


title: Jurkat cells, DMSO, 6 hours, ATF2 antibody [DMSO_ATF2]

value: Peripheral blood mononuclear cells

value: Jurkat E6-1

value: T cells


title: Th2 cells-Klrg1Cre Gata3(fl/fl) 1


title: Th2 cells-Gata3(fl/fl) 2


title: Jurkat cells, PMA Ionomycin, 6 hours, ATF2 antibody [PMA_Iono_ATF2]

value: WT

value: PMA Ionomycin


title: SHEP, H3K27ac, ABCAM, control1

value: SHEP


title: Jurkat cells, PMA Ionomycin + Selinexor, 6 hours, rep 2

data_processing:
kallisto v0.46.1
Raw reads were aligned using kallisto to the hg38 genome build
Transcripts were quantified into transcripts per million (TPM)
Gene-level TPM was generated using tximport
Differential gene expression analysis was assessed using edgeR
Assembly: hg38
Supplementary files format and content: csv file containing gene level TPM for each sample

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted using Qiagen RNEasy mini kit
Total RNA was submitted to GeneWiz for quality control, polyA selection, and library preparation

treatment_protocol:
Cells were activated with a cocktail of 50 nM PMA (Cayman Chemicals) and 1 uM Ionomycin (Cayman Chemicals)
1 uM small molecule treatments were co-administered at the same time (SP100030, synthesized in-house; Selinexor, Selleck Chemicals) and cells were incubated for 6 hours prior ot harvest

value: T cell

value: PMA Ionomycin + Selinexor


title: 55N input


title: Jurkat cells, PMA Ionomycin + Selinexor, 6 hours, rep 3


title: BE2 input


title: Rice root cells - sc_202

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

description: 10X Genomics v3.1 HT

library_source: transcriptomic single cell

data_processing:
Processed by COPILOT (https://github.com/ohlerlab/COPILOT)
Assembly: MSU 7.0
Supplementary files format and content: Seurat object

organism: Oryza sativa

source_name: Root

growth_protocol: X.kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.

extract_protocol:
For each sample, ~1 cm root tips were harvested from 15 - 40 roots and placed into a 35 mm petri dish containing a 70 μm cell strainer and 4.5 mL enzyme solution (4% [w/v] cellulase [ONOZUKA R-10, GoldBio], 1.5% Macerozyme R10 [GoldBio], 0.24% Pectolyase [Sigma P3026], 0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol). The digestion was incubated on an 85 rpm shaker at 28°C for 2.5 hours with additional pipette mixing every 30 minutes. The resulting cell solution was filtered twice through 40 μm cell strainers and centrifuged for 5 minutes at 500g in a swinging bucket rotor. The pellet was washed with 2mL washing solution (0.4 M mannitol, 20 mM MES (pH 5.7), 20 mM KCl, 10 mM CaCl2, 0.1% bovine serum albumin, and 0.000194% (v/v) -mercaptoethanol), centrifuged again at 500g for 3 minutes, and the pellet resuspended in washing solution at a concentration of ~2000 cells/uL. We loaded 16,000 cells, with the aim to capture 10,000 cells per sample with the 10X Genomics Chromium 3` Gene expression v3 or v3.1 (HT, 32,000 -> 20,000) kits.
Cell barcoding and library construction were performed following the manufacturer’s instructions. cDNA and final library quality were verified using a Bioanalyzer High Sensitivity DNA Chip (Agilent) and sequenced on an Illumina NovaSeq 6000 instrument to produce 100bp paired-end reads.

treatment_protocol: For soil growth conditions, Wedowee sand loam soil from Johnston county, Notrh Carolina (15% clay, 75% sand,15g/kg organic C, 1g/kg total N, CEC = 6.4 meg/100g,base salt = 83%, P = 199 g/m3, K = 78 g/m3, Ca = 804 g/m3, pH = 5.8) was used . Soil was air dried, crushed and then passed through a sieve with a 2 mm mesh size. To allow packing of soil to certian bulk densities, the soil was lightly sprayed with sterilized water, mixed thoroughly. Non-compacted soil condition is 1.1 g/ cm-3 (1.1 BD), Compacted soil conditions is 1.6 g/ cm-3 (1.6 BD). Soils were packed in 3D-printed mesocosms at bulk density of 1.1 BD or 1.6 BD and then saturated with water. Germinated rice seedlings (maximum 4 seedlings per mesocosm)with equivalent length radicles were inserted below the soil surface, and then grown in  a percival growth chamber set to 28°C, and consistant light for 2-3 days before harvesting.

value: Root

value: All cell types of root

value: Compacted soil stress


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, rep 3

value: PMA Ionomycin + SP100030


title: Th2 cells-Gata3(fl/fl) 1


title: Jurkat cells, PMA Ionomycin + Selinexor, 6 hours, rep 1


title: 5S, H3K27ac, ABCAM, taz2

value: H3K27ac (Abcam ab4729)


title: Rice root cells - sc_201

description: 10X Genomics v3.1 HT


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, rep 2


title: Rice root cells - sc_200

description: 10X Genomics v3.1 HT

value: Non compacted soil condition


title: SHEP, H3K27ac, ABCAM, control2

value: neuroblastoma cell line, MYCN-non-amplified


title: Jurkat cells, DMSO, 6 hours, IgG control antibody [IgG_1]

value: IgG

value: DMSO


title: Jurkat cells, PMA Ionomycin + SP100030, 6 hours, rep 1

value: Peripheral blood mononuclear cells


title: 5S, H3K27ac, ABCAM, control2

value: neuroblastoma cell line, MYCN-amplified


title: Rice root cells - sc_196

description: 10X Genomics kit v3.1


title: 5S, H3K27ac, ABCAM, taz1


title: Jurkat cells, PMA Ionomycin, 6 hours, rep 3

value: Jurkat E6-1


title: 5S, H3K27ac, ABCAM, control1


title: Jurkat cells, PMA Ionomycin, 6 hours, rep 2

value: WT


title: EGF_mIgG_2

first: Karen

last: Wong

address: 3400 Civic Center Blvd., SCTR 9-187

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Paired-end reads were demultiplexed using bcl2fastq (v2.20.0.422)
Alignment to hg38 using Bowtie2 (v2.3.5.1)
Duplicated reads were annotated using Picard MarkDuplicates
ENCODE denylist (hg38, v2) regions were removed using bedtools (v2.26.0)
Visualization tracks were generated using samtools (v1.17) to sort and index, then deepTools (v3.5.1) function "bamCoverage" with CPM normalization and parameters --SamFlagExclude 1548
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were rinsed with 1X PBS, incubated in 0.05% trypsin for 1 minute, physically scraped off the plate, then washed twice in 1X PBS by centrifugation for 3 minutes at 600 rcf.
Sequencing libraries were prepared for next-generation sequencing using a combination of the KAPA HyperPrep Kit and the NEBNext Multiplex Oligos for Illumina. Amplified libraries were quantified with Qubit and fragment size was assessed by TapeStation.

treatment_protocol: 750pM EGF or an equivalent volume of 1X PBS was added to cell media for 30 minutes. Cells were kept at 37C at 5% CO2 during treatment.

value: human lung fibroblasts


title: Rice root cells - sc_195

description: 10X Genomics kit v3.1


title: Rice root cells - sc_194

description: 10X Genomics kit v3.1


title: 55N, H3K27ac, ABCAM, taz1


title: Jurkat cells, Selinexor, 6 hours, rep 3

value: Selinexor


title: Rice root cells - sc_192

description: 10X Genomics kit v3.1


title: EGF_H3K9me2S10ph_4


title: Rice root cells - sc_193

description: 10X Genomics kit v3.1


title: 55N, H3K27ac, ABCAM, taz2


title: 55N, H3K27ac, ABCAM, control2


title: 55N, H3K27ac, ABCAM, control1


title: NBLS input

value: NBL-S

value: neuroblastoma cell line, MYCN overexpressing


title: EGF_mIgG_1


title: Jurkat cells, Selinexor, 6 hours, rep 2

value: T cell


title: EGF_H3K9me2S10ph_2


title: EGF_H3K9me2S10ph_3


title: Jurkat cells, Selinexor, 6 hours, rep 1


title: Rice root cells - sc_116

description: 10X Genomics kit v3.1

value: Root

value: All cell types of root


title: Rice root cells - sc_199

description: 10X Genomics v3.1 HT


title: Jurkat cells, SP100030, 6 hours, rep 3


title: BE2, H3K27ac, ABCAM, taz2


title: Rice root cells - sc_115

description: 10X Genomics kit v3.1


title: Jurkat cells, PMA Ionomycin, 6 hours, rep 1

value: PMA Ionomycin


title: EGF_H3K9me2S10ph_1


title: BE2, H3K27ac, ABCAM, taz1

value: H3K27ac (Abcam ab4729)


title: Jurkat cells, SP100030, 6 hours, rep 2


title: Rice root cells - sc_109

description: 10X Genomics kit v3.1


title: PBS_mIgG_3

value: PBS


title: BE2, H3K27ac, ABCAM, control2


title: Jurkat cells, SP100030, 6 hours, rep 1


title: Rice root cells - sc_108

description: 10X Genomics kit v3.1


title: PBS_mIgG_2


title: Jurkat cells, DMSO, 6 hours, rep 3


title: PBS_mIgG_1


title: Rice root cells - sc_7

description: 10X Genomics kit v3


title: Jurkat cells, DMSO, 6 hours, rep 2


title: NBLS, H3K27ac, ABCAM, taz2


title: delta_rrp6_3

city: Atlanta

first: Anita

middle: H.

last: Corbett

state: Georgia

address: 1510 Clifton Road

department: Biology

institute: Emory University

data_processing:
Trimming: NovaSeq paired-end 150-bp reads were adaptor trimmed.
Alignment: Reads were mapped to the S. cerevisiae S288C genome assembly R64-1-1, annotated with CUTs and SUTs (Xu et al. Nature. 2009) using the STAR RNA-seq aligner [v2.6.1d]
Counting: Reads were assigned to gene features (Gene_ID) and counted using featureCounts [v1.22.2; Liao et al. Bioinformatics. 2014)].
Expression estimates: Transcript and gene expression estimates were measured using StringTie [v2.1.7; Pertea et al. Nature Biotechnol.]
Differential gene expression analysis: DE analysis on raw read counts was performed using DESeq2 R package [v1.38.1; (Love et al. Genome Biology. 2014)]
Assembly: S. cerevisiae S288C R64-1-1
Supplementary files format and content: Gene Counts_Comma-separated values (CSV) files contain raw gene counts for each sample produced using featureCounts
Supplementary files format and content: DESeq2_Comma-separated values (CSV) files contain normalized abundance measurements generated using DESeq2

organism: Saccharomyces cerevisiae

source_name: MATa ura3Δ0 leu2∆0 his3∆1 met15∆0 rrp6∆::kanMX4 [LEU2, CEN6, pRS315]

growth_protocol: S. cerevisiae rrp∆ cells containing wildtype RRP or mutant rrp plasmid (pRS315, LEU2, CEN6) were grown in 10 mL Leu- minimal media in triplicate at 37°C for 5hr.

extract_protocol:
Total RNA extracted from S. cerevisiae cells using Zymo kit (Zymo Research) and rRNA was removed according to method described in Bogdanova et al. Normalization of Full-Length-Enriched cDNA, in cDNA Libraries: Methods and Applications (2011) with some modifications.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat# R3000; Zymo Research)

treatment_protocol: Growth in Leu- Glu media at 37°C for 5hr

value: BY4741 haploid

value: MATa ura3delta0 leu2delta0 his3delta1 met15delta0 rrp6delta::kanMX4 [LEU2, CEN6, pRS315]


title: delta_rrp6_2


title: PBS_H3K9me2S10ph_3


title: NBLS, H3K27ac, ABCAM, taz1


title: PBS_H3K9me2S10ph_2


title: Jurkat cells, DMSO, 6 hours, rep 1

value: DMSO


title: delta_rrp6_1


title: NBLS, H3K27ac, ABCAM, control2


title: NBLS, H3K27ac, ABCAM, control1


title: bACEseq_TET1.wt-rep2

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

data_processing:
The pre-processing (read alignment, quality filtering and read deduplication) was performed for BS-seq and bACE-seq datasets as previously described with minor modifications (Fabyanic et al., 2021). Briefly, demultiplexing of inline barcodes was first performed allowing up to 1-nt mismatch. The data quality was examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were trimmed for adaptor sequences and inline barcodes using Cutadapt (Kechin et al., 2017) with the following parameters in paired-end mode: -f fastq -q 20 -u 16 -U 16 -m 30 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. The trimmed R1 and R2 reads were mapped independently against the reference genome (mm10) using Bismark (Krueger and Andrews, 2011) (v0.18.2) with following parameters: --bowtie2 -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2 (--pbat option was turned on for mapping R1 reads). Uniquely mapped reads were filtered for minimal mapping quality (MAPQ>=10) using samtools (Li et al., 2009). PCR duplicates were removed using the Picard MarkDuplicates (http://broadinstitute.github.io/picard/). To eliminate reads from strands not deaminated by A3A, reads with three or more consecutive non-converted cytosines in the CH context were removed using filter_non_conversion in Bismark. Base calling of unmethylated and methylated cytosines was performed by bismark_methylation_extractor in Bismark in each individual nucleus. 5hmC signals were calculated as % of C/(C+T) at each cytosine base. Sequencing reads for WG-bACE-seq were pre-processed as previously reported (Schutsky et al., 2018).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and BS-seq/bACE-Seq analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in mouse genome.

growth_protocol: Human HEK293T cells were maintained at 37°C with 5% CO2 in CO2 incubators (Thermo Scientific, 51-033-774) in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco, 11965084), supplemented with 10% fetal bovine serum (Gibco, 16000044), 5% L-glutamine (Gibco, 25030081), 5% nonessential amino acid (Gibco, 11140050), and 5% sodium pyruvate (Gibco, 11360070) in 10-cm dishes and passaged every 2-3 days at 70% confluency with PBS and 0.05% Trypsin-EDTA (Gibco, 25300054).

extract_protocol: The whole genome BS-seq (WGBS) and bACE-seq (WG-bACE-seq) experiments were performed as previously described with minor modifications (Fabyanic et al., 2021). Briefly, ~15 ng of genomic DNA from each sample was first spiked in with in vitro methylated lambda phage genomic DNA (0.2%) as controls and was then subjected to bisulfite conversion (EZ DNA Methylation-Direct Kit, Zymo Research Cat# D5020).  Half of the bisulfite converted DNA was used for low input WGBS analysis (for 5mC+5hmC profiling). The other half of eluate was subjected to the low input WG-bACE-seq workflow (for 5hmC profiling).

treatment_protocol: For FACS-sorted All-in-one experiments, 2ug of Suntag platform containing scrambled or RHOXF2B sgRNA expressing constructs, and pTY-GFP (transfection control) were transiently transfected in suspension with dissociated 2x106cells per sample in Opti-MEM I Medium (Thermo Fisher Scientific, 31985062), with Lipofectamine 2000 (Invitrogen, 11668019) per manufacturer’s recommendation into 12-well plates. However, Lipofectamine 2000-DNA complexes were incubated for 45 minutes as opposed to manufacturer’s instruction. 24-hours post-transfection, the cells were expanded onto-6 well plates and incubated for an additional 48-hours prior to GFP+/DAPI- gated FACS followed by gDNA/RNA (Zymo Research, D7001), and protein isolation.

tag: experiment

value: bACE-Seq

value: TET1-wt overexpression


title: PBS_H3K9me2S10ph_1


title: bACEseq_TET1.wt-rep1


title: MCS066_RRP6_3

source_name: MATa ura3Δ0 leu2∆0 his3∆1 met15∆0 rrp6∆::kanMX4 [RRP6, LEU2, CEN6, pRS315]

value: MATa ura3delta0 leu2delta0 his3delta1 met15delta0 rrp6delta::kanMX4 [RRP6, LEU2, CEN6, pRS315]


title: WAT5

city: Heidelberg

first: Clarissa

last: Feuerstein-Akgoz

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
Data were processed with the nf-core rnaseq pipeline. Default parameters were used unless mentioned otherwise.
Sequences were aligned to the human reference genome (hg19/GRCh37) by application of the software HISAT2, with --unstranded option.
Transcripts were assembled using StringTie and gene codes gene annotation v.29 lift 37.
Gene counts were generated with the Stringties prepDE.py script (setting: -eb).
Normalized counts per million (CPM) were used for statistical analyses performed by edgeR.
Raw data will be available from the corresponding author upon reasonable request.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Normalized counts per million (CPM) as tab-delimited .txt file

source_name: white adipose tissue

extract_protocol:
Human adipose tissue was flash frozen, pulverized in liquid nitrogen and stored at -80 °C until use. RNA was extracted using TRIzol reagent (Sigma Aldrich) and the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an DNAse I digest (RNase-free DNAse set, Qiagen) and Proteinase K digest  (Puregene Proteinase K, Qiagen). RNA quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).
Illumina TrueSeq Stranded total RNA Library Prep Kit

value: white adipose tissue

tag: disease state

value: at risk of metabolic syndrome


title: MCS065_RRP6_2


title: bACEseq_TET1.var-rep2

value: TET1-var overexpression


title: ABLab_RNA_seq_WT_NF_40min_replicate2

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

data_processing:
Raw reads for the ChIP-seq results were obtained as fastq files. BWA was used in order to align the reads to the Caulobacter genome (accession number: NC_011916.1).
The aligned reads in  .bam format were converted into a .bed file format using the bamtobed option of Bedtools. Coverage was further calculated using BEDTools.
RPKM was further calculated for the samples using a custom python script.
Assembly: NC_011916.1
Supplementary files format and content: Files ending with .csv:  RPKM from RNA-seq data (column 1: gene name, column 2: RPKM)

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Overnight cultures ofCaulobactercells were back-diluted to 0.025 OD600in PYE media and grown at 30°C for 3 hours.

extract_protocol:
For RNA extraction, harvested  cells were spun down, the cell pellets were snap frozen and stored at -80°C. RNA was then extracted from these cell pellets according to a previous study (Badrinarayanan et al, 2017). RNA was isolated using Trizol extraction and purified via the Direct-zol RNA MiniPrep (Zymo, Cat. no. R2052) kit. The extracted RNA was treated with DNAse in order to remove the presence of genomic DNA from the sample. Total RNA was then purified using the RNA Clean & Concentrator-25 (Zymo, Cat. no. R1018) kit. Integrity of the RNA was assessed using Bioanalyzer instrument. mRNA was isolated from the total sample using the RiboMinus kit (Thermo, Cat. no. K155004) and submitted for sequencing.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® with sample prep beads (Cat no: E7765L)

treatment_protocol: 3 hours post back-dilution, when OD600of culture was ∼0.1, DNA damage (MMS (1.5mM) / MMC (0.25 μg/ml) / norfloxacin (8 μg/ml)) was introduced. Samples were collected at 0, 20 and 40 minutes post damage introduction.

value: Caulobacter crecentus CB15N

value: mixed population, exponential phase


title: BE2, H3K27ac, ABCAM, control1

data_processing:
raw read quality was assessed using fastqc (version 0.11.5)
Trimmomatic (version 0.36) was used to filter raw reads with a minimum Phred score of 33
Reads were aligned to GRCh38 using Bowtie2 (version 2.3.0) with default settings
Duplicate reads were eliminated using picard (version 2.18.29) with default settings.
bigWig files were generated using deepTools bamCoverage, normalized to RPKM. Blacklist regions (obtained from ENCODE) were excluded.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. After cell lysis, chromatin was sonicated using a Diagenode Bioruptor (30 seconds on and 30 seconds off) for 10 minutes in precooled conditions. Lysates were pelleted at 4˚C and the supernatant was collected.
DNA was purified using Qiagen PCR kit (Qiagen 28104). ChIP DNA libraries were made using Ovation® Ultralow System V2 kit (Tecan Genomics 0344NB-32).

value: neuroblastoma cell line, MYCN-amplified


title: bACEseq_TET1.var-rep1


title: WAT4


title: MCS064_RRP6_1


title: ABLab_RNA_seq_WT_NF_20min_replicate2


title: bACEseq_TET1.mut-rep2

value: TET1-mut overexpression


title: WAT3


title: rrp46_L191H_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp46Δ::kanMX4 [rrp46-L191H, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp46delta::kanMX4 [rrp46-L191H, LEU2, CEN6, pRS315]


title: WAT2


title: bACEseq_TET1.mut-rep1


title: WAT1


title: bACEseq_Ctrl-rep2

value: GFP overexpression


title: rrp46_L191H_1


title: H3K27me3_WAT

description: flash frozen tissue

data_processing:
Library strategy: ACT-seq
Sequencing reads (NextSeq 550 75bp paired end) were quality and adapter trimmed using Trim Galore v. 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in combination with Cutadapt v. 1.14 by deploying the non-default parameters “--paired”, “--nextera”, “--length_1 35”, “--length_2 35”.
The remaining sequences were aligned to the human reference genome hg19/GRCh37 using Bowtie2 v.2.2.6.
Aligned reads of the same library preparation that were sequenced on multiple lanes were combined using SAMtools merge v. 1.
Reads that did not map in a proper pair or that exhibited a mapping quality below 20 on the Phred scale were filtered out by means of SAMtools view.
To reconstruct the center of the original transposition events, reads aligned to the + strand were shifted by +4 bp while reads aligned to the - strand were offset by -5 bp.
The above data processing procedure was implemented as a fully dockerized workflow using the Common Workflow Language v. 1.0. and is publicly available (http://www.doi.org/10.5281/zenodo.3970149)
Raw data will be available from the corresponding author upon reasonable request.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: For bigwig files, sequencing reads overlapping with the ENCODE blacklist were removed and bw files were generated with the deeptools function bamCoverage with the options -p max -bs 20 --smoothLength 40 –e --normalizeUsing RPGC. Mean bigwig files of 3-5 WAT samples are provided.

extract_protocol:
Human adipose tissue was flash frozen, pulverized in liquid nitrogen followed by nuclear extraction.
Antibody-guided Chromatin Tagmentation (ACT-seq) was performed as described by Carter et al. 2019 with minor modifications. Shortly,  pA-transposome-antibody (pA-TnpOme-Ab) complex was generated with antibodies listed above. Anti-acetylated NEIL155 (AcNL1) was generously provided by Muralidhar Hegde and Sankar Mitra, Houston Methodist Research Institute (Sengupta et al. 2018). Nucei were incubated with pA-transposome-antibody complex for  transposition reaction and adapter ligation, followed by library amplification and purification.

tag: antibody target

value: #9733, Cell Signaling


title: rrp46_L191H_2


title: ABLab_RNA_seq_WT_MMC_40min_replicate1


title: ABLab_RNA_seq_WT_MMC_40min_replicate2


title: H3K27ac_WAT

description: flash frozen tissue


title: ABLab_RNA_seq_WT_MMC_20min_replicate2


title: bACEseq_Ctrl-rep1

value: Non-transfection control (NTC)


title: rrp46_L127T_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp46Δ::kanMX4 [rrp46-L127T, LEU2, CEN6, pRS315]

value: BY4741 haploid

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp46delta::kanMX4 [rrp46-L127T, LEU2, CEN6, pRS315]


title: ABLab_RNA_seq_WT_NF_40min_replicate1


title: BSseq_TET1.wt-rep2

value: BS-Seq


title: rrp46_L127T_2


title: ABLab_RNA_seq_WT_MMC_20min_replicate1


title: H3K4me3_WAT

description: flash frozen tissue

value: #C15410003, Diagenode


title: BSseq_TET1.wt-rep1

value: TET1-wt overexpression


title: rrp46_L127T_1


title: ABLab_RNA_seq_CB15N_0min_replicate4


title: H3K4me_WAT

description: flash frozen tissue


title: BSseq_TET1.var-rep2


title: rrp46_Q86I_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp46Δ::kanMX4 [rrp46-Q86I, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp46delta::kanMX4 [rrp46-Q86I, LEU2, CEN6, pRS315]


title: ABLab_RNA_seq_WT_NF_20min_replicate1


title: BSseq_TET1.var-rep1


title: ABLab_RNA_seq_CB15N_0min_replicate3


title: rrp46_Q86I_2


title: BSseq_TET1.mut-rep2


title: hMe-Seal WAT

description: Raw data not provided due to patient privacy concerns

data_processing:
Library strategy: hMeSEAL-seq
After sequencing, read-through adapter sequences were trimmed off using Cutadapt v1.16 and reads <30 bp were filtered out.
The remaining sequences were aligned to the human reference genome hg19/GRCh37 using Bowtie2 v.2.2.6.
Duplicate reads were marked by SAMtools v1.3.1 (RmDup) and collapsed to allow one read per alignment position.
Mapped reads with a mapping quality score of >10 were retained for further analysis.
Raw data of WAT samples will be available from the corresponding author upon reasonable request.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: For bigwig files, sequencing reads overlapping with the ENCODE blacklist were removed and bw files were generated with the deeptools function bamCoverage with the options -p max -bs 20 --smoothLength 40 –e --normalizeUsing RPGC. For hMeSeal_WAT.bw mean values of 5 samples are given.

source_name: white adipose tissue of 5 patients

growth_protocol: Human Simpson-Golabi-Behmel syndrome (SGBS) pre-adipocytes were grown to confluency in Dulbecco’s Modified Eagle’s Medium (DMEM)/F-12Nutrient Mixture (Ham) supplemented with 10 % fetal bovine serum  (FBS), 33 µM biotin, 17 µM pantothenate, 100 U/ml penicillin, 100 µg/ml streptomycin, 1ng/µl fibroblast growth factor (FGF) 1, and 90 µg/ml heparin. Three days post-confluency (day 0), SGBS cells were washed three times with PBS and stimulated to differentiate with serum-free growth medium, supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM rosiglitazone/BRL49653, 500 µM 1-methyl-3-isobuthylxanthine (IBMX), 250 nM dexamethasone (Dex), and 0.01 mg/ml human transferrin. After 6 days, FGF-1, Heparin, IBMX, Dex, rosiglitazone were removed from the medium. Cells were harvested at day 0, 1, 7 and 11.

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions, including an RNase A digest (RNase A solution, Qiagen) and Proteinase K digest  (Puregene Proteinase K, Qiagen). DNA  quality was checked by Agilent Bioanalyzer ( Agilent Technologies, Santa Clara, CA, USA) and quantified by Qubit fluorimetry (Thermo Scientific, Wilmington, USA).
Enrichment of hydroxymethylated DNA by selective chemical labeling (hMeSEAL) and spike-in amplicon generation was performed as described by Song et al. 2017 with minor modifications. Briefly, fragmented genomic (11 – 20 ng) DNA was subjected to library preparation using the KAPA HyperPrep Kit with KAPA Dual-Indexed Adapters for Illumina platforms (Roche, Mannheim, Germany). Sequencing adapters were ligated for 15 hours at 16°C, followed by library purification through double-sided size selection. The ligated DNA was spiked with unmethylated, methylated and hydroxymethylated amplicons (15 pg per amplicon) and incubated with 30 U T4 phage β-glucosyltransferase (T4-BGT), 1x NEBuffer 4 (NEB, Ipswich, MA, USA) and 3 nmol UDP-glucose (Active Motif, Carlsbad, CA, USA) for one hour at 37°C. Next, samples were purified using AMPure XP beads (Beckman Coulter, Brea, USA) and incubated for 1.5 hours at 37°C with 5 nmol dibenzylcyclooctyne-polyethylenglycol-4-distearlyether-biotin conjugate (DBCO-PEG4-biotin) (Jena Bioscience, Jena, Germany). Following AMPure XP bead-based purification, biotin-tagged DNA fragments were immobilized on streptavidin-coupled magnetic Dynabeads™ M270 (ThermoFisher Scientific, Waltham, MA, USA), pre-blocked with 50 µg sheared salmon sperm DNA. 5 µL Dynabeads™ M270 in 150 µL Buffer 1 (5 mM Tris-HCl (pH 7), 1 M NaCl, 0.5 mM EDTA, and 0.2% Tween-20) were added and rotated for 30 min at room temperature. Afterwards, the beads underwent four 5-min washing cycles at room temperature (using Buffer 1, Buffer 2 (Buffer 1 without NaCl), Buffer 3 (Buffer 1 with pH 9) and Buffer 4 (Buffer 3 without NaCl)) and were then resuspended in 27 µL water. The success of the reaction was validated by qPCR-based detection of recovered spike-in amplicons using 2 µL enriched DNA per sample. The enriched hydroxymethylated DNA fragments were amplified using 14 PCR cycles and purified by AMPure XP beads. Background libraries were prepared from the same fragmented genomic DNA (2 ng) by direct PCR amplification (11 cycles), without hydroxymethylation enrichment. Amplified libraries were subjected to paired-end 75 bp sequencing on the Illumina NextSeq 550 instrument (Illumina, San Diego, CA, USA).

value: white adipose tissue of 5 patients

tag: day

tag: replicate

tag: enrichment

value: hmC


title: BSseq_TET1.mut-rep1


title: RIP_WT_3_R1

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description: paired-end

data_processing:
Approximately 40 million paired-end 75 bp reads were sequenced for each individual cDNA library. Generated FASTQ files were mapped to F. nucleatum subsp. nucleatum ATCC 23726 (NC_003454.1) genome with custom annotation. Gene-wise read counts were normalized to TPM (transcripts per kilobase million) that takes into account sequencing depth (number of mapped reads) and transcripts length. Enrichment factors were calculated with DESeq2. RNA coimmunoprecipitated with tagged KhpA-3×FLAG or KhpB-3×FLAG (three biological duplicate each) was compared to the non-tagged WT strain to determine enrichment factors. DESeq2 utilizes Wald test to determine the P-value and the Benjamini-Hochberg to adjust P-values (P-adj). Transcripts enriched with log2 fold change ≥ 2.0 with P-adj ≤ 0.05 were considered binding ligands of KhpA or KhpB.
Assembly: NZ_CP028109.1
Supplementary files format and content: wiggle

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

source_name: cell pellets were collected from mid-exponential phase and then used as nput for coIP protocol

growth_protocol: All bacteria were grown in Columbia broth.

extract_protocol:
RNA coimmunoprecipitation was performed as previously carried out for Hfq or ProQ (Chao et al., 2012; Smirnov et al., 2016). Briefly, bacterial cultures (4 replicates) were grown to mid-exponential phase (OD=0.5) and a volume of cells equal to 100 ODs was collected. Cells were suspended in 800 μl lysis buffer (20 mM Tris pH 8.0, 150 mM KCl, 1 mM MgCl2,1mM DTT) containing 8 μl of DNase I. The resuspended cells were added to a fresh 2ml tube with 800 μl of 0.1 mm glass beads and lysed at 30 Hz for 10 min using Retsch MM200. A volume of supernatant equivalent to 0.5 OD600 cells was added to 90 μl 1x protein loading dye and used for input control. 25 μl of Flag antibody (Monoclonal ANTI-FLAG M2, Sigma, #F 1804) was added to the supernatant and rotated for 30 min at 4 °C. The sample was then added with 75 μl pre-washed Protein A Sepharose (#P6649, Sigma) and incubated at 4 °C for 30 min with rotation. Afterwards, the beads were spun down and a volume equivalent to 0.5 OD600 cells were added to 90 μl 1x protein loading dye and used for flowthrough control. The beads were then washed 5 times with the lysis buffer by inverting the tubes and centrifuged roughly. The last washing was collected in 1x protein loading dye. After washing, resuspended the beads in 532 μl lysis buffer and collected 32 μl to 8 μl 5x protein loading dye for later western blot analysis. The remaining beads were added 500 μl P: C: I for RNA precipitation. After precipitation, the RNA pellets were resuspended in H2O and further subjected to DNase I digestion and purified by P: C: I. At the end, the RNA pellets were resuspended in 15 μl H2O and used 15 μl from one replicate for northern blot verification and 3.5 μl of other three replicates for the cDNA library preparation.
For preparation cDNA library of the immunoprecipitated RNA samples, NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) was used. Briefly, 3.5 μl of RNA was mixed with 1 μl of 3’ SR Adaptor (diluted 1:10 in nuclease-free water) and incubated in a preheated thermal cycler for 2 min at 70 °C.  The samples were transferred to ice and added with the premixed 3’ ligation mix (5 μl 3’ Ligation Reaction Buffer, 1.5 μl 3’ Ligation Enzyme Mix). The ligation mixture was then incubated for 1 h at 25 °C. 0.25 μl of SR RT Primer and 2.5 μl nuclease-free water were added to the mixture and incubated at 75 °C for 5 min, 37 °C for 15 min and followed by 25 °C for 15 min. To ligate the 5’ SR adaptor, the 5’ ligation mixture (0.5 μl 1:10 diluted 5’ SR Adaptor, 0.5 μl 10x 5’ ligation reaction buffer, 1.25 μl 5’ ligation enzyme mix) was added to each sample and incubated for 1 h at 25 °C. For synthesis first strand of cDNA, reverse transcription mix (4 μl first strand synthesis reaction buffer, 0.5 μl murine RNase inhibitor, 0.5 μl M-MLV reverse transcriptase) was added to each reaction and incubated for 1 h at 50 °C followed by 15 min at 70 °C to inactivate the reverse transcription reaction. 5 μl of cDNA was then proceeded to PCR amplification with the PCR mix (12.5 μl LongAmp Taq 2x master mix, 0.625 μl SR primer, 6.25 μl nuclease-free water) and 0.625 μl index (X) primer. PCR program (30s at 94°C, 15 s at 94 °C, 30 s at 62 °C and 15 s at 70 °C for 19 cycles, 5 s at 70 °C) was carried out. PCR products were mixed with 25 μl of GLII buffer and loaded on 6 % polyAcrylamide gel containing 8 M urea. After staining the gel for 10 min in 1x TBE buffer with a 1:10,000 dilution of SYBR Gold Nucleic Acid Gel Stain (Invitrogen), the bands in the range of 130- 1000 bp were cut into small pieces and transfer to a 2 ml LoBind tube. 500 μl of DNA elution buffer was added and incubated at the room temperature for 2 h. After transferring the elute and the gel debris to centrifuge tube filters (Sigma) and centrifugation (5000 rpm, 1 min), the elute was recovered by adding 1 μl liner acrylamide (NEB) and precipitating in ethanol at -80°C for 1 h. After precipitation, the pellet was washed with 80% ethanol and resuspended in 12 μl nuclease free water (NEB). 1 μl of the prepared cDNA library was subjected to Bioanalyzer analysis.   Amplified cDNAs were pooled and sequenced on an illumine NextSeq 2000 platform by the CoreUnit Sysmed from the University of Wuerzburg.

value: WT


title: RRP46_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 rrp46Δ::kanMX4 [RRP46, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp46delta::kanMX4 [RRP46, LEU2, CEN6, pRS315]


title: RIP_WT_1_R1

description: paired-end

value: cell pellets were collected from mid-exponential phase and then used as nput for coIP protocol


title: BSseq_Ctrl-rep2


title: RIP_WT_2_R1

description: paired-end


title: RRP46_2


title: BSseq_Ctrl-rep1


title: RIP_C_BF_3_R1

description: paired-end

value: chromosomally flagged-tagged KhpB


title: RIP_C_BF_2_R1

description: paired-end


title: 451Lu_Corin_2

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

institute: Boston University

data_processing:
Fastq were trimmed using trimmomatic, aligned against gencode.v32 with salmon
Genome_build: gencode.v32
Supplementary_files_format_and_content: processed files contain gene counts for all samples

source_name: 451Lu R BRAFi-resistant melanoma cells

extract_protocol: Illumina NextSeq

value: corin treated


title: 451Lu_DMSO_2

value: DMSO treated


title: RRP46_1


title: 451Lu_DMSO_1


title: 451Lu_Corin_1


title: C4-2 cells, IPI-9119 100nM treated, rep 3

city: New York

first: Caroline

last: Ribeiro

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medicine

data_processing:
Paired-end reads were quality trimmed using Trimmomatic v.0.36 and subsequently mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Gene hit counts were quantified by featureCounts from the Subread package v.1.5.2. Differential gene expression was performed by DESeq2.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: Normalized counts separated by columns according to treatment and replicates. Genes indicated per row by ENSEMBL identifiers.

source_name: prostate

growth_protocol: Cells grown in RPMI media with 10% Fetal Bovine Serum

extract_protocol:
Frozen cell pellets submitted to Azenta Life Sciences (GENEWIZ) for RNA extraction
RNA library preparation with polyA selection performed by Azenta Life Sciences (GENEWIZ)
Standard RNA-Seq

treatment_protocol: Cells treated with IPI-9119 at 100 nM for 6 days

value: prostate

value: epithelial-like


title: rrp45_I15P_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 rrp45Δ::NEO [rrp45-I15P, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 rrp45delta::NEO [rrp45-I15P, LEU2, CEN6, pRS315]


title: NEIL1ac_WAT

description: flash frozen tissue

value: white adipose tissue

value: at risk of metabolic syndrome

value: AcNL1 (*)


title: C4-2 cells, IPI-9119 100nM treated, rep 2


title: 1205Lu_DMSO_1

source_name: 1205Lu R BRAFi-resistant melanoma cells


title: 1205Lu_DMSO_2


title: C4-2 cells, IPI-9119 100nM treated, rep 1


title: rrp45_I15P_1

value: BY4741 haploid


title: RIP_C_BF_1_R1

description: paired-end


title: RIP_AF_3_R1

description: paired-end

value: chromosomally flagged-tagged KhpA


title: rrp46_Q86I_1

value: MATalpha ura3delta0 leu2delta0 his3delta1 lys2delta0 rrp46delta::kanMX4 [rrp46-Q86I, LEU2, CEN6, pRS315]


title: RIP_AF_2_R1

description: paired-end


title: 1205Lu_Corin_2


title: C4-2 cells, DMSO treated, rep 3

value: DMSO 0.1%


title: 1205Lu_Corin_1


title: C4-2 cells, DMSO treated, rep 2


title: RIP_AF_1_R1

description: paired-end


title: MCS003_RRP45_3

source_name: MATα ura3Δ0 leu2Δ0 his3Δ1 rrp45Δ::NEO [RRP45, LEU2, CEN6, pRS315]

value: MATalpha ura3delta0 leu2delta0 his3delta1 rrp45delta::NEO [RRP45, LEU2, CEN6, pRS315]


title: MCS002_RRP45_2


title: Growth_WT_S_3

description: single-end

data_processing:
Reads from the RNA-seq experiments were trimmed and filtered using the FASTX toolkit (v.0.10.1; http://hannonlab.cshl.edu/fastx_toolkit). Mapping was performed using READemption (v.1.01)(Förstner et al., 2014) against the genome sequence for F. nucleatum subsp. nucleatum ATCC 23726 (NZ_CP028109.1) downloaded from the National Center for Biotechnology Information (NCBI). Differential gene expression analysis was carried using DEseq2 (v.1.18.01) (Love et al., 2014). All analysis for each was carried for biological triplicates and considered significant with a false-discovery rate ≤ 0.05.
Assembly: NZ_CP028109.1
Supplementary files format and content: wiggle

source_name: cells were grown to stationary phase prior to harvest

extract_protocol:
Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and snap-frozen at –80°C if not directly processed. The bacterial solution was centrifuged for 20min, 4500rpm at 4°C and the supernatant was completely discarded. Cells were suspended in 600μl of 10mg/ml lysozyme in TE buffer (pH8.0) and incubated at 37°C for 10min. Next, 60μl of 10% w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64°C, 1-2min before adding 66μl 3MNaOAc, pH5.2. Next, 750μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5min. at 64°C. Samples were briefly placed on ice to cool before centrifugation for 15min, 13,000rpm at 4°C. The aqueous layer was transferred into a 2ml phase lock gel tube (Eppendorf), 750μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12min, 13,000rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3MNaOAc, pH6.5) was added and incubated overnight at -20°C. Precipitated RNA was harvested by centrifugation, washed with cold 75% v/v ethanol and air-dried. Purified RNA was resuspended in 50µl RNase-free water and stored at -80°C.
For preparation cDNA library of the immunoprecipitated RNA samples, NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) was used. Briefly, 3.5 μl of RNA was mixed with 1 μl of 3’ SR Adaptor (diluted 1:10 in nuclease-free water) and incubated in a preheated thermal cycler for 2 min at 70 °C.  The samples were transferred to ice and added with the premixed 3’ ligation mix (5 μl 3’ Ligation Reaction Buffer, 1.5 μl 3’ Ligation Enzyme Mix). The ligation mixture was then incubated for 1 h at 25 °C. 0.25 μl of SR RT Primer and 2.5 μl nuclease-free water were added to the mixture and incubated at 75 °C for 5 min, 37 °C for 15 min and followed by 25 °C for 15 min. To ligate the 5’ SR adaptor, the 5’ ligation mixture (0.5 μl 1:10 diluted 5’ SR Adaptor, 0.5 μl 10x 5’ ligation reaction buffer, 1.25 μl 5’ ligation enzyme mix) was added to each sample and incubated for 1 h at 25 °C. For synthesis first strand of cDNA, reverse transcription mix (4 μl first strand synthesis reaction buffer, 0.5 μl murine RNase inhibitor, 0.5 μl M-MLV reverse transcriptase) was added to each reaction and incubated for 1 h at 50 °C followed by 15 min at 70 °C to inactivate the reverse transcription reaction. 5 μl of cDNA was then proceeded to PCR amplification with the PCR mix (12.5 μl LongAmp Taq 2x master mix, 0.625 μl SR primer, 6.25 μl nuclease-free water) and 0.625 μl index (X) primer. PCR program (30s at 94°C, 15 s at 94 °C, 30 s at 62 °C and 15 s at 70 °C for 19 cycles, 5 s at 70 °C) was carried out. PCR products were mixed with 25 μl of GLII buffer and loaded on 6 % polyAcrylamide gel containing 8 M urea. After staining the gel for 10 min in 1x TBE buffer with a 1:10,000 dilution of SYBR Gold Nucleic Acid Gel Stain (Invitrogen), the bands in the range of 130- 1000 bp were cut into small pieces and transfer to a 2 ml LoBind tube. 500 μl of DNA elution buffer was added and incubated at the room temperature for 2 h. After transferring the elute and the gel debris to centrifuge tube filters (Sigma) and centrifugation (5000 rpm, 1 min), the elute was recovered by adding 1 μl liner acrylamide (NEB) and precipitating in ethanol at -80°C for 1 h. After precipitation, the pellet was washed with 80% ethanol and resuspended in 12 μl nuclease free water (NEB). 1 μl of the prepared cDNA library was subjected to Bioanalyzer analysis.   Amplified cDNAs were pooled and sequenced on an illumine NextSeq 2000 platform by the CoreUnit Sysmed from the University of Wuerzburg.

value: WT


title: rrp4-2, 57h light, rep2, RNA-seq

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

description:
rrp4_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
rrp4.RNAseq.plus.bw
rrp4.RNAseq.minus.bw

data_processing:
Reads were trimmed using HOMER v4.11.1 with the following command: homerTools trim -pe -3 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -mis 2 -minMatchLength 4 -min 20. Trimmed reads were mapped to the TAIR10 genome sequence using STAR v2.7.9a with the following options: –outSAMstrandField intronMotif –outMultimapperOrder Random –outSAMmultNmax 1 –outFilterMultimapNmax 10000 –limitOutSAMoneReadBytes 10000000.
De novo transcript reconstruction was performed using a combination of two approaches. First, stringtie v2.1.4 was used with the total RNA-seq BAM files with the following options to generate de novo transcripts: -m 150 -s 1 -f 0.01. Additionally, the TSS peak summits were used to guide the creation of putative transcripts via the –ptf option. The resulting GTF files were merged from all samples and transcripts overlapping existing Araport11 transcripts filtered out using gffcompare v0.12.6. In a second approach, all total RNA-seq BAM files were filtered to remove reads with a MAPQ of less than 10, soft-clipping, or gaps, and then merged into a single file using samtools v1.14 and custom AWK scripts. A HOMER format tag directory was created using makeTagDirectory from HOMER v4.11.1, and de novo transcript reconstruction performed using findPeaks with the options -style groseq -tssSize 100 -minBodySize 100 -endFold 2078. Transcripts overlapping existing Araport11 transcripts were filtered out using gffcompare. The final HOMER and stringtie transcripts were imported into R v4.3.1 to generate a unified non-overlapping set of putative transcripts of lengths greater or equal to 200 bp, as well filtering those out whose TSS was not within 50 bp of a TSS peak discovered from the csRNA-seq, using base Bioconductor packages. The final transcript set was obtained by first converting the putative transcript set from GTF to GFF3 format using gffread v0.12.7, concatenating with the Araport11 annotations in GFF3 format, and finally sorted using GFF3sort v1.0.0.
TMM-normalized counts per million (CPM) from all samples were obtained by first reading the counts into R v4.3.1, then normalizing them using the calcNormFactors and cpm functions from the edgeR package.
Coverage tracks in bedGraph format were generated from the tag directories using the makeUCSCfile program from HOMER v4.11.1. The csRNA-seq files were further converted to bigWig using R v4.3.1 with the edgeR package to TMM-normalize the signal density.
Assembly: TAIR10
Supplementary files format and content: De novo transcripts are stored using the GFF3 format.
Supplementary files format and content: Transcript tab-separated quantification tables contain a column of transcript names and columns of counts for each RNA-seq sample.
Supplementary files format and content: RNA-seq read pileups per strand are provided in bigWig format.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized using the gas product of 100 mL of bleach mixed with 3 mL hydrochloric acid for 1 h, followed by stratification in water in the dark at 4 ˚C. Seeds were grown in 50 mL liquid ½ MS in 125 mL Erlenmeyer flasks, shaking at 180 RPM, in continuous light at 22 ˚C.

extract_protocol:
50 mg of sample (or 25 mg for dry seeds) was flash-frozen in liquid nitrogen and ground to a powder with a mortar and pestle. 1.5 mL of extraction buffer (EB; 100 mM Tris-HCl pH 9.5, 150 mM NaCl, 5 mM EDTA pH 8, 1% sarkosyl) was prepared per sample, and 7.5 µL beta-mercaptoethanol was added to each EB aliquot and briefly vortexed. After addition of the EB to the frozen ground tissue powder, the homogenate was mixed vigorously and left on ice for 10 min, with intermittent vortexing. This was followed by a 10 min max-speed centrifugation at 4 ˚C in a benchtop centrifuge. 1 mL of supernatant (avoiding the starchy upper-most layer) was transferred to a new tube and mixed with 1 mL chloroform. Following a 15 s vortexing step, the mixture was centrifuged as before and 900 µL of the upper phase transferred to a new tube. To this was added 90 µL 3 M NaOAc and 1 mL Tris-buffered phenol-chloroform, followed by vortexing for 15 s and another centrifugation as before. As much clear supernatant as possible was moved to a new tube and gently mixed by inversion with an equal volume isopropanol and incubated at 4 ˚C for 1 h. The precipitated RNA was pelleted by a 20 min max-speed centrifugation at 4 ˚C. The supernatant was discarded and the pellet washed with 800 µL ice-cold 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was discarded, further removed with a pipette after pulse-spinning, and left inverted to dry for 2 min. The pellet was dissolved in 100 µL nuclease-free water, to which 10 µL DNaseI buffer (ThermoFisher Scientific), 5 µL DNaseI (ThermoFisher Scientific), and 1 µL RiboLock (ThermoFisher Scientific) was added and left to incubate at 37 ˚C for 30 min. The resulting DNA-free RNA was isolated using a modified RNA purification protocol. Briefly, 240 µL nuclease-free water was added to the DNaseI reaction alongside 40 µL solubilization buffer (200 mM Tris-HCl pH 7.5, 10 mM EDTA pH 8, 5% SDS) and vortexed. Afterwards 40 µL 3 M NaOAc and 800 µL Tris-buffered phenol-chloroform was added and again vortexed for 15 s, followed by a max-speed centrifugation for 5 min at 4 ˚C. The supernatant was transferred to a new tube containing 800 µL chloroform and vortexed for 15 s, followed by another centrifugation as before. The supernatant was again transferred to a new tube, this time to one containing 1 mL ice-cold ethanol, gently mixed by inversion, and left at -80 ˚C overnight. The following day the tube was centrifuged as before for 20 min. The supernatant was discarded and the pellet was washed with 800 µL 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was removed, and again removed using a pipette after pulse spinning. After leaving the tubes to dry inverted for 2 min, the pellet was dissolved in 27 µL nuclease-free water (of which 1.5 µL was used for quantification with a NanoDrop (ThermoFisher Scientific)) and stored at -80 ˚C. RNA integrity was assessed by running 1 µg RNA in a denaturing RNA gel and 100 ng RNA with a Bioanalyzer RNA analysis chip (Agilent).
Total RNA was rRNA-depleted and library preparation was performed using the TruSeq Stranded Total RNA library preparation kit with Ribo-Zero (Illumina) following the manufacturer's protocol.

value: Seedlings


title: C4-2 cells, DMSO treated, rep 1


title: rrp4-2, 57h light, rep1, RNA-seq

description:
rrp4_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
rrp4.RNAseq.plus.bw
rrp4.RNAseq.minus.bw


title: hen2-4, 57h light, rep2, RNA-seq

description:
hen2_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
hen2.RNAseq.plus.bw
hen2.RNAseq.minus.bw


title: MCS001_RRP45_1


title: Growth_WT_S_2

description: single-end

value: cells were grown to stationary phase prior to harvest


title: rrp45_I15P_2


title: scRNA-Seq LG14

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

description: 10x Genomics Single cell 3' RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 from 10X
Assembly: hg38
Supplementary files format and content: cellranger output h5 of gene expression

source_name: Frontal cortex (BA9)

extract_protocol:
Human frontal cortex was homogenized by gentle manual dissociation on ice as described previously (Gosselin et al., 2017). Briefly, samples were dissociated in isolation buffer consisting of HBSS without magnesium and calcium (Life Technologies, 14175-095), 1% bovine serum albumin, and 1mM EDTA using a 2 ml polytetrafluoroethylene douncer and pestle (Wheaton, 358026). Myelin and debris was …by resuspension of the pellet in 37% isotonic Percoll (Sigma, P4937), and centrifuged at 600 x g for 30 min at 14°C with no acceleration and deceleration. Pelleted cells were washed twice with isolation buffer, filtered through a 70 µm strainer. Cells were then incubated in 1:100 with a Fc receptor blocking antibody (Human TruStain FcX) for 30 min at 4°C, and then with CD11b-PE (Biolegend), and CD45-APC (Biolegend). DAPI was used as live/dead staining. After staining, cells were centrifuged and resuspended in isolation buffer and kept on ice until FACS. CD45+ cells were sorted using Sony SA900 (100- µm nozzle, purity mode, sample chilling).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD45+ cells

value: Frontal cortex (BA9)

value: Male

tag: age

value: 59 years


title: Growth_WT_S_1

description: single-end


title: scRNA-Seq LG15

description: 10x Genomics Single cell 3' RNA

value: 88 years


title: hen2-4, 57h light, rep1, RNA-seq

description:
hen2_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
hen2.RNAseq.plus.bw
hen2.RNAseq.minus.bw


title: rrp40_W195R_2

source_name: MATa ura3Δ0 leu2Δ0 his3Δ1 rrp40Δ::NEO [rrp40-W195R, LEU2, CEN6, pRS315]

value: MATa ura3delta0 leu2delta0 his3delta1 rrp40delta::NEO [rrp40-W195R, LEU2, CEN6, pRS315]


title: Growth_WT_M_3

description: single-end

source_name: cells were grown to mid-exponential phase prior to harvest


title: Seedling, 57h light, rep2, RNA-seq

description:
L57_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L57.RNAseq.plus.bw
L57.RNAseq.minus.bw


title: scRNA-Seq LG05

description: 10x Genomics Single cell 3' RNA

value: 57 years


title: Growth_WT_M_1

description: single-end

value: cells were grown to mid-exponential phase prior to harvest


title: rrp40_S87A_3

source_name: MATa ura3Δ0 leu2Δ0 his3Δ1 rrp40Δ::NEO [rrp40-S87A, LEU2, CEN6, pRS315]

value: MATa ura3delta0 leu2delta0 his3delta1 rrp40delta::NEO [rrp40-S87A, LEU2, CEN6, pRS315]


title: Seedling, 57h light, rep1, RNA-seq

description:
L57_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L57.RNAseq.plus.bw
L57.RNAseq.minus.bw


title: rrp40_W195R_1

value: BY4741 haploid


title: Growth_dkhpB_S_3

description: single-end

value: deletion of KhpB


title: LG14

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger atac v1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: fragment tsv from cell ranger atac of 10X

extract_protocol:
Human frontal cortex was homogenized by gentle manual dissociation on ice as described previously (Gosselin et al., 2017). Briefly, samples were dissociated in isolation buffer consisting of HBSS without magnesium and calcium (Life Technologies, 14175-095), 1% bovine serum albumin, and 1mM EDTA using a 2 ml polytetrafluoroethylene douncer and pestle (Wheaton, 358026). Myelin and debris was …by resuspension of the pellet in 37% isotonic Percoll (Sigma, P4937), and centrifuged at 600 x g for 30 min at 14°C with no acceleration and deceleration. Pelleted cells were washed twice with isolation buffer, filtered through a 70 µm strainer. Cells were then incubated in 1:100 with a Fc receptor blocking antibody (Human TruStain FcX) for 30 min at 4°C, and then with CD11b-PE (Biolegend), and CD45-APC (Biolegend). DAPI was used as live/dead staining. After staining, cells were centrifuged and resuspended in isolation buffer and kept on ice until FACS. CD45+ cells were sorted using Sony SA900 (100- µm nozzle, purity mode, sample chilling).
Library was performed according to the manufacter’s instructions (single cell ATAC-seq v1 protocol, 10x Genomics). Cells were permeabilized using lysis buffer (10 mM Tris-HCl pH 7.4 (15567027, Thermo Fischer Scientific), 10 mM NaCl (ICN15194401, Fischer Scientific), 3 mM MgCl2 (194698, Mp Biomedicals Inc.), 0.1% Tween 20 (P7949, Sigma), 0.1% IGEPAL-CA630 (I8896, Sigma), 0.01% Digitonin (G9441, Promega), and 1% BSA in nuclease free water) and incubated for 5 minutes on ice. Permeabilized nuclei were washed using washing buffer (lysis buffer without IGEPAL-CA630 and Digitonin), centrifuged for 5 minutes at 500 rcf and resuspended in Nuclei buffer (10x Genomics). An aliquot was mixed with Trypan Blue and counted using a hemocytometer. Up to 10,000 nuclei were tagmented before loading onto a Chromium Controller; libraries were generated according to manufacturer specifications ((Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1, 1000175; Chromium Next GEM Chip H Single Cell Kit, 1000162; Single Index Kit N Set A, 1000212, 10x Genomics)). Libraries were amplified for 10 PCR cycles. SPRISelect reagent (Beckman Coulter) was used for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was inspected using the High Sensitivity D1000 ScreenTape assay on a Tapestation 4200 (Agilent). Libraries were sequenced using an Illumina NovaSeq 6000 using the following read lengths: Read 1: 50 cycles, Read 2: 50 cycles, Index 1: 8 cycles, Index 2: 16 cycles.


title: rrp40_S87A_2


title: Germinating seed, 26h light, rep2, RNA-seq

description:
L26_2_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L26.RNAseq.plus.bw
L26.RNAseq.minus.bw

source_name: Seeds

value: Seeds


title: LG05

description: 10x Genomics


title: Growth_dkhpB_S_2

description: single-end


title: Growth_dkhpB_S_1

description: single-end


title: Germinating seed, 26h light, rep1, RNA-seq

description:
L26_1_RNA
counts.raw.RNAseq.tsv
counts.tpm.RNAseq.tsv
denovo.RNAseq.gff3
L26.RNAseq.plus.bw
L26.RNAseq.minus.bw