title: patient# 136-42 Xenium at 2 month post-injection time point

hyb_protocol: The Xenium slide was processed according to manufacturer’s protocol (10x, CG000582 Xenium In Situ Gene Expression)

data_processing: Processed slide was scanned by Xenium Analyzer (10x, PN-1000481) and data were processed through standard 10x Xenium workflow according to manufacturer’s protocol (10x, CG000584 Xenium Analyzer) to generate cell id by gene and transcript by location coordinate.

label: Xenium multi-tissue and cancer panel (350 genes) and custom design panel (35 genes)

source_name: Skin

extract_protocol: not provided

treatment_protocol: The skin biopsies from a single subject at 2-month post-injection time point were rinsed with DPBS and stored in 4% paraformaldehyde at 4°C overnight for fixation. Tissue samples were prepared further following to manufacturer’s protocol (10x, CG000578 Xenium In Situ for FFPE Tissue Preparation Guide) in Hopkins histology core facility. Briefly, the samples were embedded in paraffin and then, tissues were cut into 5 m thick slices and three samples from vehicle, scalp fibroblast, or sole fibroblast injection sites were placed on single Xenium slide (10x, PN 300941).

tag: tag

value: skin biopsies


title: LSCC_80

status: Public on Sep 09 2024

type: SRA

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

library_source: transcriptomic

data_processing:
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads from the fq file were removed and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: 100_samples_miRNA_RPM.txt

molecule: total RNA

organism: Homo sapiens

source_name: LSCC tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumor and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US)  following the manufacturer’s instructions.

tag: tumor stage

tag: tobacco smoking

value: Yes

tag: alcohol consumption

value: No

tag: sequencing type

value: Small RNA sequencing


title: MTR4-Day-14-rep1

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: MTR4-Growing GV_rep1

data_processing:
RNA-Seq was performed with biological replicates for all samples.
Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) and ERCC spike-in sequences with Tophat v2.1.1.
Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).
Expression level  was further normalized with the ERCC spike-in.
Assembly: mm9
Supplementary files format and content: txt file includes processed FPKM with ERCC correlation for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: ovary

extract_protocol:
Oocytes were collected from indicated genotypes (10 oocytes per sample) from mice of different stages. Each sample was directly lysed with 4.2 ul lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers, and 1:1000 ERCC spike-in) and immediately used for cDNA synthesis.
RNA-seq libraries were constructed using Smart-seq2 protocal as described previously (Picelli et al, 2014).

tag: tissue

value: ovary

tag: cell type

value: Oocyte

tag: Sex

value: female

tag: genotype


title: WT-Day-21-rep1

value: WT


title: Wild-type mice, 11-month-old, Vehicle-treated, Control [03_WT_vehicle_11M_rep3]

city: Sendai

first: Akira

last: Uruno

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
Salmon quant
Assembly: GRCm38/mm10
Supplementary files format and content: CSV

source_name: Brain

extract_protocol:
Sepasol (Nakrai Tesque)
MGISP-960 sample preparation system (MGI Tech) and MGIEasy RNA Directional Library Prep Set (MGI Tech)

value: Brain

value: Wild-type

tag: treatment

value: Vehicle


title: 84_V_2

status: Public on Sep 08 2024

city: Rochester

first: Collynn

last: Woeller

state: NY

address: 601 Elmwood Avenue

country: USA

institute: University of Rochester

data_processing:
bcltofastq-2.19.0
Assembly: Human hg38, annotation H38
Supplementary files format and content: Tab delimited txt file contains raw count for each file

source_name: Orbit

growth_protocol: Cultures were maintained in DMEM/F-12 medium supplemented with 10% FBS and Antibiotic-Antimycotic. Before treatment, cells were serum starved with 0.1% FBS-DMEM/F12 for 2 days. Treatments were performed in starve medium for 24 hours.  IGF-1 was  used at 50 ng/mL. 0.01% BSA-PBS served as vehicle for IGF-1.

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy mini kit, assessed via an Agilent Bioanalyzer and prepared for analysis.
TruSeq Stranded mRNA Sample Preparation Kit.

treatment_protocol: Cells were treated with vehicle or IGF-1( 50 ng/ml) for 24 hours

value: Orbit

value: Orbital fibroblast


title: 84_IGF_3

value: IGF-1 (50 ng/mL)


title: 84_IGF_1


title: 79_V_2


title: 84_V_3


title: 79_V_1


title: Vas_after_9

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

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

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

source_name: musculus vastus lateralis

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

treatment_protocol: Ten healthy males (25-38 years old [range]; median height 1.78 m and interquartile range [1.71-1.79] m; body mass 70 [64-74] kg; BMI 24 [21-24] kg/m2) were exposed to 6 days of “dry” immersion. Samples from the soleus and vastus lateralis muscle were taken prior to and after “dry” immersion from the left leg using a modified Bergström biopsy needle with manual suction under local anesthesia (2 ml 2% lidocaine).

value: musculus vastus lateralis

value: male

tag: individual

tag: age

tag: bmi

value: 6-day dry immersion

tag: time point

value: after treatment


title: 79_IGF_2


title: Sol_before_9

source_name: musculus soleus

value: musculus soleus

value: No treatment

value: before treatment


title: 84_IGF_2


title: 79_V_3


title: Vas_before_9


title: 79_IGF_3


title: Sol_before_10


title: Vas_after_8


title: Vas_after_10


title: 79_IGF_1


title: Vas_before_10


title: Sol_after_10


title: 84_V_1


title: Sol_after_8


title: Sol_after_9


title: Sol_before_8


title: Vas_before_7


title: Vas_after_7


title: Vas_after_6


title: Sol_after_6


title: Vas_before_8


title: Sol_after_7


title: Vas_before_6


title: Vas_after_5


title: Vas_before_4


title: Vas_before_3


title: Sol_after_4


title: Sol_before_5


title: Sol_before_3


title: Sol_after_3


title: Vas_before_2


title: Sol_before_7


title: Vas_after_1


title: Sol_after_1


title: Vas_before_5


title: Sol_before_2


title: Vas_after_10

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Unique reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts_NMES.txt — uniquely aligned read counts for genes

treatment_protocol: Ten healthy males (26-39 years old [range]; median height 1.74 m and interquartile range [1.70-1.76] m; body mass 73 [70-79] kg; BMI 24 [23-26] kg/m2) were exposed to 6 days of “dry” immersion. During dry immersion, low-intensity, low-frequency electrical stimulation of the anterior and posterior surface of calf and thigh muscles was performed daily at 11:00 using a Stimul-01stimulator (Biophyspribor, Russia) for 40-45 min: stimulation – 1 s[bipolar symmetrical rectangular pulses 1 ms, 25 Hz] and pause – 2s. Every day at 17:00, low-intensity high-frequency electrical stimulation was performed for the anterior and posterior surface of calf muscles, then for the thigh muscles using an Amplidin-EST stimulator (NTC UP RAN, Russia) for 10 min: stimulation – 10 s[bipolar symmetrical pulses 2.5 kHz with sinusoidal modulating frequency 50 Hz] and pause – 50 s). Samples from the soleus and vastus lateralis muscle were taken prior to and after “dry” immersion from the left leg using a modified Bergström biopsy needle with manual suction under local anesthesia (2 ml 2% lidocaine).

value: 6-day dry immersion + NMES


title: Sol_after_2


title: Vas_after_4


title: Vas_after_2


title: Vas_before_1


title: Sol_before_6


title: Sol_before_1


title: Sol_after_10


title: Vas_before_10


title: Sol_before_4


title: Sol_after_9


title: Vas_after_9


title: Sol_before_10


title: Vas_before_9


title: Vas_after_8


title: Sol_after_5


title: Sol_after_8


title: F4-80-MycBMP4-1

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

data_processing:
RNA fastqs were aligned to the mus musculus (version mm10 from Genome Reference Consortium GRCm38) using STAR (2.6.0b) (Dobin et al., 2013), raw counts are obtained using HTSeq (Anders et. al. 2014) (python/3.6/anaconda3/bin/htseq-count, with options -m union -a 10 -s no) ( rsem-calculate-expression (1.2.3) with options --bowtie2 (2.2.3) against reference mm10.refgenes were run separated for to obtain TPM ((transcripts per million reads)) ).
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: subQ tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA samples were submitted to Cancer Genomics Center at The University of Texas Health Science Center at Houston (CPRIT RP180734). Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with NEBNext Ploy(A) mRNA Magnetic Isolation Module (E7490L, New England Biolabs), NEBNext Ultra II Directional RNA Library Prep Kit for ILLumina (E7760L, New England Biolabs) and NEBNext Multiplex Oligos for illumina (E6609S, New England Biolabs) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) , and the library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

value: subQ tumor

tag: cell line

value: CD45+, CD11b+, GR1- and F4/80+ macrophages


title: Vas_before_8


title: F4-80-MycBMP4-2


title: Sol_before_8


title: Vas_after_7


title: Sol_before_9


title: MyCp-1

value: MycCaP


title: MyCp-2


title: Sol_after_7


title: Vas_before_7


title: Sol_before_7


title: Vas_after_6


title: Sol_after_6


title: Vas_before_6


title: Vas_after_3


title: Vas_after_5


title: Sol_before_6


title: Sol_before_5


title: Vas_before_5


title: Mφ-Sca 15

type: RNA

city: Guangzhou

first: Yulan

last: Weng

state: No State

address: Guangzhou

institute: Sun Yat-sen University

description: Gene expression in HCC tissue

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were log-transformed, and then normalized with the 'sva' R package to remove batch effects and other unwanted variations. The sva algrithm identified 4 SVs, and Batch, sv2, sv3, sv4 and MRS.group were used for adjustment after careful examination.

source_name: HCC

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: HCC tissues were grinded with a mortar and pestle in liquid nitrogen, and homogenized in TRIzol Reagent (Ambion). Total RNA was extracted according to the manufacturer’s instructions and quantified with a Nanodrop Instrument (Thermo Scientific). Aliquots containing 2 μg total RNA were used to generate complimentary DNA (cDNA) using the All-in-One RT MasterMix (Applied Biological Material).

tag: batch

tag: goodprognosis

value: Good

tag: mrsgroup

value: MRSint


title: Mφ-Sca 16

description: Gene expression in HCC tissue

value: Poor

value: female


title: Mφ-Sca 12

description: Gene expression in HCC tissue


title: Sol_after_4


title: Sol_before_4


title: Sol_after_5


title: Mφ-Sca 13

description: Gene expression in HCC tissue

value: MRShi


title: Mφ-Sca 14

description: Gene expression in HCC tissue


title: Mφ-Sca 11

description: Gene expression in HCC tissue


title: Vas_after_4


title: Mφ-Sca 7

description: Gene expression in HCC tissue


title: Mφ-Sca 6

description: Gene expression in HCC tissue

value: MRSlo


title: Mφ-Sca 9

description: Gene expression in HCC tissue


title: Mφ-Sca 10

description: Gene expression in HCC tissue


title: Sol_after_3


title: Vas_before_4

value: musculus vastus lateralis


title: Sol_before_3

value: male


title: CHLA266_Pan10nM_D21_2

city: Clayton

first: Vijesh

last: Vaghjiani

state: Victoria

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Reaserch

data_processing:
Galaxy Australia workbench
Sequencing reads were trims for adapters using Galaxy Australia genomics pipeline
Assembly: GRCH38 Enseml Release version 111
Supplementary files format and content: Tab-delimited text files including raw count files for each sample

growth_protocol: BT12, BT16 and CHLA266 cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 1% Insulin-Transferrin-Selenium, 20% foetal calf serum and 1% penstrep

extract_protocol:
RNA was extracted using RNeasy mini kit and 1ug of total RNA was used to construct sequencing libraries
RNA libraries were prepared using BGI DNBSEQ library kit following manufacturers protocol

treatment_protocol: cells were treated with 10nM Panobinostat or DMSO control for 21 days

value: Brain

value: Tumour cells

value: WT

value: 10nM Panobinostat


title: CHLA266_Pan10nM_D21_3


title: Sol_after_2

value: musculus soleus

value: after treatment


title: Mφ-Sca 3

description: Gene expression in HCC tissue


title: Vas_before_3

value: No treatment

value: before treatment


title: CHLA266_Pan10nM_D21_1


title: Mφ-Sca 5

description: Gene expression in HCC tissue


title: Mφ-Agg 3

description: Gene expression in HCC tissue


title: CHLA266_DMSO_D21_3

value: DMSO Control


title: Vas_before_2


title: Mφ-Sca 1

description: Gene expression in HCC tissue


title: BT16-Pan10nM-D21-2


title: Mφ-Sca 8

description: Gene expression in HCC tissue


title: Sol_after_1

value: 6-day dry immersion + NMES


title: CHLA266_DMSO_D21_1


title: Vas_before_1


title: Vas_after_3


title: Sol_before_1


title: Mφ-Sca 4

description: Gene expression in HCC tissue

value: Good


title: Vas_after_1


title: Vas_after_2


title: Mφ-Sca 2

description: Gene expression in HCC tissue

value: Poor


title: BT16-Pan10nM-D21-1


title: BT16-DMSO-D21-3


title: CHLA266_DMSO_D21_2


title: Mφ-Agg 2

description: Gene expression in HCC tissue


title: BT16-Pan10nM-D21-3


title: Mφ-Agg 1

description: Gene expression in HCC tissue


title: BT12_Pan10nM_D21_2


title: BT12_Pan10nM_D21_3


title: BT16-DMSO-D21-1


title: BT12_DMSO_D21_2


title: BT12_DMSO_D21_3


title: BT12_DMSO_D21_1


title: BT16-DMSO-D21-2


title: Retina, 175764

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

scan_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and the limma package in R was used to perform loess normalization

organism: Rattus norvegicus

source_name: Agilent's Universal Rat Reference RNA

label_protocol: Total RNA extracted using Trizol following manufacturer's instructions

growth_protocol: growth protocol is not applicable

extract_protocol: treatment protocol is not applicable

tag: timepoint

value: Unknown

tag: diet

value: Reference

source_name: Retina

value: Sham

value: 1% LA Diet

tag: study

value: nut 4

tag: running with wheel

value: No

tag: trauma

value: UWT

value: Retina


title: Retina, 175756

tag: tissue

value: House Chow


title: Retina, 175759


title: Retina, 175771

value: 8% LA Diet


title: Retina, 175773


title: iCLIP-Seq of ZSCAN22, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: combined_CITS_0.01_ZSCAN22.merged_filtered.bed

data_processing:
library strategy: iCLIP-seq
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the cDNA sequence, were initially trimmed to 49 nt from the 3'-end, and duplicates were discarded. Reads were de-multiplexed, and the random positions, barcodes, and any 3'-bases matching Illumina adaptors were removed. Remaining reads longer than 25 nt were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using TopHat with default settings. To prevent false assignment of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis. Note that this record contains demultiplexed but un-trimmed reads.
CLIP Tool Kit (CTK) was used to identify RNA-binding sites at single-nucleotide resolution.We  called CITS peaks on individual iCLIP replicates as well as SMI samples. CITS with FDR ≤ 0.01 were considered as significant. The identified iCLIP CITS were further normalized using SMI CITS by utilizing underlying reads from each dataset and performing a differential analysis (iCLIP/SMI). Remaining peaks from individual replicates were merged for downstream analysis.   miCLIP-seq data were processed similarly to the iCLIP-seq data (except for the SMI step), and putative anti-m6A mediated CITS were identified (FDR ≤ 0.01).
Assembly: hg19
Supplementary files format and content: BED files containing merged crosslink-induced termination site (CITS) locations from multiple replicates.

growth_protocol: Cell cultures were maintained in Dulbecco's modified Eagle's medium (DMEM) (Wisent Bioproducts catalogue number 319-005-CL) supplemented with 10% FBS (Wisent Bioproducts catalogue number 080-705), sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Lysates were treated with Turbo DNase (Thermo Fisher Scientiﬁc) and RNase I (Thermo Fisher Scientiﬁc) diluted 1/250 in PBS for 5 minutes at 37°C to digest genomic DNA and partially digest RNA to short fragments of an optimal size range. RNA-protein complexes were puriﬁed using 100 mL of protein G Dynabeads (Thermo Fisher Scientiﬁc) and 10ug antibody, with 2% (20ul) of the total lysate retained for use as a size-matched input (SMI) control. SMI samples were processed as previously described (Van Nostrand et al., 2016). Following stringent high salt washes, the immunoprecipitated RNA was 3′ end dephosphorylated and ligated to a pre-adenylated adaptor at the 3′ end, as described previously. After extensive additional washes and buffer exchange, the immunoprecipitated RNA was 5′ end-labeled using ATP [γ-32P]. The puriﬁed protein-RNA complexes and SMI control samples were separated with SDS-PAGE and transferred to nitrocellulose membrane. Protein was digested using proteinase K, the RNA was puriﬁed using phenol/chloroform. miCLIP procedure was performed as decribed. Total RNA was extracted from HEK293 cells using TRIzol as per manufacturer's protocol. RNA was treated with DNase I to eliminate any contaminating genomic DNA. We used 12 μg of total RNA for miCLIP-seq. 2 μL of RNA Fragmentation Reagents was added to the RNA suspended in 20 μL of sterile water. The mixture was incubated in a heat block at 75°C for exactly 12 minutes. 2.2 μL of stop solution was added to stop the reaction. The fragmented RNA was incubated with 10 μg of m6A antibody for 2 hours at 4°C. RNA-antibody complexes were UV crosslinked twice with 0.15 J/cm2 at 254 nm in a Stratalinker 1800.  Protein G Dynabeads (100 μL) were added, and the samples were rotated for 2 hours at 4°C. Remaining steps, including dephosphorylation, adapter ligation, SDS-PAGE, and RNA-extraction are similar to the iCLIP procecure.
Purified RNA was reverse transcribed into cDNA. The cDNA was size selected by resolving samples on a 6% TBE-Urea gel, circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR ampliﬁed using AccuPrime SuperMix I (Thermo Fisher Scientiﬁc). The ﬁnal PCR libraries were puriﬁed by agarose gel electrophoresis using gel extraction columns (QIAGEN). The eluted DNA from the low, middle, and high fractions was pooled together and submitted for sequencing.

treatment_protocol: HEK293 cells were crosslinked (150mJ/cm2) at 254 nm with a Stratalinker 1800.

tag: cell type

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZSCAN22 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.

tag: clip antibody

value: anti-GFP (Thermo Fisher Scientific G10362)

tag: barcoded reverse_transcription_primer


title: iCLIP-Seq of ZSCAN22, replicate 3

tag: genotype

tag: treatment


title: iCLIP-Seq of ZSCAN22, replicate 4


title: iCLIP-Seq of ZSCAN22, replicate 1


title: Retina, 175766


title: iCLIP-Seq of ZRANB2, replicate 2

description: combined_CITS_0.01_ZRANB2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZRANB2 ORF under CMV promoter.


title: BT12_Pan10nM_D21_1

value: Brain

value: Tumour cells

value: WT

value: 10nM Panobinostat


title: Retina, 175757

value: Unknown

value: Reference


title: Retina, 175767

value: 1% LA Diet

value: nut 4


title: Retina, 175758

value: Sham

value: No

value: UWT


title: Retina, 175775

value: 8% LA Diet

value: Retina


title: Retina, 175765


title: Retina, 1621331

value: nut 2


title: Retina, 175774


title: iCLIP-Seq of ZRANB2, replicate 1

value: Human embryonic kidney cells

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: Retina, 1621324

value: House Chow


title: iCLIP-Seq of ZNF784, replicate 2

description: combined_CITS_0.01_ZNF784.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF784 ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of ZNF784, replicate 1


title: Retina, 1621339


title: iCLIP-Seq of ZNF768, replicate 2

description: combined_CITS_0.01_ZNF768.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF768 ORF under CMV promoter.


title: Retina, 1621338


title: iCLIP-Seq of ZNF768, replicate 1


title: iCLIP-Seq of ZNF654, replicate 1

description: combined_CITS_0.01_ZNF654.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF654 ORF under CMV promoter.


title: iCLIP-Seq of ZNF467, replicate 3

description: combined_CITS_0.01_ZNF467.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF467 ORF under CMV promoter.


title: iCLIP-Seq of ZNF574, replicate 1

description: combined_CITS_0.01_ZNF574.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF574 ORF under CMV promoter.


title: iCLIP-Seq of ZNF510, replicate 1

description: combined_CITS_0.01_ZNF510.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF510 ORF under CMV promoter.


title: iCLIP-Seq of ZNF510, replicate 2


title: iCLIP-Seq of ZNF467, replicate 1


title: iCLIP-Seq of ZNF467, replicate 2


title: iCLIP-Seq of ZNF449, replicate 2

description: combined_CITS_0.01_ZNF449.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF449 ORF under CMV promoter.


title: Retina, 1621337

value: Unknown

value: Reference


title: iCLIP-Seq of ZNF654, replicate 2


title: iCLIP-Seq of ZNF574, replicate 2


title: iCLIP-Seq of ZNF449, replicate 1


title: iCLIP-Seq of ZNF436, replicate 2

description: combined_CITS_0.01_ZNF436.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF436 ORF under CMV promoter.


title: Retina, 1621340

value: Sham

value: 8% LA Diet

value: No

value: UWT


title: Retina, 1621321

value: nut 2

value: Retina


title: Retina, 1621329

value: 1% LA Diet


title: Retina, 1621326

value: House Chow


title: Retina, 1621344


title: Retina, 1621322


title: Retina, 1621334


title: Retina, 1621332


title: Retina, 1621323


title: Retina, 1621343


title: Retina, 1621327


title: Retina, 1621328


title: Retina, 1621333


title: iCLIP-Seq of ZNF436, replicate 1

value: Human embryonic kidney cells

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of ZNF41, replicate 1

description: combined_CITS_0.01_ZNF41.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF41 ORF under CMV promoter.


title: iCLIP-Seq of ZNF224, replicate 2

description: combined_CITS_0.01_ZNF224.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF224 ORF under CMV promoter.


title: iCLIP-Seq of ZNF41, replicate 2


title: Retina, 1621336


title: Retina, 1621342


title: iCLIP-Seq of ZNF224, replicate 1


title: iCLIP-Seq of ZFP64, replicate 2

description: combined_CITS_0.01_ZFP64.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZFP64 ORF under CMV promoter.


title: iCLIP-Seq of ZBTB7A, replicate 4

description: combined_CITS_0.01_ZBTB7A.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZBTB7A ORF under CMV promoter.


title: iCLIP-Seq of ZFP64, replicate 1


title: Retina, 1621330

value: Unknown

value: Reference


title: Retina, 1621341

value: Sham


title: iCLIP-Seq of ZBTB7A, replicate 1


title: iCLIP-Seq of ZBTB7A, replicate 2


title: Retina, 171037

value: nut 3

value: Blast


title: iCLIP-Seq of ZBTB7A, replicate 3


title: iCLIP-Seq of ZBTB6, replicate 1

description: combined_CITS_0.01_ZBTB6.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZBTB6 ORF under CMV promoter.


title: iCLIP-Seq of ZBTB6, replicate 2


title: iCLIP-Seq of WT1, replicate 2

description: combined_CITS_0.01_WT1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/WT1 ORF under CMV promoter.


title: Retina, 171054

value: 8% LA Diet

value: No

value: Retina


title: iCLIP-Seq of WT1, replicate 1

value: Human embryonic kidney cells


title: Retina, 1621325

value: House Chow

value: nut 2

value: UWT


title: Retina, 171053

value: Blast + WD


title: Retina, 171047

value: 1% LA Diet


title: iCLIP-Seq of TRIM28, replicate 4

description: combined_CITS_0.01_TRIM28.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TRIM28 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of TRIM28, replicate 3


title: Retina, 171045

value: Unknown

value: Reference

value: Sham


title: iCLIP-Seq of TRIM28, replicate 2

value: WT

value: anti-TRIM28 (Thermo Fisher Scientific MA1-2023)


title: iCLIP-Seq of TRIM28, replicate 1


title: Retina, 171040

value: nut 3

value: Blast


title: Retina, 171048

value: No

value: Retina


title: iCLIP-Seq of SSBP1, replicate 2

description: combined_CITS_0.01_SSBP1.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SSBP1 ORF under CMV promoter.


title: Retina, 171038

value: House Chow


title: Retina, 171055

value: 8% LA Diet


title: iCLIP-Seq of SSBP1, replicate 1


title: iCLIP-Seq of SRSF2, replicate 2

description: combined_CITS_0.01_SRSF2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SRSF2 ORF under CMV promoter.


title: iCLIP-Seq of SRSF2, replicate 1


title: Retina, 171056

value: Blast + WD


title: Retina, 171039


title: Retina, 1616096

value: 1% LA Diet

value: nut 1


title: Retina, 1616090

value: Unknown


title: Retina, 1616106

value: Reference


title: Retina, 171046

value: Sham


title: Retina, 1616104


title: iCLIP-Seq of SRSF1, replicate 3

description: combined_CITS_0.01_SRSF1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SRSF1 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of SRSF1, replicate 2


title: Retina, 1616091

value: Blast


title: Retina, 1616099

value: No


title: iCLIP-Seq of RPS27A, replicate 2

description: combined_CITS_0.01_RPS27A.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/RPS27A ORF under CMV promoter.


title: Sol_before_2

value: musculus soleus

tag: Sex

value: male

tag: individual

tag: age

tag: bmi

value: No treatment

value: before treatment


title: iCLIP-Seq of RPS27A, replicate 1

tag: cell line

value: Human embryonic kidney cells


title: Retina, 1616088

value: Blast + WD

value: House Chow

value: Retina


title: Retina, 1616102

value: Unknown

value: 1% LA Diet

value: nut 1


title: iCLIP-Seq of RPRD2, replicate 2

description: combined_CITS_0.01_RPRD2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/RPRD2 ORF under CMV promoter.


title: iCLIP-Seq of RPRD2, replicate 1

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: Retina, 1616089

value: Reference


title: iCLIP-Seq of RPRD1B, replicate 2

description: combined_CITS_0.01_RPRD1B.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/RPRD1B ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: Retina, 1616107

value: Sham

value: 8% LA Diet

value: No

value: Blast


title: iCLIP-Seq of RPRD1B, replicate 1


title: iCLIP-Seq of SRSF1, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SRSF1 ORF under CMV promoter.


title: iCLIP-Seq of PRR3, replicate 2

description: combined_CITS_0.01_PRR3.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PRR3 ORF under CMV promoter.


title: iCLIP-Seq of PRR3, replicate 1


title: iCLIP-Seq of PRPF31, replicate 3

description: combined_CITS_0.01_PRPF31.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PRPF31 ORF under CMV promoter.


title: iCLIP-Seq of PRR3, replicate 3


title: iCLIP-Seq of PRPF31, replicate 1


title: iCLIP-Seq of PRPF31, replicate 2


title: Retina, 1616092

value: House Chow

value: Retina


title: Retina, 1616095

value: Unknown

value: Blast + WD

value: 1% LA Diet


title: Retina, 1616109

value: nut 1


title: Retina, 1616087

value: Reference


title: iCLIP-Seq of PPIB, replicate 2

description: combined_CITS_0.01_PPIB.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PPIB ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: Retina, 1616098

value: Sham


title: Retina, 1616105

value: 8% LA Diet


title: Retina, 1616093

value: No


title: Retina, 1616110

value: Blast


title: iCLIP-Seq of PPIB, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: Retina, 1616108


title: Retina, 1616103


title: iCLIP-Seq of ZNF594, replicate 2

data_processing:
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the cDNA sequence, were initially trimmed to 49 nt from the 3'-end, and duplicates were discarded. Reads were de-multiplexed, and the random positions, barcodes, and any 3'-bases matching Illumina adaptors were removed. Remaining reads longer than 25 nt were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using TopHat with default settings. To prevent false assignment of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis. Note that this record contains demultiplexed but un-trimmed reads.
CLIP Tool Kit (CTK) was used to identify RNA-binding sites at single-nucleotide resolution.We  called CITS peaks on individual iCLIP replicates as well as SMI samples. CITS with FDR ≤ 0.01 were considered as significant. The identified iCLIP CITS were further normalized using SMI CITS by utilizing underlying reads from each dataset and performing a differential analysis (iCLIP/SMI). Remaining peaks from individual replicates were merged for downstream analysis.  miCLIP-seq data were processed similarly to the iCLIP-seq data (except for the SMI step), and putative anti-m6A mediated CITS were identified (FDR ≤ 0.01).
Assembly: hg19
Supplementary files format and content: BED files containing merged crosslink-induced termination site (CITS) locations from multiple replicates.
Library strategy: iCLIP-Seq

treatment_protocol:
Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.
HEK293 cells were crosslinked (150mJ/cm2) at 254 nm with a Stratalinker 1800.

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF594 ORF under CMV promoter.


title: Retina, 1616097


title: Retina, 1616094


title: iCLIP-Seq of OVOL2, replicate 1

description: combined_CITS_0.01_OVOL2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/OVOL2 ORF under CMV promoter.


title: iCLIP-Seq of ZNF322, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF322 ORF under CMV promoter.


title: iCLIP-Seq of NXF1, replicate 2

description: combined_CITS_0.01_NXF1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/NXF1 ORF under CMV promoter.


title: iCLIP-Seq of ZNF322, replicate 1


title: iCLIP-Seq of OSR2, replicate 2

description: combined_CITS_0.01_OSR2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/OSR2 ORF under CMV promoter.


title: iCLIP-Seq of ZNF594, replicate 1


title: iCLIP-Seq of OVOL2, replicate 2


title: iCLIP-Seq of ZNF23, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF23 ORF under CMV promoter.


title: iCLIP-Seq of ZNF320, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF320 ORF under CMV promoter.


title: iCLIP-Seq of NXF1, replicate 1


title: Retina, 1616101

value: Unknown

value: Blast + WD

value: 1% LA Diet

value: nut 1

value: Retina


title: iCLIP-Seq of RPS15A, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/RPS15A ORF under CMV promoter.


title: iCLIP-Seq of NHP2L1, replicate 1

description: combined_CITS_0.01_NHP2L1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/NHP2L1 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of ZNF23, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of NHP2L1, replicate 2

value: Human embryonic kidney cells


title: iCLIP-Seq of RPS15A, replicate 1


title: iCLIP-Seq of MYNN, replicate 1

description: combined_CITS_0.01_MYNN.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/MYNN ORF under CMV promoter.


title: iCLIP-Seq of METTL3, replicate 2

description: combined_CITS_0.01_METTL3.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/METTL3 ORF under CMV promoter.


title: iCLIP-Seq of METTL3, replicate 1


title: iCLIP-Seq of KLF17, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF17 ORF under CMV promoter.


title: iCLIP-Seq of LSM6, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/LSM6 ORF under CMV promoter.


title: iCLIP-Seq of MBNL2, replicate 2

description: combined_CITS_0.01_MBNL2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/MBNL2 ORF under CMV promoter.


title: iCLIP-Seq of ZNF320, replicate 2


title: iCLIP-Seq of LSM6, replicate 1


title: iCLIP-Seq of OSR2, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/OSR2 ORF under CMV promoter.


title: Retina, 1616100

value: Reference

value: Sham

value: No

value: Blast


title: iCLIP-Seq of MBNL2, replicate 1


title: iCLIP-Seq of MAZ, replicate 3

description: combined_CITS_0.01_MAZ.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/MAZ ORF under CMV promoter.


title: iCLIP-Seq of MAZ, replicate 1


title: iCLIP-Seq of HuR, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/HuR ORF under CMV promoter.


title: iCLIP-Seq of MAZ, replicate 2


title: Size-matched input for PTBP1 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PTBP1 ORF under CMV promoter.


title: RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 2

description:
siZNF784_siZNF784_vs_siNT_DESeq2_results_table.tab.gz
ZBTB7A_vs_siNT_DESeq2_results_table.tab.gz

data_processing:
RNAseq reads were trimmed using Cutadapt with the following parameters : -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=25 --quality-cutoff=20
Reads were aligned to human genome GRCh38 using STAR (version 2.7.6.a).
For differential analysis, gene-level read counts were quantified using RSEM (version 1.3.3) and normalized by variance-stabilizing transformation using DESeq2 76. Adjusted p-value ≤ 0.05 and log2fold change +/- 1 were used to determine significantly regulated genes.
Assembly: hg38
Supplementary files format and content: *genes.results files are tab-delimited output of RSEM gene-level quantification, containing gene ID, transcript IDs, length, effective length, expected count, TPM and FPKM.
Supplementary files format and content: CBLL1_vs_GFP_DESeq2_results_table.tab.gz, siZNF784_siZNF784_vs_siNT_DESeq2_results_table.tab.gz, ZBTB7A_vs_siNT_DESeq2_results_table.tab.gz and ZNF645_vs_GFP_DESeq2_results_table.tab.gz are a tab-delimited output from DESeq2 analysis and contain base mean, log2-fold change, test statistic, raw and adjusted p-values from the comparison with the appropriate knockdown/overexpression knockdown.

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit.
Poly-A selected, rRNA-depleted libraries were generated from 1 μg of input RNA using the TruSeq Illumina library preparation kit (Epicenter) as per the manufacturer’s recommendations. The quantified pool was hybridized at a final concentration of 2.21 pM

value: human embryonic kidney cells (HEK293)

value: siRNA knockdowns were performed with 40-50 nM Silencer Select control siRNA (Thermo Fisher AM4611) with Lipofectamine iMax transfection reagent (Thermo Fisher 13778075) for 72 hours.

value: WT


title: Retina, 1621335

value: Unknown

value: UWT

value: 1% LA Diet

value: nut 2

value: Retina


title: iCLIP-Seq of LYAR, replicate 2

description: combined_CITS_0.01_LYAR.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/LYAR ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: RNA-seq of HEK293 cells upon overexpression of GFP, replicate 2

description:
CBLL1_vs_GFP_DESeq2_results_table.tab.gz
ZNF645_vs_GFP_DESeq2_results_table.tab.gz

value: EGFP was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to harvesting.

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus, under CMV promoter, were transfected with pDEST pcDNA5/FRT/EGFP.


title: RNA-seq of HEK293 cells upon overexpression of ZNF645, replicate 2

description: ZNF645_vs_GFP_DESeq2_results_table.tab.gz

value: ZNF645 ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF645 ORF under CMV promoter.

value: EGFP-ZNF645 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to harvesting.


title: iCLIP-Seq of KLF14, replicate 1

description: combined_CITS_0.01_KLF14.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF14 ORF under CMV promoter.


title: iCLIP-Seq of KLF14, replicate 2


title: iCLIP-Seq of LYAR, replicate 1


title: RNA-seq of HEK293 cells upon overexpression of GFP, replicate 1

value: human embryonic kidney cells (HEK293)


title: iCLIP-Seq of MYNN, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/MYNN ORF under CMV promoter.


title: RNA-seq of HEK293 cells upon control non-targeting knockdown, replicate 1

value: siRNA knockdowns were performed with 40-50 nM Silencer Select control siRNA (Thermo Fisher AM4611) with Lipofectamine iMax transfection reagent (Thermo Fisher 13778075) for 72 hours.

value: WT


title: iCLIP-Seq of KLF17, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF17 ORF under CMV promoter.


title: Size-matched input for ZFP64 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZFP64 ORF under CMV promoter.


title: RNA-seq of HEK293 cells upon overexpression of ZNF645, replicate 1


title: Size-matched input for YY1 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/YY1 ORF under CMV promoter.


title: RNA-seq of HEK293 cells upon knockdown of ZBTB7A, replicate 2

description: ZBTB7A_vs_siNT_DESeq2_results_table.tab.gz

value: siRNA knockdowns were performed with 40-50 nM siRNA against ZNF784  (s27989, Thermo Fisher Scientific Inc.)  with Lipofectamine iMax transfection reagent (Thermo Fisher 13778075) for 72 hours.


title: RNA-seq of HEK293 cells upon knockdown of ZBTB7A, replicate 1


title: Size-matched input for PRPF31 iCLIP-Seq

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PRPF31 ORF under CMV promoter.


title: RNA-seq of HEK293 cells upon overexpression of CBLL1, replicate 1

description: CBLL1_vs_GFP_DESeq2_results_table.tab.gz

value: CBLL1 ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF645 ORF under CMV promoter.

value: EGFP-CBLL1 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to harvesting.


title: iCLIP-Seq of HuR, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/HuR ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: RNA-seq of HEK293 cells upon knockdown of ZNF784, replicate 2

description: siZNF784_siZNF784_vs_siNT_DESeq2_results_table.tab.gz

value: siRNA knockdowns were performed with 40-50 nM siRNA against ZNF784  (s45060, Thermo Fisher Scientific Inc.)  with Lipofectamine iMax transfection reagent (Thermo Fisher 13778075) for 72 hours.


title: Size-matched input for CHTOP iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CHTOP ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of IFIT2, replicate 3

description: combined_CITS_0.01_IFIT2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/IFIT2 ORF under CMV promoter.


title: iCLIP-Seq of IFIT2, replicate 2


title: iCLIP-Seq of ZNF777, replicate 1

description: combined_CITS_0.01_ZNF777.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF777 ORF under CMV promoter.


title: iCLIP-Seq of ZNF777, replicate 2


title: iCLIP-Seq of HMGB2, replicate 3

description: combined_CITS_0.01_HMGB2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/HMGB2 ORF under CMV promoter.


title: iCLIP-Seq of IFIT2, replicate 1


title: iCLIP-Seq of HMGB2, replicate 2


title: iCLIP-Seq of ZNF677, replicate 2

description: combined_CITS_0.01_ZNF677.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF677 ORF under CMV promoter.


title: iCLIP-Seq of ZNF677, replicate 1


title: iCLIP-Seq of ZNF600, replicate 2

description: combined_CITS_0.01_ZNF600.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF600 ORF under CMV promoter.


title: iCLIP-Seq of H1F0, replicate 4

description: combined_CITS_0.01_H1F0.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/H1F0 ORF under CMV promoter.


title: iCLIP-Seq of ZNF384, replicate 1

description: combined_CITS_0.01_ZNF384.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF384 ORF under CMV promoter.


title: Size-matched input for PPIB iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PPIB ORF under CMV promoter.


title: iCLIP-Seq of GTF3A, replicate 3

description: combined_CITS_0.01_GTF3A.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/GTF3A ORF under CMV promoter.


title: iCLIP-Seq of ZNF384, replicate 2


title: iCLIP-Seq of H1F0, replicate 2


title: iCLIP-Seq of H1F0, replicate 1


title: iCLIP-Seq of H1F0, replicate 3


title: iCLIP-Seq of GTF3A, replicate 1


title: iCLIP-Seq of ZNF341, replicate 2

description: combined_CITS_0.01_ZNF341.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF341 ORF under CMV promoter.


title: iCLIP-Seq of ZNF341, replicate 1


title: iCLIP-Seq of ZNF32, replicate 2

description: combined_CITS_0.01_ZNF32.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF32 ORF under CMV promoter.


title: iCLIP-Seq of GFP, replicate 3

description: combined_CITS_0.01_GFP.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/GFP ORF under CMV promoter.


title: iCLIP-Seq of ZNF32, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of GTF3A, replicate 2


title: RNA-seq of HEK293 cells upon knockdown of ZNF784, replicate 1

value: human embryonic kidney cells (HEK293)

value: siRNA knockdowns were performed with 40-50 nM siRNA against ZNF784  (s45060, Thermo Fisher Scientific Inc.)  with Lipofectamine iMax transfection reagent (Thermo Fisher 13778075) for 72 hours.

value: WT


title: iCLIP-Seq of GFP, replicate 4

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of ZNF768, replicate 3

description: combined_CITS_0.01_ZNF768.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF768 ORF under CMV promoter.


title: iCLIP-Seq of GFP, replicate 2


title: iCLIP-Seq of ZNF287, replicate 2

description: combined_CITS_0.01_ZNF287.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF287 ORF under CMV promoter.


title: iCLIP-Seq of HMGB2, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/HMGB2 ORF under CMV promoter.


title: iCLIP-Seq of ZNF274, replicate 2

description: combined_CITS_0.01_ZNF274.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF274 ORF under CMV promoter.


title: iCLIP-Seq of ZNF287, replicate 1


title: iCLIP-Seq of ZNF600, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF600 ORF under CMV promoter.


title: iCLIP-Seq of EGR2, replicate 1

description: combined_CITS_0.01_EGR2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/EGR2 ORF under CMV promoter.


title: iCLIP-Seq of ZNF148, replicate 2

description: combined_CITS_0.01_ZNF148.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF148 ORF under CMV promoter.


title: iCLIP-Seq of DEK, replicate 3

description: combined_CITS_0.01_DEK.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/DEK ORF under CMV promoter.


title: iCLIP-Seq of ZBTB38, replicate 2

description: combined_CITS_0.01_ZBTB38.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZBTB38 ORF under CMV promoter.


title: iCLIP-Seq of ZNF148, replicate 1


title: iCLIP-Seq of DEK, replicate 2


title: iCLIP-Seq of ZBTB38, replicate 1


title: iCLIP-Seq of YY2, replicate 2

description: combined_CITS_0.01_YY2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/YY2 ORF under CMV promoter.


title: iCLIP-Seq of DEK, replicate 1


title: iCLIP-Seq of YY2, replicate 1


title: iCLIP-Seq of CTCF, replicate 1

description: combined_CITS_0.01_CTCF.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CTCF ORF under CMV promoter.


title: iCLIP-Seq of YY1, replicate 2

description: combined_CITS_0.01_YY1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/YY1 ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of CMTR1, replicate 2

description: combined_CITS_0.01_CMTR1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/cMTR1 ORF under CMV promoter.


title: iCLIP-Seq of YTHDF1, replicate 2

description: combined_CITS_0.01_YTHDF1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/YTHDF1 ORF under CMV promoter.


title: iCLIP-Seq of GFP, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/GFP ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of EGR2, replicate 2


title: iCLIP-Seq of YTHDF1, replicate 1


title: iCLIP-Seq of CTCF, replicate 2


title: iCLIP-Seq of CBLL2 (ZNF645), replicate 1

description: combined_CITS_0.01_CBLL2.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CBLL2 ORF under CMV promoter.


title: iCLIP-Seq of WTAP, replicate 2

description: combined_CITS_0.01_WTAP.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/WTAP ORF under CMV promoter.


title: iCLIP-Seq of CBLL2 (ZNF645), replicate 2


title: iCLIP-Seq of CMTR1, replicate 1


title: iCLIP-Seq of ZNF274, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF274 ORF under CMV promoter.


title: seedlings, jaz9-1_12_Rep3

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 5-8 seedlings/sample were grown under a 16-h-light (75 μmol m-1 s-1; cool-white fluorescent light) /8-h-dark cycle at 22 °C on half strength Murashige-Skoog (MS) liquid medium (0.5% sucrose) for 6 days.

extract_protocol:
Seedlings were flash-frozen on liquid nitrogen, and RNA was extracted using RNeasy Mini Kit (Qiagen Co. Ltd., Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Lasy-Seq v1.1 (Kamitani et al., 2019, Sci. Rep. see also　https://sites.google.com/view/lasy-seq/ )

treatment_protocol: Each compound was treated for 8 hours.

value: seedlings

tag: ecotype


title: iCLIP-Seq of WTAP, replicate 1


title: iCLIP-Seq of U2AF1, replicate 2

description: combined_CITS_0.01_U2AF1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/U2AF1 ORF under CMV promoter.


title: iCLIP-Seq of DEK, replicate 4


title: seedlings, jaz9-1_12_Rep1


title: iCLIP-Seq of U2AF1, replicate 1


title: seedlings, jaz9-1_2e_Rep3


title: iCLIP-Seq of TDP43, replicate 2

description: combined_CITS_0.01_TDP43.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TDP43 ORF under CMV promoter.


title: seedlings, jaz9-1_2e_Rep2


title: iCLIP-Seq of TDP43, replicate 1

value: Human embryonic kidney cells


title: iCLIP-Seq of YY1, replicate 1


title: iCLIP-Seq of SP6, replicate 2

description: combined_CITS_0.01_SP6.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SP6 ORF under CMV promoter.


title: seedlings, jaz9-1_2_Rep3


title: T24, RHOB OE, biol rep 3 (TR-3)

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of 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 further treated with scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same clusters. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated. Duplicate consensus sequences were removed and used for standard RNA-seq analysis. They were mapped to the human genome (assembly GRCh38) using STAR software (Version 2.5.3) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor), and then FPKMs were calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts or FPKM values for each Sample

source_name: Bladder cancer

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with Nanodrop OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with Qubit RNA Broad Range Assay kit (Life Technologies).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-Digital Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08502, Seqhealth Technology Co., Ltd. Wuhan, China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.

value: Bladder cancer

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: RHOB overexpression


title: CAF1_SP600125, RNAseq

city: Hefei

first: Yang

last: Li

state: Anhui

address: 81 Meishan Road

institute: Anhui Medical University

data_processing:
The gene count matrix was acquired by comparison with GRCH38.
Assembly: hg38
Supplementary files format and content: Tab-separated file containing row counts and FPKM for each sample.

source_name: bladder cancer

extract_protocol:
Total RNA was extracted from CAF by TRIzol reagent.
1 mg total RNA was used for the following library preparation. Subsequently, libraries with different indexes were multiplexed and loaded on an Illumina HiSeq/Illumina Novaseq/MGI2000 instrument for sequencing using a 2 x 150 paired-end configuration according to the manufacturer’s instructions.

value: bladder cancer

value: primary cancer-associated fibroblasts (CAFs)


title: CAF1_DMSO, RNAseq

value: DMSO


title: iCLIP-Seq of SP6, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: seedlings, jaz9-1_2_Rep2


title: T24, RHOB OE, biol rep 2 (TR-2)


title: seedlings, jaz9-1_12_Rep2


title: seedlings, jaz9-1_2_Rep1


title: T24, EV, biol rep 2 (TN-2)

value: Empty vector


title: iCLIP-Seq of SF3A1, replicate 1

description: combined_CITS_0.01_SF3A1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/SF3A1 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of SF3A1, replicate 2


title: T24, EV, biol rep 3 (TN-3)


title: iCLIP-Seq of PTBP1, replicate 2

description: combined_CITS_0.01_PTBP1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PTBP1 ORF under CMV promoter.


title: T24, RHOB OE, biol rep 1 (TR-1)


title: T24, SIM, biol rep 3 (S-3)

value: WT

value: Treated with simvastatin 2 μm


title: seedlings, jaz9-1_Mock_Rep2

value: seedlings

value: Mock


title: T24, EV, biol rep 1 (TN-1)


title: seedlings, jaz9-1_Mock_Rep3


title: seedlings, jaz9-1_2e_Rep1


title: iCLIP-Seq of PTBP1, replicate 1

value: Human embryonic kidney cells


title: T24, SIM, biol rep 1 (S-1)

value: Bladder cancer


title: T24, SIM, biol rep 2 (S-2)

value: T24 cell line


title: iCLIP-Seq of PRDM12, replicate 2

description: combined_CITS_0.01_PRDM12.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PRDM12 ORF under CMV promoter.


title: T24, DMSO, biol rep 2 (O-2)

value: Human bladder transitional cell cancer cells

value: Treated with DMSO


title: T24, DMSO, biol rep 1 (O-1)


title: T24, DMSO, biol rep 3 (O-3)


title: FLX1, combo, rep3 [D3]

city: Boston

first: Nabeel

last: Bardeesy

state: MA

address: 185 Cambridge St.

institute: Massachusetts General Hospital/Harvard Medical School

data_processing:
Perform alignments withHISAT2to the reference.
Gene expression level is calculated by the number of mapped reads.
Assembly: hg19
Supplementary files format and content: the xls file includes FPKM values for all samples

extract_protocol:
RNA samples were extracted using the RNeasy Plus Mini Kit (Qiagen) and subsequently stored at -80°C.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: fibrolamellar carcinoma cells

value: PKAi+SIKi


title: seedlings, Col-0_12_Rep3


title: FLX1, combo, rep2 [D2]


title: iCLIP-Seq of NAT10, replicate 2

description: combined_CITS_0.01_NAT10.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/NAT10 ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: FLX1, combo, rep1 [D1]


title: seedlings, Col-0_12_Rep1


title: seedlings, Col-0_12_Rep2


title: FLX1, PKAi, rep2 [C2]

value: PKAi


title: iCLIP-Seq of MATR3, replicate 3

description: combined_CITS_0.01_MATR3.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/MATR3 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: iCLIP-Seq of MATR3, replicate 2


title: seedlings, Col-0_2e_Rep3

value: WT


title: seedlings, Col-0_2e_Rep2


title: FLX1, PKAi, rep1 [C1]


title: iCLIP-Seq of MATR3, replicate 1


title: seedlings, jaz9-1_Mock_Rep1


title: FLX1, SIKi, rep3 [B3]

value: SIKi


title: FLX1, SIKi, rep2 [B2]


title: iCLIP-Seq of m6A, replicate 2

description: combined_CITS_0.01_m6AHek.merged_filtered.bed

value: Total RNA was extracted using Trizol (Invitrogen catalogue number 15596018) and after overnight incubation with m6A antibody, RNA was crosslinked to the antibody using UV.

value: anti-m6A (MBL RN131P)


title: seedlings, Col-0_2e_Rep1

value: seedlings


title: SP600125,replicate 1, scRNAseq

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed by the Cell Ranger pipeline (v3.0.1, 10x Genomics), including sampledemultiplexing, genome alignment (GRCm38), barcode counting, and unique molecular identifier (UMI) counting.
Assembly: mm10
Supplementary files format and content: Tab-separated file containing cell barcodes, gene features or gene expression levels.

extract_protocol:
Fresh bladder tissues were collected from BBN-induced bladder carcinogenesis mice. For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine.
Sorted cell suspension from mouse bladder was loaded on a well of 10x Chromium single cell instrument (10X Genomics). Barcoding, cDNA synthesis and library construction were administered using the manufacturer's instructions.

value: bladder cancer


title: SP600125,replicate 2, scRNAseq

description: 10X Genomics


title: anti-PD1,replicate 1, scRNAseq

description: 10X Genomics


title: seedlings, Col-0_2_Rep3


title: seedlings, Col-0_2_Rep2


title: FLX1, SIKi, rep1 [B1]


title: FLX1, DMSO, rep3 [A3]

value: DMSO


title: FLX1, PKAi, rep3 [C3]


title: iCLIP-Seq of KLF8, replicate 1

description: combined_CITS_0.01_KLF8.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF8 ORF under CMV promoter.


title: iCLIP-Seq of PRDM12, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/PRDM12 ORF under CMV promoter.


title: FLX1, DMSO, rep2 [A2]

value: fibrolamellar carcinoma cells


title: seedlings, Col-0_2_Rep1


title: iCLIP-Seq of KLF13, replicate 2

description: combined_CITS_0.01_KLF13.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF13 ORF under CMV promoter.


title: GMCSF+TGFb+IL34, replicate 2

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: University College London

data_processing:
RNA-seq transcript abundance was quantified using the salmon read mapper and an Ensembl GRCm39 transcript model
The data were imported to the R statistical environment and summarized at the gene level (that is, transcript counts summed) using tximport.
Statistical transformations for visualisation (vst and log10) and analyses of differential expression were performed using the DESeq2 package. Multiple testing adjustments of differential expression utilized the Benjamini–Hochberg false discovery rate (fdr)
Assembly: GRCm39
Supplementary files format and content: bulk_metadata.tsv.gz
Supplementary files format and content: deseq2_normalised_counts.tsv.gz

source_name: bone marrow

growth_protocol: Monocytes were isolated from whole bone marrow by MACS using Monocyte Isolation Kit (BM; Miltenyi, 130-100-629) as per manufacturer’s instructions. Monocytes were resuspended in complete RPMI and plated at 1x106 cells per well in tissue-culture treated 24-well plates. Where indicated, cells were supplemented with recombinant GM-CSF (20ng/ml), TGF bbb (5ng/ml) and IL34 (8µg/ml). Cells were cultured at 37˚C, 5% CO2. The medium was partially replaced on day 2 of culture and completely replaced on day 3, and cells were harvested on day 6.

extract_protocol:
Up to 100,000 cells were FACS sorted into RLT lysis buffer (Qiagen) supplemented with 14mM ß-mercaptoethanol. Cells were vortexed immediately after being sorted to ensure cell lysis. RNA was extracted using the RNeasy Micro kit (Qiagen) as per manufacturer’s instructions, with an additional DNA clean-up step using RNase-free DNase I (Qiagen)
Sequencing was performed on a NovaSeq 600 System (Illumina) to yield an average of 30 million reads per sample

treatment_protocol: OP9 cells were seeded into tissue-culture treated 24-well plates at 2 x 104 cells per well and incubated overnight at 37˚C. The next day, following monocyte isolation, cells were counted, and 1 x 105 monocytes were seeded on to OP9 cells. Cells were cultured at 37˚C, 5% CO2. The medium was partially replaced on day 2 of culture and completely replaced on day 3, and cells were harvested on day 6.

value: bone marrow

value: monocyte co-cultured with OP9 cell line


title: seedlings, Col-0_Mock_Rep3

value: Mock


title: FLX1, DMSO, rep1 [A1]


title: iCLIP-Seq of KLF13, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: seedlings, Col-0_Mock_Rep2


title: T24, siYY1, biol rep 3 (Y3)

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 further treated with scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster, resulting in 65,536 clusters. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated. Duplicate consensus sequences were removed and used for standard RNA-seq analysis. They were mapped to the human genome (assembly GRCh38) using STAR software (Version 2.5.3) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor), and then RPKMs were calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts or RPKM values for each Sample

value: Bladder cancer

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: YY1 knockdown

value: Use siYY1


title: GMCSF+TGFb+IL34+Jag1+FICZ, replicate 3


title: iCLIP-Seq of m6A, replicate 1

value: WT

value: Total RNA was extracted using Trizol (Invitrogen catalogue number 15596018) and after overnight incubation with m6A antibody, RNA was crosslinked to the antibody using UV.

value: anti-m6A (MBL RN131P)


title: seedlings, Col-0_Mock_Rep1

value: seedlings


title: T24, siYY1, biol rep 1 (Y1)


title: GMCSF+TGFb+IL34, replicate 1


title: DMSO,replicate 2, scRNAseq

description: 10X Genomics

value: bladder cancer

value: DMSO


title: GMCSF+TGFb+IL34+Jag1, replicate 3

description: AA48_Jag_2_EKRN230028516-1A_HV5N5DSX5_L3


title: Size-matched input for ZNF677 iCLIP-Seq

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF677 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: Size-matched input for ZNF148 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF148 ORF under CMV promoter.


title: T24, siYY1, biol rep 2 (Y2)


title: Size-matched input for ZNF274 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ZNF274 ORF under CMV promoter.


title: GMCSF+TGFb+IL34+FICZ, replicate 2

value: bone marrow

value: monocyte co-cultured with OP9 cell line


title: macTSC4_CHIR_minus_day4_rep2

city: Otsu

first: Shoma

last: Matsumoto

state: Shiga

address: Setatsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

data_processing:
The reads were mapped on cynomolgus monkey genome (macFas 5.0) using HISAT2 with a transcript assembly to guide mapping.
Putative transcripts were identified in macTSCs using Stringtie.
Reads from all samples were counted and assigned to genes in the assembled genome model using FeatureCounts.
The count table was loaded into DESeq2 to detect differentially expressed genes.
Gene set enrichment analysis (GSEA) was performed by GSEA v4.0.3 Mac App from Broad Institute.
Assembly: macFas5.0

organism: Macaca fascicularis

growth_protocol: macTSC#2 and #4 were maintained in macTS medium preciously discribed in S. Matsumoto et al (Sci Rep., 2020).

extract_protocol:
Total RNA was extracted using TRI Reagent.
cDNA libraries were constracted by Filgen.

treatment_protocol: macTSC#2 and #4 were cultured with/without CHIR99021 for four days.

value: Trophoblast stem cell

value: without CHIR99021


title: T24, siSQLE, biol rep 3 (S3)

value: Bladder cancer

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: SQLE knockdown

value: Use siSQLE


title: DMSO,replicate 1, scRNAseq

description: 10X Genomics


title: GMCSF+TGFb+IL34+Jag1+FICZ, replicate 2

description: AA47_Jag_3_EKRN230028512-1A_HV5N5DSX5_L3


title: Size-matched input for NXF1 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/NXF1 ORF under CMV promoter.


title: macTSC4_CHIR_plus_day4_rep2

value: WT

value: with CHIR99021


title: T24, siSQLE, biol rep 2 (S2)


title: Size-matched input for KLF14 iCLIP-Seq

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/KLF14 ORF under CMV promoter.


title: macTSC4_CHIR_plus_day4_rep1


title: T24, siSQLE, biol rep 1 (S1)


title: Size-matched input for CBLL1 iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CBLL1 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: macTSC2_CHIR_minus_day4_rep2


title: T24, siFDPS, biol rep 3 (F3)

value: FDPS knockdown

value: Use siFDPS


title: GMCSF+TGFb+IL34+Jag1+FICZ, replicate 1

value: bone marrow

value: monocyte co-cultured with OP9 cell line


title: Size-matched input for ALYREF iCLIP-Seq

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ALYREF ORF under CMV promoter.


title: T24, siFDPS, biol rep 2 (F2)

value: Bladder cancer


title: macTSC2_CHIR_minus_day4_rep1

value: Trophoblast stem cell

value: without CHIR99021


title: macTSC4_CHIR_minus_day4_rep1


title: Size-matched input for ADAR iCLIP-Seq


title: GMCSF+TGFb+IL34+Jag1, replicate 1

description: AA45_Jag_2_EKRN230028506-1A_HV5N5DSX5_L3


title: iCLIP-Seq of CHTOP, replicate 2

description: combined_CITS_0.01_CHTOP.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CHTOP ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: T24, siNC, biol rep 3 (N3)

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: Use siNC


title: T24, siFDPS, biol rep 1 (F1)


title: GMCSF+Jag1, replicate1


title: iCLIP-Seq of CHTOP, replicate 1

value: Human embryonic kidney cells


title: macTSC2_CHIR_plus_day4_rep1

value: WT

value: with CHIR99021


title: macTSC2_CHIR_plus_day4_rep2


title: T24, siNC, biol rep 2 (N2)


title: iCLIP-Seq of CBLL1, replicate 2

description: combined_CITS_0.01_CBLL1.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CBLL1 ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: primary chondrocytes, RPT3

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly Rnor6 (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Rat GTF file:ftp://ftp.ensembl.org/pub/release-89/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.89.gtf.gz
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited text file includes count and FPKM values for each Sample

source_name: cartilage

growth_protocol: primary rat chonrocytes were routinely cultured with DMEM plus 10% FBS, chondrocytes at passage 1 or passage 2 were used for experiments.

extract_protocol:
Chondrocytes were washed with PBS twice after culture medium were removed. RNA was harvested using Trizol reagent and  1 ug of total RNA for the constructionof sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rat chondrocytes were cultured with Rat Serum (RS  group), Rat Plasma  (RP  group), and Rat plasma plus thrombin group (RPT  group).

tag: strain

value: SD

value: cartilage

value: chondrocytes

value: treated with RPT for 24 hours


title: host CD11b+MHCII+

description:
10x genomics
male host CD45.2 C57BL/6
Host
metadata.Host.tsv.gz
normalised_expression.Host.tsv.gz

data_processing:
Generated scRNA-seq data were aligned and quantified using kallisto and bustools to the GRCm38 mouse reference genome.
Downstream QC, batch correction, and Cell Cycle informed scaling was performed using the Seurat package in R.
DoubletFinder was used to identify and remove any likely doublets. These were typically less than 1% of each batch.
Trajectory and Velocity analysis (in metadata) was performed using Slingshot and Velocyto
Assembly: GRCm38
Supplementary files format and content: Single Cell Expression and MetaData (Tab Separated Values)

source_name: epidermis

growth_protocol: BM was extracted from femurs and tibias of donors using a mortar and pestle. Red blood cells were lysed in 1ml of ammonium chloride (ACK buffer) for 1 min at room temperature. Cells were washed and resuspended in complete RPMI (RPMI supplemented with 10% FCS, 1% L-glutamine, 1% Penicillin-streptomycin) until used.

extract_protocol:
Single cell suspensions from murine epidermis were stained for FACS as described above. Donor and host CD11b+MHCII+ cells were sorted into RPMI medium supplemented 2% FCS and counted manually.
Cell concentrations were adjusted to 500-1200 cells/µl and loaded at 7,000-15,000 cells per chip position using the 10x Chromium Single cell 5’ Library, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics, V3 barcoding chemistry) according to manufacturer’s instructions. All subsequent steps were performed following standard manufacturer’s instructions. Purified libraries were analysed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.

value: epidermis

tag: donor/host

value: male host CD45.2

value: donor BMT (Bone Marrow Transplant) into male CD45.2 C57BL/6 mice


title: keratinocyte, replicate2

description:
10x genomics
male host CD45.2 C57BL/6
KCBMTT
metadata.KC.tsv.gz
normalised_expression.KC.tsv.gz

value: CD45neg keratinocytes

value: donor BMT (Bone Marrow Transplant) plus T-cells into male CD45.2 C57BL/6 mice


title: primary chondrocytes, RPT2


title: GMCSF+TGFb+IL34+Jag1, replicate 2

description: AA47_Jag_2_EKRN230028511-1A_HV5N5DSX5_L3

value: bone marrow

value: monocyte co-cultured with OP9 cell line


title: T24, siNC, biol rep 1 (N1)

value: Bladder cancer

value: T24 cell line

value: Human bladder transitional cell cancer cells

value: Use siNC


title: iCLIP-Seq of CBLL1, replicate 1

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/CBLL1 ORF under CMV promoter.

value: anti-GFP (Thermo Fisher Scientific G10362)


title: GMCSF+TGFb+IL34+FICZ, replicate 1


title: primary chondrocytes, RPT1

value: SD

value: cartilage


title: keratinocyte, replicate1

description:
10x genomics
male host CD45.2 C57BL/6
KCBMT
metadata.KC.tsv.gz
normalised_expression.KC.tsv.gz


title: iCLIP-Seq of YTHDF2, replicate 2

description: combined_CITS_0.01_YTHDF2.merged_filtered.bed

value: WT

value: anti-YTHDF2 (Proteintech 24744-1-AP)


title: iCLIP-Seq of ALYREF, replicate 2

description: combined_CITS_0.01_Alyref.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/ALYREF ORF under CMV promoter.

value: Expression was induced with doxycycline (1 μg/ml) 24 hours prior to UV crosslinking.


title: monocyte derived, replicate4

description:
10x genomics
female donor CD45.1 C57BL/6
DMBMTT
metadata.BMT.tsv.gz
normalised_expression.BMT.tsv.gz

value: epidermis

value: female donor CD45.1


title: iCLIP-Seq of YTHDF2, replicate 1


title: monocyte derived, replicate3

description:
10x genomics
female donor CD45.1 C57BL/6
DMBMT
metadata.BMT.tsv.gz
normalised_expression.BMT.tsv.gz

value: donor BMT (Bone Marrow Transplant) into male CD45.2 C57BL/6 mice


title: iCLIP-Seq of REST, replicate 2

description: combined_CITS_0.01_REST.merged_filtered.bed

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/REST ORF under CMV promoter.


title: iCLIP-Seq of ADAR1, replicate 4

description: combined_CITS_0.01_ADAR1.merged_filtered.bed

value: anti-ADAR1 (Abcam ab168809)


title: iCLIP-Seq of ALYREF, replicate 1


title: primary chondrocytes, RS2

value: chondrocytes

value: treated with RS for 24 hours


title: primary chondrocytes, RP3

value: treated with RP for 24 hours


title: anti-PD1,replicate 2, scRNAseq

description: 10X Genomics

value: bladder cancer


title: monocyte derived, replicate2

description:
10x genomics
female donor CD45.1 C57BL/6
DM2
metadata.BMT.tsv.gz
normalised_expression.BMT.tsv.gz


title: iCLIP-Seq of NAT10, replicate 1

description: combined_CITS_0.01_NAT10.merged_filtered.bed

value: Human embryonic kidney cells

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/NAT10 ORF under CMV promoter.


title: primary chondrocytes, RS1

value: SD


title: iCLIP-Seq of REST, replicate 1

value: anti-GFP (Thermo Fisher Scientific G10362)


title: iCLIP-Seq of ADAR1, replicate 3

value: WT


title: monocyte derived, replicate1

description:
10x genomics
female donor CD45.1 C57BL/6
DM1
metadata.BMT.tsv.gz
normalised_expression.BMT.tsv.gz


title: iCLIP-Seq of ADAR1, replicate 1


title: primary chondrocytes, RP2

value: cartilage


title: Size-matched input for YTHDF2 iCLIP-Seq


title: primary chondrocytes, RP1


title: iCLIP-Seq of ADAR1, replicate 2


title: D2(SHAM)

city: Xi'an

first: Yonghong

last: Wu

address: Xinwang Rd, Weiyang District

institute: Xi'an Medical University

description: GEXSCOPE

data_processing:
CeleScope (https://github.com/singleron-RD/CeleScope) v1.1.7 pipeline was used to process raw reads obtained by scRNA-seq which generated gene expression matrixes.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
The samples were rinsed 3 times with Hanks’ Balanced Salt Solution (HBSS, Gibco, Cat. No. 14025-076) and minced into 1-2 mm pieces. Then, the brain pieces were dissociated in 2 ml of GEXSCOPE Tissue Dissociation Solution (Singleron) at 37°C for 15 min under stirring conditions. The cell suspension was transferred to 40-micron sterile strainers (Falcon, Cat. No. 352340) and centrifuged (Eppendorf, 5810R) at 300 × g for 5 min to filter the cells. After the supernatant was aspirated completely, the pellets were resuspended in 1 mL of PBS (HyClone, Cat. No. SA30256.01). To destroy red blood cells, 2 mL of RBC lysis buﬀer (Roche, Cat. No. 11 814 389 001) was added to the suspension following the protocol supplied by the manufacturer. The cell suspension was transferred into a microfuge tube, centrifuged again at 500 × g for 5 min at 15-25°C, and then resuspended in PBS.
Single cell RNA-seq libraries were constructed  using the GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies) according to the manufacturer’s instructions.

value: brain

value: Sham operation


title: model-1(MCAO)

description: GEXSCOPE

value: Ischemia-reperfusion model with thread plug method


title: KOBK2

status: Public on Sep 07 2024

city: Hangzhou

first: Di

address: Yuhgang Tang Rd No.866

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw reads were processed through quality control and genome mapping and further analyzed by the DESeq2 package (1.30.1). Differential expressed genes were determined with a cutoff of FDR smaller than 0.05. Normalized transcripts per million values (TPM) were used to plot heatmap using pheatmap package (1.0.12).
none provided by the submitter

source_name: mice primary bone marrow-derived macrophages

growth_protocol: BMDMs were cultured with DMEM supplemented with 10% FBS, 1% AA.

extract_protocol:
Total RNA was extracted with RNA extraction kit following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary BMDMs from C57B6J mice were treated with B16F10 tumor cells conditioned medium supplemented with/without KCl or NaCl for 6 hours, and the final KCl and NaCl concentration was 40mM.

value: Treated with B16F10 TCM + KCl (Isotonic)


title: KOBK1


title: primary chondrocytes, RS3


title: KOBK3


title: WTBK1


title: WTBK2


title: WTNA2

value: Treated with B16F10 TCM + NaCl


title: WTNA1


title: WTK3

value: Treated with B16F10 TCM + KCl


title: WTK2


title: WTB3

value: Treated with B16F10 TCM


title: WTK1


title: WTB2


title: WTB1


title: WTNC3

value: Control group