title: Food colorant tartrazine treated N2 animals, Independent Trial 2

type: RNA

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

description: Gene expression data from animals treated with 100 uM of food colorant Tartrazine

hyb_protocol: 3.75 µg of fragmented and biotinylated ss-cDNA were included in the hybridization mix, using the GenAtlas Hybridization, Wash and Stain kit for WT Array Strips (Affymetrix, P/N 901667) according to the recommendations of the manufacturer. The resulting preparations were hybridized to GeneChip® C. elegans Gene 1.1 ST Array Strip (Affymetrix, 902157) with 26 unique sequences of each transcript. After applying hybridization (spike controls) and labeling tests it was observed that the 20 chips had fulfilled the quality criteria.

scan_protocol: GeneAtlas Microarray System from Affymetrix

data_processing:
After scanning, microarrays data were processed using Affymetrix Expression Command Console (Affymetrix) and all samples were within bounds for hybridization and labeling tests. Three independent RNA samples were employed. Samples from worms treated with food colorants were grouped as “treatment” and worms with no exposition were grouped as “control”. Data analysis was then performed with RMA (Robust Multiarray Average) allowing raw intensity values to be background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.
log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.

label: BIOTIN

organism: Caenorhabditis elegans

source_name: C. elegans treated with 100 uM Tartrazine

label_protocol: Ss-cDNA was synthetized from 3.5 ng of each sample using the GeneChip WT Pico Reagent kit (Affymetrix, P/N 703262). The amount and quality of ss-cDNA were checked by Nanodrop and Bioanalyzer. ss-cDNA targets were cleaned up, and after fragmentation and terminal labelling with biotin

growth_protocol: N2 worm  were syncronized using the bleaching protocol, from adultworms maintained in standart NGM agar plates at 20 ºC

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions, followed by a purification using  PureLink TM RNA Mini Kit from Invitrogen

treatment_protocol: 16-18 hours after haching L1 larvae were treated with 100 uM of each food colorant either Ponceau Red or Tartrazine in S. medium for 48 hours at 20 ºC

value: Whole animal

value: Wild-type N2

tag: age

value: 3 days after hacht, young adults


title: HSC_ACT_rep2

status: Public on May 05 2023

type: SRA

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

country: USA

institute: University of Illinois Chicago

library_source: transcriptomic

data_processing:
Quality check was done using FastQC v0.11.8
Sequenced reads were trimmed using cutadapt v1.18
Abundance of transcripts was quantified by kallisto v0.44.0 using kallisto index created from mm10
Read counts were normalized to counts per million reads (CPM) using edgeR v3.8
Assembly: mm10
Supplementary files format and content: tab delimited-text file including CPM values from each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mouse primary HSCs were isolated using density gradient centrifugation. Freshly isolated cells from mouse liver were considered quiescent HSCs (QS). To obtain activated mouse primary HSCs, cells were maintained for 6 days in Dulbecco’s modified Eagle’s medium (DMEM) containing 1,000 mg/L glucose supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from mouse primary HSCs using a Direct-zol RNA MicroPrep Kit. The RNA purity, concentration, and integrity were evaluated with an Agilent TapeStation 4200.
RNA libraries were prepared using Illumina TruSeq Stranded mRNA sample library preparation kit.

treatment_protocol: Mouse primary HSCs from Hk2 fl/fl mouse liver were transduced by adenovirus expressing either eGFP (ACT) or Cre recombinase fused to eGFP to delete Hk2 (KO), and cultured for 6 days. KO cells were treated with 10 mM lactate (LAC) for 24 h.

tag: tissue

value: Liver

tag: cell type

value: Hepatic stellate cell

tag: genotype

value: Hk2 fl/fl

tag: treatment

value: Ad-GFP


title: Food colorant tartrazine treated N2 animals, Independent Trial 1


title: Food colorant Ponceau Red treated  N2 animals, Independent Trial 2

description: Gene expression data from animals treated with 100 uM of food colorant Ponceau Red

source_name: C. elegans treated with 100 uM Ponceau Red


title: Trochophore larvae of crassostrea gigas

city: London

first: Laura

last: Piovani

address: Room B02, Anatomy Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v4 and v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: for details see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2023
Supplementary files format and content: Tab-separated values files and matrix files

organism: Magallana gigas

source_name: Trochophore larvae of crassostrea gigas

extract_protocol:
for protocol see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2023
for library contruction details see "Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories" Piovani et al 2024

value: trochophore larvae


title: input_0_T_Rep2

city: Wuhan

first: wu

last: bi

state: Hubei

address: wuhan hzau

country: China

institute: hzau

library_source: genomic

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30
ChIP-seq reads were aligned to the MH63RS2 and Nip genome using Bowtie. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.  files were generated using MACS v2 with default settings.
Supplementary files format and content: MH63RS2 and Nip
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Oryza sativa

source_name: input

growth_protocol: under LD condition in field

extract_protocol:
tissues were fixed with 1% formaldehyde for 15 minutes.
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for MGI (NDM607-01)

value: panicle

value: input


title: input_0_T_Rep1


title: input_0_Rep2


title: input_0_Rep1


title: HSC_ACT_rep1


title: H3K27ac_0_T_Rep1

source_name: H3K27ac Chip-seq of young panicle


title: H3K27ac_0_T_Rep2


title: HSC_QS_rep3

value: Untreated


title: 001 (SMA-adjacent)

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing: Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences. Each PCR reaction used 4 μl of indexing oligonucleotides, 4 μl of indexing PCR primers, 2 μl of Nanostring 5X PCR Master Mix. Thermocycling conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min; 18 cycles of 95 °C for 15 s, 65 °C for 1 min, 68 °C for 30 s; and 68 °C for 5 min. PCR reactions were pooled, and pooled libraries were paired-sequenced  on an Illumina Next Seq 2000 instrument. FASTQ files for each sample were converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline. DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.2.0.111 (Nanostring). A minimum of 10,000 reads were required for each sample. Probes were checked for outlier status by implementing a global Grubb’s outlier test with alpha set to 0.01. The counts for all remaining probes for a given target were then collapsed into a single metric by taking the geometric mean of probe counts. For each sample, an RNA-probe-pool-specific negative probe normalization factor was generated on the basis of the geometric mean of negative probes in each pool. To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers. Samples 003 (Pdpn-adjacent) and 006 (SMA-adjacent) were excluded from final analysis as they did not pass quality control checks.

source_name: mammary gland

growth_protocol: Paraformaldehyde-fixed frozen blocks

extract_protocol:
Slides were imaged at 20x magnification using Nanostring GeoMx DSP platform and morphologic markers SMA and Pdpn were used to select regions of interest (ROIs). Automatic segmentation of the ROIs based on ZSGreen expression were used to define areas of interest (AOIs), allowing for the separation of ZSGreen+ periostin-expressing cells from surounding cells. A total of 12 AOIs were exposed to 385 nm (UV) light, releasing the index oligonucleotides which were collected with a microcapillary and deposited into individual wells of a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 uL of DEPC-treated water.
Library was constructed at University of Minnesota Genomics Center

treatment_protocol: Fixed frozen mammary glands from 3 mice were incubated with the NanoString mouse Whole Transcriptome Atlas (WTA) panel probes overnight, then stained with Cy3-SMA (TCF C6198), Pdpn (R&D Systems AF3244;Cy5 secondary), and the DNA stain Syto83 (Thermo S11364) as morphology markers to visualize tissue architecture. Stained slides were loaded onto the GeoMx instrument and scanned for region of interest (ROI) selection.

value: mammary gland


title: H3K27ac_0_Rep2


title: HSC_QS_rep2


title: HSC_QS_rep1


title: H3K27me3_0_T_Rep1

source_name: H3K27me3 Chip-seq of young panicle


title: HSC_LAC_IgG

data_processing:
Quality check was done using FastQC v0.11.8
Sequenced reads were mapped to mm10 (UCSC) using Bowtie2 v2.4.2
Mapped reads with a MAPQ lower than 2 were filtered and sorted by samtools v1.10
Conversion of sorted bam files into bedgraph files was done using bedtools v2.30
Peaks were called using SEACR v1.3
Bigwig files were generated using deepTools v2.0
Assembly: mm10
Supplementary files format and content: bigwig files RPKM normalized by deepTools

extract_protocol:
Mouse primary HSCs were incubated with NE1 buffer on ice for 10 min. After collecting nuclear pellets, concanavalin A-coated magnetic beads were mixed and incubated for 10 min at RT. Next, the unbound supernatant was removed, and the bead-bound cells were resuspended in antibody buffer. Anti-H3K18la (PTM-1406, PTM Biolabs), anti-H3K18ac (ab1191, Abcam), and anti-IgG negative control (13-0042, EpiCypher) antibodies were added, and incubated on a nutator overnight at 4 °C. The primary antibodies were removed, and incubation with 0.5 ug of secondary antibody was performed on a nutator for 1 h at RT followed by incubation with pAG-Tn5 in 300-wash buffer for 1 h at RT. The bead/nucleus pellet was resuspended in tagmentation buffer, and the mixture was incubated for 1 h at 37 °C. Next, the bead/nucleus pellet was resuspended in TAPS buffer. The bead/nucleus pellet was then resuspended in SDS release buffer and incubated for 1 h at 58 °C. Next, SDS quenching buffer was added.
To amplify the libraries, 2 ul of a universal i5 and a uniquely barcoded i7 primer (10 uM stocks) were added. A volume of 25 ul of NEBNext High-Fidelity 2x PCR Master mix was added and mixed. The samples were placed in athermocycler with aheated lid using the following cycling conditions: 58 °C for 5 min; 72 °C for 5 min; 98 °C for 45 sec; 14 cycles of 98 °C for 15 sec and 60 °C for 10 sec; final extension at 72 °C for 1 min; and hold at 8 °C. Post-PCR clean-up was performed by adding 1.3x AMPure XP beads, and the libraries were incubated with the beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 15 ul of 10 mM Tris pH 8.0. The tubes were placed on a magnetic stand, and the liquid was withdrawn into a fresh tube.

value: Ad-Cre + Lactate

tag: antibody

value: IgG


title: H3K27me3_0_Rep1


title: H3K27me3_0_Rep2


title: H3K9me2_0_T_Rep2

source_name: H3K9me2 Chip-seq of young panicle


title: HSC_KO_IgG

value: Ad-Cre


title: Water treated N2 animals, Independent Trial 1

description: Gene expression data from control (non treated) animals

source_name: C. elegans water


title: HSC_ACT_IgG


title: H3K9me2_0_Rep2


title: H3K9me2_0_T_Rep1


title: H3K27ac_0_Rep1


title: H3K4me3_0_T_Rep2

source_name: H3K4me3 Chip-seq of young panicle


title: H3K27me3_0_T_Rep2


title: Food colorant Ponceau Red treated  N2 animals, Independent Trial 1


title: HSC_QS_IgG


title: H3K4me3_0_T_Rep1


title: Water treated N2 animals, Independent Trial 2


title: Pool154_Plate6-4-M1-H7

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: P

tag: target

value: CBX

tag: Sex

value: female


title: HSC_LAC_H3K18ac_rep2


title: H3K4me3_0_Rep2


title: H3K9me2_0_Rep1


title: G361  cells, shDCAF1 2

city: Los Angeles

first: Yonghwan

last: Shin

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to hg38 - GENCODE Genes - release 40 using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: hg38

organism: Homo sapiens

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: Melanoma

value: DCAF1 Knockdown


title: HSC_LAC_H3K18ac_rep1

value: Liver

value: Hepatic stellate cell


title: G361  cells, shControl 1

value: WT


title: G361  cells, shControl 3


title: G361  cells, shControl 2


title: HSC_LAC_H3K18la_rep2

value: Hk2 fl/fl


title: G361  cells, shDCAF1 3


title: H3K4me3_0_Rep1

value: panicle


title: HSC_LAC_H3K18la_rep1


title: POAG4

city: Changsha

first: Xiaoyu

last: Zhou

address: No. 188, Section 1, Furong South Road

department: Glaucoma Institute

institute: Changsha Aier Eye Hospital

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression. In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value). Hierarchical clustering was performed. miRNA target prediction was performed by targetscan and other popular method, then the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNAs.
Assembly: mirbase v21
Supplementary files format and content: xls format, TagCount_ALL_Isoform of miRNA

source_name: Trabecular meshwork

extract_protocol:
TM RNA samples from 4 control subjects and 4 POAG patients for microarray analyses were extracted and the RNA integrity was tested by standard denaturing agarose gel electrophoresis, as described above. RNA sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent, Santa Clara, CA). Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3′ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. One microgram of each labeled cRNA was fragmented by adding 5 μl 10 × blocking agent and 1 μl of 25 × fragmentation buffer, then the mixture was heated at 60 °C for 30 min; finally, 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 h at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (part number G2505C).
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:    1) 3'-adaptor ligation;    2) 5'-adaptor ligation;    3) cDNA synthesis;    4) PCR amplification;    5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).    The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer's instructions.

value: Trabecular meshwork

tag: disease

value: POAG


title: G361  cells, shDCAF1 1


title: HSC_KO_H3K18ac_rep2


title: POAG2

value: male


title: POAG3


title: HSC_KO_H3K18ac_rep1


title: Normal4

value: Normal


title: HSC_KO_H3K18la_rep2


title: Normal2


title: Normal1


title: HSC_KO_H3K18la_rep1


title: HUVEC PBS72h - 4

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
RNA-seq libraries were prepared using Illumina’s TruSeq protocol and were sequenced on an Illumina NextSeq 500. Reads were aligned to the hg38 genome using Rsubread v1.5.3. Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation. Gene symbols were provided by NCBI gene annotation. Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: endothelial

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVECs) were isolated in-house. Cells were assayed between passages 3 and 8. To induce IL-6 signaling, cells were plated at full confluence at a density of 8 × 104 cells/cm2 on plates precoated for 30 min with 0.1% gelatin and incubated at least 48 h prior to the start of experiments

extract_protocol:
Treated HUVECs and controls were immediately lysed in Trizol
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: Cells were then treated with a combination of 200 ng/mL recombinant human IL-6 and 100 ng/mL sIL-6Rα (IL-6+R) or PBS (control) for 72 hours.

value: endothelial

value: HUVEC

value: Endothelium

value: PBS for 72 hours


title: POAG1


title: IL6_exp1_2_72

type: genomic

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Methylation array data were processed with the statistical language R (version 4.2.1) and CHAMP Bioconductor packages. Briefly, processing of the raw HUVEC methylation data was performed with the Chip Analysis Methylation Pipeline (ChAMP) package (version 2.21.1). Raw methylation data were imported by the minfi method. Probes with a detection p-value >0.01 in one or more samples, with a bead count <3 in at least 5% of samples, non-CpG probes, probes that align to multiple locations, and sex chromosome-specific probes were removed from subsequent analyses. Data normalization was performed by the BMIQ method. Batch effect prediction was made by singular value decomposition (SVD)

label: cy3, cy5

source_name: Human Umbilical Vein Endothelial Cells

label_protocol: standard protocol

extract_protocol: DNeasy Blood & Tissue Kit (Qiagen, USA)

treatment_protocol: Cells were then treated with a combination of 200 ng/mL recombinant human IL-6 and 100 ng/mL sIL-6Rα (IL-6+R) or PBS (control) for 72 hours. After 72 hours, a subset of control and IL-6+R-treated cells were washed and incubated for 96 hours in EGM-2 Growth Medium

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: HUVEC, IL6 72h - 3

value: treated with a combination of 200 ng/mL recombinant human IL-6 and 100 ng/mL sIL-6Ralpha (IL-6+R)


title: HSC_ACT_H3K18ac_rep1

value: Ad-GFP


title: HUVEC PBS72h - 3


title: IL6_exp1_3_72


title: Normal3


title: IL6_exp1_1_72


title: HUVEC, IL6 72h - 4


title: HUVEC, IL6 72h - 2


title: HUVEC PBS72h - 1


title: HSC_ACT_H3K18la_rep1


title: HSC_ACT_H3K18ac_rep2


title: GSK3A3-Input

city: Philadelphia

first: Daniel

middle: Sungjoo

last: Park

state: PA

address: 415 Curie Blvd

department: Genetics

institute: University of Pennsylvania

description:
GSK3A3-RAD21.subtract.bw
GSK3A3-RAD21.bed
RAD21_GSK3A.bw

data_processing:
ChIP-seq:Sequencing quality was examined using FastQC (v0.11.9) to ensure that the library GC% and duplication rate were within expected range and adapters were effectively trimmed. Trimming was performed with Trimmomatic (v0.38) using a sliding window of four bases and a minimum average quality score of 20; reads shorter than 20 base pairs were discarded. Remaining reads were aligned against the GRCh38 reference genome using Bowtie2 (v2.4.1) allowing soft clipping ("--local") with the "sensitive local" preset options. Alignments were then filtered for duplicates using the Picard (v2.27.1) "MarkDuplicates" tool. Alignments that mapped to ENCODE blacklisted regions were also removed for downstream analysis using BEDtools v2.30.0.
ChIP-seq:Visualization tracks were generated using the deepTools (v3.3.1) "bamCompare" utility, in which  corresponding input controls were subtracted from IP and reads with a MAPQ score lower than 20 were discarded. Peaks were called for IP libraries against their corresponding input controls using MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff. Lost, retained, and gained sites in GSK3A KD were determined with DiffBind v3.6.2 using the DESeq2 analysis method, a false-discovery cutoff of 0.1, and only reads with a minimum MAPQ score of 20. Example ChIP-seq tracks were generated in PyGenomeTracks v3.6.
Hi-C:Raw reads for each Hi-C sample were processed with HiC-Pro (version 2.11.1) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme. For downstream analyses, ValidPairs were converted to hic files using the “hicpro2juicebox.sh” in utils of HiC-Pro. We recovered the following number of contacts in each condition: Control (507359205), GSK3A KD (445835605).
Assembly: hg38
Supplementary files format and content: ChIP-seq: Bigwig files were generated using BEDtools (v2.27.1) on each biological replicate; bed files of peaks for each biological replicate were called with MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff
Supplementary files format and content: Hi-C: .hic files for each condition were generated using HiC-Pro (version 2.11.1) and converted to .cool files using Cooltools

growth_protocol: We obtained the HCT-116 cell line from ATCC (RRID:CVCL_0291). All cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin at 37 °C with 5% CO2.

extract_protocol:
ChIP-seq: ChIP was performed based on (Shah et al., Dev Cell 2021). HCT-116 cells were cross-linked in culture medium by addition of methanol-free formaldehyde (ThermoFisher, final 1% v/v) and incubated at room temperature for 10 minutes with gentle nutation. Crosslinking was quenched by addition of glycine (final 125 mM) and incubated at room temperature for 5 minutes with gentle nutation. Media was aspirated and replaced with cold DPBS. Cells were scraped and transferred to conical tubes, then pelleted by centrifugation (1500 rpm, 3 minutes, room temperature). Pellets were flash frozen on liquid nitrogen and stored at -80C.  For ChIP, 30 uL protein G magnetic beads (per sample; ThermoFisher) were washed three times in blocking solution (0.5% BSA in DPBS). Beads were then resuspended in 250 uL blocking solution and 2 ug antibody (RAD21, Abcam ab992; CTCF, Cell Signaling Technology 3418) was added. Beads and antibody were rotated at 4C for at least six hours. Nuclei were isolated from frozen cell pellets as follows: pellet was resuspended in 10 mL cold lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40,  0.25% Triton X-100, and protease inhibitors) and rotated at 4C for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was aspirated and the pellet was resuspended in 10 mL cold lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors) and rotated at room temperature for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was discarded and nuclei were resuspended in 1 mL cold lysis buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris). Nuclei were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Sonicated chromatin was transferred to 1.5mL microcentrifuge tubes and Triton-X 100 was added (1% final v/v) followed by centrifugation (top speed, 10 minutes, 4C). Supernatant was transferred to a new tube. Antibody-conjugated protein G beads were washed three times in blocking solution, resuspended in 50 ul blocking buffer, and added to 500 ug sonicated chromatin. Chromatin was rotated overnight at 4C. 50 ug lysate was reserved in a separate tube at -20C for input.   On day 2, beads were washed five times in 1 mL RIPA buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were then washed in 1 mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes. Beads were finally resuspended in 210 uL elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS), and chromatin was eluted from beads by agitation at 65 °C for 30 minutes. 200 uL eluate was transferred to a new tube, and all samples (ChIP and input) were reverse cross-linked overnight at 65 °C with agitation for between 12 and 18 hours. 200 uL 1xTE was added to all samples, and samples were treated with RNase A (final 0.2mg/mL RNase; 37 °C for 2 hours) and proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours). DNA was purified using phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.  In situ Hi-C: Hi-C libraries were generated from 10e6 cells using the Arima-HiC+ kit (Arima Genomics) according to manufacturer's instructions
ChIP-seq: ChIP and input DNA were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for either single or dual-index sequencing. Library quality was assessed on Bioanalyzer (Agilent) and quantified by qPCR (Kapa Biosystems).   In situ Hi-C: Libraries were prepared using the Kapa Hyper Prep Kit with KAPA Library Amplification Primer Mix (KK8502), according to manufacturer’s recommendations. Libraries were validated for quality and size distribution using the Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851), KAPA Library Quantification kit (Roche, Cat# KK4824) and TapeStation 2200 (Agilent).
ChIP-seq: Quantified libraries were sequenced via Illumina sequencing using the NextSeq500 (single end, 75bp) and NovaSeq6000 (paired-end, 100bp) platforms. Data from the same libraries were merged for final analysis.  In situ Hi-C: Paired-end sequenced (61bp+61bp) on a NovaSeq 6000 (Illumina).

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium (Thermo Fisher Scientific), and pipetted onto siRNA. Plates were incubated at room temperature for 20 minutes. HCT-116 cells were trypsinized and resuspended in antibiotic-free medium, then plated on siRNA duplexes to obtain a final siRNA concentration of 25 nM. After 72 h of RNAi treatment, cells were collected for experiments.

value: wild type

value: GSK3A siRNA


title: GSK3A3-RAD21


title: HSC_QS_H3K18ac_rep2

value: Liver

value: Hepatic stellate cell

value: Untreated


title: IL6_exp3_1_72


title: HUVEC, IL6 72h - 1

value: WT


title: GSK3A1-Input

description:
GSK3A1-RAD21.subtract.bw
GSK3A1-RAD21.bed
RAD21_GSK3A.bw


title: IL6_exp2_2_72


title: HSC_QS_H3K18ac_rep1

value: Hk2 fl/fl


title: GN_attP_mix_cells_replicate2

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

data_processing:
The DNA regions of interest were sequenced by the Amplicon-EZ service provided by Genewiz (now Azenta Life Sciences), providing Illumina high throughput sequencing with read 1 and read 2 sequences of 250 nt each.
The read 1 and read 2 fastq files from each sample were paired using PEAR v0.9.6 42. The relative frequencies of the formation of various recombined DNA products were assessed by counting the frequency of particular DNA sequences in the resulting paired fastq files using the grep function in Bash.
For the excision experiments using primer set 1, excised plasmids were identified by searching for nucleotides on the right side of the attB(GA) site “ACTCCGTCGTCAGGATCATCC”, while unexcised plasmids were identified by searching for nucleotides on the right side of the attP(GA) site “ACTCAGTGGTGTACGGTACAAACC”. For the excision experiments using primer set 2, excised plasmids were identified by searching for nucleotides immediately to the left of the attP(GA) site “GATCCCCTTTAGTGAGGGTT”, while unexcised plasmids were identified by searching for nucleotides on the left of the attB(GA) site “CGACGATGTAGGTCACGGCA”.
For the orthogonal GN dinucleotide experiments, the relative numbers of recombination events for the attB sequences of each central dinucleotide within the mixture was determined by searching for and counting the instances of each resulting attR sequence present in the read. For replicates 2 and 3, each sample containing a different central dinucleotide attP sequence was amplified with a unique primer marking that sample. For example, samples where the attP sequence has a central GG dinucleotide were amplified with a primer adding a G nucleotide as the first nucleotide of read 1. This allowed us to further multiplex samples, reducing overall sequencing cost.
Sequence counts were imported into R, where they were converted into frequencies and plotted for the manuscript.
Supplementary files format and content: "Flanked_excision_results.csv" is a comma separated value table containing the counts of each excised and unexcised amplicon for each sample and each primer set, for each replicate experiment.
Supplementary files format and content: "GN_recombination_results.csv" is a comma separated value table containing the frequencies of each recombined attB sequence variant with each of the attP sequence variants, for each replicate experiment.

organism: synthetic construct

growth_protocol: DMEM with 10% FBS and 1 % Penicillin / Streptomycin

extract_protocol:
HEK 293T genomic DNA was extracted using a Qiagen DNeasy Blood and Tissue Kit
The DNA segments of interest were amplified from 500 ng DNA with 0.3125 μM forward and reverse primer in a 40 μL reaction with Phusion Flash High-Fidelity PCR Master Mix (Thermo Scientific, F548L) added as half the volume. Reaction conditions were 95℃ 3’, 95℃ 15”, 60℃ 15”, 72℃ 30”, repeated twenty-six to twenty-eight times, 72℃ 1’, 4℃ hold. In the case of excision via flanking GA sites, an extra forward or reverse primer was used so that both excised and unexcised products could be amplified from the same PCR tube. PCR products were run on a 2% TAE-agarose gel. DNA bands were excised and extracted using a GeneJet Gel Extraction and DNA Cleanup Micro Kit. The DNA regions of interest were sequenced by the Amplicon-EZ service provided by Genewiz (now Azenta Life Sciences), providing Illumina high throughput sequencing  with read 1 and read 2 sequences of 250 nt each
OTHER: Amplicon sequencing of DNA recombined within cells

value: HEK 293T

value: Cultured cells

value: Recombination into plasmid


title: GSK3A1-RAD21


title: GN_attP_mix_cells_replicate3


title: HUVEC PBS72h - 2

value: endothelial


title: HSC_QS_H3K18la_rep2


title: Scr3-CTCF

description:
Scr3-CTCF.subtract.bw
Scr3-CTCF.bed
CTCF_Scr.bw

value: control siRNA


title: Scr2-Input

description:
Scr2-RAD21.subtract.bw
Scr2-CTCF.subtract.bw
Scr3-RAD21.subtract.bw
Scr3-CTCF.subtract.bw
Scr2-RAD21.bed
Scr2-CTCF.bed
Scr2-RAD21.bed
Scr3-CTCF.bed
RAD21_Scr.bw
CTCF_Scr.bw


title: HSC_ACT_H3K18la_rep2


title: Scr2-CTCF

description:
Scr2-CTCF.subtract.bw
Scr2-CTCF.bed
CTCF_Scr.bw


title: GN_attP_GG_cells_replicate1


title: IL6_exp2_1_72


title: HSC_QS_H3K18la_rep1


title: PBS_exp1_2_72


title: PBS_exp3_2_72


title: PBS_exp3_1_72


title: CRC scRNAseq gd T cells Patent 3-6

city: Boston

first: Cathal

last: Harmon

state: MA

address: 4 Blackfan Circle, Room 625, Harvard Institutes of Medicine,

institute: Brigham and Women's Hospital

description:
BRI-294
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream data analysis was carried out using Seurat package in R
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colorectal tumor

extract_protocol:
Lymphocytes were FACS sorted from human tumor and healthy tissue. Tissue was mechanically and enzymatically digested using Type IV collagenase, Dnase I at 37C for 1 hour.
Library construction was performed as per manufacturers instructions, 10X Genomics 3' V3.0

value: Colorectal tumor

value: gd T cells


title: IL6_exp3_1_96

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: 1431.TCTCTAGCGC-CTGCTTGACG

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Hippocampus

extract_protocol:
Frozen hippocampal tissue was weighed and homogenized in RNAase-free beaded tubes in chloroform with TRIzol™ followed by RNeasy Mini Kit. 1 ug of total RNA for the construction of sequencing libraries.
Takara Clontech SMARTer Ultra-low Input HV

value: 5xFAD/ T2CV

value: F

value: SD


title: IL6_exp3_2_96


title: PBS_exp2_2_72


title: Scr3-RAD21

description:
Scr3-RAD21.subtract.bw
Scr2-RAD21.bed
RAD21_Scr.bw

value: wild type


title: GN_attP_GC_cells_replicate1


title: 1396.TCTCAGCCTC-TAACACGACG

value: Ctl


title: CRC scRNAseq MAIT cells Patent 3-6

description:
BRI-296
10X Genomics

value: MAIT cells


title: Endometrial scRNAseq Healthy tissue Patient 1 & 2

description:
BRI-184
10X Genomics

source_name: Healthy endometrium

value: Healthy endometrium

value: Lymphocytes


title: PBS_exp2_1_72


title: GN_attP_GA_cells_replicate1


title: attB_GN_plasmid_mix

value: E. coli


title: Endometrial scRNAseq Patient 2

description:
BRI-177
10X Genomics

source_name: Endometrial tumor

value: Endometrial tumor


title: 1338.TGATAATGCG-GATTCCGTCG


title: 1398.TCTATTGGTG-TAGGCGCGAA


title: IL6_exp2_1_96


title: CRC scRNAseq Patient 2

description:
BRI-117
10X Genomics


title: Excision_control_replicate3_primerB

value: HEK 293T

value: Cultured cells

value: Recombination into genomic landing pad


title: Endometrial scRNAseq Patient 1

description:
BRI-175
10X Genomics


title: CRC scRNAseq Patient 1

description:
BRI-116
10X Genomics


title: cultured_K14SOX9ARID1a_dox_rep2

city: New York

first: Yihao

last: Yang

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
transposed DNA
Biological replicate 2
K14SOX9_ARID1a_rep1_rep2_readsPOOL_RIP.bw
K14SOX9ARID1a_rep1_rep2_POOL_peaks_thresh3.bed

data_processing:
The raw sequencing reads were trimmed with skewer (v0.2.2) and aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome.
The aligned reads were deduplicated with Picard (v. 2.3.0) and shifted to correct for Tn5 insertion bias.
Bamfiles from biological replicates are combined with Samtools (1.9)
Peaks were called on replicate-pooled bamfiles with MACS2 (v. 2.1.1) with default settings.
bigwig files were generated on the combinded bamfiles using deeptools (2.5.4) bamcoverage with reads in peaks as the scalefactor.
Assembly: GRCm38 (mm10)
Supplementary files format and content: BIGWIG files generated from combined bamfiles and peak files called from replicate pooled samples in bed format

source_name: keratinocytes extracted from mouse back skin

extract_protocol:
Cells were isolated by FACS into FACS sorting buffer. Cells were pelleted and lysed using 0.01% IGEPAL CA-630. ATAC libraries were prepared on these solubilized nuclei, according to Buenrostro et al. 2015.
Illumina Nextera, Buenrostro et al., 2015

treatment_protocol: Mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time. Cells in culture are treated with 1ug/ml dox for indicated period of time

tag: mouse strain

tag: mouse age

value: K14rtTA; TRE-myc-Sox9; TRE-ARID1a

tag: mouse sex

value: male

tag: sorting scheme


title: cultured_K14SOX9ARID1a_dox_rep1

description:
transposed DNA
Biological replicate 1
K14SOX9_ARID1a_rep1_rep2_readsPOOL_RIP.bw
K14SOX9ARID1a_rep1_rep2_POOL_peaks_thresh3.bed


title: IL6_exp2_2_96


title: 1250.AATCGAACTC-TTAGACCTTC


title: PBS_exp3_2_96


title: GN_attP_GT_cells_replicate1

value: Recombination into plasmid


title: Scr2-RAD21

description:
Scr2-RAD21.subtract.bw
Scr2-RAD21.bed
RAD21_Scr.bw

value: control siRNA


title: BRG1CNR_WTSOX9_dox_rep1

description: Biological replicate 1

data_processing:
All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were trimmed with Skewer (version 0.2.2) and aligned to reference genome (mm10) using Bowtie2 (version 2.2.9) and deduplicated with Java (version 2.3.0) Picard tools (http://broadinstitute.github.io/picard). Reads were flittered to reads smaller or equal to 120bp using Samtools (version 1.3.1). BAM files for each replicate were combined using samtools.
Bigwigs were generated using Deeptools (version 3.1.2) with RPKM normalization
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles and peak files called from replicate pooled samples in bed format
Library strategy: CUT&RUN

extract_protocol:
Epidermal stem cells were FACS isolated as mentioned above and CUT&RUN was performed as previously described with minor modifications indicated in methods.
CUT&RUN sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1x ratio of SPRI beads and eluted in 15μL 0.1x TE buffer.
All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads.

value: K14rtTA; TRE-myc-Sox9

value: Male


title: CRC scRNAseqhealthy tissue Patent 3-6

description:
BRI-297
10X Genomics

source_name: Healthy colon

value: Healthy colon


title: PBS_exp1_1_72

value: Human Umbilical Vein Endothelial Cells (HUVECs)


title: PBS_exp2_2_96


title: BRG1CNR_WTSOX9_nodox_rep1

description: Biological replicate 1


title: Arid1aCNR_noHMG_dox_rep1

description: Biological replicate 1

value: K14rtTA; TRE-myc-Sox9noHMG


title: PBS_exp3_1_96


title: Excision_control_replicate2_primerB


title: SAMPLE 1_genomic DNA from a paraganglioma sample carrying the DLST-p.Y422C mutation

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011

label: Cy5 and Cy3

source_name: Paraganglioma sample carrying the DLST-p.Y422C mutation

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was obtained with the Covaris S2 System (Covaris) for FFPE tissues according to manufacturers’ instructions

tag: gender

value: DLST-p.Y422C mutation

value: Primary tumor


title: Excision_flanked_replicate3_primerB


title: 1074.AGCATGCTGT-ACACAATCCA

value: M

value: Ctl


title: BRG1CNR_noHMG_dox_rep1

description: Biological replicate 1


title: Arid1aCNR_WTSOX9_dox_rep1

description: Biological replicate 1


title: Arid1aCNR_WTSOX9_nodox_rep1

description: Biological replicate 1


title: PBS_exp2_1_96


title: Excision_flanked_replicate2_primerB


title: 1073.CAGAAGTTAG-GAAGCGGTCA


title: 1072.CCGTATCACA-TAGCTAACGT


title: JunCNR_WTSOX9_dox_rep1

description: Biological replicate 1


title: IL6_exp3_2_72


title: Excision_control_replicate2_primerA


title: JunCNR_noHMG_dox_rep1

description: Biological replicate 1


title: Excision_flanked_replicate3_primerA


title: JunCNR_WTSOX9_nodox_rep1

description: Biological replicate 1


title: cultured_K14SOX9AFOS_dox_rep2

description: Biological replicate 2

value: K14rtTA; TRE-myc-Sox9; TRE-FLAG-AFOS


title: Excision_flanked_replicate2_primerA

value: HEK 293T


title: Excision_control_replicate1_primerB

value: Cultured cells


title: cultured_K14SOX9AFOS_dox_rep1

description: Biological replicate 1


title: cultured_K14AFOS_dox_rep2

description: Biological replicate 2

value: K14rtTA; TRE-FLAG-AFOS


title: 1067.GTACCGGATA-AGTGAAGCGC

value: F


title: cultured_K14AFOS_dox_rep1

description: Biological replicate 1

value: male


title: Excision_flanked_replicate1_primerB

value: Recombination into genomic landing pad


title: 1068.TCCTACGTGC-GCATTCTCGC


title: Sox9Truncations_H3K4me1_high_MNase

data_processing:
MINT-ChIP reads were processed with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 with FASTX-Toolkit.
The demultiplexed reads were aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome The aligned reads were deduplicated with Picard for both PCR and IVT duplicates (v. 2.3.0). Bamfiles from biological replicates are combined with Samtools (1.9). H3K27ac peaks are called with MACS2 (v2.1.1), and H3K4me1 peaks are called with epic2 peak caller based on SICER (0.0.36).
bigwig files were generated on the combined bamfiles using deeptools (2.5.4) bamcoverage with (1,000,000/total reads in peaks) as the scale factor. For totalH3, RPKM is used for normalization.
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles and peak files called from replicate pooled samples in bed format

extract_protocol:
FACS sorted cells were used for MINT-ChIP according to van Galen et al (doi::10.1016/j.molcel.2015.11.003).
libraries are prepared according to van Galen et al (doi::10.1016/j.molcel.2015.11.003).
All libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads.

treatment_protocol: Mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time.

value: K14rtTA; TRE-myc-Sox9varients


title: mllCNR_WTSOX9_dox_rep1

description: Biological replicate 2

data_processing:
All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were trimmed with Skewer (version 0.2.2) and aligned to reference genome (mm10) using Bowtie2 (version 2.2.9) and deduplicated with Java (version 2.3.0) Picard tools (http://broadinstitute.github.io/picard). Reads were flittered to reads smaller or equal to 120bp using Samtools (version 1.3.1). BAM files for each replicate were combined using samtools.
Bigwigs were generated using Deeptools (version 3.1.2) with RPKM normalization
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles and peak files called from replicate pooled samples in bed format

value: MLL3/4 (Wysocka lab)

tag: antibody dilution

value: K14rtTA; TRE-myc-Sox9


title: mllCNR_WTSOX9_dox_rep2

description: Biological replicate 2

value: Male


title: mycCNR_noTA_dox_rep2

description: Biological replicate 2

value: Myc-tag (cell signaling 71D10)

value: K14rtTA; TRE-myc-Sox9noTA


title: Excision_flanked_replicate1_primerA


title: Excision_control_replicate1_primerA


title: mycCNR_WTSOX9_nodox_rep2

description: Biological replicate 2


title: mycCNR_WTSOX9_dox_rep2

description: Biological replicate 2


title: 965.AGGAGTCACT-TTCGACGCAG

value: SD

tag: age


title: mycCNR_noHMG_dox_rep2

description: Biological replicate 2

value: K14rtTA; TRE-myc-Sox9noHMG


title: CCI+THP-4

city: Beijing

first: Wu

last: Dan

address: Dongzhimennei south steet 16

institute: Institute of Chinese Materia Medica，China Academy of Chinese Medical Sciences

description: Gene expression data from spinal cord in CCI rat

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to  the manufacturer’s instructions. After cluster generation, the library preparations  were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads  were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All  the downstream analyses were based on the clean data with high quality.
Gene expression profiling was analyzed using R (http://www.rproject.org/, version 3.1.1) with Bioconductor packages (http://www.bioconductor.org/).
Assembly: rn4
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: spinal cord on postoperative day 10

extract_protocol:
RNA was harvested using TRIzol (Invitrogen, CA, USA). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNextUltra RNA Library Prep Set for Illumina (NEB, USA.) following manufacturer’s recommendations.

tag: tissue

value: spinal cord on postoperative day 10

value: WT

value: sciatic never ligation and THP teratment


title: 965.CGATCCGCTT-GCAATGATGC

value: M


title: mllCNR_noTA_dox_rep2

description: Biological replicate 2


title: 1070.AGAGTATGTG-ACAGGTATGT


title: CCI+THP-3


title: 1036.CGGAGCGATA-CTTAACAAGG


title: Sox9Truncations_H3K4me1_low_MNase


title: 1218.AAGGTGTTAG-TAAGCGCGTG

value: Ctl


title: mllCNR_noHMG_dox_rep2

description: Biological replicate 2


title: CCI+THP-2


title: 969.AACGTCCTTA-CTGCGAAGTG


title: mllCNR_WTSOX9_nodox_rep2

description: Biological replicate 2


title: 963.TCATGAGGAG-TGTGGAGAGG


title: 962.GTAGTACAGT-TGTCCAGGTG


title: CCI+THP-1


title: 1264.AGAAGTCTGT-ACCGTACACT

value: 5xFAD/ T2CV


title: cultured_noTA_dox_rep2

description: Biological replicate 2

data_processing:
The raw sequencing reads were trimmed with skewer (v0.2.2) and aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome.
The aligned reads were deduplicated with Picard (v. 2.3.0) and shifted to correct for Tn5 insertion bias.
Bamfiles from biological replicates are combined with Samtools (1.9)
Peaks were called on replicate-pooled bamfiles with MACS2 (v. 2.1.1) with default settings.
bigwig files were generated on the combinded bamfiles using deeptools (2.5.4) bamcoverage with reads in peaks as the scale factor. For cultured cell data, RPKM is used for normalization.
Assembly: GRCm38 (mm10)
Supplementary files format and content: BIGWIG files generated from combined bamfiles and peak files called from replicate pooled samples in bed format


title: cultured_WT_dox_rep2

description: Biological replicate 2


title: 961.AATGACTGGT-GCAATTAAGG


title: cultured_noHMG_dox_rep2

description: Biological replicate 2


title: cultured_WT_nodox_rep2

description: Biological replicate 2


title: 625.CGGATGAGCA-ATCCAGGTTA

value: F


title: CCI-4

value: sciatic never ligation


title: 621.AGCAGCACAA-ACAAGTGCCG


title: CCI-3


title: CCI-2


title: mycCNR_noTA_dox_rep1

description:
Biological replicate 1
noTA_dox_mycCNR_rep1_fragmentsAtOrUnder120bp.bw

data_processing:
All CUT&RUN libraries were sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were trimmed with Skewer (version 0.2.2) and aligned to reference genome (mm10) using Bowtie2 (version 2.2.9) and deduplicated with Java (version 2.3.0) Picard tools (http://broadinstitute.github.io/picard). Reads were flittered to reads smaller or equal to 120bp using Samtools (version 1.3.1). BAM files for each replicate were combined using samtools.
Bigwigs were generated using Deeptools (version 3.1.2) with RPKM normalization
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles
Library strategy: CUT&RUN

tag: strain


title: mycCNR_WTSOX9_dox_rep1

description:
Biological replicate 1
WT_dox_mycCNR_rep1_fragmentsAtOrUnder120bp.bw

tag: genotype


title: mycCNR_noHMG_dox_rep1

description:
Biological replicate 1
noHMG_dox_mycCNR_rep1_fragmentsAtOrUnder120bp.bw


title: mycCNR_WTSOX9_nodox_rep1

description:
Biological replicate 1
WT_nodox_mycCNR_rep1_fragmentsAtOrUnder120bp.bw


title: 609.AATGCACCAA-ACACGCTCCT

tag: treatment


title: mllCNR_noTA_dox_rep1

description:
Biological replicate 1
noTA_dox_mllCNR_rep1_fragments_sorted.bw

tag: antibody


title: mllCNR_noHMG_dox_rep1

description:
Biological replicate 1
noHMG_dox_mllCNR_rep1_fragments_sorted.bw


title: 594.GTAAGTGTAC-GAGCTTATGA


title: CCI-1


title: mllCNR_WTSOX9_nodox_rep1

description:
Biological replicate 1
WT_nodox_mllCNR_rep1_fragments_sorted.bw


title: Sham-4

value: sciatic nerve was exposed but not ligated


title: mllCNR_W1_rep2

description:
Biological replicate 2
Sox9_7D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw

source_name: mouse back skin

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: mllCNR_W1_rep1

description:
Biological replicate 1
Sox9_7D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw

value: MLL3/4 (Wysocka lab)


title: mllCNR_W2_rep2

description:
Biological replicate 2
Sox9_14D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw

value: K14rtTA; TRE-myc-Sox9


title: mllCNR_W2_rep1

description:
Biological replicate 1
Sox9_14D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw

value: Male


title: CRC scRNAseq NK & T cells Patent 3-6

description:
BRI-295
10X Genomics

value: Colorectal tumor

tag: cell type

value: NK & T cells


title: 268.AACAACTCCT-GCGATGGAAG


title: Sham-3


title: 265.GCTCTGGTAG-GATCTGAACA


title: SOX9CNR_W12_rep2

description:
Biological replicate 2
W12_rep1_rep2_POOL_under120bp_RPKM.bw

value: SOX9 (Millipore AB5535)

value: grafted W12


title: Sham-2

value: spinal cord on postoperative day 10


title: mllCNR_D0_rep2

description:
Biological replicate 2
Sox9_0D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw


title: 254.TCTGTTGCGG-TCACGACCAC


title: mllCNR_D0_rep1

description:
Biological replicate 1
Sox9_0D_mllF7_1to50_rep1_rep2_POOL_fragmentsAtOrUnder120bp.bw


title: SOX9CNR_W12_rep1

description:
Biological replicate 1
W12_rep1_rep2_POOL_under120bp_RPKM.bw


title: SOX9CNR_W6_rep2

description:
Biological replicate 2
W6_rep1_rep2_POOL_under120bp_RPKM.bw


title: 223.AACACGCTTG-TATCATGTCG


title: SOX9CNR_W6_rep1

description:
Biological replicate 1
W6_rep1_rep2_POOL_under120bp_RPKM.bw


title: 209.CGACTAACGT-CTCTATACTG


title: SOX9CNR_W2_rep2

description:
Biological replicate 2
W2_rep1_rep2_POOL_under120bp_RPKM.bw


title: KARPAS422 cells, 10 nM Neg2 treated, 4 hours (bio rep 1)

city: Stanford

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

data_processing:
kallisto
Sequence reads were trimmed for adaptor sequence and quality using cutadapt with options --nextseq-trim=20 --minimum-length=1
Trimmed sequence reads were pseudoaligned using kallisto quant
Assembly: human gencode v33 for human cell lines, mouse gencode vM24 for mouse tissue
Supplementary files format and content: csv files with TPMs quantified from kallisto

growth_protocol: Cell lines maintained in 10 % FBS + RPMI + antibiotics

extract_protocol:
RNA was harvested using Trisure and Zymo Direct-zol RNA purification kit
RNA libraries were made using NEB Ultra II RNA library prep kit using polyA enrichment

treatment_protocol: Drug or DMSO treated with final concentration of DMSO as 0.1% in all cases

value: DLBCL cells

value: WT

value: 10 nM Neg2

tag: time

value: 4 hours


title: KARPAS422 cells, 10 nM Neg2 treated, 4 hours (bio rep 2)


title: SOX9CNR_W1_rep2

description:
Biological replicate 2
W1_rep1_rep2_POOL_under120bp_RPKM.bw


title: SOX9CNR_W2_rep1

description:
Biological replicate 1
W2_rep1_rep2_POOL_under120bp_RPKM.bw


title: 206.CCAACGTTAG-GCAATCTGCT

value: 5xFAD/ T2CV

tag: Sex

value: SD


title: SOX9CNR_W1_rep1

description:
Biological replicate 1
W1_rep1_rep2_POOL_under120bp_RPKM.bw


title: 178.TCCTGGAACA-TCAGAACCTG

value: M


title: KARPAS422 cells, 10 nM Neg2 treated, 2 hours (bio rep 2)

tag: cell line

value: 2 hours


title: SOX9CNR_D0_rep2

description:
Biological replicate 2
D0_rep1_rep2_POOL_under120bp_RPKM.bw

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: KARPAS422 cells, 10 nM Neg2 treated, 2 hours (bio rep 1)


title: KARPAS422 cells, 10 nM Neg2 treated, 1 hours (bio rep 2)

value: 1 hr


title: 177.CGTAGATCGC-ATACGTCTCT


title: 175.AACAGGCAAG-TTCATGGAAG


title: KARPAS422 cells, 10 nM Neg2 treated, 1 hours (bio rep 1)


title: W6_totalH3_rep1_low_Mnase

description:
SOX9_6W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W6_rep1_barcode_low.txt

data_processing:
MINT-ChIP reads were processed with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 with FASTX-Toolkit.
The demultiplexed reads were aligned with Bowtie2 (v 2.2.9) to the mm10 reference genome The aligned reads were deduplicated with Picard for both PCR and IVT duplicates (v. 2.3.0). Bamfiles from biological replicates are combined with Samtools (1.9). H3K27ac peaks are called with MACS2 (v2.1.1), and H3K4me1 peaks are called with epic2 peak caller based on SICER (0.0.36).
bigwig files were generated on the combined bamfiles using deeptools (2.5.4) bamcoverage with (1,000,000/total reads in peaks) as the scale factor. For totalH3, RPKM is used for normalization.
Assembly: mm10 (UCSC release)
Supplementary files format and content: BIGWIG file generated from combined bamfiles

value: K14rtTA; TRE-myc-Sox9

value: male


title: W6_totalH3_rep2_low_Mnase

description:
SOX9_6W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W6_rep2_barcode_low.txt


title: sc6, day 100 differentiation, replicate 1

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

data_processing:
Illumina compatible RNA sequencing libraries were prepared with Quantseq and pooled and sequenced on Illumina Hiseq 4000 platform.
UMIs were extracted from the fastq files with umi_tools, and cutadapt was used to remove short and low-quality reads.
RNA-seq reads were mapped to the human reference genome (hg19) using TopHat v2.0. TopHat was run with default parameters with exception to the coverage search. Alignments were then quantified using HTSeq.
Duplicate reads were collapsed using umi_tools. Gene level counts were measured using HTSeq and compared using DESeq2.
Assembly: GRCh38

extract_protocol:
Total RNA was extracted using trizol.
First strand cDNA was synthesized with Quantseq Forward Libray preparation kit from Lexogen.

value: Schwann cell


title: W6_H3K27ac_rep2_low_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W6_rep2_barcode_low.txt


title: sc7, day 100 differentiation, replicate 2


title: 172.CCTCTAATTG-TTACTGCCTT


title: Sham-1

description: Gene expression data from spinal cord in CCI rat

value: sciatic nerve was exposed but not ligated


title: KARPAS422 cells, 10 nM Neg1 treated, 4 hours (bio rep 2)

value: 10 nM Neg1


title: sc5, day 50 differentiation, replicate 2


title: 171.CAGCATAACA-GCCATCCTTG

value: Ctl


title: W6_H3K27ac_rep1_low_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W6_rep1_barcode_low.txt


title: 170.AAGCTTCGAG-GATGTCATGC


title: KARPAS422 cells, 10 nM Neg1 treated, 2 hours (bio rep 2)


title: sc4, day 50 differentiation, replicate 1


title: KARPAS422 cells, 10 nM Neg1 treated, 4 hours (bio rep 1)


title: W6_H3K4me1_rep2_low_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W6_rep2_barcode_low.txt


title: 167.AACTCCAAGA-CTCACTACTC

value: F


title: W6_H3K4me1_rep1_low_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W6_rep1_barcode_low.txt


title: sc3, day 25 differentiation, replicate 2


title: SOX9CNR_D0_rep1

description:
Biological replicate 1
D0_rep1_rep2_POOL_under120bp_RPKM.bw

value: SOX9 (Millipore AB5535)

value: Male


title: 165.CGAGCACTGT-CTCCTCGCAA


title: sc2, day 25 differentiation, replicate 1


title: KARPAS422 cells, 10 nM Neg1 treated, 1 hours (bio rep 2)

value: DLBCL cells

value: WT


title: KARPAS422 cells, 10 nM Neg1 treated, 2 hours (bio rep 1)


title: W2_totalH3_rep2_low_Mnase

description:
SOX9_D14_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W2_rep2_barcode_low.txt


title: psc2, primary Schwann cell, replicate 2

source_name: Schwann cell


title: 164.AGATAGCACA-ATGGCGTACG


title: W2_totalH3_rep1_W12_totalH3_rep1_rep2_low_Mnase

description:
SOX9_12W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
SOX9_D14_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W2_rep1_W12_2reps_barcode_low.txt


title: W2_H3K27ac_rep2_low_Mnase

description:
SOX9_W2_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W2_rep2_barcode_low.txt


title: psc1, primary Schwann cell, replicate 1


title: KARPAS422 cells, 10 nM TCIP1 treated, 4 hours (bio rep 3)

value: 10 nM TCIP1

value: 4 hours


title: KARPAS422 cells, 10 nM Neg1 treated, 1 hours (bio rep 1)


title: 163.ACTTAACGCG-GATGCGCATA

value: M

value: SD


title: 164.AATCTCAGGC-TCACCAGGAC


title: KARPAS422 cells, 10 nM TCIP1 treated, 4 hours (bio rep 2)


title: TRAC-KVR2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: CAST-seq on sample treated with OH-TALEN (KVR-EAD scaffold) targeting TRAC

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with T-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage.
Library strategy: CAST-seq

source_name: T cells expanded from PBMCs

growth_protocol: PBMCs/ T cells were cultured at 37°C with 5% CO2. Upon thawing, PBMCs were washed with PBS (300xg, 5min) and resuspended at a density of 2x10E6 cells/ml in X-VIVO™ 15 (Lonza) medium supplemented with 200U/ml rhIL-2 (Immunotools) and seeded into 24- well plates (1ml/well) . Adherent cells were allowed to attach for 4h. After 4h, non-adherent cells were collected, counted, adjusted to a cell density of 1x10E6 cells/ml with X-VIVO™ 15 (Lonza) medium supplemented with 200U/ml rhIL-2 (Immunotools) and re-seeded into 24-well plates (1ml/well). To each well, 5μl of ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (StemCell Technologies) was added and the T cells activated for 72-96h prior to gene editing.

extract_protocol:
Genomic DNA of at least 1x10E6 cells was isolated after approximately one week using NucleoSpin Tissue Mini Kit for DNA from cells and tissue (Macherey-Nagel).
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 250-350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interes (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) on where it was performed on Illumina HiSeq or NovaSeq devices collecting 2x150 bp paired-end reads.

treatment_protocol: Prior to gene editing, activation of T cells was assessed by staining for CD25. Downstream experiments were performed only when T cells were highly activated (>85% CD25-expression). For small scale transfer of TALEN mRNAs, 1x106 cells were harvested by centrifugation (300xg, 5min) and the supernatant removed. Cells were resuspended in 50μl CliniMACS ® Electroporation Buffer (Miltenyi Biotec). Just before electroporation, 7,5μg of each left and right (or left/left, right/right) TALEN pairs were mixed with the resuspended T cells and electroporated using a CliniMACS ® Prodigy with Electroporator unit (Miltenyi Biotec) with the previously described Setting 3 (Alzubi et al., Molecular Therapy - Methods & Clinical Development, 2021). Post electroporation, cells were recovered in 400μl of pre-warmed X-VIVO™ 15 (Lonza) medium supplemented with 200U/ml rhIL-2 (Immunotools) and seeded into two wells of U-shaped 96-well plates. Half of the cells were subjected to a transient low temperature shift to 32°C for 24h before being shifted to 37°C. The other half was directly cultured at 37°C. Approximately half of the media was changed every two days and the cells split every 3-4 days.

value: T cells

tag: sample

value: CAST-seq derived amplicons from gDNA

value: KVR-EAD (OH)-TRAC-TALEN


title: TRAC-KKR2

description: CAST-seq on sample treated with OH-TALEN (KKR-ELD scaffold) targeting TRAC

value: KKR-ELD (OH)-TRAC-TALEN


title: 162.CCATTGTCAA-ACAATCGCTG


title: KARPAS422 cells, 10 nM TCIP1 treated, 4 hours (bio rep 1)


title: W2_H3K27ac_rep1_W12_H3K27ac_rep1_rep2_low_Mnase

description:
SOX9_W12_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
SOX9_W2_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W2_rep1_W12_2reps_barcode_low.txt

value: K14rtTA; TRE-myc-Sox9

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: 161.CCTGGCTATA-ACGCCACATT


title: W2_H3K4me1_rep2_low_Mnase

description:
SOX9_W2_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W2_rep2_barcode_low.txt


title: TRAC-WT2

description: CAST-seq on sample treated with wild type TALEN targeting TRAC

value: wild type TRAC-TALEN


title: KARPAS422 cells, 10 nM TCIP1 treated, 2 hours (bio rep 3)

value: 2 hours


title: TRAC-UT2

description:
Non-treated control CAST-seq sample for samples treated with TALEN targeting TRAC
used as non-treated control for TRAC-WT2, TRAC-KKR2 and TRAC-KVR2

value: non-treated


title: 160.GTCCACTCTC-ACGCCTCAAG


title: W2_H3K4me1_rep1_W12_H3K4me1_rep1_rep2_low_Mnase

description:
SOX9_W12_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
SOX9_W2_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W2_rep1_W12_2reps_barcode_low.txt


title: W1_totalH3_rep1_rep2_low_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W1_barcode_low.txt


title: KARPAS422 cells, 10 nM TCIP1 treated, 2 hours (bio rep 2)


title: TRAC-KVR1


title: KARPAS422 cells, 10 nM TCIP1 treated, 2 hours (bio rep 1)


title: 158.GTCTCCGAGA-ATGGCTAGCT

value: 5xFAD/ T2CV

value: Ctl


title: W1_H3K27ac_rep1_rep2_low_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W1_barcode_low.txt


title: 156.CACTATTCCA-TATAGGCCGA

value: F


title: W1_H3K4me1_rep1_rep2_low_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W1_barcode_low.txt


title: TRAC-KKR1


title: KARPAS422 cells, 10 nM TCIP1 treated, 1 hours (bio rep 3)

value: DLBCL cells

value: WT

value: 10 nM TCIP1

value: 1 hr


title: D0_totalH3_rep1_rep2_low_Mnase

description:
SOX9_D0_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
D0_barcode_low.txt


title: 148.CATTCCGCAA-ACAATCCGGC


title: TRAC-UT1

description:
Non-treated control CAST-seq sample for samples treated with TALEN targeting TRAC
used as non-treated control for TRAC-WT1, TRAC-KKR1 and TRAC-KVR1

value: T cells


title: D0_H3K4me1_rep1_rep2_low_MNase

description:
SOX9_D0_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
D0_barcode_low.txt


title: TRAC-WT1

value: CAST-seq derived amplicons from gDNA


title: 146.CGGAATGTTG-CTTACCATGC

value: SD


title: 146.AGGTATTCGG-GAGTCGCTTC


title: KARPAS422 cells, DMSO treated, 4 hours (bio rep 3)

value: 4 hours


title: W6_totalH3_rep2_high_Mnase

description:
SOX9_6W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W6_rep2_barcode_high.txt

value: K14rtTA; TRE-myc-Sox9


title: KARPAS422 cells, DMSO treated, 4 hours (bio rep 2)


title: CCR5-KVR-EAD2

description: CAST-seq on sample treated with OH-TALEN (KVR-EAD scaffold) targeting CCR5

value: KVR-EAD (OH)-CCR5-TALEN


title: 137.GCTCATTGTA-TATGGTTCTC


title: Excision_control_replicate3_primerA

value: HEK 293T

value: Cultured cells

value: Recombination into genomic landing pad


title: CCR5-WT2

description: CAST-seq on sample treated with wild type TALEN targeting CCR5

value: wild type CCR5-TALEN


title: 151.CAGTGGACCA-CTTCGGAATC

value: 5xFAD/ T2CV

value: M


title: 61r.GTCGAGCTGA-TTATGAGCAC


title: CCR5-UT2

description:
Non-treated control CAST-seq sample for samples treated with TALEN targeting CCR5
used as non-treated control for CCR5-WT2, CCR5-KKR-ELD2 and CCR5-KVR-ELD2

value: non-treated


title: W6_H3K27ac_rep2_high_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W6_rep2_barcode_high.txt

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: KARPAS422 cells, 100nM TCIP1 treated, 20 hours (bio rep 2)

value: DLBCL cells

value: WT

value: 100 nM TCIP1

value: 20 hours


title: CCR5-KVR-EAD1

value: T cells

value: CAST-seq derived amplicons from gDNA


title: KARPAS422 cells, 10 nM TCIP1 treated, 1 hours (bio rep 2)

value: 10 nM TCIP1

value: 1 hr


title: D0_H3K27ac_rep1_rep2_low_Mnase

description:
SOX9_D0_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
D0_barcode_low.txt

value: K14rtTA; TRE-myc-Sox9


title: CCR5-KKR-ELD1

description: CAST-seq on sample treated with OH-TALEN (KKR-ELD scaffold) targeting CCR5

value: KKR-ELD (OH)-CCR5-TALEN


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome-ZT14_F_Saline

city: Montreal

first: Valerie

last: Mongrain

state: QC

address: 333 rue Saint-Antoine Est

department: Research center

country: Canada

institute: CRCHUM

description: BAM file created by running the original sequencing file with the ''spaceranger count'' pipeline.

data_processing:
SpaceRanger1.2.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: ''spaceranger count'' pipeline and obtain h5 matrix and spatial information on the reads, and can also be processed with other RNAseq platforms, softwares and commands.

source_name: Brain

growth_protocol: Habituation to individual cage for 10 days; housing with a 12h light:12h dark cycle with food and water ad libitum.

extract_protocol:
10X Genomics protocol CG000240-Rev C
10X Genomics protocol CG000160-Rev A (Hematoxylin-Eosin staining)
10X Genomics protocol CG000239-Rev D
Paired-end dual indexed RNA sequencing with Illumina NovaSeq6000 SP100 sequencer (Genome Quebec Innovation Centre, Montreal, Canada), at a sequencing depth of approximately 150M read pairs per sample. RNAseq was performed according to instructions of 10x Genomics for the Visium Spatial Gene Expression kit: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.

treatment_protocol: Rhynchophylline (RHY, 100 mg/kg; administered with a volume of 10 mL/kg) or Saline (NaCl 0.9 %) intraperitoneal injections at ZT0 or ZT11

value: Brain

value: Female

value: control (NaCl)


title: KARPAS422 cells, 10 nM TCIP1 treated, 1 hours (bio rep 1)


title: W6_H3K4me1_rep2_high_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W6_rep2_barcode_high.txt


title: KARPAS422 cells, 100nM TCIP1 treated, 20 hours (bio rep 1)


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome-ZT4_F_RHY

value: Rhynchophylline 100 mg/kg


title: CCR5-KKR-ELD2


title: KARPAS422 cells, 10nM TCIP1 treated, 20 hours (bio rep 2)


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT14_M_RHY]

description: The matrix.h5 (processed data file 1) contains the columns barcodes (barcode sequences and their corresponding library identifiers, which is always -1 for spaceranger count runs), data (nonzero UMI counts in column-major order), features (gene information), indices (zero-based row index of corresponding element in data), indptr (zero-based index into data / indices of the start of each column, that is the data corresponding to each barcode sequence), shape (tuple of [# rows, # columns] indicating the matrix dimensions)

data_processing:
library strategy: spatial transcriptomics
Read alignment software: SpaceRanger1.2.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: Feature barcode matrices in HDF5 format that contain only tissue-associated barcodes and are used to run the Aggr pipeline and extract differentially expressed genes (DEGs)
Supplementary files format and content: Compressed file containing the spatial information: QC images to check image processing pipeline, downsampled input images, and files that describe spot barcode locations in the images. This spatial information is also used (together with the HDF5 file) to run the Aggr pipeline and extract differentially expressed genes (DEGs)
Supplementary files format and content: The matrix.h5  contains the columns barcodes (barcode sequences and their corresponding library identifiers, which is always -1 for spaceranger count runs), data (nonzero UMI counts in column-major order), features (gene information), indices (zero-based row index of corresponding element in data), indptr (zero-based index into data / indices of the start of each column, that is the data corresponding to each barcode sequence), shape (tuple of [# rows, # columns] indicating the matrix dimensions)

extract_protocol:
Tissue preparation: 10X Genomics protocol CG000240-Rev C
Slice staining: 10X Genomics protocol CG000160-Rev A (Hematoxylin-Eosin staining)
10X Genomics protocol CG000239-Rev D
Paired-end dual indexed RNA sequencing with Illumina NovaSeq 6000 (Genome Quebec Innovation Centre, Montreal, Canada), at a sequencing depth of approximately 150M read pairs per sample. RNAseq was performed according to instructions of 10x Genomics for the Visium Spatial Gene Expression kit: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.

value: Male


title: CCR5-WT1

value: wild type CCR5-TALEN


title: CCR5-UT1

description:
Non-treated control CAST-seq sample for samples treated with TALEN targeting CCR5
used as non-treated control for CCR5-WT1, CCR5-KKR-ELD1 and CCR5-KVR-ELD1

value: non-treated


title: W6_totalH3_rep1_high_Mnase

description:
SOX9_6W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W6_rep1_barcode_high.txt

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: W2_totalH3_rep2_high_Mnase

description:
SOX9_D14_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W2_rep2_barcode_high.txt


title: KARPAS422 cells, DMSO treated, 4 hours (bio rep 1)

value: DLBCL cells

value: WT

value: 4 hours


title: W2_totalH3_rep1_W12_totalH3_rep1_rep2_high_Mnase

description:
SOX9_12W_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
SOX9_D14_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W2_rep1_W12_2reps_barcode_high.txt


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT4_M_RHY]


title: Muscle, patient,3 samples pooled, scRNA-seq

first: Gilberto

last: Duran Bishop

state: Quebec

address: 110 Pine Avenue West

department: stem cells and cellular reprogramming

institute: Montreal Clinical Research Institute (IRCM)

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
DoubletFinder was used to identify putative doublets in each DGE matrix relying solely on gene expression data.
Assembly: GRCh38- 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

growth_protocol: Muscle biopsies from controls and DM1 patients were minced, digested in collagenase, and plated in a culture dish. Myoblasts were grown in Sk-MAX media complemented with Sk-MAX supplement and 20% fetal bovine serum (FBS). Myoblasts were expanded for a few days until there were enough cells for purification by FACS (Using anti-CD56 as positive myogenic marker and 7-AAD for cell viability).

extract_protocol:
Myogenic cells total RNA was extracted with Qiazol reagent according to the manufacturer’s specifications
Single cell suspensions of myogenic cells were resuspended in PBS containing 0.04% ultra-pure BSA. scRNAseq libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. Generated libraries were sequenced on an Illumina HiSeq4000.

value: Skeletal muscle

value: primary cells

value: Myogenic cells

value: DM1 patients with mutation in DMPK gene (2 males, one female)


title: W6_H3K27ac_rep1_high_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W6_rep1_barcode_high.txt

value: K14rtTA; TRE-myc-Sox9


title: W2_H3K27ac_rep2_high_Mnase

description:
SOX9_W2_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W2_rep2_barcode_high.txt


title: Muscle, control,3 samples pooled, scRNA-seq

description: 10x Genomics

value: healthy control individuals (2 males, one female)


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT4_M_Saline]

value: Brain


title: RNA_PTC_DMOG_2

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Bigwig files were generated using deeptools bamCoverage version v3.5.0, command –normalizeUsing BPM--binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Primary renal tubular cells

growth_protocol: Primary human tubular cells were isolated from tumor nephrectomy specimens and grown in Dulbecco’s modified Eagle’s medium/Ham’s F-12 supplemented with 2.5% (day 1) or 0% (day 2 onwards) fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin, and 5ng/ml selenium (Sigma), triiodothyronine (T3, Sigma) 10 ng/ml, hydrocortisone 1 mg/ml, epidermal growth factor 100 µg/ml (Peprotech). Epithelial origin was confirmed by immunocytochemistry for N- and E-Cadherin.

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on IlluminaNovaseq 6000  (Illumina).

treatment_protocol: Sub-confluent cell cultures were exposed to 1 mM dimethyloxalylglycine (DMOG, Cayman) for 16h to induce HIF stabilization.

value: Primary renal tubular cells

value: DMOG


title: W2_H3K27ac_rep1_W12_H3K27ac_rep1_rep2_high_Mnase

description:
SOX9_W12_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
SOX9_W2_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
W2_rep1_W12_2reps_barcode_high.txt


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT14_F_RHY]

value: Female

value: Rhynchophylline 100 mg/kg


title: RNA-seq of K562 cells, Day 0, wild-type replicate 2, batch 2

city: Cambridge

first: Richard

last: She

state: Massachusetts

address: 455 Main St Rm 639, Whitehead Institute

institute: Whitehead Institute

description:
K562_RNAseq_Table1.txt
K562_WT_rep2

data_processing:
RNA-seq sequencing reads were aligned to the human genome via STAR aligner, run with default parameters.
Counts for each transcript were then quantified by featureCounts
Assembly: hg19/GRCh37
Supplementary files format and content: tab-delimited text files include log2 fold-change between wild-type and sgRNA depleted cells

source_name: bone marrow

growth_protocol: K562 cells and Jurkat cells were grown in RPMI + 10% FBS + 1% penicillin-streptomycin-glutamine. HeLa cells were grown in DMEM + 10% FBS + 1% penicillin-streptomycin-glutamine.

extract_protocol:
Cell pellets were lysed with Trizol and RNA was extracted with the Zymo direct-zol RNA miniprep kit
RNA-seq libraries were constructed with the Illumina TruSeq Stranded Total RNA kit.

value: bone marrow

value: K562 cell line

value: chronic myelogenous leukemia (CML)

value: Day 0


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT14_F_Saline]

value: WT

value: control (NaCl)


title: RNA_PTC_ctrl_2

value: control


title: RNA-seq of K562 cells, Day 5, eIF4G2 sgRNA, replicate 2, batch 2

description:
K562_RNAseq_Table1.txt
K562_sgEIF4G2_rep2

value: eIF4G2 sgRNA

value: Day 5 post lentivirus infection


title: W2_H3K4me1_rep2_high_Mnase

description:
SOX9_W2_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W2_rep2_barcode_high.txt

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: RNA_PTC_ctrl_1


title: KARPAS422 cells, 10nM TCIP1 treated, 20 hours (bio rep 1)

value: DLBCL cells

value: 10 nM TCIP1

value: 20 hours


title: W2_H3K4me1_rep1_W12_H3K4me1_rep1_rep2_high_Mnase

description:
SOX9_W12_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
SOX9_W2_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W2_rep1_W12_2reps_barcode_high.txt

value: K14rtTA; TRE-myc-Sox9


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT4_F_RHY]

value: Brain

value: Female


title: KARPAS422 cells, DMSO treated, 20 hours (bio rep 2)


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT14_M_Saline]

value: Male


title: RNA-seq of K562 cells, Day 5, eIF4G2 sgRNA, replicate 1, batch 2

description:
K562_RNAseq_Table1.txt
K562_sgEIF4G2_rep1

value: bone marrow

value: K562 cell line


title: Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT4_F_Saline]


title: RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 2, batch 2

description:
K562_RNAseq_Table1.txt
K562_sgEIF3D_rep2

value: chronic myelogenous leukemia (CML)

value: eIF3D sgRNA


title: W1_totalH3_rep1_rep2_high_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
W1_barcode_high.txt


title: ChIP_PTC_DMOG_HIF1_beta

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using  BWA-mem version 0.7.17-r1188.
Reads were sorted using samtools v.1.8.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
ChIP was performed using ChIP-IT high sensitivity kit (Active Motif, Carlsbad, CA, USA). For immunoprecipitations, 20 μg of chromatin and 3-6 μl of antibodies (HIF-1α (rabbit polyclonal, PM14 or Cayman Chemicals, Cay10006421), HIF-1β (rabbit polyclonal, Novus Biologicals, NB100-110)) was used.
Novogene NGS DNA Library Prep Set (Cat No.PT004)

value: Primary renal tubular cells

value: DMOG


title: ChIP_PTC_DMOG_HIF1_alpha


title: scRNA_Mouse_ILC_Spleen and Meninges

city: Rome

first: Mattia

last: Laffranchi

address: Viale Regina Elena 291

department: Molecular Medicine

country: Italy

institute: La Sapienza University of Rome

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SevenBridges platform with the pipeline BD WTA Multiplex Rhapsody Analysis Pipeline Version 1.9.1 (https://www.sevenbridges.com/)
Supplementary files format and content: mm10
Supplementary files format and content: Comma-separated values files

source_name: multiplexed Spleen and Meninges

extract_protocol:
The meninges (50 mice divided into three samples) and spleens (two mice per sample) of C57BL/6 mice were enzymatically digested in DMEM collagenase 1mg/ml for 30 min at 37°C. Digestion reaction was stopped by addition of DMEM 10% FBS and dissociation into single cell suspension is finalized by mechanical disruption on 70 μm cell strainer (Falcon, Beckton Dickinson). The cell suspensions were washed and resuspended in staining buffer (PBS without Ca2+ Mg2+ 205 , BSA 0,5%, EDTA 2mM and NaN3 0,025%), tagged with BD single cell multiplexing kit, mixed and stained with Zombie Violet for 15 min at room temperature for exclusion of dead cells and anti-CD16/32 blocking mAb (clone 24G2) for 10 min at 4°C followed by incubation  with anti-CD45, -CD3, -NK1.1 mAbs for 25 min. CD45+CD3- NK1.1+ gated cells were sorted into PBS buffer 2% BSA 0,5mM EDTA using a FACSAriaIII (BD Biosciences) equipped with a 488, 561 210 and a 633nm laser and FACSDiva software (BD Biosciences version 6.1.3), and retained on ice. To reduce stress, cells were isolated in gentle FACS-sorting conditions using a ceramic nozzle of size 100μm, a low sheath pressure of 19.84 pound-force per square inch (psi) that maintain the sample pressure at 18.96 psi and an acquisition rate of maximum 1500 events/s.
RNA was extracted according to the manufacter’s instructions (BD Rhapsody™ Single-Cell Analysis System ).
Library was performed according to the manufacter’s instructions (BD Rhapsody™ Single-Cell Analysis System ).

value: multiplexed Spleen and Meninges

value: Primary

value: Innate lymphpocytes

value: wt

value: 10-12 weeks old


title: ChIP_PTC_DMOG_Input


title: RNA-seq of K562 cells, Day 0, wild-type replicate 1, batch 2

description:
K562_RNAseq_Table1.txt
K562_WT_rep1

value: WT

value: Day 0


title: RNA-seq of K562 cells, Day 5, eIF3D sgRNA, replicate 1, batch 2

description:
K562_RNAseq_Table1.txt
K562_sgEIF3D_rep1

value: Day 5 post lentivirus infection


title: RNA_SOX9pos_rep2

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 2
DEG_SOX9pos_vs_SOX9neg.txt

data_processing:
FASTQ files were trimmed of barcodes using Skewer (version 0.2.2) and transcript abundance quantified using Salmon with a modified Gencode transcript index (version GRCm38 release M24) to include TRE-MYC-SOX9. Gene level counts and TPMs were calculated using the tximport package in R.
To generate gene signiture of SOX9 positive and negative placodes, DESeq2 was used to generate differentially expressed gene (DEG) list.
Assembly: mm10 (UCSC release)
Supplementary files format and content: tab-delineated text file contain calculated TPM or tab-delineated text file contain DEG results from DESeq2

extract_protocol:
FACS-sorted EdpSCs were directly sorted into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer.
RNA libraries were generated using SMARTer RNA kit for low input RNA-seq and sequenced on NextSeq or NovaSeq SP 50PE.

treatment_protocol: mouse was injected with doxycycline at P21 and maintained on dox feed for indicated period of time

tag: mouse strain

value: mixed

value: CD31/45/117/140a-neg CD49f-high PCAD-lo eGFP+


title: W1_H3K4me1_rep1_rep2_high_Mnase

description:
SOX9_D7_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W1_barcode_high.txt

value: K14rtTA; TRE-myc-Sox9

value: male

value: CD31/45/117/140a-neg CD49f-high CD34-neg Ly6A-high


title: KARPAS422 cells, DMSO treated, 20 hours (bio rep 1)

value: DLBCL cells

value: 20 hours


title: D0_totalH3_rep1_rep2_high_Mnase

description:
SOX9_D0_IFE_High_Low_POOL_TOTALH3_MERGE_sorted_RC.bw
D0_barcode_high.txt


title: RNA_SOX9pos_rep1

description:
Salmon (v 1.4.0)
Tximport (v 1.12.3)
Biological replicate 1
DEG_SOX9pos_vs_SOX9neg.txt

tag: mouse age


title: W6_H3K4me1_rep1_high_Mnase

description:
SOX9_W6_IFE_High_Low_POOL_H3K4me1_MERGE_sorted_RIP.bw
W6_rep1_barcode_high.txt


title: D0_H3K27ac_rep1_rep2_high_Mnase

description:
SOX9_D0_IFE_High_Low_POOL_H3K27ac_MERGE_sorted_RIP.bw
D0_barcode_high.txt


title: ATAC_PTC_DMOG_1

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed according to the Omni-ATAC protocol published by Corces et al. (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396). In short, libraries were prepared using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA, USA) and purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 8 – 12 cycles. Library clean-up and double-sided size selection was performed using AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) according to the manufacturer’s recommendations.
ATAC-seq library preparation was carried out using the Omni-ATAC protocol. Libraries were sequenced on IlluminaNovaseq 6000 platforms following the manufacturer's protocols.

value: Primary renal tubular cells