title: fibroblasts, oligomycinA, rep11

city: LAUSANNE

first: Christopher

last: Wall

state: Schweiz

address: RUE SAINT-MARTIN 22

department: EDSV

country: Switzerland

institute: EPFL

data_processing:
Sequencing reads were trimmed with BBDuk (BBTools version 35.85, Bushnell B., sourceforge.net/projects/bbmap/).
Mapping to the human genome (built GRCh38.p2) was performed with RNA STAR version 2.3.0e (Dobin et al., 2013) using default parameters.
Gene count was performed with HTSeq (Anders et al., 2015) version 0.5.4p3.
We fit a Negative Binomial generalized linear model, estimated the dispersion across all genes and constructed a contrast matrix to assess differential expression between inhibitors using edgeR software, holding all other variables constant.
Genome_build: HG19
Supplementary_files_format_and_content: countmatrix was generated with R software

source_name: fibroblasts, oligomycinA

growth_protocol: Human primary fibroblasts (Cell Applications, cat# 106-05a) were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco cat# 11966025), containing 4 mM glutamine in a humidified incubator with 5% CO2 at 37˚C. The DMEM was supplemented with 5 mM glucose, 10% fetal bovine serum (FBS) and 100 IU/ml penicillin and 100 IU/ml streptomycin (Gibco, cat# 10270106, 15140122).

extract_protocol:
Total RNA was extracted from the treated primary fibroblasts using Agencourt RNAdvance Tissue kit (Beckman Coulter Life sciences, cat# A32646) and quantified using a Quant-iT RiboGreen RNA Assay Kit (Invitrogen, cat# R11490).
250 ng RNA was used to generate libraries using the QuantSeq 3’ mRNA-Seq library prep kit (FWD) HT for Illumina (Lexogen). The kit uses total RNA as input, hence no prior poly(A) enrichment or rRNA depletion is needed. The libraries were amplified for 17 cycles quantified with Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, cat# P7589). Size pattern was controlled with the High Sensitivity NGS Fragment Analysis kit on a Fragment Analyzer (Agilent DNF-474).
Libraries were pooled at an equimolar ratio (i.e., an equal quantity of each sample library) and clustered at a concentration of 9 pM on single read (SR) sequencing flow cell (Illumina). Sequencing was performed for 65 cycles on a HiSeq 2500 (Illumina) using the Rapid SBS Kit v2 (Illumina, cat# FC-402-4021). Sequencing reads were trimmed with BBDuk (BBTools version 35.85, Bushnell B., sourceforge.net/projects/bbmap/).

tag: time

value: 5 day treated

value: dermal fibroblasts


title: fibroblasts, oligomycinA, rep12

status: Public on Feb 25 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell type


title: PHH Mock 3

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

country: USA

institute: Gilead Sciences

data_processing:
Reads were generated using GASAVA v. 1.8.2 and clipped for low qualited bases using proprietary software developed by Q2 Solutions.
Clipped fastq files were aligned to reference genome using STAR2.7
gene level quantification using featureCounts v1.4.6-p1 with Gencode annotation v32.
Genome_build: hg38
Supplementary_files_format_and_content: Tab separated gene count matrix

source_name: Primary human hepatocyte

extract_protocol:
Qiagen Allprep kit
Illumina TruSeq Stranded mRNA

tag: tissue

value: liver

tag: timepoint

value: day 6

tag: cohort

value: Mock


title: PHH IFN J1 2

value: day 1

value: IFN


title: PHH HBV 500 3

value: HBV


title: fibroblasts, oligomycinA, rep9


title: PHH HDV 50 2

value: HDV


title: fibroblasts, oligomycinA, rep8


title: fibroblasts, oligomycinA, rep10


title: Astrocyte.shCTRL.5

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Astrocyte Control

data_processing:
Reads were aligned against the GRCm38 mouse genome using Kallisto (0.46.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: A compressed file which included the counts data in different format

organism: Mus musculus

source_name: mice undergoing progressive model of EAE

growth_protocol: CNS was harvested and digested with papain and collagenase D, myelin removed by precol gradient and Astrocytes and Microglia were isolated by flow cytometry

extract_protocol:
Arcturus® PicoPure®
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

treatment_protocol: Mice were transduced twice at day 37 and 44 after EAE induction with either shCtrl vector or pGFAPshEphB3 vector. A38 group was treated twice a day with A38 or control Vehicle starting at day 30 after EAE induction (beginning of progressive phase).

value: shCTRL

tag: strain

value: NOD/ShiLtJ

tag: Sex

value: Female

tag: age

value: 10 weeks

value: FACS Sorted Astrocytes from CNS


title: Astrocyte.shCTRL.3

description: Astrocyte Control


title: PHH HBV 500 HDV 50 2

value: HBV+HDV


title: fibroblasts, oligomycinA, rep7


title: PHH Mock 2


title: PHH HBV 500 2


title: PHH IFN J1 1


title: PHH HBV 500 HDV 50 1


title: fibroblasts, oligomycinA, rep3

value: 1 day treated


title: PHH HDV 50 3


title: PHH HDV 50 1


title: PHH HBV 500 1


title: fibroblasts, oligomycinA, rep4


title: fibroblasts, oligomycinA, rep5


title: fibroblasts, oligomycinA, rep1


title: fibroblasts, oligomycinA, rep6


title: fibroblasts, antimycinA, rep12

source_name: fibroblasts, antimycinA


title: dHepaRG IFNJ1 3

source_name: cancer cell line

value: hepatocellular carcinoma


title: fibroblasts, antimycinA, rep11

value: 5 day treated


title: fibroblasts, oligomycinA, rep2

value: dermal fibroblasts


title: dHepaRG HBV 500 + HDV 50 3


title: dHepaRG HBV 500 3


title: dHepaRG HDV 50 3


title: dHepaRG Mock 3


title: dHepaRG HBV 500 + HDV 50 2


title: fibroblasts, antimycinA, rep9


title: fibroblasts, antimycinA, rep8


title: dHepaRG HDV 50 2


title: dHepaRG HBV 500 2


title: fibroblasts, antimycinA, rep5


title: fibroblasts, antimycinA, rep6


title: dHepaRG Mock 2


title: fibroblasts, antimycinA, rep4


title: dHepaRG IFNJ1 1


title: fibroblasts, antimycinA, rep3


title: PHH Mock 1

value: liver


title: dHepaRG HBV 500 + HDV 50 1

value: day 6


title: fibroblasts, rotenone, rep12

source_name: fibroblasts, rotenone


title: fibroblasts, antimycinA, rep1


title: fibroblasts, antimycinA, rep2


title: dHepaRG Mock 1

value: Mock


title: dHepaRG HDV 50 1


title: dHepaRG HBV 500 1


title: fibroblasts, antimycinA, rep10


title: Human jejunum lymphatic vessel cells

city: Shanghai

first: Xiaodan

last: Zhang

address: 800 Dongchuan Rd

department: Biomedical Engineering

country: China

institute: Shanghai Jiao Tong University

description:
Jejunum tissue dissected from a total gastrectomy pateint and preserved in RNAlater solution for 4-8 hours, then stored in -80. After cryosection, lymphatic vessel cells were labelde with padoplanin and about 100 lymphatic vessel cells were laser-dissected by LCM. Collected into GITC lysis buffer.
Human jejunum lymphatic cells_gene level FPKM.txt, Human jejunum lymphatic cells_transcript level FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: mm10 for mouse samples, hg38 for human sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: jejunum lymphatic vessel

extract_protocol:
mouse small intestine tissue, snap frozen by liquid nitrogen, after cryosection, labeled with antibody and intersted specific labeled cells were laser-dissected by LCM. Captured cells were lysed in GITC lysis buffer. RNA were extracted by ethanol precipitation, DNA were removed by DNase treatment. cDNA library were constructed by using Ovation SoLo RNAseq Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: small intestine

value: 80 years old

tag: genotype

value: total gastrectomy patient

value: RNAlater perserved and cryosection, labeled with padoplanin


title: fibroblasts, rotenone, rep10


title: fibroblasts, rotenone, rep7


title: fibroblasts, rotenone, rep9


title: fibroblasts, rotenone, rep6


title: fibroblasts, rotenone, rep5


title: fibroblasts, antimycinA, rep7


title: fibroblasts, rotenone, rep3


title: fibroblasts, rotenone, rep4


title: fibroblasts, rotenone, rep11


title: fibroblasts, rotenone, rep2


title: fibroblasts, rotenone, rep1


title: fibroblasts, control, rep12

source_name: fibroblasts, control


title: fibroblasts, rotenone, rep8


title: siMETTL3_m6A_rep1

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

data_processing:
Raw reads were aligned to the hg19 genome using TopHat (v2.1.1) with parameter “--max-multihits 1”.
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: MCF-7 and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco), 50 units/mL penicillin and 50 μg/mL streptomycin (Hyclone SV30010).

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).

treatment_protocol: For knockdown, MCF-7 cells were seeded in a 6-well plate, and transfected with RNAiMAX (Invitrogen, 13778-150) according to the manual. Cells were harvested after three days. For construction of stable cell lines, lentiviruses expressing plasmids (PMSCV Vector, or METTL3, METTL14, WTAP, ALKBH5) were produced by co-transfection of plasmids with VSV-G and psPAX2 in a 2:1:1 ratio into HEK293T cells using Lipofectamine 2000 (Invitrogen, 11668-019). Supernatant at 48 hour post-transfection was collected. HEK293T or MCF-7 cells were seeded in a 6-well plate and infected with each lentivirus supernatant in the presence of 5 μg/mL polybrene. Medium was replaced by fresh media with Puro (2 ug/ml) for 5 days, the surviving cells were pooled as stably infected cells.

tag: cell line


title: siCtrl_Input_rep2

value: siCtrl


title: siCtrl_m6A_rep1


title: siCtrl_m6A_rep2


title: siMETTL3_Input_rep1


title: siMETTL3_m6A_rep2


title: siMETTL3_Input_rep2


title: HEK293T_WTAP_HA_ChIP_rep

library_source: genomic

data_processing:
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the hg19 (MCF-7, HEK293T) or mm10 (mNSC) genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

molecule: genomic DNA

growth_protocol: MCF-7 and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco), 50 units/mL penicillin and 50 μg/mL streptomycin (Hyclone SV30010). Mouse neural stem cells (NSCs) were kindly provided by Dr. Jian Hu (MD Anderson Cancer Center) (Shingu et al., 2017) and cultured in NeuroCult NSC Basal Medium (Stemcell, 05702) supplemented with 20ng/ml EGF (R&D, 236-EG), 20ng/ml bFGF (novoprotein, C779), 50 units/mL penicillin and 50 μg/mL streptomycin (Hyclone SV30010).

extract_protocol:
For ChIP, chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006). For Cut&Tag seq, Hyperactive In-Situ ChIP Library Prep Kit for Illumina was performed according to the manual (Vazyme, TD902).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

tag: cell line/type

value: WTAP_HA OE

tag: antibody

value: HA-Tag (Cell Signaling, 3724S)


title: HEK293T_ALKBH5_HA_ChIP_rep

value: ALKBH5_HA OE


title: fibroblasts, control, rep11


title: fibroblasts, control, rep10


title: fibroblasts, control, rep9


title: HEK293T_METTL3_HA_ChIP_rep

value: METTL3_HA OE


title: MCF7_ALKBH5_HA_ChIP_rep


title: HEK293T_METTL14_HA_ChIP_rep

value: METTL14_HA OE


title: MCF7_H3K27Ac_ChIP_rep

value: H3K27Ac (Millipore, 07-360)


title: MCF7_HnRNPG_CutAndTag_rep

value: hnRNP G (Cell Signaling, 14794S)


title: MCF7_H3K4me3_ChIP_rep

value: H3K4me3 (Cell Signaling, 9751S)


title: fibroblasts, control, rep7

value: 5 day treated

value: dermal fibroblasts


title: fibroblasts, control, rep4

value: 1 day treated


title: fibroblasts, control, rep5


title: siCtrl_Input_rep1


title: fibroblasts, control, rep6


title: fibroblasts, control, rep2


title: fibroblasts, control, rep8


title: fibroblasts, control, rep1


title: Tube_rep4

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tube cells (50-70 micrometer away from lacteal tip cells) were collected by using laser capture microdissection from the frozen sections. Four biological replicates were collected of this type sample.Replicate-4.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt

source_name: lacteal tube cells

value: 6-8 weeks

value: wild type

value: snap frozen and cryosection, labeled with Lyve1


title: HEK293T_H3K4me3_ChIP

data_processing:
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the hg19 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage bigwig files


title: HEK293T_H3K4me1_ChIP

value: H3K4me1 (Active Motif, 39297)


title: Y1

city: Guangzhou

first: Niu

last: Xingtang

state: Guangdong

address: 1838 Guangzhou North Road, Guangzhou, Guangdong, China.

institute: Nanfang Hospital, Southern Medical University

data_processing:
Illumina HiSeq X Ten software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Mapping of 150-bp paired-end reads to genes was undertaken using Hisat2 v2.0.5 software, and fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: fat

extract_protocol:
Fat tissues were collected on dry ice, and RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fat tissue

value: before grafting


title: small intestinal eosinophils_WT_F8

city: London

first: Nicola

middle: Laura

last: Diny

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Fastq files were aligned to the GRCm38 Ensembl Release 86 mouse genome using the nextflow package nf-core/rnaseq to generate gene counts.
Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). We recorded as differentially expressed those genes with adjusted p values < 0.05.
We also relied on DESeq2 for PCA of variance stabilized expression values.
All computations were performed in R version 4.0.3 (2020-10-10).
Genome_build: GRCm38 Ensembl Release 86 mouse genome
Supplementary_files_format_and_content: Tab delimited text file containing variance stabilized counts for each sample and each gene

source_name: small intestinal eosinophils

growth_protocol: Eosinophils were FACS-sorted from the intestine (CD11b+MHC-II-SiglecF+SSChi eosinophils) or bone marrow (CD11b+Ly6G-Ly6C-SiglecF+SSChi eosinophils)

extract_protocol:
RNA was extracted with TRI Reagent and the RiboPure RNA Purification Kit (ThermoFisher Scientific #AM1924) immediately after sorting. RNA quality and quantity was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Pico Kit. Only samples with RIN ≥7 were used for RNA sequencing.
RNA samples were converted into cDNA using the NuGEN Ovation RNA-Seq System v2. Illumina-compatible libraries were produced using the NuGEN Ovation Ultralow Library System V2.  Sequencing was performed on the Illumina HiSeq 4000 with single ended reads of at least 75 bp.

treatment_protocol: cells were immediately processed for RNA isolation

value: wildtype

value: small intestine

value: eosinophils

tag: cell population

value: CD11b+MHC-II-SiglecF+SSChi eosinophils


title: YY3

value: post grafting day 7


title: YY1


title: small intestinal eosinophils_WT_F7


title: fibroblasts, control, rep3


title: HEK293T_H3K27Ac_ChIP

value: H3K27Ac (Millipore, 07-360)


title: HEK293T_WTAP_HA_ChIP

value: WTAP_HA OE

value: HA-Tag (Cell Signaling, 3724S)


title: YY2


title: MCF7_H3K4me1_ChIP_rep


title: small intestinal eosinophils_WT_F6


title: Tip_rep3

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tip cells were collected by using laser capture microdissection from the frozen sections. Three biological replicates were collected of this type sample.Replicate-3.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt

source_name: lacteal tip cells


title: Y3


title: HEK293T_METTL14_HA_ChIP

value: METTL14_HA OE


title: small intestinal eosinophils_WT_F5


title: Y2


title: HEK293T_METTL3_HA_ChIP

value: METTL3_HA OE


title: Tube_rep3

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tube cells (50-70 micrometer away from lacteal tip cells) were collected by using laser capture microdissection from the frozen sections. Four biological replicates were collected of this type sample.Replicate-3.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt


title: HEK293T_ALKBH5_HA_ChIP

value: ALKBH5_HA OE


title: Tube_rep2

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tube cells (50-70 micrometer away from lacteal tip cells) were collected by using laser capture microdissection from the frozen sections. Four biological replicates were collected of this type sample.Replicate-2.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt

value: 6-8 weeks


title: Tip_rep2

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tip cells were collected by using laser capture microdissection from the frozen sections. Three biological replicates were collected of this type sample.Replicate-2.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt

value: wild type


title: Tip_rep1

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tip cells were collected by using laser capture microdissection from the frozen sections. Three biological replicates were collected of this type sample.Replicate-1.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt

value: snap frozen and cryosection, labeled with Lyve1


title: Tube_rep1

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Lymphatic lacteal cells of the small intestine were identified by Lyve-1 labeling and about 150 lacteal tube cells (50-70 micrometer away from lacteal tip cells) were collected by using laser capture microdissection from the frozen sections. Four biological replicates were collected of this type sample.Replicate-1.
Mouse small intestine lacteal tip and tube cells_gene level FPKM.txt, Mouse small intestine lacteal tip and tube cells_transcript level FPKM.txt


title: HEK293T_Vec_HA_ChIP

value: HA vector OE


title: bone marrow eosinophils_WT_F4

source_name: bone marrow eosinophils

value: bone marrow


title: RNAlater1575

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were preserved in RNAlater for 4-8 hours and stored in -80. Epithelial cells of the small intestine were identified by panCK labeling and  about  1575 cells were collected by using laser capture microdissection from the frozen sections.
Mouse small intestine epithelial cells_gene level FPKM.txt, Mouse small intestine epithelial cells_transcript level FPKM.txt

source_name: small intestine epithelial

value: RNAlater perserved and cryosection, labeled with panCK


title: Ep2300

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Epithelial cells of the small intestine were identified by panCK labeling and about 2300 cells were collected by using laser capture microdissection from the frozen sections.
Mouse small intestine epithelial cells_gene level FPKM.txt, Mouse small intestine epithelial cells_transcript level FPKM.txt

value: snap frozen and cryosection, labeled with panCK


title: Ep230

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Epithelial cells of the small intestine were identified by panCK labeling and about 230 cells were collected by using laser capture microdissection from the frozen sections.
Mouse small intestine epithelial cells_gene level FPKM.txt, Mouse small intestine epithelial cells_transcript level FPKM.txt

value: small intestine


title: MCF7_Input


title: Ep630

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Epithelial cells of the small intestine were identified by panCK labeling and about 630 cells were collected by using laser capture microdissection from the frozen sections.
Mouse small intestine epithelial cells_gene level FPKM.txt, Mouse small intestine epithelial cells_transcript level FPKM.txt


title: Ep63

description:
Small intestine tissues dissected from healthy 6-week-old  C57BL/6 mouse. Then tissues were snap frozen with liquid nitrogen and stored in -80. Epithelial cells of the small intestine were identified by panCK labeling and about 63 cells were collected by using laser capture microdissection from the frozen sections.
Mouse small intestine epithelial cells_gene level FPKM.txt, Mouse small intestine epithelial cells_transcript level FPKM.txt


title: MCF7_p300_ChIP

value: p300 (Santa Cruz, sc-584)


title: bone marrow eosinophils_WT_F2

value: wildtype

value: eosinophils


title: Microglia Healthy, 1

description: FACS Sorted Microglia from CNS

data_processing:
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.7.2) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene

source_name: Microglia

treatment_protocol: Mice were treated twice a day with A38 or control Vehicle starting at day 16 after EAE induction (peak of disease). Healthy group not inudced with EAE was also included

tag: group

value: Healthy

value: Female

value: 10 weeks


title: bone marrow eosinophils_WT_F3


title: bone marrow eosinophils_WT_F1


title: MCF7_hnRNPG_CutAndTag

value: hnRNP G (Cell Signaling, 14794S)


title: Microglia A38, 5

description: FACS Sorted Microglia from CNS

tag: agent

value: EAE


title: Microglia Healthy, 2

description: FACS Sorted Microglia from CNS


title: MCF7_ALKBH5_HA_ChIP

value: ALKBH5_HA OE

value: HA-Tag (Cell Signaling, 3724S)


title: Microglia A38, 4

description: FACS Sorted Microglia from CNS


title: Small intestinal eosinophils_Ahr-KO_M3

data_processing:
The bam files were generated using RSEM (v1.3.0 https://doi.org/10.1186/1471-2105-12-323) and STAR (v2.5.2 https://doi.org/10.1093/bioinformatics/bts635) to align against ensembl GRCm38 release 86.
Bam files were aligned to the Bioconductor gene set TxDb.Mmusculus.UCSC.mm10.knownGene using the function summarizeOverlaps from the Bioconductor package GenomicAlignments (Lawrence et al., 2013).
Differential gene discovery was done using the bioconductor package DESeq2 (Love et al., 2014). Comparisons between WT and Ahr-/- eosinophils were adjusted for sex. We also relied on DESeq2 for PCA of variance stabilized expression values.
All computations were performed in R version 4.0.3 (2020-10-10).
Genome_build: GRCm38 Ensembl Release 86 mouse genome
Supplementary_files_format_and_content: varianceStablizedExpression_counts_WT_AHR-KO_AHRR-KO.txt.gz (Tab delimited text file containing variance stabilized counts for each sample and each gene)

value: Ahr knockout

value: male

value: CD11b+MHC-II-SiglecF+SSChi eosinophils


title: Microglia A38, 2

description: FACS Sorted Microglia from CNS


title: MCF7_H3K27Ac_ChIP

value: H3K27Ac (Millipore, 07-360)


title: Microglia A38, 3

description: FACS Sorted Microglia from CNS


title: Microglia A38, 1

description: FACS Sorted Microglia from CNS


title: Microglia Control, 5

description: FACS Sorted Microglia from CNS

value: vehicle


title: Small intestinal eosinophils_Ahr-KO_M1


title: Small intestinal eosinophils_Ahr-KO_M2


title: Microglia Control, 4

description: FACS Sorted Microglia from CNS


title: MCF7_H3K4me1_ChIP

value: H3K4me1 (Active Motif, 39297)


title: Microglia Control, 3

description: FACS Sorted Microglia from CNS


title: Small intestinal eosinophils_WT_F3

value: female

value: small intestine


title: Microglia Control, 2

description: FACS Sorted Microglia from CNS


title: MCF7_sihnRNPG_INTS11_ChIP

value: sihnRNPG

value: INTS11 (Bethyl, A301-274A)


title: Microglia Control, 1

description: FACS Sorted Microglia from CNS


title: Small intestinal eosinophils_WT_F2

value: wildtype


title: Astrocyte A38, 5

description: FACS Sorted Astrocytes from CNS

source_name: Astrocytes

value: Female


title: Astrocyte Healthy, 1

description: FACS Sorted Astrocytes from CNS

value: Healthy

value: 10 weeks


title: Astrocyte Healthy, 2

description: FACS Sorted Astrocytes from CNS


title: Small intestinal eosinophils_WT_F1


title: Astrocyte A38, 3

description: FACS Sorted Astrocytes from CNS

value: EAE


title: Small intestinal eosinophils_WT_M3


title: MCF7_siMETTL14_INTS11_ChIP_rep1


title: MCF7_siWTAP_INTS11_ChIP_rep1

value: siWTAP


title: Astrocyte A38, 4

description: FACS Sorted Astrocytes from CNS


title: Small intestinal eosinophils_WT_M2


title: Astrocyte A38, 2

description: FACS Sorted Astrocytes from CNS


title: Small intestinal eosinophils_Ahrr-KO_F3

value: Ahrr knockout


title: MCF7_H3K4me3_ChIP

value: H3K4me3 (Cell Signaling, 9751S)


title: Astrocyte Control, 5

description: FACS Sorted Astrocytes from CNS


title: MCF7_siMETTL3_INTS11_ChIP_rep2


title: Astrocyte Control, 4

description: FACS Sorted Astrocytes from CNS


title: MCF7_siCtrl_for_sihnRNPG_INTS11_ChIP

value: siCtrl


title: MCF7_siMETTL3_INTS11_ChIP_rep1


title: Small intestinal eosinophils_Ahrr-KO_F2

value: CD11b+MHC-II-SiglecF+SSChi eosinophils


title: Astrocyte Control, 1

description: FACS Sorted Astrocytes from CNS


title: Astrocyte Control, 2

description: FACS Sorted Astrocytes from CNS


title: MCF7_siCtrl_INTS11_ChIP_rep2


title: Astrocyte Control, 3

description: FACS Sorted Astrocytes from CNS


title: Small intestinal eosinophils_Ahrr-KO_F1


title: Small intestinal eosinophils_Ahrr-KO_M3

value: male


title: MCF7_siCtrl_INTS11_ChIP_rep1


title: Astrocyte A38, 1

description: FACS Sorted Astrocytes from CNS


title: MCF7_WTAP_ChIP_rep2

value: WTAP (Bethyl, A301-435A)


title: MCF7_METTL14_ChIP_rep2

value: METTL14 (Sigma, HPA038002)


title: MCF7_WTAP_ChIP_rep1


title: Small intestinal eosinophils_Ahrr-KO_M1


title: MCF7_METTL14_ChIP_rep1


title: Small intestinal eosinophils_Ahr-KO_F2

value: Ahr knockout

value: female


title: Small intestinal eosinophils_Ahr-KO_F3

value: small intestine


title: Small intestinal eosinophils_Ahr-KO_F1


title: MCF7_METTL3_ChIP_rep2

value: METTL3 (Bethyl, #A301-567A)


title: MCF7_METTL3_ChIP_rep1


title: Small intestinal eosinophils_WT_M1

value: wildtype


title: Nmnat1_2

city: Bunkyo-ku

first: Hiroshi

last: Kuribayashi

state: Tokyo

address: 7-3-1 Hongo

department: Hospital

country: Japan

institute: The University of Tokyo

description:
NmnatOE_tpm.csv
N1_2

data_processing:
Illumina Casava1.8 software was used for basecalling
Sequenced reads were processed by salmon 0.11.3 with its default parameters to quantify transcript expression level
Downstream analysis including TPM calculation, differentially expressed gene detection, and visualization were performed using wasabi 0.3 and sleuth 0.30.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each samples.

source_name: retina

growth_protocol: Explant retinas were cultured on a chamber filter (Millicel) with medium (50% MEM with Hepes, 25% Hank's solution, 25% heat-inactivated HS, 200 mM L-glutamine, and 5.75 mg/ml glucose, penicillin and streptomycin) at 34ºC in 5% CO2.

extract_protocol:
Retinas were trypsinized and EGFP positive cells were sorted out using a cell sorter (FACS AriaII, BD). Total RNA was extracted using Sepasol RNA I super G reagent (nacalai). SMART-Seq v4 (Illumina) was used for cDNA synthesis with 1 ng of toal RNA.
Nextera DNA Flex Library Prep Kit (Illumina) was used for libraries preparation.

treatment_protocol: Retinas at P0.5 were electroporated with plasmids for knockdown or overexpression together with EGFP-expressing plasmids and cultured for 3 days.

value: ICR

tag: shRNA

value: Nmnat1 overexpression

value: Post natal day 0.5 - 3 day in vitro


title: Nmnat2_1

description:
NmnatOE_tpm.csv
N2_1

value: Nmnat2 overexpression


title: Nmnat1_1

description:
NmnatOE_tpm.csv
N1_1


title: Nmnat1_3

description:
NmnatOE_tpm.csv
N1_3


title: Nmnat2_2

description:
NmnatOE_tpm.csv
N2_2


title: Nmnat3_3

description:
NmnatOE_tpm.csv
N2_3


title: Small intestinal eosinophils_Ahrr-KO_M2


title: Control_3

description:
NmnatOE_tpm.csv
v3

value: Empty vector (Control for Overexpression)


title: GATA2-AS1 siRNA#2 repB

type: RNA

city: Toronto

first: Philip

middle: A

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

country: Canada

institute: University of Toronto

description: Human LncRNA Array v3.0 (8 x 60K, Arraystar)

hyb_protocol: Cy3 labeled cRNA was fragmented by adding 11ul 10x Blocking Agent and 2.2ul of 25X Fragmentation Buffer, then heated at 60C for 30min after which 55ul 2X GE Hybridization buffer was added. 100ul of hybridization solution was then despensed into the gasket slide and assembled to the LncRNA expression microarray slide. Slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the 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 the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: HUVEC

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). mRNA was purified from 1 microgram of total RNA (mRNA-ONLY eukaryotic mRNA Isolation Kit, Epicentre)

growth_protocol: HUVEC were grown as in Marsden PA, et al. (1992) Molecular cloning and characterization of human endothelial nitric oxide synthase. FEBS Lett 307(3):287-293.

extract_protocol: Total cellular RNA was extracted as in Fish JE, et al. (2010) Hypoxic repression of endothelial nitric-oxide synthase transcription is coupled with eviction of promoter histones. J Biol Chem 285(2):810-826.

treatment_protocol: RNA interference was performed using siGENOME Non-Targeting siRNA #3 (Dharmacon) for control (Ctl/Ctl siRNA) and custom siRNA designed to target GATA2-AS1 RNA (Invitrogen). HUVEC were transfected  at a final concentration of 40nM using Oligofectamine transfection reagent (Invitrogen).

value: HUVEC


title: GATA2-AS1 siRNA#1 repC


title: GATA2-AS1 siRNA#2 repC


title: GATA2-AS1 siRNA#1 repB


title: GATA2-AS1 siRNA#1 repA


title: Control siRNA repB


title: GATA2-AS1 siRNA#2 repA


title: Control_2

description:
NmnatOE_tpm.csv
v2


title: Infection2_D11p_Mock

city: Paris

first: Liliana

last: Mancio-Silva

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description:
Two processed data files represent the sequencing of the library upon its construction (pre-capture), as well as a re-sequencing post-enrichment for parasite-derived transcript (post-capture data).
Precapture_Infection2.tar
Postcapture_merged_Infection2.tar

data_processing:
For each sample, fastq files originating from multiple sequencing runs were concatenated and processed using an analytical pipeline derived from the DropSeq pipeline v. 1.12, as described in (Gierahn et al., 2017) (https://github.com/broadinstitute/Drop-seq).
Briefly, reads were converted to a bam file using picard v. 2.9.0-1-gf5b9f50-SNAPSHOT, tagged with cell and transcript barcodes, and subsequently sequencing adapters and polyadenosine tracts were trimmed. Upon regenerating fastq files, reads were aligned with STAR v. 2.5.3a (Dobin et al., 2013) against the aforementioned tri-genome reference. Genomic features of the aligned reads were annotated using the combined species-gene symbol nomenclature including gene and exon of origin when relevant. Bead synthesis errors were assessed and when possible, altered unique molecular identifiers (UMIs) were repaired. Cell barcode abundance was tallied, and gene expression was called for the top 10,000 cell barcodes.
Count matrices of genes x cells were imported in the R v. 3.6 statistical environment and Seurat v.3 was used as the primary analytical package (Satija et al., 2015). Count matrices were merged into a single Seurat object, which was split by the sample of origin. Human, murine and P. vivax genes and transcripts counts were tallied for each cell barcode.
Genome_build: Tri-genome hg19, mm10 (ENSEMBL release as used in Macosko et al. Cell 2015) and PvP01 v1.
Supplementary_files_format_and_content: Tab-delimited text files containing unfiltered genes x cell-barcode matrices in MatrixMarket format (10K cells called for each sample). Three files are reported: for "Experiment 2", a pre-parasite capture count matrix is provided (containing host and parasite data for 10K cells per sample), as well as a post-capture file, which contains data for 10K cells called upon sequencing the captured libraries, added to the corresponding reads tallied pre-capture for each matching cell barcode. For "Experiment 1" the post-capture data only (10K cells/sample).

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: day 11

growth_protocol: Primary human hepatocytes were seeded on collagen-micropatterned 96-well plates and surrounded with murine embryonic fibroblasts 3T3-J2s as detailed previously (March et al., 2015). For the scRNA-seq analysis, MPCCs were established using 3T3-J2s expressing an inducible apoptosis switch (Chen et al., 2020).

extract_protocol:
Briefly, MPCCs were first treated with AP20187 (0.5 mM) for 30 minutes at 37°C to partially deplete the fibroblast cells via apoptosis. After washing, the cultures were dissociated by Trypsin (0.25%) 5-minute treatment at 37°C.
For the scRNA-seq analysis, an updated Seq-Well protocol including a second-strand synthesis step was employed (Hughes et al., 2020). A suspension with 10-15,000 cells (pooled from duplicate MPCC wells) was then loaded onto a functionalized-polydimethylsiloxane array preloaded with uniquely barcoded mRNA capture beads. For each time-point in the two independent infections, two separate arrays were loaded with P. vivax-infected samples, and single arrays for mock and naïve samples. After cells had settled into wells, the array was sealed with a hydroxylated polycarbonate membrane with a pore size of 10 nm, facilitating buffer exchange while permitting cell lysis, mRNA transcript hybridization to beads, and bead removal before proceeding with reverse transcription. The obtained bead-bound cDNA product then underwent Exonuclease I treatment to remove excess primer before proceeding with second-strand synthesis and PCR amplification. To capture parasite reads from Seq-Well, full length cDNAs were amplified an additional 5 cycles using Kapa HiFi polymerase including a 3-minute extension time to increase concentration for capture. 200-300 ng of cDNA was concentrated using a speedvac, reconstituted in 3.4 L water and hybridized for 32 hours as previously described (Gural et al., 2018). 10 L of capture material was amplified for 15 cycles following the standard protocol. Captured cDNA was then prepared into Illumina libraries using NexteraXT (Illumina). Final libraries were quality controlled using Fragment Analyzer (Agilent) and qPCR prior to Illumina sequencing (NextSeq500). Sequencing of captured parasite transcripts was performed for the two infection batches.

treatment_protocol: MPCCs were infected with fresh sporozoites obtained through hand dissection of P. vivax-infected mosquitoes. For mock samples, MPCCs were exposed to material from non-infected mosquito salivary glands (matched number of dissected mosquitoes and processed similarly as the infected counterparts). Naïve samples received the culture media used for the infections. Pi4K treatments were conducted from days 5 to 8 after infection.

value: primary human hepatocytes, with 3T3-J2s

tag: infection

value: mock-infected


title: CaSki Input Treat

city: Hangzhou

first: Lingfang

last: Wang

state: Zhejiang Province

address: 866 Yuhangtang Road

department: Department of Obstetrics and  Gynecology

institute: Zhejiang University

description: m6A MeRIP-seq

data_processing:
Quality controlled by Q30
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of input libraries were aligned to reference genome by STAR software
Clean reads of BS-treated libraries were aligned to the reference genome by meRanGh (one component of meRanTK) software.
The methylation status of each C within the genome was extracted by meRanCall (one component of meRankTK) software
Genome_build: hg19
Supplementary_files_format_and_content: excel format: Number of raw junction read

source_name: cell line

growth_protocol: CaSki cell line was cultured in 1640 (BI, Israel) containing 10% FBS and maintained at 37°C in 5% CO2.

extract_protocol:
The total RNA of cells was extracted with RNAiso Plus (9109, Takara) under the manufacturer’s guiding.
library construction protocol

treatment_protocol: CaSki cells were subjected to heat treatment (42°C, 60 min) before the assay

value: epithelial cell

value: CaSki

tag: treatment

value: 42C 60min treatment

tag: rip antibody

value: none (input)


title: CaSki IP Treat

description: m6A MeRIP-seq

tag: cell type

value: GenSeq m6A-MeRIP Kit (GenSeq, Beijing, China)


title: Infection2_D11p_Uninfected

value: non-infected


title: shNmnat3_3

description:
shNmnat_TPM.txt
shN2_3

value: Nmnat2 knockdown


title: shNmnat2_2

description:
shNmnat_TPM.txt
shN2_2


title: Control siRNA repC


title: Control_1

description:
NmnatOE_tpm.csv
v1


title: shNmnat1_3

description:
shNmnat_TPM.txt
shN1_3

value: Nmnat1 knockdown


title: CaSki Input ctrl

description: m6A MeRIP-seq

value: control


title: Infection2_D8p_Mock

source_name: day 8


title: shNmnat2_1

description:
shNmnat_TPM.txt
shN2_1

value: ICR


title: shNmnat1_1

description:
shNmnat_TPM.txt
shN1_1


title: Infection2_D8p_Uninfected


title: Scramble_2

description:
shNmnat_TPM.txt
shCtrl_2

value: Scramble expressing plasmid (Control for knockdown)


title: Infection2_D11_Mock

value: non-treated


title: Infection2_D11_Uninfected


title: Scramble_3

description:
shNmnat_TPM.txt
shCtrl_3

value: Post natal day 0.5 - 3 day in vitro


title: Scramble_1

description:
shNmnat_TPM.txt
shCtrl_1


title: Infection2_D8_Uninfected


title: Infection2_D8_Mock


title: Infection2_D5_Mock

source_name: day 5


title: ChIP-seq Pds5-pk Smc3RR IP [CH327]

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

institute: CNRS

description: ChIP-seq Pds5-pk Smc3RR IP

data_processing:
Bowtie2 was used for two rounds of alignments, first on C. glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively mapped on S. cerevisiae (an vice-versa for C. glabrata).
The obtained SAM file was converted into a BAM file, sorted and indexed using Samtools.
ChIP-seq profiles were then normalised by the number of million sequences and converted into BigWig using bamCoverage.
Profiles were multiplied by the ORi factor
Genome_build: W303

organism: Saccharomyces cerevisiae W303

growth_protocol: cells were grown overnight in YPD

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Samples were sonicated using Covaris (DNA 300bp). For ChIP seq data: The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transfer in tubes 2mL containing glass beads before mechanical cells lysis.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

treatment_protocol: Cells were then synchronised in G1 thanks to α-factor during 2h30. Auxin (2mM final) was added to the media 1h after starting α-factor arrest. After G1 arrest cells were washed twice in fresh YP and released in rich medium (YPD) containing Nocodazole and auxin during 2h. Cells were grown exponentially to OD600 = 0.5. In triplicates, 15 OD600 units of S. cerevisiae cells were mixed with 3 OD600 units of C. glabrata to a total volume of 45 mL and fixed with 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS

tag: treatments

value: see Bastie et al, NSMB 2022

tag: chip antibody

value: Mouse anti V5-tag (Bio-Rad, MCA1360)


title: ChIP-seq Pds5-pk Smc3RR IP [CH274]

description: ChIP-seq Pds5-pk Smc3RR IP

tag: strain


title: ChIP-seq Pds5-pk WT IP [CH326]

description: ChIP-seq Pds5-pk WT IP


title: ChIP-seq Pds5-pk WT IP [CH273]

description: ChIP-seq Pds5-pk WT IP


title: ChIP-seq Scc1-pk Smc3RR IP [CH255]

description: ChIP-seq Scc1-pk Smc3RR IP


title: Infection2_D5_Uninfected

value: primary human hepatocytes, with 3T3-J2s


title: ChIP-seq Scc1-pk WT IP [CH254]

description: ChIP-seq Scc1-pk WT IP


title: ChIP-seq Scc1-pk WT IP [CH331]

description: ChIP-seq Scc1-pk WT IP


title: CaSki IP ctrl

description: m6A MeRIP-seq


title: HiC Fig S4 triple Scc3-K404E scc2-45 pds5aid 25C [CH191]

data_processing:
Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered
PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded.
Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
Genome_build: W303

treatment_protocol:
Degradation of ECO1-AID and SMC3-AID in G1 (Figure 1 and S1): To study effect of Eco1 inactivation and smc3-RR on chromosome organisation, overnight culture of the strains, FB133-20C (ECO1-AID), yNB54-4 (SMC3, SMC3-AID), yNB54-3 (smc3-RR, SMC3-AID), FB134-16C (SMC3-AID) and yLD116-1a (cdc20) were gown in a complete medium deprived of methionine (SC-met) (SC: 0.67% yeast nitrogen base without amino acids (Difco)), supplemented with a mix of amino-acids, uracil and adenine, 2% glucose). To arrest cells in metaphase, yeast cells were synchronised in G1 by adding of α-factor (Antibodies-online, ABIN399114) in the media every 30min during 2h30 (1µg/mL final). Auxin (2mM final) (Sigma-Aldrich, I3750) was added to the media 1h after starting α-factor arrest. After G1 arrest cells were washed twice in fresh YP and released in rich medium (YPD): 1%bacto pepone (Difco), 1% bacto yeast extract (Difco), and 2% glucose) supplemented with 2mM of methionine and containing auxin.
Degradation of ECO1-AID in G2 (Figure S2): To analyse effect of Eco1 depletion in metaphase on chromatin interactions strains FB133-57B (cdc20) and FB133-20C (ECO1-AID) were grown overnight in a complete medium deprived of methionine and then arrested in G1 using α-factor. After 2h30 in G1, cells were washed twice in fresh YP and released in rich medium (YPD) supplemented in methionine (2mM final) to be re-arrested in metaphase. After 2 h in metaphase, 2mM of auxin was added during two more hours.
Depletion of CDC45-AID and ECO1-AID (Figure 2): To study effect of DNA replication on chromatin loops expansion, strains FB154(CDC45-AID) and FB162-1C (CDC45-AID, ECO1-AID), were grown overnight in YPD. Cells were synchronised in G1 using α-factor during 2h30, auxin (2mM final) was added to the media 1h after starting α-factor arrest. After G1 arrest, cells were washed in fresh YP and released in rich medium (YPD) containing Nocodazole (Sigma-Aldrich, M1404-10MG) and auxin (2mM final) during 1h30.
Inactivation of Scc2 (Figure 3 and S3): To check effect of Scc2 inactivation on establishment of cohesin-dependent loops cells KN20751(scc2-45) and W303-1A (WT) were synchronised in G1 thanks to α-factor at 30°C during 2h30. Then yeasts cells were washed and released in YPD containing Nocodazole at 37°C during 1h or 2h. To determine effect of Scc2 inactivation on maintenance of cohesin dependant loop, KN20751 (scc2-45) and W303-1A (WT) was first arrest in G1 thanks to α-factor as described previously, then cells were released in G2 with Nocodazole at 30°C during 2h. After G2 arrest, cells in media containing Nocodazole were heat in a water bath at 37°C during 20min or 60min.
Degradation of Pds5 (Figure 4 and 6): To analyse effect of Pds5 depletion in G2, strains yNB33.1-8a (PDS5-AID), W303-1A (WT), yNB40-2B (Hos1∆, PDS5-AID) and yNB40-1C (Hos1∆) were grown overnight in YPD. Cells were then synchronised in G1 using α-factor and released in YPD media containing Nocodazole to arrest cells in G2 during 1h. After G2 arrest, 2mM of auxin are added during 2h to induce Pds5 degradation.
Depletion of Pds5 in Scc2-45 background (Figure 5): To study effect of Scc2 on translocase activity, strains yNB33.2-8c (scc2-45, PDS5-AID, scc3-K404E) and yNB55.1-2a (PDS5-AID, scc3-K404E) were grown overnight in YPD. Cells were synchronised using α-factor during 2h30 and released in YPD containing Nocodazole during 1h30. After G2 arrest, 4mM of auxin was added to the media during 2h to induced Pds5 degradation.
After synchronization all strains were fixed for Hi-C experiments. Two independent replicates were performed for all experiments.


title: Infection2_D1_Mock

source_name: day 1

value: mock-infected


title: Infection2_D4_Mock

source_name: day 4


title: Infection2_D1_Uninfected


title: HiC Fig S4 double scc2-45 pds5aid 25C [CH166]

description: Fig S4 double scc2-45 pds5aid 25C


title: shNmnat1_2

description:
shNmnat_TPM.txt
shN1_2


title: HiC Fig S4 triple Scc3-K404E scc2-45 pds5aid 25C repeat [CH343]


title: HiC Pds5 T1 +IAA [CH87]

description: Pds5 T1 +IAA


title: HBV/HDV+ mouse 22

data_processing:
Reads were generated using GASAVA v. 1.8.2 and clipped for low qualited bases using proprietary software developed by Q2 Solutions.
Clipped fastq files were aligned to reference genome using STAR2.7
gene level quantification using featureCounts v1.4.6-p1 with Gencode annotation v32.
Genome_build: hg38 & mm10
Supplementary_files_format_and_content: Tab separated gene count matrix

source_name: liver

tag: tissue

value: liver

tag: time

value: 12 weeks post-HBV infection, 8 weeks post-HDV infection

tag: host organism

value: FRG-NOD mice

tag: xenograft organism

value: human

tag: model

value: humanized mouse liver model FRG KO


title: HBV+ mouse 891

value: 8 week post-HBV infection


title: HBV/HDV+ mouse 24


title: HBV/HDV+ mouse 853


title: HiC Pds5 T0 [CH86]

description: Pds5 T0


title: HiC WT T1 +IAA [CH85]

description: WT T1 +IAA


title: HBV+ mouse 859


title: HiC WT T0 [CH84]

description: WT T0


title: ChIP-seq Scc1-pk Smc3RR IP [CH325]

description: ChIP-seq Scc1-pk Smc3RR IP


title: HBV+ mouse 637


title: HiC Smc3-AID [CH78]


title: HBV- mouse 858


title: HBV- mouse 851


title: miR-375-2

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the zebrafish genome using STAR (v2.5) RNA-seq aligner with the following parameter “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 0 -p –Q 10”
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw counts

organism: Danio rerio

source_name: neutrophils

growth_protocol: zebrafish embryos were grow to 3 day post fertilization in embryonic media

extract_protocol:
tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing.
mRNA sequencing library were constructed withSMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.).

treatment_protocol: transgenic zebrafish lines were used to produce embryos. For miRNA target discovery, transgenic lines expressing miR-31, 190, 375 or a vector control together with a GFP reporter were used.

tag: transgenic line


title: HiC WT 2h 37C [CH67]

description: WT 2h 37C


title: Infection2_D4_Uninfected

value: non-infected


title: HiC Scc2 37C 20min [CH66]

description: Scc2 37C 20min


title: miR-375-1


title: HBV- mouse 805


title: miR-190-1


title: HiC Scc2 2h 30C [CH64]

description: Scc2 2h 30C


title: HiC WT 30C 2h [CH63]

description: WT 30C 2h


title: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi DN_3

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi

data_processing:
Reads were aligned to mouse reference genome mm10 using TopHat
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet of raw and normalized read counts

source_name: Splenic CD4+ T cells

extract_protocol: Full-length RNA-seq from single cells using Smart-seq2

treatment_protocol: IL-21-tRFP+ CD44+ splenic CXCR6+ (Th1), CXCR5+ (Tfh), and CXCR6-CXCR5- (memory-like) CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on day 14 p.i. ( 5,000 cells per subset from 3 replicate (independent) donor mice were used to prepare RNA-seq libraries, which were prepared using SMART-seq technology (Picelli et al., 2014) and sequenced on an Illumina NextSeq.

value: C57BL/6 mice

value: LCMV Cl13 infection

value: Spleen


title: HiC WT 37C 20min [CH65]

description: WT 37C 20min


title: Day 14

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Splenic virus-specifc CD4+ T cells

extract_protocol:
10x Genomics
Single-cell RNA sequencing

treatment_protocol: IL-21-tRFP+ GP66-specific splenic CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on days 7 and 14 p.i. and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol


title: Day 7


title: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi DN_1

description: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi


title: HiC Scc2 Scc3 Pds5 +IAA R2 [CH307]

description: Scc2 Scc3 Pds5 +IAA R2


title: HiC Scc2 2h 37C [CH68]

description: Scc2 2h 37C


title: vector-2

value: vector


title: vector-3


title: RNA_seq_CXCR6+ CD4+ PD-1hi CXCR6_3

description: RNA_seq_CXCR6+ CD4+ PD-1hi


title: HiC Scc2 Scc3 Pds5 R2 [CH306]

description: Scc2 Scc3 Pds5 R2


title: PS-NPs+Pb scRNA-seq

city: Nanjing

first: Wu

last: Bing

address: No.163 Xianlin Avenue

department: School of the Environment

institute: Nanjing university

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW:  4:10) (2) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3) Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa:  2: 30: 7) (4) Drop reads below the 26 bases long (5) Discard those reads that can not form paired
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean reads.
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting.
Cell Ranger takes as input the expected number of recovered cells, N (see -- expect-cells). Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group (library) and, if the reference contains multiple genomes, for each genome.
Genome_build: Danio_rerio_Ensemble_91
Supplementary_files_format_and_content: gene-barcode expression matrix

source_name: intestine cells

extract_protocol:
The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument(10x Genomics, USA) to generate single cell Gel bead in Emulsion (GEMs).
ScRNA-seq libraries were prepared using the GemCode Single-Cell 3’ Gel Bead, Chip and Library Kits (10x Genomics, USA) as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.

treatment_protocol: Exposure solutions were prepared by adding 200μg/L PS-NPs, 50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  After 21-d exposure, zebrafish were collected and intestine were rapidly extracted on ice.

value: intestine single cell suspension

tag: age

tag: exposed pollutants

value: 200μg/L PS-NPs and 50μg/L Pb


title: HiC Pds5 Hos1 T1 +IAA R2 [CH303]

description: Pds5 Hos1 T1 +IAA R2

value: see Bastie et al, NSMB 2022


title: RNA_seq_CXCR6+ CD4+ PD-1hi CXCR6_2

description: RNA_seq_CXCR6+ CD4+ PD-1hi


title: Pb scRNA-seq

value: 50μg/L Pb


title: PS-NPs scRNA-seq

value: 200μg/L PS-NPs


title: miR-190-2


title: miR-31-3


title: RNA_seq_CXCR5+ CD4+PD-1hi CXCR5_3

description: RNA_seq_CXCR5+ CD4+PD-1hi


title: HiC Fig1 Eco1-AID IAA R2 [CH324]

description: Fig1 Eco1-AID IAA R2


title: HiC Pds5 Hos1 T0 R2 [CH302]

description: Pds5 Hos1 T0 R2


title: miR-31-1


title: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi DN_2

description: RNA_seq_CXCR6-CXCR5- CD4+PD-1hi


title: RNA_seq_CXCR5+ CD4+PD-1hi CXCR5_1

description: RNA_seq_CXCR5+ CD4+PD-1hi


title: HiC Pds5 T1 +IAA R2 [CH301]

description: Pds5 T1 +IAA R2


title: CK scRNA-seq


title: Drosophila Adult-yw-2hr-CPD_rep2

city: Chapel Hill

first: Aziz

last: Sancar

state: NC

address: 120 Mason Farm Rd. CB#7260

institute: University of North Carolina at Chapel Hill

data_processing:
Library strategy: XR-Seq
Base calling was performed with Illumina’s bcl2fastq pipeline v.2.20.0.
Quality control was done using fastqc v0.11.8.
Adapter sequences were removed with Cutadapt v2.9 using sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG.
Identical reads were removed using fastx_toolkit v0.0.14 to avoid PCR duplicates.
Reads were aligned to dm6 genome assembly of Drosophila melanogaster using Bowtie2 v2.4.1 with the option --very-sensitive.
Abundance of dimers sensitive to damage (TT for CPD; TC, CC, CT or TT for 6-4; GG for cisplatin) for each position on oligomers of the same length were calculated.
For CPD and 6-4 photoproducts, reads shorter than 26 nt an longer than 28 nt were filtered out. For cisplatin reads shorter than 27 nt an longer than 29 nt were filtered out.
Damage pinpointing was done by searcing for sensitive dimers 6 - 9 nt upstream of the 3' end of the reads for CPD and 6-4, and 7 - 9 nt for cisplatin.
Read counts on transcribed and non-transcribed strands were obatained using bedtools v2.29 with parameters -c -wa -S -F 0.5 and -c -wa -s -F 0.5 respectively.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files were created using bedtools genomecov from bedtools v2.29 and bedGraphToBigWig from UCSCtools v320.

organism: Drosophila melanogaster

source_name: Drosophila Adults

growth_protocol: Drosophila were kept at 25°C, light-dark:12hr-12hr and fed with standard cornmeal medium. S2 Cells were cultured at 27°C in Schneider’s medium with heat-inactivated fetal bovine serum at 10% and with 200 µg/ml hygromycin antibiotic. Cells were passaged when they reached 80-90% confluence.

extract_protocol:
After repair, samples (embryo, larvae, pupae ,adults or s2 cells) were collected with ice-cold PBS and washed several times. 320 µl TE pH 8.0 was added to each sample and samples were ground. After grinding, 40 µl 10% SDS was added to each sample and samples were incubated at 70°C for 30 minutes. After incubation, 100 µl 5 M NaCl was added to each sample and they were incubated at 4°C overnight.
After overnight incubation, samples from each developmental phase were centrifuged at high speed at 4 degress for one hour.  Supernatants were processed for excision or XR-Seq assay. Briefly, supernatants were incubated with 5 µL Rnase A and then 5 µL Proteinase K, purified, and then immunoprecipitated with anti-CPD, anti-6-4 (P-P) or anti-cisplatin antibodies.  Immunoprecipitates were then either radiolabeled and excision products were separated on 10-11% sequencing gels, or, for  XR-seq assay, immunoprecipitates were ligated to the adaptors, purified by a second immunoprecipitation, and DNA damages were reversed (using photoreactivation for photoproducts, and cyanide treatment for cisplatin damage). Libraries were generated by PCR and then sequenced.

treatment_protocol: For these experiments, Drosophila adults were isolated with fly food containing 5% sucrose and 6% agar for two hours during which time they laid eggs. After the adults were removed, embryos were collected and irradiated with predetermined doses of UV-B, and then were allowed to repair in the dark for predetermined times. Larvae and pupae were transferred to 100 mm plates and irradiated with UV-B and allowed to repair in the dark. After repair, samples (embryo, larvae, pupae and adults) were collected with ice-cold PBS and washed several times. 320 µl TE pH 8.0 was added to each sample and samples were ground. After grinding, 40 µl 10% SDS was added to each sample and samples were incubated at 70°C for 30 minutes. After incubation, 100 µl 5 M NaCl was added to each sample and they were incubated at 4°C overnight.S2 Cells were irradiated with 20 J/m2 UV-C or indicated concentrations of Cisplatin (150uM or 200uM). Following predetermined repair times, plates were placed on ice and cells were harvested by scraping, washed with ice-cold PBS, pelleted, and transferred to Eppendorf tubes. osophila adults were collected on a CO2 panel for UVB irradiation.  Flies were then returned to their vials and allowed to repair in the dark for predetermined times. Cells were irradiated with 20 J/m2 UV-C or indicated concentrations of Cisplatin (150uM or 200uM) and then fresh medium was added. Following predetermined repair times, plates were placed on ice and cells were harvested by scraping, washed with ice-cold PBS, pelleted, and transferred to Eppendorf tubes.

tag: repair time

value: yw

tag: damage ip antibody

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: HiC Scc3 Pds5 +IAA R2 [CH305]

description: Scc3 Pds5 +IAA R2


title: Drosophila s2 cells-1.5hr-200um cisplatin_rep2

source_name: Drosophila s2 cells

value: wild type

value: anti-Cisplatin (Abcam, ab-103261)

value: Cisplatin 200uM


title: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi DN_3

description: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files

extract_protocol: ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide (Buenrostro, Giresi et al. 2013)

treatment_protocol: CXCR6+, CXCR5+, and CXCR6-CXCR5- PD-1hi splenic CD4+ T cells were FACS-sorted from LCMV Cl13-infected WT mice on day 14 p.i. ATAC-seq was performed according to a published protocol (Buenrostro, Giresi et al. 2013). 50,000 cells of CXCR6+, CXCR5+ and CXCR6-CXCR5- PD-1hi CD4 T cell subsets (per mouse) were used for library construction. 37 cycles paired-end sequencing was performed on a Nextseq 550 sequencer and about fifty million reads were generated for each sample.

tag: infection


title: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi DN_2

description: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi


title: RNA_seq_CXCR6+ CD4+ PD-1hi CXCR6_1

description: RNA_seq_CXCR6+ CD4+ PD-1hi


title: HiC Scc3 Pds5 R2 [CH304]

description: Scc3 Pds5 R2


title: HiC Scc2 37C 20min R2 [CH296]

description: Scc2 37C 20min R2


title: HiC Scc2 1h 37C R2 [CH297]

description: Scc2 1h 37C R2


title: Drosophila s2 cells-1.5hr-150um cisplatin_rep2

tag: treatment

value: Cisplatin 150uM


title: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi DN_1

description: ATAC seq_CXCR6-CXCR5- CD4+PD-1hi


title: HiC Scc2 2h 30C R2 [CH295]

description: Scc2 2h 30C R2


title: Drosophila s2 cells-1hr-6-4_rep2

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: ATAC seq_CXCR6+ CD4+ PD-1hi CXCR6_3

description: ATAC seq_CXCR6+ CD4+ PD-1hi


title: RNA_seq_CXCR5+ CD4+PD-1hi CXCR5_2

description: RNA_seq_CXCR5+ CD4+PD-1hi


title: HiC WT 1h 37C R2 [CH294]

description: WT 1h 37C R2


title: Blood_AfterGC_4

city: Changzhou

first: Jiaqi

state: Jiangsu

address: No.68 lake Gehu Road, Wujin District, Changzhou City, Jiangsu Province, China

department: Department of Dermatology

institute: The Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University

description: Circular RNA expression after treatment of methylprednisolone

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

source_name: Peripheral Blood,

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA of 4 pairs of vitiligo samples was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. After the addition of chloroform, the samples were centrifuged at 12,000 rpm for 10 min. The aqueous phase was mixed with isopropanol and RNA pellets were collected by centrifugation (12,000 rpm, 15 min, 4 ◦C). RNA pellets were washed with 70% ethanol and dissolved in RNase-free, DEPC (diethylpyrocarbonate)-treated water (Waltham, MA, USA).

treatment_protocol: Whole blood samples (3 mL each) were collected by venipuncture into heparinized vacutainers from a total of four patients diagnosed with nonsegmental vitiligo before and after systemic glucocorticoid therapy (oral methylprednisolone tablets, 12mg daily for eight weeks).

value: whole blood


title: HiC Pds5 T0 R2 [CH300]

description: Pds5 T0 R2


title: Drosophila s2 cells-1hr-CPD_rep2


title: HiC WT 37C 20min R2 [CH293]

description: WT 37C 20min R2


title: ATAC seq_CXCR6+ CD4+ PD-1hi CXCR6_2

description: ATAC seq_CXCR6+ CD4+ PD-1hi

value: C57BL/6 mice


title: Blood_BeforGC_4

description: Circular RNA expression before treatment of methylprednisolone


title: Drosophila Adult-xpc ko-2hr-6-4_rep2

value: XPC Kockout


title: ATAC seq_CXCR6+ CD4+ PD-1hi CXCR6_1

description: ATAC seq_CXCR6+ CD4+ PD-1hi

value: LCMV Cl13 infection

value: Spleen


title: Drosophila Adult-yw-2hr-6-4_rep2


title: Blood_AfterGC_3


title: Blood_BeforGC_3


title: HiC WT 30C 2h R2 [CH292]

description: WT 30C 2h R2


title: Drosophila Adult-xpc ko-2hr-CPD_rep2


title: HiC cdc45, eco1 R2 [CH291]

description: cdc45, eco1 R2


title: Drosophila Adult-8days-6-4_rep2


title: ATAC seq_CXCR5+ CD4+PD-1hi CXCR5_2

description: ATAC seq_CXCR5+ CD4+PD-1hi


title: bos_5

city: Beijing

first: caixia

last: yu

address: No.1 Beichen West Road

institute: Beijing Institute of Bioinformatics Chinese Academy of Science

data_processing:
Basecalls performed using bcl2fastq2.
Low-quality RNA-seq reads are filtered.
The high-quality RNA-seq reads are mapped to the reference genome by STAR.
Isoform assembly and quantification are performed using RSEM with a special parameter '--single-cell-prior', for basic expression profiling.
Supplementary_files_format_and_content: GeneMatrix.txt.gz
Genome_build: ARS-UCD1.2.98
Supplementary_files_format_and_content: Matrix table contain RPKM values for every gene and every sample

organism: Bos taurus

source_name: limb

extract_protocol: cells were lysated, preamplified and library prepared according C1-HT IFC protocol of Fluidigm Corporation.

value: limb


title: HiC cdc45 R2 [CH290]

description: cdc45 R2


title: Blood_AfterGC_2


title: HiC SMC3RR+IAA R2 [CH287]

description: SMC3RR+IAA R2


title: Drosophila Adult-4days-6-4_rep2


title: bos_4

source_name: heart

value: heart


title: HiC SMC3WT+IAA R2 [CH286]

description: SMC3WT+IAA R2

value: see Bastie et al, NSMB 2022


title: 3xTg-S Cayman4

city: Villejuif

first: Gaël

last: Moquin-Beaudry

address: 114, rue Édouard-Vaillant

institute: Gustave Roussy

description: These samples were compared to 10 month samples only

data_processing:
Samples were sequenced on Nextseq 500 High Output Flowcell single-end 75nt reads
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M23, based on Ensembl 98) using STAR version 2.5.1b
Raw readcounts were obtained directly from STAR, concatenated and annotated
Genome_build: GRCm38
Supplementary_files_format_and_content: combined tab-delimited raw count matrix

source_name: Hippocampus

extract_protocol:
Hippocampi from unoperated or pump-implanted mice were dissected and immediately flash frozen on dry ice. Total RNA was extracted with TRIzol (Invitrogen) and chloroform (Invitrogen). RNA was then purified with the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. 400 ng of total RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For ICV infusions of SCDi or vehicle, mice were locally injected with buprivacaine (Hospira) and operated under isoflurane anesthesia (Baxter). Brain cannulae attached to Alzet osmotic pumps were stereotaxically implanted at 0.0mm antero-posterior and 0.9mm lateral to Bregma  and the pumps placed under the back skin according to manufacturer`s instructions. 28-day Alzet osmotic pumps were used in these experiments (0.11 μl/h infusion rate, model 1004; Durect). The SCD inhibitor (SCDi, ab142089, abcam) was dissolved in DMSO and infused at a final concentration of 80 µM in sterile aCSF. Vehicle pumps contained equal volumes as the SCDi pumps (0.8% DMSO/aCSF).

value: 10 months

value: 28 day ICV SCDi Cayman 10566


title: Drosophila Adult-4days-CPD_rep2


title: bos_3

source_name: lung

value: lung


title: 3xTg-S Cayman3


title: HiC WT +IAA S2 [CH284]

description: WT +IAA S2


title: Drosophila Adult-2days-6-4_rep2


title: HiC Smc3-AID+IAA R2 [CH285]

description: Smc3-AID+IAA R2


title: Drosophila Adult-2days-CPD_rep2

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: bos_2

source_name: skin

value: skin


title: Blood_BeforGC_1


title: ATAC seq_CXCR5+ CD4+PD-1hi CXCR5_3

description: ATAC seq_CXCR5+ CD4+PD-1hi


title: Blood_AfterGC_1


title: bos_1

source_name: brain

value: brain


title: HiC WT S2 [CH283]

description: WT S2


title: Drosophila Adult-8days-CPD_rep2


title: 3xTg-S Cayman1


title: ATAC seq_CXCR5+ CD4+PD-1hi CXCR5_1

description: ATAC seq_CXCR5+ CD4+PD-1hi


title: mNSC_Alkbh5_HA_ChIP_rep

data_processing:
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the hg19 (MCF-7, HEK293T) or mm10 (mNSC) genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

source_name: Neural Stem Cell

extract_protocol:
For ChIP, chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006). For Cut&Tag seq, Hyperactive In-Situ ChIP Library Prep Kit for Illumina was performed according to the manual (Vazyme, TD902).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: For knockdown, MCF-7 cells were seeded in a 6-well plate, and transfected with RNAiMAX (Invitrogen, 13778-150) according to the manual. Cells were harvested after three days. For construction of stable cell lines, lentiviruses expressing plasmids (PMSCV Vector, or METTL3, METTL14, WTAP, ALKBH5) were produced by co-transfection of plasmids with VSV-G and psPAX2 in a 2:1:1 ratio into HEK293T cells using Lipofectamine 2000 (Invitrogen, 11668-019). Supernatant at 48 hour post-transfection was collected. HEK293T or MCF-7 cells were seeded in a 6-well plate and infected with each lentivirus supernatant in the presence of 5 μg/mL polybrene. Medium was replaced by fresh media with Puro (2 ug/ml) for 5 days, the surviving cells were pooled as stably infected cells.

tag: cell line/type

value: mNSC

tag: antibody

value: ALKBH5 (Abcam, ab69325)


title: Blood_BeforGC_2


title: Drosophila Adult-16hr-6-4_rep2

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: HiC Eco1-AID + IAA S2 [CH282]

description: Eco1-AID + IAA S2

tag: treatments


title: Control siRNA repA

source_name: HUVEC

tag: cell type

value: HUVEC


title: mNSC_Wtap_ChIP_rep

value: WTAP (Proteintech, 10200-1-AP)


title: HiC Eco1-AID S2 [CH281]

description: Eco1-AID S2

tag: strain


title: 3xTg-S Cayman2


title: Drosophila Adult-8hr-6-4_rep2


title: Drosophila Adult-16hr-CPD_rep2


title: WT-S Cayman3


title: WT-S Cayman2


title: HiC Scc2, Scc3, Pds5 +IAA [CH251]

description: Scc2, Scc3, Pds5 +IAA


title: WT-S Cayman1


title: HiC Scc2, Scc3, Pds5 [CH250]

description: Scc2, Scc3, Pds5


title: mNSC_Mettl3_ChIP_rep

value: METTL3 (Bethyl, #A301-567A)


title: 3xTg-D4

value: 28 day ICV DMSO


title: Drosophila Adult-8hr-CPD_rep2


title: Drosophila Adult-4hr-6-4_rep3


title: HiC Scc3, Pds5 +IAA [CH249]

description: Scc3, Pds5 +IAA


title: mNSC_H3K27Ac_ChIP

data_processing:
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: Mouse neural stem cells (NSCs) were kindly provided by Dr. Jian Hu (MD Anderson Cancer Center) (Shingu et al., 2017) and cultured in NeuroCult NSC Basal Medium (Stemcell, 05702) supplemented with 20ng/ml EGF (R&D, 236-EG), 20ng/ml bFGF (novoprotein, C779), 50 units/mL penicillin and 50 μg/mL streptomycin (Hyclone SV30010).

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

treatment_protocol: For construction of stable cell lines, lentiviruses expressing plasmids (PMSCV Vector or ALKBH5) were produced by co-transfection of plasmids with VSV-G and psPAX2 in a 2:1:1 ratio into HEK293T cells using Lipofectamine 2000 (Invitrogen, 11668-019). Supernatant at 48 hour post-transfection was collected. HEK293T or MCF-7 cells were seeded in a 6-well plate and infected with each lentivirus supernatant in the presence of 5 μg/mL polybrene. Medium was replaced by fresh media with Puro (2 ug/ml) for 5 days, the surviving cells were pooled as stably infected cells.

value: H3K27Ac (Millipore, 07-360)


title: 3xTg-D3


title: Drosophila Adult-4hr-CPD_rep2


title: WT-S Cayman4


title: HiC Scc3, Pds5 [CH248]

description: Scc3, Pds5


title: mNSC_Input


title: 3xTg-D2


title: HiC WT +IAA [CH235]

description: WT +IAA


title: Drosophila Adult-1hr-6-4_rep3


title: Drosophila Adult-1hr-CPD_rep2


title: 3xTg-D1


title: mNSC_Mettl14_ChIP_rep

value: METTL14 (Sigma, HPA038002)


title: mNSC_Alkbh5_HA_ChIP

value: Alkbh5_HA OE

value: HA-Tag (Cell Signaling, 3724S)


title: WT-D4

value: 10 months


title: HiC WT FigS2 [CH233]

description: WT FigS2

value: see Bastie et al, NSMB 2022


title: HiC Eco1-AID [CH232]


title: mNSC_Wtap_ChIP

value: WTAP (Bethyl, A301-435A)


title: mNSC_Mettl14_ChIP


title: WT-D2


title: WT-D3


title: Drosophila Adult-15min-6-4_rep1


title: Drosophila Adult-30min-CPD_rep1

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: WT-D1


title: HiC fig S5 hos1 [CH231]

description: fig S5 hos1


title: mNSC_H3K4me3_ChIP

value: H3K4me3 (Cell Signaling, 9751S)


title: Drosophila Pupa-2hr-6-4_rep2

source_name: Drosophila Pupa

value: yw


title: Drosophila Adult-15min-CPD_rep1


title: mNSC_Mettl3_ChIP

value: mNSC


title: S3

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

description: partner-derived Tregs from the spleen of mouse #3

data_processing:
FASTQ reads were first processed by Trim Galore! to trim adapter and low-quality reads
Trimmed FASTQ reads were mapped to the mm10 mouse genome using TopHat2 with the default parameters.
Samtools was used to sort the resulting BAM files and generate SAM files, which were then processed by htseq-count of HTSeq to create gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq-count files that include raw counts of sequencing reads for each sample

source_name: spleen

growth_protocol: EG7.1.15 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 50 μM 2-Mercaptoethanol, 0.024 mM NaHCO3, 600 μg/mL G418, 10 μg/mL kanamycin, 200 μg/mL penicillin and streptomycin. CD45.1+ mice were injected with 3x10^6 EG7.1.15 cells intraperitoneally.

extract_protocol:
Omental tumors or spleens were excised from the tumor-bearing parabionts, and partner-derived (CD45.1-) Tregs 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.

treatment_protocol: CD45.1+ tumor-bearing mice were surgically joined with tumor-free CD45.1- mice for 14 days.

value: B6 Foxp3-DTR/GFP

tag: tissue

value: spleen

tag: sorting markers

tag: time point

value: day14 post tumor injection


title: HiC cdc45 [CH228]


title: Drosophila Pupa-2hr-CPD_rep2


title: HiC Eco1-AID + IAA [CH234]

description: Eco1-AID + IAA


title: S2

description: partner-derived Tregs from the spleen of mouse #2


title: Drosophila Larva-2hr-6-4_rep2

source_name: Drosophila Larva

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: Drosophila Adult-30min-6-4_rep1


title: HiC cdc45, eco1 [CH229]

description: cdc45, eco1


title: iUB-3

city: Edinburgh

first: Mona

last: Elhendawi

state: Midlothian

address: 7 George Square

institute: The University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt
were aligned to the Mus musculus reference genome (GRCh38; from Ensembl) using STAR
The raw count data were filtered to remove very low-expressed genes (genes consisting predominantly of near-zero counts)
Reads were normalised using the weighted trimmed mean of M-values method.
Differential analysis (comparing each ES-derived progenitor group to the E11.5 embryonic counterpart group or the E12.5 counterpart group) was carried out using edgeR4.
Genome_build: GRCh38; from Ensembl
Supplementary_files_format_and_content: Microsoft Excel Comma Separated Values file

source_name: Ureteric bud progenitor cells

extract_protocol:
Total RNA was isolated from sorted cells (35,000 – 100,000 cells) using RNeasy Plus micro kit. Organoids were dissociated and processed as per the kit protocol
100 ng of total RNA/sample was used for sequencing library preparation using an Illumina TruSeq stranded mRNA kit. Sequencing was performed using a Novaseq S1 50 Paired-end run to produce 50-64-million read-pairs per sample.

value: ES-derived ureteric bud progenitor cells

tag: cell source

value: ES-derived

tag: strain/cell line


title: OP3

description: partner-derived Tregs from omental tumors of mouse #3

source_name: omental tumors

value: omental tumors


title: iUB-4


title: iUB-2


title: HiC Smc3 RR, Smc3-AID [CH212]

description: Smc3 RR, Smc3-AID


title: mNSC_H3K4me1_ChIP

city: Shanghai

first: Yang

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

value: H3K4me1 (Active Motif, 39297)


title: OP2

description: partner-derived Tregs from omental tumors of mouse #2


title: iUB-1


title: Drosophila Larva-2hr-CPD_rep2


title: iSP-4

source_name: Stromal progenitor cells

value: ES-derived stromal progenitor cells

value: E14 mESC


title: HiC Smc3 WT,Smc3_AID [CH211]

description: Smc3 WT,Smc3_AID


title: RNA-seq_CMTR1_siRNA2_4

city: Glasgow

first: Shang

last: Liang

address: Garscube Estate

institute: CRUK Scotland Institute

data_processing:
Sequencing was performed with a read length of 2Ã—75 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
Each reads per gene was quantified using featureCounts (Liao et al., 2014)
The bigWig files were generated by deepTools (Ramírez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: Each reads per gene file contains a tab delimited table of reads per gene counted, the first column indicates the ensembl gene id, the second column shows all alignments. BigWig files showed the reads per kilobase per million (RPKM) of read densities within the 10bp windows of genomic region for each sample.

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were were grown in Glasgow's Minimum Essential Medium with 10% Knockout Serum Replacement, 1% Non-Essential Amino Acids , 2 mM L-Glutamine, 1 mM sodium pyruvate, 0.35 μM β-mercaptoethanol and 100 U/ml recombinant LIF. mESCs were cultured in 0.1% gelatin-coated flasks or dishes at 37 °C with 5 % CO2.

extract_protocol:
Total RNA was extracted using TRIzol Reagent.
Ribosomal RNA depletion was performed using the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq library preparation was carried out using the NEBNext® Ultra™ II Directional RNA Library Prep Kit and indexed with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs).

treatment_protocol: Mouse embryonic stem cells were treated with the control scramble siRNA or CMTR1 specific siRNAs for 36 hours.

value: Embryonic stem cells

tag: cell line

value: treated with the CMTR1-specific siRNA 2 for 36h


title: Drosophila Embryo-2hr-CPD_rep2

source_name: Drosophila Embryo


title: Drosophila Embryo-2hr-6-4_rep2


title: HiC WT 1h 37C Fig S3 [CH165]

description: WT 1h 37C Fig S3

value: see Bastie et al, NSMB 2022


title: HiC fig S5 WT [CH230]

description: fig S5 WT


title: RNA-seq_CMTR1_siRNA2_3


title: iSP-2


title: iSP-3


title: HiC Scc2 1h37C Fig S3 [CH164]

description: Scc2 1h37C Fig S3


title: RNA-seq_CMTR1_siRNA2_2


title: Drosophila Adult-yw-fenale-2hr-CPD_rep2

source_name: Drosophila Adults-female

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: iSP-1


title: Drosophila Adult-yw-male-2hr-CPD_rep2

source_name: Drosophila Adults-male


title: HiC Scc2 1h37C [CH129]

description: Scc2 1h37C


title: RNA-seq_CMTR1_siRNA2_1


title: HiC WT 1h 37C [CH128]

description: WT 1h 37C


title: Drosophila Adult-2hr-CPD_rep2

source_name: Drosophila Adults


title: iNP-4

source_name: Nephron progenitor cells

value: ES-derived nephron progenitor cells


title: iNP-3


title: RNA-seq_CMTR1_siRNA1_4

value: treated with the CMTR1-specific siRNA 1 for 36h


title: HiC Pds5, Hos1 T1 +IAA [CH117]

description: Pds5, Hos1 T1 +IAA


title: Drosophila Adult-2hr-6-4_rep2


title: iNP-2


title: HiC Hos1delta T1 +IAA [CH115]

description: Hos1delta T1 +IAA


title: iNP-1


title: RNA-seq_CMTR1_siRNA1_2


title: HiC Pds5, Hos1 T0 [CH116]

description: Pds5, Hos1 T0


title: E12.5_UB-4

value: E 12.5 ureteric bud progenitor cells

value: CD1 mice


title: Drosophila s2 cells-1hr-6-4_rep1

description:
Drosophila s2 cells-6-4_rep1
Low molecular DNA

data_processing:
Base calling was performed with Illumina’s bcl2fastq pipeline v.2.20.0.
Quality control was done using fastqc v0.11.8.
Adapter sequences were removed with Cutadapt v2.9 using sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG.
Identical reads were removed using fastx_toolkit v0.0.14 to avoid PCR duplicates.
Reads were aligned to dm6 genome assembly of Drosophila melanogaster using Bowtie2 v2.4.1 with the option --very-sensitive.
Abundance of dimers sensitive to damage (TT for CPD; TC, CC, CT or TT for 6-4; GG for cisplatin) for each position on oligomers of the same length were calculated.
For CPD and 6-4 photoproducts, reads shorter than 26 nt an longer than 28 nt were filtered out. For cisplatin reads shorter than 27 nt an longer than 29 nt were filtered out.
Damage pinpointing was done by searcing for sensitive dimers 6 - 9 nt upstream of the 3' end of the reads for CPD and 6-4, and 7 - 9 nt for cisplatin.
Read counts on transcribed and non-transcribed strands were obatained using bedtools v2.29 with parameters -c -wa -S -F 0.5 and -c -wa -s -F 0.5 respectively.
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files were created using bedtools genomecov from bedtools v2.29 and bedGraphToBigWig from UCSCtools v320.

source_name: Drosophila s2 cells

extract_protocol:
After repair, samples (embryo, larvae, pupae ,adults or s2 cells) were collected with ice-cold PBS and washed several times. 320 µl TE pH 8.0 was added to each sample and samples were ground. After grinding, 40 µl 10% SDS was added to each sample and samples were incubated at 70°C for 30 minutes. After incubation, 100 µl 5 M NaCl was added to each sample and they were incubated at 4°C overnight.
After overnight incubation, samples from each developmental phase were centrifuged at high speed at 4 degress for one hour.  Supernatants were processed for excision or XR-Seq assay. Briefly, supernatants were incubated with 5 µL Rnase A and then 5 µL Proteinase K, purified, and then immunoprecipitated with anti-CPD, anti-6-4 (P-P) or anti-cisplatin antibodies.  Immunoprecipitates were then either radiolabeled and excision products were separated on 10-11% sequencing gels, or, for  XR-seq assay, immunoprecipitates were ligated to the adaptors, purified by a second immunoprecipitation, and DNA damages were reversed (using photoreactivation for photoproducts, and cyanide treatment for cisplatin damage). Libraries were generated by PCR and then sequenced.
OTHER: XR-Seq

value: wild type


title: Drosophila s2 cells-1.5hr-150um cisplatin_rep1

description:
Drosophila s2 cells-150um cisplatin_rep1
Low molecular DNA

value: anti-Cisplatin (Abcam, ab-103261)

value: Cisplatin 150uM


title: Drosophila s2 cells-1.5hr-200um cisplatin_rep1

description:
Drosophila s2 cells-200um cisplatin_rep1
Low molecular DNA

value: Cisplatin 200uM


title: RNA-seq_Control_3

value: treated with the control scramble siRNA for 36h


title: HiC Eco1-AID +IAA [CH113]

description: Eco1-AID +IAA

data_processing:
Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered
PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded.
Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
Genome_build: W303


title: HiC WT Fig1 [CH112]

description: WT Fig1


title: Drosophila s2 cells-1hr-CPD_rep1

description:
Drosophila s2 cells-CPD_rep1
Low molecular DNA


title: HiC Hos1delta T0 [CH114]

description: Hos1delta T0


title: RNA-seq_Control_2


title: Drosophila Adult-xpc ko-2hr-6-4_rep1

description:
Drosophila Adult-6-4_rep2
Low molecular DNA

value: XPC Kockout

value: anti-6-4 (Cosmo Bio co. LTD, NM-DND-002)


title: E12.5_UB-3


title: E12.5_UB-2


title: Drosophila Adult-xpc ko-2hr-CPD_rep1

description:
Drosophila Adult-CPD_rep2
Low molecular DNA


title: RNA-seq_CMTR1_siRNA1_3


title: RNA-seq_Control_1


title: Input_ChIP-seq_RNAPII_siCMTR1

data_processing:
Sequencing was performed with a read length of 2×75 bp using a high output kit on Illumina NextSeq 500
The quality of sequencing reads was checked using FastQC and the adaptors were trimmed using Cutadapt (Martin, 2011)
The trimmed reads were aligned to the mouse genome assembly GRCm38/mm10 using STAR
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
The bigWig files were generated by deepTools (Ramírez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showed the reads per kilobase per million (RPKM) of ChIP read densities within the 10bp windows of genomic region for each sample.

extract_protocol:
Cells were cross-linked by 1% formaldehyde for 10 min. Then the glycine was added to quench the reaction. The cell lysates were prepared as described (Varshney et al., 2018).The chromatin was sonicated in Bioruptor (Diagenode) at high power for 20 min (30 s on/off, 20 cycles). 25-50 micrograms of the sonicated chromatin were used for each IP. 50μl (10%) from each diluted extract for IP were taken as the inputs. For ChIP using anti-HA beads, 20μL of anti-HA magnetic beads (Pierce) were added to lysates from CMTR1/RNMT KI cells (as IPs) and E14 cells (as control) for 4°C overnight incubation. For RNAP II ChIP, 2μg of anti-Rpb1 (CST 14958) were added to lysates from E14 cells for 4 °C overnight reaction before the incubation with protein G Dynabeads (Life Technologies) for additional 2 hours. The beads were washed and eluted as described (Varshney et al., 2018) before the proteinase K treatment and reverse crosslinking at 42 °C overnight. The eluted DNA was purified by the QIAquick PCR purification kit (QIAGEN).
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos (Index Primers Set 1) for Illumina.

treatment_protocol: For RNAP II ChIP, cells were treated with the control scramble siRNA or CMTR1 specific siRNAs for 36 hours.

value: treated with the CMTR1-specific siRNA for 36h


title: Drosophila Adult-8days-6-4_rep1

description:
Drosophila Adult-6-4_rep1
Low molecular DNA


title: IP_ChIP-seq_RNAPII_siCMTR1_2

value: anti-Rpb1 (CST 14958)


title: Drosophila Adult-8days-CPD_rep1

description:
Drosophila Adult-CPD_rep1
Low molecular DNA


title: E12.5_UB-1


title: IP_ChIP-seq_RNAPII_siCMTR1_1

value: Embryonic stem cells


title: E12.5_SP-3

value: E 12.5 stromal progenitor cells


title: E12.5_SP-4


title: E12.5_SP-2


title: RNA-seq_CMTR1_siRNA1_1


title: Drosophila Adult-4days-CPD_rep1


title: E12.5_SP-1


title: Drosophila Adult-4days-6-4_rep1


title: IP_ChIP-seq_RNAPII_Control_2


title: IP_ChIP-seq_RNAPII_Control_1


title: Drosophila Adult-2days-6-4_rep1


title: Drosophila Adult-2days-CPD_rep1


title: E12.5_NP-2

value: E 12.5 nephron progenitor cells


title: E12.5_NP-3


title: IP_ChIP-seq_Control_3

value: untreated

value: anti-HA magnetic beads (Pierce 88836)


title: Input_ChIP-seq_Control


title: IP_ChIP-seq_Control_2


title: E12.5_NP-4


title: Drosophila Adult-16hr-6-4_rep1


title: Drosophila Adult-8hr-6-4_rep1


title: Drosophila Adult-8hr-CPD_rep1

value: anti-CPD (Cosmo Bio co. LTD, NM-DND-001)


title: E11.5_UB-3

value: E 11.5 ureteric bud progenitor cells


title: IP_ChIP-seq_Control_1


title: Input_ChIP-seq_RNMT

value: HA-GFP-Rnmt KI E14


title: E11.5_UB-4

value: CD1 mice


title: E11.5_UB-2


title: Drosophila Adult-4hr-6-4_rep2


title: IP_ChIP-seq_RNMT_3


title: Drosophila Adult-4hr-CPD_rep1


title: Input_ChIP-seq_RNAPII_Control


title: E11.5_UB-1


title: IP_ChIP-seq_RNMT_2