title: dHfD_A55

city: New Haven

first: Stephen

middle: M

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

description: 10x Genomics

data_processing:
Reads where aligned to mm10 mouse genome referemce and masked for low quality sequences using the Cell Ranger Software v6.1.2
Scanpy (Wolf F. et al, 2018) was used to generate a merged anndata objects of all study samples for QC processing and gene filtering.
Data was log-normalized and highly variable genes were identified using Scanpy's implementation of Seurat_v3
Data integration and leiden clustering was preformed using scVI tools (Gayoso et al. 2022)
UMAP embedding, cell type cluster assigments, DEG testing, and read count extraction was performed using Scanpy's data processing pipeline.
Assembly: mm10-2020-A
Supplementary files format and content: comma separated values file contain raw gene count matrixs, one file for each sample.

molecule: nuclear RNA

source_name: Coxtex, Hippocampus

growth_protocol: Mice where aged for 11.5 months

extract_protocol:
Cerebral cortex and hippocampal tissues where disected from the left brain hemisphere. The tissues were pooled together for each mouse and processed for nuclei isolation via sucrose density gradient centrifugation with 8000-1000 nuclei used for 10x Genomics barcode mRNA sequencing.
RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3P' v3.1  Kit following the manufacturer's protocols.

treatment_protocol: Starting at ~3.5 months of age, At approximately 3-4 months of age, mice were put on either control diet (ResearchDiets #D12450K) or high fat diet (HFD) (ResearchDiets #D12492) until end of the experiment to induce Type-2 diabetes.

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI

tag: disease state

value: AD

value: Female

value: 11.5 months

value: high fat diet


title: HK-2 cells, mock, 0h, rep2

status: Public on Nov 01 2025

type: SRA

city: Shenzhen

first: Han

last: Wu

address: Liuxian Road 1066

country: China

institute: Shenzhen University

library_source: transcriptomic

data_processing:
Based on the sequencing by synthesis (SBS) technology, the Illumina high-throughput sequencing platform sequences the cDNA library.
Remove low-quality reads (including removing reads with an N ratio > 10%; removing reads with a quality value Q≤10 and a base number that accounts for more than 50% of the entire read)
Sequence reads were mapped to reference genome GRCh38 using HISAT2 software.
The StringTie algorithm normalizes the number of mapped reads and transcript length in the sample. FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) is used as an indicator to measure the expression level of transcripts or genes.
Assembly: StringTie to assemble and quantify the reads on the alignment.
Supplementary files format and content: Excel file include RPKM values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: HK-2 cells

growth_protocol: HK-2 cells were cultured in DMEM/F12 containing 10% fetal bovine serum  and 1% penicillin and streptomycin.

extract_protocol:
Total RNA from 1 × 10^7 cells was isolated by Trizol extraction with DNase I treatment for each sample.
RNA-seq library preparation and sequencing on an Illumina platform were finished by BMK Inc (Beijing, China).

treatment_protocol: HK-2 cells treated with 2 ug/ml TGFβ with the presence of HDAC11 inhibitor FT895 or vehicle (DMSO) for 1 h or 12 h.  Equal volume of PBS treated cells were serve as mock control.

tag: cell line

value: HK-2 cells

tag: cell type

value: Epithelial  cells

tag: genotype

value: WT

tag: treatment

value: Untreat control


title: DistalColon, Mouse1

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

country: USA

institute: RealSeq Biosciences

description:
Library name: DistalColon_M1
Column name in csv files: DistalColon_M1

data_processing:
Sequencing adaptors were trimmed from raw reads using cutadapt, v1.18 [--no-indels -O 15 -m 15 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC], then UMI’s were extracted using umi_tools [extract --extract-method=string --bc-pattern=NNNNNNN], finally followed by the removal of a single base added during library preparation from the 5’ end using cutadapt [-u -1 -q 10].
Reads were separated into “mature tRNAs” or “tDRs” based on read lengths of >=65 and <65nt, respectively. Reads were subsampled from each tissue sample to account for differences in sequencing depth to 200,000 reads per sample for those >=65nt and 1,000,000 reads per sample for those <65nt using seqtk [sample -s100]. These were then sequentially aligned using bowtie2 [--very-sensitive -k 100] to vector contaminants (UniVec), rRNAs, tRNAs (with the addition of the -CCA tail) identified using tRNAScan-SE (Chan and Lowe 2021), miRNAs from miRbase (Kozomara et al., 2019), snRNAs/snoRNAs/lncRNAs from Ensembl, processed mRNA transcripts (protein_coding) from Ensembl, and lastly to the genome.
Counts associated with these features were then quantified using a custom Python script, choosing the feature annotation with the largest degree of overlap. Multimapping ncRNA reads with more than one highest-scoring alignment were randomly selected.  The resulting count data underwent normalization and differential expression analysis using DESeq2 (Love 2014)
Assembly: GRCm39 (mm11)
Supplementary files format and content: MouseTissue_o65-counts.csv contains raw counts for annotated transcripts using reads >= 65nt in length.
Supplementary files format and content: MouseTissue_u65-counts.csv contains raw counts for annotated transcripts using reads < 65nt in length.

molecule: total RNA

organism: Mus musculus

source_name: DistalColon

growth_protocol: Tissues were harvested from three 6-8 week old wildtype female C57BL/6J mice at 2-3pm to best account for 12 hr light-dark cycles (7am-7pm light and 7pm-7am dark), which impact gene and protein expression during circadian variations.

extract_protocol:
Total RNA was isolated from ~15-100mg of whole bladder, brain, cecum, distal colon, duodenum, heart, ileum, kidney, liver, lung, mammary gland, ovary, proximal colon, skeletal muscle, skin, spleen, stomach, thymus, and uterus using 1mL of TRI Reagent and a tissue homogenizer, typically yielding ~50-100ug of total RNA.
OTTR-seq

tag: tissue

value: DistalColon

tag: Sex

value: female

tag: strain


title: 6-methylbenzo[a]pyrene, 0.133, 48 hpf, A

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

description: Library name: 6_0.133_48_A

data_processing:
Reads were mapped and demultiplexed by Alithia Genomics; 88% of reads were mapped to the genome, and 67% were mapped to exons.
Assembly: GRCz12tu
Supplementary files format and content: .csv file containing raw read count data

organism: Danio rerio

source_name: Whole Animal

extract_protocol:
RNA extraction was performed using the KingFisher Apex System (ThermoFisher Scientific, Waltham, MA, United States) and Quick-RNA Magbead kit (Zymo Research Corporation, Irvine, CA, United States). Samples were thawed and combined into the homogenization plate (2 mL deep 96-well plate pre-filled with 400 µL 1 mm zirconium silicate beads and 525 µL of lysis buffer) and sealed with a silicone seal. Using the Mini-BeadBeater 96 (BioSpec Products, Bartlesville, OK, United States), the plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 550µL of the supernatant was distributed over two plates, each pre-filled with 275µL of ethanol. Extraction was an automated process that using Mag beads to collect RNA, after a series of washes and treatment with DNase, the RNA is eluted in 50µL of ultra-pure water. RNA quality was assessed using the RNA ScreenTape and the 4200 TapeStation System (Agilent, Santa Clara, CA, United States). The RNA purity was assessed using the 260/230 ratio measured with the Varioskan ALF multimode plate reader (ThermoFisher Scientific, Waltham, MA, United States). RNA concentration was determined using Quant-iT broad-spectrum RNA Reagent and assay kit and Varioskan ALF multimode plate reader (standard curve R2=0.996). The four replicates of each treatment with the highest RNA concentration, which met RNA quality and purity criteria (2.3 ≥ 260/230 ≥ 1.8, RIN=10), were selected for sequencing. The resulting 80 samples were normalized using ultrapure water to the lowest concentration, 56 ng/µL.
library constructuon and RNA sequencing was performed by Alithia Genomics (Epalignes, Switzerland) using their Mercurius™ BRB-SEQ service, which is a multiplexed 3’ RNA sequencing library preparation technique. Samples were sequenced using NextSeq 200 with ~9.6 million reads/sample.

treatment_protocol: All chemicals (8-methylbenzo[a]pyrene, 6-methylbenzo[a]pyrene, and benzo[a]pyrene) were exposed at the same concentrations (0, 0.133, 1.33, and 13.3 µM).  Concentrations were picked that cause no morphological effects (0.133 µM), only x-fin (1.33 µM), and x-fin as well as cranial malformations and edema (13.3 µM). Time points were chosen to be before the observation of any morphological effects (48 hpf) and at the onset of morphological effects (72 hpf). For each chemical and concentration combination, a 96-well plate was exposed, as well as one plate of control embryos.  At 48 and 72 hpf, living embryos were collected at random regardless of morphological phenotypes, and pooled in groups of six. Five replicates of each chemical and concentration combination and control were collected at each time point, pooled sample embryo medium (EM) volume was normalized to 75 µL. Collection plates were placed on ice for one minute, immediately followed by the addition of 100 µL of RNA shield. Plates were sealed with foil seals and kept at -80°C until RNA extraction.

value: Whole Animal

value: 5D WT


title: dHfD_A2B

description: 10x Genomics

tag: time


title: HK-2 cells, mock, 0h, rep1


title: 8-methylbenzo[a]pyrene, 13.3, 48 hpf, C

description: Library name: 8_13.3_48_C


title: Cecum, Mouse3

description:
Library name: Cecum_M3
Column name in csv files: Cecum_M3

source_name: Cecum

value: Cecum


title: 8-methylbenzo[a]pyrene, 13.3, 48 hpf, D

description: Library name: 8_13.3_48_D


title: dHfD_834

description: 10x Genomics

value: Male


title: Cecum, Mouse2

description:
Library name: Cecum_M2
Column name in csv files: Cecum_M2


title: HIT-scISOseq 3d_s2

city: guangzhou

first: ming

last: zhou

address: jinsui road 7

institute: Sun Yat-sen University,

description:
HIT-scISOseq
NextSeq High Output Kits

library_source: transcriptomic single cell

data_processing:
After acquiring the HIT-scISOseq data, we used the accompanying scISA-Tools software for data preprocessing, RNA isoform identification (only the annotated genes were retained as FSM: full splice match), ISM: incomplete splice match, NIC: novel in the catalog, and NNC: novel not in catalog isoforms), gene and isoform matrix generation.
Assembly: Ensembl Macaca_fascicularis_5.0.99
Supplementary files format and content: Read count matrices for each sample were generated by CellRanger counting.

organism: Macaca fascicularis

source_name: cornea

extract_protocol:
The cells were filtered through a 30-µm cell strainer and were re-suspended in 60 µL PBS containing 0.04% BSA to achieve 1,000 cells µl-1 for capture on the 10× Genomics Chromium controller.
We obtained single-cell full-length cDNAs using the 10× Genomics platform, and then used the HIT-scISOseq method for library construction and sequencing.

value: cornea

value: corneal injury

tag: time point

value: 3-day healing stage


title: HIT-scISOseq 3d_s1

description:
HIT-scISOseq
NextSeq High Output Kits


title: dCtrD_BOA

description: 10x Genomics

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI

value: AD

value: control diet


title: 8-methylbenzo[a]pyrene, 13.3, 48 hpf, B

description: Library name: 8_13.3_48_B


title: HIT-scISOseq 1d_s2

description:
HIT-scISOseq
NextSeq High Output Kits

value: 1-day healing stage


title: Brain, Mouse3

description:
Library name: Brain_M3
Column name in csv files: Brain_M3

source_name: Brain

value: Brain

value: WT


title: 8-methylbenzo[a]pyrene, 13.3, 48 hpf, A

description: Library name: 8_13.3_48_A


title: dCtrD_B04

description: 10x Genomics

value: Female

value: 11.5 months


title: WT_1

city: Nanjing

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Assembly: GRCm39
Supplementary files format and content: xls files include counts and tpm values for each sample

source_name: mouse embryonic stem cell

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mouse embryonic stem cell


title: dCtrD_367

description: 10x Genomics


title: HIT-scISOseq 1d_s1

description:
HIT-scISOseq
NextSeq High Output Kits


title: Brain, Mouse2

description:
Library name: Brain_M2
Column name in csv files: Brain_M2

value: female


title: dCtrD_322

description: 10x Genomics


title: dHfD_D49

description: 10x Genomics

value: high fat diet


title: HIT-scISOseq 0d_s2

description:
HIT-scISOseq
NextSeq High Output Kits

value: uninjured


title: 8-methylbenzo[a]pyrene, 1.33, 48 hpf, C

description: Library name: 8_1.33_48_C

value: Whole Animal

value: 5D WT


title: Brain, Mouse1

description:
Library name: Brain_M1
Column name in csv files: Brain_M1


title: WTHfD_F59

description: 10x Genomics

value: Wildtype

value: Male


title: HIT-scISOseq 0d_s1

description:
HIT-scISOseq
NextSeq High Output Kits

value: cornea


title: Bladder, Mouse2

description:
Library name: Bladder_M2
Column name in csv files: Bladder_M2

source_name: Bladder

value: Bladder


title: WTHfD_430

description: 10x Genomics

value: Coxtex, Hippocampus


title: Bladder, Mouse1

description:
Library name: Bladder_M1
Column name in csv files: Bladder_M1


title: 8-methylbenzo[a]pyrene, 1.33, 48 hpf, A

description: Library name: 8_1.33_48_A


title: Decidua, normal, 6

city: Daejeon

first: Tae Lyun

last: Ko

address: 245, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Institute of Science and Technology Information

description: Library name: norm_Endo6

data_processing:
Sequencing data were aligned and quantified using Cell Ranger v5.0.0 (10X Genomics) against the human reference genome (GRCh38) provided by Cell Ranger
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Decidua

extract_protocol:
Decidual tissues were collected via dilation and curettage, and single-cell suspensions were prepared by mechanical and enzymatic dissociation.
Single-cell RNA libraries were prepared using the Chromium Single Cell 3′ Library Kit (10X Genomics) according to the manufacturer’s instructions and sequenced on Illumina HiSeq-X and NovaSeq 6000 platforms.

value: Decidua

tag: gestational week

tag: disease

value: Normal


title: Cecum, Mouse1

description:
Library name: Cecum_M1
Column name in csv files: Cecum_M1

value: Cecum


title: Decidua, Repeated Preagnancy Loss (RPL), 5

description: Library name: RPL_Endo5

value: Repeated Pregnancy Loss (RPL)


title: 8-methylbenzo[a]pyrene, 1.33, 48 hpf, D

description: Library name: 8_1.33_48_D


title: WTHfD_07C

description: 10x Genomics

value: WT

value: Female


title: sipink

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

institute: CHA university

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: murine adipocytes


title: 8-methylbenzo[a]pyrene, 0.133, 48 hpf, B

description: Library name: 8_0.133_48_B


title: WTCtrD_972

description: 10x Genomics

value: 11.5 months

value: control diet


title: 8-methylbenzo[a]pyrene, 0.133, 48 hpf, D

description: Library name: 8_0.133_48_D


title: 8-methylbenzo[a]pyrene, 0.133, 48 hpf, C

description: Library name: 8_0.133_48_C


title: Decidua, Repeated Preagnancy Loss (RPL), 3

description: Library name: RPL_Endo3


title: WTCtrD_73B

description: 10x Genomics


title: Decidua, normal, 2

description: Library name: norm_Endo2


title: 8-methylbenzo[a]pyrene, 0.133, 48 hpf, A

description: Library name: 8_0.133_48_A


title: Neuroepithelium of cynomolgus monkey MT2

city: Kunming

first: Peng

last: Li

state: Yunnan

address: No. 727 Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

data_processing:
hisat2 v 2.2.1
stringtie v 2.1.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to Macaca_fascicularis_6.0 using hisat2
Read count extraction and normalization were performed using stringtie
Assembly: Macaca_fascicularis_6.0
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: Embryo

extract_protocol:
RNA was harvested using trizol. 20 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by enriching and purifying mRNA, breaking it, forming cDNA, and then performing end repair, adding base A, and adding sequencing adapters, and then recovering the target size fragments for PCR amplification.

treatment_protocol: gene knockout

value: Embryo

value: ES-A

value: neuroepithelium cells

value: SHROOM3 knockout


title: Neuroepithelium of cynomolgus monkey MT3


title: WTCtrD_563

description: 10x Genomics

value: Wildtype

value: Male


title: Decidua, Repeated Preagnancy Loss (RPL), 1

description: Library name: RPL_Endo1


title: 8-methylbenzo[a]pyrene, 1.33, 48 hpf, B

description: Library name: 8_1.33_48_B

value: Whole Animal

value: 5D WT


title: WTHfD_D77

description: 10x Genomics

value: Coxtex, Hippocampus

value: high fat diet


title: Bladder, Mouse3

description:
Library name: Bladder_M3
Column name in csv files: Bladder_M3

value: Bladder

value: female


title: WTCtrD_020

description: 10x Genomics

value: WT


title: replication 1 of colony 3 knocking down METTL3 in cells

city: Tianjin

first: Junya

last: Ning

state: -- None --

address: Huanhuxi Road, Hexi District, Tianjin

institute: Tianjin Medical University Cancer Institute & Hospital

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Trim Galore, then sequence reads were mapped to mm10 genome using Hisat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include Normalized count values for each Sample.

source_name: BCPAP cells

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: thyroid cancer cells


title: Decidua, Repeated Preagnancy Loss (RPL), 4

description: Library name: RPL_Endo4

value: Decidua

value: Repeated Pregnancy Loss (RPL)


title: Neuroepithelium of cynomolgus monkey WT4


title: AMO1_RNA

city: Copenhagen N

first: Kim

middle: B

last: Jensen

address: Belgdamsvej 3B

country: Denmark

institute: University of Copenhagen

data_processing:
FASTQ files were generated using 10x Genomics Cell Ranger 6.1.0
The salmon alevin w/feature barcodes pipeline was used to pseudo-quantify the HTO and RNA reads. Salmon v1.4.0 was used with the mm10 transcriptome.
The downstream analysis was performed using Seurat v4.3.0.
Assembly: mm10
Supplementary files format and content: Processed salmon alevin output: AMO1_210702_RNA.csv
Supplementary files format and content: Processed salmon alevin output: AMO1_210702_HTO.csv

source_name: Small intestinal epithelium

extract_protocol: Five samples containing 2 biological replicates from control cultures and 3 biological replicates from mutant Etv1 cultures, subjected to cell sorting and tagged using hashtag oligos. Subsequently, samples were pooled and sequenced with Illumina NovaSeq 6000 platform.

value: Small intestinal epithelium

value: Epithelial

tag: library type

value: mRNA


title: Test

type: RNA

city: Guilin

first: gengshuo

last: chen

address: No. 212, Renmin Road, Guilin

institute: The Second Affiliated Hospital of Guilin Medical University

description: test

hyb_protocol: Cy3 labeled small RNAs were hybridized to Arraystar Human Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: The labeled RNA was hybridized onto Arraystar Human small RNA Microarray (8x15K, Arraystar) and the array was scanned by an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 6 samples were retained. Multiple probes from the same small RNA (miRNA/TsRNA (tRF&tiRNA)/pre-miRNA/tRNA/snoRNA) were combined into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmaps, scatter plots, and volcano plots were plotted to display small RNAs expression pattern among samples by R software.

source_name: ipsc

label_protocol: Each sample, 100 ng total RNA was firstly dephosphorylated to form the 3-OH end. The 3-OH ended RNA was then denatured by DMSO and enzymatically labeled with Cy3.

growth_protocol: The AF cells were dispensed into 15 ml centrifuge tubes and centrifuged at 645g (8 minutes) at room temperature. The supernatant was carefully removed using a sterile pipette, leaving approximately 2 ml of precipitate. The cell precipitates were mixed and inoculated separately into culture bottles containing medium A and B. One milliliter of mixed precipitate was added to each bottle. The inoculated bottles were placed in a CO2 incubator at 37°C with a 5% CO2 concentration. After harvesting, G-banded chromosome karyotyping was performed. The remaining AF cells from patients confirmed with DS were further cultured for the subsequent construction of iPSCs.

extract_protocol: Total RNA was extracted using TRIzol reagent (Takara) following the manufacturer's protocol. RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by Bioanalyzer 2100 or gel electrophoresis.

treatment_protocol: The AF cells were reprogrammed using the Reproeasy hiPSC Reprogramming Kit (Cellapy Beijing Biotechnology, China).  Once the clones reached a specific size, iPSC colonies were manually selected based on morphology and inoculated in PSCeasy Human Multipotent Stem Cell Resuscitation Medium (Cellapy, Cat. CA1003100). After cell adhesion, cells were transferred to PGM1 Human Multipotent Stem Cell Medium (Cellapy, Cat. CA1007500) to continue culture to the desired number of generations to obtain the target iPSCs. Finally, the iPSCs were cultured in ncEpic hPSC Medium (RP01001, Nuwacell Biotechnologies, Anhui,China) for subsequent experiments.

tag: group

value: Test

value: AF cells


title: Neuroepithelium of cynomolgus monkey WT3

value: Embryo

value: ES-A

value: neuroepithelium cells


title: D701_HTO

library_source: other

molecule: protein

value: HTO

tag: hto


title: Contral replication 2


title: Control

description: control

value: Control


title: Contral replication 1


title: Neuroepithelium of cynomolgus monkey WT2


title: RNA

data_processing:
FASTQ files were generated using 10x Genomics Cell Ranger 6.1.0
The salmon alevin w/feature barcodes pipeline was used to pseudo-quantify the HTO and RNA reads. Salmon v1.4.0 was used with the mm10 transcriptome.
The downstream analysis was performed using Seurat v4.3.0.
Assembly: mm10
Supplementary files format and content: Processed salmon alevin output: MMA_210702_RNA.csv
Supplementary files format and content: Processed salmon alevin output: MMA_210702_HTO.csv

extract_protocol: none provided

value: C57BL/6J mice


title: HTO

value: 3D culture:A0301,A0302; Engineered tissues:A0303,A0304


title: Neuroepithelium of cynomolgus monkey WT1


title: Macaca_colorectal_PostVaccine_17

city: Bethesda

first: Jay

middle: A

last: Berzofsky

state: MD

address: Building 41 Room D702D

department: Center for Immuno-Oncology

institute: National Cancer Institute

description:
Library name: Berzofsky_44
Mouse: DEK3

data_processing:
Raw FASTQ’s were trimmed for adapter sequences and low-quality sequences using CutAdapt.
Trimmed FASTQ files were aligned to the Macaca mulatta reference genome (Mmul_10) using STAR (1) in 2pass mode
Raw counts were produced using RSEM
Assembly: Mmul_10
Supplementary files format and content: Tap-delimited text file includes raw counts for each sample

organism: Macaca mulatta

source_name: colorectal

extract_protocol:
cells were thawed, and washed with R10 medium, Trizol was added to the cells, and total RNA isolation kits from Zymo research were used for RNA isolation
TruSeq Stranded mRNA kit (Illumina) was used for the RNA-Seq library construction

treatment_protocol: Mucosal SHIV vaccine was administered to a subset of macaques. Colorectal tissues were extracted before and after vaccine was administered and cut into small pieces and incubated with Liberase (Roche) at 37ÊC for 30 min after rinsing 3 times with 1XHBSS containing 5mM EDTA and 1-2mM DTT to remove intestinal intraepithelial lymphocytes. The tissue chunks were then mashed through a syringe end and filtered through a 100 μm cell strainer. After 2-3 washes with1XHBSS, the cells were re-suspended and spun down at 800xg at room temperature (25˚C) for 20 min in 40% /80 % Percoll.  The cells were washed three times with R10 medium before being cryopreserved in liquid nitrogen freezers.

value: colorectal

value: Post-Vaccine


title: Macaca_colorectal_PostVaccine_15

description:
Library name: Berzofsky_43
Mouse: DEEZ


title: Macaca_colorectal_PostVaccine_25

description:
Library name: Berzofsky_47
Mouse: 823_KLK


title: Macaca_colorectal_PostVaccine_14

description:
Library name: Berzofsky_42
Mouse: H162


title: Neuroepithelium of cynomolgus monkey MT1

value: SHROOM3 knockout


title: CN,SMC1_ETP_ChIP_2

city: Dallas

first: Morgan

last: Crewe

state: TX

address: 2201 Inwood Road, NC6.506

department: Psychiatry

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Raw fastq.gz sequencing reads were analyzed for quality control using fastq.gzC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: Primary Cortical Neuron

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. Etoposide (ETP, 50µM, Sigma E1383) was dissolved in DMSO. Cells were treated by adding drug directly to the culture media 30 minutes prior to collection

extract_protocol:
ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with appropriate antibody overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated protein-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

treatment_protocol: DIV13 primary cortical neurons were bath stimulated with 10 micromolar etoposide (ETP) for 30 minutes prior to collection or with 50 micromolar NMDA for 10 minutes followed by washout and recovery in drug-free media for 50 minutes prior to collection

value: Primary Cortical Neuron

tag: chip antibody

value: SMC1 (Bethyl, A300-055A)

value: WT

value: ETP


title: inner medulla, NFAT5-KO, rep3

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

country: Germany

institute: University Hospital Halle (Saale)

description: MedullaKO.mRp.clN.bigWig

data_processing:
ATAC-seq bioinformatics analysis was done using the nf-core atacseq pipeline v1.2.1 34, with “--genome GRCm39 --macs_gsize 2468088461”, and default settings otherwise
The broad peak results of the three replicates per tissue were merged.
For visualization, bigwig files were generated.
Assembly: GRCm39
Supplementary files format and content: mRp.clN.bigWig: bigWig files for visualization

source_name: renal inner medulla

growth_protocol: NFAT5fl/fl-AQP2-470 CRE+/- mice and Aqp2-Cre+/- mice were used.

extract_protocol:
Fresh kidneys were removed from six mice. A small piece of renal cortex tissue (approx. 2 mm) and the renal inner medulla from each single kidney were extracted.
ATAC was performed with 100.000 cells per sample using the ActiveMotif ATAC-seq kit (Carlsbad, CA), according to the manufacturer's instructions (manual version B6) for tagmentation and purification. For the library preparation a total of 10 µl of purified tagmented DNA was indexed and pre-amplified for initial 5 PCR cycles with 1x KAPA HiFi HotStart Readymix and 100 nM unique dual index P5 and P7 primers compatible with Illumina Nextera DNA barcoding, under the following PCR conditions: 72°C for 5 min, 98°C for 30 s, thermocycling for 5 cycles at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Subsequently, a qPCR on the LightCycler 480 (Roche) was performed with 1 µl of the pre-amplified material to determine the remaining PCR cycle numbers (8, 9, or 11) to avoid saturation and potential biases in library amplification 33. Purification and double-sided size selection of amplified libraries was done with AMPure XP beads (Beckmann Coulter; starting with a 1.55x volume of XP bead purification, followed by a 0.6x/1.55x double-sided size selection), checked for their quality on a Fragment Analyzer (Agilent) and quantified using qPCR.

value: renal inner medulla


title: CN,SMC1_ETP_ChIP_1


title: Patient 22, differentiated

city: Essen

first: Karim

last: Al-Ghazzawi

address: Hufelandstraße 55

department: Ophthalmology

institute: University-Clinic Duisburg-Essen

hyb_protocol: Hybridizations were performed using the high-sensitivity protocol on the nCounter Prep-Station

scan_protocol: Post-hybridization processing was performed by using the nCounter MAX/FLEX System (NanoString) and the cartridge was scanned on the Digital Analyzer (NanoString)

data_processing:
NanoString data processing was done with the “R i386 statistical programming environment” v4.0.3, Subsequently,  a biological normalization using the included RNA reference genes was performed. Additionally, all counts with p>0.05 after one-sided t-test versus negative controls plus 2x standard deviations were interpreted as not expressed to overcome basal noise
Procesed data "normalized_signal_intensity.txt" is linked as a supplementary file on the Series record.

label: fluorescent marker barcode

source_name: retinoblastoma, differentiated

label_protocol: According to nCounter protocol.

extract_protocol:
100 ng sample input were used for each reaction.
Total RNA concentrations were measured using a Nanodrop 1000 instrument (Thermo Fisher Scientific, Waltham, USA)

tag: individual

value: Patient 22

value: retinoblastoma

tag: histopathological classification

value: differentiated


title: inner medulla, NFAT5-KO, rep2

description: MedullaKO.mRp.clN.bigWig


title: CN,SMC1_NMDA_ChIP_2

value: NMDA


title: Macaca_colorectal_PostVaccine_13

description:
Library name: Berzofsky_41
Mouse: GB5V


title: inner medulla, NFAT5-KO, rep1

description: MedullaKO.mRp.clN.bigWig


title: replication 1 of colony 1 knocking down METTL3 in cells

value: thyroid cancer cells


title: Patient 20, differentiated

value: Patient 20


title: CN,SMC1_NMDA_ChIP_1


title: inner medulla, WT, rep3

description: MedullaWT.mRp.clN.bigWig


title: Macaca_colorectal_PostVaccine_20

description:
Library name: Berzofsky_45
Mouse: R298


title: Macaca_colorectal_PostVaccine_12

description:
Library name: Berzofsky_40
Mouse: DX8T


title: CN,SMC1_CON_ChIP_2


title: inner medulla, WT, rep2

description: MedullaWT.mRp.clN.bigWig


title: Patient 19, differentiated

value: Patient 19


title: CN,SMC1_CON_ChIP_1


title: Patient 18, differentiated

value: Patient 18


title: Patient 23, differentiated

value: Patient 23


title: inner medulla, WT, rep1

description: MedullaWT.mRp.clN.bigWig


title: Patient 17, differentiated

value: Patient 17


title: Macaca_colorectal_PreVaccine_4

description:
Library name: Berzofsky_4
Mouse: MAB

value: colorectal

value: Pre-Vaccine


title: CN,SMC1_Input

value: Primary Cortical Neuron


title: Macaca_colorectal_PostVaccine_11

description:
Library name: Berzofsky_39
Mouse: DX7L

value: Post-Vaccine


title: Patient 16, differentiated

value: Patient 16


title: cortex, NFAT5-KO, rep3

description: CortexKO.mRp.clN.bigWig

source_name: renal cortex

value: renal cortex


title: cortex, NFAT5-KO, rep2

description: CortexKO.mRp.clN.bigWig


title: CN, CTCF_ETP_ChIP_2

value: WT

value: ETP


title: Macaca_colorectal_PostVaccine_9

description:
Library name: Berzofsky_37
Mouse: GB7P


title: Macaca_colorectal_PostVaccine_8

description:
Library name: Berzofsky_36
Mouse: DX7E


title: Macaca_colorectal_PostVaccine_7

description:
Library name: Berzofsky_35
Mouse: DFMZ


title: Patient 15, differentiated

value: Patient 15

value: retinoblastoma


title: CN, CTCF_ETP_ChIP_1


title: CN,CTCF_NMDA_ChIP_2

value: NMDA


title: Patient 21, differentiated

value: Patient 21

value: differentiated


title: Patient 14, differentiated

value: Patient 14


title: cortex, NFAT5-KO, rep1

description: CortexKO.mRp.clN.bigWig


title: Macaca_colorectal_PostVaccine_6

description:
Library name: Berzofsky_34
Mouse: DF07


title: cortex, WT, rep3

description: CortexWT.mRp.clN.bigWig


title: CN,CTCF_NMDA_ChIP_1


title: Patient 13, differentiated

value: Patient 13


title: Macaca_colorectal_PostVaccine_5

description:
Library name: Berzofsky_33
Mouse: DEZT


title: CN,CTCF_CON_ChIP_2


title: Patient 12, undifferentiated

source_name: retinoblastoma, undifferentiated

value: Patient 12

value: undifferentiated


title: Patient 11, undifferentiated

value: Patient 11


title: Macaca_colorectal_PostVaccine_3

description:
Library name: Berzofsky_31
Mouse: ML9

value: colorectal


title: cortex, WT, rep1

description: CortexWT.mRp.clN.bigWig


title: Macaca_colorectal_PreVaccine_3

description:
Library name: Berzofsky_3
Mouse: ML9

value: Pre-Vaccine


title: CN,CTCF_Input

value: Primary Cortical Neuron


title: Patient 10, undifferentiated

value: Patient 10


title: RNA-Seq of soybean carpels replicate 1

city: Ithaca

first: Nicole

last: Szeluga

state: NY

address: 236 Tower Road

department: Plant Biology

institute: Cornell University

data_processing:
Fastp for quality control and trimming, Kallisto for alignment to the CDS and pseudocounts,
Assembly: Wm82.a4.v1.CDS
Supplementary files format and content: tsv file with effective length, estimated counts, and tpm

organism: Glycine max

source_name: Young Bud

growth_protocol: Growth Chamber

extract_protocol:
Qiagen Plant RNA mini-kit
QuantSeq FWD kit

value: Young Bud

value: Williams 82


title: Patient 9, undifferentiated

value: Patient 9


title: RNA-Seq of soybean carpels replicate 2


title: CN, RNAseq_ NMDA_2

data_processing:
Raw fastq.gz sequencing reads were trimmed using Trimmomatic and aligned to the mm10 reference genome (GRCm38.p6 assembly) using TopHat. The aligned reads were processed by the HTSeq-Count pipeline and relative transcript abundance was measured by transcripts per million mapped fragments (TPM).
Assembly: mm10
Supplementary files format and content: raw counts (.txt)

extract_protocol:
Total RNA was extracted from two biological replicates of DIV13 primary cortical neurons (~5 million cells per replicate) using the Qiagen RNeasy Plus Universal Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was assessed using an Agilent Tapestation 4200, and only RNA with RIN score of 8 or higher was used for library preparation. Prior to library preparation, samples were treated with DNase to remove any residual DNA, and RNA concentration was measured by fluorometry (RNA high sensitivity Qubit assay, Thermo).
RNA libraries were prepared for sequencing using a TruSeq stranded mRNA library prep kit with single-end adapters (Illumina) according to the manufacturer’s instructions. Prior to sequencing, library quality was assessed using an Agilent Tapestation 4200, and sample concentration was measured by fluorometry (dsDNA high sensitivity Qubit assay, Thermo). Samples were pooled and sequenced on an Illumina NextSeq 500 instrument with V2.5 reagents to an average depth of 35-45 million reads per replicate.

treatment_protocol: DIV13 primary cortical neurons were bath stimulated with 50 micromolar NMDA for 10 minutes followed by washout and recovery in drug-free media for 50 minutes prior to collection

value: WT


title: RNA-Seq of soybean carpels replicate 3


title: Macaca_colorectal_PreVaccine_28

description:
Library name: Berzofsky_28
Mouse: 822_GB5


title: RNA-Seq of soybean stamens replicate 1


title: Macaca_colorectal_PostVaccine_1

description:
Library name: Berzofsky_29
Mouse: MLP

value: Post-Vaccine


title: Patient 8, undifferentiated

value: Patient 8

value: retinoblastoma


title: CN, RNAseq_NMDA_1

value: NMDA


title: Patient 7, undifferentiated

value: Patient 7


title: Macaca_colorectal_PreVaccine_27

description:
Library name: Berzofsky_27
Mouse: 825_MG6


title: RNA-Seq of soybean stamens replicate 2


title: Macaca_colorectal_PreVaccine_26

description:
Library name: Berzofsky_26
Mouse: 824_KMV


title: cortex, WT, rep2

description: CortexWT.mRp.clN.bigWig

value: renal cortex


title: Patient 6, undifferentiated

value: Patient 6


title: RNA-Seq of soybean stamens replicate 3


title: CN, RNAseq_CON_2


title: Macaca_colorectal_PreVaccine_25

description:
Library name: Berzofsky_25
Mouse: 823_KLK


title: Macaca_colorectal_PostVaccine_4

description:
Library name: Berzofsky_32
Mouse: MAB


title: Patient 5, undifferentiated

value: Patient 5

value: undifferentiated


title: CN,CTCF_CON_ChIP_1


title: RNA-Seq of soybean petals replicate 1


title: CN, RNAseq_CON_1


title: CN, RNAseq_NMDA_3


title: Macaca_colorectal_PreVaccine_24

description:
Library name: Berzofsky_24
Mouse: 821_JHM

value: colorectal


title: Patient 4, undifferentiated

value: Patient 4


title: Patient 3, undifferentiated

value: Patient 3


title: Macaca_colorectal_PreVaccine_23

description:
Library name: Berzofsky_23
Mouse: 861

value: Pre-Vaccine


title: Patient 2, undifferentiated

value: Patient 2


title: Macaca_colorectal_PreVaccine_22

description:
Library name: Berzofsky_22
Mouse: R59


title: RNA-Seq of soybean petals replicate 3

value: Young Bud

value: Williams 82


title: RNA-Seq of soybean sepals replicate 1


title: Ptger4KO_PGE2-H3K27ac_rep1

city: Cold Spring Harbor

first: Aybuke

last: Alici

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing data was aligned and processed by CUT&RUNtools using all read fragments without filtering for read length
Peaks were called by seacr and macs2 (narrow peaks for H3K27ac)
Assembly: mm10
Supplementary files format and content: tab-separated text file of peak calls
Library strategy: Cut&Run

source_name: Intestinal Organoids

growth_protocol: Mouse intestinal organoids were generated from isolated mouse crypts and seeded into Matrigel using the media supplemented with in Advence DMEM (Gibco) media, recombinant murine EGF 40 ng/ml (PeproTech), recombinant murine Noggin 50 ng/ml (PeproTech), R-spondin 62.5 ng/ml (R&D Systems), N-acetyl-L-cysteine 1 uM (Sigma-Aldrich), CHIR-99021 5 uM (Tocris), Y-27632 20 ng/ml (Tocris), B27 1X (Gibco), N2 1X (Gibco)

extract_protocol:
Dissociated intestinal organoids were processed for CUTnRUN following protocol from https://www.nature.com/articles/nprot.2018.015. Antidobies used in our studies are anti-H3K27me3 (07-449, Millipore, 1:100), anti-H3K27ac (ab4729, Abcam, 1:100), and antiH3K4me3 (05-745R, Millipore, 1:100).
CUTnRUN libraries were prepared with Takara ThruPLEX DNA-Seq kit

treatment_protocol: Intestinal organoids were treated with vehicle, AA 25 µM and PGE2 50 nM for 6 Day

value: Intestinal Organoids

value: mouse intestinal organoids

value: Ptger4 KO

tag: time (day)


title: Macaca_colorectal_PreVaccine_21

description:
Library name: Berzofsky_21
Mouse: R51


title: Ptger4KO_AA-H3K27ac_rep2

tag: cell type

value: AA


title: Patient 1, undifferentiated

value: Patient 1

value: retinoblastoma


title: Ptger4KO_PGE2-H3K27ac_rep2

tag: genotype


title: RNA-Seq of soybean sepals replicate 3


title: CN, RNAseq_CON_3

value: Primary Cortical Neuron

value: WT

tag: treatment


title: Ptger4KO_AA-H3K27ac_rep1

tag: tissue


title: RNA-Seq of soybean sepals replicate 2


title: Macaca_colorectal_PreVaccine_20

description:
Library name: Berzofsky_20
Mouse: R298


title: Macaca_colorectal_PreVaccine_2

description:
Library name: Berzofsky_2
Mouse: A10X010


title: Ptger4KO_Vehicle-H3K27ac_rep2

value: Vehicle


title: Macaca_colorectal_PreVaccine_19

description:
Library name: Berzofsky_19
Mouse: R27


title: RNA-Seq of soybean mature flowers replicate 1

source_name: Mature Flower

value: Mature Flower


title: control

tag: cell line

value: murine adipocytes


title: Macaca_colorectal_PreVaccine_18

description:
Library name: Berzofsky_18
Mouse: DEM7

value: colorectal


title: RNA-Seq of soybean mature flowers replicate 2


title: Ptger4KO_Vehicle-H3K27ac_rep1


title: RNA-Seq of soybean mature flowers replicate 3


title: RNA-Seq of soybean petals replicate 2


title: WT_PGE2-H3K27ac_rep2


title: fibroblasts_right-sided_normal_rep1

city: Kota Bharu

first: Marahaini

last: Musa

state: Kelantan

address: Universiti Sains Malaysia, Health Campus, Kota Bharu

department: Human Genome Centre

country: Malaysia

institute: Universiti Sains Malaysia

description:
Gene expression data from primary fibroblasts derived from resected adjacent normal tissue of right-sided colon
Fibroblasts_RN-1

hyb_protocol: Following fragmentation and labeling, cDNA were hybridized to Human Clariom S Arrray for 16 hrs at 45°C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Applied Biosystems™ GeneChip™ Scanner 3000 7G.

scan_protocol: Arrays were scanned using a GeneChip™ Scanner 3000 7G (Applied Biosystems, Thermo Scientific)

data_processing: Transcriptome Analysis Software 4.0 (TAS 4.0) Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA)

label: biotin

source_name: Primary fibroblasts isolated from resected adjacent normal tissue of the right-sided colon

label_protocol: Biotin-labeled cDNA were prepared according to the standard Affymetrix protocol from 20ng total RNA (GeneChip™ WT PLUS Reagent Kit USER GUIDE)

growth_protocol: Primary fibroblast were cultured in complete medium which include DMEM supplemented with 10% FBS and 3% (10,000 U/ml penicillin 10,000 µg/ml streptomycin) and incubated in a humidified incubator (37ᵒC, 5% CO2). Epithelial colorectal cancer cell line, SW620 was cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin and in humidified incubator (37ᵒC, 5% CO2).

extract_protocol: RNA was extracted using the Rneasy Mini Kit (QIAGEN).

value: normal tissue adjacent to right-sided colorectal cancer tumour

value: primary normal fibroblasts


title: Macaca_colorectal_PreVaccine_17

description:
Library name: Berzofsky_17
Mouse: DEK3

value: Pre-Vaccine


title: RNA-Seq of soybean flower buds replicate 1

source_name: Flower Buds

value: Flower Buds


title: RNA-Seq of soybean flower buds replicate 2

value: Williams 82


title: WT_AA-H3K27ac_rep2

value: Intestinal Organoids


title: Macaca_colorectal_PreVaccine_16

description:
Library name: Berzofsky_16
Mouse: DEK2


title: WT_PGE2-H3K27ac_rep1

value: mouse intestinal organoids


title: Macaca_colorectal_PreVaccine_15

description:
Library name: Berzofsky_15
Mouse: DEEZ


title: Macaca_colorectal_PreVaccine_14

description:
Library name: Berzofsky_14
Mouse: H162


title: WT_AA-H3K27ac_rep1


title: RNA-Seq of soybean flower buds replicate 3


title: WT_Vehicle-H3K27ac_rep2


title: RNA-Seq of soybean leaves replicate 2

source_name: Young Trifoliate

value: Young Trifoliate


title: RNA-Seq of soybean leaves replicate 1


title: Macaca_colorectal_PreVaccine_13

description:
Library name: Berzofsky_13
Mouse: GB5V


title: WT_Vehicle-H3K27ac_rep1


title: Macaca_colorectal_PreVaccine_12

description:
Library name: Berzofsky_12
Mouse: DX8T


title: epithelial cell_cancer_control_rep1

description:
Gene expression data from human epithelial colorectal cancer cell line
Epithelial_SW-1

source_name: Human epithelial colorectal cancer cell line

value: human colorectal cancer cell line

value: epithelial cancer cell line


title: RNA-Seq of A2780 cells, YTHDC1 knockdown (shRNA), replicate 2

city: Xiamen

first: Hong

middle: Xiao

last: ting

state: fujian province

address: 4221 South Xiang'an Road, Xiang'an District, Xiamen, Fujian

department: Medical School

institute: Xiamen university

description:
Library name: A2780-YTHDC1-SH1-2
SH2

data_processing:
Raw sequencing reads in FASTQ format were first subjected to quality control and adapter trimming using Fastp
Assembly: Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 Gene-level counts were obtained with featureCounts
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: ovary

growth_protocol: A2780 cells were cells were cultured in Dulbecco's Modified Eagle Medium（DMEM）with 10% fetal bovine serum , 100 U/ml penicillin and 100 μg/ml streptomycin in a culture medium containing 5% carbon dioxide and at a temperature of 37℃.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using the BGI Optimal Dual-Module mRNA Library Preparation Kit (BGI-Shenzhen, China) according to the manufacturer’s instructions.

treatment_protocol: A2780 cells were transduced with lentiviral supernatant (PLKO-shCtrl or shYHTDC1) in the presence of 4 ug/mL polybrene. The transduced cells were then selected using 1 ug/mL puromycin.

value: ovary

value: ovarian carcinoma epithelial cell

value: YTHDC1 knockdown


title: RNA-Seq of A2780 cells, YTHDC1 knockdown (shRNA), replicate 3

description:
Library name: A2780-YTHDC1-SH1-3
SH3


title: RNA-Seq of soybean leaves replicate 3


title: AA-H3K4me3_rep2

data_processing:
Sequencing data was aligned and processed by CUT&RUNtools using all read fragments without filtering for read length
Peaks were called by seacr and macs2 (narrow peaks for H3K27ac, H3K4me3, broad peaks for H3K27me3)
Assembly: mm10
Supplementary files format and content: tab-separated text file of peak calls
Library strategy: Cut&Run

value: AA


title: fibroblasts_right-sided_cancer_rep2

description:
Gene expression data from primary fibroblasts derived from resected human colorectal cancer of right-sided
Fibroblasts_RC-2

source_name: Primary fibroblasts isolated from resected human colorectal cancer of right-sided

value: right-sided colorectal cancer

value: primary cancer associated fibroblasts (CAF)


title: fibroblasts_left-sided_cancer_rep2

description:
Gene expression data from primary fibroblasts derived from resected human colorectal cancer of left-sided
Fibroblasts_LC-2

source_name: Primary fibroblasts isolated from resected human colorectal cancer of left-sided

value: left-sided colorectal cancer

value: primary cancer associated fibroblasts (CAFs)


title: fibroblasts_left-sided_normal_rep2

description:
Gene expression data from embryos in slow phase of cellularisation.
Fibroblasts_LN-2

source_name: Primary fibroblasts isolated from resected adjacent normal tissue of the left-sided colon

value: normal tissue adjacent to left-sided colorectal cancer tumour

value: primary normal fibroblasts


title: fibroblasts_right-sided_cancer_rep1

description:
Gene expression data from primary fibroblasts derived from resected human colorectal cancer of right-sided
Fibroblasts_RC-1


title: Macaca_colorectal_PreVaccine_11

description:
Library name: Berzofsky_11
Mouse: DX7L

source_name: colorectal

value: colorectal

value: Pre-Vaccine


title: RNA-Seq of A2780 cells, YTHDC1 knockdown (shRNA), replicate 1

description:
Library name: A2780-YTHDC1-SH1-1
SH1


title: fibroblasts_left-sided_normal_rep1

description:
Gene expression data from primary fibroblasts derived from adjacent normal tissue of left-sided colon
Fibroblasts_LN-1


title: fibroblasts_left-sided_cancer_rep1

description:
Gene expression data from primary fibroblasts derived from resected human colorectal cancer of left-sided
Fibroblasts_LC-1


title: Macaca_colorectal_PreVaccine_10

description:
Library name: Berzofsky_10
Mouse: GB7L


title: control4

city: Beijing

first: Rui

last: Lin

address: Chaoyang District

institute: Capital Medical University Affiliated Anzhen Hospital

description: Library name: sample8

data_processing:
Rawdata(raw reads) of fastq format were firstly processed through fastp  software. In this step, clean data (clean reads) were obtained by  removing reads containing adapter, reads containing ploy-N and low  quality reads from raw data. At the same time, Q20, Q30 and GC content  the clean data were calculated. All the downstream analyses were based  on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly
Supplementary files format and content: fastq format

organism: Rattus

source_name: heart

extract_protocol:
Adult rat cardiomyocytes (ACMs) were serum-starved overnight and divided into four groups. They were then treated with palmitoyl-L-carnitine (LCAC C16) (P1645, Sigma-Aldrich), at concentrations of 0150 μM, respectively, for 4 hours.
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers followed by the second  strand cDNA synthesis. The library was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification. The  library was checked with Qubit and real-time PCR for quantification and  bioanalyzer for size distribution detection

value: heart

value: Adult rat cardiomyocytes (ACMs)

value: WT

value: control


title: AA-H3K4me3_rep1

value: Intestinal Organoids

value: mouse intestinal organoids


title: Macaca_colorectal_PreVaccine_1

description:
Library name: Berzofsky_1
Mouse: MLP


title: Vehicle-H3K4me3_rep2

value: Vehicle


title: RNA-Seq of A2780 cells, control (shRNA), replicate 3

description:
Library name: A2780-YTHDC1-shCTRL-3
Ctrl3

value: ovary

value: ovarian carcinoma epithelial cell


title: control3

description: Library name: sample7


title: control2

description: Library name: sample6


title: RNA-Seq of A2780 cells, control (shRNA), replicate 2

description:
Library name: A2780-YTHDC1-shCTRL-2
Ctrl2


title: Vehicle-H3K4me3_rep1


title: IRBP_rep3

city: Milwaukee

first: Xiaolong

last: Ma

state: Wisconsin

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description:
Library name: Sample 9
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

data_processing:
Bulk RNAseq: The aligment were done by STAR v2.7.11b, and transcripts count were done by FeatureCounts under Subread v2.0.8  package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell line

growth_protocol: BMSCs purchased from Lonza Bioscience were cultured in Mesenchymal Stem Cell Growth Medium (MSCGM, Lonza) under standard conditions (37°C, 5% CO₂, and 95% humidity), with media changes every three days.

extract_protocol:
After 7 days of culture, total RNA was extracted from all groups (n=3 per group) using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. RNA concentration was measured using the Nanodrop ND-1000, and quality was assessed via capillary electrophoresis (Agilent Technologies). RNA sequencing (RNA-Seq) was performed by Novogene Corporation Inc. Libraries were prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Illumina), and sequencing was conducted on the NovaSeq 6000 platform (Illumina) to generate paired-end reads.
Total RNA from all groups were sent to Novogene Corporation Inc. (Sacramento, CA) for library preparation and sequencing. Only samples with an RNA integrity number (RIN) ≥ 7 were considered for cDNA library preparation. cDNA libraries were generated using TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), which included an rRNA suppression step.

treatment_protocol: After 24 hours of seeding, BMSCs in the IR and IRBP groups were exposed to a single 10 Gy dose of X-ray irradiation using a Precision CellRad X-ray source. After IR exposure, cells in the IR group were maintained in standard MSCGM medium. In the IR&BP group, BPs were resuspended in MSCGM medium by sonication (final concentration: 20 μg/mL, based on BP dry weight) and added to the cells 4 hours post-IR. The BP-containing medium was maintained for 24 hours before being replaced with fresh MSCGM without BPs.

value: cell line

tag: strain

value: LONZA PT-2501

value: Human Bone marrow Mesenchymal Stem Cells

tag: age

value: exposed to a single 10 Gy dose of X-ray irradiation, 4 hours post-IR, bone nanoparticles were resuspended in MSCGM medium by sonication (final concentration:20 μg/mL, based on BP dry weight) and added to the cells and maintained for 24 hours before being replaced with fresh MSCGM without BPs.


title: RNA-Seq of A2780 cells, control (shRNA), replicate 1

description:
Library name: A2780-YTHDC1-shCTRL-1
Ctrl1


title: control1

description: Library name: sample5


title: AA-H3K27ac_rep2

value: AA


title: LCAC4

description: Library name: sample4

value: high LCAC C16 concentration (150 µM)


title: AA-H3K27ac_rep1


title: TM_4u8C_2

city: Lianyungang

first: yuzien

last: yu

state: Jiangsu

address: 59 Cangwu Road, Haizhou District

department: College of Pharmacy

institute: Jiangsu Ocean University

description:
TM_4u8C_2
MU2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample

source_name: Breast Cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Breast Cancer

value: MDA

value: Human Breast Cancer Cell


title: IRBP_rep2

description:
Library name: Sample 8
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: TM_4u8C_1

description:
TM_4u8C_1
MU1


title: IRBP_rep1

description:
Library name: Sample 7
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: IR_rep3

description:
Library name: Sample 6
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

value: exposed to a single 10 Gy dose of X-ray irradiation


title: Vehicle-H3K27ac_rep1


title: LCAC3

description: Library name: sample3

value: heart

value: Adult rat cardiomyocytes (ACMs)

value: WT


title: TM_melatonin_2

description:
TM_melatonin_2
MM2


title: AA-H3K27me3_rep2

value: Intestinal Organoids

value: mouse intestinal organoids


title: LCAC1

description: Library name: sample1


title: TM_ISRIB_2

description:
TM_ISRIB_2
MI2


title: IR_rep2

description:
Library name: Sample 5
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: TM_melatonin_1

description:
TM_melatonin_1
MM1


title: AA-H3K27me3_rep1


title: TM_ISRIB_1

description:
TM_ISRIB_1
MI1


title: IR_rep1

description:
Library name: Sample 4
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: Vehicle-H3K27me3_rep2

value: Vehicle


title: RD6 (7 DPA) Replication 2

city: Khon Kaen

first: Maysaya

last: Thitisaksakul

address: Mittrapap Road

department: Biochemistry

country: Thailand

institute: Khon Kaen University

description:
Library name: 8_2
Column name in All_FPKM.csv: RD6_7_2

data_processing:
The quality of raw sequencing reads was assessed using FastQC. Low-quality reads were removed through two steps: (I) Fastp was used to filter out reads and bases with a quality score< 30; and (II) Trimmomatic excluded adapter sequences, short reads (length < 100 bp), unpaired reads, and additional low-quality reads.
Cuffquant estimated transcript abundance based on the transcript library. The resulting transcript abundances were normalized by Cuffnorm and scaled to Fragments Per Kilobase Million (FPKM). Transcript expression values were aggregated at the gene level. Genes with FPKM < 0.5 were excluded, and a gene had to be detected in at least two replicates to be included.
Assembly: The processed reads were aligned to the Oryza sativa indica reference genome (GenBank accession: GCA_000004655.2) using HISAT2. Each sample was assembled separately using Cufflinks, guided by the reference genome.
Supplementary files format and content: csv file include FPKM values for each sample

organism: Oryza sativa Indica Group

source_name: Endosperm

growth_protocol: Grains were germinated on Petri dishes and  then transplanted into 64 8” plastic pots and placed in a net house in Completely Randomized Design (CRD) under natural light conditions.

extract_protocol:
The total RNA was extracted from the RD57 and RD6 rice grains at 7, 14, 21, and 21 DPA with three biological replications each using the modified SDS-LiCl method.
We used TruSeq Stranded mRNA Library Prep Kit as of manufacturer's protocols.

value: Endosperm

tag: time

value: 7 DPA


title: Con_rep3

description:
Library name: Sample 3
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

value: cell line

value: LONZA PT-2501

value: No treatment


title: Con_rep2

description:
Library name: Sample 2
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression

value: Human Bone marrow Mesenchymal Stem Cells


title: TM_MG132_2

description:
TM_MG132_2
MG2


title: RD6 (7 DPA) Replication 1

description:
Library name: 8_1
Column name in All_FPKM.csv: RD6_7_1


title: Vehicle-H3K27me3_rep1


title: Con_rep1

description:
Library name: Sample 1
TruSeq Stranded Total RNA Gold Sample Prep Kits, (Illumina), with rRNA suppression


title: PGE2-2

data_processing:
Trimming by TrimGalore, alignment by BWA, filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Please see nfcore atacseq pipeline for more details
Assembly: mm10
Supplementary files format and content: tab-separated text file of peaks and counts

extract_protocol:
DNAs were isolated from 50.000 freshly sorted intestinal epithelial cells by Qiagen MinElute Reaction Cleanup Kit based on Buenrostro et al. papers and Kaestner Lab protocol by using Omni-ATAC-Seq method.
Libraries generation was performed with PCR amplification followed by library purification using Agencourt AMPure XP magnetic beads .

treatment_protocol: Intestinal organoids were treated with Vehicle, AA 25 µM and PGE2 50 nM for 3 days.

value: Mouse intestinal organoids

tag: time (days)


title: RD57 (7 DPA) Replication 3

description:
Library name: 7_3
Column name in All_FPKM.csv: RD57_7_3


title: TM_MG132_1

description:
TM_MG132_1
MG1

value: Breast Cancer


title: RA503 400mM rep5

city: Richmond

first: Laura

last: Mathies

address: 1220 East Broad Street

institute: Virginia Commonwealth University

description: Library name: RA503-400-5

data_processing:
We performed initial quality control using FastQC; the sequencing libraries had high quality scores and did not contain overrepresented sequences indicative of Illumina adapters
Trimmed reads were mapped to the C. elegans genome using the STAR aligner version 2.6.0a
The STAR aligner generated gene-based read counts.
Assembly: Ensembl genome assembly release WBcel325
Supplementary files format and content: Csv file contains raw read counts for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Approximately 100 L4-stage worms from healthy, unstarved populations were placed on ethanol-treated or control plates, the plates were sealed with parafilm and incubated at 20°C for 18 hours. During this time, the animals mature into young adults

extract_protocol:
Total RNA was isolated using the miRNeasy kit with DNase I digestion performed on the column.
RNA was polyA selected and indexed sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: The worms were washed from the plates with M9 medium, rinsed once with M9, and stored in Trizol rinsed once with M9 medium, and stored in Trizol at -80°C until RNA preparation.

value: whole animal

value: hermaphrodite

value: First-day adult

value: 400 mM ethanol


title: RD57 (7 DPA) Replication 2

description:
Library name: 7_2
Column name in All_FPKM.csv: RD57_7_2


title: TM_DMSO_2

description:
TM_DMSO_2
MD2

value: MDA

value: Human Breast Cancer Cell


title: LCAC2

description: Library name: sample2

value: heart

value: Adult rat cardiomyocytes (ACMs)

value: WT

value: high LCAC C16 concentration (150 µM)


title: RA503 400mM rep4

description: Library name: RA503-400-4


title: TM_DMSO_1

description:
TM_DMSO_1
MD1


title: RD57 (7 DPA) Replication 1

description:
Library name: 7_1
Column name in All_FPKM.csv: RD57_7_1

value: Endosperm

value: 7 DPA


title: AA-2

value: Intestinal Organoids

value: AA


title: RD6 (7 DPA) Replication 3

description:
Library name: 8_3
Column name in All_FPKM.csv: RD6_7_3


title: RA503 400mM rep3

description: Library name: RA503-400-3


title: Vehicle-H3K27ac_rep2

value: mouse intestinal organoids

value: Vehicle


title: AA-1

value: Mouse intestinal organoids


title: RA503 400mM rep2

description: Library name: RA503-400-2

value: whole animal


title: TM_2_1

description:
TM_2_1
M21

value: Breast Cancer


title: RD6 (14 DPA) Replication 2

description:
Library name: 6_2
Column name in All_FPKM.csv: RD6_14_2

value: 14 DPA


title: RA503 400mM rep1

description: Library name: RA503-400-1

value: hermaphrodite

value: First-day adult

value: 400 mM ethanol


title: TM_1_2

description:
TM_1_2
M12

value: MDA

value: Human Breast Cancer Cell


title: RD6 (14 DPA) Replication 1

description:
Library name: 6_1
Column name in All_FPKM.csv: RD6_14_1


title: Vehicle-1


title: RA503 0mM rep5

description: Library name: RA503-0-5

value: 0 mM ethanol


title: TM_1_1

description:
TM_1_1
M11


title: RD57 (14 DPA) Replication 3

description:
Library name: 5_3
Column name in All_FPKM.csv: RD57_14_3


title: LSKCD150+CD48- HSCs from mutant mouse, rep3

city: New York

first: Longfei

last: Gao

address: 650 West 168th Street

institute: Columbia University

description: Mut3 samples in RawCountData.csv

data_processing:
Low-quality reads from raw fastq files were trimmed out with Trimmomatic (v0.39) with the following SLIDINGWINDOW, 4:20 and MINLEN: 20.
Trimmed reads were mapped to the mouse genome (mm10) and counted with Rsubread (v2.10.4).
Differential expressing gene analysis was performed with DESeq2 (v1.36.0).
Assembly: mm10
Supplementary files format and content: The csv files represents raw counts generated with featureCounts function in Rsubread package.

source_name: bone marrow

extract_protocol:
About 500 adult bone marrow LSKCD150+CD48- HSCs were FACS sorted into 0.2% Triton X-100 and then proceeded to library preparation following Smart-seq2 method
Following smart-seq2 method (Simone Picelli et al., Nature Protocol, 2014)

value: bone marrow

value: LSKCD150+CD48- HSCs

value: hematopoietic stem cells

value: Vav1-cre; Rbfox2-fl/fl


title: RD57 (14 DPA) Replication 2

description:
Library name: 5_2
Column name in All_FPKM.csv: RD57_14_2

value: Endosperm


title: TM_0_5_2

description:
TM_0_5_2
M02


title: RA503 0mM rep3

description: Library name: RA503-0-3


title: TM_0_5_1

description:
TM_0_5_1
M01


title: PGE2-1

source_name: Intestinal Organoids

value: Intestinal Organoids


title: LSKCD150+CD48- HSCs from mutant mouse, rep2

description: Mut2 samples in RawCountData.csv


title: RD57 (14 DPA) Replication 1

description:
Library name: 5_1
Column name in All_FPKM.csv: RD57_14_1


title: TM_2_2

description:
TM_2_2
M22


title: RD6 (21 DPA) Replication 3

description:
Library name: 4_3
Column name in All_FPKM.csv: RD6_21_3

value: 21 DPA


title: TG_4u8C_2

description:
TG_4u8C_2
GU2


title: LSKCD150+CD48- HSCs from mutant mouse, rep1

description: Mut1 samples in RawCountData.csv


title: TG_4u8C_1

description:
TG_4u8C_1
GU1


title: RA503 0mM rep1

description: Library name: RA503-0-1


title: RD6 (14 DPA) Replication 3

description:
Library name: 6_3
Column name in All_FPKM.csv: RD6_14_3


title: RD6 (21 DPA) Replication 2

description:
Library name: 4_2
Column name in All_FPKM.csv: RD6_21_2


title: Vehicle-2

value: Mouse intestinal organoids

value: Vehicle


title: LSKCD150+CD48- HSCs from control mouse, rep3

description: Ctrl3 samples in RawCountData.csv


title: RD6 (21 DPA) Replication 1

description:
Library name: 4_1
Column name in All_FPKM.csv: RD6_21_1


title: LSKCD150+CD48- HSCs from control mouse, rep2

description: Ctrl2 samples in RawCountData.csv


title: LSKCD150+CD48- HSCs from control mouse, rep1

description: Ctrl1 samples in RawCountData.csv


title: N2R 400 mM rep4

description: Library name: N2R-400-4

value: whole animal

value: wild type


title: TG_melatonin_2

description:
TG_melatonin_2
GM2

value: Breast Cancer


title: TG_melatonin_1

description:
TG_melatonin_1
GM1


title: N2R 400 mM rep3

description: Library name: N2R-400-3

value: hermaphrodite

value: First-day adult


title: RD57 (21 DPA) Replication 3

description:
Library name: 3_3
Column name in All_FPKM.csv: RD57_21_3


title: TG_ISRIB_2

description:
TG_ISRIB_2
GI2

value: MDA


title: RD57 (21 DPA) Replication 2

description:
Library name: 3_2
Column name in All_FPKM.csv: RD57_21_2


title: RA503 0mM rep4

description: Library name: RA503-0-4


title: N2R 400 mM rep2

description: Library name: N2R-400-2

value: 400 mM ethanol


title: N2R 400 mM rep1

description: Library name: N2R-400-1


title: TG_MG132_2

description:
TG_MG132_2
GG2

value: Human Breast Cancer Cell


title: RD57 (21 DPA) Replication 1

description:
Library name: 3_1
Column name in All_FPKM.csv: RD57_21_1


title: RA503 0mM rep2

description: Library name: RA503-0-2

value: 0 mM ethanol


title: TG_ISRIB_1

description:
TG_ISRIB_1
GI1


title: RD6 (28 DPA) Replication 3

description:
Library name: 2_3
Column name in All_FPKM.csv: RD6_28_3

value: 28 DPA


title: N2R 0mM rep5

description: Library name: N2R-0-5


title: RD6 (28 DPA) Replication 2

description:
Library name: 2_2
Column name in All_FPKM.csv: RD6_28_2


title: V3

city: Birmingham

first: Mingyong

last: Liu

state: AL

address: SHEL 531, 1825 University Blvd

department: Clinical Immunology and Rheumatology

institute: University of Alabama at Birmingham

data_processing:
Cell barcodes were demultiplexed, and reads were aligned to the mm10 genome and normalized across samples for aggregation using the Cell Ranger pipelines (cellranger mkfastq, count and aggr) provided by 10X Genomices.
The gathered matrix was processed using the R package Seurat (version 2.3.1). Cells with the total number of genes between 200 and 5000 and UMI lower than 60,000 were kept. We further excluded cells whose mitochondrial gene counts accounted for more than 10% of total counts.
By plotting the expression of Cd8a, Cd8b1 Cd3e, Cd247, Lck and Bst2, we found that 4 cell clusters (cluster 8, 12, 15 and 16) expressed high levels of Bst2 but not hallmark T cell genes such as Cd3e, Cd247 and Lck. This suggests that they represented non-T cell contaminants and were thus discarded from downstream analyses.
Counts from the raw data slot of the SeuratObject was extract and saved as a comma-separated values file.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values file that includes raw counts of sequencing reads for each sample

source_name: breast tumors

growth_protocol: The TS/A murine mammary adenocarcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum and 2% L-glutamine, penicillin, streptomycin solution. Mice were injected with 1x10^5 TS/A cells in the second mammary pad.

extract_protocol:
Tumors were excised and infiltrating CD8+ T cells were collected directly into PBS (Corning) with 0.04% Bovine Serum Albumin (Thermo Fisher).
Single cell libraries were prepared according to the protocol for Chromium Single Cell 3' Reagent Kit v2 (10X Genomics). Briefly, sorted CD8+ T cells, barcoded single cell 3ʹ gel beads and partitioning oil were loaded onto a Single Cell A Chip, and single cell Gel Bead-In-EMulsions (GEMs) were generated by Chromium controller. Barcoded cDNA was then produced by the incubation of GEMs and amplified by PCR after the GEMs were broken to generate sufficient mass.

treatment_protocol: Tumor-bearing mice were treated with 20mg/kg ENT or Vehicle daily starting on day 7 after tumor cell injection.

value: BALB/c

value: breast tumors

tag: sorting markers

tag: time point

value: day17 post tumor injection


title: E4

value: Entinostat (ENT)


title: V4


title: V1


title: V2


title: TG_MG132_1

description:
TG_MG132_1
GG1


title: N2R 400 mM rep5

description: Library name: N2R-400-5


title: N2R 0mM rep4

description: Library name: N2R-0-4


title: E3


title: RD6 (28 DPA) Replication 1

description:
Library name: 2_1
Column name in All_FPKM.csv: RD6_28_1

value: Endosperm


title: TG_DMSO_1

description:
TG_DMSO_1
GD1


title: TG_DMSO_2

description:
TG_DMSO_2
GD2


title: E2


title: TG_2_2

description:
TG_2_2
G22


title: N2R 0mM rep2

description: Library name: N2R-0-2


title: RD57 (28 DPA) Replication 2

description:
Library name: 1_2
Column name in All_FPKM.csv: RD57_28_2


title: N2R 0mM rep1

description: Library name: N2R-0-1


title: TG_2_1

description:
TG_2_1
G21


title: N2 400mM rep5

description: Library name: N2-400-5


title: TG_1_2

description:
TG_1_2
G12


title: Yeast PRP40 wild-type at 30 degree

city: Taipei

first: LUH

last: TUNG

address: No. 128 Sec. 2 Academia Rd. Nankang Dist

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Library name: PRP40 wild-type

data_processing:
sequencing reads are separated based on the adaptor on both 5' adaptor and 3' adaptor
The sequence without adaptors were blasted to S288C S. cerevisiae using bowtie-0.12.9
Reads from bowtie was further match to S288C gff files to identify the gene name for the corresponding position
The sel-1 intermediate reads were filtered for additional poly nucleotides using python scripts
Assembly: S288C
Supplementary files format and content: Tab-delimited text files include normalized values for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured in 50 ml of liquid YPD medium at 30°C to reach OD600=0.8.

extract_protocol:
RNA was extracted by using "MasterPure™ Yeast RNA Purification Kit (Epicentre)" followed by "Ribo-Zero™ Magnetic Gold Kit (Yeast)"
Libraries were contructed by "TruSeq Stranded mRNA Preparation Kit (illumina)"

value: Haploid


title: N2 400mM rep4

description: Library name: N2-400-4


title: TG_0_5_2

description:
TG_0_5_2
G02


title: TG_1_1

description:
TG_1_1
G11


title: d17_Con_CD8_4

data_processing:
FASTQ reads were mapped to the mm10 mouse genome using STAR with the default parameters and the UCSC KnownGene transcriptome database.
The coverage at exons for all unique Entrez genes was computed using custom R/Bioconductor scripts and the GenomicRanges package.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values file that includes raw counts of sequencing reads for each sample

extract_protocol:
Tumors were excised and infiltrating CD8+ T cells were collected directly into Qiagen RLT buffer plus 2-mercaptoethanol (Sigma). Total RNA was purified using the Quick-RNA MicroPrep kit.
Total RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). The resulting cDNA was then used as input for the NexteraXT kit (Illumina) for tagmentation, PCR amplification and indexing. Final libraries were quantitated by Qubit, pooled at equimolar ratio.

value: Vehicle


title: TG_0_5_1

description:
TG_0_5_1
G01


title: d17_Con_CD8_3


title: N2 400mM rep2

description: Library name: N2-400-2

value: whole animal


title: WT_2

city: Singapore

first: Ajay

last: Mathuru

state: Singapore

address: 28 Medical Drive, #5-COR

department: Physiology

country: Singapore

institute: NUS

data_processing:
Raw reads were first processed by Novogene-AIT to remove adapter, poly-N sequences, and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy
Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software, v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner, default parameters, and subsequently filtered to a minimum mapping quality score of > 30.
Assembly: GRCz11 genome assembly by STAR aligned
Supplementary files format and content: STAR aligned

source_name: whole brain

extract_protocol:
The quality of each sample was verified by gel electrophoresis and bio-analyser.
Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired-end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.

value: whole brain

value: WT


title: N2R 0mM rep3

description: Library name: N2R-0-3

value: hermaphrodite

value: wild type


title: N2 400mM rep3

description: Library name: N2-400-3

value: First-day adult


title: WT_3


title: FCCP_3_MA_2

description:
FCCP_3_MA_2
FM2

value: Breast Cancer

value: MDA


title: d17_Con_CD8_2


title: RD57 (28 DPA) Replication 3

description:
Library name: 1_3
Column name in All_FPKM.csv: RD57_28_3


title: d17_Con_CD8_1


title: WT_1


title: N2 400mM rep1

description: Library name: N2-400-1

value: 400 mM ethanol


title: chrna3C246X_3

value: chrna3 C246X


title: E1

value: BALB/c


title: N2 0mM rep5

description: Library name: N2-0-5

value: 0 mM ethanol


title: RD57 (28 DPA) Replication 1

description:
Library name: 1_1
Column name in All_FPKM.csv: RD57_28_1

value: 28 DPA


title: chrna3C246X_2


title: N2 0mM rep4

description: Library name: N2-0-4


title: FCCP_MG132_2

description:
FCCP_MG132_2
FG2

value: Human Breast Cancer Cell


title: chrna3C246X_1


title: d17_ENT_CD8_4

value: breast tumors

value: Entinostat (ENT)

value: day17 post tumor injection


title: d17_ENT_CD8_1


title: N2 0mM rep3

description: Library name: N2-0-3

value: whole animal


title: d10_ENT_CD8_4

value: day10 post tumor injection


title: FCCP_MG132_1

description:
FCCP_MG132_1
FG1


title: FCCP_DMSO_2

description:
FCCP_DMSO_2
FD2


title: RPA135(F301S)-HTP - treated wtih BMH-21 - sample 2

city: Toulouse

first: olivier

last: Gadal

address: 169 av. Marianne Grunberg_Manago

department: UMR5087 CNRSS

country: France

institute: centre de biologie integrative (CBI)

description: CDE12 SuperPol I + BMH

data_processing:
*library strategy: CRAC
UMI extraction with umi_tools version 1.1.2
Adapter content removal with cutadapt version 1.18
Alignment with Novoalign version 3.09.00 on yeast genome EF2.59.1 (R63-1-1)
Conversion, completion and sorting with samtools version 1.14
Deduplication with in-house script available on our github
Assembly: yeast genome EF2.59.1 (R63-1-1)
Supplementary files format and content: bedgraph files containing aligned and deduplicated sorted reads

source_name: yeast cells

extract_protocol:
CRAC method
Cross-linking and analysis of cDNAs (CRAC)

value: yeast cells

tag: strain background


title: N2 0mM rep2

description: Library name: N2-0-2

value: hermaphrodite


title: FCCP_DMSO_1

description:
FCCP_DMSO_1
FD1


title: RPA135(F301S)-HTP - treated wtih BMH-21 - sample 1


title: N2 0mM rep1

description: Library name: N2-0-1

value: wild type


title: d17_ENT_CD8_3


title: RPA135(WT)-HTP - treated wtih BMH-21 sample 2

description: CDE11 WT Pol I +BMH21


title: d10_ENT_CD8_3


title: d10_ENT_CD8_2


title: RPA135(WT)-HTP - treated wtih BMH-21 sample 1


title: RPA135(F301S)-HTP - sample 3

data_processing:
UMI extraction with umi_tools version 1.1.2
Adapter content removal with cutadapt version 1.18
Alignment with Novoalign version 3.09.00 on yeast genome EF2.59.1 (R63-1-1)
Conversion, completion and sorting with samtools version 1.14
Deduplication with in-house script available on our github
Assembly: yeast genome EF2.59.1 (R63-1-1)
Supplementary files format and content: bedgraph files containing aligned and deduplicated sorted reads
Library strategy: CRAC

molecule: other


title: FCCP_5_2

description:
FCCP_5_2
F52


title: FCCP_3_MA_1

description:
FCCP_3_MA_1
FM1


title: RPA135(F301S)-HTP - sample 2


title: d10_ENT_CD8_1


title: d17_ENT_CD8_2


title: RPA135(F301S)-HTP - sample 2


title: RPA135(F301S)-HTP - sample 1


title: FCCP_5_1

description:
FCCP_5_1
F51


title: FCCP_2.5_2

description:
FCCP_2.5_2
F22


title: RPA135(F301S)-HTP - sample 1


title: d10_Con_CD8_3

value: Vehicle


title: RPA135(WT)-HTP - sample 3


title: FCCP_2.5_1

description:
FCCP_2.5_1
F21

value: Breast Cancer


title: RPA135(WT)-HTP - sample 2


title: RPA135(WT)-HTP - sample 2


title: d10_Con_CD8_1


title: FCCP_1.25_2

description:
FCCP_1.25_2
F12

value: MDA


title: RPA135(WT)-HTP - sample 1


title: OE_5_8F

status: Public on Oct 31 2025

city: Guangzhou

first: zixuan

last: chen

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guangzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

description:
Library name: sample10
gene_fpkm.2.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: gene_fpkm.1.txt
Supplementary files format and content: gene_fpkm.2.txt

source_name: nasopharyngeal carcinoma

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer®spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of theBioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperaturein NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequentlyperformed using DNA Polymerase I and RNase H. Remaining overhangs wereconverted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure wereligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: nasopharyngeal carcinoma

value: nasopharyngeal carcinoma cell

value: UPF1 overexpressing


title: FCCP_1.25_1

description:
FCCP_1.25_1
F11


title: RPA135(WT)-HTP - sample 1


title: Emetine

description:
Library name: sample12
gene_fpkm.2.txt


title: DMSO

description:
Library name: sample11
gene_fpkm.2.txt


title: NC2

description:
Library name: sample2
gene_fpkm.1.txt

value: NC


title: N2 ChIP-seq, input, replicate 3

status: Public on Oct 24 2025

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

description:
Library name: N2_ChIP-seq_Input_replicate_3
Spike-in scaled

data_processing:
The raw sequencing reads were trimmed for low-quality base calls, with a phred33 < 22, Illumina adapter sequences using a stringency of 12, and poly-G sequences (defined as 13 Gs in a row) using a stringency of 8 with TrimGalore v0.6.5.
Trimmed reads were aligned to the Caenorhabditis elegans ce11 genome using Bowtie2 v2.3.4.3 with the maximum fragment size parameter set to 2000. Alignments were filtered by removing duplicates and multi-mapping reads with a MAPQ < 42, using Samtools v1.11.
Peaks were called with MACS2 v2.2.7.1 with the  -g option set to ce and the --broad option. Peaks that overlap with blacklisted regions, where there is artificially high signal, were removed.
Replicates with a Drosophila chromatin spike-in were processed as above, except that they were aligned to a concatenated Caenorhabditis elegans ce11 and Drosophila melanogaster dm6 genome, reads mapped to both genomes were discarded and the reads were normalized as described. Briefly, the ce11 reads were randomly subsampled using factors that reflect the total number of dm6 reads in that sample and were corrected for the ratio of dm6/ce11 reads in the corresponding input samples.
Coverage files were prepared with the BedTools v2.29.0 genomecov function using the -bga and -pc options.
Log2 transformed ChIP/Input ratios were calculated per base with deepTools v3.5.0 bigwigCompare with a pseudocount of 1.
Assembly: ce11
Supplementary files format and content: Processed data files include genome coverage levels in bigWig format, as well as peak locations in BED format (except for input samples and replicate 2 of mig-32(n4275) H2AK119ub ChIP-seq)

growth_protocol: Strains were maintained on nematode growth medium (NGM) agar with E. coli OP50-1 as a food source at 21°C unless specified otherwise. The N2 (Bristol) strain was used as wild-type. Embryos were isolated from gravid adults using standard alkaline hypochlorite treatment (“bleaching”). After three washes in M9 buffer supplemented with 0.01% (v/v) Triton X-100 (M9/Tx), embryos were allowed to develop to L1 diapause in M9/Tx buffer overnight with aeration. The arrested L1s were plated on NGM agar or added to liquid culture with OP50-1 to start synchronous growth. Arrested L1s were counted and seeded into 40 mL of S-Complete medium with OP50-1 as a food source, at a final density of ~0.5-1.5 animals per uL. Animals were grown with aeration for 71-77 hours to gravid adulthood, and embryos were isolated again by bleaching. After washes with M9/Tx, embryos were processed for ChIP as described below either immediately or after a further 3-5 hours of growth with aeration.

extract_protocol:
Embryos were collected by centrifugation (1000g, 3 min.) and washed twice in phosphate-buffered saline (PBS) containing 0.01% (v/v) Triton X-100 (PBS/Tx). To crosslink, PBS/Tx was added to at least 80 times the pellet volume, and 37% formaldehyde (Sigma F8775) was added to a final concentration of 1.8%. Samples were incubated at room temperature with rotation for 25 minutes. Glycine was added to a final concentration of 125 mM followed by incubation for an additional 5 minutes. All subsequent steps were performed on ice using pre-chilled buffers and tubes. Embryos were washed twice with PBS/Tx as above and an equal volume of resuspension buffer (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.01% Triton X-100, protease inhibitors (1 tablet per 5 mL, Roche 4693159001) was added to the embryo pellet. The resuspended embryos were aliquoted, snap-frozen in liquid nitrogen and stored at -80°C. Aliquots of cross-linked embryos were thawed in an ice-water bath, the volume was adjusted to 3-4 pellet volumes (PV) using resuspension buffer, and 100 uL was aliquoted to each polystyrene sonication tube (Evergreen 214-3721-010). An equal volume of resuspension buffer containing 2X detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA, 0.2% sodium deoxycholate, 0.7% sodium sarkosyl). Samples were sonicated in a Q800R3 water bath sonicator (QSonica Q800R3-110; 50% power, 20s on/20s off) for 4 minutes. Samples were gently mixed by pipetting and sonicated an additional 4 minutes. The lysate was transferred to an Eppendorf tube and an equal volume of resuspension buffer without detergents was added (50 mM HEPES-KOH pH7.5, 150 mM NaCl, 1 mM EDTA). The lysate was centrifuged (13,000g, 15 min. 4°C) and the supernatant was transferred to a new tube. Protein concentration was determined using the Bradford assay (Sigma B6916). For samples including a spike-in control for calibration, sonicated Drosophila chromatin (Active Motif, 53083) was added at a ratio of 1:20 or 1:30. The supernatant was aliquoted to tubes for immunoprecipitation (IP), saving 15-20% of the volume of one IP tube as the ‘input’ control, which was stored at -20°C. Triton X-100 (10%, v/v) was added to a final concentration of 1% (v/v). This step was omitted for anti-H3K27me3 (CST 9733, C36B11), for which this detergent led to increased background. After antibody addition, samples were incubated overnight at 4°C with rotation. Protein G dynabeads (Invitrogen 10003D; 7.5 uL per IP) were pre-washed twice with resuspension buffer and added to IPs, which were then incubated as above for 2 hours. Beads were collected on a magnetic stand (Permagen MSR812) and washed as follows, with each wash incubated for 5 minutes at 4°C with rotation: 2X with FA-150 (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate), 1X with FA-1M (FA-150 with 1 M NaCl), 1X with FA-0.5M (FA-150 with 0.5 M NaCl), 1X with TE-LiCl in a new tube (10 mM Tris-Cl pH 8, 1 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), 2X with TE+ (10 mM Tris-Cl pH 8, 1 mM EDTA, 50 mM NaCl, 0.005% IGEPAL CA-630). Elution was performed in a new tube at 65°C for 15 minutes using 50 uL of ChIP elution buffer (10 mM Tris-Cl pH 8, 1 mM EDTA, 200 mM NaCl, 1% SDS). Elution was repeated and the supernatants were pooled. The ‘Input’ aliquot was thawed and brought to 100 uL with ChIP elution buffer. Input and IP samples were treated with RNase A (16.5 ug, Sigma R4642) for 1 hour at 37°C and proteinase K (40 ug, Bioline BIO-37084) for 2 hours at 55°C. Crosslinks were reversed by incubation overnight at 65°C. DNA was isolated using a QIAquick PCR purification kit (Qiagen 28104).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S) according to the manufacturer’s instructions, using 25-50 ng of input DNA or half of ChIP DNA. Library concentration was quantified using NEBNext Library Quant Kit for Illumina (NEB E7630). Pooled libraries were sequenced using NextSeq500 in 50 bp paired-end mode.

value: Wild-type

tag: developmental stage

value: mixed embryo

tag: chip target

value: Input

tag: corresponding input


title: d10_Con_CD8_4

value: BALB/c

value: breast tumors


title: mig-32(n4275) ChIP-seq, input, replicate 3

description:
Library name: mig-32_n4275_ChIP-seq_Input_replicate_3
Spike-in scaled

value: whole animal

tag: chip antibody


title: UPF1_1

description:
Library name: sample4
gene_fpkm.1.txt

value: UPF1 overexpressing HK1 cells


title: Muscles of 15 individuals of the species Batrachocottus nikolskii

status: Public on Oct 30 2025

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

description: Library name: Sample 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v. 0.36.
The preprocessed reads were subjected to a de novo assembly procedure the Trinity v.2.13.2. software package
4 de-novo assemblies of different types are combined into one
The combined assembly was processed using CD-HIT version 4.8.1 to cluster sequences based on percentage similarity (95%).
Read count extrraction and normalization were perfomed using the R package EdgeR v4.0.3.
Assembly: de novo assembly
Supplementary files format and content: tab-delimited text file includes normalized FPKM values for each sample

organism: Batrachocottus nikolskii

source_name: muscle

extract_protocol:
Total RNA was isolated from the muscles of 15 individuals of each species using TRIzol reagent
The library was examined using Qubit and real-time PCR for quantification and size distribution detection. Quantified libraries were pooled in equimolar amounts and sequenced on Illumina NovaSeq 6000 High Throughput Sequencer using a NovaSeq 6000 Reagent Kit v1.5 in 150 bp paired-end reads at Novogen company (China).

value: muscle


title: UPF1_3

description:
Library name: sample6
gene_fpkm.1.txt


title: Muscles of 15 individuals of the species Batrachocottus multiradiatus

description: Library name: Sample 4

organism: Batrachocottus multiradiatus


title: N2 ChIP-seq, H3K27me3, replicate 3

description:
Library name: N2_ChIP-seq_H3K27me3_replicate_3
Spike-in scaled

value: anti-H3K27me3 rabbit monoclonal C36B11, 9733; Cell Signaling Technology

value: N2 ChIP-seq, input, replicate 3


title: Muscles of 15 individuals of the species Comephorus dybowski

description: Library name: Sample 1

organism: Comephorus dybowskii


title: UPF1_2

description:
Library name: sample5
gene_fpkm.1.txt


title: NC3

description:
Library name: sample3
gene_fpkm.1.txt


title: NC1

description:
Library name: sample1
gene_fpkm.1.txt


title: mig-32(n4275) ChIP-seq, H3K27me3, replicate 3

description:
Library name: mig-32_n4275_ChIP-seq_H3K27me3_replicate_3
Spike-in scaled

value: mig-32(n4275) ChIP-seq, input, replicate 3


title: mig-32(n4275) ChIP-seq, H2AK119ub, replicate 3

description:
Library name: mig-32_n4275_ChIP-seq_H2AK119ub_replicate_3
Spike-in scaled

value: anti-H2AK119ub rabbit monoclonal D27C4, 8240; Cell Signaling Technology