title: RNA GAS strain 854 [WT_B]

city: Boston

first: Michael

last: Wessels

address: 330 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

data_processing:
Sequencing reads from each pooled sample were demulitplexed based on their associated barcod sequence using custom scripts; allowing up to 1 mismatch in the barcode, provided this did not make assignemtn of the read to a different barcode possible. Barcode sequencese were subsequently trimmed from the first read as were terminal G's from the second read that may have been added by SMARTScirbe during template switching.
Reads were aligned to the S. pyogenes MGAS5005 genome (NCBI RefSeq NC_007297) using bowtie2 version 2.3.1
Read counts were assigned to annotated genes using HTSeq version 0.10.0
Differential expression analysis was conducted with DESeq2 version 1.20.0
Genome_build: NC_007297
Supplementary_files_format_and_content: tab-delimited text file includes read counts assigned to each feature for each sample

organism: Streptococcus pyogenes

source_name: RNA GAS strain 854

growth_protocol: Cultures were grown to mid-log-phase (OD600 of ~0.4)

extract_protocol:
Cell pellets were mechanically disrupted by bead beating in Trizol reagent. Chloroform was added and RNA was extracted from the aqueous phase via Direct-Zol RNA Miniprep Kit (Zymo Research)
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol. 500 ng - 1 µg total RNA was fragmented, depleted of genomic DNA, dephosphorylated and ligated to DNA adapters carrying 5'-AN8-3' barcodes of known sequence with a 5' phosphate and a 3' blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (EpiCentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcode adaptor with addition of an adapter to the 3' end of the cDNA by template switching using SMARTScribe (Clonetech); (ii) PCR amplification using primers whose 5' ends target the constant region of the 3' or 5' adaptors and whose 3' ends contain the full Illumina P5 or P7 sequences.

tag: genotype

value: wild-type

tag: growth phase

value: mid-log-phase (OD600 of ~0.4)

tag: molecule subtype

value: rRNA-depleted RNA


title: RNA GAS strain 854∆hsdM [DhsdM_C]

status: Public on Apr 14 2021

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: RNA GAS strain 854∆hsdM

tag: strain

value: {delta}hsdM


title: CAI-4 NA 3

city: Canterbury

first: Campbell

last: Gourlay

state: Kent

address: School of Biosciences, University of Kent

department: School of Biosciences

country: United Kingdom

institute: University of Kent

data_processing:
Illumina NextSeq 500 Real-Time Analysis software v2.4.11 used for basecalling.
Low quality ends (Phred score < 20) and any adaptor sequences were trimmed using TrimGalore! v0.4.3. Reads which became shorter than 40bp after trimming were removed from further analysis.
Processed reads were aligned with the reference C. albicans genome SC5314 version A21-s02-m09-r10 using HISAT2 v2.1.0 with single-end reads and reverse strand settings.
Number of mapped reads which overlapped CDS features in the genome (using the C. albicans_SC5314_version_A21-s02-m09-r10_features.gtf annotation file from Candida Genome Database) were determined using htseq-count v0.9.1 with default settings.
Differential gene expression analysis between conditions (0.03% and 5% CO2) was performed using DESeq2 v1.18.1 with default settings.
Genome_build: C. albicans genome SC5314 version A21-s02-m09-r10
Supplementary_files_format_and_content: tab-delimited text files include CDS feature counts for each sample.
Supplementary_files_format_and_content: xslx file with mean normalised counts and differentially expressed genes across all samples.

organism: Candida albicans

source_name: C. albicans biofilm_atmospheric CO2

growth_protocol: CAI-4 cells were seeded onto a silicone surface and grown as a biofilm for 48hr in either 0.03% or 5% CO2 at 37oC in RPMI-1640 media.

extract_protocol:
Biofilms were washed twice with ice-cold PBS, RNA was extracted using the E.Z.N.A Yeast RNA Kit (Omega Bio-Tek, R6870-01).
mRNA-Seq libraries were prepared from 500ng total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina).

tag: environment

value: Atmospheric CO2

tag: mode of growth

value: Biofilm on silicone surface at 37oC

tag: biofilm stage

value: Mature (48hr growth)


title: RNA GAS strain 854∆hsdM [DhsdM_B]


title: RNA GAS strain 854 [WT_A]


title: LA-NPC_NR18

type: RNA

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-sen University Cancer Center

description: Gene expression data from LA-NPC with no-response to induction chemotherapy

hyb_protocol: Total RNA was hybridized to Affymetrix Human Transcriptome Arrays 2.0 GeneChips (Affymetrix, Santa Clara, CA, USA) using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: All arrays were scanned with Affymetrix GeneChip® Scanner 3000 (Affymetrix). Raw data was obtained using Command Console Software 4.0 (Affymetrix) with default settings.

data_processing: Raw data were normalized using Transcriptome Analysis Console (version 4.0.1). We used empirical Bayes statistics implemented in eBayes in the 'limma package' to determine significant differentially expressed probes between response and no-response groups. Due to RNA from FFPE samples are highly and randomly fragmented, we used Fisher's exact test to confirm whether a transcript is indeed significant differentially expressed. Differential expressed transcripts were characterized according to the criterion of empirical Fold change ≥ 1.5, empirical Bayes test P-value <0.05, and Fisher p-value <0·05.

label: biotin

organism: Homo sapiens

source_name: LA-NPC_89-Stable Disease

label_protocol: Total RNA was amplified, fragmentated, labeled with Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA) and Encore Biotin Module (NuGEN) according to the manufacturer’s instructions.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Germany).

tag: tissue

value: Nasopharyngeal carcinoma

tag: response

value: stable disease


title: RNA GAS strain 854∆hsdM [DhsdM_A]


title: LA-NPC_NR20

source_name: LA-NPC_91-Stable Disease


title: LA-NPC_NR16

source_name: LA-NPC_87-Stable Disease


title: LA-NPC_NR17

source_name: LA-NPC_88-Stable Disease


title: LA-NPC_NR15

source_name: LA-NPC_86-Stable Disease


title: CAI-4 NA 2


title: LA-NPC_NR14

source_name: LA-NPC_85-Stable Disease


title: LA-NPC_NR13

source_name: LA-NPC_84-Stable Disease


title: LA-NPC_NR11

source_name: LA-NPC_82-Stable Disease


title: LA-NPC_NR12

source_name: LA-NPC_83-Stable Disease


title: RNA GAS strain 854 [WT_C]


title: L4: PAH-PASMCs

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

data_processing:
Adapters were removed by the sequencing provider. The raw fastq files were examined for sequencing quality and adapter contamination using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), after which alignment to the human transcriptome was performed using STAR (17)
After read alignment, quantification of the reads at the transcript level were performed using RSEM (18), and gene level quantification was obtained by the summarizeToGene function in the tximport R package
Genome_build: hg38
Supplementary_files_format_and_content: bam files with alignments, counts files from RSEM quantification

growth_protocol: PAH-PASMCs (n=11 cell lines) were isolated from small PAs (<1000mm diameter) from PAH patients. Controls PASMCs (n=10 cells lines) were either purchased from Cell Application (San Diego, CA) or isolated from non-PAH patients (Table 2). PASMCs were grown in high-glucose DMEM supplemented with 10% Fetal Bovine Serum (FBS) and containing 1% Penicillin/Streptomycin. The purity of the PASMCs in the primary cultures was confirmed by staining for alpha smooth muscle actin (aSMA) using immunofluorescence technique. Only cells between passages 3 to 9 were used for experiments

extract_protocol:
Total RNA was isolated from human PASMCs using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. The quality and concentration of total RNA were then determined with a spectrophotometer (NanoDrop 2000, Thermo Scientific, USA). RNA integrity was confirmed by electrophoresis on a denaturing agarose gel.
RNA sequencing analysis was carried out on total RNA extracted from PAH-PASMCs with or without siRNA-mediated silencing of EZH2. Qualitative and quantitative analysis of RNA was performed using NanoDrop2000 spectrophotometer (Thermo Scientific, USA). Library preparation and paired end RNAseq were performed by Cofactor genomics (St. Louis, MO) using Illumina HiSeq, on the PASMC samples at a read length of 150 bp and an average read depth of 50 million read pairs.
Total RNAseq (150 bp paired end, 50million clusters)

treatment_protocol: PAH-PASMCs were transfected with silencer RNA targeting EZH2 mRNA (Cat#S102665166, Qiagen, final concentration of 10nM) using Lipofectamine RNAiMAX reagent (Life Technologies) according to the manufacturer’s protocol. siRNA with scramble sequence (siSCRM) was used as negative control siRNA. Cells were cultured for 48h before collecting material for transcriptomic, proteomic and immunofluorescence analysis.

tag: cell line

tag: cell type

value: pulmonary artery smooth muscle cells

tag: treatment


title: LA-NPC_NR10

source_name: LA-NPC_81-Stable Disease


title: LA-NPC_NR21

source_name: LA-NPC_92-Stable Disease


title: L3: PAH-PASMCs


title: CAI-4 CO2 2

source_name: C. albicans biofilm_5% CO2


title: CAI-4 NA 1


title: LA-NPC_NR7

source_name: LA-NPC_78-Stable Disease


title: LA-NPC_NR3

source_name: LA-NPC_74-Stable Disease


title: L2: PAH-PASMCs


title: K3: PAH-PASMCs

value: siSCRM


title: K1: PAH-PASMCs


title: LA-NPC_NR1

source_name: LA-NPC_72-Stable Disease


title: LA-NPC_R71

description: Gene expression data from LA-NPC with response to induction chemotherapy

source_name: LA-NPC_71-Partial Response

value: partial response


title: L1: PAH-PASMCs


title: LA-NPC_NR5

source_name: LA-NPC_76-Stable Disease


title: HCT116-uS10-KI (RPS20-KI)-8hpi-VACV-WR-replicate 1 [RPS20_KI_8hpi_1]

city: san diego

first: Elayanambi

last: Sundaramoorthy

state: California

address: 9500, GILMAN DRIVE, la jolla

department: Section of cell and developmental biology

institute: University of California San Diego

description:
F1_RPS20_VaccV_8h_1_S16
cells lacking ZNF598 ubiquitylation substrate uS10 sites

data_processing:
Illumina Casava1.7 software used for basecalling.
The demultiplexed and de-indexed Fastq files were processed using galaxy platform @usegalaxy.org
Fastq files were aligned to the Human genome using HISAT2 ()
BAM files from HISAT2 were used to count  gene features using Featurecounts
Output from Featurecounts were used as input for DeSEQ2 to identify differentially expressed gene
Genome_build: Hg38
Supplementary_files_format_and_content: Tab delimited text file shows output from Featurecounts
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HCT116-uS10-KI (RPS20-KI)-8hpi-VACV-WR

growth_protocol: Cells were grown in DMEM ((high glucose, pyruvate and L-Glutamine) media supplemented with 10% FBS and maintained in humidified incubator supplied with  5% CO2 atmosphere

extract_protocol:
Cells were harvested by trypsinization and total RNA was extracted using TriZol reagent
Total RNA depleted of Ribosomal RNA using Ribozero was converted to cDNA and single read 75 bp library was sequenced on Illumina Hi-Seq instrument (IGM core UCSD)
RNA-Seq depleted of rRNA using ribozero kit

treatment_protocol: vaccinia virus was added at an MOI=5 and incubated for the indicated time before cells were harvested

value: Colon cancer cells

value: uS10-KI (RPS20-KI)

value: Vaccinia WR 8 hrs post infection


title: K4: PAH-PASMCs


title: LA-NPC_NR4

source_name: LA-NPC_75-Stable Disease


title: LA-NPC_NR6

source_name: LA-NPC_77-Stable Disease


title: LA-NPC_R70

source_name: LA-NPC_70-Partial Response


title: LA-NPC_NR2

source_name: LA-NPC_73-Stable Disease


title: K2: PAH-PASMCs


title: HCT116-uS10-KI (RPS20-KI)-8hpi-VACV-WR-replicate 3 [RPS20_KI_8hpi_3]

description:
F3_RPS20_VaccV_8h_3_S18
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: HCT116-uS10-KI (RPS20-KI)-8hpi-VACV-WR-replicate 2 [RPS20_KI_8hpi_2]

description:
F2_RPS20_VaccV_8h_2_S17
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: LA-NPC_NR9

source_name: LA-NPC_80-Stable Disease


title: LA-NPC_R69

source_name: LA-NPC_69-Partial Response


title: HCT-116- 8hpi-VACV-WR -replicate 3 [PAR_BC_8hpi_3]

source_name: HCT-116- 8hpi-VACV-WR

value: wild type


title: HCT-116- 8hpi-VACV-WR -replicate 2 [PAR_BC_8hpi_2]


title: HCT-116- 8hpi-VACV-WR -replicate 1 [PAR_BC_8hpi_1]


title: LA-NPC_R68

source_name: LA-NPC_68-Partial Response


title: LA-NPC_R67

source_name: LA-NPC_67-Partial Response


title: LA-NPC_NR8

source_name: LA-NPC_79-Stable Disease


title: HCT116-uS10-KI (RPS20-KI)-4hpi-VACV-WR-replicate 3 [RPS20_KI_4hpi_3]

description:
D3_RPS20_VaccV_4h_3_S12
cells lacking ZNF598 ubiquitylation substrate uS10 sites

source_name: HCT116-uS10-KI (RPS20-KI)-4hpi-VACV-WR

value: Vaccinia WR 4 hrs post infection


title: LA-NPC_R66

source_name: LA-NPC_66-Partial Response


title: HCT116-uS10-KI (RPS20-KI)-4hpi-VACV-WR-replicate 2 [RPS20_KI_4hpi_2]

description:
D2_RPS20_VaccV_4h_2_S11
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: HCT116-uS10-KI (RPS20-KI)-4hpi-VACV-WR-replicate 1 [RPS20_KI_4hpi_1]

description:
D1_RPS20_VaccV_4h_1_S10
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: LA-NPC_R65

source_name: LA-NPC_65-Partial Response


title: HCT-116- 4hpi-VACV-WR -replicate 3 [PAR_BC_4hpi_3]

source_name: HCT-116- 4hpi-VACV-WR


title: LA-NPC_R64

source_name: LA-NPC_64-Partial Response


title: HCT116-uS10-KI (RPS20-KI)-mock-replicate 3 [RPS20_KI_3]

description:
B3_RPS20_VaccV_mock_3_S6
cells lacking ZNF598 ubiquitylation substrate uS10 sites

source_name: HCT116-uS10-KI (RPS20-KI)-mock


title: HCT-116- 4hpi-VACV-WR -replicate 1 [PAR_BC_4hpi_1]


title: HCT116-uS10-KI (RPS20-KI)-mock-replicate 2 [RPS20_KI_2]

description:
B2_RPS20_VaccV_mock_2_S5
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: LA-NPC_R58

source_name: LA-NPC_58-Partial Response


title: LA-NPC_R57

source_name: LA-NPC_57-Partial Response


title: HCT-116- 4hpi-VACV-WR -replicate 2 [PAR_BC_4hpi_2]


title: LA-NPC_R60

source_name: LA-NPC_60-Partial Response


title: LA-NPC_R62

source_name: LA-NPC_62-Partial Response


title: LA-NPC_R55

source_name: LA-NPC_55-Partial Response


title: LA-NPC_R59

source_name: LA-NPC_59-Partial Response


title: LA-NPC_R63

source_name: LA-NPC_63-Partial Response


title: LA-NPC_R61

source_name: LA-NPC_61-Partial Response


title: HCT-116- mock -replicate 2 [PAR_2_BC]

source_name: HCT-116- mock


title: HCT-116- mock -replicate 3 [PAR_3_BC]


title: HCT-116- mock -replicate 1 [PAR_1_BC]


title: LA-NPC_R54

source_name: LA-NPC_54-Partial Response


title: HCT116-uS10-KI (RPS20-KI)-mock-replicate 1 [RPS20_KI_1]

description:
B1_RPS20_VaccV_mock_1_S4
cells lacking ZNF598 ubiquitylation substrate uS10 sites


title: microRNASeq-shBCDIN3D-RapPlus-Rep2

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

description: 10 nM Rapamycin-24h-treated shBCDIN3D MDA-MB-231 cells biological replicate #2

data_processing:
For all datasets: sequence quality was verified by FastQC, adapters were trimmed using cutadapt, and reads were filtered to require a trimmed length of 15bp or greater.
For Ribo-seq and RNA-seq: reads with remaining sequence greater than 16 bp were aligned against the hg38 build of the human reference genome using Tophat v2.0.8 with the “--b2-sensitive” set of options and the Genode v21 set of transcriptome annotations. All BAM files were filtered to require unique alignment wuth mapQ >= 5. Counts were obtained using HTSeq with default parameters
For microRNA-seq: reads were mapped with STAR v2.5.2b against either a custom small RNA reference consisting of tRNA, piRNA, miRNA, and snRNA or a reference consisting exclusively of miRNA. Reads were allowed to multi-map, and all counts were extracted using samtools idxstats.
Genome_build: hg38
Genome_build: miRBase v22
Supplementary_files_format_and_content: For RNA-seq and microRNA-seq: tab delimited text files contain the total number of reads mapped within each annotated gene or microRNA for a given sample.
Supplementary_files_format_and_content: For Rib-seq: bigWig files containing genome-wide counts per million values for a given Ribo-seq sample.

source_name: MDA-MB-231 cell line

growth_protocol: DMEM+10%FBS+PSQ+1µg/mL puromycin

extract_protocol:
Norgen RNA/protein purification kit followed by gel extraction of small RNAs < 35 nt
As in Ingolia at al, 2012

treatment_protocol: 24h with 10nM Rapamycin - collected 48h after seeding at 10^5 cells/mL

tag: shRNA status

tag: molecule type

value: Gel-fractionated small RNA


title: LA-NPC_R56

source_name: LA-NPC_56-Partial Response


title: microRNASeq-shNC-RapPlus-Rep2

description: 10 nM Rapamycin-24h-treated shNC (Control) MDA-MB-231 cells biological replicate #2

value: shNC


title: microRNASeq-shBCDIN3D-RapMinus-Rep2

description: Untreated shBCDIN3D MDA-MB-231 cells, biological replicate #2

treatment_protocol: No treatment - collected 48h after seeding at 10^5 cells/mL


title: LA-NPC_R53

source_name: LA-NPC_53-Partial Response


title: microRNASeq-shNC-RapMinus-Rep2

description: Untreated shNC (Control) MDA-MB-231 cells, biological replicate #2


title: LA-NPC_R52

source_name: LA-NPC_52-Partial Response


title: microRNASeq-shBCDIN3D-RapPlus-Rep1

description: 10 nM Rapamycin-24h-treated shBCDIN3D MDA-MB-231 cells biological replicate #1


title: LA-NPC_R51

source_name: LA-NPC_51-Partial Response


title: LA-NPC_R50

source_name: LA-NPC_50-Partial Response


title: microRNASeq-shBCDIN3D-RapMinus-Rep1

description: Untreated shBCDIN3D MDA-MB-231 cells, biological replicate #1


title: microRNASeq-shNC-RapPlus-Rep1

description: 10 nM Rapamycin-24h-treated shNC (Control) MDA-MB-231 cells biological replicate #1


title: LA-NPC_R49

description: Gene expression data from LA-NPC with response to induction chemotherapy

source_name: LA-NPC_49-Partial Response


title: microRNASeq-shNC-RapMinus-Rep1

description: Untreated shNC (Control) MDA-MB-231 cells, biological replicate #1


title: RNASeq-shBCDIN3D-RapPlus-Rep2

extract_protocol:
Norgen RNA/protein purification kit
TruSeq Stranded Total RNA

value: total RNA


title: RNASeq-shBCDIN3D-RapMinus-Rep2


title: RNASeq-shNC-RapPlus-Rep2


title: RNASeq-shBCDIN3D-RapPlus-Rep1


title: LA-NPC_R43

source_name: LA-NPC_43-Partial Response


title: LA-NPC_R41

source_name: LA-NPC_41-Partial Response


title: RNASeq-shBCDIN3D-RapMinus-Rep1


title: LA-NPC_R42

source_name: LA-NPC_42-Partial Response


title: RNASeq-shNC-RapMinus-Rep1


title: LA-NPC_R45

source_name: LA-NPC_45-Partial Response


title: LA-NPC_R38

source_name: LA-NPC_38-Partial Response


title: LA-NPC_R40

source_name: LA-NPC_40-Partial Response


title: LA-NPC_R39

source_name: LA-NPC_39-Partial Response


title: LA-NPC_R47

source_name: LA-NPC_47-Partial Response


title: RiboProfiling-shBCDIN3D-RapPlus-Rep2

data_processing:
Library strategy: Ribo-Seq
For all datasets: sequence quality was verified by FastQC, adapters were trimmed using cutadapt, and reads were filtered to require a trimmed length of 15bp or greater.
For Ribo-seq and RNA-seq: reads with remaining sequence greater than 16 bp were aligned against the hg38 build of the human reference genome using Tophat v2.0.8 with the “--b2-sensitive” set of options and the Genode v21 set of transcriptome annotations. All BAM files were filtered to require unique alignment wuth mapQ >= 5. Counts were obtained using HTSeq with default parameters
For microRNA-seq: reads were mapped with STAR v2.5.2b against either a custom small RNA reference consisting of tRNA, piRNA, miRNA, and snRNA or a reference consisting exclusively of miRNA. Reads were allowed to multi-map, and all counts were extracted using samtools idxstats.
Genome_build: hg38
Genome_build: miRBase v22
Supplementary_files_format_and_content: For RNA-seq and microRNA-seq: tab delimited text files contain the total number of reads mapped within each annotated gene or microRNA for a given sample.
Supplementary_files_format_and_content: For Rib-seq: bigWig files containing genome-wide counts per million values for a given Ribo-seq sample.

extract_protocol:
As in Ingolia at al, 2012
As in Ingolia at al, 2012

value: ribosome-protected RNA


title: LA-NPC_R48

source_name: LA-NPC_48-Partial Response


title: RiboProfiling-shNC-RapPlus-Rep2


title: LA-NPC_R37

source_name: LA-NPC_37-Partial Response


title: RiboProfiling-shBCDIN3D-RapMinus-Rep2

source_name: MDA-MB-231 cell line


title: LA-NPC_R46

source_name: LA-NPC_46-Partial Response


title: LA-NPC_R36

source_name: LA-NPC_36-Partial Response


title: RiboProfiling-shNC-RapMinus-Rep2


title: LA-NPC_R35

source_name: LA-NPC_35-Partial Response


title: RiboProfiling-shBCDIN3D-RapPlus-Rep1


title: LA-NPC_R34

source_name: LA-NPC_34-Partial Response


title: LA-NPC_R44

source_name: LA-NPC_44-Partial Response


title: RNASeq-shNC-RapMinus-Rep2


title: RNASeq-shNC-RapPlus-Rep1


title: LA-NPC_R33

source_name: LA-NPC_33-Partial Response


title: LA-NPC_R32

source_name: LA-NPC_32-Complete Response

value: complete


title: LA-NPC_R31

source_name: LA-NPC_31-Complete Response


title: RiboProfiling-shNC-RapPlus-Rep1


title: LA-NPC_R30

source_name: LA-NPC_30-Complete Response


title: LA-NPC_R28

source_name: LA-NPC_28-Complete Response


title: RiboProfiling-shNC-RapMinus-Rep1


title: LA-NPC_R29

source_name: LA-NPC_29-Complete Response


title: LA-NPC_R25

source_name: LA-NPC_25-Complete Response


title: LA-NPC_R24

source_name: LA-NPC_24-Complete Response


title: LA-NPC_R26

source_name: LA-NPC_26-Complete Response


title: LA-NPC_R22

source_name: LA-NPC_22-Complete Response


title: LA-NPC_R21

source_name: LA-NPC_21-Complete Response


title: LA-NPC_R23

source_name: LA-NPC_23-Complete Response


title: Merb 30 min rep1

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.0 with parameter -m 1.
Differentially expressed genes were identified using DEseq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample and were computed using custom R scripts that made use of the Bioconductor libraries bamsignals and edgeR.
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage function from deepTools v2.4.1 with parameters --binSize 50 –normalizeUsingRPKM. Refs: Mammana A, Helmuth J (2019). bamsignals: Extract read count signals from bam files. R package version 1.18.0, https://github.com/lamortenera/bamsignals . McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi: 10.1093/nar/gks042. Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257

source_name: retinal pigment epithelium

growth_protocol: RPE-1 cells were serum starved by 48h incubation in Dulbecco's Modified Eagle’s Medium (DMEM) F-12 (Sigma) supplemented with penicillin, streptomycin and 0.1% Fetal Bovine Serum (FBS) (Sigma) at 37ºC in 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy kit from Qiagen following instructions from the manufacturer.
cDNA libraries were prepared with TruSeq Stranded mRNA (Illumina) using 150ng of total RNA.

treatment_protocol: RPE-1 cells were treated with vehicle (DMSO) for 30 minutes or merbarone (200μM) for 30 or 120 minutes.

value: hTERT RPE-1

tag: genotype/variation

value: Merbarone, 30 min


title: DMSO 30 min rep1

value: DMSO, 30 min


title: DMSO 30 min rep3


title: LA-NPC_R20

source_name: LA-NPC_20-Complete Response

value: Nasopharyngeal carcinoma


title: LA-NPC_R19

source_name: LA-NPC_19-Complete Response


title: Merb 30 min rep2


title: DMSO 30 min rep2


title: LA-NPC_R18

source_name: LA-NPC_18-Complete Response


title: LA-NPC_R17

source_name: LA-NPC_17-Complete Response


title: RiboProfiling-shBCDIN3D-RapMinus-Rep1

source_name: MDA-MB-231 cell line


title: LA-NPC_R15

source_name: LA-NPC_15-Complete Response


title: LA-NPC_R13

source_name: LA-NPC_13-Complete Response


title: Merb 30 min rep3


title: LA-NPC_R11

source_name: LA-NPC_11-Complete Response


title: LA-NPC_R12

source_name: LA-NPC_12-Complete Response


title: conF1-F2

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

data_processing:
Sequenced reads from each biological replicate (3 from conF1-F and 3 from iAsF1-F) were aligned to mm10 using STAR aligner (v2.5.3a) with default parameters and settings.
HTSeq was applied to obtain read counts after the alignment
Expression values in normalized format, as well as differential gene expressions were obtained using DESeq2 (version 1.8.2) package
False discovery rate (FDR) threshold was set at 5% for significantly differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

organism: Mus musculus

source_name: liver

extract_protocol:
Use Rneasy kit (QIAGEN) with trizol to extrat total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: F1 generation were unexposed to iAs in drinking water, harvested at feeding status

tag: Sex

value: female

tag: group


title: iAsF1-F2


title: conF1-F1


title: iAsF1-F3


title: LA-NPC_R8

source_name: LA-NPC_8-Complete Response


title: LA-NPC_R9

source_name: LA-NPC_9-Complete Response


title: Kidney_homo_rep3

city: Shanghai

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

data_processing:
Reads were sorted using index and barcode,
Duplicated paired-end reads were removed by FastUniq (version 1.1) for QHR-4C.
Reads were aligned to mm9 using TopHat for RNA-Seq or the unique reads were aligned to mm9 using Bowtie2.
The expression levels were calculated using the Cufflinks software for RNA-Seq, or calculated using the r3Cseq program (version 1.20) in the R package for QHR-4C.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Excel/txt files include FPKM values for RNA-Seq.
Supplementary_files_format_and_content: bedGraph files include RPM values for QHR-4C.

source_name: kidney

extract_protocol:
Total RNA was extracted mouse tissues using TRIzol Reagent (Ambion). For 4C, cell pellets were lysed twice with cold lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, 5 mM EDTA, 0.5% NP-40, 1xprotease inhibitors) for nuclei. Nuclear pellet was resuspended in 225 μl of water, 30 μl of 10x DpnII buffer, and 7.5 μl of 10% SDS and incubated at 37 °C for 1 h with constant shaking at 900 rpm. After quenching SDS by adding 37.5 μl of 20% Triton X-100 and incubating at 37 °C for 1 h with shaking at 900 rpm. The nuclei were then digested with 10 μl of DpnII (10 U/μl) in situ at 37 °C with shaking at 900 rpm overnight. After enzyme inactivation at 65 °C for 20 min, nuclei were centrifuged at 2500g for 5 min, resuspended and digested in 358 μl of water, 40 μl of 10x T4 ligation buffer, and 2 μl of T4 DNA ligase (400 unit/μl) overnight at 16 °C. The ligated product was then reverse crosslinked by adding 10 μl of proteinase K (10 mg/ml) and heating at 65 °C for 4 h, followed by adding 2 μl of RNase A (37 mg/ml) and heating at 37 °C for 45 min. DNA was then extracted using phenol-chloroform. 2 μl of glycogen (20 mg/ml) was added to facilitate DNA precipitation.
RNA-Seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol. For 4C libraries, the precipitated DNA was dissolved in 50 μl water, and then sonicated using the Bioruptor system with low energy setting at a train of 30s on with 30s off for 12 cycles for DNA fragments ranging from 200 to 600 bp. With the fragmented DNA as template, a linearized amplification step was applied using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100 μl of PCR system for a total of 80 cycles. The PCR product was denatured at 95 °C for 5 min and immediately chilled on ice to obtain ssDNA. The ssDNA was enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions, and then ligated with annealed adapters in 45 μl of ligation system (20 μl of DNA-coated beads, 4.5 μl of 10x T4 ligation buffer, 10 μl of 30% PEG 8000, 1 μl of 50 μΜ adapter, 0.9 μl of T4 DNA ligase, 8.6 μl of water). The beads were then washed twice to remove the free adapters with the B/W buffer (5mM Tris-HCl, 1M NaCl, 0.5mM EDTA, Ph7.5). The DNA-coated beads were resuspended in 10 μl water. With the DNA on beads as template and a pair of primers, the QHR-4C libraries were generated by PCR amplification and purified with a PCR purification kit (Qiagen).

treatment_protocol: For 4C, cells were harvested from mice as described in ChIP-Seq. Then, about 2 million of cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the crosslinking reaction was quenched with 0.125M Glycine. Spun down and washed the cell pellets twice with 1xPBS.

value: kidney

tag: age

value: post natal day 0

tag: genotype

value: HS5-1 NRSE -/-


title: Kidney_homo_rep2


title: LA-NPC_R6

source_name: LA-NPC_6-Complete Response


title: LA-NPC_R5

source_name: LA-NPC_5-Complete Response


title: Kidney_wt_rep1


title: LA-NPC_R4

source_name: LA-NPC_4-Complete Response


title: Kidney_wt_rep2


title: Kidney_homo_rep1


title: LA-NPC_R16

source_name: LA-NPC_16-Complete Response


title: Cortex_homo_rep2

source_name: cortex

value: cortex


title: Cortex_homo_rep3


title: Cortex_homo_rep1


title: LA-NPC_R2

source_name: LA-NPC_2-Complete Response


title: LA-NPC_R14

source_name: LA-NPC_14-Complete Response


title: iAsF1-F1


title: conF1-F3


title: Cortex_wt_rep3


title: LA-NPC_R1

source_name: LA-NPC_1-Complete Response


title: LA-NPC_R10

source_name: LA-NPC_10-Complete Response


title: LA-NPC_R27

source_name: LA-NPC_27-Complete Response


title: 546_ML1_nes-msc_early_ch-

city: London

first: Dominique

last: Bonnet

state: London

address: 1 Midland Rd

institute: Francis Crick Institute

data_processing:
The RSEM package (version 1.2.29) in conjunction with the STAR alignment algorithm (version 2.5.1b)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 Ensembl genes downloaded from the UCSC Table Browser 15 on 14th April 2016
The “--forward-prob” parameter was set to “0” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3)
Genome_build: mm10 Ensembl
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: bone marrow-derived Nes-low mesenchymal cells

growth_protocol: AML cell lines were growth in RMPI supplemented with 10% FBS and 1% P/S

extract_protocol:
bones were dissected in small pieces of 2-3 mm diameter and incubated 30 min at 37 degrees in a HBSS digestion solution containing 2% FBS, DNase I (10 μg/ml, Sigma), Collagenase (1 mg/ml, Sigma), Dispase II (5 mg/ml, Sigma) and Heparin (20 U/ml, Sigma). Bone pieces were next crashed with mortar and pestle in the same digestion solution and incubated at 37 degrees for 30 min. Cell suspension was then homogenized with a micropipette and filtered with a 100 micron cell strainer. Human and Murine hematopoietic cells were eliminated using magnetic beads isolation kits, and CD31+ labelled endothelial cells were isolated via FACS in RNA extraction buffer.
Total RNA from sorted cell samples was isolated using the RNeasy Mini Kit (Qiagen, Crawley, UK). The quality and concentration of total RNA were determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay. 2 ng of Total RNA in 5 μl volume was used to generate cDNA synthesis with Nugen Ovation® RNA‑Seq System V2 kit (part No. 7102). The resulting SPIA-cDNA were normalized to 100 ng in 15 μl based on Qubit DNA HS assay. Fragmentation was done using 8 microTUBE-15 AFA Beads Strip V2 (PN 520159) on Covaris E-series at setting 20%DF, 18W, 200 burst, 20C tempt, 120s treatment time and no Intensifier.
Only 10-30 ng in 10 μl of fragmented cDNA was used starting from the End Repair step of the Ovation® Ultralow Library Systems V2 (part No. 0344NB) protocol, with 10 cycles PCR. The RNAseq libraries were quality checked on Qubit DNA HS assay, Bioanalyser and Illumina Ecoreal QPCR followed by Illumina PE51 sequencing on Hiseq 2500 V3 reagents.

treatment_protocol: AML cells were transplanted into 8- to 12-week old unconditioned Nestin+ NSG mice (Jackson Laboratory, BarHarbor, Maine, USA)

tag: host strain

value: Nestin+ NSG mice

value: engrafted with human AML cell lines

tag: tissue/cell type

tag: time point

value: isolated at early time points of the leukemic progression

tag: marker

value: cherry marker negative


title: 544_ML1_nes-msc_early_ch-

value: bone marrow-derived Nes-low mesenchymal cells


title: LA-NPC_R7

source_name: LA-NPC_7-Complete Response


title: 539_ML1_nes-msc_early_ch+

value: cherry marker positive


title: 543_ML1_nes-msc_early_ch-


title: 541_ML1_nes-msc_early_ch+


title: LA-NPC_R3

source_name: LA-NPC_3-Complete Response


title: 529_HL60_nes-msc_early_ch-


title: 527_HL60_nes-msc_early_ch-


title: 528_HL60_nes-msc_early_ch-


title: 524_HL60_nes-msc_early_ch+


title: 399_HL60_nes-msc_late

value: isolated at late time points of the leukemic progression

value: no marker


title: 538_ML1_nes-msc_early_ch+


title: 523_HL60_nes-msc_early_ch+


title: 398_HL60_nes-msc_late


title: 397_HL60_nes-msc_late


title: 525_HL60_nes-msc_early_ch+


title: 583_ML1_nes-msc_late

value: unengrafted


title: 581_ML1_nes-msc_late


title: 375_ctrl_nes-msc_ut

value: untreated


title: 582_ML1_nes-msc_late


title: 373_ctrl_nes-msc_ut


title: Cortex_wt_rep2

tag: strain

value: wild type


title: 41_HL60_osx

source_name: bone marrow-derived Osx cells

growth_protocol: Umbilical Cord Blood (CB) samples were obtained from normal full-term deliveries after signed informed consent. AML samples used for xenografts were obtained after informed consent at St Bartholomew’s Hospital (London, UK).

extract_protocol:
bones were dissected in small pieces of 2-3 mm diameter and incubated 30 min at 37 degrees in a HBSS digestion solution containing 2% FBS, DNase I (10 μg/ml, Sigma), Collagenase (1 mg/ml, Sigma), Dispase II (5 mg/ml, Sigma) and Heparin (20 U/ml, Sigma). Bone pieces were next crashed with mortar and pestle in the same digestion solution and incubated at 37 degrees for 30 min. Cell suspension was then homogenized with a micropipette and filtered with a 100 micron cell strainer. Human and Murine hematopoietic cells were eliminated using magnetic beads isolation kits, and CD31+ labelled endothelial cells were isolated via FACS in RNA extraction buffer.
Total RNA from sorted cell samples was isolated using the RNeasy Mini Kit (Qiagen, Crawley, UK). The quality and concentration of total RNA were determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay. 1-3.5 ng of Total RNA in 5 μl volume was used to generate cDNA synthesis with Nugen Ovation® RNA‑Seq System V2 kit (part No. 7102). The resulting SPIA-cDNA were normalized to 100 ng in 15 μl based on Qubit DNA HS assay. Fragmentation was done using 8 microTUBE-15 AFA Beads Strip V2 (PN 520159) on Covaris E-series at setting 20%DF, 18W, 200 burst, 20C tempt, 120s treatment time and no Intensifier.
Only 10-30 ng in 10 μl of fragmented cDNA was used starting from the End Repair step of the Ovation® Ultralow Library Systems V2 (part No. 0344NB) protocol, with 10 cycles PCR. The RNAseq libraries were quality checked on Qubit DNA HS assay, Bioanalyser and Illumina Ecoreal QPCR followed by Illumina PE51 sequencing on Hiseq 2500 V3 reagents.

treatment_protocol: AML patient-derived samples and CB were transplanted into 8- to 12-week old unconditioned NSG mice (Jackson Laboratory, BarHarbor, Maine, USA). Human bone marrow engraftment was assessed by tibia pucture.

value: bone marrow-derived Osx cells


title: 374_ctrl_nes-msc_ut


title: Cortex_wt_rep1

tag: tissue


title: 39_HL60_osx

value: 8- to 12-week old unconditioned NSG mice


title: 33_HL60_osx


title: 37_HL60_osx


title: 28_ML1_osx


title: 31_HL60_osx


title: X25_ML1_OSX


title: 2B_ctrl_osx


title: X26_ML1_OSX


title: MCF-10A_Empty_Treated-1

city: Ariel

first: Shivani

last: Patel

state: IL

address: 65, Ramat Hagolan

department: Molecular Biology

country: Israel

institute: Ariel University

data_processing:
Reads were trimmed and clipped for quality control in trim_galore (v0.5.0).
Read quality was checked for each sample using FastQC (v0.11.7).
Reads were taken to Hisat2 (v2.1.0) for alignment using hg38, GRch38.97
High-quality reads were then imported into samtools (v1.9 using htslib 1.9) for conversion of SAM files to BAM file.
Gene-count summaries were generated with featureCounts (v1.6.3): A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: hg38, GRch38.97
Supplementary_files_format_and_content: featurecounts_NeuTvsEmpty.txt :Combined Tab-delimited text file includes count for all samples.
Supplementary_files_format_and_content: ETEC_geneset.csv : List of differentially expressed genes in Empty_Treated (ET) compared to Empty_control (EC).
Supplementary_files_format_and_content: NTNC_geneset.csv :List of differentially expressed genes in Neut_Treated (NT) compared to Neut_control (NC).

source_name: Mammary gland; breast

growth_protocol: MCF10A (human breast epithelial) cells were grown in DMEM/F-12 1:1 medium supplemented with 5% horse serum (Cat#04-0041A, BI-Biologicals), 20 ng/mL epidermal growth factor (Cat#AF-100-15,Peprotech, 1 mg), 0.5 μg/mL hydrocortisone(Sigma #H-0888), 10 μg/mL human insulin (Cat#I9278, Sigma), and 100 ng/mL cholera toxin (Sigma #C-8052), L-glutamine (Cat#03-020-1B, BI-Biologicals), L-alanyl-L-glutamine (Cat#03-022-1B, BI-Biologicals), penstrep (Cat#03-031-1B, BI-Biologicals), and were grown in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from cells using Qiagen RNeasy Plus Mini kit (Cat. #74134;GmbH) as per manufacturer protocol.
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. This process was to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of sequenced by synthesis.

treatment_protocol: Empty and NeuT cells were treated with 1uM of JG-98 for 12hours or left untreated which served as controls.

value: Non-tumorigenic epithelial cell line

value: Treated with JG-98 for 12hours


title: MCF-10A_NeuT_Control-1

value: Untreated


title: MCF-10A_NeuT_Control-2


title: MCF-10A_NeuT_Treated-1


title: MCF-10A_Empty_Treated-2


title: MCF-10A_NeuT_Treated-2


title: MCF-10A_Empty_Control-1


title: X29_ML1_OSX


title: 1B_ctrl_osx


title: 12_CB_osx

value: engrafted with control human CB cells


title: 13_CB_osx


title: 2_ctrl_osx


title: MCF-10A_Empty_Control-2


title: 1_ctrl_osx


title: Tregs_1-45_1

city: Münster

first: Jan

last: Rossaint

address: Albert-Schweitzer-Campus 1, Bldg. A1

department: Dpt. of Anesthesiology

country: Germany

institute: University of Münster

data_processing:
quality control was performed with FastQC and MultiQC and adapter trimming was performed with trim-galore (v0.6.4).
Read-mapping and quantification with Salmon (v1.0.0) using the Gencode mouse reference transcriptome vM23
The transcript counts where summarized to gene-level with tximport and supplementary annotation data from Ensembl
The differential expression analysis was carried out by DESeq2 on gene level counts
The reported log foldchanges where shrunk with apeglm and s-values where calculated for statistical significance filtering. For a significant differential gene we require a s-value below 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated matrix of quantification counts of each gene per sample.

source_name: brochoalveolar lavage of mice

extract_protocol:
RNA was extracted from the sorted cells using a RNeasy Mini Kit (Qiagen).
Reverse transcription into cDNA was performed based on polyA tail. For library construction, PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The single strand circle DNA (ssCirDNA) were formatted as the final library. The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Bacterial pneumonia was induced in wildtype mice by intratracheal instillation of viable bacteria (K. pneumonia). Cells were isolated from BAL on day 5 after induction of bacterial pneumonia.

value: lung

value: regulatory t cells without bound platelets

value: 5 days after induction of bacterial pneumonia


title: 11_CB_osx


title: Treg-PLT_aggregates_1-21_1

value: regulatory t cells with bound platelets


title: 220_AML8_osx

value: engrafted with AML patient-derived cells


title: Treg-PLT_aggregates_1-20_1


title: 219_AML8_osx


title: 8_ctrl_osx


title: PLTs_1-3_1

source_name: murine peripheral whole blood

value: blood

value: platelets


title: 21_AML3_osx


title: PLTs_1-2_1


title: 22_AML3_osx


title: 218_AML8_osx


title: 19_AML2_osx


title: M2_PLT_depleted_1-32_1

value: M2 macrophages

value: cells isolated 5 days after induction of bacterial pneumonia and 3 days after platelet depletion


title: M2_PLT_depleted_1-33_1


title: PLTs_1-1_1


title: 267_AML3_NG2

source_name: bone marrow-derived Ng2 cells

value: bone marrow-derived Ng2 cells


title: 266_AML3_NG2


title: 264_AML3_NG2


title: 263_AML3_NG2


title: 268_AML3_NG2


title: M2_1-34_1

value: cells isolated 5 days after induction of bacterial pneumonia


title: 17_AML5_osx

value: bone marrow-derived Osx cells


title: 15_AML5_osx

value: 8- to 12-week old unconditioned NSG mice


title: 14_AML5_osx


title: M2_PLT_depleted_1-31_1


title: 265_AML3_NG2


title: 262_AML8_NG2


title: 259_AML8_NG2


title: 10_CB_osx


title: M1_PLT_depleted_1-24_1

value: M1 macrophages


title: 260_AML8_NG2


title: M1_PLT_depleted_1-23_1


title: 274_HL60_NG2

value: engrafted with human AML cell lines


title: 258_AML8_NG2


title: M1_PLT_depleted_1-22_1


title: 18_AML2_osx


title: 271_ML1_NG2


title: M1_1-27_1


title: 270_ML1_NG2


title: 253_ctrl_ng2

value: unengrafted


title: M1_1-26_1


title: M1_1-25_1


title: 257_CB_ng2

value: engrafted with control human CB cells


title: 251_ctrl_ng2


title: 255_CB_ng2


title: 254_CB_ng2


title: 369_AML2_ng2


title: 370_AML6_ng2


title: 116_HL60_NESLOW

source_name: bone marrow-derived Nes-low cells

value: bone marrow-derived Nes-low cells


title: 113_HL60_NESLOW


title: 114_HL60_NESLOW


title: 112_ML1_NESLOW


title: 272_HL60_NG2


title: 273_HL60_NG2


title: 111_ML1_NESLOW


title: 110_ML1_NESLOW


title: 219_ctrl_NESLOW


title: 252_ctrl_ng2


title: 218_ctrl_NESLOW


title: 217_ctrl_NESLOW


title: 129_ctrl_NESLOW


title: 135_hCB_NESLOW


title: 103_hCB_NESLOW


title: 239_AML8_NESLOW


title: 240_AML8_NESLOW


title: 238_AML8_NESLOW


title: Strain hTM72 transfect with siNC-stretched

city: Durham

first: Paloma

middle: B

last: Liton

state: NC

address: DUMC Box 3802

institute: Duke University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analysis was performed using the Partek Flow and Partek Genome Suite statistical analysis software (Partek Incorporated).

source_name: Strain hTM72 transfect with siNC-Stretch

label_protocol: standard Affymetrix protocol

growth_protocol: Human TM cells were isolated from dissected TM tissue from discarded corneal rims after surgical corneal transplantation at Duke University Eye Center and cultured as described earlier (Liton et al., 2008)

extract_protocol: At 72 h post-transfection, cells were washed with cold PBS and fixed in RNAlater (Qiagen). Total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA), following the manufacturer's protocol, and treated in-column with DNase I. RNA concentration and quality were determined using the Agilent 2100 Bioanalyzer. Total RNA (5 µg) from human TM primary cultures with transient silenced autophagy and controls were independently hybridized to human Clariom D microarrays (ThermoFisher) following the manufacturer's instructions at the Duke Microarray Core Facility.

treatment_protocol: After 24 h, the cells were transfected with either 5 pmol of siRNA against ATG5 (siAtg5, sc-41445) and ATG7 (siAtg7, sc-41447) or 5 pmol of non-targeting siRNA (siNC, sc-37007) using Lipofectamin® RNAiMAX Reagent, according to the manufacturer’s instructions. At 72 h post-transfection, cells were subjected to cyclic mechanical stress for 24 h using the Flexcell System. A regime of 15% cyclic stretch, 1 cycle/sec was applied. Non-stretched control cells were maintained under same culture conditions, but no mechanical forces were applied. Cells were washed with cold PBS and fixed in RNAlater (Qiagen).

value: trabecular meshwork cell

tag: transfection

value: siNC-Stretch


title: 118_ctrl_NESLOW


title: Strain hTM72 transfect with siatg5/7-Non stretched

source_name: Strain hTM72 transfect with siatg5/7


title: Strain hTM72 transfect with siatg5/7-stretched

source_name: Strain hTM72 transfect with siatg5/7-Stretch


title: Strain hTM67 transfect with siatg5/7- stretched

source_name: Strain hTM67 transfect with siatg5/7-Stretch


title: PCOS Normal Weight 4

city: Wuhan

first: Ruxing

last: Wu

state: Hubei

address: No.1095 Jie Fang Avenue, Hankou, Wuhan,Hubei, China.

department: Obstetrics and Gynecology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
A woman is 30 years old and whose menstrual cycle is 20-75 days.
GCS107279

hyb_protocol: Hybridization cocktail for a single probe array contained 2.5 pg of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer. GeneChip was hybridized at 45℃ for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

source_name: PCOS Normal Weight Granulosa Cells

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

tag: gender

value: female

value: 30 years old

tag: menstrual cycle

tag: disease state

value: PCOS

tag: weight

value: normal

value: Human Controlled Ovarian Stimulation Cycle Ovary Granulosa Cells


title: 237_AML8_NESLOW

tag: treatment

value: engrafted with AML patient-derived cells


title: Strain hTM72 transfect with siNC-Non stretched

source_name: Strain hTM72 transfect with siNC

tag: cell type

value: siNC


title: PCOS Obesity 4

description:
A woman is 34 years old and whose menstrual cycle is 30-50 days.
GCS107277

source_name: PCOS Obesity Granulosa Cells

value: 34 years old

value: obese


title: PCOS Normal Weight 3

description:
A woman is 25 years old and whose menstrual cycle is 45-60 days.
GCS107278

value: 25 years old


title: non-PCOS Normal Weight 4

description:
A woman is 30 years old and whose menstrual cycle is 30 days.
GCS107276

source_name: non-PCOS Normal Weight Granulosa Cells

value: 30 days

value: non-PCOS


title: 132_AML6_NESLOW

value: 8- to 12-week old unconditioned NSG mice


title: 128_AML3_NESLOW


title: non-PCOS Normal Weight 3

description:
A woman is 22 years old and whose menstrual cycle is 30 days.
GCS107273

value: 22 years old


title: Strain hTM67 transfect with siNC-stretched

source_name: Strain hTM67 transfect with siNC-Stretch


title: PCOS Obesity 3

description:
A woman is 31 years old and whose menstrual cycle is 30-60days.
GCS107275

value: 31 years old


title: Strain hTM67 transfect with siatg5/7-Non stretched

source_name: Strain hTM67 transfect with siatg5/7

value: trabecular meshwork cell


title: 126_AML3_NESLOW

value: bone marrow-derived Nes-low cells


title: 127_AML3_NESLOW


title: Strain hTM67 transfect with siNC-Non stretched

source_name: Strain hTM67 transfect with siNC


title: Strain hTM64 transfect with siatg5/7-Stretched


title: PCOS Obesity 2

description:
A woman is 30 years old and whose menstrual cycle is 35-40 days.
GCS107274

value: female


title: Strain hTM64 transfect with siNC-Stretched

value: siNC-Stretch


title: 105_AML2_NESLOW


title: 104_AML2_NESLOW


title: 107_AML2_NESLOW


title: 213_HL60_NESHIGH

source_name: bone marrow-derived Nes-high cells

value: engrafted with human AML cell lines

value: bone marrow-derived Nes-high cells


title: PCOS Obesity 1

description:
A woman is 28years old and whose menstrual cycle is 30-45 days.
GCS107272

value: 28 years old

value: PCOS

value: Human Controlled Ovarian Stimulation Cycle Ovary Granulosa Cells


title: non-PCOS Obesity 4

description:
A woman is 29 years old and whose menstrual cycle is 27 days.
GCS107271

source_name: non-PCOS Obesity Granulosa Cells

value: 29 years old

value: 27 days


title: 146_HL60_NESHIGH


title: 145_HL60_NESHIGH


title: 144_HL60_NESHIGH


title: 211_HL60_NESHIGH


title: 212_HL60_NESHIGH


title: non-PCOS Obesity 3

description:
A woman is 29years old and whose menstrual cycle is 30 days.
GCS107270

value: obese


title: Strain hTM64 transfect with siatg5/7- Non stretched

source_name: Strain hTM64 transfect with siatg5/7


title: Strain hTM64 transfect with siNC- Non stretched

source_name: Strain hTM64 transfect with siNC

value: siNC


title: 40_HL60_osx

source_name: bone marrow-derived Osx cells

value: bone marrow-derived Osx cells


title: 222_ctrl_NESHIGH

value: 8- to 12-week old unconditioned NSG mice

value: unengrafted


title: PCOS Normal Weight 2

description:
A woman is 27 years old and whose menstrual cycle is 40-60 days.
GCS107267

value: 27 years old

value: normal


title: 141_ML1_NESHIGH


title: 142_ML1_NESHIGH


title: 143_ML1_NESHIGH


title: non-PCOS Obesity 2

description:
A woman is 34 years old and whose menstrual cycle is 30 days.
GCS107269

value: 34 years old

value: 30 days

value: non-PCOS


title: 16271_ZB

city: Kunming

first: Yun

last: Yang

address: Jiao Ling Lu road

institute: Institute of Medical Biology,Chinese Academy of Medical Sciences

description: Cerebral cortex mock

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Cellranger 3.1.0
Genome_build: ftp://ftp.ensembl.org/pub/release-100/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.100.gtf.gz
Genome_build: ftp://ftp.ensembl.org/pub/release-100/fasta/macaca_mulatta/dna/Macaca_mulatta.Mmul_10.dna.toplevel.fa.gz
Supplementary_files_format_and_content: barcodes;features;matrix

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Single cell suspensions were made using a gentleMACS Octo (MiltenyiBiotec). Single-cell suspensions were loaded onto the Chromium Controller (10x Genomics) for droplet formation.
scRNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit (10x Genomics). The cell suspension (300-600 living cells/ml) was loaded onto the Chromium single cell controller (10x Genomics) by using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074).
scRNA-seq

treatment_protocol: Rhesus monkeys (3-5 kg, 3-5years old) were used for this study. One monkey were intranasally infected with 1x 10^7 PFU of SARS-CoV-2 in 1mL of PBS, and another monkey was intracranially injected with 1x10^6 of SARS-CoV-2 in 200 µl of PBS. One monkey was intranasally and intracranially treated with PBS as a control. We analyzed the tissues collected on the 4 dpi and 7dpi following intranasal inoculation and on the 9 dpi following intracranial inoculation.

value: brain

tag: tissue region

value: Cerebral cortex

value: 4 years old

tag: time

value: mock

tag: animal no.


title: 16015_XPC

description: Primary olfactory cortex on 7dpi following intranasal inoculation

value: Primary olfactory cortex

tag: age

value: 7dpi following intranasal inoculation


title: 16271_XPC

description: Primary olfactory cortex mock


title: 220_ctrl_NESHIGH

tag: host strain

value: bone marrow-derived Nes-high cells


title: non-PCOS Obesity 1

description:
A woman is 30 years old and whose menstrual cycle is 28 days.
GCS107268

value: female

value: 30 years old

value: 28 days

value: obese

value: Human Controlled Ovarian Stimulation Cycle Ovary Granulosa Cells


title: 15183_ZB

description: Cerebral cortex on 9 dpi following intracranial inoculation

value: 5 years old


title: 16271_HM

description: Hippocampus mock

value: Hippocampus


title: non-PCOS Normal Weight 2

description:
A woman is 31 years old and whose menstrual cycle is 28 days.
GCS107265

value: 31 years old

value: normal


title: 215_CB_NESHIGH

value: 8- to 12-week old unconditioned NSG mice

value: engrafted with control human CB cells

tag: tissue/cell type


title: 165_CB_NESHIGH


title: 221_ctrl_NESHIGH

value: unengrafted


title: PCOS Normal Weight 1

description:
A woman is 29 years old and whose menstrual cycle is 28-60 days.
GCS107266

value: 29 years old

value: PCOS


title: 245_AML8_NESHIGH

value: engrafted with AML patient-derived cells


title: 246_AML8_NESHIGH


title: 247_AML8_NESHIGH


title: 16149_HM

description: Hippocampus on 4dpi following intranasal inoculation

value: brain

value: 4 years old

value: 4dpi following intranasal inoculation


title: 16015_HM

description: Hippocampus on 7dpi following intranasal inoculation

value: 7dpi following intranasal inoculation


title: 244_AML8_NESHIGH

value: bone marrow-derived Nes-high cells


title: 15183_HM

description: Hippocampus on 9 dpi following intracranial inoculation


title: 156_AML3_NESHIGH


title: 153_ctrl_NESHIGH


title: 139_AML2_NESHIGH


title: 140_AML5_NESHIGH


title: 157_AML3_NESHIGH


title: 161_AML3_NESHIGH


title: 136_AML2_NESHIGH


title: 16149_XPC

description: Primary olfactory cortex on 4dpi following intranasal inoculation

value: Primary olfactory cortex


title: 567_ML1_COLLOW

source_name: bone marrow-derived Col-low cells

value: engrafted with human AML cell lines

value: bone marrow-derived Col-low cells


title: 137_AML2_NESHIGH


title: CTCF_cortex_homo_rep2

description: CTCF (Millipore, 07-729)

library_source: genomic

data_processing:
Reads were sorted  using index and barcode,
Duplicated paired-end reads were removed by FastUniq (version 1.1) for QHR-4C
Reads were aligned to mm9 using bowtie2 for ChIP-Seq or the unique reads were aligned to mm9 using Bowtie2
The peaks were calculated using the MACS for ChIP-Seq, or interactions were calculated using the r3Cseq program (version 1.20) in the R package for  QHR-4C
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files include peak information for ChIP-Seq, or bedgraph files include RPM values for QHR-4C

molecule: genomic DNA

source_name: Cortex

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody for ChIP-seq. For 4C, cell pellets were lysed twice with cold lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, 5 mM EDTA, 0.5% NP-40, 1xprotease inhibitors) for nuclei. Nuclear pellet was resuspended in 225 μl of water, 30 μl of 10x DpnII buffer, and 7.5 μl of 10% SDS and incubated at 37 °C for 1 h with constant shaking at 900 rpm. After quenching SDS by adding 37.5 μl of 20% Triton X-100 and incubating at 37 °C for 1 h with shaking at 900 rpm. The nuclei were then digested with 10 μl of DpnII (10 U/μl) in situ at 37 °C with shaking at 900 rpm overnight. After enzyme inactivation at 65 °C for 20 min, nuclei were centrifuged at 2500g for 5 min, resuspended and digested in 358 μl of water, 40 μl of 10x T4 ligation buffer, and 2 μl of T4 DNA ligase (400 unit/μl) overnight at 16 °C. The ligated product was then reverse crosslinked by adding 10 μl of proteinase K (10 mg/ml) and heating at 65 °C for 4 h, followed by adding 2 μl of RNase A (37 mg/ml) and heating at 37 °C for 45 min. DNA was then extracted using phenol-chloroform. 2 μl of glycogen (20 mg/ml) was added to facilitate DNA precipitation.
For 4C libraries, the precipitated DNA was dissolved in 50 μl water, and then sonicated using the Bioruptor system with low energy setting at a train of 30s on with 30s off for 12 cycles for DNA fragments ranging from 200 to 600 bp. With the fragmented DNA as template, a linearized amplification step was applied using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100 μl of PCR system for a total of 80 cycles. The PCR product was denatured at 95 °C for 5 min and immediately chilled on ice to obtain ssDNA. The ssDNA was enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions, and then ligated with annealed adapters in 45 μl of ligation system (20 μl of DNA-coated beads, 4.5 μl of 10x T4 ligation buffer, 10 μl of 30% PEG 8000, 1 μl of 50 μΜ adapter, 0.9 μl of T4 DNA ligase, 8.6 μl of water). The beads were then washed twice to remove the free adapters with the B/W buffer (5mM Tris-HCl, 1M NaCl, 0.5mM EDTA, Ph7.5). The DNA-coated beads were resuspended in 10 μl water. With the DNA on beads as template and a pair of primers, the QHR-4C libraries were generated by PCR amplification and purified with a PCR purification kit (Qiagen).

treatment_protocol: Mouse tissues were dispersed by 0.0125% (w/v) (for brain) or 0.0625% (w/v) (for kidney) collagenase (Sigma) treatment in DMEM supplemented with 10% (v/v) FBS for 20 min at 37 °C with rotating at 700 rpm, or directly resuspended in DMEM supplemented with 10% (v/v) FBS by pipetting (for liver). Cells were then filtered through a 40 μm cell strainer (BD) to obtain single-cell suspension.

value: Cortex

value: post natal day 0

tag: genotype

value: HS5-1 NRSE -/-


title: non-PCOS Normal Weight 1

description:
A woman is 28 years old and whose menstrual cycle is 26 days.
GCS107264

value: female

value: 28 years old

value: 26 days

value: non-PCOS

value: normal

value: Human Controlled Ovarian Stimulation Cycle Ovary Granulosa Cells


title: CTCF_cortex_wt_rep1

description: CTCF (Millipore, 07-729)

value: wild type


title: 566_ML1_COLLOW

value: 8- to 12-week old unconditioned NSG mice


title: 565_ML1_COLLOW


title: 363_HL60_COLLOW


title: 362_HL60_COLLOW


title: 361_HL60_COLLOW


title: 569_ctrl_COLLOW

value: unengrafted


title: HS51_k_wt

source_name: kidney

value: cortex


title: 338_ctrl_COLLOW


title: 337_ctrl_COLLOW


title: HS51_k_homo


title: a9_k_homo


title: APL378

first: Niu

last: Qiao

address: 197 Rui Jin Er Road

department: National Research Center for Translational Medicine (Shanghai)

data_processing:
The HISAT2 was used to align the raw RNA-seq sequences to the hg19 human reference genome. Transcript counts table files were generated using the HTSeq htseq-count subprogram with the GENCODE annotation database and processed with the BAM files created using the Hisat2.
All gene expression data from the RNA-seq experiment were normalized using the variance-stabilizing transformation in the DESeq2. Differentially expressed genes (DEGs) were obtained using the DESeq2 R package. Genes and samples were clustered using the ward.D or the ward.D2 method, and distance was calculated on the basis of the Euclidean or Pearson’s correlation coefficient in the R gplots (version 3.0.1.1) package.
The raw sequence variants of the APL RNA-seq samples without WES samples (n = 144) were called in accordance with the GATK forum-recommended analysis pipeline. The driver mutation sites from the RNA-seq only samples were reported on sites available in the WES data. The detailed screening of the candidate driver gene mutations was carried out in accordance with our previously published procedures.
The FusionCatcher was used to find somatic fusion genes, such that at least 2 split and 3 spanning reads were in the analyzed RNA-seq data.
The IPA was applied to find out whether DEGs were controlled by the same upstream regulator or by the same pathway. The gene set enrichment analysis (GSEA) was performed using the GSEA (version 3.0) with MSigDB-hallmark (H) and MSigDB-curated gene sets. For GSEA, all measured genes with phenotype labels of high and low risks were used. The GO functional and the KEGG pathway analyses were used for enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression matrix

source_name: Bone marrow mononuclear cells, APL patients

extract_protocol:
Bone marrow mononuclear cells from 18 centers were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions. After additional enrichment by purification with Ficoll, BM blasts were over 80%.
The DNase I-treated total RNA preparations were qualitatively validated by Agilent RNA 6000 Nano Kit with the 2100 Bioanalyzer system, and libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s paired-end 2 × 150 bp protocol.

value: Bone Marrow

value: acute promyelocytic leukemia

value: Female


title: APL379

value: Male


title: 334_ctrl_COLLOW

value: bone marrow-derived Col-low cells


title: a9_k_wt

value: post natal day 0


title: CTCF_cortex_homo_rep1

description: CTCF (Millipore, 07-729)

value: Cortex

value: HS5-1 NRSE -/-


title: CTCF_cortex_wt_rep2

description: CTCF (Millipore, 07-729)


title: APL377


title: 342_CB_COLLOW

value: engrafted with control human CB cells


title: CTCF_kidney_homo_rep2

description: HS5-1 NRSE -/-, post natal day 0

data_processing:
Reads were sorted  using barcode and index
Reads were aligned to mm9 genome using Bowtie2
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph were generated using Python

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated  with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform

value: kidney

tag: chip antibody

value: CTCF (Millipore, 07-729)


title: 340_CB_COLLOW


title: 339_CB_COLLOW


title: APL376


title: CTCF_kidney_homo_rep1

description: HS5-1 NRSE -/-, post natal day 0

tag: strain


title: 360_AML3_COLLOW

value: engrafted with AML patient-derived cells


title: 358_AML3_COLLOW


title: 357_AML3_COLLOW


title: 356_AML8_COLLOW


title: 355_AML8_COLLOW


title: APL375

tag: tissue


title: CTCF_kidney_wt_rep2

description: wild type, post natal day 0


title: 351_AML5_COLLOW


title: APL374


title: CTCF_kidney_wt_rep1

description: wild type, post natal day 0


title: 354_AML8_COLLOW


title: 350_AML6_COLLOW


title: 349_AML6_COLLOW


title: H3K4me3_cortex_homo_rep2

description: HS5-1 NRSE -/-, post natal day 0

value: H3K4me3 (Millipore,17-614)


title: APL373


title: APL372


title: H3K4me3_cortex_homo_rep1

description: HS5-1 NRSE -/-, post natal day 0


title: 345_AML2_COLLOW


title: APL371


title: 348_AML6_COLLOW


title: H3K4me3_cortex_wt_rep2

description: wild type, post natal day 0

value: H3K4me3 (Millipore, 17-614)


title: 344_AML2_COLLOW

value: 8- to 12-week old unconditioned NSG mice


title: APL370


title: H3K4me3_cortex_wt_rep1

description: wild type, post natal day 0


title: APL369


title: 343_AML2_COLLOW


title: 305_CB_COLHIGH

source_name: bone marrow-derived Col-high cells

value: bone marrow-derived Col-high cells


title: APL368


title: 560_ML1_COLHIGH

value: engrafted with human AML cell lines


title: 561_ML1_COLHIGH


title: 328_HL60_COLHIGH


title: APL366

value: Bone Marrow


title: APL367

value: acute promyelocytic leukemia


title: NRSF_cortex_wt_rep1

description: wild type, post natal day 0

value: NRSF (Millipore, 17-641 )


title: 563_ctrl_COLHIGH

value: unengrafted


title: 326_HL60_COLHIGH


title: NRSF_cortex_wt_rep2

description: wild type, post natal day 0


title: 304_CB_COLHIGH


title: NRSF_cortex_homo2

description: HS5-1 NRSE -/-, post natal day 0


title: NRSF_cortex_homo1

description: HS5-1 NRSE -/-, post natal day 0

value: NRSF (Millipore,17-641 )


title: 327_HL60_COLHIGH


title: 303_ctrl_COLHIGH


title: 562_ctrl_COLHIGH


title: 302_ctrl_COLHIGH


title: 299_ctrl_COLHIGH


title: APL364

value: Male


title: H3K4me3_kidney_homo_rep1

data_processing:
Reads were sorted  using barcode and index
Reads were aligned to the hg19 genome or mm9 genome using Bowtie2
Peaks were called using MACS2
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bedgraph were generated using Python

source_name: Kidney

growth_protocol: HEC-1-B and SK-N-SH cells were cultured in MEM (Hyclone), supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. Cells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-nexus libraries were performed as described (He et al., 2015), with some modifications. Briefly, The chromatin-enriched magnetic beads were then washed with buffers, repaired with the end-repair enzyme mixture (NEB) and dA-tailed with Klenow exo- (NEB) in NEB buffer 2 containing 0.2 mM dATP. After ligating the Nexus adaptors to DNA with 2x Blunt/TA Ligase Master Mix (NEB, M0367S) for 1h at 25 ℃, dealt the mixtures with Klenow exo- and followed by ligation with T4 DNA polymerase (NEB). The blunt-ended DNAs were then treated with Lambda Exonuclease in its buffer (NEB). Subsequently, samples were then digested by RecJf exonuclease (NEB) and washed three times with the RIPA buffer. DNA was then eluted, reverse-crosslinked, purified with phenol: chloroform to get ssDNA.  The ssDNA was circularized with CircLigase (Epicentre), annealed with the Cut_oligo in FastDigest buffer (Thermo), and then digested with FastDigest BamHI (Thermo),  precipitated using ethanol and sodium acetate, resuspended with 20 μl of water.DNAs were amplified by Q5 polymerase (NEB) with Illumina universal primer and index primers.  The PCR products with the sizes of 150 bp to 300bp were extracted from 2% agarose gel using MinElute Gel Extraction Kit (Qiagen).ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated  with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform

treatment_protocol: Mouse tissues were dispersed by 0.00625% (w/v) (for brain) or 0.0125% (w/v) (for kidney) collagenase (Sigma) treatment in DMEM supplemented with 10% (v/v) FBS for 45 min at 37 °C with rotating at 700 rpm, or directly resuspended in DMEM supplemented with 10% (v/v) FBS by pipetting (for liver). Cells were then filtered through a 40 μm cell strainer (BD) to obtain single-cell suspension.

value: Kidney

tag: disease/strain

value: HS5-1 NRSE -/-, post natal day 0


title: 323_AML3_COLHIGH


title: APL363

tag: gender

value: Female


title: H3K4me3_kidney_homo_rep2


title: 325_AML3_COLHIGH


title: APL362


title: H3K4me3_kidney_wt_rep2

value: wild type, post natal day 0


title: APL365


title: APL360


title: 317_AML8_COLHIGH


title: 319_AML8_COLHIGH


title: 314_AML6_COLHIGH


title: 321_AML8_COLHIGH


title: APL361


title: 320_AML8_COLHIGH


title: H3K4me3_kidney_wt_rep1


title: 313_AML6_COLHIGH


title: 86_CB_CD31

source_name: bone marrow-derived CD31 endothelial cells

value: engrafted with control human CB cells


title: 322_AML3_COLHIGH

value: engrafted with AML patient-derived cells


title: APL359


title: 573_ML1_cd31

value: bone marrow-derived CD31 endothelial cells


title: APL358


title: 83_CB_CD31


title: 49_ML1_CD31


title: 571_ML1_cd31


title: APL355


title: 85_CB_CD31


title: 82_CB_CD31


title: 201516240040_R04C01_Nonsmoker

city: Research Triangle Park

first: Dana

last: Hancock

address: 3040 E Cornwallis Rd

institute: RTI  International

data_processing:
QC metrics for potential exclusion include: sex discrepancy based on k-means clustering of PC1 values from chrY gene expression PCA, missing value for self-reported sex, RIN score <6, effective sequencing depth <10 read pairs, overall mapping rate<30%, intergenic mapping rate > 30%, overall mapping rate < 50%, Shannon diversity index < 5.92596, overall mapping rate <50%, mitochondrial proportion of gene counts <0.20, rRNA mapping proportion < 0.01
Genome alignment performed with HISAT2. Transcript quantification performed with Salmon.
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output: counts, tpm, transcript lengths

source_name: nucleus accumbens

extract_protocol:
Genomic DNA and RNA were concurrently extracted from dissected postmortem nucleus accumbens tissue using the Qiagen AllPrep DNA/RNA Mini Kit (Cat No./ID: 80204).
RNA expression was profiled on the Illumain HiSeq 3000 platform using the manufacturer's protocol.

tag: current smoking status

value: control

tag: age at death

tag: sex (m, male; f, female)

value: F

tag: ancestry (cauc, caucasian; aa, african american)

value: AA

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

value: TRUE

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 201516250050_R06C01_Nonsmoker

tag: current smoking status

tag: age at death

value: M


title: 201516240009_R03C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)


title: 201516250042_R03C01_Nonsmoker

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)


title: 201516280017_R05C01_Nonsmoker

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)


title: APL357

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

tag: age


title: 201516280017_R01C01_Nonsmoker

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: 44_ML1_CD31

tag: host strain

value: 8- to 12-week old unconditioned NSG mice

tag: treatment

value: engrafted with human AML cell lines

tag: tissue/cell type


title: APL354


title: 201516280005_R02C01_Smoker

tag: current smoking status

value: case

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 201516260028_R08C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)


title: 202_HL60_CD31

tag: host strain


title: 43_ML1_CD31

tag: treatment


title: APL356

tag: tissue

tag: disease state

tag: gender

value: Male

tag: age


title: APL353


title: 201_HL60_CD31

tag: tissue/cell type


title: 45_ML1_CD31


title: 66_HL60_CD31


title: APL352


title: 201516240031_R05C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: 65_HL60_CD31


title: 59_HL60_CD31


title: APL351


title: 64_HL60_CD31


title: 574_ctrl_cd31

value: unengrafted


title: 201516240034_R03C01_Nonsmoker

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 201516260019_R02C01_Nonsmoker

tag: current smoking status

tag: age at death


title: APL350

tag: tissue

tag: disease state

tag: gender

value: Female

tag: age


title: 96_ctrl_CD31

tag: host strain

tag: treatment

tag: tissue/cell type


title: 94_ctrl_CD31


title: 201516250010_R08C01_Smoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

value: CAUC

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: APL349


title: APL348


title: 87_ctrl_CD31


title: 180_ctrl_CD31


title: 201516250050_R03C01_Smoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 99_AML3_CD31

tag: host strain

tag: treatment

tag: tissue/cell type


title: 201516250042_R07C01_Smoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)


title: 100_AML3_CD31


title: APL346

tag: tissue

tag: disease state

tag: gender

tag: age


title: 201516240007_R05C01_indeterminant

tag: current smoking status

value: indeterminant

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

value: FALSE


title: 98_AML3_CD31

tag: host strain

tag: treatment

value: engrafted with AML patient-derived cells

tag: tissue/cell type

value: bone marrow-derived CD31 endothelial cells


title: 201516260029_R06C01_Smoker

tag: sex (m, male; f, female)

value: F

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 73_AML2_CD31


title: 575_ctrl_cd31


title: APL345

tag: tissue

tag: disease state

tag: gender

tag: age


title: APL344


title: 201516280040_R03C01_indeterminant

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)


title: 70_AML2_CD31

tag: host strain

tag: treatment

tag: tissue/cell type


title: 77_AML5_CD31


title: 79_AML5_CD31


title: 67_AML2_CD31


title: 201516250042_R01C01_Smoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

value: AA

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 95_ctrl_CD31


title: 74_AML5_CD31


title: APL347

tag: tissue

tag: disease state

tag: gender

tag: age


title: 230_AML8_CD31


title: 229_AML8_CD31


title: APL342


title: 228_AML8_CD31


title: 201516240034_R04C01_Nonsmoker

tag: current smoking status

value: control

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

value: TRUE


title: 201516260055_R07C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: 227_AML8_CD31

tag: host strain

tag: treatment

tag: tissue/cell type


title: 72_AML2_CD31


title: APL341

tag: tissue

value: Bone Marrow

tag: disease state

tag: gender

tag: age


title: 102_AML6_CD31


title: APL339

value: acute promyelocytic leukemia


title: APL338


title: APL343


title: APL337


title: 201516280017_R08C01_Nonsmoker

tag: current smoking status

tag: age at death

value: M

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 201516240042_R02C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: ST17: striatal samples from C57BL/6J mouse 14

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

data_processing:
Library strategy: scRNA-Seq
Cellranger;aggr;V 3.0;--normalize=mapped
Cellranger;count;V 3.0;mm10-3.0.0
Seurat;CreateSeuratObject;V 2.0;min.cells = 10, min.genes = 50
Seurat;FilterCells;V 2.0;NGene>500, percent.mito<.25
Genome_build: mm10
Supplementary_files_format_and_content: txt file, first 3 rows are animal number, cell type, and treatment group, remaining rows are transcripts, columns are cells

source_name: brain: striatum

growth_protocol: All animal studies were carried out in accordance with national guidelines and approved by the UNC IACUC. Animals were housed on 12 hour light/dark cycle and allowed food and water ad libitum. Eight-week old male C57BL/6J mice were purchased from Jackson Labs with ~1 week of habituation prior to dosing.

extract_protocol:
Animals were anesthetized using SomnaSol, perfused, and the brain was rapidly dissected. Brains were immediately placed in aCSF buffer in bubbling carbogen in a vibratome, and sliced coronally in 250 micron slices.The tissues were  mechanically disrupted by triturating using a patch pipet. Trituration was repeated 10 times to yield a homogenous suspension. Cell suspensions were diluted and passed through two 100 micron filters followed by two 40 micron filters. Cells were sedimented at 220 x g for 6 mins at 18°C, supernatant carefully removed, and the pellet was resuspended in 1mL aCSF-BSA. Centrifugation was repeated and pellet was resuspended in 1mL aCSF-BSA to yield an estimated 350-400 cells/microliter. Cells were then processed through a dead cell removal kit using standard methods.
10x Genomics Chromium Controller system was used for barcoding cells. Cells were concentrated by centrifuging at 300 x g for five minutes, and then diluted into PBS + BSA buffer at room temperature such that 33.8 microliters contained 500 cells. Each sample was loaded into an individual well of a Chromium Controller for generation of Gel-Bead in Emulsions (GEMS) and cell barcoding using the Chromium Single-cell 3’ Reagent Kit (v2, 10x Genomics).

treatment_protocol: Haloperidol was delivered by implanted pellets and olanzapine in food. All treatments lasted 28-29 days.

tag: strain

tag: tissue

value: brain

tag: region

value: striatum

tag: treatment

value: haloperidol


title: ST16: striatal samples from C57BL/6J mouse 13

value: olanzapine


title: ST14: striatal samples from C57BL/6J mouse 11


title: ST18: striatal samples from C57BL/6J mouse 15

value: placebo


title: ST12: striatal samples from C57BL/6J mouse 9


title: ST13: striatal samples from C57BL/6J mouse 10


title: 201516240007_R07C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)


title: ST10: striatal samples from C57BL/6J mouse 7


title: APL336

tag: disease state

tag: gender

value: Female

tag: age


title: ST11: striatal samples from C57BL/6J mouse 8


title: 201516240009_R07C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

value: CAUC

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: ST09: striatal samples from C57BL/6J mouse 6

tag: strain

tag: tissue

tag: region

tag: treatment


title: APL335

value: Male


title: ST15: striatal samples from C57BL/6J mouse 12


title: APL334


title: ST02: striatal samples from C57BL/6J mouse 2


title: 201516250010_R07C01_Smoker

tag: current smoking status

value: case

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: ST05: striatal samples from C57BL/6J mouse 4


title: APL333

tag: disease state

tag: gender

tag: age


title: ST08: striatal samples from C57BL/6J mouse 5


title: 201516240042_R01C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: rin (rna integrity number)

tag: salmon_mapping_pct (salmon software read mapping percentage)

tag: exon_mapping_pct (hisat2 software read mapping percentage to exonic regions)

tag: chry_mean_counts (mean of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: nac_sex_match (indicator variable for whether self-reported sex aligns with sex-assigned using chry gene expression counts)

tag: sex_has_value (indicator variable for whether an individual has a value assigned for self-reported sex)

tag: nac_assigned_sex_for_missing (imputed sex for individuals without a self-reported sex value (f = female, m = male). the imputation is based on chry gene expression counts)


title: 201516240031_R01C01_Nonsmoker

tag: current smoking status

tag: age at death

tag: intron_mapping_pct (hisat2 software read mapping percentage to intronic regions)

tag: intergenic_mapping_pct (hisat2 software read mapping percentage to intergenic regions)

tag: mito_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to mitochondrial genes)


title: ST04: striatal samples from C57BL/6J mouse 3

tag: strain

tag: tissue

tag: region

tag: treatment


title: ST01: striatal samples from C57BL/6J mouse 1


title: 201516250032_R05C01_Nonsmoker

tag: sex (m, male; f, female)

tag: ancestry (cauc, caucasian; aa, african american)

tag: ribo_rna_pct (percentage of median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts mapping to ribosomal genes)

tag: chry_pc1 (principal component 1 from pca on variance-stablized median-of-ratios normalized (i.e., deseq2 across sample normalization) gene counts for protein-coding genes on chry)

tag: effective_seq_depth (number of reads successfully mapped by salmon)

tag: shannon_index (shannon diversity index calculated using only median-of-ratios normalized (i.e., deseq2 across sample normalization) gene count values > 10)


title: APL332

tag: disease state

tag: gender

tag: age