title: TW-PT1-1_FRAS210076003-2

description:
From isolate TW-PT1-1, Biological Replicate 2
TW-PT1-1-2r


title: SM3746_4w Chow

status: Public on Mar 16 2024

type: SRA

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic

data_processing:
STAR v.2.4.1
Next-Generation Sequencing HOMER
Assembly: mm10
Supplementary files format and content: tab delimited file that contains raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA column purification using the RNeasy Mini Kit (74106, Qiagen, Hilden, Germany)
Transcriptomic

tag: tissue

value: Liver

tag: Sex

value: Female

tag: genotype

tag: treatment

value: 4w Chow


title: SM3747_4w Chow


title: RNA-Seq S11-kidney

city: Beijing

first: Ze

last: Yan

address: No.2, Yuanmingyuan Road (West), HaiDian District

country: China

institute: China Agricultural University

data_processing:
Sequence reads were trimmed for adaptor sequencing / low-quality bases using fastp software with default parameters.
Trimmed clean reads were mapped to Oar_rambouillet_v1.0 (GCA_002742125.1) by the program STAR (v2.7.9a)(parameter: -quantMode GeneCounts, -outFilterMismatchNmax 3, -outFilterMultimapNmax 10)
Properly paired and uniquely mapped reads were extracted by using SAMtools (v1.11)112 with the command “view -f 2”
Gene counts were generated by the featureCounts program from the Subread package suite (v2.0.3)
Assembly: Oar_rambouillet_v1.0 (GCA_002742125.1)
Supplementary files format and content: tab-delimited next file includes raw counts for each sample

molecule: total RNA

organism: Ovis aries

source_name: kidney

extract_protocol:
Total RNA was extracted from flash-frozen tissues with RNA TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
libraries were constructed by the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, CA, USA)

value: kidney


title: RNA-Seq S10-kidney


title: RNA-Seq S32-BJ

source_name: muscle

value: muscle


title: Nich-2-3-2_FRAS210075991-2

city: Hangzhou

first: lianyu

last: lin

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: Zhejiang University

description:
From isolate Nich-2-3-2, Biological Replicate 2
Nich-2-3-2-2r

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the 70-15 reference genome using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on the 70-15 reference genome annotations was determined using stringtie (v2.0) with the default parameter settings.
Transcripts per Million (TPM) were calculated for representing the expression of each gene.
Assembly: 70-15 reference genome
Supplementary files format and content: Matrix table with TPM for every gene and every sample

organism: Pyricularia oryzae

source_name: hypha

growth_protocol: For vegetative growth, the M. oryzae strains were cultured on a complete medium (CM, 6 g yeast extract, 6 g casein hydrolysate, 10 g sucrose, 20 g agar for solid medium) for 5 days at 25℃, then transfered in the liquid CM for 3 days in a shaking incubator at 25℃ and 110 rpm condition.

extract_protocol:
The RNA extraction was using a HiPure Universal RNA kit (r4130-02; Magen, China) according to the manufacturer’s instructions. 5 μg of total RNA was used for the construction of sequencing libraires.
RNA integrity and quantity were verified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and Qubit 2.0 (Life Tecnologies, China), respectively. The cDNA library was sequenced using IIIumina sequencing platform (NovaSqu 6000) with 150 bo pair-end reads length and 300 bp insert size by Novogene Co. (Tianjin, China).

tag: cell type

value: hypha


title: Nich-2-3-2_FRAS210075991-1

description:
From isolate Nich-2-3-2, Biological Replicate 1
Nich-2-3-2-1r


title: Sar-2-20-1_FRAS210075994-1

description:
From isolate Sar-2-20-1, Biological Replicate 1
Sar-2-20-1-1r


title: RNA-Seq S12-kidney


title: YN072313_FRAS210075993-1

description:
From isolate YN072313, Biological Replicate 1
YN072313-1r


title: tail_seq.WT_2

city: Riverside

first: Shiyang

last: He

state: CA

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

country: USA

institute: UCR

data_processing:
When obtained the raw fast5 file from the sequencers, guppy (version 6.3.7-gpu) was used to call bases.
Minimap2 (version 2.26-r1175) was used to map the reads to hg38 gencode v35 transcripts.
tailfindr (version 1.4) and nanopolish (version 0.14.0) were used to estimate polyA tail length
Assembly: UCSC hg38
Supplementary files format and content: tab_delimimated tail lengths estimated from tailfindr and nanopolish, and gene mapping information for individual read.
Library strategy: Poly(A)tail-seq

organism: Homo sapiens

source_name: cell line

growth_protocol: Inducible HeLa cells were maintained in Dulbecco’s Modified Eagle’s Medium, high glucose, pyruvate (Themo Fisher Scientific, 11995065) supplemented with 10% (v/v) fetal bovine serum (Thermo Fisher 10437) ; and 1% (w/v) penicillin/streptomycin Cells (Thermo Fisher Scientific, 1514022) were trypsinized and sub-cultured in incubator in 5% CO2 at 37 oC

extract_protocol:
Total RNA was extracted using Direct-zol RNA miniprep kit (Zymo Research R2050) following manufacturer's instructions. Polyadenylated RNA was selected from total RNA using Poly(A) mRNA Magnetic Isolation kit (NEB E7490).
Poly(A)tail-seq libraries were constructed using Library Kit SQK-RNA002 and either Flowcell type FLO-MIN106D or FLO-PRO002 (Oxford Nanopore Technologies). One flowcell was used for each sample.

treatment_protocol: Inducible HeLa cells were treated or not for 24 hours with doxycycline (Dox)

value: cell line

tag: cell line

value: HeLa

value: immortalized cervical cancer cell

value: WT UNK

value: Dox for 24 hours


title: RNA-Seq S26-ZW

source_name: abomasum

value: abomasum


title: RNA-Seq S14-kidney


title: SM3749_4w Chow


title: GD06-53_FRAS210075999-2

description:
From isolate GD06-53, Biological Replicate 2
GD06-53-2r


title: RNA-Seq S21-ZW


title: tail_seq.Uninduced_2

value: no Dox


title: RNA-Seq S15-kidney


title: GD06-53_FRAS210075999-1

description:
From isolate GD06-53, Biological Replicate 1
GD06-53-1r


title: TW-PT1-1_FRAS210076003-1

description:
From isolate TW-PT1-1, Biological Replicate 1
TW-PT1-1-1r


title: tail_seq.dPAM2_2

value: dPAM2 UNK


title: RNA-Seq S16-kidney


title: FJSH0703_FRAS210075998-2

description:
From isolate FJSH0703, Biological Replicate 2
FJSH0703-2r


title: tail_seq.3M_2

value: 3M UNK


title: RNA-Seq S17-kidney


title: FJSH0703_FRAS210075998-1

description:
From isolate FJSH0703, Biological Replicate 1
FJSH0703-1r


title: Ribo_seq.WT_L2

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
Flexbar(version 3.5.0) was used to demultiplex the pooled samples.
bowtie2 (version 2.4.5) was used to map the reads to human rRNA.
The rRNA unmapped reads from previous step were mapped to human lncRNA (gencode v35).
lncRNA unmapped reads from previous steps were mapped to human protein_coding genes (gencode v35).
Read counts in each gene were calculated with samtools (v1.14).
The read counts subsequently were normalized to 311 UNK unbound genes defined in the manuscript.
Differential translated genes (DTGs) were identified with DESeq2 (v1.38.2).
Assembly: UCSC hg38
Supplementary files format and content: tab_delimimated normalized read count for individual protein coding gene in all conditions.
Library strategy: Ribo-seq

extract_protocol:
Cells were lysed and treated with Rnase I. Centrifugation through a sucrose cushion was performed to enrich for ribosome-RNA complexes. RNA was extracted and size selected to enrich for ribosome protected RNA fragments (RPFs). RPFs from each condition were turned into Illumina sequencing libraries with duplicates.
Ribo-seq libraries were constructed following the protocols described in McGlinchy and Ingolia (Methods, 2017; PMID: 28579404) and Buchbender et al (Methods, 2020; PMID: 31610236)


title: RNA-Seq S18-kidney


title: RNA-Seq S13-kidney


title: FJ98099_FRAS210075996-1

description:
From isolate FJ98099, Biological Replicate 1
FJ98099-1r


title: Ribo_seq.WT_L10


title: FJ8773-19_FRAS210075992-2

description:
From isolate FJ8773-19, Biological Replicate 2
FJ8773-19-2r


title: RNA-Seq S20-kidney


title: Ribo_seq.Uninduced_L1


title: FJ8773-19_FRAS210075992-1

description:
From isolate FJ8773-19, Biological Replicate 1
FJ8773-19-1r


title: FJ81278_FRAS210076000-3

description:
From isolate FJ81278, Biological Replicate 2
FJ81278-3r


title: Ribo_seq.dPAM2_L4


title: Ribo_seq.dPAM2_L12


title: Ribo_seq.3M_L3


title: RNA-Seq S21-kidney


title: FJ78-JJ_FRAS210076001-2

description:
From isolate FJ78-JJ, Biological Replicate 2
FJ78-JJ-2r


title: RNA-Seq S22-kidney


title: FJ81278_FRAS210076000-2

description:
From isolate FJ81278, Biological Replicate 1
FJ81278-2r


title: FJ78-JJ_FRAS210076001-1

description:
From isolate FJ78-JJ, Biological Replicate 1
FJ78-JJ-1r


title: Ribo_seq.3M_L11


title: RNA-Seq S24-kidney


title: RNA-Seq S23-kidney


title: FJ72AC7-77_FRAS210075997-2

description:
From isolate FJ72AC7-77, Biological Replicate 2
FJ72ZC7-77-2r


title: iCLIP.WT_L9

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
For PABPC1 iCLIP data poly(A) sequences (more than 15 As in the end of reads) were removed before mapping.
STAR (v2.7.3a) were used to map the sequencing reads to human genome (hg38).
UMI-tools version(version 1.0.1) was used to remove PCR duplications.
RPM normalized bedgraph files were generated from bedtools v2.29.2 and subsesquently transfromed to bigwig files.
Assembly: UCSC hg38
Supplementary files format and content: RPM normalized bigwig files for crosslinking events.

extract_protocol:
After partial RNase I digestion of cell lysates, immunoprecipitation was performed using anti-Flag or anti-PABPC1 antibodies, followed by 3' adapter ligation, SDS PAGE, and transfer of protein-RNA complexes to a nitrocellulose membrane from which RNA was extracted in the presence of proteinase K.
iCLIP libraries were constructed following the protocol described in Buchbender et al (Methods, 2020; PMID: 31610236)

treatment_protocol: Inducible HeLa cells were treated or not for 24 hours with doxycycline (Dox) prior to UV crosslinking.


title: FJ72AC7-77_FRAS210075997-1

description:
From isolate FJ72AC7-77, Biological Replicate 1
FJ72ZC7-77-1r


title: RNA-Seq S25-kidney


title: RNA-Seq S26-kidney


title: iCLIP.WT_L3


title: RNA-Seq S19-kidney


title: Ribo_seq.Uninduced_L9


title: RNA-Seq S28-kidney


title: DB11-621_FRAS210076004-2

description:
From isolate DB11-621, Biological Replicate 2
DB11-621-2r


title: iCLIP.WT_L1


title: RNA-Seq S29-kidney


title: DB11-621_FRAS210076004-1

description:
From isolate DB11-621, Biological Replicate 1
DB11-621-1r


title: iCLIP.dPAM2_L20


title: RNA-Seq S33-BJ


title: BJ08-8_FRAS210076005-2

description:
From isolate BJ08-8, Biological Replicate 2
BJ08-8-2r


title: RNA-Seq S30-kidney


title: BJ08-8_FRAS210076005-1

description:
From isolate BJ08-8, Biological Replicate 1
BJ08-8-1r


title: iCLIP.dPAM2_L16


title: iCLIP.dPAM2_L15


title: RNA-Seq S32-kidney


title: RNA-Seq S31-kidney


title: iCLIP.dPAM2_L14


title: AV1-1-1_FRAS210075995-1

description:
From isolate AV1-1-1, Biological Replicate 1
AV1-1-1-1r


title: RNA-Seq S34-BJ


title: FJ98099_FRAS210075996-2

description:
From isolate FJ98099, Biological Replicate 2
FJ98099-2r


title: iCLIP.3M_L13


title: 13FM-24-1_FRAS210075990-2

description:
From isolate 13FM-24-1, Biological Replicate 2
13FM-24-1-2r


title: iCLIP.3M_L12


title: iCLIP.WT_L2


title: RNA-Seq S34-kidney


title: RNA-Seq S33-kidney


title: RNA-Seq S25-lung

source_name: lung

value: lung


title: iCLIP.3M_L11


title: iCLIP.3M_L10


title: RNA-Seq S43-BJ


title: Zip3-FLAG, 6h, biol rep 5

city: Marseille

first: Sylvain

middle: Quentin

last: Legrand

address: 27 Bd Lei Roure

country: France

institute: CNRS

library_source: genomic

data_processing:
Sequencing quality control was determined using FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aggregated across samples using MultiQC (v1.7) (Ewels et al. 2016). Reads with Phred quality score less than 30 were filtered out. Paired-end reads were mapped to CBS10367_SNP_inferred reference genome using Bowtie2 (v2.3.4.3) (Langmead et Salzberg 2012) with default parameters. Only mapped reads were filtered in using samtools (v1.9) (Li et al. 2009) (view; --exclude-flags 4). Duplicate tags were removed using Picard Tools (v2.20.2) (https://broadinstitute.github.io/picard/) (MarkDuplicates; REMOVE_DUPLICATES=true) and mapped tags were processed for further analysis. Reads mapping to the mitochondrial genome and ribosomal DNA were removed from any analysis.
For visualization purpose, mapped tags were converted into bigwig and normalized by their library size using the deepTools (v3.2.1) (Ramírez et al. 2016) (bamCoverage –scaleFactor library_size_factor –binSize 5). Reads were extended using values previously computed by deepTools (bamPEFragmentSize) and used through the –extendReads option. Untagged-subtracted bigwig files were computed from the normalized igwig files using deepTools (bigwigCompare –operation subtract). BigWig files from multiple replicates were merged into a single file using a custom bash script (bigWigMerge, bedGraphToBigWig). As t1h untagged was not available we used the t4h untagged when required.
Assembly: CBS 10367asRefSNPinferred (BioProject PRJEB60460)

molecule: genomic DNA

organism: Lachancea kluyveri

growth_protocol: L. kluyveri cells were inoculated in pre-sporulation medium (0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base, 1% potassium acetate, 1% ammonium sulfate, 0.5% potassium phthalate, pH 5.5) over day and over night at 30°C to reach an OD600 of 1, washed once with water and resuspended in 1% potassium acetate at 30°C.

extract_protocol:
1 x 10^9 cells were harvested for each ChIP-seq experiment. Cells were treated as in Sanchez and Borde 2021.
As in Sanchez and Borde 2021.

treatment_protocol: Cells were harvested 1, 4 or 6 hours after sporulation induction in potassium acetate 1% and directly treated with paraformaldehyde (1% final), quenched in glycine (0.125 M final), washed twice in PBS 1X and flash frozen in liquid nitrogen. See details in Sanchez and Borde 2021.


title: RNA.WT-3

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR (v2.7.3a) were used to map the sequencing reads to human genome (hg38).
Read counts in each gene (gencode v35) were calculated with featureCounts tools (v2.0.0) from Rsubread package
Differential expressed genes (DEGs) were identified with DESeq2 (v1.38.2)
FPKM for indivdual gene was calculated with cufflinks (version 2.2.1)
Assembly: UCSC hg38
Supplementary files format and content: tab_delimimated FPKM for individual gene in all conditions

extract_protocol:
Total RNA was extracted using Direct-zol RNA miniprep kit (Zymo Research R2050) following manufacturer's instructions. Polyadenylated RNA was selected from total RNA using Poly(A) mRNA Magnetic Isolation kit (NEB E7490).
RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB E7765)


title: RNA-Seq S26-lung


title: Zip3-FLAG, 6h, biol rep 4


title: AV1-1-1_FRAS210075995-2

description:
From isolate AV1-1-1, Biological Replicate 2
AV1-1-1-2r


title: RNA.WT-2


title: RNA-Seq S28-lung


title: Zip3-FLAG, 6h, biol rep 2


title: RNA.WT-1


title: RNA-Seq S27-lung


title: Zip3-FLAG, 6h, biol rep 3


title: Zip3-FLAG, 6h, biol rep 1


title: RNA.Uninduced-3


title: RNA-Seq S29-lung


title: Untagged, 6h, biol rep 2

value: WT


title: RNA.Uninduced-2


title: RNA.Uninduced-1


title: 13FM-24-1_FRAS210075990-1

description:
From isolate 13FM-24-1, Biological Replicate 1
13FM-24-1-1r


title: RNA-Seq S31-lung


title: RNA-Seq S30-lung


title: Untagged, 6h, biol rep 3


title: Untagged, 6h, biol rep 1


title: RNA-Seq S32-lung


title: RNA.dPAM2-2


title: RNA-Seq S33-lung


title: Red1-FLAG, 6h, biol rep 2


title: Red1-FLAG, 6h, biol rep 1


title: RNA.dPAM2-3


title: Rec8-FLAG, 6h, biol rep 2


title: RNA.dPAM2-1


title: RNA-Seq S34-lung


title: RNA.3M-3


title: RNA.3M-2


title: Hop1-FLAG, 6h, biol rep 2


title: RNA-Seq S44-BJ


title: RNA-Seq S35-lung


title: Hop1-FLAG, 6h, biol rep 1


title: RNA.3M-1


title: Rec8-FLAG, 6h, biol rep 1


title: tail_seq.WT_1


title: RNA-Seq S36-lung


title: RNA-Seq S37-lung


title: tail_seq.Uninduced_1


title: tail_seq.dPAM2_1


title: Red1-FLAG, 4h, biol rep 2


title: RNA-Seq S38-lung


title: RNA-Seq S39-lung


title: Rec8-FLAG, 4h, biol rep 1


title: RNA-Seq S40-lung


title: tail_seq.3M_1


title: Red1-FLAG, 4h, biol rep 1


title: Rec8-FLAG, 4h, biol rep 2


title: HR_Whole_embryo_No5_8CELL_S21

city: Shanghai

first: Kaile

last: Zhang

address: No. 600 Yishan Road

department: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HRMTP2014 whole genome using hisat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a clustromlized Perl script
Genome_build: Harore_MTP2014
Supplementary_files_format_and_content: HR_RPKM_AVW.xlsx includes RPKM values for each Sample.

organism: Halocynthia roretzi

source_name: Whole embryo

growth_protocol: H. roretzi were collected and cultured over generations for more than three years in the inland laboratory, as previously described (Nishide , 2012).

extract_protocol:
total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols, AVW(non-strand specific), staged RNA-Seq (strand-specific)

tag: population

value: southwestern Japanese

tag: developmental stage

value: 8 cell

value: embryo

tag: tissue region

value: Whole embryo

value: wild type


title: Hop1-FLAG, 4h, biol rep 1


title: Hop1-FLAG, 4h, biol rep 2


title: RNA-Seq S43-lung


title: HR_Whole_embryo_No4_8CELL_S15


title: HR_Whole_embryo_No5_110CELL_S24

value: 110 cell


title: RNA-Seq S41-lung


title: Untagged, 4h, biol rep 1


title: Red1-FLAG, 1h, biol rep 1


title: HR_Whole_embryo_No4_110CELL_S18


title: RNA-Seq S46-lung


title: RNA-Seq S44-lung


title: HR_Whole_embryo_No3_8CELL_S9


title: HR_Whole_embryo_No3_110CELL_S12


title: Rec8-FLAG, 1h, biol rep 1


title: Rec8-FLAG, 1h, biol rep 2


title: RNA-Seq S45-lung


title: RNA-Seq S45-BJ

value: muscle


title: Hop1-FLAG, 1h, biol rep 2


title: cKO, PN2.5, bio rep 3

first: Kai

last: Sun

address: No.22 Zhongguancun South Avenue

institute: Peking university

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (Quality limit: 0.05)
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example)
Assembly: StringTie
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: dental epithelium

extract_protocol:
RNA was harvested using TRIzol® Reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA

value: dental epithelium

value: epithelial cells

tag: age

value: postnatal 2.5


title: RNA-Seq S47-lung


title: cKO, PN2.5, bio rep 2


title: Hop1-FLAG, 1h, biol rep 1


title: RNA-Seq S48-lung


title: HR_Whole_embryo_No2_110CELL_S6


title: HR_Vegetal_No5_8CELL_S20

source_name: Vegetal hemisphere

value: Vegetal hemisphere


title: RNA.WT_CNOT9ko_2

value: cell line

value: HeLa

value: immortalized cervical cancer cell

value: WT UNK in CNOT9 KO

value: Dox for 24 hours


title: RNA-Seq S49-lung

value: lung


title: control, PN2.5, bio rep 3


title: HR_Vegetal_No5_110CELL_S23

value: southwestern Japanese


title: RNA-Seq S50-lung


title: RNA.WT_CNOT9ko_1


title: HR_Vegetal_No4_8CELL_S14

value: 8 cell


title: control, PN2.5, bio rep 2


title: RNA-Seq S01-LW

source_name: rumen

value: rumen


title: RNA.Uninduced_CNOT9ko_2

value: no Dox


title: control, PN2.5, bio rep 1


title: HR_Vegetal_No4_110CELL_S17

value: embryo

value: wild type


title: RNA.Uninduced_CNOT9ko_1


title: RNA-Seq S02-LW


title: Ribo_seq.WT_CNOT9ko_2


title: HR_Vegetal_No3_8CELL_S8


title: HR_Whole_embryo_No2_8CELL_S3

value: Whole embryo


title: P10 EXERCISE

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were trimmed for adapters and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp.
The gene count table was generated by aligning reads to the mouse transcriptome (Ensembl version 104) using kallisto and converting transcript counts to gene counts using tximport.

source_name: pancreatic islet

extract_protocol:
RNA was extracted from isolated islets using RNeasy Micro Kit (Cat No. 74004).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Kit following manufacturer's protocols.

tag: strain

value: male

value: pancreatic islet

value: EXERCISE


title: P9 EXERCISE


title: HR_Vegetal_No3_110CELL_S11

value: 110 cell

value: Vegetal hemisphere


title: Ribo_seq.WT_CNOT9ko_1

value: cell line

value: HeLa


title: cKO, PN2.5, bio rep 1

value: dental epithelium

value: epithelial cells

value: postnatal 2.5


title: RNA-Seq S04-LW


title: P7 EXERCISE


title: RNA-Seq S42-QN

source_name: hypothalamus

value: hypothalamus


title: Ribo_seq.Uninduced_CNOT9ko_1

value: immortalized cervical cancer cell

value: WT UNK in CNOT9 KO


title: HR_Vegetal_No2_8CELL_S2

value: southwestern Japanese

value: 8 cell


title: HR_Vegetal_No2_110CELL_S5

value: embryo

value: wild type


title: HR_Animal_No5_8CELL_S19

source_name: Animal hemisphere

value: Animal hemisphere


title: RNA-Seq S43-QN


title: iCLIP.PABPC1_in_uninduced_cells-2

value: WT UNK

value: no Dox


title: RNA-Seq S41-QN


title: P5 SEDENTARY

value: male

value: pancreatic islet

value: SEDENTARY


title: HR_Animal_No5_110CELL_S22

value: 110 cell


title: RNA-Seq S44-QN


title: P4 SEDENTARY


title: RNA-Seq S03-LW

value: rumen


title: iCLIP.PABPC1_in_uninduced_cells-1

value: cell line

value: HeLa


title: P3 SEDENTARY


title: iCLIP.PABPC1_in_cells_expressing_3M-1

value: 3M UNK

value: Dox for 24 hours


title: iCLIP.PABPC1_in_cells_expressing_3M-2

value: immortalized cervical cancer cell


title: RNA-Seq S46-QN

value: hypothalamus


title: RNA-Seq S45-QN


title: P2 SEDENTARY


title: HR_Animal_No3_8CELL_S7

value: southwestern Japanese

value: 8 cell


title: P8 EXERCISE

value: EXERCISE


title: HR_Animal_No4_110CELL_S16

value: embryo

value: Animal hemisphere

value: wild type


title: iCLIP.PABPC1_in_cells_expressing_dPAM2-2

value: dPAM2 UNK


title: RNA-Seq S05-CT

source_name: pituitary

value: pituitary


title: Ribo_seq.Uninduced_CNOT9ko_2

value: WT UNK in CNOT9 KO

value: no Dox


title: P6 EXERCISE

value: male

value: pancreatic islet


title: iCLIP.PABPC1_in_cells_expressing_dPAM2-1

value: cell line

value: HeLa


title: CC-seq, 6h, biol rep 2

data_processing:
As in Gittens et al. 2019, paired end reads that passed filter were aligned to the CBS 10367asRefSNPinferred genome using bowtie2 (options: -X 1000 --no-discordant --very-sensitive --mp 5,1 --np 0), using MAPQ0 settings.
SAM files were processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5’-terminal nucleotide.
Assembly: CBS 10367asRefSNPinferred (BioProject PRJEB60460)

extract_protocol:
3 x 10^10 cells were harvested for each CC-seq experiment. Cells were lyzed in 2 ml screw cap tubes with 300 microliters of glass beads (425-600 micrometer of diameter, Sigma) per tube using a Fast prep (MP Biomedicals). We used three cycles of 30 seconds at 4 m/s, with five minutes on ice between the cycles. Cell lysates were harvested by centrifuging the screw cap tubes after drilling a hole at their base for 2 minutes at 950g at 4°C. From this point, cell lysates were treated as in Gittens et al. 2019.
As in Gittens et al. 2019

treatment_protocol: Cells were harvested 6 hours after sporulation induction, which corresponds to the peak of Spo11-DSBs (Brion et al. 2017), in potassium acetate 1%, washed with water and frozen.


title: RNA-Seq S47-QN


title: HR_Animal_No3_110CELL_S10

value: 110 cell


title: HR_Animal_No2_8CELL_S1


title: RNA-Seq S48-QN


title: iCLIP.PABPC1_in_cells_expressing_WT-2

value: immortalized cervical cancer cell

value: WT UNK

value: Dox for 24 hours


title: iCLIP.PABPC1_in_cells_expressing_WT-1


title: HR_Animal_No2_110CELL_S4

value: southwestern Japanese


title: CC-seq, 6h, biol rep 1


title: SM-mito_2

status: Public on Mar 15 2024

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides.
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a  Aligned reads were filtered to remove  ribosomal reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes . The raw count matrix was normalized with DESeq2 version 1.30.1.
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: library-size normalized counts

source_name: skeletal muscle

extract_protocol:
Mitochondria and remaining tissue fraction were isolated as previosly described (10.1007/978-1-4939-2257-4_11). RNA was isolated using the TRIzol in combination with RNeasy Mini Kit (Qiagen # 217004) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen #79254) according to manufacturer’s instruction.
10ng of total RNA was used as input for Pico Input Mammalian (Takara Bio)

value: skeletal muscle

value: WT

value: isolated mitochondria


title: SM-mito_1


title: HR_Animal_No4_8CELL_S13

value: 8 cell

value: embryo

value: Animal hemisphere

value: wild type


title: SM-total_2

value: tissue minus mitochondria


title: BAT-Mito_2

source_name: brown adipose tissue

value: brown adipose tissue


title: SM-total_1


title: BAT-total_2


title: BAT-Mito_1


title: BAT-total_1


title: P1 SEDENTARY

value: male

value: pancreatic islet

value: SEDENTARY


title: Long-read sequencing of LAMA3 on-target site on sample treated with Cas9 nuclease g5

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description:
demultiplexed sequences
LAMA3_LR_read coverage analysis.xlsx
LR-Cas9-g5

data_processing:
Reads were demultiplexed directly while sequencing. Obtained reads were aligned using Minimap2 v. 2.24-r1122,60 and further processed with Samtools. Deletions and insertions were counted from the cigar string in a window of 200 bp around the cleavage site using a custom script. Deletion read coverage was calculated by subtracting the read coverage with deletions from the read coverage without the deletions, and by normalizing the reads to the total reads for each sample. The values obtained from the untreated control where subtracted from the treated samples to decrease sequencing bias.
Assembly: hg38
Supplementary files format and content: Excel table listing the number of reads at each base of the PCR amplicon. Shown is the read coverage with and without deletions. It further includes the calculation of the deletion read coverage (subtracting the read coverage with deletions from the read coverage without the deletions), and normalization of the reads to the total reads for each sample. The values obtained from the untreated control where subtracted from the treated samples to decrease sequencing bias.

source_name: Patient-derived keratinocytes

growth_protocol: Primary RDEB and JEB keratinocytes were cultivated in CNT-PRIME medium supplemented with 50 mg/mL primocin (invivoGen) and maintained at 37°C and 5% carbon dioxide in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
A 5 kb amplicon spanning the COL7A1, COL17A1 or LAMA3 target site was amplified from 200 ng of genomic DNA by a 30-cycle PCR using KAPA HiFi HotStart PCR Kit (Roche). PCR fragments were purified using AMPure XP beads (Beckman Coulter) at a 1.8 bead to sample ratio. Libraries were prepared using the Nanopore Native Barcoding Kit 24 V14 (SQK-NBD114.24) according the manufacturer’s protocol and sequenced on a MinION Flow Cell.
Libraries were prepared using the Nanopore Native Barcoding Kit 24 V14 (SQK-NBD114.24) according the manufacturer’s protocol and sequenced on a MinION Flow Cell.

treatment_protocol: Electroporation of RNPs into keratinocytes was performed using the Neon transfection system (Thermo Fisher Scientific) under the following conditions: 1,400 Volt, 20 ms, 2 pulses. 250,000 cells were treated with Alt-R™ SpCas9 Nuclease V3 or Alt-R™ SpCas9 D10A Nickase V3 (IDT) together with the gRNA (IDT) at a ratio of 4:1 (3µg + 750ng).

value: Keratinocytes

tag: sample type

value: PCR-derived amplicons from gDNA

value: JEB, homozygous c.466_467delCA


title: Long-read sequencing of COL17A1 on-target site on sample treated with Cas9 double nickase + ssODN

description:
demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-D10ACas9n-g3+4 + ssODN

value: JEB, homozygous c.3899_3900delCT


title: Long-read sequencing of COL17A1 on-target site of untreated control + ssODN

description:
used as non-treated control; demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-COL17A1-UT + ssODN

value: non-treated+ssODN


title: Long-read sequencing of LAMA3 on-target site of untreated control

description:
used as non-treated control; demultiplexed sequences
LAMA3_LR_read coverage analysis.xlsx
LR-LAMA3-UT

value: non-treated


title: Long-read sequencing of LAMA3 on-target site on sample treated with Cas9 nuclease g6

description:
demultiplexed sequences
LAMA3_LR_read coverage analysis.xlsx
LR-Cas9-g6


title: Long-read sequencing of COL17A1 on-target site of untreated control

description:
used as non-treated control; demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-COL17A1-UT


title: Long-read sequencing of COL17A1 on-target site on sample treated with Cas9 double nickase

description:
demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-D10ACas9n-g3+4


title: Long-read sequencing of COL17A1 on-target site on sample treated with Cas9 nuclease g4

description:
demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-Cas9-g4


title: Long-read sequencing of COL17A1 on-target site on sample treated with Cas9 nuclease g3

description:
demultiplexed sequences
COL17A1_LR_read coverage analysis.xlsx
LR-Cas9-g3


title: Long-read sequencing of COL7A1 on-target site on sample treated with Cas9 double nickase + ssODN

description:
demultiplexed sequences
COL7A1+ssODN_LR_read coverage analysis.xlsx
LR-D10ACas9n-g1+2 + ssODN

value: RDEB223, homozygous c.425A>G


title: Long-read sequencing of COL7A1 on-target site on sample treated with Cas9 nuclease + ssODN g2

description:
demultiplexed sequences
COL7A1+ssODN_LR_read coverage analysis.xlsx
LR-Cas9-g2 + ssODN


title: Long-read sequencing of COL7A1 on-target site of untreated control + ssODN

description:
used as non-treated control; demultiplexed sequences
COL7A1+ssODN_LR_read coverage analysis.xlsx
LR-COL7A1-UT + ssODN


title: Long-read sequencing of COL7A1 on-target site on sample treated with Cas9 nuclease + ssODN g1

description:
demultiplexed sequences
COL7A1+ssODN_LR_read coverage analysis.xlsx
LR-Cas9-g1 + ssODN


title: Amp-COL7A1-UT

description:
PCR-derived amplicons from gDNA
used as non-treated control; demultiplexed sequences

data_processing:
Reads were demultiplexed by employing a custom pipeline that allows up to 4 mismatches in the barcode sequence. Obtained reads were aligned using Minimap2 v. 2.24-r1122,60 and further processed with Samtools. Deletions and insertions were counted from the cigar string in a window of 200 bp around the cleavage site using a custom script. Deletion read coverage was calculated by subtracting the read coverage with deletions from the read coverage without the deletions, and by normalizing the reads to the total reads for each sample. The values obtained from the untreated control where subtracted from the treated samples to decrease sequencing bias. Insertion sequences were extracted from the SAM file and aligned to the reference amplicon using a blast like algorithm (LAST v.1411).
Assembly: hg38
Supplementary files format and content: table file with read coverage

source_name: Long-read sequencing of on-target site of untreated control

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
A 5 kb amplicon spanning the COL7A1 target site was amplified from 200 ng of genomic DNA by a 30-cycle PCR using KAPA HiFi HotStart PCR Kit (Roche). PCR fragments were purified using AMPure XP beads (Beckman Coulter) at a 1.8 bead to sample ratio. Libraries were prepared using the Nanopore Ligation Sequencing Kit V14 (SQK-LSK114) according the manufacturer’s protocol and sequenced on a MinION Flow Cell.
Libraries were prepared using the Nanopore Ligation Sequencing Kit V14 (SQK-LSK114) according the manufacturer’s protocol and sequenced on a MinION Flow Cell.

value: Patient-derived keratinocytes


title: Amp-D10ACas9n-g1

description:
PCR-derived amplicons from gDNA
demultiplexed sequences

source_name: Long-read sequencing of on-target site on sample treated with Cas9 single nickase


title: Amp-Cas9-g2

source_name: Long-read sequencing of on-target site on sample treated with Cas9 nuclease


title: Amp-D10ACas9n-g1+2

source_name: Long-read sequencing of on-target site on sample treated with Cas9 double nickase


title: Amp-Cas9-g1


title: 4sU-seq_Xist-KO_Female_rep5

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
On the NovaSeq platform, intensity extraction from images, base calling and quality score assignment during the sequencing were performed by software RTA2.
Adapters were removed from raw data using Trim Galore with the following parameters: (--stringency 5 -e 0.2 --length 35 --r1 36 --r2 36). After PCR duplicates removal, pre-processed reads were aligned to two parental mouse genomes separately using STAR (v2.7.10a) in the 2-pass mode, with the same parameters as they were used in the So-smart-seq alignment, except that the default maximum number of mismatches per read pair was used.
Allelic reads separation was also carried out based on the approach described in So-smart-seq analysis.
For mutation rate analysis, the comparison of each single base between each type of allelic reads (cast, mus or neutral reads) and genome template in the alignment was collected using sam2tsv, from which all types of mismatches along with their associated Reads were retrieved. Only the mutations on the sense stand of the gene exons were considered. Mismatches overlapping with CAST/EiJ SNPs were ignored. The conversion rate of each mutation type was then calculated by dividing the total coverage of a given mutation type by the total coverage (including both matched and mismatched) of the corresponding nucleotide in the whole transcriptome.
In WT crosses, genes with at least 6 allelic reads carrying T->C conversion in each sample were considered for gene category analysis, and for Xist-KO crosses, genes with at least 2 allelic reads carrying T->C conversion in each sample were used due to the slightly lower sample qualities.
assembly: mm10
processed data files format and content:  .txt files showing the number of reads carrying T->C conversion in each gene from compsoite (comp) reads
processed data files format and content:  .txt file showing total gene read counts from  compsoite (comp) reads.
processed data files format and content:  .txt file showing allelic T->C mismatch read counts for Category 1 and 4 in all replicates

organism:
Mus musculus
Mus musculus castaneus

source_name: Single preimplantation embryo

growth_protocol: One-cell zygotes at around E0.75 were collected and cultured in Advanced KSOM embryo medium (Millipore)

extract_protocol:
Single embryo was lysed in 3ul lysis solution containing 2.5ul of 200mM Sodium Phosphate buffer pH=8, 0.2ul of RNase inhibitor, 0.1ul of 4sU spike-in, and 0.2ul 10% NP-40
Libraries were prepared as previous described (Hendriks et al., 2019), with a few modifications. 10ul of Dynabeads (MyOne Dynabeads Strepavidin C1) were transferred to a clean PCR tube, and washed twice with 10ul of Buffer A (0.1M NaOH, 0.05M NaCl), twice with 10ul of Buffer B (0.1M NaCl), followed by the incubation in 20ul oligo-dT buffer containing 5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl and 50uM oligo-dT (/5Biotin-TEG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, IDT) at room temperature (RT) for 15 min with agitation. The incubated beads were then washed twice with 20ul 1x B&W buffer (5mM Tris-HCl pH7.5, 0.5mM EDTA, 1M NaCl), and resuspended in 30ul freshly prepared resuspension buffer (5.5ul RNase inhibitor (40U/ul) in 26.5ul RNase-free water) on ice. Lysis from each single embryo was kept on ice after thawing from -80C, and 2ul of processed beads were added into each tube, followed by a brief vortex and incubation for 20 minutes at RT with agitation to allow complete RNA binding to beads. 5ul of fresh alkylation solution (20mM IAA in DMSO) was added into each sample with gentle pipetting. Samples were then spined briefly and incubated at 50C for 15 min with agitation. After alkylation, samples were briefly spined and immediately put on the magnetic rack, followed by the addition of 10ul of STOP solution (2x Superscript II buffer, 0.3% Tween-20 and 60mM DTT) with gentle pipetting. The samples were spined again and kept on the magnetic rack for 5 min at RT. On the magnetic rack, after removing the supernatant from the beads that binds PolyA RNAs, 10ul of newly prepared RT mix (1X  Superscript II RT buffer, 5mM DTT, 0.8U/ul RNase inhibitor, 1M Betaine, 10mM MgCl2, 1mM dNTPs and 1uM GGrG oligo (iCiGiCGGAGTTCAGACGTGTGCTCTTCCGATCTrGrG+G)) was immediately added toward the side of the immobilized beads into the tube to perform the RT using the following temperature: 42C for 90 min, 10 cycles of 50C for 2 min followed by 42C for 2min. The samples were vortexed every 20 min during the RT. The first strand cDNA products from each embryo were next amplified by 22 cycles of PCR (F: GTGACTGGAGTTCAGACGTGTGCTCTTC; R: AAGCAGTGGTATCAACGCAGAGT) in a 30ul reaction and purified with Ampure XP beads at 1:1 ratio. The PCR products were further processed using Nextera XT DNA library preparation kit (Illumina) with multi-indexes, as previously described. The resulting libraries were pooled and subject to sequencing.

treatment_protocol: Labeled embryos were treated with 90uM 4-thiouridine (Sigma) in Advanced KSOM embryo medium, with 10-15 embryos in every 30ul of medium. Medium was changed very 6 hours.

value: Single preimplantation embryo

value: Paternal Xist-KO

value: Female

value: CAST/EiJ x 129S1/SvImJ (Xist-KO)

value: late 2-cell


title: Long-read sequencing of LAMA3 on-target site on sample treated with Cas9 double nickase

description:
demultiplexed sequences
LAMA3_LR_read coverage analysis.xlsx
LR-D10ACas9n-g5+6


title: 4sU-seq_Xist-KO_Female_rep2

data_processing:
On the NovaSeq platform, intensity extraction from images, base calling and quality score assignment during the sequencing were performed by software RTA2.
Adapters were removed from raw data using Trim Galore with the following parameters: (--stringency 5 -e 0.2 --length 35 --r1 36 --r2 36). After PCR duplicates removal, pre-processed reads were aligned to two parental mouse genomes separately using STAR (v2.7.10a) in the 2-pass mode, with the same parameters as they were used in the So-smart-seq alignment, except that the default maximum number of mismatches per read pair was used.
Allelic reads separation was also carried out based on the approach described in So-smart-seq analysis.
For mutation rate analysis, the comparison of each single base between each type of allelic reads (cast, mus or neutral reads) and genome template in the alignment was collected using sam2tsv, from which all types of mismatches along with their associated Reads were retrieved. Only the mutations on the sense stand of the gene exons were considered. Mismatches overlapping with CAST/EiJ SNPs were ignored. The conversion rate of each mutation type was then calculated by dividing the total coverage of a given mutation type by the total coverage (including both matched and mismatched) of the corresponding nucleotide in the whole transcriptome.
In WT crosses, genes with at least 6 allelic reads carrying T->C conversion in each sample were considered for gene category analysis, and for Xist-KO crosses, genes with at least 2 allelic reads carrying T->C conversion in each sample were used due to the slightly lower sample qualities.
assembly: mm10
processed data files format and content:  .txt files showing the number of reads carrying T->C conversion in each gene from compsoite (comp) reads
processed data files format and content:  .txt file showing total gene read counts from  compsoite (comp) reads.
processed data files format and content:   .txt file showing allelic T->C mismatch read counts for Category 1 and 4 in all replicates


title: 4sU-seq_Xist-KO_Female_rep7


title: 4sU-seq_Xist-KO_Female_rep3


title: bulk-RNAseq_mESC_rep2

data_processing:
On the NovaSeq platform, intensity extraction from images, base calling and quality score assignment during the sequencing were performed by software RTA2.
Similar to Alkylation Dependent RNAseq analysis, PCR duplicates were removed by Trim Galore and reads separately aligned to reconstructed mus/129 and Cast genomes using STAR with the same parameters, except that a maximum of 8 mismatches were allowed per read pair. Final allele-specific mapping to reference mm10 genome was generated based on SNPs. Uniquely aligned concordantly mapped reads overlapping with gene exons were counted using featureCounts
Allelic reads separation was also carried out based on the approach described in So-smart-seq analysis.
assembly: mm10
processed data files format and content: alignment .bw files showing RNA coverage on + and - strand from compsoite (comp) reads
processed data files format and content: .txt files showing gene counts from compsoite (comp) reads

growth_protocol: mES cells were grown in feeder-free 2i medium (DMEM/F12 media, Neurobasal media, 2% Hyclone FBS (Sigma), N2 and B27 supplements, Glutamax, 1xPen/Strep, 0.1mM βME, and 1000U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein (Sigma, ESG1107)) supplemented with 1uM PD0325901 and 3uM of CHIR99021 (Selleck Chemicals) at 37°C with 5% CO2

extract_protocol:
TRIzol
rRNAs were depleted using RiboMinus Eukaryote Kit v2 (Thermo Fisher Scientific) following manufacturer’s protocol. RNA-seq libraries were prepared in two biological replicates using NEBNext Ultra II Directional RNA Second Strand Synthesis Module and NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.

value: mouse ES cell

value: TsixTST/+

value: 129S1/SvImJ x CAST/EiJ

value: undifferentiated


title: 4sU-seq_Xist-KO_Female_rep6


title: 4sU-seq_control_Xist-KO_Female_rep6

value: no-4sU control


title: bulk-RNAseq_mESC_rep1


title: 4sU-seq_Xist-KO_Female_rep1


title: 4sU-seq_control_Xist-KO_Female_rep4


title: 4sU-seq_control_Xist-KO_Male_rep3

value: wild type (CM)

value: Male


title: 4sU-seq_control_Xist-KO_Female_rep5


title: 4sU-seq_4sU_Female_rep12

value: wild type (MC)

value: C57BL/6J x CAST/EiJ


title: 4sU-seq_Xist-KO_Female_rep4


title: 4sU-seq_4sU_Female_rep11


title: 4sU-seq_control_Xist-KO_Male_rep2


title: 4sU-seq_4sU_Female_rep10


title: 4sU-seq_4sU_Male_rep9


title: 4sU-seq_4sU_Female_rep6


title: 4sU-seq_4sU_Male_rep7


title: 4sU-seq_4sU_Female_rep5


title: Amp-D10ACas9n-g2


title: 4sU-seq_4sU_Male_rep3


title: 4sU-seq_4sU_Male_rep1


title: 4sU-seq_4sU_Female_rep2


title: 4sU-seq_no-4sU_Female_rep6


title: 4sU-seq_no-4sU_Female_rep5


title: 4sU-seq_no-4sU_Male_rep1


title: 4sU-seq_no-4sU_Female_rep3


title: RG0095 fermentation 72 h biol rep 3 [C_3]

city: NanJing

first: Chi

state: Jiangsu

address: 1 WenYuan Road

department: School of Food Science and Pharmaceutical Engineering

institute: Nanjing Normal  University

description: Sample C_3

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic. The readscontaining ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each genewere obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq (2012) functions estimate Size Factors and nbinomTest. P value < 0.05 and fold Change >2 or fold Change < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using StringTie . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofil. SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: Aspergillus niger 513.88
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample

organism: Aspergillus niger

source_name: mycelium

extract_protocol:
RNA was harvested using mirVana™ miRNA ISOlation Kit, Ambion-1561. 4 μg of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit and other kits following manufacture’s protocols.

value: mycelium

value: ATCC 1015

value: {delta}oahA, pyc, mdhC, Pgpd-C4T318


title: 4sU-seq_no-4sU_Male_rep2

value: Single preimplantation embryo


title: RG0095 fermentation 72 h biol rep 2 [C_2]

description: Sample C_2


title: 4sU-seq_control_Xist-KO_Male_rep1


title: RG0095 control seed 20 h biol rep 2 [A_2]

description: Sample A_2


title: Colon wall, Normal 51

city: Worcester

first: Jing

last: Wang

address: 100 Research Drive

institute: AbbVie

description:
GTG-039-30
log2TPM.30.samples.Wall.txt

data_processing:
The short reads in fastq format underwent quality control using FastQC (Andrews S. (2010).
Subsequently, reads were quantified at the transcript level using Kallisto [16] pseudoalignment against Ensembl human reference GRCh38 and gene annotation file and aggregated to gene-level counts using R package “tximport”
The raw RNAseq count matrix data were further normalized and processed using the "limma" package [18] from Bioconductor to generate differential expression profiles.
Assembly: Ensembl human reference GRCh38
Supplementary files format and content: TPM

source_name: Colon wall

extract_protocol:
RNA extraction was conducted using the Clontech nucleospin RNA XS kit (Takara Bio, Mountain View, CA, USA) according to the manufacturer's protocol
For sequencing library preparation, 1.5 μg of total RNA was utilized with the TruSeq mRNA Seq kit (Illumina, San Diego, CA, USA).

value: Colon wall

tag: disease state

value: Normal

tag: inflammatory state

value: Non-Inflamed


title: Colon wall, Normal 49

description:
GTG-039-25
log2TPM.30.samples.Wall.txt


title: 4sU-seq_4sU_Male_rep8

value: late 2-cell


title: embryo, 4-8 cell

city: Knoxville

first: Jianbin

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

data_processing:
Only read 1 (R1) files were processed. Reads containing two sequential telomeric repeats (TTAGGCTTAGGC or GCCTAAGCCTAA) were filtered from the data using an in-house Perl script
Reads were mapped to the appropriate genome with Bowtie2 (local alignment) and processed with SAMtools
For samples treated with restriction enzyme BEDTools intersect was used to remove reads mapped to restriction sites
The 5’-end position of each read was mapped, separated by strand, and normalized to ten million genome-mapped reads using BEDtools genomecov
The mapping results were converted to bigWig format using bedGraphToBigWig
To analyze new telomere addition during PDE developmental stages, END-seq reads containing two consecutive telomere repeats (filtered in step 1) were converted to the G-rich strand (TTAGGC).
Reads were mapped to the genome with Bowtie2 end-to-end alignment
Mapped reads were false-positive telomeric reads. Unmapped reads were trimmed with fastx_clipper “-v -n -l 25 -a TTAGGCTTAGGC” parameters.
Trimmed reads were mapped to the genome with bowtie2 (local alignment) and processed as described above except except the 3’-positions (the sites where new telomeres are added) rather than 5’-positions were obtained with BEDTools genomecov
Assembly: Ascaris suum ASM1343314v1, Parascaris univalens (Pu_v2)
Supplementary files format and content: bigWig file containing the 5' end of reads on the forward strand
Supplementary files format and content: bigWig file containing the 5' end of reads on the reverse strand
Supplementary files format and content: bigWig file with the 3' end of reads on the forward strand which contained two telomeric repeats (TTAGGCTTAGGC)
Supplementary files format and content: bigWig file with the 3' end of reads on the reverse strand which contained two telomeric repeats (TTAGGCTTAGGC)
Library strategy: END-seq

organism: Parascaris univalens

source_name: Embryo

extract_protocol:
Ascaris females were collected, and the fertilized embryos (0hr, 1-cell before prenuclear fusion) were harvested and processed as previously described (Wang et al. 2011, Wang et al. 2014). Ascaris 0hr samples were incubated at 30°C with constant shaking for the desired time (from 50hr to 98hr). For all molecular experiments, the eggshells were first de-coated with bleach treatment (0.4 M KOH, 2% sodium hypochlorite) for 1.5 hours at 30°C. Parascaris samples were collected as described (Simmons et al. 2023, Wang et al. 2017). Parascaris eggs were prepared similarly to Ascaris, except the incubation was carried out at 37°C and the embryonation time was shorter (10-14hr).
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Embryos were embedded in agarose plugs. Some plugs were treated with the restriction enzymes as internal controls. Plugs were treated with exonuclease VII and exonuclease T. Blunt ends were A-tailed and capped with END-seq adaptor 1 (Canela et al. 2016). Plugs were melted and DNA was sheared to 200-300 bp with a Covaris M220 focused ultrasonicator. DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads MyOne Streptavidin C1. END-seq adaptor 2 was ligated to the sheared ends of the A-tailed DNA fragments. The hairpins within the adaptors were digested with USER, and the DNA was amplified with Illumina TruSeq primers and barcodes. The following modifications were made to the END-seq protocol to capture break ends with different features. For the direct capture method, we excluded the exonuclease VII and exonuclease T treatments. For the all-END protocol, the plugs were treated with T4 polymerase (with dNTPs).

value: Embryo

value: 4-8 cell


title: RG0095 control seed 20 h biol rep 3 [A_3]

description: Sample A_3


title: Colon wall, Normal 50

description:
GTG-039-28
log2TPM.30.samples.Wall.txt


title: embryo, 1-2 cell

value: 1-2 cell

value: FseI


title: Colon wall, Normal 53

description:
GTG-039-38
log2TPM.30.samples.Wall.txt


title: Colon wall, Normal 47

description:
GTG-039-20C
log2TPM.30.samples.Wall.txt


title: 4sU-seq_no-4sU_Female_rep7

value: Female

value: no-4sU control


title: 4sU-seq_4sU_Female_rep4


title: RG0095 control seed 20 h biol rep 1 [A_1]

description: Sample A_1


title: RHA1-EG on 30 mM ethylene glycol, mid-log phase, rep3

city: Vancouver

first: Raphael

last: Roccor

email: r.roccor@gmail.com, leltis@mail.ubc.ca

state: BC

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: The University of British Columbia

description:
RHA1-EG_EG-vs-acetate
RHA1-EG_EG-vs-RHA1_EG
RHA1-EG_EG-vs-RHA1_glycolate

data_processing:
RNA reads were subject to quality control, filtered and trimmed using Trimmomatic 0.3.6 with default settings.
Transcripts were quantified using Salmon 0.8.1 and mapped to the RHA1 genome using the NCBI reference sequence for the chromosome and the three plasmids (NC_008268.1, NC_008269.1, NC_008270.1, NC_008271.1).
Differential expression was analyzed using DeSeq2 1.18.1 (20) in RStudio 1.3.1 and  R version 4 (21) with false discovery rate correction.
Data tables were compared by using tidyverse 1.3.0 in RStudio.
Assembly: NC_008268.1, NC_008269.1, NC_008270.1, NC_008271.1
Supplementary files format and content: tab-delimited tsv files includes base mean and log2 fold-change values for each sample compared to the reference

organism: Rhodococcus jostii

growth_protocol: 50 ml cultures at OD600 of 0.05 were grown on 30 mM acetate, ethylene glycol, or glycolate in M9 Goodies medium to mid-log phase. Ten ml cultures were centrifuged at room temperature and cell pellet was subjected to RNA extraction.

extract_protocol:
The cell pellets were suspended in 2 ml TRIzol™ (Thermo Fisher Scientific) and stored at -80 °C. One ml of cells in TRIzol™ were transferred to 2 ml screw cap tubes with glass-beads and lysed by using a MP Biochemical bead-beater (three rounds for 45 sec at power 6.5) with a 10 min incubation step at 60 °C in between. RNA extraction was then proceeded according to the manufacturer’s instructions and treated with TURBO™ DNase (Thermo Fisher Scientific). Quality and quantity of nucleic acids were assessed using 1% (w/v) agarose gel electrophoresis and Qubit fluorometric quantitation (Thermo Fisher Scientific), prior to storage at −80°C. Genomic DNA contamination was assessed by using RT-qPCR and probes for the sigA marker gene.
One μg of rRNA was depleted using the NEBNext® rRNA Depletion Kit (Bacterial) and the libraries were prepped with NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. The quality of the rRNA-depleted samples and the libraries were checked by using a Bioanalyzer 2100 and the RNA 6000 Nano kit (Agilent).

value: mid-log growth phase

value: EG adapted cells

value: 30 mM ethylene glycol


title: RHA1-EG on 30 mM ethylene glycol, mid-log phase, rep1


title: RHA1-EG on 30 mM ethylene glycol, mid-log phase, rep2


title: RHA1 on 30 mM ethylene glycol, mid-log phase, rep3

description:
RHA1_acetate-vs-EG
RHA1_EG-vs-glycolate

value: WT


title: 4sU-seq_no-4sU_Female_rep4

value: wild type (MC)

value: C57BL/6J x CAST/EiJ


title: Colon wall, Normal 48

description:
GTG-039-18
log2TPM.30.samples.Wall.txt


title: RHA1 on 30 mM ethylene glycol, mid-log phase, rep2

description:
RHA1_acetate-vs-EG
RHA1_EG-vs-glycolate


title: RHA1 on 30 mM ethylene glycol, mid-log phase, rep1

description:
RHA1_acetate-vs-EG
RHA1_EG-vs-glycolate


title: Colon wall, Normal 46

description:
GTG-039-16
log2TPM.30.samples.Wall.txt


title: RHA1 on 30 mM glycolate, mid-log phase, rep3

description:
RHA1_acetate-vs-glycolate
RHA1_EG-vs-glycolate

value: 30 mM glycolate


title: RHA1 on 30 mM glycolate, mid-log phase, rep2


title: Colon wall, Normal 52

description:
GTG-039-32
log2TPM.30.samples.Wall.txt

value: Colon wall


title: RG0095 fermentation 72 h biol rep 1 [C_1]

description: Sample C_1

value: mycelium

value: ATCC 1015

value: {delta}oahA, pyc, mdhC, Pgpd-C4T318


title: Colon wall, Normal 45

description:
GTG-039-10
log2TPM.30.samples.Wall.txt

value: Normal

value: Non-Inflamed


title: Colon wall, Crohn's disease, Non-Inflamed 44

description:
GTG-039-72
log2TPM.30.samples.Wall.txt

value: Crohn's disease


title: RHA1 on 30 mM glycolate, mid-log phase, rep1


title: Colon wall, Crohn's disease, Non-Inflamed 43

description:
GTG-039-68
log2TPM.30.samples.Wall.txt


title: RHA1 on 30 mM acetate, mid-log phase, rep1

description:
RHA1_acetate-vs-glycolate
RHA1_acetate-vs-EG

value: 30 mM acetate


title: Colon wall, Crohn's disease, Non-Inflamed 42

description:
GTG-039-64
log2TPM.30.samples.Wall.txt


title: Blood, cRBD3 immunization, rep1 [BCR-seq]

city: 昆明市

first: 然

last: 安

state: 云南省

address: 茭菱路935号医学生物学研究所

department: Institute of Medical Biology

institute: Peking Union Medical College

data_processing:
Raw sequencing data was first filtered by SOAPnuke (version 1.6.0), low-quality reads and the reads contaminated with adaptor sequences were discarded. Low-quality reads and the reads contaminated with adaptor sequences were discarded.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster.
The de-duplicated consensus sequences were used for BCR-seq analysis. They were mapped to the international ImMunoGeneTics (IMGT) database by Lefranc et al. (DOI: 10.1093/nar/gku1056) usingMiXCR software (version 3.0.3) to obtain V,D and J fragment, rearrangement and CDR3 sequences.
As the gene specific primers (GSP) for immunoglobulin subclasses (IgM, IgA, IgG, IgD, IgE, IgK, and IgL) were used for amplification during library construction, immunoglobulin subclasses information was included at the start of read2 of the sequencing data. Thus, immunoglobulin subtyping can be performed.
Assembly: mm10
Supplementary files format and content: Tab-segmented txt files contained the information of VDJ segments of IGH subtypes aligned to the database in each sample.
Library strategy: BCR-seq

source_name: Whole blood

extract_protocol:
Total RNAs were extracted from blood samples using PAXgene Blood RNA Kit (Qiagen, Cat. No. 762174) following the manufacturer's instructions. 2 μg total RNAs were used for the construction of sequencing libraries.
About 2 μg total RNA of each sample were used for BCR sequencing. Library preparation using KC-DigitalTM Stranded BCR-seq Library Prep Kit for Illumina® 150 (Seqhealth Technology Co., Ltd., Wuhan, China, Cat. No. DT0815-02) following the manufacturer’s instruction.

value: Whole blood

value: cRBD3 immunized

value: Balb/c


title: Blood, cRBD3 immunization, rep3 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: Blood, cRBD2 immunization, rep3 [BCR-seq]

address: 茭菱路935号医学生物学研究所

value: cRBD2 immunized


title: Blood, cRBD2 immunization, rep2 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: Colon wall, Crohn's disease, Non-Inflamed 41

description:
GTG-039-54
log2TPM.30.samples.Wall.txt


title: Colon wall, Crohn's disease, Non-Inflamed 40

description:
GTG-039-34037
log2TPM.30.samples.Wall.txt


title: Blood, cRBD2 immunization, rep1 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: Blood, Cntrol, rep3 [BCR-seq]

address: 茭菱路935号医学生物学研究所

value: untreated


title: Colon wall, Crohn's disease, Non-Inflamed 39

description:
GTG-039-14
log2TPM.30.samples.Wall.txt


title: Colon wall, Crohn's disease, Non-Inflamed 38

description:
GTG-039-12
log2TPM.30.samples.Wall.txt


title: Blood, Cntrol, rep2 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: Blood, cRBD1 immunization, rep1 [BCR-seq]

address: 茭菱路935号医学生物学研究所

value: cRBD1 immunized


title: Colon wall, Crohn's disease, Non-Inflamed 37

description:
GTG-039-69
log2TPM.30.samples.Wall.txt


title: Blood, cRBD1 immunization, rep3 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: RHA1 on 30 mM acetate, mid-log phase, rep3

value: mid-log growth phase

value: WT


title: Colon wall, Crohn's disease, Non-Inflamed 36

description:
GTG-039-3c
log2TPM.30.samples.Wall.txt


title: In vitro-2w-2

city: beijing,China

first: Hao

address: No. 5, Yiheyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested. The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample

source_name: Heart

extract_protocol:
RNA was harvested using ZYMO Direct-zol RNA Micro Prep (ZYMO). 1.0 ug of total RNA was used for the constructlon of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit folowing manufacturer's protocols.

value: Heart

value: MICFs

value: primary cell

value: MGTMyoS overexpression

value: vitro


title: control

data_processing:
ChIP-seq reads were trimmed by Trimmomatic software
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie. The duplicates were removed by samtools markdup command
Peaks were called uing MACS v2.1.4, differential peaks were detected by macs2 bdgdiff.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
In brief, 0.1 million cells were collected for each sample. The following primary antibodies were used rabbit anti-HA antibody HA-Tag (CST, #3724s,1:500). Goat anti-Rabbit antibody (1:100; Vazyme) was used as the secondary antibody. pAG-Tn5 was purchased from Vazyme and used for each CUT&Tag reaction building a library according to the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro protocol (Vazyme, #TD904, Nanjing, China).
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme).

tag: cut&tag antibody

value: HA-tag (CST,#3724S)


title: STAT1-i


title: Colon wall, Crohn's disease, Inflamed 35

description:
GTG-039-70
log2TPM.30.samples.Wall.txt

value: Colon wall

value: Inflamed


title: In vitro-2w-1


title: Blood, cRBD3 immunization, rep2 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: In vivo-2w-2

value: Vivo


title: RHA1 on 30 mM acetate, mid-log phase, rep2

value: 30 mM acetate


title: In vivo-2w-1


title: In vitro-1w-2


title: Colon wall, Crohn's disease, Inflamed 34

description:
GTG-039-62
log2TPM.30.samples.Wall.txt

value: Crohn's disease


title: Colon wall, Crohn's disease, Inflamed 33

description:
GTG-039-60
log2TPM.30.samples.Wall.txt


title: In vitro-1w-1


title: In vivo-1w-2


title: In vivo-1w-1


title: Colon wall, Crohn's disease, Inflamed 32

description:
GTG-039-56
log2TPM.30.samples.Wall.txt


title: Blood, Cntrol, rep1 [BCR-seq]

address: 茭菱路935号医学生物学研究所

value: Whole blood

value: Balb/c


title: Blood, cRBD1 immunization, rep2 [BCR-seq]

address: 茭菱路935号医学生物学研究所


title: Colon wall, Crohn's disease, Inflamed 31

description:
GTG-039-44
log2TPM.30.samples.Wall.txt


title: Colon wall, Crohn's disease, Inflamed 30

description:
GTG-039-41
log2TPM.30.samples.Wall.txt


title: shIfnar2


title: Liver, Wild, archival, M37976, MNase

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

country: Australia

institute: CSIRO

description:
C57BL6_Archival_MNase_pooled.wig
C57BL6_Archival_MNase_pooled-vs-C57BL6_M37810_Archival_INPUT.wig
C57BL6_Archival_MNase_pooled-vs-Wild_Archival_MNase_pooled.wig

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: For deduplication with the IDT library unique molecular identifiers (UMIs), we converted the Fastq files to BAM format using FastqToSam (PICARD v 2.9.2), extracted the UMIs with ExtractUmisFromBam (FGBio v. 1.3.0) and restored the files to FastQ format with SamToFastq (PICARD). We aligned raw reads using kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE and utilising UMIs. We computed and corrected for GC-bias with deepTools version 3.5.1 using an effective genome size of 2,818,974,548 bp
Peak analysis: We analysed regional occupancy after quantile normalisation of sequencing depth differences between treatment and control to calculate differential occupancy values with the dtriple function in DANPOS3. We analysed all mouse alignments both as individual samples and as pools of three replicates. For profiling the effect of FAIRE and MNase treatment, we used a corresponding input control. For differential peak analyses, we ran pooled laboratory strain versus pooled wild caught as input for mouse.
Assembly: GRCm38.p6 RefSeq assembly
Supplementary files format and content: WIG files are provided for all individual samples and DANPOS3 comparions with input controls and between conditions.

source_name: liver

extract_protocol:
We cryopulverised liver tissue and applied either the standard FAIRE and MNase assays (fresh-frozen tissue) or our optimised FAIRE and MNase assays (archival formalin-fixed) to recover differentially accessible gDNA fragments.
xGen cfDNA & FFPE DNA Library Prep Kit (IDT)

tag: specimen id

value: liver

tag: preservation

value: archival formalin

value: F


title: Liver, Wild, archival, M37976, INPUT

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: For deduplication with the IDT library unique molecular identifiers (UMIs), we converted the Fastq files to BAM format using FastqToSam (PICARD v 2.9.2), extracted the UMIs with ExtractUmisFromBam (FGBio v. 1.3.0) and restored the files to FastQ format with SamToFastq (PICARD). We aligned raw reads using kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE and utilising UMIs. We computed and corrected for GC-bias with deepTools version 3.5.1 using an effective genome size of 2,818,974,548 bp
Peak analysis: We analysed regional occupancy after quantile normalisation of sequencing depth differences between treatment and control to calculate differential occupancy values with the dtriple function in DANPOS3. We analysed all mouse alignments both as individual samples and as pools of three replicates. For profiling the effect of FAIRE and MNase treatment, we used a corresponding input control. For differential peak analyses, we ran pooled laboratory strain versus pooled wild caught as input for mouse.
Assembly: GRCm38.p6 RefSeq assembly
Supplementary files format and content: WIG files are provided for all individual samples and DANPOS3 comparions with input controls and between conditions.
Library strategy: Input for FAIRE-seq & Mnase-seq

tag: tissue


title: Liver, Wild, fresh, M37976, MNase

description:
Wild_Archival_MNase_pooled.wig
Wild_Archival_MNase_pooled-vs-Wild_Archival_INPUT_pooled.wig
C57BL6_Archival_MNase_pooled-vs-Wild_Archival_MNase_pooled.wig

value: fresh frozen

tag: Sex


title: Liver, Wild, fresh, M37971, MNase

description:
Wild_Archival_FAIRE_pooled.wig
Wild_Archival_FAIRE_pooled-vs-Wild_Archival_INPUT_pooled.wig
C57BL6_Archival_FAIRE_pooled-vs-Wild_Archival_FAIRE_pooled.wig


title: Liver, Wild, fresh, M37976, FAIRE


title: Liver, Wild, fresh, M37976, INPUT


title: Colon wall, Crohn's disease, Inflamed 28

description:
GTG-039-73
log2TPM.30.samples.Wall.txt


title: Colon wall, Crohn's disease, Inflamed 27

description:
GTG-039-33
log2TPM.30.samples.Wall.txt


title: Liver, Wild, archival, M37971, MNase

description:
C57BL6_Archival_FAIRE_pooled.wig
C57BL6_Archival_FAIRE_pooled-vs-C57BL6_M37810_Archival_INPUT.wig
C57BL6_Archival_FAIRE_pooled-vs-Wild_Archival_FAIRE_pooled.wig


title: Liver, Wild, fresh, M37971, FAIRE


title: Liver, Wild, archival, M37971, INPUT


title: Colon mucosa, Normal 8

description:
UM20160413-035_161
log2TPM.30.samples.Mucosa.txt

source_name: Colon mucosa

value: Colon mucosa

value: Normal

value: Non-Inflamed


title: Liver, Wild, archival, M37971, FAIRE


title: Liver, Wild, fresh, M37971, INPUT


title: Liver, Wild, fresh, M37959, INPUT

description:
Wild_Archival_INPUT_pooled.wig
Wild_Archival_FAIRE_pooled-vs-Wild_Archival_INPUT_pooled.wig
Wild_Archival_MNase_pooled-vs-Wild_Archival_INPUT_pooled.wig

value: M


title: Liver, Wild, fresh, M37959, MNase


title: flag::alg-2(CD) FLAG IP, rep2

city: Québec

first: Martin

last: Simard

address: 9 McMahon

department: Oncology

institute: CHU de Québec-Université Laval Research Center

description: small RNA analysis

data_processing:
The samples are debarcoded
The adaptors are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
The reads were normalized to the total small RNAs including miRNAs, 22G-RNAs and 21U-RNAs
Assembly: C. elegans WS215
Supplementary files format and content: Normalised Reads Per million for analysis

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were grown on NGM plates with OP50 at 25°C.

extract_protocol:
Worms suspended and frozen in M9 solution were washed and resuspended in cold lysis buffer (10mM Potassium Acetate, 25mM Hepes-Potassium Hydroxide pH 7.0, 2mM Magnesium Acetate, 1mM DTT, 0.5% [v/v] Triton X-100 and protease inhibitors) before being lysed by shaking with (Next Advance RINO) bead lysis kit using bullet blender Storm 24. Then the extracts were centrifuged at 17,000g for 20min at 4˚C and the clarified supernatants were collected and processed for FLAG Immunoprecipitation. The immunoprecipitated beads were suspended in 2X PK buffer (100 mM Tris-Cl [pH 7.5], 200 mM NaCl, 1% [w/v] SDS) and digested with proteinase K at 50°C for 20 minutes. Finally, Trizol was used to extract the RNAs.
The extracted RNA was used as input for the NEBNext Multiplex Small RNA Library Kit and size selection is performed for miRNAs on gel (Bands corresponding to ~140 bp)

value: Embryo

tag: genotype

value: flag::alg-2(qbc81[D627A]) II

value: Whole worm

tag: ip antibody

value: FLAG


title: Colon mucosa, Crohn's disease, Inflamed 25

description:
UM20160627-040_193L-M
log2TPM.30.samples.Mucosa.txt

value: Inflamed


title: Liver, Wild, fresh, M37959, FAIRE


title: Bisulfite-seq_16C_CB_Female_rep2

data_processing:
On the HiSeq 2500 platform, intensity extraction from images, base calling and quality score assignment during the sequencing was performed by software RTA.
Additional adapters at the 3’ end and first 6 nucleotide bases from the 5’ end were trimmed from the raw reads, followed by the PCR duplicates removal.
The initial alignments of Bisulfite DNAseq data were carried out as previously described (Clark, S. J. et al., 2017). The processed reads were then aligned to both mm10 and pesudo-CAST genome using Bismark with the following parameters (--non_directional).
Due to the nature of bisulfite sequencing, CAST/EiJ SNPs including C to T, T to C, G to A and A to G were excluded from downstream allelic analysis to avoid false positive allelic decisions.
mm10
processed data files format and content: .bw files showing the rate of DNA methylation

extract_protocol:
Single embryo was lysed in RLT plus buffer (Qiagen).
Bisulfite DNAseq libraries were prepared following a previously published protocol, with some minimal modifications. Briefly, single embryo was lysed in RLT plus buffer (Qiagen), followed by the addition of unmethylated lambda DNA control. Genomic DNAs were treated with CT conversion reagent (EZ methylation kit, Zyon). After the purification using PureLink PCR Purifiation kit (ThermoFisher Scientific), DNAs were amplified 5 times using Preamp oligos and Klenow exo- polymerase (NEB). Amplified DNAs were depleted of single strand DNAs by adding exonuclease I, followed by the purification using Ampure XP beads. The second round of DNA synthesis reaction was carried out using Adapter 2 Oligos. Finally, all DNAs were purified and further amplified using 14 cycles of PCR. The yielded DNAs were purified and ready for bisulfite sequencing.

value: Single preimplantation embryo

tag: cell type

value: wild type (MC)

value: Female

value: C57BL/6J x CAST/EiJ

tag: treatment


title: Liver, Wild, archival, M37959, MNase

description:
C57BL6_Archival_FAIRE_pooled-vs-C57BL6_M37810_Archival_INPUT.wig
C57BL6_Archival_MNase_pooled-vs-C57BL6_M37810_Archival_INPUT.wig

value: liver


title: flag::alg-2(CD) Input, rep2

description: small RNA analysis

extract_protocol:
Worms suspended and frozen in M9 solution were washed and resuspended in cold lysis buffer (10mM Potassium Acetate, 25mM Hepes-Potassium Hydroxide pH 7.0, 2mM Magnesium Acetate, 1mM DTT, 0.5% [v/v] Triton X-100 and protease inhibitors) before being lysed by shaking with (Next Advance RINO) bead lysis kit using bullet blender Storm 24. Then the extracts were centrifuged at 17,000g for 20min at 4˚C and the clarified supernatants were collected. The supernatant was treated with 2X PK buffer (100 mM Tris-Cl [pH 7.5], 200 mM NaCl, 1% [w/v] SDS) and digested with proteinase K at 50°C for 20 minutes. Finally, Trizol was used to extract total RNA.
The extracted RNA was used as input for the NEBNext Multiplex Small RNA Library Kit and size selection is performed for miRNAs on gel (Bands corresponding to ~140 bp)

value: none (input)


title: flag::alg-2(CD) FLAG IP, rep1

description: small RNA analysis


title: Colon wall, Crohn's disease, Inflamed 29

description:
GTG-039-4
log2TPM.30.samples.Wall.txt

value: Colon wall

value: Crohn's disease


title: Bisulfite-seq_16C_CB_Female_rep1


title: Liver, Wild, archival, M37976, FAIRE

value: archival formalin

value: F


title: Colon mucosa, Crohn's disease, Non-Inflamed 17

description:
UM20160310-028_Univolved_125NL
log2TPM.30.samples.Mucosa.txt

value: Colon mucosa

value: Non-Inflamed


title: Liver, Wild, archival, M37959, INPUT

description:
Wild_Fresh_MNase_pooled.wig
Wild_Fresh_MNase_pooled-vs-Wild_Fresh_INPUT_pooled.wig
C57BL6_Fresh_MNase_pooled-vs-Wild_Fresh_MNase_pooled.wig

value: M


title: Bisulfite-seq_8C_CB_Female_rep1


title: Colon mucosa, Crohn's disease, Inflamed 24

description:
UM20150918-024-ML1
log2TPM.30.samples.Mucosa.txt


title: Colon mucosa, Normal 6

description:
FO20160616-038_NL-M
log2TPM.30.samples.Mucosa.txt

value: Normal


title: Liver, Wild, archival, M37959, FAIRE


title: Colon mucosa, Crohn's disease, Inflamed 26

description:
UM20160615-037_173L-M
log2TPM.30.samples.Mucosa.txt


title: flag::alg-2 FLAG IP, rep2

description: small RNA analysis

value: Embryo

value: alg-2::3xflag(qe23) II

value: Whole worm


title: Bisulfite-seq_8C_CB_Female_rep2

value: Single preimplantation embryo


title: flag::alg-2 Input, rep2

description: small RNA analysis


title: Colon mucosa, Normal 5

description:
FO20160412-034
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, fresh, M37816, FAIRE

description:
C57BL6_Fresh_MNase_pooled.wig
C57BL6_Fresh_MNase_pooled-vs-C57BL6_M37810_Fresh_INPUT.wig
C57BL6_Fresh_MNase_pooled-vs-Wild_Fresh_MNase_pooled.wig

value: fresh frozen


title: Liver, C57BL6, fresh, M37816, MNase


title: flag::alg-2 FLAG IP, rep1

description: small RNA analysis

value: FLAG


title: Colon mucosa, Crohn's disease, Non-Inflamed 16

description:
UM20160712-041_NL-M_202-1a
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, archival, M37816, MNase


title: Bisulfite-seq_4C_CB_Female_rep2

value: wild type (MC)

value: Female

value: C57BL/6J x CAST/EiJ


title: Bisulfite-seq_4C_CB_Female_rep3


title: flag::alg-2 Input, rep1

description: small RNA analysis

value: none (input)


title: Colon mucosa, Crohn's disease, Inflamed 23

description:
UM20160315-029_Involved_L131-M
log2TPM.30.samples.Mucosa.txt

value: Crohn's disease

value: Inflamed


title: Bisulfite-seq_4C_CB_Female_rep4


title: flag::alg-2(CD) Input, rep1

description: small RNA analysis

value: flag::alg-2(qbc81[D627A]) II


title: Bisulfite-seq_4C_CB_Female_rep1


title: Colon mucosa, Normal 7

description:
FO20160428-036_NL-M
log2TPM.30.samples.Mucosa.txt

value: Colon mucosa


title: Liver, C57BL6, archival, M37816, FAIRE

value: liver

value: archival formalin


title: Colon mucosa, Crohn's disease, Non-Inflamed 15

description:
UM20160627-040_191NL-M
log2TPM.30.samples.Mucosa.txt

value: Non-Inflamed


title: alg-1(CD) Input, rep3

description: small RNA analysis

value: Embryo


title: Liver, C57BL6, fresh, M37811, MNase

description:
Wild_Fresh_FAIRE_pooled.wig
Wild_Fresh_FAIRE_pooled-vs-Wild_Fresh_INPUT_pooled.wig
C57BL6_Fresh_FAIRE_pooled-vs-Wild_Fresh_FAIRE_pooled.wig

value: M


title: Bisulfite-seq_late2C_CB_Female_rep5

value: late 2-cell


title: Colon mucosa, Crohn's disease, Non-Inflamed 14

description:
UM20160620-039_181NL-M_R1
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, fresh, M37811, FAIRE


title: N2 ALG-1 IP, rep3

description: small RNA analysis

extract_protocol:
Worms suspended and frozen in M9 solution were washed and resuspended in cold lysis buffer (10mM Potassium Acetate, 25mM Hepes-Potassium Hydroxide pH 7.0, 2mM Magnesium Acetate, 1mM DTT, 0.5% [v/v] Triton X-100 and protease inhibitors) before being lysed by shaking with (Next Advance RINO) bead lysis kit using bullet blender Storm 24. Then the extracts were centrifuged at 17,000g for 20min at 4˚C and the clarified supernatants were collected and processed for ALG-1 Immunoprecipitation. The immunoprecipitated beads were suspended in 2X PK buffer (100 mM Tris-Cl [pH 7.5], 200 mM NaCl, 1% [w/v] SDS) and digested with proteinase K at 50°C for 20 minutes. Finally, Trizol was used to extract the RNAs.
The extracted RNA was used as input for the NEBNext Multiplex Small RNA Library Kit and size selection is performed for miRNAs on gel (Bands corresponding to ~140 bp)

value: N2 (Bristol)

value: Whole worm


title: Liver, C57BL6, archival, M37811, MNase


title: Colon mucosa, Crohn's disease, Inflamed 22

description:
UMASS-25_involved
log2TPM.30.samples.Mucosa.txt


title: Bisulfite-seq_late2C_CB_Female_rep3

value: Single preimplantation embryo


title: Bisulfite-seq_late2C_CB_Female_rep2

value: wild type (MC)


title: Bisulfite-seq_late2C_CB_Female_rep4

value: Female


title: Colon mucosa, Crohn's disease, Inflamed 21

description:
UM20160620-039_183L-M
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, archival, M37811, FAIRE

description:
C57BL6_Fresh_FAIRE_pooled.wig
C57BL6_Fresh_FAIRE_pooled-vs-C57BL6_M37810_Fresh_INPUT.wig
C57BL6_Fresh_FAIRE_pooled-vs-Wild_Fresh_FAIRE_pooled.wig


title: Liver, C57BL6, fresh, M37810, MNase

value: fresh frozen


title: alg-1(CD) ALG-1 IP, rep2

description: small RNA analysis


title: N2 Input, rep3

description: small RNA analysis

value: none (input)


title: Bisulfite-seq_late2C_CB_Female_rep1

value: C57BL/6J x CAST/EiJ


title: Colon mucosa, Crohn's disease, Non-Inflamed 12

description:
UM20160315-029_Uninvolved_NL134-M
log2TPM.30.samples.Mucosa.txt

value: Crohn's disease


title: alg-1(CD) ALG-1 IP, rep3

description: small RNA analysis


title: N2 ALG-1 IP, rep2

description: small RNA analysis


title: Colon mucosa, Crohn's disease, Non-Inflamed 11

description:
UM20160615-037_171NL-M
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, fresh, M37810, INPUT


title: Liver, C57BL6, fresh, M37810, FAIRE

description:
Wild_Fresh_INPUT_pooled.wig
Wild_Fresh_FAIRE_pooled-vs-Wild_Fresh_INPUT_pooled.wig
Wild_Fresh_MNase_pooled-vs-Wild_Fresh_INPUT_pooled.wig


title: Colon mucosa, Crohn's disease, Inflamed 19

description:
UM20160310-028_Involved_126L_121L
log2TPM.30.samples.Mucosa.txt

value: Inflamed


title: alg-1(CD) Input, rep2

description: small RNA analysis


title: Liver, C57BL6, archival, M37810, MNase


title: Colon mucosa, Crohn's disease, Inflamed 18

description:
UM20151022-26-MI_1R
log2TPM.30.samples.Mucosa.txt

value: Colon mucosa


title: alg-1(CD) ALG-1 IP, rep1

description: small RNA analysis


title: Liver, C57BL6, archival, M37810, INPUT

value: liver


title: Colon mucosa, Normal 4

description:
UMASS-22
log2TPM.30.samples.Mucosa.txt

value: Normal


title: alg-1(CD) Input, rep1

description: small RNA analysis


title: Colon mucosa, Crohn's disease, Non-Inflamed 13

description:
UMASS-24_Uninvolved
log2TPM.30.samples.Mucosa.txt

value: Non-Inflamed


title: N2 ALG-1 IP, rep1

description: small RNA analysis

value: Embryo


title: Colon mucosa, Crohn's disease, Non-Inflamed 10

description:
UMASS-25_uninvolved
log2TPM.30.samples.Mucosa.txt


title: Liver, C57BL6, archival, M37810, FAIRE

description:
C57BL6_Fresh_FAIRE_pooled-vs-C57BL6_M37810_Fresh_INPUT.wig
C57BL6_Fresh_MNase_pooled-vs-C57BL6_M37810_Fresh_INPUT.wig

value: archival formalin

value: M


title: N2 Input, rep1

description: small RNA analysis

value: N2 (Bristol)


title: Colon mucosa, Normal 3

description:
FO20160406-032
log2TPM.30.samples.Mucosa.txt


title: Colon mucosa, Normal 2

description:
NDRI_15
log2TPM.30.samples.Mucosa.txt


title: N2 Input, rep2

description: small RNA analysis

value: Whole worm


title: alg-1(CD);alg-2(CD), rep3

description: small RNA analysis

extract_protocol:
Trizol was used to extract total RNA from frozen worm pellet
The extracted RNA was used as input for the NEBNext Multiplex Small RNA Library Kit and size selection is performed for miRNAs on gel (Bands corresponding to ~140 bp)

value: Young Adults


title: alg-1(CD);alg-2(CD), rep1

description: small RNA analysis


title: alg-2(CD), rep3

description: small RNA analysis


title: cKO_LT-HSC_rep 2

city: Tianjin

first: ZhaoFeng

last: Zheng

address: 288 Nanjing Road, Heping District, Tianjin, China

institute: Institute of Hematology & Blood Diseases Hospital,

data_processing:
Raw data  of fastq format were  processed via in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher).
The RNA sequencing libraries were prepared following standard Illumina protocols.

treatment_protocol: LT-HSC, MEP and CMP cells were isolated from Mx1cre; Atf4fl/fl mice (cKO) and  Atf4fl/fl mice (WT).

value: Bone marrow cells

value: LT-HSC cells

value: wild type

tag: cell subtype

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34-CD135-)


title: alg-1(CD);alg-2(CD), rep2

description: small RNA analysis

tag: developmental stage


title: cKO_LT-HSC_rep 1


title: alg-2(CD), rep1

description: small RNA analysis


title: CD45+ sorted tumor, L-fucose treated, day 7, RNA library

city: Tampa

first: Dongliang

last: Du

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were mapped against mm10 mouse transcriptome and processed for UMI counting using Cell Ranger (v3.0, 10X Genomics). Barcodes with UMI counts were imported to Seurat v4.0(Stuart et al., 2019) for downstream analysis. Cells with less than 200 genes detected, with greater than 10% mitochondrial UMIs, or with complexity score (log10GenesPerUMI) less than 0.8 were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet(Wolock et al., 2019), DoubletFinder(McGinnis et al., 2019), and scDblFinder(Germain et al., 2021), using 0.08% doublet rate for every 1000 cells. Cells identified as doublets by more than one method were removed. Raw UMI counts were log normalized and the top 5000 variable genes were detected in each sample separately. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function. Individual mice samples were further integrated to remove batch effects using IntegrateData function (Hao et al., 2021) in Seurat with anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData regressing against total reads count, mitochondrial UMIs percentage, cell cycle phases, and log10GenesPerUMI. Principal component analysis was performed on the integrated data and a shared nearest neighbor (SNN) graph was constructed using the first 40 principle components. Clusters were identified using the by Louvain clustering (Blondel et al., 2008) implemented in FindClusters function at resolution=0.8. Uniform manifold approximation and projection (UMAP) was used to visualize gene expression and clusters. Differential expression analysis for each cluster was performed using FindAllMarkers function in Seurat with default settings. Clusters were further annotated by comparing differential genes with markers previously associated with T cells (Cd3e, Cd3d, Cd3g), B cells (Cd79a, Cd79b, Cd19), NK cells (Gzma, Klrb1c, Ncr1), cDC1 (Xcr1, Clec9a, Itgae, Batf3), cDC2 (Lilrb4a, Itgax, Csf1r, Mgl2), mregDC (Fscn1, Ccl22, Cacnb3, Ccr7, Fabp3), monoDC (Cd7, Atp1b1, Clec10a, Cd209d), Macrophages (C1qc, C1qb, Apoe), Monocytes (Plac8, Ly6c2, Arg1), Neutrophils (S100a9, S100a8, Mmp9), and Mast cells (Cpa3, Hdc, Ifitm1) (Supplementary Figure 6c). For marker gene bubble plot, gene-level average expression was calculated for each cluster and then Z-score normalized.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: lymphocytes

extract_protocol:
For single-cell RNA sequencing of intratumoral immune cells, 4-6-weeks-old C3H/HeJ mice were injected subcutaneously into the right flank with 1x106 SW1 melanoma cells. After 14 days, a pretreatment mouse cohort (n=3) was sacrificed, and the harvested tumors were subjected to scRNAseq. The remaining mice were administered either control (n=6) or 100nM L-fuc (n=6)-supplemented water ad libitum as previously described(Lau et al., 2015;Lester et al., 2023). Upon sacrifice, tumors were removed and CD45+ cells were isolated through sorting.
Tumors were harvested at 17 and 42 days after initial tumor injection and subjected to scRNAseq analyses by 10X Genomics Chromium Single Cell Controller for single-cell RNA-sequencing library preparation (10X Genomics, Pleasanton, CA). Reverse transcription was then performed on encapsulated individual cell droplets to generate cDNA and generate cDNA libraries. These libraries were sequenced using an Illumina NextSeq 500 instrument using v2.5 flow cells; a 10X Genomics CellRanger software was used for alignment and gene counting.
Sequencing reads were mapped against mm10 mouse transcriptome and processed for UMI counting using Cell Ranger (v3.0, 10X Genomics). Barcodes with UMI counts were imported to Seurat v4.0(Stuart et al., 2019) for downstream analysis. Cells with less than 200 genes detected, with greater than 10% mitochondrial UMIs, or with complexity score (log10GenesPerUMI) less than 0.8 were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet(Wolock et al., 2019), DoubletFinder(McGinnis et al., 2019), and scDblFinder(Germain et al., 2021), using 0.08% doublet rate for every 1000 cells. Cells identified as doublets by more than one method were removed. Raw UMI counts were log normalized and the top 5000 variable genes were detected in each sample separately. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function. Individual mice samples were further integrated to remove batch effects using IntegrateData function (Hao et al., 2021) in Seurat with anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData regressing against total reads count, mitochondrial UMIs percentage, cell cycle phases, and log10GenesPerUMI. Principal component analysis was performed on the integrated data and a shared nearest neighbor (SNN) graph was constructed using the first 40 principle components. Clusters were identified using the by Louvain clustering (Blondel et al., 2008) implemented in FindClusters function at resolution=0.8. Uniform manifold approximation and projection (UMAP) was used to visualize gene expression and clusters. Differential expression analysis for each cluster was performed using FindAllMarkers function in Seurat with default settings. Clusters were further annotated by comparing differential genes with markers previously associated with T cells (Cd3e, Cd3d, Cd3g), B cells (Cd79a, Cd79b, Cd19), NK cells (Gzma, Klrb1c, Ncr1), cDC1 (Xcr1, Clec9a, Itgae, Batf3), cDC2 (Lilrb4a, Itgax, Csf1r, Mgl2), mregDC (Fscn1, Ccl22, Cacnb3, Ccr7, Fabp3), monoDC (Cd7, Atp1b1, Clec10a, Cd209d), Macrophages (C1qc, C1qb, Apoe), Monocytes (Plac8, Ly6c2, Arg1), Neutrophils (S100a9, S100a8, Mmp9), and Mast cells (Cpa3, Hdc, Ifitm1) (Supplementary Figure 6c). For marker gene bubble plot, gene-level average expression was calculated for each cluster and then Z-score normalized.

treatment_protocol: 4-6-week-old female BALB/c mice were injected with 1x105 4T1 cells into the inguinal mammary fat pad. After 10 days, the mice were supplied with either control (n=5) or 500mM L-fuc (n=5)-supplemented water ad libitum.

value: lymphocytes

tag: cell line

value: SW1 melanoma cells

value: Intratumoral CD45+ cells

value: L-fucose water ad libitum


title: CD45+ sorted tumor, control treated, day 0, VDJ library

value: control water ad libitum


title: CD45+ sorted tumor, L-fucose treated, day 7, VDJ library


title: Colon mucosa, Normal 1

description:
FO20160325_030
log2TPM.30.samples.Mucosa.txt

value: Colon mucosa

value: Normal


title: CD45+ sorted tumor, control treated, day 7, VDJ library


title: CD45+ sorted tumor, L-fucose treated, day 21, RNA library


title: CD45+ sorted tumor, control treated, day 7, RNA library


title: cKO_MEP_rep 2

value: MEP cells

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34-CD16/32-)


title: CD45+ sorted tumor, control treated, day 21, VDJ library


title: alg-1(CD), rep3

description: small RNA analysis


title: alg-2(CD), rep2

description: small RNA analysis


title: CD45+ sorted tumor, L-fucose treated, day 21, VDJ library


title: Colon mucosa, Crohn's disease, Non-Inflamed 9

description:
UMASS-26_Ileum-uninvolved
log2TPM.30.samples.Mucosa.txt

value: Crohn's disease

value: Non-Inflamed


title: cKO_CMP_rep 2

value: CMP cells

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34+CD16/32low)


title: alg-1(CD), rep2

description: small RNA analysis

value: Young Adults

value: Whole worm


title: cKO_CMP_rep 1

value: Bone marrow cells

value: wild type


title: WT_LT-HSC_rep 2

value: LT-HSC cells

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34-CD135-)


title: CD45+ sorted tumor, control treated, day 0, RNA library

value: lymphocytes

value: SW1 melanoma cells

value: Intratumoral CD45+ cells


title: PBS-1

state: Select...

address: huangpu Distinc, Ruijin Hospital

institute: 瑞金医院

data_processing:
cutadapt software, CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: mRNA Expression Profiling.xlsx

source_name: lung

extract_protocol:
Mouse AECs were isolated by fluorescence-activated cell sorting (FACS) using CD326-FITC (Thermo Fisher scientific), CD45-APC (BD Biosciences). Total mRNA was extracted from mouse AECs
mRNA-Seq:RNA libraries for RNA-Seq were preapred using SMARTER-Seq Library Prep Kit following manufatures's protocols.

value: lung

value: primary cells

value: epithelial cell

value: WT

value: PBS


title: CD45+ sorted tumor, control treated, day 21, RNA library

value: control water ad libitum


title: N2, rep1

description: small RNA analysis

value: N2 (Bristol)


title: N2, rep2

description: small RNA analysis


title: cKO_MEP_rep 1

value: MEP cells

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34-CD16/32-)


title: alg-1(CD), rep1

description: small RNA analysis

value: Young Adults

value: Whole worm


title: PBS-2


title: HDM-2

value: HDM


title: WT_MEP_rep 2

value: Bone marrow cells

value: wild type


title: embryo, 68h, direct capture

organism: Ascaris suum

value: Embryo

value: AsiSI+PmeI+AscI


title: embryo, 65h, rep2


title: embryo, 65h, rep1

value: AsiSI


title: WT_MEP_rep 1


title: PBS-1. IP

data_processing:
cutadapt software, CLC Genomics Workbench v11.0.1
Differential m6A site information, Fold change, and P-value information identified by diffReps software.
Assembly: mm10
Supplementary files format and content: Differentially_methylated_sites.mRNA.xlsx

extract_protocol:
Mouse AECs were isolated by fluorescence-activated cell sorting (FACS) using CD326-FITC (Thermo Fisher scientific), CD45-APC (BD Biosciences). Total mRNA was extracted from mouse AECs
m6A-Seq:TruSeq Stranded mRNA Sample Pre Kit (Illumina) was used to construct the library from immunoprecipitated mRNA and input mRNA following to a published protocol. mRNA-Seq:RNA libraries for RNA-Seq were preapred using SMARTER-Seq Library Prep Kit following manufatures's protocols.
m6a-seq, mRNA-seq

value: lung

value: primary airway epithelial cells

tag: fraction

value: IP


title: embryo, 62h, rep3


title: PBS-2. IP

description: Differentially_methylated_sites.mRNA.xlsx

value: WT


title: PBS-2. Input

description:
Differentially_methylated_sites.mRNA.xlsx
mRNA Expression Profiling.xlsx

value: PBS

value: Input