title: HS360-Day20-P200 [scATAC-seq]

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Day 20", "male", "maturated NPCs", "paracetamol", "P200

data_processing:
Cell Ranger ATAC version 1.2.0 was used to preprocess scATAC-seq raw sequencing data into fastq files
Single cell accessibility counts for the cells were generated from reads using the ‘cellranger-atac count’ pipeline.
Down stream analysis was perfomed using R programming languages and the R package ArchR v.1.0.1 and ArchR dev version.
Assembly: refdata-cellranger-atac-GRCh38-1.2.0
Supplementary files format and content: Output from cellranger ATAC: filtered peak matrix, fragments and singlecell.

source_name: HS360, day 20, past stage III maturation, exposed to 200 μM paracetamol

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol:
Cells were harvested using Accutase. Nuclei isolation was done according to the 10x Genomics protocol CG000169 (Rev D) using 2 minutes of incubation in lysis buffer diluted to 0.5x for Day 20 cells. Nuclei were counted and processed on the 10x Chromium controller (10x Genomics) using Next GEM Chip H Single Cell Kit (10x Genomics). The targeted nuclei recovery was 5,000 nuclei per sample.
Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10 x Genomics) and Chromium i7 Multiplex Kit N Set A (10x Genomics) were used to generate scATAC-seq libraries.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected. For cells that were exposed to either 100 or 200 μM paracetamol, fresh media with paracetamol concentrations of 100 μM and 200 μM (Merck; A7085) was added every day from Day 1 until collection day ( Day 20).

tag: gender

value: male

value: maturated NPCs

tag: treatment

value: Day 20 200 μM paracetamol


title: Glioblastoma (G) [S7-1]

status: Public on Aug 31 2023

type: SRA

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

library_source: transcriptomic

data_processing:
We used the pipeline: RiboMethSeq-nf. fastQC was used to verify sequencing quality and adapter removal was performed using Trimmomatic. The trimmed reads were aligned by Bowtie2 on the 7.2 kb-long rRNA sequence of reference (NR_046235) and the 5’ read-ends were computed using bedtool genomcov utility
The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window
Assembly: NR_046235
Supplementary files format and content: Raw counts of 5' end reads on each position of each rRNA
Supplementary files format and content: The C-score was calculated using a normalization against the median raw counts of neighbouring +/- 6 nucleotide window (Marcel et al, NAR Cancer 2020)
Library strategy: RiboMeth-Seq

molecule: total RNA

organism: Homo sapiens

source_name: brain

extract_protocol: Total RNA was extracted using either the Maxwell RSC simplyRNA Tissue Kit (Promega) with Maxwell RSC Instrument (Promega) configured with Low Elution Volume (LEV) hardware according to the manufacturer’s protocol or TRIzol (Invitrogen) according to manufacturer’s instructions.   Total RNA was partially and randomly fragmented under alkaline conditions. Libraries of 24 samples were prepared simultaneously using NEBNext Multiplex Small RNA Library kit (New England Biolabs). A calibrated source of total RNA (Human Xpress Ref Universal Total RNA, Qiagen) was introduced in each library.

tag: tissue

value: brain

tag: pfs

tag: os

tag: mitotic index

tag: rna extraction_protocol

value: Maxwell

tag: cohort

value: validation

tag: sequencing library


title: Glioblastoma (G) [S6-1]


title: Glioblastoma (G) [S5-1]


title: EF_0_3

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

country: USA

institute: Cleveland Clinic

data_processing:
TPM determined using Kallisto v0.44.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Files are given as TPM for each sample

organism: Mus musculus

source_name: ear

extract_protocol:
RNA was extracted using the Qiagen AllPrep DNA/RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: post-mortem

value: ear

tag: cell type

value: fibroblast

tag: time point

value: 0 hr

tag: replicate


title: Glioblastoma (G) [S4-1]


title: EF_12_2

value: 12 hr


title: HS360-Day20-rep2-P200

description: Day 20", "male", "maturated NPCs",  "paracetamol", "P200

library_source: transcriptomic single cell

data_processing:
mkfastq was perfomed using standard settings. cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
cellranger-3.1.0 -count was used to generate single cell feature counts for a single library,  cellranger count  run was performed with the following arguments --expect-cells for each timepoint
cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
run cellranger aggr to aggregate multiple GEM wells from a single experiment that were analyzed by cellranger count and down stream analysis was perfomed using  R programming languages and its package  Seurat version 4
Assembly: refdata-cellranger-GRCh38-3.0.0
Supplementary files format and content: Cell ranger count output: filtered count matrix, barcodes and features.

source_name: HS360, day 20, past stage III maturation, exposed to 200μM paracetamol

extract_protocol:
Cells were harvested using Accutase, counted and processed on the 10x Chromium controller (10x Genomics). Approximately 2,300 cells were loaded per channel on the Chromium Chip B (10x Genomics) to give an estimated recovery of 1,400 cells.
The Chromium Single Cell 3´ Library & Gel Bead Kit v3 (10x Genomics) and Chromium i7 Multiplex Kit (10x Genomics) were used to generate scRNA-seq libraries.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected. For cells that were exposed to either 100 or 200 μM paracetamol, fresh media with paracetamol concentrations of 100 μM and 200 μM (Merck; A7085) was added every day from Day 1 until collection day ( Day 7 or 20).


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample2

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Somatosensory Cortex

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
rna

value: Somatosensory Cortex

tag: genotype

value: WT

tag: age


title: BxPC-3 parental cells, replicate 1, scRNA-seq

city: Beijing

first: Jianlu

last: Song

state: Beijing

address: Shuaifuyuan No.1

country: China

institute: Peking Union Medical College Hospital

description:
B3_NC
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The processed data were imported into the Seurat (v4.0.6) R toolkit for quality control and further analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

extract_protocol:
Expanded cells were trypsinized into single cell and then resuspended using PBS supplemented with 20% FBS.
Library construction was performed using the 10X Chromium Next GEM Single Cell 5' Reagent Kits V2 (Dual Index) according to the manufacturer’s instructions.

tag: cell line

value: Pancreatic ductal adenocarcinoma (PDAC) cells

tag: signal

value: Parental


title: BxPC-3 double-positive cells, replicate 1, scRNA-seq

description:
B3_DP
10X Genomics

value: Double positive


title: Glioblastoma (G) [S3-1]


title: BxPC-3 single-positive cells, replicate 1, scRNA-seq

description:
B3_FACS
10X Genomics

value: Single positive


title: EF_12_1


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample3


title: 20-week SSC Grin2a WT Bulk RNA-seq Sample1


title: HS360-Day20-rep1-P200

tag: gender

value: male


title: HS360-Day20-P100 [scATAC-seq]

description: Day 20", "male", "maturated NPCs", "paracetamol", "P100

library_source: genomic

molecule: genomic DNA

source_name: HS360, day 20, past stage III maturation, exposed to 100 μM paracetamol

value: maturated NPCs

tag: treatment

value: Day 20 100 μM paracetamol


title: Glioblastoma (G) [S2-1]

tag: tissue

value: brain


title: Glioblastoma (G) [S1-1]

tag: pfs

value: Maxwell


title: H3_1

city: 南京

first: lixia

last: dong

address: 学府路12号

department: 模式动物研究所

institute: 南京大学

data_processing:
TopHat (version2.1.1) software used for basecalling.
The sequencing data were mapped to mouse genome (Ensemble GRCm38.p5).
The expression levels of each gene was calculated by FPKM (fragments per kilobase of transcript per million fragments mapped) method. gene abundances and differential expression analysis were quantified by RSEM and R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R).
Assembly: The sequencing data were mapped to mouse genome (Ensemble GRCm38.p5).
Supplementary files format and content: The file provides the original expression of the gene, including the count value of each gene for each sample, the summary of the tpm value, and the diff. file after the comparison between the experimental group and the control group.

source_name: mouse embryonic stem cell

extract_protocol: RNA-seq transcriptome librariy was prepared using TruSeqTM RNA sample preparation Kit from Illumina.

treatment_protocol: ES cells were typsined and RNA was harvested using Trizol reagent (Invitrogen) following the manufacturer’s instructions

tag: strain

value: mouse embryonic stem cell


title: EF_0_2

value: post-mortem


title: EF_0_1

value: ear


title: HS360-Day20-rep2-P100

source_name: HS360, day 20, past stage III maturation, exposed to 100μM paracetamol


title: 20-week SSC Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: HS360-Day20-rep1-P100


title: Non-neoplastic (NT) [NT-6]

tag: os

tag: mitotic index

value: test


title: 20-week SSC Grin2a -/- Bulk RNA-seq Sample2


title: LF_12_2

source_name: lung

value: lung

value: fibroblast

value: 12 hr


title: LF_12_1


title: HS360-Day7-rep2-P200

description: Day 7", "male", "neural rosettes", "neural induction",  "control

source_name: HS360, day 7, past stage I neural induction, exposed to 200μM paracetamol

value: Day 7 200 μM paracetamol

value: neural rosettes


title: Reference RNA (RNA ctrl) [R-2]

source_name: commercial RNA

value: commercial RNA

tag: rna extraction_protocol

tag: cohort


title: 20-week SSC Grin2a -/- Bulk RNA-seq Sample1

value: Somatosensory Cortex


title: HS360-Day7-rep1-P200

description: Day 7", "male", "neural rosettes", "neural induction",  "paracetamol", "P200

value: male


title: LF_0_2

tag: condition

value: 0 hr


title: 20-week SSC Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: Non-neoplastic (NT) [NT-1]

value: brain

tag: sequencing library


title: 20-week SSC Grin2a +/- Bulk RNA-seq Sample4


title: N2 PA14 R2

city: boston

first: Ayush

middle: Vasant

last: Ranawade

address: 360 Huntington Ave

department: Bioengineering

institute: Northeastern University

data_processing:
kallisto was use to map processed reads to C. elegans WS280 genome assembly to generate raw count files.
DESeq2 was used to calculate differentially expressed genes.
Assembly: C. elegans wormbase WS280
Supplementary files format and content: Each file for each sample contains raw counts for each gene

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were raised to late L4 young adult stage on E. coli OP50 at 20 degrees

extract_protocol:
Trizol extraction followed by Zymo RNA concentrator
Paired end cDNA library

treatment_protocol: Worms were washed and transffered to appropiate test bacterial lawn

value: whole animal

value: N2 (wild type)

value: P.aeruginosa PA14


title: Non-neoplastic (NT) [NT-5]

value: Maxwell


title: Non-neoplastic (NT) [NT-2]


title: hiDP_input_control

city: Daejeon

first: Minhyung

last: Lee

address: 125 Gwahak-ro

department: Stem Cell Convergence Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
iDP_Input_1_10
Fragmented DNA of hiDP

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: hg19

source_name: hiDP

growth_protocol: For hiDP reprogramming, the human fibroblasts were plated onto 24-well plates at 30,000 cells/well. The next day (0 days post transduction, dpt), the cells were transduced with Sendai virus (SeV) mixtures (CytoTune™-iPS 2.0 Sendai reprogramming kit; Thermo Fisher Scientific) at an appropriate multiplicity of infection (MOI; KOS:M:K = 4.2:4.2:2.5). After 24 h incubation, the SeV mixtures were replaced with RepM-Neural medium containing 3.0 μM CHIR99021, 0.5 μM A83-01, 50 µg/ml 2-phospho-L-ascorbic-acid (Sigma-Aldrich, St. Louis, MO, USA), 0.2 µM NaB (Sigma-Aldrich), 20 ng/ml epidermal growth factor (EGF; Peprotech), and 20 ng/ml fibroblast growth factor 2 (FGF2; Peprotech) for one week. The cells were dissociated by Accutase with 10 nM Y-27632 and re-plated onto a Geltrex-coated 6-well plate with the same medium containing 10 nM Y-27632 at 7 dpt. The next day, the culture media were replaced with RepM-Neural with 3.0 μM CHIR99021, 0.5 μM A83-01, 50 µg/ml 2-phospho-L-ascorbic-acid, 100 ng/ml FGF8 (Peprotech), and 800 ng/ml sonic hedgehog (SHH; R&D systems, Minneapolis, MN, USA). After 13–15 days, some colonies were manually isolated and maintained on Geltrex-coated plates with the same medium but a reduced SHH concentration (200 ng/ml).

extract_protocol:
We used SimpleChIP enzymatic chromatin IP kit (Cell Signaling Technology, Danvers, MA, USA) according to the manufacturer instructions with a slight modification. In brief, 4 million cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and then quenched with 0.125 M glycine for another 10 min. The cells were washed with DPBS and resuspended sequentially in three lysis buffers according to the manufacturer’s instructions. Chromatin was sonicated for 10–18 cycles (30 sec on/30 sec off) using Bioruptor Pico (Diagenode, Seraing, Belgium), and then incubated overnight at 4°C with histone and IgG control antibody. Immunoprecipitated chromatin was eluted by protein G magnetic beads followed by reversal of the cross-linking and DNA purification.
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol: Fibroblasts and hiDP samples were treatred with growth media, and reprogramming cell samples were treated with hiDP reprogramming media.

tag: cell type

value: reprogrammed hiDP cells

tag: chip antibody


title: LF_0_1

value: post-mortem

tag: time point

tag: replicate


title: HS360-Day7-rep1-P100

description: Day 7", "male", "neural rosettes", "neural induction","paracetamol", "P100

source_name: HS360, day 7, past stage I neural induction, exposed to 100μM paracetamol

value: Day 7 100 μM paracetamol


title: HS360-Day7-rep2-P100

description: Day 7", "male", "neural rosettes", "neural induction", "paracetamol", "P100

source_name: HS360, day 7, past stage I neural induction , exposed to 100μM paracetamol


title: Reference RNA (RNA ctrl) [R-1]

value: test


title: 20-week SSC Grin2a -/- Bulk RNA-seq Sample4

tag: genotype

value: Grin2a -/-

tag: age


title: N2 PA14 R1


title: N2 z11 R2

value: P.aeruginosa z11


title: hiDP_ChIP_H3K27AC

description:
iDP_H3K27AC
H3K27AC immunoprecipitated DNA of hiDP


title: 20-week SSC Grin2a +/- Bulk RNA-seq Sample3


title: Astrocytoma (A) [A-13]


title: 20-week SSC Grin2a +/- Bulk RNA-seq Sample2


title: 20-week SSC Grin2a +/- Bulk RNA-seq Sample1


title: Astrocytoma (A) [A-12]


title: hiDP_ChIP_H3K4me3

description:
iDP_H3K4me3
H3K4me3 immunoprecipitated DNA of hiDP


title: 12-week SSC Grin2a WT Bulk RNA-seq Sample5

value: WT


title: 12-week SSC Grin2a WT Bulk RNA-seq Sample4


title: hiDP-reprogramming_day16_input_control

description:
iDP-R_Input1_10
Fragmented DNA of hiDP reprogramming cells

source_name: hiDP reprogramming cells

value: Cells during hiDP reprogramming

tag: time


title: Astrocytoma (A) [A-11]


title: N2 OP50 R1

tag: treatment

value: E. coli OP50


title: Astrocytoma (A) [A-10]

tag: tissue


title: hiDP-reprogramming_day16_ChIP_H3K27AC

description:
iDP-R_H3K27AC
H3K27AC immunoprecipitated DNA of hiDP reprogramming cells


title: 12-week SSC Grin2a WT Bulk RNA-seq Sample3

value: Somatosensory Cortex


title: Astrocytoma (A) [A-9]

tag: pfs


title: Astrocytoma (A) [A-8]


title: 12-week SSC Grin2a WT Bulk RNA-seq Sample2


title: 12-week SSC Grin2a WT Bulk RNA-seq Sample1


title: Fibroblasts_input_control

description:
Fb_Input_1_10
Fragmented DNA of fibroblast

source_name: Fibroblast

value: Fibroblast


title: 12-week SSC Grin2a -/- Bulk RNA-seq Sample5


title: Fibroblasts_ChIP_H3K4me3

description:
Fb_H3K4me3
H3K4me3 immunoprecipitated DNA of fibroblast


title: hiDP-reprogramming_day16_ChIP_H3K4me3

description:
iDP-R_H3K4me3
H3K4me3 immunoprecipitated DNA of hiDP reprogramming cells


title: Fibroblasts_ChIP_H3K27AC

description:
Fb_H3K27AC
H3K27AC immunoprecipitated DNA of fibroblast


title: N2 z11 R1


title: MNT1 cells, CUTRUN-MITF

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Each ATAC-seq library was sequenced at a depth of > 40 M pair-end reads by Nextseq 550. Then, the raw fastq files were filtered using fastp (v 0.22.0)  with default settings and mapped using bowtie2 (v 2.4.1)  with parameters “--very-sensitive --maxins 1000”. Duplicates and low-quality reads were removed using MarkDuplicates from gatk (v 4.1.7.0) and samtools (v 1.13)  with parameters “-q 20 -F 1804 -f 2”. Bam files were converted to Bigwig files using deeptools2 (v 3.1.3)  with the setting “--normalizeUsing RPKM --binSize 10”. ATAC-seq peaks were called using macs2 (v 2.1.0.20150731)  with the setting “callpeak -t in.bam -g hs -f BAMPE -q 0.01 --keep-dup all”. The fraction of reads in peaks were calculated using featureCounts (v 2.0.3) . TSS enrichment plots and correlation analysis were conducted using deeptools2
Each CUT&RUN library was sequenced at a depth of > 8 M pair-end reads by Nextseq 550. First, H3K4me3 antibody specificity was determined using the SNAP-CUTANA K-MetStat Panel. Second, the raw fastq files were filtered using fastp (v 0.22.0)  with default settings and mapped using bowtie2 (v 2.4.1)  with parameters “--dovetail --very-sensitive-local -I 10 -X 700”. Duplicates and low-quality reads were removed using MarkDuplicates from gatk (v 4.1.7.0) and samtools (v 1.13)  with parameters “-q 20 -F 1804 -f 2”. Bam files were converted to Bedgraph and normalized using scaleFactor determined by spike-in Ecoli reads. Bam files were also converted to Bigwig files using deeptools2 (v 3.1.3)  with the setting “--normalizeUsing RPKM --binSize 10”. H3K27ac CUT&RUN peaks were called using macs2 (v 2.1.0.20150731)  with the setting “callpeak -t in.bam -g hs --broad --broad-cutoff 0.05 -f BAMPE --keep-dup all”. MITF, SOX10 and H3K4me3 CUT&RUN peaks were called using SEACR (v 1.3). The fraction of reads in peaks was calculated using featureCounts (v 2.0.3). TSS enrichment and correlation were conducted using deeptools2137.
Assembly: hg38
Supplementary files format and content: bigwig, bed
Library strategy: Cut&Run

growth_protocol: MNT-1 cells (ATCC, #CRL- 3450), a gift from Dr. Michael S. Marks at Children’s Hospital of Philadelphia Research Institute, were grown in DMEM (Gibco, #11965084) supplemented with 20% Fetal Bovine Serum (FBS), 1% GlutaMAX (Gibco, #35050061), 1% NEAA (Gibco, #10370021),1% penicillin/streptomycin (Gibco, #15140122), and 10% AIM-V (Gibco, # 12055-091). WM88 cells, a melanocytic patient-derived melanoma tumor cell line, a gift from Dr. Ashani Weeraratna at Wistar Institute, were cultured in Tumor Specialized medium (80% MCDB153, 20% Leibovitz’s L-15, supplemented with 2% fetal bovine serum (FBS) and 1.68 mM CaCl2).

extract_protocol:
For ATAC-seq, MNT-1 cells or WM88 cells were washed with PBS twice and detached by 0.25% trypsin. The cells were pelleted at 500g for 5 mins at 4°C and the cell density was quantified by an Automated Cell Counter. Then, 50,000 viable cells were used for ATAC-seq following the Omni-ATAC protocol. Tn5 tagmentase was purchased from Diagenode (Cat. No. C01070010). For Cut and Run, MNT-1 cells were washed with PBS twice and detached by 0.25% trypsin. The cells were pelleted at 500g for 5 mins at 4°C and then  fixed with 0.1% formaldehyde at room temperature for 1.5 min. Then, cells were quenched by adding 2.5 M glycine solution to a final concentration of 0.2 M. Finally, 500,000 cells were used for CUT&RUN using the CUT&RUN Kit (Cat. No. 14-1048) from epicypher. The antibodies used for CUT&RUN include: MITF (CST, #97800), SOX10 (CST, #89356), and H3K27Ac (abcam, # ab4729). H3K4me3 and IgG antibodies were from the CUT&RUN kit. All procedures were conducted following the manufacturer’s manual
ATAC-seq following the Omni-ATAC protocol. CUT&RUN following the manual of the CUT&RUN Kit (Cat. No. 14-1048) from epicypher

tag: cell line

value: melanoma cells

tag: antibody


title: WM88 cells, ATAC-seq

data_processing:
Each ATAC-seq library was sequenced at a depth of > 40 M pair-end reads by Nextseq 550. Then, the raw fastq files were filtered using fastp (v 0.22.0)  with default settings and mapped using bowtie2 (v 2.4.1)  with parameters “--very-sensitive --maxins 1000”. Duplicates and low-quality reads were removed using MarkDuplicates from gatk (v 4.1.7.0) and samtools (v 1.13)  with parameters “-q 20 -F 1804 -f 2”. Bam files were converted to Bigwig files using deeptools2 (v 3.1.3)  with the setting “--normalizeUsing RPKM --binSize 10”. ATAC-seq peaks were called using macs2 (v 2.1.0.20150731)  with the setting “callpeak -t in.bam -g hs -f BAMPE -q 0.01 --keep-dup all”. The fraction of reads in peaks were calculated using featureCounts (v 2.0.3) . TSS enrichment plots and correlation analysis were conducted using deeptools2
Each CUT&RUN library was sequenced at a depth of > 8 M pair-end reads by Nextseq 550. First, H3K4me3 antibody specificity was determined using the SNAP-CUTANA K-MetStat Panel. Second, the raw fastq files were filtered using fastp (v 0.22.0)  with default settings and mapped using bowtie2 (v 2.4.1)  with parameters “--dovetail --very-sensitive-local -I 10 -X 700”. Duplicates and low-quality reads were removed using MarkDuplicates from gatk (v 4.1.7.0) and samtools (v 1.13)  with parameters “-q 20 -F 1804 -f 2”. Bam files were converted to Bedgraph and normalized using scaleFactor determined by spike-in Ecoli reads. Bam files were also converted to Bigwig files using deeptools2 (v 3.1.3)  with the setting “--normalizeUsing RPKM --binSize 10”. H3K27ac CUT&RUN peaks were called using macs2 (v 2.1.0.20150731)  with the setting “callpeak -t in.bam -g hs --broad --broad-cutoff 0.05 -f BAMPE --keep-dup all”. MITF, SOX10 and H3K4me3 CUT&RUN peaks were called using SEACR (v 1.3). The fraction of reads in peaks was calculated using featureCounts (v 2.0.3). TSS enrichment and correlation were conducted using deeptools2137.
Assembly: hg38
Supplementary files format and content: bigwig, bed

value: tn5 from Diagenode (Cat. No. C01070010).


title: Astrocytoma (A) [A-7]

value: brain

tag: os

tag: mitotic index


title: N2 OP50 R2

value: whole animal

value: N2 (wild type)


title: MNT1 cells, CUTRUN-IgG

value: IgG(epicypher, Cat. No. 14-1048)


title: Oligodendroglioma (O) [O-14]

tag: rna extraction_protocol

value: Maxwell

tag: cohort


title: 12-week SSC Grin2a -/- Bulk RNA-seq Sample3


title: MNT1 cells, CUTRUN-H3K4me3

value: H3K4me3 (epicypher, Cat. No. 14-1048)


title: Astrocytoma (A) [A-6]

tag: sequencing library


title: Oligodendroglioma (O) [O-13]


title: MNT1 cells, CUTRUN-SOX10

tag: cell type


title: 12-week SSC Grin2a -/- Bulk RNA-seq Sample2


title: kidney_Organoid

city: Jinan

first: liqiang

last: guo

state: Shandong

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

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 ploy-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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney primary cells

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries for scRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Kidney primary cells

value: Organoid

value: organoid culture


title: MNT1 cells, CUTRUN-H3K27ac

value: H3K27Ac (abcam, # ab4729)


title: 12-week SSC Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: HuRflox_creNeg_MCMV_Rep2

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
TPM values generated from counts obtaind from HTseq and DESeq2
Gene Ontology was determined using DAVID_6.8
Assembly: GRCm38 vM24 mm10 (mus musculus)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample from cuffnorm

molecule: polyA RNA

source_name: NK Cell

extract_protocol:
polyA+ RNA was isolated from NK cells and proceed with downstream Illumina commercial kit
TruSeq Unstranded Illumina kit

value: NK Cell

value: HuR WT

value: MCMV Day 3


title: HuRflox_creNeg_MCMV_Rep1


title: 12-week SSC Grin2a -/- Bulk RNA-seq Sample1

value: Somatosensory Cortex


title: MNT1 cells, ATAC-seq

value: melanoma cells


title: Astrocytoma (A) [A-4]

source_name: brain

value: test


title: HuRflox_crePos_MCMV_Rep2

value: HuR KO


title: 12-week SSC Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: Astrocytoma (A) [A-5]

value: brain


title: HuRflox_crePos_MCMV_Rep3


title: HuRflox_creNeg_MCMV_Rep3


title: MR12122014.S

city: Boston

first: Youmna

last: Kfoury

address: 185 Cambridge street

department: Harvard stem cell institute

institute: Harvard 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 reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Bone Marrow

extract_protocol:
All Prep DNA/RNA Micro
Clontech SMARTER Kit (Takara)

value: Bone Marrow

value: Mesenchymal cells

value: Hip replacement


title: 12-week SSC Grin2a +/- Bulk RNA-seq Sample4

source_name: Somatosensory Cortex


title: HuRflox_crePos_MCMV_Rep1


title: MR12122014.DP


title: Astrocytoma (A) [A-1]

value: Maxwell


title: MR12122014.N


title: Astrocytoma (A) [A-2]


title: 12-week SSC Grin2a +/- Bulk RNA-seq Sample2


title: HuRflox_creNeg_Uninfected_Rep3

value: Uninfected Day 3


title: HuRflox_creNeg_Uninfected_Rep2


title: 12-week SSC Grin2a +/- Bulk RNA-seq Sample3


title: 12-week SSC Grin2a +/- Bulk RNA-seq Sample1


title: MR11142014.N


title: MR12122014.DN


title: Oligodendroglioma (O) [O-12]


title: HuRflox_creNeg_Uninfected_Rep1


title: Non-neoplastic (NT) [NT-4]


title: MR11142014.S


title: 4-week SSC Grin2a WT Bulk RNA-seq Sample5

value: WT


title: Oligodendroglioma (O) [O-10]


title: 4-week SSC Grin2a WT Bulk RNA-seq Sample3


title: Oligodendroglioma (O) [O-8]


title: MR11072014.N


title: HuRflox_crePos_Uninfected_Rep3


title: MR11072014.S


title: Oligodendroglioma (O) [O-11]


title: Astrocytoma (A) [A-3]


title: 4-week SSC Grin2a WT Bulk RNA-seq Sample2


title: MR11142014.DP


title: MR11142014.DN


title: HuRflox_crePos_Uninfected_Rep2


title: mouse CD45+_biol rep 3

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 reference genome hg19 and mm9 using STAR
Transcript abundance was calculated using Htseq
Assembly: hg19 for human and mm9 for mouse
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

value: Hematopoietic


title: MR11072014.DP


title: mouse CD45+_biol rep 2


title: Oligodendroglioma (O) [O-7]


title: 4-week SSC Grin2a WT Bulk RNA-seq Sample4


title: HuRflox_crePos_Uninfected_Rep1


title: mouse CD45+_biol rep 1


title: 4-week SSC Grin2a WT Bulk RNA-seq Sample1


title: 4-week SSC Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: Oligodendroglioma (O) [O-6]


title: mouse CD51+_biol rep 3

source_name: Digested Bones

value: Digested Bones

value: Mesenchymal


title: Non-neoplastic (NT) [NT-3]


title: MR10312014.S


title: Oligodendroglioma (O) [O-9]


title: 4-week SSC Grin2a -/- Bulk RNA-seq Sample5


title: mouse CD51+_biol rep 2


title: 4-week SSC Grin2a -/- Bulk RNA-seq Sample2


title: MR10312014.N


title: 4-week SSC Grin2a +/- Bulk RNA-seq Sample5


title: mouse Ocn+_biol rep 3


title: mouse CD51+_biol rep 1


title: MR10172014.N


title: 4-week SSC Grin2a +/- Bulk RNA-seq Sample3


title: MR11072014.DN


title: 4-week SSC Grin2a -/- Bulk RNA-seq Sample1


title: Oligodendroglioma (O) [O-4]


title: Oligodendroglioma (O) [O-5]


title: Glioblastoma (G) [G-12]


title: Oligodendroglioma (O) [O-2]


title: mouse Ocn+_biol rep 1


title: 4-week SSC Grin2a +/- Bulk RNA-seq Sample4


title: mouse Osx+_biol rep 3


title: Oligodendroglioma (O) [O-3]


title: Glioblastoma (G) [G-13]


title: MR10172014.DP


title: Glioblastoma (G) [G-11]


title: 4-week SSC Grin2a +/- Bulk RNA-seq Sample2


title: 4-week SSC Grin2a -/- Bulk RNA-seq Sample3


title: 4-week SSC Grin2a +/- Bulk RNA-seq Sample1


title: MR10172014.DN


title: MR10312014.DP


title: MR10312014.DN


title: Glioblastoma (G) [G-10]


title: MR10172014.S


title: 2-week SSC Grin2a WT Bulk RNA-seq Sample5


title: MR03202015.N


title: Glioblastoma (G) [G-8]


title: Muscle stem cells - input DNA

city: Hiroshima-shi

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima University

data_processing:
Illumina Bcl2fastq_V2.16 software used for basecalling.
The sequenced reads were mapped to mouse genome (GRCm38) using HISAT2 (version 2.10).
Peaks were called using MACS2 (version 2.1.1) with the option: callpeak -q 0.01.
Genome_build: GRCm38
Supplementary_files_format_and_content: QSC_peaks.txt: Matrix table with absolute summits of peaks, pileup counts and p-values.

source_name: muscle stem cells

growth_protocol: Muscle stem cells were isolated from mice by FACS and samples were prepared.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
Library was prepared according to NEBNext Ultra DNA Library Prep Kit (E7370) by the steps of end-polishing, dA-addition and the DNA fragments with A tail were ligated to sequencing adaptors. After 100bp-500bp size selection and PCR amplification, the DNA libraries were quantified and sequenced on HiSeq2500 platform using single-end 50bp sequencing based on manufacturer’s instructions.

tag: strain

tag: genotype/variation

value: Pax7-YFP KI

value: Muscle stem cells

value: untreated

tag: chip antibody


title: Glioblastoma (G) [G-6]

value: test


title: Muscle stem cells - GFP

value: GFP (Thermo Fisher, A-11122)


title: MR03202015.DP

tag: genotype


title: 2-week SSC Grin2a WT Bulk RNA-seq Sample1

value: Somatosensory Cortex

tag: age


title: 2-week SSC Grin2a WT Bulk RNA-seq Sample3


title: mouse Osx+_biol rep 2


title: Glioblastoma (G) [G-7]

value: brain


title: MR03202015.DN

value: Bone Marrow


title: Glioblastoma (G) [G-5]


title: 2-week SSC Grin2a -/- Bulk RNA-seq Sample5


title: MR03062015.S

value: Mesenchymal cells


title: MR03062015.N

value: Hip replacement


title: MM1-S-24hr-SR-3029

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to adaptor trimming, series of quality assessment before being aligned with STAR-2.5.3 against mouse reference genome mm10.
Quantification of read counts aligned to the region associated with each gene was performed using HTSeq v0.6.1 based on National Center for Biotechnology information (NCBI) RefSeq gene model.
Read counts of all samples were normalized using the median-of-ratios method implemented in R/Bioconductor package DESeq2 v1.6.3.
Differential expression analysis between the two groups was performed by serial dispersion estimation and statistical model fitting procedures implemented in DESeq2.
Assembly: hg19
Supplementary files format and content: Text file of normalized gene abundance

source_name: Cell Line

growth_protocol: Bone Marrow samples were maintained in Collagen I coated plates with RPMI containing 10% heat inactivated FBS

extract_protocol:
Cells were washed with 1x PBS twice and cell pellets were lysed and total RNA extracted using the MACHEREY-NAGEL NucleoSpin RNA Mini Kit for RNA purification (REF 740955.50)
Nugen_Ovation RNASeq Kit protocol

treatment_protocol: Patient Samples were treated with vehicle or SR-3029 at the indicated time points

value: Cell Line

value: Multiple Myeloma


title: 8226-24hr-SR-3029


title: MM1-S-8hr-SR-3029


title: Glioblastoma (G) [G-4]

value: Maxwell


title: 8226-8hr-SR-3029


title: mouse Osx+_biol rep 1


title: 2-week SSC Grin2a -/- Bulk RNA-seq Sample4


title: MR03202015.S


title: Glioblastoma (G) [G-9]


title: Glioblastoma (G) [G-3]


title: MR03062015.DP


title: 2-week SSC Grin2a WT Bulk RNA-seq Sample2

value: WT


title: MM1-S-24hr-Vehicle

value: Vehicle


title: 2-week SSC Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: MR03062015.DN


title: MR03022016.S


title: Glioblastoma (G) [G-1]


title: 2-week SSC Grin2a -/- Bulk RNA-seq Sample1


title: Glioblastoma (G) [G-2]


title: Oligodendroglioma (O) [O-1]


title: 2-week SSC Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: 7-24-17-Tx-250nM-SR-3029

source_name: Tumor

value: Tumor

value: Patient Sample


title: 8226-8hr-vehicle


title: MR03022016.N


title: MM1-S-8hr-Vehicle


title: MR03022016.DN


title: 2-week SSC Grin2a +/- Bulk RNA-seq Sample4


title: MR03022016.DP


title: 2-week SSC Grin2a +/- Bulk RNA-seq Sample3


title: MR02272015.S


title: 2-week SSC Grin2a +/- Bulk RNA-seq Sample2


title: 5-15-17-Trans-Vehicle


title: 5-15-17-Trans-250nM-SR-3029


title: 2-week SSC Grin2a +/- Bulk RNA-seq Sample1


title: MR02272015.N


title: 12-21-17-TX-250nM-SR-3029


title: 8226-24hr-Vehicle


title: 2-week SSC Grin2a -/- Bulk RNA-seq Sample2


title: MR02272015.DN


title: 12-21-16-TX-vehicle


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample9

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: MR02202015.S


title: 1-19-17-Tx-250nM-SR-3029


title: 7-24-17-TX-Vehicle


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample8


title: 1-19-17-Tx-vehicle


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample6


title: 1-18-17-Tx-250nM-SR-3029


title: MR02202015.DN


title: MR02202015.DP


title: MR02272015.DP


title: Exosomes, SCLC 5

city: Songpa-gu

first: Dong Ha

last: Kim

state: Seoul

address: 88, Olympic-ro 43-gil

department: Asan institute for life sciences

institute: ASAN Medical Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Quantile normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

source_name: serum exosomes

extract_protocol:
Isolation of exosomes from serum samples were centrifuged at 10,000 × g for 30 min at 4 °C to completely eliminate cellular debris. Thereafter, the supernatant was centrifuged at 100,000 × g for 70 min at 4 °C. The pellets were washed with phosphate-buffered saline (PBS), ultracentrifuged, and re-suspended in PBS. Exosomal RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

value: serum exosomes

tag: disease state

value: Small cell lung cancer

tag: tumor stage

value: LD

tag: Sex

value: male


title: Exosomes, SCLC 4


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample10

tag: tissue


title: MR02132015.N

value: Bone Marrow


title: MR02132015.DP

value: Mesenchymal cells


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample3


title: Exosomes, SCLC 3


title: MR02132015.S

value: Hip replacement


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample7


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample2


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample4


title: Exosomes, SCLC 2


title: MR02202015.N


title: Exosomes, SCLC 1


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample1


title: MR02132015.DN


title: OAW660332.S

value: MDS


title: OAW660332.N


title: 1-18-17-Tx-vehicle

tag: cell line

value: Multiple Myeloma

tag: treatment


title: 20-week PFC Grin2a -/- Bulk RNA-seq Sample3


title: OAW660332.DP


title: 20-week PFC Grin2a WT Bulk RNA-seq Sample5


title: Exosomes, Control 4

value: lung nodules


title: 20-week PFC Grin2a -/- Bulk RNA-seq Sample2


title: Exosomes, Control 3


title: OAW660332.DN


title: 20-week PFC Grin2a -/- Bulk RNA-seq Sample1


title: 20-week PFC Grin2a +/- Bulk RNA-seq Sample5


title: Exosomes, Control 2


title: OAW35389037.S


title: Exosomes, Control 1


title: OAW35389037.N


title: OAW35389037.DP


title: 20-week PFC Grin2a +/- Bulk RNA-seq Sample4


title: NGP-nutlin-spikes-1-10000_S1

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

data_processing: ddSeeker was used for alligment and quantification of the data.

source_name: NGP cell line

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10 % fetal bovine serum, 1 % of L-glutamine and 1 % penicillin/streptomycin  at 37 °C in a 5 % CO2 atmosphere.

extract_protocol:
Cells were lysed and cDNA was synthesized on the ddSeq single cell device (Bio-Rad).
polyA+ RNA-seq libraries were generated using the SureCell WTA 3’ library prep kit (Illumina) for the ddSeq system (Bio-Rad).

value: Nutlin-3 treated

value: NGP

tag: synchronization

value: cell cycle synchronization

tag: ercc spikes

value: ERCC spikes diluted to 1/10,000


title: OAW35389037.DN


title: 20-week PFC Grin2a +/- Bulk RNA-seq Sample3

value: Grin2a +/-


title: Exosomes, Control 5


title: 20-week PFC Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: 20-week PFC Grin2a +/- Bulk RNA-seq Sample2

value: Prefrontal Cortex


title: OAW35236697.S


title: NGP-nutlin-spikes-1-1000_S4

value: ERCC spikes diluted to 1/1000


title: NGP-EtOH-spikes-1-1000_S3

value: ethanol


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample10

value: WT


title: NGP-EtOH-spikes-1-10000_S2


title: OAW35236697.N


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample9


title: 20-week PFC Grin2a +/- Bulk RNA-seq Sample1


title: HEPG2 cells, 17_S9

city: Baltimore

first: Sumita

last: Mishra

state: MD

address: 720 Rutland Avenue

department: Medicine

institute: Johns Hopkins University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and for low-quality sequence, using Trim Galore v0.6.4_dev with parameters --cores 4 --paired -q 28
Gene Alignment to hg38 whole genome using bowtie v1.0.1 with parameters -p 4 -t --end-to-end
Peak locations were determined using the MACS2 algorithm (v2.2.7.1) with parameters -f BAMPE -g 2913022398 -B -q 0.03
Peaks were annotated using annotatePeaks.pl from Homer v4.11 with default parameters
Functional Analysis was performed using ChIPSeeker (v1.18.0)
DiffBind (v2.16) package was used for Differential binding analysis and generation of PCA plots and heat maps
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: ChIP Peaks Narrow Peak

source_name: HEPG2 cells

growth_protocol: HepG2, a human HCC-derived cell line, was obtained from the American Type Culture Collection (ATCC, USA). HepG2 cells were maintained in DMEM supplemented with 10% (v/v) FBS, 1% antibiotics 50 U/ml penicillin, and 50 μg/ml streptomycin (Invitrogen, Grand Island, NY) at 37°C in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol:
SimpleChIP Enzymatic Chromatin IP kit (CST) was used for immunoprecipitation following manufacturer’s instruction. Cells were washed with ice cold PBS twice and then crosslinked by incubating with 1% formaldehyde for 10 min. The reaction was stopped by the addition of 2.5 M glycine and the plates were washed twice with ice cold PBS. Chromatin was treated with nuclease and subjected to sonication. Immunoprecipitation was performed with PPARα specific antibody (Abcam ChIP-grade ab227074) and Protein G magnetic beads. Chromatin was eluted from the beads, uncrosslinked and purified.
ChIP and input DNA libraries were prepared using Clontech DNA SMART kit (Takara Bio 634866).

treatment_protocol: For each ChIP pull-down, approximately 5 × 10e6 Hepg2 cells were cultured into three 15 cm diameter plates in DMEM with 10% fetal bovine serum. Next day, the cells were transfected with expression vectors for either PPAR alpha alone (Human Tagged ORF, RC216176, Origene), or in combination with expression vector for Estrogen receptor alpha (ERa) (pCMV ERalpha, #101141, addgene) and Estrogen receptor beta (ERb) (pcDNA Flag ERbeta, #35562 addgene). 48 hrs after transfection, cells were treated with either respective agonist  for PPAR alpha alone for 2hrs- Wy13643 (Group PPARa) (10 µM, Wy14643, Cat 1312, Sigma) or with ERa specific agonist - 10 nM, PPT (Cat 1426/50, Tocris ) (Group PPARa+ERa) or with ERb specific agonist -10 nM, DPN (Cat 1494/50, Tocris) (Group PPARa+ERb) for 45 mins and then simulated for additional 2 hrs with PPARa specific agonist.

value: Transfection with PPARa+ Estrogen receptor alpha and treated with their respective agonist.

tag: agonist

value: PPARa agonist Wy13643 + Ea stimulated agonist PPT

value: anti-PPAR alpha antibody (Abcam, Catalog No.- ab227074,  Lot name- GR3201839-22)


title: HEPG2 cells, 27_S14


title: HEPG2 cells, 18_S9


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample7


title: OAW35236697.DP

value: Bone Marrow

value: Mesenchymal cells


title: OAW226719.DP

value: MDS


title: mouse Ocn+_biol rep 2

value: Digested Bones

value: Mesenchymal


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample6


title: OAW35236697.DN


title: HEPG2 cells, 6_S3

value: Transfection with PPARa+ Estrogen receptor beta and treated with their respective agonist.

value: PPARa agonist Wy13643 + Eb agonist DPN stimulated


title: HEPG2 cells, 5_S3


title: OAW226719.N


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample5


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample8


title: HEPG2 cells, 2_S1

value: Transfection with PPARa and treated with PPARa agonist.

value: PPARa agonist Wy13643 stimulated


title: HEPG2 cells, 1_S1

value: Transfection with PPARa and treated with PPARa agonist


title: KB4302014.S


title: OAW226719.DN


title: KB4302014.N


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample4

value: Prefrontal Cortex


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample3


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample2


title: KB4302014.DP


title: 12-week PFC Grin2a WT Bulk RNA-seq Sample1


title: OAW226719.S


title: KB4302014.DN


title: 12-week PFC Grin2a -/- Bulk RNA-seq Sample5

value: Grin2a -/-


title: EA09272012.S


title: 12-week PFC Grin2a -/- Bulk RNA-seq Sample4


title: SI WT Eif4a2 Rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was achieved via IP administration of 2 x 2mg tamoxifen doses, 24 hours apart.

value: Female

value: Small intestine

value: VilCreER EiF4A2fl/fl

tag: time

value: Day 4


title: SI WT Eif4a2 Rep 4


title: EA09272012.N


title: SI WT Eif4a2 Rep 2

value: Male


title: SI WT Eif4a2 Rep 1


title: SI WT Rep 5

value: VilCreER


title: EA09272012.DP

value: Bone Marrow

value: Mesenchymal cells


title: 12-week PFC Grin2a -/- Bulk RNA-seq Sample2

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample


title: EA09272012.DN

value: MDS


title: SI WT Eif4a1 Rep 6

value: VilCreER Eif4A1fl/fl


title: 12-week PFC Grin2a -/- Bulk RNA-seq Sample1


title: 12-week PFC Grin2a -/- Bulk RNA-seq Sample3


title: SI WT Rep 4


title: 12-week PFC Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: DS12152014.S


title: SI WT Eif4a1 Rep 5


title: DS12152014.N


title: 12-week PFC Grin2a +/- Bulk RNA-seq Sample4


title: SI WT Eif4a1 Rep 3

value: Day 3


title: SI WT Eif4a1 Rep 4


title: 12-week PFC Grin2a +/- Bulk RNA-seq Sample2


title: DS12152014.DN


title: DS12152014.DP


title: SI WT Eif4a1 Rep 2


title: 12-week PFC Grin2a +/- Bulk RNA-seq Sample3


title: DS06182014.S


title: SI WT Eif4a1 Rep 1


title: SI WT Rep 3


title: DS06182014.N


title: DS06182014.DP


title: DS06182014.DN


title: 4-week PFC Grin2a WT Bulk RNA-seq Sample4

value: WT


title: SI WT Rep 1


title: 4-week PFC Grin2a WT Bulk RNA-seq Sample5


title: SI WT Rep 2


title: DBS03072014.N


title: SI AK Eif4a2 Rep4

value: VilcreER Apc fl/fl KrasG12D/+ Eif4a2 fl/fl


title: DBS03072014.S


title: 4-week PFC Grin2a WT Bulk RNA-seq Sample3


title: SI AK Eif4a2 Rep3


title: 4-week PFC Grin2a WT Bulk RNA-seq Sample2


title: 4-week PFC Grin2a WT Bulk RNA-seq Sample1


title: DBS03072014.DP


title: 4-week PFC Grin2a -/- Bulk RNA-seq Sample5


title: SI AK Eif4a2 Rep2


title: 4-week PFC Grin2a -/- Bulk RNA-seq Sample4


title: SI AK Eif4a2 Rep1


title: SI AK Eif4a1 Rep4

value: VilcreER Apc fl/fl KrasG12D/+ Eif4a1 fl/fl


title: DBS01222016.S


title: 4-week PFC Grin2a -/- Bulk RNA-seq Sample2

value: Prefrontal Cortex


title: SI AK Eif4a1 Rep3


title: DBS01222016.N


title: 4-week PFC Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: 2-week SSC Grin2a WT Bulk RNA-seq Sample4

value: Somatosensory Cortex


title: 12-week PFC Grin2a +/- Bulk RNA-seq Sample1


title: DBS01222016.DP


title: SI AK Eif4a1 Rep2

value: Female

value: Small intestine


title: DBS01222016.DN


title: 4-week PFC Grin2a -/- Bulk RNA-seq Sample1


title: SI AK Eif4a1 Rep1


title: 4-week PFC Grin2a +/- Bulk RNA-seq Sample5


title: SI AK Rep4

value: VilcreER Apc fl/fl KrasG12D/+


title: BM12052011A.S


title: DBS03072014.DN


title: 4-week PFC Grin2a +/- Bulk RNA-seq Sample4


title: BM12052011A.N


title: BM12052011A.DN


title: SI AK Rep3

value: Male


title: BM12052011A.DP


title: 4-week PFC Grin2a +/- Bulk RNA-seq Sample3


title: 4-week PFC Grin2a +/- Bulk RNA-seq Sample2


title: SI AK Rep1


title: 4-week PFC Grin2a +/- Bulk RNA-seq Sample1


title: SI Apc Eif4a2 Rep4

value: VilCreER Apc f/f eIF4A2 f/f

value: Day 4


title: BM08062012A.S

value: Bone Marrow

value: Mesenchymal cells


title: BM08062012A.N

value: MDS


title: SI Apc Eif4a2 Rep3


title: 2-week PFC Grin2a WT Bulk RNA-seq Sample5


title: 2-week PFC Grin2a WT Bulk RNA-seq Sample3


title: BM08062012A.DP


title: 2-week PFC Grin2a WT Bulk RNA-seq Sample4


title: BM08062012A.DN


title: SI Apc Eif4a2 Rep2


title: SI Apc Eif4a2 Rep1


title: 2-week PFC Grin2a WT Bulk RNA-seq Sample2


title: BM07172012.S


title: HS360-Day20-P200-rep6 [35-sc2-D20-P200-D]

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

institute: University of Oslo

data_processing:
BBDuk (BBMap v. 34.56) was used to reomve and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
Reads were mapped to the human genome/transcriptome ENSEMBL GRCh38.p5 release 83 using hisat2 v2.1.0
FeatureCounts v.1.4.6-p1 was used to count the reads mapping to the features using default configurations
Downstream normalisation and differential expression analysis was performed using R software DEseq2 package v 1.30.1.
Assembly: ENSEMBL GRCh38.p5 release 83 (genome-build-accession NCBI:GCA_000001405.20)
Supplementary files format and content: Count file with data matrix with unnormalized counts for each sample. Additionaly, "normcounts.paracetamol.csv" contains a normalized count matrix for all samples.

source_name: HS360, day 20, past stage III maturation, exposed to 200μM paracetamol

extract_protocol:
Total RNA was extracted from cultured cells using Norgen RNA/DNA purification kit or Qiagen RNeasy kit and treated with DNase according to manufacturer´s instructions.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Novaseq 6000 S1 flow cell with 100bp pair end reads.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected. For cells that were exposed to either 100 or 200 μM paracetamol, fresh media with paracetamol concentrations of 100 μM and 200 μM (Merck; A7085) was added every day from Day 1 until collection day (Day 7 or Day 20).

tag: gender

value: male

value: maturated NPCs

value: Day 20 200 μM paracetamol


title: SI AK Rep2

value: Day 3


title: SI Apc Eif4a1 Rep4

value: VilCreER Apc f/f eIF4A1 f/f


title: 2-week PFC Grin2a WT Bulk RNA-seq Sample1

value: Prefrontal Cortex

value: WT


title: 2-week PFC Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: BM07172012.N

tag: cell type


title: SI Apc Eif4a1 Rep3


title: BM07172012.DP


title: HS360-Day20-P200-rep4 [33-sc2-D20-P200-B]


title: 2-week PFC Grin2a -/- Bulk RNA-seq Sample3


title: SI Apc Eif4a1 Rep2


title: BM07172012.DN


title: HS360-Day20-P200-rep3 [32-sc1-D20-P200-B]


title: 2-week PFC Grin2a -/- Bulk RNA-seq Sample2


title: SI Apc Eif4a1 Rep1


title: HS360-Day20-P200-rep2 [17-sc2-D20-P200-A]


title: 2-week PFC Grin2a -/- Bulk RNA-seq Sample1


title: BM01172012A.N


title: SI Apc Rep3

value: VilCreER Apc f/f


title: SI Apc Rep4

value: Small intestine


title: HS360-Day20-P200-rep1 [16-sc1-D20-P200-A]


title: BM01172012A.S


title: BM01172012A.DN


title: 2-week PFC Grin2a +/- Bulk RNA-seq Sample4

value: Grin2a +/-


title: 2-week PFC Grin2a +/- Bulk RNA-seq Sample5


title: BM01172012A.DP


title: SI Apc Rep2

value: Female


title: HS360-Day20-P100-rep3 [30-sc1-D20-P100-B]

source_name: HS360, day 20, past stage III maturation, exposed to 100μM paracetamol

value: Day 20 100 μM paracetamol


title: SI Apc Rep1

value: Male

value: Day 4


title: 2-week PFC Grin2a +/- Bulk RNA-seq Sample3


title: HS360-Day20-P100-rep1 [14-sc1-D20-P100-A]


title: 2-week PFC Grin2a +/- Bulk RNA-seq Sample2


title: HS360-Day20-P100-rep2 [15-sc2-D20-P100-A]


title: HS360-Day20-P200-rep5 [34-sc2-D20-P200-C]


title: AOW09202012.S

value: Bone Marrow

value: Mesenchymal cells


title: HS360-Day7-P200-rep5 [159-D7-P200-A]

description: Day 7", "male", "neural rosettes", "neural induction", "paracetamol", "P200

source_name: HS360, day 7, past stage I neural induction, exposed to 200μM paracetamol

value: male

value: neural rosettes

value: Day 7 200 μM paracetamol


title: AOW09202012.DP

value: MDS


title: 2-week PFC Grin2a +/- Bulk RNA-seq Sample1


title: 20-week HP Grin2a WT Bulk RNA-seq Sample10

source_name: Hippocampus

value: Hippocampus


title: HS360-Day20-P100-rep4 [31-sc2-D20-P100-B]

value: maturated NPCs


title: AOW04102015.S


title: 20-week HP Grin2a WT Bulk RNA-seq Sample9

value: WT


title: AOW09202012.DN


title: 20-week HP Grin2a WT Bulk RNA-seq Sample8


title: HS360-Day7-P200-rep2 [9-sc2-D7-P200-A]


title: AOW04102015.N


title: 20-week HP Grin2a WT Bulk RNA-seq Sample7


title: AOW04102015.DP


title: HS360-Day7-P200-rep1 [8-sc1-D7-P200-A]


title: HS360-Day7-P100-rep5 [156-D7-P100-A]

source_name: HS360, day 7, past stage I neural induction, exposed to 100μM paracetamol

value: Day 7 100 μM paracetamol


title: AOW04102015.DN


title: 20-week HP Grin2a WT Bulk RNA-seq Sample5


title: AOW09202012.N


title: human CD45+_biol rep 2

value: Hematopoietic


title: HS360-Day7-P200-rep4 [24-sc2-D7-P200-B]


title: human CD45+_biol rep 1


title: 20-week HP Grin2a WT Bulk RNA-seq Sample3


title: HS360-Day7-P100-rep2 [7-sc2-D7-P100-A]


title: HS360-Day7-P200-rep3 [23-sc1-D7-P200-B]


title: HS360-Day7-P100-rep1 [6-sc1-D7-P100-A]


title: human CD51+_biol rep 3

source_name: Bone Marrow+Spicules

value: Bone Marrow+Spicules

value: Mesenchymal


title: 20-week HP Grin2a WT Bulk RNA-seq Sample2


title: human CD51+_biol rep 2


title: 20-week HP Grin2a WT Bulk RNA-seq Sample1


title: human CD51+_biol rep 1


title: human SN: CD146+CD271-CD106-_biol rep 3


title: 20-week HP Grin2a -/- Bulk RNA-seq Sample4

value: Grin2a -/-


title: 20-week HP Grin2a WT Bulk RNA-seq Sample6


title: 20-week HP Grin2a -/- Bulk RNA-seq Sample2


title: 20-week HP Grin2a -/- Bulk RNA-seq Sample1


title: human SN: CD146+CD271-CD106-_biol rep 2


title: 20-week HP Grin2a -/- Bulk RNA-seq Sample3


title: 20-week HP Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: HS360-Day7-P100-rep4 [22-sc2-D7-P100-B]


title: human CD45+_biol rep 3

source_name: Bone Marrow


title: 20-week HP Grin2a +/- Bulk RNA-seq Sample4


title: KPCA.C, omental tumor, scRNAseq

city: Bosotn

first: Maeva

middle: Yvette

last: Chauvin

address: 55 fruit st

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Omental tumors (KPCA.A, KPCA.B, KPCA.C) were freshly collected from C57Bl6J mice and dissociated by incubating tumor pieces with a digestion buffer (DMEM 10% supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) at 37 °C for 30 min. The resulting mixture was transferred into a dissociation tube and processed using the MacMachine device to initiate the dissociation process. Cells were then filtered through a 70 µm strainer, washed, and resuspended in PBS. Single-cell RNA sequencing (scRNAseq) was performed on samples with >70% cell viability.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, tumor cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Fallopian tube epithelial cells

value: Tumor

tag: strain

value: 8 weeks old


title: human SP: CD146+CD271-CD106+_biol rep 3


title: 20-week HP Grin2a WT Bulk RNA-seq Sample4

city: Cambridge

first: Ally

last: Nicolella

address: 75 Ames St

institute: Broad Institute

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
rna


title: human SP: CD146+CD271-CD106+_biol rep 2


title: KPCA_Ascites, scRNAseq

description: 10x Genomics

source_name: Ascite

value: Ascite

value: 9 weeks old


title: KPCA.B, omental tumor, scRNAseq

description: 10x Genomics


title: HS360-Day7-P100-rep3 [21-sc1-D7-P100-B]

value: male

value: neural rosettes


title: human DN: CD146+CD271+CD106-_biol rep 3


title: KPCA.A, omental tumor, scRNAseq

description: 10x Genomics


title: 20-week HP Grin2a +/- Bulk RNA-seq Sample2


title: 20-week HP Grin2a +/- Bulk RNA-seq Sample3


title: human DN: CD146+CD271+CD106-_biol rep 2


title: wt_ip_rep2

city: Chicago

first: Chuan

last: He

address: 929 E 57th St, Room E319B

institute: University of Chicago

description:
the processed data file summarises peak positions in a bed format, this is a CLIP sample
CLIP_peaks_wildTypeAndMutant.xlsx

data_processing:
Adapter trimming by Cutadapt
Reads mapping by STAR to the transcriptome
Peak calling with OmniCLIP (for dataset 1), Reads calculation with RSEM (for dataset 2)
Assembly: for [Dataset 1], hg19. For [Dataset 2],hg38
Supplementary files format and content: For [Dataset 1] Excel (xlsx) files, with individual peak information in a bed format (CLIP_peaks_wildTypeAndMutant.xlsx)
Supplementary files format and content: For [Dataset 2] Excel (xlsx) files, with reads mapped to individual genes by RSEM, FPKM values and TPM values are both shown (RiboLace_reads.xlsx)

source_name: HEK293T (ATCC CRL-3216)

growth_protocol: HEK293T or HeLa cells were both kept in DMEM + 10% FBS in a regular cell culture incubator (37 degree with 5% CO2)

extract_protocol:
NEB small RNA
For [Dataset 1], HEK293T cells restored with wild-type or GlcNAcylation-null mutants were cross-linked twice with 254 nm-UV light, 0.15 J/cm2 each time (UV stratalinker 2400, Stratagene). Cells were then lysed by the lysis buffer (150 mM NaCl, 0.5% NP-40, 50 mM Tris-HCl (pH 7.5), 2 mM EDTA and 1% HaltTM protease and phosphatase inhibitor cocktail (Thermo Scientific, 78440)) at 4 °C with end-to-end rotation for 30 minutes. Cell debris were spun down at 21,000 g at 4 °C for 15 minutes. The lysates were treated with 0.2 U/μl RNase T1 (Thermo Scientific, EN0541) for 10 minutes at 22 °C with shaking. Pre-washed anti-FLAG M2 magnetic beads (MilliporeSigma, M8823-1ML) were applied to the lysates and incubated at 4 °C with end-to-end rotation for 8 hours. The beads were washed three times with 1ml IP wash buffer (50 mM Tris-HCl (pH 7.5), 300 mM KCl, 0.05% NP-40, 0.5 mM DTT, and 1% HaltTM protease and phosphatase inhibitor cocktail (Thermo Scientific, 78440)). The washed beads and input samples were resuspended in 1 vol IP wash buffer supplemented with 8 U/μl RNase T1 (Thermo Scientific, EN0541) for 10 minutes at 22 °C with shaking. Beads and input samples are resuspended in 100 ul 1 × Laemmli sample buffer (Bio-Rad, 1610747) and subjected to SDS-PAGE separation. The bands corresponding to ~70 kDa were cut with a razerblade and digested with proteinase K (Invitrogen, 25530049) for 50 minutes at 55 °C with shaking. Fragmented RNAs were extracted with TRIzolTM reagent (Invitrogen, 15596026).For [Dataset 2],  CHX (cycloheximide,  Milliporesigma C7698-1G) was added to a final concentration of 100 μg/ml to the medium and incubate for 7 minutes. Then spin down the cells, wash once with cold DPBS with 100 μg/ml CHX and spin down again, flash-freeze with LN2 and store at -80C. RPFs were prepared according to the manufacturer's instructions with riboLace kit (IMMAGINA, RL001). Total RNAs were extracted with standard TRIzol protocol.
For [Dataset 1], RNA libraries for inputs and ip samples were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with input or CLIP short RNA as inputs. For [Dataset 2], RNA libraries for rpf samples were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with end-repaired ribosome-protected fragments (RPFs) extracted as inputs. RNA libraries for input samples were constructed with TruSeq Stranded mRNA (Illumina, 20020594) with polyA-RNA extracted as inputs.

treatment_protocol: For [Dataset 1] and [Dataset 2], Wild-type HEK293T or HeLa cells were transfected with small interfering RNA (siRNA) with LipofectamineTM RNAiMAX transfection reagent (Invitrogen, 13778150) per manufacturer’s instructions. Cells were reseeded after 8 hours. The next day, cells were transfected with plasmids with LipofectamineTM 2000 transfection reagent per manufacturer’s instructions. After 24 hours, cells were harvested for western blotting or RNA extraction.

tag: dataset

value: HEK293T (ATCC CRL-3216)

value: human embryo kidney

value: Wild-type

value: siRNA-based knockdown of YTHDF1 and YTHDF3

tag: rescue

value: wild-type (wt) YTHDF1 and YTHDF3

tag: rip antibody

value: anti-FLAG M2


title: human SN: CD146+CD271-CD106-_biol rep 1

value: Bone Marrow+Spicules


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-safb∆dd2, tech rep2

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: North Carolina

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

data_processing:
reads were aligned to genome using star/2.5.4b
filtered for reads that passed quality score q30
used subread featureCounts with gencode.vM25.basic.annotation.gtf to assign sequence reads to features
deseq2
Assembly: mm10
Supplementary files format and content: wig
Supplementary files format and content: excel file of processed data

source_name: Embryonic Stem Cells

growth_protocol: RMCE embryonic Stem Cells were maintained in DMEM supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
50uL of sonicated cell lysate was prepared with Zymo Clean and Concentrator
KAPA RNA Hyperprep Kit with RiboErase, 100ng of input sequenced

value: Embryonic Stem Cells

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells

tag: genotype

value: SAFB1/2 DKO clone 13 + safb-dd2{delta}

value: 3 Days Doxycycline induction


title: wt_ip_rep1


title: human DN: CD146+CD271+CD106-_biol rep 1

value: Mesenchymal


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-FL-SAFB, bio rep #1, tech rep #2

value: SAFB1/2 DKO clone 13 + FL-SAFB


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-FL-SAFB, bio rep #1, tech rep #1


title: human DP: CD146+CD271+CD106+_biol rep 2


title: human DP: CD146+CD271+CD106+_biol rep 3


title: 12-week HP Grin2a WT Bulk RNA-seq Sample4

value: Hippocampus

value: WT

tag: age


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-eGFP, bio rep #1, tech rep #2

value: SAFB1/2 DKO clone 13 + eGFP


title: human DP: CD146+CD271+CD106+_biol rep 1


title: wt_input_rep2

description:
the processed data file summarises peak positions in a bed format, this is an input sample
CLIP_peaks_wildTypeAndMutant.xlsx

value: HEK293T (ATCC CRL-3216)


title: 12-week HP Grin2a WT Bulk RNA-seq Sample3


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-eGFP, bio rep #1, tech rep #1


title: 12-week HP Grin2a WT Bulk RNA-seq Sample2


title: human SP: CD146+CD271-CD106+_biol rep 1


title: mut_ip_rep2

value: human embryo kidney

value: O-GlcNAcylation-null mutant (mut) YTHDF1 and YTHDF3


title: mut_ip_rep1

value: Wild-type

value: siRNA-based knockdown of YTHDF1 and YTHDF3


title: 12-week HP Grin2a WT Bulk RNA-seq Sample1


title: 20-week HP Grin2a +/- Bulk RNA-seq Sample1

value: Grin2a +/-


title: MR12122014

value: Bone Marrow

value: Hip Replacement


title: wt_input_rep1

value: wild-type (wt) YTHDF1 and YTHDF3


title: 12-week HP Grin2a -/- Bulk RNA-seq Sample5

value: Grin2a -/-


title: mut_input_rep2


title: mut_input_rep1


title: MR11142014


title: CD8+CD69+CD103+Trm / D42 post DNFB / treatment: TA / sample B

city: Lyon

first: Marc

last: Vocanson

address: 21 avenue Tony Garnier

institute: INSERM

description: INS-MV-b003_HDMERGEDL_S8_R2.ReadCounts.tsv

data_processing:
Base calls were converted to FASTQ files by using bcl2fastq v2.2 and default settings.
Read 1 was used to identify the Illumina library index and CEL-Seq2 sample barcode. Read 2 was aligned to the Mus musculus (GRCm38) RefSeq transcriptome, using BWA-MEM v0.7.15-t8 and standard trimming settings
Mapping and generation of count tables was done using the HTSeq counts script
Assembly: GRCm38
Supplementary files format and content: Count table with raw gene counts for every gene per sample

source_name: Skin

extract_protocol:
FACS sorted Trm subsets were sent to Single Cell Discoveries (Utrecht, The Netherlands) for bulk RNA sequencing. Total RNA was extracted using the standard TRIzol (Invitrogen) protocol and used for library preparation and sequencing.
Library preparation followed the CEL-seq2 protocol. Samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight in vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina TruSeq small RNA primers. Paired-end sequencing was performed on the Illumina NextSeq 500 platform by sequencing paired-end at 75 bp read length, with a sequencing depth of 10 million reads/sample.

treatment_protocol: Live Nur77GFP+ and/or Nur77GFP- CD45+CD8+CD69+CD103+ TRM were FACS-sorted on a BD Biosciences FACSAria from the skin of DNFB allergic Nur77GFP animals treated with TA or Acetone, just before or 24 and 144 hours after DNFB retest (samples 1-17). In a second set of experiments, CD8+CD69+/-CD103+/- T cell subsets were purified from the skin of DNFB sensitized C57BL/6 mice at day 2, 11 or 42 post DNFB challenge (samples 18-33).

value: Skin

value: CD8+CD69+CD103+Trm / sample B

value: wild-type C57BL/6 mice

value: TA


title: 12-week HP Grin2a WT Bulk RNA-seq Sample5

value: Hippocampus


title: safb1/2 dko clone 13, embryonic stem cell, CAGGS-safb∆dd2, tech rep1

value: Embryonic Stem Cells

value: CAST/B6 Male Rosa26-RMCE

value: embryonic stem cells

value: SAFB1/2 DKO clone 13 + safb-dd2{delta}

value: 3 Days Doxycycline induction


title: 12-week HP Grin2a -/- Bulk RNA-seq Sample4


title: CD8+CD69+CD103+Trm / D42 post DNFB / treatment: TA / sample A

value: CD8+CD69+CD103+Trm / sample A


title: MR11072014


title: CD8+CD69+CD103+Trm / D42 post DNFB / treatment: Acetone / sample B

value: CD8+CD69+CD103+Trm / `sample B

value: Acetone


title: HeLa_rpf_wt_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hela_te_wt"
RiboLace_reads.xlsx

source_name: HeLa (ATCC CCL-2)

value: HeLa (ATCC CCL-2)

value: human cervix cancer

value: Wild-type

value: siRNA-based knockdown of YTHDF1 and YTHDF3


title: MR03062015

value: Bone Marrow

value: Hip Replacement


title: HeLa_rpf_wt_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hela_te_wt"
RiboLace_reads.xlsx

value: wild-type (wt) YTHDF1 and YTHDF3


title: 12-week HP Grin2a -/- Bulk RNA-seq Sample3

value: Grin2a -/-


title: 12-week HP Grin2a -/- Bulk RNA-seq Sample2

value: Hippocampus


title: HeLa_rpf_na_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hela_te_na"
RiboLace_reads.xlsx

value: no rescue (na)


title: MR03022016


title: 12-week HP Grin2a -/- Bulk RNA-seq Sample1


title: MR02272015


title: CD8+CD69+CD103+Trm / D11 post DNFB / treatment: TA / sample B

value: Skin

value: CD8+CD69+CD103+Trm / sample B

value: wild-type C57BL/6 mice

value: TA


title: CD8+CD69+CD103+Trm / D11 post DNFB / treatment: TA / sample A

value: CD8+CD69+CD103+Trm / sample A


title: 12-week HP Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: CD8+CD69+CD103+Trm / D11 post DNFB / treatment: Acetone / sample B

value: Acetone


title: 12-week HP Grin2a +/- Bulk RNA-seq Sample4


title: OAW06082011

value: MDS


title: CD8+CD69+CD103+Trm / D11 post DNFB / treatment: Acetone / sample A


title: HeLa_rpf_mut_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hela_te_mut"
RiboLace_reads.xlsx

value: HeLa (ATCC CCL-2)

value: human cervix cancer

value: O-GlcNAcylation-null mutant (mut) YTHDF1 and YTHDF3


title: HeLa_rpf_mut_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hela_te_mut"
RiboLace_reads.xlsx

value: Wild-type

value: siRNA-based knockdown of YTHDF1 and YTHDF3


title: OAW09202012

value: Bone Marrow


title: HeLa_input_wt_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hela_te_wt"
RiboLace_reads.xlsx

extract_protocol:
Truseq mRNA stranded
For [Dataset 1], HEK293T cells restored with wild-type or GlcNAcylation-null mutants were cross-linked twice with 254 nm-UV light, 0.15 J/cm2 each time (UV stratalinker 2400, Stratagene). Cells were then lysed by the lysis buffer (150 mM NaCl, 0.5% NP-40, 50 mM Tris-HCl (pH 7.5), 2 mM EDTA and 1% HaltTM protease and phosphatase inhibitor cocktail (Thermo Scientific, 78440)) at 4 °C with end-to-end rotation for 30 minutes. Cell debris were spun down at 21,000 g at 4 °C for 15 minutes. The lysates were treated with 0.2 U/μl RNase T1 (Thermo Scientific, EN0541) for 10 minutes at 22 °C with shaking. Pre-washed anti-FLAG M2 magnetic beads (MilliporeSigma, M8823-1ML) were applied to the lysates and incubated at 4 °C with end-to-end rotation for 8 hours. The beads were washed three times with 1ml IP wash buffer (50 mM Tris-HCl (pH 7.5), 300 mM KCl, 0.05% NP-40, 0.5 mM DTT, and 1% HaltTM protease and phosphatase inhibitor cocktail (Thermo Scientific, 78440)). The washed beads and input samples were resuspended in 1 vol IP wash buffer supplemented with 8 U/μl RNase T1 (Thermo Scientific, EN0541) for 10 minutes at 22 °C with shaking. Beads and input samples are resuspended in 100 ul 1 × Laemmli sample buffer (Bio-Rad, 1610747) and subjected to SDS-PAGE separation. The bands corresponding to ~70 kDa were cut with a razerblade and digested with proteinase K (Invitrogen, 25530049) for 50 minutes at 55 °C with shaking. Fragmented RNAs were extracted with TRIzolTM reagent (Invitrogen, 15596026).For [Dataset 2],  CHX (cycloheximide,  Milliporesigma C7698-1G) was added to a final concentration of 100 μg/ml to the medium and incubate for 7 minutes. Then spin down the cells, wash once with cold DPBS with 100 μg/ml CHX and spin down again, flash-freeze with LN2 and store at -80C. RPFs were prepared according to the manufacturer's instructions with riboLace kit (IMMAGINA, RL001). Total RNAs were extracted with standard TRIzol protocol.
For [Dataset 1], RNA libraries for inputs and ip samples were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with input or CLIP short RNA as inputs. For [Dataset 2], RNA libraries for rpf samples were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with end-repaired ribosome-protected fragments (RPFs) extracted as inputs. RNA libraries for input samples were constructed with TruSeq Stranded mRNA (Illumina, 20020594) with polyA-RNA extracted as inputs.

value: wild-type (wt) YTHDF1 and YTHDF3


title: CD8+CD69-CD103+Tcells / D2 post DNFB / treatment: No / sample B

value: CD8+CD69-CD103+Tcells / sample B

value: No


title: 12-week HP Grin2a +/- Bulk RNA-seq Sample2

value: Hippocampus


title: 12-week HP Grin2a +/- Bulk RNA-seq Sample3


title: OAW04092015


title: OAW04182012


title: CD8+CD69+CD103+Trm / D42 post DNFB / treatment: Acetone / sample A

value: Skin


title: 12-week HP Grin2a +/- Bulk RNA-seq Sample1


title: HeLa_input_wt_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hela_te_wt"
RiboLace_reads.xlsx


title: CD8+CD69-CD103-Tcells / D2 post DNFB / treatment: No / sample B

value: CD8+CD69-CD103-Tcells /sample B

value: wild-type C57BL/6 mice


title: HeLa_input_na_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hela_te_na"
RiboLace_reads.xlsx

value: no rescue (na)


title: OAW00226719


title: HeLa_rpf_na_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hela_te_na"
RiboLace_reads.xlsx


title: CD8+CD69-CD103-Tcells / D2 post DNFB / treatment: No / sample A

value: CD8+CD69-CD103-Tcells /sample A


title: HeLa_input_na_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hela_te_na"
RiboLace_reads.xlsx


title: CD8+CD69+CD103+Tcells / D2 post DNFB / treatment: No / sample B

value: CD8+CD69+CD103+Tcells / sample B


title: HeLa_input_mut_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hela_te_mut"
RiboLace_reads.xlsx


title: 4-week HP Grin2a WT Bulk RNA-seq Sample4

value: WT


title: HeLa_input_mut_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hela_te_mut"
RiboLace_reads.xlsx

value: HeLa (ATCC CCL-2)


title: DS12152014

value: MDS


title: DS06182014-34pos


title: 4-week HP Grin2a WT Bulk RNA-seq Sample2


title: CD8+CD69+CD103-Tcells / D2 post DNFB / treatment: No / sample B

value: CD8+CD69+CD103-Tcells / sample B


title: HEK_rpf_wt_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hek_te_wt"
RiboLace_reads.xlsx

value: HEK293T (ATCC CRL-3216)

value: human embryo kidney

value: Wild-type


title: DS06182014-34neg

value: Bone Marrow


title: HEK_rpf_wt_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hek_te_wt"
RiboLace_reads.xlsx

value: siRNA-based knockdown of YTHDF1 and YTHDF3

value: wild-type (wt) YTHDF1 and YTHDF3


title: CD8+CD69-CD103+Tcells / D2 post DNFB / treatment: No / sample A

value: CD8+CD69-CD103+Tcells / sample A

value: No


title: 4-week HP Grin2a -/- Bulk RNA-seq Sample5

value: Hippocampus

value: Grin2a -/-


title: 4-week HP Grin2a WT Bulk RNA-seq Sample1


title: OAW00660332


title: HEK_rpf_na_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hek_te_na"
RiboLace_reads.xlsx

value: no rescue (na)


title: DBS03072014


title: DBS01222016


title: 4-week HP Grin2a -/- Bulk RNA-seq Sample4


title: 4-week HP Grin2a WT Bulk RNA-seq Sample5


title: CD8+CD69+CD103+Nur77GFP-Trm / D6 post DNFB / treatment: TA / sample A

description: INS-MV-b001_HGYYWBGXH_S1_R2.ReadCounts.tsv

value: Skin

value: CD8+CD69+CD103+Nur77GFP-Trm / sample A

value: Nur77GFP mice

value: TA


title: 4-week HP Grin2a -/- Bulk RNA-seq Sample3


title: CD8+CD69+CD103+Nur77GFP- Trm / D6 post DNFB / treatment: TA / sample B

value: CD8+CD69+CD103+Nur77GFP- Trm / sample B


title: KB04302014

value: MDS


title: 769-P Lat-M2-2

city: DALLAS

first: KANGSAN

last: KIM

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
The massive raw data high-through sequencing technology must be qualified to guarantee the downstream bioinformatics analysis. Fastqc is used to generate a QC report to evaluate the raw data quality. Novogene uses FastQC to get a basic statistics of the raw reads, shown in the follows:
To obtain the qualified clean data, we trim the raw reads to filter out the contaminated adapter sequence and low-quality reads.
FastQC is also performed on the clean data obtained from trimming
Bismark software (Krueger, 2011) is used to perform alignments of bisulfite-treated reads to a reference genome. C is transformed to T and G is transformed to A (reverse complementary) in sequence reads and reference genome via Bismark, and then these sequencing reads are aligned to similarly converted versions of the genome separately.
After the alignment, site calling, and evaluation of genomic coverage/depth and C site coverage/depth of methylation data, C-site analysis of methylation is processed
Assembly: Hg19
Supplementary files format and content: WIG files

source_name: 769-P Lat-M

growth_protocol: Cells were cultured in RPM-1640 with penicillin/streptomycin, L-glutamine and 10% fetal bovine serum (FBS) at 37 degree in a humidified atmosphere with 5% CO2

extract_protocol:
DNA samples were collected using PurelinkTM Genomic DNA mini kit (Invitrogen). DNA quality was examined by agarose gel electrophoresis analysis for DNA degradation and RNA contamination and Qubit for accurate quantification of DNA.
The DNA fragments were repaired, dA-tailed to sequencing adaptors that all cytosines were methylated. After that, The DNA fragments were bisulfite treated with EZ DNA Methylation Gold Kit (Zymo Research). After treatment, cytosines without methylation changed into U, whereas cytosines with methylation remain unchanged. The final DNA library was obtained by size selection and PCR amplification. Quality of library was measured with Qubit 2.0 and sequencing was performed using Hiseq platform.

value: 769-P Lat-M

value: kidney cancer cells


title: 4-week HP Grin2a WT Bulk RNA-seq Sample3

value: WT


title: 769-P Lat-M2-1


title: HEK_rpf_mut_rpf_rep2

description:
correspond to columns starting with "rpf" and ending with "rep2" in the processed data file, subsheet "hek_te_mut"
RiboLace_reads.xlsx

value: HEK293T (ATCC CRL-3216)

value: human embryo kidney

value: Wild-type

value: O-GlcNAcylation-null mutant (mut) YTHDF1 and YTHDF3


title: CD8+CD69+CD103+Nur77GFP+ Trm / D1 post DNFB / treatment: TA / sample B

value: CD8+CD69+CD103+Nur77GFP+ Trm / sample B


title: 4-week HP Grin2a -/- Bulk RNA-seq Sample2

value: Hippocampus


title: CD8+CD69+CD103+Tcells / D2 post DNFB / treatment: No / sample A

description: INS-MV-b003_HDMERGEDL_S8_R2.ReadCounts.tsv

value: CD8+CD69+CD103+Tcells /  sample A

value: wild-type C57BL/6 mice

value: No


title: HEK_rpf_mut_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hek_te_mut"
RiboLace_reads.xlsx

value: siRNA-based knockdown of YTHDF1 and YTHDF3


title: CD8+CD69+CD103-Tcells / D2 post DNFB / treatment: No / sample A

value: Skin

value: CD8+CD69+CD103-Tcells / sample A


title: CD8+CD69+CD103+Nur77GFP+ Trm / D1 post DNFB / treatment: TA / sample A

value: CD8+CD69+CD103+Nur77GFP+ Trm /  sample A

value: Nur77GFP mice

value: TA


title: HEK_input_wt_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hek_te_wt"
RiboLace_reads.xlsx

value: wild-type (wt) YTHDF1 and YTHDF3


title: 4-week HP Grin2a -/- Bulk RNA-seq Sample1

value: Grin2a -/-


title: 769-P PA2

value: kidney cancer cells


title: CD8+CD69+CD103+Nur77GFP- Trm / D1 post DNFB / treatment: TA / sample B

value: CD8+CD69+CD103+Nur77GFP- Trm /  sample B


title: 4-week HP Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: HEK_input_wt_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hek_te_wt"
RiboLace_reads.xlsx

value: HEK293T (ATCC CRL-3216)

value: human embryo kidney

value: Wild-type


title: 769-P PA1


title: CD8+CD69+CD103+Nur77GFP-Trm / D1 post DNFB / treatment: TA / sample A

value: CD8+CD69+CD103+Nur77GFP-Trm / sample A


title: HEK_rpf_na_rpf_rep1

description:
correspond to columns starting with "rpf" and ending with "rep1" in the processed data file, subsheet "hek_te_na"
RiboLace_reads.xlsx

value: no rescue (na)


title: CD8+CD69+CD103+Nur77GFP- Trm / D0 / treatment: TA / sample B

value: CD8+CD69+CD103+Nur77GFP- Trm / sample B


title: 4-week HP Grin2a +/- Bulk RNA-seq Sample4

value: Hippocampus


title: 769-P Lat-M2-2

data_processing:
Generated libraries were run on a HiSeq2500 system and 25-50 million raw reads were collected per sample.
Raw reads were quality-checked and subsequently mapped to the human genome (hg19) using Tophat2 (2.2.4) using default settings
Read per kilobase million (RPKM) values were determined from read count of genes.
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared with either TruSeq RNA Sample Prep Kit v2 (Illumina) or Next Ultra RNA Library Prep Kit (New England Biolabs).

value: 769-P Lat-M


title: 769-P Lat-M1-2


title: HEK_input_na_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hek_te_na"
RiboLace_reads.xlsx

value: siRNA-based knockdown of YTHDF1 and YTHDF3


title: 4-week HP Grin2a +/- Bulk RNA-seq Sample2


title: HEK_input_na_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hek_te_na"
RiboLace_reads.xlsx


title: 4-week HP Grin2a +/- Bulk RNA-seq Sample1


title: 769-P Lat-M1-1


title: CD8+CD69+CD103+Nur77GFP-Trm / D6 post DNFB / treatment: Acetone / sample A

value: Skin

value: CD8+CD69+CD103+Nur77GFP-Trm /  sample A

value: Acetone


title: 2-week HP Grin2a WT Bulk RNA-seq Sample5

value: WT


title: 769-P PA3


title: HEK_input_mut_input_rep1

description:
correspond to columns starting with "input" and ending with "rep1" in the processed data file, subsheet "hek_te_mut"
RiboLace_reads.xlsx

value: O-GlcNAcylation-null mutant (mut) YTHDF1 and YTHDF3


title: HEK_input_mut_input_rep2

description:
correspond to columns starting with "input" and ending with "rep2" in the processed data file, subsheet "hek_te_mut"
RiboLace_reads.xlsx


title: 4-week HP Grin2a +/- Bulk RNA-seq Sample3


title: CD8+CD69+CD103+Nur77GFP- Trm / D6 post DNFB / treatment: Acetone / sample B

value: Nur77GFP mice


title: CD8+CD69+CD103+Nur77GFP+ Trm / D1 post DNFB / treatment: Acetone / sample B

value: CD8+CD69+CD103+Nur77GFP+ Trm / sample B


title: 2-week HP Grin2a WT Bulk RNA-seq Sample4


title: 769-P PA2

value: kidney cancer cells


title: CD8+CD69+CD103+Nur77GFP+ Trm / D1 post DNFB / treatment: Acetone / sample A

value: CD8+CD69+CD103+Nur77GFP+ Trm / sample A


title: 2-week HP Grin2a WT Bulk RNA-seq Sample3


title: 2-week HP Grin2a WT Bulk RNA-seq Sample2


title: CD8+CD69+CD103+Nur77GFP-Trm / D1 post DNFB / treatment: Acetone / sample A


title: 769-P PA1


title: CD8+CD69+CD103+Nur77GFP- Trm / D1 post DNFB / treatment: Acetone / sample B


title: 769-P Lat-M2-1


title: CD8+CD69+CD103+Nur77GFP- Trm / D0 / treatment: TA / sample A

value: CD8+CD69+CD103+Nur77GFP- Trm / sample A

value: TA


title: 2-week HP Grin2a WT Bulk RNA-seq Sample1


title: 2-week HP Grin2a -/- Bulk RNA-seq Sample5

value: Grin2a -/-


title: CD8+CD69+CD103+Nur77GFP- Trm / D0 / treatment: Acetone / sample C

value: CD8+CD69+CD103+Nur77GFP- Trm / sample C


title: InhaU-T6

city: Seoul

first: Sung Won

last: Kwon

address: 1 Gwanak-ro

department: Department of Pharmacy

institute: College of Pharmacy, Seoul National University

data_processing:
FastQC 0.10.0 before and after data trimming by Trimmomatic 0.32 (default settings)
RNA-seq reads were mapped to Homo sapiens library (hg19, genome.uscs.edu) using TopHat 2.0.13 and expression levels were determined by Cufflinks 2.2.1 with default settings.
Fragments Per Kilobase of exon per Milion fragments mapped (FPKM) was calculated.
Log transformation and quantile normalization
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Pancreas

extract_protocol:
Cut 20 μm sections from the interior of the paraffin block with a razor knife. Bring tissue slices into 1.5 ml tubes. Add 1 ml mineral oil to the sample and incubate at 70°C for 3 min to melt the paraffin. Centrifuge the sample for 1 min at 16,000 rcf. Discard the mineral oil. Wash the pellet with 1 ml 100% ethanol and air dry. Add 150 μl 1x protease K digestion buffer containing 500 μg/ml protease K, incubate at 55°C for 3 h. Add 1 ml Trizol to each sample. Incubate at RT for more than 5 min to dissociate nucleoprotein complexes. Add 0.2 ml of chloroform and vortex the tubes for 15 sec. Centrifuge the samples at 12,000 x g at 4 °C for 10 min. Transfer the aqueous phase to a new epitube. Precipitate the total RNA by mixing with equal volume  isopropyl alcohol, and put the tube at -20°C for 1 h. Centrifuge at 12,000 x g for 10 min at 2-8°C. Wash the RNA pellet with 70% ethanol, briefly air-dry. Dissolve the sample in RNase-free water for further analysis.
Library construction was prepared according to Illumina's stabdard instructions.

tag: disease

value: pancreatic cancer

tag: Stage

value: IIA


title: InhaU-T4

value: IIB


title: InhaU-T5


title: CD8+CD69+CD103+Nur77GFP- Trm / D0 / treatment: Acetone / sample B

tag: tissue

value: CD8+CD69+CD103+Nur77GFP- Trm / sample B


title: 2-week HP Grin2a -/- Bulk RNA-seq Sample4

value: Hippocampus


title: CD8+CD69+CD103+Nur77GFP- Trm / D0 / treatment: Acetone / sample A

value: Skin

value: CD8+CD69+CD103+Nur77GFP- Trm /  sample A


title: InhaU-T2


title: InhaU-T1


title: InhaU-T3


title: 2-week HP Grin2a -/- Bulk RNA-seq Sample2


title: 2-week HP Grin2a -/- Bulk RNA-seq Sample3


title: InhaU-N6

value: Adjacent controls


title: 2-week HP Grin2a +/- Bulk RNA-seq Sample5

value: Grin2a +/-


title: 2-week HP Grin2a -/- Bulk RNA-seq Sample1


title: InhaU-N5


title: Alignment_DSF2

city: Shanghai

first: Yiru

last: Wang

address: Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shan

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software   v1.8)
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter  trimmed 5'  3'-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences  then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The expression profiling of tRF & tiRNA and miRNA can be calculated based on counts of reads mapped. The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR.
Principal Component Analysis (PCA)  Correlation Analysis  Pie plots  Venn plots  Hierarchical clustering  Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF& tiRNA.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood serum

extract_protocol:
In brief  the total RNA was isolated from blood sample using TRIzol reagent (Invitrogen  Carlsbad  CA  USA) based on the manufacturer’s instructions. Before the sequencing experiment  the integrity and quantity of each RNA sample were checked using agarose gel electrophoresis and the NanoDrop ND-1000 (NanoDrop  Wilmington  DE  USA) instrument.
cDNA was synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently  ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100. We use the commercial kit for tRF & tiRNA-seq library preparation  which includes 3’ -adapter and 5’ -adapter ligation adaptor ligation  cDNA synthesis and library PCR amplification. The prepared tRF & tiRNA-seq libraries are finally quantified using Agilent BioAnalyzer 2100  then sequenced using Illumina NextSeq 500.

value: blood serum

value: atherosclerosis

value: week 20

value: high fat diet + SalB


title: Alignment_M3

institute: Longhua Hospital, Shanghai University of Traditional Chinese Medicine

value: high fat diet


title: Alignment_M2


title: 2-week HP Grin2a +/- Bulk RNA-seq Sample3


title: Alignment_DSF1


title: InhaU-N4


title: 2-week HP Grin2a +/- Bulk RNA-seq Sample4


title: Alignment_DSF3


title: Alignment_M1


title: InhaU-N2


title: 2-week HP Grin2a +/- Bulk RNA-seq Sample2


title: 2-week HP Grin2a +/- Bulk RNA-seq Sample1


title: Alignment_C57-3

value: normal diet


title: InhaU-N1


title: InhaU-N3


title: Alignment_C57-1


title: com125, EO, 6cm

city: Potsdam

first: Feng

last: Cheng

address: Meistersingerstr., 5

country: Germany

institute: University of Potsdam

data_processing:
We trimmed the adapter sequences and low quality reads using a 4 bp sliding window with a mean quality threshold of 25, and a minimum read length of 36 bp by Trimmomatic v0.39
The quality-filtered reads were mapped to the C. compressirostris genome using RSEM for gene level-quantification estimation. The estimated counts were imported into R/Bioconductor with the tximport package, which produced count matrices from gene-level quantification by taking the effective gene length into account
Supplementary files format and content: Tab-delimited text file includes length, effective_length, expected_count, TPM and FPKM on gene level

organism: Campylomormyrus compressirostris

source_name: electric organ

extract_protocol:
The RNA isolation was performed in all the electric organ samples using QIAGEN RNeasy Fibrous Tissue Mini Kit.
mRNA enrichment was performed by poly (A) capture from isolated RNA using NEXTflex Poly (A) Beads. Strand-specific transcriptomic libraries were built using NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific, USA) based on the manufacturer’s instructions.

value: electric organ


title: Alignment_C57-2