title: P1_A03_Participant_192_week_6

description:
Library name: P1_A03_S17
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT_30 at ZT10 in short day entrained 12-day seedlings

status: Public on Mar 14 2025

type: SRA

city: York

first: Daphne

last: Ezer

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description:
Library name: WT_30_C
Column name in TPM_ril_all: WT_30_C

library_source: transcriptomic

data_processing:
Illumina adapters were trimmed using CutAdapt v3.4(Martin 2011).
Reads were quantified using Salmon v1.6.0 (Patro et al. 2017) and the TAIR10 transcriptome (Berardini et al. 2015).
Variant calling was done using GATK workflow described on the GATK website (Caetano-Anolles, 2023).
Assembly: TAIR10
Supplementary files format and content: TPM_ril_all.csv is a csv table containing gene expression data (TPM).  Every row is a gene name and each column is a different sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seeds were surface-sterilized and plated onto MS medium with 3% sucrose in clusters of ~50 seeds, and then stratified for 4 days. After stratification, seedlings were entrained in two cabinets under  8/16 light dark cycle with a constant temperature of 22° for 12 days.

extract_protocol:
Total RNA was isolated from whole plant tissue using the Qiagen RNeasy Plant Mini Kit. Residual genomic DNA was removed using the Invitrogen Turbo DNA-free kit, according to the manufacturer’s protocol.
Libraries were prepared with the NEBNext Ultra II Directional Library Prep Kit for Illumina, using the NEBNext poly(A) magnetic isolation module.

treatment_protocol: On day 12, individuals in treatment cabinet left in the light at ZT8. On day 12 at ZT10 all plants were harvested and snap-frozen in liquid nitrogen.

tag: tissue

value: whole seedling

tag: genotype

tag: treatment

value: ZT10, control (dark)


title: WT_28 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_28_T
Column name in TPM_ril_all: WT_28_T

value: ZT10, 2 hours extended light


title: P1_A02_Participant_218_week_6

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description:
Library name: P1_A02_S9
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.

value: Peripheral blood

tag: age

tag: Sex

value: female

tag: timepoint


title: WT_29 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_29_C
Column name in TPM_ril_all: WT_29_C


title: WT_35 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_35_T
Column name in TPM_ril_all: WT_35_T


title: P1_B05_Participant_178_week_7

description:
Library name: P1_B05_S34
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: male


title: WT_18 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_18_C
Column name in TPM_ril_all: WT_18_C


title: WT_35 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_35_C
Column name in TPM_ril_all: WT_35_C


title: P1_A01_Participant_145_week_6

description:
Library name: P1_A01_S1
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: KO3_ROCKi_ glutamatergic neurons (DIV21)_Replicate3

city: BARCELONA

first: Patryk

last: Polinski

state: BARCELONA

address: C/ del Dr. Aiguader, 88

country: Spain

institute: EMBL Barcelona

description: KO3_ROCKi RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

data_processing:
Raw reads were mapped with vast-tools align v2.5.1
Assembly: mm10
Supplementary files format and content: Files with raw read counts to each mouse gene in Ensembl v88 and cRPKMs.

organism: Mus musculus

source_name: in vitro differentiated glutamatergic neurons from mESC

growth_protocol: We followed the protocol reported by Bibel et al., 2007 with slight modifications. More in Supplementary Methods.

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
polyA-selected stranded RNA-seq

treatment_protocol: In vitro differentiated glutamatergic neurons (DIV21) were exposed to 10 µM Y-27632 ROCK inhibitor or vehicle (water) for 2 hours

tag: cell line

tag: cell type

value: glutamatergic neurons DIV21

value: KO Cell line 3

value: ROCK inhibitor Y-27632


title: NHEM_Parental_ATAC

city: New York

first: Elena

last: Grossi

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: SW11-par-atac

library_source: genomic

data_processing:
Paired reads were trimmed with NGmerge.
Reads were aligned to GRCh38/hg38 using Bowtie2 with standard parameters and quality was assessed using fastQC.
samtools was used to generate bam files and filter out low quality, mitochondrial and duplicated reads.
bigwig files were generated from filtered bam files using deepTools bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: neonatal foreskin

growth_protocol: Melanoma cells were maintained in DMEM, 10% FBS and 1X penicillin-streptomycin. Primary normal human epithelial melanocytes (NHEM - batch SW11) were cultured in Melanocyte Growth Media 254, 1X HMGS, 0.2 mM CaCl2 and 10 ng/mL PMA.

extract_protocol:
5x104 cells were harvested, treated with Digitonin and tagmented with 2.5 ml of TDE1 Enzyme
Amplification cycles for libraries were determined by qPCR

treatment_protocol: For ATAC-seq upon ATPase inhibitor treatment, samples were treated with 1uM of BRM014 compound (MedChemExpress) or DMSO

value: neonatal foreskin

value: NHEM

tag: disease stage

value: normal


title: KO2_ROCKi_ glutamatergic neurons (DIV21)_Replicate2

description: KO2_ROCKi RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

value: in vitro differentiated glutamatergic neurons from mESC

value: KO Cell line 2


title: WT_28 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_28_C
Column name in TPM_ril_all: WT_28_C


title: A549 cells, Perth09_16hrs_Infected_Replicate_2

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

description:
Library name: Infected_16hrs_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq.gz files were generated and demultiplexed with CellRanger 6.1.1
Custom references were made using Cell Ranger 4.0.0 to combine the human and virus
Cell Ranger's (7.1.0) "count" was used to align each sample to the appropriate custom reference, collapse reads to UMIs and call cells.
Assembly: NCBI GRCh38 (Annotation Release 109) plus H3N2 (A/Perth/16/2009)
Supplementary files format and content: Tab-separated values files and matrix files.

growth_protocol: A549 cells were maintained in gibco’s F-12 with L-Glutamine supplemented with 8.3% fetal bovine serum and grown at 37°C with 5% CO2

extract_protocol:
Cells were stained with F16v3 targeting viral HA protein and sorted using Bigfoot cell sorter into infected or uninfected populations.
The library was constructed with is Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index; 10x Genomics). and sequenced on one S4 2x150nt lane in a NovaSeq 6000.

treatment_protocol: Cells were incubated with virus diluted in PBS + 0.1% BSA for 1 hr at 37°C. At 3hpi, growth media was removed, and F-12 supplemented with 50 mM HEPES and 20 mM NH4Cl was added to block secondary spread.

value: human alveolar epithelial

value: Infected H3N2 (A/Perth/16/2009)


title: A549 cells, Perth09_16hrs_Infected_Replicate_1

description:
Library name: Infected_16hrs_1
10x Genomics


title: KO1_ROCKi_ glutamatergic neurons (DIV21)_Replicate1

description: KO1_ROCKi RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

value: KO Cell line 1


title: A549 cells, Perth09_14hrs_Infected_Replicate_2

description:
Library name: Infected_14hrs_2
10x Genomics


title: P1_A06_Participant_218_week_7

description:
Library name: P1_A06_S41
Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination


title: WT3_ROCKi_ glutamatergic neurons (DIV21)_Replicate3

description: WT3_ROCKi RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

value: WT Cell line 3


title: WT_27 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_27_T
Column name in TPM_ril_all: WT_27_T

value: whole seedling


title: WT2_ROCKi_ glutamatergic neurons (DIV21)_Replicate2

description: WT2_ROCKi RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

value: WT Cell line 2


title: A549 cells, Perth09_12hrs_Infected_Replicate_2

description:
Library name: Infected_12hrs_2
10x Genomics


title: WT_27 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_27_C
Column name in TPM_ril_all: WT_27_C

value: ZT10, control (dark)


title: WT1_ROCKi_ glutamatergic neurons (DIV21)_Replicate1

description: WT1_ROCKi RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to 10 µM Y-27632 ROCK inhibitor for 2 hours

value: WT Cell line 1


title: WT_29 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_29_T
Column name in TPM_ril_all: WT_29_T

value: ZT10, 2 hours extended light


title: KO2_Veh_ glutamatergic neurons (DIV21)_Replicate2

description: KO2_Veh RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours

value: glutamatergic neurons DIV21

value: Vehicle (water)


title: KO3_Veh_ glutamatergic neurons (DIV21)_Replicate3

description: KO3_Veh RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours

value: KO Cell line 3


title: A549 cells, Perth09_12hrs_Infected_Replicate_1

description:
Library name: Infected_12hrs_1
10x Genomics


title: WT_26 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_26_T
Column name in TPM_ril_all: WT_26_T


title: 4L_Parental_ATAC

description: Library name: 4L-par-atac

source_name: skin

value: skin

value: melanoma

value: BRAFV600E subtype

value: metastatic


title: WT2_Veh_ glutamatergic neurons (DIV21)_Replicate2

description: WT2_Veh RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours

value: in vitro differentiated glutamatergic neurons from mESC


title: WT3_Veh_ glutamatergic neurons (DIV21)_Replicate3

description: WT3_Veh RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours


title: KO1_Veh_ glutamatergic neurons (DIV21)_Replicate1

description: KO1_Veh RNA-seq of in vitro differentiated KO glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours


title: A549 cells, Perth09_10hrs_Infected_Replicate_2

description:
Library name: Infected_10hrs_2
10x Genomics

value: human alveolar epithelial


title: A549 cells, Perth09_14hrs_Infected_Replicate_1

description:
Library name: Infected_14hrs_1
10x Genomics

value: Infected H3N2 (A/Perth/16/2009)


title: WT_25 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_25_T
Column name in TPM_ril_all: WT_25_T


title: WT_26 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_26_C
Column name in TPM_ril_all: WT_26_C


title: WT1_Veh_ glutamatergic neurons (DIV21)_Replicate1

description: WT1_Veh RNA-seq of in vitro differentiated WT glutamatergic neurons (DIV21) exposed to vehicle (water) for 2 hours


title: A549 cells, Perth09_10hrs_Infected_Replicate_1

description:
Library name: Infected_10hrs_1
10x Genomics


title: 4L_BRM014_6h_rep2_ATAC

description: Library name: 4L-BRM014-6h-r2


title: 4L_BRM014_6h_rep1_ATAC

description: Library name: 4L-BRM014-6h-r1


title: 4L_BRM014_1h_rep1_ATAC

description: Library name: 4L-BRM014-1h-r1


title: 4L_BRM014_1h_rep2_ATAC

description: Library name: 4L-BRM014-1h-r2


title: WT_24 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_24_T
Column name in TPM_ril_all: WT_24_T


title: 4L_BRM014_10m_rep2_ATAC

description: Library name: 4L-BRM014-10m-r2


title: A549 cells, Perth09_8hrs_Infected_Replicate_1

description:
Library name: Infected_8hrs_1
10x Genomics


title: A549 cells, Perth09_8hrs_Infected_Replicate_2

description:
Library name: Infected_8hrs_2
10x Genomics


title: 4L_BRM014_10m_rep1_ATAC

description: Library name: 4L-BRM014-10m-r1


title: A549 cells, Uninfected

description:
Library name: Uninfected
10x Genomics

value: Uninfected


title: WT_24 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_24_C
Column name in TPM_ril_all: WT_24_C


title: 4L_DMSO_rep2_ATAC

description: Library name: 4L-DMSO-r2


title: 4L_DMSO_rep1_ATAC

description: Library name: 4L-DMSO-r1


title: DOHH2_CREBBP_IL4_1

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

source_name: cell line

growth_protocol: SU-DHL4, DoHH2 and SU-DHL10 Cell lines were grown in RPMI-1640 medium+10% h.i. FBS+P.S.  OCILY7 was grown in IMDM medium+10% h.i. FBS+P.S.

extract_protocol:
Total RNA was purified using the Trizol reagent followed by RNAeasy column purification (Qiagen). RNA was assessed using the Bioanalyzer (Agilent #5067-1513) and a Qubit RNA High Sensitivity assay (Thermofisher # Q32855), and 50ng of RNA input was processed
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: The cell lines were cultured in RPMI1640 + 10% hiFCS  for 4 h in the presence or absence of 10 ng/ml of IL4.

value: cell line

value: B cell lymphoma

value: CREBBP -/-


title: WT_23 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_23_T
Column name in TPM_ril_all: WT_23_T

value: whole seedling


title: WT_23 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_23_C
Column name in TPM_ril_all: WT_23_C

value: ZT10, control (dark)


title: DOHH2_CREBBP_BSL_1

value: Baseline


title: DOHH2_AAVS_IL4_1

value: AAVS -/-


title: BoM_siPHF19_Rep3

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

description: Library name: RNAseq_BoM_siPHF19_Rep3

data_processing:
Fastq files were mapped to the human reference genome assembly hg38 using RNA STAR and then quantified using RSEM (v1.3.1).
Raw counts were used for differential gene expression analysis using DESeq2 (v1.46.0).
Assembly: hg38
Supplementary files format and content: DeSeq2 results table

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% FCS and grown under sterile conditions in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA was harvested from cells using  NucleoSpin RNA Midi kit (Macherey Nagel, #740962).
RNA integrity was assessed by gel electrophoresis, and libraries were prepared using 1 µg of RNA with the Illumina Stranded mRNA Prep Ligation Kit (Illumina, 1000000124518 v03), following the manufacturer’s protocol.

treatment_protocol: For transient knockdowns, the cells were reverse transfected using Lipofectamine™ RNAiMAX (Invitrogen) at a final concentration of 5nM total siRNA, according to manufacturer's instructions. In experiments involving siRNA mixtures, the individual siRNAs were mixed 1:1. The cells were used for experiments at 72 h post transfection. The siRNAs used were: negative control siRNA (siNT, ON-TARGETplus® non-targeting control pool D-001810-10 from Dharmacon), siPHF19 (Silencer® Select PHF19 s25161 (ss#1) and s25160 (ss#2) from ThermoFisher Scientific).

tag: disease

value: Triple Negative Breast Cancer

value: PHF19 siRNA


title: WT_25 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_25_C
Column name in TPM_ril_all: WT_25_C


title: BoM_siNT_Rep3

description: Library name: RNAseq_BoM_siNT_Rep3

value: non-targeting siRNA (NT)


title: BoM_siNT_Rep2

description: Library name: RNAseq_BoM_siNT_Rep2


title: WT_22 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_22_T
Column name in TPM_ril_all: WT_22_T

value: ZT10, 2 hours extended light


title: BoM_siPHF19_Rep1

description: Library name: RNAseq_BoM_siPHF19_Rep1


title: WT_22 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_22_C
Column name in TPM_ril_all: WT_22_C


title: DOHH2_AAVS_BSL_1


title: BoM_siPHF19_Rep2

description: Library name: RNAseq_BoM_siPHF19_Rep2


title: BoM_siNT_Rep1

description: Library name: RNAseq_BoM_siNT_Rep1


title: WT_21 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_21_T
Column name in TPM_ril_all: WT_21_T


title: 436_siPHF19_Rep3

description: Library name: RNAseq_436_siPHF19_Rep3


title: 436_siNT_Rep3

description: Library name: RNAseq_436_siNT_Rep3


title: 436_siPHF19_Rep2

description: Library name: RNAseq_436_siPHF19_Rep2


title: 436_siNT_Rep2

description: Library name: RNAseq_436_siNT_Rep2


title: SUDHL10_CREBBP_BSL_1


title: WT_21 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_21_C
Column name in TPM_ril_all: WT_21_C


title: SUDHL10_AAVS_IL4_1


title: 436_siPHF19_Rep1

description: Library name: RNAseq_436_siPHF19_Rep1


title: WT_19 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_19_T
Column name in TPM_ril_all: WT_19_T


title: 436_siPHF19_Input_Rep3

description: Library name: ChIPseq_436_siPHF19_Input_Rep3

data_processing:
Adapters were trimmed using TrimGalore (v0.6.7). Bowtie2 (v2.5.2) was used to map reads to the reference genome assembly hg38 and duplicates were marked using Picard (v3.1.0).
Bigwig files were scaled ignoring blacklist regions using bamCoverage (deeptools v3.5.6) with reads per genomic content (RPGC) normalization and scaling factors calculated as following:                                                                                1. ratio_input = spike_input_reads / (main_input_reads+spike_input_reads) 2. ratio_IP = spike_IP_reads / (main_IP_reads+spike_IP_reads) 3. scaling_factor_sample = ratio_input / ratio_IP 4. Normalize scaling factors by dividing all scaling factors by highest scaling factor
Scaled and normalized bigwigs for replicates were merged using bigwigAverage (deeptools v3.5.6).
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For ChIP, 20 million cells mixed with NIH 3T3 cells (5%) as a spike-in control and then crosslinked with 1% formaldehyde for 20 minutes. Sonicated chromatin extracts were incubated overnight with H3K27me3 antibody (Active Motif, 39155, 5 µL/IP). Protein A Sepharose beads (Cytiva, 17078001, rabbit antibodies) were subsequently added for immunoprecipitation.The immunoprecipitated chromatin was washed sequentially with high-salt buffers and TE buffer. After washing, chromatin was reverse crosslinked, and DNA was extracted.
ChIP libraries were prepared using the MicroPlex Library Preparation Kit v3 (Diagenode, C05010001), following the manufacturer’s protocol.

treatment_protocol: For transient knockdowns, the cells were reverse transfected using Lipofectamine™ RNAiMAX (Invitrogen) at a final concentration of 5nM total siRNA, according to manufacturer's instructions. In experiments involving siRNA mixtures, the individual siRNAs were mixed 1:1. The cells were used for experiments at 72 h post transfection.The siRNAs used were: negative control siRNA (siNT, ON-TARGETplus® non-targeting control pool D-001810-10 from Dharmacon), siPHF19 (Silencer® Select PHF19 s25161 (ss#1) and s25160 (ss#2) from ThermoFisher Scientific)

tag: antibody


title: SUDHL10_AAVS_BSL_1


title: 436_siNT_Rep1

description: Library name: RNAseq_436_siNT_Rep1


title: 436_siPHF19_Input_Rep1

description: Library name: ChIPseq_436_siPHF19_Input_Rep1


title: 436_siPHF19_Input_Rep2

description: Library name: ChIPseq_436_siPHF19_Input_Rep2


title: WT_18 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_18_T
Column name in TPM_ril_all: WT_18_T


title: 436_siPHF19_H3K27me3_Rep3

description: Library name: ChIPseq_436_siPHF19_H3K27me3_Rep3

value: H3K27me3 (Active Motif, #39155)


title: OCILY7_CREBBP_IL4_1


title: 436_siPHF19_H3K27me3_Rep2

description: Library name: ChIPseq_436_siPHF19_H3K27me3_Rep2


title: OCILY7_CREBBP_BSL_1


title: 436_siNT_Input_Rep3

description: Library name: ChIPseq_436_siNT_Input_Rep3


title: 436_siNT_Input_Rep2

description: Library name: ChIPseq_436_siNT_Input_Rep2


title: WT_17 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_17_C
Column name in TPM_ril_all: WT_17_C


title: OCILY7_AAVS_IL4_1


title: 436_siNT_H3K27me3_Rep3

description: Library name: ChIPseq_436_siNT_H3K27me3_Rep3


title: 436_siNT_H3K27me3_Rep2

description: Library name: ChIPseq_436_siNT_H3K27me3_Rep2


title: WT_16 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_16_T
Column name in TPM_ril_all: WT_16_T


title: 436_siNT_H3K27me3_Rep1

description: Library name: ChIPseq_436_siNT_H3K27me3_Rep1


title: SUDHL10_CREBBP_IL4_1


title: SUDHL4_CREBBP_IL4_1


title: SUDHL4_CREBBP_BSL_1


title: OCILY7_AAVS_BSL_1


title: WT_15 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_15_T
Column name in TPM_ril_all: WT_15_T


title: WT_17 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_17_T
Column name in TPM_ril_all: WT_17_T


title: SUDHL4_AAVS_IL4_1


title: BoM_siPHF19_Input_Rep3

description: Library name: ChIPseq_BoM_siPHF19_Input_Rep3


title: BoM_siPHF19_Input_Rep2

description: Library name: ChIPseq_BoM_siPHF19_Input_Rep2


title: BoM_siPHF19_H3K27me3_Rep3

description: Library name: ChIPseq_BoM_siPHF19_H3K27me3_Rep3


title: WT_19 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_19_C
Column name in TPM_ril_all: WT_19_C


title: WT_15 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_15_C
Column name in TPM_ril_all: WT_15_C


title: BoM_siPHF19_Input_Rep1

description: Library name: ChIPseq_BoM_siPHF19_Input_Rep1


title: 436_siNT_Input_Rep1

description: Library name: ChIPseq_436_siNT_Input_Rep1


title: SUDHL4_AAVS_BSL_1


title: BoM_siPHF19_H3K27me3_Rep1

description: Library name: ChIPseq_BoM_siPHF19_H3K27me3_Rep1


title: WT_14 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_14_T
Column name in TPM_ril_all: WT_14_T


title: 436_siPHF19_H3K27me3_Rep1

description: Library name: ChIPseq_436_siPHF19_H3K27me3_Rep1


title: BoM_siNT_Input_Rep3

description: Library name: ChIPseq_BoM_siNT_Input_Rep3


title: Sample_81-R9

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

data_processing:
For each bulk ATAC-seq sample, the pair-end reads from fastq files were aligned to the human genome (GRCh38) using bwa mem mode with duplicated reads removed. The 5' end of ATAC-seq reads were shifted to the actual cut-site of the Transposase using alignmentSieve module implemented in DeepTools (4). The peaks were called using Macs2 (5) with using the pair-end read information.
Gene expression was quantified with RSEM (v1.3.3) (rsem-calculate-expression --strandedness reverse --no-bam-output --paired-end --bowtie2) using the bowtie2  (v2.4.2) as the aligner and hg19 transcriptome as the reference. TPM values from RSEM were log 2 transformed (log2(TPM+1)) and the top five thousand variably expressed genes were used to perform PCA and visualize clustering of the samples.  The peak sets from multiple samples were identified as the overlap ones among samples using bUseSummarizeOverlaps function in DiffBind. We then calculated the TF activity
Assembly: GRCh38
Supplementary files format and content: bed, TPM

source_name: Donor 2 CREM KO CAR NK cells

extract_protocol:
By applying RNA  and ATAC sequencing, we want to investigate the transcriptomics and epigenetic factors that contributing for difference between optimal and suboptimcal  in NK cells
Libraries were sequenced  2 x 100 bp on an Illumina NovaSeq6000 to obtain at least 50 million high quality mapping reads per sample.

value: CBNK

value: nk

value: CREM KO CAR NK


title: WT_14 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_14_C
Column name in TPM_ril_all: WT_14_C


title: BoM_siNT_Input_Rep1

description: Library name: ChIPseq_BoM_siNT_Input_Rep1


title: BoM_siNT_Input_Rep2

description: Library name: ChIPseq_BoM_siNT_Input_Rep2


title: WT_16 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_16_C
Column name in TPM_ril_all: WT_16_C


title: Sample_80-R8

source_name: Donor 2 CREM WT CAR NK cells

value: CREM WT CAR NK


title: BoM_siNT_H3K27me3_Rep2

description: Library name: ChIPseq_BoM_siNT_H3K27me3_Rep2


title: BoM_siNT_H3K27me3_Rep1

description: Library name: ChIPseq_BoM_siNT_H3K27me3_Rep1


title: WT_13 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_13_C
Column name in TPM_ril_all: WT_13_C


title: Sample_75-R3

source_name: Donor 1 CREM KO CAR NK cells


title: BoM_siNT_H3K27me3_Rep3

description: Library name: ChIPseq_BoM_siNT_H3K27me3_Rep3


title: HeLa, siSPT6siPCF11, rep3

city: Paris

first: Fabienne

last: Bejjani

address: 27 Rue Fg St Jacques

country: France

institute: Institut Cochin

data_processing:
Initial quality control of the raw FASTQ files was performed using FastQC (version 0.12.1). FastQC reports were generated for each sample. Raw sequencing files from lane 1 (L1) and lane 2 (L2) were merged for read 1 (R1) and read 2 (R2) using the cat command (cat L1_R1.fastq.gz L2_R1.fastq.gz > merged_R1.fastq.gz).
The merged FASTQ files were aligned to the human reference genome (GRCh38) using HISAT2 (version 2.2.1) (hisat2 --dta -x genome -1 merged_R1.fastq.gz -2 merged_R2.fastq.gz -S output.sam). The SAM files were then converted to BAM format and sorted using SAMtools (version 1.3.1).
Aligned reads were quantified using StringTie (version 2.1.5) (stringtie output.bam -eB -G annotation.gtf -o output.gtf -A gene_abund.tab).
Differential expression analysis was performed using DESeq2 (version 1.30.1) in R (version 4.0.3). Read counts were imported into DESeq2, and the standard workflow was followed to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: HeLa

growth_protocol: HeLa LTR-Luc cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) + GlutaMAXTM-I (Gibco, 61965-026) supplemented with 10% of decomplemented fetal bovine serum (FBS) (Gibco, 10270-106) and 1% Antibiotic-Antimycotic (10,000 U/mL penicillin, 10,000 μg/mL streptomycin, and 25 μg/mL of Amphotericin B; Gibco, 15240-062). Cells were grown in a humidified 5% CO2 incubator at 37°C and were routinely tested for the absence of Mycoplasma contamination.

extract_protocol:
Total RNAs were extracted using the ReliaPrepTM RNA Miniprep Systems (Promega, Z6012) as per the manufacturer’s instructions. Sample quality was verified using the Bioanalyzer RNA 6000 Nano kit (Agilent)
Libraries were prepared following the Stranded Total RNA Prep Ligation with Ribo-Zero Plus protocol from Illumina, starting from 200 ng of high-quality total RNA (RIN > 9). Paired end (2 × 59) sequencing was performed on an Illumina NextSeq 2000 platform. Demultiplexing and quality control were conducted with the AOZAN software (ENS, Paris) at the GENOM’IC platform, Institut Cochin.

treatment_protocol: HeLa cells were transfected with the indicated siRNAs at a final concentration of 20nM using LipofectamineTM RNAiMAX Transfection Reagent (Invitrogen, 13778150) and Opti-MEM™ (Gibco, 31985070) according to the manufacturer’s instructions. Cells were harvested after 72 hours and RNA-seq experiments were carried out in 3 biological replicates

value: HeLa

value: epithelial cells (human cervical cancer)


title: WT_13 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_13_T
Column name in TPM_ril_all: WT_13_T


title: Sample_74-R2

source_name: Donor 1 CREM WT CAR NK cells


title: HeLa, siSPT6siPCF11, rep1


title: HeLa, siSPT6siPNUTS, rep2


title: HeLa, siSPT6siPNUTS, rep3


title: Sample_Donor-2-CREM-WT-CAR-Reg-plus-UMRC3

source_name: Donor 2 CREM WT CAR NK cells in coculture

value: CREM WT CAR NK in tumor coculture


title: WT_12 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_12_C
Column name in TPM_ril_all: WT_12_C


title: HeLa, siSPT6siPCF11, rep2


title: WT_11 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_11_T
Column name in TPM_ril_all: WT_11_T


title: Sample_Donor-2-CREM-KO-CAR-Reg-plus-UMRC3

source_name: Donor 2 CREM KO CAR NK cells in coculture

value: CREM KO CAR NK in tumor coculture


title: HeLa, siSPT6siPNUTS, rep1


title: BoM_siPHF19_H3K27me3_Rep2

description: Library name: ChIPseq_BoM_siPHF19_H3K27me3_Rep2


title: HeLa, siPCF11, rep3


title: Sample_Donor-2-CREM-WT-CAR-Reg


title: WT_11 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_11_C
Column name in TPM_ril_all: WT_11_C

value: whole seedling


title: HeLa, siPCF11, rep1


title: Sample_Donor-2-CREM-KO-CAR-Reg


title: HeLa, siPNUTS, rep3

value: siPNUTS


title: WT_10 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_10_T
Column name in TPM_ril_all: WT_10_T


title: HeLa, siPNUTS, rep2


title: Sample_Donor-1-CREM-WT-CAR-Reg-plus-UMRC3

source_name: Donor 1 CREM WT CAR NK cells in coculture


title: HeLa, siPNUTS, rep1


title: WT_10 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_10_C
Column name in TPM_ril_all: WT_10_C

value: ZT10, control (dark)


title: WT_12 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_12_T
Column name in TPM_ril_all: WT_12_T


title: Sample_Donor-1-CREM-WT-CAR-Reg


title: HeLa, siIWS1, rep3


title: Sample_Donor-1-CREM-KO-CAR-Reg-plus-UMRC3

source_name: Donor 1 CREM KO CAR NK cells in coculture


title: HeLa, siSPT6, rep3


title: WS_2 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WS_2_T
Column name in TPM_ril_all: WS_2_T


title: HeLa, siSPT6, rep2


title: HeLa, siCT, rep3

value: siCT


title: WT_1 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_1_C
Column name in TPM_ril_all: WT_1_C


title: HeLa, siPCF11, rep2


title: HeLa, siCT, rep2


title: HeLa, siCT, rep1


title: WS_2 at ZT10 in short day entrained 12-day seedlings

description:
Library name: WS_2_C
Column name in TPM_ril_all: WS_2_C


title: Sample_Donor-1-CREM-KO-CAR-Reg


title: HeLa, siSPT6, rep1


title: Sample_Input_H12

source_name: Donor C CAR70 NK cells


title: Sample_Input_H10

source_name: Donor C IL-15 NK cells


title: D48, mag-iso, preactivated

city: Hamburg

first: Michael

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

institute: UKE Hamburg

description: SMART-Seq mRNA combined with Illumina Nextera XT of resulting cDNA

data_processing:
Paired-end reads were mapped to the human reference genome (GRCh38 v110) using STAR v2.7.10a and simultaneously counted per gene
Assembly: hg38
Supplementary files format and content: Tab-separated values of raw counts for each sample

extract_protocol:
RNA was isolated from NK cells using NucleoSpin RNA Plus XS
From each sample 10 ng total quality controled RNA was used for oligo(dT)-primed, full-length cDNA synthesis with a SMART-Seq mRNA kit. The resulting cDNA samples were subjected to library preparation with the Illumina Nextera XT kit according to manufacturer’s protocols.
RNA-Seq from total RNA including rRNA depletion


title: TNZ_1 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: TNZ_1_T
Column name in TPM_ril_all: TNZ_1_T

source_name: whole seedling


title: D43, mag-iso, preactivated


title: Sample_Input_H9

source_name: Donor C NT NK cells

value: NT


title: D43, mag-iso, control


title: TNZ_1 at ZT10 in short day entrained 12-day seedlings

description:
Library name: TNZ_1_C
Column name in TPM_ril_all: TNZ_1_C


title: D41, mag-iso, preactivated


title: Sample_Input_H8

source_name: Donor B CAR70 NK cells


title: HeLa, siIWS1, rep2


title: D41, mag-iso, control


title: 4111337

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

description: FL-DLBCL, cryo-preserved

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: Cy3, Cy5

source_name: lymph node

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: FL-DLBCL, cryo-preserved


title: HeLa, siIWS1, rep1


title: D50, K562-expanded, preactivated


title: WT_1 after 2 hours extended light at ZT10 in short day entrained 12-day seedlings

description:
Library name: WT_1_T
Column name in TPM_ril_all: WT_1_T


title: 4177639

description: FL-DLBCL, cryo-preserved


title: D50, K562-expanded, control


title: Sample_Input_H7

source_name: Donor B CAR70/IL-15 NK cells


title: D48, K562-expanded, preactivated


title: Sample_Input_H6

source_name: Donor B IL-15 NK cells


title: 4142605

description: FL-DLBCL, cryo-preserved


title: D25, K562-expanded, preactivated


title: D48, K562-expanded, control


title: 4132950

description: FL-DLBCL, cryo-preserved


title: Sample_Input_H5

source_name: Donor B NT NK cells


title: D25, K562-expanded, control


title: Cell culture, elicited, 72h, rep4

city: Valencia

first: Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

data_processing:
fastp --detect_adapter_for_pe --n_base_limit 5  --cut_front_window_size 1  --cut_front_mean_quality 30  --cut_front  -- cut_tail_window_size 1  – cut_tail_mean_quality 30  –cut_tail -l 20
STAR --alignEndsProtrude 10 ConcordantPair  --alignIntronMax 100000  –twopassMode Basic
featureCounts -t "exon"
Assembly: (Jiao et al., 2020) https://doi.org/10.1016/j.molp.2020.05.005
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Morus alba

source_name: Cell suspensions

growth_protocol: Calli were subcultured every 30 days. Cell suspensions were initiated by placing 1.25 g of calli in 100 ml flasks with 25 ml of either liquid MS6 media prepared without agar and grown in darkness at 25 ºC under orbital shaking at 110 rpm. The volume of the suspension was gradually upscaled to 1L flasks containing 400mL of suspension and then maintained by subculturing every 14 days, by doubling the volume of the suspension adding fresh liquid medium and dividing it between two new sterile flasks.

extract_protocol:
The Spectrum Plant Total RNA kit (Sigma-Aldrich, SKU: STRN250-1KT) was used to extract total RNA for Illumina sequencing. For PacBio sequencing, a 4 sample pool of different elicited samples was created. DNAse-treated RNA was monitored for its integrity using an Agilent Technologies 2100 Bioanalyzer defining high quality RNA if the RNA Integrity Number (RIN) value was greater than or equal to 7.
For PacBio sequencing, cDNA synthesis was performed using Takara SMARTer PCR cDNA Synthesis Kit for ISOseq. Molecules under 4Kb were captured for library preparation. For Illumina sequencing, the TruSeq Stranded mRNA Library Construction kit was used to generate libraries.

treatment_protocol: Elicitation treatments with MBCD and MeJA were carried out in quadruplicate as previously described for grapevine cells (Lijavetzky et al., 2008), with slight modifications. Fresh cells were prepared in an aseptic environment by filtration of a 14-day old M. alba cell suspension through a sterile glass filter (90-150 μm pore size) followed by washing with sterile water under gentle vacuum.  A weighted amount of cells was transferred into shaking flasks and suspended in fresh growth medium (4 g/g of cell FW) supplemented with elicitors  (50 mM MBCD, 100 μM MeJA or 50 mM MBCD + 100 μM MeJA) and was maintained at 25ºC in a continuous rotary shaker (110 rpm) in the dark for up to 120 hours. MBCD was added to the medium before autoclave. MeJA prepared as a stock solution of 47.5mM in ethanol was filter-sterilized through a 0,2 μm PTFE filter before adding to the sterile medium. Each replicate consisted in 8 g of cells and 32 g of elicitor-supplemented MS6 liquid medium in 100 ml flasks. Controls and MBCD treatment received the same volume of ethanol than MeJA and MBCD+MeJA treatments (2.1 uL/mL cell suspension). Each flask was stored in darkness.

value: Cell suspensions

value: Stem

value: Elicited with MeJA and MBCD

tag: time after_elicitation

value: 72 hours


title: 4145177

description: FL-DLBCL, cryo-preserved


title: Cell culture, elicited, 72h, rep3


title: Cell culture, elicited, pool of samples

description: MorusElicited

value: Different timepoints pool


title: Sample_Input_H2

source_name: Donor A IL-15 NK cells

value: CBNK

value: nk


title: Cell culture, elicited, 72h, rep2


title: Cell culture, control, 72h, rep2

value: Control


title: Cell culture, elicited, 72h, rep1


title: Sample_Input_H1

source_name: Donor A NT NK cells


title: 4136702

description: FL-DLBCL, cryo-preserved


title: Cell culture, control, 72h, rep1


title: Sample_CREM_H12


title: 4177376

description: FL-DLBCL, cryo-preserved


title: Cell culture, elicited, 48h, rep4

value: 48 hours


title: Cell culture, elicited, 48h, rep3


title: Sample_CREM_H10


title: Cell culture, elicited, 48h, rep2


title: Cell culture, elicited, 48h, rep1


title: Sample_CREM_H9


title: Sample_Input_H4

source_name: Donor A CAR70 NK cells


title: 4131213

description: FL-DLBCL, cryo-preserved


title: Cell culture, control, 48h, rep2


title: 4184437

description: FL-DLBCL, cryo-preserved


title: Cell culture, control, 48h, rep1


title: Cell culture, elicited, 24h, rep4

value: 24 hours


title: Sample_CREM_H7


title: 4131744

description: FL-DLBCL, cryo-preserved


title: Cell culture, elicited, 24h, rep2


title: Cell culture, elicited, 24h, rep1


title: Cell culture, elicited, 24h, rep3


title: 4144131

description: FL-DLBCL, cryo-preserved


title: Sample_CREM_H6


title: Cell culture, control, 24h, rep2


title: 4110120

description: FL-DLBCL, cryo-preserved


title: Cell culture, elicited, 12h, rep4

value: 12 hours


title: Sample_CREM_H5


title: 4144951

description: FL-DLBCL, cryo-preserved


title: Cell culture, control, 24h, rep1


title: Cell culture, elicited, 12h, rep3


title: Sample_CREM_H4


title: 4183924

description: FL-DLBCL, cryo-preserved


title: 4113971

description: FL-DLBCL, cryo-preserved


title: Cell culture, elicited, 12h, rep2


title: Cell culture, elicited, 12h, rep1


title: Cell culture, control, 12h, rep2


title: Sample_CREM_H2


title: 4186613

description: FL-DLBCL, cryo-preserved


title: Cell culture, control, 12h, rep1


title: Sample_CREM_H1


title: Cell culture, elicited, 6h, rep3

value: 6 hours


title: Sample_CREM_H8


title: Cell culture, elicited, 6h, rep2


title: 4120468

description: FL, cryo-preserved

value: FL, cryo-preserved


title: HG00731, CTCF, FA-HiChIP , Rep_2

city: Warsaw

first: Dariusz

last: Plewczynski

state: mazovia

address: Banacha 2c

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description:
HG00731_HiChIP_CTCF.hic
HG00731_HiChIP_CTCF.bw
HG00731_HiChIP_CTCF.narrowpeak
HG00731_HiChIP_CTCF.bedpe

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Both HiChIP and ChIP-seq datasets were processed using the nf-HiChIP pipeline
HiChIP and ChIP-seq reads were aligned to the UCSC hg38 genome using Burrows-Wheeler Alignment Tool version v0.7.17
Peaks were called uing MACS3 v3.0.1 with the significance cut-off q-value <=0.01
bigWig files were generated using the deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig files include the normalized read count across the genome
Supplementary files format and content: narrowpeak files (BED 6+4 format) include peak signal
Supplementary files format and content: bedpe files include chromatin interactions (loops)
Library strategy: HiChIP

growth_protocol: HG00721 LCL was grown in RPMI 1640 (Biowest) with 15% foetal bovine albumin (Biowest) and 2mM L-glutamine (Gibco) at 37 ℃ in a humid environment containing 5% CO₂.

extract_protocol: To prepare sequencing libraries DNA fragments after tagmentation reaction were subjected  to an on-bead PCR amplification with a  total  of 12 PCR cycles using indexing primers (TruePrep Index Kit V2 for Illumina, Vazyme). Post-amplification libraries were size selected at 200-700 bp using KAPA Pure Beads from Roche. Libraries were validated using the Agilent High Sensivity DNA Kit.

value: Lymphoblastoid Cell Line

value: CTCF


title: Cell culture, control, 6h, rep2


title: Cell culture, elicited, 6h, rep1


title: HG00731, CTCF, FA-HiChIP , Rep_1


title: Cell culture, control, 6h, rep1


title: 4136095

description: FL, cryo-preserved


title: Cell culture, elicited, 0.5h, rep3

value: 0.5 hours


title: Cell culture, elicited, 0.5h, rep2


title: 4190929

description: FL, cryo-preserved


title: Cell culture, elicited, 0.5h, rep1


title: HG00731, SMC1, FA-EGS HiChIP , Rep_1

description:
HG00731_HiChIP_SMC1.hic
HG00731_HiChIP_SMC1.bw
HG00731_HiChIP_SMC1.narrowpeak
HG00731_HiChIP_SMC1.bedpe


title: 4188900

description: FL, cryo-preserved


title: Cell culture, control, 0.5h, rep1


title: 4150549

description: FL, cryo-preserved


title: 11_Sheep IgG IP (P23)

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

institute: University of Dundee

description: Sheep IgG size matched input seCLIP library

data_processing:
Libraries were sequenced using the Illumina NextSeq Mid Output (150 cycle flow cell) platform to yield 2x75bp reads. Only read 1 was processed further for analysis as read 2 does not contain additional information (consistent with single-end (se) CLIP protocol).
Barcodes were extracted using umi_tools in extract mode, then adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) trimmed from the extracted reads using cutadapt.
Reads were aligned to the mouse genome (mm10) with gencode vM12 basic annotation using STAR version 2.5.2b, then demultiplexed using umi_tools in dedup mode to remove PCR duplicates.
Bedgraph files were generated using deeptools, options -bs 10 --Offset 1 1  -of bedgraph
Assembly: mm10
Supplementary files format and content: Bedgraph files have the counts of reads starting within the 10bp windows, read start sites should be 1 nt downstream of crosslinked nucleotides.

source_name: Brain cortex

growth_protocol: Sox1-GFP mouse ES cells were cultured on gelatin coated dishes in the presence of LIF. 5x10cm dishes of cells at 80% confluency were used per sample.

extract_protocol:
Lysis steps for seCLIP were performed as described previously (Van Nostrand et al, 2017). Samples were digested with optimised high (1:20) and low (1:200) concentrations of RNase1 as indicated.
Lysates were precleared with protein G dynabeads (Thermo Fisher Scientific) at 4°C for 1hour, prior to immunoprecipitation with 50µl of protein G dynabeads preincubated with 5 µg of either RNMT, or isotype control antibody overnight at 4°C. 10% of each sample was subsequently removed to serve as the size-matched input control. IP samples were were washed three times for 5 minutes with high salt wash buffer supplemented with 2M urea. Downstream library preparation was performed as described previously (Van Nostrand et al, 2017). Libraries underwent sequencing using the Illumina MiSeq v3 150 flow cell (2x75bp reads).

treatment_protocol: Cells were washed once with cold PBS and either crosslinked using 254nm UV light (400mJ/cm2) or non-crosslinked prior to snap freezing on dry ice.

value: Post natal day 23 (P23)

value: Sox1-GFP mouse ES cells

tag: uv treatment

value: Non-crosslinked

value: Brain cortex


title: 12_Sheep IgG size matched input (P23)

description: Sheep IgG IP seCLIP library

value: Sheep IgG (Fisher, 31243)


title: Wild-type CLL patient2

city: 江苏 / 南京市 / 鼓楼区

first: Jiazhu

last: Xu

address: 广州路300号

country: China

institute: the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital

description: XJB

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length<35 bp) and low quality reads using Cutadapt v1.18(non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.35 (non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35).
Then FastQC (with default parameters) was used to ensure high reads quality. The clean reads were mapped to the human genome (assembly GRCh38) using the HISAT2 v2.1.0 (non-default parameters: --rna-strandness RF --dta) software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PB

growth_protocol: Cell mass frozen at -80℃

extract_protocol:
Total RNA was extracted using TRIzol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination.
Isolation of mRNA was performed using the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: PB

value: CLL

value: Wild-type


title: 4100049

description: FL, cryo-preserved


title: Wild-type CLL patient3

city: 江苏 / 南京市 / 鼓楼区

description: XWX


title: 10_RNMT 2 IP (P23)

description: RNMT 2 IP seCLIP library

value: RNMT (anti-sheep, in house)

value: 254nm UV crosslinked (400mJ/cm2)


title: 4100636

description: FL-DLBCL, cryo-preserved

value: FL-DLBCL, cryo-preserved


title: 4128355

description: FL, cryo-preserved


title: 8_RNMT 1 IP (P23)

description: RNMT 1 IP seCLIP library


title: POT1 mutant CLL patient3

city: 江苏 / 南京市 / 鼓楼区

description: FXM

value: POT1 mutant


title: 7_RNMT 1 size matched input (P23)

description: RNMT 1 size matched input seCLIP library


title: 9_RNMT 2 size matched input (P23)

description: RNMT 2 size matched input seCLIP library


title: 6_Sheep IgG IP (P136)

description: Sheep IgG IP seCLIP library

value: Post natal day 136 (136)


title: HG00731, SMC1, FA-EGS HiChIP ,Rep_2


title: 4177175

description: FL, cryo-preserved

value: FL, cryo-preserved


title: POT1 mutant CLL patient2

city: 江苏 / 南京市 / 鼓楼区

description: GBL


title: hlh-30(tm1978) daf-1(m40),12 hours refeeding after 48 hours ARD, replicat 4

city: Köln

first: Adam

last: Antebi

address: Joseph Stelzmann Strasse 9b

institute: Max Planck Institute for Biology of Aging

description: Library name: daf1_hlh-30_REC_REP4

data_processing:
Reads were quality trimmed with Flexbar version 2.5, then mapped to the reference genome (WBcel235.80) using hisat2 version 2.0.4. Respective assemblies were merged with cuffmerge, version 2.2.1, differential gene expression analysis was performed with Cuffquant version 2.2.1 and Cuffdiff version 2.2.1.
Assembly: Reference genome: Caenorhabditis elegans (WBcel235.80); Genome source: Ensembl;Alignment tool: HISAT2 (version 2.0.4)
Supplementary files format and content: tab-delimited text file includes DESEQ2 normaliyed counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Nematodes were cultured using standard techniques at 20 °C on nematode growth medium agar plates with the Escherichia coli strain OP50, unless otherwise noted.

extract_protocol:
For RNA sequencing, total RNA was prepared from at least 3000 worms per genotype, using the RNeasy Mini Kit (QIAGEN)
polyA+ mRNA was isolated using NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs), RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2500 at the Max Planck Genome Center (Cologne, Germany).

treatment_protocol:
ARD condition: Eggs, enriched by standard hypochlorite treatment, were grown to the mid-L3 larval stage, assessed by DIC microscopy for outgrowth of the gonad arms. Larvae were collected in M9 buffer and washed four times with M9 buffer. Animals were left to settle for 20 minutes after every wash to allow for expulsion of bacteria from the gut. Afterwards, ca. 600 worms were pipetted onto 3 cm plates containing 4 ml Nematode Growth Medium (NGM) with UltraPureTM agarose (Thermo Fisher Scientific) and 50 μg/ml ampicillin. Worms were collected 48 hours post ARD induction.
ARD refeeding condition: ARD worms were transferred to NGM plate seeded with E. coli OP50. Worms were collected 12 hours post refeeding.

value: whole worm

value: 12 hours refeeding after 48 hours ARD

tag: batch


title: POT1 mutant CLL patient1

city: 江苏 / 南京市 / 鼓楼区

description: HB


title: 5_Sheep IgG size matched input (P136)


title: 4175837

description: FL, cryo-preserved


title: 4_RNMT 2 IP (P136)

description: RNMT 2 IP seCLIP library


title: 3_RNMT 2 size matched input (P136)


title: hlh-30(tm1978) daf-1(m40), 12 hours refeeding after 48 hours ARD, replicat 2

description: Library name: daf1_hlh-30_REC_REP2


title: Tumor, UPN-625, Post-treatment, Tumor_Cells_CD45_negative, F05918-GEX_F05922-CAR

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

data_processing:
Reads with a read quality <3 were filtered and CellRanger Count v5.0.0 (10x Genomics) was used to align reads to a modified GRCh38 reference genome. V(D)J libraries were processed similarly, but with CellRanger VDJ v5.0.0 (10x Genomics).
Assembly: Modified GRCh38 Ensembl 98 with CAR construct added
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: CSV containing filtered contig annotations

source_name: Tumor

extract_protocol:
GentleMAC dissociation using Miltenyi Tumor Dissociation Kit human (Order no. 130-095-929). CD45 negative cells were separated using Miltenyi CD45 (TIL) MicroBeads human (Order no. 130-118-780). RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
scRNA-seq libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.  CAR library construction was performed using 2ng GEX cDNA and 3 nested CAR T primers.

value: Tumor

tag: gender

value: Male

tag: ethnicity

value: White

tag: diagnosis

value: Metastatic ependymoma


title: 4121974

description: FL, cryo-preserved

tag: tissue


title: Cell culture, control, 0.5h, rep2

value: Cell suspensions

value: Stem

value: Control

value: 0.5 hours


title: 4121361

description: FL, cryo-preserved


title: hlh-30(tm1978) daf-1(m40),12 hours refeeding after 48 hours ARD, replicat 3

description: Library name: daf1_hlh-30_REC_REP3

tag: genotype


title: hlh-30(tm1978) daf-1(m40),48 hours ARD, replicat 4

description: Library name: daf1_hlh-30_48_REP4

tag: treatment


title: hlh-30(tm1978) daf-1(m40), 12 hours refeeding after 48 hours ARD, replicat 1

description: Library name: daf1_hlh-30_REC_REP1


title: CAR Product, UPN-626, Product, F05565-GEX_F05629-TCR

data_processing:
Reads with a read quality <3 were filtered and CellRanger Count v5.0.0 (10x Genomics) was used to align reads to a modified GRCh38 reference genome. V(D)J libraries were processed similarly, but with CellRanger VDJ v5.0.0 (10x Genomics).
Assembly: Modified GRCh38 Ensembl 98 with CAR construct added
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes
Supplementary files format and content: CSV containing filtered contig annotations
Library strategy: TCR-seq

source_name: CAR Product

extract_protocol:
RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
TCR libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.

value: CAR Product

tag: age

value: Latino

value: DMG


title: 1_RNMT 1 size matched input (P136)

value: Sox1-GFP mouse ES cells

value: 254nm UV crosslinked (400mJ/cm2)

value: Brain cortex


title: 2_RNMT 1 IP (P136)

description: RNMT 1 IP seCLIP library

value: RNMT (anti-sheep, in house)

value: Post natal day 136 (136)


title: Wild-type CLL patient1

city: 江苏 / 南京市 / 鼓楼区

description: LXY

value: PB

value: CLL

value: Wild-type


title: Tumor, UPN-625, Post-treatment, Tumor_Cells_CD45_positive, F05917-GEX_F05921-CAR

extract_protocol:
GentleMAC dissociation using Miltenyi Tumor Dissociation Kit human (Order no. 130-095-929). CD45 positive cells were separated using Miltenyi CD45 (TIL) MicroBeads human (Order no. 130-118-780). RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
scRNA-seq libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.  CAR library construction was performed using 2ng GEX cDNA and 3 nested CAR T primers.

value: Tumor

value: Male

value: White


title: 4119702

description: FL, cryo-preserved

value: FL, cryo-preserved


title: 4113825

description: FL, cryo-preserved


title: hlh-30(tm1978) daf-1(m40),48 hours ARD, replicat 3

description: Library name: daf1_hlh-30_48_REP3

value: whole worm

value: 12 hours refeeding after 48 hours ARD


title: 4124795

description: FL, cryo-preserved


title: CAR Product, UPN-626, Product, F05565-GEX_F05607-CAR

extract_protocol:
RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
scRNA-seq libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.  CAR library construction was performed using 2ng GEX cDNA and 3 nested CAR T primers.

value: CAR Product


title: OA_T0_2

city: New Haven

first: Matthew

last: Rodeheffer

state: Connecticut

address: 316 Cedar St.

department: Comparative Medicine

institute: Yale University

data_processing:
During a run, the system's Real Time Analysis software converted signal intensities to individual base calls. Sample demultiplexing and alignment were performed with Illumina's CASAVA 1.8.2 software suite.
Reads were aligned to reference genome mm9 using TopHat.
Gene expression was quantified using Python module HTSeq with default parameters.
Genes with fewer than 20 reads in all samples were filtered out.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file with normalized counts (DESeq2 median ratio) for each sample

source_name: fibroblast

growth_protocol: Cells were maintained in DMEM with 10% FBS and 1% penicillin/streptomycin. Cells were grown in an incubator under humid conditions  with 5% CO2 at 37C.

extract_protocol:
Cells were lysed with Trizol. Zymo Research Direct-zol RNA Miniprep Kit was used to harvest RNA.
mRNA was isolated from ~250ng of total RNA using oligo-dT beads and sheared by incubation at 94C with Mg (Kapa mRNA Hyper Prep). First-strand synthesis was performed with random primers, then strand-specific sequencing libraries were made using second strand synthesis and A-tailing with dUTP. Fragments with appropriate adaptor sequences at either end were amplified, while strands marked with dUTP were not. Indexed libraries are quantified by qRT-PCR (KAPA Biosystems). Samples with at least ≥0.5ng/uL were sequenced.

treatment_protocol: Prior to treatment, cells were grown to confluence, and media was not changed for 2 days. All samples were then treated with 0.1 ug/mL insulin (Millipore Sigma), 30ug/mL 3-isobutyl-1-methylxantine (Millipore Sigma), and 0.1 ug/mL dexamethasone (Millipore Sigma) for 24h. MDI samples were treated with BSA vehicle, OA samples were treated with 100 uM oleic acid (Sigma) conjugated to BSA, and T0 samples received the OA treatment plus 5 uM T0901317 (Cayman).

value: fibroblast

value: Adipocyte precursor stem cell line

value: WT

value: Adipogenic cocktail plus oleic acid plus T0901317


title: hlh-30(tm1978) daf-1(m40), 48 hours ARD, replicat 2

description: Library name: daf1_hlh-30_48_REP2


title: Tumor, UPN-625, Pre-treatment, Tumor_Cells_myelin_depleted, F05570-GEX_F05630-TCR

extract_protocol:
GentleMAC dissociation using Miltenyi Tumor Dissociation Kit human (Order no. 130-095-929). Myelin depletion was performed with Miltenyi Myelin Removal Beads II human, mouse, rat (Order no. 130-096-731). RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
TCR libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.

value: Metastatic ependymoma


title: OA_T0_1


title: hlh-30(tm1978) daf-1(m40), 48 hours ARD, replicat 1

description: Library name: daf1_hlh-30_48_REP1


title: 4199996

description: FL, cryo-preserved


title: Tumor, UPN-625, Pre-treatment, Tumor_Cells_myelin_depleted, F05570-GEX_F05608-CAR

extract_protocol:
GentleMAC dissociation using Miltenyi Tumor Dissociation Kit human (Order no. 130-095-929). Myelin depletion was performed with Miltenyi Myelin Removal Beads II human, mouse, rat (Order no. 130-096-731). RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
scRNA-seq libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.  CAR library construction was performed using 2ng GEX cDNA and 3 nested CAR T primers.


title: OA_3

value: Adipogenic cocktail plus oleic acid


title: Mixed, F05554-GEX_F05626-TCR

source_name: Mixed

value: Mixed


title: 4145391

description: FL, cryo-preserved


title: daf-1(m40), 12 hours refeeding after 48 hours ARD, replicat 3

description: Library name: daf1_REC_REP3


title: 4138059

description: FL, cryo-preserved


title: Mixed, F05554-GEX_F05583-FB

extract_protocol:
RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
Feature barcode libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.  CAR library construction was performed using 2ng GEX cDNA and 3 nested CAR T primers.


title: OA_2


title: 4177406

description: FL, cryo-preserved


title: Tumor, UPN-574, Post-treatment, Tumor_Cells_CD45_positive, F05560-GEX_F05627-TCR

extract_protocol:
GentleMAC dissociation using Miltenyi Tumor Dissociation Kit human (Order no. 130-095-929). CD45 positive cells were separated using Miltenyi CD45 (TIL) MicroBeads human (Order no. 130-118-780). RNA was extracted via single cell GEM reactions using 10x Chromium next GEM single cell 5' reagent kit v2 (dual index) protocol according to manufacturer recommendations (CG000330revA). CAR construct specific primers were spiked in during GEM generation.
TCR libraries were generated using the 10x Chromium platform 5′ v2 library preparation kits (10x Genomics) according to the manufacturer's recommendations and targeting 5,000 to 10,000 cells per sample.

value: Female

value: Ependymoma, anaplastic


title: daf-1(m40), 12 hours refeeding after 48 hours ARD, replicat 2

description: Library name: daf1_REC_REP2


title: daf-1(m40), 12 hours refeeding after 48 hours ARD. replicat 1

description: Library name: daf1_REC_REP1


title: Tumor, UPN-574, Post-treatment, Tumor_Cells_CD45_positive, F05560-GEX_F05580-CAR


title: MDI_2

value: Adipogenic cocktail


title: OA_T0_3


title: MDI_3


title: daf-1(m40), 48 hours ARD, replicat 4

description: Library name: daf1_48_REP4


title: 4109142

description: FL, cryo-preserved


title: daf-1(m40), 48 hours ARD, replicat 3

description: Library name: daf1_48_REP3

value: 13 hours refeeding after 48 hours ARD


title: Mixed, F05555-GEX_F05625-TCR


title: MDI_1


title: Tumor, UPN-574, Post-treatment, Tumor_Cells_CD45_negative, F05561-GEX_F05581-CAR

value: Tumor


title: Mixed, F05555-GEX_F05578-FB


title: daf-1(m40), 12 hours refeeding after 48 hours ARD, replicat 4

description: Library name: daf1_REC_REP4


title: MOLM13 AML cell line, R248Q/+, Daunorubicin

city: Zurich

first: Steffen

last: Böttcher

address: Rämistrasse 100

department: Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich, University Hospital Zurich

description: Library name: MOLM13 R248Q/+ Daunorubicin

data_processing:
Fastq files were aligned to hg19 BWA Duplicate reads marked and removed with picard MarkDuplicates ChIP-seq peaks called and annotated using HOMER Peaks filtered to those that had at least 30 normalized tag counts, those found in or 1kb upstream of the Transcriptional Start Site or found in intron 1 or exon 1 of the target gene
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: bedGraph generated by HOMER, where scores represent normalized tag counts

source_name: peripheral blood

growth_protocol: MOLM13 cell lines were were cultured in RPMI, 100 U/ml penicillin and 100 mg/ml streptomycin with 10 or 20% FBS, respectively,

extract_protocol:
20x10e6 cells were crosslinked using 1% methanol-free formaldehyde (ThermoFisher, #28906) in PBS for 7 min at room temperature. Remaining formaldehyde was quenched with 100 mM Tris-HCl pH8.0 and 25 mM Glycine. Cytoplasm was stripped using 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1% SDS for 10 min at room temperature followed by precipitation of nuclei by centrifugation at 10,000g. The nuclei were then resuspended in 66 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1.7% Triton X-100, 0.5% SDS and sheared using an E220 sonicator (Covaris). Chromatin fragmentation was quality-controlled using ScreenTape D5000 (Agilent). Immunoprecipitation with anti-p53 antibodies (DO-1, abcam, #1101) and Protein G Dynabeads™ (ThermoFisher, #10003D) was performed overnight at 4 degree Celsius. Beads were washed and immunoprecipitated DNA was reverse-сrosslinked in 100 mM NaHCO3, 100 mM NaCl, 1% SDS, and quantified by ScreenTape HS D1000 (Agilent) and Qubit (ThermoFisher).
Illumina-compatible sequencing libraries were prepared using SMARTer® ThruPLEX® DNA-Seq Kit (Takara, #R400675) and sequenced using a NextSeq Sequencing System (Illumina) to obtain paired-end reads.

treatment_protocol: MOLM13 were treated with 100 nM daunorubicin for 6 hours. Control MOLM13 cells were treated with DMSO.

value: peripheral blood

value: acute myeloid leukemia

value: Daunorubicin


title: MOLM13 AML cell line, R248Q/+, DMSO

description: Library name: MOLM13 R248Q/+ DMSO

value: DMSO


title: Mixed, F04860-GEX_F05041-TCR


title: 4118156

description: FL, cryo-preserved

value: FL, cryo-preserved


title: OA_1

value: fibroblast


title: hlh-30(tm1978), 12 hours refeeding after 48 hours ARD, replicat 4

description: Library name: hlh-30_REC_REP4

value: whole worm

value: 49 hour ARD


title: 4174905

description: FL, cryo-preserved


title: Mixed, F04860-GEX_F04861-FB


title: MOLM13 AML cell line, het (+/-), Daunorubicin

description: Library name: MOLM13 het (+/-) Daunorubicin


title: 4181037

description: FL, cryo-preserved


title: hlh-30(tm1978), 12 hours refeeding after 48 hours ARD, replicat 3

description: Library name: hlh-30_REC_REP3

value: 48 hour ARD


title: MOLM13 AML cell line, het (+/-), DMSO

description: Library name: MOLM13 het (+/-) DMSO


title: HeLa, input

data_processing:
Quality control for raw FASTQ files was conducted using FastQC (version 0.12.1) to assess the quality of the sequencing reads. Raw sequencing files from different runs were merged. Sequencing adapters were trimmed using Trimmomatic (version 0.39).
Trimmed reads were aligned to the human reference genome (GRCh38) using Bowtie2 (version 2.4.2) (bowtie2 -x index_file -U input.trim.fastq.gz -S file.sam). Aligned SAM files were converted to BAM format and sorted using SAMtools (version 1.3.1).
Peaks were called using MACS2 (version 2.2.7.1) (macs2 callpeak -t file.bam -c input.bam -f BAM -B --SPMR -g hs -n sample_hg38 --outdir sample_hg38).
Processed BAM files were converted to BigWig format for visualization using bamCoverage from the deepTools suite (version 3.5.0) (bamCoverage --bam input.bam -o output.bw --normalizeUsing RPKM --effectiveGenomeSize 2747877777 --centerReads --ignoreDuplicates --minMappingQuality 20).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: HeLa

extract_protocol:
Chromatin immunoprecipitation was performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010055) according to the manufacturer’s instructions. Briefly, 2.5 million HeLa cells per IP were crosslinked with 1% formaldehyde (Thermo Scientific™, 28908) in DMEM for 10 min at room temperature. Chromatin from lysed nuclei was sheared to 200–300 bp fragments using Bioruptor® Pico sonication device (Diagenode, B01060010) and cleared by centrifugation. Sheared chromatin was incubated overnight at 4°C with 3 µg of antibody coupled to the DiaMag protein A-coated magnetic beads (from Diagenode kit). Beads and immunocomplexes were then washed and eluted per the manufacturer’s instructions. For PNUTS ChIP-seq, an additional crosslink with the ChIP cross-link Gold reagent (Diagenode, C01019027) was performed before formaldehyde crosslinking.
Sequencing libraries from immunoprecipitated DNA were prepared using the MicroPlex kit v2 (Diagenode) according to the manufacturer’s protocol. In brief, immunoprecipitated DNA was quantified using Qubit fluorometer (Thermofisher), and 1.5 to 35 ng (for SPT6, IWS1 and RNAPII ChIP) or 2 to 10 ng (for PNUTS ChIP) were used as input material. DNA was repaired and end-blunted by enzymatic treatment. Stem-loop adaptors with blocked 5’ ends were ligated to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes were added through amplification. Libraries were purified using AMPure XP beads protocol (Beckman Coulter, Indianapolis, IN) and quantified using Qubit fluorometer. Libraries’ fragment size distribution was verified using the Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA). Libraries were pooled and spike-in PhiX Control v3 (Illumina, San Diego, CA) was added to represent 1% of the total PF reads.

treatment_protocol: For transfected HeLa cells, siRNA (siCT or siPNUTS) was transfected at a final concentration of 30nM using LipofectamineTM RNAiMAX Transfection Reagent (Invitrogen, 13778150) and Opti-MEM™ (Gibco, 31985070) according to the manufacturer’s instructions. Cells were harvested after 72 hours and ChIP experiments were carried out in 2 biological replicates

value: HeLa

value: epithelial cells (human cervical cancer)

tag: chip antibody


title: Mixed, F04855-GEX_F04856-FB

value: Mixed


title: hlh-30(tm1978), 12 hours refeeding after 48 hours ARD, replicat 2

description: Library name: hlh-30_REC_REP2


title: 4124542

description: FL, cryo-preserved

source_name: lymph node

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions


title: 4139212

description: FL, cryo-preserved


title: 4110378

description: FL, cryo-preserved


title: Mixed, F04855-GEX_F05037-TCR


title: hlh-30(tm1978), 12 hours refeeding after 48 hours ARD, replicat 1

description: Library name: hlh-30_REC_REP1


title: 4101815

description: FL, cryo-preserved


title: HeLa, RNAPII, siPNUTS, ChIP, rep2

value: Santa Cruz Biotechnology, sc-55492

value: siPNUTS


title: HeLa, RNAPII, siPNUTS, ChIP, rep1


title: daf-1(m40), 48 hours ARD, replicat 2

description: Library name: daf1_48_REP2

value: 12 hours refeeding after 48 hours ARD


title: 4177987

description: FL, cryo-preserved


title: CSF, UPN-574, Cycle 8 Day 1, F04868-GEX_F05048-TCR

source_name: CSF

value: CSF

value: Female

value: White

value: Ependymoma, anaplastic


title: CSF, UPN-574, Cycle 8 Day 1, F04868-GEX_F04900-CAR


title: daf-1(m40), 48 hours ARD, replicat 1

description: Library name: daf1_48_REP1


title: hlh-30(tm1978), 48 hours ARD, replicat 4

description: Library name: hlh-30_48_REP4


title: 4198542

description: FL, cryo-preserved


title: HeLa, RNAPII, siCT, ChIP, rep2

value: siCT


title: CSF, UPN-514, Cycle 11 Day 1, F04867-GEX_F05046-TCR

value: Male

value: Recurrent metastatic ependymoma


title: 4101626

description: FL, cryo-preserved

value: FL, cryo-preserved


title: 4108992

description: FL, cryo-preserved


title: hlh-30(tm1978), 48 hours ARD, replicat 2

description: Library name: hlh-30_48_REP2

value: whole worm


title: hlh-30(tm1978), 48 hours ARD, replicat 3

description: Library name: hlh-30_48_REP3


title: CSF, UPN-514, Cycle 11 Day 1, F04867-GEX_F04898-CAR


title: HeLa, PNUTS, ChIP, rep2

value: Cell Signaling Technology, 14171


title: 4171706

description: FL, cryo-preserved


title: HeLa, PNUTS, ChIP, rep1


title: hlh-30(tm1978), 48 hours ARD, replicat 1

description: Library name: hlh-30_48_REP1

value: 48 hour ARD


title: 4151028

description: FL, cryo-preserved


title: 4145056

description: FL, cryo-preserved


title: HeLa, IWS1, ChIP, rep2

value: HeLa

value: Proteintech Group, 16943-1-AP


title: CSF, UPN-514, Cycle 5 Day 1, F04865-GEX_F05045-TCR


title: CSF, UPN-515, Cycle 4 Day 2, F04866-GEX_F04899-CAR

value: DIPG


title: CSF, UPN-515, Cycle 4 Day 2, F04866-GEX_F05047-TCR


title: N2, 12 hours refeeding after 48 hours ARD, replicat 3

description: Library name: N2_REC_REP3

value: N2 wild type


title: 4134005

description: FL, cryo-preserved


title: N2, 12 hours refeeding after 48 hours ARD, replicat 4

description: Library name: N2_REC_REP4


title: 4126692

description: FL, cryo-preserved


title: CSF, UPN-514, Cycle 5 Day 1, F04865-GEX_F04884-CAR


title: HeLa, IWS1, ChIP, rep1

value: epithelial cells (human cervical cancer)


title: N2, 12 hours refeeding after 48 hours ARD, replicat 2

description: Library name: N2_REC_REP2


title: HeLa, SPT6, ChIP, rep2

value: Abcam, ab32820


title: N2, 12 hours refeeding after 48 hours ARD, replicat 1

description: Library name: N2_REC_REP1


title: 4165379

description: FL, cryo-preserved


title: CSF, UPN-574, Cycle 3, Day 1, F04864-GEX_F05044-TCR

value: CSF


title: HeLa, RNAPII, siCT, ChIP, rep1

value: Santa Cruz Biotechnology, sc-55492


title: HeLa, SPT6, ChIP, rep1


title: 4148771

description: FL, cryo-preserved


title: CSF, UPN-574, Cycle 3, Day 1, F04864-GEX_F04908-CAR

value: Female

value: White


title: 4139483

description: FL, cryo-preserved


title: N2, 48 hours ARD, replicat 4

description: Library name: N2_48_REP4


title: CSF, UPN-515, Cycle 8 Day 1, F04863-GEX_F05043-TCR


title: immune, patient2

description: 10X Genomics Chromium Single Cell 3’ library

data_processing:
The demultiplexing, barcoded processing and gene counting were made using Cell Ranger software v3.0.2
Integration and further processing was done with Seurat v3.1.4
Cells were annotated by SingleR v1.0.6
Assembly: hg38
Supplementary files format and content: Tab-separated values and matrix files
Supplementary files format and content: Tab-separated UMAP coordinates, sample origin and annotation

source_name: bone marrow

extract_protocol:
Cell supsensions were resuspended in PBS and subjected to droplet generation via the 10X controler
Gene expression libraries were generated using the 10X Chromium Single Cell 3' Reagent Kit v3, with 3,500 cells per sample
scRNA-seq followed by Illumina short-read sequencing

value: bone marrow


title: N2, 48 hours ARD, replicat 3

description: Library name: N2_48_REP3


title: immune, patient1


title: N2, 48 hours ARD, replicat 2

description: Library name: N2_48_REP2


title: 4124432

description: FL, cryo-preserved


title: immune, healthy


title: CSF, UPN-515, Cycle 8 Day 1, F04863-GEX_F04907-CAR


title: N2, 48 hours ARD, replicat 1

description: Library name: N2_48_REP1


title: 4121263

description: FL, cryo-preserved


title: CSF, UPN-514, Cycle 8 Day 1, F04862-GEX_F05042-TCR

value: Male


title: sorted CD8+ PD-1+ CD44+ cells; control Right_tumor5

city: atlanta

first: zach

last: Buchwald

state: ga

address: 1365 Clifton Rd NE Building C

institute: Winship Cancer Institute of Emory University

description: Library name: Con-T-R5

data_processing:
ImmunoSeq raw data were processed using the standard ImmunoSeq pipeline from Adaptive Biotechnology
Assembly: mm10
Supplementary files format and content: tsv, aminoacid and nucleotide sequences of CDR3 regions, cdj alleles, counts
Library strategy: TCR-Seq

source_name: tumor

extract_protocol:
Genomic DNA (gDNA) was extracted from sorted CD8+ PD-1+ T cells using AllPrep DNA/RNA Micro Kit (QIAGEN) according to the manufacturer’s instructions
The isolated gDNA was sent to Adaptive Biotechnologies (Seattle, WA, USA) for TCR sequencing by immunoSEQ assays

value: tumor

value: Control


title: CSF, UPN-514, Cycle 8 Day 1, F04862-GEX_F04906-CAR

value: Recurrent metastatic ependymoma


title: 4142761

description: FL, cryo-preserved

value: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control Right_tumor4

description: Library name: Con-T-R4


title: CSF, UPN-574, Cycle 8 Day 1, F04859-GEX_F05040-TCR

value: Ependymoma, anaplastic


title: 4160468

description: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control Right_tumor3

description: Library name: CON-T-R3


title: Oligodendrocyte progenitors, Ehmt1/Ehmt2 cKO, rep4

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
Quality control, genome alignment and differential expression analysis were performed using Partek™ Flow™ v12.0.1 (Partek, an Illumina company).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim adapters - CUTADAPT_4_2 and Trim bases.
Trimmed sequences were aligned using STAR - 2.7.8a to mm10.
Aligned reads were quantified and annotated with Ensembl Transcripts release 102 using Quantify to annotation model (Partek E/M).
A noise reduction filter was applied to exclude features where maximum < 10.
Differential expression analysis was performed using DESeq2 with median ratio normalization to compare iCre vs RFP control using model ~ Batch + iCre
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw gene counts annotated with Ensembl

source_name: oligodendrocyte progenitors

growth_protocol: Oligodendrocyte progenitors were isolated by immunopanning from P7 Ehmt1fl/fl;Ehmt2fl/fl mouse pups (males and females) and cultured in SATO medium supplemented with growth factors PDGF-AA (10 ng/mL) and bFGF (20 ng/mL)

extract_protocol:
RNA was extracted from cells using TRIzol (Invitrogen) and RNeasy mini kit (Qiagen, 74106). Briefly, precipitated RNA samples were further purified using the RNeasy Mini Kit with on-column DNase treatment according to the manufacturer’s instruction. Quality of the RNA was assessed by Tapestation 4200 (Agilent Technologies). Only RNA with RIN>=8 was used for subsequent library construction.
mRNA-seq libraries were prepared using KAPA mRNA Hyperprep kit (Roche). Briefly, mRNA was captured using oligo-dT beads, followed by random fragmentation. First strand cDNA was synthesized using mRNA template and random hexamer primers, after which second-strand cDNA was synthesized combined with A-tailing. After a series of terminal repair, ligation and sequencing adaptor ligation, the double stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: To knock out Ehmt1 and Ehmt2 in vitro, immunopanned oligodendrocyte progenitor cells from Ehmt1fl/fl;Ehmt2fl/fl mice were infected with Ad-RFP or Ad-RFP-iCre (Vector Biolabs 1660; 1774) at an infection multiplicity of 10 (MOI = 10) followed by incubation for 6 hours in a tissue culture incubator. Virus-containing medium was replaced after 6 hours. 72 hours post infection (72hpi), cells were collected for further analysis.

value: oligodendrocyte progenitors


title: CSF, UPN-574, Cycle 8 Day 1, F04859-GEX_F04904-CAR


title: sorted CD8+ PD-1+ CD44+ cells; control Right_tumor2

description: Library name: CON-T-R2


title: 4147360

description: FL, cryo-preserved


title: Oligodendrocyte progenitors, Ehmt1/Ehmt2 cKO, rep3


title: CSF, UPN-515, Cycle 4 Day 2, F04858-GEX_F05039-TCR


title: 4113191

description: FL, cryo-preserved


title: Oligodendrocyte progenitors, control, rep6


title: CSF, UPN-515, Cycle 4 Day 2, F04858-GEX_F04903-CAR


title: sorted CD8+ PD-1+ CD44+ cells; control Left_tumor5

description: Library name: Con-T-L5


title: Oligodendrocyte progenitors, control, rep4


title: CSF, UPN-514, Cycle 11 Day 1, F04857-GEX_F05038-TCR


title: 4184011

description: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control Left_tumor4

description: Library name: Con-T-L4


title: sorted CD8+ PD-1+ CD44+ cells; control Left_tumor3

description: Library name: CON-T-L3


title: CSF, UPN-514, Cycle 11 Day 1, F04857-GEX_F04902-CAR


title: Oligodendrocyte progenitors, Ehmt1/Ehmt2 cKO, rep6


title: 4148261

description: FL, cryo-preserved


title: HEK293T, APOBEC1, replicate 2

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

data_processing:
The raw fastq sequencing data were cleaned by trimming the adapter sequences using Fastp (v0.23.1) and were aligned to the human genome (hg19) using STAR (v2.7.7) in paired-end mode. The aligned BAM files were sorted and PCR duplicates were removed using Samtools (v1.12).
Assembly: hg19
Supplementary files format and content: The cite calling pf DRAM-seq was performed using Bullseye, a previously customized pipeline to look for C-to-U or A-to-G edited sites throughout the transcriptome.Briefly, the sorted and deduplicated BAM files were initially parsed by parseBAM.pl script. Then, Find_edit_site.pl script was employed to find C-to-U or A-to-G editing events by DRAM-seq with at least 10 reads of coverage, an edit ratio of 10%-60%, an edit ratio at least 2-fold higher than NSUN2 or NSUN6-knockout samples, and at least 4 editing events at a given site. Sites that were only found in one or two replicates of each DRAM protein variant were removed. Editing events appeared in cells expressing merely APOBEC1 or TadA8e were also removed.
Supplementary files format and content: The processed data are provided in 6-column BED files, which contain the chromosome location of the edited cites by DRAM-seq system.

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (TIANGEN Biotech).
1μl of total cellular RNA was used for sequencing library generation by NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Human embryonic kidney

value: WT


title: Oligodendrocyte progenitors, control, rep3

city: New York


title: Oligodendrocyte progenitors, control, rep1


title: sorted CD8+ PD-1+ CD44+ cells; control Left_tumor2

description: Library name: CON-T-L2


title: HEK293T, APOBEC1, replicate 1


title: sorted CD8+ PD-1+ CD44+ cells; control Left_tumor1

description: Library name: CON-T-L1


title: HEK293T, TadA, replicate 2


title: GF_2X_PBS [ATAC_2_TGGATCTG]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
Paired-end ATAC-Seq reads were first assessed using FASTQC. Reads were trimmed using cutadapt to remove adapters and low quality reads below 30. Pair-end reads were then aligned against the GRCm39/mm10 mouse genome assembly with Bowtie (v2.3.0)84 in local mode, sensitive settings, and a maximum fragment size of 2000. Duplicated reads were marked using Picard (v.2.5.0). Alignments were filtered with SAMtools (v1.3) to exclude reads with mapping quality <30, not properly paired, duplicated, aligned to mitochondrial genome, and/or aligned to ENCODE blacklist regions. Alignments with an insertion size of >100bp were removed to enrich for nucleosome-free reads. ATAC-Seq peaks were called for each replicate using MACS2, using --format BAMPE and --keep-dup all. IDR (v2.0.2) was used to determine consistency of peak detection between individual replicates and peaks with a threshold below 0.10 were merged between replicates for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: gzipped tagAlign file from Picard Suite that include the reads information.

growth_protocol: Adult male and female mice, and postnatal pups were used on a C57Bl/6J background (#000664, The Jackson Laboratory); NOD/ShiLtJ (#001976, The Jackson Laboratory) mice were obtained from the Jackson Laboratory. B6.Cg-Tg(Gfap-cre)73.12Mvs/J mice65 (The Jackson Laboratory, #012886) mice were crossed with B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J mice66 (The Jackson Laboratory, #007909) to generate Gfap(Cre/+);TdTomato(f/+) (TdTomatoGfap) mice. Postnatal pups were used from the NF-kB reporter strain FVB.Cg-Tg(HIV-EGFP,luc)8Tsb/J67 (The Jackson Laboratory, #027529) at P0-P3. Mice were kept in a pathogen-free facility at the Hale Building for Transformative Medicine at Brigham and Women’s Hospital in accordance with the IACUC guidelines. 10–12-week-old mice were used for stereotactic injection and EAE induction. Pups were sacrificed between P0-P3 for harvesting and culturing astrocytes. All procedures were reviewed and approved under the IACUC guidelines at Brigham and Women’s Hospital.

extract_protocol: After isolation of nuclei, transposition was performed using the kit (Illumina, #FC-121-1030). DNA was then amplified using NEBNext High Fidelity 2X PCR Master Mix (New England Biolabs, #M0541S) for 5 cycles. DNA quantity was then measured using a Viia 7 Real-Time PCR System (Thermo Fisher Scientific) and the number of cycles required to achieve 1/3 of maximal SYBR Green fluorescence was determined and libraries were amplified accordingly. TruSeq adaptors (universal: Ad1_noMX and barcoded: Ad2.1-Ad2.24) were used according to the Buenrostro protocol. Libraries were purified using MiniElute PCR Purification Kit (Qiagen, #28006) followed by double sided Agencourt AMPure XP bead purification (Beckman Coulter, #A63881) to remove primer dimers and large DNA fragments. Libraries were analyzed on a 2100 Bioanalyzer (Agilent Technologies) and High Sensitivity DNA Kit (Agilent Technologies, #5067-4626). Libraries were sequenced by Genewiz on an Illumina HiSeq 4000 by 2x75 bp paired end sequencing.

treatment_protocol: C57Bl/6J mice at age 10-12 weeks were anesthetized using 1-3% isoflurane mixed with oxygen. Heads were shaved and cleaned using 70% ethanol and Betadine (Thermo Fisher, #19-027132) followed by a medial incision of the skin to expose the skull. Mice were injected with 100 ng/mL IL-1β (R&D Systems, #401-ML-005, 100 µg/mL stock in PBS) and 50 ng/mL TNF-α (R&D Systems, #410-MT-010, 100 µg/mL stock in PBS) diluted in PBS or PBS. At day7, mice were re-injected (2X) or injected (1X) with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. For EAE experiments, mice were injected with 100 ng/mL IL-1β and 50 ng/mL TNF-α or PBS for 18-24 hours and astrocytes were sorted for further analysis. The lateral ventricles were targeted bilaterally using the coordinates: +/- 1.0 (lateral), -0.44 (posterior), -2.2 (ventral) relative to Bregma. Mice were injected by two 5µL injections using a 25 µL Hamilton syringe (Sigma-Aldrich, #20787) on a stereotaxic alignment system (Kopf, #1900) and the incision was sutured.

value: sorted astrocytes

tag: strain

tag: Sex

value: female

value: 10 weeks

value: Germ Free Mice that are injected with PBS 2 times


title: 4128970

description: FL, cryo-preserved


title: 4103141

description: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control LN5

description: Library name: Con-LN5

value: lymph node

tag: cell type


title: Oligodendrocyte progenitors, Ehmt1/Ehmt2 cKO, rep1


title: sorted CD8+ PD-1+ CD44+ cells; control Right_tumor1

description: Library name: CON-T-R1


title: GF_2X_PBS [ATAC_2_ACCACTGT]


title: 4108588

description: FL, cryo-preserved


title: HEK293T, TadA, replicate 1

tag: cell line


title: GF_2X_PBS [ATAC_2_GTCGTGAT]


title: 4123945

description: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control LN4

description: Library name: Con-LN4


title: HEK293T, NSUN6KO-DRAM-CBE, replicate 2

value: NSUN6 knockout


title: GF_2X_PBS [ATAC_2_GTAGAGGA]


title: 4105782

description: FL, cryo-preserved


title: sorted CD8+ PD-1+ CD44+ cells; control LN3

description: Library name: CON-LN3


title: 4171908

description: FL, cryo-preserved


title: HEK293T, NSUN6KO-DRAM-CBE, replicate 1


title: GF_2X_PBS [ATAC_2_AAGAGGCA]


title: sorted CD8+ PD-1+ CD44+ cells; control LN2

description: Library name: CON-LN2


title: 4170686

description: FL, cryo-preserved


title: 4133863

description: FL, cryo-preserved


title: GF_2X_Cytokine [ATAC_2_GTGTGGTG]

value: Germ Free Mice that are injected with TNFalpha stimulation 2 times


title: HEK293T, NSUN2KO-DRAM-CBE, replicate 3

value: NSUN2 knockout


title: sorted CD8+ PD-1+ CD44+ cells; control LN1

description: Library name: CON-LN1


title: 4131095

description: FL, cryo-preserved


title: GF_2X_Cytokine [ATAC_2_AGGTTGGG]


title: HEK293T, NSUN2KO-DRAM-CBE, replicate 1


title: PT84_Tumor

city: Baltimore

first: Roy

last: Elias

state: Maryland

address: 201 N Broadway

institute: Johns Hopkins University

description:
Library name: NS145
column name in "tpm.txt" is library name

data_processing:
FASTQ files were generated from the sequencer's output using Illumina bcl2fastq2 v.2.17.1.14 (RRID:SCR_015058) with default filters to select sequence reads for subsequent analyses. Trimgalore v0.6.7 (RRID:SCR_011847) was used to trim off the adaptor sequences and low-quality bases from the reads. The reads were aligned to the human reference genome (hg38) in a splice-aware fashion using RSEM v1.3.0 (RRID:SCR_000262) with STAR (RRID:SCR_004463) as the aligner. RSEM was also used for generating gene level expression estimates.
Assembly: hg38
Supplementary files format and content: txt files include tpm values for each sample

extract_protocol:
Tumor and normal adjacent tissue regions from nephrectomy specimens were identified on hematoxylin and eosin-stained slides by a genitourinary board-certified pathologist. These areas were macrodissected, and DNA/RNA were extracted from formalin-fixed, paraffin-embedded (FFPE) tissue sections using a DNA/RNA FFPE tissue kit (AllPrep DNA/RNA, Qiagen, Hilden, Germany).
Sequencing libraries were constructed using the Illumina TruSeq RNA exome kit (Illumina, Inc.)

value: Tumor

tag: path grade

tag: Stage

tag: race

value: W

value: Female

tag: sas

tag: amr

tag: eas

tag: eur

tag: afr

tag: ancestry bin

value: EUR


title: GF_2X_Cytokine [ATAC_2_GAGGGGTT]


title: 4138885

description: FL, cryo-preserved

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

tag: tissue

value: FL, cryo-preserved


title: HEK293T, DRAM-CBE, replicate 3

tag: genotype


title: 4108988

description: FL, cryo-preserved


title: PT83_Normal

description:
Library name: NS144
column name in "tpm.txt" is library name

source_name: Normal

value: Normal

tag: age


title: GF_2X_Cytokine [ATAC_2_TGCTGGGT]

tag: treatment


title: HEK293T, DRAM-CBE, replicate 2


title: 4158268

description: FL, cryo-preserved


title: 4128477

description: FL, cryo-preserved


title: GF_2X_Cytokine [ATAC_2_CCGTTTGT]

tag: strain


title: PT83_Tumor

description:
Library name: NS143
column name in "tpm.txt" is library name

tag: Sex


title: HEK293T, NSUN6KO-DRAM-ABE, replicate 2

tag: cell type


title: SPF_3X_PBS [ATAC_1_TCCTGAGC]

value: Normal Mice that are injected with PBS 3 times


title: SPF_3X_PBS [ATAC_1_GGACTCCT]


title: 4128435

description: FL, cryo-preserved


title: HEK293T, NSUN2KO-DRAM-CBE, replicate 2

tag: cell line

value: Human embryonic kidney


title: 4120879

description: FL, cryo-preserved


title: HEK293T, NSUN6KO-DRAM-ABE, replicate 1


title: PT80_Tumor

description:
Library name: NS138
column name in "tpm.txt" is library name

tag: path grade

value: Male


title: SPF_3X_PBS [ATAC_1_AGGCAGAA]

value: sorted astrocytes


title: HEK293T, NSUN2KO-DRAM-ABE, replicate 3


title: SPF_3X_PBS [ATAC_1_TAAGGCGA]

value: female


title: PT78_Normal

description:
Library name: NS135
column name in "tpm.txt" is library name

tag: Stage


title: 4177601

description: FL, cryo-preserved


title: PT81_Normal

description:
Library name: NS141
column name in "tpm.txt" is library name

tag: race


title: HEK293T, NSUN2KO-DRAM-ABE, replicate 1


title: SPF_3X_PBS [ATAC_1_CGTACTAG]

value: 10 weeks


title: PT79_Normal

description:
Library name: NS137
column name in "tpm.txt" is library name

tag: sas


title: HEK293T, DRAM-ABE, replicate 3

value: WT


title: HEK293T, NSUN2KO-DRAM-ABE, replicate 2


title: 4189200

description: FL, cryo-preserved


title: SPF_3X_Cytokine [ATAC_1_GCTACGCT]

value: Normal Mice that are injected with TNFalpha stimulation 3 times


title: PT79_Tumor

description:
Library name: NS136
column name in "tpm.txt" is library name

tag: amr


title: SPF_3X_Cytokine [ATAC_1_CGAGGCTG]


title: PT80_Normal

description:
Library name: NS139
column name in "tpm.txt" is library name

tag: eas


title: HEK293T, DRAM-ABE, replicate 2


title: PT76_Normal

description:
Library name: NS132
column name in "tpm.txt" is library name

tag: eur


title: 4162154

description: FL, cryo-preserved


title: SPF_3X_Cytokine [ATAC_1_CAGAGAGG]


title: 4119463

description: FL, cryo-preserved


title: SPF_3X_Cytokine [ATAC_1_CTCTCTAC]


title: PT81_Tumor

description:
Library name: NS140
column name in "tpm.txt" is library name

tag: afr


title: HEK293T, DRAM-ABE, replicate 1


title: PT76_Tumor

description:
Library name: NS131
column name in "tpm.txt" is library name

tag: ancestry bin


title: 4160069

description: FL, cryo-preserved

tag: tissue


title: 4103627

description: FL, cryo-preserved


title: HEK293T, DRAM-CBE, replicate 1

tag: genotype


title: 4178655

description: FL, cryo-preserved


title: PT78_Tumor

description:
Library name: NS134
column name in "tpm.txt" is library name

tag: age


title: SPF_3X_Cytokine [ATAC_1_TAGGCATG]

tag: treatment


title: PT75_Normal

description:
Library name: NS130
column name in "tpm.txt" is library name