title: Arabidopsis_rosetta_leaf, polyA RNA, treated, rep2

description:
At6-sac-rosetta_leaf-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

tag: ecotype


title: K104334/K104973_ROI_6_well_A07

status: Public on Apr 19 2024

type: SRA

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

country: USA

institute: Indiana University School of Medicine

description: Library name:  DSP-1008870999691-D-A07

library_source: transcriptomic

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Supplementary files format and content: dcc
Library strategy: GeoMx Seq

molecule: total RNA

organism: Homo sapiens

source_name: Breast tissues from healthy woman

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: tissue

value: Breast tissues from healthy donor donated 10 years apart

tag: disease state

value: healthy donor

tag: slide id

tag: roi number

tag: segment type

value: Full ROI

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: RPE-1 hTERT XRCC1 KO double pulse dT75min+PARP_3

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: scEdUseq library

library_source: genomic

data_processing:
demultiplexing reads; extracting cell barcodes from reads
trimming adapter sequences with cutadapt
mapping to human genome with bwa -mem algorithm
custom bam tagging tool to add flags which we later select for
extracting reads wtih specific bam flags and write to tsv.gz file
Assembly: GRCh38.p12 / Ensembl release 97 for Homo Sapiens
Supplementary files format and content: Data table containing cell name, chromosome, read start, length, allele
Library strategy: DNA-seq

molecule: genomic DNA

source_name: Retinal Pigment Epithelial

growth_protocol: RPE-1 hTERT FUCCI or XRCC1 KO were maintained in DMEM/F12, 10% FCS and 1% Pen-Strep

extract_protocol:
TrypLE digestion
Custom library protocol. Briefly, EdU was clicked to Biotin-PEG3-Azide. Single cells were sorted in a 384-well plate. Subsequently, cells were lysed wioth ProtK and the genome was digested with NLAIII. Next, DNA fgragments were end-repaired by Klenow Large Fragment and PNK. On these repaired ends we ligated a custom adapter sequence followed by affininty purification of EdU-Biotin miolecules with magnetic streptadin beads. Non-modified strands were recovered by heat denaturation and the complimetary strand was re-generated by a primer extension reaction. Finally, libraries were amplified by a combination of T7 in vitro trasncription, reverse transcription and polymerase chain reaction containing Illumina handles
Illumina RPI small RNA adapters

treatment_protocol: Cells were treated with indiicated inhibitors for diverse periods of time

value: Retinal Pigment Epithelial

tag: cell line

value: RPE-1 hTERT XRCC1 KO

tag: treatment

value: 10uM PARPi

tag: genotype

value: XRCC1 KO


title: Arabidopsis_rosetta_leaf, polyA RNA, treated, rep1

city: Chicago

first: CHUAN

last: HE

state: Illinois

address: 929 East 57th Street, GCIS E313

institute: University of Chicago

description:
At6-sac-rosetta_leaf-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

data_processing:
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: TAIR-10
Supplementary files format and content: TSV
Library strategy: SAC-seq

molecule: polyA RNA

organism: Arabidopsis thaliana

extract_protocol:
A total of 50 ug total RNA for each of the two biological replicates was used for mRNA capture (Dynabeads mRNA DIRECT Purification Kit (Invitrogen)) following the manufacturer′ s instructions with modification. Briefly, 50 ug total RNA was diluted with H2O in 100ul volume and then denatured under 65°C for 2 min, and immediately put on the ice for exactly 2 min. Next, a total of 100ul Dynabeads were washed twice with 200ul lysis/binding buffer provided in the above kit. The washed beads were then eluted in 100ul lysis/binding buffer, which further mixed with the denatured total RNA. Then, the sample was put on the rotor to binding for 15 min at room temperature. After binding, wash buffer B was used to wash the beads for twice. 30ul H2O was used to elute the beads and immediately put on the 75°C for 2min. The eluted mRNA was collected after magnetic separation. The mRNA capture process was repeated as described above to obtain the more purified mRNA.
50ng mRNAs of each replicate were used for the library construction. All these libraries were constructed exactly following the previously published protocols

tag: tissue

tag: ecotype


title: K104334/K104973_ROI_5_well_A06

description: Library name:  DSP-1008870999691-D-A06

tag: disease state

tag: slide id


title: RPE-1 hTERT XRCC1 KO double pulse dT75min+PARP_2

description: scEdUseq library


title: K104334/K104973_ROI_4_well_A05

description: Library name:  DSP-1008870999691-D-A05

tag: roi number

tag: segment type


title: 3-KO-ac

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

data_processing:
Basecalls performed using Illumina NovaSeq 6000
Clean reads were aligned to mouse mm39 reference genome using bowtie2 software (v2.2.4).
Assembly: Mus musculus (mm39)
Supplementary files format and content: bigwig files were generated using macs2; Scores represent an average read coverage
Library strategy: CUT&Tag

organism: Mus musculus

source_name: bone marrow

growth_protocol: BMSCs were cultured in αMEM medium with 10% FBS.

extract_protocol:
Clarify the lysate from the nucleus treated with Protein A-Tn5 enzyme and isolate the histone DNA complex with antibodies.
Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, China) was used to perform the CUT&Tag assay. Briefly, a total of 50 000 cells were harvested and enriched by ConA magnetic beads. The samples were incubated with primary H3K18ac or H3K18cr antibody at 4°C overnight and secondary antibody at room temperature for 1 hour. Cells were incubated with the protein A-Tn5 transposon at room temperature for 1 hour, and washed thrice in Dig-300 buffer. The cells were resuspended in 50 μL of fragmentation buffer, incubated at 37 °C for 1 hour and then terminated with 1 μL of 10% SDS at 55 °C for 10 min. DNA Extract Beads Pro was used to extract the ~250bp DNA fragments. The libraries were used for sequencing on an Illumina NovaSeq 6000 platform at Novogene Science.

value: bone marrow

value: HDGFR2 knockout

tag: cell type

value: BMSC

tag: cut&tag antibody

value: H3K18ac(PTM BIO, # PTM-158)


title: RPE-1 hTERT XRCC1 KO double pulse dT75min+PARP_1

description: scEdUseq library


title: Arabidopsis_stem, polyA RNA, input, rep1

description:
At5-sac-stem-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

data_processing:
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: TAIR-10
Supplementary files format and content: TSV


title: K104334/K104973_ROI_2_well_A03

description: Library name:  DSP-1008870999691-D-A03

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads


title: RPE-1 hTERT XRCC1 KO double pulse dT75min_2

description: scEdUseq library

value: DMSO


title: Arabidopsis_stem, polyA RNA, treated, rep2

description:
At5-sac-stem-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: 2-WT-control

value: wildtype


title: K104334/K104973_ROI_3_well_A04

description: Library name:  DSP-1008870999691-D-A04

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: K104334/K104973_ROI_1_well_A02

description: Library name:  DSP-1008870999691-D-A02

tag: sequencingsaturation


title: RPE-1 hTERT XRCC1 KO double pulse dT75min_1

description: scEdUseq library

tag: tissue

tag: cell line

tag: treatment

tag: genotype


title: 1-WT-ac


title: Arabidopsis_canline_leaf, polyA RNA, input, rep2

description:
At4-sac-canline_leaf-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz

tag: ecotype


title: C25_KTBpool-25_Hispanic, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool-25_Hispanic_per_barcode_metrics.csv

library_source: transcriptomic single cell

data_processing:
cellranger-atac v2.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
Signac (v1.7) and Seurat (v4 were used to analyze the filtered barcode-peak matrices and fragment file generated from running cellragner-arc.
The gene expression and chromatin accessiblity data were process separately, WNN (weighted nearest neighbor) was used for cell clustering and visulization.
Assembly: GRCh38 (from 10X: refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: 10x Genomics cellranger-arc output files (the files needed for further analysis): filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, per_barcode_metrics.csv

molecule: nuclear RNA

source_name: Breast tissues from healthy women

growth_protocol: Cryopreserved tissues from healthy women were used.

extract_protocol:
Nuclei is isolated from these tissues using the protocol suggested for use with the chromium Next GEM Single Cell Multiome ATAC+Gene Expression protocol (CG000338).
was performed immediately as per Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338). In few instances (few samples from African American and European ancestry), the same protcol was used to generate nuclei but only snRNA-seq was performed.

value: Breast

tag: disease state

tag: donors

value: five donors

tag: ethnicity

value: Hispanic


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_7

description: scEdUseq library

value: RPE-1 hTERT FUCCI

value: 10uM DRB

value: WT


title: DISC1, replicate2, snRNA-seq

city: Shenzhen

first: Jie

last: Tu

state: Guangdong

address: 1068 Xueyuan Boulevard, Nanshan, Shenzhen 518055, China

department: The Brain Cognition and Brain Disease Institute (BCBDI)

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS)

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing an gene counting were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BLA

extract_protocol:
A vibroslicer (Leica, VT-1200S) to obtain brain slices containing the BLA region, both sides of the BLA were separated with forceps and surgical blades under a stereo microscope. To obtain a sufficient number of nuclei, we enriched bilateral BLA brain tissue from 5 mice for each group. Frozen brain tissue was placed directly into a pre-chilled Dounce homogenizer containing ice-cold homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM tricine-KOH [pH 7.8], 1mM dithiothreitol, 0.15mM spermine, 0.5mM spermidine, protease inhibitors, 5μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 beats with a pestle, the homogenate was mixed 1:1 in OptiPrep and centrifuged at 10,000× g for 20 min at 4 °C. Nuclei were collected at the bottom of the centrifuge tube, washed once to remove OptiPrep, and resuspended in Dulbecco’s modified eagle medium/F12 supplemented with 10% fetal bovine serum. We diluted the nuclei to 400 nuclei per microliter using a hemocytometer. All buffers and gradients used for nuclear extraction contained Rnase inhibitor (Promega) at 60 U/mL.
We generated snRNA-seq libraries using the Chromium Single Cell 3’ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: Six hours after intraperitoneal injection of tamoxifen, mice were anesthetized using isoflurane (3%) and the heads were decapitated to obtain the brain tissue

value: BLA

tag: strain

tag: cell type

value: all BLA cells

value: DISC-N


title: WT, replicate2, snRNA-seq

description: 10x Genomics


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_6

description: scEdUseq library

value: Retinal Pigment Epithelial


title: Arabidopsis_canline_leaf, polyA RNA, input, rep1

description:
At4-sac-canline_leaf-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_5

description: scEdUseq library


title: 5-WT-ac

tag: cut&tag antibody


title: 4-KO-control


title: WT, replicate1, snRNA-seq

description: 10x Genomics


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_4

description: scEdUseq library


title: DISC1, replicate1, snRNA-seq

description: 10x Genomics


title: Arabidopsis_stem, polyA RNA, input, rep2

description:
At5-sac-stem-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: αMHC_7_days_post_delivery_ECs_scRNA-seq

city: Helsinki

first: Ibrahim

last: Sultan

address: Haartmaninkatu 8

country: Finland

institute: Helsinki University

description: 10x Genomics

data_processing:
Cellranger 3’ RNAseq pipeline analysis of sequencing data was run using 10x Genomics Cell Ranger v3.1.0 count and aggr pipelines.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix

source_name: Heart

extract_protocol:
Heart digestion and cardiac endothelial cell isolation was performed as previously described in our study in Circulation (PMID: 33203221 DOI: 10.1161/CIRCULATIONAHA.120.050635). Briefly, hearts from 2-3 mice per condition/genotype were digested and pooled and subsequently treated as 1 sample. The pooled hearts were rinsed with DPBS containing CaCl2, manually minced and digested with a mixture of Collagenases (type I, II, and IV) at 37°C followed by washing and straining. The obtained cells were subjected to downstream steps for SVF or stained and FAC sorted to obtain ECs.
The cells were loaded into Chromium Next GEM Single Cell 3’ Chip v3.1 (Dual index) (10x Genomics, Pleasanton, CA) and gel beads in emulsion (GEM) generation was performed aiming at 10 000 cell captures/sample. Subsequent cDNA purification, amplification (11 cycles), and library construction (sample index PCR 12 cycles for WT-EC and αMHC-VEGF-B-EC samples, 13 cycles for aP2-VEGF-B-SVF and αMHC-VEGF-B-SVF samples, and 14 cycles for all other samples) was performed as instructed in manufacturer's kit.

value: Heart

value: Endothelial cells

tag: Sex

value: Female

tag: operation

value: {alpha}MHC-VEGF-B

tag: age

value: 10-12 weeks


title: KTBpool15_Asian, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool15_Asian_per_barcode_metrics.csv

value: healthy donor

value: Asian


title: Arabidopsis_silique, polyA RNA, input, rep2

description:
At3-sac-silique-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: WT_7_days_post_delivery_ECs_scRNA-seq

description: 10x Genomics

value: Wildtype (WT)


title: Arabidopsis_silique, polyA RNA, input, rep1

description:
At3-sac-silique-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: KTBpool17_Asian, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool17_Asian_per_barcode_metrics.csv

value: Breast

value: five donors


title: Arabidopsis_stem, polyA RNA, treated, rep1

description:
At5-sac-stem-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: αMHC_18_days_pregnant_ECs_scRNA-seq

description: 10x Genomics


title: Arabidopsis_canline_leaf, polyA RNA, treated, rep1

description:
At4-sac-canline_leaf-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_1

description: scEdUseq library

value: RPE-1 hTERT FUCCI


title: Arabidopsis_canline_leaf, polyA RNA, treated, rep2

description:
At4-sac-canline_leaf-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: KTBpool12-White American, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool9_per_barcode_metrics.csv

value: White American


title: C23_KTBpool-23_Hispanic, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool-23_Hispanic_per_barcode_metrics.csv

value: Hispanic


title: Arabidopsis_silique, polyA RNA, treated, rep2

description:
At3-sac-silique-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_7

description: scEdUseq library

value: 10uM PARPi

value: WT


title: KTBpool11-White American, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool12_per_barcode_metrics.csv


title: WT_18_days_pregnant_ECs_scRNA-seq

description: 10x Genomics


title: KTBpool_13-Indigenous American, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool_13_per_barcode_metrics.csv

value: Indigenous American


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_2

description: scEdUseq library

value: Retinal Pigment Epithelial

value: 10uM DRB


title: KTBpool_14-Indigenous American, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool_14_per_barcode_metrics.csv


title: Arabidopsis_silique, polyA RNA, treated, rep1

description:
At3-sac-silique-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: αMHC_2_days_post_LAD_ECs_scRNA-seq

description: 10x Genomics

value: Heart

value: Endothelial cells

value: LAD


title: KTBpool9-White American, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool11_per_barcode_metrics.csv


title: Arabidopsis_seedling, polyA RNA, input, rep2

description:
At2-sac-seedling-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: Arabidopsis_seedling, polyA RNA, input, rep1

description:
At2-sac-seedling-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: Pool8_BRCA1Positive, scRNA-seq

description:
All samples are from healthy donors with no diseases
Pool8_BRCA1Positive_per_barcode_metrics.csv

value: healthy donor (BRCA1 mutation carriers)


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_5

description: scEdUseq library


title: WT_2_days_post_LAD_ECs_scRNA-seq

description: 10x Genomics

value: Female

value: 10-12 weeks


title: RPE-1 hTERT FUCCI double pulse dT75min+DRB_3

description: scEdUseq library


title: αMHC_ECs_scRNA-seq

description: 10x Genomics

value: {alpha}MHC-VEGF-B


title: aP2_ECs_scRNA-seq

description: 10x Genomics


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_4

description: scEdUseq library


title: Arabidopsis_seedling, polyA RNA, treated, rep2

description:
At2-sac-seedling-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_3

description: scEdUseq library


title: KTBpool6_Ashkenazi_jew, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool6_Ashkenazi_jew_per_barcode_metrics.csv

value: Breast

value: healthy donor


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_2

description: scEdUseq library

value: RPE-1 hTERT FUCCI


title: Arabidopsis_seedling, polyA RNA, treated, rep1

description:
At2-sac-seedling-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: KTBpool5_Ashkenazi_jew, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTBpool5_Ashkenazi_jew_per_barcode_metrics.csv

value: five donors


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_1

description: scEdUseq library


title: KTB_pool-4-Ashkenazi_jew, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTB_pool-4_per_barcode_metrics.csv


title: aP2_SVF_scRNA-seq

description: 10x Genomics

value: Stromovascular fraction


title: Pool7_BRCA2Positive, scRNA-seq

description:
All samples are from healthy donors with no diseases
Pool7_BRCA2Positive_per_barcode_metrics.csv

value: healthy donor (BRCA2 mutation carriers)


title: Arabidopsis_flower, polyA RNA, input, rep1

description:
At1-sac-flower-input1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: WT_ECs_scRNA-seq

description: 10x Genomics

value: Wildtype (WT)


title: Arabidopsis_flower, polyA RNA, input, rep2

description:
At1-sac-flower-input2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min+PARP_6

description: scEdUseq library

value: 10uM PARPi

value: WT


title: αMHC_SVF_scRNA-seq

description: 10x Genomics


title: RPE-1 hTERT FUCCI double pulse dT75min_8

description: scEdUseq library

value: Retinal Pigment Epithelial

value: DMSO


title: KTB_pool-3-Ashkenazi_jew, scRNA-seq

description:
All samples are from healthy donors with no diseases
KTB_pool-3_per_barcode_metrics.csv


title: RPE-1 hTERT FUCCI double pulse dT75min_7

description: scEdUseq library


title: Ashkenazi_NormalBreastSample_multiome_Pool1, scRNA-seq

description:
All samples are from healthy donors with no diseases
Ashkenazi_NormalBreastSample_multiome_Pool1_per_barcode_metrics.csv


title: Arabidopsis_flower, polyA RNA, treated, rep1

description:
At1-sac-flower-treated1
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: RPE-1 hTERT FUCCI double pulse dT75min_6

description: scEdUseq library


title: C25_KTBpool-25_Hispanic, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool-25_Hispanic_per_barcode_metrics.csv

library_source: genomic single cell

value: Hispanic


title: NC, scRNAseq

city: Nanjing

first: Jiawen

last: Cui

state: Jiangsu

address: TongJiaXiang #24

institute: China Pharmaceutical University

description: 10X Genomics

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Assembly: Ensembl_release109
Supplementary files format and content: Tap-separated values files and matrix files

source_name: lung cancer xenograft

extract_protocol:
Take a small amount of single cell suspension, add an equal volume of 0.4% trypan blue dye, count the cells with Countess@IlAutomated cellCounter, and adjust the viable cell concentration to the ideal concentration (1000~2000 cells/uL)
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: lung cancer xenograft

value: lung cancer

value: LLC

value: control


title: SH, scRNAseq

description: 10X Genomics

value: shRNA to knock down GFPT2


title: RPE-1 hTERT FUCCI double pulse dT45min_8

description: scEdUseq library


title: Prostate cancer, Testosterone, rep 3

city: Québec

first: Étienne

last: Audet-Walsh

state: Québec

address: 2705, boulevard Laurier

country: Canada

institute: CRCHU de Québec

data_processing:
Trimming: Trim Galore/Cutadapt
Quality check: FastQC/MultiQC
Pseudoalignement: Kallisto
Differential analysis and normalization : tximport/DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: normalized_counts.csv.gz: comma separated values containing normalized expression for each sample
Supplementary files format and content: raw_counts.csv.gz: comma separated values containing raw counts for each sample

source_name: Prostate

growth_protocol: Thirty mice in total (16 C57BL/6J Ptenfl/fl [normal or WT] and 14 C57BL/6J PB-Cre4+/-;Ptenfl/fl [prostate cancer]) were bred and housed in a 12 hour light, 12h dark cycle at 22°C.

extract_protocol:
24 hours after injections, mice prostates were harvested, and RNA was extracted and purified with the QIAGEN RNeasy Mini Kit.
mRNA library was generated using NEBNext Ultra II Directional RNA library prep kit.

treatment_protocol: Mice of at least 24 weeks old where firstly castrated, and 72h later, they received sub-cutaneous injections of either vehicule (1:10 ethanol 96% / vegetable oil), Estradiol (30 µg/g of mouse weight) and/or Testosterone (30 µg/g of mouse weight). Estradiol will activate the estrogen receptor alpha (ERa), whereas Testosterone will activate the androgen receptor (AR).

value: Prostate

value: C57BL/6J PB-Cre4+/-;Ptenfl/fl

value: Testosterone (30 µg/g of mouse weight)


title: RPE-1 hTERT FUCCI double pulse dT45min_7

description: scEdUseq library

value: RPE-1 hTERT FUCCI


title: KTBpool17_Asian, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool17_Asian_per_barcode_metrics.csv

value: Breast

value: healthy donor

value: five donors

value: Asian


title: Arabidopsis_flower, polyA RNA, treated, rep2

description:
At1-sac-flower-treated2
Arabidopsis_gene_expression.tsv.gz
Arabidopsis_m6a_modification.tsv.gz


title: WT_SVF_scRNA-seq

description: 10x Genomics

value: Heart

value: Stromovascular fraction

value: Female

value: Wildtype (WT)

value: 10-12 weeks


title: TRBP KO cervical cancer cells, SeV_D234A

type: RNA

city: Bunkyo-ku, Tokyo

first: Tomoko

last: Takahashi

country: Japan

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy-3 labeled RNAs were fragmented by Gene Expression Hybridization kit (Agilent Techinologies) and hybridized to SurePrint G3 Human GE microarray ver.3 (Agilent Techinologies) at 65°C for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing:
Signals were quantified by Feature Extraction 10.5.1.1 (Agilent Techinologies).
~10k analyzed probes that passed filers with enough quality for analysis.

label_protocol: Cy-3 labeled RNA were synthesized by Quick Amp Labeling kit for One color (Agilent Techinologies).

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (Wako) containing 10% fetal bovine serum (NICHIREI) at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the FastGene RNA Premium Kit.

treatment_protocol: SeV was incubated with serum-free medium for 1 h at 37℃.

value: female

value: cervical cancer cells

value: TRBP knockout

tag: expressing

tag: infection

value: SeV


title: Prostate cancer, Testosterone, rep 1

value: Prostate


title: KTBpool15_Asian, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool15_Asian_per_barcode_metrics.csv


title: RPE-1 hTERT FUCCI double pulse dT105min_2

description: scEdUseq library

value: Retinal Pigment Epithelial

value: DMSO

value: WT


title: C23_KTBpool-23_Hispanic, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool-23_Hispanic_per_barcode_metrics.csv

value: Breast

value: Hispanic


title: Prostate cancer, Estradiol + Testosterone, rep 4

value: C57BL/6J PB-Cre4+/-;Ptenfl/fl

value: 17β-Estradiol and Testosterone (each 30 µg/g of mouse weight)


title: RPE-1 hTERT FUCCI double pulse dT105min_1

description: scEdUseq library

value: RPE-1 hTERT FUCCI


title: KTBpool_13-Indigenous American, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool_13_per_barcode_metrics.csv

value: healthy donor

value: five donors

value: Indigenous American


title: RPE-1 hTERT FUCCI double pulse dT75min_5

description: scEdUseq library


title: KTBpool12-White American, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool9_per_barcode_metrics.csv

value: White American


title: RPE-1 hTERT FUCCI double pulse dT75min_4

description: scEdUseq library


title: TRBP KO cervical cancer cells, C

description: Gene expression

data_processing:
Signals were quantified by Feature Extraction 10.5.1.1 (Agilent Techinologies).
~11.5k analyzed probes that passed filers with enough quality for analysis.

source_name: C

treatment_protocol: TRBP expression plasmid was transfected.

value: female

value: TRBP-C


title: KTBpool11-White American, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool12_per_barcode_metrics.csv


title: TRBP KO cervical cancer cells, mock_D234A

description: Gene expression

value: cervical cancer cells

value: TRBP knockout

value: mock


title: Prostate cancer, Estradiol + Testosterone, rep 1

value: Prostate


title: Prostate cancer, Testosterone, rep 2

value: Testosterone (30 µg/g of mouse weight)


title: TRBP KO cervical cancer cells, N

description: Gene expression

source_name: N

value: TRBP-N


title: TRBP KO cervical cancer cells, WT

description: Gene expression

source_name: WT

value: TRBP-WT


title: RPE-1 hTERT FUCCI double pulse dT45min_6

description: scEdUseq library

value: Retinal Pigment Epithelial

value: DMSO

value: WT


title: RPE-1 hTERT FUCCI double pulse dT75min_3

description: scEdUseq library

value: RPE-1 hTERT FUCCI


title: KTBpool_14-Indigenous American, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool_14_per_barcode_metrics.csv

value: Breast

value: healthy donor


title: TRBP KO cervical cancer cells, SeV_WT

description: Gene expression

value: SeV


title: endometrial organoid, 3 fat, rep4

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
The quality of DNA reads was evaluated using FastQC and MultiQC. Cutadapt was used to trim adapters,76 STAR was used to align reads to the genome (hg19),77 and htseq-count was used to calculate read counts78 using gene annotation from Ensembl (http://useast.ensembl.org/index.html). Data were normalized using the DESeq2 method, and multifactorial differential expression analysis was performed using DESeq2.79 The analysis was paired, controlling for patients as a second factor. Genes with a false discovery rate-adjusted p-value of less than 0.05 were considered to be significantly differentially expressed.
Supplementary files format and content: Raw counts of sequencing reads for each gene.
Supplementary files format and content: Individual file for each sample. Files are tab separated with dot counts (.counts) extension.

source_name: organoid comprised of epithelial and stromal cells from benign endometrium

extract_protocol:
Endometrial organoids were removed from agarose micro-molds by pipetting and lysed in TRI Reagent® (Sigma-Aldrich T9424). Total RNA was isolated using the Direct-zol RNA Microprep Kit (Zymo Research R2062) according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq mRNA-Seq Library Prep kit according to the manufacturer’s instructions.

treatment_protocol: Cocultures were performed in a 24-well, ultra-low attachment plate by culturing endometrial organoids inside an agarose micro-mold and adipose spheroids in the well outside the agarose micro-mold, physically separated from the organoids.  Cocultures were treated in a stepwise fashion with estradiol (E2) and progesterone (P4) and with or without testosterone (T) for 14 days to represent a condensed version of previously described menstrual cycle hormone treatment

value: coculture with 3 fat spheroids and fluctuating concentrations of estradiol, progesterone, testosterone over 14 days to mimic menstrual cycle


title: RPE-1 hTERT FUCCI double pulse dT75min_2

description: scEdUseq library


title: Prostate cancer, Estradiol, rep 4

value: C57BL/6J PB-Cre4+/-;Ptenfl/fl

value: 17β-Estradiol (30 µg/g of mouse weight)


title: endometrial organoid, 3 fat, rep3

value: organoid comprised of epithelial and stromal cells from benign endometrium


title: Prostate cancer, Estradiol + Testosterone, rep 3

value: 17β-Estradiol and Testosterone (each 30 µg/g of mouse weight)


title: Pool8_BRCA1Positive, scATAC-seq

description:
All samples are from healthy donors with no diseases
Pool8_BRCA1Positive_per_barcode_metrics.csv

value: healthy donor (BRCA1 mutation carriers)

value: five donors


title: endometrial organoid, 3 fat, rep2


title: Prostate cancer, Estradiol, rep 3

value: Prostate


title: Pool7_BRCA2Positive, scATAC-seq

value: healthy donor (BRCA2 mutation carriers)


title: Prostate cancer, Estradiol, rep 2


title: TRBP KO cervical cancer cells, mock_WT

description: Gene expression

value: female

value: cervical cancer cells

value: TRBP knockout

value: TRBP-WT

value: mock


title: RPE-1 hTERT FUCCI double pulse dT75min_1

description: scEdUseq library

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI

value: DMSO

value: WT


title: RPE-1 hTERT FUCCI double pulse dT45min_5

description: scEdUseq library


title: TRBP KO cervical cancer cells, empty

description: Gene expression

source_name: empty

value: empty


title: Prostate cancer, Estradiol + Testosterone, rep 2

value: C57BL/6J PB-Cre4+/-;Ptenfl/fl


title: endometrial organoid, 3 fat, rep1

value: organoid comprised of epithelial and stromal cells from benign endometrium

value: coculture with 3 fat spheroids and fluctuating concentrations of estradiol, progesterone, testosterone over 14 days to mimic menstrual cycle


title: Prostate cancer, Estradiol, rep 1

value: 17β-Estradiol (30 µg/g of mouse weight)


title: KTBpool9-White American, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool11_per_barcode_metrics.csv

value: Breast

value: healthy donor

value: five donors

value: White American


title: RPE-1 hTERT FUCCI double pulse dT45min_4

description: scEdUseq library


title: KTBpool5_Ashkenazi_jew, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool5_Ashkenazi_jew_per_barcode_metrics.csv


title: RPE-1 hTERT FUCCI double pulse dT45min_3

description: scEdUseq library


title: endometrial organoid, 30 fat, rep4

value: coculture with 30 fat spheroids and fluctuating concentrations of estradiol, progesterone, testosterone over 14 days to mimic menstrual cycle


title: KTB_pool-4-Ashkenazi_jew, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTB_pool-4_per_barcode_metrics.csv


title: Prostate cancer, Vehicle, rep 2

value: Prostate

value: Vehicle (1:10 v/v Ethanol 96%:vegetable oil)


title: RPE-1 hTERT FUCCI double pulse dT45min_2

description: scEdUseq library


title: KTB_pool-3-Ashkenazi_jew, scATAC-seq


title: endometrial organoid, 30 fat, rep3


title: Prostate cancer, Vehicle, rep 3


title: endometrial organoid, 30 fat, rep2


title: Prostate cancer, Vehicle, rep 1


title: Ashkenazi_NormalBreastSample_multiome_Pool1, scATAC-seq


title: Normal prostate, Testosterone, rep 2

value: C57BL/6J Ptenfl/fl

value: Testosterone (30 µg/g of mouse weight)


title: endometrial organoid, 0 fat, rep4

value: fluctuating concentrations of estradiol, progesterone, testosterone over 14 days to mimic menstrual cycle


title: KTBset4_nulliparous

data_processing:
CellRanger 7 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Seurat 4 was used for hashtag demultiplexing, data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis.
Assembly: GRCh38
Supplementary files format and content: HDF5 file of filtered gene-barcode matrices

extract_protocol:
Nuclei is isolated from these tissues using the protocol suggested for use with the chromium Next GEM Single Cell Multiome ATAC+Gene Expression protocol (CG000338).
10x Genomics protocol for chromium single cell 3' reagent kits V3

value: White

tag: pregnancy status

value: nulliparous


title: KTBpool6_Ashkenazi_jew, scATAC-seq

description:
All samples are from healthy donors with no diseases
KTBpool6_Ashkenazi_jew_per_barcode_metrics.csv

tag: tissue


title: RPE-1 hTERT FUCCI double pulse dT45min_1

description: scEdUseq library

value: Retinal Pigment Epithelial

tag: cell line

value: RPE-1 hTERT FUCCI

value: DMSO

value: WT


title: endometrial organoid, 30 fat, rep1

value: organoid comprised of epithelial and stromal cells from benign endometrium

tag: treatment


title: Normal prostate, Testosterone, rep 4

tag: genotype


title: KTBset_2_AAF

value: Breast

value: African American


title: Pooled CARs 10X Lane 1 GEX Library

city: Cambridge

first: Caleb

middle: R

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

description: Contains six different biological samples pooled prior to sequencing, which can be deconvoluted by hashing antibody. Hash1 = CAR6 Donor1; Hash2 = CAR9 Donor1; Hash3 = 13BBz Donor1; Hash 4 = CAR6 Donor2; Hash5 = CAR9 Donor2; Hash6 = 13BBz Donor2

data_processing:
Reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), and a cell–gene matrix was generated using the CellRanger pipeline (10X Genomics; v4.0.0). Downstream analysis was performed using the Seurat package (v4.0.0).
Cells were first assigned sample identity based on the detection of a single hashing antibody following normalization of antibody reads using the HTODemux algorithm. Next, low-quality cells were filtered out on the basis of mitochondrial reads (>25%). Filtered data for each cell were normalized to total expression, and cell cycle-related genes were regressed out using the ScaleData function. To identify distinct transcriptional states, linear dimensionality reduction was performed on the scaled, normalized data, followed by shared nearest neighbors clustering on the basis of the first 40 principal components. Differentially expressed genes, both within clusters and across samples, were identified by a Wilcoxon rank-sum test between the populations of interest. For pathway-level analyses, individual cells were assigned scGSVA scores on the basis of their relative expression of genes within all canonical pathways, immunologic signature gene sets (Broad Institute; C2 and C7 gene sets, respectively) or T-cell-specific curated pathways (Supplementary Table 4), as previously described.
Assembly: GRCh38
Supplementary files format and content: Fastq files from both 10X lanes were processed using the CellRanger pipeline to generate cell-feature matrices of UMI counts for both feature barcode and gene expression libraries. The matrices are provided in sparse matrix format as a single filtered_feature_bc_matrix.tar.gz file.

source_name: Lymphocyte

extract_protocol:
Human primary CD3+ T cells from two donors expressing two novel CARs, CAR 6 and CAR 9, and one control CAR, 13BBz, were subject to antigen stimulation with mitomycin treated IL13Ra2+ U87 cells four times in vitro every 4 days. Residual tumor cells were removed by sorting for bicistronically expressed EGFP
Cells were stained with TotalSeq-C hashing prior to sorting and pooled before encapsulation in two channels of the Chromium Single Cell 3′ v3.1 platform (10X Genomics). Gene expression (GEX) libraries were constructed based on manufacturer’ instructions, while hashing antibody libraries were constructed as reported previously. The resulting libraries were pooled at 12.5% antibody to 87.5% GEX before sequencing on an Illumina NextSeq500 to a depth of 34,380 reads per cell.

value: Lymphocyte

value: Primary T cell

value: T cell


title: KTBset5_Parous

value: healthy donor

value: five donors

value: parous


title: Pooled CARs 10X Lane 2 Feature Barcode Library

library_source: other

molecule: protein


title: endometrial organoid, 0 fat, rep1


title: endometrial organoid, 0 fat, rep3


title: Normal prostate, Estradiol + Testosterone, rep 4

value: Prostate

value: C57BL/6J Ptenfl/fl

value: 17β-Estradiol and Testosterone (each 30 µg/g of mouse weight)


title: Normal prostate, Testosterone, rep 3

value: Testosterone (30 µg/g of mouse weight)


title: FUUR1_input

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

data_processing:
All Chip-Seq data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Assembly: hg19
Supplementary files format and content: Processed ChIP-Seq data files are in wiggle format

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for paired-end 37 bp sequencing on an Illumina NextSeq 550 were prepared with a ThruPLEX DNA-seq Kit (Takara).

value: tRCC

tag: chip antibody


title: Normal prostate, Testosterone, rep 1


title: endometrial organoid, 0 fat, rep2

value: fluctuating concentrations of estradiol, progesterone, testosterone over 14 days to mimic menstrual cycle


title: Pooled CARs 10X Lane 2 GEX Library


title: Pooled CARs 10X Lane 1 Feature Barcode Library


title: GLUP_TEAD4

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Basecalls were performed using bol2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChiP-seq reads were aligned to the UCSC h19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seg reads were extended to 150 bp to represent sequenced fragments,renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianificance cut-off a-value <=0.01.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: 1640, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HT Library Preparation Kit complemented with NEXTflex DNA Barcodes from Boo Scientific.10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler.Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: gastric cancer cells

tag: antibody

value: GLUP peptide


title: Normal prostate, Estradiol + Testosterone, rep 3


title: 3808_Uninfected

city: Stanford

first: Jason

last: Nideffer

state: CA

address: 240 Pasteur Drive

department: Medicine

institute: Stanford University

data_processing:
FASTQ files were generated using the bcl2fastq2 Conversion v2.19 tool.
The STAR aligner tool was used to trim reads and align them to the reference genome (GRCh38), generating a gene expression count matrix.
Differential expression of genes across disease states was analyzed using DeSeq2
Assembly: GrCh38
Supplementary files format and content: paired_UninSymp_DeSeq2.csv includes a count matrix for all paired uninfected/symptomatic samples as well as diffferential gene expression comparining disease states (DeSeq2).
Supplementary files format and content: paired_UninAsymp_DeSeq2.csv includes a count matrix for all paired uninfected/asymptomatic samples as well as diffferential gene expression comparining disease states (DeSeq2).

source_name: whole-blood

growth_protocol: Whole blood collected in RNA protect was cryopreserved before shipment to Stanford University. For RNA extraction, the mixes of whole blood cells and RNAprotect Cell Reagents were thawed.

extract_protocol:
350 ul QIAGEN Buffer RLT plus was added to dissolve the thawed cell pellets. The QIAGEN RNeasy Plus mini (QIAGEN, Cat. #74134) kit was used for RNA purification on QIAcube automation (QIAGEN, Cat.# 9002864). RNA samples were eluted in 30ul RNase-free water. All RNAs were checked on a NANODRP1000 and Agilent bioanalyzer 2100 RNA NANO analysis for RNA yield, purity, and integrity.
The KAPA mRNA HyperPrep Kits (KK8580) with the IDT forIlluminaDual Index Adapter kit (Cat. #20021454) were used for library preparation per the manufacturer’s protocol. Extra hemoglobin RNA removal and rRNA depletion using the Kapa specific reagents (RiboErase Globin) were added to the protocol. Briefly, mRNA was captured using magnetic oligo-dT beads then RiboErase Globin capture beads were applied. Fragmentation was performed using heat and magnesium. 1st strand cDNA synthesis was completed using random priming. Combined 2nd strand synthesis and A-tailing, adapter ligation, library amplification, and KAPA Pure Beads clean-ups were performed for library preparation. The strand marked with dUTP is not amplified, allowing strand-specific sequencing. All final libraries were checked on Agilent’s bioanalyzer 2100 High Sensitivity DNA Chip. An equal amount of cDNA library from each sample was pooled for sequencing on the Illumina Hiseq 4000 platform.

value: whole-blood

tag: date sampled

value: Female

tag: disease state

value: Uninfected


title: KTBset_1_AAF

value: Breast

tag: donors

tag: ethnicity

value: African American


title: Con_TEAD4

tag: cell type


title: GLUP_input 2


title: Normal prostate, Estradiol + Testosterone, rep 2


title: FUUR1_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: ASPS-KY_HA

source_name: ASPS-KY

value: ASPS-KY

value: ASPS


title: 3744_Asymptomatic

tag: Sex

value: Male

value: Asymptomatic


title: 3744_Uninfected


title: Normal prostate, Estradiol + Testosterone, rep 1

value: Prostate

value: C57BL/6J Ptenfl/fl


title: Normal prostate, Estradiol, rep 4

value: 17β-Estradiol (30 µg/g of mouse weight)


title: Con_input 2


title: ASPS-KY_input


title: ASPS-KY_H3K27ac


title: GLUP_H3K27me3

data_processing:
Basecalls were performed using bol2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChiP-seq reads were aligned to the UCSC h19 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seg reads were extended to 150 bp to represent sequenced fragments,renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the sianificance cut-off a-value <=0.01.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)


title: 3742_Asymptomatic


title: ASPS-1_input


title: Normal prostate, Estradiol, rep 3


title: 3742_Uninfected


title: Con_H3K27me3


title: Normal prostate, Estradiol, rep 2


title: ASPS-1_H3K27ac


title: Normal prostate, Estradiol, rep 1


title: ASPS_PDX_input

source_name: ASPS PDX

value: ASPS PDX


title: Normal prostate, Vehicle, rep 4

value: Vehicle (1:10 v/v Ethanol 96%:vegetable oil)


title: 3720_Uninfected


title: 3808_Asymptomatic


title: Con_H3K27ac

value: gastric cancer cells


title: ASPS_PDX_H3K27ac


title: GLUP_input

value: GLUP peptide


title: 3719_Asymptomatic

value: whole-blood


title: ASPS_Tumor-4_input

source_name: ASPS Tumor

value: ASPS Tumor


title: Con_input


title: 3719_Uninfected

value: Uninfected


title: Normal prostate, Vehicle, rep 3


title: Normal prostate, Vehicle, rep 2


title: 3665_Uninfected

value: Female


title: ASPS_Tumor-4_H3K27ac


title: ASPS_Tumor-3_input


title: Normal prostate, Vehicle, rep 1


title: Con_2

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Assembly: GRCh38.p10
Supplementary files format and content: xls file includes RPKM values for each Sample.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: 3665_Asymptomatic


title: GLUP_H3K27ac


title: ASPS_Tumor-3_H3K27ac


title: 3720_Asymptomatic


title: Con_1


title: Knockout

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The sequence data were generated from the base call (BCL) files by the Cell Ranger pipeline (v. 3.0.1) and mapped to the mouse reference genome GRCm39 by STAR aligner.
The count data was processed by Seurat.
The cell types of the predicted clusters were annotated based on expression of marker genes.
Differential expression analysis of genes between control and cKO samples was performed using the ‘FindAllMarkers’ function of Seurat for each cell type.
Assembly: GRCm39
Supplementary files format and content: text files, conatin count data, features and barcodes

source_name: Whole brain

extract_protocol:
Single nuclei were isolated using Pure Prep Nuclei Isolation kit (Sigma, St. Louis, MO, USA) as per manufacturer’s instructions.
The freshly prepared nuclei were used to prepare sequencing libraries using 10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 at the University of Missouri Genomics Technology Core. The libraries were quantified using a Qubit HS DNA kit. The fragment size was analyzed using an Agilent Fragment Analyzer system.  Libraries were sequenced on an Illumina NovaSeq 6000 with a sequencing configuration of 28 base pair (bp) on read1 and 98 bp on read2. Each library was sequenced to a depth of 20,000 paired-end (single-indexing) reads per nucleus.
Single-nuclei RNA-seq

value: Whole brain

tag: developmental stage

value: week-8 old adult knockout offspring


title: GLUP_1


title: 3630_Uninfected

tag: age


title: Control

value: week-8 old adult control offspring


title: 3630_Asymptomatic


title: 3629_Asymptomatic


title: ASPS_Tumor-2_input

value: ASPS


title: ASPS_Tumor-1_input


title: 3629_Uninfected

value: Male


title: Spl replicate 3

city: Milwaukee

first: Subramaniam

last: Malarkannan

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Microbiology & Immunology

institute: Medical college of wisconsin

data_processing:
The demultiplexing, barcode processing,and gene counting and aggregation were made using 10X Genomics CellRanger software v3.0.0 using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Spleen

extract_protocol:
Freshly isolated human LN, spleen were flushed with ice-cold PBS. Fat tissues were removed from the samples. 0.5 g of the tissue was cut it into small pieces of 2-4 mm in length and transferred into the GentleMACS C Tube containing the enzyme mix and RPMI-1640 medium on ice. GentleMACS Program for the tissue type of interest (i.e., 37° C ‘multi.B’ preset program for human spleen) was selected.BM samples were collected in anticoagulated tubes and processed on the same day. Density gradient separation of BM samples was performed using Lymphoprep, StemCell. Cells were sorted using FACSAria III or FACSMelody (BD Biosciences, San Jose, CA).
Library construction was performed using the 10X Genomic Chromium Single Cell 3’ Reagent Kit per manufacturer’s protocols. Briefly, cells were resuspend in master mix and loaded into the chip with partitioning oil and gel beads to generate GEM. The mRNA will concvert to cDNA and cleaned up with Silane DynaBeads. After amplification, the size selection was doen using SPRIselect beads for library construction. In the library construction part, the adaptors for sequencing and index were added for sequencing.

value: Spleen


title: cKO adult brain 1

data_processing:
The quality of raw sequences was checked with FastQC followed by trimming the adaptors from the sequence reads by cutadapt.
The trimmomatic tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides).  GRCm39 using Hisat2 aligner.
The quality reads were then mapped to the mouse reference genome.
Read counting from the alignment data was performed by FeatureCounts.
The count data was used for differential expression analysis by edgeR.
Assembly: GRCm39
Supplementary files format and content: Text file containing read count data
Supplementary files format and content: Text file and it conatins read counts

source_name: whole brain

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) was used to isolate total RNA following the manufacturer’s instruction.
Stranded bulk RNA-Seq libraries using a poly A enrichment method.

value: whole brain

value: Week-8 adult (W8)

value: M

value: REST Knockout


title: cKO adult brain 3


title: GLUP_2


title: ASPS_Tumor-1_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: Spl replicate 4


title: Spl replicate 2


title: cKO adult brain 2


title: 3597_Asymptomatic

value: Asymptomatic


title: Spl replicate 1


title: Control adult brain 2

value: Control


title: 3597_Uninfected

value: whole-blood


title: RPE-1 hTERT FUCCI single pulse 15min_8

description: scEdUseq library

data_processing:
demultiplexing reads; extracting cell barcodes from reads
trimming adapter sequences with cutadapt
mapping to human genome with bwa -mem algorithm
custom bam tagging tool to add flags which we later select for
extracting reads wtih specific bam flags and write to tsv.gz file
Assembly: GRCh38.p12 / Ensembl release 97 for Homo Sapiens
Supplementary files format and content: Data table containing cell name, chromosome, read start, length, allele
Library strategy: DNA-seq

source_name: Retinal Pigment Epithelial

extract_protocol:
TrypLE digestion
Custom library protocol. Briefly, EdU was clicked to Biotin-PEG3-Azide. Single cells were sorted in a 384-well plate. Subsequently, cells were lysed wioth ProtK and the genome was digested with NLAIII. Next, DNA fgragments were end-repaired by Klenow Large Fragment and PNK. On these repaired ends we ligated a custom adapter sequence followed by affininty purification of EdU-Biotin miolecules with magnetic streptadin beads. Non-modified strands were recovered by heat denaturation and the complimetary strand was re-generated by a primer extension reaction. Finally, libraries were amplified by a combination of T7 in vitro trasncription, reverse transcription and polymerase chain reaction containing Illumina handles
Illumina RPI small RNA adapters

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI

value: DMSO

value: WT


title: RPE-1 hTERT FUCCI single pulse 15min_9

description: scEdUseq library


title: BM replicate 4

source_name: Bone marrow

value: Bone marrow


title: 3580_Asymptomatic


title: Control adult brain 1


title: ASPS_Tumor-2_H3K27ac

value: ASPS Tumor


title: 3580_Uninfected

value: Uninfected


title: cKO post-natal brain 3

value: Post-natal day 7 (P7)


title: RPE-1 hTERT FUCCI single pulse 15min_7

description: scEdUseq library


title: RPE-1 hTERT FUCCI single pulse 15min_6

description: scEdUseq library


title: BM replicate 2


title: 3570_Asymptomatic

value: Female


title: RPE-1 hTERT FUCCI single pulse 15min_5

description: scEdUseq library


title: cKO post-natal brain 2

value: whole brain


title: 3570_Uninfected


title: cKO post-natal brain 1


title: RPE-1 hTERT FUCCI single pulse 15min_4

description: scEdUseq library


title: BM replicate 1


title: Control adult brain 3

value: Week-8 adult (W8)


title: 3444_Asymptomatic

value: Male


title: Control post-natal brain 3

value: M


title: RPE-1 hTERT FUCCI single pulse 15min_3

description: scEdUseq library


title: RPE-1 hTERT FUCCI single pulse 15min_2

description: scEdUseq library


title: LN thoracic replicate 3

source_name: Lymph node

value: Lymph node


title: LN thoracic replicate 2


title: 3393_Asymptomatic

value: Asymptomatic


title: BM replicate 3


title: LN thoracic replicate 1


title: LN abdominal replicate 3


title: RPE-1 hTERT FUCCI single pulse 15min_1

description: scEdUseq library


title: Control post-natal brain 1

value: Control


title: cKO fetal brain 3

value: Embryonic day 15 (E15)

value: REST Knockout


title: RPE-1 hTERT FUCCI single pulse 15min_11

description: scEdUseq library

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI


title: 3393_Uninfected

value: whole-blood


title: 3444_Uninfected


title: RPE-1 hTERT FUCCI single pulse 15min_10

description: scEdUseq library

value: DMSO

value: WT


title: ASPS_PDX_Palbo-2

data_processing:
fastq files wre aligned using STAR, and transcript quantitation performed using cufflinks.
Assembly: hg19
Supplementary files format and content: Gene expresion in FPKM are in text format

source_name: PDX

extract_protocol:
Total RNA was isolated using an RNeasy Plus Kit (Qiagen).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs Cat# E7645S). Paired-end 150 bp sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: In indicated conditions, cells and xenografts were treated with palobciclib for 24 hours or 3 days, respectively.

value: PDX

value: Palbociclib


title: cKO fetal brain 2


title: LN abdominal replicate 1


title: LN abdominal replicate 2


title: cKO fetal brain 1


title: RPE-1 hTERT FUCCI bulk single pulse 120min late S

description: bulk EdUseq library


title: 3046_Uninfected

value: Female

value: Uninfected


title: ASPS_PDX_Palbo-1


title: 31821_Uninfected


title: Control fetal brain 3

value: whole brain


title: RPE-1 hTERT FUCCI bulk single pulse 120min  early S

description: bulk EdUseq library


title: 31821_Symptomatic

value: Symptomatic


title: Control fetal brain 2

value: M


title: ASPS_PDX_Control-2

value: Vehicle


title: 31803_Symptomatic


title: Control fetal brain 1


title: H5

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were mapped to the mm10 genome using HISAT2 (D. Kim, Langmead, and Salzberg 2015)
Read counts mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation (Liao, Smyth, and Shi 2019).
Differential expression analysis was performed using the DESeq2 package (Love, Huber, and Anders 2014). DEGs were determined using a p-value of < 0.05 and log2(fold change) > 0.3.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing counts

source_name: Nucleus accumbens

extract_protocol:
Animals were euthanized via cervical dislocation, the brain was rapidly extracted and placed in chilled PBS. Coronal brain sections were performed at 1 mm thickness, the NAc was collected using a 14-gauge needle and placed on dry ice. RNA isolation was performed using the Qiagen RNeasy Micro Kit according to the manufacturer’s instructions. cDNA conversion was performed using the Bio-Rad iScript cDNA Synthesis Kit. qPCR reactions were performed in triplicate using the TaqMan Fast Advanced Master Mix (Applied Biosystems) with TaqMan probes directed towards Pde1b (Cat. #: 4331182). Expression levels were calculated using the ∆∆Ct method relative to Hprt1 (Cat. #: 4331182).
RNA-seq libraries were generated using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio; Cat. #: 634417) and the Indexing Primer Set HT for Illumina® v2 (Takara Bio; Cat. #: 634420). Library sequencing was performed by Azenta with >20 million reads per sample.

value: Nucleus accumbens

value: female

tag: virus

value: Cocaine


title: 3046_Asymptomatic

value: Asymptomatic


title: ASPS_PDX_Control-1


title: 31787_Symptomatic


title: H3

value: Saline


title: 31803_Uninfected


title: biol rep 2- KPC-Trip12 knockout tumor derived cell line (KO-c1762)

city: Toulouse

first: Marlène

last: DUfresne

address: 2 Avenue Hubert Curien

country: France

institute: Inserm

data_processing:
read alignment on Mouse_GRCm39 version 2.7.4a indexed genome with STAR version 2.7.10a
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCM39/mm39 using STAR version 2.7.10a
Read count extraction and normalization were performed using STAR version 2.7.10a
Assembly: mm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: pancreatic tumor

growth_protocol: the tumor murine cell lines were grown in DMEM/F12 medium (Gibco-BRL) supplemented with 10% fetal calf serum, antifungics and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA were isolated using Trizol reagent (Life Technologies) following manufacturer's recommendations. Preliminary quality control of total mRNA was ensured by agarose gel electrophoresis and NanoDrop measurement. Sample quantitation and integrity were performed by Nanodrop and Agilent 2100, respectively.
mRNA libraries were constructed using poly A enrichment preparation. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount

treatment_protocol: no treatment

value: pancreatic tumor


title: biol rep 3- KPC-Trip12 knockout tumor derived cell line (KO-c1763)


title: H2

value: mCherry


title: ASPS-1_Palbo-3


title: ASPS-1_Palbo-2


title: biol rep 1- KPC-Trip12 heterozygous tumor derived cell line (KO-H-c1901)


title: 31777_Symptomatic

value: whole-blood


title: H1


title: G5


title: biol rep 3- KPC tumor derived cell line (WT-c166)


title: 31787_Uninfected


title: 31777_Uninfected


title: biol rep 1- KPC-Trip12 heterozygous tumor derived cell line (WT-H-c28)


title: H4


title: biol rep 2- KPC tumor derived cell line (WT-c99)


title: G3


title: ASPS-1_DMSO-3

value: DMSO


title: ASPS-1_Palbo-4


title: ASPS-1_DMSO-4


title: G4


title: G2


title: ASPS-1_DMSO-2


title: 31752_Symptomatic

value: Male


title: ASPS-1_DMSO-1


title: 31752_Uninfected


title: 31763_Uninfected


title: G1


title: biol rep 2- pancreatic Trip12 knockout acinar cells (KO_64)

source_name: pancreatic acinar cells

value: pancreatic acinar cells

value: adult


title: ASPS-1_Palbo-1

value: Palbociclib


title: KYdTAG_6h-4

value: ASPS-KY


title: biol rep 1- pancreatic Trip12 knockout acinar cells (KO_1)


title: F5


title: KYdTAG_6h-3


title: 31763_Symptomatic

value: Symptomatic


title: 31738_Uninfected

value: Uninfected


title: F4


title: biol rep 3- pancreatic control acinar cells (WT_484)


title: biol rep 3- pancreatic Trip12 knockout acinar cells (KO_787)


title: F3


title: 31736_Symptomatic


title: biol rep 1- pancreatic control wt acinar cells (WT_24)


title: KYdTAG_6h-2


title: F2


title: KYdTAG_6h-1


title: 31736_Uninfected


title: KYdTAG_24h-4


title: F1


title: 31704_Symptomatic


title: murine_glioma_ATRA_tcr

city: Pittsburgh

first: Nduka

last: Amankulor

state: PA

address: 200 Lothrop Street

department: Neurological Surgery

institute: University of Pittsburgh

description: TCR sequencing data

data_processing:
bcl2fastq (version 2.20.0) to demultiplex reads
cellranger (version 3.1.0) to align reads and generated gene barcode matrices
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_barcode_matrix, cellranger gene barcode expression matrix consisting of features (genes), cell barcodes, and UMI counts. filtered_contig_annotations, cellranger output of vdj

source_name: glioma tissue

growth_protocol: Neurospheres were maintained in DMEM-F12 with 20 ng/mL bEGF, bFGF and 1 ug/mL Normocin.

extract_protocol:
Tumors were dissected with normal surrounding brain tissue, chopped into 1-2 mm pieces and incubated in Accutase for 10 minutes at 37degreesC. The suspension was then passed through 25 mL, 10 ml and 5 mL pipettes beforre finally being passed through 18G needle 3 times and filtered through a 100 micron strainer. Immune cells were sorted from dissected tissue by CD45 expression.
Libraries were contructed accoding to the manufactuerer's protocol for the 5-prime v1 kit from 10X Genomics.

treatment_protocol: Mice were treated with 10 mg/kg all-trans retinoic acid or control every other day.

tag: strain

value: brain (glioma tissue)

value: ATRA


title: murine_glioma_control_tcr

description: TCR sequencing data

value: control


title: E5

value: Nucleus accumbens

value: female


title: murine_glioma_ATRA_gex

description: gene expression data


title: KYdTAG_24h-3


title: KYdTAG_24h-2


title: biol rep 2- pancreatic control acinar cells (WT_27)


title: 31738_Symptomatic


title: murine_glioma_control_gex

description: gene expression data


title: KYdTAG_24h-1


title: PBS-3

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

description: Mouse CRC tissue was obtained from wild-type C57 mice with AOM/DSS model

data_processing:
Using Cell, the official 10X Genomics analysis software Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to the raw data to identify the data filtering, alignment, quantitative, recycling cells, Finally, the gene expression matrix of each cell was obtained.
The Seurat (https://satijalab.org/seurat/) for further cell filtration, standardization, the classification of the cells, each subgroup analysis and Marker gene screening differentially expressed genes.
Genome_build: Mus_musculus.GRCm38.96
Supplementary_files_format_and_content: Sample name.gz:contains three files:barcodes.tsv.gz,features.tsv.gz and matrix.mtx.gz.
Supplementary_files_format_and_content: cell_batch.tsv.gz:includes cell - sample correspondence.

source_name: PBS administration

extract_protocol:
Chromium™ Single Cell 3'Solution is a microfluidics platform built on GemCode technology that combines gel beads with barcodes and primers. Individual cells are encapsulated in oil droplets to form GEM(Gel bead in emulsion).The gel beads in the GEM dissolve and the cells cleave to release mRNA, which is then reverse transcribed to produce cDNA with barcodes for sequencing. After the liquid oil layer is destroyed, cDNA amplification reaction is carried out. After purification, quality inspection is carried out.
Enzymatic digestion interrupted the fragments, end patching was carried out, and base A was added to connect the joints, and the target size fragments were recovered for library quality inspection and quantification.
10X scRNA-seq

treatment_protocol: C57BL/6J wild-type (WT) mice were housed and reared in specific pathogen free and barrier conditions with autoclaved food and water. The body weight of mice was measured every week. For AOM/DSS model, 6- to 7-week-old male mice were treated with metronidazole(2mg/ml) in drinking water for 5 consecutive days to ensure the consistency of regular microbiota and facilitate Fn colonization. PBS-resuspended 109 CFU Fn or PBS were administrated into mice by gavage every other day. Then mice were given a single intraperitoneal injection of carcinogen azoxymethane at 12 mg/kg body weight. After 8 days of intraperitoneal injection, 2% dextran sodium sulfate (DSS) was added in the drinking water for 7 consecutive days. Then mice were given regular drinking water. After a week, mice were again given 2% dextran sodium sulfate in drinking water for 7 consecutive days. During the DSS intervention, the bacteria administration was suspended. Bacteria, or PBS administration was given for a period of 10 weeks. To investigate the effect of related therapy on the Fn induced gut tumor progression, At the indicated time intervals, the mice were anaesthetized with 40 mg/kg pentobarbital sodium and sacrificed for tumor statistics.

tag: the mice model

value: C57BL/6J wild-type mice

tag: treatment type

value: colorectal tumor tissues PBS administration


title: E2

tag: tissue

value: Saline


title: E3

value: mCherry

tag: treatment

value: Cocaine


title: 31698_Uninfected

value: whole-blood

value: Male


title: 31694_Symptomatic


title: PBS-2


title: KYdTAG_0h-3

tag: cell line


title: E1


title: 31694_Uninfected


title: PBS-1


title: D5

value: male


title: KYdTAG_0h-2


title: E4


title: 31704_Uninfected


title: Fn-3

source_name: Fn administration

value: colorectal tumor tissues Fn administration


title: 31685_Symptomatic

source_name: whole-blood


title: D4


title: 31698_Symptomatic


title: Fn-2


title: KYdTAG_0h-1

source_name: ASPS-KY

value: ASPS-KY


title: D3


title: 31629_Symptomatic

value: Symptomatic


title: Fn-1


title: ASPS_Tumor-3

source_name: ASPS tumor

value: ASPS tumor


title: D2


title: D1


title: ASPS_Tumor-1


title: 31629_Uninfected

value: Uninfected


title: ASPS_Tumor-2


title: KYdTAG_0h-4


title: 31604_Symptomatic

value: Female


title: WBCminusNeu_ZT85_replicate

type: genomic

city: Vilnius

first: Karolis

last: Koncevičius

address: Saulėtekio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description: White blood cells left over after magnetically activated cell sorting isolation of neutrophils

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing:
Processeing was done using the R “minfi” package. First, all samples having more than 3% of probes with poor detection p-values (detection p < 0.05) using an alternative detection p-value approach(Heiss and Just 2019) were removed as outliers. Then array normalization was performed using “noob” background correction followed by functional normalization, and signals from the methylated and unmethylated channels were combined to obtain the methylation beta values. Additional outliers were identified by measuring Pearson’s correlations among all the sample pairs and removing samples with an average inter-sample correlation value more than three standard deviations below the mean. Finally, for the datasets that contained technical replicates for every sample, all the samples with only a single replicate remaining after quality control were discarded.
R "minfi" package computed Average Beta values after "noob" background correction and "functional" normalization

label: Cy3 and Cy5

source_name: Whole blood depleted of neutrophils

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The remaining fraction of white blood cells depleted of neutrophils were snap-frozen and stored in -80 °C before DNA extraction. DNA was extracted with NucleoSpin® Blood XL (Macherey-Nagel) using the standard protocol

tag: ct


title: WBCminusNeu_ZT85


title: 31604_Uninfected


title: ASPS-KY


title: C5


title: WBCminusNeu_ZT82_replicate


title: 31578_Symptomatic


title: FUUR1


title: 31685_Uninfected


title: WBCminusNeu_ZT82


title: C3


title: ASPS_Tumor-5


title: WBCminusNeu_ZT79_replicate


title: 31578_Uninfected


title: WBCminusNeu_ZT79


title: ASPS_Tumor-4


title: C2


title: ASPS-1_CLX

source_name: Cell line xenograft

value: Cell line xenograft


title: 31538_Symptomatic


title: WBCminusNeu_ZT76_replicate


title: C1

value: Nucleus accumbens


title: 31538_Uninfected


title: B5


title: B4


title: ASPS-1


title: 31277_Uninfected


title: Control post-natal brain 2

value: whole brain

value: Post-natal day 7 (P7)

value: M

tag: genotype

value: Control


title: WBCminusNeu_ZT76


title: WBCminusNeu_ZT73_replicate


title: ASPS_PDX_F4

value: PDX


title: ASPS_PDX_F0


title: C4

value: Saline


title: WBCminusNeu_ZT70_replicate


title: zhx8-9

first: Xiang

last: Zhong

address: Tongwei Road

institute: Nanjing agricultural university

description: immunoprecipitation

data_processing:
Reads were quality controlled using FastQC (v0.11.5) and TrimGalore (v0.6.0).
rRNA sequence were removed by using bowtie2(v2.3.4.1) with --ungz or --un-conc-gz parameter.
The retained reads were aligned to GRCm38/mm10 by HISAT2 (v2.2.1) with default parameters.
Bigwig files were obtained by using bamCoverage function in deepTools (v3.5.1) and visualized in IGV (v11.0.19).
Read counts were quantified by using featureCounts (v1.6.0).
Assembly: Sscrofa 11.1,porcine_rotavirus
Supplementary files format and content: bigwig

organism: Porcine rotavirus

source_name: PoRV

extract_protocol:
The experiment was carried out according to the procedure previously reported. mRNA was isolated from total RNA using the Dynabeads™ mRNA DIRECT™ kit (Ambion, Cat NO. 61012). The purified mRNA was then fragmented by 30 cycles of ultrasound, with each cycle comprising 30 s on and 30 s off. The concentration of fragmented mRNA was determined using a QubitTM RNA HS assay kit (Invitrogen, Cat NO. Q32852). Next, 500 ng of mRNA was taken as the Input control for sequencing. A total of 950 ng of fragmented mRNA was incubated with 1 μL of m6A antibody (NEB, Cat. E1610S) at 4°C for 1 h. After incubation, the mixture was washed twice in reaction buffer (150 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), twice in low salt buffer (50 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40), and twice in high salt buffer (500 mM NaCl, 10 mM Tris-HCl, pH 7.5, 0.1% NP-40). Bound mRNA was eluted using 100 μL of elution buffer (QIAGEN, Cat. 1015762). Library preparation was conducted using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara) per the manufacturer’s instructions. Briefly, the immunoprecipitated mRNA fragments and an equal amount of input control were subjected to cDNA synthesis using the kit components SMART Pico Oligos Mix v2, 5X First-Strand Buffer, SMART TSO Mix v2, and SMARTScribe Reverse Transcriptase. The cDNA was then ligated with Illumina adapters and indexes, followed by PCR amplification. The libraries were then purified using AMPure beads to remove excess primers and nucleotides. Ribosomal cDNA removal was performed using the ZapR v2 and R-Probes v2 reagents provided in the kit. The library fragments underwent a second round of PCR enrichment to amplify the libraries to sufficient quantity for sequencing. Before sequencing on an Illumina HiSeq4000, the libraries were analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit version 2-Pico Input Mammalian (Takara), according to the manufacturer’s protocol.
m6a-seq

value: PoRV


title: B1


title: B3

value: Cocaine


title: WBCminusNeu_ZT70

value: male


title: B2

value: mCherry


title: zhx8-8

description: immunoprecipitation


title: WBCminusNeu_ZT67_replicate


title: 1833shp27 input

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Adapters trimmed with TrimGalore
Genome alignment with bwa v0.7.12
Peaks called with MACS2 v2.1.2
Assembly: hg19
Supplementary files format and content: NarrowPeak files obtained from MACS2

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY, USA) with 10% fetal bovine serum, 1% glutamine, 1% sodium pyruvate. Cells were cultured at 37C at 5% CO2.

extract_protocol:
ChIP assay was performed by ChIP-IT High Sensitivity®(HS) Kit (Avtive motif; 53040)according to kit’s instruction. Briefly, after cells were crosslinked with 1% formaldehyde, the cells were lysed and sonicated. For the immunoprecipitation, sonicated samples were incubated with p27 (Cell Signaling; 3686s), STAT3 (Cell Signaling; 12640s), cJun (Cell Signaling; 9165s), CBP (Cell Signaling; 7389s), H3K27ac (Cell Signaling; 8173s), SIN3A (Abcam; ab3479), YY1 (Abcam; ab12132), HDAC1 (Santa Cruz; sc-7872), IgG Rabbit (Cell Signaling; 2729s), and IgG mouse (Santa Cruz; sc-2025) antibodies overnight at 4°C. Samples were collected on A/G plus-agarose. DNA was eluted after washing of the beads and decrosslinking. Eluted DNA was used for sequencing.
The ChIP DNA library was made using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads kit (NEB; E7103S) per kit’s instruction.

treatment_protocol: 10 ng/ml IL-6 for 30 minutes

value: breast cancer

value: 10 ng/ml IL-6 for 30 minutes


title: 1833shp27-STAT3 ChIP-Rep1

tag: chip antibody

value: STAT3 (Cell Signaling, Cat#12640)


title: A5


title: zhx8-23

description: Input


title: MDA-MB-231-1833-STAT3 ChIP-Rep1


title: zhx8-22

description: Input


title: P2-3

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
The paired-end libraries were prepared using a NEBNext UltraTM RNA Library Prep Kit for Illumina
Sequencing was performed using the Illumina NovaSeq 6000 platform.
A fold change of   >2 and P value of <0.05 were set as the criteria for identifying significantly differentially expressed genes
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Text file for rpkm values of each gene

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Human ovarian cancer cell line

value: SNX29P2 overexpression


title: WBCminusNeu_ZT73


title: 31277_Symptomatic

value: whole-blood

tag: date sampled

value: Male

tag: disease state

value: Symptomatic


title: A2

value: Nucleus accumbens


title: A3


title: P2-2


title: zhx8-7

description: immunoprecipitation


title: ChIPWT H3K4me1 Mesoderm Rep 2

city: Irvine

first: Kitt

middle: D.

last: Paraiso

address: 4410 Nat Sci II, University of California, Irvine

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
H3K4me1 ChIP-seq reads from biological replicates were concatenated and then aligned to the X. tropicalis genome v9.0 (Mitros et al., 2019; Karimi et al., 2018) using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 10 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.0000000001 but otherwise default options.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: ChIP-Seq: NarrowPeak (BED)

organism: Xenopus tropicalis

source_name: Early Embryo

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8. After 10 minutes, embryos are washed with 1/9x MMR and transferred to 1/9x MMR.

extract_protocol:
Samples were dissected from 100 fixed embryos and were then homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 ¼L Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4C with rotation. Meanwhile, another 20 ¼L Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4C to block non-specific binding. This second 20 ¼L Protein G Dynabeads were then pre-bound with 3 ug anti-H3K4me1 antibody at 4C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4¡C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
Library Construction Protocol: Nextflex ChIP-seq kit (Bioo Scientific)

tag: tissue type

value: Marginal Zone (Mesoderm)

value: Nieuwkoop Faber 10.25

tag: antibody

tag: clock time (hours post-fertilization)

tag: agent

value: untreated


title: WBCminusNeu_ZT64_replicate

tag: Sex

tag: age


title: zhx8-21

description: Input


title: 1833 input

tag: cell type


title: A1

tag: virus

value: Saline


title: WBCminusNeu_ZT64


title: ChIPWT H3K4me1 Mesoderm Rep 1

tag: developmental stage


title: A4

tag: tissue


title: B2-3

value: OTUB2 overexpression


title: WBCminusNeu_ZT61


title: Gpr124-/- bEC E15.5 ME5

first: Kanako

last: Yuki

address: 265 CAMPUS DRIVE

description: Gpr124-/- bEC E15.5

data_processing:
The sequencing libraries were multiplexed and clustered on a lane of a flowcell.
The samples were sequenced using a 2x150 Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
One mismatch was allowed for index sequence identification.
Assembly: mm10

source_name: CD31+ brain endothelial cells

extract_protocol:
RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
RNA libraries for ultra-low input RNA-seq were prepared using SmartSeq V4 Ultra-Low RNA Library Prep following manufacturer's protocols.

value: CD31+ brain endothelial cells

tag: time


title: WBCminusNeu_ZT67

value: male


title: ChIPWT H3K4me1 Ectoderm Rep 2

value: Animal Cap (Ectoderm)


title: Gpr124-/- bEC E15.5 ME4

description: Gpr124-/- bEC E15.5


title: P2-1

tag: cell line


title: WBCminusNeu_ZT61_replicate

tag: ct


title: WBCminusNeu_ZT58_replicate


title: ChIPWT H3K4me1 Ectoderm Rep 1


title: B2-1

tag: genotype


title: B2-2


title: WBCminusNeu_ZT58


title: V-3

value: empty vector


title: Gpr124-/- bEC E15.5 KE4

description: Gpr124-/- bEC E15.5


title: RNAseq Clutch C Sample 5

data_processing:
Paired-end reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version 9.0 (Mitros et al., 2019; Karimi et al., 2018). Gene expression in transcripts per million were extracted from RSEM results output.
Genome_build: Xenopus tropicalis v9.0
Supplementary_files_format_and_content: RNA-Seq:The first column is populated by the gene models in the X. tropicalis v9.0 genome annotation. Each subsequent column is the expression of the gene from the 15 RNA-seq datasets.

extract_protocol:
Total RNA was extracted using the acid guanidinium thiocyanate method of Chomczynski and Sacchi (1987: Analytical Biochemistry 162:156-159). Final RNA pellets were resuspended in DEPC-treated water and then precipitated overnight at 4C in 2.5M LiCl to remove contaminating genomic DNA.
Library Construction Protocol: Smart-seq2 cDNA synthesis, Tagmentation

value: Whole Embryo


title: RNAseq Clutch C Sample 4


title: WBCminusNeu_ZT55_replicate


title: Gpr124ΔC/ΔC bEC E15.5 LE5

description: Gpr124ΔC/ΔC bEC E15.5


title: RNAseq Clutch C Sample 3


title: V-2


title: WBCminusNeu_ZT55


title: Gpr124ΔC/ΔC bEC E15.5 LE2

description: Gpr124ΔC/ΔC bEC E15.5


title: RNAseq Clutch C Sample 2


title: WBCminusNeu_ZT49_replicate


title: Gpr124ΔC/ΔC bEC E15.5 JE4

description: Gpr124ΔC/ΔC bEC E15.5


title: KELLY cells, DMSO, 48 hours, replicate 3

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
ATAC-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/atac-seq/). Briefly, quality control for the paired-end unmapped reads was performed with the FastQC v.0.11.9 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were trimmed and filtered for Nextera adapters using Trimmomatic v0.39 (Bolger et al., 2014).
The trimmed reads were mapped to the hg38 reference genome using bowtie2-2.3.5 (Langmead and Salzberg, 2012)with the –local –very sensitive –X 2000 options. Bam files were deduplicated using Picard tools ( “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute).  Only reads mapping to chromosomes 1-22 and chrX with MAPQ ≥ 5 were retained. Reads were shifted with 4 bp on the positive strand and -5 bp on the negative strand using AlignmentSieve available in deepTools v3.5.1 (Ramírez et al., 2016).
Replicate correlations were computed with the multiBamSummary and bamCorrelate tools available in deepTools v3.5.1  and visualized as dendrograms and in PCA plots. Fragment size distributions were computed with the bamPEFragmentSize tool available in deepTools v3.5.1 and then inspected for QC. Properly aligned reads for replicates were merged for each condition. Replicate correlations were computed with the multiBamSummary and bamCorrelate tools available in deepTools v3.5.1  and visualized as dendrograms and in PCA plots. Fragment size distributions were computed with the bamPEFragmentSize tool available in deepTools v3.5.1 and then inspected for QC. Properly aligned reads for replicates were merged for each condition.
Peak calling was performed for properly aligned and for the merged reads with MACS2 v2.1.1.20160309 software (Zhang et al., 2008), with the –nomodel, --extsize to fragment length and –q 0.01 options. Area under curve (AUC) binding signal for peaks was computed with the bwtool software (Pohl and Beato, 2014).
The peaks were annotated with the closest hg38 genes by using the annotatePeaks function implemented in the Homer v4.11 platform (Heinz et al., 2010) and the GREAT annotation platform (McLean et al., 2010).  Gene promoter regions were defined as the +/- 3.0 kb intervals around the hg38 gene transcription start site (TSS). Enhancer regions were defined as the H3K27ac binding regions outside TSS +/- 3.0 kb gene promoter regions. The samtools v1.9 (Li et al., 2009)  and the BEDTools v2.29 suite (Quinlan and Hall, 2010)  were used to perform various genomic analyses.
Assembly: hg38
Supplementary files format and content: bigwig RPKM normalized signal file for each replicate sample, for merged replicates and for merged CRISPR knocked out conditions.

source_name: KELLY

growth_protocol: ATAC-seq was performed as previously described with modifications (Buenrostro et al., 2013; 2015). KELLY dTAG TADA2B cells were cultured under standard conditions, then treated with DMSO or 500nM BNN4 for 48 hours. The Tn5 transposition reaction was performed using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, cat.# 20034197 ). Cells were trypsinized, 100,000 collected, and washed once with cold PBS, A resuspension buffer was prepared (10nM Tris-HCl, pH7.5, 10mM NaCl, 3mM MgCl2). Cells were lysed in 50ul lysis buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin in resuspension buffer) for 3 minutes on ice, then washed with 1mL Wash buffer (0.1% Tween-20 in resuspension buffer). Lysates were cleared by centrifugation at 500g for 10 minutes at 4C. Tn5 transposition reaction was performed with the Nextera kit (Illumina). The nuclear pellet was resuspended in transposition reaction mix (25ul Tagment DNA Buffer, 16.5ul PBS, 0.5ul 10% Tween-20, 0.5ul 1% Digitonin, 2.5ul Tagment DNA Enzyme 1, 5ul nuclease-free water) and incubated for 30 minutes at 37C on a thermomixer with 1,000 rpm. For KELLY cells with sgRNAs, nuclei isolation and transposition reaction procedures were same as above except 100ul lysis buffer and 100ul transposition reaction mix were used for 100,000 cells.

extract_protocol:
DNA was isolated using the Qiagen MinElute Reaction Cleanup Kit (Qiagen cat.#28204) and eluted in 10ul EB.
Library generation was performed with NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat.# M0541S), SYBR Green I (ThermoFisher, cat.# S7563), Ad1_noMX and Ad2.* primers at 25uM.

value: KELLY

value: neuroblastoma cell line

value: WT

tag: treatment

value: 48 hours


title: RNAseq Clutch B Sample 5


title: RNAseq Clutch C Sample 1


title: Gpr124ΔC/ΔC bEC E15.5 JE3

description: Gpr124ΔC/ΔC bEC E15.5


title: WBCminusNeu_ZT49


title: KELLY cells, DMSO, 48 hours, replicate 2


title: WT bECs E15.5 LE6

description: WT bECs E15.5


title: Gpr124-/- bEC E15.5 ME1

description: Gpr124-/- bEC E15.5


title: WBCminusNeu_ZT46_replicate


title: KELLY cells, DMSO, 48 hours, replicate 1