title: Specimen_1

status: Public on Apr 19 2022

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Basecalls performed using BCL2fastq
RNAseq reads were aligned to the hg38 genome assembly using STAR 2.7.6a
Data processing was preprocessed using Drop-seq-1.13
Genome_build: hg38

source_name: human hippocampus

extract_protocol:
Briefly, 14 mL of sucrose cushion (1.8 M sucrose (Sigma-Aldrich, RNase & DNase free, ultra pure grade), 10 mM Tris-HCl pH 8.0 (Invitrogen), 3 mM MgAc2 (Sigma-Aldrich), protease inhibitor cocktail (Roche)) was added to the bottom of centrifuge tubes (Beckman Coulter). Using a glass homogenizer (Wheaton), a freshly isolated or frozen mouse cortex sample was subjected to dounce homogenization (21 times with loose pestle followed by 7 times with tight pestle) in 12 mL of homogenization buffer (0.32M sucrose, 5 mM CaCl2 (Sigma-Aldrich), 3mM MgAc2, 10 mM Tris-HCl pH 8.0, 0.1% Triton X-100 (Sigma-Aldrich), 0.1 mM EDTA (Invitrogen), protease inhibitor cocktail). For in vitro cultured cells, cell pellets (~ 5 million cells) were resuspended in homogenization buffer and dounced 20 times with a loose pestle. Homogenates (12 mL) were layered onto the sucrose cushion in the centrifuge tubes, and 10 mL of homogenization buffer was added atop of the homogenates. The tubes were then centrifuged in a Beckman Coulter L7-65 Ultracentrifuge at 25,000 rpm at 4C for 2 hr using a Beckman Coulter SW28 swinging bucket rotor (Beckman Coulter). The supernatant was carefully removed via aspiration. 1 mL of chilled DPBS with RNase inhibitor (Lucigen) was added to resuspend the nuclear pellet, and nuclei were subsequently transferred to a 1.5-mL tube. Nuclei were pelleted at 5,000 rpm for 10 min at 4C, and then resuspended in 0.01% BSA (Sigma-Aldrich) in DPBS. After resuspension, nuclei were filtered through a 40-mm cell strainer (Fisher Scientific), visually inspected for morphology and quality assurance, and counted using a Fuchs-Rosenthal counting chamber before droplet microfluidic encapsulation.
Drop-seq

tag: tissue

value: hippocampus

tag: development stage

value: Infant


title: Sm1-Ctrl2

status: Public on Apr 27 2022

type: SRA

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

country: USA

institute: National Jewish Health

library_source: genomic

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’, duplicates were removed using picard tools MarkDuplicates (v. 2.26.6) and then resulting BAM files were sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.29.2) with arguments ‘-bg -ibam -g hg38 -strand +’.
Assembly: hg38
Supplementary files format and content: BedGraph files are non-normalized coverage files.

molecule: genomic DNA

organism: Homo sapiens

source_name: Sm1 small airway epithelial cells

growth_protocol: De-identified primary human small airway epithelial cells (< 2 mm diameter) were obtained from the National Jewish Health Biobank from subjects with no history of deployment or chronic lung disease. Cells were first co-cultured with irradiated NIH/3T3 (ATCC) fibroblasts in F-medium containing 1 uM Y-27632 (APEX Bio) and then passaged onto tissue culture dishes double-coated with Type I bovine collagen solution (Advanced Biomatrix) and grown to confluence in BronchiaLife Epithelial Medium with the complete LifeFactors Supplement Kit (Lifeline Cell Technology).

extract_protocol:
Cells were washed twice with 1X PBS and collected by scraping or pelleting prior to counting. Approximately 50K cells were pelleted and processed in duplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 37 bp paired-end reads.

treatment_protocol: Afghan Desert Particulate Matter (APM) were obtained generously from Drs. Gregory Downey and Hong Wei Chu and exposed to cells by suspension in cell culture medium for 20 hours. Wood Smoke Particles (WSP) were generated as described [Ghio 2012] and generously gifted by Dr. Andrew Ghio at the Environmental Protection Agency Laboratory in North Carolina. Particles were dehydrated for transportation and resuspended in PBS. Particles were disaggregated by sonication and sterilized under UV light for 20 minutes prior to addition directly to cell culture media at a concentration of 1 mg/ml for all experiments.

tag: cell type

value: small airway epithelial cells


title: Sm3-APM1

source_name: Sm3 small airway epithelial cells


title: Sm1-APM2


title: Sm3-Ctrl1


title: Sm1-APM1


title: Sm2-APM2

source_name: Sm2 small airway epithelial cells


title: Sm2-WSP1


title: Sm3-APM2


title: Sm3-Ctrl2


title: Sm2-veh1


title: Sm2-APM1


title: 64294_4

status: Public on Mar 31 2022

city: London

first: Thu

middle: Hong

last: Le

address: Gower Street

country: United Kingdom

institute: UCL

library_source: transcriptomic

data_processing:
alignment reads to the reference to generate the BAM files, using STAR
sort the raw bam files and mark duplications using Picard
assemble the GTF reference file based on your BAM files using CUFFLINK and CUFFMERGE
estimate the gene counts and then calculate the RPKMs using featureCounts and DESeq2
normalize the RPKMs of each gene and detect the significant different expression genes [using DESeq2]
Genome_build: Rn6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Adipose cells

extract_protocol:
Adipose tissue was dissected, and then snap-frozen. RNA was extracted using Trizol
Library preps were created using Illumina kits and run on an Illumina HiSeq 2500 to obtain 75bp single-end reads for adipose tissue

value: adipose

tag: age

value: 17 weeks


title: 64304_1


title: 64297_6


title: 64305_5


title: 64299_4


title: Sm2-Ctrl2


title: 64299_3


title: 64297_3


title: 64297_5


title: 64267_3


title: 64293_3


title: 64295_4


title: 64251_3


title: Sm2-Ctrl1


title: 64257_4


title: 64244_4


title: 64305_6


title: 64246_4


title: 64247_3


title: 64246_5


title: 64231_4


title: 64238_3


title: 64230_5


title: 64235_5


title: 64238_4


title: 64248_3


title: 64231_3


title: 64262_4


title: 64185_4


title: 64227_3


title: 64199_4


title: 64199_5


title: 64186_4


title: 64194_3


title: 64213_4


title: 64230_4


title: 64205_3


title: 64197_3


title: 64177_4


title: 64183_3


title: 64249_4


title: 64235_3


title: 64170_4


title: 64170_3


title: 64171_3


title: 64167_3


title: 64168_4


title: 64166_4


title: 64226_4


title: 64164_3


title: 64162_3


title: 64154_4


title: 64160_2


title: 64159_4


title: 64159_3


title: 64162_4


title: 64148_4


title: 64149_3


title: 64148_3


title: 64142_4


title: 64134_5


title: 64119_3


title: 64119_4


title: 64134_6


title: 64113_3


title: 64116_4


title: 64131_4


title: 64113_4


title: 64112_3


title: 64111_3


title: 64110_3


title: 64109_4


title: 64105_4


title: 64106_5


title: 64106_3


title: 64105_3


title: 64104_3


title: 64146_4


title: 64114_5


title: 64043_3


title: 64060_3


title: 64027_3


title: 64064_4


title: 64016_6


title: 64057_4


title: 64045_3


title: 64024_3


title: 64057_3


title: 64024_4


title: 64027_4


title: 64034_3


title: 64009_3


title: 64038_4


title: 64039_3


title: 64023_4


title: 64016_4


title: 64070_4


title: 64045_4


title: 64003_3


title: 64000_4


title: 64011_3


title: 64003_5


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title: 64000_3


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title: 63991_3


title: 63997_3


title: 63984_4


title: 64038_3


title: 63959_4


title: 63974_4


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title: 63912_4


title: 63913_4


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title: 63016_4


title: 63014_4


title: 63008_4


title: 63032_4


title: 63032_3


title: 63032_5


title: 62996_4


title: 63000_4


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title: 63000_3


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title: 62978_6


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title: 62381_6


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title: 62044_5


title: 62315_4


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title: 62298_4


title: 62324_6


title: 62310_4


title: 61821_6


title: 61646_4


title: 61646_3


title: 61644_4


title: 61643_5


title: 61641_3


title: 61638_4


title: 61638_5


title: 61645_3


title: 61357_4


title: 62309_4


title: 61163_4


title: 61172_3


title: 61160_3


title: 61158_4


title: 61038_4


title: 60645_3


title: 61040_5


title: 60444_5


title: 60650_3


title: 60641_3


title: 60444_7


title: 60644_4


title: 60214_5


title: 60444_3


title: 59114_4


title: 59108_3


title: 61638_6


title: 60213_3


title: 60214_3


title: 59114_3


title: 58774_4


title: 58779_3


title: 61160_4


title: 58779_4


title: 58771_4


title: 58765_4


title: 58566_4


title: 58769_3


title: 58572_4


title: 61038_5


title: 58566_3


title: 58570_3


title: 58564_4


title: 58343_4


title: 58342_3


title: 58294_4


title: 58337_3


title: 58301_3


title: 58293_4


title: 58295_4


title: 59104_4


title: 58125_4


title: 58293_3


title: U2_organoid_scRNA-seq

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
cellranger 4.0.0 was used to demultiplex and map the raw sequencing data
The downstream analysis was performed using Seurat 3.2.1 on R 3.6.2
Genome_build: GRCh38-2020A (pre-built GRCh38 genome reference provided by 10X Genomics)
Supplementary_files_format_and_content: Normalized gene count for every gene and every cell (where raw counts were divided by total transcipts per cell and expressed as transcripts per 10000)

molecule: polyA RNA

source_name: human ureter-derived organoid

extract_protocol:
10x Chromium Next GEM Single Cell 3ʹ Kit v3.1
barcoded single cell RNA seq libraries were prepared for each sample and subjected to 150 base paired-end sequencing on Illumina NovaSeq. Each sample library was loaded on 4 lanes of flowcell generating 4 sets of fastq files

tag: Sex

value: M

tag: disease state

value: normal

value: human ureter-derived organoid


title: U2_visium

data_processing:
spaceranger 1.3.0 was used to create a GEM from fastq files provided by 10X
Downstream normalization of expression counts was done by Seurat (v4.0.3) in R (4.0.3)
Genome_build: GRCh38-2020A (pre-built GRCh38 genome reference provided by 10X Genomics)
Supplementary_files_format_and_content: Normalized gene count for every gene and every cell (normalized by a negative binomial regression model SCTransform)

source_name: human ureter

extract_protocol:
10X Chromium Spatial Gene Expression Slide & Reagent Kit, 16 rxns PN-1000186
10X Chromium Library Construction Kit, 16 rxns PN-1000190
A Visium Spatial Gene Expression library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The 16 bp Spatial Barcode and 12bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. I7 and i5 sample index sequences are incorporated. TruSeq Read 1 and TruSeq Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing.

value: human ureter


title: U2_thawed_scRNA-seq


title: U1_visium

value: F


title: 58301_4


title: Patient 15 CLL Alone

status: Public on Mar 22 2022

city: BRIGHTON

first: Chris

last: Pepper

address: Falmer

department: Brighton and Sussex Medical School

institute: University of Sussex

description: Processed data column name: TB222

data_processing:
Sequenced reads were trimmed for adaptor sequences and for quality (minimum 20) using trim-galore v0.6.5.
Trimmed reads were mapped separately to the mouse GRCm39 genome and the human GRCh38 genome using HISAT2 generating separate bam files
Human reads in each sample were identified by analysing the mouse and human bam files for each sample using the R package XenofilteR v1.6
Human reads in the XenofilteR output were quantified against human GRCh38 transcripts using kallisto quant
kallisto quantifications were converted to gene level by tximport, then normalised and analysed for differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file. Matrix table with raw gene counts for every gene and every sample, generated by tximport

source_name: CLL Cells

extract_protocol:
RNA was extracted using the RNeasy Micro Kit
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacturer’s instructions

tag: condition

value: CLL cells alone

tag: patient source


title: Patient 16 Co-culture

description: Processed data column name: TB225

value: CLL on CD40L Fibroblast Co-culture


title: Patient 17 Co-culture

description: Processed data column name: TB227


title: Patient 18 CLL Alone

description: Processed data column name: TB228


title: Patient 13 Co-culture

description: Processed data column name: TB215


title: Patient 18 Co-culture

description: Processed data column name: TB229


title: Patient 14 CLL Alone

description: Processed data column name: TB216


title: Patient 15 Co-culture

description: Processed data column name: TB223


title: Patient 14 Co-culture

description: Processed data column name: TB217


title: Patient 17 CLL Alone

description: Processed data column name: TB226


title: Patient 16 CLL Alone

description: Processed data column name: TB224


title: Patient 12 Co-culture

description: Processed data column name: TB213


title: Patient 12 CLL Alone

description: Processed data column name: TB212


title: Patient 11 Co-culture

description: Processed data column name: TB211


title: Patient 11 CLL Alone

description: Processed data column name: TB210


title: Patient 13 CLL Alone

description: Processed data column name: TB214


title: 58041_6


title: 58125_3


title: 58105_4


title: 58096_4


title: 57810_3


title: 57604_6


title: 58095_3


title: 57909_4


title: 57215_3


title: 57241_4


title: 57914_3


title: 58096_6


title: 58041_3


title: 57241_5


title: RNA-Seq Patient 9 Circ

description: Processed data column name: TB30

data_processing:
Sequenced reads were trimmed for adaptor sequences and for quality (minimum 20) using cutadapt
Trimmed reads were quantified against the human GRCh38 transcriptome using kallisto quant
kallisto quantifications were converted to gene level by tximport, then normalised and analysed for differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file. Matrix table of raw gene counts for every gene and every sample, generated by tximport.

value: Circulating CLL cells


title: RNA-Seq Patient 7 Circ

description: Processed data column name: TB66


title: RNA-Seq Patient 10 Circ

description: Processed data column name: TB9


title: RNA-Seq Patient 7 Mig

description: Processed data column name: TB67

value: Migrating CLL cells


title: RNA-Seq Patient 8 Circ

description: Processed data column name: TB40


title: RNA-Seq Patient 9 Mig

description: Processed data column name: TB32


title: RNA-Seq Patient 6 Mig

description: Processed data column name: TB63


title: RNA-Seq Patient 8 Mig

description: Processed data column name: TB41


title: RNA-Seq Patient 6 Circ

description: Processed data column name: TB62


title: RNA-Seq Patient 4 Circ

description: Processed data column name: TB52


title: RNA-Seq Patient 3 Mig

description: Processed data column name: TB51


title: RNA-Seq Patient 5 Circ

description: Processed data column name: TB54


title: RNA-Seq Patient 4 Mig

description: Processed data column name: TB53


title: RNA-Seq Patient 3 Circ

description: Processed data column name: TB50


title: RNA-Seq Patient 10 Mig

description: Processed data column name: TB10


title: miRNA-Seq Patient 7 Mig

description: Processed data column name: TB65

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt v2.1 with a command based on the kit manufacturers’ recommendations (cutadapt -m 15 -u 3 --max-n 0.9 -a AAAAAAAAAA)
miRNA counts were obtained  using MiRDeep2 and miRNAs obtained from miRBase v22.1
Raw count count data was processed and analysed for differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file. Matrix table with raw miRNA counts for every miRNA and every sample

extract_protocol:
RNA was extracted using the RNeasy Micro Kit
SMARTer smRNA-Seq Kit for Illumina


title: RNA-Seq Patient 2 Mig

description: Processed data column name: TB49


title: miRNA-Seq Patient 8 Mig

description: Processed data column name: TB67


title: miRNA-Seq Patient 8 Circ

description: Processed data column name: TB66


title: miRNA-Seq Patient 5 Circ

description: Processed data column name: TB54


title: RNA-Seq Patient 1 Mig

description: Processed data column name: TB47


title: miRNA-Seq Patient 6 Circ

description: Processed data column name: TB62


title: RNA-Seq Patient 1 Circ

description: Processed data column name: TB46


title: miRNA-Seq Patient 3 Circ

description: Processed data column name: TB50


title: miRNA-Seq Patient 4 Circ

description: Processed data column name: TB52


title: miRNA-Seq Patient 6 Mig

description: Processed data column name: TB63


title: miRNA-Seq Patient 2 Circ

description: Processed data column name: TB48


title: 95_S21_L003_R1_001

status: Public on Mar 06 2022

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. normals were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.

tag: ptid

tag: lesion

value: Control

tag: subtype


title: miRNA-Seq Patient 1 Circ

description: Processed data column name: TB46


title: 94_S20_L003_R1_001


title: miRNA-Seq Patient 4 Mig

description: Processed data column name: TB53


title: RNA-Seq Patient 2 Circ

description: Processed data column name: TB48


title: RNA-Seq Patient 5 Mig

description: Processed data column name: TB55


title: 93_S19_L003_R1_001


title: miRNA-Seq Patient 7 Circ

description: Processed data column name: TB64


title: miRNA-Seq Patient 1 Mig

description: Processed data column name: TB47


title: miRNA-Seq Patient 5 Mig

description: Processed data column name: TB55


title: miRNA-Seq Patient 3 Mig

description: Processed data column name: TB51


title: miRNA-SeqPatient 2 Mig

description: Processed data column name: TB49


title: 96_S22_L003_R1_001


title: 9_S9_L002_R1_001

value: LS

value: CIE


title: 90_S17_L003_R1_001


title: 91_S50_L007_R1_001


title: 92_S16_L002_R1_001


title: 89_S15_L002_R1_001


title: 88_S14_L002_R1_001


title: 87_S13_L002_R1_001


title: 64_S57_L008_R1_001


title: 7_S7_L001_R1_001

value: LI


title: 59_S54_L007_R1_001


title: 62_S56_L007_R1_001


title: 56_S51_L007_R1_001


title: 86_S12_L002_R1_001


title: 58_S53_L007_R1_001


title: 52_S47_L006_R1_001


title: 5_S5_L001_R1_001


title: 49_S44_L006_R1_001


title: 8_S8_L001_R1_001

value: EI


title: 47_S42_L006_R1_001


title: 57_S52_L007_R1_001


title: 48_S43_L006_R1_001


title: 41_S36_L005_R1_001


title: 53_S48_L006_R1_001

value: NS


title: 44_S39_L005_R1_001


title: 51_S46_L006_R1_001


title: 50_S45_L006_R1_001


title: 40_S35_L005_R1_001


title: 4_S4_L001_R1_001


title: 42_S37_L005_R1_001


title: 43_S38_L005_R1_001


title: 39_S34_L005_R1_001


title: 54_S49_L007_R1_001


title: 60_S55_L007_R1_001


title: 6_S6_L001_R1_001


title: 55_S50_L007_R1_001


title: 35_S30_L004_R1_001


title: 34_S29_L004_R1_001


title: 36_S31_L004_R1_001


title: 33_S28_L004_R1_001


title: 27_S23_L003_R1_001


title: 22_S22_L003_R1_001


title: 31_S49_L007_R1_001


title: 32_S27_L004_R1_001


title: 20_S20_L003_R1_001


title: 3_S3_L001_R1_001


title: 21_S21_L003_R1_001


title: 28_S24_L003_R1_001


title: 18_S18_L003_R1_001


title: 17_S17_L003_R1_001


title: 15_S15_L002_R1_001


title: 133_S23_L003_R1_001


title: 132_S40_L005_R1_001


title: 16_S16_L002_R1_001


title: 130_S38_L005_R1_001


title: 14_S14_L002_R1_001


title: 13_S13_L002_R1_001


title: 125_S55_L007_R1_001


title: 127_S37_L005_R1_001 2


title: 30_S26_L004_R1_001


title: 2_S2_L001_R1_001


title: 124_S47_L006_R1_001


title: 122_S54_L007_R1_001


title: 126_S48_L006_R1_001


title: 118_S43_L006_R1_001


title: 120_S35_L005_R1_001


title: 131_S39_L005_R1_001


title: 19_S19_L003_R1_001


title: 117_S53_L007_R1_001


title: 12_S12_L002_R1_001


title: 109_S32_L004_R1_001


title: 108_S31_L004_R1_001


title: 11_S11_L002_R1_001


title: 121_S18_L003_R1_001


title: 106_S29_L004_R1_001


title: 107_S30_L004_R1_001


title: 110_S51_L007_R1_001


title: 123_S36_L005_R1_001


title: 104_S27_L004_R1_001


title: 105_S28_L004_R1_001


title: 128_S44_L006_R1_001


title: 119_S46_L006_R1_001


title: 100_S25_L004_R1_001


title: 1_S1_L001_R1_001


title: 103_S26_L004_R1_001


title: 115_S34_L005_R1_001


title: 114_S45_L006_R1_001


title: PH-mut-25MNase Replicate2-

status: Public on Feb 12 2022

city: Srinagar

first: Ajazul

last: Wani

address: Hazratbal

country: India

institute: University of Kashmir

data_processing:
The sequenced paired-end reads obtained at each MNase concentration were mapped to dm3, Drosophila melanogaster genome using Bowtie aligner. Reads with no more than two mismatches, mapping uniquely were retained and having insert size between 50-500 bp were retained. Read frequencies were computed in 300 bp non- overlapping bins. For comparison read frequencies were normalized by their corresponding library size and represented as reads per million.
MACC scores were computed (as described in earlier (Mieczkowski et al., 2016). for 300 bp genomic bins by fitting the normalized read frequencies obtained at each MNase concentration with linear regression. MNase concentration was taken on log scale and bins devoid of any reads were excluded.
Supplementary_files_format_and_content: MACC
Supplementary_files_format_and_content: wig

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were procured from Expression Systems and were grown at 27oC in ESF921 media

extract_protocol: library preparation protocol described in Bowman et al. 60. Bowman, S. K. Simon, M. D. Deaton, A. M. Tolstorukov, M. Y. Borowsky, M. L. Kingston, R. E. Multiplexed illumina sequencing libraries from picogram quantities of DNA. BMC Genomics 14, 466 (2013)

treatment_protocol: Cells were grown for three days after induction with 0.5mM CuSO4 to induce the expression

tag: genotype/variation

value: S2 cells

tag: replicate


title: PH-mut-100MNase Replicate2-


title: 116_S42_L006_R1_001


title: PH-mut-6.25MNase Replicate2-


title: PH-mut-1.65MNase Replicate2-


title: PH-WT-400MNase Replicate2-


title: PH-WT-100MNase Replicate2-


title: S2-400MNase Replicate2-


title: S2-25 MNase Replicate2-


title: S2-100 Mnase Replicate2-


title: PH-WT-1.65MNase Replicate2-


title: S2-1.65 MNase Replicate2-


title: S2-6.25 MNase Replicate2-


title: PH-mut-400MNase Replicate2-


title: PH-mut-25MNase Replicate1-


title: PH-mut-400MNase Replicate1-


title: PH-mut-6.25MNase Replicate1-


title: PH-mut-100MNase Replicate1-


title: PH-mut-1.65MNase Replicate1-


title: PH-WT-400MNase Replicate1-


title: PH-WT-100MNase Replicate1-


title: PH-WT-6.25MNase Replicate2-


title: PH-WT-1.65MNase Replicate1-


title: PH-WT-25MNase Replicate1-


title: PH-WT-6.25MNase Replicate1-


title: S2-25 MNase Replicate1-


title: S2-6.25 MNase Replicate1-


title: S2-400MNase Replicate1-


title: S2-100 Mnase Replicate1-


title: PH-WT-25MNase Replicate2-


title: S2-1.65 MNase Replicate1-


title: 29_S25_L004_R1_001


title: iCLIP-seq of SP1, replicate A

status: Public on Jan 28 2022

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Extracted RNA was reverse transcribed using primer Rt13clip: /5Phos/NNTCCGNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNCGGANN, where N are random bases.
This sample was not analyzed in Song et al., Mol Cell (2022), PMID: 35914531.

data_processing:
Base calls were processed with bcl2fastq2 (Illumina) version 2.18.
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the actual read were initially trimmed to 45 nt from the 3'-end, and duplicates were discarded.
Reads were de-multiplexed (note that they are already de-multiplexed in this GEO record), and the random positions, barcode, and 3'-bases matching Illumina adaptors were removed.
Reads shorter than 25 nt were filtered out and remaining reads trimmed to 35 nt. These steps were carried out using Trimmomatic (Bolger et al., 2014). Surviving reads were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using tophat (Trapnell et al., 2009) with default settings. To prevent false assignments of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis.
Sites of crosslink-induced mutation sites (CIMS) and crosslink-induced truncation sites (CITS) were derived using the CLIP Tool Kit (Shah A. et al., Bioinformatics 2017). Peaks from CITS and CIMS analyses were thresholded at a p-value (or FDR for CIMS) of 10e-10 and concatenated into one BED file.
Genome_build: hg19
Supplementary_files_format_and_content: Concatenated CIMS and CITS derived with  CLIP Tool Kit, in BED format.
Supplementary_files_format_and_content: bigWig file; crosslinks were approximated as being position 1 of the read, binned to 50 nt, and normalized to counts per million.

source_name: Human embryonic kidney cells

extract_protocol:
Cells were crosslinked (0.4 J/cm2) at 254 nm with a Stratalinker 1800 prior to immunoprecipitation.  Lysates generated from the crosslinked cells were treated with Turbo DNAse (Ambion) and diluted RNAse I (Ambion) for 5 minutes at 37°C to digest the genomic DNA and trim the RNA to short fragments of an optimal size range. RNA-protein complexes were immunoprecipitated using 100 μL of protein A/G Dynabeads (Life Technologies) and 5-10 μg of indicated antibodies. Following stringent high salt washes, the immunoprecipitated RNA was 3´ end dephosphorylated and a pre-adenylated adaptor was ligated at the 3´ end as described for a previously described enhanced CLIP ligation method (Van Nostrand et al., Nat. Methods 2016) for adaptor ligation. After additional washes, the immunoprecipitated RNA was 5´ end-labeled with radioactive 32P isotopes using T4 polynucleotide kinase (New England Biolabs). The immunoprecipitated complexes were separated with SDS-PAGE and transferred to a nitrocellulose membrane (Protran). For the input sample, the membrane was cut to match the size of the immunoprecipitated material. RNA was recovered by digesting proteins using proteinase K (Thermo Fisher).
RNA was reverse transcribed into cDNA using reverse transcription primers that include barcode sequences to enable multiplexing,  a unique molecular identifier, and a BamHI restriction site. The cDNA was size selected (low: 70 to 85 nt, middle: 85 to 110 nt, and high: 110 to 180 nt), circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR amplified using AccuPrime SuperMix I (Thermo Fisher). The final PCR libraries were purified on PCR purification columns (QIAGEN).  Eluted DNA was mixed at a ratio of 1:5:5 from the low, middle, and high fractions and submitted for sequencing.

treatment_protocol: Crosslinking (0.4 J/cm2) was done at 254 nm with a Stratalinker 1800.

tag: cell line

tag: growth protocol

value: Human embryonic kidney cells (HEK293) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin, and maintained at 37°C with 5% CO2.

tag: genotype

value: wild-type cells

tag: antibody

value: Sp1 monoclonal antibody (SANTA CRUZ  Biotechnology)


title: iCLIP-seq of SP1, replicate B

description:
Extracted RNA was reverse transcribed using primer Rt9clip: /5Phos/NNGCCANNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC. Reads start with 5'-NNNTGGCNN, where N are random bases.
This sample was not analyzed in Song et al., Mol Cell (2022), PMID: 35914531.


title: Sample 4-R: Pit_Pedia_HM1_fragm_snRNA

status: Public on Jan 10 2022

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
sn-RNAseq data were processed using the Cell Ranger pipeline v5.0.0 with the --include-introns option.
Samples were aligned to the CellRanger GRCh38 reference transcriptome, introns included.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count matrices in Hierarchical Data Format HDF5 for cell barcodes

source_name: Pituitary gland

growth_protocol: Frozen post-mortem human pituitaries were obtained from the National Institutes of Health (NIH) NeuroBioBank, and kept at -80C until processing.

extract_protocol:
Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X PBS/0.04% BSA for snRNAseq (10X Genomics).
snRNAseq were performed as described (10x Genomics, Pleasanton, CA; (24)), following the Chromium Next GEM Single Cell 3’ Reagents Kits V3.1 User Guidelines. Nuclei were filtered and counted on a Countess instrument. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell Chip kit G PN-2000177) was loaded to target a minimum of 1,000 nuclei final. Reverse-transcription was performed in the emulsion and cDNA was amplified before library construction following the Chromium protocols v2 or v3. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex kit PN-220103). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.

treatment_protocol: Frozen post-mortem pituitaries were broken into small pieces in a frozen mortar on dry-ice, and one piece was thawed on ice and prepared for nuclei extraction based on a modified protocol from (Mathys, Davila-Velderrain et al. 2019).  The remainder of one pituitary was pulverized.  Part of the powder was collected to be also processed following the same protocol. The remaining powder and pituitary fragments were stored back at -80C.

tag: pmi

tag: source tissue type

value: frozen post-mortem pituitary

tag: gender

value: Male

tag: ethnicity

value: White


title: Sample 1P-R: Pit_Pedia_HF1P_pulver_snRNA

tag: age

value: Female

value: Black or African American


title: Sample 5-R: Pit_Adult_HM2_fragm_snRNA


title: Sample 1-R: Pit_Pedia_HF1_fragm_snRNA


title: Sample 6-R: Pit_Aged_HM3_fragm_snRNA


title: Sample 3-R: Pit_Aged_HF3_fragm_snRNA


title: Sample 2-R: Pit_Adult_HF2_fragm_snRNA


title: Sample 3-A: Pit_Aged_HF3_fragm_snATAC

data_processing:
Single Nuclei ATAC-seq data of frozen post-mortem human pituitary samples were processed using Cell Ranger-ATAC pipeline version 1.2.0.
Samples were aligned to the CellRanger-ATAC GRCh38 reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak accessibility count matrices for cell barcodes in Hierarchical Data Format HDF5.
Supplementary_files_format_and_content: Metadata files that include per barcode QC, ATAC signal and cell calling metrics in comma-separated values (CSV) format.
Supplementary_files_format_and_content: BED-like tabular files listing all unique fragments captured by the assay in tab-separated values (TSV) format.

extract_protocol:
Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei dilution buffer for snATACseq (10X Genomics).
snATACseq was performed as described (10x Genomics, Pleasanton, CA), following the Chromium Next GEM Single Cell ATAC Reagent Kits V1.1 User Guide. Nuclei were counted on a Cellometer instrument, and the final concentration was used to calculate the volume of nuclei stock to use. Transposition was performed in 10 microliter at 37C for 60min. Then the Chromium Chip H (PN-2000180) was loaded to target 1,000-10,000 nuclei. Barcoding was performed in the emulsion for 12 cycles following the Chromium protocol. Each library was tagged with a different index for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262). Quality control and quantification of the libraries were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.


title: Sample 1P-A: Pit_Pedia_HF1P_pulver_snATAC


title: Sample 4-A: Pit_Pedia_HM1_fragm_snATAC


title: Sample 1-A: Pit_Pedia_HF1_fragm_snATAC


title: Sample 5-A: Pit_Adult_HM2_fragm_snATAC


title: Sample 2-A: Pit_Adult_HF2_fragm_snATAC


title: Sample 6-A: Pit_Aged_HM3_fragm_snATAC


title: Sample 1P-M: Pit_Pedia_HF1P_pulver_snMultiome

data_processing:
Library strategy: snATAC+RNA-Seq
Single nuclei Multiome (ATAC + Gene Expression) data were processed using the Cell Ranger ARC pipeline version 1.0.0.
Indices from two GEM wells were pooled together and processed as a single sample.
Samples were aligned to the CellRanger-ARC GRCh38 reference transcriptome.  Intron-aligned reads were included in the gene expression counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrices for cell barcodes in Hierarchical Data Format HDF5.  File includes both Gene Expression UMI counts and ATAC peak fragment counts.
Supplementary_files_format_and_content: BED-like tabular file listing all unique fragments captured by the ATAC assay in tab-separated values (TSV) format.

molecule: other

growth_protocol: The frozen post-mortem human pituitary used for multiome was obtained from the National Institutes of Health (NIH) NeuroBioBank, and kept at -80C until processing.

extract_protocol:
Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei buffer for sn multiome (10X Genomics).
sn Multiome was performed as described (10x Genomics, Pleasanton, CA; (24)), following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guidelines. Nuclei were filtered and counted on a Countess instrument. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit J  PN-200264) was loaded to target 10,000 nuclei final. After transposition, linear amplification was performed in the emulsion and cDNA was amplified before the RNA and ATAC library constructions were performed following the Chromium multiome protocol. The library was tagged with an index for multiplexing (Chromium i7 Sample Index Plate N Set A for ATAC PN-3000427; Chromium i7 Sample Dual Index Plate TT Set A for ATAC PN-3000431). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.

treatment_protocol: The frozen post-mortem pituitary was pulverized in a frozen mortar on dry-ice and part of the obtained powder was thawed on ice and prepared for nuclei extraction based on a modified protocol from (Mathys, Davila-Velderrain et al. 2019). The remainder of the pituitary was stored back at -80C.


title: ENZ_8

status: Public on Nov 07 2021

first: Dana

last: Pe'er

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions withre enzalutamide (ENZ) exposure

data_processing:
SEQC alignment
EmptyDrops for empty droplet detection
DoubletDetection for doublet detection
sctransform for normalization
scanpy for downstream analysis
Genome_build: mm38
Supplementary_files_format_and_content: counts matrices (.csv)
Supplementary_files_format_and_content: adata objects (.h5ad)
Supplementary_files_format_and_content: obs cell annotations (.csv)

organism: Mus musculus

source_name: Prostate organoid cell line

growth_protocol: Organoids were cultured under standard conditions (Karthaus et al 2014. Cell).

extract_protocol:
For single-cell analysis, organoids were isolated from basement membrane extract and digested to single-cell suspension by incubating with TRYPLE (Life technologies) supplemented with Y-27632 (10 μM) for 10 min at 37 °C with shaking, followed by a 2-min incubation with EDTA (1 mM), Y-27632 (10 μM) in PBS0 and a second digestion with TRYPLE (Life technologies) supplemented with Y-27632 for 5 min at 37 °C with shaking. Cells were filtered and resuspended in PBS0, Y-27632 (10 μM) and BSA (0.04%) before processing further for single-cell sequencing. Cells were checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II) and all sequencing experiments were performed on samples with a minimum of 80% viable cells.
Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2). Each sample loaded onto the cartridge contained approximately 5,000 cells at a final dilution of ~500 cells/µl. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina HiSeq (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads/cell).

treatment_protocol: Organoids were transduced using cre expressing lentivirus followed by culturing under standard conditions

tag: tissue

value: Prostate organoid cell line

tag: treatment


title: DHT_8

description: Prostate organoid at 8 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: ENZ_4

description: Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions withre enzalutamide (ENZ) exposure


title: DHT_2

description: Prostate organoid at 2 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: 10_S10_L002_R1_001


title: DHT_4

description: Prostate organoid at 4 weeks following cre mediated RB1 and TP53 deletion and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: DHT_0

description: Wild-type prostate organoid isolated from TP53 loxP/loxP and RB1 loxP/loxP mice and cultured under standard organoid conditions with dihydrotestosterone (DHT) exposure


title: 89R

status: Public on Oct 07 2021

city: Freising

first: Frank

last: Johannes

state: Bavaria

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

country: Germany

institute: Technical University of Munich

data_processing:
WGBS data was analyzed using the Methylstar pipeline (Shahryary et al.2020).
WGBS reads were aligned to the A. thaliana TAIR10 reference genome (Berardini et al., 2015)
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed file (*.tsv) are tab-separated text file in allc format. "allc" stands for all cytosine (C). Each row in an allc file corresponds to one cytosine in the genome. An allc file contain 7 column. 1:chromosome; 2:position; 3:strand; 4:sequence context; 5:count of methylated reads; 6:reads coverage; 7:indicator of significant methylation (0 or 1)

organism: Arabidopsis thaliana

growth_protocol: The 169 epiRILs were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark )conditions.

extract_protocol:
Genomic DNA was extracted from each sample using the DNAeasy plant mini kit from Qiagen
At least 1 μg of DNA were submitted to the Beijing Genome Institute where they were prepared for WGBS libraries.
WGBS library

treatment_protocol: Aerial rosette tissue 27 days after sowing (DAS) was harvested.

value: Aerial rosette

value: Harvested at 27 days after sowing (DAS)

tag: line

value: ddm1-derived epiRIL


title: 81R


title: 97R


title: 93R


title: 80R


title: 79R


title: 96R


title: 9R


title: 568R


title: 59R


title: 579R


title: 578R


title: 56R


title: 54R


title: sample 15, healthy control 15

status: Public on Dec 14 2021

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Gene expression data for a healthy individual

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: healthy control

tag: therapy

tag: Sex

value: male

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: sample 13, healthy control 13


title: 573R


title: 99R


title: 574R


title: 63R


title: sample 14, healthy control 14

value: female


title: 52R


title: 62R


title: 538R


title: 518R


title: 531R


title: 539R


title: 519R


title: 497R


title: 503R


title: 504R


title: 48R


title: 479R


title: 50R


title: 4R


title: 467R


title: 494R


title: 466R


title: 469R


title: 513R


title: 461R


title: 462R


title: 457R


title: 455R


title: 44R


title: 447R


title: 432R


title: 424R


title: 430R


title: 423R


title: 442R


title: 419R


title: 410R


title: 391R


title: 463R


title: 426R


title: 40R


title: 393R


title: 383R


title: 388R


title: 401R


title: 402R


title: 384R


title: 389R


title: 113_S41_L006_R1_001

tag: ptid

tag: lesion

value: Control

tag: subtype


title: 413R


title: 394R


title: 380R


title: 37R


title: 382R


title: 41R


title: 454R


title: 379R


title: 373R


title: 412R


title: 362R


title: 350R


title: 368R


title: 344R


title: 390R


title: 367R


title: 348R


title: 337R


title: 353R


title: 339R


title: 328R


title: 354R


title: 35R


title: 334R


title: 319R


title: 352R


title: 330R


title: 327R


title: 318R


title: 313R


title: 310R


title: 30R


title: 340R


title: 300R


title: 309R


title: 302R


title: 329R


title: 31R


title: 305R


title: 28R


title: 2R


title: 275R


title: 286R


title: 295R


title: 273R


title: 262R


title: 266R


title: 26R


title: 250R


title: 245R


title: 239R


title: 24R


title: 241R


title: 229R


title: 231R


title: 223R


title: 219R


title: 220R


title: 21R


title: 216R


title: 234R


title: 225R


title: 211R


title: 214R


title: 215R


title: 18R


title: 210R


title: 19R


title: 204R


title: 213R


title: 208R


title: 207R


title: 184R


title: 189R


title: 17R


title: 200R


title: 185R


title: 203R


title: 188R


title: 176R


title: 171R


title: 158R


title: 152R


title: 168R


title: 157R


title: 153R


title: 161R


title: 150R


title: 160R


title: 13R


title: 12R


title: 136R


title: 146R


title: 16R


title: 118R


title: 128R


title: 139R


title: 120R


title: 106R


title: 141R


title: 102R


title: 126R


title: 125R


title: 131R


title: 10R


title: 103R


title: Emb.07-viscera-1

status: Public on Sep 01 2021

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

country: China

institute: Tongji University

data_processing:
Raw reads were demultiplexed, filtered and mapped to the human reference genome (GRCh38) using Cell Ranger 3.0.2 with default settings. The filtered feature-barcode matrices generated by Cell Ranger were used for further analysis.
To exclude low-quality cells and doublets, cells with fewer than 1000 genes or over 60000 UMIs were discarded. The expression matrix was normalized into UMIs per 10000 by size factors.
Iterative clustering was performed to identify cell types. First, we partitioned cells into main clusters with Seurat (r=0.5, PCs=20) using only transcription factors in highly variable genes (HVGs). Second, for each main cluster, we performed one or two rounds of clustering with HVGs of the particular cluster.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix table with raw gene counts; csv files with gene and cell annotations.

growth_protocol: Aborted embryos from donations were washed with PBS, transferred into cold Hibernate-E medium (Gibco) and immediately transported to the laboratory. Embryos with good quality were staged based on anatomical characters.

extract_protocol:
Samples were incubated at 37°C for 10 minutes and were pipetted up and down thoroughly and gently every 3 minutes. To quench the dissociation, we added 300μl FBS into each tube and centrifuge cells at 300xg for 5 min at 4°C. Cells were then resuspended in 500μl cold PBS, filtered through a 35μm strainer. Single cells were subsequently washed twice with cold PBS, centrifuged at 300xg for 5 min at 4°C and resuspended in cold PBS.
To generate sequencing libraries, a suspension of 10,000 single cells per sample was processed following the 10x Genomics protocol using Single Cell 3’ Reagent Kits v2 (10x Genomics).

treatment_protocol: We dissected each embryo on ice into four main sections, i.e., head, trunk, viscera and limb. After the dissection, each sample was placed into separate tubes, washed twice with cold PBS, cut into pieces and suspended in 300μl Hibernate-E medium with 0.05mg/ml Liberase TM (Roche).

value: embryo viscera

tag: gender

tag: Stage

value: Carnegie Stages 15-16


title: Emb.07-viscera-3


title: 107R

tag: age


title: Emb.07-viscera-2

tag: tissue


title: Emb.07-limb viscera-4

source_name: Emb.07-limb and viscera

value: embryo limb and viscera


title: Emb.07-limb viscera-3


title: 104R


title: Emb.07-limb viscera-2


title: Emb.07-limb viscera-1


title: Emb.06-limb-12

value: embryo limb


title: Emb.06-limb-6


title: Emb.07-viscera-4


title: Emb.06-limb-8


title: Emb.06-limb-5


title: Emb.06-limb-4


title: Emb.06-limb-10


title: Emb.06-limb-11


title: Emb.06-limb-2


title: Emb.06-trunk-11

value: embryo trunk


title: Emb.06-trunk-10

value: Male


title: Emb.06-limb-3


title: Emb.06-limb-1


title: Emb.06-trunk-8


title: Emb.06-trunk-9


title: Emb.06-limb-9


title: Emb.06-head b-11

value: embryo head


title: Emb.06-trunk-6


title: Emb.06-trunk-1


title: Emb.06-trunk-2


title: Emb.06-head b-10


title: Emb.06-limb-7


title: Emb.06-trunk-3


title: Emb.06-trunk-5


title: Emb.06-trunk-4


title: Emb.06-head b-12


title: Emb.06-head b-7


title: Emb.06-head b-9


title: Emb.06-head b-8


title: Emb.06-trunk-12


title: Emb.06-head b-4


title: Emb.06-head b-5


title: Emb.06-head b-6


title: Emb.06-trunk-7


title: Emb.06-head b-2


title: Emb.06-head b-1


title: Emb.06-head b-3


title: Emb.06-head a-5


title: Emb.06-head a-6


title: Emb.06-head a-7


title: Emb.06-head a-4


title: Emb.06-head a-2


title: Emb.05-viscera limb-4

source_name: Emb.05-limb and viscera

value: Female


title: Emb.05-limb viscera-4


title: Emb.05-limb viscera-2


title: Emb.05-viscera limb-1


title: Emb.05-viscera limb-2


title: Emb.05-trunk-4


title: Emb.05-limb viscera-1


title: Emb.05-trunk-3


title: Emb.05-limb viscera-3


title: Emb.05-trunk-2


title: Emb.06-head a-3


title: Emb.05-head-2


title: Emb.05-head-1


title: Emb.06-head a-8


title: Emb.05-viscera limb-3


title: Adult_eWAT_SVF

status: Public on Aug 23 2021

city: Durham

first: Rana

middle: K

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

description: SVF from 5-weeks old eWAT

data_processing:
Data was analyzed using Cell Ranger (v3.1.0) to perform demultiplexing, aligning reads,
Cells with less than 200 genes and genes expressed less than 3 cells were removed; cells with mitochondria proportion greater than 25% were removed; cells with ribosome proportion less than 5% were removed; cells with abnormally high counts were removed.
Cells from different developmental stages were integrated and normalized using SCTransform from Seurat (v4.0.3)
Cell clusters were identified with the resolution of 1 using Seurat (v4.0.3) and were annotated with cell-specific marker genes
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files contain the filtered barcodes, matrix, and genes.

source_name: epidydimal white adipose tissue

extract_protocol:
Both SVF and mesothelial cells were isolated from gonadal WAT as previously described (Hepler et al. Elife 2017).  The library was generated according to manufacturer's instructions (10X Genomics).
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i7=8cycles

tag: strain

value: 5-weeks old


title: P3_eWAT_SVF

description: SVF from Postnatal day 3 eWAT

value: Postnatal day 3


title: HY_P0

status: Public on Aug 05 2021

city: Beijing

first: yuhong

address: No.1 West Beichen Road

department: Institute of Genetics and Developmental Biology (IGDB)

institute: Chinese Academy of Sciences (CAS)

data_processing:
Sequencing was performed on an Illumina NovaSeq6000 platform
We used 10x genomics cellranger count pipeline 3.0.2 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were integrated together by Seurat pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts matrix file with gene and barcode annotations

source_name: Hypothalamus

extract_protocol:
Hypothalamus was derived from Rax-CreERT2::Ai14 mice induced at E9.5, microdissected at both embryonic and postnatal days (E11.5, E14.5, P0 and P7) and dissociated into single-cell suspension. Live tdTomato+ cells were purified by fluorescent-activated cell sorting for single-cell transcriptomic sequencing(10x Genomics).
Single-cell RNA-seq libraries were constructed  according to the manufacturer’s protocol accompanying single cell 3 'Library and Gel Bead Kit V3 (10xGenomics, 1000075). Cell suspensions (300-600 living cells per microliter determined by Count Star) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in the emulsion. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Using a S1000TM Touch Thermal Cycler (Bio Rad) to reverse transcribe, the GEMs were programed at 53°C for 45 min, followed 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and the quality was assessed using the Agilent 4200 (performed by CapitalBio, Beijing). Finally sequencing was performed on the Illumina Novaseq6000 sequencer following the manufacturer's introduction.
scRNA-Seq

tag: genotype

tag: stain


title: HY_E14


title: HY_E11


title: HY_P7


title: Emb.06-head a-1


title: Emb.05-trunk-1


title: Patient 8

status: Public on Jul 21 2021

first: Daniel

middle: Bernard

last: Zamler

state: TX

department: Genomic Medicine

institute: M.D. Anderson Cancer Center

description:
Term Source REF: EFO
Term Accession Number: UO_0000036
Human_Aggregate_features.tsv.gz

data_processing:
FastQ preparation: mkfastq (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation: count (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Aggregation of samples: aggr (cellranger): https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/aggregate
Visualization and comparisons: Adapted Seurat Pipeline (Zamler): Aggregate All.R
Data Normalization: scTransform (Satija): https://satijalab.org/seurat/v3.1/sctransform_vignette.html
genome build: mm10-3.0.0 (mouse): GRCh38-3.0.0 (human)
Supplementary_files_format_and_content: Zipped Matrices - Single Cell Gene Counts

source_name: Mixed Immune Cells

extract_protocol:
Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9N sucrose solution to remove myelin. Cell pellets were then frozen. Upon bringing samples back up CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

tag: developmental stage

value: adult

value: brain

tag: individual

value: Patient 8

tag: cell type

value: leukocyte

tag: disease state

value: glioblastoma multiforme

tag: sampling site

value: left parietal lobe

tag: tumor grading

value: IDHmut, Negative for MGMT promoter methylation, positive for IDH1 R132H and p53 and negative for ATRX (loss of nuclear staining). MIB-1 (Ki67) immunostaining reveals a low proliferation index peaking at 4.2%

tag: cell line

tag: age in years


title: Patient 9

tag: Sex

value: male

value: Patient 9

value: diffuse astrocytoma

value: left parieto-occipital lobe

value: IDH1 protein status (IHC):NEGATIVE for IDH1 p.R132H expression ATRX protein status (IHC):Retained nuclear expression MGMT status (methylation specific PCR):Negative for promoter methylation


title: Emb.05-head-4

value: Carnegie Stages 15-16


title: Patient 3

value: Patient 3

value: right temporal lobe

value: BRAFv600e negative, P53 focally positive, ATRX +


title: Patient 5

value: Patient 5

value: right basal ganglia

value: MGMT methylation negative, Mutation of :TP53, TERT, MBM4, KRAS


title: Patient 4

value: adult

value: brain

value: Patient 4

value: right frontal lobe


title: Emb.05-head-3

value: embryo head

value: Female


title: Patient 6

value: female

value: Patient 6

value: leukocyte

value: glioblastoma multiforme

value: right temporo-occipital lobe

value: BRAF negative, P53 5% positive, ATRX retained


title: Patient 2

value: male

value: Patient 2

value: right temporal lobe

value: P53 negative, ATRX retained


title: MTD_control1, H3K9m-me3

status: Public on Jul 01 2021

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

description: control

data_processing:
QC control: FASTQC report with basic sequencing quality statistics
mapping reads:Bowtie
Peak Calling: MACS2/HOMER
Genome_build: Drosophila release  6
Supplementary_files_format_and_content: bgiwig

source_name: 16hr embryos

growth_protocol: flies were grown on standard bottle food supplemented with yeast paste

extract_protocol:
H3K9me3 antibody (Abcam, ab8898)
DNA was isolated from 400 16hr embryos and subjected to H3K27-me3 immunoprecipatation
Ttakara hruPLEX® DNA-Seq Kit

tag: antibody

value: H3Kk9-me3 ChIP sample


title: MTD_control2, H3K9m-me3

description: control


title: Mouse - Implanted 2

description:
Term Source REF: EFO
Term Accession Number: UO_0000036
Mouse_Implanted_Aggregate_features.tsv.gz

value: adult

value: Mouse 5

value: Tumor Containing Hemisphere

value: Wild Type


title: Mouse - Implanted 1

value: brain

value: Mouse 4


title: Mouse - Spontaneous 2

description:
Term Source REF: EFO
Term Accession Number: UO_0000036
Mouse_Spontaneous_Aggregate_features.tsv.gz

value: not determined

value: Mouse 2

value: Nestin-CreERT2; Quaking L/L, tp53 L/L, Pten L/L

value: Mixed Background


title: Mouse - Implanted 3

value: female

value: Mouse 6

value: leukocyte

value: glioblastoma multiforme


title: MTD_IR_DN2, H3K9m-me3

description: InR-DN progeny


title: MTD_IR_DN1, H3K9m-me3

description: InR-DN progeny


title: Patient 7

value: male

value: Patient 7

value: diffuse astrocytoma

value: left temporal lobe

value: No loss ATRX (IHC), TERT 124 promotor mutation, EGFRvIII, +MGMT, MIB=70%


title: scRNA-seq Inner POD14 [18092510]

status: Public on Jun 24 2021

city: Stanford

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Inner POD14

data_processing:
Fastq files were aligned to the mm10 mouse genome using STAR v2.5.3a.
Counts were extracted from individual bam files using the featureCounts function from the Rsubread library in R.
mRNA counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
genome build: mm10 v3.0.0
processed data files format and content: Counts matrix

source_name: Dorsal wound

extract_protocol:
Single cell RNAseq was performed via the method described by Picelli et al (42). Lysis buffer plates were thawed on ice, then heated at 72 oC/3 min in a Biorad C1000 Touch thermal cycler to denature RNA.
scRNA-seq: First strand cDNA synthesis was performed in a 10 ul reaction with 100 Units of Clontech’s Smartscribe reverse transcriptase (Cat. No. 639538), 10 Units RRI, 1X First Strand Buffer (Clontech), 5 mM DTT, 1M Betaine (Sigma B0300-5VL), 6mM MgCl2, 1 M Template Switch Oligo (TSO, (5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′, Exiqon) at 42oC/90 min, 70oC/5 min. PCR pre-amplification was performed in a 25 ul reaction with 1X Kapa HiFi HotStart, 0.1 uM ISPCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′, IDT) at 98oC/3 min, then 25 cycles of 98oC/20 sec, 67 oC/15 sec, 72 oC/6 min, then 72 oC/5 min. Amplified cDNAs were purified by SPRI beads using a Biomek FX automated platform and eluted in 25 ul water, and 2 ul aliquots were run on an Fragment Analyzer High Sensitivity NGS 1-6000 kit for quantitation. Barcoded sequencing libraries were made using the miniaturized Nextera XT protocol of Mora-Castilla et al(43) in a total volume of 4 ul. Pooled libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a NextSeq 500 Illumina platform aiming for 50,000 reads per cell.
scRNA-seq: cDNA libraries were sequenced on a NextSeq 500 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Skin tissue from mouse specimens was minced on ice and digested in DMEM-F12 (GIBCO®) with 0.5mg/ml LiberaseTM (Roche) for 30 minutes at 37º in an orbital shaker. The digests were quenched with quench media (DMEM-F12 with 10% Fetal Bovie Serum (FBS, Sigma)), centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, filtered through 100, 70, and 40um cell strainers (Falcon cell strainer, ThermoFisher), centrifuged once more, and resuspended in FACS buffer.

value: Rainbow

value: Dorsal wound

value: Splinted excisional wound healing

value: Fibroblasts


title: scRNA-seq Inner POD2 [18101622]

description: Inner POD2


title: scRNA-seq Inner POD14 [18092509]

description: Inner POD14


title: scRNA-seq Inner POD2 [18101621]

description: Inner POD2


title: scRNA-seq Inner POD7 [18101613]

description: Inner POD7


title: Mouse - Spontaneous 3

value: adult

value: not determined

value: brain

value: Mouse 3

value: Tumor Containing Hemisphere


title: scRNA-seq Outer POD2 [18101615]

description: Outer POD2


title: scRNA-seq Outer POD2 [19031328]

description: Outer POD2


title: Patient 1

value: Patient 1

value: oligodendroglioma

value: right frontal lobe

value: IDHmut, 1p19q deletion, 1 and 19 monosomy


title: Patient 10

value: female

value: Patient 10

value: leukocyte

value: glioblastoma multiforme

value: left frontal lobe

value: IDHmut, Positive for MGMT promoter methylation, IDH1 protein status (IHC):POSITIVE for mutant IDH1 p.R132H, 1p/19q status (FISH):NEGATIVE for codeletion (isolated 1p deletion; 19q intact) ATRX protein status (IHC):LOSS of expression in tumor cell population p53 protein status (IHC):POSITIVE for nuclear expression (strong, diffuse)


title: Mouse - Spontaneous 1

value: Mouse 1

value: Nestin-CreERT2; Quaking L/L, tp53 L/L, Pten L/L

value: Mixed Background


title: scRNA-seq Outer POD7 [18101612]

description: Outer POD7

value: Rainbow

value: Dorsal wound

value: Splinted excisional wound healing

value: Fibroblasts


title: scRNA-seq Outer POD14 [19031326]

description: Outer POD14


title: scRNA-seq Outer POD7 [18101611]

description: Outer POD7


title: scRNA-seq Outer POD2 [18101614]

description: Outer POD2


title: PAO1161 EV_3 RNA-seq

status: Public on Jun 17 2021

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description: gene expression data from empty vector control

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Genome_build: CP032126
Supplementary_files_format_and_content: Raw counts of sequencing (FeatureCounts output summarized for all samples).
Supplementary_files_format_and_content: A table with DE data for all genes and normalized abundance measurements (EdgeR output).

organism: Pseudomonas aeruginosa

source_name: empty vector control (EV), biological rep3

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pMEB63 carrying lacIQ-tacp-bsrA and empty vector pAMB9.37 (lacIQ-tacp) to obtain PAO1161/pMEB63 (lacIQ-tacp-bsrA) and PAO1161/pAMB9.37 (lacIQ-tacp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml-1 chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 mg/ml-1 chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 mg/ml-1) and IPTG (0.05 mM) and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
Ribosomal RNA was depleted using RiboZero Bacteria kit (Illumina). Obtained mRNA was used for cDNA library construction using KAPA Stranded RNASeq kit. Library was further quality checked on 1% agarose gel and concentration was measured using qPCR KAPA Library Quantification Kit.

treatment_protocol: All cultures were incubated at 37°C in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.05 mM IPTG with shaking until reaching exponential phase of growth (OD600= 0.5).

value: PAO1161/pAMB9.37 (lacIQ-tacp)

value: empty vector control (EV)

value: logarithmic phase of liquid culture


title: PAO1161 EV_2 RNA-seq

source_name: empty vector control (EV), biological rep2


title: PAO1161 EV_1 RNA-seq

source_name: empty vector control (EV), biological rep1


title: CD34 HiChIP

status: Public on May 19 2021

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Library strategy: HiChIP
HiChIP data were processed and analyzed using MAPS41 v1.9 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig coverage tracks

source_name: cord blood CD34

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine. CD34+ cells were isolated by positive selection from human umbicilal cord blood and expanded for 3 days in StemSpan SFEM II (StemCell Technologies 09655) supplemented with the following cytokines each at 100 ng/mL: IL6 (Peprotech 200-06), thrombopoietin (Peprotech 300-18), SCF (300-07), and FLT3-ligand (Peprotech 300-19), and 1 uM StemRegenin 1 (Cayman Chemical 10625).

extract_protocol:
for cell lines and CD34+ cells, freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 10 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then crosslinked in a volume of 5 mL PBS with 2% formaldehyde for 10 minutes at room temperature, followed by quenching with Stop Solution 1 according to the Arima protocol. For cryopreserved patient samples, one vial of cells was thawed in a 37°C water bath and the entire contents of the vial were immediately transferred to 5 mL PBS where cells were counted before proceeding with crosslinking as above. The total number of cells used per patient sample ranged from 1.6 million to 8 million cells.
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ Document numbers A160168 v00 (HiChIP) and A160169 v00 (library preparation)),

treatment_protocol: no treatment

value: primary sample (CD34+ progeintors isolated from human umbilical cord blood)

tag: chip antibody

value: H3K27ac (Active Motif am91193 lot#22420004)

tag: treatment

value: untreated


title: SJALL068279_D1 HiChIP

source_name: primary sample

value: primary sample (leukemia)


title: SJAUL068292_D1 HiChIP


title: SJMPAL011911_D1 HiChIP


title: DND41_rep1 HiChIP

value: cell line

value: T-ALL cell line DND41


title: SJTALL005006_D2 HiChIP


title: Macrophages derived from M-MDSC from non-small lung cancer patient p6 [derivedMF.MDSC.3]

status: Public on Dec 14 2020

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: Macrophages

extract_protocol:
Cell pellets containing 500,000 - 1 million cells were lysed in 300 ul of Tri- Reagent (Sigma, St. Louis, MO) and RNA was extracted using the Direct-Zol RNA Mini-Prep Kit (Zymo Research, Irvine, CA), including an on-column DNAseI treatment.
3’ mRNA-seq libraries were generated from DNAseI treated total RNA using the QuantSeq FWD Library Preparation kit (Lexogen, Vienna, Austria), according to manufacturer’s directions.

value: Macrophages derived from M-MDSC

tag: patientid

tag: disease

value: non-small lung cancer


title: Macrophages derived from Monocytes from non-small lung cancer patient p6 [derivedMF.Mono.3]

value: Macrophages derived from Monocytes


title: RNA-seq siEGFP rep 2

status: Public on Jan 03 2021

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
total RNA
batch 2

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
TT-seq/RNA-seq: the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
TT-seq/RNA-seq: the BAM files were filtered to contain only uniquely mapped reads with Samtools
TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
TT-seq/RNA-seq: TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
3'-seq: reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
3'-seq: the data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
3'-seq: 5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig; normalized and bias corrected coverage generated with…

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
TT-seq/RNA-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA. 4sU-labeled RNA was first biotinylated with EZ-Link HPDP-Biotin (Pierce) and isolated with µMACS Streptavidin Kit (Miltenyi). 4sU-labeld RNA was eluted by cleaving off the biotin with DTT. Both total RNA and 4sU-labeled RNA purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNse I treatment to remove genomic DNA.
3'-seq:
TT-seq/RNA-seq RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).
3'-seq libraries were generated with standard and modified Lexogen 3'-seq protocols. The modified preapration included 3'end polydenylation in vitro using E.coli poly(A) polymerase ('xPAP') preceeding the NGS library preparation with the QuantSeq REV kit according to manufacturer's protocol (Lexogen).
RNA-Seq, paired-end; RNA 3'end seq, single-end

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labelled for 5 min or 10 min for TT-seq or 3'-seq, respectively, with 500 µM 4-thiouridine minutes and harvested.

value: HeLa Kyoto

tag: tissue

value: cervix

value: epithelial

tag: sirna

value: EGFP


title: RNA-seq siCPSF3 rep 1

description:
total RNA
batch 1


title: RNA-seq siINTS11 rep 2

description:
total RNA
batch 2


title: Macrophages derived from Monocytes from non-small lung cancer patient p5 [derivedMF.Mono.2]


title: Macrophages derived from Monocytes from non-small lung cancer patient p7 [derivedMF.Mono.4]


title: RNA-seq siINTS11 rep 1

description:
total RNA
batch 1


title: Macrophages derived from M-MDSC from non-small lung cancer patient p4 [derivedMF.MDSC.1]


title: DND41_rep2 HiChIP


title: RNA-seq siEGFP rep 1

description:
total RNA
batch 1


title: Macrophages derived from Monocytes from non-small lung cancer patient p4 [derivedMF.Mono.1]


title: Monocytes from non-small lung cancer patient p2 [source.Mono.2]

source_name: Monocytes

value: Monocytes


title: Macrophages derived from M-MDSC from non-small lung cancer patient p5 [derivedMF.MDSC.2]


title: RNA-seq siCPSF3 rep 2

description:
total RNA
batch 2


title: M-MDSC from non-small lung cancer patient p2 [source.MDSC.2]

source_name: M-MDSC

value: M-MDSC


title: Monocytes from non-small lung cancer patient p3 [source.Mono.3]


title: M-MDSC from non-small lung cancer patient p1 [source.MDSC.1]


title: M-MDSC from non-small lung cancer patient p3 [source.MDSC.3]


title: Monocytes from non-small lung cancer patient p1 [source.Mono.1]


title: SJMPAL011914_D1 HiChIP


title: Macrophages derived from M-MDSC from non-small lung cancer patient p7 [derivedMF.MDSC.4]


title: Single cell RNA-seq

status: Public on Oct 22 2020

city: Chengdu

first: Guanghui

last: Zhu

state: Sichuan

address: 8 Linyin Street

institute: Sichuan University

description:
Collected from patients who had undergone radical prostatectomy at Shanghai Changhai Hospital.
The number following the barcode (the name of each column) reflects the patient number. The relation between this number and patient ID is as follows: 1->patient ID 59, 2->patient ID 62, 3->patient ID 74, 4->patient ID 72, 5->patient ID 73, 6->patient ID 71, 7->patient ID 75, 8->patient ID 77, 9->patient ID 76, 10->patient ID 54, 11->patient ID 55, 12->patient ID 56, 13->patient ID 53.

data_processing:
We applied fastp(Chen et al., 2018) with default parameter filtering the adaptor sequence and removed the low-quality reads to acquire the clean data.   Umi-tools (v1.0.0) was applied to identify the cell barcode whitelist. Raw data was mapped using STAR (v2.5.2b) with default parameters from UMI-tools standard pipeline to obtain the UMI counts of each sample.
For each cell, we calculated three quality measures: percent of mitochondrion genes, number of total genes and housekeeping genes expressed(Tirosh et al., 2016). We remove cells that have higher than 20% expression on mitochondrion genes, lower than 200 or higher than 5218 total genes expressed, or lower than 56 housekeeping genes expressed (Tirosh et al., 2016).
The resultant gene expression matrix was imported into R (v3.5.1) statistical environment for further analysis. Data normalization and annotation was performed using R package scran (v1.10.2) (Lun et al., 2016). To calculate pool-based normalization factor, cells for each sample were first splited into sensible clusters using quickCluster function (max.size = 3000).
Genome_build: ensemble hg38, v91
Supplementary_files_format_and_content: plain text files for raw count and normalized count (log scale)

source_name: Single-cell transcriptional profiles of 13 prostate tumors

extract_protocol:
Using a S1000TM Touch Thermal Cycler (Bio Rad) to reverse transcribe, the GEMs were programed at 53°C for 45 min, followed 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and the quality was assessed using the Agilent 4200 (performed by CapitalBio, Beijing).
According to the manufacture’s protocol, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library Gel Bead Kit V2. Sequencing was performed on the Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell and 150 bp (PE150) paired end reads (performed by CapitalBio, Beijing).

treatment_protocol: Fresh tissue samples were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small, ~1mm cubic pieces on ice and enzymatically digested with protocol as following: DNase I (Worthington)(30U/ml), collagenase IV (Worthington) (195U/ml), collagenase I (Worthington) (10U/ml) and 30% FBS for 1 hour at 37°C, with agitation to achieve single cell.   After digestion, samples were sieved through a 70µm cell strainer (Corning), and centrifuged at 300~500g for 8 mins. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer and incubated for 2 min to lyse red blood cells. After washing with RPMI-1640 medium, the cell pellets were re-suspended in RPMI-1640 medium and re-filtered through a 35μm cell strainer (Corning).   Cell capture and cDNA synthesis: Using single cell 3 'Library and Gel Bead Kit V2 (10xGenomics, 120237) and Chromium Single Cell A Chip Kit (10xGenomics, 120236), the cell suspension (300-600 living cells per microliter, determined by Count Star) was loaded onto the Chromium single cell controller (10xGenomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 7000 cells were added to each channel, and the target cell recovery rate was estimated to be 3000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017).

value: 12 primary prostate tumors and one lymphatic metastasis of prostate tumor

tag: patient diagnosis

value: prostate cancer


title: PCa2

status: Public on Oct 20 2020

city: Shenzhen

first: Xiaoshi

last: Ma

address: No.1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic.
Alignment,reads  counts were analysed by the cellranger  (3.1.0) pipeline from 10X (https://www.10xgenomics.com/).
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Matrix table with  gene counts for every gene and every cell in every sample

source_name: Cancerous prostate tissue

extract_protocol:
Cancerous prostate tissues were cut into small pieces and digested in a lyase cocktail for the isolation of single cells. Cells were combined with barcoded Gel Beads, cells enzyme and partitioning oil to generate GEMs. After GEMs generation, copartitioned cells were lysed and the polyA mRNA were released and incubated with a Master Mix containing reverse transcription reagents to synthesize the full-lengh cDNA.
Libraries were prepared according to Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (PN-1000121). Briefly, silane magnetic beads were used to purify the first-strand cDNA from the  post GEM-RT reaction mixture.The full-length cDNA were amplifed via PCR to generate sufficient mass for library construction. After end repair, A-tailing,  adaptor ligation and PCR amplification, the  final libraries were ready for sequencing.

value: Cells isolated from cancerous prostate

value: Cancerous prostate tissue

tag: tumor stage

value: Prostate cancer with a Gleason score of 7 (3 + 4)


title: PCa1

value: Prostate cancer with a Gleason score of 6 (3 + 3)


title: P09: Primary tumor 09 (10x 3' v2)

status: Public on Oct 01 2020

city: Allen

first: Wei

last: Lin

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

data_processing:
Cell Ranger
Genome_build: hg19
Supplementary_files_format_and_content: csv format that contains the umi count for each gene in each barcodes (cells)

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Tumor dissociated using a dissociation kit from Miltenyi Biotec
10x Genomics Chromium v2

tag: tissue type

value: Primary

tag: age

tag: gender

value: M

value: Pancreatic ductal adenocarcinoma


title: P07: Primary tumor 07 (10x 3' v2)

value: F

tag: disease state


title: P08: Primary tumor 08 (10x 3' v2)


title: P05: Primary tumor 05 (10x 3' v2)


title: P06: Primary tumor 06 (10x 3' v2)


title: P10: Primary tumor 10 (10x 3' v2)


title: P04: Primary tumor 04 (10x 3' v2)


title: P03: Primary tumor 03 (10x 3' v2)


title: P01: Primary tumor 01 (10x 3' v1)


title: P02: Primary tumor 02 (10x 3' v2)


title: MOB [Nanopore]

status: Public on Aug 26 2020

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Visium Spatial Transcriptomics of mouse hippocampus of adult mouse.
spot barcode in the bam files is the SAM tag BC, and the UMI is SAM tag U8

data_processing:
The Space Ranger pre-release was used to perform Visium Spatial Transcriptomics Illumina profiling.
Processing of Nanopore reads for scNaUMI-seq is describe at https://github.com/ucagenomix/Sicelore
Genome_build: mm10
Supplementary_files_format_and_content: Space Ranger filtered gene barcodes matrices. SiT gene/isoform/junction/editing matrices.
Supplementary_files_format_and_content: The rds files refer to the final statistical analysis of the 3 samples, consisting of an analysis using Illumina and Nanopore sequencing.

source_name: Mouse olfactory bulb

extract_protocol:
The Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics, Pleasanton, CA, USA) was used to optimize permeabilization conditions for mouse brain tissue. Spatially barcoded full-length cDNA was generated using Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) following the manufacturer’s protocol. Tissue permeabilization was performed for 6 and 9 min (CBS1, CBS2) and 12 min (MOB). cDNA amplification was conducted with 12 (CBS) and 17 (MOB) cycles.
10µl of cDNA library followed 10x Genomics Visium library preparation protocol of fragmentation, adapter ligation, and indexing. The libraries were sequenced on a NextSeq500 (Illumina), with 28 bases from read 1 and 91 from read 2.
Nanopore sequencing libraries were prepared with the LSK-109 kit from Oxford Nanopore (1 µg cDNA) following the instructions from the manufacturer. PromethION flowcells were loaded with 200 ng library each. PCR amplifications for Nanopore library preparations were made with Kapa Hifi Hotstart polymerase (Roche Sequencing Solutions): initial denaturation, 3 min at 95°C; cycles: 98°C for 30 sec, 64°C for 30 sec, 72°C for 5 min; final elongation: 72°C for 10 min, primer concentration was 1 µM.

value: olfactory bulb

tag: strain

tag: developmental stage

value: 2 months old


title: CBS1 [Nanopore]

source_name: Mouse hippocampus

value: hippocampus


title: MOB [Illumina]

description:
Visium Spatial Transcriptomics of mouse hippocampus of adult mouse.
spot barcode in the bam files is the SAM tag CB, and the UMI is SAM tag UB (standard tags of Space Ranger)


title: CBS2 [Nanopore]


title: ICC_24_Tumor1: CCC24T

status: Public on Jun 06 2020

first: Min

state: Beijing

address: No. 8 East Road, Fengtai District

department: The Fifth Medical Center of Chinese PLA General Hospital

institute: Academy of Military Medical Sciences

data_processing:
Illumina CASAVA version 1.8 used for basecalling.
Sequencing data from 10x was aligned and quantified using the CellRanger version 2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

source_name: tumor

extract_protocol:
Single-cell suspensions were stained for 7AAD (Invitrogen) per the manufacturer’s recommendations, washed with cold PBS, and re-suspended for flow cytometric analyses.
Fluorescence-activated cell sorting (FACS) -sorted viable cells (7-AAD-negative) were loaded into a well of a microfluidic chip to generate a cDNA library using a commercial 10x Genomics platform. Single-cell transcriptomic amplification and library preparation was performed using single-cell 3′ v2 chemistry (10X Genomics) according to manufacturer’s instructions.
The libraries were then pooled and sequenced across six lanes on an Illumina Xten or NovaSeq 6000 system.

treatment_protocol: All the freshly resected surgical specimens were immediately washed with phosphate-buffered saline (PBS) and divided into two equal parts. One part was processed to generate single-cell suspensions, while the second part was used for other experiments, including pathology examination.Tissue digestion was performed in a 15 ml centrifuge tube containing 10 ml pre-warmed RPMI 1640 (ThermoFisher Scientific), 2 mg/ml dispase (Roche), 1 mg/ml type IV collagenase (Sigma) and 10 U/µl DNase I (Roche) for 60 minutes at 37°C. The reaction was deactivated by 10% FBS. Cell suspensions were filtered using a 70 μm filter and then centrifuged at 500 rpm for 6 min at 4°C to pellet dead cells and red blood cells. The cells were washed twice and suspended in PBS with 0.5% bovine serum albumin (BSA, Sigma).

value: human intrahepatic cholangiocarcinoma


title: ICC_24_Tumor2: FACS24T


title: ICC_23_Adjacent: 171239E-ccc23N

source_name: adjacent

value: human intrahepatic cholangiocarcinoma adjacent


title: ICC_23_Tumor: 171239E-ccc23T


title: CBS2 [Illumina]


title: CBS1 [Illumina]


title: ICC_20_Tumor: 171239A-ccc20T


title: ICC_18_Adjacent: BAJD-20180619-12-171239-18N


title: LUNG_T34

status: Public on Mar 27 2020

city: Seoul

first: Hae-Ock

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

country: South Korea

institute: College of Medicine, The Catholic University of Korea

description:
Single-cell RNA-seq
Lung_Cancer_raw_UMI_matrix.txt
Lung_Cancer_normalized_log2TPM_matrix.txt

data_processing:
Fastq files were quantified to unique molecular identifiers (UMI) count values with Cell Ranger toolkit (version 2.1.0) with default parameters.
For each cell, we applied the three quality measures of mitochondrial genes (≤20%), and UMI and gene count (range from 100 to 150,000 and range from 200 to 10,000, respectively), which was applied to the raw gene-cell-barcode matrix.
UMI count for a gene in each cell was log-normalized to TPM-like values and then finally used in the scale of log2 (TPM+1), as previously described.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: UMI counts (Lung_Cancer_raw_UMI_matrix.txt); normalized data as described above (Lung_Cancer_normalized_log2TPM_matrix.txt)

source_name: Tumour lung

growth_protocol: Single-cell suspensions of the collected tissues were prepared by mechanical dissociation and enzymatic digestion within 16 hours after the surgery without any in vitro culture.

extract_protocol:
Single cell isolation was differently performed following each sample conditions. (1) Tumour and distant normal lung tissue dissociation was performed using tumor dissociation kit (Miltenyi Biotech, Germany) following the manufacturer’s instruction. Briefly, tissue was cut into 2-4 mm pieces and transferred to C tube containing the enzyme mix (Enzyme H, R, and A in RPMI1640 media). GentleMACS programs; h_tumor_01, 02, and 02 were run with two 30 min incubation in the MACSmix tube rotator at 37 oC. (2) Normal lymph node tissue and biopsy samples of metastatic lymph node and lung tumour tissue were dissociated using Collagenase/Hyaluronidase and DNase I. The tissue was chopped into 2-4 mm pieces with a sterile scissor in a 35 mm dish and incubated in an enzyme solution (Collagenase/Hyaluronidase (STEMCELL Technologies, Vancouver, Canada) and DNase I (QIAGEN, Hilden, Germany) in RPMI1640 media) at 37 oC for 1 hour. Tissue pieces are re-mixed by gentle pipetting at an interval of 20 min during incubation. (3) Metastatic brain tissue was chopped into 2-4 mm pieces with a sterile scissor in a 100 mm dish and incubated in an enzyme solution (Collagenase (Gibco, Waltham, MA, USA), DNase1 (Roche,  Basel, Switzerland), and Dispase1 (Gibco, Waltham, MA, USA) in DMEM media) at 37 oC within 1 hour. Tissue pieces are re-mixed by gentle pipetting at an interval of 15 min during incubation. (4) Pleural fluids were transferred to a 50 ml tube and spun down at 300g.  The cell suspension was transferred into a new 50 ml (or 15 ml; for biopsy samples) tube through 70um strainer. The volume in the tube was readjusted to 50 ml (or 15ml) with RPMI1640 media and spun down to remove enzymes. The supernatant was aspirated out and the cell pellet was resuspended in 4 ml of RPMI1640 media and dead cells were removed by Ficoll-Paque PLUS (GE Healthcare, Chicago, IL, USA) separation.
Each cell suspension was subjected to 3’ single-cell RNA sequencing using the GemCode system (10x genomics, Pleasanton, CA, USA) with cell recovery target at 5000, following the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq2500.

tag: patient id

value: I

tag: tissue origin abbrevation

value: tLung

tag: lung cancer subtype

value: lung adenocarcinoma


title: LUNG_T25


title: LUNG_T28

value: III