title: HNO, D72, HET, Bio Rep 2

description: 10x Genomics Chromium

value: Human iPSC derived neural organoids (HNOs)

value: iPSC F11362.11F10 (HET:MAPT R406W/R406R heterozygous)

value: 5 HNOs pooled per library


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 1 hour, biol rep 2

status: Public on Mar 17 2025

type: SRA

city: Gif-sur-Yvette

first: Mathieu

last: Rougemaille

address: 1 avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell

library_source: transcriptomic

data_processing:
Demultiplexing was performed with bcl2fastq v2.20 and adapters were trimmed with fastp v0.23.1.
Reads were aligned using STAR v2.6.1d (--outSAMtype BAM SortedByCoordinate \ --quantMode GeneCounts \ --outSAMunmapped Within \ --outSAMattributes Standard \)
Read count was performed using featureCounts from subread v2.0.6
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa.gz and Schizosaccharomyces_pombe_all_chromosomes.gff3.gz from Pombase
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: haploid, h- cells

growth_protocol: Schizosaccharomyces pombe cells carrying the pat1-L95G allele were grown in EMM at 30°C prior to over-night (15 to 16h) incubation in EMM lacking nitrogen (EMM-N) to synchronize cells in G1. The following day, cultures were supplemented with 50 mg/L L-leucine, 500 µg/mL NH4Cl and 25 µM 3-MB-PP1 to induce meiosis and aliquots were harvested every hour for up to 8h.

extract_protocol:
Total RNAs were extracted using the hot acid phenol method.
PolyA RNAs were enriched from total RNAs using oligodT-attached magnetic beads and mRNA librairies were constructed using the Novogene NGS RNA Library Prep Set (PT042).

treatment_protocol: Meiosis was induced by adding 25 µM 3-MB-PP1 to cell cultures for up to 8 hours.

tag: cell type

value: haploid, h- cells

tag: genotype

value: leu1-32, pat1-L95G::kanR

tag: treatment

value: meiosis induction, 25 uM 3-MB-PP1

tag: time

value: 1 hour


title: HNO, D120, HET, Bio Rep 1

city: Columbus

first: Hongjun

last: Fu

state: OH

address: 616 Biomedical Research Tower, 460 W. 12th Ave

department: Department of Neuroscience

country: USA

institute: The Ohio State University Wexner Medical Center

description: 10x Genomics Chromium

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20. Cell Ranger v6.1.2 (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the human reference genome GRCh38.
Assembly: Human reference genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Human iPSC derived neural organoids (HNOs)

extract_protocol:
On Day 70 and Day 120, ten healthy HNOs of similar size were selected from each line. Five HNOs were combined to form a technical replicate. Each replicate was gently dissociated following the Single Cell Preparation Guide established by 10x Genomics.
Approximately 10,000 live cells were used to generate scRNA-seq libraries with the 10x Chromium single-cell 3′ V2 library kit (10x Genomics) according to the manufacturer's instructions and paired-end sequencing was performed with a NovaSeq600 S2 flow cell using an Illumina NovaSeq 600 sequencer.

tag: tissue

tag: cell line

tag: technical replication


title: allS inducible 1

city: Boston

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: ChIP-Seq of inducible allS with C-terminal FLAG tag

library_source: genomic

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
For Library-ChIP: Inserted sequences were counted from raw reads by identifying the anchor sequence (from the flank of the insertion site) "GGACGGATCCTCGAGCATGC", and taking the following 37 nucleotides after the anchor.
For Library-ChIP: Low abundance hits were dropped out (< 0.1% of preIP reads)
For Library-ChIP: Counts were normalized within-sample for sequencing depth by dividing counts by average counts for each insertion sequence
For Library-ChIP: Enrichment was determined as the ratio of normalized postIP:preIP counts
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps
Supplementary files format and content: Library-ChIP: TSV file where first column is the inserted sequence identified in processing step 1, columns 2 and 3 are the number of times sequence was identified in R1 and R2 reads, column 4 is the identifier of the sequence from the designed insertion pool, and column 5 is the sum of R1 and R2 reads

molecule: genomic DNA

organism: Escherichia coli K-12

growth_protocol: Cells were grown in indicated media at 30°C with shaking in vented flasks

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  For in vivo ChIP-Seq, cells were sheared via sonication; for in vitro ChIP-Seq, DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-FLAG, anti-V5, or anti-6xHis mAb (indicated in metadata).  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  For Library-ChIP, preIP samples used sheared DNA purified via ProteinaseK digestion and Qiaquick PCR purification kit prior to addition of anti-tag antibody; postIP samples used sheared DNA that was immunoprecipitated, washed, purified, and extracted in the same way as ChIP-Seq.
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).  For Library-ChIP, libraries were constructed similarly to Illumina's 16S metagenomic library prep (Illumina Ref #15044223 Rev. B).  Briefly, an initial PCR was performed on DNA with a universal primer pair targeting flanks of the insertion site on the pAMD plasmid where designed sequences were inserted.  These primers contained overhangs that could be targeted by Illumina Nextera XT Index Kit v2 (Illumina Cat. No. FC-131-2001) primers.  First PCR was cleaned up with Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  Second PCR used a unique pair of primers from the Illumina Nextera kit for each sample, and were cleaned up with AMPureXP beads (Fisher Scientific Cat. No. NC9933872).

treatment_protocol: Inducible strains were treated with arabinose prior to crosslinking, some native strains were treated with GlcNac for 5 minutes prior to crosslinking (treatments indicated in metadata).

tag: strain

tag: transcription factor

value: allS

tag: chip antibody

value: anti-FLAG mAb

tag: antibody vendor/catalog#

value: Sigma/Cat. No. F1804

tag: media

value: M9 Minimal with 0.4% glycerol

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: Sheep pancreas CF 120 day scRNAseq donor 5 scRNA-seq

city: Cleveland

first: Ann

last: Harris

address: 2109 Adelbert Road

department: Genetics

institute: Case Western Reserve University

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.1.0
Assembly: Oar_v4.0/oviAri4 (Texel)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Pancreas

extract_protocol:
For single cell isolation from fresh pancreas, ~ 300 mg of tissue was cut into 2-3 mm pieces and subjected to two rounds of digestion: First in 5ml of collagenase solution (200 U/ml collagenase, 40 IU/mL, DNAse I 250 μg/mL, soybean trypsin inhibitor (SBTI) (all from Worthington), 3 mM CaCl2, at 37°C, with continuous stirring for 30-40 min. Tissue clumps were then disassociated by pipetting 10 times in a 5 ml serological pipette and left to settle for 3-4 minutes at which point the supernatant was collected and stored on ice as cell suspension 1. Second, 5 ml of fresh collagenase digestion solution as above was added to the settled tissue clumps remaining after the first digestion and again stirred at 37°C for 30-40 min, at which point very little tissue debris remained. The supernatant (cell suspension 2) was pooled with cell suspension 1 and together passed through a cell strainer (200 µm, pluriSelect) to remove any tissue debris. The strained cell suspension was then centrifuged at 300 ×g for 5 min, washed once in HBSS (Sigma Aldrich) + 2% FBS and centrifuged again. 4 ml of 1× Red Blood Cell Lysis Solution (Miltenyi Biotec 130-094-183) was added to the cell pellet which was vortexed for 5 seconds and then incubated for 5 minutes at room temperature. After 10 mL of HBSS with 2% FBS was added, the mixture was centrifuged at 300 ×g for 5 min, and the supernatant was removed. The cell pellet was then digested with 3 mL of Accutase (Stem Cell Technologies) for 15-25 min with frequent gentle pipetting with a wide-bore pipette, after which time the cells were visualized under a microscope. If any cell clumps persisted, they were collected by centrifugation and further digested with replace with 3 mL of Accutase, and digested for 10-15 min. Accutase was removed by washing the cells with 5 mL HBSS + 2% FBS, followed by centrifugation to collect the cells. The supernatant was discarded, and the cell pellet was resuspended in 0.5-1.0 ml HBSS, passed through a 20-µm mini cell strainer (pluriSelect) and cells counted. ~ 2000 - 6,000 cells were used for scRNA-seq using the 10x Genomics Chromium system.
Libraries generated from single cells according to the manufacturer's protocol for 10X Genomics Chromium Single Cell 3' Reagent Kits v3 or 3.1.

value: Pancreas

tag: Sex

value: Female

tag: disease state

value: CF


title: allR native 6

description: ChIP-Seq of native allR with C-terminal SPA tag

value: allR

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: allR native 5


title: wt nitrogen-starved cells, EMM-N, biol rep 2

value: over-night nitrogen starvation


title: Sheep pancreas CF 120 day scRNAseq donor 4 scRNA-seq

description: 10x Genomics

value: Male


title: HNO, D72, HET, Bio Rep 1

description: 10x Genomics Chromium

value: Human iPSC derived neural organoids (HNOs)

value: iPSC F11362.11F10 (HET:MAPT R406W/R406R heterozygous)

value: 5 HNOs pooled per library


title: allR native 10

description: ChIP-Seq of native allR with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: HNO, D72, WT, Bio Rep 2

description: 10x Genomics Chromium

value: WT:CRISPR-Cas9 edited isogenic control


title: vegetative wt cells, EMM, biol rep 2

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: none, vegetative growth


title: allR native 4

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: Sheep pancreas CF 120 day scRNAseq donor 2 scRNA-seq

description: 10x Genomics

value: Pancreas

value: CF


title: HNO, D72, WT, Bio Rep 1

description: 10x Genomics Chromium


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 8 hours, biol rep 1

value: meiosis induction, 25 uM 3-MB-PP1

value: 8 hours


title: Q6_3, case batch 3

city: New York

first: Joseph

middle: A.

last: Gogos

state: NY

address: 3227 Broadway

department: Zuckerman Institute

institute: Columbia University

data_processing:
Cutadap (Martin, EMBnet Journal 2011) and in house perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Sequence quality was subsequently verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
HISAT2 (Kim et al., Nat Methods 2015) was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/. The mapped reads of each sample were assembled using StringTie (Pertea et al., Nat Biotechnol 2015). Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and GffCompare. After the ﬁnal transcriptome was generated, StringTie and edgeR81 were used to estimate the expression levels of all transcripts. StringTie was used to assess expression levels for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Assembly: Hg38, Ensembl version 98

source_name: hiPSC-derived cortical neurons

growth_protocol: Human iPSC-derived cortical neurons at DIV8 were generated using combined small molecule inhibitors as described in Thakur et al.

extract_protocol:
Total RNA extraction with miRNA enrichment was performed using the Vana™ miRNA Isolation Kit (Thermo Fisher Scientific, AM1561).
Poly(A) RNA sequencing library was prepared by using approximately 1 ug of total RNA following Illumina’s TruSeq-stranded-mRNA (Illumina, San Diego, CA, USA) sample preparation protocol. RNA integrity was checked with Bioanalyzer 2100 (Agilent, CA, USA). Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip (Agilent, CA, USA). Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 (LC Sciences, Houston, TX, USA) sequencing system.

value: hiPSC-derived cortical neurons


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 7 hours, biol rep 1

value: 7 hours


title: allR native 2

value: allR


title: Sheep pancreas CF 80 day scRNAseq donor 3 scRNA-seq

description: 10x Genomics

value: Male


title: Q6_2, case batch 2


title: allR native 1


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 6 hours, biol rep 1

value: 6 hours


title: Sheep pancreas CF 80 day scRNAseq donor 2 scRNA-seq

description: 10x Genomics


title: Pancreas, term CF, rep2

data_processing:
Bulk RNA-seq mapped to the sheep (texel, Oar_v4.0) genome with STAR 2.6 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Assembly: Texel (ovis aries) sheep genome Oar_v4.0
Supplementary files format and content: Feature assignment of aligned reads to annotated sheep genes in TSV format.

source_name: pancreas

extract_protocol:
50-100mg of sample was excised from frozen tissue and mixed with 1mL TRIzol Reagent and ceramic beads over ice. Tissue was homogenized and incubated at RT to dissociate the nucleoprotein complex. Solution was then mixed with 200uL chloroform, centrifuged, and the aqueous phase removed. RNA was precipitated with 100% isopropanol, washed with 75% ethanol, and solubilized in water.
RNA concentration and purity were measured by nanodrop and 1ug was used for oligo-dt mRNA directional library preperation

value: pancreas

tag: developmental stage

value: Day 147 (term)

tag: sample


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 5 hours, biol rep 1

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: 5 hours


title: Q6_1, case batch 1


title: Pancreas, term CF, rep1


title: Q5_3, ctrl batch 3

value: Wild type


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 4 hours, biol rep 1

value: 4 hours


title: Q5_2, ctrl batch 2


title: Sheep pancreas CF 120 day scRNAseq donor 3 scRNA-seq

description: 10x Genomics


title: agaR inducible 1

description: ChIP-Seq of inducible agaR with C-terminal FLAG tag

value: agaR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: aaeR inducible 1

description: ChIP-Seq of inducible aaeR with C-terminal FLAG tag

value: aaeR


title: Pancreas, d120 CF, rep2

value: Day 120

value: CF


title: Q5_1, ctrl batch 1

value: hiPSC-derived cortical neurons


title: agaR native 1

description: ChIP-Seq of native agaR with C-terminal SPA tag


title: Pancreas, d120 CF, rep1

value: pancreas


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 2 hours, biol rep 1

value: meiosis induction, 25 uM 3-MB-PP1

value: 2 hours


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 3 hours, biol rep 1

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: 3 hours


title: Pancreas, d100 CF, rep2

value: Day 100


title: MS_99

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Microbial reads were discriminated against human reads with BMTagger (ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/).
To perform the analysis at order/family/species levels, reads were mapped to the collection of all available genomes (https://www.ncbi.nlm.nih.gov/genome/) with Kraken2 for exact alignment of k-mers and accurate read classification.
Species alpha diversity index was calculated with vegan (https://cran.r-project.org/web/packages/vegan).
Assembly: n/a
Supplementary files format and content: Kraken2 raw counts (https://ccb.jhu.edu/software/kraken/MANUAL.html#output-format)

source_name: RRMS patient stool-associated microbiome

extract_protocol:
Fecal samples that were collected in DNA/RNA Shield Fecal Collection Tubes (Euroclone). DNA was extracted from fecal samples using the QIAamp powerFecal Pro DNA Kit (Qiagen) following the manufacturer’s instructions.
Sequencing libraries were prepared using the Nextera DNA Flex Library Preparation Kit (Illumina), following the manufacturer’s guidelines.
Sequencing was performed on the Illumina NovaSeq 6000 platform following the manufacturer’s protocol on an S4 flow cell for 150bp paired-end.

value: Stools

tag: subject status

value: RRMS patient


title: allR native 3

value: allR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: vegetative wt cells, total RNA, biol rep 1

data_processing:
For total RNA samples, demultiplexing was performed with bcl2fastq2 v2.18.12 and adapters were trimmed with Cutadapt v1.15.
For polyA RNA samples, demultiplexing was performed with bcl2fastq v2.20 and adapters were trimmed with fastp v0.23.1.
Reads were aligned using STAR v2.6.1d (--outSAMtype BAM SortedByCoordinate \ --quantMode GeneCounts \ --outSAMunmapped Within \ --outSAMattributes Standard \)
Read count was performed using featureCounts from subread v2.0.6
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa.gz and Schizosaccharomyces_pombe_all_chromosomes.gff3.gz from Pombase
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.

growth_protocol: Schizosaccharomyces pombe cells  were cultured in minimal medium (EMM) for 2 days at 30°C. Cells were harvested at OD = 0.8 - 1.0.

extract_protocol:
Total RNAs were extracted using the hot acid phenol method.
Total RNAs were subjected to ribosomal RNA depletion and directional RNA-seq librairies were constructed using the TruSeq Stranded Total RNA library prep Gold kit (Illumina, #20020598).
PolyA RNAs were enriched from total RNAs using oligodT-attached magnetic beads and mRNA librairies were constructed using the Novogene NGS RNA Library Prep Set (PT042).

tag: cell type


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 1 hour, biol rep 1

tag: genotype

value: 1 hour


title: MS_98


title: Pancreas, d100 CF, rep1


title: wt nitrogen-starved cells, EMM-N, biol rep 1

tag: treatment

value: over-night nitrogen starvation


title: Patient 7, bone marrow, post-IFN-gamma

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

description:
Library name: Post_Ifng_7_BM_GEX
10X Genomics

data_processing:
Illumina BCL files were then demultiplexed and processed using Cellranger v6.0.2 for alignment, barcode processing and gene counting (10x Genomics).
Assembly: GRCH38
Supplementary files format and content: Tab separated values files (barcodes, features), Comma- separated values files (metadata, filtered contig annotations) and matrix files.
Supplementary files format and content: sparse matrix file, metadata csv, genes.csv
Supplementary files format and content: sparse matrix file, metadata csv, genes.csv

source_name: Bone marrow

extract_protocol:
Single cells were captured with Chromium Controller (10x Genomics)
Libraries were generated using the Chromium Next GEM Single Cell 5′ v2 (Dual Index) kit (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced using a NextSeq 2000  (Illumina P3/P4 kit) , with a target of 20,000 reads per cell for gene expression.

treatment_protocol: Interferon-gamma 100mcg fixed dose

tag: individual

value: Patient 7

value: Male

value: Acute myeloid leukemia

value: Bone marrow

value: Post-IFN-gamma


title: Pancreas, d80 CF, rep2

tag: tissue

value: pancreas

value: Day 80

value: CF


title: MS_96


title: Patient 7, bone marrow, pre-IFN-gamma

description:
Library name: Pre_Ifng_7_BM_GEX
10X Genomics

value: Pre-IFN-gamma


title: vegetative wt cells, EMM, biol rep 1

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: none, vegetative growth


title: MS_89

value: Stools

value: RRMS patient


title: Pancreas, d80 CF, rep1


title: vegetative wt cells, polyA RNA, biol rep 2


title: Patient 5, bone marrow, post-IFN-gamma

description:
Library name: Post_Ifng_5_BM_GEX
10X Genomics

value: Patient 5


title: MS_88


title: MS_87


title: vegetative wt cells, total RNA, biol rep 2


title: Patient 1, bulk bone marrow, post-IFN-gamma

description:
Library name: Post_Ifng_1_BM_GEX
10X Genomics

value: Patient 1

value: Myelodysplastic syndrome


title: Patient 5, bone marrow, pre-IFN-gamma

description:
Library name: Pre_Ifng_5_BM_GEX
10X Genomics


title: Pancreas, term WT, rep2

value: Day 147 (term)

value: WT


title: Pancreas, d65 CF, rep1

value: Day 65


title: Patient 1, bulk bone marrow, pre-IFN-gamma

description:
Library name: Pre_Ifng_1_BM_GEX
10X Genomics

value: Male

value: Bone marrow


title: Pancreas, d65 CF, rep2

value: pancreas


title: Pancreas, term WT, rep1


title: Patient 1, CD34 cells, post-IFN-gamma

description:
Library name: Post_Ifng_1_34_GEX
10X Genomics

value: Post-IFN-gamma


title: MS_58


title: EtOH_WT5

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

description: Library name: EtOH_WT5

data_processing:
FASTQC, TRIMMOMATIC, hisat2, samtools, featureCounts, DEseq2
Assembly: Mus_musculus.GRCm38.102.gtf
Supplementary files format and content: TXT file and raw counts

organism: Mus musculus

source_name: Liver

extract_protocol:
Trizol
PolyA selection for mRNA species (eukaryotic)

value: Liver

tag: agent

value: EtOH

value: female


title: EtOH_WT3

description: Library name: EtOH_WT3


title: vegetative wt cells, polyA RNA, biol rep 1

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR


title: EtOH_WT4

description: Library name: EtOH_WT4


title: MS_108

value: Stools


title: Pancreas, d120 WT, rep2

value: Day 120


title: EtOH_WT2

description: Library name: EtOH_WT2


title: MS_76

value: RRMS patient


title: MS_107


title: Pancreas, d120 WT, rep1


title: EtOH_WT1

description: Library name: EtOH_WT1


title: Patient 1, CD34 cells, pre-IFN-gamma

description:
Library name: Pre_Ifng_1_34_GEX
10X Genomics

value: Patient 1

value: Pre-IFN-gamma


title: MS7_N_NS

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

data_processing:
sequana_rnaseq 0.15.2 from the pipeline Sequana 0.14.1 (Ref. https://joss.theoj.org/papers/10.21105/joss.00352)
Reads were trimmed from adapters using Cutadapt 2.10 then mapped to the human genome (hg38) using STAR 2.7.8 with the following paramaters “--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq TGGAATTCTCGGGTGCCAAGG TGGAATTCTCGGGTGCCAAGG --clip3pAdapterMMp 0.1 0.1”.
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: human HG38 (GRCh38, NCBI_Assembly:GCA_000001405.15)
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted from thawed QIAzol cell lysates using miRNeasy Mini
Small RNA libraries were prepared from 100 ng of Total RNA using the Netflex Small RNA-Seq Kit v4 with UDIs

treatment_protocol: PBMCs were obtained by Ficoll gradient centrifugation of blood samples and CD4+ T cells were isolated by negative magnetic selection using the CD4+ T cell isolation kit and an autoMACS Pro Separator (Miltenyi Biotec).

value: Blood

tag: disease

value: relapsing-remitting multiple sclerosis

value: CD4+ T cell

value: Naive


title: MS_106


title: EtOH_ApoE5

description: Library name: EtOH_ApoE5

value: ApoE


title: MS7_EM_NS

value: Effector memory


title: Pancreas, d100 WT, rep1

value: pancreas

value: Day 100

value: WT


title: MS_105


title: EtOH_ApoE4

description: Library name: EtOH_ApoE4

value: Liver

value: EtOH

value: female


title: MS6_N_NS


title: MS_104

value: Stools


title: Pancreas, d80 WT, rep2

value: Day 80


title: MS_103

value: RRMS patient


title: MS6_EM_NS


title: EtOH_ApoE2

description: Library name: EtOH_ApoE2


title: EtOH_ApoE1

description: Library name: EtOH_ApoE1


title: Pancreas, d80 WT, rep1


title: Ctrl_WT4

description: Library name: Ctrl_WT4

value: Ctrl


title: MS5_N_NS


title: MS5_EM_NS


title: MS_101


title: Pancreas, d65 WT, rep1

value: Day 65


title: Ctrl_WT3

description: Library name: Ctrl_WT3


title: Pancreas, d65 WT, rep2


title: MS1_N_NS

value: Blood


title: MS1_EM_NS

value: relapsing-remitting multiple sclerosis


title: Pancreas, d100 WT, rep2


title: Sheep pancreas CF term scRNAseq donor 2 scRNA-seq

description: 10x Genomics

value: Pancreas

value: Female

value: CF


title: MS_3


title: MS_100


title: D6_N_NS

value: healthy

value: CD4+ T cell

value: Naive


title: MS_2


title: Ctrl_ApoE5

description: Library name: Ctrl_ApoE5

value: ApoE


title: D6_EM_NS

value: Effector memory


title: MS_1


title: Sheep pancreas CF 120 scRNAseq donor 1B scRNA-seq

description: 10x Genomics

value: Male


title: Ctrl_ApoE4

description: Library name: Ctrl_ApoE4

value: Liver

value: female


title: D5_N_NS


title: MS_102

value: Stools


title: HC_42

source_name: Healthy control stool-associated microbiome

value: Healthy control


title: Sheep pancreas CF 120 scRNAseq donor 1A scRNA-seq

description: 10x Genomics


title: Ctrl_ApoE3

description: Library name: Ctrl_ApoE3

value: Ctrl


title: D5_EM_NS


title: HC_41


title: Ctrl_ApoE1

description: Library name: Ctrl_ApoE1


title: Sheep pancreas WT Term scRNAseq donor 2 scRNA-seq

description: 10x Genomics


title: D4_EM_NS


title: Ctrl_WT2

description: Library name: Ctrl_WT2

value: WT


title: Sheep pancreas CF term scRNAseq donor 1B scRNA-seq

description: 10x Genomics


title: HC_40


title: Sheep pancreas CF 80 day scRNAseq donor 1 scRNA-seq

description: 10x Genomics


title: HC_38


title: Sheep pancreas WT Term scRNAseq donor 1 scRNA-seq

description: 10x Genomics


title: Huh7-TR cells, replicate 3

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
The transcriptome analysis involved RNA sequencing using Illumina's NextSeq 500 platform, followed by quality control to remove low-quality reads. The remaining reads were aligned to the human reference genome (GRCh38) and annotated using Ensembl database data. Gene expression levels were quantified using RSEM, and statistical analysis was conducted using DESeq2 in the R environment. Visualization was done using TPM values, and genes showing significant differential expression were identified. Functional analysis was performed using clusterProfiler or ComplexHeatmap R packages. This comprehensive workflow provides insights into gene expression patterns and their potential functional implications.
Assembly: Homo Sapiens GRCh38 Ensemble v94
Supplementary files format and content: tab delimited

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Nucleospin RNA mini kit (MN).
Services have been procured, and EMBL has conducted this stage.

treatment_protocol: Senescence was induced by treating cells with 5 ng/mL TGF-β.

tag: cell line

value: hepatocellular carcinoma

value: Res

value: TGF-β


title: Sheep pancreas CF term scRNAseq donor 1A scRNA-seq

description: 10x Genomics

value: Pancreas

value: Female


title: HC_39


title: LB1 pA-DamID, R4-5 truncation, t6, clone 26, replicate 2, dam-LB1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: pA-DamID_Sample_290

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 25 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Assembly: mm10
Supplementary files format and content: BigWig files of log2-normalized LaminB1 pA-DamID scores for 25 kb genomic bins.
Library strategy: pA-DamID

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) female mouse embryonic stem cells (mESCs) F1 hybrid cell line and derived clones were cultured in 2i+LIF condition, according to the 4D Nucleome guidelines (https://data.4dnucleome.org/biosources/4DNSRMG5APUM/). Briefly, cells were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1), supplemented with N-2 (Gibco), B-27 (Gibco), 0.05% BSA (Gibco), 10 × 4 U leukemia inhibitory factor (LIF; Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress), 1.5 × 10−4 M 1-thioglycerol (Sigma-Aldrich), and 1% penicillin-streptomycin (Gibco, 15070063) on 0.1% gelatin-coated plates. Cells were passaged every 2 days. Cells were seeded and incubated overnight before harvesting. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
One million cells were collected by centrifugation (500 g, 3 min) and washed sequentially in PBS and digitonin wash buffer (DigWash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 h at 4 °C in 200 μL DigWash with 1:100 LaminB1 antibody (Abcam, ab16048, rabbit) or 1:100 H3K9me3 antibody (Diagenone, C15410193, Rabbit), followed by a wash step with DigWash. This was repeated with a 1:200 pA-Dam solution (~60 NEB Dam units), followed by 2 wash steps. Dam activity was induced by an incubation for 30 min at 37 °C in 100 μL DigWash supplemented with 80 μM SAM. For every condition, another 1 million cells were processed in only DigWash and during Dam activation incubated with 4 units of Dam enzyme (NEB, M0222L). This Dam only control sample serves to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C).

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: recombined + CRISPR/Cas9 edited

tag: antibody


title: Sheep pancreas WT 120 scRNAseq donor 3 scRNA-seq

description: 10x Genomics


title: Ctrl_WT1

description: Library name: Ctrl_WT1


title: Huh7-TR cells, replicate 2


title: HC_37


title: LB1 pA-DamID, R4-5 truncation, t6, clone 26, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_289


title: Sheep pancreas WT 120 scRNAseq donor 2 scRNA-seq

description: 10x Genomics


title: Huh7-TR cells, replicate 1


title: Ctrl_ApoE2

description: Library name: Ctrl_ApoE2

value: ApoE


title: Sheep pancreas WT 120 scRNAseq donor 1 scRNA-seq

description: 10x Genomics


title: D4_N_NS

value: Blood

value: healthy

value: CD4+ T cell

value: Naive


title: Senescent Huh7 cells (Huh7-S), replicate 3


title: HC_35

value: Stools


title: LB1 pA-DamID, R4-5 truncation, t5, clone 26, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_286


title: Sheep pancreas HZ 80 scRNAseq donor 4 scRNA-seq

description: 10x Genomics

value: Male


title: LB1 pA-DamID, R4-5 truncation, t5, clone 26, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_285


title: Senescent Huh7 cells (Huh7-S), replicate 1


title: Sheep pancreas WT 80 scRNAseq donor 3 scRNA-seq

description: 10x Genomics


title: LB1 pA-DamID, R4-5 truncation, t5, clone 21, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_284


title: Huh7 cells, control, replicate 3

value: Vehicle


title: HC_29

value: Healthy control


title: LB1 pA-DamID, R4-5 truncation, t5, clone 21, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_283


title: Huh7 cells, control, replicate 2

value: hepatocellular carcinoma

value: WT


title: Sheep pancreas WT 80 scRNAseq donor 1 scRNA-sq

description: 10x Genomics


title: Experimental WT 16

city: Birmingham

first: Abolfazl

last: Zarjou

state: AL

address: 618 Zeigler Research Building, 703 South 19th Street

institute: University of Alabama at Birmingham

description:
Library name: Sample 8
FtHfl/fl (wild-type)

data_processing:
Basecalls were performed using bcl2fastq version 2.18.0.12
Sequence reads were aligned to reference genome using STAR version 2.7.7a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from STAR alignment BAM files using HTSEq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm38.p6.ReleaseM25
Supplementary files format and content: tab delimited Excel file containing raw gene counts for each gene in each sample

source_name: Kidney

extract_protocol: Total RNA was isolated from kidney of wild-type (FtHfl/fl) n=4 and myeloid specific FtH deficient (FtHΔ/Δ) n=4 mice treated with iron using Trizol

treatment_protocol: All mice received intraperitoneal injection of 0.4 mg/gram body weight iron dextran on five subsequent days. Three days following last injection all mice were sacrificed for analysis.

value: Kidney

value: FtHfl/fl (wild-type)

value: Iron (0.4mg/g)


title: LB1 pA-DamID, R4-5 truncation, t4, clone 68, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_282

value: F1 hybrid 129/Sv:CAST/EiJ


title: LB1 pA-DamID, R4-5 truncation, t6, clone 11, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_288

value: mESC


title: HC_36


title: LB1 pA-DamID, R4-5 truncation, t6, clone 11, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_287

value: recombined + CRISPR/Cas9 edited


title: Experimental WT 15

description:
Library name: Sample 7
FtHfl/fl (wild-type)


title: HC_27


title: LB1 pA-DamID, R4-5 truncation, t4, clone 68, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_281


title: HC_26


title: SecondaryScreen_HUDEP2_Rep3_D12

city: Ann Arbor

first: Rami

last: Khoriaty

state: Michigan

address: 109 Zina Pitcher Pl

department: Internal Medicine

institute: University of Michigan

description: Library name: SS_H2_R3_D12

library_source: other

data_processing:
Reads matching sgRNA sequence were compiled and counted to obtain raw counts. Raw counts from the CRISPR screen were analyzed using MAGeCK.
Assembly: Reference Free
Supplementary files format and content: counts_matrix.txt

molecule: other

extract_protocol:
Qiagen Blood & Tissue Kit
For sgRNA sequencing, a 1 step PCR approach was used to amplify the region of sgRNA region after genomic DNA extraction using primers containing standard P7/P5 adapters and staggered barcodes.

value: Erythroid Precursor

tag: sample group


title: SecondaryScreen_HUDEP2_Rep2_D12

description: Library name: SS_H2_R2_D12


title: Senescent Huh7 cells (Huh7-S), replicate 2

value: TGF-β


title: HC_33


title: HC_25


title: HC_32


title: Experimental WT 13

description:
Library name: Sample 5
FtHfl/fl (wild-type)


title: LB1 pA-DamID, R4-5 truncation, t4, clone 13, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_279


title: SecondaryScreen_HUDEP2_Rep1_D12

description: Library name: SS_H2_R1_D12


title: LB1 pA-DamID, R4-5 truncation, t4, clone 13, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_280


title: Experimental KO 12

description:
Library name: Sample 4
FtHΔ/Δ (myeloid-specific FtH-deficient)


title: LB1 pA-DamID, R4-5 truncation, t3, clone 96, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_278


title: SecondaryScreen_HUDEP2_Rep3_D0

description: Library name: SS_H2_R3_D0


title: Experimental KO 11

description:
Library name: Sample 3
FtHΔ/Δ (myeloid-specific FtH-deficient)


title: LB1 pA-DamID, R4-5 truncation, t3, clone 96, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_277


title: Experimental WT 14

description:
Library name: Sample 6
FtHfl/fl (wild-type)


title: HC_24


title: Huh7 cells, control, replicate 1


title: SecondaryScreen_HUDEP2_Rep2_D0

description: Library name: SS_H2_R2_D0


title: HC_19


title: Experimental KO 10

description:
Library name: Sample 2
FtHΔ/Δ (myeloid-specific FtH-deficient)


title: HC_20


title: SecondaryScreen_HUDEP2_Rep1_D0

description: Library name: SS_H2_R1_D0


title: HC_15


title: LB1 pA-DamID, R4-5 truncation, t3, clone 93, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_276


title: LB1 pA-DamID, R4-5 truncation, t3, clone 93, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_275


title: Sheep pancreas HZ 80 scRNAseq donor 2 scRNA-seq

description: 10x Genomics

value: Pancreas


title: GenomeScale_HUDEP2_Rep3_Day12

description: Library name: GS_H2_R3_D12


title: HC_14


title: GenomeScale_HUDEP2_Rep2_Day12

description: Library name: GS_H2_R2_D12


title: LB1 pA-DamID, R4-5 truncation, t2, clone 2, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_274


title: GEX_60R

city: Jacksonville

first: Zonghua

last: Li

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

description: 10X Genomics

data_processing:
SnRNA-Seq data were aligned and quantified using the 10X Genomics Cell Ranger Software Suite (v3.1.0) against a custom "pre-mRNA" human reference (GRCh38-1.2.0.pre-mrna) generated according to the steps detailed by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Assembly: GRCh38-1.2.0.pre-mrna
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain (temporal cortex)

extract_protocol:
To isolate nuclei, the frozen tissue (50-60 mg) was thawed for 2 minutes in 2 mL of ice-cold Nuclei EZ Lysis Buffer (Sigma, Cat # NUC-101), supplemented with EDTA-free protease inhibitors (Sigma, Cat # 11836170001) and 0.4 U μL−1 recombinant RNase inhibitors (Takara Bio USA, Cat # 2313A) before homogenizing with a glass Dounce tissue grinder (10-15 strokes with pestle A, followed by 10 strokes with pestle B. Sigma, Cat # D8938). An additional 2 mL of lysis buffer supplemented with protease and RNase inhibitor was added to the homogenized tissue and incubated for 5 minutes. The nuclei suspension was then filtered through a 40-μm cell strainer (Corning, Cat # 352340), followed by centrifugation at 300 x g for 5 minutes. The nuclei pellet was resuspended with 900 μL debris removal solution (Miltenyi Biotech, Cat # 130-109-398) containing 0.4 U μL−1 RNase inhibitors and 3.1 mL of Dulbecco's phosphate-buffered saline (DPBS) without calcium and magnesium. Next, 4 mL of DPBS was overlaid carefully onto the top of the nuclei resuspension. The nuclei were then pelleted again by centrifugation for 5 minutes at 3,000 x g. After removing the supernatant, the nuclei were resuspended in 500 µL of 1% BSA in DPBS with 0.4 U μL−1 RNase inhibitors. All procedures for nuclei isolation were carried out on ice or at 4°C. The density of the nuclei suspension was determined using a C-chip-disposable hemocytometer (INCYTO, Cat # DHC-B02-5) with trypan blue staining (Bio-Rad, Cat # 1450013).
The 59 samples were processed in 10 batches. Each batch had 5 to 6 samples from individuals of the same sex randomly selected from each of the AD and APOE genotype groups, i.e., control APOE2 carriers, control APOE3 homozygotes, control APOE4 carriers, AD APOE2 carriers, AD APOE3 homozygotes, and AD APOE4 carriers (6 groups in total). The samples from males and females were processed in alternating batches. A total of 5000 nuclei per sample were loaded to the Chromium microfluidic chip for cDNA library preparation using the Chromium Single Cell 3' Library and Gel Bead kit v3 (10X Genomics, Cat # 1000075) following the manufacturer's instructions.

value: Brain (temporal cortex)

tag: pathological diagnosis

value: AD

value: male


title: EWS502 cell line expressing FKBP(F36V)-EWS/FLI1 BAK-04-212 treated - 24 hours - replicate 2

first: Kimberly

last: Stegmaier

address: 450 Brookline Ave

institute: Dana Farber Cancer Institue

description: Library name: EWS502_BAK212_R2

data_processing:
ATAC-Seq analysis was performed according to the ENCODE standards (https://www.encodeproject.org/atac-seq/). Quality control was performed on the unmapped paired end reads with FastQC v.0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)  and MultiQC v.1.14. Adapters were then trimmed and filtered using Trimmomatic v.0.36. Using bowtie2 v.2.5.1, the trimmed paired end reads were aligned to the hg38 genome
Reads mapped to the hg38 genome to chromosomes 1 to 22 with a MAPQ > 5 were kept. Duplicates were removed using Picard Mark Duplicates method implemented in the sambamba 0.7.1 tool. deepTools v.3.5.1 AlignemntSieve tool was used to shift reads 4bp on the positive strand and -5bp on the negative strand. Replicate correlations were calculated and visualized using multiBamsummary and bamCorrelate, along with fragment size distributions using PEFragmentSize within the deepTools v.3.5.1 package Replicates were merged and then peak calling was performed with MACS2 v.2.1.1.20160309
Assembly: hg38
Supplementary files format and content: bigWig RPKM binding signal

source_name: EWS502 FKBP(F36V)-EWS/FLI1

growth_protocol: EWS502 cells expressing exogenous FKBP12(F36V)-EWS/FLI1 concurrent with Cas9 and a guide targeting an intron/exon junction of endogenous EWS/FLI1 were grown in RPMI media supplemented with 15% FBS and 1% penicllin-streptomycin

extract_protocol:
Cells were harvested by trypsinization and counted. 100,000 cells from each sample were lysed in ATAC lysis buffer from the ActiveMotif ATAC-seq kit (53150). Samples were processed using this kit according to the manufacturer's protocol.
Q5-High-Fidelity DNA Polymerase and i7/i5 indexing primers were used to prepare ATAC libraries using the Active Motif ATAC-seq kit (53150) according to the manufacturer's protocol.

treatment_protocol: Cells were treated for 24 hours with DMSO or 1 µM of the designated compound

value: EWS502 FKBP(F36V)-EWS/FLI1

value: Ewing sarcoma

value: EB-TCIP

tag: batch


title: GEX_59R

description: 10X Genomics

value: Control

tag: Sex

value: female


title: LB1 pA-DamID, R4-5 truncation, t2, clone 2, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_273


title: HC_28

value: Stools

value: Healthy control


title: GenomeScale_HUDEP2_Rep1_Day12

description: Library name: GS_H2_R1_D12


title: GEX_58R

description: 10X Genomics


title: GenomeScale_HUDEP2_Rep3_Day0

description: Library name: GS_H2_R3_D0


title: EWS502 cell line expressing FKBP(F36V)-EWS/FLI1BAK-04-212 treated - 24 hours - replicate 1

description: Library name: EWS502_BAK212_R1


title: EWS502 cell line expressing FKBP(F36V)-EWS/FLI1DMSO treated - 24 hours - replicate 2

description: Library name: EWS502_DMSO_R2


title: LB1 pA-DamID, R4-5 truncation, t2, clone 18, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_271


title: GenomeScale_HUDEP2_Rep2_Day0

description: Library name: GS_H2_R2_D0


title: GEX_56R

description: 10X Genomics


title: LB1 pA-DamID, R4-5 truncation, t1, clone 9, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_270


title: GenomeScale_HUDEP2_Rep1_Day0

description: Library name: GS_H2_R1_D0


title: Secondary_Plasmid_Library

description: Library name: SS_Library


title: GEX_55R

description: 10X Genomics


title: Experimental KO 9

description:
Library name: Sample 1
FtHΔ/Δ (myeloid-specific FtH-deficient)

value: Kidney

value: Iron (0.4mg/g)


title: LB1 pA-DamID, R4-5 truncation, t1, clone 9, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_269

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: GECKOv2_Plasmid_Library

description:
Library name: GS_Library
Sequenced using shared flowcell, library barcodes are CAGATC & CTTGTA

value: Erythroid Precursor


title: A498 shBMAL1 IP HIF2a 4

city: SAN DIEGO

first: Rebecca

last: Mello

state: CA

address: 11093 CLAIREMONT MESA BLVD

institute: The Scripps Research Institute

description: Library name: A498 shBMAL1 IP HIF2a 4

data_processing:
There are two lanes (L001, L002) and two reads (paired end 2 x 75 – R1, R2), The data from each lane can be combined for each sample.
reads underwent alignment to both the human genome hg19 and the yeast genome sacCer3 using Bowtie2 2.5.3, with the following parameters: --local --very-sensitive --fr --dovetail --no-mixed -I 10 -X 700
Alignment files (SAM) were then converted to BAM format, and subjected to filtering, and duplicate reads were removed using samtools 1.6 and sambamba 1.0
Peak calling was performed using MACS2 2.2.9.1, specifying parameters --keep-dup all --max-gap 400 –p 1e-5
Post-peak calling, filtering against the hg19 blacklist was executed using bedtools 2.31.1 with the intersect option
annotation and motif analysis of the peaks was carried out using HOMER 4.11, using annotatePeaks.pl and findMotifsGenome.pl options with the human genome hg19 reference
Peak functional annotation was directly done by Homer using -go option, or with WEB-based GEne SeT AnaLysis Toolkit -WebGestalt (https://www.webgestalt.org/) to identify gene ontologies and KEGG-related pathways after crossing peaks annotation with RNA-seq data.
Spike-in normalization with the aligned reads was achieved against the yeast genome sacCer3 with deeptools 3.5.5 using bamCoverage –scaleFactor --smoothLength 60 --extendReads 150 –centerReads to produce BigWig files. Spike-in scale factor values were calculated as described in the manufacturer protocol (CST #86652).
Profiles and heatmap were obtained by using computeMatrix –referencePoint center after spike-in normalization.  BigWig files were uploaded to the UCSC genome browser (https://genome-euro.ucsc.edu/index.html) and tracks were visualized against the human genome hg19
Assembly: hg19
Supplementary files format and content: bigWig, peak file (.bed) (except for negative control)

source_name: kidney

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium + 10% fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco), and maintained in an atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) were performed using CUT&RUN assay kit (CST #86652) following the manufacturer protocol. DNA purification was performed by phenol/chloroform extraction followed by ethanol precipitation.
Next generation sequencing libraries were prepared using DNA Library Prep Kit for Illumina (CST #56795) and Multiplex Oligos for Illumina (CST #29580).

treatment_protocol: To generate cell lines expressing shRNA, lentiviral shRNA constructs encoded in PLKO.1 vectors were produced by transient transfection in HEK293T cells. Target cells were infected with lentivirus for 4-6 hours before selection in DMEM + 10% fetal bovine serum and 1% penicillin-streptomycin containing 2.5 µg/mL puromycin for 1 week. After initial selection, cells were maintained in DMEM containing 1.25 µg/mL.

value: kidney

value: Adenocarcinoma; Renal Cell

value: BMAL1 knockdown

tag: chip antibody

value: HIF-2α rabbit mAb (CST #59973)


title: GEX_52R

description: 10X Genomics

value: Brain (temporal cortex)

value: male


title: LB1 pA-DamID, R4-5 truncation, t1, clone 36, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_268

value: recombined + CRISPR/Cas9 edited


title: GEX_50R

description: 10X Genomics

value: AD


title: A498 shBMAL1 IP HIF2a 2

description: Library name: A498 shBMAL1 IP HIF2a 2


title: LB1 pA-DamID, R4-5 truncation, t1, clone 36, replicate 1, dam-LB1

description: Library name: pA-DamID_Sample_267


title: CBMCs, IL-5 biol rep8

city: Halifax

first: Tobias

middle: K

last: Karakach

state: NS

address: 5058 College Street

department: Pharmacology

country: Canada

institute: Dalhousie University

description:
400 million reads and 2x75bp paired end reads
Combined Data
795-IL5

data_processing:
Raw files were pre-processed following standard QC workflows that include demultiplexing, adaptor sequences removal and trimming. This was done in-house on a linux machine running RHEL 7.
Sequence reads that passed QC were subsequently mapped to the reference human genome GRCh38 assembly (hg38) using STAR, with the --quantMode GeneCounts option which yielded read counts per gene while mapping.
Read counts per gened were obtained using the --quantMode GeneCounts option in STAR
Assembly: GRCh38
Supplementary files format and content: tab delimited text format for processed files compristing of raw counts of 60,234 gene transcripts for each of the 16 donor samples

source_name: Cord blood-derived

growth_protocol: Primary cultures of human mast cells were derived from mononuclear cells isolated from human umbilical cord blood and are referred to as CBMCs. Cord blood was drawn into syringes with heparin and diluted with twice the volume of PBS. Up to 30 mL of diluted blood was layered onto 15 mL Lymphoprep (Stem Cell Technologies) and centrifuged at 480 x g for 25 minutes at 22ºC. The buffy layer containing mononuclear cells was harvested, washed with 1X PBS, and centrifuged at 300 x g for 10 minutes at 4ºC. Red blood cells were lysed by incubation of sterile water for 30 seconds, followed by two washes with 1X PBS at 300 x g for 20 minutes at 4°C. Mononuclear leukocytes were cultured at 10^6  cells/mL and passaged once per week for 4 weeks in StemSpan SFEM medium (Stem Cell Technologies) containing 10 ng/mL human IL-3 (IL-3; present only for the first week of culture, eBiosciences), 10 ng/mL human IL-6 (IL-6) and 100 ng/mL human SCF (SCF; Peprotech) in 5% CO2  at 37°C in humidified atmosphere. At 5 weeks of culture, the medium was replaced by RPMI 1640 (Sigma) supplemented with 10% fetal bovine serum (FBS; Sigma), 2 mM L-glutamine (Hyclone Labs, Thermo Scientific), 1 x penicillin/streptomycin (HyClone), 50 uM 2-mercaptoethanol (Sigma), 15 mM HEPES (HyClone), 0.1 mM nonessential amino acids (HyClone), 100 ng/mL SCF and 10 ng/mL IL-6. After 5 weeks of culture, cord blood-derived mast cells (CBMCs) were stained for CD117 (anti-human CD117, Invitrogen) and analyzed by flow cytometry for mast cell purity. CBMCs were used for experiments when the purity was determined to be ≥ 95%.

extract_protocol:
RNA was harvested in TRIzol and purified with the RNAeasy Plus kit (Qiagen) including DNAse I treatment step. The quality of the RNA samples was assessed with the Experion automated electrophoresis system (Bio-Rad).
Sequencing libraries were constructed according to the Illumina Stranded Total RNA Prep kit and the Ribo-Zero Plus kit (Illumina) following manufacturer’s instructions

treatment_protocol: CBMCs (10^6 cells/mL) were cultured with 10 ng/mL of human IL-5 (IL-5; BioLegend) or left non stimulated at 37°C for 24 hours in their corresponding culture medium (containing 100 ng/mL of SCF and 10 ng/mL of IL-6). Then, cells were cultured in 10 ng/mL of IL-5 and 10 ng/mL of SCF for 18 hours prior to RNA harvest. Total treatment protocol is 42 hours.

value: Cord blood-derived

value: primary mast cells (CBMCs)

value: 10 ng/mL of human IL-5


title: A498 shBMAL1 IP HIF2a 3

description: Library name: A498 shBMAL1 IP HIF2a 3


title: CBMCs, Mock biol rep8

description:
400 million reads and 2x75bp paired end reads
Combined Data
795-med

value: Media


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 2, dam-LB1, control for truncation experiment

description: Library name: pA-DamID_Sample_266


title: GEX_51R

description: 10X Genomics

value: Control


title: LB1 pA-DamID, R4-5 truncation, t2, clone 18, replicate 2, dam-LB1

description: Library name: pA-DamID_Sample_272


title: GEX_57R

description: 10X Genomics

value: female


title: CBMCs, Mock biol rep7

description:
400 million reads and 2x75bp paired end reads
Combined Data
794-med


title: EWS502 cell line expressing FKBP(F36V)-EWS/FLI1 DMSO treated - 24 hours - replicate 1

description: Library name: EWS502_DMSO_R1

value: EWS502 FKBP(F36V)-EWS/FLI1

value: Ewing sarcoma


title: A498 shBMAL1 IP HIF2a 1

description: Library name: A498 shBMAL1 IP HIF2a 1


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 1, dam-LB1, control for truncation experiment

description: Library name: pA-DamID_Sample_265

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: CBMCs, IL-5 biol rep7

description:
400 million reads and 2x75bp paired end reads
Combined Data
794-IL5


title: GEX_49R

description: 10X Genomics


title: LB1 pA-DamID, R4-5 truncation, t6, clone 26, replicate 2, dam only

description: Library name: pA-DamID_Sample_264


title: A498 shBMAL1 IP BMAL1 3

description: Library name: A498 shBMAL1 IP BMAL1 3

value: kidney

value: Adenocarcinoma; Renal Cell

value: BMAL1 rabbit mAb (CST #14020)


title: GEX_47R

description: 10X Genomics

value: Brain (temporal cortex)


title: A498 shBMAL1 IP BMAL1 4

description: Library name: A498 shBMAL1 IP BMAL1 4

value: BMAL1 knockdown


title: LB1 pA-DamID, R4-5 truncation, t6, clone 26, replicate 1, dam only

description: Library name: pA-DamID_Sample_263

value: recombined + CRISPR/Cas9 edited


title: GEX_48R

description: 10X Genomics


title: CBMCs, Mock biol rep6

description:
400 million reads and 2x75bp paired end reads
Combined Data
793-med


title: LB1 pA-DamID, R4-5 truncation, t6, clone 11, replicate 2, dam only

description: Library name: pA-DamID_Sample_262


title: GEX_46R

description: 10X Genomics


title: A498 shBMAL1 IP BMAL1 2

description: Library name: A498 shBMAL1 IP BMAL1 2


title: CBMCs, Mock biol rep5

description:
400 million reads and 2x75bp paired end reads
Combined Data
792-med


title: GEX_45R

description: 10X Genomics

value: AD


title: A498 shBMAL1 IP BMAL1 1

description: Library name: A498 shBMAL1 IP BMAL1 1


title: A498 shBMAL1 IP IgG 2

description: Library name: A498 shBMAL1 IP IgG 2

value: rabbit mAb IgG isotype  (CST #66362)


title: CBMCs, IL-5 biol rep5

description:
400 million reads and 2x75bp paired end reads
Combined Data
792-IL5

value: Cord blood-derived

value: primary mast cells (CBMCs)


title: A498 shBMAL1 IP IgG 1

description: Library name: A498 shBMAL1 IP IgG 1


title: CBMCs, Mock biol rep4

description:
400 million reads and 2x75bp paired end reads
Combined Data
790-med

value: Media


title: LB1 pA-DamID, R4-5 truncation, t6, clone 11, replicate 1, dam only

description: Library name: pA-DamID_Sample_261


title: LB1 pA-DamID, R4-5 truncation, t5, clone 26, replicate 2, dam only

description: Library name: pA-DamID_Sample_260


title: LB1 pA-DamID, R4-5 truncation, t5, clone 26, replicate 1, dam only

description: Library name: pA-DamID_Sample_259


title: GEX_43R

description: 10X Genomics


title: CBMCs, IL-5 biol rep4

description:
400 million reads and 2x75bp paired end reads
Combined Data
790-IL5

value: 10 ng/mL of human IL-5


title: GEX_42R

description: 10X Genomics

value: Control

value: male


title: A498 shCNT IP HIF2a 3

description: Library name: A498 shCNT IP HIF2a 3

value: WT

value: HIF-2α rabbit mAb (CST #59973)


title: CBMCs, Mock biol rep3

description:
400 million reads and 2x75bp paired end reads
Combined Data
788-med


title: CBMCs, IL-5 biol rep6

description:
400 million reads and 2x75bp paired end reads
Combined Data
793-IL5


title: LB1 pA-DamID, R4-5 truncation, t5, clone 21, replicate 2, dam only

description: Library name: pA-DamID_Sample_258

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: GEX_41R

description: 10X Genomics


title: LB1 pA-DamID, R4-5 truncation, t5, clone 21, replicate 1, dam only

description: Library name: pA-DamID_Sample_257


title: CBMCs, IL-5 biol rep3

description:
400 million reads and 2x75bp paired end reads
Combined Data
788-IL5


title: A498 shCNT IP HIF2a 2

description: Library name: A498 shCNT IP HIF2a 2

value: kidney

value: Adenocarcinoma; Renal Cell


title: A498 shCNT IP HIF2a 1

description: Library name: A498 shCNT IP HIF2a 1


title: GEX_40R

description: 10X Genomics

value: Brain (temporal cortex)


title: CBMCs, Mock biol rep2

description:
400 million reads and 2x75bp paired end reads
Combined Data
780-med


title: LB1 pA-DamID, R4-5 truncation, t4, clone 68, replicate 1, dam only

description: Library name: pA-DamID_Sample_255


title: LB1 pA-DamID, R4-5 truncation, t4, clone 68, replicate 2, dam only

description: Library name: pA-DamID_Sample_256


title: CBMCs, IL-5 biol rep2

description:
400 million reads and 2x75bp paired end reads
Combined Data
780-IL5


title: GEX_39R

description: 10X Genomics


title: GEX_38R

description: 10X Genomics


title: A498 shCNT IP BMAL1 4

description: Library name: A498 shCNT IP BMAL1 4

value: BMAL1 rabbit mAb (CST #14020)


title: LB1 pA-DamID, R4-5 truncation, t4, clone 13, replicate 2, dam only

description: Library name: pA-DamID_Sample_254

value: recombined + CRISPR/Cas9 edited


title: A498 shCNT IP BMAL1 3

description: Library name: A498 shCNT IP BMAL1 3


title: CBMCs, Mock biol rep1

description:
400 million reads and 2x75bp paired end reads
Combined Data
779-med


title: LB1 pA-DamID, R4-5 truncation, t4, clone 13, replicate 1, dam only

description: Library name: pA-DamID_Sample_253


title: CBMCs, IL-5 biol rep1

description:
400 million reads and 2x75bp paired end reads
Combined Data
779-IL5


title: GEX_37R

description: 10X Genomics

value: AD


title: A498 shCNT IP HIF2a 4

description: Library name: A498 shCNT IP HIF2a 4


title: A498 shCNT IP BMAL1 2

description: Library name: A498 shCNT IP BMAL1 2


title: GEX_36R

description: 10X Genomics

value: female


title: LB1 pA-DamID, R4-5 truncation, t3, clone 96, replicate 2, dam only

description: Library name: pA-DamID_Sample_252


title: A498 shCNT IP BMAL1 1

description: Library name: A498 shCNT IP BMAL1 1


title: TILs, Ctrl_GEX

city: Professor

first: David

last: Nemazee

address: 10550 N Torrey Pines Rd

description:
Library name: CTRL_GEX
10X Genomics

data_processing:
Sequenced raw reads were processed using the Cell Ranger (v6.0.0, 10X Genomics) "multi" pipeline. Reads were aligned to the GRCm38 mouse reference genome.
Assembly: Mouse mm10 (gene expression reads); GRCm38 (VDJ reads)
Supplementary files format and content: Tab-separated feature and barcode files, and matrix files

source_name: tumor-infiltrating lymphocytes (TILs)

extract_protocol:
MC38 tumor cells were cultured and transferred subcutaneously (s.c.) into Prdm1f/f and Prdm1f/f CD19cre recipient mice. On DPI 18, inoculated MC38 tumors were collected from 11 recipients in each group. Immune cells were enriched by percoll gradients (30% and 70%) first, then sorted as single B220+ cells and single CD138+ cells from living cells (the viability dye negative population) using the Sony MA900 cell sorter. The sorted cells were combined and resuspended in 10% FBS, PBS buffer. Then samples were processed with the VDJ and GEX library preparations.
Libraries were loaded onto 100-cycle flowcells for sequencing using the NextSeq2000 (Ilumina) and sequenced as follows: read1 = 26 cycles, i7 index = 10 cycles, i5 index = 10 cycles, read 2 = 90 cycles. 1400 cells were targeted per sample ("BLIMP", "CTRL") with 6,000 reads/cell for VDJ/B cell enriched library, and 24,000 reads/cell for 5' GEX library.

value: tumor-infiltrating lymphocytes (TILs)

value: a combination of CD138+ and B220+ cells

tag: strain

value: Prdm1 f/f

tag: age

value: 12-16 weeks old


title: GEX_35R

description: 10X Genomics

value: Control


title: LB1 pA-DamID, R4-5 truncation, t3, clone 96, replicate 1, dam only

description: Library name: pA-DamID_Sample_251


title: GEX_34R

description: 10X Genomics


title: A498 shCNT IP IgG 2

description: Library name: A498 shCNT IP IgG 2

value: rabbit mAb IgG isotype  (CST #66362)


title: LB1 pA-DamID, R4-5 truncation, t3, clone 93, replicate 2, dam only

description: Library name: pA-DamID_Sample_250


title: TILs, Ctrl_VDJ

description:
Library name: CTRL_VDJ
10X Genomics


title: TILs, Blimp-1 KO_GEX

description:
Library name: BLIMP_GEX
10X Genomics

value: Prdm1 f/f CD19cre


title: GEX_33R

description: 10X Genomics


title: TILs, Blimp-1 KO_VDJ

description:
Library name: BLIMP_VDJ
10X Genomics


title: GEX_32R

description: 10X Genomics


title: xnp-1_L4_biological_replicate_3, RNA-Seq

city: St Andrews

first: Helder

middle: C

last: Ferreira

address: North Haugh

country: United Kingdom

institute: University of St Andrews

description:
Library name: X4_EKRN240004842-1A
all_samples_counts_L4_25C.txt

data_processing:
Quality control with fastQC before and after trimming with Trim_galore.
Trimmed reads were mapped to WS280 genome build (BioProject PRJNA13758) using STAR without limits on mapped length and with max. number of mismatches per pair = 2.
The reads were re-sorted by read name using Samtools. FeatureCounts was used to generate a count matrix.
Assembly: WS280
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Adult C. elegans were grown on standard NGM with OP50 at 20°C and lysed with hypochlorite to obtain embryos. L1 larvae were obtained by incubating embryos in M9 for ~11hrs at 20°C. L4 larvae were grown at 25°C from L1.

extract_protocol:
For each 100 μl of worm pellet, 1 ml of Trizol was added. 5 cycles of freeze‐cracking were carried out, freezing in liquid nitrogen, followed by thawing in a water bath at 37°C. Tubes were vortexed for 30 s on, 30 s off, for 5 min and incubated for 5 min at room temperature. 200 μl chloroform per ml of Trizol were added, tubes were shaked vigorously, incubated 2–3 min at room temperature and centrifuged at full speed for 10 min at 4°C. The top layer was transferred to a new tube, and RNA was precipitated overnight at −20°C with 1 μl glycogen and an equal volume of isopropanol.
RNA sequencing of embryos and L1 was carried out at the Oxford Genomics Centre and for the L4 samples was carried out at Novogene, Cambridge. All genotypes where sequences in biological triplicate. For small RNA library preparation, 1-2 µg (see Beltran et al., Nat Ecol Evo 2020 for details) of RNA were incubated for 1 h at 37 °C with RNA 5′ polyphosphatase (Epicentre) at a final concentration of 1 U µl−1 in a total volume of 20 µl to convert 5′-triphosphate 22G-RNAs into clonable 5′-phosphate 22G-RNAs. RNA was phenol–chloroform-extracted and precipitated overnight with 1 µl of glycogen, 1/10 volume 3M AcNA and 3 volumes of 100% ethanol. Small RNA libraries were generated using the Illumina TruSeq Small RNA Library Preparation Kit according to the manufacturer’s instructions and gel-purified to size-select 21–23-nucleotide (nt) inserts. The libraries were sequenced on an Illumina HiSeq2500 system.

treatment_protocol: L4 larvae were grown at 25°C from L1 to L4.

value: whole organism

tag: developmental stage

tag: biological replicate


title: LB1 pA-DamID, R4-5 truncation, t2, clone 2, replicate 2, dam only

description: Library name: pA-DamID_Sample_248

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

tag: genotype


title: LD_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description:
Library name: Sample 12
Actg1 knockout (full locus deletion)

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1.20160309 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples and counts were produced with bigWigAverageOverBed (UCSC Toolkit).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 101.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of unified peaks.

extract_protocol:
Cells were grown in 6-well plates, detached by TrypLE, and resuspended in PBS. Each sample contains 25,000 cells.
The Cell pellet was resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing Primers was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform using V2 chemistry and paired-end setup.

value: Fibroblast

value: Actg1 knockout (full locus deletion)


title: xnp-1_L4_biological_replicate_2, RNA-Seq

description:
Library name: X3_EKRN240004841-1A
all_samples_counts_L4_25C.txt


title: GEX_31R

description: 10X Genomics


title: LD_2

description:
Library name: Sample 11
Actg1 knockout (full locus deletion)


title: xnp-1_L4_biological_replicate_1, RNA-Seq

description:
Library name: X2_EKRN240004840-1A
all_samples_counts_L4_25C.txt


title: LB1 pA-DamID, R4-5 truncation, t2, clone 18, replicate 2, dam only

description: Library name: pA-DamID_Sample_246

value: mESC


title: LB1 pA-DamID, R4-5 truncation, t2, clone 2, replicate 1, dam only

description: Library name: pA-DamID_Sample_247


title: GEX_30R

description: 10X Genomics

value: Brain (temporal cortex)

value: male


title: N2_L4_biological_replicate_3, RNA-Seq

description:
Library name: N4_EKRN240004836-1A
all_samples_counts_L4_25C.txt


title: GEX_29R

description: 10X Genomics


title: LB1 pA-DamID, R4-5 truncation, t2, clone 18, replicate 1, dam only

description: Library name: pA-DamID_Sample_245

value: recombined + CRISPR/Cas9 edited


title: PTC2_3

description:
Library name: Sample 9
Actg1 knockout, Actg1-202:r.1096_1097insn[4036](premature termination codon exon 5)


title: A498 shCNT IP IgG 1

description: Library name: A498 shCNT IP IgG 1

value: kidney

value: Adenocarcinoma; Renal Cell

value: WT


title: PTC2_2

description:
Library name: Sample 8
Actg1 knockout, Actg1-202:r.1096_1097insn[4036](premature termination codon exon 5)


title: GEX_28R

description: 10X Genomics


title: LB1 pA-DamID, R4-5 truncation, t1, clone 9, replicate 1, dam only

description: Library name: pA-DamID_Sample_243


title: LB1 pA-DamID, R4-5 truncation, t1, clone 9, replicate 2, dam only

description: Library name: pA-DamID_Sample_244


title: GEX_27R

description: 10X Genomics

value: AD


title: N2_L4_biological_replicate_2, RNA-Seq

description:
Library name: N3_EKRN240004835-1A
all_samples_counts_L4_25C.txt


title: LB1 pA-DamID, R4-5 truncation, t3, clone 93, replicate 1, dam only

description: Library name: pA-DamID_Sample_249


title: PTC2_1

description:
Library name: Sample 7
Actg1 knockout, Actg1-202:r.1096_1097insn[4036](premature termination codon exon 5)


title: GEX_26R

description: 10X Genomics


title: PTC1_3

description:
Library name: Sample 6
Actg1 knockout, c.280_281insT and c.[280A>G; 280_281insT](premature termination codon in exon 3)


title: LB1 pA-DamID, R4-5 truncation, t1, clone 36, replicate 2, dam only

description: Library name: pA-DamID_Sample_242


title: GEX_24R

description: 10X Genomics

value: female


title: gsox-1_L4_biological_replicate_2, RNA-Seq

description:
Library name: F3_EKRN240004838-1A
all_samples_counts_L4_25C.txt


title: LB1 pA-DamID, R4-5 truncation, t1, clone 36, replicate 1, dam only

description: Library name: pA-DamID_Sample_241


title: gsox-1_L4_biological_replicate_3, RNA-Seq

description:
Library name: F4_EKRN240004839-1A
all_samples_counts_L4_25C.txt


title: PTC1_2

description:
Library name: Sample 5
Actg1 knockout, c.280_281insT and c.[280A>G; 280_281insT](premature termination codon in exon 3)


title: gsox-1_L4_biological_replicate_1, RNA-Seq

description:
Library name: F2_EKRN240004837-1A
all_samples_counts_L4_25C.txt


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 2, dam only, control for truncation experiment

description: Library name: pA-DamID_Sample_240


title: PTC1_1

description:
Library name: Sample 4
Actg1 knockout, c.280_281insT and c.[280A>G; 280_281insT](premature termination codon in exon 3)


title: LD_1

description:
Library name: Sample 10
Actg1 knockout (full locus deletion)


title: Wildtype_3

description: Library name: Sample 3


title: GEX_22R

description: 10X Genomics


title: xnp-1;gsox-1_L4_biological_replicate_2, RNA-Seq

description:
Library name: DM3_EKRN240004844-1A
all_samples_counts_L4_25C.txt


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 1, dam only, control for truncation experiment

description: Library name: pA-DamID_Sample_239


title: N2_L4_biological_replicate_1, RNA-Seq

description:
Library name: N2_EKRN240004834-1A
all_samples_counts_L4_25C.txt


title: GEX_21R

description: 10X Genomics


title: xnp-1;gsox-1_L4_biological_replicate_1, RNA-Seq

description:
Library name: DM2_EKRN240004843-1A
all_samples_counts_L4_25C.txt


title: Wildtype_1

description: Library name: Sample 1


title: vegetative wt cells, biol rep 2

city: Gif-sur-Yvette

first: Mathieu

last: Rougemaille

address: 1 avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell

data_processing:
Data were base-called on super accuracy mode using dorado 7.2.13-1.
Sequences were mapped on the S. pombe genome with minimap2 with -x splice parameter.
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa.gz and Schizosaccharomyces_pombe_all_chromosomes.gff3.gz from Pombase
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.

source_name: haploid, h- cells

extract_protocol:
Total RNAs were extracted using the hot acid phenol method.
Total RNAs were subjected to ribosomal RNA depletion using the TruSeq Stranded Total RNA library prep Gold kit (Illumina, #20020598).
350 ng RNA was polyadenylated in vitro and librairies were prepared using the Direct RNA Sequencing kit (Oxford Nanopore Technologies, SQK-RNA004).
direct RNA-seq (Oxford Nanopore Technologies)

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR


title: GEX_20R

description: 10X Genomics


title: Wildtype_2

description: Library name: Sample 2


title: GEX_19R

description: 10X Genomics


title: AD14CWT-2

city: Los Angeles

first: Lianjiu

last: Su

address: 500 Landfair Ave.

institute: University of California, Los Angeles

description: Library name: AD14CWT-2

data_processing:
Fastq files were generated with Cell Ranger (version 3.0.2), and the reads were aligned to the mouse reference genome using the cellranger count function. The resulting digital expression matrix was analyzed with Seurat (version 3.0.2), which identified different cell types and their signature genes. Cells with less than 500 unique molecular identifiers (UMIs), fewer than 100 genes, or more than 10% mitochondrial gene expression were removed. The data were normalized, scaled, and subjected to PCA, t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) for dimensionality reduction. Clustering was performed with the FindClusters function, and marker genes were identified with the FindAllMarkers function.
Assembly: GRCm39
Supplementary files format and content: filtered_feature_bc_matrix.h5 of each sample includes barcodes, genes ,and matrix

extract_protocol:
For single-cell RNA sequencing (scRNA-seq), kidney tissue from the adenine-induced injury model was collected two weeks post-injury and digested with Liberase, following a specific protocol. The kidney tissue was cut into 1mm pieces on ice, washed with cold PBS. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no.25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no.11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. Kidney tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 45 min. Cell suspensions were filtered using a 40um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no.14190144) to check the viability.
Libraries were created using the Chromium Single Cell 3' Library Construction kit (10x Genomics) and sequenced on the NovaSeq6000 (Illumina) platform.

value: Wild type (cre-)

tag: treatment

value: Adenine diet for 14 days


title: AD14CWT-3

description: Library name: AD14CWT-3

tag: tissue


title: GEX_18R

description: 10X Genomics

value: Control


title: AD14CWT-1

description: Library name: AD14CWT-1


title: vegetative wt cells, biol rep 1


title: AD14CKO-Cilengitide-4

description: Library name: AD14CKO-Cilengitide-4

value: Col5a1 CKO

value: Adenine diet + Cilengitide for 14 days


title: Fig2a_VDJ_JP0037

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: JP0037_VDJ
VDJ library

data_processing:
Gene expression unique molecular identifier (UMI) sample HTO counts were generated with CellRanger v6.0.1, v7.0.1, or v8.0.1 with mm39 reference.
BCR libraries were processed with CellRanger “vdj” with default parameters.
Transciptomic analysis was carried out using Seurat v. 5.1.0.
Assembly: Mus Musculus mm39
Supplementary files format and content: Tab separated value files and matrix files

source_name: Lymph node

extract_protocol:
Single cell suspension from lymph nodes was prepared in PBS supplemented with 0.5% BSA and 2 mM EDTA (PBE). Live GC cells were sorted using BD FACSymphony S6 or BD S8 FACSDiscover sorter
Library was  generated using a Chromium Next GEM Single Cell 5' Reagent Kit v2 or v3(Dual Index) with Feature Barcode technology for Cell Surface Protein, according to the manufacturer’s protocol.

value: Lymph node

value: GC B cell

tag: library type

value: mRNA


title: Fig2a_HTO_JP0037

description:
Library name: JP0037_HTO
HTO library

value: HTO


title: GEX_23R

description: 10X Genomics

value: Brain (temporal cortex)


title: AD14CKO-Cilengitide-3

description: Library name: AD14CKO-Cilengitide-3

value: kidney


title: xnp-1;gsox-1_L4_biological_replicate_3, RNA-Seq

description:
Library name: DM4_EKRN240004845-1A
all_samples_counts_L4_25C.txt

value: whole organism


title: GEX_17R

description: 10X Genomics

value: male


title: Fig2a_GEX_JP0037

description:
Library name: JP0037_GEX
GEX (5') library


title: T4-2

city: guiyang

first: Wang

middle: xin

last: Zhang

state: guizhousheng

address: Guiyang

department: Tobacco College

country: China

institute: Guizhou University

data_processing:
cLc Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: FPKM_anno.txt

organism: Nicotiana tabacum

source_name: leaves

extract_protocol:
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA)
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing liboraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kt following manufacturer's protocols.

value: leaves

value: nitrogen excess, 150 kg/hm2 (T4)


title: GEX_15R

description: 10X Genomics

value: AD


title: ki-iT3H48_3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109.
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform (Illumina) using P2 flowcell with 2x 61bp paired-end setup.

tag: knock-in

value: Inactive T3H48-HHR ribozyme


title: AD14CKO-Cilengitide-2

description: Library name: AD14CKO-Cilengitide-2


title: T4-1


title: AD14CKO-Cilengitide-1

description: Library name: AD14CKO-Cilengitide-1


title: GEX_14R

description: 10X Genomics


title: T3-3

value: standard application, 105 kg/hm2 (T3)


title: ki-iT3H48_2

tag: cell line


title: AD14CKO-4

description: Library name: AD14CKO-4

value: Adenine diet for 14 days


title: GEX_13R

description: 10X Genomics


title: ki-iT3H48_1


title: GEX_12R

description: 10X Genomics

value: female


title: T3-2


title: AD14CKO-3

description: Library name: AD14CKO-3

value: Col5a1 CKO


title: ki-aT3H48_3

value: Active T3H48-HHR ribozyme


title: T3-1


title: GEX_11R

description: 10X Genomics

value: Control


title: AD14CKO-2

description: Library name: AD14CKO-2


title: T2-3

value: nitrogen deficiency, 60 kg/hm2 (T2)


title: T4-3


title: ki-aT3H48_2


title: GEX_10R

description: 10X Genomics


title: AD14CKO-1

description: Library name: AD14CKO-1


title: ki-aT3H48_1


title: GEX_9R

description: 10X Genomics


title: sg3-KD_3

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples and counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 101.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of unified peaks.

value: Fibroblast

value: CRISPR-Cas13d knock-in

value: Transfection with Actg1-specific guide RNA


title: T2-2


title: CKO-IRI-29

city: Changsha

first: Jinrong

last: He

address: Tongzipo Road

department: Department of Nephrology

institute: The Third Xiangya Hospital, Central South University

description: Library name: sample12

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: GRCh38
Supplementary files format and content: txt file contains the FPKM value of gene in every sample

extract_protocol:
The joint capsule tissues were washed by phosphate buffer saline, and then synovium tissues were removed from joint capsules. The isolated joint capsule tissues were used in following study，RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit(Illumina). Briefly,Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: kidney

value: GPX3 knockout specifically in renal tubular epithelial cells

value: IRI-AKI


title: T1-3

value: leaves

value: no nitrogen fertilizer, 0 kg/hm2 (T1)


title: sg3-KD_2


title: GEX_8R

description: 10X Genomics

value: Brain (temporal cortex)

value: AD


title: CKO-IRI-15

description: Library name: sample11


title: T2-1


title: GEX_7R

description: 10X Genomics


title: CKO-IRI-7

description: Library name: sample10


title: sg3-KD_1


title: GEX_6R

description: 10X Genomics

value: male


title: T1-2


title: WT-IRI-49

description: Library name: sample9

value: WT


title: GFP-KD_3

value: Transfection with GFP-specific guide RNA


title: GEX_5R

description: 10X Genomics


title: WT-IRI-24

description: Library name: sample8


title: GFP-KD_2


title: native pdhR libV2 postIP 2

city: Boston

first: James

last: Galagan

address: 36 Cummington Mall

institute: Boston University

description: Sequencing of Library-ChIP sequences in native-SPA-tagged PdhR strain after IP

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
For Library-ChIP: Inserted sequences were counted from raw reads by identifying the anchor sequence (from the flank of the insertion site) "GGACGGATCCTCGAGCATGC", and taking the following 37 nucleotides after the anchor.
For Library-ChIP: Low abundance hits were dropped out (< 0.1% of preIP reads)
For Library-ChIP: Counts were normalized within-sample for sequencing depth by dividing counts by average counts for each insertion sequence
For Library-ChIP: Enrichment was determined as the ratio of normalized postIP:preIP counts
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps
Supplementary files format and content: Library-ChIP: TSV file where first column is the inserted sequence identified in processing step 1, columns 2 and 3 are the number of times sequence was identified in R1 and R2 reads, column 4 is the identifier of the sequence from the designed insertion pool, and column 5 is the sum of R1 and R2 reads
Library strategy: Library-ChIP

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  For in vivo ChIP-Seq, cells were sheared via sonication; for in vitro ChIP-Seq, DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-FLAG, anti-V5, or anti-6xHis mAb (indicated in metadata).  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  For Library-ChIP, preIP samples used sheared DNA purified via ProteinaseK digestion and Qiaquick PCR purification kit prior to addition of anti-tag antibody; postIP samples used sheared DNA that was immunoprecipitated, washed, purified, and extracted in the same way as ChIP-Seq.
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).  For Library-ChIP, libraries were constructed similarly to Illumina's 16S metagenomic library prep (Illumina Ref #15044223 Rev. B).  Briefly, an initial PCR was performed on DNA with a universal primer pair targeting flanks of the insertion site on the pAMD plasmid where designed sequences were inserted.  These primers contained overhangs that could be targeted by Illumina Nextera XT Index Kit v2 (Illumina Cat. No. FC-131-2001) primers.  First PCR was cleaned up with Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  Second PCR used a unique pair of primers from the Illumina Nextera kit for each sample, and were cleaned up with AMPureXP beads (Fisher Scientific Cat. No. NC9933872).

tag: transcription factor

value: pdhR

value: anti-FLAG mAb

tag: antibody vendor/catalog#

value: Sigma/Cat. No. F1804

tag: media

value: M9 Minimal with 0.4% glycerol

tag: time

value: Log-Phase

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: WT-IRI-13

description: Library name: sample7


title: GEX_4R

description: 10X Genomics

tag: pathological diagnosis

value: Control

tag: Sex


title: native pdhR libV2 postIP 1

tag: strain

tag: chip antibody


title: GEX_3R

description: 10X Genomics


title: Heart, TAB, sorbs2 knock-out, biol rep 4

city: Utrecht

first: Louk

last: Timmer

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Quality control of sequencing reads from FASTQ files was performed using FastQC (v0.11.8)
Reads were trimmed based on quality and adapter presence by TrimGalore (v0.6.5) and again checked for quality using FastQC.
rRNA reads were removed using SortMeRNA (v4.3.3)
reads were aligned to using the STAR (v2.7.3a) aligner
Mapped (bam) files were subjected to quality control using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3). and annotated against reference genome to generate readcounts using the Subread FeatureCounts module (v2.0.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Heart (ventricular)

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher)
TruSeq Stranded mRNA libraries (Illumina, #20020594) were prepared using a total of 100ng RNA according to the manufacturers protocol.

value: Heart (ventricular)

value: sorbs2 knock-out

value: TAB


title: native pdhR libV1 postIP


title: GEX_2R

description: 10X Genomics


title: CKO2

description: Library name: sample5

value: kidney

value: GPX3 knockout specifically in renal tubular epithelial cells

value: Sham


title: Heart, TAB, sorbs2 knock-out, biol rep 3


title: CKO3

description: Library name: sample6


title: GFP-KD_1

value: Fibroblast

value: CRISPR-Cas13d knock-in


title: inducible pdhR libV2 postIP 2

description: Sequencing of Library-ChIP sequences in inducible-FLAG-tagged PdhR strain after IP

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: inducible pdhR libV2 postIP 1


title: Heart, TAB, sorbs2 knock-out, biol rep 2


title: CKO1

description: Library name: sample4


title: WT3

description: Library name: sample3

value: WT


title: Heart, TAB, sorbs2 knock-out, biol rep 1


title: inducible pdhR libV1 postIP

value: pdhR


title: T1-1

value: leaves

value: no nitrogen fertilizer, 0 kg/hm2 (T1)


title: ulaR in vitro 10x 2

description:
Library name: invitro_ulaR_500_rep2
in vitro ChIP-Seq of 500ng ulaR with C-terminal 6xHis tag

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-6xHis mAb.  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).

treatment_protocol: Purified proteins were allowed to bind with 500ng sheared genomic DNA in IPP150 buffer at room temp for 1 hour prior to crosslinking and immunoprecipitation with anti-6xHis antibody.

value: ulaR

value: anti-6xHis mAb

value: Invitrogen/Cat. No. MA1-21315

value: 1 hour


title: WT2

description: Library name: sample2


title: Heart, sham, sorbs2 knock-out, biol rep 4

value: Heart (ventricular)

value: wildtype


title: inducible glnG libV2 postIP 2

description: Sequencing of Library-ChIP sequences in inducible-FLAG-tagged GlnG strain after IP

value: glnG

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: ulaR in vitro 1x 2

description:
Library name: invitro_ulaR_50_rep2
in vitro ChIP-Seq of 50ng ulaR with C-terminal 6xHis tag

source_name: Escherichia coli str. K-12 substr. MG1655


title: WT1

description: Library name: sample1

value: kidney

value: Sham


title: inducible glnG libV2 postIP 1

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: ulaR in vitro 1x 1

description:
Library name: invitro_ulaR_50_rep1
in vitro ChIP-Seq of 50ng ulaR with C-terminal 6xHis tag

value: Escherichia coli str. K-12 substr. MG1655


title: Heart, sham, sorbs2 knock-out, biol rep 2

value: TAB


title: inducible glnG libV1 postIP


title: nac in vitro 10x 2

description:
Library name: invitro_nac_500_rep2
in vitro ChIP-Seq of 500ng nac with C-terminal 6xHis tag

value: nac


title: ADR+SI2

city: Zhengzhou

first: Mingyang

last: Hu

state: Henan

address: jinshui

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

data_processing:
The quality of the constructed library was verified with an Agilent 2100 Bioanalyzer and quantified via qPCR.
Sequencing was then performed using the Illumina NovaSeq 6000 sequencer.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

extract_protocol:
Total RNA samples were extracted and assessed for quality using agarose gel electrophoresis, followed by quantification with a nanodrop. RNA samples that met the quality criteria were enriched for mRNA using oligo(dT) magnetic beads.
For RNA sequencing library construction, the RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers, followed by second-strand cDNA synthesis with dUTP incorporation. The double-stranded cDNA was subjected to end repair, A-tailing, adapter ligation, and polymerase chain reaction (PCR) amplification to generate the final library.

value: podocytes