title: LX-2 cells, PBS-treated, biol rep3

city: Nanjing

first: Hao

last: Peng

state: State...

address: Dingjiaqiao

institute: Southeast University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (Parameter-quality limit: 0.05 )
Trimmed sequence reads  were mapped to Ensembl_v101  using CLC Genomics Workbench (Parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8  )
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: Ensembl_v101
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

growth_protocol: LX-2 cells were maintained in DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in humidified air with 5% CO2

extract_protocol:
RNA were havested using TRIzol reagent kit (thermofisher), 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following maufacture's protocols.

treatment_protocol: LX-2 cells were treated with 300ng/ml of rhSema3C or PBS for 48 hours.

value: hepatic stellate cell

value: WT

value: PBS stimulation


title: LX-2 cells, PBS-treated, biol rep2

status: Public on Jul 10 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: LX-2 cells, PBS-treated, biol rep1


title: P487.FF

type: RNA

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

data_processing: Raw count data from nCounter was normalized

label: fluorescence barcode

source_name: tumor

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

tag: tissue

value: FF

tag: Stage

value: III

tag: age

tag: gender

value: Male

value: right

tag: ptstage

tag: pnstage

tag: death

tag: recurrence


title: P2273.FFPE

value: FFPE

value: Female


title: P605.FF

value: left


title: LX-2 cells, rhSema3C-treated, biol rep1

value: rhSema3C stimulation


title: P1226.FF


title: P171.FF


title: P938.FF


title: P549.FF


title: X7

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

data_processing:
FastQC v0.11.8 for Sequencing QC
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Counts for sample sequenced with multiple lanes were added to produce a single column of value
Assembly: GRCh37
Supplementary files format and content: target.mod.tsv: Tab delimited raw gene counts of each sample

source_name: Keratinoocyte cell

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit and the On-column DNase digestion (Qiagen, Hilden, Germany).
RNA samples were analyzed by quantitative real-time polymerase chain reaction (PCR) using TaqMan Fast Virus 1-Step Master Mix with the QuantStudio 7 Flex Real-Time PCR System (All from Thermo Fisher Scientific).

value: Keratinoocyte cell


title: LX-2 cells, rhSema3C-treated, biol rep3


title: P1868.FF


title: Lung_16_tumor

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expresison count using Space Ranger's default settings
hg38
barcodes.tsv.gz: list of spatial barcodes
features.tsv.gz: list of gene IDs
matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
aligned_fiducials.jpg: aligned fiducials of the tissue image
detected_tissue_image.jpg: image of tissue and spots
scalefactors_json.json: scalefactors in json format
Assembly: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Lung tumor

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Lung tumor


title: X12


title: P2886.FF


title: P152.FF


title: Lung_15_tumor


title: P126.FF


title: P1880.FF


title: LX-2 cells, rhSema3C-treated, biol rep2


title: P1331.FF


title: Lung_14_tumor


title: P2999.FF


title: Lung_13_tumor


title: P1887.FF


title: P3039.FF


title: P2887.FF


title: P2916.FF


title: Lung_11_tumor


title: Lung_12_tumor


title: Lung_8_tumor


title: Lung_9_tumor


title: Lung_7_tumor


title: P2840.FF


title: Lung_4_tumor


title: Lung_3_tumor


title: P2807.FF


title: Lung_6_tumor


title: P2772.FF


title: P2846.FF


title: Lung_2_tumor


title: P2802.FF


title: Tumor_16_Input

description: BED file: Tumor 16, low exposure to violence neighborhood, Tumor relative to Input

library_source: genomic

data_processing:
The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
Adaptors were trimmed from the 3'-end of the reads. The quality-scores line in fastq files used an ASCII offset of 33 known as Sanger scores.
Paired-end FASTQ files were aligned to human reference (GRCh38) using Bowtie2 (v2.4.5)
BAM files were prepared using SAMtools (v1.17)
Narrow peak calling was performed using MACS (v2.2.5) with a p-value cutoff and FDR of 0.001.
Assembly: Tumor-specific narrowPeak files were generated by filtering out binding regions also found in healthy tissue bed files. Normal-specific narrowPeak files were similarly generated via the removal of binding regions found in tumor bed files.
Supplementary files format and content: hg38
Supplementary files format and content: bed
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
Tumor samples were homogenized using 30 strokes of a Dounce homogenizer
Libraries were constructed with the Ovation Ultralow System V2 kit from Tecan following the manufacturer’s protocol. The individually barcoded libraries were run on a Fragment Analyzer (Agilent, CA) to confirm the absence of free primers and primer dimers and to confirm the presence of DNA of the expected size range. Libraries were pooled in equimolar concentration and the pool was further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA).

value: low exposure to violence neighborhood


title: P2798.FF


title: P2712.FF


title: Normal_16_GR

description: BED file: Normal 16, low exposure to violence neighborhood, Normal relative to Tumor

source_name: Healthy lung tissue

value: Healthy lung tissue


title: Lung_1_tumor


title: P3043.FF


title: Tumor_16_GR

description: BED file: Tumor 16, low exposure to violence neighborhood, Tumor relative to Normal


title: Lung_10_tumor


title: P2700.FF


title: P2711.FF


title: P2694.FF


title: Normal_15_Input

description: BED file: Normal 15, high exposure to violence neighborhood, Normal relative to Input

value: high exposure to violence neighborhood


title: P2746.FF


title: Tumor_15_Input

description: BED file: Tumor 15, high exposure to violence neighborhood, Tumor relative to Input


title: Normal_15_GR

description: BED file: Normal 15, high exposure to violence neighborhood, Normal relative to Tumor


title: P2763.FF


title: P2731.FF


title: Normal_16_Input

description: BED file: Normal 16, low exposure to violence neighborhood, Normal relative to Input


title: Normal_14_Input

description: BED file: Normal 14, mid exposure to violence neighborhood, Normal relative to Input

value: mid exposure to violence neighborhood


title: Normal_14_GR

description: BED file: Normal 14, mid exposure to violence neighborhood, Normal relative to Tumor


title: P2654.FF


title: P2513.FF


title: Tumor_14_Input

description: BED file: Tumor 14, mid exposure to violence neighborhood, Tumor relative to Input


title: Tumor_14_GR

description: BED file: Tumor 14, mid exposure to violence neighborhood, Tumor relative to Normal


title: P2495.FF


title: P2715.FF


title: P2519.FF


title: Normal_13_Input

description: BED file: Normal 13, mid exposure to violence neighborhood, Normal relative to Input


title: Tumor_13_Input

description: BED file: Tumor 13, mid exposure to violence neighborhood, Tumor relative to Input


title: P2518.FF


title: Tumor_13_GR

description: BED file: Tumor 13, mid exposure to violence neighborhood, Tumor relative to Normal


title: P2486.FF


title: P2326.FF


title: Normal_13_GR

description: BED file: Normal 13, mid exposure to violence neighborhood, Normal relative to Tumor


title: P2621.FF


title: Normal_12_Input

description: BED file: Normal 12, low exposure to violence neighborhood, Normal relative to Input


title: P2304.FF


title: P2428.FF


title: Tumor_15_GR

description: BED file: Tumor 15, high exposure to violence neighborhood, Tumor relative to Normal


title: P2305.FF


title: Normal_11_Input

description: BED file: Normal 11, low exposure to violence neighborhood, Normal relative to Input


title: Tumor_12_GR

description: BED file: Tumor 12, low exposure to violence neighborhood, Tumor relative to Normal


title: P2341.FF


title: Normal_12_GR

description: BED file: Normal 12, low exposure to violence neighborhood, Normal relative to Tumor


title: P2298.FF


title: P2361.FF


title: Normal_11_GR

description: BED file: Normal 11, low exposure to violence neighborhood, Normal relative to Tumor


title: P2283.FF


title: Tumor_11_Input

description: BED file: Tumor 11, low exposure to violence neighborhood, Tumor relative to Input


title: Tumor_11_GR

description: BED file: Tumor 11, low exposure to violence neighborhood, Tumor relative to Normal


title: Normal_9_Input

description: BED file: Normal 9, high exposure to violence neighborhood, Normal relative to Input


title: Normal_9_GR

description: BED file: Normal 9, high exposure to violence neighborhood, Normal relative to Tumor


title: P2046.FF


title: Tumor_9_Input

description: BED file: Tumor 9, high exposure to violence neighborhood, Tumor relative to Input


title: P2173.FF


title: P2236.FF


title: P2099.FF


title: Tumor_9_GR

description: BED file: Tumor 9, high exposure to violence neighborhood, Tumor relative to Normal


title: Normal_8_Input

description: BED file: Normal 8, mid exposure to violence neighborhood, Normal relative to Input


title: Normal_8_GR

description: BED file: Normal 8, mid exposure to violence neighborhood, Normal relative to Tumor


title: P2194.FF


title: P2037.FF


title: Tumor_8_Input

description: BED file: Tumor 8, mid exposure to violence neighborhood, Tumor relative to Input


title: Tumor_7_Input

description: BED file: Tumor 7, high exposure to violence neighborhood, Tumor relative to Input


title: Normal_7_Input

description: BED file: Normal 7, high exposure to violence neighborhood, Normal relative to Input


title: Normal_6_Input

description: BED file: Normal 6, low exposure to violence neighborhood, Normal relative to Input


title: Normal_7_GR

description: BED file: Normal 7, high exposure to violence neighborhood, Normal relative to Tumor


title: Tumor_8_GR

description: BED file: Tumor 8, mid exposure to violence neighborhood, Tumor relative to Normal


title: P1975.FF


title: Normal_6_GR

description: BED file: Normal 6, low exposure to violence neighborhood, Normal relative to Tumor


title: P1946.FF


title: P1921.FF


title: P1928.FF


title: P1899.FF


title: P1881.FF


title: Tumor_6_GR

description: BED file: Tumor 6, low exposure to violence neighborhood, Tumor relative to Normal


title: Normal_4_Input

description: BED file: Normal 4, mid exposure to violence neighborhood, Normal relative to Input


title: Normal_4_GR

description: BED file: Normal 4, mid exposure to violence neighborhood, Normal relative to Tumor


title: P1920.FF


title: P1846.FF


title: P2197.FF


title: P1962.FF


title: Tumor_4_Input

description: BED file: Tumor 4, mid exposure to violence neighborhood, Tumor relative to Input


title: P1795.FF


title: P2148.FF


title: P895.FF


title: P2060.FF


title: P1816.FF


title: Tumor_7_GR

description: BED file: Tumor 7, high exposure to violence neighborhood, Tumor relative to Normal


title: P1903.FF


title: Normal_3_Input

description: BED file: Normal 3, low exposure to violence neighborhood, Normal relative to Input


title: Normal_3_GR

description: BED file: Normal 3, low exposure to violence neighborhood, Normal relative to Tumor


title: Tumor_3_Input

description: BED file: Tumor 3, low exposure to violence neighborhood, Tumor relative to Input


title: P524.FF


title: Tumor_6_Input

description: BED file: Tumor 6, low exposure to violence neighborhood, Tumor relative to Input


title: P404.FF


title: P341.FF


title: Tumor_3_GR

description: BED file: Tumor 3, low exposure to violence neighborhood, Tumor relative to Normal


title: Tumor_4_GR

description: BED file: Tumor 4, mid exposure to violence neighborhood, Tumor relative to Normal


title: Normal_2_GR

description: BED file: Normal 2, high exposure to violence neighborhood, Normal relative to Tumor


title: P237.FF


title: Tumor_2_GR

description: BED file: Tumor 2, high exposure to violence neighborhood, Tumor relative to Normal


title: P185.FF


title: Normal_1_Input

description: BED file: Normal 1, high exposure to violence neighborhood, Normal relative to Input


title: P1754.FF


title: P309.FF


title: Tumor_1_Input

description: BED file: Tumor 1, high exposure to violence neighborhood, Tumor relative to Input


title: Normal_1_GR

description: BED file: Normal 1, high exposure to violence neighborhood, Normal relative to Tumor


title: Tumor_2_Input

description: BED file: Tumor 2, high exposure to violence neighborhood, Tumor relative to Input


title: P1650.FF


title: P1779.FF


title: P547.FF


title: P1648.FF


title: Amuc_0904 rep3

city: 天津市

first: Liu

last: yang

state: 天津市

address: qixiangtai Road

institute: Tianjin medical university

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RAW counts for each sample.
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: colon

extract_protocol:
Total RNA was extracted from theSW480 cells using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

value: Human colorectal adenocarcinoma


title: P1705.FF


title: Amuc_0904 rep2

value: WT


title: Amuc_0904 rep1


title: Normal_2_Input

description: BED file: Normal 2, high exposure to violence neighborhood, Normal relative to Input


title: P1706.FF

value: FF


title: P1604.FF

value: III


title: Control rep1

value: buffer


title: P1576.FF

value: right


title: Control rep2


title: P1637.FF


title: Tumor_1_GR

description: BED file: Tumor 1, high exposure to violence neighborhood, Tumor relative to Normal


title: Meni_Y_5

city: Wuhan

first: Jun

last: Zhang

state: hubei

address: No. 169, Donghu Road

institute: wuhan university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Clean Reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/） using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: meniscus

growth_protocol: The meniscal tissue was immediately transferred to RNAlater solution (Thermo Fisher Scientific) following surgery, refrigerated overnight at 4 °C, and stored at −80 °C

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: meniscus

value: healthy (non-OA)


title: Meni_Y_4


title: P1533.FF

value: Female


title: P1314.FF

value: Male

value: left


title: Meni_Y_3


title: P1306.FF


title: Meni_Y_2


title: Meni_O_5

value: osteoarthritis (OA)


title: Meni_Y_1


title: P1327.FF


title: Meni_O_4


title: Meni_O_3


title: P1537.FF


title: Control rep3


title: P1373.FF


title: Meni_O_1


title: P1098.FF


title: Meni_O_2


title: P1175.FF


title: P1642.FF


title: P1143.FF


title: PUS1-/- mock treated biol rep 6

city: Lausanne

first: Leon

last: Kleemann

address: Station 19

country: Switzerland

institute: EPFL

description:
Flp-In™ T-REx™ 293
processed data file contains information from all treated and untreated replicates of PUS1-/-, columns contain headers
PUS1plusandminus.txt.gz

data_processing:
First, technical replicates were concatenated to one fastq file. Reads were adapter clipped and random nucleotides were trimmed using Cutadapt (DOI: https://doi.org/10.14806/ej.17.1.200).
Reads were then mapped to the transcriptome (MANE GRCh38 v1.0 ensemble rna) after mitochondrial transcripts from the human cDNA collection (Homo_sapiens.GRCh38.cdna.all.fa) were included using bowtie version 2.5.0.
The analysis was performed based on calculating the ratio of 5' read ends (earlier RT stops) over the overall coverage at each transcript position as reported before (Finet et al. 2022).
Resulting SAM files were sorted and indexed using samtools version 1.15.1. Afterwards, the 5' coverage as well as the overall coverage at each transcript position was calculated using bedtools version 2.30.0 and bedops 2.4.41. Both files of all replicates (CMC and mock treated) were combined in one table.
GNU Awk 4.0.2 was used to calculate the average coverage and the average 5' coverage/coverage. The Ψ score was calculated by dividing the average 5' coverage/coverage of one condition by the average 5' coverage/coverage of another.
Assembly: MANE.GRCh38.v1.0.ensembl_rna.fna.gz
Supplementary files format and content: tab-delimited text files including transcript id, transcript position, coverage, 5' coverage, average coverage, 5' coverage/coverage, average 5'coverage/coverage, the Ψ score and nucleotide at the specific transcript position of all replicates of either WT, PUS3-/- or PUS1-/-
Library strategy: Pseudo-Seq

molecule: polyA RNA

source_name: mock

growth_protocol: HEK293TRex FlpIn cells were grown in Dulbecco's Modified Eagle's Medium DMEM (D5671, Sigma) supplemented with 10% FBS (G3031P-500, Lucerna-Chem), 100 units penicillin, 100 µg streptomycin (P4333, Sigma), 2 mM Ala-Gln (G8541, Sigma) in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
total RNA was extracted using 1ml TRIzol per 10cm dish following the manufacturers protocol. 200µg total RNA per replicate was used for the construction of sequencing libraries.
Pseudo-seq libraries were prepared as described before (Carlile et al., 2015) with some adaptations. Poly-A RNA enrichment was performed with Poly(A)Purist™ MAG Kit (AM1922, Thermofisher) using 200 µg total RNA input. RNA was fragmented in 10 mM ZnCl2 for 55 s at 94 °C and quenched with 20 mM EDTA followed by ethanol precipitation. RNA was then either CMC treated (0.4 M, +CMC) or mock treated (-CMC) in BEU buffer for 45 min at 40 °C and 1000 rpm. After ethanol precipitation, unspecific CMC labelling was removed by incubating the RNA in sodium carbonate buffer for 2 h at 50 °C and 1000 rpm followed by ethanol precipitation. RNA ends were repaired with T4 PNK (M0201L, NEB) for 2 h at 37 °C, precipitated and size selected (120-140 nt) by Urea-PAGE. A 3′ adenylated adapter (5′-AppGATATCGTCAAGATCGGAAGAGCACACGTCTGAA-ddC-3′) was then ligated to the RNA fragments using T4 RNA ligase (M0373L, NEB) for 4 h at 22 °C followed by ethanol precipitation. The reverse transcription was performed with AMV RT (M5108, Promega) and RT primer: 5′-pRNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG-iSp18-GTGACTGGAGTTCAGACGTGTGCTC-3′. Truncated cDNAs (110-180 nt) were size selected using Urea-PAGE. Gel purified cDNA was circularized using CircLigase ssDNA ligase II (CL9025K, Epicentre) and PCR amplified with forward primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCT*C-3′) and barcode reverse primer (NEBNext® Multiplex Oligos for Illumina®, Index Primers Set 1-4, NEB E7335S, E7500S, E7710S, E7730S). PCR products were PAGE purified and sequenced on an Illumina NovaSeq 6000 using an SP or S2 flow cell in SR75 mode to yield a total of 130 million reads per library.

treatment_protocol: no treatment

value: mock

value: HEK293TRex FlpIn

value: Human embryonic kidney

value: total RNA extraction with TRIzol, polyA enrichment, mock labelling of pseudouridines during library preparation


title: P1024.FF


title: P1209.FF


title: P658.FF


title: PUS1-/- mock treated biol rep 4


title: PUS1-/- mock treated biol rep 3


title: P1055.FF


title: PUS1-/- mock treated biol rep 2


title: PUS1-/- mock treated biol rep 1


title: PUS1-/- CMC treated biol rep 6

source_name: CMC

value: CMC

value: total RNA extraction with TRIzol, polyA enrichment, CMC labelling of pseudouridines during library preparation


title: PUS1-/- CMC treated biol rep 5


title: P1231.FF


title: P844.FF


title: P1186.FF


title: PUS1-/- CMC treated biol rep 3


title: Ribo_Sc_ribopools_2

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools
Ribo_Sc.csv

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms
Library strategy: Ribo-seq

organism: Saccharomyces cerevisiae

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer. Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer. The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice. S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer. E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker. For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.  0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)


title: PUS1-/- CMC treated biol rep 1


title: P949.FF


title: P919.FF


title: PUS1-/- CMC treated biol rep 2


title: PUS1-/- mock treated biol rep 5


title: PUS3-/- mock treated biol rep 6

description:
Flp-In™ T-REx™ 293
processed data file contains information from all treated and untreated replicates of PUS3-/-, columns contain headers
PUS3plusandminus.txt.gz


title: PUS3-/- mock treated biol rep 5


title: Ribo_Sc_ribopools_1


title: PUS3-/- mock treated biol rep 3


title: P712.FF


title: P720.FF


title: PUS3-/- mock treated biol rep 4


title: PUS3-/- mock treated biol rep 2


title: Ribo_Sc_CT_2

description:
Ribosome profiling_and_rRNA_depletion_with_None
Ribo_Sc.csv


title: P1051.FF


title: Ribo_Sc_CT_1


title: PUS3-/- mock treated biol rep 1


title: P651.FF


title: P641.FF


title: PUS3-/- CMC treated biol rep 6


title: P948.FF


title: PUS1-/- CMC treated biol rep 4


title: PUS3-/- CMC treated biol rep 5


title: Ribo_Sc_ribopools_Ribo-Filterout_2

description:
Ribosome profiling_and_rRNA_depletion_with_ribopools,Ribo-FilterOut
Ribo_Sc.csv


title: PUS3-/- CMC treated biol rep 3


title: PUS3-/- CMC treated biol rep 2


title: Ribo_Sc_ribopools_Ribo-Filterout_1


title: P848.FF


title: Ribo_Sc_Ribo-Filterout_2

description:
Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut
Ribo_Sc.csv


title: P633.FF


title: wild-type mock treated biol rep 5

description:
Flp-In™ T-REx™ 293
processed data file contains information from all treated and untreated replicates of WT, columns contain headers
WTplusandminus.txt.gz

value: WT


title: wild-type mock treated biol rep 6


title: Ribo_Sc_Ribo-Filterout_1


title: wild-type mock treated biol rep 4


title: P538.FF

value: FF


title: wild-type mock treated biol rep 3


title: wild-type mock treated biol rep 2


title: P463.FF

value: III


title: Plasmid-1

city: Seoul

first: Tackhoon

last: Kim

state: 서울

address: L3671, KIST, 5 Hwarangro-14-gil, SeongbukGu

country: South Korea

institute: Korea Institute of Science and Tech

data_processing: The sgRNA sequence was detected from the NGS reads using the custom code described in Github (https://github.com/tackhoonkim)

organism: synthetic construct

source_name: non-cell

extract_protocol:
Genomic DNA extracted with Accuprep genomic DNA extraction kit (Bioneer)
PCR amplicons were generated with primers F: 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNGGACTATCATATGCTTACCGTAACTTG-3′ R: 5′-AATGATACGGCGACCACCGAGATCTACAC AAGCAGCGTATCCACATAGC-3′
Amplicon sequencing

value: non-cell


title: wild-type mock treated biol rep 1


title: Plasmid-2


title: P646.FF

value: right


title: PUS3-/- CMC treated biol rep 4


title: SK-N-SH, DA+

city: Shanghai

first: Yang

last: Yaqi

address: No.1678 Dongfang Road, Pudong, Shanghai, China

institute: Shanghai Children Medical Centre

data_processing:
Upon removal of low-quality reads and adapters, quality control was executed using FastQ Screen (version 0.13.0) and FastQC (version 0.11.9)
The Burrows-Wheeler Aligner (version 0.7.17-r1188) was then employed to align the data to the human hg19 genome reference, with non-uniquely mapping reads being discarded.
Duplicate reads were marked with the MarkDuplicates feature in Picard (version 2.22.9, http://broadinstitute.github.io/picard).
BigWig files standardized by spike-in were generated using the bamCoverage tool of deepTools (version 3.4.3)
Assembly: hg19
Supplementary files format and content: BigWig

source_name: SK-N-SH

growth_protocol: EMEM/F12 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
1 x 107 SK-N-SH cells in culture dishes were fixed with 1% formaldehyde at room temperature for 10 min, and the fixation was stopped via addition of cool 0.125 M glycine solution at room temperature for 5 min. The cells were collected and washed with PBS and scraped into cold lysis buffer (10 mM tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.5% NP-40). Chromatin pellets obtained by centrifugation were resuspended with 0.8 ml of RIPA buffer (50 mM tris-HCl, pH 7.5, 300 mM NaCl, 1.0% Triton X-100, 0.5% sodium deoxycholate, and 0.1% SDS, and 1 × protease inhibitor cocktail) and sonicated at 25% amplitude for a total of 8 min (with intervals). Sonicated chromatin was then incubated with 2 mg of anti-histone H4Q27dop or control IgG precoated on protein A/G magnetic beads (Thermo fisher, no. 88803) at 4°C overnight. Immunoprecipitants were washed twice with RIPA buffer and additional three times with LiCl washing buffer (100 mM tris-HCl, pH 7.5, 500 mM LiCl, 1% NP-40, and 1% sodium deoxycholate). Chromatin precipitated was then eluted by protease K digestion, cross-link reversed at 65°C overnight, and purified using a QIAquick PCR purification kit (Qiagen). The immunoprecipitated DNA fragments were either sent for high-throughput sequencing (Novogene) or assessed by qPCR as described above. To normalize the sequencing data, samples were standardized by the inclusion of Drosophila DNA as a spike-in control
1.DNA fragment Adjust the volume of the combined gDNA sample to a total volume of 41 μL using 1×TE and fragment the DNA to 300 bp using the Biorupter.  2.End repair Blunt-ended fragments are created by filling in or chewing back 3’ and 5’ overhangs. Phosphorylation of the 5’ ends ensures the fragments are suitable for ligation. 3.dA-Tailing This step is dA-tailing of the 3’end of the end-repaired, phosphorylated fragments. This single A overhang enables ligation to adaptors with single T overhangs. 4.Adaptor ligation Adaptor containing sequences required downstream in the sequencing workflow are ligated to the dA-tailed fragment.  5.PCR amplification The KAPA HiFi DNA Polymerase has been inactivated, enabling amplification of DNA. 6.2 % agarose gel select the fragment 200~500bp.

treatment_protocol: SK-N-SH cells were cultured for 24 hours in standard medium, and then cells were treated with medium (control) or DA at 40 M for 6 h.

value: SK-N-SH

value: neuroblastoma cells

value: Wild Type

value: dopamine


title: wild-type CMC treated biol rep 6


title: SK-N-SH, DA+ input


title: PUS3-/- CMC treated biol rep 1


title: P598.FF

value: Female

value: left


title: wild-type CMC treated biol rep 5


title: DEL_3

city: Nashville

first: Eric

middle: P

last: Skaar

state: Tennessee

address: 1161 21st Avenue South, A5303B MCN

institute: Vanderbilt University Medical Center

data_processing:
*library strategy: Transpson sequencing
Sequencing data were analyzed using the TRANSIT software package for TnSeq analysis
Reads were processed and mapped to the S. aureus FPR3757 genome using the TnSeq Pre-Processor (TPP) tool.
Gene essentiality was determining using the Gumbel method in TRANSIT
Log2 fold changes between antibiotic exposed biofilms and the no antibiotic controls were calculated using the Resampling method in TRANSIT with beta-geometric normalization and correction for multiple comparisons using the Benjamini-Hochberg procedure
Assembly: Staphylococcus aureus subsp. aureus USA300_FPR3757 (CP000255.1)
Supplementary files format and content: File is in .xlsx format. Contains normalized read counts along with calculated log2FC, z-scores, and adjusted p-value for comparisons

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: S. aureus was inoculated on a polycarbonate filter disc on trypic soy agar and allowed to grow for 48 hours at 37 degrees Celsius  with change to a fresh plate every 24 hours. After 48 hours, 1 set of filters were removed for the "48hr_biofilm" sample while the other filters were transferred to TSA plates containing a vehicle control or antibiotics. Colonies were allowed to grow for another 48 hours in the presence of antibiotics before being harvested ("96hr_biofilm" is the vehicle control, while VAN, LZD, CPT, or DEL are the antibiotic treated biofilms.

extract_protocol:
The frozen bacteria pellets from the transposon library screen were thawed on ice and genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). Genomic DNA was sheared to 350 bp by sonication using a Covaris LE220 and prepared by sequencing using the homopolymer tail-mediated ligation PCR (HTML-PCR) as outlined in van Opijnen et. al. with the modification of the use of the KAPA HiFi HotStart DNA Polymerase (Roche) for the PCR cycles and the use of the transposon-specific primers olj510 and olj511 as previously outlined. Replicates were all individually barcoded and then multiplexed for sequencing.
A transposon library was constructed in the JE2 strain using the plasmids pBursa and pMG020 as described in Grosser et. al. The library construction process was repeated multiple times until enough transposon mutants could be pooled together to make a single library. This pooled library was grown for an additional 4 hours in TSB (without antibiotics) before being frozen in individual aliquots at a concentration of roughly 1x1011 CFUs/ml at -80°C. Spot plating of the inoculum on TSA plates containing antibiotics (either 10 µg/ml tetracycline or 10 µg/ml chloramphenicol 10 µg/ml) confirmed curing of plasmids pBursa and pMG020 in greater than 99.98% of bacterial cells. The library was confirmed to have roughly 150,000 independent transposon mutants as verified by Illumina sequencing analysis. Pooled aliquots of this high-density library were frozen at -80°C until used.

treatment_protocol: Biofilms were grown on TSA for 48 hours prior to being transferred to TSA plates either without antibiotics or with vancomycin, ceftaroline, delafloxacin, or linezolid added. The biofilms were grown for an additional 48 hours. After 48 hours of antibiotic exposure, the filters containing the biofilms were transferred to a microcentrifuge tube, washed with 1 mL PBS, and vortexing to separate the biofilm from the filters and resuspend the bacteria. The resulting suspension was then diluted 1:500 into fresh TSB without antibiotics and outgrown for 4 hours to enrich for viable bacteria.

value: Bacteria

value: Delafloxacin 9 mcg/ml


title: SK-N-SH, DA-


title: DEL_1


title: SK-N-SH, DA- input


title: P588.FF


title: P447.FF


title: P434.FF


title: wild-type CMC treated biol rep 3

value: HEK293TRex FlpIn

value: Human embryonic kidney


title: CPT_3

value: Ceftaroline 20 mcg/ml


title: P582.FF

value: Male


title: RNA-seq_ESRRAKO-rep3

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
FastQC (v0.11.3) was used to check the quality of raw sequencing reads.
Alignment to the mouse reference genome (MGSCv37/mm9) was performed using Kallisto (v2.1.0)
DESeq2 (v.2.2.1) was used to calculate the fragments per kilobase of transcript per million mapped reads (FPKM) and for differential expression analysis.
Assembly: mm9
Supplementary files format and content: tab delimited text file contains FPKM output from each replicate of WT and ESRRAKO
Supplementary files format and content: Differential enrichment analysis was generated as a csv file by DESeq2

organism: Mus musculus

source_name: duodenal epithelium

extract_protocol:
The initial third of the small intestine (duodenum) was dissected and opened longitudinally to wash the inter-lumen space and expose epithelial cells. Tissue was cut into 1-inch pieces and rinsed with ice-cold PBS. Tissue was treated with 3mM EDTA/PBS for 35 minutes, with changes in EDTA solution at the initial 5- and 10-minute time points. Mechanical force was applied to release the epithelial cell layer from the underlying mesenchyme. The epithelial cells were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.RNA extraction was performed using the RNeasy Micro Kit (Qiagen, 74004).
Illumina TruSeq RNA Library Prep kit v2

value: duodenal epithelium

value: ESRRAKO


title: CPT_2


title: P568.FF

value: FF

value: III


title: wild-type CMC treated biol rep 2

value: CMC

value: WT

value: total RNA extraction with TRIzol, polyA enrichment, CMC labelling of pseudouridines during library preparation


title: P492.FF

value: right


title: RNA-seq_ESRRAKO-rep2


title: wild-type CMC treated biol rep 1


title: CPT_1


title: RNA-seq_ESRRAKO-rep1


title: P415.FF


title: LZD_3

value: Linezolid 20 mcg/ml


title: Q19B052024AB6

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Illumina DRAGEN BCL, then fastq files were analysed with salmon to get counts data. The counts were imported to DESeq2.
Assembly: GRCh38
Supplementary files format and content: DESeq2 normalised counts

source_name: bone

growth_protocol: These are FFPE samples of the osteosarcoma.

extract_protocol:
The formalin-fixed paraffin-embedded tissue (FFPE) samples (n=90: 50 OS + 40 normal) were obtained through PathWest Nedlands (QEII Medical Centre, Australia) and total RNA was extracted using the Norgen FFPE RNA purification kit (#25300) using manufacturer’s standard protocol. The purified RNA samples were sent to the Australian Genome Research Facility (AGRF) in Melbourne for sequencing.
whole transcriptome library preparartion with ribominus depletion for rRNA

value: bone

tag: disease state

value: NORMAL

tag: Sex

value: M

value: no

tag: status

value: alive

tag: ageatdiagnosis


title: Q19B052024AB2

value: TUMOUR


title: RNA-seq_WT-rep2


title: LZD_2

value: Bacteria


title: RNA-seq_WT-rep3


title: P408.FF

value: Male

value: left


title: wild-type CMC treated biol rep 4

value: HEK293TRex FlpIn

value: Human embryonic kidney


title: P449.FF

value: FF

value: III


title: Q19B051495PB19

value: F

value: chemo


title: RNA-seq_WT-rep1

value: duodenal epithelium

value: WT


title: P452.FF

value: right


title: Q19B051495PA2

value: bone

value: NORMAL


title: LZD_1

value: Linezolid 20 mcg/ml


title: VAN_3

value: Vancomycin 400 mcg/ml


title: VAN_2


title: Q19B035672TA12

value: TUMOUR

value: M

value: alive


title: wound _cornea

city: Qingdao,Shandong

first: Di

last: Sun

address: No.5 Yanerdao Road, Shinan District, Qingdao City, Shandong Province

institute: Eye Institute of Shandong First Medical University

description: corneal epithelial wounded

library_source: transcriptomic single cell

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (3.1.0) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
Cells with gene counts falling below 500 or exceeding 8000, or exhibiting a mitochondrial gene ratio surpassing 10%, were excluded. Genes expressed in fewer than 5 cells were eliminated.
After filtering, this matrix was used for UMAP projection and graph based clustering. Following cell-embeddings and clustering, the original non-downsampled UMI data was used for all analysis and is provided as the Corneal_count_matrix.txt.gz.
Assembly: mm9
Supplementary files format and content: Corneal_count_matrix.txt.gz with UMI counts per gene per cell. Corneal_metadata.txt.gz contains information about each cell in the count matrix.

source_name: Cornea

extract_protocol:
The eyes from 4 normal unwound (UW) mice and 4 mice 24 hours post-wound (W) were collected to extract corneas. The corneas of mice underwent an 18-hour digestion using dispase II (Roche) at 4°C to facilitate the separation of the epithelial layer from other components. Subsequently, the epithelial layer underwent trypsin digestion (Sigma-Aldrich), while the residual tissue was subjected to collagenase A digestion (Roche) at 37°C for a duration of 1 hour (Kawakita et al., 2004). Following this, the dissociated corneal cells from UW and W groups were severally combined and suspended anew, in preparation for 10x Genomic sequencing.
Library generation was performed following the Chromium Single Cell 3' Reagents Kits v3 where we target 10,000 cellls per sample for capture.

value: Cornea

value: corneal epithelial wounded


title: P374.FF

value: Female


title: Q19B035672TA1


title: VAN_1

value: Bacteria


title: P369.FF

value: FF

value: III


title: P304.FF

value: left


title: 96hr_biofilm_3

value: Vehicle


title: Q19B021879LA21

value: chemo


title: P373.FF

value: Male


title: miRNA_Prostatic urethral trauma tissue 4

city: GuiYang

first: XiaoHu

last: Tang

address: No. 83 Zhongshan East Road

institute: Guizhou Provincial People's Hospital

description: Biological replicate 4 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat miRNA Microarray Kit,Release 21.0,8x15K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Rattus norvegicus

source_name: Prostatic urethral trauma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: SD rats were reared under standard laboratory conditions (12/12 hour light/dark cycle, 22±2°C with a relative humidity of 55±5%) and allowed to consume standard laboratory food pellets and water ad libitum.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: SD rats underwent simulating transurethral laser prostatectomy

value: male

tag: strain

value: SD rat

value: Urethral tissue

value: Prostatic urethral trauma


title: Q19B021879LA19

value: bone

value: TUMOUR


title: 96hr_biofilm_2


title: P316.FF


title: Q19B013567KA1

value: M

value: deceased


title: miRNA_Prostatic urethral trauma tissue 3

description: Biological replicate 3 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.


title: 96hr_biofilm_1


title: miRNA_Prostatic urethral trauma tissue 1

description: Biological replicate 1 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.


title: miRNA_Prostatic urethral trauma tissue 2

description: Biological replicate 2 of 4.Prostatic urethral trauma tissue, treated, harvested after 5 days after sham surgery.


title: 48hr_biofilm_3

value: 48hr control


title: Q19B007088FB22

value: NORMAL

value: F

value: alive


title: P244.FF

value: FF

value: III

value: Female

value: right


title: P210.FF

value: Male

value: left


title: unwound_cornea

description: normal

value: Cornea

value: normal


title: Q19B007088FB10

value: chemo


title: Q19B005830YA2

value: bone


title: P251.FF


title: 48hr_biofilm_1

value: Bacteria


title: 48hr_biofilm_2


title: miRNA_Control Prostate urethral tissue 4

description: Biological replicate 4 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.

source_name: Prostatic urethral tissue

value: male

value: SD rat

value: Urethral tissue

value: control


title: P183.FF


title: P184.FF


title: miRNA_Control Prostate urethral tissue 3

description: Biological replicate 3 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.


title: Q19B001229RA22

value: NORMAL

value: F


title: Q19B001229RA30

value: TUMOUR

value: alive


title: osteoblast, ad-Hif2a 3, Day6

city: Gwangju

first: Su-Jin

address: 77, Yongbong-ro, Buk-gu, Gwangju, Republic of Korea

institute: Chonnam National University

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: osteoblast

growth_protocol: Primary culture of calvarial pre-osteoblasts were maintained in DMEM containing 10% fetal bovine serum and 1% penicillin/streptomycin, in incubators with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: Primary calvarial pre-osteoblasts from WT mice were cultured in the medium containing 50 μg/ml L-AA and 5 mM β-Gp for up to 6 days for osteogenic differentiation.

tag: cell line

value: osteoblast

value: primary cultured calvarial pre-osteoblasts

value: Hif2a overexpression

value: osteoblast differentiation


title: P241.FF

source_name: tumor

value: FF

value: III

value: Male

value: left


title: Input_2

tag: cell type

value: Bacteria

value: Input


title: Q18B051017FA16

value: bone

value: M

value: chemo

value: deceased


title: Input_1


title: P178.FF


title: Q18B051017FA1


title: LB2 pA-DamID,HCT116, replicate 3, dam-only

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

description: pADamID-HCT116_TOP2AAID_WT_r3_Lmnb2-20kb.bw

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 20 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig files of log2-normalized LaminB2  pA-DamID scores for 20 kb genomic bins.
Library strategy: pA-DamID

growth_protocol: HCT116 (Top2A-AID, from Vassilis Roukos, Goethe Mol cell 2019) cell line were grown in McCoy's Modified Medium (Gibco, 16600082) FBS0 10%, 1% penicillin-streptomycin (Gibco, 15070063). HeLa cell line were grown in DMEM (Gibco, 16600082) FBS0 10%, 1% penicillin-streptomycin (Gibco, 11965092)  Cells were passaged every 2 days. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
LMNB2 pA-DamID maps were generated as previously described (van Shaik, 2022, 36050765). Briefly, one million of HAP1 were collected by centrifugation (500 g, 3 min) and washed sequentially in ice-cold PBS and digitonin wash buffer (D-Wash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 hours at 4 °C in 200 μL D-Wash with 1:200 LMNB2 (Abcam, ab8983) followed by a wash step with D-Wash. Following this step, cells were incubated with a solution of D-Wash buffer and Rabbit-anti-mouse IgG (1:200, Abcam, ab6709), followed by a wash step. This incubation was repeated with a 1:200 pA-Dam solution (equivalent to nearly 60 Dam units from NEB), followed by two wash steps. Dam activity was induced by incubation for 30 min at 37 °C in 100 μL D-Wash supplemented with the methyl donor SAM (30 µM) while gently shaking (500 rpm). Genomic DNA was isolated and processed similarly to DamID, except that the DpnII digestion was omitted, and 65-bp reads were sequenced. For every condition, another 1 million cells were processed in only D-Wash and, during Dam activation, incubated with 4 units of Dam enzyme (NEB, M0222L). We use Dam control samples to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C). Libraries were sequenced on Illumina platform Hiseq2500 with single end 65 bp reads.

treatment_protocol: No treatment

tag: genotype

value: control

tag: antibody


title: P224.FF

data_processing: Raw count data from nCounter was normalized

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

tag: tissue


title: Q18B034715YA6

value: TUMOUR

value: F

tag: treatment


title: LB2 pA-DamID,HCT116, replicate 3, dam-LB2


title: osteoblast, ad-Hif1a 3, Day6

value: osteoblast

value: Hif1a overexpression


title: Input_3


title: LB2 pA-DamID,HCT116, replicate 2, dam-only

description: pADamID-HCT116_TOP2AAID_WT_r2_Lmnb2-20kb.bw


title: osteoblast, ad-Hif1a 2, Day6

value: primary cultured calvarial pre-osteoblasts


title: Q18B034715YA11

value: NORMAL

value: alive


title: miRNA_Control Prostate urethral tissue 2

description: Biological replicate 2 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.

value: male

value: SD rat

tag: age

value: Urethral tissue


title: Q18B028621HA4


title: P187.FF

value: FF

tag: Stage

value: III

tag: gender

value: Male

value: left


title: LB2 pA-DamID,HCT116, replicate 1, dam-only

description: pADamID-HCT116_TOP2AAID_WT_r1_Lmnb2-20kb.bw


title: LB2 pA-DamID,HCT116, replicate 2, dam-LB2


title: osteoblast, ad-Hif1a 1, Day6

value: osteoblast differentiation


title: osteoblast, ad-Hif2a 1, Day6

value: Hif2a overexpression


title: Q18B018266YE1

value: bone

value: M

value: chemo

value: deceased


title: miRNA_Control Prostate urethral tissue 1

description: Biological replicate 1 of 4.Control prostatic urethral tissue, untreated, harvested after 5 days after sham surgery.

value: control


title: P11.FF

tag: ptstage

tag: pnstage


title: P193.FF

value: right

tag: death

tag: recurrence


title: LB2 pA-DamID,HCT116, replicate 1, dam-LB2


title: osteoblast, ad-Hif2a 2, Day6

value: osteoblast

value: primary cultured calvarial pre-osteoblasts


title: P18.FF


title: Q18B018266YA1

tag: disease state

value: TUMOUR

tag: Sex


title: P77.FF


title: P1237.FF


title: osteoblast, ad-Control 2, Day6

value: WT


title: Q18B015603EA52

tag: status

value: alive

tag: ageatdiagnosis


title: osteoblast, ad-Control 1, Day6

tag: cell line


title: P812.FF

value: FF


title: Q18B028621HA1

value: NORMAL


title: P186.FF

value: III

value: Female


title: Q18B014955AA23

value: F


title: J1 with OP9 coculture

city: Atlanta

first: Kyuwon

last: Cho

state: GA

address: 201 Dowman Dr

institute: Emory University

description: all.cloupe

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger 7.1.0 at 10X Genomics Cloud Analysis.
Assembly: mm10
Supplementary files format and content: cloupe file which contains the expression data for all cells,  a tSNE projection split into groups by two methods and some initial differential expression analysis.

source_name: Embryonic stem cells with bone marrow stromal cells

extract_protocol:
Cultured cells were washed with PBS three times and treated with  accutase for 10 minutes at 37 C degree. PBS containing 10% fetal bovine serum (FBS) were used to collect cells. Cells were pelleted and resuspended with PBS.
Library was constructed using NextGEM Single Cell 3' Kit via Dual Index Protocol

tag: cell type


title: ChIP-seq_Input

data_processing:
FastQC (v0.11.3) was used to check the quality of raw sequencing reads.
Alignment to the mouse reference genome (MGSCv37/mm9) was done using bowtie2 (v2.2.6) (30) and alignments were sorted using Samtools (v0.1.19).
Replicates were merged, sorted and indexed using Samtools (v0.1.19) [6].
deepTools2 (31) bamCoverage (v2.4.2) was used to generate RPKM-normalized bigwig files from individual and merged bam files.
Assembly: mm9
Supplementary files format and content: Merged bigwig files from ESRRA replicate ChIP samples
Supplementary files format and content: bigwig files for merged ESRRA ChIP replicates
Supplementary files format and content: bed file with ESRRA binding sites from merged ESRRA ChIP replicate samples

extract_protocol:
The initial third of the small intestine (duodenum) was dissected and opened longitudinally to wash the inter-lumen space and expose epithelial cells. Tissue was cut into 1-inch pieces and rinsed with ice-cold PBS. Tissue was treated with 3mM EDTA/PBS for 25 minutes for mutant mice and 35 minutes for wild-type, with changes in EDTA solution at the initial 5- and 10-minute time points. Mechanical force was applied to release the epithelial cell layer from the underlying mesenchyme. Crypts and villi were separated with a 70uM filter. The smaller crypts pass through the pores of the filter while the larger villi stay on top. Villus cells were collected and washed twice with ice-cold PBS and pelleted by centrifugation at 300 rcf at 4°C. Cell pellets were cross-linked in 2 mM DSG (Thermo Scientific, 20593) for 45 min, and then further cross-linked in 1% formaldehyde (Sigma, F8775) for 20 min at room temperature, pelleted and washed with ice-cold PBS. Fixed cells were lysed in 3X volume of lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, 1X protease inhibitor cocktail (G-Biosciences, 786-433) and sonicated for 8 minutes (30sec on-off, 20% amplitude) using a QSonica Q800R3 sonicator to shear chromatin to 300-600bp. Protein A/G beads (Invitrogen, 10001D and 10004D) were washed with 1% BSA in PBS and pre-loaded with 5μg of anti-Esrra antibody (Santa Cruz sc-65718). Antibody-conjugated beads were incubated with sheared chromatin in dilution buffer with SDS at a final concentration of 0.24% on a rotator at 4°C overnight. Antibody-conjugated beads were collected by magnetic separation and washed five times with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Sodium deoxycholate, 1% NP-40, 0.5M LiCl), and once with TE buffer (10mM Tris, 0.1mM EDTA). Cross-links were reversed in 0.1M NaHCO3 and 1% SDS overnight at 65°C. DNA was column purified using the MinElute PCR purification kit (Qiagen, 28004) and quantified using Picogreen (Invitrogen, P7581).
ThruPLEX DNA-Seq kit (Takara, R400675)

value: duodenal epithelium

value: adult villus cells

tag: genotype


title: RNASEQ, clone SC9, NELFE, replicate 2

data_processing:
RNA-seq reads were subjected to quality control using FastQC v0.11.6. Reads were aligned to the human reference genome (GRCh38, GRCh38_no_alt_analysis_set_GCA_000001405.15;https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/) using STAR 2.5.4a (Dobin et al. 2013) with parameters --clip5pNbases 0 --outWigStrand Unstranded. Gene-level count tables were generated while mapping using Gencode v24 primary assembly annotations.
Genome_build: GRCh38
Assembly: hg38
Supplementary files format and content: BigWig files  and Rawcounts

source_name: HAP1 dCAS9-KRAB cSC9

growth_protocol: HAP1 cell line were grown in IMDM (Gibco, 15070063) FBS0 10%, 1% penicillin-streptomycin (Gibco, 15070063) . Cells were passaged every 2 days. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
One million cells were harvested, washed once in cold PBS, resuspended in 600 µL of RTL buffer (RNeasy Mini kit, 74104, Qiagen) and stored at -80°C until subsequent RNA isolation. RNA was isolated using the RNeasy Mini kit (74104, Qiagen).
Libraries were prepared using the TruSeq® RNA LT kit and TruSeq RNA Single Indexes (Illumina). Libraries were sequenced with single-end 65-bp reads on a HiSeq 2500 platform

treatment_protocol: The cell line was infected with lentiviral vectors (Lentiguide Puro: Addgene #52963) containing guide RNA for: ADAM22 (negative control), NELFE or NELFB. We produced lentiviral particles by transfecting HEK293T with Calcium Phosphate transfection and using pREV, pMDL, and pVSV as packaging vec-tors. Supernatants from a 10 cm dish were collected 48 hours after transfection, filtered, and concentrated to 250 µl using Amicon filters, aliquoted, and stored at -80°C. HAP1 cells were infected with 30 µl of concentrated virus and then selected for puromycin resistance 48 hours after transduction. We performed mRNA extraction 144 hours following lentiguide transduction for RNAseq

value: HAP1 dCAS9-KRAB cSC9

value: NELFE Knockdown

tag: antibody


title: RNASEQ, clone SC9, NELFB, replicate 1

value: NELFB Knockdown


title: Q18B014955AA15

tag: tissue

value: bone

value: chemo

value: deceased


title: Q18B015603EA5

value: M

tag: treatment


title: RNASEQ, clone SC9, NELFE, replicate 1


title: ChIP-seq_EsrraChIP_rep2

value: Esrra


title: P794.FF

city: Amsterdam

first: Arezo

address: Meibergdreef 9

institute: Amsterdam UMC

tag: age

value: left


title: Q18B009680HA12

value: TUMOUR


title: Undifferentiated J1

description: all.cloupe

source_name: Embryonic stem cells

value: Embryonic stem cells


title: P824.FF

value: FF

tag: Stage

value: Male


title: ChIP-seq_EsrraChIP_rep1

value: WT


title: RNASEQ, clone SC9, NELFB, replicate 2


title: Q18B009680HA1


title: P119.FF

value: III

tag: gender

value: right


title: HF, Hippocampus, ATAC, rep2

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

description:
HF_rep2_snATAC
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)

library_source: genomic single cell

data_processing:
cellranger-arc-2.0.1 count function to quantify reads into single set barcodes.tsv.gz, feature.tsv.gz and matrix.mtx.gz
Using R Seurat::Read10X() and split the result into two set of files for GEX and Peak, respectively
Assembly: mm10
Supplementary files format and content: CellRanger output files: Gene Expression barcodes.tsv.gz, Gene Expression features.tsv.gz,Gene Expression matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Peak barcodes.tsv.gz, Peak features.tsv.gz, Peak matrix.mtx.gz

source_name: Hippocampus

growth_protocol: Adult female C57BL/6J mice (8 weeks) were purchased from Jaxson laboratory and maintained in a 12-hour light/dark cycle under standard pathogen-free conditions.

extract_protocol:
Pups were harvested on postnatal day 21 (P21) and fresh hippocampus tissues were dissected and used to prepare debris-free single nuclei suspension.
Single nuclei RNA-seq (snRNA-seq) and single nuclei ATAC-seq (snATAC-seq) libraries were simultaneously constructed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, cat# 1000285) according to the manufacturer’s User Guide (CG000338).
single nuclei multiome (snRNA-seq and snATAC-seq)

treatment_protocol: Adult female mice (8 weeks old) were randomly assigned to either a control folic acid (FA) diet (2mg/kg) or an excessive FA diet (20mg/kg) for two weeks before mating with males. These diets were maintained throughout pregnancy and lactation.

value: Hippocampus

value: HF

value: wild-type


title: Q18B006524DA8

value: NORMAL

value: F

value: no


title: P782.FF

last: Torang

tag: ptstage


title: P602.FF

value: Female

tag: pnstage


title: HF, Hippocampus, ATAC, rep1

description:
HF_rep1_snATAC
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)


title: RNASEQ, clone SC9, pLB187, replicate 1

value: HAP1 dCAS9-KRAB cSC9

value: control


title: P102.FF

tag: death


title: LB2 pA-DamID, clone SC9, parental, replicate 2, dam-LB2

treatment_protocol: The cell line was infected with lentiviral vectors (Lentiguide Puro: Addgene #52963) containing guide RNA for, CCSER1 (negative control). We produced lentiviral particles by transfecting HEK293T with Calcium Phosphate transfection and using pREV, pMDL, and pVSV as packaging vec-tors. Supernatants from a 10 cm dish were collected 48 hours after transfection, filtered, and concentrated to 250 µl using Amicon filters, aliquoted, and stored at -80°C. HAP1 cells were infected with 30 µl of concentrated virus and then selected for puromycin resistance 48 hours after transduction. We performed mRNA extraction 144 hours following lentiguide transduction for RNAseq


title: Q18B006524DA28

value: bone

value: deceased


title: MF, Hippocampus, ATAC, rep2

description:
MF_rep2_snATAC
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)

value: MF


title: Q17B045995JA5

value: TUMOUR


title: LB2 pA-DamID, clone SC9, parental, replicate 2, dam only


title: MF, Hippocampus, ATAC, rep1

description:
MF_rep1_snATAC
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)


title: Q17B045995JA29


title: P64.FF

value: FF

tag: recurrence


title: RNASEQ, clone SC9, pLB187, replicate 2


title: LB2 pA-DamID, clone SC9, parental, replicate 1, dam-LB2


title: DEL_2

value: Bacteria

value: Delafloxacin 9 mcg/ml


title: LB2 pA-DamID, clone SC9, parental, replicate 1, dam only


title: Q17B045840YA23

tag: disease state

value: alive


title: P88.FF

value: III

value: right


title: HF, Hippocampus, GEX, rep1

description:
HF_rep1_snRNA
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)

molecule: nuclear RNA

value: Hippocampus

value: HF

value: wild-type


title: HF, Hippocampus, GEX, rep2

description:
HF_rep2_snRNA
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)


title: P345.FF


title: Q17B045840YA17

value: NORMAL

tag: Sex

value: F

value: no


title: RNASEQ, clone SC9, pLB187, replicate 3

value: HAP1 dCAS9-KRAB cSC9

value: control


title: MF, Hippocampus, GEX, rep2

description:
MF_rep2_snRNA
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)


title: A375VR-2

value: melanoma


title: A375VR-1


title: P79.FF

value: Female


title: Q17B034037YB20

value: bone

value: TUMOUR

value: M

value: chemo

tag: status

value: deceased


title: MF, Hippocampus, GEX, rep1

description:
MF_rep1_snRNA
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)

value: MF


title: P34.FF

value: FF

value: III

value: Male

value: left


title: Q17B034037YB2

value: NORMAL

tag: ageatdiagnosis


title: P74.FF


title: Q17B029593MA7

value: F


title: A375-1

tag: cell line


title: HF, coronal, rep2

description: FFPE spatial transcriptome sequencing

data_processing:
*library strategy: Spatial transcriptomics
Fastq files were mapped to mm10 genome to quantify gene expression using Space ranger default setting
The data were further analyze using R package Seurat
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.ipg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors ison.ison.gz:scalefactors in ison format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots

source_name: brain

extract_protocol:
Pups were harvested on postnatal day 21 (P21) and fresh mouse brain tissues were fixed in 10% neutral buffered formalin (NBF) at room temperature (RT) overnight for preparing formalin-fixed paraffin-embedded (FFPE) tissue blocks.
Visium Spatial Gene Expression (VGSE) libraries were prepared using the Visium Spatial Gene Expression Slide Kit (10x genomics, cat# PN-1000185) following the manufacturer’s User Guide (CG000407).

value: brain

value: wild-type

value: high folate


title: P68.FF


title: HF, coronal, rep1

description: FFPE spatial transcriptome sequencing


title: shVDR, 48h, rep3

city: Jinan City

first: Yan

last: Xu

address: No. 44 Wenhua West Road

institute: Shandong University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)   was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Text Document  include Raw read counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ  platform.

value: VDR knockdown


title: shVDR, 48h, rep2


title: MF, coronal, rep2

description: FFPE spatial transcriptome sequencing

value: median folate


title: Q17B018941HA12

value: bone


title: MF, coronal, rep1

description: FFPE spatial transcriptome sequencing


title: shVDR, 48h, rep1


title: P1015.FF

value: Female


title: iRGCs, Shtn1-KD_c

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: read counts for each genes were given in the Excel file

source_name: RGC-like neurons (iRGCs)

growth_protocol: MEFs were cultured in DMEM+10% FBS, at 37℃ in incubator.

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

treatment_protocol: MEFs were infected with Ascl1+Brn3b+Islet1 overexpressing lentiviruses, doxycycline was added on day 0 to induce exogenous gene expression, cells were switched to neuronal medium (DMEM/F12+GlutaMAX+N2+B27) on day 2 of reprogramming; medium was half-changed every other day.

tag: cell type

value: RGC-like neurons (iRGCs)

value: Shtn1 knockdown


title: P521.FF


title: Q17B009637RB1

value: M

value: chemosurg

value: alive


title: shNC, 48h, rep3

value: shNC


title: iRGCs, Shtn1-KD_b

tag: genotype


title: P1173.FF

value: FF

value: III

value: Male

value: right


title: A375-2

data_processing: The sgRNA sequence was detected from the NGS reads using the custom code described in Github (https://github.com/tackhoonkim)

extract_protocol:
Genomic DNA extracted with Accuprep genomic DNA extraction kit (Bioneer)
PCR amplicons were generated with primers F: 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNGGACTATCATATGCTTACCGTAACTTG-3′ R: 5′-AATGATACGGCGACCACCGAGATCTACAC AAGCAGCGTATCCACATAGC-3′
Amplicon sequencing

value: melanoma


title: Q17B009637RA2

value: TUMOUR


title: shNC, 48h, rep2


title: Ribo_Harringtonin_180s_2

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero, Ribo-FilterOut

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms
Library strategy: Ribo-seq

source_name: cultures

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer.
Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer.
The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice.
S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer.
E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker.
For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.
0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

value: cultures

value: Human Embryonic Kidney cells293

tag: rrna depletion

value: Ribo zero and Ribo-Filterout

value: 2 ug/ml harringtonine,180s

value: 2 ug/ml harringtonine


title: iRGCs, Shtn1-KD_a

value: RGC-like neurons (iRGCs)


title: Ribo_Harringtonin_180s_1

tag: tissue


title: Q17B029593MA23

value: bone

value: NORMAL

value: F

tag: treatment

value: chemo

value: deceased


title: shNC, 48h, rep1

value: shNC


title: Q17B018941HB1

value: M


title: iRGCs, Ctrl_c

value: control


title: Ribo_Harringtonin_120s_2

value: 2 ug/ml harringtonine,120s


title: P45.FF

value: FF

value: III

tag: age

value: Female

value: right


title: Q17B001640BB1

value: chemosurg

value: alive


title: iRGCs, Ctrl_b


title: Ribo_Harringtonin_120s_1

value: cultures

value: Human Embryonic Kidney cells293

value: Ribo zero and Ribo-Filterout

value: 2 ug/ml harringtonine


title: RNASEQ, clone SC9, NELFE, replicate 3

value: HAP1 dCAS9-KRAB cSC9

value: NELFE Knockdown

tag: antibody


title: E2A-PBX1-KM-1

first: Wei

last: Liu

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

description:
E2A-PBX1-KM-1_fpkm
E2A-PBX1-KM-1_count

data_processing:
To get high-quality clean reads, reads were further filtered by fastp (version 0.18.0). Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNA differential expression analysis was performed by DESeq2  software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\KEGG pathways\Reactome pathways\DO terms shows significant differences in the two groups. Briefly, we input the gene expression matrix and rank genes by the SignaltoNoise normalization method. Enrichment scores and p-value were calculated in default parameters.
Assembly: GRCz11 Ensembl release 108
Supplementary files format and content: gene exppression.txt

organism: Danio rerio

source_name: kidney marrow

extract_protocol:
Kidney marrows were isolated from 6-month-old fish, placed in PBS with 5% fetal bovine serum, triturated by pipet, and filtered through a 40-μm cell strainer. Total RNA was extracted using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase-free agarose gel electrophoresis
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads(1.0X). And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

tag: development stage

value: kidney marrow

value: blood cells


title: Q16B040208XA33

value: bone

value: TUMOUR

value: M

value: deceased


title: E2A-PBX1-KM-2

description:
E2A-PBX1-KM-2_fpkm
E2A-PBX1-KM-2_count


title: iRGCs, Ctrl_a

value: RGC-like neurons (iRGCs)

value: control


title: WT-KM-2

description:
WT-KM-2_fpkm
WT-KM-2_count

value: wt


title: Q16B040208XA25

value: NORMAL

value: chemosurg


title: Ribo_Harringtonin_60s_1

value: cultures

value: 2 ug/ml harringtonine,60s


title: WT-KM-1

description:
WT-KM-1_fpkm
WT-KM-1_count


title: Q16B037369BA8

value: alive


title: Ribo_Harringtonin_0s_2

value: Human Embryonic Kidney cells293

value: Ribo zero and Ribo-Filterout

value: control condtion

value: 2 ug/ml harringtonine


title: WT, mammary tissue, scRNA seq, rep1

city: Beijing

first: Qianchen

last: Li

address: Beijing

institute: PKU

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines /latest/what-is-cell-ranger) using default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mammary gland

extract_protocol:
Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification.
Amplified cDNA was then used for 3’gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads, and sequenced on an NovaSeq platform (Illumia) to generate 150 bp paired-end Reads

value: mammary gland

value: WT


title: WT, mammary tissue, scRNA seq, rep2


title: Frmd3 KO, mammary tissue, scRNA seq, rep3

value: KO


title: Ribo_Harringtonin_60s_2

first: Shintaro

address: 2-1, Hirosawa

institute: RIKEN


title: Q16B027819YA23

data_processing:
Illumina DRAGEN BCL, then fastq files were analysed with salmon to get counts data. The counts were imported to DESeq2.
Assembly: GRCh38
Supplementary files format and content: DESeq2 normalised counts

extract_protocol:
The formalin-fixed paraffin-embedded tissue (FFPE) samples (n=90: 50 OS + 40 normal) were obtained through PathWest Nedlands (QEII Medical Centre, Australia) and total RNA was extracted using the Norgen FFPE RNA purification kit (#25300) using manufacturer’s standard protocol. The purified RNA samples were sent to the Australian Genome Research Facility (AGRF) in Melbourne for sequencing.
whole transcriptome library preparartion with ribominus depletion for rRNA

value: bone

value: TUMOUR

value: M


title: Ribo_Harringtonin_0s_1


title: REC_GVC1(LP) [LP_3499]

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCh38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: hg38
Supplementary files format and content: Counts

source_name: Brain

growth_protocol: GVC were maintained in Endothelial Growth media supplemented with 2% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37*C. GBM cells were maintained in DMEM:F12 with B27 minus vitamin A, and supplemented with FGF, EGF and heparin plus antibiotics

extract_protocol:
Total RNA was extracted using Qiagen RNEasy microkit.
Library was prepared using TruSeq Stranded RNA (100ng) +Ribozero Gold.
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end, 2X75bp with Illumina Hiseq 4000

treatment_protocol: No treatment was performed on these cultures

value: Brain

value: TEC

value: endothelial


title: Q17B001640BB5

value: F

value: chemosurg


title: RNA_Fibro2

city: Wako city

last: Iwasaki

description: RNAseq_and_rRNA_depletion_with_Ribo-Zero

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms

value: HDFn

value: cultures

value: human fibrobrast cells


title: Frmd3 KO, mammary tissue, scRNA seq, rep2


title: Q16B027819YA16

value: NORMAL

value: alive


title: REC_GVC1(EP) [EP_3499]


title: Frmd3 KO, mammary tissue, scRNA seq, rep1


title: PRI_GVC1 (LP) [LP_3367]


title: Q15B001034YA15

value: chemo

value: deceased


title: RNA_Fibro1

description: RNAseq_and_rRNA_depletion_with_Ribo-Zero_Ribo-Calibration

value: Ribo zero and Ribo-Filterout


title: RNA_Kera2

value: HEKn

value: human keratynocyte cells


title: Q15B001034YB1

value: bone


title: PPGS_2_H3K27me3

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
CL Convert Conversion Software v4.0 was used to generate de-multiplexed Fastq files
TrimGalore(TrimGalore)(v0.4.5) and cutadapt(Martin)(v1.15) were used with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20
trimmed reads were aligned to mm10 with Bowtie2(v2.3.4.1) using default parameters with the exception of the following flags: -X 2000
Duplicate reads are marked with Picard(v2.20.2)
Alignments are filtered with samtools(v1.2) using the flags: -F4 -F8 -f3 -q10 -F1024
Alignments completely overlapping blacklisted regions(ENCODE Blacklist Regions)are removed with bedtools(v2.28.0)
Sample-wise peaks are called with macs2 (v2.1.2) with flags: –format BAMPE –gsize mm
Assembly: mm10
Supplementary files format and content: .bed peak files

source_name: breast tumor

growth_protocol: CCN6KOT primary Cells were growth in DMEM/F12  10%FBS and trasnduced with lentivirus  of DNTCF4 construct and control followed by  puromycin selection

extract_protocol:
samples were fixed with 1% formaldehyde, quenched with glycine, and frozen as a pellet.
The Diagenode ChIPmentation kit with dual indices was used, following the manufacturer’s protocol. Briefly, the cells were lysed and resuspended in 130ul of chromatin shearing solution. Shearing was done in a Covaris S2 instrument. A 15ul aliquot of the sheared chromatin was taken for assessment of the shearing size. The remaining sheared chromatin split for immunoprecipitation in the presence of H3K27me3 antibody (purchased Cell Signaling, provided by the investigator) and IgG as input. Four ug of each antibody was used per immunoprecipitation. Immunoprecipitation was done overnight at 4C with rotation. The immunoprecipitates were next washed before on-bead tagmentation at 37C for 10 minutes with agitation. The reaction was stopped by putting the samples on ice and additional washes, before processing for stripping, end filling and reverse crosslinking. qPCR was used to determine the optimal cycle number for enrichment PCR, according to the manufacturer’s protocol. The final amplified libraries were cleaned using AMPure XP beads at a 1.8:1 bead:DNA ratio, quantitated with Qubit HS dsDNA, and fragment size assessed on a TapeStation HS D1000 kit. The libraries were qPCR quantitated for pooling using the KAPA Illumina qPCR quantitation kit

treatment_protocol: treatment with puromycin

value: breast tumor

value: Breast Cancer cell line

tag: condition

value: Spindle Metaplastic

value: Control

tag: fraction

value: IP


title: HBEC [HBEC_S1]

value: Brain

value: HBEC

value: endothelial


title: PPGS_1_H3K27me3


title: Q16B037369BA40

source_name: bone

value: M

value: chemosurg


title: Q14B024855KA29

value: NORMAL

value: alive


title: dnTCF4_2_H3K27me3


title: Q14B024855KA15

value: TUMOUR


title: TEC [TEC_3465]

value: TEC


title: RNA_Mela2

value: HEMn-DP

value: cultures

value: human melanocyte cells

value: Ribo zero and Ribo-Filterout


title: RNA_Kera1

value: HEKn

value: human keratynocyte cells


title: RNA_Mela1


title: osteoblast, ad-Control 3, Day6

last: Kim

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

value: osteoblast

value: primary cultured calvarial pre-osteoblasts

value: WT

value: osteoblast differentiation


title: dnTCF4_4_H3K27me3

value: breast tumor

value: Breast Cancer cell line

value: Spindle Metaplastic

value: IP


title: GBM [GBM_3465]

value: Brain

value: GBM

value: tumor


title: HBEC [HBEC_S45]

growth_protocol: GVC were maintained in Endothelial Growth media supplemented with 2% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37*C

value: brain

value: HBEC

value: Endothelial cells


title: Q14B020064NA9

value: bone

value: TUMOUR

value: F

value: chemo

value: alive


title: dnTCF4_3_H3K27me3


title: RNA_IPSC2

value: cultures

value: human iPS cells

value: Ribo zero and Ribo-Filterout


title: LGG_GVC3 [3746TEC]

value: TEC


title: RNA_IPSC1


title: LGG_GVC5 [3788TEC]


title: LGG_GVC4 [3761TEC]


title: Q13B020599EC3

value: NORMAL

value: chemosurg

value: deceased


title: Ribo_Fibro1

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero, Ribo-FilterOut_Ribo-Calibration

value: HDFn

value: human fibrobrast cells


title: LGG_GVC2 [3744TEC]

value: brain


title: Q13B012216BA21

value: M


title: dnTCF4_2_IgG

value: breast tumor

value: Breast Cancer cell line

value: Spindle Metaplastic

value: Input


title: Q13B012216BA7

value: bone


title: Q13B020599EB5

value: TUMOUR

value: F


title: Ribo_Fibro2

value: cultures


title: dnTCF4_1_IgG


title: PPGS_4_H3K27me3

value: Control

value: IP


title: PPGS_3_IgG


title: dnTCF4_4_IgG


title: Q13B011918YB36

value: NORMAL

value: alive


title: Ribo_Kera2

value: HEKn

value: human keratynocyte cells

value: Ribo zero and Ribo-Filterout


title: PRI_GVC1 [3706TEC]

value: brain

value: TEC

value: Endothelial cells


title: PPGS_3_H3K27me3

value: breast tumor

value: Breast Cancer cell line


title: Ribo_Mela2

value: HEMn-DP

value: human melanocyte cells


title: LGG_GVC1 [3707TEC]


title: Q13B011918YB10

value: bone

value: TUMOUR

value: M

value: chemosurg


title: Q14B020064NA1

value: F

value: chemo


title: PRI_GVC2 [3383TEC]


title: Q13B008611LA5

value: NORMAL

value: alive


title: dnTCF4_1_H3K27me3

value: Spindle Metaplastic

value: IP


title: PRI_GVC3 [3810TEC]

value: brain


title: Ribo_Kera1

value: HEKn

value: cultures

value: human keratynocyte cells

value: Ribo zero and Ribo-Filterout


title: Q13B008611LA13


title: PPGS_2_IgG

value: breast tumor

value: Breast Cancer cell line

value: Control

value: Input


title: Ribo_IPSC2

value: human iPS cells


title: REC_GVC1 [3499TEC]

value: TEC

value: Endothelial cells


title: PPGS_1_IgG


title: dnTCF4_3_IgG


title: Q13B004130DA9

value: bone

value: TUMOUR

value: M

value: chemosurg

value: deceased


title: Q13B004130DA3

value: NORMAL


title: Ribo_IPSC1


title: RNA_HS_2_1

value: Human Embryonic Kidney cells293

value: Heatshock 2h and Recovery 1 h


title: PPGS_4_IgG

value: Spindle Metaplastic


title: DNTCF4-SET-3 (RNA-seq)

data_processing:
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3
Data were pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab delimited text file containing raw counts
Supplementary files format and content: tab delimited text file containing rlog normalized counts

growth_protocol: CCN6KOT primary Cells were growth in DMEM/F12  10%FBS and transduced with lentivirus  of DNTCF4 construct and control followed by  puromycin selection

extract_protocol:
Cells were collected   trypsin and then RNA extracted using QIAGEN RNA protocol.
Qiagen RNA protocol for cells.

value: Lentivirus DNTCF4-SET


title: Q13B003269YA35

value: F


title: RNA_HS_2_4

value: cultures

value: Ribo zero and Ribo-Filterout

value: Heatshock 2h and Recovery 4 h


title: Q12B044305AA45

value: chemo

value: alive


title: REC_GVC4 [3811TEC]

value: brain

value: TEC

value: Endothelial cells


title: RNA_HS_2_0.5

value: Heatshock 2h and Recovery 0.5 h


title: REC_GVC2 [3768TEC]


title: DNTCF4-SET-2 (RNA-seq)

value: breast tumor

value: Breast Cancer cell line


title: Ribo_Mela1

value: HEMn-DP

value: human melanocyte cells


title: RNA_HS_2

value: Human Embryonic Kidney cells293

value: Heatshock 2h


title: Q12B044305AA16

value: bone

value: NORMAL

value: M


title: REC_GVC3 [3778TEC]


title: PRI_GVC4 [3815TEC]


title: DNTCF4-SET-1 (RNA-seq)

value: Spindle Metaplastic

value: Lentivirus DNTCF4-SET


title: Q12B042591TA1

value: TUMOUR

value: F

value: chemosurg

value: deceased


title: REC_GVC5 [3812TEC]

value: brain

value: TEC

value: Endothelial cells


title: Ribo_HEK_Ribo_zero_Ribo-Filterout_2

value: cultures

value: WT

value: Ribo zero and Ribo-Filterout


title: RNA_HS_0.5

value: Human Embryonic Kidney cells293

value: Heatshock 0.5 h


title: Q12B019249NA34

value: bone


title: Ribo_HEK_Ribo_zero_Ribo-Filterout_1


title: Q12B019249NA28


title: DNTCF4-Vector-3 (RNA-seq)

value: breast tumor

value: Breast Cancer cell line


title: Ribo_HEK_Ribo-Filterout_2

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-FilterOut

value: Ribo-Filterout


title: Q11B045903JA5

value: M

value: alive


title: Q11B045903JA31

value: NORMAL


title: Ribo_HEK_Ribo-Filterout_1


title: RNA_HS_CT1

value: control condtion


title: Ribo_HS_2_1

value: Heatshock 2h and Recovery 1 h


title: Ribo_HS_2_4

value: Heatshock 2h and Recovery 4 h


title: DNTCF4-Vector-2 (RNA-seq)

value: Spindle Metaplastic


title: Q10B040965MA55

value: F

value: chemosurg


title: DNTCF4-EZH2-3 (RNA-seq)

value: Lentivirus DNTCF4-EZH2


title: RNA_HS_1

value: cultures

value: Ribo zero and Ribo-Filterout

value: Heatshock 1h


title: Ribo_HEK_Ribo_zero_1

description: Ribosome profiling_and_rRNA_depletion_with_Ribo-Zero

value: WT

value: Ribo zero


title: DNTCF4-EZH2-2 (RNA-seq)

value: breast tumor

value: Breast Cancer cell line


title: DNTCF4-Vector-1 (RNA-seq)


title: RNA_HS_CT2

value: Human Embryonic Kidney cells293


title: Ribo_HS_2_0.5

value: Heatshock 2h and Recovery 0.5 h


title: PPGS-Vector-3 (RNA-seq)

value: lentivirus Control


title: Q10B040965MA4

value: bone

value: TUMOUR

value: alive


title: Ribo_HS_2

value: Heatshock 2h


title: Q09B042936FB9

value: NORMAL

value: M


title: PPGS-Vector-2 (RNA-seq)

value: Spindle Metaplastic


title: DNTCF4-EZH2-1 (RNA-seq)

value: Lentivirus DNTCF4-EZH2


title: Ribo_HEK_CT2

description: Ribosome profiling_and_rRNA_depletion_with_None

value: cultures

value: control condtion


title: Ribo_HEK_CT1

value: WT


title: Q09B042936FB21

value: chemosurg


title: Ribo_HS_1

value: Ribo zero and Ribo-Filterout

value: Heatshock 1h