title: 18992X72 Ctrl 1

city: Salt Lake City

first: Marcus

last: Pezzolesi

state: Utah

address: HELIX Building, 30 N Mario Capecchi Dr, 3rd floor South

department: Internal Medicine

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 110 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: whole blood

extract_protocol:
PAXgene Blood RNA Kit
Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus Kit

value: whole blood

tag: subject status

value: non-ESKD


title: 293T cells, MLL2 KO, rep1

status: Public on Oct 21 2024

type: SRA

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

library_source: transcriptomic

data_processing:
RNA-seq reads were filtered by FastQC (v0.11.4) and trimmed with TrimGalore (v0.6.10).
Reads were aligned to hg38 using STAR (v2.7.5a) with default parameters.
Bam file quantification was performed using featureCount (v1.5.0-p1) with parameter -Q 10.
DEG analysis was performed using DESeq2 (v1.36.0).
Assembly: hg38
Supplementary files format and content: Bigwig files include CPM values.
Supplementary files format and content: Tab-delimited text files include featureCount count values. These files are used for DESeq2 input.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was prepared using TRIzol (Invitrogen).
RNA libraries were generated using TruSeq Stranded Total RNA Library Prep Gold (Illumina).

tag: cell line

tag: genotype

value: MLL2 knockout

tag: treatment


title: RFB_9

city: Nanjing

first: Ma

last: Ce

address: weigang

department: nanjingnongyedaxue

country: China

institute: Nanjing

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
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 following reads: (1) reads with 5’ adapter; (2) reads without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more than 50% nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C. Adapter trimming for the removal of adapter sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Clean reads for each sample were first mapped to a reference genome with the software HISAT2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: R498_mbkbase
Supplementary_files_format_and_content: Matrix table with fpkm for every gene and every sample

organism: Oryza sativa

source_name: filling panicles

growth_protocol: All the tested lines were routinely planted in the experimental field of Dafeng base.

extract_protocol:
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. Briefly, the ribosomal RNA was depleted from total RNA using the rRNA Removal Kit following manufacturer’s instruction. RNA was then fragmented into 250~300 bp fragments, and first strand cDNA was reversetranscribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP). RNA was degraded using RNase H, and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/ polymerase activities. After adenylation of 3’ ends of DNA fragments,  equencing adaptors were ligated to the cDNA. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Uridine digestion was performed using Uracil-N-Glycosylase, which was followed by the cDNA amplification using PCR
RNA librarys were prefared for secquencing using standard Illumina protocls

treatment_protocol: Three replicates were setted.

tag: tissue

value: filling panicles

tag: line

value: RFB (Parent)


title: RFB_8


title: WFB_1

source_name: young seedlings

value: young seedlings

value: WFB (Parent)


title: wounding 2H, rep3

city: Montpellier

first: Anne-Sophie

last: PETITOT

address: 911 avenue Agropolis

department: UMR DIADE

country: France

institute: IRD

description:
wildtype-t2_3
wildtype-t2_3

data_processing:
The quality of each library was controlled using FastQC.
Reads were trimmed with CutAdapt using the following criteria: the first 10 bases of all reads were eliminated, contaminating adapters were removed, low quality bases (Q<30) were trimmed out from both the 5- and 3-ends of reads, and reads less than 50 nt were discarded.
Clean reads were mapped against the Oryza sativa subsp. japonica ‘Nipponbare’ reference genomes (MSU7 and RAP-DB) using HiSat2. Mapped reads were assembled into transcripts with StringTie using  reference annotations. Count files were generated from GTF files with an in-house script.
Assembly: msu7 and rapdb
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: leaves

growth_protocol: Seeds were sterilized in 70% ethanol for 1 minute, and then 30 minutes in 40% commercial bleach, following by 6-8 times rinsed in sterilized water. Disinfected seeds were then pregerminated on half‐strength Murashige & Skoog (MS) medium including Gamborg B5 vitamins medium (Duchefa Biochemie BV, Haarlem, the Netherlands) supplied with 0.7% plant agar (Duchefa Biochemie BV, Haarlem, the Netherlands) for 2 days. Seedlings with both coleoptile and primary root were then transferred into the square petri dish (one plant per plate) containing ½ MS including Gamborg B5 supplied with 0.7% plant agar (Duchefa Biochemie BV, Haarlem, the Netherlands) and allowed to growth for 7 days in the growth chamber at 26°C under a 12 : 12 h, light : dark photoperiod, humidity at 70%.

extract_protocol:
Total RNAs were extracted from rice leaves samples using the RNeasy Plant mini kit (Qiagen) with addition of an on-column DNase I digestion.
For each sample, 500 ng of the extracted total RNA was used for library construction. Libraries were constructed using Truseq RNA Sample Preparation Kit V2 (Illumina, CA, USA), following the manufacturer's instructions. Adapters with index sequences were attached to the libraries. After the average length of the libraries was confirmed, the concentration of each library was adjusted to 10 nM.

treatment_protocol: The first complete leaf was wound 3 times with the forceps. The wounded leaves were then sampled for RNA extraction, following a kinetic from 0-16 hours. A total of 10 samples were harvested for each biological replicate at 0, 1, 2, 4, 6, 8, 10, 12, 14, and 16 h. For each time point, 5 leaves were pooled.The experiment was repeated 3 times.

value: leaves

value: Kitaake

value: wounding 2H


title: wounding 6H, rep2

description:
wildtype-t6_2
wildtype-t6_2

value: wounding 6H


title: 18992X70 Ctrl 1

country: USA


title: E12.5_mouse_distal_forelimb_WT_H3K27ac_ChIPseq

city: Montréal

first: Fanny

last: GUERARD-MILLET

state: Quebec

address: 110 AVENUE DES PINS OUEST

country: Canada

institute: IRCM

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x. Sam files were converted into bam files using Samtools v1.4.1. Duplicates were removed using Picard MarkDuplicates v.2.9.0. ChIP-seq data were visualized on the IGV software using BigWig files generated using bamCoverage tools using the following parameters : --normalizeUsing CPM -bs 1.
Mouse (MM10) and human (HG38) genome FASTA files were downloaded from the UCSC Genome Browser Website on September 15th 2022. Adapter sequences were removed from reads using robtools (https://github.com/francoisrobertlab/robtools) with the command “robtools trimmomatic --trimmers "ILLUMINACLIP:adapters.fa:2:30:10: TRAILING:3 MINLEN:25"” which requires Trimmomatic . Robtools version 2.0 and Trimmomatic version 0.36 was used. Reads were aligned to the genome using robtools with the commands “robtools bowtie2 -x mm10.fa.index -is -paired" and “robtools bowtie2 -x hg38.fa.index -is -paired" which require Bowtie2 (https://github.com/BenLangmead/bowtie2). Bowtie2 version 2.3.4.3 was used. Unmapped reads, low quality reads and duplicated reads were removed using robtools with the command “robtools filterbam” which requires samtools (https://github.com/samtools/samtools). Samtools version 1.9 was used. BAM files of replicates were merged together using robtools with the command “robtools mergebam --suffix -dedup” which requires samtools. Fragments were converted to BED format using robtools with the command “robtools bam2bed” which requires bedtools. Bedtools version 2.27.1 was used. Genome coverage files were generated using robtools with the command “robtools genomecov -g mm10.chrom.sizes --spike-suffix -human” which requires bedtools.
From the BED files containing the fragments, we counted the number of fragments per transcript for each category obtained from the SUZ12 and RING1B ChIP-seq data using a custom script called “TssFragmentCount.py” which requires bedtools. The number of fragments were scaled using a custom script called “TssScaleFragmentCount.py”. These custom scripts are available at https://github.com/francoisrobertlab/kmita-202210.
Peak calling was done using a custom script called macs2.py that requires MACS2. MACS2 version 2.2.7.1 was used. For each peak, TSSs from “knownGene.txt.gz” that are within a window size of 500bp around peak were keep for further analysis using a custom script called “TssWithPeaks.py”. Scaled number of fragments for each TSS were obtained using custom scripts “TssFragmentCount.py” and “TssScaleFragmentCount.py”. TSSs for which the EED mutant fragment count are between half and twice the WT counts are considered as maintained genes in the EED mutant. TSSs for which the EED mutant fragment count are above twice the WT counts are considered as gain genes in the EED mutant.
Scaled number of fragments for each TSS from “knownGene.txt.gz” were obtained using custom scripts “TssFragmentCount.py” and “TssScaleFragmentCount.py”. TSSs for which the WT fragment count is twice above the input fragment count were kept for further analysis. From these TSSs, only TSSs for which the WT fragment count is twice above the median of non-zero input fragment count of all TSSs were kept for further analysis. TSSs for which the EED mutant fragment count are between half and twice the WT counts were considered as additional maintained genes in the EED mutant.
Comparison of fragment counts were done using Perseus  version 1.6.14.0.
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: distal forelimb

extract_protocol:
ChIP experiments were performed in dissected proximal and distal forelimb buds of CD1 (wild type) and Prrx1Cre; EedDel/Flox (Eedc/-) mice at E12.5 following the same conditions as previously described (Berlivet et al., 2013). Chromatin was cross-linked for 13 minutes using formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4℃ with 5ug of antibody. The chromatin was coupled to the beads overnight at 4℃. The immunoprecipitated samples were then washed with different wash buffers depending on the antibody present. Lastly, the DNA was purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: distal forelimb

tag: age

value: WT

tag: antibody

value: H3K27ac abcam :ab4729


title: RFB_7


title: 18992X71 Ctrl 1


title: E12.5_mouse_distal_forelimb_WT_H2AK119ub_ChIPseq

value: H2AK119ub Cell Signaling :8240


title: RFB_6

source_name: young panicles

value: young panicles


title: wounding 2H, rep2

description:
wildtype-t2_2
wildtype-t2_2


title: E12.5_mouse_distal_forelimb_EED_H2AK119ub_ChIPseq


title: 18992X69 Ctrl 1


title: RFB_5


title: wounding 2H, rep1

description:
wildtype-t2_1
wildtype-t2_1


title: 293T cells, Control, rep1


title: 18992X68 Ctrl 1


title: E12.5_mouse_distal_forelimb_WT_CBX8_ChIPseq

value: CBX8 abcam :ab259849


title: wounding 1H, rep3

description:
wildtype-t1_3
wildtype-t1_3

value: wounding 1H


title: wounding 4H, rep1

description:
wildtype-t4_1
wildtype-t4_1

value: wounding 4H


title: RFB_4


title: control sample, rep3

description:
wildtype-t0_3
wildtype-t0_3

value: control sample


title: RFB_3


title: RFB_2


title: 18992X67 Ctrl 1

value: whole blood

value: non-ESKD


title: wounding 1H, rep1

description:
wildtype-t1_1
wildtype-t1_1


title: RFB_1

value: young seedlings

value: RFB (Parent)


title: E12.5_mouse_distal_forelimb_EED_CBX2_ChIPseq

value: CBX2 abcam :ab80044


title: 18992X66 Ctrl 1


title: 18992X65 Ctrl 1


title: 18992X63 Ctrl 1


title: R308_9

value: filling panicles

value: R308 (Parent)


title: e12.5_mouse_proximal_forelimb_Eed448_RNAseq

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using TopHat 2
Bam files were converted to tagDirectory using HOMER
BigWig were generated using the makeUCSCfile HOMER command
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER with the following parameters:-fsize 1e20 -fragLength 150 –bigWig. Scores represent reads normalized per 10000000 reads

source_name: forelimb bud

extract_protocol:
RNA was extracted from dissected proximal and distal limb buds from 3 independent pools of wild type limb buds (n=3) and from two independent pools of Eedc/- limb buds (n=2). The extraction was performed using the RNAeasy Plus mini kit. Ribosomal depleted RNA. Next, mRNA enrichment, library preparation and flow-cell preparation for sequencing were performed by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations. Sequencing was done on a HiSeq 2000 instrument with a paired-end 50 cycles protocol.
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: proximal forelimb bud

tag: developmental stage

tag: strain

value: mixed background C57Bl/6 x 129

value: Prrx1Cre; EedDel/Flox


title: control sample, rep1

description:
wildtype-t0_1
wildtype-t0_1

value: leaves

value: Kitaake


title: 18992X64 Ctrl 1


title: R308_7


title: e12.5_mouse_proximal_forelimb_Eed445_RNAseq


title: e12.5_mouse_distal_forelimb_Eed445_RNAseq

value: distal forelimb bud


title: E12.5_mouse_distal_forelimb_WT_CBX2_ChIPseq

value: distal forelimb

value: WT


title: e12.5_mouse_distal_forelimb_Eed448_RNAseq


title: 18992X61 Ctrl 1


title: wounding 1H, rep2

description:
wildtype-t1_2
wildtype-t1_2

value: wounding 1H


title: E12.5_mouse_distal_forelimb_EED_CBX8_ChIPseq

value: CBX8 abcam :ab259849


title: e12.5_mouse_proximal_forelimb_Eed427_RNAseq


title: control sample, rep2

description:
wildtype-t0_2
wildtype-t0_2

value: control sample


title: empty-vector-control_CLS_d6_biolRep3

city: London

first: Shajahan

last: Anver

address: Gower Street London

department: Genetics, Evolution and Environment

country: United Kingdom

institute: University College London

data_processing:
All quality control steps including quality filtering, demultiplexing and adapter removal were performed with Illumina BaseSpace in-house tools leaving unique molecular indices (UMIs) intact.
The quality of the sequences was confirmed with FastQC (ver 0.11.2, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads for each sample from the two lanes were concatenated and the UMIs were clipped and added to the read header by je (ver. 1.2, http://gbcs.embl.de/je) with the following code : je clip F1=pair1.fastq.gz F2=pair2.fastq.gz LEN=8.
Reads were aligned with STAR (ver. 2.6.1a, https://github.com/alexdobin/STAR) against the S. pombe genome sequence with the following code: STAR --genomeDir dir --runThreadN 8 --readFilesIn pair1.fastq.gz pair2.fastq.gz --readFilesCommand gunzip -c --outFileNamePrefix prefix --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType wiggle --clip5pNbases 9 --limitBAMsortRAM 2552288998.
Sorted bam files were used to count the number of reads per gene using htseq (version 0.12.3, https://htseq.readthedocs.io/en/master/index.html; the code used was: htseq-count -s reverse -f bam -t gene -i ID file.bam Spombe.gff3 > gene.counts).
We performed the differential expression analysis with edgeR (version 3.46.0). Very lowly expressed genes were removed by retaining genes with a mean read count of 1 per million in at least 3 samples. TMM normalization was performed on the filtered counts. Common (overall variability across the genome) and tagwise (measure of the degree of inter-library variation of each gene) negative binomial dispersions were estimated by weighted likelihood empirical Bayes using limma (ver 3.46.0). and fitted in to a generalised linear model with strains as a categorical variable with evc (empty-vector control) strain as the reference. Benjamini and Hochberg method was used to control FDRs (False Discovery Rates).
Assembly: The genome sequence and gene annotation gff3 files were downloaded from pombase.org on December 2018
Supplementary files format and content: raw gene counts files combined as a table with each column representing a sample. As .xlsx format (excel sheet)
Supplementary files format and content: as described above

organism: Schizosaccharomyces pombe

source_name: cell culture

extract_protocol:
RNA was extracted with the Qiagen RNeasy Mini Kit. RNA was extracted with RNeasy spin columns and digested with DNase I (Qiagen) for 30 minutes at room temperature followed by a column cleanup with RNeasy spin columns. The rRNA was removed using the Ribo-Zero rRNA removal kit (Illumina) as per recommendations.
RNA quality was assessed in an Agilent 2100 Bioanalyzer and strand-specific cDNA libraries were made with NEXTflex™ Rapid Directional qRNA-Seq™ Kit (PerkinElmer, formerly BiooScientific) with molecular indexing. Libraries were quantified in a Qubit, pooled and 4 nM of the pooled library was sequenced in an Illumina HiSeq2500 sequencer, 50 bp paired-end reads in two lanes.

treatment_protocol: cells grown in minimal media (EMMG) until CLS day6

tag: cell type

value: cell culture

value: cells expressing an empty vector (control) in 972h-/leu1-32 background

value: Grown in minimal medium


title: 18992X60 Ctrl 1

value: whole blood

value: non-ESKD


title: R308_8

value: filling panicles

value: R308 (Parent)


title: 18992X62 Ctrl 1


title: empty-vector-control_CLS_d6_biolRep1


title: e12.5_mouse_distal_forelimb_Eed427_RNAseq

value: mixed background C57Bl/6 x 129


title: aal1OE_CLS_d6_biolRep3

value: aal1 overexpressed in a plasmid with a thiamine-repressible P41nmt1 promoter in  972h-/leu1-32 background


title: R308_5

value: young panicles


title: 18992X58 Case 1

value: ESKD


title: empty-vector-control_CLS_d6_biolRep2


title: R308_6


title: e12.5_mouse_distal_forelimb_WT514_RNAseq

value: distal forelimb bud


title: R308_4


title: e12.5_mouse_proximal_forelimb_WT514_RNAseq

value: proximal forelimb bud


title: e12.5_mouse_distal_forelimb_WT512_RNAseq

value: WT


title: 18992X56 Ctrl 1


title: aal1OE_CLS_d6_biolRep2


title: 18992X54 Ctrl 1


title: XF-DISC ISC, rep2

first: Sung Gap

last: Im

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed of adapters and sequencing quality lower than 20 (using cutadapt and sickle)
The RNAseq reads were aligned to hg38 whole genome using Hisat2
Fragments Per Kilobase of transcript per Million (FPKM) was calculated using StringTie with gene level.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Human intestinal stem cells from human pluripotent stem cell-drived 3D intestinal organoids

extract_protocol:
Illumina TruSeq kit for paired-end reads, poly-A selection, non-strand-specific
The NEBNext RNA first-strand synthesis module and NEBNExt Ultra Directional second strand synthesis kit (New England BioLabs) were used for the preparation of RNA sequencing (RNA-Seq) libraries.

value: Human intestinal stem cells

value: XF-DISC dishes


title: aal1OE_CLS_d6_biolRep1


title: R998_9

value: R998 (Parent)


title: e12.5_mouse_proximal_forelimb_WT512_RNAseq


title: 18992X57 Ctrl 1


title: XF-DISC ISC, rep1

value: Human intestinal stem cells from human pluripotent stem cell-drived 3D intestinal organoids


title: 18992X55 Ctrl 1


title: XF-DISC ISC, rep3


title: R308_1

value: young seedlings


title: 18992X59 Ctrl 1


title: R308_3


title: 18992X53 Ctrl 1


title: e12.5_mouse_distal_forelimb_WT469_RNAseq


title: R308_2


title: Matrigel ISC, rep3

value: Matrigel-coated dishes


title: R998_7


title: e12.5_mouse_INPUT (FG-KMI_CD1)

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HOMER with the following parameters:-fsize 1e20 -fragLength 150 –bigWig. Scores represent reads normalized per 10000000 reads

extract_protocol:
ChIP experiments were performed in dissected proximal and distal forelimb buds of CD1 (wild type) and Prrx1Cre; EedDel/Flox (Eedc/-) mice at E12.5 following the same conditions as previously described (Berlivet et al., 2013). Chromatin was cross-linked for 13 minutes using formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4℃ with 5ug Suz12 (D39F6, Cell Signaling), 4ug H3K27Ac (ab-4729, Abcam), and 4ug Ring1b (39663, Active Motif). The chromatin was coupled to the beads overnight at 4℃. The immunoprecipitated samples were then washed with different wash buffers depending on the antibody present. For SUZ12 antibody, 6 sequential RIPA washes (50mM Hepes-KOH (pH7.5), 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) were performed. For both H3K27Ac and RING1B sequential washes in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA) were performed. Lastly, the DNA was purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: forelimb bud

tag: chip antibody


title: 18992X52 Ctrl 1

value: whole blood

value: non-ESKD


title: R998_6


title: Matrigel ISC, rep2


title: Matrigel ISC, rep1


title: 18992X51 Ctrl 1


title: e12.5_mouse_INPUT (FG_CD1)


title: e12.5_mouse_distal_forelimb_WT_RYBP_ChIPseq

value: RYBP Millipore Sigma :ab3637


title: R998_5


title: 18992X50 Ctrl 1


title: e12.5_mouse_distal_forelimb_EEDc/-_RYBP_ChIPseq

value: mixed background C57Bl/6 x 129

value: Prrx1Cre; EedDel/Flox


title: 18992X48 Ctrl 1


title: 18992X49 Ctrl 1


title: R998_3


title: stim2KO, repllicate 1, scRNASeq

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads from fastq files were mapped to the zebrafish reference genome (GRCz11) and gene expression were quantified with STARSolo mode of STAR, for each sample (with the following parameters: --soloType CB_UMI_Simple, --soloCBwhitelist 3M-february-2018.txt [from Cell Ranger], --soloUMIlen 12, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloUMIfiltering MultiGeneUMI_CR, --soloUMIdedup 1MM_CR, --soloCellFilter  EmptyDrops_CR)
Assembly: Danio rerio GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: head

extract_protocol:
5 dpf larvae were anesthetized by tricaine methanesulfonate (MS222), a neuromuscular blocker, and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12; with Ca2+, and L-glutamine, and without HEPES, and Phenol Red; Gibco) with 10% fetal bovine serum (FBS; Gibco). Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single-cell suspensions were obtained by enzymatic and mechanical digestion of heads without eyes isolated from two fish lines: stim2 KO and Tg (control). Immediately after isolation of single-cell suspension, the cells were sorted based on GCaMP5G fluorescence (with 488 nm excitation and 510 nm emission) to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter, which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II (BD Biosciences, Franklin Lakes, NJ). Cell viability was measured using the trypan blue staining method, and when the viability of cells was ~80%, the cells were immediately loaded on the 10X Chromium system for droplet encapsulation.
Approximately 8000 cells were sorted and suspended in ~40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol (V3 chemistry). To prepare the cells for droplet-based sequencing, GCaMP5G-positive single-cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system, the standard manufacturer’s protocol. During the encapsulation, the cells were lysed within the droplet, and they released polyadenylated RNA bound to the barcoded bead, which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines, the droplets were directly subjected to reverse transcription, the emulsion was broken, and cDNA was purified using Silane beads. After the amplification of cDNA with 13 cycles, purification and quantification were performed. The 10X Genomics single-cell RNA-sequencing library preparation – involving fragmentation, dA-tailing, adapter ligation, and 12-cycle indexing PCR – was performed.

value: head

value: neuronal

value: (stim2a;stim2b)-/- ; Tg(HuC:GCaMP5G)

value: 5 dpf larvae


title: e12.5_mouse_distal_forelimb_WT_H2AK119ub_ChIPseq

value: distal forelimb bud

value: WT

value: H2AK119ub Cell Signaling  :8240


title: stim2KO, repllicate 2, scRNASeq

description: 10x Genomics


title: Tg, repllicate 2, scRNASeq

description: 10x Genomics


title: R998_2

value: R998 (Parent)


title: R998_4

value: young panicles


title: 18992X47 Ctrl 1


title: R998_8

value: filling panicles


title: R998_1

value: young seedlings


title: e12.5_mouse_distal_forelimb_EEDc/-_CBX2_ChIPseq

value: CBX2 Abcam :ab80044


title: e12.5_mouse_proximal_forelimb_WT469_RNAseq

value: proximal forelimb bud


title: Tg, repllicate 1, scRNASeq

description: 10x Genomics


title: 18992X46 Ctrl 1

value: whole blood

value: non-ESKD


title: e12.5_mouse_distal_forelimb_WT_CBX2_ChIPseq

value: mixed background C57Bl/6 x 129


title: Patient 6 biopsy B

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

data_processing:
Transcriptomic maps of single-end reads were generated using STAR v2.5 against the hg38 reference genome.
Transcript counts were assessed by HTSeq-0.6.1 using the no strand setting and intersection-non-empty mode and counts were assigned to Ensembl gene ids.
Assembly: hg38
Supplementary files format and content: Count data in .TXT format.

molecule: polyA RNA

source_name: Mid luteal endometrial cells

extract_protocol:
RNA was purified using RNA STAT-60 (AMS Bio) according to manufacturer's instructions and treated using Amplification Grade DNase I (Invitrogen) followed by ethanol precipitation and clean-up. Quality control, library preparation and sequencing were performed by the Wellcome Trust Centre for Human Genetics.
Libraries were prepared using the Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions. Single-end 75bp sequencing was performed on Illumina HiSeq4000.

value: Mid luteal endometrial cells

tag: patient

tag: lh+

tag: nk

tag: previous losses

tag: previous live births

tag: cycle type

value: Normal


title: Patient 6 biopsy A


title: e12.5_mouse_distal_forelimb_EEDc/-_H3K27me3_ChIPseq

value: Prrx1Cre; EedDel/Flox

value: H3K27me3 Millipore :07-449


title: 18992X45 Ctrl 1

tag: subject status


title: BTK_L_brain_2

city: Seoul

first: Jeung Hee

last: An

address: 47 Kkachisan-ro 24-gil, Gangseo-gu

institute: Gangseo University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: brain

growth_protocol: The animals were housed under standardized conditions, maintaining a temperature of 21–22 °C, a 12-h light/dark cycle, and 70% humidity, with ad libitum access to chow and water.

extract_protocol:
Total RNA was extracted from the cells with the use of a TruSeq Stranded mRNA Kit (Illumina) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: a 1-week acclimation period, the mice were randomly divided into five groups, with eight mice in each group: (1) normal control group, (2) MPTP-induced group, (3) MPTP + levodopa (2 mg/kg/day; Sigma Aldrich) group, (4) MPTP + BTK low-dose (1 µg/kg/day) group, and (5) MPTP + BTK high-dose (2 µg/kg/day) group. The normal group received a standard diet for 6 weeks. The MPTP-induced group received intraperitoneal injections of MPTP (20 mg/kg/day) for 1 week. Groups 3–5 received MPTP (20 mg/kg/day) intraperitoneally for 1 week, followed by oral administration of levodopa (2 mg/kg/day) or BTK inhibitor at low (1 µg/kg/day) and high doses (2 µg/kg/day) for 4 weeks.

value: brain

tag: time

value: 6 week

value: 7 days of stabilization, MPTP treatment for 1 week followed by BTK 25pM for 4 weeks


title: BTK_L_brain_3

tag: treatment


title: 18992X43 Ctrl 1

tag: tissue


title: Patient 5 biopsy B

description:
P5.B
Excessive senescence

value: Abnormal


title: Patient 5 biopsy A


title: BTK_L_brain_1


title: e12.5_mouse_proximal_forelimb_EEDc/-_H3K27me3_ChIPseq

tag: genotype


title: e12.5_mouse_distal_forelimb_WT_H3K27me3_ChIPseq

value: distal forelimb bud

value: WT


title: BTK_H_brain_3

value: 7 days of stabilization, MPTP treatment for 1 week followed by BTK 50pM for 4 weeks


title: 18992X44 Ctrl 1


title: Patient 4 biopsy B

tag: age


title: BTK_H_brain_1


title: 18992X41 Ctrl 1


title: Testit mirVana Purified OTTR Control Rep 2

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt v2.9, when UMI was present reads were deduplicated with seqkit v0.14.0 and UMI sequence was trimmed with cutadapt.
Trimmed reads where then mapped to sacCer3 or mm10 with tRAX using default settings.
Assembly: mm10, sacCer3
Supplementary files format and content: Each processed data file contains information about read-start/stop site, coveage, and  misinicorporation rate.

source_name: Testis

growth_protocol: For full length tRNA experiments, yTG66 and yTG109 were grown overnight in selective synthetic media containing 2% dextrose, saturated cultures were diluted to OD600=0.1 and grown in selective synthetic media containing 2% dextrose until they reached OD600=0.5-07. For tRF experiments, yTG72 were grown overnight in selective synthetic media containing 2% raffinose. Saturated cultures were diluted to OD600=0.1 in selective synthetic media containing 2% raffinose and grown until early-midlog (OD600= 0.3-0.4). Cells were then centrifuged and diluted in selective synthetic media containing 2% galactose to an OD600 so that they reach OD600=0.5-0.7 in 360 minutes (“WT” samples were resuspended in selective synthetic media containing 2% galactose, centrifuged, and snap frozen immediately).

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.

value: FVB/NJ


title: BTK_H_brain_2


title: e12.5_mouse_proximal_forelimb_WT_H3K27me3_ChIPseq


title: Patient 4 biopsy A


title: Patient 3 biopsy B


title: 18992X40 Ctrl 1


title: 18992X42 Ctrl 1


title: Testit mirVana Purified OTTR Control Rep 1


title: MPTP_brain_2

value: 7 days of stabilization, MPTP treatment for 1 week followed by Normal diet for 4 weeks


title: Patient 3 biopsy A


title: MPTP_brain_3


title: 18992X39 Ctrl 1


title: 18992X38 Ctrl 1


title: Testit mirVana Purified OTTR AlkB Rep 2


title: MPTP_brain_1


title: Patient 2 biopsy B

description:
P2.B
Excessive senescence


title: Patient 2 biopsy A


title: 18992X37 Ctrl 1


title: 18992X36 Case 1

value: ESKD


title: Levo_brain_3

value: 7 days of stabilization, MPTP treatment for 1 week followed by intraperitoneal injection of levodopa for 4 weeks.


title: Levo_brain_2


title: Cauda Tissue mirVana Purified OTTR AlkB Rep 6

source_name: Cauda Tissue


title: Cauda Tissue mirVana Purified OTTR Control Rep 6


title: Cauda Tissue mirVana Purified OTTR AlkB Rep 5


title: Patient 1 biopsy A

description:
P1.A
Excessive senescence


title: 18992X35 Case 1

value: whole blood


title: 18992X34 Case 1


title: Cauda Tissue mirVana Purified OTTR Control Rep 5


title: Levo_brain_1


title: 18992X33 Case 1


title: tomo_Polyp6_intact

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

data_processing:
Sequencing reads were mapped against the Nematostella transcriptome (Zimmermann et al. 2022) using kallisto.
Kallisto | bustools (Melsted & Booeshaghi et al. 2021) was also used to count UMIs and to generate slice/gene matrices per sample.
Assembly: Nematostella transcripome Nvec200 (Zimmermann et al. 2022)
Supplementary files format and content: tomo_stella_allSlices.RDS, Seurat object containing all final slices including meta data information across all time points.
Supplementary files format and content: tomo_stella_intactSlices.RDS, Seurat object containing all final slices including meta data information for intact polyps only.

organism: Nematostella vectensis

source_name: tomo-seq slices

growth_protocol: 3 week old unfed polyps were used

extract_protocol:
cDNA from tissue slices was generated using CEL-seq2 (Hashimshony et al. 2016). Experiments were performed by Single Cell Discoveries.
Illumina TruSeq small RNA sample preperation was performed by Single Cell Discoveries.

treatment_protocol: amputation of the aboral tip

value: tomo-seq slices

value: unfed polyp, 3 week old

value: intact


title: tomo_Polyp10_12hpa

value: 12 hpa


title: Con_brain_3

value: 7 days of stabilization, Normal diet for 5 weeks


title: tomo_Polyp18_96hpa

value: 96 hpa


title: 18992X32 Case 1


title: Cauda Tissue mirVana Purified OTTR Control Rep 4


title: Con_brain_1

value: brain

value: 6 week


title: 18992X31 Case 1


title: tomo_Polyp16_48hpa

value: 48 hpa


title: Testit mirVana Purified OTTR AlkB Rep 1


title: Patient 1 biopsy B

value: Mid luteal endometrial cells

value: Normal


title: 18992X30 Case 1


title: e12.5_mouse_distal_forelimb_EEDc/-_H2AK119ub_ChIPseq

value: distal forelimb bud

value: mixed background C57Bl/6 x 129

value: Prrx1Cre; EedDel/Flox

value: H2AK119ub Cell Signaling  :8240


title: Cauda Tissue mirVana Purified OTTR Control Rep 3

value: FVB/NJ


title: tomo_Polyp5_intact


title: tomo_Polyp17_96hpa


title: Testes, WT, P56

city: Wuhan

first: Weihua

last: Wang

address: No.8, Sanjiaohu Rd

institute: Jianghan University

data_processing:
The quality of raw data was evaluated using FastQC (v0.11.9).
Sequencing reads were trimmed for adaptor/low-quality sequence using Trimmomatic (v0.39). Parameter: ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:8:true MINLEN:8.
Sequence alignment was completed using Bowtie2 (v2.4.4). Parameter: -X 1000 --very-sensitive.
Peak calling was performed using MACS2 (v2.1.4). Parameter: -f BAMPE --keep-dup=all.
Peak annotation was completed using R/ChIPseeker.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: testes

extract_protocol:
The spermatogenic cells were enriched using a two-step enzymatic digestion process, and the collected cells with the proportion of live cells no less than 90% were used for CUT&Tag.
CUT&Tag libraries for sequencing were prepared according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).

value: testes

value: WT


title: Testes, WT, P16


title: Cauda Tissue mirVana Purified OTTR Control Rep 2


title: 18992X27 Ctrl 1

value: whole blood

value: non-ESKD


title: Con_brain_2


title: 18992X28 Ctrl 1


title: 18992X26 Ctrl 1


title: Thyroid, TSH-MMI, 4week, rep2

city: Kyoto

first: Ichiro

last: Yamauchi

address: 54 Kawaharacho, Shogoin, Sakyo-ku

department: Department of Diabetes, Endocrinology and Nutrition

country: Japan

institute: Kyoto University Graduate School of Medicine

data_processing:
Quality control metrics of raw sequencing reads were performed with FastQC version 0.11.7; low-quality reads were removed with Trimmomatic version 0.38.
Reads were mapped to the mm10 reference sequence with HISAT2 version 2.1.0 and assembled into transcripts with StringTie version 2.1.3b.
Assembly: mm10
Supplementary files format and content: Spreadsheet includes read counts.

source_name: Thyroid gland

extract_protocol:
Total RNA was extracted using a Nucleospin RNA Plus kit (Macherey-Nagel).
The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA) was used to construct libraries.

value: Thyroid gland

value: TSH-MMI, 4week

value: Hyperthyroidism induction


title: Thyroid, TSH, 4week, rep3

value: TSH, 4week


title: tomo_Polyp15_48hpa

value: tomo-seq slices

value: unfed polyp, 3 week old


title: Cauda Sperm mirVana Purified OTTR AlkB Rep 6

source_name: Cauda Sperm


title: 18992X25 Ctrl 1

source_name: whole blood


title: Thyroid, TSH-MMI, 4week, rep1


title: tomo_Polyp11_24hpa

value: 24 hpa


title: Cauda Tissue mirVana Purified OTTR AlkB Rep 3


title: Cauda Sperm mirVana Purified OTTR AlkB Rep 4


title: Cauda Sperm mirVana Purified OTTR Control Rep 6


title: tomo_Polyp20_96hpa

value: 96 hpa


title: 18992X24 Ctrl 1


title: 18992X29 Case 1

value: ESKD


title: Cauda Tissue mirVana Purified OTTR AlkB Rep 2


title: tomo_Polyp8_12hpa

value: 12 hpa


title: tomo_Polyp9_12hpa


title: 18992X23 Ctrl 1


title: Cauda Sperm mirVana Purified OTTR Control Rep 4


title: Thyroid, TSH, 4week, rep1


title: Cauda Sperm mirVana Purified OTTR AlkB Rep 3


title: Thyroid, Empty-MMI, 4week, rep3

value: Empty-MMI, 4week


title: 18992X22 Ctrl 1


title: tomo_Polyp13_24hpa


title: Thyroid, TSH-MMI, 4week, rep3


title: Cauda Sperm mirVana Purified OTTR Control Rep 3


title: Thyroid, Empty-MMI, 4week, rep2


title: tomo_Polyp4_intact

value: intact


title: Thyroid, Empty-MMI, 4week, rep1


title: Thyroid, TSH, 4week, rep2


title: Cauda Sperm mirVana Purified OTTR AlkB Rep 2

value: FVB/NJ


title: tomo_Polyp12_24hpa


title: 18992X20 Ctrl 1


title: Thyroid, Empty, 4week, rep3

value: Empty, 4week


title: tomo_Polyp7_12hpa


title: 18992X18 Ctrl 1


title: tomo_Polyp19_96hpa


title: Cauda Sperm mirVana Purified OTTR Control Rep 2


title: 18992X19 Ctrl 1


title: Thyroid, Empty, 4week, rep2


title: tomo_Polyp14_48hpa

value: 48 hpa


title: Thyroid, Empty, 4week, rep1


title: Cauda Sperm mirVana Purified OTTR AlkB Rep 1


title: 18992X17 Case 1

value: whole blood


title: Thyroid, TSH-MMI, 1week, rep3

value: TSH-MMI, 1week


title: Cauda Sperm mirVana Purified OTTR Control Rep 1


title: GFP_ Setdb1-KO nTnG, replicate 2, scRNA

city: Heraklion

first: Dimitrios

last: Botskaris

address: Nikolaou Plastira 100

country: Greece

institute: IMBB FORTH

description: 10x Genomics

data_processing:
Initial preprocessing was performed using the CellRanger pipeline (version 6.1.1, 10x Genomics), including alignment to the reference genome, barcode demultiplexing, and unique molecular identifier (UMI) counting. The CellRanger web summary report provided metrics such as the estimated number of cells, median genes per cell, and the percentage of reads mapping to the genome (Ref 44). To identify and remove potential doublets, the DoubletFinder algorithm (Ref 45) was applied using the following parameters: pN = 0.25, pK = 0.09, the expected number of doublets (nExp), and the first 10 principal components (PCs = 1:10). The doublet detection rate was based on nExp, calculated from the estimated number of cells and the experimental protocol. Cells identified as doublets were excluded from further analysis. Post-doublet removal, quality control filtering was performed using the Seurat package (version 5.0.3) (Ref 46) to retain high-quality cells. Cells were filtered based on the following criteria: a number of detected features (genes) per cell between 200 and 4000, a mitochondrial gene expression percentage below 5%, and a total RNA count not exceeding 18,000. Normalization was conducted using the "LogNormalize" method, followed by the identification of the top 2,000 highly variable genes with the variance-stabilizing transformation (vst) method. The data were then centered and scaled, and principal component analysis (PCA) was used for dimensionality reduction. A nearest neighbor graph was constructed using the top 10 principal components, and cells were clustered using the Louvain algorithm at a resolution of 0.5 via the Seurat FindClusters function. Clustering was visualized with Uniform Manifold Approximation and Projection (UMAP). Cell-to-cell heterogeneity in mRNA expression was assessed by calculating the coefficient of variation (CV) in gene expression (Ref 38) separately for wild-type and knockout cells. Gene count matrices were generated for each condition, and the CV for each gene was computed as the standard deviation of gene expression divided by the mean expression, multiplied by 100. Boxplots were generated to visualize differences in CV between conditions, and statistical significance was assessed using a Wilcoxon rank-sum test. The single-cell ATAC-seq (scATAC-seq) data were analyzed in bulk format. Initial preprocessing was performed using the CellRanger pipeline (version 6.1.1, 10x Genomics), including alignment of reads to the reference genome and generation of BAM files. The BAM files were normalized using the bamCoverage tool from deepTools (version 3.3.2) (Ref 48) with the BPM (Bins Per Million) method. Peak calling was performed using MACS2 (Ref 49), with a p-value cutoff of 0.00001. For the analysis of H3K9me3 CUT&Tag data, the quality of all FASTQ files was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc). Low-quality bases and adapter sequences were trimmed using Trimmomatic (version 0.39) (Ref 51). The cleaned FASTQ files were aligned to the UCSC mm10 mouse genome using HISAT2 (version 2.1.0) (Ref 52) with default settings, retaining only reads with a mapping quality score greater than 30. BAM files were converted to BigWig format using deepTools (version 3.3.2) (Ref 48) and visualized in the UCSC Genome Browser. Read counts were standardized by down sampling to match the sample with the fewest reads, and peak regions were identified using SICER2 (Ref 53). Transposable element (TE) and gene expression levels were quantified using TEtranscripts (version 2.2.3).
Assembly: mm10
Supplementary files format and content: fastq.gz, barcodes.txt.gz, features.txt.gz, matrix.txt.gz

source_name: Intestine

growth_protocol: We used livers dissected from 60-65 days old mice with the following genotypes: 1) Lgr5-GFP-CreERT2; 2) Lgr5-GFP-CreERT2/ Setdb1lox/lox; 3) Lgr5-GFP-CreERT2/nTnG ; 4) Lgr5-GFP-CreERT2/ Setdb1lox/lox/nTnG. All mice were in C57Bl6 background.

extract_protocol:
Cell Isolation from the Intestinal Epithelium: To isolate crypts, the ileum was dissected and washed with cold phosphate buffered saline (PBS) using blunt-ended syringe, opened longitudinally with a scissor and cut into 3-5 mm pieces. After extensive washing with cold PBS, the tissue fragments were resuspended in 30 volumes of cold PBS, containing 20 mM EDTA and incubated with constant shaking for 30 min. The tissue fragments allowed to settle by gravity to remove supernatant and resuspended in cold PBS. After vigorous shaking and trituration with 10 ml pipette the tissue pieces were collected by gravity sedimentation. The supernatant was discarded and the PBS extraction was repeated 9 to 12 times, until the supernatant contained mainly crypts, as verified by microscopic examination. The final supernatant containing enriched crypt fraction was passed through 70 m cell strainer and centrifuged at 400g for 5 min. To isolate epithelial cells, the crypt pellets were incubated in 10 volumes of preheated TrypLE Express (Gibco) for 4.5 min at 37 0C. The reactions were stopped by the addition of equal volume of Defined Trypsin Inhibitor (Gibco). The cells were passed through 40 m cell strainer, centrifuged at 400g for 5 min and resuspended in ice-cold PBS containing 1 mM EDTA and 2% FBS. GFP+ cells were sorted using BD FACSAria III cell sorter gated by forward scatter, side scatter and pulse width parameter at a flow rate of 3-5000 events/second.                                                                                Total RNA isolation: Total RNAs were purified from liver tissues by brief homogenization in 10 volumes of Trizol reagent using Polytron device, followed by incubation at room temperature for 5 min and the addition of 0.2 volumes of chloroform and further incubation at room temperature for 3 minutes. The samples were centrifuged at 12000 g for 15 minutes at 40C and the aqueous phase was collected, precipitated by the addition of equal volume of isopropanol. After 10 minutes at room temperature, the RNA was collected by centrifugation at 12000g for 15 minutes. The pellet was resuspended in H2O and re-precipitated with ethanol. The RNA samples were further purified by digestion with 10 units of DNase-I for 10 min at 370C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation.                                                  CUT&Tag assay: CUT&Tag assays were performed as described in (Ref 43). Briefly, nuclei were prepared from the isolated, FACS-sorted GFP+ intestinal epithelial cells by resuspension in 10 volumes of ice-cold Swelling Buffer, containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2 and protease inhibitor cocktail (CompleteTM EDTA-free, Roche). After centrifugation at 400g for 5 min at 40C, the pellet was resuspended in Lysis Buffer, containing 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 1% NP40 and protease inhibitor cocktail. After incubation in ice for 3 min the nuclei were collected by centrifugation for 5 min at 400g, at 40C, washed twice with PBS. Then, 105 nuclei were resuspended in a buffer containing 20 mM HEPES–KOH pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, protease inhibitor cocktail and incubated for 10 min with Concanavalin A-conjugated magnetic beads (Epicypher) that were previously activated by repeated washings with a buffer containing 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2. The reactions were supplemented with 0.5 volume of a buffer containing 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin, 2 mM EDTA and 0.5 g of the anti-H3K9Me3 or IgG negative control primary antibodies. The samples were incubated overnight at 40C by gentle agitation. The beads were then supplemented with a buffer containing 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail, 0.01% Digitonin and 0.5 g of anti-rabbit secondary antibody (Epicypher). After incubation at room temperature for 30 min, the beads were washed twice with the same buffer and resuspended in the same buffer containing 300 mM NaCl. Protein A/G-fused Tn5 transposase protein (CUTANA pA/G-Tn5, Epicypher) was added and the samples were incubated for 1 hour at room temperature followed by washing with a buffer containing 20 mM HEPES-NaOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail and 0.01% Digitonin. The beads were collected and resuspended in the above buffer containing 10 mM MgCl2, and incubated for 1 hour at room temperature, washed once with 10 mM TAPS pH 8.5 and 0.2 mM EDTA. And incubated with 10 mM TAPS pH 8.5 and 0.1% SDS for 1 hour at 580C, to release DNA. After quenching by the addition of 3 volumes of 0.67% Triton-X100, the samples were used for PCR reaction (14 cycles) using universal i5 primers and barcoded i7 primers. After cleanup with AMPure beads (Beckman Coulter), quantification and quality evaluation in Agilent Bionalyzer, the libraries were sequenced using Illumina NextSeq500 platform Roche).
Total RNA-seq libraries were generated using CORALL Total RNA Library preparation kit from Lexogen and sequenced in an Illumina NextSeq 500 system. Single cell RNA-seq libraries were prepared using 10x Genomics Single Cell 3′ Reagent Kit. Single cell ATAC-seq libraries were prepared using Chromium Next GEM Single Cell ATAC Reagent Kit.

treatment_protocol: Mice were treated with single intraperitoneal injection of 70 mg/kg Tamoxifen in corn-oil and analyzed 5 days after the injection

value: Intestine

value: Stem Cells

value: Lgr5-GFP-CreERT2/ Setdb1lox/lox/nTnG

value: Tamoxifen


title: tomo_Polyp2_intact

value: tomo-seq slices


title: 18992X16 Case 1

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 110 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
PAXgene Blood RNA Kit
Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus Kit


title: 18992X21 Ctrl 1

value: non-ESKD


title: Thyroid, TSH-MMI, 1week, rep2

value: Thyroid gland

value: Hyperthyroidism induction


title: 18992X15 Ctrl 1


title: tomo_Polyp1_intact

value: unfed polyp, 3 week old


title: Thyroid, TSH-MMI, 1week, rep1


title: GFP_ WT nTnG, replicate 2, scRNA

description: 10x Genomics


title: Thyroid, TSH, 1week, rep3

value: TSH, 1week


title: pmr1 Deletion Biofilm, Spider Medium, One Week, Rep 3

city: ANN ARBOR

first: Anuj

last: Kumar

state: MI

address: 1105 N. University Avenue, BSB Room 3210

department: MCDB

institute: University of Michigan

description:
gene_count.xls
gene_fpkm_group.xls
gene_fpkm.xls

data_processing:
Quality control: 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 1 containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: 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.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Candida Genome Database. Strain: SC5314. Assembly 22
Supplementary files format and content: Excel spreadsheet indicating expression read counts for all genes identified by sequencing. Columns indicate read counts for the indicated gene (row) in the respective sample.
Supplementary files format and content: Excel file summarizing transcript expression levels as fragments per kilobase of transcript per million reads mapped; the data account for sequencing depth and feature length.

organism: Candida albicans

source_name: strain BWP17

extract_protocol:
RNA was isolated from frozen cell pellets using the RiboPure Yeast Kit (Thermo Fisher Scientific). RNA samples were treated with DNase, and RNA concentrations were determined using the NanoDrop microvolume spectrophotometer. RNA quality control, sequencing, and analysis was performed by Novogene (CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries were prepared for sequencing as follows. Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: strain BWP17

value: WT


title: GFP_ WT nTnG, replicate 1, scRNA

description: 10x Genomics


title: pmr1 Deletion Biofilm, Spider Medium, One Week, Rep 2


title: 18992X13 Ctrl 1


title: tomo_Polyp3_intact

value: intact


title: Thyroid, TSH, 1week, rep2


title: GFP_Setdb1KO, scATAC

description: 10x Genomics

library_source: genomic single cell

value: Lgr5-GFP-CreERT2/ Setdb1lox/lox


title: 18992X12 Ctrl 1


title: GFP_WT , scATAC

description: 10x Genomics


title: Thyroid, TSH, 1week, rep1


title: pmr1 Deletion Biofilm, Spider Medium, One Week, Rep 1


title: Thyroid, Empty, 1week, rep3

value: Empty, 1week


title: 18992X11 Case 1

value: whole blood

value: ESKD


title: kre5 Deletion Biofilm, Spider Medium, One Week, Rep 3


title: GFP_Setdb1KO_Setdb1_H3K9me3., replicate 2, ChIP

value: Intestine


title: 18992X10 Case 1


title: Thyroid, Empty, 1week, rep2


title: 18992X9 Ctrl 1


title: GFP_ Setdb1-KO nTnG, replicate 1, scRNA

description: 10x Genomics

value: Stem Cells


title: Thyroid, Empty, 1week, rep1


title: kre5 Deletion Biofilm, Spider Medium, One Week, Rep 1


title: GFP_WT_H3K9me3., replicate 2, ChIP


title: 18992X8 Ctrl 1


title: 18992X14 Ctrl 1


title: alg11 Deletion Biofilm, Spider Medium, One Week, Rep 3


title: GFP_WT_H3K9me3., replicate 1, ChIP


title: alg11 Deletion Biofilm, Spider Medium, One Week, Rep 2


title: DG_control, snRNA-Seq

first: fan

last: meng

address: Longmian Avenue 101

institute: Nanjing Medical University

description: 10X Genomics

data_processing:
The Cell Ranger Analysis Pipeline(version 6.1.2) was used to create sequencing libraries from single cell transcriptomes without specifying a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file（human：GRCh38,mouse:mm10）and a transcriptome annotation file（human:GENCODE v32/Ensembl 98,mouse:GENCODE vM23/Ensembl 98）for sequence alignment. The pipeline generates a unique molecular identifier (UMI) count matrix which will be processed using python package Scanpy (version 1.8) for further analysis. To remove low quality cells, which is a major concern in microdroplet-based experiments, we filtered out cells with UMI/gene numbers smaller than the threshold(UMI ≤100000，gene numbers≤6000). Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >5% of the counts belonged to mitochondrial genes. After applying these QC criteria, xxxx single cells in total remained and were included in the downstream analyses. Library size normalization was performed with pp. normalize_total function in Scanpy to obtain the normalized counts. Specifically, the global-scaling normalization method normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), pp. log1p function and then logtransformed.
Top variable genes across single cells were identified using the method described by Macosko et al. The most variable genes were selected using pp.highly_variable_genes function in Scanpy.  Principal component analysis (PCA) was performed to reduce the dimensionality of the dataset with tl.pca function in Scanpy. Graph-based clustering was performed to cluster cells according to their gene expression profiles using the pp.neighbors function in Scanpy. Cells were visualized using 2-dimensional and 3-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm with the tl.umap function in Scanpy. We used the FindAllMarkers function (test.use = wilcox) in Seurat to identify marker genes of each cluster. For a given cluster, FindAllMarkers identified positive markers compared with all other cells(Adjust P value < 0.05 and |foldchange| > 2 was set as the threshold of significant markers gene). Then, we used the R package g:Profiler2 to perform a functional enrichment analysis of marker genes. The marker genes for each cluster were mapped to known sources of functional pathway, and the hypergeometric distribution was used to check whether these biological processes were over-represented. Including pathways from Gene Ontology (GO),KEGG,Reactome ,WikiPathways,etc.
Assembly: mouse: GENCODE vM23/Ensembl 98
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: dentate gyrus

extract_protocol:
The tissues samples were surgically removed and snap frozen in liquid nitrogen for intact nucleus isolation. The nucleus was isolated and purified as previously described with some modifications. Briefly, the frozen tissue was homogenized in NLB buffer which contain 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton X-100 (SigmaAldrich, USA), 0.1 mM EDTA, 0.2U/μL RNase Inhibitor (Takara, Japan). Various concentration of sucrose was used to purify the nucleus. The concentration of nucleus was adjusted to about 1000 nuclei/μL for snRNA-Seq.
The snRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to approximately 1000 nuclei/μL than loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent, USA). All libraries were sequenced by Novaseq6000 (Illumina, USA) on a 150 bp paired-end run.

value: dentate gyrus

tag: condition

value: control


title: 18992X7 Case 1

first: Marcus

last: Pezzolesi


title: GFP_Setdb1KO, replicate 2, Total RNA-seq

value: Tamoxifen


title: DG_epilepsy, snRNA-Seq

description: 10X Genomics

value: epilepsy


title: 18992X6 Case 1


title: GFP_ Setdb1KO, replicate 1, Total RNA-seq


title: S4KO_EB+AC_Dnmt3b_ChIP

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads were trimmed by using cutadapt tool with parameters --trim-n  -m 30 -q 20,20.
Sequencing reads were aligned to mm10 genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely and properly paired mapping reads were retained.
Peaks for ChIP-seq data were called using MACS v2.2.7 with the sinificance cut-off P-value <=0.05 and fold change >=3; Peaks for CUT & Tag data were called using MACS v2.2.7 with the sinificance cut-off Q-value <=0.01 and fold change >=4
Assembly: mm10
Supplementary files format and content: bigWig files for each samples.

extract_protocol:
For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB505124 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis. For CUT&Tag, 1*10^5 ME cells or EB cells treated either with or without Activin as indicated, were harvested and crosslinked with 0.1% formaldehyde if necessary. Followed steps were performed using a commercially available kit (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904).
For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Qubit and AATI Fragment Analyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with VAHTS® Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608) according to manufacturer’s instructions. For CUT&Tag library construction, purified DNA samples were carried out following manual (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904)

treatment_protocol: Recombinant human Activin A (R&D Systems, 338-AC) were used at 50ng/ml. SB505124 (10uM, selleck, S2186) were used at 10μM.

tag: cell line

value: Smad4 knockout

value: Day 3.5 EBs were treated with 50ng/ml Activin A (R&D Systems, 338-AC) for 2 hours.


title: kre5 Deletion Biofilm, Spider Medium, One Week, Rep 2


title: 18992X5 Case 1

address: HELIX Building, 30 N Mario Capecchi Dr, 3rd floor South

institute: University of Utah


title: GFP_Setdb1KO_H3K9me3., replicate 1, ChIP


title: alg11 Deletion Biofilm, Spider Medium, One Week, Rep 1


title: GFP_ WT, replciate 2, Total RNA-seq


title: WT_EB+AC_Dnmt3b_ChIP

value: Wildtype


title: GFP_ WT, replicate 1 Total RNA-seq


title: WT Biofilm, Spider Medium, One Week, Rep 3


title: 18992X4 Ctrl 1

value: non-ESKD


title: WT Biofilm, Spider Medium, One Week, Rep 2

value: strain BWP17


title: 18992X3 Ctrl 1


title: WT Biofilm, Spider Medium, One Week, Rep 1

value: WT


title: 18992X2 Ctrl 1


title: S4KO_EB+AC_Dnmt3a_ChIP


title: WT_EB+AC_Dnmt3a_ChIP


title: matPΔtetra, IP

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

institute: CNRS

data_processing:
Cutadapt was used to trim the first 9 basepairs of the reads
BWA software was used for the alignment of reads on genomes
MatLab was used to create the files with the matS sites in the genome
Assembly: N16961.fa
Assembly: MCH1.fa
Assembly: EPV496.fa
Assembly: EPV487.fa
Supplementary files format and content: Table containing ChIP and Input data per base pair position

organism: Vibrio cholerae

source_name: O1 biovar El Tor str. N16961

growth_protocol: V. choleraestrains were grown in M9 minimal medium supplemented with 0.2% fructose, 1 μg/ml thiamine at 37°C until exponential phase

extract_protocol:
Cells were crosslinked with 1% formaldehyde final concentration. After quenching and cells lysis, samples were sonicated with Covaris.
For inmunoprecipitation, Anti-FLAG M2 affinity gel (Sigma) was added to the samples and elution was performed with 3xFLAG. Samples were de-crosslinked and gDNA for Input and IP was extracted with Qiagen PCR Purification Kit. Illumina libraries were prepared using DNA SMART ChIP-Seq Kit (TAKARA)

tag: strain

value: O1 biovar El Tor str. N16961

value: ChapR  matP{delta}20C:SPA

value: FLAG


title: GFP_Setdb1KO replicate 2, scRNA

description: 10x Genomics

tag: cell type

value: Lgr5-GFP-CreERT2/ Setdb1lox/lox


title: GFP_Setdb1KO replicate 1, scRNA

description: 10x Genomics


title: 18992X1 Case 1

city: Salt Lake City

value: whole blood

value: ESKD


title: scRNA-seq of LysM CRE mouse CAC

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

data_processing:
Cellranger v7.2.0 software (10x Genomics) was used to align reads to the refdata-gex-mm10-2020-A mouse reference transcriptome and generate the gene-cell unique molecular identifier (UMI) count matrix for each cell.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: normalized counts

source_name: colitis associated colon tumors

extract_protocol:
6-8 CACs from 3 mice per genotype were isolated and dissociated according to 10x Genomics protocol “Tumor Dissociation for Single Cell RNA Sequencing” (CG000147 Rev B). To increase the percentage of viable cells, we then proceeded with the 10 x Genomics protocol “Removal of Dead Cells for Single Cell RNA Sequencing” (CG000093 Rev C) according to manufactors instructions.
Barcoded sequencing libraries were prepared with the Chromium Single Cell 3’ v.3.1 Gene Expression Kit (10x Genomics).

treatment_protocol: Mice at 6-10 weeks of age were intraperitoneally (i.p.) injected with azoxymethane (AOM, 10 mg/kg) 5 days prior to the first and second dextran sodium sulfate (DSS) induced colitis period. The first and second colitis period were induced by giving 2.5% DSS dissolved in drinking water for a period of 5 days, followed by 16 days of regular water. Subsequently, the third colitis period was induced by giving 2% DSS for 5 days. All mice were sacrificed 110 days after the first AOM injection.

value: colitis associated colon tumors

value: tumor cells

value: AOM/DSS


title: scRNA-seq of Flox mouse CAC


title: matPΔtetra, Input

tag: chip antibody


title: GFP_WT replicate 2, scRNA

description: 10x Genomics

value: Intestine

value: Stem Cells

value: Tamoxifen


title: S4KO_EB+AC_S2/3_ChIP

data_processing:
Sequencing reads were trimmed by using cutadapt tool with parameters --trim-n  -m 30 -q 20,20.
Sequencing reads were aligned to mm10 genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely and properly paired mapping reads were retained.
Peaks were called using MACS v2.2.7 with the sinificance cut-off P-value <=0.05 and fold change >=3.
bigWig files were generated using the bamCoverage command of the deeptools package with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig files for each samples.

extract_protocol:
For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB431542 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis.
For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Recombinant human Activin A (R&D Systems, 338-AC) were used at 50ng/ml. SB431542 (Tocris, #1614) were used at 10μM

value: Smad4 knockout

value: Day 3.5 EBs were treated with 50ng/ml Activin A (R&D Systems, 338-AC) for 2 hours (Tocris, #1614).


title: WK12, scRNAseq

city: Cardiff

first: Laura

last: Howard

address: Maindy Road

institute: Cardiff University

data_processing:
Cell Ranger 6.1.1 using default parameters
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
Cells were harvested at successive timepoints spanning 0 – 12 weeks and single cell suspensions were prepared according to current 10x Genomics guidelines.
Libraries were constructed according to user guidelines for Chromium Next GEM Single Cell 3ʹ Reagent Kits with v3.1 chemistry


title: MatS15, terII, Input

value: ChapR {delta}vc1488 vca0560::vc1488 matP:SPA


title: WK10, scRNAseq


title: GFP_WT replicate 1, scRNA

description: 10x Genomics


title: S4KO_EB+SB_S2/3_ChIP

value: Day 3.5 EBs were treated with 10microM SB431542 for 4-6 hours (Tocris, #1614).


title: S4KO_EB_Input

value: LIF removal and form EB for 3.5 days.


title: WK8, scRNAseq


title: Ter inverted, IP

value: O1 biovar El Tor str. N16961

value: ChapR  INV(attP-dif)  matP:SPA


title: WK4, scRNAseq


title: FtsZ84, 42, Input

value: ChapR  ftsZts matP:SPA


title: WK2, scRNAseq


title: 26mo keto diet R

city: Columbus

first: Matthew

last: Stratton

state: OH

address: 473 W 12th Ave

institute: Ohio State University

data_processing:
fastqc (galaxy)
trimmomatic (galaxy)
mapping - RNA STAR (galaxy)
reads per gene - RNA STAR (galaxy)
Assembly: mm10
Supplementary files format and content: txt - reads per gene

extract_protocol:
Qiazol -> column purification and DNAse I treatment
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: brain

value: ketogenic diet


title: WK6, scRNAseq


title: FtsZ84, 42, IP

value: FLAG


title: S4KO_ES_S2/3_ChIP

value: Undifferentiated mESC


title: Ter inverted, Input


title: S4KO_ES_Input


title: MatS15, terII, IP


title: WK1, scRNAseq


title: 26mo keto diet P


title: FtsZ84, 30, IP


title: 26mo control diet N

value: control diet


title: CtL_12LM

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description: RNA extracted from liver tumor tissue

data_processing:
Demultiplexed and trimmed fastq's are generated from Illumina BaseSpace with FastqGeneration app
Alignment and raw counts are generated with nf-core/rnaseq v3.3 pipline. The pipiline are running with default parameters
Assembly: GRCh37
Supplementary files format and content: Matrix table with fpkm counts for every gene and each sample. Merged fpkm matrix table with all samples

source_name: liver metastasis

extract_protocol: RNA will be extracted from 5µm FFPE tissue sections using the AllPrep DNA/RNA FFPE kit (Qiagen). The quality of the RNA will be assessed with the Bioanalyzer. Libraries for RNA-Seq will be prepared using the TruSeq RNA Exome kit which is perfectly suited for low input and low quality RNA (Illumina). The procedure consists of two steps, the first one is a general whole transcriptome strand specific library preparation followed by a specific exon targeting enrichment. The quality of the resulting libraries will be controlled via the Bioanalyzer (High Sensitivity DNA Kit). The intermediate library before exon enrichment will be quantified with Qubit, the final library with qPCR. Samples will be sequenced in paired-end mode

value: liver metastasis tumor sample

tag: disease

value: tumor


title: MCH1, IP

value: MCH1 ChapR matP:SPA


title: FtsZ84, 30, Input


title: WT, IP

value: ChapR  matP:SPA


title: 26mo control diet L


title: CtL_10LM

description: RNA extracted from liver tumor tissue


title: 26mo control diet K


title: 26mo keto diet O


title: CtL_7LM

description: RNA extracted from liver tumor tissue


title: WT_DIST_E12_5_REP2

city: Montréal

first: Fanny

last: GUERARD-MILLET

address: 110 AVENUE DES PINS OUEST

institute: IRCM

data_processing:
Mouse (GRCm38.p6) genome FASTA and GTF files were downloaded from the Ensembl Website (http://useast.ensembl.org/info/about/publications.html) on October 4th 2022. Adapter sequences were removed from reads using robtools (https://github.com/francoisrobertlab/robtools) with the command “robtools trimmomatic --trimmers "ILLUMINACLIP:adapters.fa:2:30:10 HEADCROP:10 SLIDINGWINDOW:4:15 TRAILING:20 MINLEN:40"” which requires Trimmomatic. Reads were aligned to the genome using STAR (https://github.com/alexdobin/STAR ) using the command “STAR --readFilesCommand zcat --readFilesIn "$sample"-paired_R1.fastq.gz "$sample"-paired_R2.fastq.gz --genomeDir mouse-star-index --genomeLoad NoSharedMemory --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --outSAMheaderHD @HD VN:1.4 SO:unsorted --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFileNamePrefix "$sample".star/"$sample"_“ where “$sample” is replaced by the sample name. STAR version 2.7.9a was used. The number of fragments per transcript were counted using RSEM (http://deweylab.github.io/RSEM/ ) with the command “rsem-calculate-expression --alignments --paired-end "$sample".star/"$sample"_Aligned.toTranscriptome.out.bam rsem-index/Mus_musculus "$sample".rsem/"$sample"” where “$sample” is replaced by the sample name. RSEM version 1.3.3 was used.
Assembly: mm10

source_name: distal forelimb

extract_protocol:
RNA was extracted from dissected proximal and distal limb buds from 2 independent pools of wild type limb buds (n=2) and from two independent pools of mutant limb buds (n=2). The extraction was performed using the RNAeasy Plus mini kit. Next, mRNA enrichment, library preparation and flow-cell preparation for sequencing were performed by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations. Sequencing was done on a Nextseq500 instrument with a paired-end 50 cycles protocol.
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina in a 50 cycles paired-end configuration.

value: distal forelimb

value: WT


title: Cauda Tissue mirVana Purified OTTR AlkB Rep 4

value: FVB/NJ


title: MCH1, Input


title: 26mo control diet M


title: CtL_8LM

description: RNA extracted from liver tumor tissue


title: WT, Input


title: N2_30C_eemb_rep1

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Adapter were trimmed using Trimmomatic v0.39. Reads were aligned to the C. elegans genome (ce10) with the R package QuasR v1.42.1, (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html). The command “proj <-qAlign(“samples.txt“,“BSgenome. Celegans.UCSC.ce10”, splicedAlignment=TRUE)” instructs hisat296 to align using default parameters, considering unique reads for genes and genome wide distribution.
Count Tables of reads mapping within annotated exons in WormBase (WS220) (expr_mRNA.tab) were constructed using the qCount function of the QuasR package to quantify the number of reads in each window (qCount(proj, GRange_object,orientation=“same”)) and normalized by division by the total number of reads in each library and multiplied by the average library size. Transformation into log2 space was performed after the addition of a pseudocount of 8 to minimize large changes in abundance fold change (FC) caused by low count numbers.
Assembly: ce10
Supplementary files format and content: Tab delimited table with first column indicating the WormBase ID followed by coumns with the read counts for each condition and replica

organism: Caenorhabditis elegans

source_name: embryo

extract_protocol:
RNA was extracted from early wild-type (N2 Bristol) C. elegans embryos from a synchronized culture grown at 20°C and exposed to indicated temperatures for 2 h, using Trizol. Embryos were freeze cracked five times, then RNA was extracted with choloroform followed by isopropanol precipitation. Further purification was performed with the RNA Clean and Concentrator kit (Zymo).
Libraries were produced using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina). rRNA was depleted using the Ribo-Zero Plus kit supplemented with custom made C. elegans specific rDNA oligos (IDT).
Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyser (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Life technologies). Equimolar amounts of indexed libraries were pooled and sequenced on a NextSeq 2000 (Illumina).

treatment_protocol: adults containing embryos were shifted to indicated temperatures for 2 hours, prior to isolation of embryos by bleaching.

value: embryo

value: wild-type (N2 Bristol)


title: N2_30C_eemb_rep3

growth_protocol: RNA was extracted from early wild-type (N2 Bristol) C. elegans embryos from a synchronized culture grown at 20°C


title: WT_PROX_E12_5_REP2

source_name: proximal forelimb

value: proximal forelimb


title: N2_25C_eemb_rep3


title: 13mo keto diet G

source_name: brain


title: CtL_1LM

description: RNA extracted from liver tumor tissue


title: WT_DIST_E12_5_REP1


title: CtL_6LM

description: RNA extracted from liver tumor tissue


title: 26mo keto diet Q


title: CtL_20C

description: RNA extracted from primary colon tumor tissue

source_name: colon cancer

value: primary colon tumor sample


title: N2_30C_eemb_rep2


title: WK0, scRNAseq


title: CtL_5LM

description: RNA extracted from liver tumor tissue


title: 13mo keto diet H


title: 13mo keto diet J


title: CtL_12C


title: CtL_20LM

description: RNA extracted from liver tumor tissue


title: Dmel, genitalia, 30 hAPF

city: Durham

first: Javier

last: Figueras Jimenez

address: South Road

department: Biosciences

institute: Durham University

data_processing:
Raw reads generated from 30 hAPF male pupae were mapped to D. melanogaster genome version r6.55 Dec 2023 using Bowtie2 (version 2.4.5)
We used Samtools (version 1.9) to convert sam files to bam files and remove duplicates
Bedtools (version 2.31.1) was used to convert generated datafiles into bed format and we re-centered the reads according to (BUENROSTRO et al. 2013).
Peak calling was then performed using MACS2 (version 2.2.7.1) with the parameters -extsize 50, -q 0.01.
bigWig files were generated using deeptools (version 3.5.2) normalizing using CPM, binzise 10 and smoothlenght 50. Narrowpeaks obtained using MACS2 (version 2.2.7.1) with the parameters -extsize 50, -q 0.01.
Assembly: dm6 (D. melanogaster genome version r6.55)
Supplementary files format and content: bigWig and narrowPeak

organism: Drosophila melanogaster

source_name: Pupal terminalia

growth_protocol: Drosophila melanogaster prepupae were collected and aged at 25 ºC for 30 hours.

extract_protocol:
Pupae were dissected in ice-cold 1XPBS, followed by incubation in lysis buffer (10 mM Tris-HCL, pH = 7.5; 10 mM NaCl; 3 mM MgCl2; 0.1% IGEPAL and 0.1% digitonin). After the lysis was stopped, the nuclei were collected by centrifuging at 500g for 10 minutes. 50000 nuclei were resuspended in Tagmentation Mix [25 ul tagmentation buffer (20 mM Tris-CH2COO-, pH = 7.6; 10 mM MgCl2; 20 % Dimethylformamide); 2.5 Tn5 transposase; 22.5 ul H2O] and incubated for 30 minutes at 37 ºC. 3 ul of 2 M NaAC, pH = 5.2 was added to the sample and then purified using a QIAGEN MinElute Kit
ATAC-seq library amplification was performed using NEBNext High Fidelity 2X PCR Mix with primers indexed with primers compatible with Nextera adaptors from Diagenode. 150 bp paired-end sequencing was carried out by Novogene (UK).

value: Pupal terminalia

value: Wt (OR-R)


title: CtL_10C


title: CtL_8C


title: CtL_4LM

description: RNA extracted from liver tumor tissue


title: N2_20C_eemb_rep1


title: 13mo control diet A

value: brain


title: N2_25C_eemb_rep2


title: 13mo keto diet F

value: ketogenic diet


title: N2_25C_eemb_rep1


title: Tg, repllicate 3, RNASeq

city: Poznań

first: Arkadiusz

last: Kajdasz

address: ul. Z. Noskowskiego 12/14

institute: Institute of Bioorganic Chemistry PAS

data_processing:
Raw RNA-seq data were converted to FASTQ format with bcl2fastq2 (v2.17, Illumina), and FastQC (v0.11.4) was used to assess the quality of each sequencing run. We then utilized the SQuIRE pipeline45 for subsequent steps. STAR version 2.5.3a, StringTie version 1.3.3b, and DESeq2 version 1.16.149 were used within the SQuIRE pipeline for read alignment, transcript assembly, and quantification for each replicate, and differential gene expression analysis, respectively.
Assembly: Danio rerio GRCz11
Supplementary files format and content: Tab-separated files with raw reads for each sample

source_name: eye

extract_protocol:
Total RNA was isolated for RNA-seq using TRIzol reagent. Thirty five larvae were pooled together to comprise one RNA sample. The quality of RNA was checked by measuring absorbance at 260, 280, and 230 nm, and Bioanalyzer Nano RNA chip (Agilent, USA) analysis. Samples with 260/280 nm and 230/280 nm absorbance ratio >1.8 and RNA integrity number values >8 were used for further processing. Total RNA was first digested by DNase I and purified using the RNA Clean and Concentrator Kit (ZYMO Research, Irvine, CA, USA) according to the manufacturer’s recommendations.
Library construction was conducted using stranded Illumina TruSeq protocol.

value: eye

value: AB

value: 5 dpf


title: 13mo control diet E

value: control diet


title: 13mo control diet C


title: WT_PROX_E12_5_REP1


title: N2_10C_eemb_rep2


title: N2_20C_eemb_rep2


title: 13mo control diet B


title: stim2KO, repllicate 3, RNASeq


title: N2_20C_eemb_rep3


title: CtL_5C

value: tumor


title: stim2KO, repllicate 1, RNASeq


title: WT_ME_S2/3 CUT&Tag

data_processing:
Sequencing reads were trimmed by using cutadapt tool with parameters --trim-n  -m 30 -q 20,20.
Sequencing reads were aligned to mm10 genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely and properly paired mapping reads were retained.
Peaks for ChIP-seq data were called using MACS v2.2.7 with the sinificance cut-off P-value <=0.05 and fold change >=3; Peaks for CUT & Tag data were called using MACS v2.2.7 with the sinificance cut-off Q-value <=0.01 and fold change >=4
Assembly: mm10
Supplementary files format and content: bigWig files for each samples.
Library strategy: CUT&Tag

value: Wildtype

value: EpiLC to mesendoderm induction with 3uM CHIR99021 (Cayman, 13122)


title: E14_EB_D4_ATAC

data_processing:
Sequencing reads were trimmed by using cutadapt tool with parameters --trim-n  -m 30 -q 20,20.
Sequencing reads were aligned to mm10 genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely and properly paired mapping reads were retained.
Peaks for ChIP-seq data were called using MACS v2.2.7 with the sinificance cut-off P-value <=0.05 and fold change >=3; Peaks for CUT & Tag or ATAC-seq data were called using MACS v2.2.7 with the sinificance cut-off Q-value <=0.01 and fold change >=4
Assembly: mm10
Supplementary files format and content: bigWig files for each samples.

extract_protocol:
For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB505124 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis. For CUT&Tag, 1*10^5 ME cells or EB cells treated either with or without Activin as indicated, were harvested and crosslinked with 0.1% formaldehyde if necessary. Followed steps were performed using a commercially available kit (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904; Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904). For ATAC-seq, 8*10^4 single-celled EB cells were treated with NP-40(10%), Tween-20(10%) and digitonin(1%), and the reaction was stopped after the cell membrane burst. The Tn5 transposase (Illumina #FC-121-1030) was mixed with the nucleus at 1000 RPM at 37ºC for 30 minutes, and the DNA fragments were purified using the DNA Clean and Concentrator kit (Zymo #D4014).
For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Qubit and AATI Fragment Analyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with VAHTS® Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608) according to manufacturer’s instructions. For CUT&Tag library construction, purified DNA samples were carried out following manual (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904). For ATAC-seq library construction, DNA fragments were amplified using NEBNext High-Fidelity 2X PCR Master Mix (NEB #M0541L) and index primers (adaptors), which were further purified.

value: LIF removal and form EB for 4 days.


title: HEK293T_Mock-c

city: guangzhou

first: Ye

last: Shaotang

address: No. 483, Wushan Road, Tianhe District, Guangzhou

institute: South China Agricultural University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Human embryonic kidney cells

growth_protocol: DMEM with 2% FBS

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfection by Lipo8000 (Beyotime, China)

value: Human embryonic kidney cells

tag: passages

value: wild type


title: N2_10C_eemb_rep3

value: embryo

value: wild-type (N2 Bristol)


title: CtL_1C

value: primary colon tumor sample


title: S4KO_ME_S2/3 CUT&Tag

value: Smad4 knockout


title: CtL_7C


title: stim2KO, repllicate 2, RNASeq


title: Tg, repllicate 1, RNASeq


title: CtL_6C


title: S4KO+Dnmt3b-shRNA_EB_S2/3 CUT&Tag

value: Smad4 knockout infected by Dnmt3b-shRNA

value: LIF removal and form EB for 3.5 days.


title: E14-Dnmt3b-3xFlag_EB_Flag CUT&Tag

value: 3xFlag tag insertion at C-terminus of Dnmt3b


title: Ei2: Mtb, E-ALF, after infection, rep2

city: San Antonio

first: Anna

last: Allue Guardia

state: Texas

address: 8715 Military Dr W

institute: Texas Biomedical Research Institute

description:
Sample 13
ALF-Mtb_AOF_raw.txt

data_processing:
Raw sequencing reads were trimmed and aligned to the M.tb H37Rv reference genome (Genbank NC_000962.3) with the STAR aligner v2.5.3a in the Partek Flow Genomic Analysis software using default settings.
Data were filtered to remove poorly expressed genes and differentially expressed genes (DEGs) were identified using the DESeq2 method with an FDR cut-off of 0.1 and a minimum fold change (FC) of 2 in the iDEP.94 software.
Assembly: H37Rv (Genbank NC_000962.3)
Supplementary files format and content: Raw counts

organism: Mycobacterium tuberculosis

growth_protocol: Before infection: M.tb Erdman were cultured from frozen stocks for 14 days at 37°C in 7H11 agar plates (Remel), supplemented with oleic acid, albumin, dextrose and catalase (OADC). After infection: A549 cell line (ATs) were infected with M.tb Erdman for 72 hours at 37°C with 5% CO2.

extract_protocol:
Bacterial RNA was extracted using the Quick-RNA Fungal/Bacterial Miniprep kit (Zymo Research). Briefly, bacterial pellets were suspended in RNA lysis buffer and transferred to a ZR BashingBead Lysis tube containing 0.1 mm and 0.5 mm ceramic beads. Samples underwent a bead beating procedure in a Disruptor Genie (10 cycles of 1 min at maximum speed with 1 min intervals on ice), facilitating the breaking down of the M.tb cell envelope. RNA in the supernatant was isolated using the Zymo-spin columns, including an in-column DNAse I treatment, and was finally eluted in nuclease-free water. A second DNAse treatment was performed on the extracted RNA using the TURBO DNAse reagent (Thermo Fisher Scientific, Waltham, MA, USA). RNA was further purified using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA),  MA, USA). Conversely, infected ATs (at 72 hpi) were washed twice with culture media and then lysed with GTC solution (4M guanidinium thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM tri-sodium citrate, 0.1M 2-mercaptoethanol, 0.5% Tween 80, pH 7.0) 34, 35 for 5 min at RT and then centrifuged at 5000 x g for 30 min at RT to recover bacteria. M.tb pellets were washed in GTC lysis solution to combine the content from all flasks (4 x 150 cm2 flasks/ condition) into one single tube, centrifuged, and suspended in RNA lysis buffer. RNA was then extracted using the Quick-RNA Fungal/Bacterial Miniprep kit, treated with TURBO DNAse, and purified with the RNA Clean & Concentrator kit, as previously described.
A whole-stranded transcriptome RNA library was generated using the Zymo-Seq RiboFree Total RNA kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol. RNA (250 ng) was used as input to construct the library, which included a rRNA depletion step of 30 min followed by 15 cycles of PCR. Using a NextSeq 500 Mid Output Illumina platform, a 75-bp paired-end (PE) sequencing was conducted. RNA sequencing was performed on three independent experiments (n = 3 per condition), except for E-ALF-exposed M.tb before infection (n=2), where one of the replicates was not included in the study due to low RNA concentration and quality.

treatment_protocol: Single bacterial suspensions were obtained and exposed to human ALFs for 12 ± 2 hours at 37°C. Following exposure, bacteria were thoroughly washed to remove any unbound ALF; the bacterial pellet was either stored at -80°C for further RNA extraction [after incubation in RNAProtect (Qiagen, Hilden, Germany) for 10 min at room temperature, RT] or suspended in culture media for ATs infection. Infected ATs (at 72 hpi) were washed twice with culture media and then lysed with GTC solution (4M guanidinium thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM tri-sodium citrate, 0.1M 2-mercaptoethanol, 0.5% Tween 80, pH 7.0) 34, 35 for 5 min at RT and then centrifuged at 5000 x g for 30 min at RT.

value: Erdman

value: Elderly ALF

value: After infection


title: N2_10C_eemb_rep1


title: E16, IgG, WT, rep2

city: Ann Arbor

first: Shigeki

last: Iwase

state: Michigan

address: 1241 E. Catherine St.

department: Human Genetics

data_processing:
Reads were aligned to the UCSC mm10 genome using Bowtie2. Non-unique alignments (MAPQ > 10) and reads < 140-nt were filtered out.
bigWig files were generated using bamCoverage (deepTools), with files normalized to BPM for each replicate.
Average coverage was calculated from biological replicates within each genotype using bigWigCompare (operation set to “mean”).
To reduce background noise, final normalization to IgG samples was performed using bigWigCompare (operation set to “ratio”).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: cortex

extract_protocol:
The digested target chromatin was released and purified by phenol, chloroform, and ethanol.
Sequencing libraries were prepared with NEBNxt Ultra II DNA (NEB #E7645L) and NEB UDI plate 1 (NEB #E6440L)

treatment_protocol: E16.5 cortices are taken from two embryos per genotype (the sex was balanced between genotypes) and washed with HHGN solution78 then washed 4 times with HHGN containing 10% FBS, treated with 0.1 mg/ml DNaseI for 5 mins at RT, triturated using a P1000 pipet. Dissociated cells were precipitated by a centrifugation at 1500 rpm for 5 min, and washed with dPBS (Gibco, 14190). 1 million cells per sample were re-suspended in Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM spermidine, 1X protease inhibitor cocktail), and Concanavalin A-coated beads (Bangs Laboratories, Inc., #BP531) were added into the cell suspension and incubated for 10 min. Bead-bound cells were then incubated overnight at 4°C in Wash buffer supplemented with EDtA and digitonin (EMD Millipore, #300410, Wash buffer D) and 1 µg antibody. The beads were then washed three times with Wash buffer D, followed by an incubation with 200 µl pA-MNase (0.7 ng/µl) for 1 hour at 4°C. The beads were washed three times Wash buffer D before 2 mM of CaCl2 were added to activate the pA-MNase for 30 min on ice. The reaction was quenched by 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 50 µg/ml RNase A (QIAGEN, #19101), 50 µg/ml glycogen (Roche, #10901393001) and 2 pg/ml Drosophila spike-in DNA) at 37°C for 10 min.

value: cortex

value: WT

tag: cut&run antibody

value: IgG (Abcam, ab171870)


title: E16, IgG, KO, rep2


title: E16, IgG, WT, rep1


title: HEK293T_Mock-b


title: E16, IgG, KO, rep1


title: Tg, repllicate 2, RNASeq

value: eye

value: AB

value: 5 dpf


title: Ei3: Mtb, E-ALF, after infection, rep3

description:
Sample 14
ALF-Mtb_AOF_raw.txt


title: E16, H4K20me2, KO, rep2

value: H4K20me2 (Abcam, ab9052)


title: HEK293T_R-M2-2

value: Human embryonic kidney cells

value: transfected with CIV M2 and canine RIG-I


title: E14-Dnmt3a-3xFlag_EB_Flag CUT&Tag

value: 3xFlag tag insertion at C-terminus of Dnmt3a


title: HEK293T_Mock-a

value: wild type


title: HEK293T_R-M2-3


title: HEK293T_R-M2-1


title: Ei1: Mtb, E-ALF, after infection, rep1

description:
Sample 12
ALF-Mtb_AOF_raw.txt


title: E14+Dnmt3b-shRNA_EB_Dnmt3b CUT&Tag_2

value: Wildtype infected by Dnmt3b-shRNA


title: CtL_4C

value: primary colon tumor sample

value: tumor


title: Ai2: Mtb, A-ALF, after infection, rep2

description:
Sample 10
ALF-Mtb_AOF_raw.txt

value: Erdman

value: Adult ALF


title: E16, H4K20me2, WT, rep1


title: S4KO_EB_S2/3 CUT&Tag

value: Smad4 knockout

value: LIF removal and form EB for 3.5 days.


title: HEK293T_R-M1-3

value: transfected with CIV M1 and canine RIG-I


title: S4KO+Dnmt3b-shRNA_EB_Dnmt3b CUT&Tag_2

value: Smad4 knockout infected by Dnmt3b-shRNA


title: Ai3: Mtb, A-ALF, after infection, rep3

description:
Sample 11
ALF-Mtb_AOF_raw.txt

value: After infection


title: S4KO_EB_Dnmt3b CUT&Tag_2