title: patient 2, PBMC, post-chemotherapy, scRNA-seq

first: Siyuan

last: Huang

state: Beijing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

description:
P2_B2
10x Genomics

data_processing:
The Cell Ranger toolkit (v7.0.1) provided by 10x Genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix using the human reference genome hg38.
Assembly: hg38
Supplementary files format and content: h5 files containing UMI count matrix

source_name: PBMC

extract_protocol:
Fresh tumor samples were dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s guidelines. Peripheral blood mononuclear cells were isolated using Ficoll-Paque Plus (Cytiva, Sweden).
According to the manufacturer’s instructions, single-cell RNA-seq libraries were prepared by using the Chromium Single Cell 3’ Library and Gel Bead Kit. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and then subjected to end repair and adapter ligation. Next, the products were purified and enriched using PCR to create a final cDNA library. Finally, the libraries were sequenced using the Illumina sequencing platform.

value: PBMC

value: Male

tag: tumor stage

value: docetaxel, cisplatin, 5-fluorouracil


title: patient 2, tumor, post-chemotherapy, scRNA-seq

status: Public on Mar 06 2024

type: SRA

city: Beijing

country: China

description:
P2_T2
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

source_name: tongue

tag: tissue

value: tongue

tag: Sex

tag: age

tag: treatment


title: patient 2, tumor, pre-chemotherapy, scRNA-seq

description:
P2_T
10x Genomics


title: small RNA golden hamster 1

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs, tsRNA (tRNA-derived small non-coding RNA), rsRNA (rRNA-derived small non-coding RNA), small snoRNAs, lncRNA, and mRNA, successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo-siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others.
We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM (transcripts per kilobase of exon model per million mapped reads) by StringTie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM values or raw counts for each Sample

organism: Mesocricetus auratus

source_name: oocyte

extract_protocol:
Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively.
Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel.
mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.

value: oocyte

value: female

tag: Stage

value: MII

tag: genotype

value: wild type

tag: molecule subtype

value: small RNA


title: patient 1, tumor, pre-chemotherapy, scRNA-seq

description:
P1_T
10x Genomics


title: patient 1, tumor, post-chemotherapy, scRNA-seq

description:
P1_T2
10x Genomics


title: patient 2, PBMC, pre-chemotherapy, scRNA-seq

description:
P2_B
10x Genomics


title: patient 1, PBMC, pre-chemotherapy, scRNA-seq

description:
P1_B
10x Genomics


title: Endogenous, amplicon A (DMS-seq)

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description: DMS-MaP-seq

data_processing:
Reads were mapped to the NORAD and alternative sequences using STAR (Dobin et al. 2013) and mutations in individual positions in the sequence were quantified using JACUSA2 (Piechotta et al. 2022).
Assembly: hg19
Supplementary files format and content: Tab-separated value files and matrix table
Library strategy: Amplicon sequencing

extract_protocol:
HCT116 NORAD WT and NORAD–/– cells were seeded in a 6-well plate (200,000 cells per well). After 24 hr, NORAD–/– cells were transfected with NORAD constructs using PEI reagent. Cells were washed 48 hr post-transfection and incubated with warm DMEM containing 2% DMS for 5 min at 37°C. In parallel, as a control, 2% of DDW was added to another well of cells. Media with DMS was decanted, and cells were washed with 30% of beta-mercaptoethanol solution in PBS. The adherent cells were dislodged using a cell-scraper, and collected by centrifugation at 1000 × g at 4 °C for 5 min. Cells were resuspended in TRI reagent and RNA was isolated according to the manufacturer protocol. Total RNA was DNase-treated for 30 min at 37 °C in 1× TURBO DNase buffer with 1 μl TURBO DNase enzyme (Thermo Fisher Scientific).
Reverse transcription was performed in a 10 μl volume with 1 pmol of gene specific primer (Table S7). To begin, a mixture of 3-6 µg of RNA with primer was incubated at 95°C for 30 sec to denature the template, and then it was returned to ice to anneal the primer to the template. To initiate the reaction, 20 U Marathon RT (company, cat#) with RT buffer (100 mM Tris-HCl pH 8.3, 400 mM KCl, 2 mM MnCl2, 10 mM DTT, 40% glycerol)  and 5 mM dNTPs were added to annealed substrate, and allowed the reaction to proceed for 1 h at 420C  (Guo et al. 2020; Mitchell et al. 2023).  Two ∼ 300 nt amplicons tiled around NRU 7 to 8 were designed to obtain sequencing coverage of the structured region of NORAD (Table S6). Amplicons had an overlapping of 65 nucleotides. Amplicons were generated using Q5 High-Fidelity DNA Polymerase (NEB) with NORAD specific forward and reverse primers, and 2 µl of cDNA per reaction carried out in a 25 µl total volume per amplicon.

tag: cell line

value: WT


title: alt. sequence1, amplicon B (DMS-seq)

description: DMS-MaP-seq

value: NORAD-/-


title: RNAseq golden hamster 2

molecule: polyA RNA


title: alt. sequence2, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: alt. sequence2, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: patient 1, PBMC, post-chemotherapy, scRNA-seq

description:
P1_B2
10x Genomics


title: Full NORAD OE, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: mini-NORAD7/8, rep1, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: mini-NORAD7/8, rep2, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: golden hamster oxidation

value: NaIO4 oxidation


title: mini-NORAD7/8, rep2, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: mini-NORAD7/8, rep1, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: Delta-disordered (DMS-seq)

description: DMS-MaP-seq


title: control, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: LK-2_control_1st

city: Yonago

first: Takahiro

last: Matsushige

state: Tottori

address: 86 Nishi-cho

department: Faculty of Medicine

country: Japan

institute: Tottori University

data_processing:
Adapter trimming and quality trimming were performed using trimmomatic (ver. 0.39).
Cleaned RNA-seq reads were aligned to the GRCh38.p13 genome assembly using BWA (ver. 0.7.17).
Calculating mapping statistics from BAM file were performed using SAMtools (ver. 1.12).
The analysis data of mapping statistics of transcript IDs was compiled for each gene using gene IDs.
Nromalization using the Trimmed Mean of M-values (TMM) method for comparing the expression levels of each genes was performed using edgeR (ver. 3.16.5). Normalization; ( Read of the gene/total reads of  sample)x(total reads of the sample with the least total reads)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts, normalized total counts, and TMM values for each sample

source_name: Lung

growth_protocol: LK2-control and -maspin cells were seeded at a density of 3.6 × 10^5 in 6-well plates, and maintained in RPMI1640.

extract_protocol:
Total RNA from LK2-maspin and LK2-control cells was recovered using RNeasy Mini Kit according to the manufacturer’s instructions.
To purify the strand-specific mRNA library, the mRNA was reverse transcribed into cDNA using random primers, and then the synthesized double-strand cDNA was fragmented, and the cDNA was subsequently ligated adapters. Transcriptome sequencing in strand-specific mRNA-seq library was performed using illumine NovaSeq 6000 Sequencing System.

value: Lung

tag: cell type

value: Squamous cell carcinoma

value: ZsGreen overexpression


title: LK-2_Maspin_3rd

value: Maspin and ZsGreen overexpression


title: LK-2_Maspin_2nd


title: LK-2_Maspin_1st


title: LK-2_control_2nd


title: LK-2_control_3rd


title: Endogenous, amplicon B (DMS-seq)

description: DMS-MaP-seq


title: JHU_AD_07

city: Baltimore

first: Dimitrios

last: Avramopoulos

state: Maryland

address: 733 North Broadway

department: Genetic Medicine

country: USA

institute: Johns Hopkins University

data_processing:
Hisat2 (version 2.2.1)
SAMtools (version 1.1.4)
stringtie (version 2.1.7)
Bioconductor package DESeq2
Assembly: hg38
Supplementary files format and content: csv format, gene expression levels (normalized reaad counts from the DEseq2 package) for each sample

source_name: hiPSC derived excitatory neurons

growth_protocol: Neural maturation medium (Neurobasal medium A (Gibco, Grand Island, NY, USA),

extract_protocol:
Quick-RNA MiniPrep Kit (Zymo Research #R1054)
250~300 bp insert , strand-specific libraries with rRNA removal.
Fragmentation, Reverse Transcription, Second strand cDNA synthesis, End repair and A-tailing, , adapter ligation, Size selection, PCR amplification

value: hiPSC derived excitatory neurons

tag: disease state

value: Alzheimers


title: JHU_AD_08


title: JHU_AD_05


title: Full NORAD OE, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: JHU_AD_03


title: alt. sequence1, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: JHU_AD_02


title: JHU_AD_01


title: JHU_AD_04


title: JHU_WT_04

value: healthy


title: JHU_WT_01


title: JHU_WT_08


title: JHU_WT_03


title: JHU_WT_07


title: control, amplicon A (DMS-seq)

description: DMS-MaP-seq


title: Donor 2 AOI 164

city: Ann Arbor

first: Jun

last: Li

state: Michigan

address: 1141 Catherine St

department: Human Genetics

institute: University of Michigan

description:
NanoString GeoMx
DSP-1001660016230-D-F10

data_processing:
*library strategy: nanoString GeoMx
GeoMx NGS Pipeline software v2.3.3.10
Assembly: GRCh38
Supplementary files format and content: Digital count conversion files (DCC), comma seperated values files

source_name: ovary

extract_protocol:
Selected slides were deparaffinized and rehydrated, followed by antigen retrieval for 15 minutes at 90C in Tris-EDTA. RNA targets were exposed using proteinase K (1 ug/ml) in PBS for 15 minutes at 37C. For in situ hybridization, GeoMx reagents and protocols were used according to the manufacturer's instructions. Slides were stained with morphology markers prior to RNA collection.
Slides were covered with Buffer S (Nanostring) and loaded into the GeoMx DSP instrument. Regions of interest were defined by the user and RNA molecules which were affixed by photocleavable linkers are released using programmable UV light then collected into microtiter wells for sequencing. After pooling, purification, and quality control process the library was then sequenced on an Illumina NGS platform.

treatment_protocol: Tissue was fixed in 4% paraformaldehyde for 24 hours at 4C then rinsed five times for 24 hours each in PBS at 4C. Tissue was then embedded in paraffin for sectioning. Every other 5 um section was stained with hematoxylin and eosin to select an unstained slide for spatial analysis.

value: ovary

tag: subject id

value: Donor 2

tag: subject status

value: healthy donor


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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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title: Donor 2 AOI 152

description:
NanoString GeoMx
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title: JHU_WT_05


title: Donor 2 AOI 148

description:
NanoString GeoMx
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description:
NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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description:
NanoString GeoMx
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description:
NanoString GeoMx
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title: Donor 2 AOI 48

description:
NanoString GeoMx
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description:
NanoString GeoMx
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description:
NanoString GeoMx
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title: Donor 2 AOI 50

description:
NanoString GeoMx
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NanoString GeoMx
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description:
NanoString GeoMx
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title: Donor 2 AOI 47

description:
NanoString GeoMx
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title: Donor 2 AOI 45

description:
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title: Donor5

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregationi were made using Cell Ranger software v2.1.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
After removal of dead DAPI+ cells, the cell suspension was submitted to the University of Michigan Advanced Genomics Core and loaded into the 10X Genomics Chromium controller for droplet-based single-cell capture. Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, Product Code 120237.
Library was performed according to the manufacter's instructions (single cell v2 protocol, 10x Genomics)

treatment_protocol: Tissue was cut in 1x1x1 mm pieces and digested in 0.5mg/ml collagenase IA with 0.01 mg/ml DNase I in PBS at 37C for 30 minutes, then strained through 70 then 30 um filters. Single cell suspension was quenched with ice cold PBS with 10% fetal bovine serum and remaining tissue from the 70 um strainer was digested using the same process for an additional 30 minutes, after which additional single cell suspension was combined with that from the first 30 minute digest. The suspension was treated with red blood cell lysis buffer, rinsed with 1% then 0.04% bovine serum albumin solutions in PBS, then immediately sent for DAPI live/dead cell sorting.


title: Donor3

description: 10x Genomics


title: Donor4

description: 10x Genomics


title: C9_833_2DG_2

city: philadelphia

first: Davide

last: Trotti

state: Pennsylvania

address: 900 WALNUT ST, JEFFERSON HOSPITAL FOR NEUROSCIENCE BUILD

institute: PROFESSOR OF NEUROSCIENCE, THOMAS JEFFERSON UNIVERSITY

data_processing:
Raw reads were processed through Novogene in-houser perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Q20, Q30, and GC content of clean data were calculated and downstream analyses were performed on clean data with high quality.
Reads were mapped using Hisat2. Mapped reads of each sample were assembled by StringTie (v1.3.3b). featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Assembly: Index of reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were laigned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: Supplementary files format and content: excel file includes FPKM values for each Sample
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include TMM values for each Sample

source_name: Human induced pluripotent stem cell

growth_protocol: Human induced pluripotent stem cell-derived i3Neurons were differentiated to maturity by exposure to doxycycline and neuronal growth factors (see Fernandopulle et al, Curr Protoc Cell Biol 2018).

extract_protocol:
Zymo Quick-RNA Miniprep Kit was used to extract RNA. 0.5 micrograms of RNA from each sample was submitted for library preparation.
RNA libraries for RNA-seq were prepared following Novogene's protocols and sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The cells were then cultured for 48 hours in one of the three following media types: 1) complete/normal media containing 25 mM glucose, 2) glucose-deprived media containing 0 mM glucose and 25 mM mannitol as an osmotic control, or 3) media in which 40% of the glucose was replaced with the glucose analog and glycolytic inhibitor 2-deoxglucose (2DG).

tag: disease

value: C9orf72 ALS/FTD

tag: patient

value: patient B

value: 2-deoxyglucose-containing media


title: C9_833_2DG


title: C9_833_NG_2

value: glucose-deprived media


title: Donor 1 AOI 9

description:
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title: C9_4a_NG_2

value: patient A


title: C9_4a_2DG


title: C9_833_com_2

value: complete media


title: C9_4a_comp_2


title: C9_4a_comp


title: C9_4a_NG


title: A3_V4

city: Graz

first: Theresa

last: Benezeder

address: Auenbruggerplatz 8

department: Department of Dermatology and Venereology

country: Austria

institute: Medical University of Graz

data_processing:
After passing initial quality control with FastQC (v0.73) and MultiQC (v1.11) reads were trimmed with trimmomatic (v0.38.1, minimum length 40 bp and removing Illumina specific adaptor sequences).
Reads were aligned against the reference genome GRCh38.p13 using Ensembl gene annotation Homo_sapiens.GRCh38.108.gtf with RNASTAR (v2.78) in 2 pass mode with standard settings.
From the 62703 annotated genes a total of 40435 low count genes were filtered out because either the median over all samples was below 10 counts or no group had a non-zero count in at least in 90% of groups’ samples with a group median count > 10.
For differential gene expression the model Patient_ID + group with multiple test adjustment by Benjamini-Hochberg (BH) was used (cut-off adjusted p‑value<0.05), since addition of Patient_ID was found to be significant for most differentially expressed genes (DEG).
Assembly: GRCh38.p13
Supplementary files format and content: counts_RNASeq_Benezeder_2023.txt: tab delimited text file with decimal separator = "," includes raw counts of all annotated genes for each sample
Supplementary files format and content: counts_genes_filtered_RNASeq_Benezeder_2023: tab delimited text file with decimal separator = "," includes raw counts of included genes for each sample
Supplementary files format and content: vst_variance_stabilizing_transformation_RNASeq_Benezeder_2023: tab delimited text file with decimal separator = "," includes DESeq2 normalized and vst transformed values of included genes for each sample

source_name: skin

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen, Hilden, Germany), as per manufacturer's instructions.
Library preparation was done with the NEBnext Ultra II Directional RNA Library Prep Kit for Illumina Kit with beads (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Psoriasis patients were daily topically treated with dithranol for 2-3 weeks;  ClinicalTrials.gov Identifier: NCT02752672

value: skin

value: female

value: psoriasis skin lesion after treatment

value: dithranol


title: 5246,SI-GA-H3

city: Boston

first: Samia

last: Ali

state: Massachusetts

address: 800 Washington Street

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: 10x Genomics, S4 Flow Cell

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1
Assembly: Fca126, GRCh38, mm10
Supplementary files format and content: Tab-separated values files, and matrix files

molecule: nuclear RNA

source_name: Septal Tissue

extract_protocol:
Cryopreserved tissue was thawed in a 37°C water bath for 75 seconds. Nuclei were released from the tissue via dounce homogenization using a buffer containing Triton X-100 (0.1 v/v). The homogenate was filtered through a 10µM cell strainer and nuclei were pelleted (500 x g for 5 minutes at 4°C) and washed before being resuspended in 1% w/v BSA, 1X PBS, and  0.2 U/µL RNase inhibitor
Library was constructed according to manufacturers instructions (single cell 3' v3.1, 10x Genomics).

value: Septal Tissue

value: Heart Tissue

value: POS


title: 5042,SI-GA-G3

description: 10x Genomics, S4 Flow Cell


title: A9_V4

value: male


title: A12_V4


title: No treatment_1 (Cinnamic acid control)

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

data_processing:
Data processing were conducted using NovaSeq Control Software v1.7.5, Real Time Analysis (RTA) v3.4.4, bcl2fastq2 v2.20, and DRAGEN Bio-IT Platform v3.9.3
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes row counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: hair follicle

growth_protocol: Adult human DP cells were obtained from PromoCell (Heidelberg, Germany), passaged up to passage four, and used for 2D culture.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen) from DP cells with/without 100 μg/mL Cinnamic acid treatment for 3 days.
RNA library for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit

treatment_protocol: Dermal papilla cells (2 × 104 cells) were suspended in 0.5 mL culture medium supplemented with 0 or 100 μg/mL Cinnamic acid and seeded into the wells of a 24-well cell culture plate (Corning Inc., Corning, NY, USA). Gene expression in DP cells was assessed  after 3 days of culture.

value: hair follicle

value: dermal papilla cells


title: Cinnamic acid treatment_1


title: A10_V4


title: A7_V4


title: A9_V1a

value: psoriasis skin lesion


title: C9_4a_2DG_2

value: C9orf72 ALS/FTD


title: A7_V1a


title: A15_V1a


title: A11_V4


title: A1_V4


title: C9_833_NG

value: patient B


title: A3_V1a


title: A10_V1a


title: C9_833_comp


title: A1_V1a


title: A7_V1b

value: non-lesional skin


title: 2883,SI-GA-C3

description: 10x Genomics, S4 Flow Cell


title: A11_V1a


title: A9_V1b


title: A11_V1b


title: tissue biopsy of thigh muscle [PSQ86_MUO_ThMuscle_S59_L004]

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: The metabolic grouping was defined by features of normal insulin sensitivity.

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned with STAR v2.5.1a, and quantitated with Subread:featureCount v1.4.6-p5
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: thigh.muscle_all.gene_count.txt, tab separated text file, contains gene counts for all samples, each sample in a column
Supplementary files format and content: thigh.muscle_all.gene_CPM.txt, tab separated text file, contains counts per million (CPM) reads for all samples, each sample in a column
Supplementary files format and content: thigh.muscle_all.gene_moderated_log2cpm.txt, tab separated text file, contains log2-transformed (0.5+CPM) values for all samples, each sample in a column

source_name: thigh muscle

extract_protocol: an oligo-dT based SMARTer Ultra Low RNA kit from the Takara-Clontech was used to prepare the libraries

value: thigh muscle

tag: metabolic group

value: MUO


title: A10_V1b


title: A15_V4


title: tissue biopsy of thigh muscle [PSQ70_MUO_ThMuscle_S58_L004]


title: tissue biopsy of thigh muscle [PSQ397_MUO_ThMuscle_S68_L004]


title: tissue biopsy of thigh muscle [PSQ469_MUO_ThMuscle_S70_L004]


title: tissue biopsy of thigh muscle [PSQ441_MUO_ThMuscle_S69_L004]


title: A12_V1a


title: tissue biopsy of thigh muscle [PSQ379_MUO_ThMuscle_S67_L004]


title: tissue biopsy of thigh muscle [PSQ354_MUO_ThMuscle_S65_L004]


title: tissue biopsy of thigh muscle [PSQ366_MUO_ThMuscle_S66_L004]


title: tissue biopsy of thigh muscle [PSQ251_MUO_ThMuscle_S62_L004]


title: tissue biopsy of thigh muscle [PSQ297_MUO_ThMuscle_S63_L004]


title: tissue biopsy of thigh muscle [PSQ48_MUO_ThMuscle_S57_L004]


title: tissue biopsy of thigh muscle [PSQ1_MUO_ThMuscle_S55_L004]


title: tissue biopsy of thigh muscle [PSQ185_MUO_ThMuscle_S61_L004]


title: tissue biopsy of thigh muscle [PSQ164_MUO_ThMuscle_S60_L004]


title: tissue biopsy of thigh muscle [PSQ333_MUO_ThMuscle_S64_L004]


title: tissue biopsy of thigh muscle [PE9_MUO_ThMuscle_S72_L004]


title: tissue biopsy of thigh muscle [PE6_MUO_ThMuscle_S71_L004]


title: A15_V1b


title: tissue biopsy of thigh muscle [PE12_MUO_ThMuscle_S73_L004]


title: tissue biopsy of thigh muscle [PE40_MUO_ThMuscle_S74_L004]


title: tissue biopsy of thigh muscle [PSQ428_MHO_ThMuscle_S53_L004]

value: MHO


title: tissue biopsy of thigh muscle [PSQ472_MHO_ThMuscle_S54_L004]


title: tissue biopsy of thigh muscle [PSQ34_MHO_ThMuscle_S40_L004]


title: tissue biopsy of thigh muscle [PSQ89_MHO_ThMuscle_S42_L004]


title: tissue biopsy of thigh muscle [PSQ26_MHO_ThMuscle_S39_L004]


title: tissue biopsy of thigh muscle [PSQ7_MUO_ThMuscle_S56_L004]


title: tissue biopsy of thigh muscle [PSQ393_MHO_ThMuscle_S52_L004]


title: tissue biopsy of thigh muscle [PSQ256_MHO_ThMuscle_S49_L004]


title: tissue biopsy of thigh muscle [PSQ168_MHO_ThMuscle_S47_L004]


title: tissue biopsy of thigh muscle [PSQ291_MHO_ThMuscle_S50_L004]


title: tissue biopsy of thigh muscle [PSQ162_MHO_ThMuscle_S46_L004]


title: tissue biopsy of thigh muscle [PSQ332_MHO_ThMuscle_S51_L004]


title: tissue biopsy of thigh muscle [PSQ115_MHO_ThMuscle_S43_L004]


title: tissue biopsy of thigh muscle [PSQ73_MHL_ThMuscle_S25_L004]

value: MHL


title: tissue biopsy of thigh muscle [PSQ120_MHO_ThMuscle_S44_L004]


title: tissue biopsy of thigh muscle [PSQ454_MHL_ThMuscle_S35_L004]


title: tissue biopsy of thigh muscle [PSQ146_MHO_ThMuscle_S45_L004]


title: tissue biopsy of thigh muscle [PSQ23_MHO_ThMuscle_S38_L004]


title: tissue biopsy of thigh muscle [PSQ252_MHL_ThMuscle_S34_L004]


title: tissue biopsy of thigh muscle [PSQ250_MHL_ThMuscle_S33_L004]


title: tissue biopsy of thigh muscle [PSQ150_MHL_ThMuscle_S29_L004]


title: tissue biopsy of thigh muscle [PSQ141_MHL_ThMuscle_S28_L004]


title: tissue biopsy of thigh muscle [PSQ211_MHL_ThMuscle_S31_L004]


title: tissue biopsy of thigh muscle [PSQ116_MHL_ThMuscle_S26_L004]


title: tissue biopsy of thigh muscle [PSQ72_MHO_ThMuscle_S41_L004]


title: tissue biopsy of abdominal fat [PSQ86_tube265_MUO_AbFat_S42_L003]

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined, aligned with STAR v2.5.1a, and quantitated with Subread:featureCount v1.4.6-p5
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: abdominal.fat_all.gene_count.txt, tab separated text file, contains gene counts for all samples, each sample in a column
Supplementary files format and content: abdominal.fat_all.gene_CPM.txt, tab separated text file, contains counts per million (CPM) reads for all samples, each sample in a column
Supplementary files format and content: abdominal.fat_all.gene_moderated_log2cpm.txt, tab separated text file, contains log2-transformed (0.5+CPM) values for all samples, each sample in a column

source_name: abdominal fat

value: abdominal fat


title: tissue biopsy of abdominal fat [PSQ7_tube964_MUO_AbFat_S44_L003]


title: tissue biopsy of abdominal fat [PSQ469_tube981_MUO_AbFat_S11_L003]


title: tissue biopsy of abdominal fat [PSQ441_tube980_MUO_AbFat_S68_L003]


title: tissue biopsy of abdominal fat [PSQ397_tube977_MUO_AbFat_S46_L003]


title: tissue biopsy of thigh muscle [PSQ194_MHO_ThMuscle_S48_L004]


title: tissue biopsy of thigh muscle [PSQ475_MHL_ThMuscle_S36_L004]


title: tissue biopsy of abdominal fat [PSQ297_tube968_MUO_AbFat_S37_L003]


title: tissue biopsy of abdominal fat [PSQ366_tube975_MUO_AbFat_S22_L003]


title: tissue biopsy of abdominal fat [PSQ251_tube556_MUO_AbFat_S47_L003]


title: tissue biopsy of abdominal fat [PSQ379_tube976_MUO_AbFat_S77_L003]


title: tissue biopsy of abdominal fat [PSQ333_tube971_MUO_AbFat_S83_L003]


title: tissue biopsy of abdominal fat [PSQ354_tube973_MUO_AbFat_S78_L003]


title: tissue biopsy of thigh muscle [PSQ236_MHL_ThMuscle_S32_L004]


title: tissue biopsy of thigh muscle [PSQ204_MHL_ThMuscle_S30_L004]


title: tissue biopsy of abdominal fat [PSQ185_tube553_MUO_AbFat_S42_L003]


title: tissue biopsy of thigh muscle [PSQ128_MHL_ThMuscle_S27_L004]


title: tissue biopsy of abdominal fat [PE6_tube271_MUO_AbFat_S4_L003]


title: tissue biopsy of abdominal fat [PSQ1_tube260_MUO_AbFat_S18_L003]


title: tissue biopsy of abdominal fat [PSQ89_tube248_MHO_AbFat_S6_L003]


title: tissue biopsy of abdominal fat [PE12_tube275_MUO_AbFat_S24_L003]


title: tissue biopsy of abdominal fat [PSQ164_tube267_MUO_AbFat_S4_L003]


title: tissue biopsy of abdominal fat [PSQ72_tube247_MHO_AbFat_S57_L003]


title: tissue biopsy of abdominal fat [PSQ472_tube963_MHO_AbFat_S14_L003]


title: tissue biopsy of abdominal fat [PE9_tube273_MUO_AbFat_S29_L003]


title: tissue biopsy of abdominal fat [PSQ70_tube264_MUO_AbFat_S75_L003]


title: tissue biopsy of abdominal fat [PSQ428_tube962_MHO_AbFat_S45_L003]


title: tissue biopsy of thigh muscle [PSQ13_MHO_ThMuscle_S37_L004]


title: tissue biopsy of abdominal fat [PSQ426_tube961_MHO_AbFat_S5_L003]


title: tissue biopsy of abdominal fat [PSQ291_tube957_MHO_AbFat_S73_L003]


title: tissue biopsy of abdominal fat [PSQ168_tube258_MHO_AbFat_S19_L003]


title: tissue biopsy of abdominal fat [PSQ23_tube240_MHO_AbFat_S78_L003]


title: tissue biopsy of abdominal fat [PSQ393_tube960_MHO_AbFat_S20_L003]


title: tissue biopsy of abdominal fat [PSQ34_tube244_MHO_AbFat_S34_L003]


title: tissue biopsy of abdominal fat [PSQ13_tube237_MHO_AbFat_S48_L003]


title: tissue biopsy of abdominal fat [PSQ146_tube255_MHO_AbFat_S79_L003]


title: tissue biopsy of abdominal fat [PSQ4_tube235B_MHO_AbFat_S35_L003]


title: tissue biopsy of abdominal fat [PSQ73_tube229_MHL_AbFat_S81_L003]


title: tissue biopsy of abdominal fat [PSQ115_tube251_MHO_AbFat_S32_L003]


title: tissue biopsy of abdominal fat [PSQ194_tube259_MHO_AbFat_S63_L003]


title: tissue biopsy of abdominal fat [PSQ64_tube552_MHL_AbFat_S56_L003]


title: tissue biopsy of abdominal fat [PSQ332_tube958_MHO_AbFat_S1_L003]


title: tissue biopsy of abdominal fat [PSQ162_tube257_MHO_AbFat_S29_L003]


title: tissue biopsy of abdominal fat [PSQ256_tube559_MHO_AbFat_S60_L003]


title: tissue biopsy of abdominal fat [PSQ211_tube951_MHL_AbFat_S72_L003]


title: tissue biopsy of abdominal fat [PSQ236_tube566_MHL_AbFat_S86_L003]


title: tissue biopsy of abdominal fat [PSQ454_tube954_MHL_AbFat_S17_L003]


title: tissue biopsy of abdominal fat [PSQ44_tube195_MHL_AbFat_S40_L003]


title: tissue biopsy of abdominal fat [PSQ475_tube982_MHL_AbFat_S46_L003]


title: tissue biopsy of abdominal fat [PE40_tube563_MUO_AbFat_S60_L003]


title: tissue biopsy of abdominal fat [PSQ147_tube232_MHL_AbFat_S16_L003]


title: tissue biopsy of abdominal fat [PSQ150_tube233_MHL_AbFat_S13_L003]


title: tissue biopsy of abdominal fat [PSQ141_tube231_MHL_AbFat_S12_L003]


title: tissue biopsy of abdominal fat [PSQ252_tube557_MHL_AbFat_S7_L003]


title: tissue biopsy of abdominal fat [PSQ128_tube230_MHL_AbFat_S63_L003]


title: tissue biopsy of abdominal fat [PSQ120_tube252_MHO_AbFat_S72_L003]


title: tissue biopsy of abdominal fat [PSQ116_tube194_MHL_AbFat_S27_L003]


title: DIPG-1376-1

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks, which is provided here

source_name: TUMOR-DIPG

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

value: TUMOR-DIPG

tag: tumor full_name

value: diffuse intrinsic pontine glioma

value: F

value: Presentation


title: Normal-frontal-1359-X

source_name: NORMAL-cortex

value: NORMAL-cortex

value: normal brain

value: M

tag: tumor stage


title: MED-1494

source_name: TUMOR-MED

tag: tissue

value: TUMOR-MED

value: medulloblastoma


title: EPNPFA2-770-1

value: ependymoma, posterior fossa group A2

tag: Sex


title: MEDGP4-186


title: GBM-1276-1

source_name: TUMOR-GBM

value: TUMOR-GBM

value: glioblastoma


title: MEDSHH-1325

source_name: TUMOR-MEDSHH

value: TUMOR-MEDSHH

value: medulloblastoma, SHH group


title: tissue biopsy of abdominal fat [PSQ250_tube555_MHL_AbFat_S3_L003]


title: EPNPFA1-1400-1

value: ependymoma, posterior fossa group A1


title: DIPG-1359-1


title: EPNPFA2-1101


title: GG-749-1

source_name: TUMOR-GG

value: TUMOR-GG

value: ganglioglioma


title: EPNPFA1-1239


title: EPNPFA1-NCH-1


title: PHGG2

value: Recurrence


title: ACP-TK756-1

source_name: TUMOR-ACP

value: TUMOR-ACP

value: adamantinomatous craniopharyngioma


title: ACP-TK34-1

value: Presentation


title: PHGG4


title: tissue biopsy of abdominal fat [PSQ204_tube234_MHL_AbFat_S71_L003]

value: abdominal fat

value: MHL


title: MED-1490

value: F


title: EPNPFA-1269-1

value: M


title: PHGG1


title: ACP-G10-4-1


title: NORMAL-PIT-A16-32

source_name: NORMAL-pituitary

value: NORMAL-pituitary

value: normal brain


title: phoB-FLAG3_2

city: Wuhan

first: wencan

last: zheng

state: Hubei

address: NO.152 Luoyu Road

department: School of Life Sciences

institute: Central China Normal University

library_source: genomic

data_processing:
The first part is data preprocessing. Delinker sequences, polluting sequences, and low-quality bases, clean data sequences were obtained, and relevant data statistics were performed.
In the second part, the clean data is mapped to the reference genome to obtain a BAM file, and the repetitive sequences are removed, and the uniquely aligned sequences are retained.
In the third part, the BAM file was tested for Peak to obtain information on the enrichment region, and the distribution of Peak in gene functional elements, recent gene search and motif prediction were performed.
In the fourth part, the distribution of Peak was counted, and the functional annotation and enrichment of GO and KEGG of the nearest Peak genes were carried out, and transcription factor prediction was carried out.
Assembly: ASM972v1
Supplementary files format and content: PhoB_Flag.peak_annotation.xls

molecule: genomic DNA

organism: Synechocystis sp. PCC 6803

source_name: phoB-FLAG3 strains

growth_protocol: The phoB-FLAG3 strains were grown in phosphate limited medium of YBG11

extract_protocol:
The samples were cross-linked with formaldehyde at a final concentration of 1%, and the cross-linking reaction was terminated with glycine. Ultranic interruption of the DNA-protein complexes formed by cross-linking; The target protein antibody is added to form an antibody-target protein-DNA complex; This complex was precipitated using Protein G beads, specifically enriching DNA fragments bound to the protein of interest; Multiple washes to remove non-specifically bound chromatin and purify the complex; Unraveling cross-links and purifying DNA fragments; q-PCR or sequencing analysis.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method

value: phoB-FLAG3 strains


title: ACP-UAB-1


title: NORMAL-PIT-A14-31


title: PHGG3

value: TUMOR-GBM

value: glioblastoma


title: EPNPFA2-965-1b

value: ependymoma, posterior fossa group A2


title: EPNPFA2-987-1


title: H3K18lac-L2C-G+N-L

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
We aligned paired-end CUT&Tag reads of H3K18lac to the mm39 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed. Next, we pooled the biological replicates for each stage and performed downstream analysis. For peak calling, we converted sequence alignments in BAM format into BEDPE records using the BEDTools function bamtobed. CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. Peak comparisons and overlaps were evaluated using the BEDTools suite for autosomal chromosomes. For quantitative analysis, we normalized the read counts by computing the number of RPKMs using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: mm39
Supplementary files format and content: bw
Library strategy: Cut&Tag

organism: Mus musculus

source_name: late 2-cell

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used.
CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech). Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C. For single-cell CUT&Tag of human embryos, CUT&Tag was performed in well of a microplate. After tagmentation, single human embryos were transferred to 200µl tubes containing 5% Proteinase K. After embryos lysis, PCR buffer and adaptors were directly added to tubes, normal PCR cycle was performed. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (Vazyme Biotech). Libraries were sequenced on the Illumina NovaSeq 6000 platform according to the manufacturer’s instructions.

value: late 2-cell

tag: chip antibody

value: H3K18lac(Cat# PTM-1406RM)


title: WT_2


title: ACP-F21-4-1

tag: treatment


title: H3K18lac-L2C-G+N


title: NORMAL-FRONTAL-E03

source_name: TUMOR-FRONTAL

value: TUMOR-FRONTAL


title: EPNPFA2-965-1a


title: MEDGP4-934-1

value: TUMOR-MED

value: medulloblastoma


title: phoB-FLAG3_1


title: MEDGP4-961-1


title: NORMAL-PONS-953-X

source_name: NORMAL-PONS

value: NORMAL-PONS


title: EPNPFA1-943-1

value: ependymoma, posterior fossa group A1

value: Presentation


title: KO-female-DRG3

city: durham

first: sangsu

last: Bang

state: North Carolina

address: 3 genome st, 6200 MSRB3

institute: duke

data_processing:
Cutadapt(V:1.10)and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
sequence quality was verified using FastQC (V:0.10.1)
We used HISAT2(V: 2.0)to map reads to the genome. The mapped reads of each sample were assembled using StringTie(V:1.3.4).
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare
The ﬁnal transcriptome was generated, StringTieand ballgown was used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: tab-deliminited text file including raw counts and RPKM value for each Sample

source_name: DRG

extract_protocol:
RAA was harvstd using Qiagen mini prep kit. 6~7 ug of total RNA was used for the construction of sequencing libraies.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

value: DRG

value: female

value: Gpr37L1 KO

value: Control


title: NORMAL-912-X-CEREB

source_name: NORMAL-Cerebellum

value: NORMAL-Cerebellum

value: normal brain

value: M


title: H3K18lac-L2C-G+N-L+A


title: EPNST-RELA-909-1

source_name: TUMOR-RELA

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion


title: WT-female-PTX-DRG3

value: WT


title: KO-male-DRG1

value: male


title: KO-male-PTX-DRG1


title: EPNPFA1-928-1


title: EPNPFA2-930-1

value: ependymoma, posterior fossa group A2


title: WT-male-PTX-DRG2


title: WT_1

value: phoB-FLAG3 strains


title: ATRT-TYR-908-1

source_name: TUMOR-ATRT

value: TUMOR-ATRT

value: atypical teratoid rhabdoid tumor

value: F

value: Recurrence


title: WT-female-DRG3

value: DRG


title: WT-male-PTX-DRG1


title: KO-female-PTX-DRG2

value: female


title: WT-male-DRG2


title: WT-male-DRG1


title: EPNPFA1-871-1

value: ependymoma, posterior fossa group A1

value: Presentation


title: EPNPFA1-816-1


title: NORMAL-CEREB-897-X

value: NORMAL-Cerebellum


title: EPNPFA2-811-1


title: 19512X24 Female SMC

city: Salt Lake City

first: Katsuhiko

last: Funai

state: UT

department: Molecular Medicine

institute: University of Utah

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 104
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.34.0
Assembly: mm39
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited raw count matrix

source_name: Skeletal Muscle

extract_protocol:
Direct-zol RNA Miniprep Plus kit
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion kit

value: Skeletal Muscle

value: Female

tag: strain

value: 8 weeks of small mouse cage (SMC) intervention


title: 19512X21 Female SMC


title: EPNST-RELA-870-1

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion

value: M


title: 19512X23 Female SMC


title: MEDSHH-831-1

value: TUMOR-MED

value: medulloblastoma


title: 19512X20 Female SMC


title: 19512X22 Female SMC


title: EPNPFA2-80-1

value: ependymoma, posterior fossa group A2


title: EPNPFA1-781-1


title: KO-male-DRG2

value: male

tag: genotype

value: Gpr37L1 KO

value: Control


title: 19512X18 Male SMC

value: Male


title: GG-794-1

value: TUMOR-GG

value: ganglioglioma

value: F


title: 19512X19 Female SMC


title: 19512X16 Male SMC


title: EPNPFA1-758-1

value: ependymoma, posterior fossa group A1

value: Presentation


title: 19512X17 Male SMC

value: Skeletal Muscle


title: ATRT-SHH-737-1

source_name: TUMOR-ATRTSHH

value: TUMOR-ATRTSHH

value: atypical teratoid rhabdoid tumor


title: EPNPFA2-727-1


title: EPNPFA2-897-1


title: 19512X15 Male SMC

value: 8 weeks of small mouse cage (SMC) intervention


title: 19512X14 Male SMC


title: EPNPFA2-700-1

value: M


title: 19512X13 Male SMC


title: EPNPFA2-723-1


title: MEDGP3-674-1

value: medulloblastoma group 3


title: 19512X12 Female Sham

value: Female

value: Sham


title: MEDGP4-655-1

value: TUMOR-MED

value: medulloblastoma


title: 19512X10 Female Sham


title: 19512X11 Female Sham


title: ACP-646-1

value: TUMOR-ACP

value: adamantinomatous craniopharyngioma


title: 19512X9 Female Sham


title: ATRT-SHH-605-1

value: TUMOR-ATRT


title: 19512X8 Female Sham


title: 19512X7 Female Sham


title: NORMAL-CEREB-514-X

value: NORMAL-Cerebellum

value: normal brain


title: MEDGP4-554-1

value: medulloblastoma group 4


title: 19512X4 Male Sham

value: Male


title: EPNPFA1-64-1

value: ependymoma, posterior fossa group A1

value: Presentation


title: EPNPFA1-492-1


title: GG-487-1

value: TUMOR-GG

value: ganglioglioma


title: 19512X3 Male Sham

value: Skeletal Muscle


title: ATRT-MYC-514-1

value: atypical teratoid rhabdoid tumor

value: M


title: 19512X2 Male Sham

value: Sham


title: MED-WNT-613-1

value: TUMOR-MED


title: EPNPFA1-483-1


title: 19512X1 Male Sham


title: EPNPFA1-419-1


title: EPNPFA1-393-1

value: F


title: 19512X5 Male Sham


title: RNA-con-in vitro 1

city: 33-浙江省

first: Ming

last: Zong

address: University Town, Chashan, Wenzhou

institute: Wenzhou Medical University

description: count.txt

data_processing:
CUT&Tag paired-end reads were aligned to the mouse genome (mm10) using Bowtie 2 (version 2.2.5) with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). Reads from PCR duplicates were removed using Picard ‘MarkDuplicates’. After confirming reproducibility between replicates, they were merged using Samtools‘merge’. Final bam files were converted to bigWig files of read coverages normalized to RPKM using deepTools (version 3.5.1) bamCoverage.
For RNA-seq analysis of all data, we downloaded the mouse reference genome (genome assembly: mm10) from the Ensembl database and used the HISAT2 software for read alignment with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. The expression level of each gene was quantified in terms of the normalized fragments per kilobase of transcript per million mapped reads (FPKM). Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10

source_name: oocyte

extract_protocol:
Oocytes were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Single Cell Full Length mRNA-Amplification Kit(N712, Vazyme) according to the manufacturer’s instructions.
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) according to the manufacturer’s instructions.

value: oocyte


title: EPNPFA2-392-1

value: ependymoma, posterior fossa group A2


title: pho84Δ-1

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing: The online Galaxy platform was used (www.usegalaxy.org). Programs: HiSAT2, FeatureCounts, edgeR.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Strains were grown overnight at 30 °C in phosphate free YNB medium (Formedium) supplemented with 7.2 mM potassium phosphate and 50 mM KCl, supplemented with leucine, histidine, methionine and uracil. This culture was used to inoculate two or three times 50 ml of supplemented YNB medium containing 7.2 mM potassium phosphate and 50 mM KCl yielding A620nm 0.1. These cultures were grown at 180 rpm at 30 °C to A620nm 0.5. The cultures were poured into plastic tubes and frozen in liquid nitrogen. Prior to RNA isolation, the frozen cultures were thawed on ice and cells were collected by centrifugation and transferred to Eppendorf tubes using ice-cold water.

extract_protocol:
RNA was isolated using the Ambion RiboPure yeast RNA Purification Kit (Life Technologies).
The Illumina TruSeq stranded RNA-seq library preparation kit is used and the purified mRNA is fragmented and converted to double-stranded cDNA. DNA adapters with sample-specific barcodes are ligated and a PCR amplification is performed. .

value: yeast


title: EPNPFA1-507-1


title: RNA-PSMPs & OE-Hdac3 1

description: count.txt


title: EPNST-RELA-388-1

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion


title: pho4Δ-1


title: pho84Δ-2


title: RNA-SAHA 2

description: count.txt


title: ume6Δ-2


title: 19512X6 Male Sham


title: ume6Δ-3


title: ATRT-TYR-370-1

value: TUMOR-ATRT


title: RNA-SAHA 1

description: count.txt


title: ume6Δ-1


title: EPNPFA2-321-1


title: BY4741ΔU-3


title: RNA-in vitro PSMPs 2

description: count.txt


title: BY4741ΔU-1


title: BY4741ΔU-2


title: EPNPFA1-319-1


title: RNA-in vitro PSMPs 1

description: count.txt


title: BY4741-5


title: EPNPFA1-318-1


title: RNA-PSMPs & OE-Hdac3 2

description: count.txt


title: BY4741-4


title: RNA-in vivo PSMPs 2

description: count.txt


title: MEDSHH-288-1

source_name: TUMOR-MED

value: medulloblastoma


title: Tpho84-Tcyc1-3


title: pho4Δ-2


title: Tpho84-Tcyc1-2


title: Tpho84-Tcyc1-1


title: RNA-in vivo PSMPs 1

description: count.txt


title: MEDGP3-277-1


title: RNA-con 2

description: count.txt


title: BY4741ΔP-2


title: MEDSHH-258-1


title: RNA-con 1

description: count.txt


title: BY4741ΔP-1


title: H4K16ac-con-invitro 2

data_processing:
CUT&Tag paired-end reads were aligned to the mouse genome (mm10) using Bowtie 2 (version 2.2.5) with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). Reads from PCR duplicates were removed using Picard ‘MarkDuplicates’. After confirming reproducibility between replicates, they were merged using Samtools‘merge’. Final bam files were converted to bigWig files of read coverages normalized to RPKM using deepTools (version 3.5.1) bamCoverage.
For RNA-seq analysis of all data, we downloaded the mouse reference genome (genome assembly: mm10) from the Ensembl database and used the HISAT2 software for read alignment with a default setting after removing adaptor sequences and low-quality reads by fastp (version 0.12.4). The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. The expression level of each gene was quantified in terms of the normalized fragments per kilobase of transcript per million mapped reads (FPKM). Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10
Library strategy: Cut&Tag

extract_protocol:
Oocytes were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG/A-Tnp and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h.The reaction was stopped with 5 μl Proteinase K、100 μl Buffer L/B, and extraction with DNA Extract beads.
CUT&Tag was performed using the Hyperactive Universal CUT & Tag Assay Kit for Illumina (TD903, Vazyme).Oocytes were incubated in 50 µL antibody buffer;    0.5 μg antibody was added and the mixture was incubated at 4℃ overnight.After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 2 µL pA/G-Tnp and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer.We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 5 μl Proteinase K、100 μl Buffer L/B; After extraction with DNA Extract beads PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C.

tag: antibody


title: BY4741-1


title: BY4741-2


title: MEDGP3-241-1


title: EPNPFA1-246-1

value: ependymoma, posterior fossa group A1


title: ALFA-EGR1

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

library_source: other

data_processing:
Barcodes from sequencing libraries were mapped to the associated TFBS based on previously obtained TFBS-BC pairings. Barcode counts per TFBS were obtained for each library and merged into a single data frame. For differential activity analysis, read counts for the DBD-of-interest and a ‘No-DBD’ control, across 3 replicates each, were analyzed using DESeq2. TFBS significantly bound by the DBD-of-interest were identified by applying a false discovery rate (FDR) threshold of 5%.
Assembly: Custom: TFBS_BC_Combinations_all_10-mers_library.csv and TFBS_BC_Combinations_Output_UNIQUE.txt
Supplementary files format and content: TFBS_BC_Combinations_all_10-mers_library.csv: Comma separated strings of 10-bps TFBS, 25-bps Barcode, and count.
Supplementary files format and content: ReadCounts_perTFBS_all10mers_DF.txt: Tab separated read count matrix
Supplementary files format and content: dds_results_HOXD13_df.txt: DESeq2 output comparing read counts from ALFA-HOXD13 to the No-DBD control.
Supplementary files format and content: dds_results_EGR1_df.txt: DESeq2 output comparing read counts from ALFA-EGR1 to the No-DBD control
Supplementary files format and content: TFBS_BC_Combinations_Output_UNIQUE.txt: Tab separated strings of 9-bps TFBS, and 20-bps Barcodes.
Supplementary files format and content: ReadCounts_perTFBS_DF_DuplicatesNotRemoved_Tag_Linker.txt: Tab separated read count matrix
Library strategy: PADIT-seq

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
PADIT-seq experiment: To remove any supercoiling, PADIT-seq reporter libraries were first linearized with DrdI (NEB), which cuts a 12-bp DNA sequence (GACNNNN/NNGTC) only once in the pGL4.23 vector. For every DBD being tested, the following 30ul PURExpress IVTT reactions (NEB) were assembled: 10ul Solution A, 7.5ul Solution B, 1ul Murine RNase Inhibitor, 3ul 100mM rNTPs, 0.45ul 1000mM Magnesium Acetate, 3ul previously purified nbALFA-T7-RNA-Polymerase, ~300 ng linearized PADIT-seq reporter plasmid library, ‘pT7-ALFA-DBD-T7Term’. The linearized PADIT-seq reporter plasmid library was mixed with ‘pT7-ALFA-DBD-T7Term’ amplicons in an approximately 2:1 molar ratio. The 30ul PURExpress IVTT reactions were split into three wells, and all subsequent steps were performed separately (3 biological replicates).   cDNA synthesis of PADIT-seq reporter RNAs: After 4 hours at 37°C, the 10ul reactions were purified with RNAClean XP as per manufacturer’s instructions, eluting in 35ul Nuclease-free water. 2ul barcoded cDNA synthesis primers (0.1uM final each) were added to 18ul purified RNA, incubated at 75°C for 3 mins, then placed on ice. cDNA was synthesized by adding 10ul 2X Multiscribe reaction mix (Thermo Fisher), and incubating at 25°C for 20 minutes, followed by 37°C for 120 minutes. Minus reverse transcriptase controls were performed in parallel. Excess primers were removed from the cDNA:RNA duplexes by adding Exonuclease I and incubating at 37°C for 60 mins, followed by heat inactivation at 80°C for 20 mins. Quantitative PCR was performed to verify degradation of all excess primers, and to determine the threshold cycle of sample cDNAs.    PADIT-seq library preparation for Illumina Sequencing: For the small-scale PADIT-seq library, barcoded cDNAs synthesized from the reporter RNAs were pooled prior to PCR amplification. The pooled cDNA was amplified in a single PCR reaction using KAPA HiFi polymerase with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated a PCR-1 product that was then used as template for a second PCR with primers '#34_MPRA' and ‘169_TruSeq_Multiplex_220_2’ to attach Illumina adapters and sample barcodes. In contrast, for the all-10mers PADIT-seq library, barcoded cDNAs were kept separate and amplified in individual PCR reactions rather than pooled. For each DBD, cDNA was amplified using KAPA HiFi HotStart Polymerase with primers 'MPRA_AmpliconEZ_FWD' and 'MPRA_AmpEZ_REV2.0'. This generated PCR-1 products that were cleaned and quantified. In the second PCR, '#34_MPRA' and indexed TruSeq primers were used to attach Illumina adapters and sample barcodes.
Construction of the all-10mers PADIT-seq reporter library: We designed and ordered two IDT Ultramers - one containing all possible 10-bp DNA sequences as candidate TFBS (‘All10mersTFBS_Top’), and another containing all possible 25-bp DNA sequences to serve as barcodes (‘25bpsBC_Bottom’). The two Ultramers were mixed in an equimolar ratio and double stranded in a single PCR cycle using KAPA HiFi polymerase. The pGL4.23 plasmid vector backbone was again PCR amplified in 2 steps with Q5 High-Fidelity 2X Master Mix. First, the backbone was amplified with primers ‘pGL4.23_FWD’ and ‘pGL4.23_REV’ to exclude the luciferase open reading frame. The resulting amplicon (2359-bps) was then further amplified with primers 'T7Term_pGL4.23_F_2.0' and 'pGL4.23_REV' to add a 56-bps DNA sequence as an overlapping region for Gibson Assembly, which was performed with the resulting amplicon (2415-bps) and the double-stranded oligo-pool mixed in equimolar ratios. Following desalting with a mixed cellulose esters (MCE) hydrophilic membrane (0.025 um), the assembled reporter library plasmid was electroporated into E. cloni 10G Supreme cells (n = 13 transformations). Based on plating experiments, the total number of transformants obtained was estimated to be 110 million, providing an average of ~100 barcodes per TFBS. The transformed cells were recovered, grown for 6.5 hrs, and maxi-prepped to obtain the complete all-10mers PADIT-seq reporter plasmid library containing over 100 million clones. Correct library assembly was validated by diagnostic PCR and Sanger sequencing of 10 colonies.   Obtaining TFBS-BC pairing in the all-10mers PADIT-seq reporter library: To obtain TFBS-BC pairings, the all-10mers PADIT-seq reporter library was PCR amplified using KAPA HiFi polymerase. Four forward primers were designed with partial Illumina adapters, 6N randomized bases, and 2-bps staggers (‘All_10mers_LibSeq_F1-4’). These were used individually with a single reverse primer (‘All_10mers_LibSeq_R’) to generate 4 PCR-1 products of expected sizes 213-219-bps (9 cycles). The 4 PCR-1 products were then used as template in PCR-2 (5 cycles) with TruSeq indexed primers to attach Illumina sample indexes. This generated 4 PCR-2 products of expected size 272-278-bps. After PCR amplification, the 4 products were SPRI cleaned and analyzed on Tapestation to confirm expected sizes. The 4 indexed libraries were sequenced separately on a NovaSeq6000 (2x150 bp reads). The sequencing data from each of the 4 indexed libraries (F1-F4) was combined and processed using custom scripts to extract unique TFBS-BC combinations along with their counts by matching the constant flanking regions. Barcodes unambiguously associated with only 1 TFBS across all 4 libraries were classified as ‘single TFBS barcodes’ and retained. The all-10mers PADIT-seq reporter plasmid library was amplified in 4 separate PCR reactions (F1-F4) with different TruSeq indexes to identify potential PCR-mediated recombination artifacts in the following way: for barcodes associated with multiple TFBS, an initial filter retained only TFBS observed independently in at least 2 of the 4 libraries. The rationale being that TFBS-BC occurrence in multiple independent libraries indicates likely true pairings versus artifacts of PCR-mediated recombination. After this first multi-library filtering step, any barcodes still associated with multiple TFBS were removed entirely to eliminate ambiguities. As an additional filter, barcodes where the top TFBS had fewer reads than the sum of discarded TFBS were removed. The ‘single TFBS barcodes’ and  vetted multiple TFBS barcodes were combined to obtain high-confidence 1:1 TFBS-BC pairs for downstream analysis. This multi-step filtering process leveraged the independently prepared sequencing libraries to remove incorrect and ambiguous TFBS-BC pairings arising from PCR-mediated recombination. It enabled retaining high-confidence barcode-TFBS pairs reproducibly identified across multiple libraries while discarding likely PCR artifacts and errors.

value: synthetic construct


title: H4K16ac-con-invitro 1

tag: cell line


title: GG-199

source_name: TUMOR-GG

value: TUMOR-GG

value: Presentation


title: TFBS-BC-Combinations_small-scale-library


title: H4K16ac-PSMPs & OE-Hdac3 2


title: ALFA-HOXD13


title: No_DBD


title: H4K16ac-PSMPs & OE-Hdac3 1


title: TFBS-BC-Combinations_All-10mers-library


title: H4K16ac-SAHA 2


title: BY4741ΔP-3

tag: cell type


title: Liver_finasteride_65

city: Urbana

first: Jaume

last: Amengual

state: IL

address: 905 S Goodwin Ave

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Salmon (v1.4.0) was used to quasi-map reads of the NCBI Mus musculus Annotation Release 109 transcriptome using the entire GRCm39 genome as the decoy sequence and additional options(--seqBias --gcBias --numBootstraps=30)
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v1.20.0) in R (v4.1.0)
Assembly: GRCm39, NCBI Annotation Release 109
Supplementary files format and content: Amengual_rawCounts_2021-07-16.txt: gene level annotations and counts in tab-delimited text format

source_name: Liver

extract_protocol:
Liver RNA was isolated using a Zymo Research mini prep tissue kit (Irvine, CA), following a DNaseI treatment, according to the manufacturer's instructions.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were pooled; quantitated by qPCR and sequenced on one SP lane for 101 cycles from one end of the fragments on a NovaSeq 6000.

value: Liver

value: Ldlr-/-

value: Male

value: 1000 mg/kg of finasteride


title: Liver_finasteride_64


title: EPNPFA1-195-1

value: M


title: Liver_finasteride_63


title: Liver_finasteride_61


title: ATRT-MYC-1545-1

value: atypical teratoid rhabdoid tumor


title: H4K16ac-SAHA 1

value: oocyte


title: Liver_finasteride_41


title: MED-1520

value: TUMOR-MED


title: H4K16ac-in vitro PSMPs 2


title: BY4741-3

value: yeast


title: Liver_finasteride_40


title: Liver_finasteride_26


title: Liver_finasteride_25


title: Liver_control_72

value: 0 mg/kg of finasteride


title: EPNPFA-1513-1


title: H4K16ac-in vitro PSMPs 1


title: Liver_control_71


title: H4K16ac-in vivo PSMPs 2


title: GBM-1485-1

source_name: TUMOR-GBM

value: TUMOR-GBM

value: glioblastoma


title: Liver_control_69


title: Liver_control_70


title: Liver_control_34


title: Liver_control_33


title: EPNPFA-1536-1

value: ependymoma, posterior fossa group A2


title: PA-1459-1

source_name: TUMOR-PA

value: TUMOR-PA

value: pilocytic astrocytoma


title: H4K16ac-con 1


title: EPNST-RELA-1464

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion


title: GG-1455-1

value: TUMOR-GG

value: ganglioglioma

value: F

value: Presentation


title: J774A.1 cells, B. pseudomallei + Mip inhibitor AN_CH_37, 4 hr, replicate4

city: Crawley

first: Jua

last: Iwasaki

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Pass filter data of fastq format were processed by Trimmomatic (v0.30)
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL.
Hisat2 (v2.0.1) was used to index reference genome sequence.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1)
Assembly: mm10
Supplementary files format and content: 1 excel sheet containing FPKM values for each sample

source_name: Ascites

growth_protocol: J774A.1 murine macrophage cells were maintained in DMEM (Gibco, Life Technologies) supplemented with a final concentration of 1% GlutaMAX (Gibco, Life Technologies) and 10% heat-inactivated fetal calf serum (Gibco, Life Technologies) at 37°C with 5% CO2

extract_protocol:
RNA was extracted using the RNeasy Micro Plus kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq was prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit following manufacturers protocols

value: Ascites

value: Macrophage

value: WT

value: B. pseudomallei + AN_CH_37


title: H4K16ac-con 2

value: oocyte


title: GBM-1484-1


title: 2205,SI-GA-G6

description: 10x Genomics, S4 Flow Cell

source_name: Whole Heart

value: Whole Heart

value: Heart Tissue

value: HET


title: J774A.1 cells, B. pseudomallei + Mip inhibitor SF235, 4 hr, replicate4

value: B. pseudomallei + SF235


title: Periodontal tissues of ligature-induced periodontitis mice

city: Tokyo

first: Masayuki

last: Tsukasaki

state: --None--

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

description: 10x Genomics

data_processing:
Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Periodontal tissue

extract_protocol:
Single-cell RNA-sequencing was performed on live cells derived from periodontal tissues of control mice and ligature-induced periodontitis mice.
The sequencing libraries were generated using the 10x Genomics Single-cell 3′ Solution Kit (v.3) and then subjected to Illumina sequencing (HiSeq 4000 Sequencing System).

value: Periodontal tissue

tag: age

value: 8 weeks old

value: Ligature-induced periodontitis


title: H4K16ac-in vivo PSMPs 1


title: Liver_control_48

value: Liver

value: Ldlr-/-

value: Male

value: 0 mg/kg of finasteride


title: Liver_control_47


title: GG-1491-1

value: TUMOR-GG

value: ganglioglioma

value: Presentation


title: J774A.1 cells, DMSO, 4 hr, replicate4

value: Ascites

value: Macrophage

value: WT

value: DMSO


title: 953,SI-GA-F6

description: 10x Genomics, S4 Flow Cell

value: Whole Heart

value: Heart Tissue


title: PA-1453-1

value: TUMOR-PA

value: pilocytic astrocytoma


title: J774A.1 cells, B. pseudomallei + Mip inhibitor AN_CH_37, 4 hr, replicate3

value: B. pseudomallei + AN_CH_37


title: J774A.1 cells, B. pseudomallei + DMSO, 4 hr, replicate3

value: B. pseudomallei + DMSO


title: J774A.1 cells, B. pseudomallei + Mip inhibitor SF235, 4 hr, replicate3

value: B. pseudomallei + SF235


title: MEDGP3-1433

value: medulloblastoma group 3

value: M


title: GBM-1437-1

value: TUMOR-GBM

value: glioblastoma


title: 1505,SI-GA-F1

description: 10x Genomics, S4 Flow Cell


title: J774A.1 cells, DMSO, 4 hr, replicate3


title: PA-1428

value: F


title: J774A.1 cells, B. pseudomallei + Mip inhibitor SF235, 4 hr, replicate2


title: 4674,SI-GA-H6

description: 10x Genomics, S4 Flow Cell

value: HET


title: J774A.1 cells, B. pseudomallei + Mip inhibitor AN_CH_37, 4 hr, replicate2

value: Ascites


title: 955,SI-GA-E1

description: 10x Genomics, S4 Flow Cell


title: Periodontal tissues of control mice

description: 10x Genomics

value: Periodontal tissue

value: 8 weeks old


title: J774A.1 cells, B. pseudomallei + DMSO, 4 hr, replicate4

value: Macrophage

value: WT


title: 1931,SI-GA-G1

description: 10x Genomics, S4 Flow Cell

value: Whole Heart

value: Heart Tissue


title: J774A.1 cells, B. pseudomallei + DMSO, 4 hr, replicate2


title: GBM-1421

value: Presentation


title: EPNST-RELA-1418-3

value: TUMOR-RELA

value: ependymoma, supratentorial ZFTA-RELA fusion

value: Recurrence


title: 2440,SI-GA-H1

description: 10x Genomics, S4 Flow Cell


title: J774A.1 cells, B. pseudomallei + Mip inhibitor AN_CH_37, 4 hr, replicate1

value: B. pseudomallei + AN_CH_37


title: J774A.1 cells, B. pseudomallei + DMSO, 4 hr, replicate1

value: B. pseudomallei + DMSO


title: 2439,SI-GA-A3

description: 10x Genomics, S4 Flow Cell


title: J774A.1 cells, DMSO, 4 hr, replicate1

value: DMSO


title: J774A.1 cells, DMSO, 4 hr, replicate2


title: MEF cells- HF 3

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 N. Barnhill Dr. MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: HF treated sample for tRNA Charge-Seq in MEF cells

data_processing:
Pooled Samples were demultiplexed using python script to identify the sample specific barcode contained within the ligated adapter (5’- PO4-NNNNNXXXXXAGATCGGAAGAGCACACGTCTGAA-ddC-3’) where XXXXX is the unique sample-specific barcode.
Due to the small library footprint and long sequencing reads, it was necessary to trim the 5' ends of the reads using trimgalore
The trimmed reads were then aligned using bowtie2 to a custom reference consisting of mature tRNA sequences constructed from the GRCm38/mm10 (for MEF cells) or GRCh38/hg38 (for NTERT cells)-- references for both are supplied in this submission, and each reference was constructed from the UCSC gtRNAdb.
tRNA charging was assessed by parsing the aligned reads using a custom python script to identify the presence or absence of a 3' adenine base. The NaIO4 treatment performed during library prep  results in cleavage of the 3'-A if not protected by an amino-acyl bond.
Counts of charged and uncharged tRNA were then used to create plots and calculate statistical significance using R.
Assembly: Custom genome containing mature tRNA sequences from GRCm38/mm10 and GRCh38/hg38-- each supplied as fasta sequences
Supplementary files format and content: tab delimited text files containing counts of charged and uncharged tRNA
Library strategy: tRNA Charge-Seq

source_name: Cell Line

growth_protocol: MEF cells grown in high-glucose DMEM supplemented with 10% Fetal Bovine Serum and 1x Penicilin/Streptomycin. NTERT cells were maintained and passaged in low calcium EpiLife Complete media (Themo Fisher Scientific) supplemented with human keratinocyte growth supplement (HKGS; Themo Fisher Scientific) and 1000 U Penicillin-Streptomycin (PS) (Gibco Laboratories).

extract_protocol:
For genome-wide tRNA-charging assay, total RNA were extracted with Trizol reagent according to manufacturer's protocol. RNA were then oxidized by NaIO4 followed by deacylation at high pH. Next RNA were purified using ethanol precipitation and used for library preparation.
For genome-wide tRNA-charging assay: The purified tRNA samples were then treated with PNK (M0201, New England BioLabs) to remove the 3’-PO4 group from the uncharged tRNA. Next, 5’-adenylated adaptors carrying unique barcode (5’- PO4-NNNNNXXXXXAGATCGGAAGAGCACACGTCTGAA-ddC-3’; N-random nucleotides, XXXXX- is sample specific pentamer barcode, ddc-dideoxy cytidine) were ligated to the tRNAs using T4 RNA ligase2 truncated KQ (M0351L, New England BioLabs). tRNAs were then ligated to a 5’-adaptor (5’-rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC-3’) followed by reverse transcription using SuperScript IV RT kit (18090050, Invitrogen) and RT primer (5’-AGACGTGTGCTCTTCCGATCT-3’). Next the tRNA library was PCR amplified for 10 cycles by using Illumina multiplex PCR primer (5’-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’) and Illumina barcode PCR Primer (5’-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’). PCR products were separated by an 8% non-denaturing polyacrylamide TBE gel (EC6215BOX, Invitrogen) and ~210 nt bands were excised, purified and subjected to HiSeq paired-end Illumina sequencing.

treatment_protocol: Cells treated with 100nM halofuginone for 6Hrs in high-glucose DMEM supplemented with 10% dialyzed Fetal bovine Serum and 1x Penicilin/Streptomycin. Control samples were treated with same dialyzed FBS containing media without halofuginone for 6Hrs. NTERT cells were treated with 400 J/m2 UV-B or left untreated (NT), followed by recovery for 3 hours.

value: Cell Line

value: MEF

value: Mouse Embryonic Fibroblast

value: 100nM Halofuginone for 6hrs


title: MEF cells- HF 2


title: 472,SI-GA-D1

description: 10x Genomics, S4 Flow Cell

data_processing:
Demultiplexing, barcode processing, gene counting were done using Cell Ranger software v6.0.1
Assembly: Fca126, GRCh38, mm10
Supplementary files format and content: Tab-separated values files, and matrix files


title: 2204,SI-GA-C2

description: 10x Genomics, S4 Flow Cell

value: HOM


title: MEDSHH-1416

source_name: TUMOR-MEDSHH

value: TUMOR-MEDSHH

value: medulloblastoma, SHH group

value: M


title: GBM-1414-1

value: TUMOR-GBM

value: glioblastoma


title: MEF cells- HF 1


title: GG-1417-1

value: TUMOR-GG

value: ganglioglioma

value: F

value: Presentation


title: MEF cells- Control 3

description: Control for tRNA Charge-Seq in MEF cells

value: untreated


title: 945,SI-GA-B2

description: 10x Genomics, S4 Flow Cell

value: Whole Heart

value: Heart Tissue


title: MEF cells- Control 2

value: Cell Line


title: GBM-1402


title: EPNPFA1-1400-2

value: ependymoma, posterior fossa group A1

value: Recurrence


title: 2TFP-Myc/2TFP-Myc mouse, WGS

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: R1:150 and R2:150

data_processing:
CNV analysis on WGS has been perform using CNVnator (https://www.ncbi.nlm.nih. gov/pmc/articles/PMC3106330/) with a sliding window of 10 and 20kbs. The following filter was applied subsequently: Both t-Test (columns 5 and 7) <  0.05 and the ratio of mQ0 (column 9) < 0.01.
Assembly: mm10
Supplementary files format and content: CNV files: Table of several columns indicating the type of alteration (deletion/duplication), the segment size, read depth of the segment normalized to 1, t-Test for the distribution of the RD of the bins with in the segments compared to all segments, probability of RD values within the region to be in the tails of a gaussian distribution describing frequencies of RD values in bins, t-Test for the segment for the middle of the segment, probability of being in the tails of a Gaussian distribution for the middle of the segment and proportion of reads mapped with mapping quality == 0.

source_name: tail tissue

extract_protocol:
For WGS DNA was extracted from mouse tails by Salt lysis buffer and Isopropanol DNA precipitation.
For WGS, library was generated using Illumina TrueSeq standard protocol.

value: tail tissue


title: MEF cells- Control 1

value: MEF

value: Mouse Embryonic Fibroblast