title: CTRL_4

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
FASTQ files were assessed using fastQC version 0.11.8. We used Salmon version 1.0.0 to quantify the abundance at the transcript level with the fragment-level GC bias correction option (gcBias flag) and the appropriate option for the library type (l flag set to A) against the GENCODE release 32 of the human transcriptome (GRCh38.p13). Transcript-level quantification was imported into R and collapsed onto gene-level quantification using the tximport R package version 1.8.0 according to the gene definitions provided by the same GENCODE release. We filtered out genes in non-canonical chromosomes and scaffolds. Transcripts encoded by the mitochondrial genome, except for the protein-coding mitochondrial genes, were also removed. Genes were filtered out if their level of expression was below 10 reads in more than 75% of the samples. Transcript counts were aggregated into gene counts. Sample correlations were calculated with the information of DV200, library size, cell type and mutation, and sample outliers were excluded. Differential expression analysis was conducted using DEseq2. Multiple comparisons were adjusted by using the false discovery rate method. Adjusted P value (q value) <0.05 was considered statistically significant. KEGG pathway and KEGG module enrichment analysis were conducted using Clusterprofiler.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: Brain organoid

growth_protocol: IPSCs were dissociated and The single cells were cultured in suspension to form embryoid body (EB). After 10 days, the organoids were transferred into a 6-well ultra-low attachment tissue culture plates in neural differentiation media  minus vitamin A for next 8 days using an orbital shaker to induce cerebral organoids. On day 18, the organoids were subsequently matured in neural differentiation media with vitamin A  with media changes every 3-4 days.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Kit (QIAGEN, 74104) following manufacturer’s instructions. Samples were sent to BGI, Wu Han, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample
Library preparation (BGISEQ-500RS High-throughput sequencing kit, PE50, V3.0, MGI Tech Co, Ltd, Shenzhen, China), hybridization and sequencing were performed according to the manufacturer's standard procedure provided by BGI (BGI-Shenzhen).

value: IPSC derived brain organoid

value: wild type

value: No treatment


title: high target, g11, rep 2 [XP005]

status: Public on Feb 24 2023

type: SRA

city: New York

first: Xuebing

last: Wu

state: NY

address: 630 West 168th Street

department: Medicine/Systems Biology

country: USA

institute: Columbia University

library_source: transcriptomic

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 (Human: GRCh38) using kallisto (0.44.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: kallisto counts and tpm file (txt)

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK293T_high target_g11

growth_protocol: HEK293T cells were cultured with DMEM and 10% FBS

extract_protocol:
Total RNA were extracted using Trizol
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry. Libraries are then sequenced using Illumina NovaSeq 6000. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: Transfection in HEK293T cells was with Lipofectamine 3000 following the manufacture’s protocol. All samples were transfected with RfxCas13d (CasRx with NLS), target reporter (DsRed), control reporter (BFP), and gRNA (g3: targeting, g11: control). Unless noted, all samples were mixed with 10% mouse MEF cells prior to total RNA extraction

tag: cell line

tag: sample group

value: high target_g11


title: TFAP2A_KO_rep2

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

library_source: genomic

data_processing:
HiC-pro pipeline is used to align and generate contact matrix
FitHiChIP is used to call loops and differential loops
HiC file is generate using juicer_tools pre command
Assembly: hg38
Supplementary files format and content: hic file
Library strategy: HiChIP

molecule: genomic DNA

source_name: H9 day7

growth_protocol: Human embryonic stem cells (H9, female) were maintained in E8 medium (Life Technologies) on Matrigel (Stem Cell Technologies) coated plates, dissociated using 0.5mM EDTA, and passaged at 1:10 ratio.

extract_protocol:
Cells were removed from the plate and singularized with Accutase.
Cohesin HiChIP library prep was performed as previously described (Mumbach et al., 2016). Briefly, 25x106 cells were crosslinked and digested with MboI (NEB). After digest, biotin was incorporated into the sticky ends of fragments before ligation. Cohesin ChIP was performed to enrich for proximity ligations bound to cohesin, using an SMC1 antibody (Bethyl, A300-055A). The paired-end library quality was assessed on a MiSeq sequencer before sequencing on an Illumina HiSeq 4000. Three replicates were pooled and sequenced across two HiSeq lanes for a total of 1200 million reads per sample.

treatment_protocol: For differentiations, the media was changed to Essential 6 (Life Technologies) supplemented with 1μM retinoic acid (Sigma) and 5ng/mL Recombinant Human BMP4 (R&D Systems) and replaced every two days for seven days. On day 7, cells were collected for downstream analysis.

tag: genotype

value: AP2a KO

tag: age

tag: chip antibody

value: Cohesin


title: CTRL_3

molecule: total RNA

tag: cell type

tag: treatment


title: TFAP2A_KO_rep1


title: CTRL_2


title: CTRL_1


title: high target, g11, rep 1 [XP004]


title: high target, g3, rep 3 [XP003]

source_name: HEK293T_high target_g3

value: high target_g3


title: Serum-Healthy Individual-Control6-Rep1

type: RNA

city: Istanbul

first: Tuba

last: Gunel

state: Fatih

address: Balabanaga mahallesi sehzadebasi cad.

country: Turkey

institute: Istanbul University

description:
MiRNA expressions in healthy individual serum samples of control 6
Serum sample, Healthy Individual, Control6, Replicate 1

hyb_protocol: The labelled miRNAs were hybridized for 24 h on “Human miRNA Microarray Version 16” (Agilent Technologies, Santa Clara, CA, USA) slides. Labelled miRNAs were blocked by “10X GE Blocking agent” and were washed using Gene Expression Wash Buffer 1 and 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (Model G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing: The images provided after scanning were analyzed by “Agilent Feature Extraction (v.11.0.1.1)” software using default parameters (protocol miRNA_1100_Jul11 and Grid: 070156_D_F_20141006).

label_protocol: For labelling, miRNA Labelling and Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA) was used according to the manufacturer's instructions. Total RNAs extracted from both serum and tissue were labelled by cyanine 3-cytidine bisphosphate (pCp-Cy3).

growth_protocol: About 500 mg of tissue samples were taken in sterile centrifuge tubes containing RNAlater Solution (Ambion, Life Technology, USA) stabilization and storage solution, stored at +4°C overnight and then stored at -80°C until studied. Peripheral blood was collected into EDTA tubes (5 ml).

extract_protocol: Total RNA was isolated with “QIAGEN RNeasy Plus Mini Kit” (QIAGEN, Germany) from tissue samples. The quantity of obtained total RNA was measured by NanoDrop IMPLEN P-Class (Thermo Fisher Scientific, Waltham, MA, USA), and the quality controls of them were done by Agilent RNA 6000 Nano Kit on Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). After RNA extracts were evaluated with bioanalyzer, 8 samples with the highest quality (RNA Integrity Number (RIN) value >5) according to RIN were selected for microarray study. To extract total RNA including miRNA from serum (500ul input), “mirVana™ PARIS™ RNA and Native Protein Purification Kit” (Ambion, Life Technology, USA) was used following the manufacturer’s protocol. The purity and concentration of RNA samples of serum were determined by NanoDrop IMPLEN P-Class (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: Tissues are digested with liquid nitrogen before isolation of total RNA from tissue samples. Crushed samples (30-60 mg is preferred) are placed in 2 ml microcentrifuge tubes. Blood samples were immediately centrifuged at 3500xg for 15 min at 4°C. The supernatant serum was transferred to RNase-free tubes after centrifugation. Sample serum fractions were collected and stored at -80°C until laboratory workup.

tag: tissue

value: Serum


title: Alpers_3 derived NSC

data_processing:
FASTQ files were trimmed using Trimmomatic version 0.39 to remove potential Illumina adapters and low-quality bases with the following parameters: ILLUMINACLIP: truseq. fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW: 4:15. FASTQ files were assessed using fastQC version 0.11.8 prior and following trimming. We used Salmon version 1.0.0 to quantify the abundance at the transcript level with the fragment-level GC bias correction option (gcBias flag) and the appropriate option for the library type (l flag set to A) against the GENCODE release 32 of the human transcriptome (GRCh38.p13). Transcript-level quantification was imported into R and collapsed onto gene-level quantification using the tximport R package version 1.8.0 according to the gene definitions provided by the same GENCODE release. We filtered out genes in non-canonical chromosomes and scaffolds. Transcripts encoded by the mitochondrial genome, except for the protein-coding mitochondrial genes, were also removed. Genes were filtered out if their level of expression was below 10 reads in more than 75% of the samples. Transcript counts were aggregated into gene counts. Sample correlations were calculated with the information of DV200, library size, cell type and mutation, and sample outliers were excluded. Differential expression analysis was conducted using DEseq2. Multiple comparisons were adjusted by using the false discovery rate method. Adjusted P value (q value) <0.05 was considered statistically significant. KEGG pathway and KEGG module enrichment analysis were conducted using Clusterprofiler.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: NSC

growth_protocol: iPSCs were grown under feeder-free condition using E8 medium (Invitrogen, cat. no. A1517001) on 6 well Geltrex-coated plates. NSCS were cultured using StemPro™ NSC medium plus bFGF, EGF (Thermo Fisher, cat. no. A1050901) and 1X GlutaMAX™.

extract_protocol:
Total RNA was isolated from NSCs and iPSCs using RNeasy Mini Kit (QIAGEN).  RNA quality and concentration were checked using Bioanalyzer and QubitTM.  RNA sequencing libraries were established by the PolyA enrichment method. For iPSCs and NSCs, RNA sequencing was performed by HudsonAlpha.
Library preparation was conducted by HudsonAlpha, following the guide of the standard protocol.

value: IPSC derived NSC

value: mutation


title: Alpers_2 derived NSC


title: Serum-Healthy Individual-Control5-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 5
Serum sample, Healthy Individual, Control5, Replicate 1


title: Serum-Healthy Individual-Control8-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 8
Serum sample, Healthy Individual, Control8, Replicate 1


title: Alpers_1 derived NSC


title: high target, g3, rep 2 [XP002]


title: Alpers2_3NR

value: NR treated


title: high target, g3, rep 1 [XP001]


title: Alpers2_2NR


title: Alpers_3

source_name: IPSC

value: IPSC


title: Serum-Healthy Individual-Control4-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 4
Serum sample, Healthy Individual, Control4, Replicate 1


title: Serum-Healthy Individual-Control7-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 7
Serum sample, Healthy Individual, Control7, Replicate 1


title: Alpers_2


title: Alpers2_1NR


title: Serum-Healthy Individual-Control3-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 3
Serum sample, Healthy Individual, Control3, Replicate 1


title: Alpers2_3


title: Serum-Healthy Individual-Control2-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 2
Serum sample, Healthy Individual, Control2, Replicate 1


title: Serum-Healthy Individual-Control1-Rep1

description:
MiRNA expressions in healthy individual serum samples of control 1
Serum sample, Healthy Individual, Control1, Replicate 1


title: Alpers_1


title: CTRL3_3 derived NSC


title: Alpers2_2


title: Alpers2_1


title: CTRL3_2 derived NSC


title: Alpers1_3NR


title: CTRL3_1 derived NSC


title: Microbiota of skin from subject C1

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human skin microbiome

data_processing:
library strategy:
demultiplexing: 16S amplicon DNA-seq
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming:
qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check:
qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
ASV generation:
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 223 --p-trunc-len-r 219 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
taxonomic assignment:
qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs_V3V4.qza --i-reference-reads ~/Scrivania/Tools/Database/silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search.results vsearch_hits.qza --verbose 2> ASV_matched_in_SILVA.txt
further analyses:
R software (see the relative script publicly available at github.com/LeandroD94/Papers)
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

source_name: Skin

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Skin

tag: patient id

tag: age group

value: C

tag: facial skin_hydration_level

value: Dry


title: Alpers1_2NR


title: Microbiota of skin from subject B4

value: B


title: Microbiota of skin from subject A3

value: A

value: Not dry


title: Microbiota of skin from subject A1


title: Microbiota of skin from subject B1


title: Alpers1_1NR

value: IPSC derived brain organoid


title: Serum-Epithelial Ovarian Cancer-Sample6-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 6
Serum sample, Epithelial Ovarian Cancer, Sample6, Replicate 1


title: Serum-Epithelial Ovarian Cancer-Sample7-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 7
Serum sample, Epithelial Ovarian Cancer, Sample7, Replicate 1


title: Serum-Epithelial Ovarian Cancer-Sample5-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 5
Serum sample, Epithelial Ovarian Cancer, Sample5, Replicate 1


title: Microbiota of skin from subject B2


title: Microbiota of skin from subject A2


title: CTRL3_2

value: wild type


title: CTRL3_1


title: Serum-Epithelial Ovarian Cancer-Sample8-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 8
Serum sample, Epithelial Ovarian Cancer, Sample8, Replicate 1


title: Serum-Epithelial Ovarian Cancer-Sample3-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 3
Serum sample, Epithelial Ovarian Cancer, Sample3, Replicate 1


title: Mel167-R-H5

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

library_source: transcriptomic single cell

data_processing:
Illumina CASAVA version 1.8 were used to do the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases. For single cell RNA-seq, the cleaned reads were aligned to the human hg19 reference using Tophat (v2.0.12) with default settings and the --no-novel-juncs argument (Trapnell et al., 2009).
PCR duplicates were removed using samtools (v1.3.1)(Li et al., 2009), gene counts were computed using HTseq (v0.6.1) (Anders et al., 2015)
Assembly: hg19
Supplementary files format and content: counts.csv is a comma-separated-values file with rows corresponding to a gene, columns corresponding to a sample, and values giving the number of reads aligned to the gene.

extract_protocol:
Single cells were picked or sorted into lysate buffer and RNA was released.
single cell cDNA was amplified using SMART-seq2 protocol

value: circulating tumor cell (CTC)


title: Microbiota of skin from subject C4


title: Serum-Epithelial Ovarian Cancer-Sample4-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 4
Serum sample, Epithelial Ovarian Cancer, Sample4, Replicate 1


title: Alpers1_2

value: No treatment


title: CTRL2_3 derived NSC


title: CTRL3_3


title: Microbiota of skin from subject C5


title: Serum-Epithelial Ovarian Cancer-Sample2-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 2
Serum sample, Epithelial Ovarian Cancer, Sample2, Replicate 1


title: Serum-Epithelial Ovarian Cancer-Sample1-Rep1

description:
MiRNA expressions in epithelial ovarian cancer serum samples of sample 1
Serum sample, Epithelial Ovarian Cancer, Sample1, Replicate 1


title: Mel167-R-H4


title: Alpers1_1


title: CTRL2_2 derived NSC


title: CTRL2_1 derived NSC


title: Microbiota of skin from subject C2


title: Mel167-R-H3


title: Mel167-R-H2


title: Mel167-R-H1


title: Adam10 knockout replicate 2

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
Raw sequences were aligned to the murine reference cDNA (mm10) obtained from the Ensembl using kallisto (v0.48.0).
Transcript abundances were aggregated into gene level by the R package tximport (v1.22.0).
Genes with an average read count below 5 were removed. In addition, only protein-coding genes were included.
Assembly: GRCm39.v107
Supplementary files format and content: exp_counts.tsv
Supplementary files format and content: tab-delimited text files include read count values for each sample

organism: Mus musculus

source_name: Aorta

extract_protocol:
Total RNA was extracted from the samples using the Direct-zol RNA MiniPrep Plus Kit (Zymo Research), including an in-column DNase I treatment.
1) Oligo(dT) magnetic beads are used to select mRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target  RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adapt or with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

value: Aorta

value: KO

value: AAV8-PCSK9 + 10w WTD


title: CTRL2_2


title: Adam10 knockout replicate 3


title: CTRL2_3


title: Microbiota of skin from subject C3


title: Alpers1_3


title: Mel167-R-G5


title: Microbiota of skin from subject A5


title: Wildtype replicate 3

value: WT


title: CTRL2_1


title: Microbiota of skin from subject B3


title: Mel167-R-G4


title: Wildtype replicate 2


title: CTRL1_3 derived NSC

value: IPSC derived NSC


title: Mel167-R-G3


title: CTRL1_2 derived NSC


title: Microbiota of skin from subject B5


title: CTRL1_1 derived NSC


title: Mel167-R-G2


title: Microbiota of skin from subject A4


title: Mel167-R-G1


title: CTRL1_3


title: Liver, Fast-3, miRNA-seq

city: shanghai

first: NANA

last: JI

address: Dongan road 130

country: China

institute: Fudan university

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: mm10
Supplementary files format and content: Excel format representing TPM and count values of miRNAs

source_name: Liver

extract_protocol:
Total RNA was harvested using Trizol reagent and used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: 10-week-old male C57BL/6J mice were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). Mice were fed ad libitum or fasted for 24 hour. Then, mice were sacrificed and livers were harvested for RNA extraction.

value: Liver

tag: Sex

value: male

tag: strain

value: Wild-type

value: Fasted for 24 hour


title: Liver, Refed-2h-3, miRNA-seq

value: Refed 2h


title: Liver, Refed-2h-1, miRNA-seq


title: CTRL1_2

value: IPSC


title: Liver, Refed-2h-2, miRNA-seq


title: Liver, Fast-2, miRNA-seq


title: Mel167-R-F3


title: Mel167-R-F5


title: Mel167-R-F2


title: Klf4_flox_CD11c_Cre_R2__HTO

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: 10x Genomics

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v4.0.0) to perform quality control and sample de-multiplexing (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Single cell capture, cDNA and library preparations were performed with the Single Cell 3’ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions. GEX sequencing libraries were loaded on an Illumina NovaSeq with high output cycle kits and sequenced paired-end using the following read length: Read1-28 cycles / Read2-8 cycles / Read3-91 cycles. HTO libraries were prepared according to manufacturer instruction and loaded on an Illumina NextSeq 500 with high output cycle kits and sequenced paired-end using the following read length: Read1 28 cycles / Read2 8 cycles / Read3 56 cycles for HTO libraries. The first 15 bases of R3 represented HTO barcode sequence.
Samples were aligned to the UCSC mouse (mm10) genome using and expression of ensembl genes (v102) was quantified with "STARsolo" (version 2.7.9a) with recommended parameters (-- soloFeatures Gene GeneFull SJ Velocyto, --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB, --soloCBwhitelist 3M-february-2018.txt (provided by 10x), --soloCellFilter None) for all 6 samples. Additionally, the expression of Cre was quantified by including these sequences during mapping and quantification step.
Similarly, also hashtags-tags (HTO) were quantified with "STARsolo" after aligning the sample data only to HTO barcode sequences (with additional parameter: --clip3pNbases 41). The information obtained from HTO quantification was used only as additional annotation for cells (tissue of origin).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, RDS file with SingleCellExperiment
Supplementary files format and content: The raw_counts.mtx contains UMI counts (expression values), row names (ensembl gene ids) are stored in raw_genes.tsv and column names (cell barcodes) in raw_barcodes.tsv. The gene information is in raw_rowdata.tsv (rowData) and cell information in raw_coldata.tsv (colData). The raw_hto.mtx contains UMI counts for HTO, rownanes are stored in raw_hto.tsv.
Supplementary files format and content: The filtered dataset is stored in SingleCellExperiment.rds, with individual components: final_counts.mtx (UMI counts), final_logcounts.mtx (log2 UMI counts), column names in final_barcodes.tsv and row names in final_genes.tsv, gene annotation is stored in final_rowdata.tsv and cell information is in final_coldata.tsv.

source_name: spleen, skin draining lymph node (sLN), mesenteric lymp node (mLN)

extract_protocol:
Sort purified CD11c+ cells derived from C57BL/6 or Klf4fl/fl ItgaxCre+ spleens, sLNs and mLNs were multiplexed individually by labeling each sort purified cell suspension with a unique Hashtag (HTO) antibody. 10K sort purified CD11c+ cells from the spleen, sLN and mLN of either C57BL/6 or Klf4fl/fl ItgaxCre+ mice were mixed and loaded on a 10x Genomics Chromium Single Cell Controller.
Single cell capture, cDNA and library preparations were performed with the Single Cell 3’ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions. GEX sequencing libraries were loaded on an Illumina NovaSeq with high output cycle kits and sequenced paired-end using the following read length: Read1-28 cycles / Read2-8 cycles / Read3-91 cycles.
HTO libraries were prepared according to manufacturer instruction and loaded on an Illumina NextSeq 500 with high output cycle kits and sequenced paired-end using the following read length: Read1 28 cycles / Read2 8 cycles / Read3 56 cycles for HTO libraries. The first 15 bases of R3 represented HTO barcode sequence.

value: CD11c+ cells

value: Klf4 fl/fl CD11c Cre

value: 6-14 weeks old

tag: library type

value: HTO -- hash tags


title: Klf4_flox_CD11c_Cre_R3__HTO

description: 10x Genomics

value: spleen, skin draining lymph node (sLN), mesenteric lymp node (mLN)


title: Adam10 knockout replicate 1


title: Klf4_flox_CD11c_Cre_R1__HTO

description: 10x Genomics


title: ESC3_3 derived NSC

value: ESC derived NSC

value: wild type


title: Mel167-R-F1

value: circulating tumor cell (CTC)


title: Liver, Fed-3, miRNA-seq

value: Fed ad libitum


title: Klf4_flox_CD11c_Cre_R3__GEX

description: 10x Genomics

value: GEX -- gene expression


title: Klf4_flox_CD11c_Cre_R2__GEX

description: 10x Genomics


title: Liver, Fast-1, miRNA-seq


title: ESC3_2 derived NSC


title: Wildtype replicate 1

value: Aorta

value: WT

value: AAV8-PCSK9 + 10w WTD


title: Mel167-R-E6


title: Liver, Fed-2, miRNA-seq

value: Liver

value: male

value: Wild-type


title: Liver, Fed-1, miRNA-seq


title: Mel167-R-E5


title: ESC3_3

source_name: ESC

value: ESC


title: Mel167-R-E3


title: ESC3_1


title: ESC3_2


title: ESC2_3 derived NSC


title: CTRL1_1

value: IPSC


title: Mel167-R-D4


title: Mel167-R-E1


title: Mel167-R-D3


title: ESC2_2 derived NSC


title: ESC2_1 derived NSC


title: mm_Min6_Untreated_Input_ChIPseq_B

city: La Jolla

first: Matthew

last: Wortham

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

data_processing:
ChIP-seq: Bowtie2 v 2.2.7 was used for mapping of ChIP-seq data to the human reference genome hg19 with a seed length of 33 bp and a maximum of 2 mismatches allowed in the seed region, discarding reads aligning to multiple sites. Duplicate reads were removed using SAMtools.
ChIP-seq: Two biological replicates were used for ChIP-seq data analysis, and replicates were merged prior to analysis
ChIP-seq: Peak calling was performed using the findPeaks program of the HOMER suite of bioinformatics tools with the options -style histone, -P 0.0000001 for H3K27ac or -style factor for Lsd1 (with default P-value cutoff of P < 0.0001) with replicate-matched ChIP-seq input used as background.
mRNA-seq: mRNA-seq reads were mapped to NCBI37/mm9 (mouse) or GRCh37/hg19 (human) genomes by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files were generated from merged replicates. Peak files are provided in BED format. mRNA-seq: Cuffdiff output comparing experimental groups

growth_protocol: Min6 cells were cultured in Dulbecco's modified Eagle's Medium with 25 mM glucose, 4% FBS, 23.8 mM NaHCO3, 1 mM sodium pyruvate, 4 mM L-glutamine, 143 μM β-mercaptoethanol, and 80 μg/mL Gentamicin at 37°C with 5% CO2.

extract_protocol:
ChIP-seq: Islets were processed for ChIP immediately following isolation. Mouse islets were hand-picked twice under a dissecting microscope to minimize acinar cell contamination. For histone ChIP, islets were washed once in Hanks Balanced Salt Solution (Hyclone) and then fixed for 10 min in DPBS containing 1.11% formaldehyde. Cross-linking was quenched as before, then islets were lysed by passage through a 25 gauge needle in lysis buffer (10 mM Tris-Hcl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 1% NP-40, 1% SDS, 0.5% sodium deoxycholate). ChIP was then performed as described above using 10 or 30 μg of sheared chromatin and 4 μg of anti-H3K27ac (39133, Active Motif) antibodies, respectively.  For Lsd1 ChIP of islets from fed or fasted mice, 1000 islets from each condition were first dissociated by briefly washing in StemPro Accutase (Life Technologies) and then incubating in StemPro Accutase for at 37 °C for 12 minutes with frequent trituration. Digestion was quenched with HBSS supplemented with 0.3% BSA and 2.8 mM glucose, then islet cells were pelleted via centrifugation for 5 minutes at 1200 rpm in a swing-out rotor centrifuge. Cells were washed briefly in DPBS and then fixed at room temperature on a rocker using 2 mM disuccinimidyl glutarate (Proteochem) for 30 min followed by 1.11% formaldehyde for 15 min. Fixation was quenched with 0.125 M glycine, then cells were washed twice in ice-cold DPBS containing 0.5% BSA. Nuclei were isolated by resuspending cells in lysis buffer (10 mM HEPES-KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 1% NP-40, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) and incubation for 5 min on ice followed by centrifugation at 1100 x rcf for 8 min at 4°C to pellet nuclei. Nuclear lysis buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.2% sodium deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) was then added and chromatin was sheared using a Covaris E220 for 30 cycles with the following settings: Peak power: 140, duty factor: 5, cycles/burst: 200, Avg. Power: 7.0. Immunoprecipitation as performed by overnight rotation at 4°C using 30 μL of Dynabeads Protein A beads (Life Technologies) conjugated to 4 μg anti-Lsd1 antibody (ab17721, Abcam). Beads were then washed using a magnetic rack for 30 s each with the following: 3 washes of RIPA-NR wash buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% sodium deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail (Sigma)), 6 washes RIPA-LiCl wash buffer (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 1x protease inhibitor cocktail (Sigma)), 3 washes TET buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.2% Tween-20), 1 wash TEN buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl), and 1 wash IDTE buffer (10 mM Tris-HCl pH 8.0, 100 μM EDTA). DNA was then eluted by adding proteinase K (80 μg) and RNase A (40 μg) in reverse crosslinking buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% SDS) and incubating at 50°C for 1 hour then at 65°C overnight. DNA was eluted a second time using 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS and combined with the first elution. The same protocol was followed for Srf ChIP-seq in Min6 cells with the following modifications: cells were harvested using a cell scraper and sonicated using a Covaris E220 for 18 cycles with the above settings, then chromatin from 1.25 x10^7 cells was used for immunoprecipitation using 4 μl of Srf antibody (5147, Cell Signaling). mRNA-seq: Mouse islets were processed for RNA purification immediately following isolation. Following mouse islet isolation, islets were hand-picked twice under a dissecting microscope to minimize acinar contamination, and were then pooled from at least 2 animals per biologicla replicate. For all mRNA-seq experiments, RNA was isolated using the RNeasy Micro kit (QIAGEN) according to the manufacturer’s instructions.
ChIP-seq ibraries were constructed from purified DNA using the KAPA DNA Library Preparation Kit for Illumina (Kapa Biosystems). Input libraries were prepared from each experimental replicate using 10 ng of DNA purified immediately following shearing. Libraries were sequenced using NovaSeq 6000 (Illumina). mRNA-seq libraries were prepared from 35 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: treatment/condition/replicate

value: Rep 2


title: mm_Min6_Untreated_Input_ChIPseq_A

value: Rep 1


title: Mel167-R-D1


title: ESC2_1


title: Klf4_flox_CD11c_Cre_R1__GEX

description: 10x Genomics

value: CD11c+ cells

value: Klf4 fl/fl CD11c Cre

value: 6-14 weeks old


title: Mel167-R-C3


title: mm_Min6_Untreated_Srf_ChIPseq_A

value: Srf (Cell Signaling, 5147)


title: mm_Min6_Untreated_Srf_ChIPseq_B


title: ESC2_2

value: wild type


title: Mel167-R-C4

value: circulating tumor cell (CTC)


title: ESC2_3


title: ESC1_3 derived NSC

value: ESC derived NSC


title: Mel167-R-C2


title: ESC3_1 derived NSC


title: ESC1_2 derived NSC


title: mm_Islets_KOD7Fast_RNAseq_A

source_name: Pancreatic islets

value: Fasted (16h) Wk1 Lsd1 KO Rep 1


title: Mel167-R-C1


title: mm_Islets_KOD7Fast_RNAseq_B

value: Fasted (16h) Wk1 Lsd1 KO Rep 2


title: Fucci sample 2

city: Tianjin

first: Yao

last: Ma

address: Nanjing Street

institute: Chinese Academy of Medical Sciences

description: 3' ends mRNA

data_processing:
Raw sequencing reads were demultiplexed and assigned to each single cell according to the unique barcode sequences pooled in sequencing libraries.
We next trimmed polyA tails, artificial sequences introduced during sequencing library construction, including TSO and UMI, and low quality bases from the 5’ prime or 3’ prime of each paired reads
Sequencing reads that passed quality control were aligned to the mouse reference genome (genome version: mm10) by using hisat2 with default settings (version 2.2.1 ).
HTSeq package (version 0.11.3) was used to summarize the uniquely aligned reads for each gene and duplicated transcripts were removed referring to UMI sequences.The number of transcripts for each gene was calculated as the number of different UMIs aligned.
Low quality cells were further removed based on the number of genes and transcripts detected in each cell referring to  Scater R package (version 1.18.3) .
We also removed genes with low expression abundance across all cells as described in Seurat package.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

source_name: Bone marrow

extract_protocol:
Single cells were sorted or transferred directly into cell lysis buffer. The reverse transcription and template switch steps were then performed following the modified Smart-seq2* protocol. Amplified cDNA was sonicated to ~300-base-pair (bp) fragments by the Covaris S2 system. The 3' ends of the transcripts are enriched by Dynabeads Myone streptavidin C1 beads (invitrogen) after biotin-primer PCR.
The cDNA libraries were generated using a KAPA Hyper Prep Kit for Illumina (KAPA). Finally, the samples were ready for sequencing on an Illumina Hiseq platform (Novogene).
Modified Smart-seq2

value: Bone marrow

value: 8 weeks

tag: cell markers

value: mKO2high, mKO2low


title: Mel167-R-D6


title: Mel167-R-B6


title: ESC1_1 derived NSC


title: mm_Islets_KOD7Fed_RNAseq_B

value: Fed (4h) Wk1 Lsd1 KO Rep 2


title: N302

city: Hongo

first: Akihiro

last: Iguchi

state: Bunkyo-ku

department: Pharmaceutical Sciences

country: Japan

institute: The University of  Tokyo

data_processing:
Obtained reads were mapped onto the mouse GRCm38.p6 (mm10) genome using STAR (version 2.7.3a).
Reads on annotated genes were counted using featureCounts (version 1.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWif files for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: microglia

extract_protocol:
Microglia was isolated using flow cytometry, and total RNA was extracted from isolated microglia using RNeasy Plus Micro Kit (QIAGEN)
Double-stranded cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TaKaRa)

value: Brain

value: microglia

value: 9-10 months

value: NLGF


title: Mel167-R-B5


title: ESC1_3

value: ESC


title: mm_Islets_KOD7Fed_RNAseq_A

value: Fed (4h) Wk1 Lsd1 KO Rep 1


title: N261


title: Mel167-R-B4


title: mm_Islets_CtrlD7Fast_RNAseq_B

value: Fasted (16h) Control for Wk1 Lsd1 KO Rep 2


title: Mel167-R-B3


title: N253


title: Mel167-R-B2


title: mm_Islets_CtrlD7Fast_RNAseq_A

value: Fasted (16h) Control for Wk1 Lsd1 KO Rep 1


title: 4C-AG

first: Wange

last: Lu

address: 94 Weijin Road

institute: Nankai University

data_processing:
library strategy: 4C-seq
Raw fastq files (paired-end data) were first trimmed to remove adaptor sequences using Trim Galore and then processed through the HiC-Pro pipeline to create valid interacting pairs and raw contact count matrices.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph, read count of restriction fragments

source_name: Prostate

growth_protocol: 22Rv1 cell lines were obtained from ATCC. Cells were incubated at 37 ℃ in 5% CO2 and cultured in complete RPMI1640 (Gibco) supplemented with 10% FBS (Bio-logical Industries) and 1% Penicillin/Streptomycin (Gibco).

extract_protocol:
The 4C assay was carried out in SNP rs10486567 heterozygous cell clones, using a published protocol 61 with some modification. Briefly, 1 × 107 cells were cross-linked in 1 % formaldehyde at room temperature for 10 min and quenched by 0.125 M glycine. Nuclei were isolated in 5 ml of cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 10 mM EGTA, 0.2% NP-40 and 1 mM PMSF) and then digested with 400 U HindIII(NEB, R3104S) at 37°C with rotation, followed by adding 4000 U T4 DNA ligase (NEB, M2020M) for in-situ ligation at 16°C overnight. The ligated DNA was de-crosslinked with proteinase K at 65 °C overnight. Purified DNA was digested with 100 U CviQ1 enzyme (NEB, RO639S) and then circularized using 4000 U T4 DNA ligase.
Circularized DNA was amplified with SNP-specific inverse primers (see table s6). Each 4C library was sequenced as 150 bp paired-end reads using the Illumina Hiseq 4000 system.

tag: restriction enzyme

value: HindIII, CviQI


title: I259

value: Inpp5d+/-; NLGF


title: Mel167-R-B1

tag: cell line

value: circulating tumor cell (CTC)


title: 22Rv1_ChIP_input

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to hg19 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Peaks were called with MACS version 2.1.1 to define broad peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
1× 107 22Rv1 cells were cross-linked in 1% formaldehyde and quenched in 0.125 M g lycine. Cell pellets were harvested in Farnham lysis buffer [50 mM tris-HCl (pH 7.5), 150 mM NaCl, 0.5% NP-40, 5 mM EDTA, 1% Triton X-100, 1× protease inhibitor co cktail (Roche) and 1 mM PMSF] and incubated 30 min on ice to isolate nuclei. Nuclei  were suspended in SDS lysis buffer [1% SDS, 50 mM Tris-HCl, 10 mM EDTA and 1 × protease inhibitor cocktail (Roche)] and sheared to 100-500 bp by sonication. Super natants were collected and precleared 1 h with 50 μl protein G (Invitrogen). 2% of the precleared sample served as input, and the remainder was immunoprecipitated with 5 μg antibody [H3K27ac, (ab4729), Abcam] bound to 50 μl protein G beads at 4°C over night. Beads were washed 5 times with LiCl IP washing buffer [100 mM Tris-HCl (pH 7.5), 500 mM LiCl, 1% NP-40 and 1% sodium deoxycholate] and reversed cross-links  with Proteinase K overnight at 65°C. Finally, DNA was purified using a PCR Purifica tion Kit (Qiagen) and eluted in 30 μl H2O
Input and precipitated DNA were sequence d using an Illumina Hiseq4000 platform.


title: mm_Islets_CtrlD7Fed_RNAseq_A

value: Fed (4h) Control for Wk1 Lsd1 KO Rep 1


title: 22Rv1_H3K27ac

value: H3K27ac, (ab4729), Abcam


title: Fucci sample 1

description: 3' ends mRNA

value: Bone marrow

value: mKO2neg, mAG+


title: I245


title: Mel167-R-A6


title: mm_islets_LsdKIwk3_RNAseq_C

value: Wk3 Lsd1 KI Rep 3


title: DI233

value: Tyrobp-/-; Inpp5d+/-; NLGF


title: 22Rv1_HiC_rep2

data_processing:
Raw fastq files (paired-end data) were first trimmed to remove adaptor sequences using Trim Galore and then processed through the HiC-Pro pipeline to create valid interacting pairs and raw contact count matrices.
Genome_build: hg19
Supplementary_files_format_and_content: HIC

extract_protocol: In situ Hi-C experiments were performed in 22Rv1 cells, using a previously described protocol 25 with minor modifications. Briefly, 1× 107 cells were digested and cross-linked in 1% formaldehyde. Chromatin was digested with 150 U MboⅠ (NEB, R0147) at 37 ℃ with rotation. To fill in restriction fragment overhangs, 50 U DNA Polymerase Ⅰ, Large Fragment (NEB, M0210), combined with dNTPs containing biotin-dATP (Thermofisher, 19524016), were added and incubated at 37℃ for 1 h. For ligation, 4000 U T4 DNA ligase (NEB, M0202) was added and incubated at room temperature for 4 h with slow rotation. To reverse cross-links, 25 μl proteinase K (20 mg/ml) was added and incubated at 65 ℃ overnight. Purified Hi-C samples were sheared to 200-300 bp by sonication. Biotin pull-down was performed using Streptavidin C-1 beads (Life Technologies, 65002) with 2× biotin binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA and 2 M NaCl). The Hi-C library was amplified with 8 cycles using Illumina primers.

value: MboI


title: Mel167-R-A4


title: DI231

value: Brain

value: microglia


title: 22Rv1_HiC_rep1


title: Mel167-R-A3


title: Mel167-M-H5

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All bisulfite sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads that passed quality control were mapped to human reference genome (version: hg19) or mouse reference genome (version: mm9) using bismark (version: 0.7.6) in single-end alignment mode.
Assembly: hg19
Supplementary files format and content: bigWig (1 if a methylated CpG, 0 if an unmethylated CpG, no value otherwise)

extract_protocol:
Single cell were either manully picked or sorted into the scBS lysis buffer by FACS, and DNA was released after proteinase treatment at 50C and then bisulfite converted.
After bislfite purification, DNA was complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.

tag: cpg coverage

tag: bisulfite conversion_rate


title: mm_islets_LsdKIwk3_RNAseq_B

value: Wk3 Lsd1 KI Rep 2


title: ESC1_2

value: ESC

tag: genotype

value: wild type


title: ESC1_1


title: mm_islets_LsdKIwk3_RNAseq_A

tag: chip antibody

value: Wk3 Lsd1 KI Rep 1


title: DI230

tag: cell type

tag: age

value: 9-10 months


title: I250

tag: tissue


title: rs10486567_KO2 [RNA-seq]

data_processing:
Clean reads were mapped to the Ensemble hg19 human genome using Hisat2 with default parameters.
Gene reads were counted by Htseq. Fold changes (FC) were computed as a log2 ratio of normalized reads per gene using the DEseq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent (ThermoFisher Scientific, 15596018) based on the manufacturer’s protocol. 2 μg RNA was reverse transcribed to cDNA using the PrimeScript RT reagent with a gDNA eraser Kit (Takara, no. RRO47B).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

tag: genotype/variation


title: D234

value: Tyrobp-/-; NLGF


title: Mel167-M-H4

value: circulating tumor cell (CTC)


title: rs10486567_KO1 [RNA-seq]


title: mm_islets_CtrlforLsdKI_RNAseq_D

value: Control for Wk3 Lsd1 KI Rep 4


title: mm_Islets_CtrlD7Fed_RNAseq_B

value: Fed (4h) Control for Wk1 Lsd1 KO Rep 2


title: D232


title: Mel167-M-H3


title: 22Rv1_WT2 [RNA-seq]

value: WT


title: mm_islets_CtrlforLsdKI_RNAseq_C

value: Control for Wk3 Lsd1 KI Rep 3


title: mm_islets_LsdKIwk3_RNAseq_D

value: Wk3 Lsd1 KI Rep 4


title: Mel167-M-H2


title: 22Rv1_WT1 [RNA-seq]


title: IAA_Input_6_Rep2

city: Pittsburgh

first: Mitchell

middle: A

last: Ellison

email: mae92@pitt.edu, mae133@pitt.edu, melliso46@gmail.com, ellisoniima@upmc.edu

state: PA

address: Langley Hall / 3477 Euler Way

department: Pathology / Biological Sciences

institute: University of Pittsburgh

data_processing:
ChIP-seq reads were aligned to the S. pombe genome (Ensembl EF2) and then unaligned reads were aligned to the S. cerevisiae genome (Ensembl R64-1-1), using Bowtie2 (75) before SAM to BAM conversion, and PCR duplicate removal with the SAMtools suite (76). Spike-in normalization factors were calculated via a custom bash script using established methods (77). BAM to BigWig conversion was conducted while simultaneously applying the normalization factors (74). This was done by multiplying each base pair of the genome by the normalization factor using deepTools3 bamCoverage.
Assembly: S. cerevisiae genome (Ensembl R64-1-1)
Supplementary files format and content: bigwig files containing ChIP-seq occupancy data after spike-in normalization

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol:
cells were grown to mid log phase in YPD
Cells were grown to log phase at 30 °C in YPD medium (48) supplemented with 400 µM tryptophan (W).

extract_protocol:
ChIP was performed essentially as described previously (70,71). Briefly, 200 or 250 mL of cell cultures were grown to log phase (OD600 = 0.8 - 1.0). Cells were crosslinked for 20 min at room temperature by addition of formaldehyde to 1% (v/v). Lysates were prepared in FA lysis buffer (72). Chromatin was sheared in Bioruptor® Pico 15 mL tubes with 300 µL beads (Diagenode C30010017) by 25 cycles of 30 sec on and 30 sec off using a Bioruptor® (Diagenode B01060010). Sonicated chromatin was brought up to a volume of 6 mL in FA lysis buffer and centrifuged at 50,000 rpm for 20 min at 4˚C. Chromatin in the supernatant was aliquoted, flash-frozen, and stored at -80˚C.
S. cerevisiae chromatin was mixed with Schizosaccharomyces pombe chromatin (KP07 or KP08) at a 1:10 ratio (S. pombe : S. cerevisiae) based on protein concentration (Pierce BCA protein assay kit; Thermo Fisher Scientific 23227), and IP reactions were conducted with anti-V5 (Invitrogen R960-25, 1 µL/225 µg or 10 µL/1800 µg), anti-Rpb1-CTD (8WG16; BioLegend 664906, 1 µL/225 µg or 8 µL/1800 µg), anti-HSV (Sigma-Aldrich H6030, 1.75 µL/450 µg or 7 µL/1800 µg), anti-HA (Santa Cruz sc-7392 AC, 15 µL/225 µg), anti-Spt5 (gift from Grant Hartzog, 4 µL/1800 µg), anti-H2BK123ub (Cell Signaling 5546, 5 µL/1000 µg), anti-total H3 (Abcam ab1791, 2 µL/1000 µg), anti-H3K4me2 (Millipore 07-030, 5 µL/1000 µg), anti-H3K4me3 (Active motif 39159, 5 µL/1000 µg), or anti-Myc (gift from John Woolford, used as a non-specific IgG control, 5 µL/1000 µg) primary antibodies. While S. pombe chromatin was included for the ChIP assays in Fig. S4, it was not used for normalization of the S. cerevisiae data as it increased variance in the qPCR measurements. IP reactions were incubated overnight at 4˚C on an end-over-end roller. Protein A or G beads (Cytiva 17-5280-01 or 17-0618-01) were washed with FA lysis buffer with 275 mM NaCl and added to the chromatin-antibody mixture and placed on the roller for 1 hr at room temperature. Beads were washed and DNA recovered as previously described (71). DNA was purified using the QIAquick PCR Purification Kit (Qiagen, 28106).
ChIP-sequencing (ChIP-seq) libraries were prepared using a NEBNext Ultra II kit and indices (E7645, E7335, E7500, E7710, E7730). Libraries were quantified by Qubit and fragment length distribution was assessed by agarose gel electrophoresis. DNA sequencing was conducted by the University of Pittsburgh Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh on an Illumina NextSeq2000.

treatment_protocol:
IAA (Indole-3-acetic acid; Sigma-Aldrich, I3750), dissolved in DMSO, was added to the culture at a final concentration of 500 mM before incubation at 30 °C for 60 minutes proir to crosslinking and cell harvest.
For auxin-induced degradation experiments, indole-3-acetic acid (IAA; Sigma-Aldrich, I3750), dissolved in DMSO, was added to the culture at a final concentration of 500 mM and incubated at 30 °C for one hour. All chromatin was crosslinked with formaldehyde and prior to chromatin immunoprecipitation (ChIP).

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

tag: spike in species

value: Schizosaccharomyces pombe

tag: spike in type

value: DNA

tag: spike in to sample ratio


title: mm_islets_CtrlforLsdKI_RNAseq_B

value: Control for Wk3 Lsd1 KI Rep 2


title: Mel167-M-H1


title: mm_islets_CtrlforLsdKI_RNAseq_A

value: Control for Wk3 Lsd1 KI Rep 1


title: IAA_Input_6_Rep1

tag: strain


title: IAA_Input_5_Rep2


title: IAA_Input_5_Rep1


title: mm_islets_10pmFast_Input_ChIPseq_Z

value: Fasted (16h) Rep 2


title: Hu_islets_TCP_RNAseq_E

description:
RRID: SAMN08774189
TCP_gene_exp.diff

data_processing:
ChIP-seq: Bowtie2 v 2.2.7 was used for mapping of ChIP-seq data to the human reference genome hg19 with a seed length of 33 bp and a maximum of 2 mismatches allowed in the seed region, discarding reads aligning to multiple sites. Duplicate reads were removed using SAMtools.
ChIP-seq: Two biological replicates were used for ChIP-seq data analysis, and replicates were merged prior to analysis
ChIP-seq: Peak calling was performed using the findPeaks program of the HOMER suite of bioinformatics tools with the options -style histone, -P 0.0000001 for H3K27ac or -style factor for Lsd1 (with default P-value cutoff of P < 0.0001) with replicate-matched ChIP-seq input used as background.
mRNA-seq: mRNA-seq reads were mapped to NCBI37/mm9 (mouse) or GRCh37/hg19 (human) genomes by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files were generated from merged replicates. Peak files are provided in BED format. mRNA-seq: Cuffdiff output comparing experimental groups

extract_protocol:
ChIP-seq: Islets were processed for ChIP immediately following isolation (for mouse islets) or shipping (for human islets). Mouse islets were hand-picked twice under a dissecting microscope to minimize acinar cell contamination. Human islets selected for ChIP-seq analysis were of > 90% purity to facilitate analysis of large quantities of islets without the need for dithizone staining. For Lsd1 ChIP, islets were transferred to complete islet media (CMRL 1066 with 13 mM glucose, 10% FBS, 2 mM L-glutamine, 100 U/mL Pen/Strep, 1 mM sodium pyruvate, 10 mM HEPES, and 0.25 mg/mL amphoterecin B) containing 1.11% formaldehyde and fixed on a rocker for 15 minutes. The reaction was quenched for 5 minutes in 0.125 M glycine. Cells were then washed in DPBS containing 0.5% NP-40 then once again in DPBS supplemented with 0.5% NP-40 and 1 mM PMSF. Islets were lysed and ChIP was performed using the ChIP-IT High Sensitivity Kit (Active Motif) with 30 μg of sheared chromatin and 4 μg anti-Lsd1 antibody (ab17721, Abcam). For histone ChIP, islets were washed once in Hanks Balanced Salt Solution (Hyclone) and then fixed for 10 min in DPBS containing 1.11% formaldehyde. Cross-linking was quenched as before, then islets were lysed by passage through a 25 gauge needle in lysis buffer (10 mM Tris-Hcl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 1% NP-40, 1% SDS, 0.5% sodium deoxycholate). ChIP was then performed as described above using 10 or 30 μg of sheared chromatin and 4 μg of anti-H3K4me1 (ab8895, Abcam) or anti-H3K27ac (39133, Active Motif) antibodies, respectively. mRNA-seq: Human islets were first treated as described under the "treatment protocol"  section above, while mouse islets were processed for RNA purification immediately following isolation. Following mouse islet isolation, islets were hand-picked twice under a dissecting microscope to minimize acinar contamination, and were then pooled from at least 2 animals per biologicla replicate. For all mRNA-seq experiments, RNA was isolated using the RNeasy Micro kit (QIAGEN) according to the manufacturer’s instructions.
ChIP-seq ibraries were constructed from purified DNA using the KAPA DNA Library Preparation Kit for Illumina (Kapa Biosystems). Input libraries were prepared from each experimental replicate using 10 ng of DNA purified immediately following shearing. Libraries were sequenced using HiSeq 4000 (Illumina). mRNA-seq libraries were prepared from 35 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with the exception of db/db mouse islets and their respective controls, from which libraries were generated with 1 μg of total RNA as described in (Xie, R. et al. Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Cell Stem Cell 12, 224-237, 2013).

treatment_protocol: Human islet mRNA-seq: Upon receipt, human islets were stained with dithizone and positively-staining material was hand-picked using a dissection microscope. Islets were allowed to recover 18-48 hours in complete media (CMRL 1066 with 13 mM glucose, 10% FBS, 2 mM L-glutamine, 100 U/mL Pen/Strep, 1 mM sodium pyruvate, 10 mM HEPES, and 0.25 mg/mL amphoterecin B) at 37°C with 5% CO2 prior to treatments. For LSD1 inhibition studies, 2 mM tranylcypromine (Sigma) was included in the culture media for 24 hours prior to analysis.

value: tranylcypromine Rep 5


title: Hu_islets_UT_RNAseq_E

description:
RRID: SAMN08774189
TCP_gene_exp.diff

value: vehicle Rep 5


title: Hu_islets_TCP_RNAseq_D

description:
RRID: SAMN08774194
TCP_gene_exp.diff

value: tranylcypromine Rep 4


title: Mel167-M-G4


title: IAA_Input_4_Rep2


title: Mel167-M-G3


title: mm_islets_10pmFed_Input_ChIPseq_Z

value: Fed (4h) Rep 2


title: Mel167-M-G2


title: IAA_Input_4_Rep1


title: Hu_islets_UT_RNAseq_D

description:
RRID: SAMN08774194
TCP_gene_exp.diff

value: vehicle Rep 4


title: mm_islets_10pmFast_Input_ChIPseq_Y

value: Fasted (16h) Rep 1


title: mm_islets_10pmFed_Input_ChIPseq_Y

value: Fed (4h) Rep 1


title: IAA_Input_3_Rep2


title: Hu_islets_TCP_RNAseq_C

description:
RRID: SAMN08773777
TCP_gene_exp.diff

value: tranylcypromine Rep 3


title: Hu_islets_UT_RNAseq_C

description:
RRID: SAMN08773777
TCP_gene_exp.diff

value: vehicle Rep 3


title: IAA_Input_3_Rep1


title: mm_islets_10pmFast_Lsd1_ChIPseq_Z

value: LSD1 (abcam, ab17721)


title: Mel167-M-F5

value: circulating tumor cell (CTC)


title: mm_islets_10pmFast_Lsd1_ChIPseq_Y


title: Hu_islets_TCP_RNAseq_B

description:
RRID: SAMN08774953
TCP_gene_exp.diff

value: tranylcypromine Rep 2


title: Mel167-M-G5


title: IAA_Input_2_Rep2

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: Schizosaccharomyces pombe


title: Hu_islets_UT_RNAseq_B

description:
RRID: SAMN08774953
TCP_gene_exp.diff

value: vehicle Rep 2


title: IAA_Input_2_Rep1

value: DNA


title: Mel167-M-F3


title: Mel167-M-F2


title: mm_islets_10pmFed_Lsd1_ChIPseq_Y


title: IAA_Input_1_Rep2


title: Mel167-M-F1


title: IAA_Input_1_Rep1


title: mm_islets_10pmFast_H3K27ac_ChIPseq_2C

value: H3K27ac (Active Motif 39133)

value: Fasted (16h) Rep 3 Batch 2


title: Mel167-M-G1


title: Hu_islets_UT_RNAseq_A

description:
RRID: SAMN08930500
TCP_gene_exp.diff

value: vehicle Rep 1


title: Hu_islets_TCP_RNAseq_A

description:
RRID: SAMN08930500
TCP_gene_exp.diff

value: tranylcypromine Rep 1


title: Hs_islets_input_B3

description:
RRID: SAMN08769028
HuIsletInputforLsdOld+B.ucsc.bedGraph.gz


title: Mel167-M-E5


title: Mel167-M-E6


title: mm_islets_10pmFast_H3K27ac_ChIPseq_2B

value: Fasted (16h) Rep 2 Batch 1


title: IAA_V5_IP_Rep1

value: anti-V5 (Invitrogen R960-25)


title: mm_islets_10pmFast_H3K27ac_ChIPseq_2A

value: Fasted (16h) Rep 1 Batch 1


title: Hs_islets_LSD1_ChIPseq_B

description:
RRID: SAMN08769028
HuIsletLsd1Old+B.ucsc.bedGraph.gz


title: IAA_Spt5_IP_Rep2

value: anti-Spt5 (gift from Grant Hartzog)


title: mm_islets_10pmFed_H3K27ac_ChIPseq_2B

value: Fed (4h) Rep 2 Batch 1


title: mm_islets_10pmFed_H3K27ac_ChIPseq_2C

value: Fed (4h) Rep 3 Batch 2


title: Mel167-M-E1


title: Hs_islets_input_A

description:
RRID: SAMN08784602
HuIsletInputforLsdOld+B.ucsc.bedGraph.gz


title: Hs_islets_LSD1_ChIPseq_A

description:
RRID: SAMN08784602
HuIsletLsd1Old+B.ucsc.bedGraph.gz

value: LSD1 (abcam, ab17721)


title: IAA_Spt5_IP_Rep1


title: mm_islets_10pmFed_Lsd1_ChIPseq_Z

value: Fed (4h) Rep 2


title: Mel167-M-D6

value: circulating tumor cell (CTC)


title: R20

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
ShortRead, v1.52.0
HISAT2, v2.2.1
Htseq-count, v0.13.5
DESeq2
Genome_build: mm39
Supplementary_files_format_and_content: DESeq2 table

extract_protocol:
RNeasy Plus Mini Kit (Qiagen #74134)
mRNA-sequencing library preparation (1.5ug total RNA/ sample; plant and animal eukaryotic strand-specific mRNA and sequencing)

tag: regime

value: Methionine and Choline Deficient Diet (Safe #AIN-76)

tag: treatment

value: Antibody anti-ACBP/DBI (Fred Hutch Antibody Technology)

tag: disease state

value: NASH

value: Liver


title: Mel167-M-D4


title: sample23

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
unfiltered_mRNA_count_data
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: text tab separated file

organism: Bos taurus

source_name: blastocyst

extract_protocol:
We extracted RNA using Trizol protocol.
We produced the libraries following the mcSCRB-seq protocol with minor modifications

value: blastocyst


title: IAA_Myc_IP_Rep2

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: anti-Myc (gift from John Woolford, used as non-specific IgG control)

value: Schizosaccharomyces pombe

value: DNA


title: IAA_V5_IP_Rep2

value: anti-V5 (Invitrogen R960-25)


title: R19


title: Mel167-M-D3


title: IAA_Myc_IP_Rep1


title: sample21


title: Mel167-M-D1


title: R18


title: sample20


title: Mel167-M-E3


title: Mel167-M-C4


title: R17


title: R16


title: sample18


title: sample19


title: R15

value: Antibody IgG (Bioxcell #BE0085)


title: mm_islets_10pmFed_H3K27ac_ChIPseq_2A

value: H3K27ac (Active Motif 39133)

tag: treatment/condition/replicate

value: Fed (4h) Rep 1 Batch 1


title: IAA_HSV_IP_Rep1

value: anti-HSV (Sigma-Aldrich H6030)


title: sample16


title: Mel167-M-C1

tag: cell line


title: IAA_H3_IP_Rep1

value: anti-total H3 (Abcam ab1791)


title: Mel167-M-C2

tag: cpg coverage


title: IAA_H3_IP_Rep2


title: Mel167-M-C3

tag: bisulfite conversion_rate


title: IAA_H3K4me3_IP_Rep2

tag: genotype

value: anti-H3K4me3 (Active motif 39159)


title: R14


title: sample22


title: sample15


title: IAA_H3K4me3_IP_Rep1

tag: chip antibody


title: Mel167-M-B6

tag: cell type

value: circulating tumor cell (CTC)


title: R13

value: Methionine and Choline Deficient Diet (Safe #AIN-76)


title: sample14


title: Mel167-M-B5


title: IAA_H3K4me2_IP_Rep2

value: anti-H3K4me2 (Millipore 07-030)


title: R12

value: NASH


title: sample13


title: IAA_HSV_IP_Rep2


title: IAA_H3K4me2_IP_Rep1


title: sample12


title: Mel167-M-B4


title: Mel167-M-B3


title: R11

value: Liver


title: IAA_H2Bub_IP_Rep2

value: anti-H2BK123ub (Cell Signaling 5546)


title: R10

value: Regular chow diet (Safe #A04)

value: Antibody anti-ACBP/DBI (Fred Hutch Antibody Technology)

value: Healthy


title: sample11

value: blastocyst


title: Mel167-M-B2


title: sample10


title: IAA_H2Bub_IP_Rep1

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: Schizosaccharomyces pombe

value: DNA


title: Mel167-M-B1


title: R8


title: IAA_8WG16_IP_Rep2

value: anti-8WG16 (BioLegend 664906)


title: Mel167-M-A6


title: sample09


title: DMSO_Input_6_Rep2

treatment_protocol:
DMSO (same volume as IAA+DMSO to achive 500mM IAA) was added to the culture before incubation at 30 °C for 60 minutes proir to crosslinking and cell harvest.
For auxin-induced degradation experiments, indole-3-acetic acid (IAA; Sigma-Aldrich, I3750), dissolved in DMSO, was added to the culture at a final concentration of 500 mM and incubated at 30 °C for one hour. All chromatin was crosslinked with formaldehyde and prior to chromatin immunoprecipitation (ChIP).


title: IAA_8WG16_IP_Rep1


title: sample08


title: R6


title: Mel167-M-A4


title: DMSO_Input_6_Rep1


title: sample07


title: R5

value: Antibody IgG (Bioxcell #BE0085)


title: sample06


title: Mel167-M-A3


title: sample05


title: 7 mixed samples of PBMCs, PBgdT cells and igdT cells    (resequence of SampleTag library)

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

description:
Processed data file "_1_Combined_mRNA_panel_DBEC_MolsPerCell.csv" was created by integrating all the raw data files.
Processed data file "_1_mRNA_panel_Sample_Tag_Calls.csv" was also created by integrating all the raw data files.

data_processing:
Raw sequence files (FASTQ) were processed with BD Rhapsody targeted Analysis Pipeline on Seven Bridges Genomics platform.
Supplementary_files_format_and_content: Multiplexed processed data files (_1_Combined_mRNA_panel_DBEC_MolsPerCell.csv and _1_mRNA_panel_Sample_Tag_Calls.csv) were generated and used for single cell analysis using Seurat. Demultiplexed seven processed data files were also attached.

source_name: freshly isolated PBMCs, CD3+gdTCR+ sorted PB-γδT cells, CD3+gdTCR+ sorted γδ Tcells differentiated from iPSCs (n=3), non-sorted γδ Tcells differentiated from iPSCs (n=2)

extract_protocol:
Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System, according to the manufacturer's instructions.
Libraries were prepared using a pre-designed primer panel (BD Immuno Response panel hs) containing 399 probes targeting 397 genes, according to the manufacturer's instructions. Protein(Abseq) and sample barcording libraries were also amplified in parallel and pooled for sequencing.
single-cell RNA-seq

value: PBMCs, PBgdT cells and igdT cells

tag: library

value: SampleTag


title: R9

tag: tissue


title: R3


title: sample04


title: DMSO_Input_5_Rep1


title: R2


title: 7 mixed samples of PBMCs, PBgdT cells and igdT cells (cDNA library and SampleTag library)

value: cDNA and SampleTag


title: 500035_AA_Pre

city: Charlestown

first: Neal

middle: Patrick

last: Smith

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10x Genomics) to demultiplex FASTQ reads, align reads to the human reference genome (GRCh38, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Matrices from individual samples were aggregated using thew aggregate matrices function from Pegasus (version 0.17.2)
Cell quality was assessed using the qc_metrics function from Pegasus (version 0.17.2) and cells with >30% mitochondrial UMIs or <500 unique genes detected were filtered out of the matrix
UMI counts were log-normalized with Pegasus (version 0.17.2)
Data matrices were saved in .h5 format using the write_output function from Pegasus (version 0.17.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw Count matrix file includes the UMI counts for the cells that passed QC in .h5 format.  .h5 file includes sample ID information for each cell.
Supplementary_files_format_and_content: log-adjusted count matrix file includes the log-adjusted counts for the cells that passed QC in .h5 format. .h5 file includes sample ID information for each cell.

source_name: Lung

extract_protocol:
Endobronchial brush samples were collected in phenol-free RPMI (ThermoFisher) with 2% human AB serum and ROCK inhibitor (Y-27632, Tocris Bioscience) on ice and processed within 60 minutes of collection. Cells were gently removed from cytology brushes and resuspended in phenol-free RPMI. Single cell suspensions were depleted of dead cells using annexin V conjugated beads (Stemcell Technologies) and of red blood cells using antibodies directed against glycophorin A (Stemcell Technologies). Viable cells were resuspended at a concentration of 500-1000 cells/µl in preparation for loading on the 10x Chromium controller instrument (10x Genomics)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: isolation method

value: endobronchial brushing

tag: subject id

tag: sample (ag = allergen; dil = diluent; pre = baseline)

value: Pre

tag: phenotype (aa = allergic asthmatic; ana = allergic non-asthmatic control)

value: AA


title: R7

tag: strain

value: Liver


title: 500035_AA_Ag

value: Ag


title: R1

tag: regime

value: Regular chow diet (Safe #A04)


title: DMSO_Input_4_Rep2

tag: spike in species

tag: spike in type

tag: spike in to sample ratio


title: sample03


title: 500023_AA_Pre


title: sample02


title: DMSO_Input_4_Rep1


title: DMSO_Input_3_Rep2


title: W23

data_processing:
ShortRead, v1.52.0
HISAT2, v2.2.1
Htseq-count, v0.13.5
Genome_build: mm39 (GRCm39)
Supplementary_files_format_and_content: seq_res_Gerasimos_final.txt: HTSeq-count output in txt file.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen #74134).
mRNA-sequencing library preparation (1.5ug total RNA/ sample; plant and animal eukaryotic strand-specific mRNA and sequencing).

value: Gabrg2tm1Wul/J +/+

tag: Sex

value: Male

tag: treatment

value: High-fat chow diet (Safe #260 HF)


title: sample01

value: blastocyst


title: DMSO_Input_3_Rep1

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: Schizosaccharomyces pombe

value: DNA


title: V22

value: Gabrg2tm1Wul/J F77I/F77I


title: DMSO_Input_5_Rep2


title: 500023_AA_Ag


title: Pep30, HEK293T WT, GFP low

first: Xuebing

last: Wu

address: 630 West 168th Street, P&S 10-401

data_processing:
Reads were aligned to a custom index for the Pep30 library generated with the command bowtie-build in bowtie version 1.2.3 and the option -v 3 --best (best alignment with up to 3 mismatches). The counts of each Pep30 sequence were extracted from the alignment with the bash command cut -f 3 | sort | uniq -c.
Assembly: Custom
Supplementary files format and content: Pep30lib-GFP-high-vs-low.txt: tab-delimited. Columns are: ID, DNA sequence, GFP_high read count, GFP_low read count, Peptide
Supplementary files format and content: Pep30lib-GFP-mCherry-ratio.txt: space-delimited. Columns are: ID Seq Peptide KO_high KO_midhigh KO_midlow KO_low WT_high WT_midhigh WT_midlow WT_low

growth_protocol: HEK293T cells used in this study were purchased from ATCC, from which the BAG6 KO cells were derived using CRISPR/Cas9. Cells were cultured in DMEM with 4.5 g/L D-Glucose supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin was added except when producing lentivirus. Low passage number cells were used and maintained under 90% visual confluency. Cells were maintained at 5% CO2 and 37 °C. HEK293T cells used in this study were confirmed to be negative for Mycoplasma Contamination and routinely tested using the MycoAlertTM Mycoplasma Detection Kit (Lonza, LT07-418).

extract_protocol:
Genomic DNA was isolated from the cell populations using QIAGEN QIAamp DNA mini kit or Machery Nagel Nucleospin Tissue kit
genomic DNA was eluted in 50 uL of elution buffer. Libraries were then amplified using PCR with custom Illumina adapters, using Q5 high-fidelity PCR mix with 1000 ng input gDNA per sample. Libraries were amplified for a total of 24-27 cycles. After amplification, libraries were cleanup up using SPRISelect beads at a ratio of 0.7x. Purified library size was confirmed via gel and libraries were quantified using the KAPA qPCR Illumina library quantification kit. Libraries were subsequently pooled in a ratio based on the number of total cells collected from each sample.
DNA amplicon sequencing

treatment_protocol: Sorting based on EGFP alone in HEK293T cells: cells were transduced with Pep30 lentivirus at low MOI, grown for 6 days, then FACS sort top and bottom 20% GFP cells. Sorting based on mCherry/EGFP ratio of WT and BAG6 KO cells: HEK293T as well as a clonal BAG6 knockout cell line were reverse transduced with the Pep30 library such that less than 30% of cells were transduced (thus are most likely a single integration per cell). The virus-containing media was removed after 24 hours and fresh media with 10% FBS and 1% PenStrep was added to the plates. After another 24 hours, transduced cells were purified based on their expression of mCherry. The transduced populations were returned to culture and allowed to grow out for an additional 6 days, with passaging as necessary to maintain confluence below 80%. After 6 days, both populations were sorted into 4 bins based on the ratio of EGFP/mCherry expression (High, mid-high, mid-low, and low) using a FACSAria cell sorter. The same mCherry/EGFP ratio gates were used for both WT and BAG6 KO cells. Sorted cells were spun down at 500 RCF for 5 minutes, washed once with 1000 uL PBS, spun down again, then frozen at -20 as a cell pellet.

tag: cell line

value: Human embryonic kidney

value: wild-type


title: R4

value: Antibody IgG (Bioxcell #BE0085)

tag: disease state

value: Healthy


title: U21

tag: genotype


title: DMSO_Input_2_Rep2

tag: chip antibody


title: Pep30, HEK293T WT, GFP high

tag: cell type


title: DMSO_Input_2_Rep1


title: 500030_AA_Dil

tag: tissue

value: Lung

value: endobronchial brushing

value: Dil


title: T20

value: Liver


title: AlpineDingo_blood_WGBS

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Adaptor sequences and low quality bases were removed using trimmomatic tool (Bolger et al, 2014)
Sequencing reads were aligned to in-silico bisulphite-converted reference genome Canis lupus dingo using WALT mapping tool (Chen et al, 2016)
DNA methylation calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel)
Assembly: Canis lupus dingo: GCA_012295265.2_UNSW_AlpineDingo_1.0_genomic.
Supplementary files format and content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting methylated bases; 6. The number of alignments/pairs reporting unmethylated bases
Supplementary files format and content: bigtable.tsv / For bigtable.tsv" processed data files the column headers are as follows: column 1 - assembly (chromosome). column 2 - position: coordinate for the cytosine position on the chromosome. column 3 (.C) - number of reads depicting a methylated cytosine. column 4 (.cov) - total number of reads at that position.
Library strategy: MethylC-seq

organism: Canis lupus dingo

source_name: Blood-derived DNA subject to WGBS

growth_protocol: Alpine Dingo's whole blood

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue kit (Qiagen, USA).
MethylC-seq library generation was performed as described previously (Ulrich et al, 2015; Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 300 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA).

treatment_protocol: no treatment

tag: tissue type

value: blood


title: S19

value: Gabrg2tm1Wul/J +/+


title: 500024_ANA_Pre

tag: isolation method

tag: subject id

value: Pre

value: ANA


title: Ovary, anestrus

city: Lanzhou

first: Jie

last: Pei

state: Gansu

address: No. 335 Jiangouyan ST, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
Raw scRNA-seq data was converted using the Cell Ranger analysis pipeline provided by 10X Genomics (v2.2.0) and reads were aligned to the yak genome version BosGru3.0 using the STAR aligner.
Assembly: BosGru3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens

source_name: Ovary

extract_protocol:
The pieces of ovarian tissue were washed in cooled RPMI 1640 medium containing 0.04% bovine serum albumin twice. The ovarian samples were further minced into approximate 0.5 mm3 pieces with a sterile scalpel blade in RPMI 1640 medium containing 0.04% BSA. The pieces were incubated with 1 mg/ml collagenase Type II in 0.25% trypsin-EDTA on ice overnight. The digestion was stopped by adding 10% of fetal calf serum. Next, the dissociated cells were collected by centrifugation at 160 × g for 3 min and incubated with advanced DMEM/F12 Glutamax containing 1% insulin-transferrin-selenium , 1% penicillin-streptomycin, and 27 IU/ml RNase-free DNase I at 37 °C for 1 h. The ovarian cells were resuspended in DPBS containing 2% FBS and passed through a 40 μm cell strainer.
The cell suspensions containing high viability cells were prepared immediately. Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Chromium, PN-1000128) was used for gel beads in emulsion (GEM) formation. The cell suspensions, gel beads, and partitioning oil were loaded into a Chromium Single Cell Controller to produce single-cell GEM. Then, a primer containing Illumina TruSeq Read 1, 10X Barcode, and unique molecular identifier (UMI) was applied to produce barcoded full-length cDNA by reverse transcriptase reaction. The GEMs were broken and the pooled fractions were recovered. The first-strand cDNAs were purified with silane magnetic beads and amplified to generate sufficient mass for library construction. Enzymatic fragmention and size selection were used to optimize cDNA amplicon size. P5, P7, a sample index, and a TruSeq Read 2 were added to the amplicon via end repair, A-tailing, adaptor ligation, and PCR.

value: Ovary

tag: age

value: 4 years old


title: DMSO_Input_1_Rep2

tag: strain

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: Schizosaccharomyces pombe


title: DMSO_Input_1_Rep1

value: DNA


title: R18

value: Gabrg2tm1Wul/J F77I/F77I

value: Male

value: High-fat chow diet (Safe #260 HF)


title: 500024_ANA_Dil

tag: sample (ag = allergen; dil = diluent; pre = baseline)

tag: phenotype (aa = allergic asthmatic; ana = allergic non-asthmatic control)


title: 500024_ANA_Ag

value: Ag


title: Monkey fecal DNA - Maltreated 6

city: Atlanta

first: Mar

last: Sanchez

state: GA

address: 954 Gatewood Road NE

institute: Emory University

data_processing:
Bioconductor workflow in R was used to trim, filter, and test this data using the packages dada2 and phyloseq
Supplementary files format and content: comma-separated text file, percentage of total reads belonging to a specific clade
Library strategy: 16S rRNA DNA-seq

organism: feces metagenome

source_name: feces

extract_protocol:
E.Z.N.A. Stool DNA Kit
prepared for sequencing using standard Illumina protocols
primer pair sequences for the V4 region of the 16s rRNA gene

treatment_protocol: Infant maltreatment is defined by co-morbid experience of maternal physical abuse, rejection and neglect of the infant during the first three months of life, resulting in pain, emotional distress, and elevations in stress hormones. Animals in the Control group did not receive such maltreatment.

value: feces

tag: host

value: Macaca mulatta

value: gram-positive bacteria


title: 500030_AA_Pre

value: Lung

value: endobronchial brushing

value: AA


title: Q17

value: Gabrg2tm1Wul/J +/+

value: Liver


title: Monkey fecal DNA - Control 7


title: N14


title: DMSO_Spt5_IP_Rep2

value: anti-Spt5 (gift from Grant Hartzog)

tag: spike in species

tag: spike in type

tag: spike in to sample ratio


title: P16

tag: Sex

tag: treatment


title: DMSO_V5_IP_Rep2

tag: genotype

value: anti-V5 (Invitrogen R960-25)


title: O15


title: Monkey fecal DNA - Maltreated 4


title: 500021_AA_Pre

value: Pre


title: M13


title: 500021_AA_Ag


title: DMSO_Spt5_IP_Rep1

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

tag: chip antibody

value: Schizosaccharomyces pombe


title: Monkey fecal DNA - Control 6

tag: cell type


title: 500030_AA_Ag

tag: tissue


title: Monkey fecal DNA - Control 5


title: 500015_ANA_Pre

value: ANA


title: L12

value: Male


title: 500021_AA_Dil

value: Dil


title: DMSO_Myc_IP_Rep2

value: anti-Myc (gift from John Woolford, used as non-specific IgG control)

value: DNA


title: Monkey fecal DNA - Maltreated 5

value: feces

value: Macaca mulatta


title: Monkey fecal DNA - Maltreated 2

value: gram-positive bacteria


title: K11

value: High-fat chow diet (Safe #260 HF)


title: DMSO_HSV_IP_Rep2

value: anti-HSV (Sigma-Aldrich H6030)


title: 500015_ANA_Ag

value: Lung

value: endobronchial brushing

value: Ag


title: DMSO_HSV_IP_Rep1


title: DMSO_V5_IP_Rep1

value: anti-V5 (Invitrogen R960-25)


title: DMSO_Myc_IP_Rep1


title: Monkey fecal DNA - Maltreated 3


title: J10

value: Gabrg2tm1Wul/J F77I/F77I

value: Liver


title: Monkey fecal DNA - Maltreated 1


title: DMSO_H3_IP_Rep2

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: anti-total H3 (Abcam ab1791)

value: Schizosaccharomyces pombe


title: Monkey fecal DNA - Control 4


title: I9

value: Gabrg2tm1Wul/J +/+

value: Male


title: 500012_ANA_Dil

value: Dil

value: ANA


title: DMSO_H3_IP_Rep1

value: DNA


title: 500012_ANA_Ag


title: G7

value: Regular chow diet (Safe #A04)


title: DMSO_H3K4me3_IP_Rep2

value: anti-H3K4me3 (Active motif 39159)


title: 500008_ANA_Pre

value: Pre


title: DMSO_H3K4me3_IP_Rep1


title: 500008_ANA_Dil

value: Lung


title: Monkey fecal DNA - Control 2

value: feces

value: Macaca mulatta

value: gram-positive bacteria


title: F6

value: Gabrg2tm1Wul/J F77I/F77I


title: 500008_ANA_Ag

value: endobronchial brushing

value: Ag


title: Monkey fecal DNA - Control 1


title: E5

value: Liver


title: 500012_ANA_Pre


title: DMSO_H3K4me2_IP_Rep1

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: anti-H3K4me2 (Millipore 07-030)

value: Schizosaccharomyces pombe


title: YUMM1.7 cells, protrusions, biol rep 1

city: Dallas

first: Megan

middle: L

last: Norris

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Fastq files were quality checked using fastqc and fastq_screen.
Fastq files were mapped to mm10 using STAR
Read counts were generated using featureCounts
differential expression analysis was performed using edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text file with TPM and differential expression measurements for each sample calculated using edgeR

extract_protocol:
PET Millicell Hanging Cell Culture Inserts with 1 mm pores sized for 6 well plates were coated on the bottom side with 30 ug/mL fibronectin. Fibronectin was diluted in sterile PBS and inserts were coated for 15 minutes, then aspirated and allowed to dry. 6x105 to 8x105 cells were plated per membrane and placed in an incubator overnight. For fractionation, media was aspirated, cells were rinsed with RNase-free PBS and aspirated, then cell bodies were scraped using a cell scraper and collected into Qiazol. Inserts were rinsed with RNase-free PBS and cleaned with a cotton swab three times. The cleaned insert was carefully dislodged, placed inside a new tube with Qiazol and briefly vortexed. After cell bodies and protrusions were collected, the standard protocol the Qiagen miRNeasy kit was followed. RNA was eluted with 30 μl RNase-free water. There were two RNA seq replicates, each with 6 inserts. 0.69 - 9.4 ug Total RNA was extracted for each sample.
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring  only high quality RNA is used (RIN Score 8 or higher).   The Qubit fluorometer is used to determine the concentration prior to staring library prep.  One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Total RNA is depleted of its rRNA and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated.   After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.  Before being normalized and pooled, samples are quantified by Qubit then run on the Illumina NextSeq 500 using V2.5 reagents.

tag: cell line

value: melanoma cells

value: wildtype

value: fractionated cell protrusions


title: YUMM1.7 cells, protrusions, biol rep 2


title: DMSO_H3K4me2_IP_Rep2

value: DNA


title: DMSO_H2Bub_IP_Rep2

value: anti-H2BK123ub (Cell Signaling 5546)


title: mm_islets_LsdKIWk3_H3K27ac_ChIPseq_3

description: LsdKIWk3_H3K27ac_H3K27ac1e8.ucsc.bedGraph.gz

data_processing:
ChIP-seq: Bowtie2 v 2.2.7 was used for mapping of ChIP-seq data to the human reference genome hg19 with a seed length of 33 bp and a maximum of 2 mismatches allowed in the seed region, discarding reads aligning to multiple sites. Duplicate reads were removed using SAMtools.
ChIP-seq: Two biological replicates were used for ChIP-seq data analysis, and replicates were merged prior to analysis
ChIP-seq: Peak calling was performed using the findPeaks program of the HOMER suite of bioinformatics tools with the options -style histone, -P 0.0000001 for H3K27ac or -style factor for Lsd1 (with default P-value cutoff of P < 0.0001) with replicate-matched ChIP-seq input used as background.
mRNA-seq: mRNA-seq reads were mapped to NCBI37/mm9 (mouse) or GRCh37/hg19 (human) genomes by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Assembly: mm9
Supplementary files format and content: ChIP-seq: Bedgraph files were generated from merged replicates. Peak files are provided in BED format. mRNA-seq: Cuffdiff output comparing experimental groups

organism: Mus

extract_protocol:
ChIP-seq: Islets were processed for ChIP immediately following isolation. Mouse islets were hand-picked twice under a dissecting microscope to minimize acinar cell contamination. For histone ChIP, islets were washed once in Hanks Balanced Salt Solution (Hyclone) and then fixed for 10 min in DPBS containing 1.11% formaldehyde. Cross-linking was quenched as before, then islets were lysed by passage through a 25 gauge needle in lysis buffer (10 mM Tris-Hcl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 1% NP-40, 1% SDS, 0.5% sodium deoxycholate). ChIP was then performed as described above using 10 or 30 μg of sheared chromatin and 4 μg of anti-H3K27ac (39133, Active Motif) antibodies, respectively.  For Lsd1 ChIP of islets from fed or fasted mice, 1000 islets from each condition were first dissociated by briefly washing in StemPro Accutase (Life Technologies) and then incubating in StemPro Accutase for at 37 °C for 12 minutes with frequent trituration. Digestion was quenched with HBSS supplemented with 0.3% BSA and 2.8 mM glucose, then islet cells were pelleted via centrifugation for 5 minutes at 1200 rpm in a swing-out rotor centrifuge. Cells were washed briefly in DPBS and then fixed at room temperature on a rocker using 2 mM disuccinimidyl glutarate (Proteochem) for 30 min followed by 1.11% formaldehyde for 15 min. Fixation was quenched with 0.125 M glycine, then cells were washed twice in ice-cold DPBS containing 0.5% BSA. Nuclei were isolated by resuspending cells in lysis buffer (10 mM HEPES-KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 1% NP-40, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) and incubation for 5 min on ice followed by centrifugation at 1100 x rcf for 8 min at 4°C to pellet nuclei. Nuclear lysis buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.2% sodium deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) was then added and chromatin was sheared using a Covaris E220 for 30 cycles with the following settings: Peak power: 140, duty factor: 5, cycles/burst: 200, Avg. Power: 7.0. Immunoprecipitation as performed by overnight rotation at 4°C using 30 μL of Dynabeads Protein A beads (Life Technologies) conjugated to 4 μg anti-Lsd1 antibody (ab17721, Abcam). Beads were then washed using a magnetic rack for 30 s each with the following: 3 washes of RIPA-NR wash buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% sodium deoxycholate, 1% NP-40, 0.5 mM DTT, 1x protease inhibitor cocktail (Sigma)), 6 washes RIPA-LiCl wash buffer (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 1x protease inhibitor cocktail (Sigma)), 3 washes TET buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.2% Tween-20), 1 wash TEN buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl), and 1 wash IDTE buffer (10 mM Tris-HCl pH 8.0, 100 μM EDTA). DNA was then eluted by adding proteinase K (80 μg) and RNase A (40 μg) in reverse crosslinking buffer (10 mM Tris-HCl pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% SDS) and incubating at 50°C for 1 hour then at 65°C overnight. DNA was eluted a second time using 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% SDS and combined with the first elution. The same protocol was followed for Srf ChIP-seq in Min6 cells with the following modifications: cells were harvested using a cell scraper and sonicated using a Covaris E220 for 18 cycles with the above settings, then chromatin from 1.25 x10^7 cells was used for immunoprecipitation using 4 μl of Srf antibody (5147, Cell Signaling). mRNA-seq: Mouse islets were processed for RNA purification immediately following isolation. Following mouse islet isolation, islets were hand-picked twice under a dissecting microscope to minimize acinar contamination, and were then pooled from at least 2 animals per biologicla replicate. For all mRNA-seq experiments, RNA was isolated using the RNeasy Micro kit (QIAGEN) according to the manufacturer’s instructions.
ChIP-seq ibraries were constructed from purified DNA using the KAPA DNA Library Preparation Kit for Illumina (Kapa Biosystems). Input libraries were prepared from each experimental replicate using 10 ng of DNA purified immediately following shearing. Libraries were sequenced using NovaSeq 6000 (Illumina). mRNA-seq libraries were prepared from 35 ng of total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: tissue/cell type

value: Pancreatic islets

value: H3K27ac (Active Motif 39133)

tag: treatment/condition/replicate

value: LsdKI Wk3 Rep 3


title: D4

value: Male

value: Regular chow diet (Safe #A04)


title: H8

value: Gabrg2tm1Wul/J +/+


title: mm_islets_LsdKIWk3_H3K27ac_ChIPseq_2

value: LsdKI Wk3 Rep 2


title: Monkey fecal DNA - Control 3

value: feces

value: Macaca mulatta

value: gram-positive bacteria


title: YUMM1.7 cells, cell bodies, biol rep 2

value: fractionated cell bodies


title: B2

value: Liver


title: DMSO_H2Bub_IP_Rep1

value: MATa his3D200::HIS3-osTIR lys2-128d leu2D1 ura3-52 3XHSV-PAF1 SPT6-V5-IAA7(AID)-KANMX

value: Schizosaccharomyces pombe


title: mm_islets_CtrlforLsdKI_H3K27ac_ChIPseq_2

description: CtrlforLsdKI_H3K27ac1e8.ucsc.bedGraph.gz

value: CtrlforLsdKI Wk3 Rep 2


title: mm_islets_LsdKIWk3_H3K27ac_ChIPseq_1

value: LsdKI Wk3 Rep 1


title: YUMM1.7 cells, cell bodies, biol rep 1

value: melanoma cells

value: wildtype


title: DMSO_8WG16_IP_Rep2

value: anti-8WG16 (BioLegend 664906)

value: DNA


title: A1

value: Male


title: DMSO_8WG16_IP_Rep1


title: mm_islets_CtrlforLsdKI_H3K27ac_ChIPseq_1

value: Pancreatic islets

value: H3K27ac (Active Motif 39133)

value: CtrlforLsdKI Wk3 Rep 1


title: CBS 118892 - Sertraline - 3 hours, replicate II

status: Public on Feb 23 2023

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

data_processing:
FastQC v0.11.9 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the T. rubrum genome using the STAR v2.6.1d.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Assembly: Broad T. rubrum strain CBS118892 genome
Supplementary files format and content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism: Trichophyton rubrum

source_name: fungal cells

growth_protocol: Trichophyton rubrum strain CBS118892 from Westerdijk Fungal Biodiversity Institute (formerly CBS-KNAW Collections), the Netherlands, was maintained on malt extract agar [2% glucose, 2% malt extract, 0.1% peptone (w/v), pH 5.7].

extract_protocol:
Total RNA was isolated from ~100 mg mycelia using an Illustra RNAspin mini-RNA isolation kit (GE Healthcare, Chicago, IL, USA).
Equal amounts of RNA from three independent biological replicates at each time point (3, and 12 h) were used for the synthesis of cDNA with the TruSeq RNA library Kit (Illumina, San Diego, CA, USA) and sequenced using the Illumina technology (HiSeq 2000 sequencer) according to the manufacturer’s instructions.

treatment_protocol: Conidia suspensions were obtained by flooding 21-day-old plates with sterilized 0.9% NaCl. Approximately 106 conidia mL-1 were inoculated into 100 mL Sabouraud dextrose broth [SDB; 2% (w/v) glucose, 1% (w/v) peptone], and incubated under agitation (120 rpm) at 28 °C for 96 h. Next, we aseptically transferred mycelia into a new flask containing 100 mL SDB media with 70 µg/mL of sertraline hydrochloride (Cayman Chemical Co., Ann Arbor, MI, USA). After 3 or 12 h of incubation at 28 °C under agitation, the resultant mycelia were collected and stored at −80 °C until RNA isolation.

value: fungal cells

value: Sabouraud and Sertraline

tag: time

value: 3 hours


title: CBS 118892 - Sertraline - 12 hours, replicate II

tag: strain

value: 12 hours


title: CBS 118892 - Sertraline - 3 hours, replicate III


title: CBS 118892 - Sertraline - 12 hours, replicate III


title: CBS 118892 - Sertraline - 12 hours, replicate I


title: CBS 118892 - Control - 12 hours, replicate I

value: Sabouraud


title: CBS 118892 - Control - 12 hours, replicate II


title: CBS 118892 - Control - 12 hours, replicate III


title: CBS 118892 - Control - 3 hours, replicate III


title: C3

value: Gabrg2tm1Wul/J F77I/F77I

value: Liver

value: Regular chow diet (Safe #A04)


title: CBS 118892 - Control - 3 hours, replicate I


title: FXRa treated APOB-/- organoids from donor 2

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: hg19
Supplementary files format and content: csv file including feature raw counts for all samples

growth_protocol: Organoids were cultured in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)

treatment_protocol: Organoids were treated for 7 days with the indicated drug or vehicle

tag: individual

value: donor 2

value: Human hepatocyte organoid

value: Hepatocyte

value: APOB-mutant

value: FXRa 7 days


title: FASi treated APOB-/- organoids from donor 2

value: FASi 7 days


title: FXRa treated APOB-/- organoids from donor 1

value: donor 1


title: vehicle treated APOB-/- organoids from donor 2

value: vehicle 7 days


title: ACCi treated APOB-/- organoids from donor 2

value: ACCi 7 days


title: CBS 118892 - Control - 3 hours, replicate II

value: fungal cells


title: FGF19 treated APOB-/- organoids from donor 2

value: FGF19 7 days


title: FGF19 treated APOB-/- organoids from donor 1


title: DGAT2i treated APOB-/- organoids from donor 2

value: DGAT2i 7 days


title: vehicle treated APOB-/- organoids from donor 1


title: ACCi treated APOB-/- organoids from donor 1


title: CBS 118892 - Sertraline - 3 hours, replicate I

value: Sabouraud and Sertraline

value: 3 hours