title: JJN3 cells treated with NT antisenses  for 1 week, Replicate 1

description: cells treated with oligonucleotides


title: JJN3 cells treated with NT antisenses  for 1 week, Replicate 2

status: Public on Nov 28 2023

type: SRA

city: Indianapolis

first: Caleb

middle: A

last: Class

state: IN

address: 4600 Sunset Ave

department: Pharmaceutical Sciences

country: USA

institute: Butler University

description: cells treated with oligonucleotides

library_source: transcriptomic

data_processing:
FASTQ files were pseudo-aligned using Kallisto with the default options, resulting in pseudo-counts and TPM estimates for each transcript.
Genome_build: human genome GRCh38.p12 (Ensembl version 94)
Supplementary_files_format_and_content: One TSV file (Kallisto output) for each sample, including Ensembl transcript ID, transcript length, effective length, estimated counts, and estimated TPM

molecule: total RNA

organism: Homo sapiens

growth_protocol: KMS11 and JJN3 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 0.1% amphotericin B (all from Gibco). Cell cultures were maintained at 37°C in 5% CO2. Cells were constantly seeded at a density of 200,000 cells/mL independently of the type of treatment they received.

extract_protocol:
RNA was extracted from KMS11 or JJN3 cells treated with NT or ILF2 ASOs using the RNeasy kit (Qiagen).
Quality checks and quantification were performed with the 2100 Expert Bioanalyzer (Agilent). cDNA libraries were prepared at MD Anderson’s Advanced Technology Genomics Core facility using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to manufacturer’s specifications. Libraries were sequenced on the HiSeq 4000 System (Illumina) using the standard paired-end protocol.

treatment_protocol: KMS11 and JJN3 cells were treated with  0.5 or 1 mM ASOs for 1 or 3 weeks.

tag: cell line

tag: cell type

value: myeloma cell

tag: treatment

value: control NT

tag: time

value: 1 week


title: JJN3 cells treated with NT antisenses  for 1 week, Replicate 3

description: cells treated with oligonucleotides


title: CCS20_D5_S2071_00010

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) and gene annotated with their corresponding GTF file (GENCODE GRCh38 release 25) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts (Dobin A, et al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013;29(1):15–21). DEseq2 was used to perform differential gene expression analysis and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values for each gene (Love et al., 2014).
Assembly: GRCh38

source_name: OPM2 cells

growth_protocol: OPM2 cells were obtained from  the DSMZ cell repository and cultured in RPMI containing 10% FBS supplemented with 2mM L-glutamine before injecting into NOD-SCID mice.

extract_protocol:
Total RNA was extracted from THP1 cells treated with either DMSO or CCS1477 using the RNeasy Plus Mini Kit (Qiagen, 74134), according to manufacturer’s instructions. RNA quality was analyzed using the Agilent Bioanalyzer.
Libraries were prepared using Roche KAPA HyperPrep with RiboErase. Then, libraries were sequenced using the NextSeq500 (Illumina) with 50 million reads per sample.

tag: xenograft tumour tissue

value: Xenograft tissue


title: CCS20_D5_S2071_00012


title: CCS20_D5_S2071_00009


title: R273H_PLVX_2

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

description: mRNA

data_processing:
Tophat was used to align the sequence to the human genome hg38.
samtools was used to sort the bam files.
samtools was used to convert bam files to sam files.
HTSeq was used to count the read number of genes.
Filtered out genes with reads count less than 5 in all the samples.
DESeq was used to normalize the data and to the Variance Stabilizing Transformation.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Text files were generated containing reads count.

source_name: head neck cancer UM-SCC-1 stable cells

growth_protocol: Subconfluent cells grown in DMEM medium with 10% FBS.

extract_protocol: RNeasy Plus Mini kit (QIAGENE, #74134) was used for RNA isolation following the manufacturer protocol.

treatment_protocol: No treatment.

value: oral squamous cell carcinoma UM-SCC-1 stable cells

tag: genotype/variation

value: expressing retroviral pBabe-mutant p53 R273H and lentiviral pLVX-control vectors


title: D5_veh_S2071_00003


title: D5_veh_S2071_00004


title: R273H_PLVX_1

description: mRNA


title: R273H_MCM5_3

description: mRNA

value: expressing retroviral pBabe-mutant p53 R273H and lentiviral pLVX-MCM5 vectors


title: R273H_PLVX_3

description: mRNA


title: D5_veh_S2071_00002


title: R273H_MCM5_2

description: mRNA


title: TS185_04_OPM-2_CCS1477_48h_S4

library_source: genomic

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) using BWA-MEM version 0.7.15 (Li and Durbin 2009). Reads were filtered using Samtools (version 0.1.9) (Li et al., 2009) to keep only reads that mapped to standard chromosomes and Bedtools version 2.25.0 (Quinian and Hall, 2010) to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje). Peaks were called with Model-based Analysis of ChIP-Seq version 2 (MACS2) using the following parameters -f BAMPE, --keep-dup 5 to keep only paired-end reads with up to 5 duplicates (Zhang et al. 2008). Annotation of peaks was performed with Homer version 4.10 (Heinz et al. 2010).
Assembly: GRCh38

molecule: genomic DNA

growth_protocol: Human myeloma cell lines were obtained from ATCC and the DSMZ cell repositories and cultured in RPMI containing 10% FBS supplemented with 2mM L-glutamine.

extract_protocol:
The Assay for Transposase Accessible Chromatin (ATAC-seq) was performed following the Omni- ATAC improved version of the conventional protocol (Corces et al., 2017) using 5x10^4 viable OPM2 cells. Cell pellets were washed once in cold PBS, re-suspended in 50μl of cold lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% Digitonin) and further incubated on ice for 3min. Cells were then washed in 1ml of wash buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% v/v Tween-20) and nuclei were pelleted by centrifugation for 10min at 500xg at 4°C. Supernatant was discarded and the nuclei were re-suspended in 50μl of transposition reaction buffer (Nextera DNA Sample Preparation Kit, Illumina) containing 16.5μl PBS, 0.1% v/v Tween-20, 0.01% Digitonin, 5μl nuclease-free water, 25μl 2X TD Buffer and 2.5μl Tn5 Transposase. The reaction was incubated at 37°C for 30min at 1,000rpm and purified using the MinElute Reaction Cleanup Kit (QIAGEN). DNA was amplified using NEB Next High-Fidelity PCR Master Mix (New England Biolabs) and 1.25μM of custom PCR primers and conditions (Buenrostro et al., 2013). The PCR reaction was monitored to reduce GC and size bias by pre-amplifying the full libraries for five cycles and taking an aliquot to run for 25 cycles using the same PCR cocktail and SYBR Green. The remaining 45μl reaction was amplified for 6-7 additional cycles as determined by qPCR and DNA libraries were purified using the MinElute Reaction Cleanup Kit (QIAGEN). Fragments of 200– 1000bp were selected using AMPure beads (Beckman Coulter) and quantified by quantitative PCR with a KAPA Library Quantification Kit (Kapa Biosystems).
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a Novaseq SP sequencer system (Illumina) generating around 60 million reads per sample.

value: OPM2 cells

tag: agent

tag: time point


title: D5_veh_S2071_00001


title: R273H_MCM5_1

description: mRNA


title: JJN3 cells treated with ILF2 antisenses  for 1 week, Replicate 3

description: cells treated with oligonucleotides

value: ILF2 ASO 09


title: pBabe_PLVX_3

description: mRNA

value: expressing retroviral control pBabe and lentiviral pLVX-control vectors


title: pBabe_PLVX_2

description: mRNA


title: pBabe_PLVX_1

description: mRNA


title: TS185_03_OPM-2_DMSO_48h_S3

value: DMSO


title: TS185_01_OPM-2_DMSO_6h_S1


title: TS185_02_OPM-2_CCS1477_6h_S2


title: pBabe_MCM5_3

description: mRNA

value: expressing retroviral control pBabe and lentiviral pLVX-MCM5 vectors


title: CF-tCT1

city: Lausanne

first: Gilles

last: Willemin

state: VD

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: Université de Lausanne

data_processing:
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.
Transcript quantification was done using rsem v 1.3.068. The resulting counts matrix was used for subsequent analysis.
Analysis was done in R on the three cohorts, independently; gene filtering based on the rule of 1 count per M (cpm) in at least 1 sample, library size scaling using TMM normalization (EdgeR package v 3.32.1 (Robinson et al. 2010)) and log-transformation using the Limma voom function . Unwanted variation was removed with RUVr (RUVseq package v 1.24.0, Risso et al. 2014).
Statistically significant differentially expressed genes were identified from log-transformed, TMM-scaled values using lmFit of the Limma package by fitting a linear model on the selected samples. P-values calculated using eBayes were adjusted for multiple testing using the Benjamini & Hochberg correction. RUVr-computed factors were added in the design matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rsem counts per gene for each sample

organism: Mus musculus

source_name: Liver

growth_protocol: Male mice were fed either a Chow diet (Kliba Nafag diet #3436) or a High Fat diet (HF, with 60% of calories coming from lard – BioServ diet #F3282) from 4-5 weeks of age. Animals were housed under 12h light/dark conditions, at a constant temperature of 22°C and fed ad-libitum with free access to water.

extract_protocol:
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.

treatment_protocol: Animals were weighed, fasted overnight, refed for 4 hours, and then sacrificed to provide samples for ChIPseq, RNAseq, and proteomic analyses.

tag: tissue

value: Liver

tag: strain

tag: genotype

value: Control

tag: diet

value: CHOW


title: CCS20_D5_S2071_00011


title: pBabe_MCM5_2

description: mRNA


title: TS186_11_H3K27ac_48h_CCS1477_OPM-2_S11

growth_protocol: Human AML and myeloma cell lines were obtained from ATCC and the DSMZ cell repositories and cultured in RPMI containing 10% FBS supplemented with 2mM L-glutamine.

extract_protocol:
100x10^6 cells were treated for 1-, 2-, 6- and/or 48- hours with CCS1477. Cells were counted and cross-linked using 1% formaldehyde (F8775, Sigma Aldrich) in PBS for 10 minutes (for H3K27ac), or double cross-linked (for EP300, MYB, IRF4, CBP, TCF3/E2A and RUNX1) with ChIP Cross-link Gold (C01019027, Diagenode) for 30 minutes in PBS with 1mM MgCl2 and then with 1% formaldehyde for 10 minutes. The reaction was stopped by addition of 0.125M glycine for 5 minutes. Cell pellets were then washed twice with cold PBS containing protease inhibitors (Complete EDTA-free tablets, 11873580001, Roche). ChIP was performed as described in Lee et al. (2006, doi: 10.1038/nprot.2006.98). Briefly, nuclear lysates were sonicated by using a Bioruptor Pico for 8 and 16 cycles for THP1 and OPM2, respectively (30 seconds ON, 30 seconds OFF settings). Chromatin Immunoprecipitation was carried out overnight at 20 rpm, 4°C in a rotating wheel with 180μl Dynabeads Protein G (10004D, Invitrogen) previously conjugated with 15μg antibody.  Beads were then washed six times with the RIPA buffer (50mM HEPES pH7.5, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and once with TE buffer (10mM Tris pH8.0, 1mM EDTA). Later, chromatin IP-bound fractions were extracted and de-crosslinked with Odom elution buffer (50mM TrisHCl pH8.0, 10mM EDTA, 1% SDS) and incubated in a thermomixer at 65°C, 900 rpm overnight.   The day after, RNaseA (0.2mg/ml) and proteinase K (0.2 μg/ml) were added to remove any RNA and protein from the samples. Finally, DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and precipitated with ethanol: two volumes of ice-cold 100% ethanol, glycogen (20 μg/μl) and 200mM NaCl were added to each sample, which were then incubated overnight at −80°C. Pellets were washed with 70% ethanol and resuspended in 30μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using NEBNext UltraII (New England Biolabs) starting from 1-5ng of ChIP DNA, according to the manufacturer’s instructions. Fragments of 200–800 bp were selected using AMPure beads (Beckman Coulter, Pasadena, CA). Sequencing was performed using either a NovaseqSP (2x100 cycles) or a Novaseq 2x150 with 100-bp, paired-end high output generating between 50-90 million reads per sample.

tag: chip antibody

value: ab4729 from Abcam


title: TS186_10_MYB_48h_CCS1477_OPM-2_S10

value: ab45150 from Abcam


title: pBabe_MCM5_1

description: mRNA


title: TS186_09_MYB_6h_CCS1477_OPM-2_S9


title: TS186_06_MYB_6h_DMSO_OPM-2_S6


title: TS186_04_H3K27ac_48h_DMSO_OPM-2_S4


title: TS186_03_H3K27ac_6h_CCS1477_OPM-2_S3


title: shp53_shMCM5G_b

data_processing:
Tophat was used to align the sequence to the  human genome hg38
samtools was used to sort the bam files
samtools was used to convert bam files to sam files
HTSeq was used to count the read number of genes
Filtered out genes with reads count less than 5 in all the samples
DESeq was used to normalize the data and to the Variance Stabilizing Transformation
Genome_build: hg38
Supplementary_files_format_and_content: tex file were generated containing reads count

growth_protocol: Subconfluent cells grow in DMEM medium with 10% FBS

extract_protocol: Rneasy Plus Mini kit (QIAGENE, #74134) was used for RNA isolation following the manufacturer protocol.

treatment_protocol: No treatment

value: oral squamous cell carcinoma MDA1586 stable cells

value: expressing lentiviral shp53 and the second independent lentiviral  shMCM5 vectors


title: shp53_shMCM5C_c

source_name: head neck cancer MDA1586 stable cells

value: expressing lentiviral shp53 and lentiviral  shMCM5 vectors


title: shp53_shMCM5G_c


title: shp53_shMCM5G_a


title: shp53_c

value: expressing lentiviral shp53 and lentiviral control shRNA vectors


title: TS186_01_H3K27ac_6h_DMSO_OPM-2_S1


title: TS184_08_E2A_48h_CCS1477_OPM-2_S16

value: 12258S from Cell Signalling Technology


title: liver tissue pair-fed 3weeks, rep3

city: New York

first: Lorraine

middle: J

last: Gudas

state: NY

address: 1300 York Ave E405

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
HTseq-count v0.11.2
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm10 reference genome using Tophat2 v2.0.11.
Raw reads counts were extracted using htseq-count v1.6.3
Assembly: mm10
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini kit with DNAse I digestion (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using TrSeq RNA protocol (Illumina)

value: liver

value: wild type

value: 3 weeks


title: liver tissue pair-fed 3weeks, rep1


title: TS184_07_E2A_6h_CCS1477_OPM-2_S15


title: TS184_06_RUNX1_6h_DMSO_OPM-2_S14

value: ab23980 from Abcam


title: shp53_b


title: shp53_shMCM5C_a


title: TS184_05_RUNX1_6h_CCS1477_OPM-2_S13


title: liver tissue ethanol-fed 3weeks, rep2


title: R273H_shSting_c

value: oral squamous cell carcinoma UM-SCC-1 stable cells

value: expressing retroviral R273H mutant p53 and Lentiviral shSting control vectors


title: liver tissue ethanol-fed 3weeks, rep3


title: TS184_04_RUNX1_48h_DMSO_OPM-2_S12


title: Sox4 hepatocytes, replicate3

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

description:
After alignment, 3 bam files were merged into one file, and converted to bigwig files
ATAC_Sox4_3rep_merged_RPGC.bw

data_processing:
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by aligning the sequence tags to mm10 by bowtie2 with default parameters and converting the bam files to bigwig using bamCoverage by RPGC normalization.
Supplementary files format and content: Peak calling was performed using MACS2 with the options ‘--nomodel --extsize 200 --shift -100’.

extract_protocol:
Nuclei were isolated from sorted cells using a solution of 10 mM Tris-HCl pH 7.4/10 mM NaCl/3 mM MgCl2/0.1% IGEPAL CA-630.
Immediately following isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 30 minutes at 37 °C.
Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded, and PCR amplified for xx cycles using NEBNext High Fidelity 2x PCR master mix (New England Biolabs), and then the libraries were purified with AMPure XP beads.

treatment_protocol: AAV8-TBG-Cre (EV) or AAV8-TBG-HA-Sox4-P2A-Cre (Sox4) were retro-orbitally injected. 4 days post injection, hepatocytes were harvsted.

value: Hepatocyte

value: AAV8-TBG-HA-Sox4-P2A-Cre injected; harvested 4 days post injection


title: liver tissue ethanol-fed 3weeks, rep1


title: R273H_shSting_b


title: TS186_02_MYB_48h_DMSO_OPM-2_S2


title: TS184_03_RUNX1_48h_CCS1477_OPM-2_S11


title: shp53_shMCM5C_b


title: Sox4 hepatocytes, replicate2

value: Liver


title: R273H_shSting_a


title: EV hepatocytes, replicate3

description:
After alignment, 3 bam files were merged into one file, and converted to bigwig files
ATAC_EV_3rep_merged_RPGC.bw

value: WT

value: AAV8-TBG-Cre injected; harvested 4 days post injection


title: TS184_02_E2A_6h_DMSO_OPM-2_S10


title: Sox4 hepatocytes, replicate1


title: R273H_shRelB_c

value: expressing retroviral R273H mutant p53 and Lentiviral shRelB vectors


title: liver tissue pair-fed 3weeks, rep2


title: TS184_01_E2A_48h_DMSO_OPM-2_S9


title: R273H_shRelB_b


title: shp53_a

value: oral squamous cell carcinoma MDA1586 stable cells


title: R273H_shRelB_a


title: EV hepatocytes, replicate1


title: R273H_c

value: expressing retroviral R273H mutant p53 and Lentiviral shRNA control vectors


title: TS183_04_p300_48h_DMSO_1000nM_S4

source_name: THP1 cells

value: MCA6390 from Biorad


title: TS183_05_p300_6h_DMSO_1000nM_S5


title: Hep_Sox4_3

data_processing:
Reads were mapped to GRCm39 mouse genome using the STAR aligner (version 2.7.10b).
Read counts were obtained using the featureCounts package (v2.0.1)
Read counts were imported to DESeq2, and normalization was performed using the "median of ratios normalization" method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized data including all the samples.

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Library was prepared by Novogene (Sacramento, CA)

treatment_protocol: Mice were injected with adeno-associated viruses (AAVs) packaged with mouse Sox4 expression vector (AAV8-TBG-HA-Sox4-P2A-Cre) or empty vector (AAV8-TBG-Cre). Hepatocytes were harvested 4 days post injection by a standard 2-step liberase digestion method followed by a Percoll enrichment step.

value: Hepatocytes

value: AAV8-TBG-HA-Sox4 (Sox4 expression vector) injected


title: R273H_b


title: TS183_02_p300_48h_CCS1477_1000nM_S2


title: R273H_a


title: Hep_Sox4_2


title: TS181_06_OPM2CBP6hDMSO_S6

value: ab253202 from Abcam


title: Hep_EV_3

value: AAV8-TBG-Cre (empty vector) injected


title: Hep_EV_2


title: TS181_05_THP1CBP6hDMSO_S5


title: Hep_Sox4_1


title: pBabe_b

value: expressing retroviral control pBabe and Lentiviral shRNA control vectors


title: EV hepatocytes, replicate2


title: TS183_07_p300_6h_CCS1477_1000nM_S7


title: Oocyte_Magnet sorting_rep1

type: RNA

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

label: biotin

source_name: oocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPre RNA Amplification kit(IL1791) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit according to the prescribed protocol provided with the kit. Quality control was performed with nanodrop-1000 and electrophoresis.

value: oocytes


title: PFGC_Magnet sorting_rep3

description: replicate 3

source_name: putative female germ cells

value: putative female germ cells


title: Oocyte_Magnet sorting_rep2

description: replicate 2


title: Oocyte_Magnet sorting_rep3

description: replicate 3


title: PFGC_Magnet sorting_rep1

description: replicate 1


title: PFGC_Magnet sorting_rep2

description: replicate 2


title: TS181_04_OPM2CBP6hCCS1477_S4


title: SSC_cultured_rep2

description: replicate 2

source_name: spermatogonial stem cells

value: spermatogonial stem cells


title: SSC_cultured_rep3

description: replicate 3


title: Hep_EV_1


title: lenti_c

value: expressing two lentiviral control shRNA vectors


title: pBabe_a

value: oral squamous cell carcinoma UM-SCC-1 stable cells


title: 19_Control_Input

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Input 2-DG

data_processing:
BWA was used for alignment
Picard was used for removing duplicates
MACS2 was used for peak calling
DiffBind for differential peak calling
Assembly: mm10
Supplementary files format and content: peaks

source_name: Mouse immature neurons

growth_protocol: Primary immature neurons were cultured from E14 mouse embryos and plated on poly-D-Lysine coated plates in the EMEM plus GlutMAX medium added with 10% fetalk bovine serum, 5% horse serum, and 1% Penicillin/Streptomycin. These neurons (two days in vitro) were treated with 2-Deoxyglucose (2-DG).

extract_protocol:
Purified RNA was extracted from these samples using Nucleospin RNA kit (Macherey-Nagel) and follwing its protocol. RNA concentration determined by Nanodrop 1000 (Thermofisher scientific).
Libraries were prepared according to Illumina's instructions

treatment_protocol: These primary immature neurons were either untreated (Control), or treated with 10mM 2-DG for 6h.

value: immature neurons

value: ATF4 antibody (Sigma-Millipore:catalog number ABE387)

tag: condition

value: Input


title: TS181_02_OPM2CBP48hCCS1477_S2


title: SSC_cultured_rep1

description: replicate 1


title: lenti_b


title: 18_2DG_IP

description: IP Control

value: IP

value: Control


title: TS180_04_IRF4_48h_CCS1477_OPM2_S4

value: 4964S from Cell Signalling Technology


title: pBabe_c


title: 17_Control_IP

description: IP 2-DG


title: TS181_03_THP1CBP6hCCS1477_S3


title: 16_2DG_Input

description: Input Control


title: TS180_03_IRF4_48h_DMSO_OPM2_S3


title: 14_2DG_IP

description: IP 2-DG


title: TS180_01_IRF4_6h_CCS1477_OPM2_S1


title: R273H_shSting_2_HU

molecule: polyA RNA

treatment_protocol: Cells were treated with 100 mM hydroxyurea (HU) for 48hrs before the harvest for RNA preparation

tag: cel type

value: expressing  pBabe-R273H mutp53+ shSting1


title: R273H_shSting_3_HU


title: lenti_a

value: oral squamous cell carcinoma MDA1586 stable cells


title: TS180_02_IRF4_6h_DMSO_OPM2_S2


title: TS181_01_OPM2CBP48hDMSO_S1


title: 12_2DG_Input

description: Input 2-DG


title: 13_Control_IP

description: IP Control


title: R273H_shRelB_2_HU

value: expressing pBabe-R273H mutp53+ shRelB


title: R273H_shRelB_3_HU


title: 11_Control_Input

description: Input Control


title: TS179_11_p300_1h_DMSO_S23

value: 61401 from Active Motif


title: TS179_09_MYB_2h_CCS1477_S21

value: ab45150 from Abcam


title: 9_Control_IP

description: IP Control


title: R273H_shRelB_1_HU


title: R273H_3_HU

value: expressing  pBabe-R273H mutp53


title: R273H_2_HU


title: TS179_07_MYB_6h_DMSO_S19


title: TS179_06_MYB_1h_DMSO_S18


title: R273H_1_HU


title: 8_2DG_Input

description: Input 2-DG


title: 7_Control_Input

description: Input Control


title: TS179_05_MYB_6h_CCS1477_S17


title: INPUT_HF-hCT-C

data_processing:
Reads were mapped simultaneously on both Human Hg19 and Mouse Mm10 genome releases with STAR using a merged index with the following options : --outFilterMultimapNmax 50 --outFilterMatchNminOverLread 0.4. up to 30 redundant reads were kept for further analysis.
Mouse and Human scores for Pol3 loci (+/- 150 nucleotides) were normalized according to the library size and the gene length
Factors from human spikes were used for between-samples Mouse data correction
bigWig files were generated using bamCoverage with reads extension set to 300 and bin size set to 10
Assembly: UCSC Mm10/UCSC Hg19
Supplementary files format and content: Genome-wide CPM-normalized bigWig files

extract_protocol:
Preparation of chromatin immunoprecipitation was as described in (Mange et al. 2017)
Preparation of  libraries and high throughput sequencing were as described in (Mange et al. 2017)

value: Liver

value: High Fat


title: pBabe_3_HU

value: expressing pBabe vector


title: R273H_shSting_1_HU


title: TS179_14_p300_2h_DMSO_S26


title: pBabe_2_HU


title: TS179_04_MYB_2h_DMSO_S16


title: 5_Control_IP

description: IP Control


title: 10_2DG_IP

description: IP 2-DG


title: 4_2DG_Input

description: Input 2-DG


title: TS179_03_p300_2h_CCS1477_S15


title: TS179_02_MYB_1h_CCS1477_S14


title: pBabe_1_HU

value: expressing  pBabe vector


title: 3_Control_Input

description: Input Control


title: 2_2DG_IP

description: IP 2-DG


title: 1_Control_IP

description: IP Control


title: TS181_09_48hDMSOREP1_S9

growth_protocol: Human AML cell lines were obtained from ATCC and the DSMZ cell repositories and cultured in RPMI containing 10% FBS supplemented with 2mM L-glutamine.

extract_protocol:
Total RNA was extracted from THP1 cells treated with either DMSO or CCS1477 using the RNeasy Plus Mini Kit (Qiagen, 74134), according to manufacturer’s instructions. RNA quality was analyzed using the Agilent Bioanalyzer.
Libraries were prepared using the NEB Next Ultra II RNA (total). Then, libraries were sequenced using the Novaseq SP sequencing system (Illumina) with 65 million reads per sample.

treatment_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10percent  fetal bovine serum (Sigma Aldrich).

value: DMSO


title: TS181_08_48hCCS1477REP2_S8


title: Liver, Degarelix+FSH, biolrep3

city: Aurora

first: Paul

last: MacLean

state: CO

department: Endocrinology, Metabolism, & Diabetes

institute: University of Colorado Anschutz Medical Campus

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the rat genome (rn6) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Raw counts were imported into Integrated Differential Expression and Pathway analysis (iDEP version .95).  iDEP.95 is an online graphical user interface that provides access to a number of Bioconductor packages required for RNAseq analysis within RStudio.  Low abundance signals were filtered by using a minimum of 0.5 counts per million (CPM) in at least one library.  Counts were transformed using the EdgeR package for differential gene expression analysis throughput using a CPM of 0.5 and a pseudocount (c) of 1.  The DESeq2 package was utilized to calculate differentially-expressed genes (DEG).
Assembly: rn6
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts/reads) and columns include samples. A single file is included for all samples.

organism: Rattus norvegicus

extract_protocol:
RNA was extracted from snap-frozen liver tissue from individual ovariectomized rats receiving either degarelix-only (n=5) or degarelix+FSH (n=4) using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (Illumina, Cat. No. RS-122-2303) on a Perkin Elmer Sciclone G3 platform. An additional standard 1.0x manual bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit
Paired-end, opposing strand directional libraries

treatment_protocol: Ten-week-old female Wistar rats were placed on western diet for 6 weeks and then ovariectomized. Rats were given the GnRH antagonist degarelix and then implanted with osmotic pumps.  5 of the rats had vehicle-only in their pumps.  4 of the rats had FSH delivered in their pumps at 6 ug/kg/day. Rats were calorically-limited on western diet to maintain their pre-OVX body weight for 12 days for metabolic measurement.  Rats were then allowed to eat ad libitum for 7 days.  Finally, rats were fasted for 4 hours and then harvested for liver tissue at 19 weeks of age.

value: Wistar

tag: age

value: 19 Weeks

value: Degarelix + FSH


title: Liver, Degarelix+FSH, biolrep4


title: Liver, Degarelix+FSH, biolrep1


title: TS181_07_48hDMSOREP2_S7


title: Liver, Degarelix-only, biolrep5

value: Degarelix-only


title: RNA-seq of MSCs in 2D culture-3

city: Hiroshima-city

first: MAI

last: YOSHINO

address: 1-2-3 Kasumi Minami-ku

country: Japan

institute: Hiroshima University

data_processing:
The construction and sequencing of the cDNA library were carried out by the Beijing Genomics Institute using the DNBSEQ platform.
The sequence data was filtered using SOAPnuke 1.5.2, and the clean reads were mapped to the reference genome using HISAT2 2.0.4.
After performing alignment using Bowtie2 2.2.5, the expression levels of individual genes were quantified using RSEM 1.2.8.
Assembly: GRCh38
Supplementary files format and content: Counts matrix showing gene-level counts for each sample

source_name: bone marrow

growth_protocol: MSCs were cultured in DMEM (Sigma-Aldrich, Osaka, Japan) supplemented with 10% fetal bovine serum (FBS; Hyclone, Logan, UT), 100 U/mL penicillin (Sigma-Aldrich), and 100 mg/ml streptomycin (Sigma-Aldrich).

extract_protocol:
RNA extraction was carried out using RNA-iso (Takara, Otsu, Japan) and the concentration of the extracted RNA was quantified spectrophotometrically at wavelengths of 260 and 280 nm. The construction and sequencing of the cDNA library were carried out by the Beijing Genomics Institute using the DNBSEQ platform
1) mRNA enrichment and purification:Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis 7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

value: bone marrow

value: primary mscs

value: mesenchymal stem cells


title: P-1572

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

library_source: transcriptomic single cell

data_processing:
We aligned single nuclei RNA-seq (snRNA-seq) reads to the human genome (GRCh38.p13) for each output with the turn-key single-cell transcriptomics method STARsolo, which is folds faster than the CellRanger pipeline and equally accurate (v2.7.9a) 1. We chose parameters for the STARsolo UMI quantification to closely replicate the 10X Cell-Ranger pipeline v6 and use the filtered genome and gene annotation available from 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest, Human reference 2020-A). We ran STARsolo to allow for pre-mRNA gene counts as well as exonic counts for nuclear RNA and to separately count introns and exons for RNA velocity analyses, (--soloFeatures GeneFull Velocyto). We used the following parameters to correct cell barcodes, de-duplicate transcripts by their unique molecular identifier (UMI), assign UMI counts to genes, and pre-filter cells that are likely empty droplets (--soloType Droplet --soloCBmatchWLtype 1MM --soloCellFilter EmptyDrops_CR --soloMultiMappers EM --soloUMIdedup 1MM_CR). We pre-process the UMI gene x cell count matrix to reduce inherent biases in the technology. We identified likely ambient RNA contamination with SoupX 2, empty droplets with DropletQC 3, doublets with scds 4, and damaged nuclei with miQC 5. For each of these analyses, each sample (GEM well) was analyzed separate from each other. We ran SoupX as described to estimate the fraction of ambient RNA from both raw and unfiltered UMI count matrices from STARsolo and perform ambient RNA removal aware of the cell clusters in the filtered matrix. For just the SoupX analyses, we clustered the cells with Seurat v4 6 with FindClusters(algorithm = 2, resolution = 0.5). For DropletQC, we used the intronic and exonic UMI counts per cell per gene from STARsolo to get the fraction of intronic UMI per cell (referred to as the nuclear fraction). We identified empty droplets with default DropletQC parameters (nf_rescue = 0.50, umi_rescue = 1000). We identified droplets with scds’s hybrid algorithm using the function cxds_bcds_hybrid to estimate doublet scores and called doublets on cells with scds.hybrid_score > 1.0. We identified damaged cells with miQC which uses a Bayesian EM algorithm to learn the relationship between mitochondria UMI counts and number of captured genes. We used the posterior probability cutoff of 0.75 to call damaged cells by miQC.
To combine cells together across samples, we normalize the UMI counts with the variance-stabilizing SCTransform and glmGamPoi on each sample 7,8 and  jointly embed cells across samples with reciprocal PCA integration 6 as outlined in https://satijalab.org/seurat/articles/integration_rpca.html. In this joint embedding, we over-clustered the dataset with FindClusters(algorithm = 2, resolution = 1)and removed any cluster with more than 10% of cells flagged by miQC, scds, or DropletQC as low-quality biased-clusters in the data.
We annotated our cells from the human striatum to a recently published high-resolution snRNA-seq reference dataset of the non-human primate striatum 9 using Seurat v4. We downloaded the monkey snRNA-seq processed, annotated gene UMI counts for all cells and MSNs from GSE167920. He, Kleyman et al. had aligned the snRNA-seq reads to the rheMac10 genome using the GRCh38 gene annotation liftover to rheMac10, so the gene-wise labels represent the UMI counts on the rheMac10 genome most orthologous to human. For both full nuclei and MSN subset datasets, we re-processed the macaque cells with SCTransform , glmGamPoi, and reciprocal PCA with default parameters as above to enable label transfer using the most recent integration algorithms in Seurat.
To transfer cell annotations from the reference macaque striatum dataset to the human striatum cells, we perform two label transfers at increasing resolutions: one with all cells and another with just MSNs. As He, Kleyman et al. described, the differences between transcriptionally and anatomically distinct MSN subtypes are subtle, so we split the annotations into two steps to optimally annotate the cells. The first label transfers the cell classes (Oligodendrocytes, MSNs, Interneurons, etc.) from the macaque to the human dataset with the Seurat functions FindTransferAnchors(reduction = ‘rpca’) and  TransferData. Next, we identified cells or cell clusters that were labeled as MSNs and transferred MSN subtype labels (D1.Striosome, D2.Striomsome, etc.) from the macaque to human datasets. We filtered out cells where the cell class or cell subtype labels have max prediction scores less than 0.5 as these tend to represent noisy predictions due to low quality cells from either datasets. We confirmed accurate label transfer at the cell class and cell subtype levels with published marker genes and similar proportions across subjects and samples.
Even with the robust cutoffs that we applied to this dataset to remove likely low quality or doublet cells, we find a residual subset of the data that contain these cells. Upon clustering, doublet cells tend to project into the UMAP space as long streaks between two well-defined cell types. Low-quality cell types would project into the UMAP space as amorphous cell types without clear boundaries. Using these embedding features, we selected these clusters with Seurat’s FindClusters(resolution = 1) function, confirmed that they have the indicative QC metrics, and removed them from analyses.
Assembly: hg38
Supplementary files format and content: Annotated seurat h5 object with raw, processed, and integrated gene counts by cell aggregating samples across the entire dataset
Supplementary files format and content: Annotated scanpy h5ad object with raw, processed, and integrated gene counts by cell aggregating samples across the entire dataset

molecule: nuclear RNA

source_name: postmortem brain tissue

extract_protocol:
Nuclei were isolated from 24 samples of frozen human postmortem brain tissue. Samples weighing 40mg were homogenized in 5mL glass douncers with 1mL lysis buffer containing DAPI using glass pestles using ~10 strokes per pestle. Homogenate was filtered using a 40um mesh strainer (FisherScientific #48680). Nuclei were sorted for DAPI fluorescence using a BD FACS Aria at the Boston University Flow Cytometry Core. Approximately 100,000 nuclei were sorted into 7ul of 0.04% bovine serum albumin (MilliporeSigma #126615) in phosphate buffered saline (ThermoFisher #10010031). Nuclei were counted using a hemocytometer and assessed for concentration and debris. 7,000 nuclei were targeted per sample except for two samples with lower concentrations where 5,000 nuclei were targeted. The 10x Chromium process was performed and next generation sequencing libraries were prepared using the 10x genomics single cell 3’ gene expression dual index kit.
Libraries were sequenced at the Boston University Single Cell Sequencing Core. The pool of snRNA-seq libraries were sequenced on 7 Next-seq P3 flow cells with intermediate re-pooling scheme to optimize for 50-80% sequencing saturation, > 8,000 average UMI per cell. Between sequencing runs, we preliminarily aligned the sequencing reads as outlined below to assess quality per sample and estimate the number of viable nuclei and sample complexity. We identified two samples, C-13291 and C-612, to have low quality QC metrics due to wetting failures, mean UMI per cell <1,000 and estimated # cells >50,000. These samples were excluded from subsequent re-pooling and further analyses (Supplemental Table 1.3 tab STARsolo QC).
snRNA-seq

value: Putamen

value: striatal cells

tag: pair

tag: subject

tag: Sex

value: F

tag: race

value: W

tag: bmi

tag: pmi

tag: ph

tag: rin

tag: dx oud

value: OUD

tag: dx substances

value: OUD-only

tag: dx comorbid

value: Opioid Dependence

value: Methadone, Methadone Metabolite, Trazodone

value: Osteoarthritis; Degenerative Changes of Cervical Spine

value: B, O, Z

value: Y

value: Accidental

value: Combined Drug Overdose


title: RNA-seq of MSCs in 2D culture-2

tag: tissue

tag: cell line

tag: cell type


title: Liver, Degarelix-only, biolrep4

value: Liver

tag: strain

value: Wistar

value: 19 Weeks

tag: treatment

value: Degarelix-only


title: RNA-seq of MSCs in 2D culture-1

value: bone marrow

value: primary mscs

value: mesenchymal stem cells


title: RNA-seq of MSCs spheroids-3


title: 6_2DG_IP

description: IP 2-DG

value: immature neurons

tag: chip antibody

value: ATF4 antibody (Sigma-Millipore:catalog number ABE387)

tag: condition

value: IP


title: C-1572

value: Caudate

value: striatal cells

tag: pair

tag: subject

value: F

value: W

tag: age

value: OUD

value: OUD-only

value: Opioid Dependence


title: RNA-seq of MSCs spheroids-2


title: P-1034

value: Putamen

tag: Sex

tag: race

tag: bmi

value: No substances detected

value: N

value: Natural

value: Endocardial Fibroelastosis


title: C-1034

tag: pmi

tag: ph

tag: rin


title: RNA-seq of MSCs spheroids-1

value: bone marrow

value: primary mscs


title: TS179_01_p300_1h_CCS1477_S13

value: 61401 from Active Motif


title: Liver, Degarelix-only, biolrep2

value: Liver

value: Wistar

value: 19 Weeks

value: Degarelix-only


title: TS181_10_48hCCS1477REP1_S10

tag: time point

tag: agent


title: Liver, Degarelix+FSH, biolrep2

tag: tissue

value: Degarelix + FSH


title: Liver, Degarelix-only, biolrep1


title: RNA-seq of C-MSCs-3

tag: cell line

tag: cell type

value: mesenchymal stem cells


title: Liver, Degarelix-only, biolrep3

tag: strain

tag: treatment


title: CD4+ T cell, healthy, replicate 1

city: Clayton

first: Peter

middle: James

last: Eggenhuizen

state: VIC

address: Monash Medical Centre, 246 Clayton Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: matrix.h5 files

source_name: blood

extract_protocol:
CD4+ cells expanded in vitro in the presence of Smith peptide were FACS sorted based on CD4+ and CellTrace dye dilution selecting the proliferated cells. Sorted cells were counted on a hemocytometer with 0.4% trypan blue. Single-cell concentration was adjusted to between 700-1200 single cells/μL  in 0.04% BSA/PBS and processed as per library construction protocol.
Cells were loaded onto a 10x Chromium Controller (10x Genomics) to perform single-cell partitioning and barcoding. scRNA-seq libraries were constructed using 10x Genomics Chromium Single Cell Single Cell 5' R2-only chemistry according to the manufacturer’s instructions (10x Genomics). Sample quality was determined by CE integrity analysis by AATI Fragment Analyzer and fluorimetric quantitation by Qubit (Invitrogen).

value: blood

value: CD4+ T cell

value: cultured in vitro with SmB/B'58-72-pulsed mature dendritic cells


title: RNA-seq of C-MSCs-2


title: P-13291

value: Putamen

value: striatal cells

value: M

value: B

tag: dx oud

tag: dx substances

tag: dx comorbid

value: U

value: Cardiac Tamponade


title: P-1488

tag: pair

tag: subject

tag: age

value: No substances detected

value: Asthma

value: N

value: Y

value: Natural

value: Pulmonary Embolism


title: Col-0 normal-light rep5

city: Loughborough

first: Zoe

last: Wilson

address: Sutton Bonington Campus

department: Plant Sciences

institute: University of Nottingham

data_processing:
BGI’s internal software SOAPnuke was used to filter reads: removing reads with adaptors, reads in which unknown bases (N) are more than 1%, and removing low quality reads (percentage of bases with less than 15% quality more than 40%). Clean reads were mapped to Arabidopsis thaliana Reference Transcript Dataset 2 (AtRTD2) using Salmon then read counts and transcript per million reads (TPMs) were generated using tximport R package version 1.10.0 and length Scaled TPM method.
Assembly: AtRTD2
Supplementary files format and content: CSV file containing TPMs per gene
Supplementary files format and content: CSV file containing gene read counts

organism: Arabidopsis thaliana

source_name: whole flowers, pre-mitosis I anthers

growth_protocol: Arabidopsis thaliana Columbia (Col-0) ecotype and bhlh89,91 (SALK-123106 x GK-345C06) T-DNA mutants were sown onto a 3:1 mix of Levington M3 compost: Vermiculite with T34 biological control. Plants were grown at 22°C  in a controlled environment room with 16h day length provided by fluorescent lighting.

extract_protocol:
Total RNA was isolated from pre-mitotic buds, containing anther stages 1-10, from 4 factor groups (bhlh89,91 Low, bhlh89,91 Norm, Col-0 Low, Col-0 Norm), each with 4 biological replicates, using RNeasy Kit (Qiagen)
Poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. mRNA was fragmented into small pieces using divalent cations under elevated temperature. Cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. A single 'A' base was then added to cDNA fragments and adapter was ligated. Products were then purified and enriched with PCR amplification. PCR yield was quantified by Qubit and samples were pooled to make single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform, combining the DNB nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: At the onset of flowering, just before bolting, treatments were commenced. In normal light conditions, plants were illuminated with a Photosynthetic Photon Flux Density (PPFD) of 205(± 8.6 SD) μmol/m2/s, while the low light plants received 53 (± 5) μmol/m2/s PPFD through use of net shading. Trays were rotated weekly to minimise localised environmental effects.

value: whole flowers, pre-mitosis I anthers

tag: genotype

value: normal light (200umol/m2/s)


title: Col-0 normal-light rep4


title: RNA-seq of C-MSCs-1

value: bone marrow

value: primary mscs

value: mesenchymal stem cells


title: P-612

value: Putamen

tag: Sex

tag: race

value: W

tag: bmi

tag: pmi

value: Accidental

value: Aspiration


title: P-13151

value: striatal cells

value: F

tag: ph

tag: rin

value: Degenerative Joint Disease

value: O

value: Cardiovascular Disease


title: P-13114

tag: tissue

value: B

value: No substances detected

value: Arthritis

value: Y


title: P-1262

tag: cell type

value: M

value: OUD

value: Poly-SUD

value: Opioid Dependence; Cocaine Dependence; Sedative or Hypnotic or Anxiolytic Dependence

value: Fentanyl, Norfentanyl, Lidocaine, Butalbital, Cocaine Metabolites, Trazodone, Alprazolam, Citalopram,  Acetaminophen

value: B, D

value: N

value: Combined Drug Overdose


title: Col-0 normal-light rep2

value: whole flowers, pre-mitosis I anthers

value: normal light (200umol/m2/s)


title: Col-0 low-light rep5

value: low light (50umol/m2/s)


title: Col-0 low-light rep4


title: Col-0 normal-light rep3


title: P-1670

value: Putamen

value: striatal cells

value: W

value: OUD-only

value: Opioid Dependence

value: Morphine, Oxycodone

value: Osteomyelitis with Non-healing Ulcer; Recurring Foot Infections

value: O, Z

value: Accidental


title: Col-0 low-light rep3


title: Wild type RD2715, rep2

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

description: Barley

data_processing:
Fastp, an ultra-fast FASTQ processor with useful quality control and data-filtering and QC
Filtered reads were further used for alignment by using hisat2 splice-ware aligner and available Hordenum valgare reference genome/ gene annotation from ensembl.org (http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/hordeum_vulgare/dna/).
Differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: Reference genome
Supplementary files format and content: tab-delimited text files include COUNT matrix for each Sample

organism: Hordeum vulgare

source_name: Meristem

extract_protocol:
Inflorescence meristem tissues at Double ridge stage of contrasting cultivars RD2715 and GP were processed as per the manufacturer’s protocol for total RNA extraction using SV Total RNA Isolation System, Promega (WI, USA), followed by an on-column DNase treatment. Quality of RNA extracted is confirmed by 1 % agarose gel electrophoresis and visualised in gel doc, and quantity assessed using Agilent nano-drop.
NEBNext® Ultra II Directional RNA library Prep Kit was used to prepare high quality libraries, according to manufacturer’s protocols and paired end sequencing reads were generated with Ilumina HiSeq-X sequencing platform.

value: Meristem

tag: cultivar


title: P-1366

value: F

value: OUD

value: Poly-SUD

value: Pain Disorder

value: Opioid Dependence; Sedative or Hypnotic or Anxiolytic Dependence

value: Pain Disorder Associated with Both Psychological Factors and a General Medical Condition

value: Methadone, Tramadol, Alprazolam, Diphenhydramine

value: Asthma; Recurrent Bronchitis

value: B, O, Z

value: Y


title: bhlh89,91 normal-light rep5

value: whole flowers, pre-mitosis I anthers

tag: treatment

value: normal light (200umol/m2/s)


title: P-1252

value: Putamen

value: striatal cells

value: M

value: W

tag: dx oud

value: MDD

value: Opioid Dependence; Alcohol Dependence; Cocaine Dependence; Polysubstance Dependence

value: Major Depressive Disorder, Single Episode, Severe without Psychotic Features

value: Morphine, Phenobarbital, Cocaine Metabolites

value: Arthritis

value: Combined Drug Overdose


title: Rat5 day14 ipsilateral

city: Guangzhou

first: Guangyin

last: Yu

address: No. 74 Zhongshan Road 2, Guangzhou 510080, P.R. China

institute: Zhongshan School of Medicine, Sun Yat-sen University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using homemade scripts.

source_name: ipsilateral

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The rats were sacrificed on the 3rd day or the 14th day after root avulsion. They were given a lethal dose of 10% chloral hydrate (Kermel, China). Under the surgical microscope, the cervical spinal cord of each rat was exposed, and the ipsilateral half of the spinal cord segments with a complete ventral and dorsal root avulsion were evaluated and success of avulsion confirmed. Then, the C5 to T1 spinal segments were removed and dissected into ipsilateral and contralateral halves as quickly as possible. Total RNA was isolated using TRIzol (TIANGEN, China) according to the manufacturer's instructions. Total RNA from each sample was quantified using a Nanodrop 2000 (Thermo fisher, US), and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Subsequently, we stored the remaining RNA at − 80 °C for later use.

treatment_protocol: In the supine position, the right brachial plexus was exposed, and the right C5-C8 and T1 spinal nerve roots were isolated under a surgical microscope (Chenghe Microsurgical Instruments Factory, China)，and then were pull out one by one using micro hemostatic forceps. The avulsed ventral and dorsal roots together with the dorsal root ganglia were cut away from the distal ends of the spinal nerves and success of avulsion model confirmed under the microscope. The muscle and skin were sutured in successive layers following avulsion. The animals were placed in a heated recovery chamber and returned to their cage once they were awake.

tag: strain

value: Sprague-Dawley

value: spinal cord - C5 to T1 spinal segments

tag: gender

value: female

tag: weight

value: 14 days after the unilateral BPRA in the spinal cord


title: P-13281

tag: pair

tag: subject

value: F

value: OUD

tag: dx substances

value: Poly-SUD

tag: dx comorbid

value: Opioid Dependence; Sedative or Hypnotic or Anxiolytic Dependence

value: Fentanyl, Meprobamate

value: B, C, D, L, O, P

value: Y

value: Accidental

value: Fentanyl Overdose


title: Rat6 day 14 contralateral

source_name: contralateral


title: Wild type, GP,  rep2

description: Barley

value: Meristem

value: GP


title: Rat6 day 14 ipsilateral


title: Rat4 day14 contralateral


title: Rat5 day14 contralateral


title: bhlh89,91 normal-light rep4

value: whole flowers, pre-mitosis I anthers

tag: genotype

value: normal light (200umol/m2/s)


title: Col-0 low-light rep2

value: low light (50umol/m2/s)


title: Wild type RD2715, rep1

description: Barley


title: Wild type, GP,  rep1

description: Barley


title: C-1488

value: Caudate

value: striatal cells

tag: Sex

value: M

tag: race

value: B

tag: age

tag: bmi

value: No substances detected

value: Asthma

value: N

value: Natural

value: Pulmonary Embolism


title: bhlh89,91 normal-light rep3

tag: tissue


title: TS186_07_MYB_KD6_H3K27ac_THP1_S7

extract_protocol:
100x10^6 cells were treated for 1-, 2-, 6- and/or 48- hours with CCS1477. Cells were counted and cross-linked using 1% formaldehyde (F8775, Sigma Aldrich) in PBS for 10 minutes (for H3K27ac), or double cross-linked (for EP300, MYB, IRF4, CBP, TCF3/E2A and RUNX1) with ChIP Cross-link Gold (C01019027, Diagenode) for 30 minutes in PBS with 1mM MgCl2 and then with 1% formaldehyde for 10 minutes. The reaction was stopped by addition of 0.125M glycine for 5 minutes. Cell pellets were then washed twice with cold PBS containing protease inhibitors (Complete EDTA-free tablets, 11873580001, Roche). ChIP was performed as described in Lee et al. (2006, doi: 10.1038/nprot.2006.98). Briefly, nuclear lysates were sonicated by using a Bioruptor Pico for 8 and 16 cycles for THP1 and OPM2, respectively (30 seconds ON, 30 seconds OFF settings). Chromatin Immunoprecipitation was carried out overnight at 20 rpm, 4°C in a rotating wheel with 180μl Dynabeads Protein G (10004D, Invitrogen) previously conjugated with 15μg antibody. Beads were then washed six times with the RIPA buffer (50mM HEPES pH7.5, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and once with TE buffer (10mM Tris pH8.0, 1mM EDTA). Later, chromatin IP-bound fractions were extracted and de-crosslinked with Odom elution buffer (50mM TrisHCl pH8.0, 10mM EDTA, 1% SDS) and incubated in a thermomixer at 65°C, 900 rpm overnight.  The day after, RNaseA (0.2mg/ml) and proteinase K (0.2 μg/ml) were added to remove any RNA and protein from the samples. Finally, DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and precipitated with ethanol: two volumes of ice-cold 100% ethanol, glycogen (20 μg/μl) and 200mM NaCl were added to each sample, which were then incubated overnight at −80°C. Pellets were washed with 70% ethanol and resuspended in 30μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using NEBNext UltraII (New England Biolabs) starting from 1-5ng of ChIP DNA, according to the manufacturer’s instructions. Fragments of 200–800 bp were selected using AMPure beads (Beckman Coulter, Pasadena, CA). Sequencing was performed using either a NovaseqSP (2x100 cycles) or a Novaseq 2x150 with 100-bp, paired-end high output generating between 50-90 million reads per sample.

tag: chip antibody

value: ab4729 from Abcam


title: Rat3 day3 contralateral

value: Sprague-Dawley

value: spinal cord - C5 to T1 spinal segments

value: female

value: 3 days after the unilateral BPRA in the spinal cord


title: Rat3 day3 ipsilateral


title: bhlh89,91 normal-light rep2

value: whole flowers, pre-mitosis I anthers


title: TS186_05_shx_H3K27ac_THP1_S5


title: bhlh89,91 low-light rep5


title: PBMC, Patient 6, scRNAseq

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger 6.1.2
Assembly: hg38
Supplementary files format and content: Tab-separated feature files, matrix files and barcode files.

source_name: Blood

extract_protocol:
PBMCs were isolated from blood using Ficoll-Paque density gradient method. CD15+ granulocyte depletion was done post-thawing of SENSE method’s cryopreserved whole blood samples EasySep cd15 positive selection kit.
ScRNA-seq libraries were prepared from viably thawed whole blood (WB) and PBMCs single-cell samples prepared in the previous section according to manufacturer’s (10x genomics) instructions.  Cellplexing kit (10x genomics, 1000261), which allows the pooling of samples prior to GEMs generation by labeling samples with unique cell multiplexing oligos (CMOs), was used to multiplex samples. The pooled samples were used to generate GEMs, followed by RT-PCR steps and cDNA amplification using Next GEM single cell 3’v3.1 kits (10x genomics, 1000268). Following the cDNA amplification step, size selection beads were used to separate the CMO and gene expression (GEX) cDNAs that were then used to prepare the CMO and GEX libraries respectively.

tag: individual

value: Patient 6

tag: cell type

value: PBMC

value: Blood

tag: method


title: C-13291

value: Caudate

value: striatal cells

tag: pmi

tag: ph

tag: rin

tag: dx oud

value: U

value: Cardiac Tamponade


title: bhlh89,91 low-light rep3

tag: treatment

value: low light (50umol/m2/s)


title: PBMC, Patient 5, scRNAseq

value: Patient 5


title: fenster2020-TTATGCGA

description:
inDrops v3
S8_2

data_processing:
The demultiplexing was performed using a custom shell script. Reads were aligned to the rheMac10 genome and counted at cell and gene level with STARsolo using a reference annotation lifted from the human genome to the rheMac10 genome.
To combine cells together across samples, we normalize the UMI counts with the variance-stabilizing SCTransform and glmGamPoi on each sample 7,8 and jointly embed cells across samples with reciprocal PCA integration 6 as outlined in https://satijalab.org/seurat/articles/integration_rpca.html. In this joint embedding, we over-clustered the dataset with FindClusters(algorithm = 2, resolution = 1)and removed any cluster with more than 10% of cells flagged by miQC, scds, or DropletQC as low-quality biased-clusters in the data.
We annotated our cells from the human striatum to a recently published high-resolution snRNA-seq reference dataset of the non-human primate striatum 9 using Seurat v4. We downloaded the monkey snRNA-seq processed, annotated gene UMI counts for all cells and MSNs from GSE167920. He, Kleyman et al. had aligned the snRNA-seq reads to the rheMac10 genome using the GRCh38 gene annotation liftover to rheMac10, so the gene-wise labels represent the UMI counts on the rheMac10 genome most orthologous to human. For both full nuclei and MSN subset datasets, we re-processed the macaque cells with SCTransform , glmGamPoi, and reciprocal PCA with default parameters as above to enable label transfer using the most recent integration algorithms in Seurat.
To transfer cell annotations from the reference macaque striatum dataset to the human striatum cells, we perform two label transfers at increasing resolutions: one with all cells and another with just MSNs. As He, Kleyman et al. described, the differences between transcriptionally and anatomically distinct MSN subtypes are subtle, so we split the annotations into two steps to optimally annotate the cells. The first label transfers the cell classes (Oligodendrocytes, MSNs, Interneurons, etc.) from the macaque to the human dataset with the Seurat functions FindTransferAnchors(reduction = ‘rpca’) and TransferData. Next, we identified cells or cell clusters that were labeled as MSNs and transferred MSN subtype labels (D1.Striosome, D2.Striomsome, etc.) from the macaque to human datasets. We filtered out cells where the cell class or cell subtype labels have max prediction scores less than 0.5 as these tend to represent noisy predictions due to low quality cells from either datasets. We confirmed accurate label transfer at the cell class and cell subtype levels with published marker genes and similar proportions across subjects and samples.
Even with the robust cutoffs that we applied to this dataset to remove likely low quality or doublet cells, we find a residual subset of the data that contain these cells. Upon clustering, doublet cells tend to project into the UMAP space as long streaks between two well-defined cell types. Low-quality cell types would project into the UMAP space as amorphous cell types without clear boundaries. Using these embedding features, we selected these clusters with Seurat’s FindClusters(resolution = 1) function, confirmed that they have the indicative QC metrics, and removed them from analyses.
Assembly: rheMac10
Supplementary files format and content: Annotated seurat h5 object with raw, processed, and integrated gene counts by cell aggregating samples across the entire dataset

organism: Macaca mulatta

source_name: nucleus accumbens

extract_protocol:
After sacrifice, brains were rapidly dissected into slabs and frozen on metal plates in liquid nitrogen vapor. Time between animal sacrifice and tissue freezing was between 1-2 hours for all animals. Brains were kept stored at -80 C until punching, when they were punched on a microtome with guidance from a macaque anatomist (Dr. S. Haber). Punches were stored at -80 C until the day of nuclear isolation and encapsulation.
Nuclei were isolated as in previous studies130, with minor modifications. Punches were placed into buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5mM spermidine, protease inhibitors) and placed in a Dounce homogenizer for 10 strokes each with loose and tight pestles. A 5% IGEPAL solution was added to a final concentration of 0.3% followed by five additional dounce strokes, then the lysate was filtered through a 40-μm strainer. Nuclei were mixed with an equal volume of 50% iodixanol and then layered on top of an iodixanol gradient of 40% and 30% layers in a 2 mL dolphin microcentrifuge tube. Nuclei were spun by centrifuging at 10,000 x g for 4 min at 4°C and then collected by aspiration at the interface of the 30% and 40% iodixanol layers. Nuclear concentration and prep quality were ascertained by loading on a hemocytometer and were diluted to a concentration of 80-100K and 15% iodixanol with Buffer HB prior to loading on InDrops platform. Single-nuclei suspensions were encapsulated into droplets, lysed, and the RNA within each droplet was reverse-transcribed using a unique nucleotide barcode as described previously131. Approximately 6,000 nuclei, in two batches of 3,000 nuclei each were processed per library and sequenced on Illumina NovaSeq 6000 chips (at a density of approximately 20,000 reads/nucleus).

treatment_protocol: Each morphine-treated subject was trained to come to the front of the enclosure for twice daily intramuscular (IM) injections (<0.5 cc) of morphine sulfate (NIDA Drug Supply Program) dissolved in 0.9% saline. Injections were administered at 09:30 and 17:00 hours. A gradual dosing escalation method (0.5 log unit increase every 3 days) was used to achieve the terminal dosage of 9 mg/kg/day (i.e., 4.5 mg/kg, BID). This dosage was selected to produce moderate opioid dependence128,129. All subjects received approximately 1500 mg of morphine over the 5-6-month period of chronic dosing. On the last day and approximately 3 hrs following the last IM morphine injection, each subject received an IM injection of ketamine (10 mg/kg) followed by 5.0 ml IV of a pentobarbital-based euthanasia solution (Beuthanasia-D).

value: M

tag: weight (kg)

value: morphine

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

value: ~1500 mg/kg morphine (2018)

tag: pair

value: D


title: C-13114

tag: subject

tag: Sex

value: F

tag: race

value: B

tag: age

tag: bmi

tag: dx substances

tag: dx comorbid

value: No substances detected

value: Arthritis

value: O

value: Y

value: Natural

value: Cardiovascular Disease


title: bhlh89,91 low-light rep1

tag: tissue

value: whole flowers, pre-mitosis I anthers

tag: genotype


title: Rat2 day3 ipsilateral

tag: strain

value: Sprague-Dawley

value: spinal cord - C5 to T1 spinal segments

tag: gender

value: female

tag: weight

value: 3 days after the unilateral BPRA in the spinal cord


title: Rat4 day14 ipsilateral

tag: treatment

value: 14 days after the unilateral BPRA in the spinal cord


title: Rat1 day3 ipsilateral


title: Rat1 day3 contralateral


title: C-1262

value: Caudate

tag: cell type

value: striatal cells

value: M

value: W

tag: pmi

tag: ph

tag: rin

tag: dx oud

value: OUD

value: Poly-SUD

value: Opioid Dependence; Cocaine Dependence; Sedative or Hypnotic or Anxiolytic Dependence

value: Fentanyl, Norfentanyl, Lidocaine, Butalbital, Cocaine Metabolites, Trazodone, Alprazolam, Citalopram,  Acetaminophen

value: B, D

value: N

value: Accidental

value: Combined Drug Overdose


title: C-1670

tag: pair

tag: subject

tag: Sex

value: OUD-only

value: Opioid Dependence

value: Morphine, Oxycodone

value: Osteomyelitis with Non-healing Ulcer; Recurring Foot Infections

value: O, Z

value: Y


title: PBMC, Patient 3, scRNAseq

tag: individual

value: Patient 3

value: PBMC

value: Blood

tag: method


title: PBMC, Patient 4, scRNAseq

value: Patient 4


title: fenster2020-GAGCCTTA

description:
inDrops v3
S8_1

value: M

tag: weight (kg)

value: morphine

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

value: ~1500 mg/kg morphine (2018)

value: D


title: fenster2020-AAGGCTAT

description:
inDrops v3
S7_2

value: control

tag: tissue

value: ~1250 mg/kg cocaine (2012 ‚Äì 2016) - drug free 2 yrs prior to brain collection

value: A


title: C-1252

value: Caudate

value: striatal cells

tag: race

value: W

tag: age

tag: bmi

value: OUD

tag: dx substances

value: Poly-SUD

tag: dx comorbid

value: MDD

value: Opioid Dependence; Alcohol Dependence; Cocaine Dependence; Polysubstance Dependence

value: Major Depressive Disorder, Single Episode, Severe without Psychotic Features

value: Morphine, Phenobarbital, Cocaine Metabolites

value: Arthritis

value: Accidental

value: Combined Drug Overdose


title: PBMC, Patient 2, scRNAseq

value: Patient 2

tag: cell type

value: PBMC

value: Blood


title: 4d non-exposed control.3

city: Cajamar

first: Juliana

last: Lago

state: SP

address: Via de Acesso, KM30,5, Prédio C

department: R&D

country: Brazil

institute: Natura Cosméticos S/A

description: 3D skin samples non-exposed, 4 day incubation, replicate 3

data_processing:
Software Version:   Torrent Suite 5.10.0  host figo  ion-analysis 5.10.10-1  ion-dbreports 5.10.26-1  ion-gpu 5.10.0-1  ion-pipeline 5.10.8-1  ion-torrentpy 5.10.8-1  ion-torrentr 5.10.9-1  S5 Script 0.1.31  LiveView 2389  DataCollect 3602  OIA 51000  OS 34  Graphics 97
Run Name R 2018 09 06 22 44 33 user S5-CEC-75  Run Date Oct. 4, 2018, 3:15 p.m.  Run Flows 500
Chip Type 540  Chip Data tiled  Chip Lot Number QSC156  Chip Wafer 19  Barcode Set IonXpress
Analysis Args Analysis {args-json /opt/ion/config/args 540 analysis.json  Pre-BaseCaller BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0  {max-phasing-levels 2 {wells-normalization on  Calibration Args Calibration  BaseCaller Args BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0  {max-phasing-levels 2 {num-unfiltered 1000 {barcode-filter-postpone 1  {wells-normalization on  Alignment Args tmap mapall -q 50000 ... stage1 map4  IonStats Args ionstats alignment  Analysis Parameters default
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (.xlsx)

source_name: non-exposed control

extract_protocol:
The mRNA from 3D skin was extracted using MINI KIT PURELINK PURIFIC RNA 50 PREPS (INVITROGEN) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard NGS platform (ION chef e ION5S) protocols:
A26325: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit
Q32852: Qubit™ RNA high sensitivity (HS), broad range (BR) and extended range (XR) Assay Kits
468802: Ion Library TaqMan® Quantitation Kit
A27759: ION 540 kit-Chef

treatment_protocol: 3D skin samples, in triplicate, was irradiated using LED light

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

tag: treatment

value: 4d non-exposed control


title: fenster2020-CTATTAAG

description:
inDrops v3
S7_1

tag: Sex

value: M

value: control

value: nucleus accumbens

value: ~1250 mg/kg cocaine (2012 ‚Äì 2016) - drug free 2 yrs prior to brain collection

tag: pair

value: A


title: C-13281

value: Caudate

value: striatal cells

tag: subject

value: F

value: W

tag: pmi

tag: ph

tag: rin

tag: dx oud

value: OUD

value: Poly-SUD

value: Opioid Dependence; Sedative or Hypnotic or Anxiolytic Dependence

value: Fentanyl, Meprobamate

value: B, C, D, L, O, P

value: Y

value: Fentanyl Overdose


title: pR_fib

type: genomic

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description:
methylation profiling using bisulfite converted
Matrix_processed_with_skin_fibroblasts.txt
Matrix_signal_intensities_with_skin_fibroblasts.txt

hyb_protocol: DNA was treated with sodium bisulfite and bisulfite-converted DNA was subjected to genome-wide methylation profiling using Infinium MethylationEPIC 850K Bead Chip (Illumina Inc., USA).

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Methylation array data analysis was carried out in the R (v 3.6.1) environment using “ChAMP R package” (v 2.20.1). Raw IDAT files and the sample sheet was imported using the “champ.load” function. The quality control parameters were set as default while probes overlapping SNP positions, sex chromosomes and detection p-value < 0.01 were filtered-out. The filtering process retained 729682 probes, which were normalized by the BMIQ (Beta MIxture Quantile dilation) method. The normalized beta-values were tagged with genomic features using Illumina Manifest file, which was originally in hg19 version but converted to hg38 genome version using liftOver R package v 1.16.0 (Bioconductor Package Maintainer).

label: Cy5 and Cy3

source_name: genomic DNA from Skin Fibroblast

label_protocol: Standard llumina Protocol

growth_protocol: iPSCs were plated on tissue culture plates coated with Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Gibco™), and grown StemMACS™ iPS-Brew XF, human (Miltenyi Biotec).Cells were passaged every 4–6 days. Cell were dissociated from plates with StemPro™ Accutase™ Cell Dissociation Reagent (Gibco™), and following each passage, 1X of RevitaCell™ Supplement (100X) (Gibco™), was added to the media.

extract_protocol: Genomic DNA was extracted from iPSCs using the Wizard Genomic DNA Kit following the manufacturer's instruction (A1125, Promega).

tag: gender

value: Female

tag: disease state

value: Skin Fibroblast


title: 4d non-exposed control.1

description: 3D skin samples non-exposed, 4 day incubation, replicate 1

tag: tissue

value: 3D equivalent human skin

value: primary fibroblast + Col type1

value: primary keratinocyte

value: 4d non-exposed control


title: 4d non-exposed control.2

description: 3D skin samples non-exposed, 4 day incubation, replicate 2


title: C-1366

value: Caudate

tag: race

tag: age

tag: bmi

value: Pain Disorder

value: Pain Disorder Associated with Both Psychological Factors and a General Medical Condition

value: Methadone, Tramadol, Alprazolam, Diphenhydramine

value: Asthma; Recurrent Bronchitis

value: B, O, Z

value: Accidental

value: Combined Drug Overdose


title: fenster2020-GCGTAAGA

description:
inDrops v3
S6_2

value: M

tag: weight (kg)

value: morphine

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

value: ~1500 mg/kg morphine (2018)

value: A


title: SENSE, Patient 6, scRNAseq

tag: individual

value: Patient 6

tag: cell type

value: Whole Blood

value: Blood

tag: method

value: SENSE


title: PBMC, Patient 1, scRNAseq

value: Patient 1

value: PBMC


title: fenster2020-CCTAGAGT

description:
inDrops v3
S6_1

tag: Sex

tag: treatment

tag: pair


title: TS169_08_THP1_CCS1477_48h_100nM

city: Manchester

first: Tim

last: Somervaille

institute: Cancer Research UK

data_processing:
Reads were aligned to the human genome (GRCh38 GENCODE release 25) using BWA-MEM version 0.7.15 (Li and Durbin 2009). Reads were filtered using Samtools (version 0.1.9) (Li et al., 2009) to keep only reads that mapped to standard chromosomes and Bedtools version 2.25.0 (Quinian and Hall, 2010) to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje). Peaks were called with Model-based Analysis of ChIP-Seq version 2 (MACS2) using the following parameters -f BAMPE, --keep-dup 5 to keep only paired-end reads with up to 5 duplicates (Zhang et al. 2008). Annotation of peaks was performed with Homer version 4.10 (Heinz et al. 2010).
Assembly: GRCh38

extract_protocol:
The Assay for Transposase Accessible Chromatin (ATAC-seq) was performed following the Omni- ATAC improved version of the conventional protocol (Corces et al., 2017) using 5x10^4 viable THP1 cells. Cell pellets were washed once in cold PBS, re-suspended in 50μl of cold lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% Digitonin) and further incubated on ice for 3min. Cells were then washed in 1ml of wash buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% v/v Tween-20) and nuclei were pelleted by centrifugation for 10min at 500xg at 4°C. Supernatant was discarded and the nuclei were re-suspended in 50μl of transposition reaction buffer (Nextera DNA Sample Preparation Kit, Illumina) containing 16.5μl PBS, 0.1% v/v Tween-20, 0.01% Digitonin, 5μl nuclease-free water, 25μl 2X TD Buffer and 2.5μl Tn5 Transposase. The reaction was incubated at 37°C for 30min at 1,000rpm and purified using the MinElute Reaction Cleanup Kit (QIAGEN). DNA was amplified using NEB Next High-Fidelity PCR Master Mix (New England Biolabs) and 1.25μM of custom PCR primers and conditions (Buenrostro et al., 2013). The PCR reaction was monitored to reduce GC and size bias by pre-amplifying the full libraries for five cycles and taking an aliquot to run for 25 cycles using the same PCR cocktail and SYBR Green. The remaining 45μl reaction was amplified for 6-7 additional cycles as determined by qPCR and DNA libraries were purified using the MinElute Reaction Cleanup Kit (QIAGEN). Fragments of 200– 1000bp were selected using AMPure beads (Beckman Coulter) and quantified by quantitative PCR with a KAPA Library Quantification Kit (Kapa Biosystems).
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a Novaseq SP sequencer system (Illumina) generating around 80 million reads per sample.

tag: cell line


title: 1d non-exposed control.2

description: 3D skin samples non-exposed, 1 day incubation, replicate 2

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

value: 1d non-exposed control


title: 1d non-exposed control.1

description: 3D skin samples non-exposed, 1 day incubation, replicate 1

tag: tissue


title: SENSE, Patient 4, scRNAseq

value: Patient 4


title: fenster2020-TTCTAGCT

description:
inDrops v3
S5_2

value: control

value: ~500 mg/kg cocaine (2011-2016)- drug free ~2 yrs prior to brain collection

value: C


title: pG

description: methylation profiling using bisulfite converted

source_name: genomic DNA from iPSCs

extract_protocol: Genomic DNA was extracted from iPSCs using the Wizard Genomic DNA Kit following the manufacturer's instruction  (A1125, Promega).

tag: gender

value: Male

tag: disease state

value: iPSC


title: Full visible spectrum 2h.3

description: 3D skin samples exposed to full visible spectrum light, for 2 hour, simulating acute exposure, replicate 3

source_name: full visible spectrum 2h

value: full visible spectrum 2h


title: TS169_07_THP1_DMSO_6h

source_name: THP1 cells


title: C-13151

value: Caudate

value: striatal cells

tag: subject

value: F

tag: race

value: W

tag: age

tag: bmi

tag: pmi

tag: ph

tag: rin

tag: dx oud

tag: dx substances

tag: dx comorbid

value: No substances detected

value: Degenerative Joint Disease

value: O

value: N

value: Natural

value: Cardiovascular Disease


title: fenster2020-TCGACTAG

description:
inDrops v3
S5_1

tag: Sex

value: M

tag: weight (kg)

tag: treatment

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

tag: pair


title: Rat2 day3 contralateral

tag: strain

value: Sprague-Dawley

tag: tissue

value: spinal cord - C5 to T1 spinal segments

tag: gender

value: female

tag: weight

value: 3 days after the unilateral BPRA in the spinal cord


title: bhlh89,91 low-light rep2

value: whole flowers, pre-mitosis I anthers

tag: genotype

value: low light (50umol/m2/s)


title: SENSE, Patient 3, scRNAseq

tag: individual

value: Patient 3

tag: cell type

value: Whole Blood

value: Blood

tag: method

value: SENSE


title: TS169_06_THP1_DMSO_48h

tag: cell line


title: SENSE, Patient 5, scRNAseq

value: Patient 5


title: SENSE, Patient 2, scRNAseq

value: Patient 2


title: TS169_05_THP1_CCS1477_6h_100nM


title: pR

value: Female

tag: disease state

value: iPSC


title: fenster2020-TCTCTCCG

description:
inDrops v3
S4_2

tag: Sex

tag: weight (kg)

value: control

value: ~2000 mg/kg cocaine (2008 -2017) - drug free ~1 yr prior to brain collection

value: D


title: Full visible spectrum 4h.2

description: 3D skin samples exposed to full visible spectrum light, for 4 hour, simulating acute exposure, replicate 2

source_name: full visible spectrum 4h

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

tag: treatment

value: full visible spectrum 4h


title: UN

value: Male

value: Control


title: TS172_05_OPM2_p300_6h_CCS1477_100nM

source_name: OPM2 cells

extract_protocol:
100x10^6 cells were treated for 6- and/or 48- hours with CCS1477. Cells were counted and cross-linked using 1% formaldehyde (F8775, Sigma Aldrich) in PBS for 10 minutes (for H3K27ac, RNA-Pol II, phosphoS2 RNA-Pol II, phosphoS5 RNA-Pol II and CEBPA), or double cross-linked (for EP300) with ChIP Cross-link Gold (C01019027, Diagenode) for 30 minutes in PBS with 1mM MgCl2 and then with 1% formaldehyde for 10 minutes. The reaction was stopped by addition of 0.125M glycine for 5 minutes. Cell pellets were then washed twice with cold PBS containing protease inhibitors (Complete EDTA-free tablets, 11873580001, Roche). ChIP was performed as described in Lee et al. (2006, doi: 10.1038/nprot.2006.98). Briefly, nuclear lysates were sonicated by using a Bioruptor Pico for 8 and 16 cycles for THP1 and OPM2, respectively (30 seconds ON, 30 seconds OFF settings). Chromatin Immunoprecipitation was carried out overnight at 20 rpm, 4°C in a rotating wheel with 180μl Dynabeads Protein G (10004D, Invitrogen) previously conjugated with 15μg antibody.  Beads were then washed six times with the RIPA buffer (50mM HEPES pH7.5, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and once with TE buffer (10mM Tris pH8.0, 1mM EDTA). Later, chromatin IP-bound fractions were extracted and de-crosslinked with Odom elution buffer (50mM TrisHCl pH8.0, 10mM EDTA, 1% SDS) and incubated in a thermomixer at 65°C, 900 rpm overnight.   The day after, RNaseA (0.2mg/ml) and proteinase K (0.2 μg/ml) were added to remove any RNA and protein from the samples. Finally, DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and precipitated with ethanol: two volumes of ice-cold 100% ethanol, glycogen (20 μg/μl) and 200mM NaCl were added to each sample, which were then incubated overnight at −80°C. Pellets were washed with 70% ethanol and resuspended in 30μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using NEBNext UltraII (New England Biolabs) starting from 1-5ng of ChIP DNA, according to the manufacturer’s instructions. Fragments of 200–800 bp were selected using AMPure beads (Beckman Coulter, Pasadena, CA). Sequencing was performed using either a NovaseqSP (2x100 cycles) or a Novaseq 2x150 with 100-bp, paired-end high output generating between 50-90 million reads per sample.

tag: chip antibody

value: anti-EP300 (61401 from Active Motif)


title: fenster2020-CGTCTAAT

description:
inDrops v3
S4_1

value: M

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

tag: pair


title: SENSE, Patient 1, scRNAseq

value: Patient 1

value: Whole Blood

tag: tissue

value: Blood

value: SENSE


title: C-612

value: Caudate

value: striatal cells

tag: subject

tag: race

value: W

tag: age

tag: bmi

tag: pmi

tag: ph

tag: rin

tag: dx oud

tag: dx substances

tag: dx comorbid

value: No substances detected

value: N

value: U

value: Accidental

value: Aspiration


title: Full visible spectrum 2h.2

description: 3D skin samples exposed to full visible spectrum light, for 2 hour, simulating acute exposure, replicate 2

value: 3D equivalent human skin

tag: dermis

value: primary fibroblast + Col type1

tag: epidermis

value: primary keratinocyte

tag: treatment

value: full visible spectrum 2h


title: TS172_04_OPM2_p300_6h_DMSO

tag: cell line

tag: chip antibody

value: anti-EP300 (61401 from Active Motif)


title: cG13

tag: gender

value: Male

tag: disease state

tag: cell type

value: iPSC


title: fenster2020-CTAAGCCT

description:
inDrops v3
S3_2

tag: Sex

value: F

tag: weight (kg)

value: control

tag: tissue

value: nucleus accumbens

tag: date of_sacrifice

tag: date of_birth

tag: age (year)

tag: drug history

value: ~200 mg/kg nicotine (2015 ‚Äì 2017) - drug free ~1 yr prior to brain collection

tag: pair

value: B


title: cG50


title: D2SU

value: Control


title: Full visible spectrum 1h.2

description: 3D skin samples exposed to full visible spectrum light, for 1 hour, simulating acute exposure, replicate 2

source_name: full visible spectrum 1h

value: full visible spectrum 1h


title: TS172_03_OPM2_INPUT

value: input


title: Blue wavelenght 1h".2

description: 3D skin samples exposed to blue wavelength light, for 1 hour for 4 sequential days simulating chronic exposure, replicate 2

source_name: blue wavelength 1h"

value: blue wavelength 1h"


title: fenster2020-ACTGCATA

description:
inDrops v3
S2_2

value: M

value: morphine

value: ~1500 mg/kg morphine (2018)

value: C


title: TW3

city: La Jolla

first: Michael

last: Croft

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: Stimulated for 24 hrs and then bulk RNAseq performed

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: HEK (Primary human keratinocyte cells from skin)

growth_protocol: Human epidermal keratinocytes from neonates (nHEK) were obtained from American Type Culture Collection (ATCC) (NHEK, PS-200-010, ATCC, Manassas, VA) and maintained in dermal cell basal medium (PCS-200-030, ATCC).

extract_protocol:
Cells were harvested using TRIzol and further subjected to transcriptomic analysis.
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: Cells were seeded at 3 × 105 cells per well in triplicates in six-well plates and treated with preoptimized concentrations of human rTWEAK (100 ng/ml), human rIL-13 (100 ng/ml), or human rIL-22 (100 ng/ml), or a combination of rTWEAK with rIL-13 or rIL-22 at the above concentrations, for 24 hr. Control cells received the same volume of PBS.

value: Human Epidermal Keratinocyte

value: 100 ng/ml TWEAK stimulation, 24 hr


title: CR35

value: Female


title: TW2


title: TW1


title: TS172_02_OPM2_p300_48h_CCS1477_100nM

address: Wilmslow Rd

value: anti-EP300 (61401 from Active Motif)


title: Blue wavelenght 4h.2

description: 3D skin samples exposed to blue wavelength light, for 4 hours, simulating acute exposure, replicate 2

source_name: blue wavelength 4h

value: 3D equivalent human skin

value: primary fibroblast + Col type1

value: primary keratinocyte

value: blue wavelength 4h


title: fenster2020-AAGGAGTA

description:
inDrops v3
S3_1

value: F

value: control

value: nucleus accumbens

value: ~200 mg/kg nicotine (2015 ‚Äì 2017) - drug free ~1 yr prior to brain collection

value: B


title: TS172_01_OPM2_p300_48h_DMSO


title: fenster2020-GTAAGGAG

description:
inDrops v3
S2_1

value: M


title: Blue wavelenght 1h.2

description: 3D skin samples exposed to blue wavelength light, for 1 hours, simulating acute exposure, replicate 2

source_name: blue wavelength 1h

value: blue wavelength 1h


title: TW_22_3

value: TWEAK_plus_IL22, 100 ng/ml each; 24 hrs


title: Blue wavelenght 2h.2

description: 3D skin samples exposed to blue wavelength light, for 2 hours, simulating acute exposure, replicate 2

source_name: blue wavelength 2h

value: blue wavelength 2h


title: TS171_04_THP1_p300_48h_DMSO


title: cR7

value: iPSC


title: fenster2020-TATCCTCT

description:
inDrops v3
S1_2

value: morphine

value: ~1500 mg/kg morphine (2018)


title: TW_22_1

value: Human Epidermal Keratinocyte


title: Full visible spectrum 1h".1

description: 3D skin samples exposed to full visible spectrum light, for 1 hour for 4 sequential days simulating chronic exposure, replicate 1

source_name: full visible spectrum 1h"

value: 3D equivalent human skin

value: full visible spectrum 1h"


title: Full visible spectrum 4h.1

description: 3D skin samples exposed to full visible spectrum light, for 4 hour, simulating acute exposure, replicate 1

value: primary fibroblast + Col type1

value: primary keratinocyte

value: full visible spectrum 4h


title: TW_13_3

value: TWEAK_plus_IL13, 100 ng/ml each; 24 hrs


title: TS171_02_THP1_p300_6h_CCS1477_100nM

value: anti-EP300 (61401 from Active Motif)


title: TW_22_2


title: RNA-Seq_HCT116_siITGB8-AS1rep

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using STAR version 2.7.0e.
Genome_build: hg19

source_name: colorectal cancer

growth_protocol: HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using Trizol (Takara) following the manufacturer’s protocol followed by DNase I digestion to remove residual DNA.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 platform.

treatment_protocol: HCT116 cells were transfected with NC-siRNA or ITGB8-AS1-siRNA for 48 hours, respectively.


title: RNA-Seq_HCT116_siITGB8-AS1


title: TS171_01_THP1_p300_48h_CCS1477_100nM


title: TS171_03_THP1_p300_6h_DMSO


title: Full visible spectrum 2h.1

description: 3D skin samples exposed to full visible spectrum light, for 2 hour, simulating acute exposure, replicate 1

value: full visible spectrum 2h


title: TW_13_1


title: Full visible spectrum 1h".2

description: 3D skin samples exposed to full visible spectrum light, for 1 hour for 4 sequential days simulating chronic exposure, replicate 2


title: Chicken, male, scRNAseq

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
Cell Ranger v5.0.0 was used for demultiplexing
Assembly: GRCg6a
Supplementary files format and content: barcodes.tsv, features.tsv, and Matrix.mtx files

organism: Gallus gallus

source_name: Gonadal cells

extract_protocol:
Gonads were collected from chicken embryos at Hamburger Hamilton stage 28. Seven male and seven female embryonic gonads were pooled in 100 ul trypsin 0.05% with same-sex and incubated at 37℃ for 5 min with gentle pipetting. The digestion was stopped with 100 ul of Dulbecco’s Modified Eagle Medium containing 10% fetal bovine serum and washed with 500 ul PBS. Cells were pelleted down and resuspended in PBS. Single cell libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol.
Libraries were prepared using Chromium Next GEM Single Cell 3p RNA library v3.1. Single Cell 3' GEX and feature barcode libraries are sequenced on the Illumina sequencing system.

value: Gonadal cells

value: Male

tag: developmental stage

value: Hamburger Hamilton stage 28


title: Full visible spectrum 1h.1

description: 3D skin samples exposed to full visible spectrum light, for 1 hour, simulating acute exposure, replicate 1

tag: dermis

value: full visible spectrum 1h


title: Pol2DMSO_6h

value: anti-RNA Pol II (ab26721 from Abcam)


title: Chicken, female, scRNAseq

description: 10x Genomics

value: Female


title: pG_fib

description:
methylation profiling using bisulfite converted
Matrix_processed_with_skin_fibroblasts.txt
Matrix_signal_intensities_with_skin_fibroblasts.txt

value: Skin Fibroblast


title: Pol2CCS1477_6h_100nM


title: PBS_3

value: PBS


title: Blue wavelenght 1h".1

description: 3D skin samples exposed to blue wavelength light, for 1 hour for 4 sequential days simulating chronic exposure, replicate 1

tag: epidermis

value: blue wavelength 1h"


title: phosphoS5Pol2DMSO_6h

value: anti-phospho S5 RNA Pol II (ab5408 from Abcam)


title: smallRNA_seq _F2

city: TaiAn

first: min

last: zhang

state: ShanDong

address: 61 Daizong Street

department: College of Animal Science and Technology

institute: ShanDongAgricultural University

data_processing:
Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The sequences were processed and analyzed by GENEWIZ.
Hisat2 (v2.0.1) was used to index reference genome sequence. And, clean data were aligned to reference genome via software Hisat2 (v2.0.1).

source_name: cumulus cells

extract_protocol:
Total RNA was extracted from CC samples using RNeasy Mini Kit (Qiagen) or miRNeasy Mini Kit (Qiagen) for mRNA and miRNA sequencing, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols

value: granulosa cells in the antral follicles

tag: strain

value: Mice of Kunming

tag: treatment

value: treated with FSH and FBS for 18 hours


title: smallRNA_seq _F3


title: Blue wavelenght 4h.1

description: 3D skin samples exposed to blue wavelength light, for 4 hours, simulating acute exposure, replicate 1

value: 3D equivalent human skin

value: primary fibroblast + Col type1

value: primary keratinocyte

value: blue wavelength 4h


title: PBS_1

value: Human Epidermal Keratinocyte


title: phosphoS2Pol2DMSO_6h

tag: cell line

tag: chip antibody

value: anti-phospho S2 RNA Pol II (ab5095 from Abcam)


title: phosphoS5Pol2CCS1477_6h_100nM


title: IL_22_3

value: 100 ng/ml IL22 stimulation, 24 hr


title: smallRNA_seq _F1


title: PBS_2


title: phosphoS2Pol2CCS1477_6h_100nM


title: smallRNA_seq _X3

value: untreated


title: IonXpress_009: Full visible spectrum 1h'

description: 3D skin samples exposed for 1 hour for 4 sequential days simulating chronic exposure

data_processing:
Software Version: Torrent Suite 5.10.0; host figo; ion-analysis 5.10.10-1; ion-dbreports 5.10.26-1; ion-gpu 5.10.0-1; ion-pipeline 5.10.8-1; ion-torrentpy 5.10.8-1; ion-torrentr 5.10.9-1; S5 Script 0.1.31; LiveView 2389; DataCollect 3602; OIA 51000; OS 34; Graphi
Run Name R 2018 09 06 22 44 33 user S5-CEC-75; Run Date Oct. 4, 2018, 3:15 p.m.; Run Flows 500
Chip Type 540; Chip Data tiled; Chip Lot Number QSC156; Chip Wafer 19; Barcode Set IonXpress
Analysis Args Analysis {args-json /opt/ion/config/args 540 analysis.json; Pre-BaseCaller BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0; {max-phasing-levels 2 {wells-normalization on; Calibration Args Calibration; BaseCaller Args BaseCaller {barcode-filter-minreads 10 {phasing-residual-filter=2.0; {max-phasing-levels 2 {num-unfiltered 1000 {barcode-filter-postpone 1; {wells-normalization on; Alignment Args tmap mapall -q 50000 ... stage1 map4; IonStats Args ionstats alignment; Analysis Parameters default
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

value: full spectrum 1h'


title: smallRNA_seq _X2


title: Blue wavelenght 1h.1

description: 3D skin samples exposed to blue wavelength light, for 1 hours, simulating acute exposure, replicate 1

value: blue wavelength 1h


title: TS162_10_Input-THP1

value: input


title: Blue wavelenght 2h.1

description: 3D skin samples exposed to blue wavelength light, for 2 hours, simulating acute exposure, replicate 1

value: blue wavelength 2h


title: IL_22_1


title: TS162_09_H3K27ac-DMSO_6h

value: anti-acetyl H3K27 (ab4729 from Abcam)


title: smallRNA_seq _X1


title: IL_22_2


title: TW_13_2

value: TWEAK_plus_IL13, 100 ng/ml each; 24 hrs


title: IL_13_3

value: 100 ng/ml IL13 stimulation, 24 hr


title: RNA_seq _X3

value: granulosa cells in the antral follicles

value: Mice of Kunming


title: IL_13_2


title: TS162_05_H3K27ac-CCS1477_6h_100nM


title: IL_13_1


title: IonXpress_005: Blue wavelenght 1h'

source_name: 3D skin samples exposed for 1 hour for 4 sequential days simulating chronic exposure

value: 3D equivalent human skin

value: blue 1h'


title: RNA_seq _X2