title: BY-batch2-2nd-000

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: RNA-seq_97H_R2

status: Public on Jan 09 2023

type: SRA

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

country: China

institute: Dalian University of Technology

library_source: transcriptomic

data_processing:
SOAP nuke software (v2.1.0) was used to remove reads with unknown bases more than 10% and low-quality reads (the ratio of the bases with quality value Q ≤ 15 greater than 50%).
Bowtie2 and HISAT (v2.1.0) were used to align clean reads to the reference genome hg19.
RSEM (v1.2.4) was then used to quantify the gene-expression level through the fragments per kilobase of transcript per million mapped reads (FPKM) method.
The differentially expressed genes (DEGs) were determined by DESeq2 (v1.18.1, fold change ≥ 2 and p value ≤ 0.05).
Assembly: hg19
Supplementary files format and content: TXT

molecule: total RNA

organism: Homo sapiens

source_name: liver

growth_protocol: DMEM medium with 10% fetal calf serum.

extract_protocol:
MHCC-97H and MHCC-97L cells were maintained in DMEM medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for ChIP-seq assay. For Flag-OGT ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-Flag-magnetic beads. For ZNF263, H3K4me3, or H3K27ac ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-ZNF263, anti-H3K4me3, or anti-H3K27ac antibody.  For HA-ZNF263-WT and HA-ZNF263-S662A ChIP-seq, crosslinked chromatin complexes were immunoprecipitated with anti-HA-magnetic beads. For RNA-seq, total RNA was extracted from the Flag-OGT expressing cells using Trizol reagent (Invitrogen). RNA quality was checked by Hiseq 2000 instrument (Illumina). RNA libraries were prepared for sequencing using standard protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit.

treatment_protocol: The sequence coding human full-length (1-1036aa) wild type (WT) human OGT were subcloned into lentiviral luciferase expressing pLVX-IRES-Luc-G418 vector containing an C-terminal 3 × Flag tag. ZNF263 was transiently knockdown by ZNF263 shRNA. The sequence coding human full-length (1-683aa) wild type (WT) human ZNF263 and O-GlcNAcylation site mutants (Ser662 → Ala) ZNF263 were subcloned into lentiviral luciferase expressing pLVX-IRES-Luc-Hygro vector containing an C-terminal HA tag.  Transfection of the MHCC-97H and MHCC-97L cells were performed with geneticin  according to the manufacturer’s instructions. The stably transfected cells were then selected by the addition of neomycin or hygro to the medium.  ~2x10e7 cells were used as a unit of cells for each experiment.

tag: tissue

value: liver

tag: cell line

tag: cell type

value: hepatocellular carcinoma


title: 39B

city: Athens

first: Ioanna

last: Papadatou

state: Greece

address: Thivon & Papadiamantopoulou 1

department: "Agia Sophia" Children's Hospital

country: Greece

institute: National and Kapodistrian University of Athens

description: Healthy, after 2nd dose

data_processing:
Basecalling on Illumina NextSeq550
Alignement with STAR on hg38 with pipeline provided by Lexogen and BlueBee
Bam used for bedgraph construction
bigWig constructed through bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from whole blood, stored in paxgene, using the ExtractionMonarch® Total  RNA Miniprep Kit (NEB #T2010). Upon blood isolation, Monarch DNA/RNA Protection Reagent  (supplied as a 2x concentrate) was added undiluted to an equal volume of blood. Addition of the  protection reagent and the following RNA isolation was performed as described in the Kit's manual  for Total RNA Purification from Mammalian Whole Blood Samples.
After quantification on a NanoDrop ND-1000 (Thermofisher) and Bioanalyzer RNA 6000 Nano  assay (Agilent), 140-300ng of total RNA from samples passing quality control were processed  using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, 015.96) for library  preparation. Libraries were assessed for molarity and median library size using Bioanalyzer High  Sensitivity DNA Analysis (Agilent, 5067-4626)
RNA sequencing. The kit creates Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

value: Blood

tag: age

tag: gender

value: Female

tag: status

value: Post


title: CASCADE_NCOR1_JURKAT_rep2

type: other

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

country: USA

institute: Boston University

hyb_protocol: Microarray DNA double stranding and PBM protocols are as previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937)

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing: Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006). Processed data corresponds to z-scores normalized against the fluorescence distribution obtained at sets of random background probes

label: Alexa fluor conjugated antibody

molecule: other

source_name: Jurkat cells, rep2

label_protocol: PBM experiments using cell extracts were performed following the protocols previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937) and outlined here. The double-stranded microarray was pre-wetted in HBS+TX-100 (20mM HEPES, 150mM NaCl, 0.01% Triton X-100) for 5 min and then de-wetted in an HBS bath. Each of the microarray chambers were then incubated with 180 mL of nuclear extract binding mixture for 1 h in the dark. Nuclear extract binding mixture (per chamber): 400-600 mg of nuclear extract; 20mM HEPES (pH 7.9); 100mM NaCl; 1mM DTT; 0.2mg/mL BSA; 0.02% Triton X-100; 0.4mg/mL salmon testes DNA (Sigma-Aldrich, Catalog #D7656)). The microarray was then rinsed in an HBS bath containing 0.1% Tween-20 and subsequently de-wetted in an HBS bath. After the nuclear extract incubation, the microarray was incubated for 20 min in the dark with 20mg/mL primary antibody for the TF or COF of interest. The primary antibody was diluted in 180 mL of 2% milk in HBS. The array was then rinsed in an HBS bath containing 0.1% Tween-20, de-wetted in an HBS bath, and incubated with 10mg/mL of either Alexa488- or Alexa647-conjugated secondary antibody for 20 min in the dark. The secondary antibody was diluted in 180 mL of 2% milk in HBS. Excess antibody was removed by washing the array twice for 3 min in 0.05% Tween-20 in HBS and once for 2 min in HBS in Coplin jars as described above. After the washes, the microarray was de-wetted in an HBS bath and scanned

growth_protocol: Jurkat cells were grown in suspension in RPMI 1640 Glutamax media (Thermofisher Scientific, Catalog #72400120) with 10% heat-inactivated fetal bovine serum (FBS) (Thermofisher Scientific, Catalog #132903). Cells were grown in 50mL of media in T175 (Thermofisher Scientific, Catalogue #132903) non-treated flasks. SK-MEL-28 cells were grown in EMEM media (ATCC, Catalog #30-2003) with 10% heat-inactivated FBS (Thermofisher Scientific, Catalog #132903). Cells were grown in 30mL of media in T225 flasks for adherent cells (Corning, Catalog #35138).

extract_protocol: Nuclear extracts were obtained as previously described (Bray et al. PMID: 35252945, Mohaghegh et al. PMID: 30657937) with modifications detailed below. To harvest nuclear extracts from Jurkat cells, the cells were collected in a 15 ml falcon tube and placed on ice. To harvest nuclear extracts from SK-MEL-28 cells, the media was aspirated off and the cells were washed once with 1X PBS (Thermofisher Scientific, Catalog #100010049). Once the 1X PBS used to wash the cells was aspirated off, enough 1X PBS was mixed with 0.1mM Protease Inhibitor (Sigma-Aldrich, Catalogue #P8340) to cover the cells was added to each flask. A cell scraper was used to dislodge the cells from the flask, and cells were collected in a 15 ml falcon tube and placed on ice. Jurkat and SK-MEL28 cells were pelleted by centrifugation at 500xg for 5 min at 4˚C. Both pellets were washed with 2mL of 1X PBS with Protease Inhibitor and pelleted again at 500xg for 2 min at 4˚C. To lyse the plasma membrane, the cells were resuspended in Buffer A (1 mL Buffer A for Jurkat cells, 1.5 mL Buffer A for SK-MEL28 cells) (10mM HEPES, pH 7.9, 1.5mM MgCl, 10mM KCl, 0.1mM Protease Inhibitor, Phosphatase Inhibitor (Santa-Cruz Biotechnology, Catalog #sc-45044), 0.5mM DTT (Sigma-Aldrich, Catalog #4315) and incubated for 10 min on ice. After the 10 min incubation, Igepal detergent (final concentration of 0.1%) was added to the cell and Buffer A mixture and vortexed for 10 s. To separate the cytosolic fraction from the nuclei, the sample was centrifuged at 500xg for 5 min at 4˚C to pellet the nuclei. The cytosolic fraction was collected into a separate microcentrifuge tube. The pelleted nuclei were then resuspended in Buffer C (100 µL for Jurkat nuclei and 150 µL for SK-MEL-28 nuclei) (20mM HEPES, pH 7.9, 25% glycerol, 1.5mM MgCl, 0.2mM EDTA, 0.1mM Protease Inhibitor, Phosphatase Inhibitor, 0.5mM DTT, and 420mM NaCl) and then vortexed for 30 s. To extract the nuclear proteins (i.e., the nuclear extract), the nuclei were incubated in Buffer C for 1 h while mixing at 4˚C. To separate the nuclear extract from the nuclear debris, the mixture was centrifuged at 21,000xg for 20 min at 4˚C. The nuclear extract was collected in a separate microcentrifuge tube and flash frozen using liquid nitrogen. Nuclear extracts were stored at -80˚C

treatment_protocol: Jurkat and SK-MEL-28 cells were untreated. For each condition, nuclear lysates were harvested. For all nuclear lysates assayed using PBM experiments.

tag: treatment

value: untreated

tag: target protein

tag: primary antibody

tag: primary antibody concentration

value: 20 mg/mL

tag: secondary antibody

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)

tag: secondary antibody concentration

value: 10 mg/mL

tag: molecule type

value: Nuclear extract


title: RNA-seq_97H_R1


title: BY-batch2-1st-3h

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: rRNA depleted RNA

data_processing:
For RNASEQ. The genome assembly and annotation for the RNA-Seq data analysis was downloaded from SGD database (version 64-1-1) (Xu et al., 2009). The quality of the RNA-Seq data was assessed with FastQC (Andrews, 2010). The reads were aligned to the genome with STAR and parameters --outFilterMismatchNmax 4 --alignIntronMin 13 --alignIntronMax 2482.  Read counts were then summarised using featurecounts with parameter -s 2 -C . chimeric fragments was excluded from fragment counting.  MultiQC was used to assess the performance of the preprocessing steps (Ewels et al., 2016). Differential gene expression analysis was perfomed with DESEQ2 package in R. The counts were normalized by coding transcriptome.   For ChIPseq and MNase-seq Illumina adptor was detected and trimmed by TrimGalore. Trimmed reads were then alignment with BWA to Saccharomyces_cerevisiae genome assembly R64-1-1. High repetitive Ribosome DNA region was provided as blacklist and removed from alignment.  PCR duplicates were marked with Picard MarkDuplicates and then removed for subsequent analysis. Deduplicted reads from biological replicates were then merged together. Bigwig files were then generated from merged bam files by deeptools bamcoverage command. Parameter --binSize 1 --MNase --minFragmentLength 100 --maxFragmentLength 200 --normalizeUsing CPM were used to take only mononucleosome, deconvolute and take only the center dyad genomic coordinate of each nucleosome. Bed files contains gene groups gerenerated from RNAseq data were provided to deepltools computatematrix command to extract the nucleosome occupancy and histone modification level of each gene within particular group. Deeptools plotProfile tool were then used to summarise above matrix into metagene plot with parameter –perGroup.  SLAMseq: SLAMseq data was anaysed with slamdunk provided by nextflow pipeline(v 1.0.0). https://nf-co.re/slamseq . As stranded library was prepared with dUTP method and fastq files were first converted to reverse complementary reads to feed into slamdunk nf core pipeline.  Adapter contamination and low quality region was trimmed with TrimGalore, trim length 30bp was used instead of default value. When aligned to genome, transcript annotation downloaded from SGD database (version 64-1-1) (Xu et al., 2009) were first converted into bed file and then used as input for parameter utrbed. At least 2 conversions cooccur in one reads is regarded as a confident call for nascent RNA. SNP masking was employed to uncouple Single Nucletide Polymorphism from converted nucleotides.
Assembly: V64-1-1
Supplementary files format and content: bigwig for ChIP-seq, txt files of normalised RNASEQdata and slamseq data

organism: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae grown in YPD at 30°C

extract_protocol:
RNA was extracted with MasterPure RNA extraction kit from Lucigene  The DNA was purified with phenol, precipitated with ethanol and sodium acetate at -20 °C, washed with cold 70% ethanol, and resuspended in 30 µl TE buffer.
RNA-Seq: First rRNA was depleted  from total RNA with Illumina ribozero Gold kit. Then stranded RNA library was generated with NEBnext Ultra Directional RNA Library Prep kit for illumina.  MNase and ChIPSeq-Seq:  100 ml culture per S. cerevisiae sample and 30 ml of S. pombe culture was crosslinked using 1% formaldehyde for 15 minutes at room temperature. Formaldehyde was quenched by 0.125 M glycine for 5 minutes. Then cells were washed three times with cold TBS, flash-frozen in liquid nitrogen and stored at -80 °C.  Frozen cell pellets were resuspended in zymolyase solution (1 M sorbitol, 50 mM Tris-HCl pH 7.5, 1% beta-mercaptoethanol, 0.1 U/µl zymolyase). The zymolyase digestion proceeded at +37 °C for 30 min (S. cerevisiae) or 90 min (S. pombe). Spheroplasts were isolated by centrifugation at 6000xg for 10 minutes at +4 °C. Spheroplasts were resuspended in NP buffer (10 mM Tris-HCl pH 7.5, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40 (Tergitol), 1% beta-mercaptoethanol, 0.5 mM spermidine, 1% yeast protease inhibitor cocktail). The suspensions were pre-warmed and then 0.5 U/µl of MNase for S. cerevisiae and 2 U/µl for S. pombe was added per sample. MNase digestion proceeded at 37 °C for 40 min (S. cerevisiae) or 30 min (S. pombe) and stopped by addition of EGTA. The supernatants containing chromatin fragments were collected and  diluted with 1 ml RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate) with 1% yeast protease inhibitor cocktail. Equal volumes of S. pombe chromatin were spiked in to S. cerevisiae chromatin samples at this point, corresponding to around 3% of S. cerevisiae DNA.  Each sample was immunoprecipitated with anti-H3K4me3 (Abcam ab8580) and anti-H3K4me2 (Abcam ab7766) antibodies. Protein A/G beads (Pierce) were coupled to antibodies and resuspended in diluted chromatin and rotated o/n at 4 °C.  The next day, beads were washed with RIPA buffer, RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% v/v NP-40, 0.5% w/v sodium deoxycholate), and TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). Volume of each wash was 150 µl. Chromatin was eluted from beads in 2x10 µl ChIP elution buffer (Tris-HCl pH 8 50 mM, 1% SDS, 10 mM EDTA pH 8). The immunoprecipitated chromatin as well as a 20 µl sample of input chromatin were decrosslinked by TE, RNase cocktail, Proteinase K and 6 µl SDS (10% w/v), incubating overnight at 65 °C. DNA was purified by ethanol precipitation. Illumina sequencing libraries were prepared from the DNA using the NEBNext Ultra II kit without dual size selection and using 1.4X volume of AMPure XP beads for the purification steps. The libraries were sequenced on Illumina’s NextSeq 500, paired-end, 39 bases from each end     SLAMSeq: Metabolic labeling of newly synthesized RNA molecules was done as previously described (Voichek et al., 2016). Briefly, 4-thiouracil (4tU) (Sigma) was dissolved in NaOH(83mM), Newly synthesized RNA was labeled for indicated  time  spans  (10  min)  at  a  final  concentration  of  5mM  4-thiouridine  (4sU,  Carbosynth). MES buffer with a final concentration 10mM PH 5.9 was added to media to avoid pH change as a result of NaOH addition. At each time points before harvesting, 4tU was added to media for ten minutes ahead of desired time point.  cells were snap frozen in liquid nitrogen immediately at the time point required and RNA purification was done with MasterPure Yeast RNA Purification Kit. Total RNA was subjected to thiol(SH)-linked alkylation by iodoacetamide (Sigma, 10 mM) at 50C for 15 minutes (Herzog et al., 2017), the reaction was stopped by 20 mM DTT and RNA  was  re-purified by ethanol precipitation. After rRNA depletion with RiboPool Depletion Kit, library was prepared by Ultra™ II Directional RNA Library Prep Kit for Illumina® and sequenced single end with read length 150bp on Nextseq 500 Illumina sequencer.

treatment_protocol: cells were shifted to pre-warmed YPG and then grown at 30°C for 3 hours harvesting at time point 0min, 30 min, 60min and 180 min for the first Galactose treatment. After put in YPD for middle resting for 3 hours, cells were shifted back to prewarmed YPG for second induction and harvested at 0min, 15min, 30min and 60 min.

tag: genotype

value: time 3 hour of FIRST Galactose treatment


title: control-2

city: Shaanxi

first: Xueni

last: You

state: 陕西省

address: 22 Xi-nong Road

department: College of Animal Science and Technology

institute: Northwest A&F University

data_processing:
none provided by the submitter
Supplementary files format and content: FPKM

organism: Sus scrofa

source_name: testis

extract_protocol: none provided by the submitter

value: testis

value: porcine primitive spermatogonia

value: 0.1% ethanol in place of retinoic acid was applied


title: RNA-seq_97H_OGT_R2

value: Flag-OGT expressed


title: BY-batch2-1st-30min

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: RA-1

value: 2 umol/L all-trans-retinoic acid


title: 39A

description: Healthy, before 2nd dose

value: Pre


title: CASCADE_RBBP5_JURKAT_rep2


title: 30B

description: Healthy, after 2nd dose


title: CASCADE_SRC1_JURKAT_rep1

source_name: Jurkat cells, rep1

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: SNP_screen_BRD4_JURKAT_rep1


title: CASCADE_SRC1_JURKAT_rep2


title: control-1


title: RNA-seq_97H_OGT_R1

value: liver

value: hepatocellular carcinoma


title: 30A

description: Healthy, before 2nd dose

value: Blood

value: Female


title: CASCADE_RBBP5_JURKAT_rep1

value: untreated

value: 20 mg/mL


title: ChIP-seq_97L_OGT_input_R2

library_source: genomic

data_processing:
base-calling: in-house Illumina software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
Deeptools was used for generating bigwig files. ChIPseeker for the annotation of peaks.
Assembly: ChIP-Seq: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

tag: genotype/antibody


title: BY-batch2-1st-1h

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 1 hour of FIRST Galactose treatment


title: BY-batch2-1st-000

description: rRNA depleted RNA

value: time 0 of FIRST Galactose treatment


title: 29B

description: Healthy, after 2nd dose

value: Post


title: ChIP-seq_97L_OGT_input_R1


title: BY-batch1-2nd-30min

description: rRNA depleted RNA

value: time 30 minutes  of SECOND Galactose treatment


title: 29A

description: Healthy, before 2nd dose


title: ChIP-seq_97L_OGT_IP_HA_ZNF263_WT_R2


title: BY-batch1-2nd-1h

description: rRNA depleted RNA

value: time 1 hour of SECOND Galactose treatment


title: CASCADE_TBL1XR1_JURKAT_rep2

value: 10 mg/mL

value: Nuclear extract


title: BY-batch1-2nd-15min

description: rRNA depleted RNA

value: time 15 minutes of SECOND Galactose treatment


title: ChIP-seq_97L_OGT_IP_HA_ZNF263_WT_R1


title: ChIP-seq_97L_OGT_IP_HA_ZNF263_S662A_R2


title: CASCADE_BRD4_JURKAT_rep2

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: CASCADE_TBL1XR1_JURKAT_rep1

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: CASCADE_BRD4_JURKAT_rep1


title: 25B

description: Healthy, after 2nd dose


title: BY-batch1-2nd-000

description: rRNA depleted RNA

value: time 0 of SECOND Galactose treatment


title: 27B

description: Healthy, after 2nd dose


title: 25A

description: Healthy, before 2nd dose

value: Pre


title: BY-batch1-1st-30min

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: BY-batch1-1st-3h

description: rRNA depleted RNA

value: time 3 hour of FIRST Galactose treatment


title: 27A

description: Healthy, before 2nd dose

value: Blood

value: Female


title: 21B

description: Healthy, after 2nd dose

value: Male


title: ChIP-seq_97L_OGT_IP_ZNF263_R1

value: liver

value: hepatocellular carcinoma


title: BY-batch1-1st-1h

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 1 hour of FIRST Galactose treatment


title: 21A

description: Healthy, before 2nd dose


title: ChIP-seq_97L_OGT_IP_H3K4me3_R2


title: ChIP-seq_97L_OGT_IP_HA_ZNF263_S662A_R1


title: R-2-NCX-48

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from NCI/ADR-RES tumor cells with 48hr NCX4040 treatment

hyb_protocol: Five and one-half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

label: biotin

source_name: NCI/ADR-RES tumor cells with 48hr NCX4040 treatment, replicate 2

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: OVCAR-8 and Its resistant variant (OVCAR-8R) tumor cells were grown in RPMI 1640 media containing 10% FBS.

extract_protocol: RNA was extracted using Triazol method.

treatment_protocol: Cell were left untreated or treated with NCX-4040 for 4, 24 and 48 h


title: ChIP-seq_97L_OGT_IP_ZNF263_R2


title: R-3-NCX-48

source_name: NCI/ADR-RES tumor cells with 48hr NCX4040 treatment, replicate 3


title: BY-batch1-1st-000

description: rRNA depleted RNA

value: time 0 of FIRST Galactose treatment


title: ChIP-seq_97L_OGT_IP_H3K4me3_R1


title: RA-2

value: testis

value: porcine primitive spermatogonia

value: 2 umol/L all-trans-retinoic acid


title: 18A

description: Healthy, before 2nd dose


title: SLAMSEQ_rrp03_2nd_T30

description: rRNA depleted RNA

data_processing:
For RNASEQ. The genome assembly and annotation for the RNA-Seq data analysis was downloaded from SGD database (version 64-1-1) (Xu et al., 2009). The quality of the RNA-Seq data was assessed with FastQC (Andrews, 2010). The reads were aligned to the genome with STAR and parameters --outFilterMismatchNmax 4 --alignIntronMin 13 --alignIntronMax 2482.  Read counts were then summarised using featurecounts with parameter -s 2 -C . chimeric fragments was excluded from fragment counting.  MultiQC was used to assess the performance of the preprocessing steps (Ewels et al., 2016). Differential gene expression analysis was perfomed with DESEQ2 package in R. The counts were normalized by coding transcriptome.   For ChIPseq and MNase-seq Illumina adptor was detected and trimmed by TrimGalore. Trimmed reads were then alignment with BWA to Saccharomyces_cerevisiae genome assembly R64-1-1. High repetitive Ribosome DNA region was provided as blacklist and removed from alignment.  PCR duplicates were marked with Picard MarkDuplicates and then removed for subsequent analysis. Deduplicted reads from biological replicates were then merged together. Bigwig files were then generated from merged bam files by deeptools bamcoverage command. Parameter --binSize 1 --MNase --minFragmentLength 100 --maxFragmentLength 200 --normalizeUsing CPM were used to take only mononucleosome, deconvolute and take only the center dyad genomic coordinate of each nucleosome. Bed files contains gene groups gerenerated from RNAseq data were provided to deepltools computatematrix command to extract the nucleosome occupancy and histone modification level of each gene within particular group. Deeptools plotProfile tool were then used to summarise above matrix into metagene plot with parameter –perGroup.  SLAMseq: SLAMseq data was anaysed with slamdunk provided by nextflow pipeline(v 1.0.0). https://nf-co.re/slamseq . As stranded library was prepared with dUTP method and fastq files were first converted to reverse complementary reads to feed into slamdunk nf core pipeline.  Adapter contamination and low quality region was trimmed with TrimGalore, trim length 30bp was used instead of default value. When aligned to genome, transcript annotation downloaded from SGD database (version 64-1-1) (Xu et al., 2009) were first converted into bed file and then used as input for parameter utrbed. At least 2 conversions cooccur in one reads is regarded as a confident call for nascent RNA. SNP masking was employed to uncouple Single Nucletide Polymorphism from converted nucleotides.
Assembly: V64-1-1
Supplementary files format and content: bigwig for ChIP-seq, txt files of normalised RNASEQdata and slamseq data
Library strategy: SLAM-seq

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 30 minutes  of SECOND Galactose treatment


title: ChIP-seq_97L_OGT_IP_H3K27ac_R2


title: 17B

description: Healthy, after 2nd dose

value: Post


title: SLAMSEQ_rrp03_2nd_T0

description: rRNA depleted RNA

value: time 0 of SECOND Galactose treatment


title: R-1-NCX-48

source_name: NCI/ADR-RES tumor cells with 48hr NCX4040 treatment, replicate 1


title: ChIP-seq_97L_OGT_IP_H3K27ac_R1


title: R-2-NCX-24

description: Gene expression from NCI/ADR-RES tumor cells with 24hr NCX4040 treatment

source_name: NCI/ADR-RES tumor cells with 24hr NCX4040 treatment, replicate 2


title: R-3-NCX-4

description: Gene expression from NCI/ADR-RES tumor cells with 4hr NCX4040 treatment

source_name: NCI/ADR-RES tumor cells with 4hr NCX4040 treatment, replicate 3


title: 17A

description: Healthy, before 2nd dose

value: Pre


title: ChIP-seq_97L_input_Flag_OGT_R2


title: 18B

description: Heathy, after 2nd dose


title: SLAMSEQ_rrp03_1st_T30

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: ApoE, scRNAseq

city: Nanjing

first: Mulong

last: Du

state: Jiangsu

address: 101 Longmian Avenue

institute: Nanjing Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, aggregation, and analysis were made using the Cell Ranger and Seurat package of R.
Assembly: mm10

organism: Mus musculus

source_name: aortas

extract_protocol:
Mouse aortas were cut into fine pieces and placed in 6.5 mL enzyme solution at 37°C for 1.5 hours (5 mL DMEM, 1 mL trypsin, collagenase type I 10 mg/mL, collagenase type IV 10 mg/mL , 50 µL elastin (2.5 mg/mL stock), collagenase type II 200 µL (stock: 1 mg/mL), Collagenase XI 200 µL (stock: 1 mg/mL), Hydrolase 200 µL (stock: 1 mg/mL), Liberase 100 µL (stock: 3.85 mg/mL, Roche), DNase I 10 µL (stock: 5U/µL, Sigma).  This solution was then filtered using a 40 µm strainer (Falcon, NC), centrifuged (400xg for 5 min) and the cell pellet was suspended in 90 µL FEB buffer containing 0.5% BSA and 2 mM EDTA in PBS. 10 µL of CD31 Microbeads (MACS) was added to the suspension at 4°C for 15 min.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: aortas

value: all cells

value: ApoE


title: SLAMSEQ_rrp02_2nd_T30

description: rRNA depleted RNA


title: ChIP-seq_97L_OGT_IP_Flag_OGT_R2

value: liver


title: ChIP-seq_97L_input_Flag_OGT_R1

value: hepatocellular carcinoma


title: DKO, scRNAseq

description: 10x Genomics

value: DKO


title: SLAMSEQ_rrp03_1st_T0

description: rRNA depleted RNA


title: R-1-NCX-24

source_name: NCI/ADR-RES tumor cells with 24hr NCX4040 treatment, replicate 1

value: Female


title: R-3-NCX-24

source_name: NCI/ADR-RES tumor cells with 24hr NCX4040 treatment, replicate 3


title: Soleus ERRalpha/ERRgamma dmKO 3

city: Baltimore

first: Anastasia

last: Kralli

state: Maryland

address: 725 N. Wolfe Street

department: Phys Physiology

institute: Johns Hopkins School of Medicine

data_processing:
The data were aligned to the GRCm38 reference genome using the CLCGenomicsServer with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 9.1.1 as above
FPKM vaues log2 converted (FPKM = 0 ignored as NULL) and quantile normalized with Partek Genomics Suite v6.6
Assembly: GRCm38_p6 mm10
Supplementary files format and content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples, contains NULLs for Zeros.

source_name: skeletal muscle

growth_protocol: C57Bl6 mice housed at room temperature (~22oC), on a 12-hour light-dark cycle, and fed a standard chow breeder diet

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) and the RNeasy mini kit with on-column DNase digestion (Qiagen)
RNA libraries were prepared using 400 ng of RNA amplified via 10 PCR cycles and the NEBNext UltraII Directional RNA Library Prep Kit (NEB) for Illumina

treatment_protocol: All mice were were backcrossed to the C57BL/6JBom background (Taconic Biosciences) for at least 10 generations. To generate mice with muscle-specific deletions of ERRs, ERR floxed mice were crossed to mice expressing CRE recombinase under the control of the human α-skeletal actin (HSA) promoter. Muscles were harvested from 1 year old males.

value: skeletal muscle

value: C57BL/6JBom background

value: ERRalpha/ERRgamma dmKO


title: ChIP-seq_97L_OGT_IP_Flag_OGT_R1


title: Soleus ERRalpha/ERRgamma dmKO 2


title: R-3-C

description: Gene expression from control NCI/ADR-RES tumor cells

source_name: Control NCI/ADR-RES tumor cells, replicate 3


title: ChIP-seq_97H_OGT_input_R2


title: SLAMSEQ_rrp02_1st_T30

description: rRNA depleted RNA


title: WT-3-NCX-48

description: Gene expression from tumor cells with 48hr NCX4040 treatment

source_name: Tumor cells with 48hr NCX4040 treatment, replicate 3


title: R-2-C

source_name: Control NCI/ADR-RES tumor cells, replicate 2


title: ChIP-seq_97H_OGT_input_R1

source_name: liver


title: SLAMSEQ_rrp01_2nd_T30

description: rRNA depleted RNA


title: SLAMSEQ_rrp02_1st_T0

description: rRNA depleted RNA

value: time 0 of FIRST Galactose treatment


title: Soleus ERRalpha/ERRgamma dmKO 1


title: SLAMSEQ_rrp02_2nd_T0

description: rRNA depleted RNA

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ChIP-seq_97H_OGT_IP_HA_ZNF263_WT_R2


title: Soleus ERRalpha/ERRgamma WT 2

value: WT


title: WT-2-NCX-48

source_name: Tumor cells with 48hr NCX4040 treatment, replicate 2


title: ChIP-seq_97H_OGT_IP_HA_ZNF263_WT_R1


title: R-1-NCX-4

source_name: NCI/ADR-RES tumor cells with 4hr NCX4040 treatment, replicate 1


title: SLAMSEQ_rrp01_2nd_T0

description: rRNA depleted RNA


title: WT-1-NCX48

source_name: Tumor cells with 48hr NCX4040 treatment, replicate 1


title: ChIP-seq_97H_OGT_IP_HA_ZNF263_S662A_R2


title: Soleus ERRalpha/ERRgamma WT 3


title: Soleus ERRbeta/ERRgamma dmKO 3

value: ERRbeta/ERRgamma dmKO


title: ChIP-seq_97H_OGT_IP_HA_ZNF263_S662A_R1


title: SLAMSEQ_rrp01_1st_T30

description: rRNA depleted RNA


title: WT-3-NCX-24

description: Gene expression from tumor cells with 24hr NCX4040 treatment

source_name: Tumor cells with 24hr NCX4040 treatment, replicate 3


title: R-1-C

source_name: Control NCI/ADR-RES tumor cells, replicate 1


title: Soleus ERRbeta/ERRgamma dmKO 2


title: ChIP-seq_97H_OGT_IP_ZNF263_R2


title: SLAMSEQ_rrp01_1st_T0

description: rRNA depleted RNA


title: Soleus ERRalpha/ERRgamma WT 1


title: ChIP-seq_97H_OGT_IP_ZNF263_R1


title: ChIP-seq_97H_OGT_IP_H3K4me3_R2


title: Soleus ERRbeta/ERRgamma WT 3


title: Soleus ERRbeta/ERRgamma dmKO 1


title: SLAMSEQ_BY03_1st_T30

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: SLAMSEQ_BY03_2nd_T0

description: rRNA depleted RNA

value: time 0 of SECOND Galactose treatment


title: Soleus ERRbeta/ERRgamma WT 2


title: WT-2-NCX-24

source_name: Tumor cells with 24hr NCX4040 treatment, replicate 2


title: WT-3-NCX-4

description: Gene expression from tumor cells with 4hr NCX4040 treatment

source_name: Tumor cells with 4hr NCX4040 treatment, replicate 3


title: WT-1-NCX-24

source_name: Tumor cells with 24hr NCX4040 treatment, replicate 1


title: SLAMSEQ_BY03_1st_T0

description: rRNA depleted RNA


title: ChIP-seq_97H_OGT_IP_H3K4me3_R1


title: SLAMSEQ_BY02_2nd_T30

description: rRNA depleted RNA

value: time 30 minutes  of SECOND Galactose treatment


title: IAV4-B16

city: Hangzhou

first: Yushi

last: Yao

state: Zhejiang

address: 866 Yu Hang Tang Road

institute: Zhejiang University

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts to get the clean data
paired-end clean reads were aligned to the reference genime using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numberes mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
differential expression ananlysis of two condtions/groups(two or more biologcal replicates per condition) was performed usig the DESeq2 R package(1.16.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Count values for each Sample

source_name: Lung

extract_protocol:
RNA was extracted with Trizol method
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Alveolar Macrophages

value: Lung

value: IAV-exposed mouse treated with B16 tumor cells


title: IAV3-B16


title: SLAMSEQ_BY03_2nd_T30

description: rRNA depleted RNA


title: WT-1-NCX-4

source_name: Tumor cells with 4hr NCX4040 treatment, replicate 1


title: ChIP-seq_97H_OGT_IP_H3K27ac_R2

value: liver


title: Soleus ERRbeta/ERRgamma WT 1


title: IAV2-B16


title: WT-2-NCX-4

source_name: Tumor cells with 4hr NCX4040 treatment, replicate 2


title: Soleus ERRalpha mKO 3

value: ERRalpha mKO


title: ChIP-seq_97H_OGT_IP_H3K27ac_R1

value: hepatocellular carcinoma


title: SLAMSEQ_BY02_1st_T30

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: WT-2C

description: Gene expression from control tumor cells

source_name: Control tumor cells, replicate 2

value: Female


title: PBS3-B16

value: B16 tumor cells


title: Soleus ERRalpha mKO 1

source_name: skeletal muscle

value: skeletal muscle

value: C57BL/6JBom background


title: SLAMSEQ_BY02_1st_T0

description: rRNA depleted RNA

value: time 0 of FIRST Galactose treatment


title: Soleus ERRalpha WT 3

value: WT


title: PBS2-B16


title: IAV1-B16


title: ChIP-seq_97H_input_Flag_OGT_R1


title: WT-1C

source_name: Control tumor cells, replicate 1


title: Soleus ERRalpha WT 2


title: PBS1-B16


title: SLAMSEQ_BY02_2nd_T0

description: rRNA depleted RNA


title: WT-3C

source_name: Control tumor cells, replicate 3


title: ChIP-seq_97H_OGT_IP_Flag_OGT_R1


title: SLAMSEQ_BY01_2nd_T0

description: rRNA depleted RNA


title: IAV3

value: IAV


title: R-2-NCX-4

source_name: NCI/ADR-RES tumor cells with 4hr NCX4040 treatment, replicate 2


title: ChIP-seq_97H_OGT_IP_Flag_OGT_R2

source_name: liver


title: Soleus ERRalpha mKO 2


title: ChIP-seq_97H_input_Flag_OGT_R2


title: Soleus ERRalpha WT 1


title: EDL ERRalpha/ERRgamma dmKO 3

value: ERRalpha/ERRgamma dmKO


title: IAV1


title: 4OHT p53 KO rep 3

city: Milan

first: Davide

last: Mazza

address: via Olgettina 58

country: Italy

institute: Università Vita-Salute San Raffaele

description: mRNA Stranded TruSeq protocol

data_processing:
Sequencing reads were trimmed using fastp (v0.21.0) with options set to: --qualified_quality_phred 15.
Reads were mapped against the GRCh37/hg19, genome assembly (Ensembl release 87) using hisat2 (v2.1.0) with options set to; --rna-strandness R.
Differential expression (DE) analysis was performed using the R package DESeq2 (v1.3.6). Genes with an adjusted p-value (FDR) of <0.05 and with a log2 fold change (log2FC) greater or equal to the absolute value of 1, were considered as differentially expressed.
To identify the genes that are directly regulated by p53 in the DIvA cell line, we intersected upregulated genes (FDR<0.05, log2FC≥1) with the p53 cistrome derived from a previous meta-analysis (PMID: 30107566)
Assembly: GRCh37/hg19
Supplementary files format and content: A tab-separated values file named 'RNAseqCounts' which contains RNA-seq reads for each replicate.
Supplementary files format and content: A tab-separated values file named 'DEGs' containing the differential gene expression analysis. The file includes a column indicating the intersection of upregulated genes with the p53 cistrome (PMID: 30107566).

molecule: polyA RNA

source_name: osteosarcoma cell line

growth_protocol: Cells were plated on 6-cm dishes (12.000 cells/dish) two days before treatment and grown in DMEM supplemented with 10% heat-inactivated Qualified Fetal Bovine Serum and antibiotics, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After 4OHT treatment, cells were washed once in cold PBS and lysed in 750 μL of TRIzol reagent (Thermo-Fisher, cat. 15596018) to extract the total RNA. Lysates were purified using silica membrane columns (Machery-Nagel, NucleoSpin RNA Plus). RNA quality was confirmed running samples on Tapestation 4100 (Agilent).
TruSeq Stranded mRNA (Illumina) protocol

treatment_protocol: A batch of DMEM containing 300nM 4OHT was prepared just before the treatment. Cells were incubated with the 4OHT-containing DMEM for 5 hours.

value: osteosarcoma cell line

value: DIvA

value: U2OS-derived cells

value: p53 KO

value: 300 nM 4-OHT


title: SLAMSEQ_BY01_1st_T0

description: rRNA depleted RNA

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ChIPseq_Input_rrp6_t2_rep3

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of SECOND Galactose treatment


title: 4OHT p53 KO rep 2

description: mRNA Stranded TruSeq protocol


title: IAV2

value: Alveolar Macrophages

value: Lung


title: SLAMSEQ_BY01_2nd_T30

description: rRNA depleted RNA

value: time 30 minutes  of SECOND Galactose treatment


title: ChIPseq_Input_rrp6_t2_rep2


title: PBS3

value: PBS


title: SLAMSEQ_BY01_1st_T30

description: rRNA depleted RNA

value: time 30 minutes  of FIRST Galactose treatment


title: 4OHT p53 WT rep 3

description: mRNA Stranded TruSeq protocol

value: p53 WT


title: ChIPseq_Input_rrp6_t2_rep1


title: 4OHT p53 WT rep 2

description: mRNA Stranded TruSeq protocol


title: PBS2

value: WT


title: EDL ERRalpha/ERRgamma WT 2

value: skeletal muscle

value: C57BL/6JBom background


title: ChIPseq_Input_rrp6_t1_rep3

value: time 0 of FIRST Galactose treatment


title: EDL ERRalpha/ERRgamma WT 3


title: ATAC_IAV3-B16

data_processing:
Raw ATAC-seq fastq files from paired-end sequencing were trimmed by using fastp (v0.19.11) followed by quality control using fastqc(v0.11.5).
Clean data were aligned to the GRCm38/mm10 reference genome using BWA(v0.7.12-r1039). Samtools(v1.11) was used to remove unmapped, unpaired and mitochondrial reads. PCR duplicates were removed by using Picard.
Peak calling was performed using MACS2(v2.1.2, -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all).
The number of reads in each peak was determined using DiffBind(v3.4).
Differentially accessible peaks were identified following DESeq2 normalization using an FDR cut-off <0.05.
Tracks were visualized using Integrative Genomics Viewer (v.2.3.77, Broad Institute).
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Lung Primary Macrophages

extract_protocol:
50,000 AMs were washed with cold PBS and resuspend in cold lysis buffer(10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Detail protocol could be find in Curr Protoc Mol Biol. ; 109: 21.29.1–21.29.9. doi:10.1002/0471142727.mb2129s109.
Cell lysates were centrifuged at 500g for 10 min at 4℃ and nuclei were resuspended in 50 µL of transposition reaction mix (25 µL of TD buffer + 2.5 µL of Tn5 Transposase + 22.5 µL of nuclease-free water; Illumina, San Diego, CA) and incubated for 30 min at 37 °C. Transposed DNA fragments were purified by using a Qiagen Reaction MiniElute Kit (Qiagen, Hilden, Germany), barcoded with Nextera single indexes (New England Biolabs, Ipswich, MA), and amplified by PCR for 11 cycles using NEBNext High Fidelity 2× PCR Master Mix (New England Biolabs, Ipswich, MA). PCR products were purified using a PCR Purification Kit (Qiagen, Hilden, Germany) and amplified fragment size was verified on an Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA). ATAC-seq libraries were quantified by quantitative PCR.

value: Lung Primary Macrophages

value: IAV-exposed mouse treated with B16 tumor cells


title: ChIPseq_Input_rrp6_t1_rep2


title: EDL ERRalpha/ERRgamma WT 1


title: EDL ERRalpha/ERRgamma dmKO 2

value: ERRalpha/ERRgamma dmKO


title: ATAC_IAV2-B16


title: EDL ERRbeta/ERRgamma dmKO 3

value: ERRbeta/ERRgamma dmKO


title: 4OHT p53 KO rep 1

description: mRNA Stranded TruSeq protocol

value: osteosarcoma cell line

value: DIvA

value: U2OS-derived cells

value: p53 KO

value: 300 nM 4-OHT


title: stressed IVD 1

city: Los Angeles

first: Wensen

last: Jiang

state: CA

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Cell Ranger 3.0.0
Loupe Cell Browser 3.0.0
bcl2fastq v2.20 (Illumina, San Diego, CA)
Converted into fastq format
Supplementary files format and content: .csv or .tsv.zg or .mtx.gz

source_name: Cells harvested from the whole IVD, in vitro cultured with stress

extract_protocol:
The IVDs were dissected, nucleus pulposus identified and washed with Phosphate Buffered Saline (PBS). The tissue was manually minced and enzymatically digested. Tissue was digested with Pronase Protease (Millipore, Temecula, CA) in growth media, followed by ~18 hour digestion of Collagenase Type 1S in growth media. The resulting sample was pushed through a 70μm cell strainer and cells were isolated via centrifugation. The pellet was resuspended in phosphate buffered saline at a concentration of 1,500 cells/μL and 100uL of sample was processed for single-cell RNA sequencing. For the sIVD and nsIVD group, IVD cells were cryopreserved, thawed, plated, and cultured in vitro with (sIVD) or without (nsIVD) stressors.
Chromium Single-cell 3' v2 libraries were prepared on a Chromium Controller with chips and reagents from Single-cell Gene Expression v2 kits following the manufacturer’s protocols (10x Genomics). The libraries were then sequenced using paired-end sequencing on an Illumina NovaSeq. Samples were sequenced with raw sequencing data analyzed and visualized with pre-release versions of Cell Ranger 3.0.0 and Loupe Cell Browser 3.0.0. Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, CA). Fragment analysis of indexed libraries was performed on the Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA).

tag: group

value: stress


title: non-stressed IVD 1

source_name: Cells harvested from the whole IVD, in vitro cultured without stress

value: no stress


title: ChIPseq_Input_rrp6_t1_rep1

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ATAC_IAV1-B16


title: ChIPseq_Input_WT_t2_rep3

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of SECOND Galactose treatment


title: back pain IVD 3

source_name: Cells harvested from the whole IVD

value: back pain


title: EDL ERRbeta/ERRgamma dmKO 2

value: skeletal muscle

value: C57BL/6JBom background


title: EDL ERRalpha/ERRgamma dmKO 1


title: ATAC_PBS3-B16

value: Lung Primary Macrophages

value: B16 tumor cells


title: back pain IVD 2


title: PBS1

value: Alveolar Macrophages

value: Lung

value: WT

value: PBS


title: ChIPseq_Input_WT_t2_rep2


title: EDL ERRbeta/ERRgamma dmKO 1

value: ERRbeta/ERRgamma dmKO


title: 4OHT p53 WT rep 1

description: mRNA Stranded TruSeq protocol

value: osteosarcoma cell line

value: DIvA

value: U2OS-derived cells

value: p53 WT


title: ChIPseq_Input_WT_t2_rep1


title: EDL ERRbeta/ERRgamma WT 3


title: ATAC_PBS2-B16


title: back pain IVD 1


title: ChIPseq_Input_WT_t1_rep3

value: time 0 of FIRST Galactose treatment


title: ATAC_IAV3

value: IAV


title: asymptomatic IVD 4

value: asymptomatic


title: EDL ERRbeta/ERRgamma WT 1


title: EDL ERRbeta/ERRgamma WT 2


title: ChIPseq_Input_WT_t1_rep2

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ChIPseq_Input_WT_t1_rep1


title: ATAC_IAV2


title: EDL ERRalpha mKO 3

value: skeletal muscle

value: ERRalpha mKO


title: asymptomatic IVD 2


title: ATAC_IAV1

value: Lung Primary Macrophages


title: asymptomatic IVD 1


title: EDL ERRalpha mKO 2

value: C57BL/6JBom background


title: ATAC_PBS3


title: ChIPseq_H3_rrp6_t2_rep2

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of SECOND Galactose treatment


title: ATAC_PBS1-B16

value: B16 tumor cells


title: ATAC_PBS2

value: PBS


title: 4481 rep1, scATACseq

city: Huntsville

first: Lindsay

last: Rizzardi

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
Processed files include paired scRNAseq and scATACseq counts from the same cells
Assembly: hg38
Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data

extract_protocol:
Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess.
Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).

tag: disease state

value: AD

tag: Sex

value: M


title: ChIPseq_H3_rrp6_t2_rep1


title: EDL ERRalpha WT 3

tag: tissue

value: WT


title: EDL ERRalpha WT 2

tag: cell type


title: ChIPseq_H3_rrp6_t1_rep3


title: ATAC_PBS1


title: 4481 rep2, scATACseq

description: 10x Genomics

tag: age


title: 3586 rep2, scATACseq

description: 10x Genomics

value: control


title: 3586 rep1, scATACseq

description: 10x Genomics


title: 12_AM+4: alpha-amanitin treated 10h one-cell embryo

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw sequence reads (fastq) were trimmed using the fastx_trimmer command from fastx-Toolkit (version 0.0.13; respectively 4 nt from 5' and 15 nt from 3' ends)
Sequencing adapter sequences were removed by Cutadapt (1.7.1)
Mapping of the trimmed reads was by STAR (2.5.0a) using the GRCm38 genome and gene level count was performed (with STAR) against Ensembl V100 reference gene model
Assembly: Grcm38
Supplementary files format and content: Raw gene-level counts in tab-delimited text format

source_name: one-cell embryo

growth_protocol: Embryos were generated by standard B6D2F1 × B6D2F1 IVF. Sperm were collected from mature males by epididymidal puncture followed by dispersal for 5 min in pre-warmed human tubal fluid (HTF; Millipore) in humidified CO2 (5% [v/v] in air) at 37°C. Of the 400 μl dispersal droplet, 10 μl were transferred to a fresh fertilization dish containing 200 μl HTF and incubation continued for 1 h before placing ~30 cumulus oophorous complexes freshly-isolated from superovulated 8-week-old B6D2F1 females and incubating in the CO2 incubator at 37°C. The resultant embryos were washed in fresh HTF and dead and clearly unfertilized oocytes removed. Embryos were then washed 5x in KSOM and incubated until required in KSOM droplets equilibrated under mineral oil in humidified 5% CO2 (v/v air) at 37°C.

extract_protocol:
Single-cell embryo were directly lysed using Takara Clontech Smartseq lysis buffer with RNAse inhibitor
Whole transcriptome amplification and library preparation was performed using Takara Clontech Smarter Stranded Total RNA-Seq Kit Pico Input version 2

treatment_protocol: To inhibit the trans-activation of c-Myc target gene expression, embryos produced by IVF 2 h after sperm-oocyte mixing were washed and transferred to KSOM supplemented with 5-[(4- Ethylphenyl)methylene]-2-thioxo-4-thiazolidinone (10058-F4; Merck) or NUCC-0200975 1015 (MYCi975; Selleckchem, UK) and incubation for 10 h. For the inhibition of Pol II-mediated transcription, embryos were generated by sperm-oocyte mixing for 1 h and then incubated in KSOM containing a-amanitin (100 μg/ml) for a further 10 h, when bi-pronuclear embryo samples (with or without exposure to a-amanitin) were collected.

value: one-cell embryo

tag: strain

value: alpha-amanitin

tag: replicate


title: EDL ERRalpha WT 1


title: asymptomatic IVD 3


title: PAM3

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

data_processing:
Cutadapt and Trimmomatic were used to clip or remove low quality reads. The Illuminaclip function was used to remove Illumina adapters. The SLIDINGWINDOW function was applied to discard reads shorter than 20 bases.
Good quality reads were mapped to the mouse genome with STAR and default parameters
Raw read counts for each sample were extracted with the featureCounts tool from Rsubread using the Gencode M29 annotation as reference
Assembly: mm10
Supplementary files format and content: Tab-separated text files with raw read counts extracted with featureCounts

source_name: Lin- cells Pam3-treated

growth_protocol: Purified Lin- cells were cultured in complete cell culture medium (RPMI 1640 medium supplemented with 2 nM L-glutamine, 5% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin stock solution supplemented with 20 ng/ml stem cell factor)

extract_protocol:
aRNA was extracted from whole cell lysates using an RNeasy mini kit (QIAGEN)
RNA libraries were prepared using with the Illumina TruSeq stranded mRNA library preparation kit following manufacturer's protocols.

treatment_protocol: Lin- cells were treated with 1 µg/ml Pam3CSK4 for 24h

value: C57BL/6 mice

value: Hematopoietic stem and progenitor cells

value: WT-TREATED

tag: treatment

tag: time


title: ChIPseq_H3_rrp6_t1_rep2

value: time 0 of FIRST Galactose treatment


title: 11_AM+3: alpha-amanitin treated 10h one-cell embryo


title: 1224 rep2, scATACseq

description: 10x Genomics

source_name: DLPFC

value: DLPFC

value: F


title: PAM2


title: EDL ERRalpha mKO 1

value: skeletal muscle

value: C57BL/6JBom background

value: ERRalpha mKO


title: ChIPseq_H3_WT_t2_rep3

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of SECOND Galactose treatment


title: ChIPseq_H3_rrp6_t2_rep3

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ChIPseq_H3_rrp6_t1_rep1


title: PAM1


title: 9_AM+1: alpha-amanitin treated 10h one-cell embryo


title: ChIPseq_H3_WT_t2_rep2


title: 10_AM+2: alpha-amanitin treated 10h one-cell embryo


title: 1224 rep1, scATACseq

description: 10x Genomics


title: 4627 rep1, scATACseq

description: 10x Genomics

value: AD


title: ChIPseq_H3_WT_t2_rep1


title: ChIPseq_H3_WT_t1_rep3


title: CONTROL2

source_name: Lin- cells untreated

value: WT-CONTROL

value: untreated


title: 7_AM-3: control 10h one-cell embryo

description: control 10h one-cell embryo

value: one-cell embryo

value: Control


title: 6_AM-2: control 10h one-cell embryo

description: control 10h one-cell embryo


title: CONTROL3

value: C57BL/6 mice


title: CONTROL1

value: Hematopoietic stem and progenitor cells


title: 8_AM-4: control 10h one-cell embryo

description: control 10h one-cell embryo


title: ChIPseq_H3_WT_t1_rep2


title: 1238 rep1, scATACseq

description: 10x Genomics

value: control

value: M


title: 1238 rep2, scATACseq

description: 10x Genomics

value: DLPFC


title: 5_AM-1: control 10h one-cell embryo

description: control 10h one-cell embryo


title: input DNA

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

description: Pooled Input

data_processing:
All sequencing data were processed with snakePipes (v. 1.1.1).
Fastq Quality Control using FastQC.
 high quality and uniquely mapping reads were retained (mapq > 5).
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Input-normalised bigwig files from treated and control samples were compared and normalised to log2ratio using bigwigCompare Galaxy Version 3.3.2.0.0. Parameters:
Genome_build: mm10
Supplementary_files_format_and_content: bw and narrow peak

source_name: Primary Hippocampal Neurons

growth_protocol: Primary hippocampal tissue isolation and culture was done following a protocol modified after Brewer et al., 1993. Hippocampal tissue was isolated from E18.5 mouse embryos and dissociated by trypsinisation and trituration. Cells were counted and seeded 150,000/well in 24 well-plates and were grown in Neurobasal medium with B27 supplement (DIV0). Half-volume medium change was done every 48 hours.

extract_protocol:
Cells were fixed according to instructions of Active Motif. Freshly prepared Formaldehyde solution (11% FA, 0.1 M NaCl, 1mM EDTA, 1M HEPES) was added to the existing media in 1:10 ratio. Cells were agitated at room temperature for 15 minutes. Fixation was stopped by adding 2.5 M glycine solution in 1:20 ratio and incubating at room temperature for 5 minutes. After glycine incubation, cells were scraped from the surface and colelcted. Cells were washed 2x with ice-cold PBS-Igepal, and lastly with PBS-Igepal-PMSF solutions. Cells were centrifuged at 800g (4C,10 min). Pellets were snap frozen and kept at -80 C until all samples were ready. Lysates were clarified from sonicated nuclei and TF-DNA complexes were isolated with antibody.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads.

treatment_protocol: On DIV4,  cytosine arabinoside (Ara-C, final: 2mM) was addedto stop the proliferation of non-neuronal cells.. Half-volume medium changes were continued every 48 hours until DIV11.

tag: days in vitro(div)

value: hippocampus

tag: dissection age

tag: antibody

value: WT


title: ChIPseq_H3_WT_t1_rep1

value: time 0 of FIRST Galactose treatment


title: ChIPseq_H3K4me3_rrp6_t2_rep3


title: ChIPseq_H3K4me3_rrp6_t2_rep2


title: 2_mII2: control mii oocyte

description: control mii oocyte

source_name: MII oocyte

value: MII oocyte


title: 4627 rep2, scATACseq

description: 10x Genomics

value: F


title: ChIPseq_H3K4me3_rrp6_t2_rep1

value: time 0 of SECOND Galactose treatment


title: 1_mII1: control mii oocyte

description: control mii oocyte


title: 3_mII3: control mii oocyte

description: control mii oocyte


title: NEUROD1_WT_N2

value: NEUROD1 (Active Motif)


title: Control_Pooled Input

data_processing:
Sequencing data was processed in usegalaxy.eu platform.
Fastq Quality Control using FastQC  (v0.11.9).
 high quality and uniquely mapping reads were retained (mapq > 5).
Adapter trimming and quality filtering was done using Trimmomatic (v 0.38)with the following configurations: ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_PATH/TruSeq3-SE.fa:2:30:10 MINLEN:20 -trimlog trimlog 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz'
Trimmed and quality filtered reads were aligned to mm10 genome assembly using Bowtie 2(v 2.3.4.1) using the following command: set -o | grep -q pipefail && set -o pipefail;   ln -s '/data/dnb05/galaxy_db/files/0/2/f/dataset_02fe6c06-864b-43e2-8311-2fc1e1a81253.dat' input_f.fastq.gz.gz &&   bowtie2  -p ${GALAXY_SLOTS:-4}  -x '/data/db/reference_genomes/mm10/bowtie2_index/mm10'   -U 'input_f.fastq.gz.gz'               --sensitive         2> '/data/jwd/main/033/625/33625182/outputs/galaxy_dataset_fb42ac29-feb2-48ce-bc4d-15a12528fe2a.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -O bam -o '/data/jwd/main/033/625/33625182/outputs/galaxy_dataset_0fc27fd7-4cc2-4fde-996a-c523cb87f985.dat'
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Input-normalised bigwig files (bamcompare) from treated and control samples were compared and normalised to log2ratio using bigwigCompare. deeptools Galaxy Version 3.3.2.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and narrowpeaks

extract_protocol:
virally transduced (shFoxg1, shNeurod1 or shLuciferase) primary hippocampal neurons were fixed and collected for subsequent ChIP-seq experiments according to the instructions of the servicing company (Active Motif). Briefly, cells were fixed by adding 1/10 volume formaldehyde solution (11% Formaldehyde, 0.1 M NaCl, 1 mM EDTA pH=8.0, 50 mM HEPES pH=7.9) directly to the medium and incubated at room temperature (RT) with agitation. Fixation was stopped by adding 1/20 volume 2.5 M Glycine solution (Roth, Germany) and incubating for 5 min at RT. Cells were scraped from the plates and transferred into conical tubes, and centrifuged at 800 rpm at 4°C for 10 min. Cells were resuspended and washed twice in chilled PBS-Igepal solution (0.5% Igepal CA-360 (Sigma) in 1X PBS pH 7.4 (Gibco)), and a third time in PBS-Igepal-PMSF (phenylmethylsulfonyl fluoride) solution (0.5% Igepal, 1 mM PMSF (Sigma) in 1X PBS pH 7.4). The supernatant was completely removed and cell pellets were snap frozen in liquid nitrogen and stored at -80°C until following ChIP-seq experiments.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara)
ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads.

treatment_protocol: Lentiviral particles were prepared using plko.1-CMV.Puro-tGFP-shNeurod1, plko.1-CMV.Puro-tGFP-shFoxg1 or plko.1-CMV.Puro-tGFP-shLuciferase (Genscript) plasmids. Cells were transduced with lentiviral particles on day-in-vitro (DIV) 1. At DIV4, transduced cells were selected using 0.3 µg/ml puromycin (P9620, Sigma) and cell proliferation was inhibited by addition of 2 µM Arabinocytosine (AraC, C1768, Sigma), while performing a half-volume medium change. Medium was changed again at DIV7 and DIV9 including 0.3 µg/ml puromycin and 2 µM AraC.

tag: knockdown


title: ChIPseq_H3K4me3_rrp6_t1_rep3

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: NEUROD1_WT_N1


title: Foxg1KD_Pooled Input


title: ChIPseq_H3K4me3_rrp6_t1_rep2


title: 4313, scATACseq

description: 10x Genomics

value: AD


title: 4443, scATACseq

description: 10x Genomics


title: ChIPseq_H3K4me3_rrp6_t1_rep1


title: Neurod1KD_Pooled Input


title: 4482, scATACseq

description: 10x Genomics


title: NT1271, scATACseq

description: 10x Genomics


title: FOXG1_ChIP_Control

value: FOXG1 (Active Motif)


title: NEUROD1_ChIP_Control


title: 14-F7: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo

value: one-cell embryo


title: 15-C8: control 10h one-cell embryo

description: control 10h one-cell embryo

value: Control


title: 4_mII4: control mii oocyte

description: control mii oocyte


title: 16-F8: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: 3329, scATACseq

description: 10x Genomics


title: ChIPseq_H3K4me3_WT_t2_rep2

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: 4305, scATACseq

description: 10x Genomics


title: ChIPseq_H3K4me3_WT_t2_rep3


title: 13-C7: control 10h one-cell embryo

description: control 10h one-cell embryo


title: 1230, scATACseq

description: 10x Genomics


title: FOXG1_ChIP_Neurod1KD_n2


title: NT1261, scATACseq

description: 10x Genomics


title: ChIPseq_H3K4me3_WT_t2_rep1


title: 11-C6: control 10h one-cell embryo

description: control 10h one-cell embryo


title: NEUROD1_ChIP_Foxg1KD_n2


title: ChIPseq_H3K4me3_WT_t1_rep3


title: 4481 rep2, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
Processed files include paired scRNAseq and scATACseq counts from the same cells
Assembly: hg38
Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix


title: 10-F5: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: 9-C5: control 10h one-cell embryo

description: control 10h one-cell embryo


title: ChIPseq_H3K4me3_WT_t1_rep2

data_processing:
For RNASEQ. The genome assembly and annotation for the RNA-Seq data analysis was downloaded from SGD database (version 64-1-1) (Xu et al., 2009). The quality of the RNA-Seq data was assessed with FastQC (Andrews, 2010). The reads were aligned to the genome with STAR and parameters --outFilterMismatchNmax 4 --alignIntronMin 13 --alignIntronMax 2482.  Read counts were then summarised using featurecounts with parameter -s 2 -C . chimeric fragments was excluded from fragment counting.  MultiQC was used to assess the performance of the preprocessing steps (Ewels et al., 2016). Differential gene expression analysis was perfomed with DESEQ2 package in R. The counts were normalized by coding transcriptome.   For ChIPseq and MNase-seq Illumina adptor was detected and trimmed by TrimGalore. Trimmed reads were then alignment with BWA to Saccharomyces_cerevisiae genome assembly R64-1-1. High repetitive Ribosome DNA region was provided as blacklist and removed from alignment.  PCR duplicates were marked with Picard MarkDuplicates and then removed for subsequent analysis. Deduplicted reads from biological replicates were then merged together. Bigwig files were then generated from merged bam files by deeptools bamcoverage command. Parameter --binSize 1 --MNase --minFragmentLength 100 --maxFragmentLength 200 --normalizeUsing CPM were used to take only mononucleosome, deconvolute and take only the center dyad genomic coordinate of each nucleosome. Bed files contains gene groups gerenerated from RNAseq data were provided to deepltools computatematrix command to extract the nucleosome occupancy and histone modification level of each gene within particular group. Deeptools plotProfile tool were then used to summarise above matrix into metagene plot with parameter –perGroup.  SLAMseq: SLAMseq data was anaysed with slamdunk provided by nextflow pipeline(v 1.0.0). https://nf-co.re/slamseq . As stranded library was prepared with dUTP method and fastq files were first converted to reverse complementary reads to feed into slamdunk nf core pipeline.  Adapter contamination and low quality region was trimmed with TrimGalore, trim length 30bp was used instead of default value. When aligned to genome, transcript annotation downloaded from SGD database (version 64-1-1) (Xu et al., 2009) were first converted into bed file and then used as input for parameter utrbed. At least 2 conversions cooccur in one reads is regarded as a confident call for nascent RNA. SNP masking was employed to uncouple Single Nucletide Polymorphism from converted nucleotides.
Assembly: V64-1-1
Supplementary files format and content: bigwig for ChIP-seq, txt files of normalised RNASEQdata and slamseq data


title: 8-F4: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: NEUROD1_ChIP_Foxg1KD_n1


title: 3586 rep2, scRNAseq

description: 10x Genomics


title: FOXG1_invivo_input

data_processing:
All sequencing data were processed with snakePipes (v. 1.1.1).
Fastq Quality Control using FastQC.
 high quality and uniquely mapping reads were retained (mapq > 5). RELACS custom barcodes were designed with integrated UMI, so duplicate removal was performed using UMITools.
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Genome_build: mm10
Supplementary_files_format_and_content: bw and narrow peak

growth_protocol: Mice were sacrificed, and CA and DG regions of the hippocampus were dissected separately and snap frozen in liquid nitrogen. An aliquot of chromatin (12 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against FOXG1 (Active Motif, cat# 61211, lot# 34711001). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (QPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad). The resulting signals were normalized for primer efficiency by carrying out QPCR for each primer pair using Input DNA.

extract_protocol:
Frozen tissue was sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.
ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads.

tag: region

value: Pooled


title: ChIPseq_H3K4me3_WT_t1_rep1

tag: genotype


title: FOXG1_ChIP_CA_n2

value: CA

value: FOXG1 (Activ Motif)


title: ChIPseq_H3K4me2_rrp6_t2_rep3


title: 6-F3: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: 3586 rep1, scRNAseq

description: 10x Genomics

value: control

value: M


title: FOXG1_ChIP_CA_n1

value: hippocampus

value: WT


title: 1224 rep2, scRNAseq

description: 10x Genomics

value: DLPFC


title: FOXG1_ChIP_DG

value: DG


title: 1224, rep1, scRNAseq

description: 10x Genomics

value: F


title: 4-F2: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: FOXG1_ChIP_Neurod1KD_n1


title: 3-C2: control 10h one-cell embryo

description: control 10h one-cell embryo


title: ChIPseq_H3K4me2_rrp6_t2_rep1

value: time 0 of SECOND Galactose treatment


title: 4627 rep2, scRNAseq

description: 10x Genomics


title: Input_N2

data_processing:
All sequencing data were processed with snakePipes (v. 1.1.1).
Fastq Quality Control using FastQC.
 high quality and uniquely mapping reads were retained (mapq > 5).
Adapter trimming and quality filtering was done using Cutadapt 2.1 with Python 3.6.7 with the following configurations: -j 8 -e 0.1 -q 16 -O 3 --trim-n --minimum-length 25 -a AGATCGGAAGAGC
Trimmed and quality filtered reads were aligned to mm10 genome assembly using STAR_2.6.1d with the following configurations: STAR --runThreadN 20 --sjdbOverhang 100 --readFilesCommand zcat --outSAMunmapped Within --outSAMtype BAM Unsorted --outStd BAM_Unsorted --sjdbGTFfile
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files.
Input-normalised bigwig files from treated and control samples were compared and normalised to log2ratio using bigwigCompare Galaxy Version 3.3.2.0.0. Parameters:
Genome_build: mm10
Supplementary_files_format_and_content: bw and narrowpeak

treatment_protocol: On DIV4,  cytosine arabinoside (Ara-C, final: 2mM) was added to stop the proliferation of non-neuronal cells.. Half-volume medium changes were continued every 48 hours until DIV11.


title: ChIPseq_H3K4me2_rrp6_t1_rep3

value: rrp6delta parental strain background:BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)

value: time 0 of FIRST Galactose treatment


title: 4627 rep1, scRNAseq

description: 10x Genomics

value: AD


title: 1-C1: control 10h one-cell embryo

description: control 10h one-cell embryo

value: one-cell embryo


title: 4481 rep1, scRNAseq

description: 10x Genomics


title: ChIPseq_H3K4me2_rrp6_t1_rep2


title: 2-F1: 10058-F4 treated 10h one-cell embryo

description: 10058-F4 treated 10h one-cell embryo


title: Input_N1


title: 7-C4: control 10h one-cell embryo

description: control 10h one-cell embryo

value: Control


title: FOXG1_WT_N2


title: ChIPseq_H3K4me2_rrp6_t1_rep1


title: ChIPseq_H3K4me2_rrp6_t2_rep2


title: FOXG1_WT_N1


title: 1238 rep1, scRNAseq

description: 10x Genomics


title: 4305, scRNAseq

description: 10x Genomics


title: ChIPseq_H3K4me2_WT_t2_rep2

value: BY4741 (MAT a his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ChIPseq_H3K4me2_WT_t2_rep1


title: Sorted beta cells from db/+ lean control mouse #3

city: NEW YORK

first: Jinsook

last: Son

state: NY

address: 1150 st Nicholas ave, Russ Berrie Pavilion, Ste. 238

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Assembly: Mouse: GRCm38
Supplementary files format and content: Tab-delimited text file

source_name: Pancreatic beta cells

extract_protocol:
RNA extraction using Qiagen RNeasy Plus Micro Kit
Illumina TruSeq chemistry

value: Pancreatic beta cells

value: db/+


title: Sorted beta cells from db/+ lean control mouse #2


title: 4443, scRNAseq

description: 10x Genomics


title: Sorted beta cells from db/db control mouse #2

value: db/db


title: ChIPseq_H3K4me2_WT_t1_rep3


title: ChIPseq_H3K4me2_WT_t1_rep2


title: maize_leaf, SA, 48hpi, rep3

city: Cologne

first: Gunther

last: Doehlemann

address: Zuelpicher Str. 47a

institute: University of Cologne

description: 48hpi, SA treatment, rep3

data_processing:
Trimmomatic (0.39) was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
samtools (1.9) were used to dort the BAM files.
Htseq-count (2.0.1) was used to count the mapped reads.
edgeR (3.36.0) was used for the differential gene expression analysis.
Assembly: Zea mays reference genome Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: Gzipped text files containing transcript counts for each sample.

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: leaf

value: SA

tag: time point


title: Sorted beta cells from db/db control mouse #1


title: maize_leaf, SA, 48hpi, rep2

description: 48hpi, SA treatment, rep2


title: maize_leaf, SA, 48hpi, rep1

description: 48hpi, SA treatment, rep1


title: 4313, scRNAseq

description: 10x Genomics


title: 1238 rep2, scRNAseq

description: 10x Genomics

value: control

value: M


title: ChIPseq_H3K4me2_WT_t1_rep1

extract_protocol:
RNA was extracted with MasterPure RNA extraction kit from Lucigene  The DNA was purified with phenol, precipitated with ethanol and sodium acetate at -20 °C, washed with cold 70% ethanol, and resuspended in 30 µl TE buffer.
RNA-Seq: First rRNA was depleted  from total RNA with Illumina ribozero Gold kit. Then stranded RNA library was generated with NEBnext Ultra Directional RNA Library Prep kit for illumina.  MNase and ChIPSeq-Seq:  100 ml culture per S. cerevisiae sample and 30 ml of S. pombe culture was crosslinked using 1% formaldehyde for 15 minutes at room temperature. Formaldehyde was quenched by 0.125 M glycine for 5 minutes. Then cells were washed three times with cold TBS, flash-frozen in liquid nitrogen and stored at -80 °C.  Frozen cell pellets were resuspended in zymolyase solution (1 M sorbitol, 50 mM Tris-HCl pH 7.5, 1% beta-mercaptoethanol, 0.1 U/µl zymolyase). The zymolyase digestion proceeded at +37 °C for 30 min (S. cerevisiae) or 90 min (S. pombe). Spheroplasts were isolated by centrifugation at 6000xg for 10 minutes at +4 °C. Spheroplasts were resuspended in NP buffer (10 mM Tris-HCl pH 7.5, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.075% NP-40 (Tergitol), 1% beta-mercaptoethanol, 0.5 mM spermidine, 1% yeast protease inhibitor cocktail). The suspensions were pre-warmed and then 0.5 U/µl of MNase for S. cerevisiae and 2 U/µl for S. pombe was added per sample. MNase digestion proceeded at 37 °C for 40 min (S. cerevisiae) or 30 min (S. pombe) and stopped by addition of EGTA. The supernatants containing chromatin fragments were collected and  diluted with 1 ml RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate) with 1% yeast protease inhibitor cocktail. Equal volumes of S. pombe chromatin were spiked in to S. cerevisiae chromatin samples at this point, corresponding to around 3% of S. cerevisiae DNA.  Each sample was immunoprecipitated with anti-H3K4me3 (Abcam ab8580) and anti-H3K4me2 (Abcam ab7766) antibodies. Protein A/G beads (Pierce) were coupled to antibodies and resuspended in diluted chromatin and rotated o/n at 4 °C.  The next day, beads were washed with RIPA buffer, RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% v/v NP-40, 0.5% w/v sodium deoxycholate), and TE buffer (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8). Volume of each wash was 150 µl. Chromatin was eluted from beads in 2x10 µl ChIP elution buffer (Tris-HCl pH 8 50 mM, 1% SDS, 10 mM EDTA pH 8). The immunoprecipitated chromatin as well as a 20 µl sample of input chromatin were decrosslinked by TE, RNase cocktail, Proteinase K and 6 µl SDS (10% w/v), incubating overnight at 65 °C. DNA was purified by ethanol precipitation. Illumina sequencing libraries were prepared from the DNA using the NEBNext Ultra II kit without dual size selection and using 1.4X volume of AMPure XP beads for the purification steps. The libraries were sequenced on Illumina’s NextSeq 500, paired-end, 39 bases from each end     SLAMSeq: Metabolic labeling of newly synthesized RNA molecules was done as previously described (Voichek et al., 2016). Briefly, 4-thiouracil (4tU) (Sigma) was dissolved in NaOH(83mM), Newly synthesized RNA was labeled for indicated  time  spans  (10  min)  at  a  final  concentration  of  5mM  4-thiouridine  (4sU,  Carbosynth). MES buffer with a final concentration 10mM PH 5.9 was added to media to avoid pH change as a result of NaOH addition. At each time points before harvesting, 4tU was added to media for ten minutes ahead of desired time point.  cells were snap frozen in liquid nitrogen immediately at the time point required and RNA purification was done with MasterPure Yeast RNA Purification Kit. Total RNA was subjected to thiol(SH)-linked alkylation by iodoacetamide (Sigma, 10 mM) at 50C for 15 minutes (Herzog et al., 2017), the reaction was stopped by 20 mM DTT and RNA  was  re-purified by ethanol precipitation. After rRNA depletion with RiboPool Depletion Kit, library was prepared by Ultra™ II Directional RNA Library Prep Kit for Illumina® and sequenced single end with read length 150bp on Nextseq 500 Illumina sequencer.


title: NL05_21 [Pool #4]

city: Stanford

first: Myung Chang

last: Lee

address: 265 Campus Drive, G2065

department: Pediatrics and Genetics

institute: Stanford University

description: Pool #4

data_processing:
Library strategy: Tuba-seq
Illumina RTA software was used for basecalling, fastq files were generated by bcl2fastq software
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
We kept only the sgID-BC reads with perfect match between forward and reverese sequences, and we calculated the overall counts of sgID-BC to determine enrichment or depletion in the tumor samples.
Tumor size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmark cell lines (1 * 10^5 cells for each) added to each sample.
Assembly: sgID-BC reference (8N followed by GCNNNNNTANNNNNGCNNNNNTANNNNNGC)

source_name: Transformed lung epithelial cell

extract_protocol:
Genomic DNA isolation from tumor-bearing mouse lung was performed via phenol:chloroform isolation and ethanol precipitation. Three benchmark control cell lines (1 * 10^5 cells per control) were added to correlate sgID-BC reads with cell number. Q5 High-Fidelity 2X Master Mix (New England Biolabs M0494X) was used to amplify the sgID-BC region using unique dual-indexed primers.
For sgID-BC amplicon libraries, we performed PCR with dual-indexed primers and purified the amplicon using MinElute kit as well as two-sided bead purification with Sera-Mag Select beads or Ampure XP beads.

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: Sorted beta cells from Aldh1a3 KO_db/db mouse #2

value: CKO


title: maize_leaf, SA, 12hpi, rep2

description: 12hpi, SA treatment, rep2


title: 4482, scRNAseq

description: 10x Genomics


title: NL05_18 [Pool #4]

description: Pool #4


title: NL05_20 [Pool #4]

description: Pool #4


title: maize_leaf, SA, 12hpi, rep3

description: 12hpi, SA treatment, rep3


title: NT1271, scRNAseq

description: 10x Genomics

value: DLPFC

value: F


title: 1230, scRNAseq

description: 10x Genomics


title: NL05_10 [Pool #4]

description: Pool #4


title: ChIPseq_H3K4me2_WT_t2_rep3

value: time 0 of SECOND Galactose treatment


title: NT1261, scRNAseq

description: 10x Genomics


title: maize_leaf, FB1, 48hpi, rep2

description: 48hpi, FB1 treatment, rep2


title: Sorted beta cells from Aldh1a3 KO_db/db mouse #1


title: NL05_12 [Pool #4]

description: Pool #4


title: maize_leaf, SA, 12hpi, rep1

description: 12hpi, SA treatment, rep1


title: maize_leaf, FB1, 48hpi, rep1

description: 48hpi, FB1 treatment, rep1


title: NL05_9 [Pool #4]

description: Pool #4


title: 1242 MEF2C Input

data_processing:
Each sample has a fastq for sonicated input control. Remove optical duplicates with clumpify and remove adapter reads with Cutadapt (v1.16)
Experiments were analyzed with ENCODE chip-seq-pipeline2. Pipeline was run with default settings
Peaks were called using IDR overlapping method with a threshold of 0.05
Processed files are pooled from both tissue samples
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Post-mortem brain tissue was homogenized and fixed for 10 minutes at room temperature, followed by 5 minutes of quenching with Glycine. Fixed nuclei were isolated by ultracentrifuging 24,000 RPM for 2 hours  at 4C. If sorted, nuclei were stained for NeuN/OLIG overnight and sorted the next day. Sorted nuclei were pelleted and resuspended in RIPA for 8 rounds of sonication using the Diagenode Bioruptor Pico.
Libraries were prepared by blunting and ligating ChIP DNA fragments to sequencing adapters for amplification with barcoded primers (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 15 cycles; 5 min at 72°C). Libraries were quantified with Qubit dsDNA HS Assay kit and visualized with Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical DNF-473) and Fragment Analyzer 5200 (Agilent).

value: Bulk

tag: chip antibody

value: none (input)


title: maize_leaf, DMSO, 48hpi, rep3

description: 48hpi, control of FB1/SA, rep3

value: DMSO (control)


title: 1242 MEF2C ChIPseq

tag: disease state

value: anti-MEF2C (proteintech 18290-1-AP)


title: NL05_8 [Pool #4]

description: Pool #4


title: maize_leaf, FB1, 48hpi, rep3

description: 48hpi, FB1 treatment, rep3


title: NL05_7 [Pool #4]

description: Pool #4


title: maize_leaf, DMSO, 48hpi, rep2

description: 48hpi, control of FB1/SA, rep2


title: 1238 MEF2C Input

tag: Sex


title: Sorted beta cells from db/+ lean control mouse #1

tag: tissue

value: Pancreatic beta cells


title: maize_leaf, DMSO, 48hpi, rep1

description: 48hpi, control of FB1/SA, rep1


title: 1238 MEF2C ChIPseq

tag: cell type


title: 3329, scRNAseq

description: 10x Genomics

value: AD

tag: age


title: NL05_5 [Pool #4]

description: Pool #4


title: NL05_6 [Pool #4]

description: Pool #4


title: maize_leaf, FB1, 24hpi, rep3

description: 24hpi, FB1 treatment, rep3


title: 1241 ZEB2 Input

value: NeuN


title: NL05_3 [Pool #4]

description: Pool #4


title: maize_leaf, FB1, 24hpi, rep2

description: 24hpi, FB1 treatment, rep2

value: leaf


title: 1241 ZEB2 ChIPseq

value: anti-ZEB1 (Bethyl A301-921A)


title: maize_leaf, FB1, 24hpi, rep1

description: 24hpi, FB1 treatment, rep1


title: NL05_2 [Pool #4]

description: Pool #4


title: maize_leaf, SA, 24hpi, rep3

description: 24hpi, SA treatment, rep3

value: SA


title: maize_leaf, SA, 24hpi, rep2

description: 24hpi, SA treatment, rep2


title: 1238 ZEB1 Input

value: control

value: M


title: 48_5P

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
FASTQs were generated using cellranger (v6.0.0) mkfastq with default parameters.
Raw counts were generated by aligning FASTQs to a combined custom reference using cellranger (v6.0.0) count with default parameters.
Assembly: made using cellranger mkref with default parameters using GRCh38
Supplementary files format and content: Raw counts are provided in sparse matrices and were generated by aligning FASTQs using cellranger (v6.0.0) count with default parameters.

source_name: seizure-affected brain tissue

extract_protocol:
Surgically resected brain tissue was dissociated in a glass dounce homogenizer and then nuclei were washed and stained with Hoechst dye, as previously described [Koboldt et al., 2021]. Approximately 10,000 Hoechst-positive nuclei per sample were sorted on a BD Influx cell sorter directly into master mix from the 10x Genomics Next GEM Single-Cell 3’ or 5’ reagent kits.
10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol.
paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 91 (R2) (3'v3.1) or paired-end sequencing using the following read configuration: 28 (R1), 8 (i7), 0 (i5), 90 (R2) (5'v2)

value: seizure-affected brain tissue

tag: diagnosis

value: Focal cortical dysplasia type IC


title: NL03_13 [Pool #3]

description: Pool #3

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre


title: 49_5P

value: Focal cortical dysplasia type IIID


title: maize_leaf, SA, 24hpi, rep1

description: 24hpi, SA treatment, rep1


title: NL05_1 [Pool #4]

description: Pool #4


title: 48_3P


title: maize_leaf, DMSO, 24hpi, rep2

description: 24hpi, control of FB1/SA, rep2


title: 1238 ZEB1 ChIPseq

value: DLPFC


title: maize_leaf, DMSO, 24hpi, rep3

description: 24hpi, control of FB1/SA, rep3


title: maize_leaf, DMSO, 24hpi, rep1

description: 24hpi, control of FB1/SA, rep1


title: NL03_12 [Pool #3]

description: Pool #3


title: NL03_9 [Pool #3]

description: Pool #3


title: 49_3P


title: NL05_4 [Pool #4]

description: Pool #4


title: NL03_8 [Pool #3]

description: Pool #3


title: maize_leaf, FB1, 12hpi, rep2

description: 12hpi, FB1 treatment, rep2


title: maize_leaf, FB1, 12hpi, rep3

description: 12hpi, FB1 treatment, rep3


title: NL03_7 [Pool #3]

description: Pool #3


title: 47_3P

value: Focal cortical dysplasia type IIA


title: maize_leaf, FB1, 12hpi, rep1

description: 12hpi, FB1 treatment, rep1


title: NL03_6 [Pool #3]

description: Pool #3


title: H2CKO

city: Indianapolis

first: Anthony

last: Firulli

email: tfirulli@iupui.edu, tfirulli@iu.edu

state: IN

address: 1044 W Walnut R4302E

department: pediatrics

institute: IU school of medicine

description: 10x Genomics

data_processing:
Sequenced reads were aligned to a mouse transcriptome reference built from GRCm38.p6 (Genome Reference Consortium Mouse Build 38 patch release 6) combined with eGFP and dTomato gene sequences using the software 10x Genomics Cell Ranger 5.0.1 (Zheng, Terry et al. 2017).
Reads from the cells associated with a total more than 1000 UMIs from Hemoglobin related genes (Hbb-bt, Hbb-bs, Hbb-bh2, Hbb-bh1, Hbb-y, Hba-x, Hba-a1, Hbq1b, Hba-a2 and Hbq1a) were excluded from further analysis.
The downstream data exploration and differential gene expression analysis was conducted using the R package, Seurat V4 (Hao, Hao et al. 2021).
As per the standard pre-processing workflow for scRNA-seq data in Seurat, cells with more than 2500 unique features were filtered out. The feature expression values for each cell were normalized using the standard “LogNormalize” method with default parameter values. The Seurat objects derived from WT and MT data were integrated using the anchors found using Canonical Correlation Analysis (CCA) with the neighbor search space specified using 1 to 20 dimensions (FindIntegrationAnchors(reduction=”cca”, dims = 1:20)). The integrated dataset was subjected to linear transformation followed by linear dimensionality reduction using Principal Component Analysis (PCA).
Clusters were identified from the Shared Nearest Neighbor graph (FindNeighbors(reduction = "pca", dims = 1:20)) with the resolution set to 0.5 (FindClusters(resolution = 0.5)) and were visualized using the Uniform Manifold Approximation and Projection (UMAP) non-linear dimensional reduction technique.
Assembly: GRCm38.p6 (Genome Reference Consortium Mouse Build 38 patch release 6) combined with eGFP and dTomato gene sequences
Supplementary files format and content: *.UMI_matrix.csv files are the UMI count matrices in comma separated file format. These are created by exporting the cellranger output from Market Exchange Format (MEX) using cellranger mat2csv command (ver 5.0.1)
Supplementary files format and content: *.umap_rna.csv files are the cell-level annotations provided in the form of UMAP coordinates in comma separated file format as generated using the Seurat package (ver V4)

source_name: Embryonic heart at E11.5

extract_protocol:
E11.5 embryos were dissected in cold PBS and placed in PBS with 1% FBS solution on ice until dissociation (approximately 3 hours). Yolk-sac DNA was extracted (QuickExtract DNA Extraction Solution, Epicentre) and used for genotyping to distinguish heterozygous and homozygous Hand2 conditional allele. The RosamTmG allele fluorescence was used to determine Nfatc1cre status. Dissected cardiac tissue was incubated in 750 μl TrypLE (ThermoFisher) for 5 min at 370C, triturated with a 200-μl wide-bore pipette tip. The cell suspension was quenched with 750 μl DMEM with 10% FBS. Cells were filtered through a 30-μm cell strainer (MACS SmartStrainer), centrifuged at 300g for 5 min, and washed once with 750 μl PBS with 0.5% BSA. Cells were resuspended in 30 μl PBS with 0.5% BSA (10x Genomics).
Single-cell droplet libraries were generated using the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide, CG000204 Rev D (10X Genomics, Inc). according to the manufacturer’s instructions. Briefly, each clean single cell suspension was counted with hemocytometer under microscope for cell number and cell viability. Only single cell suspensions with a viability of >90% and minimal cell debris and aggregation were used for further processing. The resulting library was sequenced in a custom program for 28b plus 91b paired-end sequencing on Illumina NovaSeq 6000. About 50K reads per cell were generated and 91% of the sequencing reads reached Q30 (99.9% base call accuracy). A Phred quality score (Q score) was used to measure the quality of sequencing.

value: Embryonic heart at E11.5


title: NL03_11 [Pool #3]

description: Pool #3


title: maize_leaf, DMSO, 12hpi, rep3

description: 12hpi, control of FB1/SA, rep3

value: DMSO (control)


title: P26

city: San Diego

first: Diane

middle: M

last: Simeone

address: 3855 Health Sciences Drive

institute: UCSD Health

description: 10x Genomics

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software, version 5.0.1.
Assembly: hg38/GRCh38
Supplementary files format and content: raw barcodes
Supplementary files format and content: raw genes
Supplementary files format and content: raw gene-barcode matrix

source_name: Primary PDAC

extract_protocol:
Within 4-6 h of tissue acquisition, the specimen was placed in ice-cold RPMI 1640 medium (Gibco, Cat. No. 11875101). Tissue samples were washed in ice-cold phosphate-buffered saline (PBS; Corning, Cat. No. 21- 040-CM) and grossly assessed for adequacy (solid tissue component, free of large hemorrhagic or necrotic areas). Next, the tissue was manually minced with a scalpel blade and filtered through a 40 μm mesh filter (Falcon; Cat. No. 352340) to remove any excess debris or blood. The tissue was then transferred to a sterile gentleMACS C tube (Miltenyi Biotec, Cat. No. 130096334), resuspended in 3-5 mL of Miltenyi Tumor Dissociation Kit buffer (Cat. No. 130-095-929), and mechanically minced to submillimeter particles. The suspension was then digested utilizing the gentleMACS Octo Dissociator (Miltenyi Biotec, Cat. No. 130-095-937) for 25-30 min using the “37C_h_TDK_3'' program for tumor tissue. Dissociated cells were then quenched with ice-cold RPMI 1640 containing 10% fetal bovine serum (FBS; Gibco, Cat. No. 10082147) and filtered through a 40 μm mesh filter. Red blood cells were removed by treatment with 3-5 mL of ACK lysis buffer (Gibco, Cat. No. A1049201) and a subsequent washing step in RPMI 1640 with 10% FBS. Final cell counts were established with 0.4% trypan blue solution and a Countess II Automated Cell Counter (Applied Biosystems, Cat. No. A27977). The final concentration was titrated to 300-500 viable cells/μL for further analysis.
Chromium Single Cell 3′ Reagent Kits (v3)—the Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), the Chromium Next GEM Chip G Single Cell Kit (PN-100120), and the i7 Multiplex Kit (PN-120262) (10x Genomics)

value: Primary PDAC

value: Untreated

tag: procedure

value: EUS-Biopsy

tag: Stage

value: Metastatic


title: P25

description: 10x Genomics

source_name: PDAC liver met

value: PDAC liver met

tag: treatment

value: Liver-Biopsy


title: NL03_4 [Pool #3]

description: Pool #3


title: maize_leaf, DMSO, 12hpi, rep1

description: 12hpi, control of FB1/SA, rep1

value: leaf


title: P24

description: 10x Genomics


title: P23

description: 10x Genomics

value: Resection

value: Resectable


title: Control

description: 10x Genomics


title: BMDMs, SREBP1 ko, LPS, 4h, biol, rep3

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Aligned read files were analyzed using HOMER. Batch effects were removed using ComBat-seq. Differentially expressed genes were analyzed using DESeq2.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Srebf1-/- BMDMs treated with LPS for 4 h

extract_protocol:
Total RNA was isolated and purified using Rneasy columns and Rnase-free Dnase digestion according to the manufacturer’s instructions (QIAGEN).
Poly-A mRNA was extracted from total RNA using Oligo-dT beads in a NEBNext Poly (A) RNA Magnetic Isolation Module (New England Biolabs), after which RNA-seq libraries are prepared using a RNA-Seq library preparation kit for Illumina (New England Biolabs) according to the manufacturer’s protocols.

value: Bone marrow-derived macrophage

value: LPS


title: BMDMs, SREBP1 ko, LPS, 4h, biol, rep2


title: 47_5P

value: seizure-affected brain tissue


title: NL03_10 [Pool #3]

description: Pool #3

value: Lung

value: Naphthalene (200 mg/kg) i.p. two days prior to intratracheal transduction with HIV-sgTSG_Pool/PGK-Cre