title: H4VOE_H4V_ChIP_normal_Rep1

data_processing:
The reads obtained were trimmed using cutadapt and aligned to IRGSP rice genome with parameters -q -v 1 -k 1 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 5bp bin size.
Assembly: Oryza sativa japonica Nipponbare genome – IRGSP1
Supplementary files format and content: The coverage files of the ChIP seq alignments were provided in bigwig format.

source_name: 20d old seedlings

growth_protocol: For seedlings, seeds were germinated on half-strength Murashige-Skoog medium with 0.3% Phytagel. Germinated seedlings were kept in dark for 5 days and then grown in growth chamber with 16h light and 8h dark day-night cycles for 15 days.

extract_protocol:
Sheared chromatin from the equally developed pre emerged panicle of WT and kd plants were incubated with appropriate antibodies bound to Protein G Dynabeads (Thermo Fisher, catalog number 10003D).  Washes, elution, de-crosslinking and DNA purification was done as described. The purified DNA was taken for library preparation.
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. For paired end reads, the adapters used were AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (mate1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (mate2). The sequencing was done on a Illumina platform.

value: seedlings

tag: chip antibody


title: Wild type DBA/2J 28 weeks

status: Public on Feb 09 2025

type: SRA

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

description: Library name: WT28

library_source: transcriptomic single cell

data_processing:
Generated FASTQ files were mapped to mouse (mm10) transcriptome references provided by 10x Genomics using Cell Ranger v6.0.0.
Assembly: mm10
Supplementary files format and content: tsv, mtx

molecule: polyA RNA

organism: Mus musculus

source_name: hindlimb muscle

extract_protocol:
All muscle samples were processed and snRNA-seq data generated by GENINUS (Seoul, Republic of Korea). After the frozen tissue was homogenized and nuclei were counted, the nuclei were isolated using flow cytometry. Single-cell capture, barcoding and library preparation were performed following the 10x Genomics Single cell Chromium 3’ protocols (V3: CG000183).
cDNA library quality was determined using an Agilent Bioanalyzer. Paired-end 200 bp reads were generated on an Illumina NovaSeq6000.

tag: tissue

value: hindlimb muscle

tag: cell type

value: muscle

tag: treatment

value: no treatment


title: N59903, Input

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

country: China

institute: Sun Yat-sen University

library_source: transcriptomic

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using fastp.
We used HISAT2 to map reads to the genome of Homo sapiens (Version: V90) with default parameters. Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software.
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house. Called peaks were annotated by intersection with gene architecture using ChIPseeker. Then, StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM.
Genome_build: GRCh38 (V90)
Supplementary_files_format_and_content: peak files (xlsx)

molecule: total RNA

organism: Homo sapiens

source_name: tumor-adjacent normal tissue from colorectal cancer patients

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was ~100±50 bp. we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.
MeRIP-seq

tag: individual

tag: disease state

value: colorectal cancer

value: normal

tag: rip antibody

tag: Sex

value: female

tag: age


title: D2mdx 7 weeks with steroid

description: Library name: DMD7s

value: deflazacort


title: D2mdx 28 weeks with steroid

description: Library name: DMD28s


title: h4v_sdlng_salt_Rep1

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome (IRGSP1) using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Tab delimited text files including FPKM for all the genes in the experimental samples.

organism: Oryza sativa

source_name: 20d old Seedlings

growth_protocol: For collecting mature leaves, the plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius. For seedlings, seeds were germinated on half-strength Murashige-Skoog medium with 0.3% Phytagel. Germinated seedlings were kept in dark for 5 days and then grown in growth chamber with 16h light and 8h dark day-night cycles for 15 days

extract_protocol:
Total RNA was isolated from tissues mentioned. RNA was extracted using TRIzol reagent following manufaturer’s protocol.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT and transgenic lines were handled in the same manner. For salt stress treatment, all conditions were followed exactly as described for seedlings growth except that media contained 120mM of sodium chloride.

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)

value: Seedlings

value: 20d old

value: salt

tag: genotype


title: 100 Tail_experimental

type: genomic

city: Baltimore

first: Caitlin

last: Bowen

address: 1800 Orleans

country: USA

institute: Johns Hopkins

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Genomic DNA extracted from tail was genotyped using GIGA-Muga Array (Illumina)

label: Cy5, Cy3

molecule: genomic DNA

source_name: Tail

label_protocol: Standard Illumina Protocol

extract_protocol: Extraction of genomic DNA from fresh tissue was performed using phenol-chloroform extraction.

value: Female

tag: group


title: 86 Tail_experimental


title: OE_CHMR_leaf_Rep2

source_name: Mature leaf

value: leaf

value: Mature


title: T61521, IP

source_name: primary tumor tissue from colorectal cancer patients

value: tumor

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)

value: male


title: D2mdx 28 weeks

description: Library name: DMD28

value: hindlimb muscle

value: muscle


title: 33 Tail_experimental


title: OE_CHMR_leaf_Rep1


title: WT_LN1_Clean_Data

city: Shenzhen

first: Bingxin

last: Guo

address: No. 1088 Xueyuan Avenue, Nanshan District Shenzhen

institute: Southern University of Science and Technology

description: Library name: WT_LN1_Clean_Data

data_processing:
Raw sequencing data were trimmed using Trimmomatic, followed by aligning reads to a reference genome with Bowtie2. Differential analysis is performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

growth_protocol: BMDM were maintained in DMEM supplemented with10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
Total RNA from BMDMs was extracted using Trizol/chloroform/isopropanol precipitation.
Fast RNA-seq Lib Prep Kit V2

value: Bone marrow

tag: cell line

value: BMDM

value: Macrophage

value: BMDM cells from Mettl3fl/fl mice were stimulated overnight with LPS (50 ng/ml), and then incubated with nigericin (10 μM) for 3 h.


title: D2mdx 7 weeks with GSK126

description: Library name: GP


title: T71860, IP

value: colorectal cancer


title: 70 Tail_experimental


title: H4VOE_H4V_ChIP_normal_Rep2

library_source: genomic

value: Indica

value: Pusa Basmati 1 (PB1)

value: seedlings

value: normal


title: 25 Tail_experimental

value: Female


title: T72190, IP


title: H4VOE_H4K5Ac_ChIP_normal_Rep2

value: 20d old


title: OE_H4C_leaf_Rep2

value: leaf

value: Mature


title: OE_H4C_leaf_Rep1


title: T59903, IP

value: tumor

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)

value: female


title: Wild type DBA/2J 7 weeks

description: Library name: WT7

value: hindlimb muscle

value: muscle

value: no treatment


title: 42 Tail_experimental


title: 26 Tail_experimental


title: OE_H4V_leaf_Rep2


title: WT_CC1_Clean_Data

description: Library name: WT_CC1_Clean_Data

value: Bone marrow

value: BMDM

value: Macrophage

value: BMDM cells from Mettl3fl/fl mice were stimulated with PBS


title: KO_LN2_Clean_Data

description: Library name: KO_LN2_Clean_Data

value: BMDM cells from Lyz2-Cre-Mettl3fl/fl mice were stimulated overnight with LPS (50 ng/ml), and then incubated with nigericin (10 μM) for 3 h.


title: T73568, IP

value: colorectal cancer


title: WT_CC2_Clean_Data

description: Library name: WT_CC2_Clean_Data


title: 47 Tail_experimental


title: 6 Tail_Control


title: N71040, IP

value: normal


title: N71860, IP

value: male


title: N72190, IP


title: OE_H4V_leaf_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)


title: 5 Tail_Control

value: Male


title: WT_LN2_Clean_Data

description: Library name: WT_LN2_Clean_Data

value: BMDM cells from Mettl3fl/fl mice were stimulated overnight with LPS (50 ng/ml), and then incubated with nigericin (10 μM) for 3 h.


title: KO_LN1_Clean_Data

description: Library name: KO_LN1_Clean_Data


title: healthy individual 3

city: guangdong

first: wenzhen

last: he

address: 57 Changping Road, Shantou, Guangdong

institute: First Affiliated Hospital of Shantou University Medical College

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: brain

extract_protocol:
HiSeq RNA-Seq
RNA libraries were prepared for sequencing using standard illumina protocol

value: blood

tag: disease

value: healthy


title: N73568, IP

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)

value: female


title: N61521, IP


title: WT_leaf_Rep1

value: leaf

value: Mature

value: WT


title: KO_CC2_Clean_Data

description: Library name: KO_CC2_Clean_Data

value: Bone marrow

value: BMDM

value: Macrophage

value: BMDM cells from Lyz2-Cre-Mettl3fl/fl mice were stimulated with PBS


title: WT_sdlng_Rep2

value: Seedlings

value: 20d old

value: normal


title: large-artery atherosclerotic ischemic stroke patient 3


title: healthy individual 2


title: large-artery atherosclerotic ischemic stroke patient 2


title: RAW-DMSO-2h

city: Beijing

first: Xuefei

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description:
Library name: Sample 17
RAW 264.7 cells were collected for total RNA extraction with DMSO treatment for 2 hours.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The DESeq2 software was used to identify the differantially expressed genes (DEGs).
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: CSV file includes the FPKM value for each sample.

source_name: cell line

growth_protocol: RAW 264.7 were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent (TIANGEN). 1.5 ug of total RNA was used for the construction of sequencing libraries.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: RAW 264.7 macrophages were treated with DMSO, LPS, LPS-Co68, and Co68 for durations of 1, 2, and 3 hours, respectively.

value: cell line

value: macrophages


title: healthy individual 1


title: RAW-DMSO-3h

description:
Library name: Sample 18
RAW 264.7 cells were collected for total RNA extraction with DMSO treatment for 3 hours.


title: KO_CC1_Clean_Data

description: Library name: KO_CC1_Clean_Data


title: WT_sdlng_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)


title: h4v_sdlng_Rep1


title: h4v_sdlng_Rep2


title: WT_H4V_ChIP_Salt_Rep2

value: seedlings

value: Salt


title: RAW-LPS-Co68-2h

description:
Library name: Sample 14
RAW 264.7 cells were collected for total RNA extraction with LPS and Co68 treatment for 2 hours.


title: RAW-DMSO-1h

description:
Library name: Sample 16
RAW 264.7 cells were collected for total RNA extraction with DMSO treatment for 1 hour.


title: small-artery occlusion ischemic stroke patient 1

value: blood


title: RAW-LPS-Co68-1h

description:
Library name: Sample 13
RAW 264.7 cells were collected for total RNA extraction with LPS and Co68 treatment for 1 hour.


title: large-artery atherosclerotic ischemic stroke patient 1


title: cysts, evaginated, TA-, 120h, replicate 1

city: Lima

first: Cristina

last: Guerra-Giraldez

state: Lima

address: Honorio Delgado 430

department: Facultad de Ciencias e Ingeniería

country: Peru

institute: Universidad Peruana Cayetana Heredia

description: Library name: POST_SAT_1

data_processing:
Removal of Illumina adapter sequences and trimming of reads with a phred+33 quality score below 20 was done using BBDuk (BBMap version 38.90)
Reads were mapped to the Taenia Solium genome (assembly GCA_001870725.1)  using the default settings of RSubread (version 2.17.4)
Gene abundance was calculated with GenomicFeatures (v. 1.52.1) using predicted gene annotations available in the WormBase ParaSite database (version WBPS18)
Differential expression analysis was performed using a generalized linear model that assumes a negative binomial distribution of count data, implemented by DESeq2 (v.1.40.2)
Assembly: GCA_001870725.1
Supplementary files format and content: csv file includes raw counts for all samples

organism: Taenia solium

source_name: whole cyst

growth_protocol: Cysts arrived at the laboratory approximately 16 hours after collection and were washed three times with transport solution before in vitro culture. Following shipment, most cysts retained their characteristics, appearing as intact, white, or translucent oblong vesicles filled with clear fluid and without atypical coloration. The cysts were then allocated for different purposes, with 84 selected for the present study. Twelve cysts were washed in 1 mL of RNAlater® solution (R-0901, Sigma Aldrich) and stored at -20°C for RNA extraction and gene transcription analysis. These ex vivo cysts were classified as non-cultured (NC). The remaining 72 cysts were incubated individually in 1.5 mL of filtered, sterilized RPMI 1640 medium (pH 7.4), supplemented with 2 g/mL NaHCO₃ (Merck®, Burlington, MA), 1.6 µM β-mercaptoethanol, and Gibco™ Antibiotic-Antimycotic at the previously described concentrations. Each cyst was placed in a separate well of three Costar® 24-well culture plates (Corning®, Corning, NY, USA) and maintained at 37°C with 5% CO₂ in a sterile incubator (VWR Symphony Incubator) for up to five days. The culture medium was replaced every 24 hours.

extract_protocol:
RNA was extracted from 12 samples (cysts) of each of the seven groups (NC, PRE TA+, PRE TA-, EV TA+, EV TA-, POST TA+, POST TA-; n=84 cysts) using the Quick-RNA Miniprep Plus Kit (Zymo Research, R1058). Briefly, samples were independently embedded in 600 µL of DNA/RNA Shield (Zymo Research, R1058) and admixed with a tissue homogenizer tip (Omni International, Kennesaw, GA) on ice, followed immediately by a 30-min treatment with 60 mg of Proteinase K (Zymo Research, D3001-2-60). RNA was isolated following the manufacturer’s protocol, with an extra washing step with 400 µL of RNA Wash Buffer (Zymo Research, R1058) before final RNA isolation. The protocol included DNAse I treatment (Zymo Research, E1009-A (250 U)). As recommended by the manufacturer, a mix of 5 µL of DNase I (1 U/µL) and 75 µL of DNA Digestion Buffer (Zymo Research, R1058) was added directly to the silica column matrix (Zymo-Spin™ IIICG Columns) containing processed samples, for a 15-min incubation at room temperature (20-30°C).
A total of 21 libraries were constructed, three for each one of the seven groups (NC, PRE TA+, PRE TA-, EV TA+, EV TA-, POST TA+, POST TA-). Each library was made from four cysts, pooling 125 ng each of independently extracted RNA, for a total of 500 ng/library. Following the manufacturer's instructions, the Illumina® Stranded mRNA Prep Ligation Kit (Illumina, 20040532) was used to construct libraries indexed with the IDT for Illumina RNA Unique dual (UD) Indexes. Briefly, polyA selection for ribosomal RNA depletion was performed using Oligo(dT) RNA purification magnetic beads (RPBX, Illumina, 20040532). Fragmentation of purified mRNA, cDNA synthesis of the first and second strands, and ligation of the Illumina RNA UD Indexes Set A followed. Thirteen PCR cycles were performed for library amplification.

treatment_protocol: Half of the cultured cysts (36/72) were exposed to 0.1% taurocholic acid (TA) (Sigma, St. Louis, MO, USA), creating two experimental groups: TA+ and TA-. Cysts were collected at three distinct time points based on their evagination stage. Pre-evagination (PRE TA+ and PRE TA-) included cysts with a non-evaginated scolex after 6 hours in vitro, while recent evagination (EV TA+ and EV TA-) corresponded to cysts with a newly exposed scolex, typically observed after 24-48 hours in vitro. Finally, post-evagination (POST TA+ and POST TA-) consisted of fully evaginated cysts displaying initial proglottid formation, collected between 48-120 hours in vitro. Following culture, all parasites were washed with 1X PBS to remove residual media and preserved at -20°C in 1 mL of RNAlater® solution for RNA extraction and gene transcription analysis. Evagination curves were generated over a 240-hour in vitro period.

value: whole cyst


title: N59903, IP

value: colorectal cancer

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)

value: female


title: cysts, evaginated, TA+, 120h, replicate 1

description: Library name: POST_AT_1


title: cysts, evaginated, TA+, 120h, replicate 3

description: Library name: POST_AT_3


title: small-artery occlusion ischemic stroke patient 2


title: cysts, evaginated, TA-, 120h, replicate 2

description: Library name: POST_SAT_2


title: WT_H4V_ChIP_normal_Rep3

value: WT


title: small-artery occlusion ischemic stroke patient 3


title: cysts, evaginated, TA-, 120h, replicate 3

description: Library name: POST_SAT_3


title: WT_leaf_Rep2

value: leaf

value: Mature


title: WT_H4V_ChIP_Salt_Rep1


title: RAW-LPS-3h-2

description:
Library name: Sample 12
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 3 hours. (replication 2)


title: cysts, evaginated, TA+, 24-48h, replicate 3

description: Library name: EV_AT_3


title: cysts, evaginated, TA+, 120h, replicate 2

description: Library name: POST_AT_2


title: RAW-LPS-Co68-3h

description:
Library name: Sample 15
RAW 264.7 cells were collected for total RNA extraction with LPS and Co68 treatment for 3 hours.


title: RAW-LPS-3h-1

description:
Library name: Sample 11
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 3 hours. (replication 1)


title: NHK 601 PMC

city: Frankfurt am Main

first: Magdalena

last: Jahn

address: Theodor-Stern-Kai 7

country: Germany

institute: University Hospital Frankfurt

description: Library name: Sample_601_PMC

data_processing:
Reads were trimmed with Trimmomatic 0.39.
Trimmed reads were aligned to the hg19 reference genome using Hisat2 (2.2.1)
Output files were sorted using SAMtools (1.10)
Reads were counted with HTSeq (1.99.2)
Counts were normalized using DESeq2 (1.32.0)
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw-counts for each sample

source_name: primary keratinocytes

growth_protocol: Primary keratinocytes were isolated from human juvenile foreskin or various adult body regions after skin reduction surgery. Cells were cultivated in KGM-2 (PromoCell)

extract_protocol:
RNA was isolated using NucleoSpin RNA isolation kit (Macherey-Nagel). 500 ng total RNA was used to prepare the library
RNA-libraries were prepared with the TruSeq RNA Library Prep Kit v2 from Illumina

treatment_protocol: Culture plates were coated with 100 µg/ml collagen IV from human placenta for 2h at 37°C or at least 24h at 4°C. Cells attaching within 5 min at 37°C were considered keratinocyte stem cells (KSC). Non-attached cells were transferred into another coated well, cells attached overnight were regarded as transiently amplifying cells (TAC), while cells not attaching were considered as being post-mitotic cells (PMC). Non-separated cells (all) were cultivated in non-coated plates.

value: primary keratinocytes

value: no attachment collagen IV


title: WT_H4V_ChIP_normal_Rep2

value: 20d old

value: normal


title: NHK 601 TAC

description: Library name: Sample_601_TAC

value: attachment to collagen IV, overnight


title: RAW-LPS-2h-2

description:
Library name: Sample 10
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 2 hours. (replication 2)

value: cell line

value: macrophages


title: WT_H4V_ChIP_normal_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)

value: seedlings


title: NHK 601 KSC

description: Library name: Sample_601_KSC

value: attchment to collagen IV, 5 min


title: cysts, evaginated, TA+, 24-48h, replicate 1

description: Library name: EV_AT_1

value: whole cyst


title: cysts, evaginated, TA+, 24-48h, replicate 2

description: Library name: EV_AT_2


title: WT_H4K5Ac_ChIP_Salt_Rep2

value: Salt


title: RAW-LPS-2h-1

description:
Library name: Sample 9
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 2 hours. (replication 1)


title: NHK 601 all

description: Library name: Sample_601_all


title: RAW-LPS-1h-2

description:
Library name: Sample 8
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 1 hour. (replication 2)


title: cysts, evaginated, TA-, 24-48h, replicate 3

description: Library name: EV_SAT_3


title: RAW-LPS-1h-1

description:
Library name: Sample 7
RAW 264.7 cells were collected for total RNA extraction with LPS treatment for 1 hour. (replication 1)


title: cysts, evaginated, TA-, 24-48h, replicate 2

description: Library name: EV_SAT_2


title: WT_H4K5Ac_ChIP_Salt_Rep1


title: NHK 595 PMC

description: Library name: Sample_595_PMC


title: WT_H4K5Ac_ChIP_normal_Rep2


title: WT_H4K5Ac_ChIP_normal_Rep1


title: cysts, evaginated, TA-, 24-48h, replicate 1

description: Library name: EV_SAT_1


title: WT_H4C_ChIP_normal_Rep1


title: NHK 595 TAC

description: Library name: Sample_595 TAC


title: RAW-Co68-3h-1

description:
Library name: Sample 5
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 3 hours. (replication 1)


title: cysts, non-evaginated, TA+, 6h, replicate 3

description: Library name: PRE_AT_3


title: cysts, non-evaginated, TA+, 6h, replicate 2

description: Library name: PRE_AT_2


title: NHK 595 KSC

description: Library name: Sample_595_KSC


title: RAW-Co68-3h-2

description:
Library name: Sample 6
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 3 hours. (replication 2)


title: cysts, non-evaginated, TA+, 6h, replicate 1

description: Library name: PRE_AT_1


title: cysts, non-evaginated, TA-, 6h, replicate 3

description: Library name: PRE_SAT_3


title: RAW-Co68-1h-2

description:
Library name: Sample 2
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 1 hour. (replication 2)


title: H4VOE_H4K5Ac_ChIP_normal_Rep1


title: NHK N10 PMC

description: Library name: Sample_N10_PMC


title: h4vko_H4V_ChIP_normal_Rep2


title: cysts, non-evaginated, TA-, 6h, replicate 2

description: Library name: PRE_SAT_2


title: NHK N10 KSC

description: Library name: Sample_N10_KSC


title: h4vko_H4K5Ac_ChIP_Salt_Rep2


title: RAW-Co68-2h-1

description:
Library name: Sample 3
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 2 hours. (replication 1)


title: h4vko_H4V_ChIP_normal_Rep1


title: RAW-Co68-1h-1

description:
Library name: Sample 1
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 1 hour. (replication 1)


title: NHK N9 PMC

description: Library name: Sample_N9_PMC


title: RAW-Co68-2h-2

description:
Library name: Sample 4
RAW 264.7 cells were collected for total RNA extraction with Co68 treatment for 2 hours. (replication 2)


title: RAW-LPS-Co68

description:
Library name: Sample 3
RAW 264.7 cells were collected for ATAC-seq with LPS and Co68 treatment for 1 hour.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to mouse mm10 genome using Bowtie2, which produced the BAM type file directly.
The peaks was called using MACS3 software.
Then the peaks was annotated by the ChIPseeker R package.
The TOBIAS software was used to perform the footprint analysis.
Assembly: UCSC mm10 genome was used as reference genome.
Supplementary files format and content: narrowPeak file includes the peaks was identified for each sample.
Supplementary files format and content: bw file includes the peaks signal intensity for each sample.

extract_protocol:
Total DNA was extracted using ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711)  for library following the manufacturer’s recommendations.
ATAC-seq library for sequencing was generated using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, TD711) following the manufacturer’s recommendations

treatment_protocol: RAW 264.7 were treated with by DMSO, LPS, LPS-Co68 and Co68 for 1 hour.

value: LPS and Co68 treatment for 1h


title: NHK N10 TAC

description: Library name: Sample_N10_TAC

value: WT


title: NHK N10 all

description: Library name: Sample_N10_all


title: h4vko_H4K5Ac_ChIP_Salt_Rep1


title: h4vko_H4K5Ac_ChIP_normal_Rep2


title: NHK 595 all

description: Library name: Sample_595_all


title: cysts, non-evaginated, TA-, 6h, replicate 1

description: Library name: PRE_SAT_1


title: cysts, non-cultured, replicate 3

description: Library name: NC3


title: DRG: AAV MEF2 rep 3

status: Public on Feb 08 2025

city: Amsterdam

first: Matthew

last: Mason

address: Meibergdreef 47

department: Neuroregeneration

country: Netherlands

institute: Netherlands Institute for Neuroscience

data_processing:
Image analysis, base-calling and quality check were performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Reads were aligned to a composite sequence comprised of the rat genome plus transgene and other viral vector elements, using TopHat v2.1.1 with option transcriptome-only. Gene counts were dervied using featureCounts with multimapping and fractional counts enabled
Assembly: Rnor6.0
Supplementary files format and content: Raw gene counts

organism: Rattus norvegicus

source_name: L4/L5 dorsal root ganglia

extract_protocol:
DRG were cryosectioned at 20µm thickness onto polyethylene-naphtalate (PEN) membrane slides. Sections were briefly dehydrated and then laser dissected using a PALM MicroBeam (Carl Zeiss, Germany) and PALM Robosoftware. Large diameter (>40µm) neurons labelled with fluorophore/ tracer were dissected and catapulted into an adhesive cap. An average of 184 neurons per animal were collected. Trizol Reagent was added to the samples. To isolate RNA, chloroform extraction was performed and then the RNeasy® Micro Kit (QIAGEN, Germany) was used following an adapted version of the manufacturer’s protocol. RNA quality numbers, determined by Fragment Analyzer, were in the range 5.5-8.1.
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used, following the manufacturer's protocol (NEB #E7420S/L), in conjunction with ribosomal RNA depletion.

value: L4/L5 dorsal root ganglia

value: Transduction with AAV vector expressing MEF2/GFP

tag: time

value: 28 days


title: cysts, non-cultured, replicate 2

description: Library name: NC2


title: RAW-DMSO

description:
Library name: Sample 2
RAW 264.7 cells were collected for ATAC-seq with DMSO treatment for 1 hour.

value: DMSO treatment for 1h


title: h4vko_H4K5Ac_ChIP_normal_Rep1

value: 20d old


title: NHK N9 KSC

description: Library name: Sample_N9_KSC

value: primary keratinocytes


title: NHK N9 TAC

description: Library name: Sample_N9_TAC

value: attachment to collagen IV, overnight


title: NHK N9 all

description: Library name: Sample_N9_all


title: DRG: AAV ATF3/KLF7/MEF2 rep 1

value: Transduction with 3 AAV vectors expressing KLF7/mCherry, MEF2/GFP and ATF3/mitoYFP


title: DRG: AAV KLF7 rep 3

value: Transduction with AAV vector expressing KLF7/mCherry


title: RAW-LPS

description:
Library name: Sample 4
RAW 264.7 cells were collected for ATAC-seq with LPS treatment for 1 hour.

value: macrophages

value: LPS treatment for 1h


title: RAW-Co68

description:
Library name: Sample 1
RAW 264.7 cells were collected for ATAC-seq with Co68 treatment for 1 hour.

value: Co68 treatment for 1h


title: h4vko_H4C_ChIP_normal_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)

value: seedlings

value: normal


title: cysts, non-cultured, replicate 1

description: Library name: NC1

value: whole cyst


title: DRG: AAV MEF2 rep 4 (excluded)

value: L4/L5 dorsal root ganglia

value: Transduction with AAV vector expressing MEF2/GFP (excluded)


title: DRG: AAV MEF2 rep 2

value: Transduction with AAV vector expressing MEF2/GFP

value: 28 days


title: DRG: AAV ATF3 rep 4

value: Transduction with AAV vector expressing ATF3/mitoYFP


title: DRG: AAV ATF3 rep 3


title: DRG: AAV MEF2 rep 1


title: DRG: AAV GFP rep 4

value: Transduction with AAV vector expressing GFP


title: DRG: AAV KLF7 rep 4


title: DRG: AAV ATF3 rep 2


title: DRG: AAV ATF3/KLF7/MEF2 rep 4


title: DRG: AAV ATF3 rep 1


title: DRG: AAV GFP rep 3


title: DRG: AAV ATF3/KLF7/MEF2 rep 3


title: DRG: AAV ATF3/KLF7/MEF2 rep 2


title: DRG: AAV KLF7/MEF2 rep 2

value: Transduction with 2 AAV vectors expressing KLF7/mCherry and MEF2/GFP


title: DRG: sciatic nerve injury, 7 days rep 4

value: Sciatic nerve injury

value: 7 days


title: DRG: sciatic nerve injury, 7 days rep 1


title: DRG: sciatic nerve injury, 1 days rep 4

value: 1 day


title: DRG: sciatic nerve injury, 1 days rep 3


title: DRG: AAV KLF7 rep 2

value: Transduction with AAV vector expressing KLF7/mCherry


title: DRG: sciatic nerve injury, 1 days rep 2


title: DRG: sciatic nerve injury, 1 days rep 1


title: DRG: AAV KLF7 rep 1


title: DRG: AAV KLF7/MEF2 rep 4


title: DRG: AAV GFP rep 1


title: DRG: AAV GFP rep 2


title: Mus musculus,FA4_IP RNA

city: Zhengzhou

first: Linxiao

last: Lv

address: Longhu Central Ring Road No.1

institute: the first affiliated hospital of Zhengzhou university

description: Library name: FA4_IP

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/). Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome Mus musculus (Version: v101). Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
Assembly: Mus musculus (Version: v101)
Supplementary files format and content: 1_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)

source_name: kidney

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000, and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: kidney


title: DRG: AAV KLF7/MEF2 rep 1


title: DRG: AAV KLF7/MEF2 rep 3


title: Mus musculus,FA1_input RNA

description: Library name: FA1_input


title: DRG: sciatic nerve injury, 7 days rep 3


title: Mus musculus,control4_input RNA

description: Library name: control4_input


title: DRG: sciatic nerve injury, 7 days rep 2


title: DRG: Naive, 0 days rep 4

value: Naive


title: Mus musculus,control2_input RNA

description: Library name: control2_input


title: DRG: Naive, 0 days rep 1


title: Mus musculus,control1_input RNA

description: Library name: control1_input


title: DRG: Naive, 0 days rep 2


title: Crypts, NT

city: Shanghai

first: Guoying

last: Zhang

address: 320 Yueyang Road

institute: SHANGHAI INSTITUTE OF NUTRITION AND HEALTH. CAS

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed  using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). For dimension reduction, we employed Uniform Manifold Approximation and Projection (UMAP) algorithm. The resulting measurements yielded an average of 3698.5 cells per sample, totaling 7397 cells, with an average detection of 3443 genes per cell.
Assembly: mm10
Supplementary files format and content: features, barcodes and matrix files for all samples

source_name: Intestine

extract_protocol:
Single-cell RNA-sequencing (scRNA-seq) including paired intestinal crypt samples from NT and ES mice. Duodenal crypts were isolated through a meticulous procedure involving longitudinal opening of the duodenum, cold DPBS washing, and a 30-minute incubation with 5 mM EDTA on ice. Following this, crypts were mechanically separated from the intestinal tissue, filtered through a 70 µm mesh into a 50 mL tube for isolation from villus. To achieve a single-cell suspension, crypts were dissociated into individual cells using Tryple Express (GIBCO) for 5min and filtered through a 40 µm mesh. Subsequently, 5 animals per condition were pooled to minimize sample variation.
The scRNA-seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 30 V3 Reagent Kits (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. The experiments were performed by NovelBio Bio-Pharm Technology Co.,Ltd.

value: Intestine

value: Crypts

value: NT


title: DRG: Naive, 0 days rep 3


title: Mus musculus,FA4_input RNA

description: Library name: FA4_input


title: Mus musculus,FA3_IP RNA

description: Library name: FA3_IP


title: Mus musculus,FA3_input RNA

description: Library name: FA3_input


title: Mus musculus,FA2_IP RNA

description: Library name: FA2_IP


title: Mus musculus,FA2_input RNA

description: Library name: FA2_input


title: Mus musculus,control4_IP RNA

description: Library name: control4_IP


title: ISCs, NT, Chrm3_WT, rep1

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The read length was 2×150 bp. The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per million mapped reads) using Perl. Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package in R between different groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count  values for NT_WT, NT_KO, ES_WT and ES_KO samples
Supplementary files format and content: tab-delimited text files include count  values for young and old samples

extract_protocol:
RNA was extracted using Trizol purification from Lgr5-positive ISCs, 1µg total RNA was used for the construction of sequencing libraries
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina) following manufacturer's protocols

value: intestinal stem cells

value: WT


title: Mus musculus,control2_IP RNA

description: Library name: control2_IP


title: Mus musculus,control1_IP RNA

description: Library name: control1_IP


title: Mus musculus,control3_input RNA

description: Library name: control3_input


title: ISCs, ES, Chrm3_WT, rep1

value: ES


title: H_M2

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: FPKM values for each Sample

growth_protocol: bEnd.3 endothelial cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNeasy Mini kit ( Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA).
RNA libraries for RNA-seq were prepared using Stranded mRNA-seq Library Prep Kit (Vazyme)following manufacturer's protocols.

treatment_protocol: Sample H_M1-3 were co-incubated with isolated mitochondria reconsituted by 100ul of culture medium; Sample H1-3 were treated with equal amount of culture medium alone.

value: endothelial cells

value: Mitochondrial transplantation


title: Crypts, ES


title: ISCs, old_18month, rep2


title: ISCs, old_18month, rep3


title: ISCs, old_18month, rep1


title: ISCs, young_2month, rep2


title: ISCs, young_2month, rep1


title: ISCs, ES, Chrm3_KO, rep1

value: Chrm3 knockout


title: ISCs, NT, Chrm3_KO, rep2


title: ISCs, young_2month, rep3


title: ISCs, NT, Chrm3_KO, rep1


title: ISCs, ES, Chrm3_WT, rep2


title: CD200R_Ear, Replicate 2, ADT-derived cDNA

city: San Diego

first: Anja

last: Koester

state: CA

address: 10290 Campus Point Dr

department: Immunology Research

institute: Eli Lilly and Company

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
CD200REar-2_barcodes.tsv.gz
CD200REar-2_features.tsv.gz
CD200REar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv

library_source: other

data_processing:
Quantification was done with CellRanger v6.1.2 (10x Genomics) xenograft pipeline against mouse (mm10) and human (HGRC38) genomes.
Only cells derived from the humanized mouse model harboring transcripts that uniquely mapped to the human genome (HGRC38 built) were retained for downstream analysis and cell clustering.
Assembly: HGRC38 / mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: For each unique Feature Barcode used, this file declares a feature name and identifier, the unique Feature Barcode sequence associated with this reagent, and a pattern indicating how to extract the Feature: Antibody_tag_feature_reference.csv
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Ear

growth_protocol: Female huNOG-EXL mice (NOD.Cg-Prkdcscid  Il2rgtm1Sug Tg(SV40/HTLV-IL3, CSF2)10-7Jic/JicTac)  were purchased from Taconic at 20 weeks of age and allowed to acclimate for > 1 week.  Mice were housed 4/cage at 72º C under a 12h light:dark cycle and allowed food and water ad libitum.

extract_protocol:
Both ears from groups of 2-3 mice within the same treatment group were pooled together into two biological replicates for digestion using the Multi Tissue Dissociation Kit 1 (Milenyi) according to manufacturer’s recommendations in the Dissociation of mouse Ear protocol. The resulting single cell suspensions were incubated in Cell Staining Buffer (BioLegend) containing Human TruStain FcX (BioLegend) on ice for 15 minutes protected from light prior to addition of Live/Dead Fixable Near-IR (Invitrogen), AlexaFluor700-conjugated anti-human CD45 (clone 2D1, eBioscience), anti-human CD200R (clone OX-108, BioLegend) that was previously biotinylated using the EZ-Link Sulfo-NHS-LC-Biotin kit (ThermoFisher), and TotalSeq-B conjugated anti-human antibodies (CD20, CD3, CD33, CD4, CD8a, HLA-DR, and CD123, BioLegend) for 30 minutes on ice, protected from light. Cells were washed twice in Cell Staining Buffer prior to incubation with TotalSeq-B-PE-conjugated Streptavidin (BioLegend) diluted in Cell Staining Buffer for 20 minutes on ice and washed twice in Cell Staining Buffer. Cells were diluted in Cell Staining Buffer to 2x10^7 cells/mL (500 uL minimum volume) and collected in RPMI (ThermoFisher) supplemented with 50% FBS (ThermoFisher) using a FACSAria III cell sorter (BD Biosciences). Following cell sorting, if yields were higher than 20, 000 cells, cells were counted and diluted to 1x10^6 cells/mL in DPBS and 10, 000 cells from each sample were loaded onto separate lanes of a Chromium Controller instrument (10x Genomics). For samples with yields lower than 20, 000 cells, the entire sample was loaded onto an individual lane of a Chromium Controller.
The resulting GEMs were processed according to the standard 10x Genomics single cell 3’ v3.1 assay protocol. After library preparation and i7 indexing of individual samples, the final pooled library was comprised of 90% mRNA-derived library and 10% ADT library.

treatment_protocol: On day 0, mice were anesthetized with 5% isoflurane, their abdomens were shaved, and 100 uL of 3% oxazalone in ethanol was applied to the shaved area.  Five days after sensitization LSN3454738 was administered at 1 and 10 mg/kg subcutaneously (SC); LSN2435695 IgG4P isotype was administered at 10 mg/kg SC for comparison.  Four hours after mAb administration, mice were anesthetized with 5% isoflurane, ear thickness was measured with calipers, and ears were challenged with 10 uL of 2% oxazalone in ethanol on each side of both ears.  The challenge procedure was repeated on days 10 and 14.  The hypersensitivity reaction was assessed by measuring the difference between ear thickness pre- and 24hours post-challenges. Ears were harvested one day following the third challenge.

value: Ear

tag: cells

value: Human CD45+ cells isolated from ears of humanized mice

value: Human CD45+

tag: library type

value: ADT

tag: antibodies/tags

value: anti-human CD200R (clone OX-108, BioLegend) that was previously biotinylated using the EZ-Link Sulfo-NHS-LC-Biotin kit (ThermoFisher), and TotalSeq-B conjugated Streptavidin-PE and anti-human antibodies (CD20, CD3, CD33, CD4, CD8a, HLA-DR, CD123, BioLegend).

tag: strain


title: ISCs, ES, Chrm3_KO, rep2

tag: tissue

tag: cell type

tag: treatment


title: Dupilumab_Ear, Replicate 1, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
DupilumabEar-1_barcodes.tsv.gz
DupilumabEar-1_features.tsv.gz
DupilumabEar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv

value: mRNA

value: NOD.Cg-Prkdcscid Il2rgtm1Sug Tg(SV40/HTLV-IL3, CSF2)10-7Jic/JicTac)

value: Dupilumab


title: H3

value: Control


title: H2


title: Isotype_Ear, Replicate2, ADT-derived cDNA

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
IsotypeEar-2_barcodes.tsv.gz
IsotypeEar-2_features.tsv.gz
IsotypeEar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv

value: Human IgG4 Isotype control


title: Isotype_Ear, Replicate1, ADT-derived cDNA

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
IsotypeEar-1_barcodes.tsv.gz
IsotypeEar-1_features.tsv.gz
IsotypeEar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: H1


title: H_M1


title: Dupilumab_Ear, Replicate2, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
DupilumabEar-2_barcodes.tsv.gz
DupilumabEar-2_features.tsv.gz
DupilumabEar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: Dupilumab_Ear, Replicate2, ADT-derived cDNA

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
DupilumabEar-2_barcodes.tsv.gz
DupilumabEar-2_features.tsv.gz
DupilumabEar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: Dupilumab_Ear, Replicate 1, ADT-derived cDNA

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
DupilumabEar-1_barcodes.tsv.gz
DupilumabEar-1_features.tsv.gz
DupilumabEar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: CD200R_Ear, Replicate 1, ADT-derived cDNA

description:
10x Genomics 3' v3.1
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
CD200REar-1_barcodes.tsv.gz
CD200REar-1_features.tsv.gz
CD200REar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: H_M3


title: X7T

first: Jinlong

last: Lin

address: Dongfeng dong road

institute: Sun Yat-sen university cancer center

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: hg19
Supplementary files format and content: all.gene.FPKM.mRNA_processed.txt: Tab-delimited text file includes all FPKM values for each Sample.

source_name: colorectal tumor11

extract_protocol:
RNA was harvested using Trizol.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: colorectal tumor11


title: Isotype_Ear, Replicate1, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
IsotypeEar-1_barcodes.tsv.gz
IsotypeEar-1_features.tsv.gz
IsotypeEar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: Isotype_Ear, Replicate2, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
IsotypeEar-2_barcodes.tsv.gz
IsotypeEar-2_features.tsv.gz
IsotypeEar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: CD200R_Ear, Replicate 1, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
CD200REar-1_barcodes.tsv.gz
CD200REar-1_features.tsv.gz
CD200REar-1_matrix.mtx.gz
Antibody_tag_feature_reference.csv


title: X7pre

source_name: colorectal adenoma11

value: colorectal adenoma11


title: X5pre

source_name: colorectal adenoma10

value: colorectal adenoma10


title: X2800N

source_name: normal colorectal tissue11

value: normal colorectal tissue11


title: X8pre

source_name: colorectal adenoma9

value: colorectal adenoma9


title: OCI-AML2 cells, shControl, Replicate 1

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

description: Library name: Sample 1

data_processing:
Transcript abundance was quantified from RNA-sequencing reads using Salmon (version 1.4.0).
Trimmed sequences were mapped to the human reference genome (GENCODE GRCh38; RRID: SCR_014966) using STAR (RRID:SCR_004463).
Salmon quant.sf files were converted into a count matrix for subsequent gene-level analysis using the tximport pipeline (RRID: SCR_016752; version 1.30.0).
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet; normalised gene expression (using DESeq2 package in R).

source_name: Bone. Marrow

growth_protocol: OCI-AML2 cells were cultured in IMDM prior to extract preparation.

extract_protocol:
Total RNA from control and SOCS1 overexpressed OCI-AML2 cells were isolated using RNeasy Mini Kits (Qiagen), and cDNA was synthesized from the isolated mRNA using QuantiTect Reverse Transcription Kit (Qiagen) in accordance with the manufacturer protocols.
RNA-sequencing libraries were prepared using Illumina Stranded Total RNA prep (ligation with Ribo-zero Plus kit)

value: Bone. Marrow

value: Acute Myeloid Leukemia

value: Scambled Control


title: OCI-AML2 cells, shControl, Replicate 2

description: Library name: Sample 2


title: OCI-AML2 cells, SOCS1 Overexpression, Replicate 1

description: Library name: Sample 3

value: SOCS1 Overexpression


title: N5,Healthy control

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to genome(hg38) using STAR/bowtie2/BWA
circRNAs were identified by CIRI2/CIRCexplorer2/circRNA_cinder/find_circ
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count

source_name: PBMC

extract_protocol:
For PBMC, total RNA was extracted and treated with the RiboZero rRNA Removal Kit. Then, the RNA was fragmented and synthesized cDNA with random primer. Purified the PCR amplification products of cDNA, then the libraries were quality controlled and sequenced.For cell lines, total RNA was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PBMC


title: N6,Healthy control


title: CD200R_Ear, Replicate 2, mRNA-derived cDNA

description:
10x Genomics 3' v3.1
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
CD200REar-2_barcodes.tsv.gz
CD200REar-2_features.tsv.gz
CD200REar-2_matrix.mtx.gz
Antibody_tag_feature_reference.csv

value: Ear

value: Human CD45+ cells isolated from ears of humanized mice

value: Human CD45+


title: HCCLM3 cells,YTHDF2-Input-2

city: tianjin

first: meixi

last: wang

address: Tianjin Sports Institute North Road Huanhu West Road

institute: Tianjin Medical University Cancer Hospital

data_processing:
For RIP-seq, reads were aligned to the UCSC hg38 genome using hisat2. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: For RIP-seq, CSV files inclued peak information for each sample.

source_name: Liver

extract_protocol:
For RIP-seq, RNAs from INPUT and IP were extracted using Magna RIPTM Kit according to the manufacturer’s protocol.
For RIP-seq, RNA libraries were prepared using SMARTer Stranded Total RNA-Seq kit- Pico Input Mammalian following manufacturer’s protocols.

value: Liver

value: Human liver

value: WT


title: N4,Healthy control


title: X3376T

source_name: colorectal tumor10

value: colorectal tumor10


title: HCCLM3 cells, YTHDF2-RIP-2


title: X2536T

source_name: colorectal tumor8

value: colorectal tumor8


title: X3T

source_name: colorectal tumor9

value: colorectal tumor9


title: HCCLM3 cells, YTHDF2-RIP-1


title: X2800T

source_name: colorectal tumor7

value: colorectal tumor7


title: HCCLM3 cells, m6A-RIP

data_processing:
For m6A-seq, reads were aligned to the UCSC hg38 genome using hisat2. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: For m6A-seq, CSV files inclued peak information for each sample.

extract_protocol:
For m6A-seq, RNAs from INPUT and IP were extracted using Magna RIPTM Kit according to the manufacturer’s protocol.
For m6A-seq, RNA libraries were prepared using SMARTer Stranded Total RNA-Seq kit- Pico Input Mammalian following manufacturer’s protocols.


title: HCCLM3 cells, m6A-Input


title: X6pre

source_name: colorectal adenoma6

value: colorectal adenoma6


title: X2637T

source_name: colorectal tumor6

value: colorectal tumor6


title: HCCLM3 cells, CRTC2-RIP


title: HCCLM3 cells,CRTC2-Input


title: X2798N

source_name: normal colorectal tissue9

value: normal colorectal tissue9


title: X2pre

source_name: colorectal adenoma5

value: colorectal adenoma5


title: RNA ShTRMT6 rep 3

first: En-Wei

last: Tao

address: 145 Middle Shandong Road

institute: Shanghai Jiao Tong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low   quality bases which will affect the following assembly and analysis. Thus, to get high quality   clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the   reference genome using HISAT2. 2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a   reference-based approach. For each transcription region, a FPKM (fragment per kilobase of   transcript per million mapped reads) value was calculated to quantify its expression   abundance and variations, using RSEM software.
Assembly: ensembl_release104

source_name: RKO

extract_protocol:
Total RNA samples were extracted with the TRIzol reagent (Takara, #9109) according to the manufacturer’s instructions
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit (New England Biolabs, # E7530L) for Illumina.

value: RKO

value: Colorectal cancer cells

value: TRMT6 knockdown


title: RNA ShTRMT6 rep 2


title: RNA ShTRMT6 rep 1


title: X2525N

source_name: normal colorectal tissue8

value: normal colorectal tissue8


title: RNA ShControl rep 3


title: X2740T

source_name: colorectal tumor5

value: colorectal tumor5


title: RNA ShControl rep 1


title: RNA ShControl rep 2


title: HCCLM3 cells,YTHDF2-Input-1


title: U937 sh circRNA_01 3

value: sh circRNA_01


title: X10pre

source_name: colorectal adenoma7

value: colorectal adenoma7


title: X4pre

source_name: colorectal adenoma8

value: colorectal adenoma8


title: X2740N

source_name: normal colorectal tissue6

value: normal colorectal tissue6


title: X2525T

source_name: colorectal tumor4

value: colorectal tumor4


title: U937 control 3


title: X7N

source_name: normal colorectal tissue10

value: normal colorectal tissue10


title: U937 sh circRNA_01 1


title: X2712N

source_name: normal colorectal tissue5

value: normal colorectal tissue5


title: X2712T

source_name: colorectal tumor3

value: colorectal tumor3


title: X1pre

source_name: colorectal adenoma4

value: colorectal adenoma4


title: U937 control 2


title: Mus musculus,FA1_IP RNA

description: Library name: FA1_IP

source_name: kidney

value: kidney


title: X2637N

source_name: normal colorectal tissue3

value: normal colorectal tissue3


title: X2476N

source_name: normal colorectal tissue4

value: normal colorectal tissue4


title: X11pre

source_name: colorectal adenoma2

value: colorectal adenoma2


title: X3N

source_name: normal colorectal tissue7

value: normal colorectal tissue7


title: THP-1 control 2


title: THP-1 control 3


title: THP-1 sh circRNA_01 2


title: U937 control 1


title: X2476T

source_name: colorectal tumor2

value: colorectal tumor2


title: X3376N

source_name: normal colorectal tissue2

value: normal colorectal tissue2


title: THP-1 sh circRNA_01 1


title: X9pre

source_name: colorectal adenoma3

value: colorectal adenoma3


title: SU-DIPG36, SUV39H1,CST

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

data_processing:
Cut&Run-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference humant genome version hg38 with the program BOWTIE v2.3.4.1.
Peaks were called using the program MACS v2.1.2 using the narrow and broad peaks mode for Cut&Run-Seq.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: Cut&Run

growth_protocol: SU-DIPG36 and SU-DIPG13 cells  were cultured as TSM basic medium supplied with B27(-vitamin A), hEGF, hFGF, h-PDGF-AA, h-PDGF-BB and Heparin.

extract_protocol:
Cut &Run cleaved fragments were purified by Qiagen MinElute PCR Purification Kit.
Libraries were prepared for Illumina sequencing with Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).

value: patient-derived DIPG cells

tag: chip antibody


title: X3pre

source_name: colorectal adenoma1

value: colorectal adenoma1


title: On_4h_3

city: Chicago

first: Michael

last: Federle

state: IL

address: 900 S. Ashland Avenue

department: Pharmaceutical Sciences

institute: Universiry of Illinois - Chicago

description:
Library name: Sample 27
ON_4C_1.fq.out.bam

data_processing:
Data quality control was performed on FASTQ files using FASTQC and the raw sequencing reads were aligned to the mouse genome (GRCm39) using STAR. Raw sequencing reads of genomic features were enumerated using featureCounts and DESeq2 was used to normalize the counts, and provide differential expression analysis, and pre-ranked test-statistic data.
Assembly: raw sequencing reads were aligned to the mouse genome (GRCm39) using STAR
Supplementary files format and content: Tab delimited text file that contains Ensembl ID, chromosome #, start and end loci, strand, gene length, and raw counts for each sample

extract_protocol:
RNA was collected using Rneasy Mini kit (Qiagen)
Completed by Novogene. mRNA was enriched using oligo(dT) beads and rRNA was removed using Ribo-Zero kit (Illumina). mRNA was randomly fragmented using fragmentation buffer and cDNA synthesized by second strand synthesis using random primers and a custom second-strand synthesis buffer (Illumina). The cDNA was end-repaired, followed by 3’ polyadenylation and sequencing adaptor ligation. The library was then size selected and enriched by PCR

value: Macrophage

value: WT

tag: infection

value: QS-ON GAS Infection


title: On_8h_3

description:
Library name: Sample 30
ON_8C_1.fq.out.bam


title: On_4h_2

description:
Library name: Sample 26
ON_4B_1.fq.out.bam


title: On_8h_2

description:
Library name: Sample 29
ON_8B_1.fq.out.bam


title: SU-DIPG13, SUV39H1,CST


title: X2798T

city: Guangzhou

source_name: colorectal tumor1

value: colorectal tumor1


title: SU-DIPG13, H3K9me3, CST


title: SU-DIPG36, H3K9me3,CST


title: On_8h_1

description:
Library name: Sample 28
ON_8A_1.fq.out.bam


title: Prostate epithelial tissues (PN20)

first: Zezhong

last: Xiong

address: 1095 Jiefang Ave. Wuhan, P.R.China

institute: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

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 FastUniq（version 1.1）to eliminate duplication.
Deduplicated reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip） from using bowtie2 software (version 2.2.6) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis. The insert length was counted by Collect Insert Size Metrics tools from picard software (version 2.8.2).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: normal prostate

extract_protocol:
ATAC assay was performed on prostate cancer and normal prostate tissues by SeqHealth (Wuhan, China). 10000-50000 cells were treated with cell lysis buffer and nucleus was collected by centrifuging for 5min at 500g(500mg tissue was frozen in liquid nitrogen, and grinded by tissue lyser；The grinded powder was treated with cell lysis buffer and nucleus was collected by centrifuging for 5min at 2000g).
Transposition and high-throughput DNA sequencing library were carried out by TruePrep DNA Library Prep Kit V2 for Illumina kit（Catalog NO. TD501, Vazyme）.

value: normal prostate

tag: gender

value: male

tag: age


title: On_4h_1

description:
Library name: Sample 25
ON_4A_1.fq.out.bam


title: Prostate epithelial tissues (PN18)


title: On_2h_3

description:
Library name: Sample 24
ON_2C_1.fq.out.bam


title: Prostate epithelial tissues (PN17)


title: On_2h_1

description:
Library name: Sample 22
ON_2A_1.fq.out.bam


title: Prostate epithelial tissues (PN16)


title: Off_8h_3

description:
Library name: Sample 21
OFF_8C_1.fq.out.bam

value: QS-OFF GAS Infection


title: Prostate epithelial tissues (PN15)


title: Prostate epithelial tissues (PN14)


title: Off_8h_2

description:
Library name: Sample 20
OFF_8B_1.fq.out.bam


title: Prostate epithelial tissues (PN13)


title: Prostate epithelial tissues (PN19)


title: Off_8h_1

description:
Library name: Sample 19
OFF_8A_1.fq.out.bam


title: Prostate epithelial tissues (PN12)


title: Prostate epithelial tissues (PN11)


title: Off_4h_3

description:
Library name: Sample 18
OFF_4C_1.fq.out.bam


title: Off_4h_2

description:
Library name: Sample 17
OFF_4B_1.fq.out.bam


title: Off_2h_3

description:
Library name: Sample 15
OFF_2C_1.fq.out.bam


title: Prostate epithelial tissues (PN10)


title: Prostate epithelial tissues (PN8)


title: On_2h_2

description:
Library name: Sample 23
ON_2B_1.fq.out.bam


title: Prostate epithelial tissues (PN9)


title: Mus musculus,control3_IP RNA

description: Library name: control3_IP

value: kidney


title: Prostate epithelial tissues (PN7)


title: Off_2h_2

description:
Library name: Sample 14
OFF_2B_1.fq.out.bam


title: Off_2h_1

description:
Library name: Sample 13
OFF_2A_1.fq.out.bam


title: Prostate epithelial tissues (PN6)


title: ISCs, NT, Chrm3_WT, rep2

source_name: Intestine

value: Intestine

value: intestinal stem cells

value: NT


title: U937 sh circRNA_01 2

value: sh circRNA_01


title: Prostate epithelial tissues (PN4)


title: Mix_8h_2

description:
Library name: Sample 11
Mix_8B_1.fq.out.bam

value: QS-ON + QS-OFF GAS Infection


title: Prostate epithelial tissues (PN5)


title: Mix_8h_3

description:
Library name: Sample 12
Mix_8C_1.fq.out.bam


title: Mix_8h_1

description:
Library name: Sample 10
Mix_8A_1.fq.out.bam


title: Mix_4h_3

description:
Library name: Sample 9
Mix_4C_1.fq.out.bam


title: Prostate epithelial tissues (PN3)


title: Prostate epithelial tissues (PN2)


title: Off_4h_1

description:
Library name: Sample 16
OFF_4A_1.fq.out.bam


title: Mix_4h_2

description:
Library name: Sample 8
Mix_4B_1.fq.out.bam


title: Prostate epithelial tissues (PN1)


title: Mix_4h_1

description:
Library name: Sample 7
Mix_4A_1.fq.out.bam


title: Prostate cancer tissues (PC19)

source_name: prostate cancer

value: prostate cancer


title: Mix_2h_2

description:
Library name: Sample 5
Mix_2B_1.fq.out.bam


title: Mix_2h_3

description:
Library name: Sample 6
Mix_2C_1.fq.out.bam


title: Mix_2h_1

description:
Library name: Sample 4
Mix_2A_1.fq.out.bam


title: Prostate cancer tissues (PC18)


title: Uninfected 2h_3

description:
Library name: Sample 3
Med_2C_1.fq.out.bam


title: Prostate cancer tissues (PC16)


title: Uninfected 2h_1

description:
Library name: Sample 1
Med_2A_1.fq.out.bam


title: Prostate cancer tissues (PC13)


title: Prostate cancer tissues (PC12)


title: iWAT, Kmo-KO, HFD, rep3

city: ANN ARBOR

first: Jorge

middle: L

last: Ruas

state: Michigan

address: 2800 Plymouth RD, B025-2681 NCRC - Ruas Lab NCRC B025

institute: University of Michigan

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Reads aligning to gene exons (Mus_musculus.GRCm38.94.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: .txt file of raw read counts of all samples
Supplementary files format and content: s
Supplementary files format and content: .csv file of normalized counts of all samples
Supplementary files format and content: .csv file of differetial gene expression analysis output from DESeq2 of chow samples
Supplementary files format and content: .csv file of differetial gene expression analysis output from DESeq2 of HFD samples

source_name: Inguinal adipose tissue (iWAT)

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma-Aldrich, T9424) according to the manufacturer's instructions. RNA was further purified, and DNase treated (Zymo, R1013), and integrity confirmed prior to sequencing (Agilent Technologies, 2100 Bioanalyzer), with an RNA integrity number (RIN) greater than 7 as a threshold. Samples were purified by poly-A enrichment before library preparation using the Illumina NovaSeq X Plus Series platform with a paired-end 150 base pair strategy.
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA

value: Inguinal adipose tissue (iWAT)

value: Kmo-KO

value: High-fat diet


title: iWAT, Kmo-KO, HFD, rep4


title: Prostate cancer tissues (PC14)


title: iWAT, Kmo-KO, HFD, rep2


title: Prostate cancer tissues (PC11)


title: iWAT, Kmo-KO, HFD, rep1


title: iWAT, wild-type, HFD, rep4

value: Wild-type


title: Prostate cancer tissues (PC20)


title: Prostate cancer tissues (PC9)


title: iWAT, wild-type, HFD, rep3


title: Prostate cancer tissues (PC8)


title: iWAT, wild-type, HFD, rep2


title: Prostate cancer tissues (PC7)


title: Uninfected 2h_2

description:
Library name: Sample 2
Med_2B_1.fq.out.bam

value: Macrophage

value: WT


title: iWAT, Kmo-KO, chow, rep3

value: Chow diet


title: Prostate cancer tissues (PC6)


title: Prostate cancer tissues (PC15)


title: Prostate cancer tissues (PC5)


title: iWAT, wild-type, HFD, rep1


title: Prostate cancer tissues (PC4)


title: Prostate cancer tissues (PC17)


title: iWAT, Kmo-KO, chow, rep1


title: ATAC-seq of shSND1-KYSE150 esophageal carcinoma cells with SND1 knockdown

city: Luzhou

first: Jian

middle: Yan

address: No. 25, TaiPing Road, JiangYang District, Luzhou, Sichuan

institute: The Affiliated Hospital of Southwest Medical University

description: ATAC-seq profile of KYSE-150 human esophageal squamous cell carcinoma cells with SND1 knockdown via shRNA. This sample was generated to examine the impact of SND1 suppression on chromatin accessibility and gene expression, providing insights into the role of SND1 in esophageal carcinoma progression

data_processing:
Raw fastq files were quality checked (e.g., FastQC), adapter sequences were trimmed, and reads were aligned to the reference genome (e.g., human genome GRCh38)
Peak calling was performed using tools such as MACS2 to identify regions of open chromatin
Normalization and visualization of the data were done using appropriate software (e.g., deepTools for bigWig files).
Assembly: GRCh38/hg38" (assuming you used the human genome reference GRCh38, which is the standard for human studies)
Supplementary files format and content: The processed data files are in BigWig format, representing normalized chromatin accessibility data. The content includes the signal intensity of ATAC-seq data across the genome for each sample

source_name: Esophageal

growth_protocol: Cells (KYSE150) were cultured in appropriate media and conditions (e.g., RPMI, DMEM, incubator temperature, and CO₂) until they reached the desired confluence. For tissue samples, fresh or frozen tissue was prepared to create single-cell or cell nucleus suspensions.

extract_protocol:
Chromatin was extracted from cells by resuspending in chilled cell lysis buffer, followed by gentle pipetting and low-speed centrifugation to pellet chromatin. For frozen tissue samples, cells/nuclei were isolated by homogenization and similar chromatin extraction steps were applied
Chromatin was subjected to Tn5 transposition for fragmenting DNA and attaching adapters, followed by PCR amplification with high-fidelity polymerase. The PCR amplification was carried out for 12-15 cycles, after which the libraries were purified using magnetic beads
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing). Paired-end sequencing was performed using the Illumina HiSeq 2500 platform with a 2×150 bp read length.

treatment_protocol: Cells were transfected with shRNA constructs targeting SND1 (shSND1) or a control shRNA. The knockdown was confirmed via appropriate methods, such as qPCR or western blot, before proceeding with ATAC-seq. For tissue samples, fresh tissue was processed into single-cell suspensions (or nuclei) for chromatin preparation

value: Esophageal

value: squamous cell carcinoma

value: TP53 mutation, CDKN2A deletion, SND1 knockdown

value: SND1 knockdown by shRNA


title: iWAT, Kmo-KO, chow, rep2


title: iWAT, Kmo-KO, chow, rep4


title: Prostate cancer tissues (PC10)

value: male


title: sh-SUV39H1-1

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg19 (human) whole genome using Tophat using default options.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SU-DIPG36  cells  were cultured as TSM basic medium supplied with B27(-vitamin A), hEGF, hFGF, h-PDGF-AA, h-PDGF-BB and Heparin.

extract_protocol:
Total RNA from DIPG cells  were extracted using Trizol (Life Technologies) protocol followed by purification using an RNeasy Micro Kit (Qiagen)
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit

treatment_protocol: 25nM Cheatocin treatment  for 24 hours

value: patient-derived DIPG cells

value: SUV39H1 knockdown


title: Prostate cancer tissues (PC2)


title: sh-ctrl-2


title: iWAT, wild-type, chow, rep4


title: sh-ctrl-1


title: Prostate cancer tissues (PC1)


title: iWAT, wild-type, chow, rep3


title: Chaetocin-2

value: Chaetocin

value: 24 hours


title: Chaetocin-1


title: Prostate epithelial tissues (PN20) [RNA-Seq]

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/） using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the deseq2 package (version 3.12.1).
Assembly: hg38
Supplementary files format and content: csv

extract_protocol:
Total RNAs were extracted from prostate cancer and adjacent normal tissues using TRIzol (Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: normal prostate


title: DMSO-2


title: Prostate epithelial tissues (PN19) [RNA-Seq]


title: DMSO-1


title: iWAT, wild-type, chow, rep2

value: Inguinal adipose tissue (iWAT)


title: ATAC-seq of KYSE-150 esophageal squamous carcinoma cells

description: ATAC-seq profile of untreated KYSE-150 human esophageal squamous cell carcinoma cells to assess chromatin accessibility under baseline conditions. This sample serves as the control in comparison with shSND1 knockdown-treated cells to investigate the effects of SND1 knockdown on chromatin structure and gene regulation

value: TP53 mutation, CDKN2A deletion

value: Untreated


title: iWAT, wild-type, chow, rep1

value: Wild-type


title: QVD_2

city: Balitmore

first: Charles

middle: Scott

last: Kirby

state: Maryland

address: 1551 Orleans Street, Koch CRBII Suite 216

institute: Johns Hopkins

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Illumina CASAVA 1.8 software was used for basecalling
Reads with adaptor contamination were removed, reads with uncertain nucleotids for more than 10% of either read were removed, reads with low quality nucleotides (base quality < 20) for more than 50% of read were removed
Mapping: STAR(v2.6.1d), Quantification: FeatureCounts (v1.5.0-p3)
Assembly: Genome build:  hg38
Supplementary files format and content: tab-delimited text file including read count for each gene for each Sample

source_name: NHEK, Q-VD-Oph

growth_protocol: Keratinocytes were cultured in keratinocyte growth medium (KGM-Gold)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina®  following manufacturer’s recommendations

treatment_protocol: NHEKs were treated with either a DMSO vehicle or 120μM/mL of Q-VD-Oph, for 48 hours

value: Foreskin

value: Normal Human Epidermal Keratinocytes (NHEK)

value: Q-VD-OPh


title: sh-SUV39H1-2


title: whole worm, Suppressor-Fed-3MBPP1-3

city: Genève

first: François-Xavier

last: Stubbe

state: Genève

address: 30, quai Ernest-Ansermet

department: MOCEL

country: Switzerland

institute: University of Geneva

data_processing:
Basecalls were performed using bcl2fastq for NovaSeq output
RNA-seq reads were aligned to WBCel235 genome using hisat2 (with parameters –no-discordant –min-intronlen 20 –max-intronlen 5000)
Read Count extraction was performed using FeatureCount
DGE analysis was performed usig DESEQ2
Assembly: WBCel235
Supplementary files format and content: FeatureCount matrix: tab-delimited text files includes raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: L1 were synchornized by hypochlorite treatment and hatched over night

extract_protocol:
RNA was harvested using TriZol reagent. DNA was removed Ambion Turbo DNAse and cleaned by phenol/cloroform extraction
RNA-seq libraries were made following the Illumina TRUESeq protocol

treatment_protocol: 100k L1s were grown in liquid in presence or absence of food and in presence or absence of 3MB-PP1

tag: developmental stage

value: whole worm

tag: feeding time

value: Fed

value: 3MB-PP1 (2uM)


title: Prostate epithelial tissues (PN18) [RNA-Seq]


title: DMSO_2

source_name: NHEK, DMSO

tag: genotype

value: WT

value: DMSO


title: Prostate epithelial tissues (PN17) [RNA-Seq]

value: male


title: whole worm, Suppressor-Fed-3MBPP1-2


title: DMSO_1


title: Prostate epithelial tissues (PN16) [RNA-Seq]


title: whole worm, Suppressor-Fed-3MBPP1-1


title: CRF_CHP [RNA_68]

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

institute: École polytechnique fédérale de Lausanne

description: CRF CHP 3

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles rn6_modified_chrm_names.fa --sjdbGTFfile Rattus_norvegicus.Rnor_6.0.99.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.
SMARTER mRNA-Seq Library Prep Kit

treatment_protocol: 5/6 nephrectomy rat model was used to ascertain the effect of CHP on fibrosis, which is associated with CKD progression. Sprague Dawley rat (250 g, 6~7 weeks old; Koatech) were treated with CHP 20 mg/L orally, from 10 days before nephrectomy to 8 weeks after 5/6 Nx established. Rats underwent 5/6 Nx under anesthesia with isoflurane 3% in N2O/O2 (1:2). After 3 days, animals received ligation of 2 or 3 main branches of the left renal artery by silk ligature. One week later, rats received right nephrectomy to remove 5/6 renal mass and the 5/6 nephrectomy rats were treated for 8 weeks. Eight weeks later, rats underwent necropsy to collect blood and kidneys. The renal cortex was immediately snap frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated using Trizol reagent (Invitrogen).

tag: strain background

value: Sprague Dawley

tag: condition

value: CRF

tag: tratment

value: CHP

value: kidney


title: CRF_CHP [RNA_67]

description: CRF CHP 2


title: CRF_Control [RNA_58]

description: CRF Control 3

value: Control


title: whole worm, Suppressor-Fed-DMSO-3


title: Prostate epithelial tissues (PN14) [RNA-Seq]

value: normal prostate


title: QVD_3


title: whole worm, Suppressor-Fed-DMSO-2


title: Sham_Control [RNA_53-1]

description: Sham Control 2

value: Sham


title: Sham_Control [RNA_52-1]

description: Sham Control 1


title: QVD_1


title: DMSO_3


title: Prostate epithelial tissues (PN13) [RNA-Seq]


title: Prostate epithelial tissues (PN12) [RNA-Seq]


title: OCI-AML2 cells, SOCS1 Overexpression, Replicate 2

description: Library name: Sample 4

source_name: Bone. Marrow

value: Bone. Marrow

tag: cell line

value: Acute Myeloid Leukemia

value: SOCS1 Overexpression


title: whole worm, Suppressor-Fed-DMSO-1


title: CRF_Control [61]

description: CRF Control 1


title: CRF_CHP [65]

description: CRF CHP 1


title: WT-Fla-pNET-rep1

city: Beijing

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

data_processing:
The paired-end reads were trimmed as follows: cutadapt -a TGGAATTCTCGGGTGCCAAGG -O 10 -e 0.1  -m 10 inputfile_R1.fq.gz -o outputfile_R1_trim.fq.gz, cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGA -O 15 -e 0.1 -m 10 inputfile_R2.fq.gz -o outputfile_R2_trim.fq.gz. Then the trimed reads were aligned to the Arabidopsis reference genome (TAIR10) using Bowtie 2. The reduplication-removed bam files were converted to bigWig using RPKM normalization method in deeptools v3.5.1.
Assembly: TAIR10
Supplementary files format and content: The bigwig files were generated using the bamCoverage from deeptools.

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 7-day seedlings growth on 1/2 MS media.

extract_protocol:
Seedlings were harvested from 1/2MS liquid media and were grounded in liquid nitrogen and resuspended in ice-cold lysis buffer (50mM HEPES pH 7.5, 150mM NaCl, 1mM EDTA pH 8.0, 1% Triton X-100, 10% glycerol, 5mM β-mercaptoethanol, 1mM PMSF, 2μg/μl Aprotinin and 2μg/μl Pepstatin A) for 30 mins on ice. After lysis mixture was filtered and centrifuged to discard the supernatant, Nuclear pellet was washed once with ice-cold HBB (25mM Tris-HCl pH7.6, 0.44M sucrose, 10mM MgCl2, 0.10% Triton-100, 10mM β-mercaptoethanol) and HBC (20mM Tris-HCl pH7.6, 0.352M sucrose, 8mM MgCl2, 0.08% Triton-100, 8mM β-mercaptoethanol and 20% glycerol) buffers, respectively. Washed nuclear pellet was resuspended in MNase reaction buffer (20mM Tris-HCl pH 8.0 , 5mM NaCl, and 2.5mM CaCl2, 20U MNase (NEB)). The reaction mixture was incubated at 37°C for 5 minutes and the reaction was later stopped with final con. 0.02M EDTA. Then sonication was performed 1s ON/OFF for 10 cycles to release chromatin and centrifuged to obtain the supernatant. The collected supernatant was diluted 5-8 times with ice-cold NET-2 buffer (50mM Tris-HCl pH7.4, 150mM NaCl, and 0.05% NP-40). The diluted supernatant was incubated with Pol II Ser2p antibody (ab5095) coated Dynabeads (Invitrogen, 11201D) for 2 hours at 4°C and the beads containing complex was washed 8 times with ice-cold NET-2 buffer. Finally, beads were resuspended with PNK reaction mixture containing 75 μl PNK buffer, 10 μl PNK enzymes (NEB) and 15 μl of 10mM ATP and incubated at 37°C for 10 mins on a Thermomixture (1400 rpm). After that supernatant was removed and beads were washed once with NET-2 buffer. Then beads was followed RNA extraction with Trizol reagent. The extracted RNA was conducted to library construction.
The recovered RNA was used to construct the small RNA libraries with NEXTflex TM small RNA-Seq Kit V4. Finally, the libraries were recovered from the 6% PAGE gel corresponding to 140-250 bp size and undergone high throughput deep sequencing.
small RNA-seq

treatment_protocol: 7-day seedlings were transfered to 1/2 MS liquid media adding DMSO or 10 μM flavopiridol and incubated for 1 hour.

value: seedlings

tag: ecotype

value: Columbia

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS antibody (ab5095)

value: 10 μM flavopiridol, 1 hour


title: WT-Fla-pNET-rep2


title: whole worm, Suppressor-Starved-DMSO-3

value: whole worm

value: Starved


title: Prostate epithelial tissues (PN11) [RNA-Seq]

value: male


title: whole worm, Suppressor-Starved-DMSO-2

value: DMSO


title: WT-DMSO-pNET-rep2

value: DMSO, 1 hour


title: WT-DMSO-pNET-rep1


title: Prostate epithelial tissues (PN15) [RNA-Seq]


title: Prostate epithelial tissues (PN10) [RNA-Seq]


title: IVT_DRS_ac4C

first: Xiang

last: Yu

address: 800 Dongchuan Road

description: In vitro transcripts from Oryza sativa cDNA library

data_processing:
The fast5 files containing raw electric signals were basecalled using Guppy(v6.1.5 with options ‘--recursive --fast5_out --config rna_r9.4.1_70bps_hac.cfg’)
Multi-fast5 files were converted to single-fast5 files using ont_fast5_api(v4.0.0)
Basecalled sequences were corrected according to reference and aligned to corresponding raw electric signals using tombo resquiggle(v1.5.1 with options ‘--overwrite --basecall-group Basecall_1D_000 --fit-global-scale --include-event-stdev’).
Raw current signals were normalized by median and median absolute deviation.
Then, mean, standard deviation, median, signal length and base quality were extracted as features for each event. 5-mer sequence was also considered as one event-level feature in this work and was embedded to vectors.
Assembly: Osativa_323_v7.0

source_name: leaf and inflorescence

extract_protocol:
The IVT products were treated with RNase-free DNase I (NEB, M0303S, USA) to remove residual DNA, and then purified using the RNeasy Mini Kit (QIAGEN, 74104, USA). The tailing reaction was catalyzed by E. coli Poly(A) Polymerase (NEB, M0276S, USA). The products were purified again using the RNeasy Mini Kit, followed by overnight ethanol precipitation to obtain poly(A)-tailed RNA for nanopore direct RNA sequencing.
Sequencing libraries were prepared according to the ONT’s SQK-RNA002 protocol.
Nanopore Direct RNA-seq

value: leaf and inflorescence


title: CRF_Control [RNA_57]

description: CRF Control 2

value: Sprague Dawley

value: CRF

value: kidney


title: Prostate epithelial tissues (PN9) [RNA-Seq]

value: normal prostate


title: whole worm, Suppressor-Starved-DMSO-1


title: THP-1 sh circRNA_01 3

value: sh circRNA_01


title: WT2 Xenium

type: RNA

description: WT2_output-XETG00089__0025303__Region_2__20240426__181528

data_processing:
Output files were generated by the Xenium Onboard Analysis pipeline to generate gene transcript by cell and transcript by tissue location data matrices.
cell_boundaries.csv.gz: compressed dimensions of cell boundaries
experiment.xenium: executable file to open data in Xenium Explorer
features.tsv.gz: gene expression feature names
matrix.mtx.gz: gene expression matrix
barcodes.tsv.gz: cell barcode names
gene_panel.json: gene panel list
cell_feature_matrix.h5: compressed cell expression data
cell_feature_matrix.zarr.zip: compressed cell expression data
cells.csv.gz: compressed cell locations
transcripts.csv.gz: zcompressed transcripts

source_name: SD0 Wounded back skin

label_protocol: Spatial transcriptome sequencing libraries were prepared with 10X Xenium spatial gene expression slides & reagent kit according to manufacturer's construction

extract_protocol: Wound samples were formalin-fixed and paraffin-embedded (FFPE) then underwent sectioning, and H&E staining. Samples were then trimmed to match Xenium slides, then analyzed according to manufacturers protocols. Post xenium H&E staining was then performed.

treatment_protocol: Using surgical scissors  approximately 1.26 cm2 X 1.25cm2 of skin was excised creating wounds deep into the fascia

tag: strain

value: Formalin-fixed and paraffin-embedded (FFPE) wounded back skin at SD0


title: whole worm, CDK12as-Fed-3MBPP1-3

tag: tissue

value: Fed

value: 3MB-PP1 (2uM)


title: whole worm, CDK12as-Fed-3MBPP1-2


title: WT1 Xenium

description: WT1_output-XETG00089__0025303__Region_1__20240426__181528


title: Prostate epithelial tissues (PN8) [RNA-Seq]


title: WT3 Xenium

description: WT3_output-XETG00089__0025303__Region_3__20240426__181528


title: RLKO2 Xenium

description: RLKO2_output-XETG00089__0025300__Region_2__20240426__181528


title: 5572

city: Philadelphia

first: Thomas

middle: G

last: Brooks

address: 3400 Civic Center Blvd

department: ITMAT

institute: University of Pennsylvania

description: Library name: ZT11.LD.female.5572

data_processing:
RNA-seq reads were quantified using Salmon v1.9.0to the GRCm38 genome with Ensembl v102 annotation. Quantifications were imported with the tximeta package v1.20.3] for use with DESeq2 v1.42.0 and aggregated to gene level quantifications.
Assembly: GRCm38
Supplementary files format and content: salmon.genes.TPM.txt is a tab-separated file containing gene-level transcripts-per-million (TPM) values for each sample

source_name: Lung

growth_protocol: Specific pathogen-free 8-12 week-old C57bl/6J mice were placed in circadian cabinets on reverse light-dark cycle. This allowed us to simultaneously infect mice or harvest tissues across all experimental groups. After 4-6 weeks of acclimatization in these cabinets, mice were anesthetized lightly with isoflurane prior to being infected intranasally (i.n.) with mouse-adapted influenza virus (PR8 ). Given the use of circadian cabinets, mice were simultaneously infected at either ZT23 or ZT11 and maintained in 12 hr light-dark cycle. The dose chosen was likely to cause >50% mortality when mice were infected at ZT11. On day four p.i. a subset of ZT23-LD mice were moved to constant light (LL) until the end of the study.

extract_protocol:
TRIzol (Life Technologies) was used to extract and isolate RNA from the inferior lobe of the mouse lung. The RNeasy Mini Elute Clean Up Kit (Qiagen) was used to further purify the RNA as per the manufacturer’s protocol. The NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc) was used to assess the quality and quantity of the extracted RNA. Only samples with RINS>7 after QC were sent for sequencing to Azenta Life Sciences.
Strand-specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

value: Lung

tag: Sex

value: female

tag: time

value: LD


title: whole worm, CDK12as-Fed-3MBPP1-1

value: whole worm

tag: treatment


title: whole worm, CDK12as-Fed-DMSO-3


title: Prostate epithelial tissues (PN5) [RNA-Seq]


title: 4716

description: Library name: ZT11.LD.female.4716


title: 4715

description: Library name: ZT11.LD.female.4715


title: whole worm, CDK12as-Fed-DMSO-2


title: 4714

description: Library name: ZT11.LD.female.4714


title: Prostate epithelial tissues (PN4) [RNA-Seq]


title: whole worm, CDK12as-Starved-DMSO-3

value: Starved


title: 5574

description: Library name: ZT11.LD.female.5574


title: 4713

description: Library name: ZT23.LL.female.4713

value: LL


title: 5196

description: Library name: ZT23.LL.female.5196


title: whole worm, CDK12as-Fed-DMSO-1

value: DMSO


title: Prostate epithelial tissues (PN3) [RNA-Seq]

value: male