title: iDART_SMART-seq APOBEC1-YTH Cell 770


title: iDART_SMART-seq APOBEC1-YTH Cell 772

status: Public on Jan 25 2022

type: SRA

city: Durham

first: Matthew

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Alignment to hg38 and UMI deduplication using Cell Ranger 3.1.0 (10x Genomics scRNA-seq samples only)
SMART-seq2 and bulk RNAseq samples: Trimming of adaptor sequences (Flexbar 3.0.3)
SMART-seq2 and bulk RNAseq samples:  Alignment using STAR 2.7.5c, and deduplication using SAMtools (1.11) fixmate and markdup
All samples: Identification of m6A sites using Bullseye
All samples: Expression normalization and integrated clustering of cells using Seurat (3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Bed files for bulk RNAare a list of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 APOBEC1-YTH replicates
Supplementary_files_format_and_content: a bed file consisting of APOBEC1-mediated C-to-U editing sites identified by downstream analysis

molecule: polyA RNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: HEK293T cells expressing APOBEC1-YTH or APOBEC1-YTHmut (iDART cells) were cultured in DMEM +10% FBS with penicillin/streptomycin.

extract_protocol:
SMART-seq2 cells: Single cells were sorted using a FACS Aria II (BD) directly into lysis buffer provided with the SMART-seq HT Kit (Takara, Cat. 634438). The SMART-seq HT Kit was then used for reverse transcription and cDNA amplification. Sequencing libraries were constructed from cDNA using the Nextera XT kit (Illumina, FC-131-1096) and dual Nextera-compatible CDI indexes from IDT. Samples were pooled and sequenced targeting 5,000,000 reads/library (150bp paried-end) on a Novaseq6000 using the S4 flowcell.   10X Genomics cells: A single cell suspension was prepared according to manufacturer's instruction for Chromium v3 3' end sequencing (10x Genomics, Manual Part #CG00053). Samples were sequenced targeting 80,000 reads per cell on a Novaseq6000 using the S1 flowcell.  Bulk RNA-seq: Trizol was used to extract total RNA from iDART cells. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA. The samples were sequenced targeting ~30 million reads (50bp paired-end sequencing) per sample on a Novaseq6000 using the S1 flowcell.
SMART-seq2 scRNA-seq: cDNA libraries were generated using the SMART-seq HT Kit (Takara, Cat. 634438). Final libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096).   10x scRNA-seq: Libraries were generated from a single cell suspension using the 10x Genomics NextGEM Single Cell 3' Kit, v3.1 chemistry (10x Genomics)  Bulk-RNA seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA.

treatment_protocol: When cells were 60-70% confluent, iDART cells were treated with 1µg/µL doxycycline for 24 hours for bulk RNA-seq, 10x Genomics scRNA-seq, and SMART-seq2 scRNA-seq

tag: cell line

value: HEK293T Cells

tag: transgene

tag: treatment

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 774


title: iDART_SMART-seq APOBEC1-YTH Cell 794


title: iDART_SMART-seq APOBEC1-YTH Cell 767


title: iDART_SMART-seq APOBEC1-YTH Cell 768


title: iDART_SMART-seq APOBEC1-YTH Cell 765


title: iDART_SMART-seq APOBEC1-YTH Cell 761


title: iDART_SMART-seq APOBEC1-YTH Cell 766


title: iDART_SMART-seq APOBEC1-YTH Cell 782


title: iDART_SMART-seq APOBEC1-YTH Cell 760


title: iDART_SMART-seq APOBEC1-YTH Cell 763


title: iDART_SMART-seq APOBEC1-YTH Cell 762


title: iDART_SMART-seq APOBEC1-YTH Cell 764


title: iDART_SMART-seq APOBEC1-YTH Cell 758


title: iDART_SMART-seq APOBEC1-YTH Cell 754


title: iDART_SMART-seq APOBEC1-YTH Cell 776


title: iDART_SMART-seq APOBEC1-YTH Cell 756


title: iDART_SMART-seq APOBEC1-YTH Cell 759


title: iDART_SMART-seq APOBEC1-YTH Cell 757


title: iDART_SMART-seq APOBEC1-YTH Cell 755


title: iDART_SMART-seq APOBEC1-YTH Cell 752


title: iDART_SMART-seq APOBEC1-YTH Cell 753


title: iDART_SMART-seq APOBEC1-YTH Cell 750


title: iDART_SMART-seq APOBEC1-YTH Cell 751


title: WT_H3K56ac_ChIP_BMRC210004706-1A

city: KunMing

first: Lu

last: Zhang

state: YunNan

address: WuJiaYing Street

country: China

institute: YunNan University

library_source: genomic

data_processing:
software used for basecalling
ChIP-seq reads were aligned to the NC10 genome assembly using Bowtie 2 version 2.3.4.1 with the following configurations…
Data were filtered using the following specifications…
peaks were called using masc2 version 2.2 with the following setting
Genome_build: NC10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage 3.5.1
Supplementary_files_format_and_content: bedGraph files were generated using Bismark Version v0.23.1

molecule: genomic DNA

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Conidia of indicated strains were inoculated in petri dishes with 50 mL minimal medium (1× Vogel's and 2% glucose) and cultured at 25°C in constant light until the exponential growth phase of mycelia. The mycelial mats were cut with a specific puncher for quantification. Then, these small mycelial disks were transferred to Erlenmeyer flasks with 50 mL minimal medium and were grown at 25°C with shaking for 18 hours under constant light.

extract_protocol:
Lysates were clarified from sonicated mycelia and histone-DNA complexes were isolated with antibody.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genotype/variation

value: wild type

tag: antibody


title: WT_HP1_ChIP_BMRC210004457-1A


title: WT_HP1_input_BMRC210004447-1A


title: WT_H3K56ac_input_BMRC210004705-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 769


title: iDART_SMART-seq APOBEC1-YTH Cell 749


title: iDART_SMART-seq APOBEC1-YTH Cell 748


title: WT_H2A.Z_input_BMRC210004713-1A


title: WT_H2A.Z_ChIP_BMRC210004714-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 745


title: iDART_SMART-seq APOBEC1-YTH Cell 747


title: iDART_SMART-seq APOBEC1-YTH Cell 746


title: iDART_SMART-seq APOBEC1-YTH Cell 744


title: H3K56Rdmm-1KO_HP1_input_BMRC210004455-1A


title: H3K56R_HP1_ChIP_BMRC210004454-1A

tag: genotype/variation:

tag: antibody:


title: iDART_SMART-seq APOBEC1-YTH Cell 742


title: H3K56Q_HP1_input_BMRC210004701-1A


title: H3K56Rdmm-1KO_HP1_ChIP_BMRC210004456-1A


title: H3K56Q_HP1_ChIP_BMRC210004702-1A


title: H3K56R_HP1_input_BMRC210004453-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 743


title: iDART_SMART-seq APOBEC1-YTH Cell 859


title: H3K56Qdmm-1KO_HP1_ChIP_BMRC210004704-1A


title: H3K56Qdmm-1KO_HP1_input_BMRC210004703-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 739


title: iDART_SMART-seq APOBEC1-YTH Cell 740


title: iDART_SMART-seq APOBEC1-YTH Cell 741


title: WT_H3_input_BMRC210004709-1A


title: H2A.ZKO_HP1_ChIP_BMRC210004451-1A


title: H2A.ZKO_HP1_input_BMRC210004450-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 738


title: iDART_SMART-seq APOBEC1-YTH Cell 736


title: H2A.ZKO_dmm-1KO_HP1_input_BMRC210004452-1A


title: WT_H3_ChIP_BMRC210004710-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 735


title: H2A.ZKO_dmm-1KO_HP1_ChIP_BMRC210004458-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 733


title: dmm-1_KO_H3K56ac_input_BMRC210004707-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 734


title: dmm-1_KO_HP1_input_BMRC210004448-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 862


title: iDART_SMART-seq APOBEC1-YTH Cell 730


title: dmm-1_KO_HP1_ChIP_BMRC210004449-1A


title: dmm-1_KO_H3_input_BMRC210004711-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 728


title: dmm-1_KO_H3_ChIP_BMRC210004712-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 729


title: dmm-1_KO_H2A.Z_input_BMRC210004715-1A


title: dmm-1_KO_H2A.Z_ChIP_BMRC210004716-1A


title: iDART_SMART-seq APOBEC1-YTH Cell 727


title: iDART_SMART-seq APOBEC1-YTH Cell 726


title: iDART_SMART-seq APOBEC1-YTH Cell 725


title: iDART_SMART-seq APOBEC1-YTH Cell 724


title: iDART_SMART-seq APOBEC1-YTH Cell 737


title: iDART_SMART-seq APOBEC1-YTH Cell 723


title: dmm-1_KO_H3K56ac_ChIP_BMRC210004708-1A


title: EpiLC_Cdh1-Tg_rep2

city: Fukuoka city

first: Yuki

last: Naitou

state: Japan

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka city

country: Japan

institute: Kyushu university

data_processing:
Obtained reads were mapped to the mouse mm10 genome using Hisat2. Mapped reads were counted by featureCounts. Principal component analysis (PCA) was performed using R software with FactoMineR. For differentially expressed gene (DEG) analysis, the false discovery rate (FDR) and log2 fold-change were calculated using edgeR. The DAVID database was used for Gene ontology (GO) analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

organism: Mus musculus

source_name: epiblast like cells of Cdh1 OE

extract_protocol:
Total RNAs were extracted and purified using an RNeasy Micro Kit, and mRNAs were isolated with the NEBNext poly(A) mRNA magnetic isolation module (NEB).
Purified RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNAs were enriched by 12-cycle PCR.

tag: strain

tag: cell type

value: embryonic stem cells

tag: genotype

value: Cdh1 OE


title: d2PGCLC_Cdh1-Tg_rep1

source_name: primordial germ cell like cells at day 2 of Cdh1 OE


title: EpiLC_Cdh1-Tg_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 721


title: iDART_SMART-seq APOBEC1-YTH Cell 722


title: ESC_Cdh1-Tg_rep2

source_name: embryonic stem cells of Cdh1 OE

value: primordial germ cell like cells


title: d2PGCLC_Cdh1-Tg_rep2


title: ESC_Cdh1-Tg_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 732


title: iDART_SMART-seq APOBEC1-YTH Cell 720


title: d2PGCLC_Ovol2a/2b-Tg_rep2

source_name: primordial germ cell like cells at day 2 of Ovol2a/2b OE

value: Ovol2a/2b OE


title: iDART_SMART-seq APOBEC1-YTH Cell 731


title: iDART_SMART-seq APOBEC1-YTH Cell 718


title: EpiLC_Ovol2a/2b-Tg_rep2

source_name: epiblast like cells of Ovol2a/2b OE

value: epiblast like cells


title: iDART_SMART-seq APOBEC1-YTH Cell 716


title: iDART_SMART-seq APOBEC1-YTH Cell 717


title: d2PGCLC_Ovol2a/2b-Tg_rep1


title: ESC_Ovol2a/2b-Tg_rep2

source_name: embryonic stem cells of Ovol2a/2b OE


title: iDART_SMART-seq APOBEC1-YTH Cell 715


title: iDART_SMART-seq APOBEC1-YTH Cell 714


title: iDART_SMART-seq APOBEC1-YTH Cell 713


title: iDART_SMART-seq APOBEC1-YTH Cell 712


title: ESC_Ovol2a/2b-Tg_rep1


title: EpiLC_Ovol2a/2b-Tg_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 709


title: Ovol2b_input_rep1

data_processing:
ChIP-seq reads were aligned using Bowtie v2.3.5 (Langmead and Salzberg, 2012) to the mouse reference genome (GRCm38/mm10). Peaks were called with MACS version 2.2.6 (Zhang et al., 2008) with default settings and visualized using an Integrative Genomics Viewer (Thorvaldsdottir et al., 2013). The consensus sequences of OVOL2A and OVOL2B were identified by HOMER (Heinz et al., 2010). Genomic annotation of the peaks identified from the ChIP-seq data was performed using bedtools (Quinlan and Hall, 2010). Unsupervised hierarchical clustering (UHC) was performed using the hclust function with Pearson correlation distances and Ward’s method (ward.D2). The normalized IP/input ratios were determined as peak density divided by input within 1 kb from the TSSs.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: primordial germ cell like cells at day 2 of Ovol2b OE

extract_protocol:
For crosslinking, the pellets were resuspended in PBS containing 1% formaldehyde, incubated for 10 min, and quenched with 125 mM glycine. The fixed cells were resuspended in 1 ml of LB1 (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TritonX-100), and pelleted by centrifugation at 4000 rpm for 5 min. The pellets were resuspended in 1 ml of LB2 (20 mM Tris [pH 7.5], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and pelleted by centrifugation at 4000 rpm for 5 min. The pellets were resuspended in 1 ml of LB3 (20 mM Tris [pH 7.5], 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate, 0.1% SDS), and pelleted by centrifugation at 4000 rpm for 5 min. The nuclei were lysed in 200 µl of SDS buffer (20 mM Tris [pH 7.5], 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium-deoxycholate, 1% SDS, and protease inhibitor cocktail). The lysed nuclei were sonicated using a sonicator (Branson) for 10 cycles. Protein-DNA complexes were immunoprecipitated at 4℃ overnight using 2 µg of antibodies bound to 50 µl of Dynabeads Protein G (Invitrogen). Immunoprecipitates were washed with 1ml of LB3 twice, high salt buffer (20 mM Tris [pH7.5], 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium-deoxycholate, 0.1%SDS), RIPA buffer (50 mM HEPES-KOH [pH 7.4], 0.25M LiCl, 1 mM EDTA, 0.5% sodium-deoxycholate, 1% NP-40), and TE buffer (50 mM Tris [pH 8.0], 10 mM EDTA). For collection of the protein-DNA complexes, beads were resuspended with 100 µl of elution buffer (50 mM Tris [pH 8.0], 10 mM EDTA, 1% SDS). The immunoprecipitated and input DNA were reverse-crosslinked by incubating at 65℃ overnight. The mixtures were supplemented with 20 µg of RNaseA and incubated at 37℃ for 1 h. After Proteinase K digestion, the DNA was purified by using a PCR purification kit (Fastgene, FG-91302) and dissolved with distilled water.
Sonicated DNA fragments were end-repaired, ligated to sequencing adapters, and amplified according to the manufacturer’s instructions (NEB, E7645).

value: Ovol2b OE


title: Ovol2a_input_rep2

source_name: primordial germ cell like cells at day 2 of Ovol2a OE

value: Ovol2a OE


title: Ovol2b_ChIP_rep1


title: Ovol2a_ChIP_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 710


title: Ovol2a_ChIP_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 708


title: iDART_SMART-seq APOBEC1-YTH Cell 711


title: Ovol2b_input_rep2


title: Ovol2a_input_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 705


title: iDART_SMART-seq APOBEC1-YTH Cell 719


title: iDART_SMART-seq APOBEC1-YTH Cell 704


title: iDART_SMART-seq APOBEC1-YTH Cell 706


title: iDART_SMART-seq APOBEC1-YTH Cell 703


title: 1-222mut_PAPI-CLIP=seq_rep3

city: Tokyo

first: Yuka

middle: W.

last: Iwasaki

address: 35 Shinanomachi, Shinjuku-ku,

department: Department of Molecular Biology

institute: Keio University School of Medicine

data_processing:
Reads were trimmed by a 3′ adapter sequence using Cutadapt (Martin, 2011), and those shorter than 27bp were discarded. PCR duplicates were removed by collapsing all identical reads containing the same random barcode using fastx-collapser from FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit), followed by the removal of 5′-end random barcode at positions 1–9 of the reads. Mapping was performed against the Bombyx mori genome assembly (Nov.2016) from the SilkBase database (Kawamoto et al., 2019) using STAR (Dobin et al., 2013).
Genome_build: Bombyx mori genome assembly (Nov.2016) from the SilkBase database (Kawamoto et al., 2019)
Supplementary_files_format_and_content: 3′ adapter sequence trimmed, size selected, PCR duplicates removed, and barcodes are removed. Then reads were mapped to the silkworm genome, and mapped reads were extracted. For each unique CLIP tag sequences, read counts are indicated in tab delimited format.

molecule: total RNA

organism: Bombyx mori

source_name: BmN4 cells

growth_protocol: BmN4 cells were cultured at 26 °C in EX-CELL® 420 Serum-Free Medium for insect cells (Sigma) supplemented with 10% fetal bovine serum (FBS) (Equitech-Bio) and penicillin-streptomycin-glutamine (Thermo Fisher Scientific).

extract_protocol:
10 cm dish BmN4 cells transfected Papi-Flag or Papi1-222-Flag were used for each iCLIP experiment. For UV crosslinking, BmN4 cells were washed once with ice-cold PBS. The UV crosslinking was performed with irradiance of 200 mJ/cm2 at 254 nm. Cells were pelleted and lysed with lysis buffer [20 mM HEPES (pH7.3), 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin]. RNA–protein complexes were immunoprecipitated using 12 μg of anti-FLAG M2 antibody and 120 μL of Dynabeads Protein G at 4 °C for 2 h. Beads were washed three times with wash buffer [20 mM HEPES (pH7.3), 300 mM sodium chloride, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin], followed by partial RNA digestion with 1 U/μL RNase T1 for 15 min at room temperature. Beads were washed three times with high-salt wash buffer [20 mM HEPES (pH7.3), 500 mM sodium chloride, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin]. After 3' end RNA dephosphorylation with T4 PNK, the RNAs were ligated at their 3' end s to a preadenylated RNA adaptor with T4 RNA ligase2, truncated KQ (New England Biolabs), and then radioactively labeled. The samples were analyzed by NuPAGE gel electrophoresis (Life Technologies) and RNA–protein complexes were transferred to nitrocellulose. After cutting out the region of nitrocellulose containing RNA–protein complexes, RNAs were removed from the membrane by Proteinase K (Roche) digestion.
Extracted samples were processed for reverse transcription, cDNA purification, and cDNA circularization as previously described (Flynn et al., 2015). Libraries were then amplified with Q5 DNA polymerase (New England Biolabs) and size-selected via polyacrylamide gel electrophoresis.
iCLIP libraries were sequenced using the MiSeq platform as single-end 51-bp reads.

treatment_protocol: BmN4 cells were transfected with 2 μg of plasmids (per 6 × 105 cells) using FuGENE HD (Promega). After 48 h, transfected cells were harvested for FAST-iCLIP analysis.


title: WT_PAPI-CLIP-seq_rep3

value: WT


title: iDART_SMART-seq APOBEC1-YTH Cell 702


title: 1-222mut_PAPI-CLIP=seq_rep1

extract_protocol:
10 cm dish BmN4 cells transfected Papi-Flag or Papi1-222-Flag were used for each iCLIP experiment. For UV crosslinking, BmN4 cells were washed once with ice-cold PBS. The UV crosslinking was performed with irradiance of 200 mJ/cm2 at 254 nm. Cells were pelleted and lysed with lysis buffer [20 mM HEPES (pH7.3), 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin]. RNA–protein complexes were immunoprecipitated using 12 μg of anti-FLAG M2 antibody and 120 μL of Dynabeads Protein G at 4 °C for 2 h. Beads were washed three times with wash buffer [20 mM HEPES (pH7.3), 300 mM sodium chloride, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin], followed by partial RNA digestion with 1 U/μL RNase T1 for 15 min at room temperature. Beads were washed three times with high-salt wash buffer [20 mM HEPES (pH7.3), 500 mM sodium chloride, 1 mM DTT, 0.5% Triton X-100, 2 μg/mL pepstatin, 2 μg/mL leupeptin, 0.5% aprotinin]. After 3' end RNA dephosphorylation with T4 PNK, the RNAs were ligated at their 3' end s to a preadenylated RNA adaptor with T4 RNA ligase2, truncated KQ (New England Biolabs), and then radioactively labeled. The samples were analyzed by NuPAGE gel electrophoresis (Life Technologies) and RNA–protein complexes were transferred to nitrocellulose. After cutting out the region of nitrocellulose containing RNA–protein complexes, RNAs were removed from the membrane by Proteinase K (Roche) digestion.
Extracted samples were processed for reverse transcription, cDNA purification, and cDNA circularization as previously described (Flynn et al., 2015). Libraries were then amplified with Q5 DNA polymerase (New England Biolabs) and size-selected via polyacrylamide gel electrophoresis.


title: WT_PAPI-CLIP-seq_rep2


title: Ovol2b_ChIP_rep2


title: WT_PAPI-CLIP-seq_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 696


title: iDART_SMART-seq APOBEC1-YTH Cell 699


title: iDART_SMART-seq APOBEC1-YTH Cell 707


title: iDART_SMART-seq APOBEC1-YTH Cell 698


title: leg 72h APF rep2

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

state: Bayern

address: Großhaderner Str. 9

department: Physiological Chemistry

country: Germany

institute: Ludwig-Maximilians-University München, Biomedical center

description:
leg72h2
wildtype sample, dissected whole leg

data_processing:
basecalling and demultiplexing by LC Sciences or GENEWIZ using Illumina software
Sequenced reads were mapped to the Ensembl BDGP6.22 whole genome using STAR v2.7.3a
mapped reads were sorted and indexed using samtools v1.1
bam files were converted into bigwig for visualisation using ucsc-wigtobigwig v377, or visualized directly as .bam files in IGV
Counting the mapped reads on the gene and exon level using featureCounts in subread v.2.0.0
novel alternative splice event discovery and annotation using fortuna
differential gene expression analysis using the R package DESeq2 v1.32.0
differential exon usage with the R package DEXSeq v1.38.0
Genome_build: BDGP6.22 from ENSEMBL
Supplementary_files_format_and_content: tab delimited text files including counts and results from DESeq2 analysis (all pairwise comparisons)
Supplementary_files_format_and_content: tab delimited text files including counts and results from DEXSeq analysis (all pairwise comparisons)
Supplementary_files_format_and_content: tab delimited text files of output from fortuna

organism: Drosophila melanogaster

source_name: whole leg

growth_protocol:
grown at 27C, staged 0h white pre-pupae
flies were grown at 27C on standard medium using standard fly husbandry

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selection by LC Sciences (brain and leg) or GENEWIZ (IFM)
RNA libraries were prepared for sequencing by LC Sciences (Houston, TX, USA) or GENEWIZ (South Plainfield, NJ, USA) using standard Illumina protocols

treatment_protocol: tissues were dissected for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction (see Kao et al., JoVE, 2019 for details)

tag: developmental stage

value: 72h APF

tag: muscle type

value: tubular


title: brain 72h APF rep1

description:
brain72h1
wildtype sample, dissected brain

source_name: brain

value: non-muscle


title: leg 72h APF rep1

description:
leg72h1
wildtype sample, dissected whole leg


title: IFM 72h APF rep2

description:
IFM72h2
wildtype sample, dissected IFM

source_name: indirect flight muscle

value: fibrillar


title: iDART_SMART-seq APOBEC1-YTH Cell 697


title: iDART_SMART-seq APOBEC1-YTH Cell 692


title: iDART_SMART-seq APOBEC1-YTH Cell 689


title: DFR2_CDNA

city: Esch-sur-Alzette

first: Dirk

last: Brenner

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

description:
10x Genomics with CITE-seq
DFR2_hashtag1 to DFR2_hashtag4
mRNA and protein

data_processing:
Library strategy: CITE-seq
The Cell Ranger pipeline (10x Genomics version 3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression and cell surface protein libraries.
Read 2 of the gene expression libraries was mapped to the reference genome (mouse mm10, v3.0.0) using STAR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pre-processed feature counts (filtered matrices, .h5 files).

source_name: spleen

extract_protocol:
The cell pellet was resuspended and incubated for 30 min on ice with 25μL of staining mix in PBS containing 0.04% BSA, TruStain FcX Block (BioLegend 101320) and the mouse cell surface protein antibody panel containing the following oligo-conjugated anti-mouse antibodies (TotalSeq-A BioLegend) diluted 1:500.
Sorted single-cell suspensions were resuspended at an estimated final concentration of 1000 cells/μl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). Biological replicates (n=4 for each group) were multiplexed using TotalSeq-A Cell Hashing Antibodies.
The scRNA/CITE-seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version 3 (10x Genomics 1000128) according to the manufacturer’s instructions with the addition of amplification primer (3nM, 5’CCTTGGCACCCGAGAATT*C*C) during cDNA amplification to enrich the TotalSeq-A cell surface protein oligos.

value: B cell-specific Gclc KO

tag: age

value: 8 weeks

value: Splenic B cells


title: DFR1_CDNA

description:
10x Genomics with CITE-seq
DFR1_hashtag1 to DFR1_hashtag4
mRNA and protein


title: DFR1_HTO


title: iDART_SMART-seq APOBEC1-YTH Cell 688

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: 1-222mut_PAPI-CLIP=seq_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 701


title: IFM 72h APF rep1

description:
IFM72h1
wildtype sample, dissected IFM


title: DFR1_ADT


title: iDART_SMART-seq APOBEC1-YTH Cell 695


title: iDART_SMART-seq APOBEC1-YTH Cell 687


title: brain 72h APF rep2

description:
brain72h2
wildtype sample, dissected brain


title: iDART_SMART-seq APOBEC1-YTH Cell 691


title: iDART_SMART-seq APOBEC1-YTH Cell 694


title: iDART_SMART-seq APOBEC1-YTH Cell 700


title: DFR2_ADT


title: FRT CD4 Rorc mutant rep5

city: Davis

first: Stephen

middle: J

last: McSorley

state: CA

address: One Shields Avenue

department: Center for Immunology and Infectious Diseases

institute: University of California Davis

data_processing:
Data processing was performed by the UC Davis Bioinformatics Core. Raw reads were processed with HTStream v.1.1.0 (https://s4hts.github.io/HTStream/) to perform raw sequence data QA/QC, remove adapter contamination and low-quality bases/sequences.
The trimmed reads were aligned to the Mus musculus GRCm38 primary assembly genome with GENCODE v.M23 annotation, using the aligner STAR v. 2.7.0f (Dobin, et al. 2013, Reference at https://www.ncbi.nlm.nih.gov/pubmed/23104886) to generate raw counts per gene.
Differential expression analyses were conducted using limma-voom  (edgeR version 3.20.9, limma version 3.34.9, R version 3.4.4).
Gene ontology enrichment analysis of the whole transcriptome was conducted using Kolmogorov-Smirnov test as implemented in the Bioconductor package topGO, version 2.30.1.
Mus musculus Ensembl gene identifiers and annotations were used in this study.
Genome_build: Mus musculus GRCm38 primary assembly genome with GENCODE v.M23 annotation
Supplementary_files_format_and_content: matrix table of processed counts per gene per sample

source_name: Sorted FRT CD4 T cells

extract_protocol:
Five samples for each group were prepared by pooling three mice per sample to accumulate enough cells for RNA isolation. Lymphocytes were isolated from the FRT of mice 17 days post infection i.vag. with Chlamydia muridarum via collagenase IV digestion and a percoll gradient. Cells were then stained for flow sorting using Zombie Yellow (BioLegend) and antibodies for surface markers APC-B220 (RA3-6B2, eBioscience), APC-F4/80 (BM8.1, Tonbo Biosciences), APC-CD11b (M1/70, Tonbo Biosciences), APC-CD11c (N418, Tonbo Biosciences, eF450-CD4 (RM4-5, eBioscience), and PerCP-Cy5.5-CD8a (53-6.7, eBioscience). CD4 T cells were collected passing through single cell, live, dump (B220, F4/80, CD11b, CD11c) negative, and CD4+CD8- gates. RNA was isolated using the Qiagen RNeasy Mini Kit.
Barcoded sequencing libraries were prepared using the 3' mRNA-seq QuantSeq FWD kit (Lexogen, Vienna, Austria). Library preparation was performed by the UC Davis DNA Tech Core.

tag: tissue

value: CD4 T cells from female reproductive tract

value: Rorc mutant (JAX 031393)

tag: batch


title: iDART_SMART-seq APOBEC1-YTH Cell 693


title: DFR2_HTO


title: FRT CD4 Rorc mutant rep4


title: iDART_SMART-seq APOBEC1-YTH Cell 686


title: iDART_SMART-seq APOBEC1-YTH Cell 685


title: iDART_SMART-seq APOBEC1-YTH Cell 690


title: FRT CD4 Rorc mutant rep3


title: FRT CD4 Rorc mutant rep1


title: FRT CD4 Rorc mutant rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 683


title: FRT CD4 Tbet-/- rep5


title: iDART_SMART-seq APOBEC1-YTH Cell 680


title: iDART_SMART-seq APOBEC1-YTH Cell 682


title: iDART_SMART-seq APOBEC1-YTH Cell 678


title: FRT CD4 Tbet-/- rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 681


title: FRT CD4 Tbet-/- rep2


title: FRT CD4 Tbet-/- rep4


title: iDART_SMART-seq APOBEC1-YTH Cell 677


title: iDART_SMART-seq APOBEC1-YTH Cell 679


title: FRT CD4 WT rep3


title: FRT CD4 WT rep5


title: iDART_SMART-seq APOBEC1-YTH Cell 674


title: iDART_SMART-seq APOBEC1-YTH Cell 684


title: FRT CD4 WT rep1


title: FRT CD4 WT rep4


title: FRT CD4 Tbet-/- rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 673


title: iDART_SMART-seq APOBEC1-YTH Cell 676


title: FRT CD4 WT rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 675


title: Liver LXR double knockout rep2 ATAC [LXRDKO_4_ATAC]

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

data_processing:
For RNA-Seq, aata quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Genes were annotated using biomaRt package in R (https://www.R-project.org/).
For ATAC-Seq, samples were demultiplexed and quality control was done using FastQC.
Cutadapt was used to trim adapters.
Trimmed sequences were aligned to the mm10 mouse genome assembly using bowtie2.
Mitochondrial, unmapped, multi-mapped and duplicate reads were removed using samtools.
Peaks were called using MACS2.
Quantitated across samples using Seqmonk and normalized to million reads per sample.
Peaks were annotated to genomic features and nearest promoter via Homer.
Bam files were merged using samtools. Bedgraphs were created using Homer.
Genome_build: mm10
Supplementary_files_format_and_content: excel file showing the RNA-Seq results from DESeq2
Supplementary_files_format_and_content: csv file showing the normalized counts from RNA-Seq for each gene for each sample obtained from DESeq2
Supplementary_files_format_and_content: Excel file containing the ATAC-Seq quantification of each peak for each sample.
Supplementary_files_format_and_content: Bedgraphs for merged WT and LXRDKO ATAC-Seq samples.

source_name: Liver LXR double knockout

extract_protocol:
For RNA-Seq, total RNA from frozen tissue was extracted through TRIzol (Invitrogen) and Qiagen RNeasy Mini Kit. For ATAC-Seq, Approximately 50 -100 mg of fresh tissue was homogenized via dounce homogenizer in 1 ml of nuclear isolation buffer (20 mM Tris-HCl, 50 mM EDTA, 5 mM Spermidine, 0.15 mM Spermine, 0.1% mercaptoethanol, 40% glycerol, 1mM EGTA, 60 mM KCl, 1% IGEPAL pH 7.5) and filtered through a 40 M nylon filter. Samples were centrifuged at 4 °C at 1000 × g for 10 min and the pellet was resuspended with 1 ml cold resuspension buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH 7.4). Approximately 50,000 nuclei from these samples were removed and centrifuged at 4 °C at 500 × g for 5 min. Supernatant was removed and the transposase reaction was performed immediately as described in Buenrosto et al., 2015.
For RNA-Seq, total RNA libraries were made with KAPA Stranded kit with mRNA capture. For ATAC-Seq, size selection was done with AMPure XP magnetic beads. Libraries were quantified by qPCR using NEBNext Library Quant Kit for Illumina

treatment_protocol: Mice were fasted 4 to 6 hours before sacrifice.

tag: strain background

value: 8 weeks old

value: LXRa/b double knockout

value: Left lobe of liver


title: Liver wildtype rep2 ATAC [WT_2_ATAC]

source_name: Liver wildtype

value: wild type


title: iDART_SMART-seq APOBEC1-YTH Cell 670

source_name: Kidney


title: iDART_SMART-seq APOBEC1-YTH Cell 672


title: iDART_SMART-seq APOBEC1-YTH Cell 671


title: Liver wildtype rep1 ATAC [WT_1_ATAC]


title: iDART_SMART-seq APOBEC1-YTH Cell 668


title: iDART_SMART-seq APOBEC1-YTH Cell 669


title: F-IgG, rep 2

city: Providence

first: Megan

last: Gura

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

data_processing:
The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on flowcells. After clustering, the flowcells were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using bcl2fastq (v. 2.20). One mismatch was allowed for index sequence identification.
Reads were quality-trimmed and had adapters removed using Trim Galore! (v 0.5.0) with the parameter -q 10.
Samples before and after trimming were analyzed using FastQC (v 0.11.5) for quality and then aligned to the Ensemble GRCm39 using Bowtie2 (v 2.3.0). Fastq screen (v 0.13.0) was used to determine the percentage of reads uniquely mapped to the mouse genome in comparison to other species.
Resulting sam files were converted to bam files, then unmapped, duplicated reads, and low quality mapped were removed using Samtools (v1.9). Resulting bam files were split into size classes using a unix script.
For calling peaks, annotating peaks, and identifying coverage around TSSs, Homer (v 4.10) was used. For signal visualization, IGV was used.
Genome_build: GRCm39
Supplementary_files_format_and_content: Peaks called by Homer for female H3K4me3 replicate 1 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for female TAF4b replicate 1 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for female H3K4me3 replicate 2 with annotation
Supplementary_files_format_and_content: Peaks called by Homer for female TAF4b replicate 2 with annotation

source_name: oocytes

extract_protocol:
Mice that were homozygous for an Oct4-EGFP transgene (The Jackson Laboratory: B6;129S4-Pou5f1tm2Jae/J) were mated for germ cell collections. Timed matings were estimated to begin at day 0.5 by evidence of a copulatory plug. To dissociate gonadal tissue into a single-cell suspension, embryonic gonads were harvested and placed in 0.25% Trypsin/EDTA and incubated at 37°C for 25 minutes, as previously described (Gura et al., 2020). Eppendorf tubes were flicked to dissociate tissue halfway through and again at the end of the incubation. Trypsin was neutralized with FBS. Cells were pelleted at 1,500 RPM for 5 minutes, the supernatant was removed, and cells were resuspended in 100 μL PBS. The cell suspension was strained through a 35 μm mesh cap into a FACS tube (Gibco REF # 352235). Propidium iodide (1:500) was added to the cell suspension as a live/dead distinguishing stain. Fluorescence-activated cell sorting (FACS) was performed using a Becton Dickinson FACSAria III in the Flow Cytometry and Cell Sorting Core Facility at Brown University. A negative control of a non-transgenic mouse gonad was used for each experiment to establish an appropriate GFP signal baseline. Dead cells were discarded and then cells were sorted at 4°C in PBS based on GFP signal into GFP+ or GFP- samples.
For library preparation, the KAPA HyperPrep kit (Roche Cat. No 07962363001) was used with New England Biolabs NEBNext Multiplex Oligos for Illumina (NEB #E7335). After library amplification through PCR, libraries were size selected through gel extraction (~150-650 bp) and cleaned up using the Qiagen QIAquick Gel Extraction Kit (Cat. # 28704). CUT&RUN libraries in EB buffer were shipped to GENEWIZ (GENEWIZ Inc., NJ) on dry ice. Sample QC, sequencing, and initial bioinformatics were done at GENEWIZ.
CUT&RUN

tag: Sex

value: female


title: F-H3K4me3, rep 2


title: F-IgG, rep 1


title: F-TAF4b, rep 2


title: iDART_SMART-seq APOBEC1-YTH Cell 665

tag: cell line


title: F-TAF4b, rep 1


title: iDART_SMART-seq APOBEC1-YTH Cell 667

tag: transgene


title: iDART_SMART-seq APOBEC1-YTH Cell 664

tag: treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 663


title: iDART_SMART-seq APOBEC1-YTH Cell 662


title: F-H3K4me3, rep 1


title: iDART_SMART-seq APOBEC1-YTH Cell 661


title: Liver LXR double knockout rep1 ATAC [LXRDKO_3_ATAC]


title: IKO 4 [Trigeminal ganglia]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCm39 genome using 2 mismatches within 50 bases
featureCounts version 2.0.1 was used to quantify reads for genes in GRCm39 version 104
Genome_build: GRCm39 version 104
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Trigeminal ganglia

growth_protocol: dissected tissues were microdissected in ice-cold PBS and directly stored at -80°C in 1ml TRIZOL

extract_protocol:
TriZol reagent according to manufacturer recommendation
non stranded mRNA usinf the TruSeq RS-122-2001 accord to manufacturer recommendation

treatment_protocol: the dissected samples have not been treated by any reagents and have not been cultured before RNA extraction

value: Adult

value: Rosa26Cre ERT2; Fl/Fl

tag: agent

value: injected with tamoxyfene

value: male


title: Control 4 [Trigeminal ganglia]

value: Rosa26Cre ERT2; +/+


title: iKO 3 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 660


title: Control 3 [Trigeminal ganglia]


title: iKO 2 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 658


title: Control 2 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 657


title: iDART_SMART-seq APOBEC1-YTH Cell 666


title: iKO 1 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 656


title: iDART_SMART-seq APOBEC1-YTH Cell 655


title: iDART_SMART-seq APOBEC1-YTH Cell 654


title: iKO 5 [Trigeminal ganglia]


title: Control 1 [Trigeminal ganglia]

value: Rosa26Cre ERT2; Fl/+


title: iDART_SMART-seq APOBEC1-YTH Cell 652


title: control 6 [Trigeminal ganglia]

value: injected with corn oil


title: iDART_SMART-seq APOBEC1-YTH Cell 653


title: iDART_SMART-seq APOBEC1-YTH Cell 651


title: icKO 5 Non Injected

source_name: Dorsal Root ganglia

value: AdvCreERT2; P12 Fl/Fl TAM


title: control 5 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 650

value: HEK293T Cells


title: iDART_SMART-seq APOBEC1-YTH Cell 649

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 659


title: icKO 5 Formalin

value: Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 646


title: icKO 4 Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 647


title: icKO 4 Non Injected


title: iDART_SMART-seq APOBEC1-YTH Cell 648


title: Control 4 Non Injected

value: P12 Fl/Fl TAM


title: iDART_SMART-seq APOBEC1-YTH Cell 645


title: Control 5 Formalin


title: Control 4 Formalin


title: iKO  6 [Trigeminal ganglia]


title: iDART_SMART-seq APOBEC1-YTH Cell 643


title: Control 3 Non Injected


title: Control 3 Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 644


title: iDART_SMART-seq APOBEC1-YTH Cell 642


title: iDART_SMART-seq APOBEC1-YTH Cell 641


title: icKO 3 Non Injected


title: iDART_SMART-seq APOBEC1-YTH Cell 639


title: icKO 3 Formalin


title: icKO 2 Non Injected


title: iDART_SMART-seq APOBEC1-YTH Cell 638


title: iDART_SMART-seq APOBEC1-YTH Cell 640


title: iDART_SMART-seq APOBEC1-YTH Cell 637


title: iDART_SMART-seq APOBEC1-YTH Cell 636


title: icKO 1 Non Injected


title: icKO 1 Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 635


title: Control 5 Non Injected


title: Control 2 Non Injected


title: Control 2 Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 633


title: Control 1 Non Injected


title: iDART_SMART-seq APOBEC1-YTH Cell 632


title: IKO 4

source_name: Dorsal root ganglia

extract_protocol:
With TriZol reagent according to manufacturer recommendation
non stranded mRNA usinf the TruSeq RS-122-2001 accord to manufacturer recommendation


title: iDART_SMART-seq APOBEC1-YTH Cell 631


title: Control 4


title: iDART_SMART-seq APOBEC1-YTH Cell 630


title: iDART_SMART-seq APOBEC1-YTH Cell 629


title: iKO 3


title: Control 1 Formalin


title: iKO 2


title: Control 3


title: iKO 1


title: icKO 2 Formalin


title: iDART_SMART-seq APOBEC1-YTH Cell 627


title: Control 2


title: iDART_SMART-seq APOBEC1-YTH Cell 623


title: Control 1


title: iDART_SMART-seq APOBEC1-YTH Cell 628


title: iKO 6


title: iDART_SMART-seq APOBEC1-YTH Cell 625


title: iKO 5


title: control 6


title: iDART_SMART-seq APOBEC1-YTH Cell 634


title: iDART_SMART-seq APOBEC1-YTH Cell 622


title: iDART_SMART-seq APOBEC1-YTH Cell 624


title: iDART_SMART-seq APOBEC1-YTH Cell 619


title: E16.5, Taf4b-Def rep5

data_processing:
Reads were quality-trimmed and had adapters removed using Trim Galore! (v 0.5.0) with the parameters –nextera -q 10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Samples before and after trimming were analyzed using FastQC (v 0.11.5) for quality and then aligned to the Ensemble GRCm38 using HiSat2 (v 2.1.0) with the optional -dta setting enabled. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; Kim et al., 2019).
Resulting sam files were converted to bam files using Samtools (v 1.9) (Li et al., 2009).
To obtain transcripts per million (TPMs) for each sample, StringTie (v 1.3.3b) was used with the optional parameters -A and -e (Pertea et al., 2016).
To obtain count tables, featurecounts (Subread v 1.6.2) was used (Liao et al., 2014).
DESeq2 was  used for differential gene expression analysis, where the Subread count table was used as input (Love et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-delimited text file of gene counts for each sample
Supplementary_files_format_and_content: comma-delimited text file of TPMs and gene information for each sample
Supplementary_files_format_and_content: comma-delimited text file of DESeq2 differential gene expression analysis

extract_protocol:
Mice that were homozygous for an Oct4-EGFP transgene (The Jackson Laboratory: B6;129S4-Pou5f1tm2Jae/J) and heterozygous for the Taf4b-deficiency mutation were mated for mRNA collections. Timed matings were estimated to begin at day 0.5 by evidence of a copulatory plug. To dissociate gonadal tissue into a single-cell suspension, embryonic gonads were harvested and placed in 0.25% Trypsin/EDTA and incubated at 37°C for 25 minutes, as previously described (Gura et al., 2020). Eppendorf tubes were flicked to dissociate tissue halfway through and again at the end of the incubation. Trypsin was neutralized with FBS. Cells were pelleted at 1,500 RPM for 5 minutes, the supernatant was removed, and cells were resuspended in 100 μL PBS. The cell suspension was strained through a 35 μm mesh cap into a FACS tube (Gibco REF # 352235). Propidium iodide (1:500) was added to the cell suspension as a live/dead distinguishing stain. Fluorescence-activated cell sorting (FACS) was performed using a Becton Dickinson FACSAria III in the Flow Cytometry and Cell Sorting Core Facility at Brown University. A negative control of a non-transgenic mouse gonad was used for each experiment to establish an appropriate GFP signal baseline. Dead cells were discarded and then cells were sorted at 4°C in PBS based on GFP signal into GFP+ or GFP- samples. These cells were then spun down at 1,500 RPM for 5 minutes, had PBS removed, and were then resuspended in Trizol (ThermoFisher # 1556026). If samples had roughly less than 50 µL of PBS in the tube, Trizol was added immediately. Samples were stored at -80°C.
Embryonic germ cells in Trizol were shipped to GENEWIZ (GENEWIZ Inc., NJ) on dry ice. Sample RNA extraction, sample QC, library preparation, sequencing, and initial bioinformatics were done at GENEWIZ. RNA was extracted following the Trizol Reagent User Guide (Thermo Fisher Scientific). Glycogen was added (1 µL, 10 mg/mL) to the supernatant to increase RNA recovery. RNA was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with TapeStation (Agilent Technologies, Palo Alto, CA, USA) to see if the concentration met the requirements.
SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. The sequencing libraries were multiplexed and clustered on a lane of a flowcell. After clustering, the flowcell was loaded onto an Illumina HiSeq 4000 according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument.  Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using bcl2fastq (v. 2.17). One mismatch was allowed for index sequence identification.

value: oocytes

tag: litter date


title: iDART_SMART-seq APOBEC1-YTH Cell 621


title: iDART_SMART-seq APOBEC1-YTH Cell 620


title: E16.5, Taf4b-Def rep4


title: E16.5, Taf4b-Def rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 618


title: E16.5, Taf4b-Def rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 617


title: iDART_SMART-seq APOBEC1-YTH Cell 615


title: E16.5, Taf4b-Def rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 626


title: iDART_SMART-seq APOBEC1-YTH Cell 616


title: iDART_SMART-seq APOBEC1-YTH Cell 614


title: E16.5, Taf4b-Het rep5


title: E16.5, Taf4b-Het rep4


title: iDART_SMART-seq APOBEC1-YTH Cell 613


title: iDART_SMART-seq APOBEC1-YTH Cell 612


title: iDART_SMART-seq APOBEC1-YTH Cell 611


title: E16.5, Taf4b-Het rep3


title: E14.5, Taf4b-Wt rep2

data_processing:
Reads were quality-trimmed and had adapters removed using Trim Galore! (v 0.5.0) with the parameters –nextera -q 10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Samples before and after trimming were analyzed using FastQC (v 0.11.5) for quality and then aligned to the Ensemble GRCm38 using HiSat2 (v 2.1.0) with the optional -dta setting enabled. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; Kim et al., 2019).
Resulting sam files were converted to bam files using Samtools (v 1.9) (Li et al., 2009).
E14.5 heterozygous bam files were downsampled using Samtools because they had been sequencing more deeply than their wild-type and deficient counterparts.
To obtain transcripts per million (TPMs) for each sample, StringTie (v 1.3.3b) was used with the optional parameters -A and -e (Pertea et al., 2016).
To obtain count tables, featurecounts (Subread v 1.6.2) was used (Liao et al., 2014).
DESeq2 was  used for differential gene expression analysis, where the Subread count table was used as input (Love et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-delimited text file of gene counts for each sample
Supplementary_files_format_and_content: comma-delimited text file of TPMs and gene information for each sample
Supplementary_files_format_and_content: comma-delimited text file of DESeq2 differential gene expression analysis

tag: phenotype

value: fertile


title: E16.5, Taf4b-Het rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 610


title: iDART_SMART-seq APOBEC1-YTH Cell 609


title: iDART_SMART-seq APOBEC1-YTH Cell 606


title: E14.5, Taf4b-Het rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 605


title: iDART_SMART-seq APOBEC1-YTH Cell 604


title: E14.5, Taf4b-Wt rep1


title: E14.5, Taf4b-Het rep1


title: E14.5, Taf4b-Het rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 603


title: iDART_SMART-seq APOBEC1-YTH Cell 608


title: iDART_SMART-seq APOBEC1-YTH Cell 602


title: E14.5, Taf4b-Def rep2

value: infertile


title: E14.5, Taf4b-Def rep4


title: iDART_SMART-seq APOBEC1-YTH Cell 601


title: E14.5, Taf4b-Def rep3


title: iDART_SMART-seq APOBEC1-YTH Cell 600


title: iDART_SMART-seq APOBEC1-YTH Cell 599


title: E16.5, Taf4b-Het rep2


title: Ctrl 4

data_processing:
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using to fastq files using bcl2fastq v2.20.0.422
STAR version 2.5.2a was used to align the reads to the mm10 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 96
Genome_build: mm10 gene version 96
Supplementary_files_format_and_content: Tab-delimited gene counts

extract_protocol:
Tissues were microdissected in ice-cold PBS and stored at -80°C in 1ml TRIZOL (Thermofisher). RNA was extracted using the illustra RNAspin Mini RNA isolation kit from GE Healthcare (25-0500-70)
RNA libraries were prepared for sequencing using standard mRNA-seq Illumina protocols

value: wild type


title: Ctrl 3


title: iDART_SMART-seq APOBEC1-YTH Cell 597


title: iDART_SMART-seq APOBEC1-YTH Cell 596


title: E14.5, Taf4b-Het rep4

value: female


title: iDART_SMART-seq APOBEC1-YTH Cell 607


title: iDART_SMART-seq APOBEC1-YTH Cell 595


title: SAMPLE 3_11R

type: RNA

city: Bern

first: Andrea

last: Karolin

address: Freiburgstrasse 15

country: Switzerland

institute: University of Bern

description: treatment

data_processing:
extraction of raw Ct values from software; ActB was used as a housekeeping gene and to calculate normalized score; dCt method was used
dCt (non-normalized Ct - non-normalized housekeeping gene ActB) --> ddCt (normalized samples- normalized control = sample 1) --> 2^-ddCt (--> fold change)

label: SYBR

source_name: MCT

label_protocol: cDNA: PrimeScript RT Reagent Kit (Takara, RR037A)

growth_protocol: DMEM/10% FBS

extract_protocol: total RNA with TRIzol

value: MCT

value: kidney:convoluted tubule


title: SAMPLE 4_SB203580

description: treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 593


title: iDART_SMART-seq APOBEC1-YTH Cell 594


title: SAMPLE 2_CsA

description: treatment

value: CsA


title: iDART_SMART-seq APOBEC1-YTH Cell 592


title: Ctrl 1

value: Adult


title: WT

data_processing:
software used for basecalling
Bisulfit-Seq reads were aligned to the NC10 genome assembly using Bismark Version v0.23.1 and Bowtie 2 version 2.4.4 with the following configurations…
Data were filtered using the following specifications…
peaks were called using Bismark Version v0.23.1 with the following setting
Genome_build: NC10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage 3.5.1
Supplementary_files_format_and_content: bedGraph files were generated using Bismark Version v0.23.1

source_name: mycelia

extract_protocol:
Lysates were clarified from sonicated mycelia and histone-DNA complexes were isolated with antibody.
Bisulfite-sequencing sample preparation was performed using the MGIEasy WGBS Library Prep Kit (1000005251; MGI) for DNBSEQ platform (MGI) and the EZ DNA Methylation-Gold Kit (Zymo Research).

tag: genotype/variation


title: iDART_SMART-seq APOBEC1-YTH Cell 591

extract_protocol:
SMART-seq2 cells: Single cells were sorted using a FACS Aria II (BD) directly into lysis buffer provided with the SMART-seq HT Kit (Takara, Cat. 634438). The SMART-seq HT Kit was then used for reverse transcription and cDNA amplification. Sequencing libraries were constructed from cDNA using the Nextera XT kit (Illumina, FC-131-1096) and dual Nextera-compatible CDI indexes from IDT. Samples were pooled and sequenced targeting 5,000,000 reads/library (150bp paried-end) on a Novaseq6000 using the S4 flowcell.   10X Genomics cells: A single cell suspension was prepared according to manufacturer's instruction for Chromium v3 3' end sequencing (10x Genomics, Manual Part #CG00053). Samples were sequenced targeting 80,000 reads per cell on a Novaseq6000 using the S1 flowcell.  Bulk RNA-seq: Trizol was used to extract total RNA from iDART cells. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA. The samples were sequenced targeting ~30 million reads (50bp paired-end sequencing) per sample on a Novaseq6000 using the S1 flowcell.
SMART-seq2 scRNA-seq: cDNA libraries were generated using the SMART-seq HT Kit (Takara, Cat. 634438). Final libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096).   10x scRNA-seq: Libraries were generated from a single cell suspension using the 10x Genomics NextGEM Single Cell 3' Kit, v3.1 chemistry (10x Genomics)  Bulk-RNA seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 900ng of input RNA.


title: icKO 5

tag: strain

value: Prdm12 inducible conditional knock-out


title: iDART_SMART-seq APOBEC1-YTH Cell 590


title: iDART_SMART-seq APOBEC1-YTH Cell 589


title: iDART_SMART-seq APOBEC1-YTH Cell 588


title: icKO 4


title: icKO 3


title: SAMPLE 1_control

description: no treatment

value: control


title: iDART_SMART-seq APOBEC1-YTH Cell 586


title: H3K56R_dmm1ko


title: iDART_SMART-seq APOBEC1-YTH Cell 598


title: iDART_SMART-seq APOBEC1-YTH Cell 587


title: E14.5, Taf4b-Def rep1

tag: cell type


title: H3K56R


title: iDART_SMART-seq APOBEC1-YTH Cell 585


title: icKO 2

tag: genotype


title: Ctrl 2


title: iDART_SMART-seq APOBEC1-YTH Cell 583


title: H3K56Q_dmm1ko


title: iDART_SMART-seq APOBEC1-YTH Cell 584


title: H3K56Q


title: iDART_SMART-seq APOBEC1-YTH Cell 581


title: iDART_SMART-seq APOBEC1-YTH Cell 580


title: H2A.Z_dmm1ko


title: iDART_SMART-seq APOBEC1-YTH Cell 578


title: H2A.Z


title: iDART_SMART-seq APOBEC1-YTH Cell 579


title: dmm1KO


title: iDART_SMART-seq APOBEC1-YTH Cell 577


title: iDART_SMART-seq APOBEC1-YTH Cell 576


title: iDART_SMART-seq APOBEC1-YTH Cell 574


title: iDART_SMART-seq APOBEC1-YTH Cell 575


title: iDART_SMART-seq APOBEC1-YTH Cell 572


title: iDART_SMART-seq APOBEC1-YTH Cell 573


title: icKO 1


title: iDART_SMART-seq APOBEC1-YTH Cell 582


title: Lean Nonviable Liver - 6 hours perfusion - replicate 2

first: Jennifer

middle: Ann

last: Sanders

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

data_processing:
The sequencing libraries were clustered on 3 lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Raw hit counts table in text file format.

source_name: Liver

extract_protocol:
Tissues samples from livers taken immediately prior to perfusion and after 3 and 6 hours of perfusion were used for bulk transcriptome sequencing. Core needle biopsies from the right liver lobe were collected in RNAlater solution (Sigma-MilleporeMillipore, Waltham, MA, USA) and stored overnight at 4 Celsius. Tissue samples were then removed from solution and stored at -80 Celsius. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer guidelines.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Grafts were perfused for 12 hours on the Liver Assist device (Organ Assist, Groningen, Netherlands) using a previously described protocol (Raigani et al. Clin Transplant. 2020 Nov;34(11):e14069, PMID 32860634). Briefly, perfusate composition consisted of O+ packed red blood cells, human albumin, Lactated Ringer’s solution, and heparin. Bile salts (taurocholate) and lipid-free parenteral nutrition were continuously infused. Perfusate, bile, and tissue biopsies were collected and analyzed at multiple time points. Livers were deemed to be "viable" if they satisfied the following criteria: perfusate lactate < 2.5mmol/L and two or more of the following minor criteria within 4 hours of starting perfusion: a) perfusate pH >7.30, b) arterial flow > 150mL/min and portal flow > 500mL/min, c) evidence of glucose metabolism, d) bile production, and e) visually assessed homogenous perfusion. Livers that failed to meet these criteria were deemed "nonviable".

tag: lean or fatty

tag: liver id

value: Lean

tag: transplant viability

value: Nonviable

tag: perfusion time

value: 6 hours

tag: condition replicate


title: iDART_SMART-seq APOBEC1-YTH Cell 569

data_processing:
Alignment to hg38 and UMI deduplication using Cell Ranger 3.1.0 (10x Genomics scRNA-seq samples only)
SMART-seq2 and bulk RNAseq samples: Trimming of adaptor sequences (Flexbar 3.0.3)
SMART-seq2 and bulk RNAseq samples:  Alignment using STAR 2.7.5c, and deduplication using SAMtools (1.11) fixmate and markdup
All samples: Identification of m6A sites using Bullseye
All samples: Expression normalization and integrated clustering of cells using Seurat (3.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: Bed files for bulk RNAare a list of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 APOBEC1-YTH replicates
Supplementary_files_format_and_content: a bed file consisting of APOBEC1-mediated C-to-U editing sites identified by downstream analysis

value: HEK293T Cells

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 570


title: C-H12-6d_S131

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each sample (columns)

source_name: EpCAM-high Kaede Sequenced Airway Epithelial Cells

extract_protocol: Full length RNAseq (SMART-Seq2)

treatment_protocol: Injury with So2 gas

value: Injury with So2

tag: time point

value: Distal trachea that were not moving post SO2

value: Wild Type


title: C-H11-6d_S123


title: C-H10-6d_S115


title: C-H09-6d_S107


title: iDART_SMART-seq APOBEC1-YTH Cell 568


title: iDART_SMART-seq APOBEC1-YTH Cell 567


title: Fibroblasts with hypoxia T3

city: Changsha

first: HE

last: Xinglan

address: No. 139 Renmin Middle Road, Furong District

department: Department of Dermatology

institute: The Second Xiangya Hospital

description:
Fibroblasts with hypoxia
Gene expression after hypoxia

hyb_protocol: Briefly, total RNA was transcribed to double-strand cDNA, which was synthesized into cRNA and labeled with cyanine-3-CTP.

scan_protocol: After washing, the arrays were scanned using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: The Feature Extraction software (version 10.7.1.1; Agilent Technologies) was used to analyze array images and obtain raw data. GeneSpring (version 13.1; Agilent Technologies) was used to analyze the raw data. The raw data were normalized using the quantile algorithm. Probes that had 100% of the values flagged as detected under at least one condition were selected for further analysis.

source_name: hypoxia 26h

label_protocol: Sample labeling, microarray hybridization, and washing were performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was quantified using NanoDrop ND-2000 (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

tag: gender

tag: age


title: Fibroblasts with hypoxia T2

source_name: hypoxia 25h


title: Fibroblasts with hypoxia T1

source_name: hypoxia 24h

value: male


title: Fibroblasts without hypoxia C2

description:
Fibroblasts without hypoxia
Gene expression after without hypoxia

source_name: control


title: Lean Nonviable Liver - 0 hours perfusion - replicate 1

value: 0 hours


title: C-H08-6d_S99


title: iDART_SMART-seq APOBEC1-YTH Cell 565

tag: cell line

tag: transgene


title: Fibroblasts without hypoxia C3

value: female


title: Lean Viable Liver - 6 hours perfusion - replicate 3

value: Viable


title: Fibroblasts without hypoxia C1


title: iDART_SMART-seq APOBEC1-YTH Cell 564

tag: treatment


title: iDART_SMART-seq APOBEC1-YTH Cell 563


title: Lean Viable Liver - 3 hours perfusion - replicate 1

value: 3 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 562


title: iDART_SMART-seq APOBEC1-YTH Cell 571


title: C-H07-6d_S91


title: C-H06-6d_S83


title: Lean Nonviable Liver - 6 hours perfusion - replicate 1


title: C-H05-6d_S75


title: iDART_SMART-seq APOBEC1-YTH Cell 561


title: iDART_SMART-seq APOBEC1-YTH Cell 560


title: iDART_SMART-seq APOBEC1-YTH Cell 559


title: Lean Nonviable Liver - 3 hours perfusion - replicate 1


title: iDART_SMART-seq APOBEC1-YTH Cell 558


title: C-H04-6d_S67


title: iDART_SMART-seq APOBEC1-YTH Cell 557


title: iDART_SMART-seq APOBEC1-YTH Cell 556


title: Lean Viable Liver - 6 hours perfusion - replicate 1


title: iDART_SMART-seq APOBEC1-YTH Cell 566


title: iDART_SMART-seq APOBEC1-YTH Cell 555


title: C-H02-6d_S51


title: iDART_SMART-seq APOBEC1-YTH Cell 552


title: iDART_SMART-seq APOBEC1-YTH Cell 554


title: Lean Viable Liver - 3 hours perfusion - replicate 3


title: C-H01-6d_S43


title: iDART_SMART-seq APOBEC1-YTH Cell 550


title: Lean Nonviable Liver - 0 hours perfusion - replicate 2


title: C-G12-6d_S130


title: C-G11-6d_S122


title: Lean Nonviable Liver - 0 hours perfusion - replicate 3


title: Lean Nonviable Liver - 3 hours perfusion - replicate 3


title: iDART_SMART-seq APOBEC1-YTH Cell 549


title: iDART_SMART-seq APOBEC1-YTH Cell 548


title: iDART_SMART-seq APOBEC1-YTH Cell 546


title: iDART_SMART-seq APOBEC1-YTH Cell 545


title: Lean Viable Liver - 0 hours perfusion - replicate 1


title: Lean Viable Liver - 0 hours perfusion - replicate 3


title: control 5

value: Rosa26Cre ERT2; Fl/Fl

tag: agent

value: injected with corn oil

tag: Sex


title: C-G09-6d_S106


title: iDART_SMART-seq APOBEC1-YTH Cell 547


title: iDART_SMART-seq APOBEC1-YTH Cell 544


title: C-H03-6d_S59


title: iDART_SMART-seq APOBEC1-YTH Cell 543


title: iDART_SMART-seq APOBEC1-YTH Cell 553


title: iDART_SMART-seq APOBEC1-YTH Cell 541


title: C-G08-6d_S98


title: C-G07-6d_S90


title: Lean Nonviable Liver - 3 hours perfusion - replicate 2


title: iDART_SMART-seq APOBEC1-YTH Cell 551


title: iDART_SMART-seq APOBEC1-YTH Cell 539


title: iDART_SMART-seq APOBEC1-YTH Cell 540


title: C-G06-6d_S82


title: iDART_SMART-seq APOBEC1-YTH Cell 538


title: Lean Nonviable Liver - 6 hours perfusion - replicate 3


title: iDART_SMART-seq APOBEC1-YTH Cell 536


title: C-G05-6d_S74


title: iDART_SMART-seq APOBEC1-YTH Cell 535


title: C-G10-6d_S114


title: C-G04-6d_S66


title: C-G03-6d_S58


title: circRNA_BGI EC109 plenti ADAR2

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description: circRNA-Seq

data_processing:
Clean raw reads were mapped to the reference human genome (hg19) by using STAR with the chimeric junction reads option on (--chimSegmentMin 20).
The gtf file from the GENCODE (gencode.v27lift37.annotation.gtf) was used for the gene and junction annotations.
The expression of the circRNAs were quantified as read counts that map to the junctions.
To identify differentially expressed circRNAs in ADAR1/2 OE and KD samples compared to the control, the below criteria were applied:
1. Total reads in both (EV + ADAR OE) and (Scr + ADAR KD) >= 10;
2. ADAR/EV ratio <= 0.5 (repressing) or >= 2 (promoting), while shADAR/shScr ratio <= 0.5 (promoting) or >= 2 (repressing) and in the opposite directions.
which resulted in 1,406 circRNAs for further analysis.
To identify differentially expressed circRNAs in ADAR1/2 OE samples compared to the control, the below criteria were applied:
1. Total reads (EV + ADAR) >= 50
2. ADAR/EV ratio <= 0.5 (repressing) or >= 2 (promoting)
which resulted in 1,118 circRNAs for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: spreadsheet file including ADAR1/2 KD and/or OE specific circRNA events and their expression quantification as read counts. The above filters must be applied on this list to obtain the DE circRNAs.

source_name: human esophageal squamous carcinoma cells

extract_protocol:
circular RNA samples were extracted using Qiagen Rneasy Mini Kit and subjected to rRNA depletion and RNase R treatment to digest all the linear RNAs.
cDNA library according to Illumina's TruSeq Library Prep Kit using a modified protocol.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silecing ADAR1/2 or transfected with expression construct for overexpressing ADAR1/2.

value: ADAR2 over expression

tag: rna population

value: circular RNA


title: iDART_SMART-seq APOBEC1-YTH Cell 534


title: iDART_SMART-seq APOBEC1-YTH Cell 532


title: iDART_SMART-seq APOBEC1-YTH Cell 533


title: iDART_SMART-seq APOBEC1-YTH Cell 531


title: C-G02-6d_S50

tag: strain


title: Lean Viable Liver - 3 hours perfusion - replicate 2

value: Lean


title: iDART_SMART-seq APOBEC1-YTH Cell 542


title: iDART_SMART-seq APOBEC1-YTH Cell 530


title: circRNA_BGI EC109 plenti ADAR1

description: circRNA-Seq

tag: cell type

value: human esophageal squamous carcinoma cells

value: ADAR1 over expression


title: iDART_SMART-seq APOBEC1-YTH Cell 529

value: HEK293T Cells


title: Lean Viable Liver - 0 hours perfusion - replicate 2


title: circRNA_BGI EC109 shAR2 #942

description: circRNA-Seq

value: ADAR2 knockdown


title: iDART_SMART-seq APOBEC1-YTH Cell 527

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 528


title: iDART_SMART-seq APOBEC1-YTH Cell 526


title: iDART_SMART-seq APOBEC1-YTH Cell 537


title: circRNA_BGI EC109 shAR1 #3

description: circRNA-Seq

value: ADAR1 knockdown


title: C-F11-6d_S121

value: Injury with So2

value: Distal trachea that were not moving post SO2

tag: genotype

value: Wild Type


title: iDART_SMART-seq APOBEC1-YTH Cell 525


title: iDART_SMART-seq APOBEC1-YTH Cell 524


title: iDART_SMART-seq APOBEC1-YTH Cell 523


title: Lean Viable Liver - 6 hours perfusion - replicate 2

tag: lean or fatty

value: 6 hours


title: circRNA_BGI EC109 scr

description: circRNA-Seq

value: scramble shRNA treated


title: iDART_SMART-seq APOBEC1-YTH Cell 522


title: C-F09-6d_S105


title: C-F10-6d_S113


title: iDART_SMART-seq APOBEC1-YTH Cell 520


title: iDART_SMART-seq APOBEC1-YTH Cell 521


title: C-F07-6d_S89


title: iDART_SMART-seq APOBEC1-YTH Cell 519


title: iDART_SMART-seq APOBEC1-YTH Cell 518


title: iDART_SMART-seq APOBEC1-YTH Cell 516


title: C-F08-6d_S97


title: iDART_SMART-seq APOBEC1-YTH Cell 515


title: iDART_SMART-seq APOBEC1-YTH Cell 517


title: circRNA_BGI EC109 plenti6

description: circRNA-Seq

value: empty vector control


title: C-G01-6d_S42


title: C-F12-6d_S129


title: C-F06-6d_S81


title: iDART_SMART-seq APOBEC1-YTH Cell 514


title: iDART_SMART-seq APOBEC1-YTH Cell 513


title: C-F05-6d_S73


title: siLAS1L_RNAseq_HEK293FT_rep2

city: boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

description: mRNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were mapped to the human genome (GRCh37/hg19) with Kallisto (version 1.15.0).
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Differentially expressed genes were identified by DESeq2 ((v1.18.1)) with fold change>2 and Benjamini–Hochberg false discovery rate adjusted P < 0.05.
deeptool (v/3.0.2) was used to generate bigwig files for visualization in IGV tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file normalized to RPGC for each Sample

extract_protocol:
For mRNA-seq, total RNA was isolated from human cells with an RNA purification kit (Qiagen, 74134) and genomic DNA was removed by genomic DNA binding columns in the kit.
For RNA-seq, two μg of total RNA was used to start RNA-seq library construction. Poly(A)-containing mRNA was isolated by poly-A selection beads and further reverse transcribed to cDNA. The resulting cDNA was ligated with adapters, amplified by PCR, and further cleaned to obtain the final library. Libraries were sequenced on an Illumina Hiseq machine (Novogene) to obtain 150 bp paired-end reads.

tag: sirna

tag: knockout

value: wild type

tag: medium

value: DMEM

tag: antibody


title: siNOL9_RNAseq_HEK293FT_rep2

description: mRNA-seq


title: siNOL9_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 512


title: iDART_SMART-seq APOBEC1-YTH Cell 511


title: siLAS1L_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 510


title: C-F04-6d_S65

tag: time point


title: iDART_SMART-seq APOBEC1-YTH Cell 509


title: RING1B_HEK293FT_Q137AQ138A_rep2

description: ChIP-seq

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5)
Pooled libraries were demultiplexed using fastx
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding  input files for background normalization
Genome_build: hg19
Supplementary_files_format_and_content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.

extract_protocol:
Cells for ChIP were cultured in 15 cm plates. Cell were first washed with cold PBS, crosslinked at room temperature with 10 mM DMP (ThermoFisher Scientific) for 30 min, and then 1% formaldehyde (ThermoFisher Scientific) for 15 min. Crosslinking reactions were quenched by addition of 125 mM glycine for 5 min. Crosslinked cells were separated by 3 min treatment of 0.05% trypsin (Gibco), and then washed with cold PBS 3 times. In every wash, cells were centrifuged for 3 min at 1000xg at 4℃.Cell were then resuspended in sonication buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.5% SDS) and sonicated to shear chromatin into ~300 bp fragments using a Branson sonicator. Sonicated samples were diluted 5-fold with ChIP dilution buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate) to obtain a final concentration of 0.1% SDS. Diluted samples were centrifuged at13,000 rpm for 10 min. The supernatant was pre-cleared with protein A/G or Dynabeads M-280 Streptavidin beads (ThermoFisher) and immunoprecipitated for 3-12 h using 3 μg antibodies and 40 μl protein A/G or Dynabeads M-280 Streptavidin beads. The beads were washed twicewith high salt wash buffer A (pH 7.9, 50 mM Hepes, 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.1% SDS), and once with wash buffer B (pH 7.9, 50 mM Hepes, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, 0.5% NP-40). The bound chromatin fragments were eluted with elution buffer (pH 8.0, 50 Mm Tris, 10 mM EDTA, 1% SDS) for 5 min at 65℃. Eluted DNA-proteins complexes were treated with RNase A and crosslinks were reversed overnight at 65℃. Proteinase K was then added to digest proteins for 1 h at 55℃. DNA was further purified using PCR Purification Kit (QIAGEN) and analyzed by PCR on a QuantStudio 7 Flex Real Time PCR System (Applied Biosystem). PCR parameters were 95℃for 2 min and 40 cycles of 95℃ for 15s, 60℃ for 15s, and 72℃ for 15 s, followed by 72℃ for 1 min. All the ChIP-qPCR data presented were at least three biological replicates. Primer sequences are in the table. Error bar represent standard deviation (three biological replicates).
For ChIP-seq, sequencing library was constructed using TruSeq DNA sample Prep Kits (Illumina) and adapter dimers were removed by agarose gels electrophoresis. Sized selected and purified DNA libraries were sequenced on an Illumina Hiseq 2500 machine (Bauer core facility at Harvard University) to obtain 50 bp single-end reads.

tag: mutagenesis


title: iDART_SMART-seq APOBEC1-YTH Cell 508


title: C-F03-6d_S57


title: iDART_SMART-seq APOBEC1-YTH Cell 507


title: RING1B_HEK293FT_Q137AQ138A_rep1

description: ChIP-seq


title: C-F02-6d_S49


title: iDART_SMART-seq APOBEC1-YTH Cell 505


title: iDART_SMART-seq APOBEC1-YTH Cell 504


title: iDART_SMART-seq APOBEC1-YTH Cell 503


title: C-F01-6d_S41


title: RING1B_HEK293FT_WT_rep2

description: ChIP-seq

value: RING1B Q137AQ138A


title: C-E12-6d_S128


title: RING1B_HEK293FT_WT_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 501


title: C-E11-6d_S120


title: iDART_SMART-seq APOBEC1-YTH Cell 499


title: H2AK119ub1_HEK293FT_WT_rep2

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 500


title: C-E10-6d_S112


title: H2AK119ub1_HEK293FT_WT_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 497


title: iDART_SMART-seq APOBEC1-YTH Cell 496


title: iDART_SMART-seq APOBEC1-YTH Cell 498


title: H2AK119ub1_HEK293FT_RING1BQ137AQ138A_rep2

description: ChIP-seq


title: H2AK119ub1_HEK293FT_RING1BQ137AQ138A_rep1

description: ChIP-seq


title: C-E09-6d_S104


title: iDART_SMART-seq APOBEC1-YTH Cell 494


title: C-E08-6d_S96


title: iDART_SMART-seq APOBEC1-YTH Cell 493


title: siTEX10_RNAseq_HeLa_rep2

description: mRNA-seq

source_name: HeLa

value: HeLa


title: iDART_SMART-seq APOBEC1-YTH Cell 492


title: C-E07-6d_S88


title: iDART_SMART-seq APOBEC1-YTH Cell 491


title: iDART_SMART-seq APOBEC1-YTH Cell 506


title: iDART_SMART-seq APOBEC1-YTH Cell 489


title: iDART_SMART-seq APOBEC1-YTH Cell 488


title: C-E06-6d_S80


title: C-E05-6d_S72


title: siNOL9_RNAseq_HeLa_rep2

description: mRNA-seq


title: siTEX10_RNAseq_HeLa_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 502


title: iDART_SMART-seq APOBEC1-YTH Cell 490


title: iDART_SMART-seq APOBEC1-YTH Cell 487


title: siNOL9_RNAseq_HeLa_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 486


title: C-E04-6d_S64


title: iDART_SMART-seq APOBEC1-YTH Cell 485


title: iDART_SMART-seq APOBEC1-YTH Cell 484


title: C-E03-6d_S56


title: siNC_RNAseq_HeLa_rep2

description: mRNA-seq

value: siNC


title: iDART_SMART-seq APOBEC1-YTH Cell 483


title: iDART_SMART-seq APOBEC1-YTH Cell 495


title: C-E02-6d_S48


title: siNC_RNAseq_HeLa_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 482


title: iDART_SMART-seq APOBEC1-YTH Cell 481


title: iDART_SMART-seq APOBEC1-YTH Cell 480


title: C-E01-6d_S40


title: iDART_SMART-seq APOBEC1-YTH Cell 479


title: siLAS1L_RNAseq_HeLa_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 478


title: iDART_SMART-seq APOBEC1-YTH Cell 477


title: C-D12-6d_S127


title: iDART_SMART-seq APOBEC1-YTH Cell 476


title: C-D11-6d_S119


title: siEZH2_RNAseq_HeLa_rep1

description: mRNA-seq


title: RING1A_KO_siRING1B_RNAseq_HeLa_rep2

description: mRNA-seq

value: RING1A knockout


title: C-D10-6d_S111


title: iDART_SMART-seq APOBEC1-YTH Cell 473


title: iDART_SMART-seq APOBEC1-YTH Cell 471


title: RING1A_KO_siRING1B_RNAseq_HeLa_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 469


title: iDART_SMART-seq APOBEC1-YTH Cell 470


title: siEZH2_RNAseq_HeLa_rep2

description: mRNA-seq


title: C-D07-6d_S87


title: iDART_SMART-seq APOBEC1-YTH Cell 467


title: C-D08-6d_S95


title: iDART_SMART-seq APOBEC1-YTH Cell 472


title: siLAS1L_RNAseq_HeLa_rep2

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 468


title: siRING1B_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 474


title: iDART_SMART-seq APOBEC1-YTH Cell 466


title: C-D06-6d_S79


title: iDART_SMART-seq APOBEC1-YTH Cell 464


title: C-D05-6d_S71


title: iDART_SMART-seq APOBEC1-YTH Cell 465


title: siNC_RNAseq_HEK293FT_rep2

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 463


title: siNC_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 462


title: iDART_SMART-seq APOBEC1-YTH Cell 475


title: C-D04-6d_S63


title: iDART_SMART-seq APOBEC1-YTH Cell 461


title: iDART_SMART-seq APOBEC1-YTH Cell 460


title: C-D09-6d_S103


title: siEZH2_RNAseq_HEK293FT_rep2

description: mRNA-seq


title: siEZH2_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 459


title: RING1AB_KO_RNAseq_HEK293FT_rep2

description: mRNA-seq

value: RING1A and RING1B double knockout


title: iDART_SMART-seq APOBEC1-YTH Cell 458

value: HEK293T Cells


title: C-D03-6d_S55


title: C-D01-6d_S39


title: iDART_SMART-seq APOBEC1-YTH Cell 455


title: iDART_SMART-seq APOBEC1-YTH Cell 457


title: iDART_SMART-seq APOBEC1-YTH Cell 456


title: RING1AB_KO_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: C-D02-6d_S47


title: EZH_KO_RNAseq_HEK293FT_rep2

description: mRNA-seq

value: EZH1 and EZH2 double knockout


title: iDART_SMART-seq APOBEC1-YTH Cell 453

value: 1microg/mL doxycycline; 24 hours


title: iDART_SMART-seq APOBEC1-YTH Cell 454


title: iDART_SMART-seq APOBEC1-YTH Cell 452


title: C-C11-6d_S118


title: iDART_SMART-seq APOBEC1-YTH Cell 451


title: EZH_KO_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: C-C10-6d_S110


title: iDART_SMART-seq APOBEC1-YTH Cell 450


title: EED_KO_RNAseq_HEK293FT_rep2

description: mRNA-seq

value: EED knockout


title: C-C09-6d_S102

value: Injury with So2


title: iDART_SMART-seq APOBEC1-YTH Cell 448


title: iDART_SMART-seq APOBEC1-YTH Cell 447


title: iDART_SMART-seq APOBEC1-YTH Cell 446


title: EED_KO_RNAseq_HEK293FT_rep1

description: mRNA-seq


title: C-C08-6d_S94

value: Distal trachea that were not moving post SO2


title: iDART_SMART-seq APOBEC1-YTH Cell 444


title: iDART_SMART-seq APOBEC1-YTH Cell 445


title: iDART_SMART-seq APOBEC1-YTH Cell 443


title: iDART_SMART-seq APOBEC1-YTH Cell 441


title: C-C05-6d_S70

value: Wild Type


title: iDART_SMART-seq APOBEC1-YTH Cell 440


title: C-C06-6d_S78


title: iDART_SMART-seq APOBEC1-YTH Cell 438


title: C-C04-6d_S62


title: iDART_SMART-seq APOBEC1-YTH Cell 439


title: C-C12-6d_S126


title: iDART_SMART-seq APOBEC1-YTH Cell 437


title: C-C03-6d_S54


title: iDART_SMART-seq APOBEC1-YTH Cell 436


title: MDN1-HeLa_siNC_rep2

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 434


title: C-C02-6d_S46


title: iDART_SMART-seq APOBEC1-YTH Cell 449


title: iDART_SMART-seq APOBEC1-YTH Cell 433


title: MDN1-HeLa_siMDN1_rep2

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 432


title: iDART_SMART-seq APOBEC1-YTH Cell 431


title: iDART_SMART-seq APOBEC1-YTH Cell 430


title: MDN1-HeLa_siMDN1_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 429


title: C-B12-6d_S125


title: C-C07-6d_S86


title: INPUT-HeLa_rep2

description: ChIP-seq


title: C-B11-6d_S117


title: iDART_SMART-seq APOBEC1-YTH Cell 442


title: iDART_SMART-seq APOBEC1-YTH Cell 427


title: INPUT-HeLa_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 426


title: H3K27me3-HeLa_rep2

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 425


title: iDART_SMART-seq APOBEC1-YTH Cell 428


title: iDART_SMART-seq APOBEC1-YTH Cell 424


title: iDART_SMART-seq APOBEC1-YTH Cell 423


title: C-B10-6d_S109


title: H3K27me3-HeLa_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 435


title: iDART_SMART-seq APOBEC1-YTH Cell 422


title: MDN1-HeLa_siNC_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 421


title: H2AK119ub1-HeLa_rep2

description: ChIP-seq


title: C-B07-6d_S85


title: C-B08-6d_S93


title: C-C01-6d_S38


title: iDART_SMART-seq APOBEC1-YTH Cell 418


title: iDART_SMART-seq APOBEC1-YTH Cell 419


title: iDART_SMART-seq APOBEC1-YTH Cell 417


title: H2AK119ub1-HeLa_rep1

description: ChIP-seq


title: TEX10-HEK293FT_RING1DKO_rep2

description: ChIP-seq

value: RING1 A/B double knockout


title: C-B06-6d_S77


title: iDART_SMART-seq APOBEC1-YTH Cell 415


title: TEX10-HEK293FT_RING1DKO_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 414


title: iDART_SMART-seq APOBEC1-YTH Cell 413


title: iDART_SMART-seq APOBEC1-YTH Cell 416


title: TEX10-HEK293FT_siTEX10_rep2

description: ChIP-seq


title: C-B03-6d_S53


title: C-B04-6d_S61


title: C-B09-6d_S101


title: iDART_SMART-seq APOBEC1-YTH Cell 410


title: iDART_SMART-seq APOBEC1-YTH Cell 411


title: C-B02-6d_S45


title: C-B05-6d_S69


title: iDART_SMART-seq APOBEC1-YTH Cell 409


title: iDART_SMART-seq APOBEC1-YTH Cell 412


title: iDART_SMART-seq APOBEC1-YTH Cell 420


title: C-B01-6d_S37


title: iDART_SMART-seq APOBEC1-YTH Cell 407


title: TEX10-HEK293FT_siNC_rep2

description: ChIP-seq


title: TEX10-HEK293FT_siNC_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 405


title: iDART_SMART-seq APOBEC1-YTH Cell 404


title: MDN1-HEK293FT_RING1DKO_rep2

description: ChIP-seq


title: C-A11-1p_S116

value: Proximal trachea that were migratory post SO2


title: C-A12-1p_S124


title: iDART_SMART-seq APOBEC1-YTH Cell 406


title: MDN1-HEK293FT_RING1DKO_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 403


title: iDART_SMART-seq APOBEC1-YTH Cell 402


title: TEX10-HEK293FT_siTEX10_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 401


title: iDART_SMART-seq APOBEC1-YTH Cell 400


title: C-A10-1p_S108


title: C-A09-1p_S100


title: iDART_SMART-seq APOBEC1-YTH Cell 399


title: iDART_SMART-seq APOBEC1-YTH Cell 408


title: H2AK119ub1-HEK293FT_siNOL9_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 398


title: iDART_SMART-seq APOBEC1-YTH Cell 397


title: iDART_SMART-seq APOBEC1-YTH Cell 396


title: C-A07-1p_S84


title: siRING1B_RNAseq_HEK293FT_rep2

description: mRNA-seq


title: H2AK119ub1-HEK293FT_siNOL9_rep2

description: ChIP-seq


title: C-A08-1p_S92


title: iDART_SMART-seq APOBEC1-YTH Cell 395


title: iDART_SMART-seq APOBEC1-YTH Cell 394


title: C-A06-1p_S76


title: TEX10-ES_siTEX10_rep1

description: ChIP-seq

source_name: human ES cell

value: human ES cell


title: iDART_SMART-seq APOBEC1-YTH Cell 393


title: TEX10-ES_rep2

description: ChIP-seq

value: wild type


title: C-A05-1p_S68


title: iDART_SMART-seq APOBEC1-YTH Cell 392


title: iDART_SMART-seq APOBEC1-YTH Cell 391


title: TEX10-ES_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 390


title: C-A04-1p_S60


title: iDART_SMART-seq APOBEC1-YTH Cell 388


title: C-A03-1p_S52


title: INPUT-ES_rep2

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 385


title: C-A02-1p_S44


title: iDART_SMART-seq APOBEC1-YTH Cell 383


title: iDART_SMART-seq APOBEC1-YTH Cell 387


title: TEX10-ES_siTEX10_rep2

description: ChIP-seq


title: H2AK119ub1-ES_rep1

description: ChIP-seq


title: iDART_SMART-seq APOBEC1-YTH Cell 384


title: H2AK119ub1-ES_rep2

description: ChIP-seq


title: C-A01-1p_S36


title: B-C11-1p_S35


title: EED-KO-proseq-rep-2

description:
PRO-seq
EED-KO_F_norm_N2_10ntBins_noZeros_cleaned.bw
EED-KO_R_norm_N2_10ntBins_noZeros_cleaned.bw

extract_protocol:
For PRO-seq, total nascent RNA with biotin labeled was isolated from human cells.
For PRO-seq, two μg of total RNA was used to start RNA-seq library construction. Nascent RNA was isolated and further reverse transcribed to cDNA. The resulting cDNA was ligated with adapters, amplified by PCR, and further cleaned to obtain the final library. Libraries were sequenced on an Illumina Hiseq machine to obtain 150 bp paired-end reads.

value: siControl

value: DMEM

value: nascent RNA


title: iDART_SMART-seq APOBEC1-YTH Cell 381


title: iDART_SMART-seq APOBEC1-YTH Cell 380


title: B-C10-1p_S34


title: iDART_SMART-seq APOBEC1-YTH Cell 378


title: iDART_SMART-seq APOBEC1-YTH Cell 379


title: B-C09-1p_S33


title: siNOL9-proseq-rep-2

description:
PRO-seq
siNOL9_F_norm_N2_10ntBins_noZeros_cleaned.bw
siNC_R_norm_N2_10ntBins_noZeros_cleaned.bw


title: iDART_SMART-seq APOBEC1-YTH Cell 377


title: iDART_SMART-seq APOBEC1-YTH Cell 376


title: iDART_SMART-seq APOBEC1-YTH Cell 389


title: B-C08-1p_S32


title: iDART_SMART-seq APOBEC1-YTH Cell 386


title: INPUT-ES_rep1

description: ChIP-seq

value: siNC


title: iDART_SMART-seq APOBEC1-YTH Cell 375


title: siNOL9-proseq-rep-1


title: iDART_SMART-seq APOBEC1-YTH Cell 374


title: iDART_SMART-seq APOBEC1-YTH Cell 373


title: B-C06-1p_S30


title: iDART_SMART-seq APOBEC1-YTH Cell 372


title: iDART_SMART-seq APOBEC1-YTH Cell 382


title: iDART_SMART-seq APOBEC1-YTH Cell 370


title: iDART_SMART-seq APOBEC1-YTH Cell 371


title: iDART_SMART-seq APOBEC1-YTH Cell 369


title: B-C05-1p_S29


title: EED-KO-proseq-rep-1


title: iDART_SMART-seq APOBEC1-YTH Cell 368


title: iDART_SMART-seq APOBEC1-YTH Cell 367


title: H2AK119ub1-HEK293FT_rep1

description: ChIP-seq

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5)
Pooled libraries were demultiplexed using fastx
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding  input files for background normalization
Genome_build: hg20
Supplementary_files_format_and_content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.

value: WT

value: H2AK119ub1 (cell signaling technology 8240S)


title: iDART_SMART-seq APOBEC1-YTH Cell 366

value: HEK293T Cells


title: B-C02-1p_S26


title: iDART_SMART-seq APOBEC1-YTH Cell 363


title: iDART_SMART-seq APOBEC1-YTH Cell 362


title: siNC-proseq-rep-2

description:
PRO-seq
siNC_F_norm_N2_10ntBins_noZeros_cleaned.bw
siNC_R_norm_N2_10ntBins_noZeros_cleaned.bw


title: B-C01-1p_S25


title: B-B12-1p_S24


title: iDART_SMART-seq APOBEC1-YTH Cell 360


title: iDART_SMART-seq APOBEC1-YTH Cell 359


title: B-C07-1p_S31


title: siNC-proseq-rep-1


title: MDN1_siMDN1_rep2

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5).
Pooled libraries were demultiplexed using fastx.
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding input files for background normalization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.

extract_protocol:
Cells for ChIP were cultured in 15 cm plates. Cell were first washed with cold PBS, crosslinked at room temperature with 10 mM DMP (ThermoFisher Scientific) for 30 min, and then 1% formaldehyde (ThermoFisher Scientific) for 15 min. Crosslinking reactions were quenched by addition of 125 mM glycine for 5 min. Crosslinked cells were separated by 3 min treatment of 0.05% trypsin (Gibco), and then washed with cold PBS 3 times. In every wash, cells were centrifuged for 3 min at 1000xg at 4℃.Cell were then resuspended in sonication buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.5% SDS) and sonicated to shear chromatin into ~300 bp fragments using a Branson sonicator. Sonicated samples were diluted 5-fold with ChIP dilution buffer (pH 7.9, 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate) to obtain a final concentration of 0.1% SDS. Diluted samples were centrifuged at 13,000 rpm for 10 min. The supernatant was pre-cleared with protein A/G or Dynabeads M-280 Streptavidin beads (ThermoFisher) and immunoprecipitated for 3-12 h using 3 μg antibodies and 40 μl protein A/G or Dynabeads M-280 Streptavidin beads. The beads were washed twice with high salt wash buffer A (pH 7.9, 50 mM Hepes, 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.1% SDS), and once with wash buffer B (pH 7.9, 50 mM Hepes, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, 0.5% NP-40). The bound chromatin fragments were eluted with elution buffer (pH 8.0, 50 Mm Tris, 10 mM EDTA, 1% SDS) for 5 min at 65℃. Eluted DNA-proteins complexes were treated with RNase A and crosslinks were reversed overnight at 65℃. Proteinase K was then added to digest proteins for 1 h at 55℃. DNA was further purified using PCR Purification Kit (QIAGEN).
For ChIP-seq, sequencing library was constructed using TruSeq DNA sample Prep Kits (Illumina) and adapter dimers were removed by agarose gels electrophoresis. Sized selected and purified DNA libraries were sequenced on an Illumina Hiseq 2500 machine (Bauer core facility at Harvard University) to obtain 50 bp single-end reads.

value: MDN1 (Bethyl Laboratories A304-739A-T)


title: iDART_SMART-seq APOBEC1-YTH Cell 357

value: 1microg/mL doxycycline; 24 hours


title: B-C04-1p_S28


title: B-B10-1p_S22


title: H2AK119ub1-HEK293FT_rep2

description: ChIP-seq

data_processing:
ChIP-seq reads were quality controlled with fastqc (v0.11.5)
Pooled libraries were demultiplexed using fastx
Reads were aligned to the reference genome using bowtie2 with default parameters.
The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.
ChIP-seq peaks were called with macs2 (v2.1.1.20160309) and broad peak calling option using corresponding  input files for background normalization
Genome_build: hg21
Supplementary_files_format_and_content: The mapped reads were normalized to reads per genome content using Deeptools, saved as bw files and visualized in IGV.


title: iDART_SMART-seq APOBEC1-YTH Cell 358


title: B-C03-1p_S27


title: MDN1_siNC_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 361


title: MDN1_siMDN1_rep1


title: B-B11-1p_S23


title: H3K27me3_siNOL9_rep1

value: H3K27me3 (Diagenode C15410069)


title: MDN1_siNC_rep2


title: B-B09-1p_S21

value: Injury with So2


title: iDART_SMART-seq APOBEC1-YTH Cell 356


title: iDART_SMART-seq APOBEC1-YTH Cell 354


title: iDART_SMART-seq APOBEC1-YTH Cell 365


title: H3K27me3_siNOL9_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 364


title: iDART_SMART-seq APOBEC1-YTH Cell 353


title: iDART_SMART-seq APOBEC1-YTH Cell 352


title: H3K27me3_siNC_rep2


title: B-B08-1p_S20


title: iDART_SMART-seq APOBEC1-YTH Cell 355


title: iDART_SMART-seq APOBEC1-YTH Cell 351


title: H3K27me3_siNC_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 350


title: iDART_SMART-seq APOBEC1-YTH Cell 349


title: H3K9me3_rep2

value: H3K9me3 (Diagenode C15500003)


title: B-B07-1p_S19

value: Wild Type


title: iDART_SMART-seq APOBEC1-YTH Cell 348


title: iDART_SMART-seq APOBEC1-YTH Cell 347


title: iDART_SMART-seq APOBEC1-YTH Cell 345


title: B-B06-1p_S18


title: H3K9me3_rep1


title: INPUT_siNOL9_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 346


title: iDART_SMART-seq APOBEC1-YTH Cell 342


title: INPUT_siNOL9_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 343


title: iDART_SMART-seq APOBEC1-YTH Cell 344


title: INPUT_siNC_rep2


title: iDART_SMART-seq APOBEC1-YTH Cell 340


title: B-B05-1p_S17


title: B-B02-1p_S14


title: B-B03-1p_S15


title: iDART_SMART-seq APOBEC1-YTH Cell 339


title: iDART_SMART-seq APOBEC1-YTH Cell 338


title: iDART_SMART-seq APOBEC1-YTH Cell 336


title: iDART_SMART-seq APOBEC1-YTH Cell 337


title: INPUT_siMDN1_rep2


title: B-A12-1p_S12


title: iDART_SMART-seq APOBEC1-YTH Cell 335


title: B-B04-1p_S16


title: B-B01-1p_S13


title: INPUT_siMDN1_rep1


title: iDART_SMART-seq APOBEC1-YTH Cell 333


title: B-A11-1p_S11


title: iDART_SMART-seq APOBEC1-YTH Cell 334


title: B-A10-1p_S10


title: iDART_SMART-seq APOBEC1-YTH Cell 332


title: iDART_SMART-seq APOBEC1-YTH Cell 330


title: iDART_SMART-seq APOBEC1-YTH Cell 328


title: iDART_SMART-seq APOBEC1-YTH Cell 331


title: iDART_SMART-seq APOBEC1-YTH Cell 329


title: iDART_SMART-seq APOBEC1-YTH Cell 327


title: B-A09-1p_S9


title: INPUT_siNC_rep1


title: B-A08-1p_S8


title: iDART_SMART-seq APOBEC1-YTH Cell 325


title: B-A07-1p_S7


title: iDART_SMART-seq APOBEC1-YTH Cell 326


title: B-A06-1p_S6


title: iDART_SMART-seq APOBEC1-YTH Cell 324


title: iDART_SMART-seq APOBEC1-YTH Cell 322


title: iDART_SMART-seq APOBEC1-YTH Cell 321


title: B-A05-1p_S5


title: iDART_SMART-seq APOBEC1-YTH Cell 323


title: iDART_SMART-seq APOBEC1-YTH Cell 320


title: iDART_SMART-seq APOBEC1-YTH Cell 319


title: iDART_SMART-seq APOBEC1-YTH Cell 318


title: B-A03-1p_S3


title: B-A02-1p_S2


title: iDART_SMART-seq APOBEC1-YTH Cell 317


title: iDART_SMART-seq APOBEC1-YTH Cell 314


title: iDART_SMART-seq APOBEC1-YTH Cell 315


title: iDART_SMART-seq APOBEC1-YTH Cell 312


title: B-A01-1p_S1


title: Terminal Ileum KO 3

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
For total RNA-seq: Sequencing analysis was done using RNA-seq for Eukaryotes Analysis v3 by Banana Slug Genomics Center at University of California Santa Cruz
For total RNA-seq: Raw sequencing reads (paired-end reads) that  were produced by Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC. Adapter sequences and primers were trimmed from the sequencing reads using Trimmomatic, then followed by removing the polyA tail, polyN, and read portions with quality score below 28 using PRINSEQ
For total RNA-seq: Trimmed reads were mapped to the reference genome (GRCm38/mm10) using (STAR) with NCBI RefSeq annotated genes as transcriptome index data. Read alignment coverage and summary statistics for visualization were computed using SAMtools, BEDtools, and UCSC Genome Browser utilities
For total RNA-seq: Using Cufflinks work flow, the sequencing reads aligned to RefSeq annotated genes were quanti fied using Cuffquant. Cuffnorm was then used to normalize the gene expression levels across the studied samples with FPKM computed for sample correlation assessment. Differential expression analysis between samples was performed using Cuffidff with the computed results from Cuffquant.
Genome_build: mm10

source_name: Murine small intestinal tissue

extract_protocol:
Mice were given DSS in drinking water. On day 6 terminal ileum tissues were extracted and stored at -20°C in RNAlater. RNA from the terminal ileum of DSS treated Il17rafl/fl;Atoh1-cre+ and their littermate cre- mice was isolated using TRIZOL extraction methods as per manufacture instructions (Life Technologies).
Libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to manufacturer’s supplied protocol. Library quality was confirmed by size analysis using Bioanalyzer High Sensitivity DNA Analysis (Agilent). All the libraries were sequenced on an Illimuna NextSeq 500 using high-output kit

tag: tissue

value: Terminal Ileum

tag: age

value: 6 weeks


title: iDART_SMART-seq APOBEC1-YTH Cell 310

first: Matthew

last: Tegowski

address: 153 Research Dr.

institute: Duke University

source_name: Kidney

tag: cell line

tag: transgene


title: iDART_SMART-seq APOBEC1-YTH Cell 311

tag: treatment


title: Terminal Ileum KO 2


title: B-A04-1p_S4

value: Proximal trachea that were migratory post SO2