title: 30 μM CuCl2 stimulated 4 hr, biol rep1

data_processing:
library strategy: N3-kethoxal-assisted ssDNA sequencing (KAS-seq)
Sequence reads from two separate Illumina sequencing runs were catenated
First, the fastqc (0.11.9) and trim-galore (0.6.7) packages were used for (i) quality control and (ii) to remove low-qualified bases and adapter-containing reads from raw KAS-seq data, respectively. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the hg19 reference genome using bowtie2 (2.4.4) under default parameters.
Bed files were converted to bedGraph files using bedtools (2.30.0). Bedgraph files were then normalized to total read counts using the normalize_KAS-seq script (KAS-pipe) and normalized bedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Differential analysis was then performed using the diff_KAS-seq script (KAS-pipe: which applies DESeq2 (1.26.0) differential analysis)
Assembly: hg19
Supplementary files format and content: bigWig, read density

growth_protocol: A549 cells were maintained in [Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% pen/strep] (referred to as sDMEM) in humidified atmosphere with 5% CO2 at 37*C

extract_protocol:
After labeling, genomic DNA was isolated using a PureLink Genomic DNA mini kit. 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin. The mixture was shaken at 37 °C for 1.5 h, after which 5 µL RNase A was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. 5% of the sonicated DNA was set aside and saved, and the rest was used for enrichment with 10 µL Dynabeads MyOne Streptavidin C1. The beads were washed with three times with 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. Binding was performed at room temperature for 15 min. The beads were then washed 5 times in 1× B&W buffer and were subsequently resuspended in 15 μL H2O. Beads were then heated at 95 °C for 10 min to elute DNA; DNA eluate solution was then moved onto ice for library construction.
Sonicated/sheared enriched DNA libraries were constructed using a Accel-NGS Methyl-Seq DNA library kit

treatment_protocol:
Cells were treated with sDMEM or [sDMEM + CuCl2] for various timepoints as indicated above
To detect ssDNA levels, following sDMEM or [sDMEM + CuCl2] supplementation for the aforementioned times, cells were treated with 5 mM N3-kethoxal in DMSO into the growth media

value: Non-small cell lung adenocarcinoma

value: WT

value: sDMEM + 30 uM CuCl2

value: 4 hours


title: 30 μM CuCl2 stimulated 4 hr, biol rep2

status: Public on Aug 07 2023

type: SRA

city: Chicago

first: Matthew

middle: Oliver

last: Ross

state: United States

address: 929 E 57th St (loading dock behind 5741 S. Drexel Ave) GCIS E507

department: Chemistry

country: USA

institute: University of Chicago

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: time


title: 10 μM CuCl2 stimulated 4 hr, biol rep2

value: sDMEM + 10 uM CuCl2


title: sDMEM 4 hr, biol rep2

value: sDMEM


title: wildtype PDH effector T-cell sample 1

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

data_processing:
Raw ATAC-seq data were trimmed to remove residual adapter sequences using Trimmomatic. Adapter seqeunces were supplied by the developed of Trimmomatic in NexteraPE-PE.fa file.
Trimmed reads were mapped to mouse genome reference seqeunce GRCm38 using BWA MEM (v. 0.7.17)
Reads mapping low mappability regions (supplied in ENCFF547MET.bed) were filtered using samtools.
ATAC-seq peaks were identfied using MACS2 software (v. 2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: narrowPeak, bedgraph files

organism: Mus musculus

source_name: wildtype T-effector

extract_protocol: Tagmented DNA samples were amplified to add single indexed adapters using the Kapa HiFi PCR MasterMix (Roche). The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt).

value: wildtype T-effector

value: effector T-cell

value: TPdh+/+


title: wildtype PDH effector T-cell sample 2


title: Wild-type pollen RNA, CMC-treated, replicate 1

city: Dunedin

first: Rowan

middle: Paul

last: Herridge

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

library_source: transcriptomic

data_processing:
Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
feature counts (bedtools v2.29.0)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: pollen

extract_protocol:
tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)

treatment_protocol: N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)

tag: tissue

value: pollen

value: CMC


title: 10 μM CuCl2 stimulated 4 hr, biol rep1


title: Embryonic stage16 Hand-GFP+ cells from wild type Drosophila [Hrt24_25hr]

city: Baltimore

first: Hangnoh

middle: Joseph

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

description: Single cell RNA-Seq of Drosophila embryonic heart (25hr)

data_processing:
CASAVA version 1.8.2 (Illumina, San Diego, CA) was used for basecalling.
We used Cell Ranger pipeline version 3.0.2 (10X Genomics, Pleasanton, CA) for demultiplexing of raw reads, aligning them to the reference genome, filtering and counting of the mapped reads.
The supplementary file (count matrix) was generated using Seurat package (Stuart*, Butler*, et al., 2019. PMID: 31178118)
Genome_build: Drosophila BDGP Release 6
Supplementary_files_format_and_content: Combined_Count_Matrix.tsv.gz

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Embryonic heart

growth_protocol: Hand-GFP+ wild type files were maintained at 25°C on standard diet and one-week-old flies were collected. Flies were put in a collection cage and juice plates were changed 3 times before egg collection. Eggs were collected at 1h intervals at 25°C, and then transferred to 18°C for development. Samples were collected at the indicated time points.

extract_protocol:
Collected embryos were washed thoroughly with ice-cold 1X phosphate buffered saline (PBS) and then dechorionated in fresh 4-5% bleach (sodium hypochlorite solution; Sigma) for 3 min at room temperature. Dechorionated embryos were extensively rinsed with H2O. Then embryos (~150 mg) were transferred to a Dounce homogenizer (15 ml Tissue Grinder; Dounce). A 5 ml suspension of embryos (Schneider medium) was subjected to mechanical disruption using the Dounce homogenizer, achieved by five strokes using a pestle. Homogenized samples were transferred to 15 ml centrifuge tubes. Collagenase (Type I) (20 U/ml; Worthington), 100 U total, was added to the Schneider medium with the embryos and incubated at room temperature for 10 min. Next, 10 μl of ethylenediaminetetraacetid acid (EDTA) (0.5 M; final concentration of 1 mM) and 0.5 ml 2.5% Trypsin were added to the 5 ml cell solution to digest the samples for 20 min at room temperature. The trypsin reaction was stop by adding 20% fetal bovine serum (FBS) and cells were filtered out using a 70 μm mesh. The cells were then pelleted by centrifugation (1000xg, 5 min, 4°C) and resuspended in 2 ml pre-chilled artificial hemolymph. Isolated embryonic cells were sorted by flow cytometry (BD Influx cell sorter).
The library preparation (Single Cell 3’ Reagent Kits v3, 10x Genomics, CA, USA) and sequencing were performed using Illumina HiSeq by Novogene Corporation Inc (Sacramento, CA).
Single-cell RNA-Seq (Single Cell 3’ Reagent Kits v3, 10x Genomics, CA, USA)

tag: developmental stage

value: Stage 16

value: Embryonic heart


title: sDMEM 4 hr, biol rep1


title: Wild-type pollen RNA, mock-treated, replicate 1

value: mock (CMC)


title: Wild-type pollen RNA, mock-treated, replicate 2


title: knockout PDH effector T-cell sample 3

source_name: TPdh-/- T-effector

value: TPdh-/- T-effector

value: TPdh-/-


title: HHV57DSXY_19005484_S64,TT4_A,WT_EFFECTOR

data_processing:
RNA-seq data QC with QoRTs (version 1.3.6)
Sequence reads were aligned to mm10 with STAR (version 2.7.6a)
Transcript abundances from RNA-Seq data were quantified by usig RSEM (version 1.3.3)
Expected counts of the transcripts were then analyzed for differential expression with R package DESeq2
Assembly: mm10 (GRCm38.101)
Supplementary files format and content: tab-delimited text files

source_name: EFFECTOR

extract_protocol: Poly-A selected RNA-seq libraries were constructed from 1 mg total RNA using the Illumina TruSeq RNA Sample Prep Kits, version 2.  The resulting cDNA was fragmented using a Covaris E210. Library amplification was performed using 11 cycles to minimize the risk of over amplification.  Unique barcode adapters were applied to each library.  Libraries were quantitated by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) and pooled in an equimolar ratio.  The pooled libraries were sequenced on a NovaSeq 6000 with version 1 chemistry.  At least 90 million 150-base read pairs were generated for each individual library.  Data was processed using RTA 3.4.4.

value: wildtype

value: EFFECTOR


title: Embryonic stage15 Hand-GFP+ cells from wild type Drosophila [Hrt23_24hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (23hr)

value: Stage 15


title: 30 μM CuCl2 stimulated 2 hr, biol rep2

value: Non-small cell lung adenocarcinoma

value: WT

value: sDMEM + 30 uM CuCl2

value: 2 hours


title: HHV57DSXY_19005482_S54,TT3_A,WT_EFFECTOR


title: WT Poly 72020

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Reads trimmed and filtered with fastp v0.12.2
Assembled with Ensembl GRCm39 cDNA index using Kallisto v0.46.0
Counts extracted with tximport
Counts imported to DESeq2
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized counts per sample per Ensembl transcript ID exported from DESeq2

source_name: Neocortex

growth_protocol: Wild type (WT) littermate control and Celf4 conditional-deletion animals were generated by crossing Celf4f/f (B6.129-Celf4tm1.1Frk/Frk (Celf4f/f mice; Jax strain: 018126) from Jackson Laboratory) mice with B6.129S2-Emx1tm1(cre)Krj/J (Emx1-Cre mice, Jax strain: 005628) transgenic line that drives the expression of Cre recombinase in the cortical progenitors and postmitotic neurons of neocortex.

extract_protocol:
Mouse embryonic neocortices at postnatal day 0 (P0) were dissected in ice-cold HBSS media supplemented with 5mg/ml glucose and 20 mM HEPES (pH 7.2), followed by freezing on dry ice. Three mouse cortices were pooled and homogenized in freshly prepared polysome extraction buffer supplemented with EDTA-free protease inhibitor, RNaseOut, DTT, and cycloheximide. Lysis was performed by pipetting gently up and down on ice for 15 minutes.  Lysate was centrifuged at 5k rpm for 10 min at 4C and the resulting supernatant was spun at 14k for 5 min at 4C.  Following quantification, 120 ug neocortical input was layered onto 10-50% sucrose density gradients in thin wall polypropylene tubes. A portion (25%) was stored for processing as input. Gradients were spun at 39K rpm at 4C for 120 min.  Polysome profiles were generated with a continuous flow Fluorinert FC-40 and A254 recording with a Brandel fraction collector with UV absorbance recorder.  Samples were frozen at -80C until use.  Pooled monosomes (40S-60S-80S) and polysomes fractions were pooled for isolation of RNA by extraction with TRIzol LS.  RNA was precipitated with one volume of isopropanol/glycogen, then washed with 75% ethanol and air-dried.  Following resuspension, genomic DNA was destroyed with DNase treatment.
Illumina TruSeq RNA Library Kit

value: Neocortex

tag: fraction

value: Poly


title: 30 μM CuCl2 stimulated 2 hr, biol rep1


title: WT Mono 72020

value: Mono


title: Embryonic stage14-late Hand-GFP+ cells from wild type Drosophila [Hrt22_23hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (22hr)

value: Stage 14-late


title: Yeast_total_RNA_ModSeq_Mn

city: New Haven

first: Rafael

middle: de Cesaris

last: Araujo Tavares

state: Connecticut

address: 260 Whitney Ave

institute: Yale University

data_processing:
ShapeMapper2 (Busan et al.2018)
Mg libraries = untreated samples; Mn libraries = modified samples; use ‘--output-counted-mutations’ flag to output counted mutations
Assembly: human 18S rRNA (NCBI ID: 100008588), human 28S rRNA (NCBI ID: 100008589), human 5.8S rRNA (NCBI ID: 100008587), E. coli 16S rRNA (GeneBank ID: J01859.1), E coli 23S rRNA (GeneBank ID: V00331.1), S cerevisiae 18S rRNA (RNAcentral ID: URS00005F2C2D_4932), S cerevisiae 25S rRNA (RNAcentral ID: URS000061F377_4932)
Supplementary files format and content: profile.txt files = csv containing calculated mutation rates for each nucleotide position in the reference sequence; mutation_counts.txt files = csv containing mutation rate compositions for each nucleotide position in the reference sequence

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Human cell lines were grown in DMEM supplemented with 10% fetal bovine serum and 1X antimycotic-antibiotic at 37 deg C; E coli cells were grown in Luria Broth media at 37 deg C; Saccaramyces cerevisiae were grown in YPD at 30 deg C

extract_protocol:
Trizol
cDNA was prepared from total RNA from each source using random nonamer primers and MarathonRT enzyme in the presence of either Mg or Mn as enzymatic cofactors; second-strand synthesis was carried out from each cDNA sample using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module; library preparation was carried out from the resulting dsDNA sample using the Nextera XT DNA kit
Illumina Nextera XT DNA

tag: strain

value: WT strain


title: wildtype PDH effector T-cell sample 4

value: wildtype T-effector

value: effector T-cell

value: TPdh+/+


title: HHV57DSXY_19005480_S55,TT2_A,WT_EFFECTOR


title: WT Input 72020

value: Input


title: 10 μM CuCl2 stimulated 2 hr, biol rep2

value: sDMEM + 10 uM CuCl2


title: HHV57DSXY_19005496_S43,TT1_A,WT_EFFECTOR

value: wildtype


title: cKO Poly 72020

value: cKO


title: HHV57DSXY_19005478_S46,TT16_A,PDH_MEMORY

source_name: MEMORY

value: MEMORY


title: Embryonic stage14-early Hand-GFP+ cells from wild type Drosophila [Hrt21_22hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (21hr)

value: Stage 14-early

value: Embryonic heart


title: 10 μM CuCl2 stimulated 2 hr, biol rep1

value: Non-small cell lung adenocarcinoma

value: WT


title: HHV57DSXY_19005476_S68,TT15_A,PDH_MEMORY


title: Embryonic stage13 Hand-GFP+ cells from wild type Drosophila [Hrt20_21hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (20hr)

value: Stage 13


title: Embryonic stage13 Hand-GFP+ cells from wild type Drosophila [Hrt18_19hr]

description: Single cell RNA-Seq of Drosophila embryonic heart (18hr)


title: cKO Input 72020

value: Neocortex


title: cKO Mono 72020

value: Mono


title: HHV57DSXY_19005474_S56,TT14_A,PDH_MEMORY


title: WT Poly 71920

value: Poly


title: sDMEM 2 hr, biol rep2

value: sDMEM

value: 2 hours


title: 20 μM CuCl2 stimulated 15 min, biol rep2

value: sDMEM + 20 uM CuCl2

value: 15 min


title: HHV57DSXY_19005470_S47,TT12_A,WT_MEMORY


title: MKN28_deltaTM

city: Songpa

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: Soongsil University

data_processing:
Sequenced reads were filtered using the following criteria; reads containing more than 10% of skipped bases (marked as ‘N’), reads containing more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores are less than 20. Filtered reads were mapped to the human genome GRCh37 (Ensemble release 72) using Tophat. Gene expression levels were measured with Cufflinks v2.1.1 using the gene annotation database of Ensembl release 72. Non-coding gene regions were removed with the mask option. To improve the accuracy of measurement, multi-read-correction, and frag-bias-correct options were applied. All other options were set to default values.
Assembly: GRCh37

source_name: MKN28, a human gastric adenocarcinoma cell line

extract_protocol:
We performed RNAseq on total RNA from Luc, KIAA1324 WT-, 3NQ-, and ΔTM-expressing MKN28 cells.
RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, California, USA). Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs were subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, California, USA). The suitable fragments that were automatically purified by BluePippin 2% agarose gel cassette (Sage Science, Massachusetts, USA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies and the fragment was found to be between 350–450 bp.


title: MKN28_3NQ


title: WT Mono 71920


title: HHV57DSXY_19005468_S45,TT11_A,WT_MEMORY


title: MKN28_1324


title: WT Input 71920

value: Input


title: MKN28_Luc


title: HHV57DSXY_19005466_S70,TT10_A,WT_MEMORY


title: 20 μM CuCl2 stimulated 15 min, biol rep1


title: 10 μM CuCl2 stimulated 15 min, biol rep2

value: sDMEM + 10 uM CuCl2


title: 10 μM CuCl2 stimulated 15 min, biol rep1


title: HHV57DSXY_19005464_S57,TT9_A,WT_MEMORY

value: wildtype


title: GFP-CD34+_CBFA2T3

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

data_processing:
Sequencing reads were mapped to the human hg38 genome build using Bowtie2.
Regions of enrichment (peaks) were identified using SEACRv1.4 in stringent mode and IgG control normalization.
CBFA2T3-GLIS2 (C/G) peaks were identified by intersection of the high confidence peaks from CBFA2T3 and GLIS2 from C/G transduced cord blood samples using Bedtools intersect.
Motif enrichment and peak annotations were completed using Homerversion 4.11 with hg38 promoter sets.
Assembly: GRCh38
Supplementary files format and content: bigWig
Supplementary files format and content: bed, peak calls from SEACR
Library strategy: Cut & Run

source_name: Blood

growth_protocol: Cells were grown as described in PMID: 36136600, 500K cells were used for all CUT&RUN samples

extract_protocol:
Fresh CB samples were processed with red blood cell lysis buffer, enriched for CD34+ cells using CliniMACS CD34 MicroBeads (Miltenyi Biotec, 130-017-501), and frozen down for the future use. On the day of sort, CD34+ cells from multiple pooled CB samples (8 units each) were thawed and stained with the following antibodies: CD45RA-APC-Cyanine7, CD38-PECy7 (Invitrogen), CD34-PerCP, CD90-BV421, EPCR-BV786, Lineage cocktail (CD3, 14, 16,19,20,56)-FITC (BD Biosciences) and DAPI (to exclude dead cells)
Cut&Run data were generated from human umbilical cord blood samples transduced with CBFA2T3-GLIS2 or GFP control

treatment_protocol: The M07e cell line was seeded at 1x106 cells/ml and cultured in RPMI (Gibco) +10%FBS +1X Glutamax (Gibco) + 10ng/ml IL-3 (STEMCELL Technologies). The WSU-AML cell line was also seeded at 1x106 cells/ml, cultured in RPMI (Gibco) +10%FBS +1X Glutamax (Gibco). Both cell lines were treated with FHD-186 or BRM-014 for 48 hours. FHD-286 was added at 1nM, 10 nM, and 100 nM. BRM-014 was added at 10 nM, 100 nM, and 1000 nM. A DMSO control group was included with each drug treatment. For the CUT&RUN experiments, the M07e line was treated with 100 nM FHD-286 for 24 hours, while the WSU-AML line was treated with 10 nM FHD-286 for 24 hours.

value: Blood

value: cord blood cells

tag: antibody


title: WT Mono 71820


title: WT Input 71820


title: sDMEM 15 min, biol rep2


title: GFP-CD34+_Glis2


title: sDMEM 15 min, biol rep1


title: cKO Poly 71320

value: cKO


title: sDMEM 2 hr, biol rep1


title: HHV57DSXY_19005472_S50,TT13_A,PDH_MEMORY

value: MEMORY


title: HHV57DSXY_19005458_S52,TT6_A,PDH_EFFECTOR

value: EFFECTOR


title: HHV57DSXY_19005460_S53,TT7_A,PDH_EFFECTOR


title: GFP-CD34+_H3K27me3


title: GFP-CD34+_H3K4me3


title: HHV57DSXY_19005462_S61,TT8_A,PDH_EFFECTOR


title: cKO Mono 71320


title: HHV57DSXY_19005456_S48,TT5_A,PDH_EFFECTOR


title: cKO Input 71320


title: HNP SCZ MPRA Rep 9

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

description: Barcoded RNA

library_source: other

data_processing:
Using the barcode-variant relationship decoded from the barcode mapping step, RNA and DNA barcodes from RNA- and DNA-sequencing were mapped back to their corresponding variants. We counted the number of barcodes mapped to each variant and found that each variant was mapped to ~1000 barcodes on average. Next, we aggregated the RNA and DNA barcode counts for each variant. Because different combinations of barcodes could be introduced to different biological replicates, using the same DNA counts measured from the AAV-MPRA library for all biological replicates could lead to incorrect normalization. To mitigate this, if a given RNA barcode was missing in one biological replicate, that barcode was not counted in aggregating DNA counts for that replicate. This way, even when the DNA from the AAV-MPRA library was used, each biological replicate could have different DNA barcode counts guided by RNA barcodes. For example, if barcodes 1, 2, and 3 were mapped to the variant1, and barcode 2 was missing from the RNA barcode count, we would simply sum up the counts for barcodes 1 and 3 for both DNA and RNA. In contrast, if none of the barcodes were measured, that corresponding variant will have NA count. After merging both DNA and RNA counts by those criteria, we discarded any variants that had more than eight NAs across ten replicates.
Assembly: hg19
Supplementary files format and content: Sequenced barcodes from each replicates.

molecule: other

source_name: Human neural progenitor

growth_protocol: Human neural progenitors (HNPs) from Donor number 54 was used for all experiments. 6-well plates were coated with PBS with Poly-L-Ornithine (10 μg/ml; Sigma-Aldrich, cat#P3655-100MG) and PBS with fibronectin (5 μg/ml; Sigma-Aldrich, cat#F1141-5MG). HNPs were plated at 400K cells/well. The cells were plated in Neurobasal A media (Thermo Fisher, cat#10888022) supplemented with primocin (100 μg/ml; Invitrogen, cat#ant-pm-2), BIT 9500 (10%; STEMCELL, cat#09500), glutamax 100X (1%; Fisher Scientific, cat#5112367), Heparin (1 μg/ml; Sigma-Aldrich, cat#H3393-100KU), and growth factors: EGF (20 μg/ml; PeproTech, cat#AF-100-15), FGF (20 μg/ml; PeproTech, cat#AF-100-15), PDGF (20 ng/ml; PeproTech, cat#100-00AB), and LIF (2 ng/ml; PeproTech, cat# 300-05).

extract_protocol:
RNA was extracted from each well using Qiagen RNeasy kit (Qiagen, cat#74004), using 10 uL of Mercaptoethanol (Sigma-Aldrich, cat#60-24-2) per 1 mL of Qiagen RLT buffer. The columns were treated with DNase (Qiagen, cat#79256). To acquire an initial input of DNA put into the cells, DNA was extracted from the AAV which contained the AAV-MPRA library using a NucleoSpin virus kit (Macherey-Nagel, cat#740983.50).
The variant and barcode region of the AAV-variant-barcode library was PCR amplified using NEBNext 2X Q5 Hifi HS Mastermix with primers that contain Illumina P5 and P7 adapters (Bcmap_P5_AAV_R and Bcmap_P7_AAV_F). The PCR product was cleaned up using Zymo PCR clean and concentrator-5. The resulting library was sequenced using custom sequencing primers (BCmap_R1Seq_AAV_R and BCmap_R2Seq_AAV_F) via Novaseq 6000 SP (2x250bp) by the UNC High-Throughput Sequencing Facility (HTSF).

treatment_protocol: Each well was transduced with the AAV-MPRA library at 7,000 multiplicity of infection (MOI). One well per plate was a no-virus control to monitor general cell health. After the AAV-MPRA library was added to the cells, the plates were spun in a centrifuge for 5 minutes at 37°C at 1000 rcf. Cells were half-fed with 2X growth factors every other day for two weeks after transduction.

tag: disease state

value: Schizophrenia

value: Human neural progenitor


title: CBF-Glis CD34+_IgG_rep2

value: CBF-Glis CD34+

value: IgG


title: HNP SCZ MPRA Rep 10

description: Barcoded RNA


title: cKO Poly 71220

value: Neocortex

value: Poly


title: HNP SCZ MPRA Rep 8

description: Barcoded RNA


title: CBF-Glis CD34+_Glis2_rep2


title: PDH_Mutant 3

description: acetyl K18

data_processing:
Quality control checks were performed using FastQC (0.11.9) on raw sequence data in fastq files generated from sequencer
The fastq files were aligned to the mouse reference genome (GRCm38 or mm10) using BWA-mem(0.7.17)
The output BAM files were filtered to retain only uniquely mapping reads using Samtools(1.15.1) view
The reads overlapping with backlisted regions were removed from bam files using Samtools view. Blacklisted regions were downloaded from the ENCODE project. (https://www.encodeproject.org/files/ENCFF547MET/)
broad peak calling was performed using MACS2(2.2.6)
Diffbind(3.2) was used to identify the differentially enriched peaks between Wildtype and PDH_Mutant samples
The peak profiles were annotated using ChIPseeker(1.28.3) in R (version 4.1.0)
For visualization of peaks in UCSC Genome Browser, the bam files were first sorted and indexed using Samtools sort and Samtools index respectively and the bedGraph files were converted to bigWig files using UCSC bedGraphToBigWig tool
Assembly: GRCm38
Supplementary files format and content: broadPeak,bigWig

extract_protocol:
ABCAM (AB1191)
Chip-Seq libraries were constructed from 50 ng of ChIP DNA using Ovation Ultralow System V2 1-96 with 15 cycles of PCR amplification.  The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt).  The libraries were pooled and then quantitated by qPCR. The pool balance was checked by performing a MiSeq run using a MiSeq Nano kit, version 2. The percentage of each library in the pool was determined from the demultiplexing and was used to rebalance the pool before sequencing. The pooled libraries were sequenced on a NovaSeq 6000 using version 1.5 chemistry to achieve a minimum of 37 million 51-base reads.  The data was processed using RTA version 3.4.4.

value: memory type

tag: chip antibody

value: Acetyl histone antibodies


title: WT Poly 71820

value: WT


title: HNP SCZ MPRA Rep 7

description: Barcoded RNA


title: PDH_Mutant 2

description: acetyl K18


title: cKO Mono 71220

value: Mono


title: cKO Input 71220

value: Input


title: PDH_Mutant 1

description: acetyl K18


title: CBF-Glis CD34+_IgG_rep1


title: HNP SCZ MPRA Rep 6

description: Barcoded RNA


title: CBF-Glis CD34+_H3K4me3_rep2


title: HNP SCZ MPRA Rep 5

description: Barcoded RNA


title: Wildtype 2

description: acetyl K18

value: wildtype


title: CBF-Glis CD34+_Glis2_rep1

value: Blood


title: Wildtype 1

description: acetyl K18


title: CREB_antibody_2

city: Cold Spring Harbor

first: Lingbo

last: Zhang

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Fragmented genomic DNA from BFU-E was immunoprecipitated with anti-CREB antibody

data_processing:
RNA-Seq reads were alligned to the mm10 genome using STAR mapper.
ChIP-seq reads were aligned to the mm10 genome
MACS platform was used for peak calling
Genome_build: mm10

source_name: BFU-E

growth_protocol: BFU-Es were isolated and cultured in StemSpan SFEM II medium

extract_protocol:
For RNA-Seq, cells were collected for RNA extraction using Rneasy mini kit by Qiagen. For ChIP-Seq, genomic DNA samples were prepared using ChIP-IT high sensitivity kit by Active Motif.
RNA-Seq and ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-Seq (sample 1 to 6), BFU-Es were cultured in StemSpan SFEM II medium with either DMSO or 100uM of compound OB, and for RNA-Seq (sample 7 to 12), BFU-Es were cultured with either DMSO or 3nM of compound PD.

value: fetal liver

value: early erythroid progenitor

value: anti-CREB


title: HNP SCZ MPRA Rep 3

description: Barcoded RNA


title: Input_control_1

description: Fragmented genomic DNA from BFU-E was used to prepare  control library sample


title: CBF-Glis CD34+_CBFA2T3_rep1

value: cord blood cells


title: HNP SCZ MPRA Rep 4

description: Barcoded RNA

value: Schizophrenia


title: Compound PD_3

value: Treated with compound PD 3nM


title: Compound PD_2


title: HNP SCZ MPRA Rep 1

description: Barcoded RNA

value: Human neural progenitor


title: CBF-Glis CD34+_CBFA2T3_rep2

value: CBF-Glis CD34+


title: HFSC_media_rep2

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm10) using Salmon (v 1.4.0)
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts with Tximport (v 1.12.3) in R (v 3.6.1)(Salmon aligned data)
Assembly: mm10 (UCSC release)
Supplementary files format and content: tab-delineated text files contain raw counts and tab-delineated text files contain calculated TPM

source_name: wild type mouse HFSC, cultured

extract_protocol:
Cells were isolated by FACS, and collected into trizol. RNA was extracted using the Direct-zol RNA extraction kit (Zymo) following manufacturer's instructions.
RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit. Libraries were sequenced on an Illumina HiSeq 4000 or NovaSeq instrument as indicated.

tag: mouse age

value: 8 wks

tag: mouse strain

value: cultured hair follicle stem cells

tag: passage #

tag: sorting scheme

tag: read alignment program

value: Salmon (v 1.4.0)

tag: read quantification program

value: Tximport (v 1.12.3)

tag: biological replicate

value: Biol rep 2


title: CBF-Glis CD34+_H3K4me1

tag: cell line

tag: cell type


title: Compound PD_1

tag: treatment


title: HFSC_media_rep1

tag: genotype

value: Biol rep 1


title: PD_Control DMSO_3

tag: tissue

value: Treated with DMSO


title: CBF-Glis CD34+_H3K4me3_rep1


title: ATAC non-Treg non-Tfh IL10(-) Young

city: Cincinnati

first: Joseph

last: Wayman

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

data_processing:
We aligned reads to mm10 using Bowtie2 (option: --very-sensitive). Using SAMtools (v1.9.0), we filtered reads (option: -q 30), removed duplicates, kept reads aligning to autosomal or X chromosomes, and removed reads aligning to ENCODE blacklist regions. We shifted aligned fragment ends by 5 bp to identify Tn5 transposase cut sites. To compare population-level and single-cell ATAC-seq, the population-level cut sites were mapped to the scATAC-seq reference peak set using the featureCounts function from Rsubread.
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: Spleen

extract_protocol:
Young (≤4 months) and old (≥18 months) IL-10-GFP x Foxp3-RFP mice were generated by crossing IL-10-reporter (VertX) mice to Foxp3-IRES-mRFP mice and aged in house. Spleens were harvested and crushed through 100-um filters to generate single-cell suspensions. CD4+ memory T cells were enriched using the negative selection magnetic-activated cell sorting CD4+ T cell isolation kit II. Enriched CD4+ T cells were stained with fluorescent antibodies against CD4, CD44, CD62L, CXCR5 and PD1 and the following sorting strategy was used to isolate T cells into 3 groups for bulk RNA-seq and ATAC-seq: "Tfh10" (CD4+CD44hiCD62LloCXCR5+PD1+GFP+RFP-), Treg (CD4+RFP+) and non-Treg-non-Tfh-IL10- (CD4+CD44hiCD62LloCXCR5-PD1-RFP-GFP-).
ATAC-seq was performed using the OMNI-ATAC protocol.

value: Spleen

value: CD4+TM Foxp3-RFP-CXCR5-PD1-IL10-GFP-

value: Foxp3-RFP; IL10-GFP double-reporter

tag: age

value: ≤4 months


title: ATAC non-Treg non-Tfh IL10(-) Old

tag: strain

value: ≥18 months


title: Atac 33947_shR-3

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis

data_processing:
At least 45 million omni-ATAC reads per sample were processed by Partek Flow® Software Analysis Pipeline.
AIAP trims adapters using Cutadapt
AIAP aligns fragments using BWA to the hg38 human reference genome
AIAP normalizes count signal by 10 million input single end reads
AIAP call peaks by GSA with p-value less than 0.05
Assembly: hg38
Supplementary files format and content: bigWig files of biological replicates for ATAC-seq experiments

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)

value: NHCDR ND33947

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L

tag: shRNA


title: Atac 33947_shR-2


title: Neocortex Late N.A.4 [18 PCW]

library_source: transcriptomic single cell

data_processing:
Base-calling was performed by GeneWiz using Illumina software.
Fastq files were filtered, aligned with combined hg38 and mm10 reference index, and assigned to barcodes using 10X Genomics cellranger software v 4.0.0
Counts files (filtered_feature_bc_matrix.h5) were loaded into Seurat v 4.0.2 for sample merging, filtering, clustering and analysis of gene expression
Assembly: hg38
Supplementary files format and content: Output from combined Seurat data object with the GetAssay(slot="counts") command.  File is tab-delimited text file containing counts for sample-barcodes x genes.

growth_protocol: Human prefrontal cortex samples (11-18 PCW) were dissected and frozen.

extract_protocol: Single-cell cDNA libraries were generated using the Chromium Next GEM Single Cell 3’ GEM Reagent Kits v3.1 (10X Genomics).

treatment_protocol: Samples were delivered to GeneWiz/Azenta for preparation, library construction, and sequencing.

value: Neocortex

value: 18 PCW

tag: developmental stage

value: Late


title: ATAC Treg Old

value: CD4+TM Foxp3-RFP+IL10-GFP+


title: PD_Control DMSO_2

value: fetal liver

value: early erythroid progenitor


title: Atac 33947_shR-1


title: Neocortex Late N.A.3 [18 PCW]


title: PD_Control DMSO_1


title: HNP SCZ MPRA Rep 2

description: Barcoded RNA

tag: disease state

value: Schizophrenia

value: Human neural progenitor


title: Atac 33947_shCN-3

value: shCalcineurin


title: CBF-Glis CD34+_H3K27me3

value: Blood

value: CBF-Glis CD34+

value: cord blood cells

tag: antibody


title: Neocortex Late N.A.4 [17 PCW]

value: 17 PCW


title: ATAC Tfh10 Old Rep 2

value: Spleen

value: CD4+TM Foxp3-RFP-CXCR5+PD1+IL10-GFP+

value: Foxp3-RFP; IL10-GFP double-reporter


title: Compound_OB_3

value: Treated with compound OB 100uM


title: Atac 33947_shCN-2

value: NHCDR ND33947

value: CTIP2, DLX1, DLX2, MYT1L


title: Neocortex Late N.A.3 [17 PCW]

value: Neocortex

value: Late


title: Atac 33947_shCN-1


title: ATAC Tfh10 Old Rep 1

value: ≥18 months


title: Compound OB_2

value: fetal liver

value: early erythroid progenitor


title: ATAC Tfh10 Young Rep 2

value: ≤4 months


title: Neocortex Mid N.A.4 [15 PCW]

value: 15 PCW

value: Mid


title: ATAC Tfh10 Young Rep 1


title: Neocortex Mid N.A.3 [15 PCW]


title: Atac 33947_shC-3

value: shControl


title: Atac 33947_shC-2


title: Neocortex Mid N.A.4 [14 PCW]

value: 14 PCW


title: OB_Control DMSO_2

value: Treated with DMSO


title: ATAC Treg Young

value: Spleen

value: CD4+TM Foxp3-RFP+IL10-GFP+


title: Atac 33947_shC-1


title: RNA non-Treg non-Tfh IL10(-) Old Rep 1

data_processing:
We aligned reads to mm10 using Bowtie2 (option: --very-sensitive). Using SAMtools (v1.9.0), we filtered reads (option: -q 30), removed duplicates, and kept reads aligning to autosomal or X chromosomes. We generated a gene-level counts matrix for all samples using the featureCounts function from the R package Rsubread.
Assembly: mm10
Supplementary files format and content: Tab-separated values files

extract_protocol:
Young (≤4 months) and old (≥18 months) IL-10-GFP x Foxp3-RFP mice were generated by crossing IL-10-reporter (VertX) mice to Foxp3-IRES-mRFP mice and aged in house. Spleens were harvested and crushed through 100-um filters to generate single-cell suspensions. CD4+ memory T cells were enriched using the negative selection magnetic-activated cell sorting CD4+ T cell isolation kit II. Enriched CD4+ T cells were stained with fluorescent antibodies against CD4, CD44, CD62L, CXCR5 and PD1 and the following sorting strategy was used to isolate T cells into 3 groups for bulk RNA-seq and ATAC-seq: "Tfh10" (CD4+CD44hiCD62LloCXCR5+PD1+GFP+RFP-), Treg (CD4+RFP+) and non-Treg-non-Tfh-IL10- (CD4+CD44hiCD62LloCXCR5-PD1-RFP-GFP-).
RNA-seq libraries were constructed using the NEBNext Ultra II directional (dUTP) RNA-seq kit.

value: CD4+TM Foxp3-RFP-CXCR5-PD1-IL10-GFP-

value: Foxp3-RFP; IL10-GFP double-reporter


title: Neocortex Mid N.A.3 [14 PCW]


title: Atac 30013_shR-3

value: NHCDR ND30013


title: OB_Control DMSO_1


title: Neocortex Early N.A.2 [12 PCW]

value: 12 PCW

value: Early


title: Atac 30013_shR-2

value: CTIP2, DLX1, DLX2, MYT1L


title: Neocortex Early 15154.1 [12 PCW]

value: Neocortex


title: RNA Treg Old Rep 2

value: ≥18 months


title: Atac 30013_shR-1


title: Neocortex Early N.A.3 [11 PCW]

value: 11 PCW


title: IMCISION, scRNAseq

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: UMI count table on the transcript profiling of CD45+ cells

data_processing:
Gene expression, antibody, and TCR sequencing reads were respectively mapped to the GRCh38 human reference genome, antibody reference sequences, and IMGT reference using CellRanger Version 3.1 (10x Genomics). The unfiltered UMI matrices for gene expression and antibody libraries were used. Demultiplexing of the sample hashtags was done using the HTOdemux function, part of the Seurat package Version 4.0.1, with the positive quantile set to 0.99.
Cells were filtered based on the following criteria: less than 800 unique molecular identifiers (UMIs), a fraction of mitochondrial gene expression that exceeded 0.5, or with more than one hashtag (multiplets). Downstream analysis were performed with the MetaCell package (V0.3.5).
Supplementary files format and content: Table of UMI counts. Columns: cell ids Rows: gene names
Assembly: hg38
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: tumor

extract_protocol:
Single cell suspensions were generated using enzymatic digestion of biopsied material. CD45+ immune cells were isolated from single cell suspension using fluorescence-associated flow sorting (FACS).
Single cell RNA, antibody barcode, and TCR libraries were constructed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 for human (10X Genomics), according to the manufacturer’s protocol. Libraries were sequenced on a NextSeq instrument (Illumina) with read lengths of 26/58 for RNA and antibody libraries and 26/91 or 26/130 for TCR libraries, aiming for 30,000 read pairs per cell for RNA libraries and 5,000 reads for both antibody and TCR libraries.

value: tumor

tag: patient

value: mixed samples (Pat04, Pat10, Pat12, Pat15, Pat17, Pat21, Pat22, Pat26, Pat27, Pat29, Pat30, Pat31, Pat33, Pat34, Pat36, Pat37, Pat38, Pat39)

value: CD45+ cells

tag: timepoint

value: mixed samples (post, pre)

tag: response

value: mixed samples (RE, NR)


title: RNA Treg Old Rep 1


title: IMCISION, meta data (scTCRseq and scRNAseq)

description: Annotation data per cell

data_processing:
Gene expression, antibody, and TCR sequencing reads were respectively mapped to the GRCh38 human reference genome, antibody reference sequences, and IMGT reference using CellRanger Version 3.1 (10x Genomics). The unfiltered UMI matrices for gene expression and antibody libraries were used. Demultiplexing of the sample hashtags was done using the HTOdemux function, part of the Seurat package Version 4.0.1, with the positive quantile set to 0.99.
Cells were filtered based on the following criteria: less than 800 unique molecular identifiers (UMIs), a fraction of mitochondrial gene expression that exceeded 0.5, or with more than one hashtag (multiplets). Downstream analysis were performed with the MetaCell package (V0.3.5).
Supplementary files format and content: Table with the annotation data per cell, including cell state, patient ID, clone ID, timepoint and response. The "cell_id" column corresponds to column names in the count table.
Assembly: hg38
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)


title: HkNR [MK_EOG_015]

city: Boston

first: Stefano

last: Monti

state: Massachusetts

address: 72 East Concord Street,

department: Medicine

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing:
Host Alignment and Mapping: featureCounts() from Rsubread
Microbiome Alignment and Mapping: Pathoscope 2.0
Assembly: GRCh38.99
Supplementary files format and content: tab-delimited host gene expression profiles
Supplementary files format and content: tab-delimited microbial abundance
Supplementary files format and content: tab-delimited sample annotations

source_name: oral mucosa

extract_protocol:
Total RNA integrity was verified using RNA 6000 Pico Assay chips run on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). To deplete ribosomal RNA, 100 ng of total RNA from each sample was incubated with RiboErase Mouse rRNA depletion oligos per the manufacturer’s instructions using Kapa RiboErase (HMR) Module (Kapa Biosystems, USA). Resulting rRNA duplexed with DNA oligos were digested with RNase H treatment.
Libraries were then prepared using Kapa RNA HyperPrep Library Preparation Kit according to the manufacturer’s protocol. Briefly, after rRNA depletion, the RNA was fragmented at 94C for 6 minutes. First strand cDNA was generated, and dUTP was incorporated during synthesis of second strand cDNA. Next, double-stranded cDNA underwent A-tailing, adaptor ligation, and incorporation of sample-specific multiplex indices before PCR amplification (12 cycles) according to the manufacturer’s protocol (Kapa Biosystems, USA). Size distribution and molarity of amplified cDNA libraries were assessed via the Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA). All cDNA libraries were sequenced on an Illumina NextSeq 500 instrument with 1.45 pM input and 1% PhiX control library spiked in (Illumina, USA) targeting 30-40 Million reads pairs per sample.

value: oral mucosa

tag: group

value: premalignant lesions


title: OB_Control_DMSO_3

value: fetal liver

value: early erythroid progenitor

value: Treated with DMSO


title: Neocortex Early 15155.3 [11 PCW]


title: Atac 30013_shCN-3

tag: cell line

value: NHCDR ND30013

value: shCalcineurin


title: Compound OB_1

tag: cell type

value: Treated with compound OB 100uM


title: RNA non-Treg non-Tfh IL10(-) Old Rep 2

value: Spleen

value: CD4+TM Foxp3-RFP-CXCR5-PD1-IL10-GFP-

value: Foxp3-RFP; IL10-GFP double-reporter


title: HkNR [MK_EOG_009]


title: RNA Tfh10 Old Rep 2

value: CD4+TM Foxp3-RFP-CXCR5+PD1+IL10-GFP+

value: ≥18 months


title: RNA Treg Young

value: CD4+TM Foxp3-RFP+IL10-GFP+

value: ≤4 months


title: PFC_IGG_15506_17

data_processing:
Primers trimmed with Trimmomatic v0.3.6
Aligned with GRCh38 reference assembly with STAR v2.5.2b
Counts extracted with featureCounts from the Subread package (v1.5.2)
Counts imported to DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited normalized counts per sample per Ensembl gene ID exported from DESeq2

source_name: Prefrontal cortex

growth_protocol: Human prefrontal cortex samples (11-20 PCW) were dissected and frozen.

extract_protocol: Illumina TruSeq RNA Library Kit

treatment_protocol: Cell lysate was incubed with EZ-Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore) beads precoated with either CELF4 antibody (Invitrogen) or IgG rabbit antibody (Millipore).  Following binding overnight, beads were washed, proteins were digested, and RNA extracted with Phenol:chloroform:isoamyl alcohol, and precipitated with salt solutions.  RNA was treated with TURBO DNA-free kit (Invitrogen) prior to library construction.

value: Prefrontal cortex

value: IGG


title: Control [MK_EOG_005]

value: oral mucosa

value: Control


title: Atac 30013_shCN-1

value: CTIP2, DLX1, DLX2, MYT1L


title: RNA Tfh10 Old Rep 1


title: Atac 30013_shCN-2


title: RNA Tfh10 Young


title: PFC_IGG_15296_15


title: Atac 30013_shC-2

value: shControl


title: PFC_CELF4_15296_15


title: Atac 30013_shC-1


title: Control [MK_EOG_001]


title: scATAC CD4+TM Old IL10(+) Rep 2

description: 10x Genomics

library_source: genomic single cell

data_processing:
Alignment, initial cell barcode filtering, identification of transposase cut sites, and initial peak calling was performed using Cell Ranger ATAC version 2.0.0 and the 10x Genomics pre-built mm10 genome reference 2020-A. Cell barcodes were retained that had greater than 5,000 cut sites in peaks, greater than 50% fragments in peaks, and a minimum TSS enrichment score of 3. The Seurat workflow was used for normalization, dimension reduction, sample integration and clustering. Integration and clustering was performed using a reference peak set based on the MACS2 peak-calling algorithm. Pseudobulk accessibility profiles were generated by aggregating transposase cut sites from cells from each cell-type and sample. Pseudobulk accessibility was normalized using DESeq2 variance-stabilization transformation and batch correction by ComBat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: R data format of Seurat object containing integrated samples and meta data.

extract_protocol:
Spleens were harvested and crushed through 100-um filters to generate single-cell suspensions. CD4+ memory T cells were enriched using the negative selection magnetic-activated cell sorting CD4+ T cell isolation kit II. Enriched cells were stained with anti-CD4, anti-CD44, and anti-CD62L antibodies and sorted for memory CD4+ T cells (CD4+CD44hiCD62Llo) that were either GFP+ (IL10+) or GFP- (IL10-) by flow. Nuclei were isolated from sorted cell populations by resuspending sorted cell pellets in pre-chilled lysis buffer (Tris-Hcl (10mM), NaCl (10mM), MgCl2 (3mM), Tween20 (0.1%), Nonidet P40 substitute (0.1%), Digitonin (0.01%), BSA (1%) in Nuclease-free water) for 3 minutes. Chilled wash buffer was added, mixed by pipetting, centrifuged at 500 x g, and nuclei were resuspended in Nuclei buffer (10x Genomics).
Nuclei were prepared for droplet-based scATAC-seq using the 10x Genomics Single-Cell ATAC Reagent Kit. Barcoded cDNA were isolated with Dynabeads MyOne SILANE bead cleanup mixture and SPRI bead cleanup.

value: CD4+ memory T cells

tag: sorted cells

value: IL10-GFP-reporter (VertX)


title: Control [MK_EOG_012]


title: Dysplasia [MK_B-0024]

value: premalignant lesions


title: Atac 4230_shR-3

value: Coriell GM04230


title: scATAC CD4+TM Old IL10(-) Rep 2

description: 10x Genomics

value: Spleen

tag: genotype


title: PFC_IGG_15294_18

tag: tissue


title: scATAC CD4+TM Young IL10(-) Rep 2

description: 10x Genomics

tag: age


title: scATAC CD4+TM Young IL10(+) Rep 2

description: 10x Genomics

tag: strain


title: Atac 4230_shR-2

tag: overexpression 1


title: Atac 4230_shR-1

tag: overexpression 2


title: PFC_CELF4_15506_17


title: Cancer [MK_B-0022]

value: OSCC


title: PFC_CELF4_15295_14


title: Control [MK_B-0021]


title: scATAC CD4+TM Old IL10(+) Rep 1

description: 10x Genomics


title: Control [MK_EOG_004]


title: PFC_CELF4_15294_18


title: Atac 30013_shC-3

value: NHCDR ND30013

tag: shRNA


title: PFC_IGG_15293_20


title: Atac 4230_shCN-3

value: shCalcineurin


title: scATAC CD4+TM Old IL10(-) Rep 1

description: 10x Genomics

value: ≥18 months


title: Cancer [MK_B-018]


title: PFC_CELF4_15293_20


title: Dysplasia [MK_B-016]


title: scATAC CD4+TM Young IL10(+) Rep 1

description: 10x Genomics


title: PFC_IGG_15158_11


title: Dysplasia [MK_B-014]


title: PFC_IGG_15295_14


title: PFC_IGG_15154_12


title: Cancer [MK_B-0019]


title: scRNA CD4+TM Old IL10(-) Rep 2

description: 10x Genomics

data_processing:
Alignment, initial cell barcode filtering, and UMI counting was performed using Cell Ranger version 3.1.0 and the 10x Genomics pre-built mm10 genome reference 2020-A. Downstream quality control and analyses was performed in R version 4.0.2, using workflows from Seurat v4.04. Cell doublets using DoubletFinder. Cell barcodes were retained that had at least one UMI count from 500 genes, greater than 1,000 total UMI counts, and less than 15% of UMIs corresponding to mitochondrial transcripts. The Seurat workflow was used for normalization, dimension reduction, sample integration and clustering. Pseudobulk expression profiles were generated by aggregating UMIs from cells from each cell-type and sample. Pseudobulk expression was normalized using DESeq2 variance-stabilization transformation and batch correction by ComBat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: R data format of Seurat object containing integrated samples and meta data.

extract_protocol:
Spleens were harvested and crushed through 100-um filters to generate single-cell suspensions. CD4+ memory T cells were enriched using the negative selection magnetic-activated cell sorting CD4+ T cell isolation kit II. Enriched cells were stained with anti-CD4, anti-CD44, and anti-CD62L antibodies and sorted for memory CD4+ T cells (CD4+CD44hiCD62Llo) that were either GFP+ (IL10+) or GFP- (IL10-) by flow.
Cells were prepared for droplet-based scRNA-seq using the 10x Genomics v3 Single Cell 3ʹ Reagent Kit. Barcoded cDNA was amplified by PCR and purified using SPRI bead cleanup. Gene expression libraries were prepared with 50 ng of amplified cDNA.


title: scRNA CD4+TM Old IL10(+) Rep 2

description: 10x Genomics


title: scATAC CD4+TM Young IL10(-) Rep 1

description: 10x Genomics


title: Atac 4230_shC-3


title: Atac 4230_shC-1


title: Dysplasia [MK_B-013]


title: Control [MK_B-0012]


title: Control [MK_B-0008]


title: scRNA CD4+TM Young IL10(-) Rep 2

description: 10x Genomics


title: Atac 4230_shC-2


title: PFC_CELF4_15154_12


title: PFC_IGG_15053_12


title: Atac 4230_shCN-2


title: RNA non-Treg non-Tfh IL10(-) Young

value: CD4+TM Foxp3-RFP-CXCR5-PD1-IL10-GFP-

value: Foxp3-RFP; IL10-GFP double-reporter


title: scRNA CD4+TM Young IL10(+) Rep 2

description: 10x Genomics

value: ≤4 months


title: Atac 4198_shR-3

value: Coriell GM04198


title: PFC_CELF4_15053_12

value: Prefrontal cortex


title: Atac 4198_shR-2


title: scRNA CD4+TM Old IL10(+) Rep 1

description: 10x Genomics


title: Control [MK_B-0005]

value: oral mucosa

value: Control


title: Atac 4230_shCN-1

value: CTIP2, DLX1, DLX2, MYT1L


title: Control [MK_B-0004]


title: 120520-Human-PFC-15293-2-20PCW-Poly

description: 20PCW Poly

extract_protocol:
Human fresh frozen neocortices from 11 to 20 PCW were homogenized in freshly prepared polysome extraction buffer supplemented with EDTA-free protease inhibitor, RNaseOut, DTT, and cycloheximide. Lysis was performed by pipetting gently up and down on ice for 15 minutes.  Lysate was centrifuged at 5k rpm for 10 min at 4C and the resulting supernatant was spun at 14k for 5 min at 4C.  Following quantification, 120 ug neocortical input was layered onto 10-50% sucrose density gradients in thin wall polypropylene tubes. A portion (25%) was stored for processing as input. Gradients were spun at 39K rpm at 4C for 120 min.  Polysome profiles were generated with a continuous flow Fluorinert FC-40 and A254 recording with a Brandel fraction collector with UV absorbance recorder.  Samples were frozen at -80C until use.  Pooled monosomes (40S-60S-80S) and polysomes fractions were pooled for isolation of RNA by extraction with TRIzol LS.  RNA was precipitated with one volume of isopropanol/glycogen, then washed with 75% ethanol and air-dried.  Following resuspension, genomic DNA was destroyed with DNase treatment.
Illumina TruSeq RNA Library Kit

value: Neocortex

tag: developmental stage

tag: fraction

value: Poly


title: scRNA CD4+TM Old IL10(-) Rep 1

description: 10x Genomics

value: CD4+ memory T cells

value: IL10-GFP-reporter (VertX)


title: Dysplasia [MK_B-0003]

value: premalignant lesions


title: PFC_CELF4_15158_11

tag: antibody


title: Atac 4198_shR-1


title: Control [MK_B-0002]


title: 120520-Human-PFC-15293-2-20PCW-Mono

description: 20PCW Mono

value: Mono


title: scRNA CD4+TM Young IL10(+) Rep 1

description: 10x Genomics

value: Spleen


title: Atac 4198_shCN-3

value: shCalcineurin


title: Dysplasia [MK_B-0007]


title: 120520-Human-PFC-15293-2-20PCW-Input

description: 20PCW Input

value: Input


title: Atac 4198_shCN-2


title: Atac 4198_shCN-1


title: 120420-Human-PFC-15293-1-20PCW-Mono

description: 20PCW Mono


title: Atac 4198_shC-3

value: shControl


title: Dysplasia [MK_B6A]


title: 120420-Human-PFC-15293-1-20PCW-Poly

description: 20PCW Poly


title: BVSC Gastruloid, 120h, Blimp1-Venus+SSEA1+, rep1

city: London

first: Naomi

last: Moris

address: 1 Midland Way

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Base calling by bcl2fastq 2.20.0
Quantification using Cell Ranger 6.1.2 against refdata-gex-mm10-2020-A
Downstream analysis using Seurat 4.0.3 in R 4.1.1
Assembly: mm10
Supplementary files format and content: Tarball archive of Cell Ranger raw and filtered feature matrices
Supplementary files format and content: Plain text file of cell barcodes used in the analysis

source_name: Mouse gastruloid

growth_protocol: Mouse ESC lines were routinely cultured in 2iLif in N2B27 (NDiff227 Takara Bio, Y40002, supplemented with 3µM CHIR99021 (Chi), 1µM PD0325901 (PD03) and 11ng/ml mLIF) on gelatinised (0.1% gelatin) tissue culture flasks or 6-well plates kept in humidified incubators at 37°C, 5% CO2. Cells were passaged into new flasks or plates every two days with media exchanged daily.

extract_protocol:
Gastruloids were collected and washed twice in PBS before incubating at room temperature for 8 mins in Trypsin-EDTA before quenching with 10% FBS in PBS. Cells were pelleted at 230xg for 5mins before resuspending in filtered 1% FBS in PBS. Cell solution was passed through tube filter (35µm) then counted and divided into tubes before antibody addition. Incubated at 4°C on rotator for 1 hour then centrifuged at 800 rpm for 5 mins at 4°C. Supernatants were aspirated and sample washed with filtered 1% FBS in PBS before repeating wash and transferring to chilled flow tubes. Cells were loaded onto a BD FACSAria™ Fusion III (BD Biosciences) for sorting. Sorting was based on the reporters Stella::CFP, Blimp1::mVenus or PECAM1-PE and SSEA1-A647 antibodies. Sorted cells were transferred to DNA low-bind tubes and centrifuged at 300 rcf for 5 mins at 4°C. The supernatant was aspirated and, using cut tips, 1ml of chilled PBS pipetted up and down 10 times. This was repeated twice more, and after the final centrifugation step the cells were resuspended in 200µl chilled PBS then 800µl of chilled 100% methanol added dropwise and with stirring. Fixed cells were stored at -80°C until ready for 10x preparation for scRNAseq.
The sorted, fixed and frozen cells were thawed on ice for 5 minutes before centrifugation at 1,000 xg for 5 minutes (at 4°C). Supernatant was carefully aspirated without disturbing the pellet before resuspending the pellet in the appropriate volume of Wash-Resuspension buffer; 3x SSC Buffer (Invitrogen, 15557-044) supplemented with 0.04% Bovine Serum Albumin (BSA) (Invitrogen, AM2616), 1mM DL-Dithiothreitol solution (DTT) (Sigma-Aldrich, 646563) and 0.2U/µl Protector RNase inhibitor (Roche, 3335399001) to give 1000 cells/µl in 50µl or minimum volume of 50µl if not possible to obtain that concentration. Quality control on the cells and counts were performed on a Luna FX7 cell counter (Logos biosystems) prior to applying to 10x Chromium library preparation performed according to manufacturer’s instructions. Single cell libraries of 100 bp paired-end reads were pooled and sequenced on HiSeq 4000 to perform single cell RNA sequencing (scRNAseq).

treatment_protocol: Gastruloids were prepared following published protocols. Briefly, mESCs were trypsinized and pelleted, with the cell pellet washed in PBS before repeating the process then resuspending in N2B27. The cells were counted and diluted to provide 300 cells per well, before pipetting into cell-repellent, ultra-low attachment 96-well plates (Greiner). Aggregates were incubated at 37°C, 5% CO2 in a humidified incubator. After 48 hours, N2B27 supplemented with 3µM Chi was added, and every subsequent 24 hours the media was aspirated and replaced with fresh N2B27.

value: Mouse gastruloid

value: 120h after aggregation

tag: sorted population


title: scRNA CD4+TM Young IL10(-) Rep 1

description: 10x Genomics

value: ≤4 months


title: 120420-Human-PFC-15293-1-20PCW-Input

description: 20PCW Input


title: Control [MK_B6C]


title: Atac 4198_shC-1

value: Coriell GM04198


title: Atac 4198_shC-2


title: 120320-Human-PFC-15294-2-18PCW-Poly

description: 18PCW Poly


title: BVSC Gastruloid, 120h, STELLA+, rep1

tag: timepoint

value: STELLA+


title: Skin - Gut axis, scRNAseq 2

city: San Diego

first: Tatsuya

last: Dokoshi

state: California

address: 9500 Gilman

department: Department of Dermatology

institute: Univeristy of California, San Diego

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole colon

extract_protocol:
Freshly collected whole colon  were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissues were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2.5 mg/mL Collagenase D and 30 ng/mL DNAse1) and incubated at 37 °C for 40 min. Tissues were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: whole colon

value: section of the large intestine

value: C57BL/6 back ground mouse

tag: treatment


title: BVSC Gastruloid, 120h, PECAM1+, rep1


title: HkNR [MK_4]

value: oral mucosa

tag: group


title: 120320-Human-PFC-15294-2-18PCW-Mono

description: 18PCW Mono

value: Neocortex


title: Patient 3 Group: Exercise (End-of-Study) rep_3

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fastq files were processed to GeoMx readable digital counts (DCC) files by GeoMx NGS Pipeline software
Raw count was normalized by Q3 method
Assembly: hg38
Supplementary files format and content: NanoString GeoMx Digital Count Conversion (DCC) file.
Supplementary files format and content: normalized count in tab seperated files

source_name: colorectal mucosa

extract_protocol:
Formalin‐fixed paraffin‐embedded (FFPE) normal colorectal mucosa specimens from participants for the usual and exercise groups with pre and post intervention) were used to perform GeoMx Digital Spatial Profiling (DSP). Each sample was scanned to generate a digital image. Region of interest (ROIs) were selected in the epithelium (2-6 per ROI per sample, size of each ROI between 27000-340000 mm2), including areas rich in crypts, at least 3 mm away of the edges, and avoiding tissue artifacts such as wrinkles and tears of the tissue. The selection of the ROIs was supervised by a trained pathologist
The library was prepared by GeoMx Human Whole Transcriptome Atlas kit as the manufactures' manual.

value: colorectal mucosa

tag: patient diagnosis

value: Lynch syndrome

value: Exercise

tag: patient id

tag: gender

value: M

tag: race

value: White or Caucasian

tag: ethinicity

value: Not Hispanic or Latino

tag: gene mutated

tag: visit

value: End-of-Study


title: Skin - Gut axis, scRNAseq 1

tag: tissue

tag: cell type

tag: strain


title: Patient 3 Group: Exercise (End-of-Study) rep_2

tag: age


title: 120320-Human-PFC-15294-2-18PCW-Input

description: 18PCW Input

tag: developmental stage

tag: fraction

value: Input


title: Dysplasia [MK_6]

value: premalignant lesions


title: Patient 3 Group: Exercise (End-of-Study) rep_1


title: Skin - Gut axis, spatialRNAseq 4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the space Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: spatialRNA-seq

extract_protocol:
Colonic tissues from untreated and DSS-treated mice from WT and K14/HYAL1 mouse were cleaned from adipose tissue and cut longitudinally; the luminal content was removed by washing it in cold phosphate buffered saline (PBS). Starting from the most proximal portion (i.e., Cecum) and with the luminal side facing upward, the colon was rolled resulting in a roll with the proximal colon in the center and the distal colon in the outer portion of the roll. The roll was placed in a histology plastic cassette and snap frozen for 1 min in a bath of liquid nitrogen-cooled isopentane. The frozen tissue was then embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at −80 °C. OCT blocks were cut with a pre-cooled cryostat at 10um thickness, and sections were transferred to fit the 6.5mm2 oligo-barcoded capture areas on the Visium 10x Genomics slide. Before performing the complete protocol, Visium Spatial Tissue Optimization (10x Genomics) was performed according to manufacturer’s instructions, and the fluorescent footprint was imaged using a Metafer Slide Scanning Platform (Metasystems). 9 minutes was selected as optimal permeabilization time.
The experimental slide with colonic tissue was fixed and stained with hematoxylin and eosin (H&E) and imaged using a Keyence BZX-700 Fluorescent Microscopy (Keyence) at 2X magnification. Sequence libraries were then processed according to manufacturer’s instructions (10x Genomics, Visium Spatial Transcriptomic)

value: 2.5% DSS for 7 days


title: Skin - Gut axis, spatialRNAseq 3


title: 120220-Human-PFC-15294-1-18PCW-Poly

description: 18PCW Poly

value: Poly


title: Patient 3 Group: Exercise (Baseline) rep_3

value: Baseline


title: Control [MK_3]

value: Control


title: Cancer [MK_54]

value: OSCC


title: 120220-Human-PFC-15294-1-18PCW-Mono

description: 18PCW Mono

value: Mono


title: Patient 3 Group: Exercise (Baseline) rep_2


title: 120220-Human-PFC-15294-1-18PCW-Input

description: 18PCW Input


title: Patient 3 Group: Exercise (Baseline) rep_1


title: 120120-Human-PFC-N-A-1-17PCW-Poly

description: 17PCW Poly


title: Skin - Gut axis, spatialRNAseq 2

value: whole colon

value: section of the large intestine

value: C57BL/6 back ground mouse


title: Skin - Gut axis, spatialRNAseq 1


title: Control [MK_27]

value: oral mucosa


title: HkNR [MK_51]


title: HkNR [MK_36]


title: Dysplasia [MK_A]


title: CAFs Tumor 15

city: Rochester

first: Scott

last: Gerber

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

description: deSeq2_d14_CAF_1-5_vs_d14_CAF_A.txt; deSeq2_d14_CAF_1-5_vs_d14_CAF_B.txt; deSeq2_d14_CAF_A_vs_d14_CAF_B.txt

data_processing:
Raw fastq files were prepared by trimming and filtering for quality using fastp-0.20.1, followed by the removal of the adapter sequences. Files were aligned to m39 mouse reference genome using STAR-2.7.6a aligner and converted to gene counts using featurcounts-2.0.1 and mouse annotation M27. DESeq2-1.28.1 package in R-4.0.2 was used to perform differential expression and normalization. For low expression genes, ifcShrink was applied. The differentially expressed genes were identified using a Wald test statistic with adjusted P value threshold of ≤.05.
Assembly: mm39
Supplementary files format and content: Tab-delineated text file includes raw and normalized read counts for every gene across each sample.

source_name: Rectal Tumor

growth_protocol: MC38 cells grown in MAT/P media supplemented with 2% FBS

extract_protocol:
tumors were harvested, dissocaited in collagenase, and cells lysed in buffer RLT
Total RNA was extracted following the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol before being sequenced by the Genomics Research Core. Quality control was determined by RNA concentration using the NanopDrop 1000 Spectrophotometer (NanoDrop), and RNA quality was measured using the Agilent Bioanalyzer 2100 (Agilent). The SMARTer Ultra Low Input kit v4 (Clontech) was used to preamplify 1 ng of total RNA, and the resulting cDNA product was assessed for quality and quantity using the Qubit Flourometer (Life Technologies) and the Agilent Bioanalyzer 2100 (Agilent). Sequencing libraries were generated using 150 pg of cDNA and the NexteraXT library preparation kit (Illumina) before being amplified and hybridized to the Illumina flow cell and sequenced using the NovaSeq 6000 sequencer (Illumina) on the S1 flow cell. Approximately 25 million reads were collected per sample and single end reads of 100 nt were generated.

treatment_protocol: Tumor cells implanted intrarectally in C57BL6 mice and treated (a)  IgG or anti-IFNAR antibodies with Short course radiotherapy (5Gy x 5 fractions), OR (b) just SCRT

value: Rectal Tumor

value: CAF

value: SCRT


title: Patient 7 Group: Exercise (Baseline) rep_2

value: colorectal mucosa

value: Lynch syndrome

value: Exercise

value: F

value: White or Caucasian

value: Not Hispanic or Latino


title: 120120-Human-PFC-N-A-1-17PCW-Mono

description: 17PCW Mono

source_name: Neocortex

value: Neocortex


title: CAFs Tumor 14


title: Patient 7 Group: Exercise (Baseline) rep_3

value: Baseline


title: Dysplasia [MK_13]

value: premalignant lesions


title: 120120-Human-PFC-N-A-1-17PCW-Input

description: 17PCW Input

value: Input


title: HkNR [MK_32]


title: Patient 7 Group: Exercise (Baseline) rep_1


title: CAFs Tumor 12


title: Patient 8 Group: Exercise (Baseline) rep_3

value: M

value: Asian


title: 113020-Human-PFC-N-A-2-17PCW-Mono

description: 17PCW Mono

value: Mono


title: Control [MK_24]

value: oral mucosa

value: Control


title: HkNR [MK_18]


title: Dysplasia [MK_14]


title: CAFs Tumor 10

value: Rectal Tumor

value: CAF


title: Patient 8 Group: Exercise (Baseline) rep_2

value: colorectal mucosa


title: 113020-Human-PFC-N-A-2-17PCW-Input

description: 17PCW Input


title: Patient 8 Group: Exercise (Baseline) rep_1

value: Lynch syndrome


title: 112420-Human-PFC-15296-15PCW-Poly

description: 15PCW Poly

value: Poly


title: 112420-Human-PFC-15296-15PCW-Mono

description: 15PCW Mono


title: CAFs Tumor 9

value: SCRT


title: CAFs Tumor 8


title: CAFs Tumor 13


title: 112420-Human-PFC-15296-15PCW-Input

description: 15PCW Input


title: Dysplasia [MK_30]


title: CAFs Tumor 7


title: CAFs Tumor 6


title: Patient 7 Group: Exercise (End-of-Study) rep_1

value: Exercise

value: F

value: White or Caucasian

value: End-of-Study


title: 113020-Human-PFC-N-A-2-17PCW-Poly

description: 17PCW Poly

value: Neocortex


title: HkNR [MK_23]

value: premalignant lesions


title: 112320-Human-PFC-N-A-2-15PCW-Poly

description: 15PCW Poly


title: 112320-Human-PFC-N-A-2-15PCW-Mono

description: 15PCW Mono


title: Patient 8 Group: Exercise (End-of-Study) rep_3

value: M

value: Not Hispanic or Latino


title: CAFs Tumor 5

value: untreated


title: HkNR [MK_22]

value: oral mucosa


title: CAFs Tumor 4


title: 112320-Human-PFC-N-A-2-15PCW-Input

description: 15PCW Input

value: Input


title: CAFs Tumor 11

value: Rectal Tumor


title: Patient 8 Group: Exercise (End-of-Study) rep_1

value: Asian


title: Cancer [MK_40]

value: OSCC


title: Cancer [MK_16]


title: CAFs Tumor 3

value: CAF


title: 112220-Human-PFC-15295-14PCW-Poly

description: 14PCW Poly

value: Poly


title: Patient 7 Group: Exercise (End-of-Study) rep_3

value: colorectal mucosa

value: Lynch syndrome


title: 112220-Human-PFC-15295-14PCW-Mono

description: 14PCW Mono

value: Mono


title: HkNR [MK_33]


title: Cancer [MK_37]


title: CAFs Tumor 2


title: 112020-Human-PFC-N-A-2-14PCW-Poly

description: 14PCW Poly


title: Dysplasia [MK_29]


title: Patient 19 Group: Control (End-of-Study) rep_4

value: Control

value: F

value: White or Caucasian


title: HkNR [MK_20]

value: premalignant lesions


title: Control [MK_26]


title: Tumor cells Tumor 15

description: deSeq2_d14_tumor_1-5_vs_d14_tumor_A.txt; deSeq2_d14_tumor_1-5_vs_d14_tumor_B.txt; deSeq2_d14_tumor_A_vs_d14_tumor_B.txt

value: Tumor cell

value: SCRT


title: Control [MK_19]


title: Patient 19 Group: Control (End-of-Study) rep_5

value: Not Hispanic or Latino

value: End-of-Study


title: Tumor cells Tumor 14


title: CAFs Tumor 1

value: untreated


title: 112020-Human-PFC-N-A-2-14PCW-Mono

description: 14PCW Mono

value: Neocortex


title: Patient 8 Group: Exercise (End-of-Study) rep_2

value: Exercise

value: M

value: Asian


title: Patient 21 Group: Control (End-of-Study) rep_2


title: Dysplasia [MK_17]

value: oral mucosa


title: 112020-Human-PFC-N-A-2-14PCW-Input

description: 14PCW Input

value: Input


title: Tumor cells Tumor 12

value: Rectal Tumor


title: Tumor cells Tumor 13


title: Patient 21 Group: Control (Baseline) rep_5

value: colorectal mucosa

value: Lynch syndrome

value: Baseline


title: 112220-Human-PFC-15295-14PCW-Input

description: 14PCW Input


title: Patient 21 Group: Control (End-of-Study) rep_1

value: Control

value: White or Caucasian


title: Dysplasia [MK_12]

value: premalignant lesions


title: Patient 21 Group: Control (Baseline) rep_3


title: Patient 21 Group: Control (Baseline) rep_4


title: 111920-Human-PFC-15154-12PCW-Mono

description: 12PCW Mono

value: Mono


title: 111920-Human-PFC-15154-12PCW-Poly

description: 12PCW Poly

value: Poly


title: Control [MK_10]


title: Tumor cells Tumor 11

value: Tumor cell

value: SCRT


title: 111920-Human-PFC-15154-12PCW-Input

description: 12PCW Input

value: Neocortex


title: Tumor cells Tumor 10


title: Patient 21 Group: Control (Baseline) rep_2

value: Not Hispanic or Latino


title: Tumor cells Tumor 9


title: HkNR [MK_7]


title: 111920-Human-PFC-15053-12PCW-Mono

description: 12PCW Mono


title: Dysplasia [MK_9]


title: Patient 21 Group: Control (Baseline) rep_1

value: M


title: Dysplasia [MK_8]


title: 111920-Human-PFC-15053-12PCW-Input

description: 12PCW Input


title: Tumor cells Tumor 8


title: Patient 19 Group: Control (End-of-Study) rep_2

value: F

value: End-of-Study


title: Cancer [MK_5]

value: oral mucosa

value: OSCC


title: 111820-Human-PFC-15158-11PCW-Poly

description: 11PCW Poly


title: Patient 19 Group: Control (End-of-Study) rep_1

value: colorectal mucosa


title: Tumor cells Tumor 6

value: Rectal Tumor


title: Patient 19 Group: Control (Baseline) rep_3

value: Lynch syndrome

value: Baseline


title: 111820-Human-PFC-15158-11PCW-Mono

description: 11PCW Mono


title: Dysplasia [MK_46]


title: Tumor cells Tumor 5

value: untreated


title: Dysplasia [MK_45]

value: premalignant lesions


title: 111820-Human-PFC-15158-11PCW-Input

description: 11PCW Input

value: Input


title: Tumor cells Tumor 4


title: 111920-Human-PFC-15053-12PCW-Poly

description: 12PCW Poly

value: Poly


title: Patient 19 Group: Control (Baseline) rep_2

value: Control

value: White or Caucasian


title: 111720-Human-PFC-15155-1-11PCW-Poly

description: 11PCW Poly

value: Neocortex


title: Patient 19 Group: Control (Baseline) rep_1

value: Not Hispanic or Latino


title: HkNR [MK_43]


title: Tumor cells Tumor 3

value: Tumor cell


title: Cancer [MK_42]


title: Patient 1 Group: Exercise (Baseline) rep_3

value: Exercise

value: F


title: Tumor cells Tumor 2


title: 111720-Human-PFC-15155-1-11PCW-Mono

description: 11PCW Mono

value: Mono


title: HkNR [MK_34]

value: oral mucosa


title: Patient 19 Group: Control (End-of-Study) rep_3

value: colorectal mucosa

value: End-of-Study


title: Patient 1 Group: Exercise (Baseline) rep_2

value: Lynch syndrome


title: Tumor cells Tumor 7

value: Rectal Tumor

value: SCRT


title: Tumor cells Tumor 1

value: untreated


title: HkNR [MK_31]

value: premalignant lesions


title: 111720-Human-PFC-15155-1-11PCW-Input

description: 11PCW Input

value: Input


title: Patient 1 Group: Exercise (Baseline) rep_1

value: Baseline


title: Dysplasia [MK_52]


title: CD8 WT Tumor 14

description: deSeq2_nonresponders_vs_untreated.txt; deSeq2_responders_vs_nonresponders.txt; deSeq2_responders_vs_untreated.txt;

value: CD8 T cell


title: CD8 WT Tumor 15


title: HkNR [MK_53]


title: FAP20-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP20)

data_processing:
Generated sequencing files underwent quality assessment using FastQC24 and were aligned to the human genome (hg19) with STAR in a 2-stage mapping process
Quality assessment of the resultant .bam files was carried out using samtools.
Reads were counted with HTSeq-count in union mode, retaining only those reads that mapped uniquely
Genome_build: hg19
Supplementary_files_format_and_content: output from rsem

source_name: Normal mucosa

extract_protocol:
RNA samples were extracted from tissue biopsies utilised the AllPrep DNA/RNA/protein mini kit (Qiagen) as per the manufacturer’s recommendations.
120 ng RNA starting material, using the TruSeq Stranded Total RNA Kit with Ribo-Zero Gold. Sample preparation, library construction, and sequencing was performed at the Genomics Core at UTMDACC Sequencing Core for 16 tubular adenomas and 10 normal mucosa samples.

tag: disease

value: patient with Familial Adenomatous Polyposis (FAP20)

tag: location

value: Duodenum

tag: size (mm)


title: Patient 1 Group: Exercise (End-of-Study) rep_3

tag: treatment

value: White or Caucasian

value: Not Hispanic or Latino


title: Patient 1 Group: Exercise (End-of-Study) rep_2

tag: patient diagnosis

value: Exercise

value: F


title: FAP20-TA-1

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP20)

source_name: Tubular adenoma with LGD


title: FAP20-TA-2


title: FAP18-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP18)

value: patient with Familial Adenomatous Polyposis (FAP18)


title: CD8 WT Tumor 12


title: CD8 WT Tumor 13


title: Control [MK_50]

value: oral mucosa

tag: group

value: Control


title: Patient 1 Group: Exercise (End-of-Study) rep_1

value: colorectal mucosa

value: Lynch syndrome

tag: patient id

tag: gender

value: End-of-Study


title: Patient 7 Group: Exercise (End-of-Study) rep_2

tag: race

tag: ethinicity


title: Patient 2 Group: Exercise (Baseline) rep_3

tag: gene mutated

tag: visit


title: CD8 WT Tumor 11

tag: tissue

value: Rectal Tumor

tag: cell type

value: SCRT


title: Dysplasia [MK_47]

value: premalignant lesions


title: FAP18-TA-1

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP18)


title: CD8 WT Tumor 10


title: HkNR [MK_39]


title: FAP17-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP17)

value: patient with Familial Adenomatous Polyposis (FAP17)


title: Patient 2 Group: Exercise (Baseline) rep_2

tag: age

value: Baseline


title: Dysplasia [MK_35]


title: CD8 WT Tumor 9

value: CD8 T cell


title: FAP17-TA-1

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP17)

value: Duodenum


title: Patient 2 Group: Exercise (Baseline) rep_1

value: White or Caucasian


title: Patient 2 Group: Exercise (End-of-Study) rep_3

value: Not Hispanic or Latino


title: FAP14-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP14)

value: patient with Familial Adenomatous Polyposis (FAP14)


title: FAP14-TA-2

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP14)


title: HEK293_total_RNA_ModSeq_Mg

data_processing:
ShapeMapper2 (Busan et al.2018)
Mg libraries = untreated samples; Mn libraries = modified samples; use ‘--output-counted-mutations’ flag to output counted mutations
Assembly: human 18S rRNA (NCBI ID: 100008588), human 28S rRNA (NCBI ID: 100008589), human 5.8S rRNA (NCBI ID: 100008587), E. coli 16S rRNA (GeneBank ID: J01859.1), E coli 23S rRNA (GeneBank ID: V00331.1), S cerevisiae 18S rRNA (RNAcentral ID: URS00005F2C2D_4932), S cerevisiae 25S rRNA (RNAcentral ID: URS000061F377_4932)
Supplementary files format and content: profile.txt files = csv containing calculated mutation rates for each nucleotide position in the reference sequence; mutation_counts.txt files = csv containing mutation rate compositions for each nucleotide position in the reference sequence

source_name: HEK293 cell line

extract_protocol:
Trizol
cDNA was prepared from total RNA from each source using random nonamer primers and MarathonRT enzyme in the presence of either Mg or Mn as enzymatic cofactors; second-strand synthesis was carried out from each cDNA sample using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module; library preparation was carried out from the resulting dsDNA sample using the Nextera XT DNA kit
Illumina Nextera XT DNA

value: Embryonic kidney


title: Patient 2 Group: Exercise (End-of-Study) rep_2

value: Exercise

value: F


title: CD8 WT Tumor 8


title: CD8 WT Tumor 7


title: HeLa_total_RNA_ModSeq_Mn

source_name: HeLa cell line

value: cervical cancer


title: Patient 2 Group: Exercise (End-of-Study) rep_1

value: colorectal mucosa


title: FAP14-TA-1


title: CD8 WT Tumor 6


title: CD8 WT Tumor 5

value: untreated


title: Patient 17 Group: Control (Baseline) rep_3

value: Lynch syndrome

value: Control


title: HeLa_total_RNA_ModSeq_Mg


title: Patient 17 Group: Control (Baseline) rep_2


title: Huh7.5_total_RNA_ModSeq_rep2_Mn

source_name: Huh7.5 cell line

value: hepatocellular carcinoma


title: FAP12-TA-2

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP12)

value: patient with Familial Adenomatous Polyposis (FAP12)


title: FAP12-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP12)


title: Huh7.5_total_RNA_ModSeq_rep2_Mg


title: CD8 WT Tumor 4

value: Rectal Tumor


title: Patient 17 Group: Control (End-of-Study) rep_6

value: End-of-Study


title: CD8 WT Tumor 2

value: CD8 T cell


title: CD8 WT Tumor 3


title: Patient 17 Group: Control (End-of-Study) rep_5


title: Huh7.5_total_RNA_ModSeq_rep1_Mn


title: Huh7.5_total_RNA_ModSeq_rep1_Mg


title: FAP10-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP10)

value: patient with Familial Adenomatous Polyposis (FAP10)

value: Duodenum


title: HEK293_total_RNA_ModSeq_Mn


title: CD8 WT Tumor 1


title: FAP10-TA-1

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP10)


title: CD8 IFNAR Tumor 11

value: SCRT, anti-IFNAR


title: FAP08-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP08)

value: patient with Familial Adenomatous Polyposis (FAP08)


title: CF39622_pre_39, bulk TCR-seq

description: Count data of TCRb clone IDs in PBMCs, including a column containing the clone ID that matches the scTCRseq data (of the matching patient)

data_processing:
Preprocessing of raw data, including filtering and V/J segment identification was performed using Adaptive's immunoSEQ Analyzer pipeline (Adaptive Biotechnologies, Seattle, WA). Clone IDs were assigned to the unique TCR β chain sequences.
Supplementary files format and content: Table containing the number of templates from each clone IDs detected in the PBMC sample. Overlapping clone IDs based on the TCR β chain detected in the corresponding tumor sample (single cell TCRseq) are indicated in the column “overlapping_clone_ID_tumor”.
Assembly: hg38
Library strategy: bulk TCR-seq

source_name: PBMCs

extract_protocol:
DNA from the PBMCs was extracted in line with the standard protocol for the ImmunoSEQ assay (Adaptive Biotechnologies, Seattle, WA)
Libraries were prepared according to Illumina protocol (by Adaptive Biotechnologies, Seattle, WA.)

value: PBMCs

tag: patient

tag: response

value: RE

tag: timepoint

value: pre


title: Patient 17 Group: Control (End-of-Study) rep_3

value: F

value: White or Caucasian

value: Not Hispanic or Latino


title: CF71327_post_36, bulk TCR-seq

value: post


title: CD8 IFNAR Tumor 10


title: CF39616_pre_36, bulk TCR-seq


title: Patient 17 Group: Control (End-of-Study) rep_2

value: colorectal mucosa

value: Lynch syndrome

value: Control


title: Patient 17 Group: Control (Baseline) rep_1

value: Baseline


title: FAP06-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP06)

tag: disease

value: patient with Familial Adenomatous Polyposis (FAP06)

tag: location


title: Patient 17 Group: Control (End-of-Study) rep_1

tag: treatment

value: End-of-Study


title: CD8 IFNAR Tumor 9

value: Rectal Tumor

value: CD8 T cell


title: CD8 IFNAR Tumor 8

value: SCRT, anti-IFNAR


title: FAP12-TA-1

value: patient with Familial Adenomatous Polyposis (FAP12)

value: Duodenum

tag: size (mm)


title: FAP06-TA-2

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP06)


title: CF71332_post_31, bulk TCR-seq

value: PBMCs

value: RE


title: Diabetic Heart Organoids

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

description: 10x Genomics

data_processing:
Output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0
After demultiplexing reads from each of the sample libraries was further processed using 10x Genomics cellranger count (v6.1.1).
This program uses the read 1 data to identify reads from individual cells and remove duplicate reads (based on UMIs) as well as align the corresponding read 2 to the reference transcriptome (GRCh38).
Assembly: the reference transcriptome (GRCh38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC-derived heart organoids at day 15

extract_protocol:
hHOs were dissociated into single cell suspensions using STEMDiff Cardiomyocyte dissociation media (Stemcell Technologies), and 4 organoid were condition were pooled.
The libraries were prepared using the 10x Chromium Next GEM Single Cell 3' Kit, v3.1 and associated components. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays. The libraries were pool in equimolar proportions and the pool quantified again using the Invitrogen Collibri qPCR assay. It was loaded onto one lane of an Illumina NovaSeq 6000 SP flow cell (v1.5) and sequencing was performed in a custom paired end format, 28 cycles for read 1, 2 10 cycle index reads and 90 cycles for read 2. A v1.5, 100 cycle NovaSeq reagent cartridge was used for sequencing. The 28bp read 1 includes the 10x cell barcodes and UMIs, read 2 is the cDNA read.

value: iPSC-derived heart organoids at day 15

tag: cell line

value: Hyperglycemia and hyperinsulinemia


title: CF71331_post_29, bulk TCR-seq


title: FAP06-TA-1


title: Healthy Heart Organoids

description: 10x Genomics


title: CF39581_pre_31, bulk TCR-seq

value: pre


title: CD8 IFNAR Tumor 7


title: FAP05-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP05)

value: patient with Familial Adenomatous Polyposis (FAP05)


title: DLD-1 CBP HAT sg1 H3K4me1

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Danpos2 (v2.2.2).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

extract_protocol: Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).  Libraries were constructed using Illumina standard protocols.

tag: antibody

tag: genotype/treatment

value: CBP HAT sg1


title: CD8 IFNAR Tumor 6


title: CF71333_post_39, bulk TCR-seq

value: post


title: FAP08-TA-1

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP08)

value: patient with Familial Adenomatous Polyposis (FAP08)


title: CD8 IFNAR Tumor 5

value: SCRT, IgG


title: Patient 17 Group: Control (End-of-Study) rep_4

value: colorectal mucosa

tag: patient diagnosis

value: Lynch syndrome

value: Control

tag: patient id

tag: gender

value: F

tag: race

value: White or Caucasian

value: Not Hispanic or Latino


title: FAP05-TA-2

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP05)

value: Duodenum


title: CF39580_pre_29, bulk TCR-seq

tag: tissue

value: PBMCs


title: FAP05-TA-1


title: DLD-1 CBP TAZ2 sg2 H3K4me1

value: CBP TAZ2 sg2


title: CD8 IFNAR Tumor 4

value: Rectal Tumor

tag: cell type

value: CD8 T cell


title: CF71330_post_27, bulk TCR-seq

value: RE


title: CF39579_pre_27, bulk TCR-seq

value: pre


title: FAP01-NM-1

description: Normal mucosa sample from a patients with Familial Adenomatous Polyposis (FAP01)

value: patient with Familial Adenomatous Polyposis (FAP01)


title: FAP01-TA-2

description: Tubular adenoma with LGD sample from a patients with Familial Adenomatous Polyposis (FAP01)


title: CD8 IFNAR Tumor 3


title: CD8 IFNAR Tumor 2


title: CF71329_post_22, bulk TCR-seq

value: post


title: DLD-1 p300 TAZ2 sg2 H3K4me1

value: p300 TAZ2 sg2


title: CF71328_post_21, bulk TCR-seq


title: CD8 IFNAR Tumor 1

value: SCRT, IgG


title: CF39575_pre_22, bulk TCR-seq


title: DLD-1 p300 TAZ2 sg1 H3K4me1

value: p300 TAZ2 sg1


title: cyp71-3_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

description: 18- 26 nt sRNA

data_processing:
The adapters were removed using cutadapt version 3.1 with parameters: -m 16 -M 26 -a AGATCGGA.
Clean small RNA reads were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie 1.3.0, allowing no mismatches under parameters: -n 0 -v 0 -k 1.
Small RNA abundance was calculated as reads per million (RPM).
All scripts used for data analysis were uploaded to https://github.com/Chipeyown/cyp71_analysis.
Assembly: Arabidopsis TAIR10
Supplementary files format and content: txt text format. Column1 is the sRNA sequence mapped to TAIR10 genome; column2 is the RPM value of the sRNA.

source_name: 2-week-old seedling

growth_protocol: All plants were grown under long photoperiod conditions (16 h light, 22 °C/8 h dark, 18 °C). Two-week-old seedlings were collected for small RNA isolation.

extract_protocol:
Total RNA was extracted from 2-week-old seedlings using RNAiso Plus reagent (Takara, 9109). Small RNAs were enriched with 5% PEG8000 (Sigma, P5413) and 0.5 M NaCl (Sigma, S3014).
Small RNAs (20 μg) were resolved on a 15% Urea-PAGE gel. RNAs that are 16–26 nt were excised and purified. Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep system (NEB, E7300L) essentially according to the manufacturer’s instructions. The libraries were paired-end sequenced in 150 bp on an Illumina HiSeqX-Ten platform.

value: 2-week-old seedling

tag: genotype


title: DLD-1 GFP sg1 H3K4me1

value: GFP


title: CF39574_pre_21, bulk TCR-seq

tag: patient


title: OVCAR3 p300 HAT sg1 rep3 [ATAC-seq]

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Danpos2 (v2.2.2).
Genome_build: hg38

growth_protocol: OVCAR3 is cultured in DMEM/F-12 with 10% FBS.

extract_protocol:
DNA were extracted by ATAC-Seq Kit (Active Motif, Cat. 53150).
Libraries were constructed using Illumina standard protocols.

value: p300 HAT sg1


title: CF71325_post_17, bulk TCR-seq

tag: response


title: Inguinal White Adipose, Young, Thermoneutral

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

description: YTN

data_processing:
Data was processed using the Cell Ranger pipeline (10x Genomics, v.3.1.0) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices.
The cell ranger output files were read into R (version 4.1.1) and processed utilizing the standard Seurat CCA integrated workflow (version 4.3.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Inguinal white adipose

extract_protocol:
As previously described (Merrick et al 2019, Wang et al 2019), iWAT tissue was dissected, minced gently and digested with Collagenase Type I (1.5 units/ml; Worthington) and Dispase II (2.4 units/ml; Roche) in DMEM/F12 containing 1% fatty acid–free bovine serum albumin (Gold Biotechnology) in a gentleMACS dissociator (Miltenyi Biotec) on program “37 MR ATDK-1.” The digestion was quenched with DMEM/F12 containing 10% FBS, and the dissociated cells were passed through a 100 uM filter and spun at 400 xg for 4 mins. The pellet was resuspended in red blood cell lysis buffer (Biolegend), incubated for 4 mins at RT, then quenched with DMEM/F12 containing 10% serum. Cells were passed through a 70 uM filter, spun, resuspended, then passed through a final 40 uM filter, spun at 400 xg for 4 minutes and plated or underwent further processing for FACS. Cells were flow sorted to isolate live (DAPI(−)) cells and remove debris. We enriched non-immune cells by sorting out CD45+ cells.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium Single Index Kit T Set A, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run by the CHOP Center for Applied Genomics at the University of Pennsylvania. Sequencing for each library targeted 20,000 mean reads per cell.

value: Inguinal white adipose

tag: age

value: Young

value: Thermonetural

tag: time

value: 0 Days


title: Inguinal White Adipose, Young, 3 Days Cold

value: Cold

value: 3 Days


title: cyp71-3_rep1

description: 18- 26 nt sRNA


title: OVCAR3 p300 HAT sg1 rep2 [ATAC-seq]


title: Inguinal White Adipose, Young, 14 Days Cold

value: 14 Days


title: cyp71-2_rep3

description: 18- 26 nt sRNA


title: DLD-1 CBP TAZ2 sg1 H3K4me1

value: CBP TAZ2 sg1


title: Inguinal White Adipose, Aged, Thermoneutral

description: OTN

value: Aged


title: DLD-1 p300 HAT sg1 H3K4me1


title: Inguinal White Adipose, Aged, 3 Days Cold


title: cyp71-2_rep2

description: 18- 26 nt sRNA


title: FAP01-TA-1

tag: disease

value: patient with Familial Adenomatous Polyposis (FAP01)

tag: location

value: Duodenum


title: OVCAR3 p300 TAZ2 sg2 rep3 [ATAC-seq]

value: p300 TAZ2 sg2


title: CF30578_pre_15, bulk TCR-seq

value: PBMCs

value: RE

tag: timepoint

value: pre


title: Inguinal White Adipose, Aged, 14 Days Cold

tag: treatment


title: OVCAR3 p300 TAZ2 sg2 rep2 [ATAC-seq]

tag: cell line


title: cyp71-3_rep2

description: 18- 26 nt sRNA

value: 2-week-old seedling


title: Col-0_rep3

description: 18- 26 nt sRNA


title: cyp71-2_rep1

description: 18- 26 nt sRNA


title: KP gastric organoids

first: Gengyi

last: Zou

state: Texas

institute: MD Anderson

data_processing:
The barcoded processing and gene counting were performed using the Cell Ranger ( v6.1.2)
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: stomach

extract_protocol:
organoids from WT, KP, and EKP were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min.
cDNA library was prepared with the 10x Genomics 3’ v2 kit.

value: gastric organoids

value: epithelial cell

value: KrasG12D;Trp53 KO


title: EKP gastric organoids

value: Cdh1 KO; KrasG12D;Trp53 KO


title: DND41_GSI_Resistance_H3K27ac_ChIPseq_rep2

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

data_processing:
Reads from H3K27ac ChIP-seq experiments were trimmed with Trim Galore (version 606 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (H. Li and Durbin 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6 and paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) from ChIP-seq were generated with bedtools genomecov. Genome-wide uploadable bigWig files were generated with UCSC tools (version 329) (Kent et al. 2010) bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

source_name: DND-41 cell line

growth_protocol: DND-41 cells (DSMZ, cat# ACC525) were purchased from the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Lines. Cells were cultured in RPMI 1,640 (Corning, 538 cat# 10-040-CM) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, cat# 539 SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg mL−1 peni-540 cillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 541 11140-050), 1 mM sodium pyruvate (Gibco, cat# 11360-070) and 0.1 mM of 2-mercaptoethanol (Sigma, cat# M6250). All cells were grown at 37 °C and 5% CO2 with media refreshed every 3-4 days.

extract_protocol:
We performed H3K27ac ChIP-seq as previously described (Petrovic et al. 2019). Briefly, we sonicated and cleared chromatin samples prepared from 107 fixed cells with recombinant protein G–conjugated Agarose beads (Invitrogen, cat# 15920-010) and subsequently immunoprecipitated these cells with antibodies recognizing H3K27ac (Active Motif, cat# 39133). We captured Antibody-chromatin complexes with recombinant protein G–conjugated Agarose beads, washed them with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and TE buffer with 50mM NaCl and eluted them. After reversal of cross-linking, we performed RNase and Proteinase K (Invitrogen, cat# 25530-049) treatment and purified DNA with QIAquick PCR Purification Kit (Qiagen, cat# 28106).
We then prepared libraries using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB, cat# E7645S). We validated indexed libraries for quality and size distribution using a TapeStation 2200  (Agilent). We performed paired-end sequencing (38 bp+38 bp) on a NextSeq 550.

treatment_protocol: To generate GSI-resistant cells, DND-41 treatment-naïve cells were cultured in the presence of 125 nM GSI for at least six weeks. The establishment of GSI-resistance was determined with IC50 assay as described above. GSI-resistant DND-41 cells can tolerate 10 μM GSI with less than 20% cell death. Short-term DMSO treatment was performed on treatment-naïve DND-41 cells with 125 nM DMSO for 24 hours.

value: T Acute Lymphoblastic Leukemia

tag: chip antibody

tag: drug response

value: GSI resistance


title: DND41_GSI_Resistance_H3K27ac_ChIPseq_rep1


title: OVCAR3 p300 TAZ2 sg1 rep3 [ATAC-seq]

tag: genotype/treatment

value: p300 TAZ2 sg1


title: Col-0_rep2

description: 18- 26 nt sRNA


title: CF39571_pre_17, bulk TCR-seq


title: Col-0_rep1

description: 18- 26 nt sRNA


title: OVCAR3 p300 HAT sg1 rep1 [ATAC-seq]

value: p300 HAT sg1


title: Wild type gastric organoids

value: wild type