title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_belt_deletion plasmid repeat 3

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
We removed the adapters from the raw reads, joined the pair-end reads and collected high-quality reads using cutadapt (Martin, 2011), fastq-join (Aronesty, 2013) and fastq_quality_filter. The remaining reads were mapped to the human genome (hg38) using Bowtie2 (Langmead, & Salzberg, 2012). The unambiguously mapped reads allowing a maximum of 2 mismatches at their 3p-ends were collected. Next, the miRNA annotation downloaded from miRBase v22 (Kozomara et al., 2019, miRbase.org) was used to label the unambiguous reads mapped to the miRNA loci. The raw counts were normalized by the geometric mean of the expression of hsa-miR-320a-3p and hsa-miR-320b, generated from two DROSHA-independent pri-miRNAs. The normalized counts were rescaled by multiplying with 10,000 to obtain the normalized counts higher than 1.
Assembly: hg38
Supplementary files format and content: rawcount.txt: Tab-delimited text file contains the raw read counts of miRNAs in all samples

source_name: DROSHA-KO HCT116 cell line

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
The small RNAs (19–24 nt) from 10 μg of each total RNA sample were size-selected in a 15% urea-PAGE. The purified small RNAs were cloned using the NEBNext® Small RNA Library Prep Set for Illumina® (NEB) to generate the small RNA libraries.

treatment_protocol: 4.5 μg of pXC-NLS-DG4 plasmid and 4.5 μg of pCK-DROSHA (WT or mutants) were transfected to DROSHA-KO cells.

value: DROSHA-KO

tag: transfection

value: pXC-NLS-DG4 + pCK-DROSHA_belt_deletion plasmid

tag: repeat

value: repeat 3


title: REB1_DMSO_60_B_S41_RNA-seq

status: Public on Aug 01 2023

type: SRA

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Center

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-REB1

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

tag: genotype

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-REB1


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_belt_deletion plasmid repeat 2

organism: Homo sapiens

tag: cell line

value: repeat 2


title: REB1_DMSO_60_C_S47_RNA-seq


title: proximal_colon_day_9_replicate_3

city: Gainesville

first: Jake

last: Boles

state: FL

address: LG-152, 1149 Newell Dr

department: Neuroscience

institute: University of Florida

description: colon_clean_VST_counts.csv column 86

data_processing:
Reads were filtered to remove adapters, reads with polyA or polyG, reads with more than 5% unknown nucleotides, and reads with more than 20% low-quality bases (Q-value < 20) with Cutadapt.
Reads were mapped to the GRCmm39 genome assembly using STAR (v. 2.7.9)
Reads were counted with Subread (v. 2.0.3) in paired-end mode
Quality control and normalization was performed in R with the WGCNA, DESeq2, and edgeR packages.
Assembly: GRCmm39
Supplementary files format and content: comma-separated file gives raw read counts for each sample
Supplementary files format and content: comma-separated file gives variance-stabilized counts of only high-quality genes and samples

organism: Mus musculus

extract_protocol:
RNA was extracted using the TRIzol-chloroform based method. Tissue was lysed in TRIzol (ThermoFisher 15596018), and lysate was mixed with phenol:choloroform:isoamyl alcohol (ThermoFisher 15593049) in a 5:1 ratio. Protein and nucleic acids were separated into phases via centrifugation. The top aqueous layer containing the RNA was passed through a QIAshredder column (Qiagen 79656). Eluent was mixed 1:1 with 70% ethanol and applied to an RNease Mini column (Qiagen 74104). After a brief centrifugation, columns were washed once with RW1 buffer and twice with RPE buffer, as per manufacturer's recommendations. RNA was eluted in nuclease-free water. 1µg of total RNA in a concentration of 20ng/µL was shipped to LC Sciences (Houston, TX) for library preparation and RNA sequencing.
Total RNA was enriched for mRNA, fragmented, and reverse transcribed into complementary DNA (cDNA). Second-stranded DNA was synthesized, A-bases were added to the blunt ends of either strand, and DNA was ligated to dual-index adapters. Size selection was performed and DNA was treated with a heat-labile UDG enzyme. Ligated products were amplified with PCR before sequencing.

treatment_protocol: Mice received 2.5% DSS in their drinking water for 7d followed by a recovery period of 14d, and tissue was harvested at the following time points: day 0, 5, 7, 9, 12, 14, 21. Mice were euthanized via rapid decapitation and tissues were flash-frozen in liquid nitrogen immediately upon removal.

tag: tissue

tag: day

tag: Sex

value: F

tag: strain


title: proximal_colon_day_9_replicate_2

description: colon_clean_VST_counts.csv column 85


title: W1118 flies, Day 2, cycloheximide, rep5 [D2Cx2]

city: Houston

first: Andrew

middle: M

last: Pickering

state: tx

address: 6431 Fannin St

institute: UTHealth Houston

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.18.0.12
Raw FASTQ sequence files were aligned to the reference genome using STAR version 2.7.10a_alpha_220601 with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using HTSeq-count version 0.12.3 with parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Ensembl Drosophila melanogaster BDGP6.32.Release107
Supplementary files format and content: tab delimited text file containing raw counts for each gene (Ensembl ID#) for each sample

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: flies were maintained in an 24C incubator on 10% sugar/yeast food

extract_protocol: RNA was extracted by RNAeasy qiagen extraction kit

treatment_protocol: 1uM cycloheximide was mixed directly into food

value: Whole fly

tag: treatment

value: Cycloheximide


title: REB1_DMSO_60_A_S35_RNA-seq


title: proximal_colon_day_9_replicate_6

description: colon_clean_VST_counts.csv column 84

value: M


title: W1118 flies, Day 2, cycloheximide, rep4 [D2Cx1]


title: proximal_colon_day_7_replicate_6

description: discarded during WGCNA network construction


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_m4 plasmid repeat 3

value: pXC-NLS-DG4 + pCK-DROSHA_m4 plasmid


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_belt_deletion plasmid repeat 1

value: repeat 1


title: REB1_DMSO_30_C_S46_RNA-seq


title: REB1_DMSO_30_B_S40_RNA-seq


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_m4 plasmid repeat 2


title: W1118 flies, Day 2, cycloheximide, rep3 [D2Cx-3]


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA_m4 plasmid repeat 1


title: W1118 flies, Day 2, cycloheximide, rep2 [D2Cx-2]


title: proximal_colon_day_0_replicate_12

description: colon_clean_VST_counts.csv column 82


title: W1118 flies, Day 2, cycloheximide, rep1 [D2Cx-1]


title: REB1_DMSO_10_C_S51_RNA-seq


title: REB1_DMSO_120_A_S36_RNA-seq


title: proximal_colon_day_0_replicate_10

description: colon_clean_VST_counts.csv column 81


title: W1118 flies, Day 0, rep6 [D03]

value: Control


title: REB1_DMSO_10_B_S50_RNA-seq


title: REB1_DMSO_30_A_S34_RNA-seq


title: W1118 flies, Day 0, rep5 [D02]


title: proximal_colon_day_0_replicate_9


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA wild type plasmid repeat 2

value: pXC-NLS-DG4 + pCK-DROSHA wild type plasmid


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA wild type plasmid repeat 3


title: proximal_colon_day_12_replicate_4

description: colon_clean_VST_counts.csv column 80


title: REB1_DMSO_10_A_S49_RNA-seq


title: W1118 flies, Day 0, rep4 [D01]


title: DROSHA-KO HCT116 cells transfected with pCK empty plasmid repeat 3

value: pXC-NLS-DG4 + pCK empty plasmid


title: DROSHA-KO HCT116 cells transfected with pCK-DROSHA wild type plasmid repeat 1


title: proximal_colon_day_9_replicate_5

description: colon_clean_VST_counts.csv column 79


title: REB1_3IAA_120_C_S51_RNA-seq


title: proximal_colon_day_0_replicate_13

description: colon_clean_VST_counts.csv column 83


title: DROSHA-KO HCT116 cells transfected with pCK empty plasmid repeat 1


title: DROSHA-KO HCT116 cells transfected with pCK empty plasmid repeat 2


title: W1118 flies, Day 0, rep2 [D0-2]


title: W1118 flies, Day 0, rep3 [D0-3]


title: proximal_colon_day_12_replicate_1

description: colon_clean_VST_counts.csv column 77


title: REB1_3IAA_120_A_S39_RNA-seq


title: W1118 flies, Day 0, rep1 [D0-1]


title: proximal_colon_day_14_replicate_1

description: colon_clean_VST_counts.csv column 78


title: REB1_3IAA_120_B_S45_RNA-seq


title: proximal_colon_day_9_replicate_1

description: colon_clean_VST_counts.csv column 76


title: REB1_3IAA_60_C_S50_RNA-seq


title: hsp70_day_47_3

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference D. melanogaster BDGP6.94 primary genome assembly using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (BDGP6.94)
TPM values calculated using kallisto v0.44.0
Assembly: BDGP6.94 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

molecule: polyA RNA

source_name: legs

extract_protocol:
Legs from 15 flies were homogenized in the RLT buffer (Qiagen, Germany) with 1% beta-mercaptoethanol using a drill and incubated (55ºC, 10 min) with protein kinase K (Evrogen, Russia). Total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration was evaluated by a fluorimetric assay (Qubit 4, Thermo Scientific). RNA integrity was evaluated in an aliquot of total RNA (200 μg) after DNase I (Thermo Scientific) treatment using capillary electrophoresis (TapeStation, Agilent, Germany).
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

value: legs

value: male

value: No treatment

value: Df(3R)Hsp70A, Df(3R)Hsp70B

tag: age

value: 47 days


title: proximal_colon_day_5_replicate_2

description: colon_clean_VST_counts.csv column 75


title: hsp70_day_47_4


title: REB1_3IAA_60_B_S44_RNA-seq


title: hsp70_day_47_1


title: proximal_colon_day_5_replicate_7

description: colon_clean_VST_counts.csv column 73


title: REB1_3IAA_30_C_S49_RNA-seq


title: proximal_colon_day_5_replicate_6


title: REB1_3IAA_30_B_S43_RNA-seq


title: w_day_47_4


title: hsp70_day_47_2


title: proximal_colon_day_5_replicate_5

description: colon_clean_VST_counts.csv column 72


title: w_day_47_3


title: REB1_3IAA_10_C_S54_RNA-seq


title: REB1_3IAA_10_B_S53_RNA-seq


title: CE81T2-4_sh6, shPI3 group

city: Kaohsiung

first: Ming-Tsang

last: Wu

address: No.100, Shih-Chuan 1st Road, Sanmin Dist

department: Research Center for Environmental Medicine

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Read quality was checked for each sample using FastQC 0.11.2.
High-quality reads were then imported into HISAT2 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of cufflinks, version 2.2.1 .
we set p-value cutffoff to 0.05 & FC2X for discovering differential genes.
Differential expressed genes of each experiment design would followed by enrichment test for functional assay by clusterProfiler, version 3.5.
Assembly: Alignment was initially to the transcriptome (hg38, GRCh38.p10), and then to the genome (hg38, GRCh38).
Supplementary files format and content: file format: .xlsx; Content: normalized abundance gene measurements
Supplementary files format and content: file format: .xlsx; Content: normalized abundance Transcript measurements

extract_protocol: RNA was harvested using  Trizol® Reagent

tag: cell type

value: esophageal squamous cell carcinoma

value: Knock down

value: Transform with PI3 knockdown plasmid


title: w_day_47_2


title: CE81T2_PI3 cell, overexpression group

value: overexpression

value: Transform with PI3 overexpression plasmid


title: CE81T2-4_scr, shRNA conreol group

value: WT

value: Transform with scramble plasmid


title: REB1_3IAA_30_A_S37_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-REB1


title: proximal_colon_day_0_replicate_11

description: colon_clean_VST_counts.csv column 69

value: M


title: RDS2_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RDS2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RDS2-3xV5 IAA7::URA3


title: w_day_47_1


title: proximal_colon_day_0_replicate_8

description: colon_clean_VST_counts.csv column 68

value: F


title: REB1_3IAA_10_A_S52_RNA-seq


title: hsp70_day_23_trained_4

value: training

value: 23 days


title: hsp70_day_23_trained_3

value: legs

value: male


title: ChIP-Seq_Input

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description:
Sample 15
Input DNA
ChIP-Seq_TSS_counts.csv

library_source: genomic

data_processing:
Genomic alignment with bowtie 2.2.3, --very-sensitive --dovetail --fr -I 0 -X 1500
Sam to bam conversion, samtools 0.1.19 samtools view -b -S
Sort and index, samtools 0.1.19 samtools sort, samtools index
Enrichment compared to input calculation of respective ChIP-tracks in 1kb windows centered on the TSS with R 3.3.0
Genome_build: HG19
Supplementary_files_format_and_content: CSV file detailing the enrichment of EZH2, H3K27me3, H3K4me3, Input, PHC1, PHC1-dFCS and RNAPII relative to Input 1kb around the TSS together with the associated region and gene

molecule: genomic DNA

source_name: HEK293T T-Rex cells

growth_protocol: DMEM  suppl. with 10% FCS and 5 µM Glutamine

extract_protocol:
HEK293T cells were cultured to 80-90% confluence, reaching approximately 30 million cells per 15 cm plate. The plate was washed once with PBS before adding 10 mL of fixative solution (50 mM HEPES pH 7.5 at 25 °C, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 M NaHCO3, 1% Formaldehyde Methanol free – Thermo Fisher Scientific) and incubating for 6 minutes at 25 °C while shaking gently. Directly afterwards, glycine was added to 125 mM and the plate was incubated for an additional 5 minutes. Cells were scraped off, pelleted at 4 °C, resuspended in 5 mL PBS and 15 mL water and 5 mL 5x nuclear isolation buffer (1.28 M sucrose, 40 mM Tris pH 8 at 4 °C, 20 mM MgCl2, 5 mM EDTA, 2.5 mM EGTA, 4% Triton X100, 1 µg/mL each for Leupeptin, Pepstatin A, Aprotinin) were added. The resulting suspension was rotated at 4 °C for 10 minutes. Nuclei were pelleted and resuspended in 1 mL of sonication buffer (10 mM Tris pH 8 at 4 °C, 1 mM EDTA, 0.1 % SDS, Roche cOmplete protease inhibitors) kept on ice for 5 minutes, transferred to a milliTube (Covaris) and sonicated in a S220 (Covaris) for 12 minutes at 5 % duty cycle, 200 cycles per burst and 140 W max incidence power. Sample was diluted with 250 µL 5x ChIP dilution buffer (10 mM Tris pH 8 at 4 °C, 1 mM EDTA, 0.1 % SDS, 750 mM NaCl, 5 % Triton X-100, 0.5 % Na-Deoxycholate, Roche cOmplete protease inhibitors). The mix was kept on ice for 5 minutes and cleared at maximum speed in a tabletop centrifuge. The supernatant was transferred, aliquoted and flash frozen in siliconized epis using liquid nitrogen.  For each IP one aliquot was thawed on ice and pre-cleared with 10 µL of protein A or G dynabeads (Thermo Fisher Scientific) washed three times with wash buffer (10 mM Tris pH 8, 1 mM EDTA, 150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 0.1 % Na-Deoxycholate). After 15 minutes at 4 °C the beads were removed and 2 µg of the respective antibody added. The IP was performed overnight at 4 °C while rotating. Next 10 µL of washed protein A or G dynabeads were added and incubated at 4 °C for 4 hours.   After the IP the beads were washed 5 times with 400 µL of wash buffer, once with 400 µL high salt wash buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 0.1 % Na-Deoxycholate) and once with 400 µL TE, each for 8 minutes at 4 °C. Next the Protein-DNA was eluted from the beads by resuspending the them in 100 µL elution buffer (1 % SDS, 100 mM NaHCO3) and incubated at 65 °C and 1000 rpm in a thermomixer. The elution was repeated twice and to the resulting 300 µL eluate 12 µL 5 M NaCl were added and de-crosslinked at 65 °C overnight.   To remove RNA from the de-crosslinked DNA, 8 µL of RNase A (Roche) was added and the sample was incubated for 1.5 hours at 37 °C. Afterwards, 3 µL of 20 mg / mL Proteinase K (Roche) was added and incubated at 55 °C for 1 hour. The DNA was purified using QIAquick PCR purification kit (Qiagen).
Kapa Hyper Prep

value: HEK293T T-Rex

tag: transgene

tag: chip antibody/reagent


title: proximal_colon_day_5_replicate_1

description: colon_clean_VST_counts.csv column 74


title: proximal_colon_day_0_replicate_16

description: colon_clean_VST_counts.csv column 71


title: RDS2_DMSO_B_S20_RNA-seq


title: CE81T2_myc cell, overexpression control group

value: Transform with control plasmid


title: proximal_colon_day_0_replicate_7

description: colon_clean_VST_counts.csv column 67


title: hsp70_day_23_trained_2

value: Df(3R)Hsp70A, Df(3R)Hsp70B


title: ChIP-Seq_H3K4me3

description:
Sample 14
K4me3 modified histone bound DNA
ChIP-Seq_TSS_counts.csv

value: aH3K4me3 - CST 9751


title: REB1_3IAA_60_A_S38_RNA-seq


title: proximal_colon_day_0_replicate_6

description: colon_clean_VST_counts.csv column 66


title: ChIP-Seq_H3K27me3

description:
Sample 13
K27me3 modified histone bound DNA
ChIP-Seq_TSS_counts.csv

value: aH3K27me3 - Millipore 07-449


title: proximal_colon_day_0_replicate_15

description: colon_clean_VST_counts.csv column 70


title: hsp70_day_23_trained_1


title: ChIP-Seq_EZH2

description:
Sample 12
EZH2 bound DNA
ChIP-Seq_TSS_counts.csv

value: aEZH2 - Active Motif 39639


title: hsp70_day_23_4

value: No treatment


title: RDS2_3IAA_C_S24_RNA-seq


title: RDS2_3IAA_A_S22_RNA-seq


title: cortex_day_0_replicate_15

description: brain_clean_VST_counts.csv column 4

source_name: cortex

value: cortex


title: hsp70_day_23_1


title: ChIP-Seq_PHC1_dFCS_r1

description:
Sample 9
PHC1-dFCS bound DNA
ChIP-Seq_TSS_counts.csv

growth_protocol: DMEM  suppl. with 10% FCS and 5 µM Glutamine, 100 µg / mL Hygromycin

value: Streptavidin Dynabeads MyOne T1


title: proximal_colon_day_0_replicate_14

description: colon_clean_VST_counts.csv column 65


title: RDR1_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 RDR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RDR1-3xV5 IAA7::URA3


title: striatum_day_0_replicate_4

description: brain_clean_VST_counts.csv column 244

source_name: striatum

value: striatum


title: ChIP-Seq_RNAPII

description:
Sample 11
RNAPII bound DNA
ChIP-Seq_TSS_counts.csv

value: aRNAPII ctd - abcam ab817


title: RDS2_3IAA_B_S23_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RDS2-3xV5 IAA7::URA3


title: RDR1_DMSO_A_S13_RNA-seq


title: midbrain_day_0_replicate_1

description: brain_clean_VST_counts.csv column 111

source_name: midbrain

value: midbrain

value: F


title: hsp70_day_23_3

value: legs

value: 23 days


title: ChIP-Seq_PHC1_r1

description:
Sample 7
PHC1 bound DNA
ChIP-Seq_TSS_counts.csv

value: HEK293T T-Rex


title: midbrain_day_9_replicate_10

description: brain_clean_VST_counts.csv column 110

value: M


title: striatum_day_21_replicate_2

description: brain_clean_VST_counts.csv column 236


title: RDR1_3IAA_C_S18_RNA-seq


title: RNA-Seq_total_nuclear_r2

description:
Sample 6
total nuclear RNA
RNA-Seq_total_nuclear.csv

data_processing:
Genomic alignment with TopHat 2.0.11, -g 1
Determining expression via RPKM
Genome_build: HG19
Supplementary_files_format_and_content: CSV file containing the raw readcounts and normalized RPKM

extract_protocol:
Nuclei were isolated from crosslinked cells by scraping, resuspending, washing once with cold PBS and resuspending in 9 mL of cold PBS, 27 mL of cold ddH2O and 9 mL of 5x Nuclear isolation buffer (1.28 M sucrose, 40 mM Tris pH 7.5 at 4 °C, 20 mM MgCl2, 4% Triton X100, 1 µg/mL each for Leupeptin, Pepstatin A, Aprotinin). After 15 minutes rotating at 4 °C nuclei were pelleted at 1800 rcf for 10 minutes at 4°C. Nuclei were washed once in the same buffer then resusended in Trizol.
RiboZero Gold, TruSeq Stranded TotalRNA


title: w_day_23_trained_2

value: male

value: training


title: w_day_23_trained_3


title: RNA-Seq_total_nuclear_r1

description:
Sample 5
total nuclear RNA
RNA-Seq_total_nuclear.csv


title: w_day_23_trained_4


title: ChIP-Seq_PHC1_dFCS_r2

description:
Sample 10
PHC1-dFCS bound DNA
ChIP-Seq_TSS_counts.csv


title: ChIP-Seq_PHC1_r2

description:
Sample 8
PHC1 bound DNA
ChIP-Seq_TSS_counts.csv


title: hippocampus_day_5_replicate_8

description: brain_clean_VST_counts.csv column 147

source_name: hippocampus

value: hippocampus


title: RDR1_DMSO_C_S15_RNA-seq


title: RDS2_DMSO_A_S19_RNA-seq


title: RDR1_3IAA_B_S17_RNA-seq


title: midbrain_day_7_replicate_2

description: brain_clean_VST_counts.csv column 79


title: w_day_23_trained_1


title: hsp70_day_23_2

value: Df(3R)Hsp70A, Df(3R)Hsp70B


title: w_day_23_4

value: No treatment


title: RAP1_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-RAP1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-RAP1


title: striatum_day_0_replicate_5

description: brain_clean_VST_counts.csv column 245


title: striatum_day_0_replicate_3

description: brain_clean_VST_counts.csv column 243


title: w_day_23_3


title: RAP1_DMSO_B_S2_RNA-seq


title: RNAseq Mettl3 knockout MEF replicate 3

city: New York

first: Brian

middle: Frederick

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
Low-quality bases, reads with more than two ambiguous base calls, and adapter sequence were removed using FLEXBAR tool (--max-uncalled 2 --min-read-length 15 --pre-trim-phred 30, 3’ adapter: AGATCGGAAGAGCGGTTCAG). Then, PCR-duplicated reads of identical sequences were removed using the pyDuplicateRemover.py script of the pyCRAC tool suite (version 1.2.2.3). Unique reads were mapped with Burrows-Wheeler Aligner (bwa-0.7.1) using mm10 as reference genome. Further analysis including the identification of CITS CIMS was performed as using the CTK package (v1.1.3).
Assembly: mm10
Supplementary files format and content: bed files contain called FMRP iCLIP sites from the CTK package or called m6A sites from wild-type MEFs

source_name: embryonic fibroblast

growth_protocol: Cells were grown in DMEM +10% FBS

extract_protocol:
For iCLIP, cells were washed twiced with ice-cold PBS and crosslinked with UV254 at 150 mJ/cm^2/sec.  Cross-linked cells were then lysed in lysis buffer (20 mM Tris pH 7.4, 1% SDS, 5 mM EDTA).  For miCLIP, RNA was extracted with Trizol followed by two rounds of poly-A purification.
iCLIP and miCLIP libraries were prepared as previously described (PMID: 27602518, PMID 30874375)
iCLIP, miCLIP, RNAseq

treatment_protocol: Mettl3 was knocked out by inducing Cre-ERT2 with 500 nM 4-OHT for 8 days

value: embryonic fibroblast

value: fibroblast

value: Mettl3 knockout

value: 4-hydroxytamoxifen, 500 nM, 8 days


title: RNAseq Mettl3 knockout MEF replicate 2


title: RNAseq Mettl3 knockout MEF replicate 1


title: striatum_day_9_replicate_5

description: brain_clean_VST_counts.csv column 241

value: striatum


title: RAP1_DMSO_A_S1_RNA-seq


title: RAP1_3IAA_C_S6_RNA-seq


title: striatum_day_21_replicate_8

description: brain_clean_VST_counts.csv column 240


title: RNAseq wild type MEF replicate 3

value: Mettl3 wild-type

value: vehicle control


title: w_day_23_1

value: legs


title: RDR1_3IAA_A_S16_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 RDR1-3xV5 IAA7::URA3


title: RNAseq wild type MEF replicate 2


title: hsp70_day_7_exercised_3

value: exercise

value: 7 days


title: striatum_day_21_replicate_4

description: brain_clean_VST_counts.csv column 238

value: F


title: striatum_day_9_replicate_10

description: brain_clean_VST_counts.csv column 239

value: M


title: RAP1_3IAA_B_S5_RNA-seq


title: RAP1_3IAA_A_S4_RNA-seq


title: RNAseq wild type MEF replicate 1


title: FMRP iCLIP Mettl3 knockout MEF replicate 3


title: hsp70_day_7_exercised_2

value: male


title: hsp70_day_7_exercised_4

value: Df(3R)Hsp70A, Df(3R)Hsp70B


title: striatum_day_21_replicate_3

description: brain_clean_VST_counts.csv column 237


title: PUT3_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PUT3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PUT3-3xV5 IAA7::URA3


title: FMRP iCLIP Mettl3 knockout MEF replicate 2


title: hsp70_day_7_exercised_1


title: PUT3_DMSO_B_S8_RNA-seq


title: striatum_day_0_replicate_2

description: brain_clean_VST_counts.csv column 242


title: w_day_23_2

value: No treatment

value: 23 days


title: FMRP iCLIP Mettl3 knockout MEF replicate 1

value: embryonic fibroblast

value: fibroblast


title: striatum_day_21_replicate_1

description: brain_clean_VST_counts.csv column 235


title: hsp70_day_7_4


title: striatum_day_21_replicate_7

description: brain_clean_VST_counts.csv column 234


title: PUT3_DMSO_A_S7_RNA-seq


title: FMRP iCLIP wild type MEF replicate 3


title: FMRP iCLIP wild type MEF replicate 2


title: hsp70_day_7_2


title: PUT3_3IAA_B_S11_RNA-seq


title: FMRP iCLIP wild type MEF replicate 1


title: striatum_day_21_replicate_5

description: brain_clean_VST_counts.csv column 232


title: striatum_day_5_replicate_10

description: brain_clean_VST_counts.csv column 231


title: hsp70_day_7_1


title: PUT3_3IAA_A_S10_RNA-seq


title: w_day_7_exercised_4


title: PPR1_DMSO_C_S45_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PPR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PPR1-3xV5 IAA7::URA3


title: striatum_day_5_replicate_9

description: brain_clean_VST_counts.csv column 230

value: striatum


title: MPTPKD2

city: Guangzhou

first: Chen

last: Shiyu

state: Guangdong

address: 253 Gongye Middle Ave

country: China

institute: Zhujiang Hospital

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10

source_name: mice brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's protocols.

value: substantia nigra pars compacta

value: MPTP + MCT-KD


title: w_day_7_exercised_3

value: legs


title: MPTPKD3


title: PPR1_DMSO_B_S44_RNA-seq


title: w_day_7_exercised_2


title: striatum_day_5_replicate_4

description: brain_clean_VST_counts.csv column 228


title: PPR1_DMSO_A_S43_RNA-seq


title: MPTP3

value: MPTP


title: hsp70_day_7_3


title: striatum_day_21_replicate_6

description: brain_clean_VST_counts.csv column 233


title: PUT3_3IAA_C_S12_RNA-seq


title: w_day_7_exercised_1

value: exercise


title: w_day_7_4

value: 7 days


title: PPR1_3IAA_B_S47_RNA-seq


title: striatum_day_14_replicate_7

description: brain_clean_VST_counts.csv column 226


title: PPR1_3IAA_C_S48_RNA-seq


title: MPTP1


title: striatum_day_12_replicate_8

description: brain_clean_VST_counts.csv column 225


title: striatum_day_14_replicate_8

description: brain_clean_VST_counts.csv column 227


title: striatum_day_7_replicate_4

description: brain_clean_VST_counts.csv column 229

value: F


title: w_day_7_2


title: MPTPKD1


title: POG1_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 POG1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 POG1-3xV5 IAA7::URA3


title: striatum_day_7_replicate_3

description: brain_clean_VST_counts.csv column 224


title: Ctrl3

value: Ctrl


title: PPR1_3IAA_A_S46_RNA-seq


title: Ctrl2


title: Ctrl1


title: POG1_DMSO_A_S37_RNA-seq


title: striatum_day_5_replicate_3


title: patient12_ACTP_TCRbeta

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

data_processing:
Deep sequencing of the TCR beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Assembly: IMGT data base was used to identifiy TCR
Supplementary files format and content: txt files containing the list of TCR and their frequencies
Library strategy: TCR-seq

source_name: expanded TILs

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction and as described in Genolet et al., Cell Report Methods, 2013.
Libraries were prepare using targeted TCR amplification

value: expanded TILs

tag: patient

tag: time

value: ACT product


title: patient11_ACTP_TCRbeta


title: MPTP2


title: striatum_day_14_replicate_3

description: brain_clean_VST_counts.csv column 222


title: WT JAX distal colon 002

city: Boston

first: Roni

last: Nowarski

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

data_processing:
Mapping the read to the transcriptome was performed with tophat(v.2.1.1) and bowtie2(v.2.3.4.3).
Assembling the transcripts and estimating their abundances was performed with cufflinks (v.2.2.1)
Assembly: GRCm39 (Ensembl Release 104.39)
Supplementary files format and content: We provided individual tab-separated FPKM tracking files(named isoforms_fpkm_tracking) containing transcript FPKMs

source_name: Distal colon

extract_protocol:
RNA was extracted from distal colon tissue using TRIzol (Ambion)
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Library Prep Kit

value: JAX

value: Distal colon

value: WT

value: steady-state


title: POG1_3IAA_C_S42_RNA-seq


title: striatum_day_12_replicate_3

description: brain_clean_VST_counts.csv column 223


title: patient10_T30stable_TCRbeta

source_name: tumor

value: tumor

value: tumor-infiltrating lymphocytes (TILs)

value: post-ACT


title: WT JAX distal colon 003


title: w_day_7_3

source_name: legs

value: male

value: No treatment


title: WT JAX distal colon 001


title: patient10_T30inresp_TCRbeta


title: POG1_3IAA_B_S41_RNA-seq


title: POG1_3IAA_A_S40_RNA-seq


title: striatum_day_12_replicate_2

description: brain_clean_VST_counts.csv column 221

value: striatum


title: w_day_7_1

value: legs


title: NK cells, anti-NK1.1, 6 hours, rep 3 [S12]

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

data_processing:
Reads were aligned to the mouse genome GRCm38/mm10 primary assembly (GENCODE) and gene annotation Ver.M16 with STAR 2.5.4a
The raw read counts were generated by featureCounts and normalized with DESeq2 package from R/Bioconductor.
Assembly: mouse genome GRCm38/mm10 primary assembly (GENCODE) and gene annotation Ver.M16 with STAR 2.5.4a
Supplementary files format and content: tab-delimited text file include log2CPM gene count values for each sample

source_name: natural killer

extract_protocol:
RNA was isolated using Dynabeads mRNA DIRECT Kit (Invitrogen), and then reverse transcribed using the AffinityScript Multiple Temperature cDNA Synthesis Kit (Agilent Technologies) to synthesize cDNA.
After first strand synthesis, samples were pooled together based on ACTB qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixtures were then PCR enriched for17 - 20cycles and SPRI purified to yield final strand specific RNA-seq libraries. Individual librarieswere then pooled into two final librarypools for sequencing based on ACTB qPCR values. Final library QCwas performed using the Agilent TapeStation system. Libraries were sequenced on HiSeq 2500 (Illumina) using 40 bp X 10 bp paired-end sequencing.

value: natural killer

value: 6 hours


title: striatum_day_9_replicate_9

description: brain_clean_VST_counts.csv column 220

value: M


title: patient10_B30_TCRbeta

source_name: blood

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: striatum_day_9_replicate_8

description: brain_clean_VST_counts.csv column 219


title: PIP2_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PIP2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PIP2-3xV5 IAA7::URA3


title: POG1_DMSO_B_S38_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 POG1-3xV5 IAA7::URA3


title: NK cells, anti-NK1.1, 6 hours, rep 2 [S10]


title: striatum_day_7_replicate_9

description: brain_clean_VST_counts.csv column 218


title: patient10_T0siteB_TCRbeta

value: pre-ACT


title: patient10_ACTP_TCRbeta

value: expanded TILs

value: ACT product


title: PIP2_DMSO_B_S32_RNA-seq


title: NK cells, anti-NK1.1, 6 hours, rep 1 [S11]

value: WT


title: PIP2_DMSO_A_S31_RNA-seq


title: patient10_T0siteA_TCRbeta

value: tumor

value: tumor-infiltrating lymphocytes (TILs)


title: NK cells, anti-NK1.1, 3 hours, rep 3 [S5]

value: 3 hours


title: PIP2_3IAA_C_S36_RNA-seq


title: striatum_day_14_replicate_6

description: brain_clean_VST_counts.csv column 215


title: patient10_B0_TCRbeta


title: PIP2_3IAA_B_S35_RNA-seq


title: NK cells, anti-NK1.1, 3 hours, rep 2 [S4]


title: striatum_day_7_replicate_7

description: brain_clean_VST_counts.csv column 216


title: patient9_T30_TCRbeta

value: post-ACT


title: PIP2_3IAA_A_S34_RNA-seq


title: patient9_B30_TCRbeta


title: NK cells, unstimulated, 0.5 hours, rep 3 [S3]

value: media/unstimulated

value: 0.5 hours


title: striatum_day_5_replicate_8

description: brain_clean_VST_counts.csv column 213

value: striatum


title: striatum_day_9_replicate_7

description: brain_clean_VST_counts.csv column 214


title: PHO4_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PHO4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PHO4-3xV5 IAA7::URA3


title: patient9_ACTP_TCRbeta


title: NK cells, unstimulated, 0.5 hours, rep 2 [S2]

value: natural killer


title: striatum_day_14_replicate_5

description: brain_clean_VST_counts.csv column 212

source_name: striatum

value: M


title: patient9_T0_TCRbeta


title: NK cells, IL-12+IL-18, 3 hours, rep 3 [S9]


title: striatum_day_14_replicate_4

description: brain_clean_VST_counts.csv column 211


title: PHO4_DMSO_A_S13_RNA-seq


title: NK cells, unstimulated, 0.5 hours, rep 1 [S1]


title: patient9_B0_TCRbeta

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: striatum_day_7_replicate_8

description: brain_clean_VST_counts.csv column 217


title: NK cells, anti-NK1.1, 3 hours, rep 1 [S6]


title: striatum_day_12_replicate_7

description: brain_clean_VST_counts.csv column 210


title: PHO4_3IAA_B_S17_RNA-seq


title: patient8_T30_TCRbeta


title: striatum_day_9_replicate_4

description: brain_clean_VST_counts.csv column 209

value: F


title: striatum_day_14_replicate_2

description: brain_clean_VST_counts.csv column 208


title: PHO4_3IAA_A_S16_RNA-seq


title: NK cells, IL-12+IL-18, 6 hours, rep 3 [S15]

value: 6 hours


title: patient8_ACTP_TCRbeta

value: expanded TILs


title: PHO4_DMSO_C_S15_RNA-seq


title: patient8_T0_TCRbeta

value: pre-ACT


title: PHO2_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PHO2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PHO2-3xV5 IAA7::URA3


title: striatum_day_7_replicate_2

description: brain_clean_VST_counts.csv column 207


title: patient8_B0_TCRbeta


title: PHO2_DMSO_B_S38_RNA-seq


title: NK cells, IL-12+IL-18, 6 hours, rep1 [S13]

value: WT


title: PHO4_3IAA_C_S18_RNA-seq


title: NK cells, IL-12+IL-18, 3 hours, rep 2 [S7]


title: striatum_day_12_replicate_6

description: brain_clean_VST_counts.csv column 205


title: striatum_day_7_replicate_1

description: brain_clean_VST_counts.csv column 206


title: PHO2_DMSO_A_S37_RNA-seq


title: striatum_day_9_replicate_3

description: brain_clean_VST_counts.csv column 204


title: NK cells, LD IL-15, anti-NK1.1 [C3]

data_processing:
NOT PROVIDED; REQUESTED
Assembly: mm10
Supplementary files format and content: tab-delimited text file include log2CPM gene count values for each sample

extract_protocol:
RNA was isolated using Dynabeads mRNA DIRECT Kit (Invitrogen), and then reverse transcribed using the AffinityScript Multiple Temperature cDNA Synthesis Kit (Agilent Technologies) to synthesize cDNA.
After first strand synthesis, samples were pooled together based on ACTB qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixture was then PCR enriched for 14 cycles and SPRI purified to yield final strand specific RNA-seq libraries.

value: LD IL-15, 72 hours

value: 72 hours

tag: stimulation

value: anti-NK1.1, 6 hours


title: patient7_ACTP_TCRbeta

value: ACT product


title: PHO2_3IAA_C_S42_RNA-seq


title: NK cells, IL-12+IL-18, 3 hours, rep 1 [S8]

value: 3 hours


title: striatum_day_9_replicate_2

description: brain_clean_VST_counts.csv column 203

value: striatum


title: PHO2_3IAA_B_S41_RNA-seq


title: patient7_T0_TCRbeta

value: tumor

value: tumor-infiltrating lymphocytes (TILs)


title: PHO2_3IAA_A_S40_RNA-seq


title: striatum_day_9_replicate_6

description: brain_clean_VST_counts.csv column 202

value: M


title: NK cells, naive, anti-NK1.1 [B4]

value: natural killer


title: NK cells, naive, unstimulated [A4]


title: PHD1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PHD1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PHD1-3xV5 IAA7::URA3


title: patient7_B0_TCRbeta

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: striatum_day_7_replicate_6

description: brain_clean_VST_counts.csv column 201


title: NK cells, naive, anti-NK1.1 [B1]

value: 6 hours


title: NK cells, IL-12+IL-18, 6 hours, rep2 [S14]


title: patient6_T30_TCRbeta

value: post-ACT


title: striatum_day_7_replicate_5

description: brain_clean_VST_counts.csv column 200


title: NK cells, naive, unstimulated [A1]


title: patient7_T30_TCRbeta


title: patient7_B30_TCRbeta


title: PHD1_DMSO_A_S25_RNA-seq


title: patient6_B30_TCRbeta


title: striatum_day_0_replicate_13

description: brain_clean_VST_counts.csv column 199


title: patient6_ACTP_TCRbeta

value: expanded TILs


title: striatum_day_0_replicate_12

description: brain_clean_VST_counts.csv column 198


title: NK cells, naive, anti-NK1.1 [B5]

value: WT


title: NK cells, naive, unstimulated [A6]


title: PHD1_3IAA_C_S30_RNA-seq


title: patient6_T0_TCRbeta

value: pre-ACT


title: PHD1_3IAA_B_S29_RNA-seq


title: NK cells, HD IL-15, anti-NK1.1 [E1]

value: HD IL-15, 72 hours

value: 72 hours


title: PDR3_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PDR3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PDR3-3xV5 IAA7::URA3


title: patient6_B0_TCRbeta


title: striatum_day_0_replicate_10

description: brain_clean_VST_counts.csv column 197


title: NK cells, HD IL-15, anti-NK1.1 [E2]

value: anti-NK1.1, 6 hours


title: NK cells, LD IL-15, anti-NK1.1 [C1]

value: LD IL-15, 72 hours


title: patient5_T30_TCRbeta

value: tumor


title: striatum_day_0_replicate_9

description: brain_clean_VST_counts.csv column 196

value: striatum


title: striatum_day_14_replicate_1

description: brain_clean_VST_counts.csv column 194

value: F


title: PHD1_3IAA_A_S28_RNA-seq


title: striatum_day_12_replicate_4

description: brain_clean_VST_counts.csv column 195

value: M


title: PHD1_DMSO_B_S26_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PHD1-3xV5 IAA7::URA3


title: NK cells, HD IL-15, unstimulated [D1]

value: natural killer


title: patient5_B30_TCRbeta

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: striatum_day_12_replicate_1

description: brain_clean_VST_counts.csv column 193


title: PDR3_DMSO_B_S32_RNA-seq


title: patient5_ACTP_TCRbeta

value: ACT product


title: PDR3_3IAA_C_S36_RNA-seq


title: NK cells, HD IL-15, unstimulated [D2]


title: patient5_T0_TCRbeta

value: tumor-infiltrating lymphocytes (TILs)


title: NK cells, HD IL-15, anti-NK1.1 [E3]

value: WT


title: striatum_day_9_replicate_1

description: brain_clean_VST_counts.csv column 192


title: sPool_WT

first: Iñigo

last: Landa

state: Massachusetts

address: 77 Avenue Louis Pasteur, 4BF Building, Room 645A

department: Medicine/Endocrinology

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing: none provided

source_name: thyroid tumor

extract_protocol: none provided

value: thyroid tumor

value: thyrocytes (YFP-sorted)

value: Wildtype, pooled samples

value: Naïve

value: 20 weeks


title: patient5_B0_TCRbeta

value: pre-ACT


title: striatum_day_5_replicate_2

description: brain_clean_VST_counts.csv column 191


title: sPool_Tert_123

value: Tert-123C>T, pooled samples


title: patient4_T30_TCRbeta

value: tumor

value: post-ACT


title: PDR3_3IAA_B_S35_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PDR3-3xV5 IAA7::URA3


title: PDR3_3IAA_A_S34_RNA-seq


title: striatum_day_5_replicate_1

description: brain_clean_VST_counts.csv column 190

value: striatum

value: F


title: striatum_day_5_replicate_7

description: brain_clean_VST_counts.csv column 189

value: M


title: PDR1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PDR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PDR1-3xV5 IAA7::URA3


title: s67425


title: patient4_ACTP_TCRbeta

value: expanded TILs

value: ACT product


title: PDR3_DMSO_A_S31_RNA-seq


title: sPool_K5_Tert_only

value: K5-Tert, pooled samples


title: PDR1_DMSO_B_S26_RNA-seq


title: s66661

value: thyroid tumor


title: patient4_T0_TCRbeta

value: tumor-infiltrating lymphocytes (TILs)


title: striatum_day_5_replicate_6

description: brain_clean_VST_counts.csv column 188


title: s66264

value: thyrocytes (YFP-sorted)


title: patient4_B0_TCRbeta

value: blood

value: peripheral blood mononuclear cell (PBMC)


title: PDR1_DMSO_A_S25_RNA-seq


title: striatum_day_5_replicate_5

description: brain_clean_VST_counts.csv column 187


title: s66262

value: Naïve

value: 20 weeks


title: patient3_T30_TCRbeta

value: tumor


title: PDR1_3IAA_C_S30_RNA-seq


title: PDR1_3IAA_B_S29_RNA-seq


title: striatum_day_0_replicate_16

description: brain_clean_VST_counts.csv column 186


title: s63594


title: striatum_day_0_replicate_15

description: brain_clean_VST_counts.csv column 185


title: PDR1_3IAA_A_S28_RNA-seq


title: s63590


title: patient3_ACTP_TCRbeta


title: PDC2_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 PDC2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 PDC2-3xV5 IAA7::URA3


title: patient3_T0_TCRbeta

value: pre-ACT


title: striatum_day_0_replicate_14

description: brain_clean_VST_counts.csv column 184

value: striatum


title: striatum_day_0_replicate_11

description: brain_clean_VST_counts.csv column 183


title: patient3_B0_TCRbeta


title: PDC2_DMSO_B_S20_RNA-seq


title: s63711


title: striatum_day_0_replicate_8

description: brain_clean_VST_counts.csv column 182

value: F


title: PDC2_DMSO_A_S19_RNA-seq


title: s63608


title: patient2_T30_TCRbeta

value: post-ACT


title: PDC2_3IAA_C_S24_RNA-seq


title: striatum_day_0_replicate_7

description: brain_clean_VST_counts.csv column 181


title: patient2_ACTP_TCRbeta


title: striatum_day_0_replicate_6

description: brain_clean_VST_counts.csv column 180


title: patient2_T0_TCRbeta


title: hippocampus_day_0_replicate_5

description: brain_clean_VST_counts.csv column 179

source_name: hippocampus

value: hippocampus


title: s63593


title: PDC2_3IAA_A_S22_RNA-seq


title: s63592


title: patient2_B0_TCRbeta


title: hippocampus_day_0_replicate_4

description: brain_clean_VST_counts.csv column 178


title: s64033


title: s63587


title: patient1_ACTP_TCRbeta

value: expanded TILs


title: hippocampus_day_0_replicate_3

description: brain_clean_VST_counts.csv column 177


title: s63610


title: patient1_T30_TCRbeta


title: OPI1_DMSO_B_S29_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 OPI1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 OPI1-3xV5 IAA7::URA3


title: hippocampus_day_0_replicate_2

description: brain_clean_VST_counts.csv column 176


title: s63609


title: patient1_T0_TCRbeta


title: OPI1_DMSO_A_S51_RNA-seq


title: hippocampus_day_21_replicate_8

description: brain_clean_VST_counts.csv column 174

value: M


title: hippocampus_day_0_replicate_1

description: brain_clean_VST_counts.csv column 175


title: OPI1_3IAA_C_S31_RNA-seq


title: s63584

value: thyroid tumor


title: PDC2_3IAA_B_S23_RNA-seq


title: hippocampus_day_9_replicate_10

description: brain_clean_VST_counts.csv column 173


title: OPI1_3IAA_A_S53_RNA-seq


title: WT stimulated

city: SUZHOU

first: Mengyun

address: 199 Renai Road, Industrial Park, Suzhou City, Jiangsu Province, China

institute: Soochow University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through cutadapt-1.7.1 and fastx-toolkit-0.0.14.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Comparison of WT and Cbl-b-/- CD4+ T cells

source_name: WT CD4+T cells, anti-CD3 stimulated  for 48 h

growth_protocol: CD4+ T cells were isolated from WT and Cbl-b-/- mice and were cultured in RPMI-1640 medium (HyClone) with 10% FBS (Gibco) and 1% penicillin-streptomycin solution  at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA were extracted with Trizol (Tiangen, Beijing) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
A total amount of 3ug total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEB Next®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: T cells were unactivated or stimulated by anti-CD3 for 48h.

value: WT


title: Cbl-b-/-

source_name: Cbl-b-/- CD4+T cells, naive

value: Cbl-b-/-


title: OPI1_DMSO_C_S52_RNA-seq


title: hippocampus_day_21_replicate_4

description: brain_clean_VST_counts.csv column 172


title: Cbl-b-/- stimulated

source_name: Cbl-b-/- CD4+T cells, anti-CD3 stimulated for 48 h


title: OPI1_3IAA_B_S30_RNA-seq


title: NRM1_DMSO_C_S50_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 NRM1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 NRM1-3xV5 IAA7::URA3


title: WT

source_name: WT CD4+T cells, naive


title: hippocampus_day_21_replicate_3

description: brain_clean_VST_counts.csv column 171


title: Dex

city: Beijing

first: Liu

last: Zhiwen

address: NO.15 Of North Three-ring East Road,Chao Yang District

institute: Beijing University of Chemical Technolgoy

description: Dex-FPKM

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:
1) Remove the reads containing the adaptor(adaptor pollution);
2) Remove reads whose N content is greater than 5%;
3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GCF_006088835.1_ASM608883v1
Supplementary files format and content: processed data.csv

organism: Staphylococcus aureus

source_name: biofilm

extract_protocol:
2.1 Incubate 10% SDS at 37℃，add 60-100 µL elution buffer for each sample in 2.0 mL tube and incubate at 95℃.
2.2 Add 500 µL ice-cold Zirconia Beads to 2.0 mL screwed tube，add 480 µL Phenol/chloroform/iso-amyl alcohol 25:24:1）、480 µL Lysis Buffer and 48 µL 10% SDS.
2.3 Transfer appropriate microbial sample to 2.0 mL screwed tube, homogenize at 65Hz for 60 s，stay at room temperature for 5 min.
2.4 Centrifuge at 15,000×g for 5 min at room temperature.
2.5 Transfer supernatant to new 5.0 mL tube，add 1.9 mL Binding Buffer、1.2 mL ethanol absolute and mix thoroughly.
2.6 Transfer 700 µL mixed solution to Filter Cartridge with collection tube，centrifuge for 15,000×g for 30 s at room temperature and discard the filtrate.
2.7 Repeat 2.6，until all mixed solution pass the Filter Cartridge.
2.8 Add 700 µL Wash Solution 1，centrifuge at 10,000×g for 30 s at room temperature and discard the filtrate.
2.9 Add 500 µL Wash Solution 2/3，centrifuge at 10,000×g for 30 s at room temperature and discard the filtrate.
2.10 加入500 µL Wash Solution 2/3，centrifuge at 10,000×g for 30 s at room temperature and discard the filtrate.
2.11 Centrifuge at 15,000×g for 2 min at room temperature, transfer the Filter Cartridge to a new 2.0 mL collection tube.
2.12 Add 60-100 µL prewarmed elution buffer to Filter Cartridge and stay for 2 min，centrifuge at 15,000×g for 1min and collect the RNA solution.
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: biofilm

value: Dex


title: DexBS

description: DexBS-FPKM

value: DexBS


title: hippocampus_day_21_replicate_2

description: brain_clean_VST_counts.csv column 170


title: Ctrl

description: Ctrl-FPKM

value: Ctrl


title: BS

description: BS-FPKM

value: BS


title: DYRK1A-ChIP, mESCs

city: Barcelona

first: Chiara

last: Di Vona

state: Spain

address: Carrer Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

data_processing:
Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference (or to the mm9 mouse genome reference) using Bowtie and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10-8 and a false discovery rate (FDR) < 1%.
Genome_build: hg38 or mm9
Supplementary_files_format_and_content: peak text files and bigwig files

source_name: mESC

growth_protocol: Human cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and antibiotics (100 U/ml penicillin and 100 µg/ml streptomycin). mESCs were maintained in 0.1% gelatin (Millipore ES-006-B)-coated plates mESC medium, which consisted of DMEM supplemented with 15% FBS, L– glutamine (2 mM), penicillin (100 U/ml), streptomycin (100 µg/ ml), sodium pyruvate (1 mM), non-essential amino acid (NEAA) (0,1 mM), 2-mercaptoethanol (0,5 mM) and ESGRO mLif (1000 U/ml).

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen).
DNA libraries were generated by using the OvationÒ Ultralow Library System V2 (NuGEN) following the manufacturer’s instructions. To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition.

treatment_protocol: For cell transduction, the virus was added to the medium with the cells in suspension, and replaced with fresh complete DMEM 24 h after infection and seeding. Selection of infected cells was performed by adding 1.25 mg/ml of puromycin (Sigma) for 48-72 h, and cells were allowed to recover in the absence of puromycin for 24 h.

value: mESC

value: Mouse Embrionic Stem cells

tag: chip antibody

value: DYRK1A (Abcam, ab69811)

value: untreated


title: NRM1_DMSO_B_S25_RNA-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.


title: RRMM16_T2

city: Heidelberg

first: Alexandra

last: Poos

address: Im Neuenheimer Feld 410

country: Germany

institute: University Hospital Heidelberg

description: 10X Genomics

library_source: other

data_processing:
CellRanger ATAC version 1.2
Assembly: hg38
Supplementary files format and content: For each sample the fragments.tsv.gz, raw_peak_bc_matrix.h5 and singlecell.csv have been uploaded.

molecule: other

source_name: bone marrow

extract_protocol:
Viably frozenCD138+-enriched or CD138+-depleted (RRMM7) BMMCswere thawed at 37 ºC, resuspended in RPMI with 10% FBS and washed once in ice-cold PBS with cells being collected by centrifugation at 500 g for 5 min.
Library was performed according to the manufactur's instructions (scATAC-seq, v1.0 protocol, 10X Genomics)

value: bone marrow

value: CD138-positive fraction

value: post


title: RRMM16_T1

description: 10X Genomics

value: pre


title: NRM1_DMSO_A_S24_RNA-seq


title: RRMM15_T2

description: 10X Genomics


title: NRM1_3IAA_C_S28_RNA-seq


title: RRMM15_T1

description: 10X Genomics


title: NRM1_3IAA_B_S27_RNA-seq


title: hippocampus_day_21_replicate_6

description: brain_clean_VST_counts.csv column 167

data_processing:
Reads were filtered to remove adapters, reads with polyA or polyG, reads with more than 5% unknown nucleotides, and reads with more than 20% low-quality bases (Q-value < 20) with Cutadapt.
Reads were mapped to the GRCmm39 genome assembly using STAR (v. 2.7.9)
Reads were counted with Subread (v. 2.0.3) in paired-end mode
Quality control and normalization was performed in R with the WGCNA, DESeq2, and edgeR packages.
Assembly: GRCmm39
Supplementary files format and content: comma-separated file gives raw read counts for each sample
Supplementary files format and content: comma-separated file gives variance-stabilized counts of only high-quality genes and samples

extract_protocol:
RNA was extracted using the TRIzol-chloroform based method. Tissue was lysed in TRIzol (ThermoFisher 15596018), and lysate was mixed with phenol:choloroform:isoamyl alcohol (ThermoFisher 15593049) in a 5:1 ratio. Protein and nucleic acids were separated into phases via centrifugation. The top aqueous layer containing the RNA was passed through a QIAshredder column (Qiagen 79656). Eluent was mixed 1:1 with 70% ethanol and applied to an RNease Mini column (Qiagen 74104). After a brief centrifugation, columns were washed once with RW1 buffer and twice with RPE buffer, as per manufacturer's recommendations. RNA was eluted in nuclease-free water. 1µg of total RNA in a concentration of 20ng/µL was shipped to LC Sciences (Houston, TX) for library preparation and RNA sequencing.
Total RNA was enriched for mRNA, fragmented, and reverse transcribed into complementary DNA (cDNA). Second-stranded DNA was synthesized, A-bases were added to the blunt ends of either strand, and DNA was ligated to dual-index adapters. Size selection was performed and DNA was treated with a heat-labile UDG enzyme. Ligated products were amplified with PCR before sequencing.

value: hippocampus

value: M


title: RRMM10_T2

description: 10X Genomics


title: hippocampus_day_21_replicate_5

description: brain_clean_VST_counts.csv column 166


title: NRG1_DMSO_C_S20_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 NRG1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 NRG1-3xV5 IAA7::URA3


title: NRM1_3IAA_A_S26_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 NRM1-3xV5 IAA7::URA3


title: hippocampus_day_5_replicate_10

description: brain_clean_VST_counts.csv column 165


title: RRMM10_T1

description: 10X Genomics


title: hippocampus_day_21_replicate_1

description: brain_clean_VST_counts.csv column 169

value: F


title: RRMM9_T2

description: 10X Genomics


title: hippocampus_day_5_replicate_9

description: brain_clean_VST_counts.csv column 164


title: RRMM7_BME2

description: 10X Genomics

value: CD138-negative fraction


title: NRG1_DMSO_B_S19_RNA-seq


title: hippocampus_day_5_replicate_4

description: brain_clean_VST_counts.csv column 163


title: NRG1_DMSO_A_S18_RNA-seq


title: hippocampus_day_21_replicate_7

description: brain_clean_VST_counts.csv column 168


title: NRG1_3IAA_C_S23_RNA-seq


title: hippocampus_day_14_replicate_8

description: brain_clean_VST_counts.csv column 162


title: RRMM7_BME1

description: 10X Genomics


title: NRG1_3IAA_B_S22_RNA-seq


title: hippocampus_day_14_replicate_7

description: brain_clean_VST_counts.csv column 161


title: DM+RYGB, rep2

type: RNA

city: ChongQing

first: Xiao

last: Wei

address: ChangJiang Zhi Road 10, YuZhong District

department: Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases

institute: Daping Hospital, Army Medical University of PLA

hyb_protocol: Finally, 55 μl of 2 × GE Hybridization buffer was added to dilute the labeled cRNA. One hundred microliters of hybridization solution were dispensed into the gasket slide and assembled to create the gene expression microarray slide. The slides were incubated for 17 h at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed using the Gene Spring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes for which at least 46 out of 92 samples had Detected (“All Targets Value”) flags were chosen for further analysis. Differentially expressed genes with a statistically significant difference between the two groups were identified through Volcano Plot filtering.
Differentially expressed genes between the two samples were identified through Fold Change filtering.

organism: Rattus norvegicus

source_name: Renal cortex

label_protocol: The Rat 4 × 44 K Gene Expression Array was manufactured by Agilent. The updated content provided full coverage of rat genes and transcripts. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, the total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified with a RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured with a NanoDrop ND-1000. Each labeled cRNA (1 μg) was fragmented in 11 μl of 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer. Then, the mixture was heated at 60 ℃ for 30 min.

extract_protocol: Total RNA was extracted from the frozen tissues by using TRIzol (Invitrogen). The RNA quantity and quality were measured with a NanoDrop ND-1000. RNA integrity was assessed by using standard denaturing agarose gel electrophoresis.

treatment_protocol: SD rats are as controls, and type 1 diabetes was induced by STZ. 4 weeks later, control and diabetes rats were treated with Sham or RYGB surgery. Then renal cortex was collected 4 weeks later.

tag: disease state

value: DM

value: RYGB


title: Control+RYGB, rep3

value: Control


title: DM+RYGB, rep1


title: Control+RYGB, rep2


title: Control+RYGB, rep1


title: RRMM7_T2

description: 10X Genomics


title: hippocampus_day_12_replicate_8

description: brain_clean_VST_counts.csv column 160


title: RRMM7_T1

description: 10X Genomics


title: NRG1_3IAA_A_S21_RNA-seq

first: Lakshmi

address: 1100 FAIRVIEW AVE N

institute: Fred Hutchinson Cancer Center


title: DM+Sham, rep2

value: Sham


title: hippocampus_day_7_replicate_3

first: Jake

address: LG-152, 1149 Newell Dr

institute: University of Florida

description: brain_clean_VST_counts.csv column 159


title: NDD1_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 NDD1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 NDD1-3xV5 IAA7::URA3


title: hippocampus_day_5_replicate_3

description: brain_clean_VST_counts.csv column 158


title: DM+Sham, rep3


title: RRMM6_T1

description: 10X Genomics


title: Control+Sham, rep3


title: DM+Sham, rep1


title: RRMM9_T1

description: 10X Genomics


title: NDD1_DMSO_C_S15_RNA-seq


title: NDD1_DMSO_A_S13_RNA-seq


title: RRMM5_T2

description: 10X Genomics


title: hippocampus_day_12_replicate_3

description: brain_clean_VST_counts.csv column 157


title: Control+Sham, rep2


title: RRMM3_T2

description: 10X Genomics


title: hippocampus_day_14_replicate_3

description: brain_clean_VST_counts.csv column 156


title: Control+Sham, rep1


title: RRMM3_T1

description: 10X Genomics


title: hippocampus_day_12_replicate_2

description: brain_clean_VST_counts.csv column 155


title: RRMM6_T2

description: 10X Genomics


title: RRMM2_T2

description: 10X Genomics


title: hippocampus_day_9_replicate_9

description: brain_clean_VST_counts.csv column 154


title: DCUN1D1 Knockdown (biological rep2)

city: Cape Town

first: Luiz

middle: F

last: Zerbini

address: Wernher and Beit Building (South), Anzio Road

country: South Africa

institute: ICGEB

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HT_HG-U133_Plus_PM
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: DU145 shDCUN1D1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 µg total RNA.1 µg of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688)

growth_protocol: DU145 cells were grown in DMEM medium (BioWhitaker, Walkersville, MD, USA).The medium was supplemented with 10% fetal bovine serum (FBS), 50 units/ml penicillin, and 50 µg/ml streptomycin (all from Life Technologies, Inc.). Cells were maintained in a 5% CO2-humidified incubator at 37°C

extract_protocol: Total RNA was obtained using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: DU145 shDCUN1D1 and DU145 shGFP (control)  were grown in DMEM medium for 16h. Cells were washed with PBS 1X and RNA were extracted. DMSO.  Biological duplicates were used for this analysis.

value: Prostate Cancer cell line

tag: genotype/variation

value: DCUN1D1 Knockdown


title: DCUN1D1 Knockdown (biological rep1)


title: U-937 FOXO3A KO3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: hg38

growth_protocol: U-937 were maintained inRPMI1640 with 15% fetal bovine serum (FBS) (Gibico) and 1% penicillin/streptomycin (Hyclone).

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

treatment_protocol: we generated knock-out (KO) cells of FOXO3A using small guide RNAs (sgRNAs)

value: acute myeloid leukemia cell

tag: genotype

value: FOXO3A knock-out


title: Control (biological rep2)

source_name: DU145 shGFP

tag: cell line

value: control


title: U-937 FOXO3A KO2


title: hippocampus_day_9_replicate_8

city: Gainesville

description: brain_clean_VST_counts.csv column 153

tag: tissue


title: MSS11_DMSO_B_S14_RNA-seq

city: SEATTLE

last: Mahendrawada

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MSS11-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSS11-3xV5 IAA7::URA3


title: RRMM1_T1

description: 10X Genomics

value: bone marrow

value: CD138-positive fraction

value: pre


title: U-937 FOXO3A KO1


title: RRMM1_T2

description: 10X Genomics

value: post


title: NDD1_3IAA_C_S17_RNA-seq


title: MSS11_DMSO_A_S13_RNA-seq


title: hippocampus_day_7_replicate_8

last: Boles

description: brain_clean_VST_counts.csv column 151

value: hippocampus

tag: day

value: M


title: MSS11_DMSO_C_S15_RNA-seq


title: NDD1_3IAA_B_S16_RNA-seq


title: hippocampus_day_7_replicate_9

description: brain_clean_VST_counts.csv column 152

tag: Sex


title: NDD1_3IAA_A_S49_RNA-seq


title: hippocampus_day_7_replicate_7

description: brain_clean_VST_counts.csv column 150

tag: strain


title: MSS11_3IAA_C_S18_RNA-seq


title: U-937 Control2

value: WT


title: Control (biological rep1)


title: HeLa cell culture, UV crosslinked, RNA binding protein-RNA fraction, replicate two

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

institute: Duke University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were first processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapters or the insert tag, containing poly A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, reads from 18-40 bp from the clean reads record was used to perform the downstream analyses.
Read mapping to the reference sequence: The small RNA tags were mapped to the reference sequence by Bowtie without mismatch. Known miRNA alignment: mapped small RNA tags were used to identify known miRNAs. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and predict the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNAs and on each position of all identified miRNAs, respectively.
Small RNA annotation summary: In the initial alignment and annotation analysis, some small RNA tags may be mapped to more than one category. To restrict small RNA mapping to a single annotation, we used the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a sample quality metric.
Novel miRNA prediction: The characteristics of hairpin structure of miRNA precursors can be used to predict novel miRNAs. The available software miREvo and mirdeep2 were integrated to predict novel miRNAs through exploring secondary structure, Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified
Supplementary files format and content: Mapped Counts_LEAP-RBP_R1. An Excel file containing gene ID, gene symbol, count, fpkm, and tpm values are included. NB: These are the refseq mapping counts. For small RNA searches, the raw and processed read data can be mapped for miRNA analysis with miREvo_v1.1 and mirdeep2
Supplementary files format and content: Mapped Counts_LEAP-RBP_R2. An Excel file containing gene ID, gene symbol, count, fpkm, and tpm values are included. NB: These are the refseq mapping counts. For small RNA searches, the raw and processed read data can be mapped for miRNA analysis with miREvo_v1.1 and mirdeep2

source_name: HeLa cell culture

growth_protocol: HeLa cells were maintained in Dulbecco’s Modified Eagle’s Medium (D6428, Sigma) supplemented with 10% FBS (35-010-CV, Corning) at 37 ˚C, 5% CO2.

extract_protocol:
Cells were lysed on plate, scraped, and transferred to a 2.0 mL microcentrifuge tube using two 400 µL aliquots of guanidinium thiocyanate (−phenol) buffer. Guanidinium thiocyanate (GT) buffer (4 M GT, 25 mM sodium citrate pH 7.0, 0.5% N-lauryl sarcosine, 5 mM EDTA pH 8.0, and 0.1 M 2-mercaptoethanol) was prepared as described in  [23, 24], with the following stock solutions prepared in DEPC-treated DI water: 5 M guanidinium thiocyanate (00522, Chemimpex), 750 mM sodium citrate pH 7.0 (BDH-9288, VWR; C-0759, Sigma), 10% N-lauryl sarcosine (L9150, Sigma), 0.5 M EDTA pH 8.0 (0105, VWR).
Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ ends of the small RNA fraction, respectively. Then, first strand cDNA was synthesized after hybridization with the reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing on Illumina sequencing with SE50.

treatment_protocol: Cells were cultured in 100- or 150-mm dishes until 60–90% confluent, washed twice with ice-cold 1X PBS, and UV-crosslinked on ice with 100–800 mJ/cm2 at 254 nm

value: HeLa cell culture

value: HeLa

tag: treatment

value: UV crosslinked


title: U-937 Control3


title: HeLa cell culture, UV crosslinked, RNA binding protein-RNA fraction, replicate one


title: MSS11_3IAA_B_S17_RNA-seq


title: hippocampus_day_14_replicate_6

description: brain_clean_VST_counts.csv column 149

source_name: hippocampus


title: U-937 Control1


title: hippocampus_day_9_replicate_7

description: brain_clean_VST_counts.csv column 148


title: 95D cell, LCMR1 ko, Pol II ChIP-seq

city: Nanjing

first: Lu

last: Liu

state: -- None selected --

address: Key Laboratory of Human Functional Genomics of Jiangsu Province

institute: Nanjing Medical University

data_processing:
Alignment by BWA;Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Assembly: GRCh38
Supplementary files format and content: BigWig files, Narrow peaks files

source_name: lung cancer

growth_protocol: 95D cells were cultured in RPMI 1640 medium (Gibco, USA) with 10% of fetal bovine serum, 100 U/mL penicillin, and 100µg/mL streptomycin in an incubator at 37 °C, 5% CO2, 95% humidity.

extract_protocol:
For RNA-seq, total RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer.  For RNA Pol II ChIP-seq,native nuclei were purified from 95D cell，and washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 1x10^5 nuclei bound to Concanavalin A-coated beads were incubated with RNA Pol II first antibody (39097, Thermo)  and second antibody (anti-mouse IgG antibody, goat polyclonal: Millipore AP124). Transposase pA-Tn5 was used to induce DNA tagmentation, followed by Proteinase K digestion and PCI extraction. The ethanol precipitated DNA was immediately subjected to PCR amplification by Universal and barcoded i7 primer using NEBNext HiFi 2x PCR Master mix. The amplified library was purified without size selection.
For RNA-seq, 1.5 μg of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following manufacturer's protocols. For RNA Pol II ChIP-seq, libraries were prepared from 3-5ng DNA using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Post-amplification libraries were size selected at 250–450bp in length using AMPure XP beads ((Beckman Counter)) and were quantified using the Library Quantification Kit for Illiumina (Kapa Biosystems, KK4603).

treatment_protocol: 95D cells were stable infected with either LCMR1 shRNA or scramble shNC lentivirus.

value: lung cancer

value: 95D cell

value: Large-cell lung cancer

value: LCMR1 KO

value: 95D cells were infected with either LCMR1 shRNA or scramble shNC lentivirus.


title: U-937_CUT2

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were mapped to the hg38 reference genome using Bowtie2 with -×2000
Reads that aligned to the mitochondrial genome were filtered and PCR duplicates were removed with picard MarkDuplicates.
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

growth_protocol: RPMI1640 with 15% fetal bovine serum (FBS) (Gibico) and 1% penicillin/streptomycin (Hyclone)

extract_protocol:
Cells were harvested and washed twice in 1 mL wash buffer (20 mM HEPES PH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 1x PIC (Bimake)), and then resuspended in 300 μL wash buffer. Concanavalin A coated beads were activated by washing twice in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). 10 μL activated beads were then added to the cell suspension. After 30 min’s incubation at room temperature, the supernatant was removed and the beads were resuspended in 50 μL antibody buffer (20 mM HEPES pH 7.5,150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1x PIC). Then 0.5 μL antibody (FOXO3A) was added and incubated for 2 hours at room temperature. After the supernatant was gently removed on DynaMag (Thermo), the beads were resuspended in 100 μL Dig wash buffer (20 mM HEPES pH 7.5,150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 1x PIC) containing 1 μL Guinea Pig anti-Rabbit IgG antibody. After incubation for 1 hr at room temperature, the beads were then washed three times in 800 μL Dig wash buffer, followed by resuspended in 100 μL Dig 300 wash buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.0125% Digitonin, 1x PIC). Then 0.04 μM pA-Tn5 adapter complex (Vazyme S603) was added and incubated for 1 h at room temperature. Beas were washed three times in 800 μL Dig 300 wash buffer and resuspended in 300 μL tagmentation buffer (20 mM HEPES pH 7.5, 300 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 10 mM MgCl2, 1x PIC) and incubated for 1 hr at 37°C. And then 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 1 µL of 20 mg/mL Proteinase K were added and incubated at 55°C for 1 hr to stop tagmentation.The DNA was extracted by PCI and amplified with i5 and i7 primers (Vazyme, TD202) by 16-18 cycles’ PCR.
DNA libraries were prepared for sequencing using standard Illumina protocols. The amplified products were purified by Ampure XP beads to remove >1 kb fragment and to enrich the 200-1000 bp fragments for high-throughput sequencing.

value: acute myeloid leukemia cell

tag: antibody


title: MSN4_DMSO_B_S38_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MSN4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSN4-3xV5 IAA7::URA3


title: hippocampus_day_14_replicate_4

description: brain_clean_VST_counts.csv column 145


title: 95D cell, control, RNA-seq rep2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapped to GRCh38 whole genome using STAR(v2.6.1a) with default parameters. Reference genome and gene model annotation files were downloaded from NCBI.
FeatureCounts (v1.6.3) was used to count the reads numbers mapped to each gene.
The abundance of each gene was calculated by stringtie (v2.0). Deseq2 for differential analysis
Assembly: GRCh38
Supplementary files format and content: FPKMs_allsamples.txt

tag: cell type

value: wild type


title: THP-1_CUT2


title: 95D cell, control, RNA-seq rep1


title: hippocampus_day_12_replicate_7

description: brain_clean_VST_counts.csv column 144


title: MSN4_3IAA_C_S42_RNA-seq


title: hippocampus_day_9_replicate_4

description: brain_clean_VST_counts.csv column 143

value: F


title: MSN4_DMSO_A_S37_RNA-seq


title: MSN4_3IAA_B_S41_RNA-seq


title: THP-1_CUT1


title: hippocampus_day_14_replicate_2

description: brain_clean_VST_counts.csv column 142


title: MSS11_3IAA_A_S16_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSS11-3xV5 IAA7::URA3


title: 95D cell, control, Pol II ChIP-seq


title: MSN4_3IAA_A_S40_RNA-seq


title: 95D cell, LCMR1 ko, RNA-seq rep3


title: HEK293A, Sh Cry1 replicate 2

city: Charlestown

first: Xu

last: Wu

address: 149, 13th Street

department: Dermatology, Harvard Medical School,

institute: Cutaneous Biology Research Center, Massachusetts General Hospital

data_processing:
The following low quality reads and adapters were filtered at Novogene. Reads containing adapters, reads with N > 10% and reads with low quality (Qscore<= 5) base which is over 50% of the total base. Sequence quality was further verified using FastQC
Assembly: human genome version (hg38).
Transcriptome quantification was performed using feature Counts.
Differential expression was performed using edgeR, using TMM normalization method. Benjamini-Hochberg correction was used to correct for multiple comparisons (with a false discovery cut-off <0.05).
Supplementary files format and content: tab-delimited text files containing normalized read cound  for each Sample

growth_protocol: HEK293A cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA were isolated using TRI reagent then purified with RNeasy Mini Kit (QIAGEN#74004). Quality control, library preparation and sequencing was performed by Novogene.
Performed by Novogene strandard RNA seq protocol

value: epithelial

tag: shRNA

value: Sh Cry2


title: 95D cell, LCMR1 ko, RNA-seq rep2


title: hippocampus_day_7_replicate_2

description: brain_clean_VST_counts.csv column 141

value: hippocampus


title: 95D cell, LCMR1 ko, RNA-seq rep1


title: HEK293A, Sh Cry1 replicate 1

value: Sh Cry1


title: MSN4_DMSO_C_S39_RNA-seq


title: HEK293A, Sh control replicate 2

value: Sh control


title: 95D cell, control, RNA-seq rep3

description:
MED19ct3_count
Sample MED19ct3 was excluded from the study after cluster analysis of all samples.


title: MSN2_DMSO_37_C_S52_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MSN2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSN2-3xV5 IAA7::URA3

value: heat shock


title: THP-1_CUT3


title: hippocampus_day_14_replicate_5

description: brain_clean_VST_counts.csv column 146

value: M


title: U-937_CUT1


title: hippocampus_day_7_replicate_1

description: brain_clean_VST_counts.csv column 140


title: HUWE1-CS, shWRNIP1, DSBseq, rep3

city: Tübingen

first: Elias

last: Einig

address: Otfried-Müller Straße 14

department: Medical Oncology and Pulmonology

institute: University Hospital Tübingen

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to human genome (hg19) with STAR (2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: hg19
Supplementary files format and content: Bedgraph
Library strategy: DSB capture and sequencing

source_name: colon

growth_protocol: HCT116 cells were cultured in Dulbecco’s Modified Eagle’s Medium with high glucose (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; PAN-Biotech), 1% (v/v) penicillin-streptomycin, 1% (v/v) non-essential amino acids and 50 µM 2-mercaptoethanol. Cells were maintained in a humidified atmosphere at 37°C in 7.5% CO2.

extract_protocol:
Double strand break sequencing was performed based on the DSBCapture protocol (Lensing et al., 2016). In brief, 5 million cells were fixed with 90% methanol. Cells were permeabilized in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% Triton-X100) for 10 min on ice and bound to Con-A Sepharose (Sigma) in binding buffer (20 mM HEPES, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). DNA ends were repaired using Klenow fragment (NEB) in NEB buffer 2 for 30 min at 25°C followed by A-tailing in dA-tailing buffer (NEB) with Klenow (3'→5' exo-) for 30 min at 37°C. Biotinylated NEB adaptors were ligated to A-tailed DSBs with T4 DNA ligase (NEB) in the corresponding buffer overnight at 16°C. Cells were lysed in 10 mM Tris, pH 8.5, 5 mM EDTA, 0.5% SDS, 250 mM NaCl, 1.2 U Proteinase K (Thermo) at 50°C overnight followed by sonication for 5 min on ice and DNA purification using phenol/chloroform/isoamyl and ethanol. Biotinylated DNA was captured on streptavidin C1 beads (NEB) and washed with 10 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.02 % TritonX100.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

treatment_protocol: 100 ng/ml doxycycline was added for 4 days  to induce shRNA expression

value: colon

value: Colorectal carcinoma cell line

value: HUWE1-CS, shWRNIP1


title: MSN2_DMSO_37_B_S51_RNA-seq


title: hippocampus_day_12_replicate_6

description: brain_clean_VST_counts.csv column 139


title: MSN2_DMSO_37_A_S50_RNA-seq


title: HUWE1-CS, shCtrl, DSBseq, rep3

value: HUWE1-CS, shCtrl


title: hippocampus_day_12_replicate_5

description: brain_clean_VST_counts.csv column 138


title: HEK293A, Sh control replicate 1


title: HUWE1-WT, shWRNIP1, DSBseq, rep3

value: HUWE1-WT, shWRNIP1


title: PANC-1 cell line GATA1-shHDAC5-IP #2

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

data_processing:
Basecalls performed using star v2.7.10a
Sequencing read quality was inspected using the fastqc v0.11.9. Adapter removal and read trimming were performed using fastp v0.23.2. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 20).
Paired-end reads were aligned to the hg38.featureCounts v2.0.1 was used to count the reads numbers mapped to each gene.
deepTools v3.5.0 was used to generate bigWig files.
macs2 v2.2.7.1 was used to call peaks.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read-counts and peaks for each Sample.

extract_protocol: not provided

value: human pancreatic cancer cells

value: HDAC5 knockdown

value: Day 3


title: MSN2_DMSO_30_C_S46_RNA-seq


title: HUWE1-WT, shCtrl, DSBseq, rep3

value: HUWE1-WT, shCtrl


title: hippocampus_day_9_replicate_3

description: brain_clean_VST_counts.csv column 137

value: F


title: MSN2_DMSO_30_B_S45_RNA-seq


title: PANC-1 cell line GATA1-shHDAC5-Input #2

value: Input


title: hippocampus_day_9_replicate_2

description: brain_clean_VST_counts.csv column 136

value: hippocampus


title: PANC-1 cell line GATA1-shHDAC5-IP #1


title: PANC-1 cell line GATA1-shHDAC5-Input #1


title: MSN2_DMSO_30_A_S44_RNA-seq


title: hippocampus_day_9_replicate_6

description: brain_clean_VST_counts.csv column 135


title: hippocampus_day_7_replicate_6

description: brain_clean_VST_counts.csv column 134


title: HUWE1-CS, shCtrl, DSBseq, rep2


title: MSN2_3IAA_37_C_S55_RNA-seq


title: hippocampus_day_7_replicate_5

description: brain_clean_VST_counts.csv column 133


title: PANC-1 cell line GATA1-NC-IP #1

value: WT

value: shControl


title: HUWE1-WT, shWRNIP1, DSBseq, rep2


title: PANC-1 cell line GATA1-NC-IP #2


title: MSN2_3IAA_37_B_S54_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSN2-3xV5 IAA7::URA3


title: HUWE1-WT, shCtrl, DSBseq, rep2


title: MSN2_3IAA_37_A_S53_RNA-seq

value: heat shock


title: hippocampus_day_0_replicate_12

description: brain_clean_VST_counts.csv column 132

value: M


title: PANC-1 cell line GATA1-NC-Input #2


title: MSN2_3IAA_30_C_S49_RNA-seq


title: Fibroblasts, EtOH 075%/CBD 075uM, 12h, K27

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

source_name: skin

extract_protocol:
Standard procedure of TRIzol Reagent
Standard protocol of QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen)

value: skin

value: fibroblasts


title: HUWE1-CS, shWRNIP1, DSBseq, rep2

value: colon

value: Colorectal carcinoma cell line

value: HUWE1-CS, shWRNIP1


title: PANC-1 cell line GATA1-NC-Input #1

value: human pancreatic cancer cells


title: Fibroblasts, EtOH 075%/CBD 075uM, 12h, K26


title: MSN2_3IAA_30_B_S48_RNA-seq


title: hippocampus_day_0_replicate_9

description: brain_clean_VST_counts.csv column 130


title: Fibroblasts, EtOH 075%/CBD 075uM, 12h, K25


title: Fibroblasts, EtOH 025%/CBD 075uM, 12h, K30


title: hippocampus_day_12_replicate_4

description: brain_clean_VST_counts.csv column 129


title: BxPC-3 cell line shHDAC5 #3

value: HDAC5 knockdown


title: MSN2_3IAA_30_A_S47_RNA-seq


title: hippocampus_day_9_replicate_5

description: brain_clean_VST_counts.csv column 128


title: hippocampus_day_9_replicate_1

description: brain_clean_VST_counts.csv column 127


title: MSA2_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MSA2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MSA2-3xV5 IAA7::URA3


title: BxPC-3 cell line shHDAC5 #1

value: Day 3


title: Fibroblasts, EtOH 025%/CBD 075uM, 12h, K29


title: BxPC-3 cell line shControl #3


title: MSA2_DMSO_A_S37_RNA-seq


title: Fibroblasts, EtOH 025%/CBD 075uM, 12h, K28


title: BxPC-3 cell line shControl #2


title: MSA2_3IAA_C_S42_RNA-seq


title: hippocampus_day_5_replicate_2

description: brain_clean_VST_counts.csv column 126

value: F


title: hippocampus_day_0_replicate_10

description: brain_clean_VST_counts.csv column 131


title: Fibroblasts, EtOH 075%/CBD 075uM, 6h, K42


title: BxPC-3 cell line shControl #1


title: MSA2_3IAA_B_S41_RNA-seq


title: LY1_VitC3

city: Huddinge

first: Martin

last: Bergo

address: MBE Group, Neo bldn. SE-141 83 Huddinge Sweden

department: BioNut

country: Sweden

institute: Karolinska Institutet

data_processing:
Preprocessed reads were aligned to the GRCh38 transcriptome using the STAR Aligner, and genes were quantified with the featureCounts tool. Tests for differential expression of genes identified in RNA-seq analyses were done with DESeq2. Differentially expressed genes with a false-discovery rate < 0.01 were considered statistically significant.
Assembly: GRCh38

growth_protocol: LY1, and Ramos  were cultured in RPMI1640 medium (61870044, ThermoFisher) supplemented with 10% fetal bovine serum (FBS, 26140079, ThermoFisher) and 1% penicillin/streptomycin (15070063, ThermoFisher).

extract_protocol:
Total RNAs were extracted with the RNeasy Plus Mini kit (74136, QIAGEN).
RNA-seq libraries were prepared and sequenced on the Illumina HiSeq 2000 platform at Bioinformatics and Expression Analysis core facility (BEA, Karolinska Institutet, Sweden).

treatment_protocol: Reagents used were N-acetylcysteine (NAC, A7250), and vitamin C (VitC, A5960). Ramos and LY1 were treated with or without NAC, VitC for 24h.

value: Diffuse large B-cell lymphoma

value: Treatment with Vitamin C (VitC)

value: High CMYC expression


title: BxPC-3 cell line shHDAC5 #2


title: Fibroblasts, EtOH 075%/CBD 075uM, 6h, K40


title: hippocampus_day_5_replicate_6

description: brain_clean_VST_counts.csv column 123

value: hippocampus


title: hippocampus_day_5_replicate_7

description: brain_clean_VST_counts.csv column 124


title: MSA2_3IAA_A_S40_RNA-seq


title: hippocampus_day_5_replicate_5

description: brain_clean_VST_counts.csv column 122


title: MSA2_DMSO_B_S38_RNA-seq


title: Fibroblasts, EtOH 025%/CBD 075uM, 6h, K37


title: Fibroblasts, EtOH 025%/CBD 075uM, 6h, K38


title: LY1_VitC1


title: MIG2_DMSO_B_S8_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MIG2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MIG2-3xV5 IAA7::URA3


title: hippocampus_day_0_replicate_16

description: brain_clean_VST_counts.csv column 121


title: hippocampus_day_0_replicate_15


title: hippocampus_day_5_replicate_1

description: brain_clean_VST_counts.csv column 125


title: MIG2_3IAA_C_S12_RNA-seq


title: LY1_NAC2

value: Treatment with N-acetylcysteine (NAC)


title: hippocampus_day_0_replicate_14

description: brain_clean_VST_counts.csv column 120

value: M


title: LY1_NAC1


title: MIG2_DMSO_A_S7_RNA-seq


title: Fibroblasts, EtOH 075%, 12h, K10

value: skin


title: Fibroblasts, EtOH 075%, 12h, K11

value: fibroblasts


title: hippocampus_day_0_replicate_11

description: brain_clean_VST_counts.csv column 119


title: LY1_Ctrl3

value: Control


title: Fibroblasts, EtOH 025%/CBD 075uM, 6h, K39


title: MIG2_3IAA_B_S11_RNA-seq


title: Fibroblasts, EtOH 025%, 12h, K8


title: MIG2_DMSO_C_S9_RNA-seq


title: MIG2_3IAA_A_S10_RNA-seq


title: LY1_VitC2


title: LY1_Ctrl2