title: 7F_M_2680


title: 7F_M_2677

status: Public on Jul 06 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: GP

tag: age

tag: strain


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title: 7F_M_1462


title: 7F_M_1463


title: 7F_M_1464


title: 7F_M_1460


title: 7F_M_1465


title: 7F_M_1459


title: 7F_M_1461


title: 7F_M_1455


title: 7F_M_1453


title: 7F_M_1456


title: 7F_M_1451


title: 7F_M_1448


title: 7F_M_1452


title: 7F_M_1446


title: 7F_M_1454


title: 7F_M_1444


title: 7F_M_1445


title: 7F_M_1447


title: 7F_M_1438


title: 7F_M_1443


title: 7F_M_1457


title: 7F_M_1434


title: 7F_M_1436


title: 7F_M_1437


title: 7F_M_1429


title: 7F_M_1442


title: 7F_M_1439


title: 7F_M_1428


title: 7F_M_1430


title: 7F_M_1426


title: 7F_M_1435


title: 7F_M_1449


title: 7F_M_1450


title: 7F_M_1425


title: 7F_M_1424


title: 7F_M_1441


title: 7F_M_1422


title: 7F_M_1421


title: 7F_M_1423


title: 7F_M_1420


title: 7F_M_1440


title: 7F_M_1458


title: 7F_M_1433


title: 7F_M_1419


title: 7F_M_1432


title: 7F_M_1417


title: 7F_M_1427


title: 7F_M_1418


title: 7F_M_1416


title: 7F_M_1414


title: 7F_M_1415


title: 7F_M_1412


title: 7F_M_1409


title: 7F_M_1413


title: 7F_M_1405


title: 7F_M_1410


title: Cell216-253 Alpha and Beta Chains

first: Luc

last: Teyton

address: 10550 North Torrey Pines Road

department: Immunology and Microbiology

institute: Scripps Research

description: total RNA:TCR mRNA

library_source: transcriptomic

data_processing:
Raw sequencing files were processed using Bcl2Fastq, files were then passed through Trimmomatic and paired with Fastq, and then processed using custom R scripts
Once, TCRBeta and Alpha were separated by cell barcode first, then chain, sequences were then aligned to IMGT.
This data was then parsed to remove sequences that were unproductive. This final data was used for figure generation.
N/A
N/A
Assembly: Homo sapiens
Supplementary files format and content: GEO-AlphaChains_TCRSeq_Used_For_Analysis.csv: Contains the processed data from the TCR sequencing pipeline
Supplementary files format and content: GEO-BetaChains_TCRSeq_Used_For_Analysis.csv: Contains the processed data from the TCR sequencing pipeline
Library strategy: TCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were isolated via ficoll/density centrifugation
Detailed in Holt et al. (https://doi.org/10.1007/978-1-4939-7514-3_14)
Amplicon Sequencing: sequencing of TCR amplicons from single cells

treatment_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were stained with either DQ8-Ins12-20, DQ8-13021, DQ8-CP11 or DQ8-CP18 tetramers for 1 hour at 4C in the dark. The cells were then stained with surface antibodies for 30 minutes at 4C in the dark. Single tetramer positive CD4 T cells were then single cell sorted directly into lysis buffer.

tag: tissue

value: Blood

tag: cell line

tag: cell type

value: CD4 T cell

tag: cohort

value: Monitored

tag: treatment

value: dq8 tetramer_specificity:DQ8:_12-20_, or DQ8:_13-21_,or DQ8:CP11 or DQ8:CP18


title: 7F_M_1408


title: 7F_M_1402


title: 7F_M_1407


title: Cell279-294 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: Cell113-138 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: Cell254-278 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: 7F_M_1406


title: Cell182-215 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: 7F_M_1144


title: 7F_M_1403


title: 7F_M_1404


title: Cell156-181 Alpha and Beta Chains

description: total RNA:TCR mRNA

value: Established


title: Cell37-70 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: Cell139-155 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: 7F_M_1401


title: Cell94-112 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: Cell79-93 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: Cell1-36 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: 7F_M_1141


title: 7F_M_1145


title: Cell71-78 Alpha and Beta Chains

description: total RNA:TCR mRNA


title: 7F_M_1143


title: 7F_M_1142


title: siMAFB +IVIg+CL B1 12h

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 12 hours #1

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocyte-derived macrophages (at day 6 along the differentiation protocol) were transfected with MAF and MAFB-specific siRNA or control siRNA, kept in culture for 24 hours, and then stimulated (or not) with IVIg (10mg/ml) and CL264 (1 microgram/ml). After 4 and 12 hours, cells were lysed and RNA isolated for transcriptional analysis.

value: Monocyte-derived M-CSF macrophages

tag: knockdown

value: MAFB-specific siRNA

value: Exposed to IVIg and CL264


title: siMAFB +IVIg B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 12 hours #5

value: Exposed to IVIg


title: siMAFB+IVIg+CL B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 12 hours #4


title: 7F_M_1139


title: 7F_M_1137


title: siMAFB+IVIg B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 12 hours #4


title: 7F_M_1140


title: siMAFB +IVIg B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 12 hours #1


title: 7F_M_1135


title: siMAFB +IVIg+CL B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 12 hours #5


title: siMAFB +CL B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 12 hours #5

value: Exposed to CL264


title: 7F_M_1138


title: 7F_M_1134


title: siMAFB+CL B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 12 hours #4


title: 7F_M_1133


title: 7F_M_1136


title: 7F_M_1132


title: siMAFB-B5 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #5

value: untreated


title: siMAFB +CL B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 12 hours #1


title: 7F_M_1131


title: 7F_M_1130


title: SLE_2

type: genomic

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

hyb_protocol: not provided

scan_protocol: not provided

data_processing: DNA methylation analysis was performed using the GenomeStudio (v2011.1) Methylation Module (v1.9.0; Illumina, San Diego, CA). Red and green channel values were normalized to internal, non-CpG control probes and array background subtracted using unhybridized in-array control probes. The normalization setting used in GenomeStudio was controls. Methylation beta values (β) were calculated on a scale of 0% to 100% methylation using normalized, background-corrected signal values.

label: Cy5 and Cy3

source_name: Keratinocyte DNA

label_protocol: not provided

growth_protocol: 6-mm punch skin biopsy samples were taken from lupus patients with a history of cutaneous lupus erythematosus and healthy control subjects. Biopsy samples were placed in Hank's balanced salt solution overnight and then incubated in basal media (100 mmol/L NaCl, 22.5 mmol/L HEPES, 7.6 mmol/L glucose, 2.25 mmol/L KCl, 0.75 mmol/L Na2HPO4) with 0.17% trypsin for 2 hours at 37 °C. Keratinocytes were then cultured in keratinocyte-specific medium (Epilife, Gibco Thermo-Fisher Scientific, Waltham, MA, with keratinocyte growth supplement) and carefully passaged at 60% confluency to avoid differentiation. Keratinocyte culture purity was confirmed by morphology.

extract_protocol: At passage two, DNA was collected from approximately 3x10^5 cells for methylation studies. DNA was extracted from primary keratinocytes using the DNeasy Blood and Tissue Kit (Qiagen, MD, USA) according to manufacturer’s instructions. DNA concentration was measured using a Qubit dsDNA Broad Range Assay Kit (Thermo Fisher Scientific, MA, USA). DNA was bisulfite converted for DNA methylation studies using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA) using the provided protocol and thermocycler settings recommended by Zymo for Illumina DNA methylation array samples included in the product literature.

value: keratinocyte

tag: disease

value: systemic lupus erythematosus

tag: Sex

value: Female

tag: race/ethnicity

value: White, Non-Hispanic


title: 7F_M_1431


title: siMAF +IVIg+CL B5 12h

description: Only the R2 file was submitted. The R1 file was corrupted and there was no replacement.

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIgCL264 for 12 hours #5

value: MAF-specific siRNA


title: 7F_M_1129

value: GP


title: SLE_5

value: Male

value: Asian


title: siMAFB-B4 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #4


title: siMAF +IVIg B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 12 hours #5


title: siMAF +IVIg+CL B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg+CL264 for 12 hours #4


title: SLE_1


title: siMAF +IVIg B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 12 hours #4


title: 7F_M_1126

source_name: C57BL/6J Male P56 Mouse Brain


title: 7F_M_1127


title: siMAF +IVIg+CL-B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg+CL264 for 12 hours #1


title: siMAFB-B1 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #1


title: SLE_6


title: siMAF +IVIg-B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 12 hours #1


title: 7F_M_1125


title: 7F_M_1124


title: Control_6

value: healthy control


title: 7F_M_1123


title: Control_1


title: SLE_3

value: Black


title: 7F_M_1121


title: 7F_M_1122


title: SLE_4

value: White, Hispanic


title: siMAF +CL B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 12 hours #1

value: Monocyte-derived M-CSF macrophages


title: Control_3


title: Control_5


title: 7F_M_1119


title: siCNT +IVIg+CL-B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 12 hours #1

value: Control siRNA


title: 7F_M_1120


title: siMAF +CL B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 12 hours #4


title: siCNT +IVIg+CL-B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 12 hours #4

value: Exposed to IVIg and CL264


title: siMAF-B1 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #1


title: siMAF +CL B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 12 hours #5


title: Control_4


title: 7F_M_1114


title: 7F_M_1118


title: siMAF-B5 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #5


title: siMAF-B4 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #4


title: 7F_M_1117


title: siCNT +IVIg-B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 12 hours #5

value: Exposed to IVIg


title: siCNT +IVIg-B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 12 hours #4


title: 7F_M_1116


title: 7F_M_1112


title: 7F_M_1111


title: 7F_M_1115


title: 7F_M_1113


title: siCNT +IVIg+CL-B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 12 hours #5


title: 7F_M_1109


title: Control_2

source_name: Keratinocyte DNA


title: siCNT +CL B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 12 hours #4

value: Exposed to CL264


title: siCNT +CL B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 12 hours #5


title: siCNT +IVIg-B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 12 hours #1


title: siCNT-B5 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA #5

value: untreated


title: 7F_M_1108

source_name: C57BL/6J Male P56 Mouse Brain


title: siCNT-B4 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA #4


title: 7F_M_1110


title: siCNT-B1 12h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a control siRNA #1


title: 7F_M_1105


title: 7F_M_1104


title: siMAFB +IVIg+CL B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 4 hours #5

value: MAFB-specific siRNA


title: 7F_M_1107


title: 7F_M_1106


title: siMAFB+IVIg+CL B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 4 hours #4


title: siCNT +CL B1 12h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 12 hours #1


title: siMAFB +IVIg+CL B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg+CL264 for 4 hours #1


title: siMAFB+IVIg B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 4 hours #4


title: 7F_M_1103


title: 7F_M_1101


title: siMAFB +IVIg B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 4 hours #5


title: 7F_M_1096


title: 7F_M_1100


title: siMAFB +CL B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 4 hours #5


title: 7F_M_1097


title: 7F_M_1099


title: 7F_M_1102


title: siMAFB +IVIg B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to IVIg for 4 hours #1


title: 7F_M_1095


title: siMAFB +CL B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 4 hours #1


title: siMAFB-B5 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #5


title: siMAFB-B4 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #4


title: 7F_M_1098


title: 7F_M_1091


title: siMAF +IVIg B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 4 hours #5


title: 7F_M_1128


title: siMAF +IVIg+CL B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIgCL264 for 4 hours #5


title: 7F_M_1093


title: siMAF +IVIg+CL-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg+CL264 for 4 hours #1


title: siMAFB+CL B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA and exposure to CL264 for 4 hours #4


title: 7F_M_1090

source_name: C57BL/6J Male P56 Mouse Brain


title: siMAFB-B1 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAFB-specific siRNA #1


title: siMAF +IVIg+CL B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg+CL264 for 4 hours #4


title: siMAF +IVIg B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 4 hours #4


title: 7F_M_1094


title: 7F_M_1088


title: 7F_M_1089


title: siMAF +IVIg-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to IVIg for 4 hours #1


title: 7F_M_1086


title: 7F_M_1087


title: siMAF +CL B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 4 hours #5


title: siMAF +CL-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 4 hours #1


title: siMAF-B5 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #5


title: 7F_M_1085


title: 7F_M_1092


title: siMAF +CL B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA and exposure to CL264 for 4 hours #4


title: siMAF-B4 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #4


title: 7F_M_1083


title: 7F_M_1082


title: 7F_M_954


title: 7F_M_1084


title: 7F_M_952


title: siCNT +IVIg+CL-B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 4 hours #5


title: 7F_M_953


title: siCNT +IVIg+CL-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 4 hours #1


title: siCNT +IVIg+CL-B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg+CL264 for 4 hours #4


title: 7F_M_951


title: siCNT +IVIg-B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 4 hours #5


title: 7F_M_950


title: siCNT +IVIg-B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 4 hours #4


title: siCNT +IVIg-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to IVIg for 4 hours #1


title: 7F_M_949


title: 7F_M_948


title: 7F_M_947


title: siCNT +CL-B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #4


title: siCNT +CL-B1 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #1


title: 7F_M_945

source_name: C57BL/6J Male P56 Mouse Brain


title: siCNT-B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA #5


title: siMAF-B1 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a MAF-specific siRNA #1


title: siCNT-B1 4h

source_name: RNA from monocyte-derived macrophages 24 hours after transfection with a control siRNA #1


title: 7F_M_943


title: 7F_M_946


title: 7F_M_941


title: 7F_M_940


title: 7F_M_939


title: 7F_M_938


title: siCNT +CL-B5 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #5


title: siCNT-B4 4h

source_name: RNA from  monocyte-derived macrophages 24 hours after transfection with a control siRNA #4


title: 7F_M_937


title: 7F_M_934


title: 7F_M_936


title: 7F_M_933


title: 7F_M_931


title: 7F_M_932


title: 7F_M_929


title: 7F_M_942


title: 7F_M_944


title: 7F_M_928


title: 7F_M_927


title: 7F_M_935


title: 7F_M_926


title: 7F_M_925


title: 7F_M_923


title: 7F_M_924


title: 7F_M_930


title: 7F_M_919


title: 7F_M_918


title: 7F_M_917


title: 7F_M_916


title: 7F_M_921


title: 7F_M_915


title: 7F_M_914


title: 7F_M_920


title: 7F_M_912


title: 7F_M_913


title: 7F_M_911


title: 7F_M_910


title: 7F_M_908


title: genomic DNA from Liver from ShamYoungIso4

city: Boston

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Young isochronic sham parabiosis
206604260006_R04C01

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: For mammalian microarray analysis, raw methylation data were first normalized and beta values were calculated using the SeSAMe R package.

source_name: Liver from ShamYoungIso4

label_protocol: Standard Illumina protocol

growth_protocol: This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.

extract_protocol: DNA was isolated from whole blood using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Both mice were anesthetized by isoflurane and opposing lateral sides of the abdomen were sutured from elbow to knee (the same distance as standard parabiosis) to create a physical attachment between the two mice. Importantly, for the mock parabiosis, no incisions were made to the skin or fascia prior to attachment thus preventing the generation of shared vasculature. We confirmed separation of circulation by testing the blood glucose response in both parabionts to an IP glucose bolus delivered to one of the partners. All mock parabiosis pairs were attached for 5 weeks.

tag: age (years)

tag: mouse strain

value: C57BL/6 WT

tag: mouse id

value: Liver


title: genomic DNA from Liver from ShamYoungIso1

description:
Young isochronic sham parabiosis
206604260011_R04C01

source_name: Liver from ShamYoungIso1

value: Female


title: genomic DNA from Blood from ShamYoungIso5

description:
Young isochronic sham parabiosis
206604260005_R06C01

source_name: Blood from ShamYoungIso5

value: Blood


title: genomic DNA from Blood from ShamYoungIso3

description:
Young isochronic sham parabiosis
206604260005_R03C02

source_name: Blood from ShamYoungIso3


title: genomic DNA from Liver from ShamYoungIso5

description:
Young isochronic sham parabiosis
206604260011_R05C02

source_name: Liver from ShamYoungIso5


title: genomic DNA from Liver from ShamYoungIso3

description:
Young isochronic sham parabiosis
206604260006_R06C02

source_name: Liver from ShamYoungIso3


title: genomic DNA from Liver from ShamYoungHet1

description:
Young heterochronic sham parabiosis
206604260006_R06C01

source_name: Liver from ShamYoungHet1


title: genomic DNA from Liver from ShamOldIso3

description:
Old isochronic sham parabiosis
206604260006_R04C02

source_name: Liver from ShamOldIso3


title: genomic DNA from Blood from ShamOldIso1

description:
Old isochronic sham parabiosis
206604260006_R05C02

source_name: Blood from ShamOldIso1


title: genomic DNA from Blood from ShamYoungIso1

description:
Young isochronic sham parabiosis
206604260003_R04C01

source_name: Blood from ShamYoungIso1


title: 7F_M_909

value: GP


title: genomic DNA from Liver from ShamYoungIso2

description:
Young isochronic sham parabiosis
206604260005_R05C02

source_name: Liver from ShamYoungIso2


title: genomic DNA from Liver from ShamOldIso6

description:
Old isochronic sham parabiosis
206604260003_R01C01

source_name: Liver from ShamOldIso6


title: genomic DNA from Liver from ShamOldIso4

description:
Old isochronic sham parabiosis
206604260011_R02C01

source_name: Liver from ShamOldIso4


title: 7F_M_905

source_name: C57BL/6J Male P56 Mouse Brain


title: 7F_M_904


title: genomic DNA from Liver from ShamYoungHet4

description:
Young heterochronic sham parabiosis
206604260003_R04C02

source_name: Liver from ShamYoungHet4


title: genomic DNA from Liver from ShamYoungHet2

description:
Young heterochronic sham parabiosis
206604260006_R03C02

source_name: Liver from ShamYoungHet2


title: genomic DNA from Liver from ShamYoungHet5

description:
Young heterochronic sham parabiosis
206604260011_R03C02

source_name: Liver from ShamYoungHet5


title: genomic DNA from Blood from ShamOldIso2

description:
Old isochronic sham parabiosis
206604260003_R05C02

source_name: Blood from ShamOldIso2


title: genomic DNA from Liver from ShamOldIso5

description:
Old isochronic sham parabiosis
206604260005_R03C01

source_name: Liver from ShamOldIso5


title: genomic DNA from Liver from ShamYoungHet3

description:
Young heterochronic sham parabiosis
206604260006_R01C01

source_name: Liver from ShamYoungHet3


title: 7F_M_906


title: 7F_M_903


title: genomic DNA from Blood from ShamOldIso4

description:
Old isochronic sham parabiosis
206604260011_R01C02

source_name: Blood from ShamOldIso4


title: genomic DNA from Blood from ShamYoungIso2

description:
Young isochronic sham parabiosis
206604260005_R04C01

source_name: Blood from ShamYoungIso2


title: genomic DNA from Blood from ShamOldIso3

description:
Old isochronic sham parabiosis
206604260005_R02C02

source_name: Blood from ShamOldIso3


title: 7F_M_907


title: genomic DNA from Liver from ShamOldIso2

description:
Old isochronic sham parabiosis
206604260005_R01C02

source_name: Liver from ShamOldIso2


title: genomic DNA from Blood from ShamYoungIso4

description:
Young isochronic sham parabiosis
206604260005_R01C01

source_name: Blood from ShamYoungIso4


title: genomic DNA from Liver from ShamOldIso1

description:
Old isochronic sham parabiosis
206604260003_R01C02

source_name: Liver from ShamOldIso1


title: 7F_M_901


title: 7F_M_902


title: 7F_M_900


title: genomic DNA from Blood from ShamOldIso5

description:
Old isochronic sham parabiosis
206604260003_R03C01

source_name: Blood from ShamOldIso5


title: genomic DNA from Blood from ShamOldHet2

description:
Old heterochronic sham parabiosis
206604260011_R03C01

source_name: Blood from ShamOldHet2


title: 7F_M_899


title: 7F_M_896


title: 7F_M_897


title: eHAP, control for SF1_265 target site

city: San Francisco

first: Irene

last: Beusch

state: California

address: 600 16th Street

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
fastq.gz sequencing read files were directly used to quantify editing at the base editing window using CRISPResso2 v.2.1
CRISPRESSO2 was run with the following parameters: [--exclude_bp_from_left 18 --exclude_bp_from_right 0 --quantification_window_center -12 --quantification_window_size 15 --min_average_read_quality 30 --default_min_aln_score 60 --plot_window_size 20 --base_editor_output --output_folder 20210531_pos -p 12].
For analysis we used the “Alleles_frequency_table_around_[sgRNA].txt” output files or in the single case where editing occurred far outside the editing window “Alleles_frequency_table.txt” was used for information extraction.
Assembly: hg38
Supplementary files format and content: tab-delimited textfile corresponding to CRISPRESSO2 output file “Alleles_frequency_table_around_[sgRNA].txt”
Library strategy: sequencing of genomic loci corresponding to target site of CRISPR-Cas9 base editing

source_name: eHAP

growth_protocol: All cell lines were maintained at 37 °C with 5% CO2 and were regularly tested negative for mycoplasma infection. Cells were passaged every 2-3 days.  Human eHAP cell lines and derivatives thereof were cultured in IMDM (with L-glutamine, with HEPES; Cytiva #SH30228), supplemented with 10% FBS and 1:100 penicillin/streptomycin. eHAP cell lines were at all times maintained at sub-confluent conditions and ploidy was regularly assessed with flow cytometry.

extract_protocol:
Genomic DNA was extracted using QuickExtractTM DNA Extraction Solution (Lucigen #QE09050) according to the manufacturer's protocol.
1 µl (qsp. >200 cells) and was used for target site amplification using a 2-step PCR. In addition, each reaction contained 10 µl NEBnext Ultra II Q5 master mix as well as 1 µM of each forward and reverse primer. Primer pairs for PCR 1 were selected such that forward annealing primer is not closer than 7 nt to editing window position 1  but still allowing that 75 sequencing cycles will read the sequence. Primers were verified to anneal to a single position within the genome using BLAT11 and tested before use. Primers for PCR 1 (12 cycles) were flanked for the forward primer by: 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ and for the reverse primer by 5′-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’. 1.5 µl of PCR 1 were used as template for PCR 2 (14 cycles) and used forward primers 5′-AATGATACGGCGACCACCGAGATCTACAC-NNNNNNNN-ACACTCTTTCCCTACACGAC-3’ (compatible to Illumina i5) and reverse primers 5′-CAAGCAGAAGACGGCATACGAGAT- NNNNNNNN- GTGACTGGAGTTCAGACGTG-3’ (compatible to Illumina i7), with both containing 8N barcodes for multiplexing.  Primers were removed after the second PCR step with AMPure XP Reagent (Beckman #A63882). Library was quantified (QuantiFluor® dsDNA System; Promega #E2670) before being pooled (10 fmol per sample) for each time point & condition, run on 8% TBE-PAGE gel, then size selected for a range of 250-500 bp. Pooled libraries were then run on Bioanalyzer High Sensitivity DNA Kit, Agilent #5067-4626) before final pooling and subsequent run on a MiniSeq Sequencing System using the Miniseq High Output Kit (75 cycles) (Illumina #FC-420-1001) with a 10% of phiX spike-in.

treatment_protocol: Lentivirus carrying individual sgRNAs was used to transduce 2e5 eHAP FNLS cells at MOI 0.3 in a 6-well dish. After puromycin selection on day 6 (= t0), 2x 11000 cells were seeded in 96-well plates and split into treatment arms the next day (DMSO vs. 2 nM PB). Cells were propagated and harvested at t8 and t15 for gDNA extraction.

value: eHAP

tag: genotype

value: expressing FNLS

value: no base editing, no treatment


title: eHAP, control for SF3B3_378 target site


title: 7F_M_895


title: 7F_M_894


title: eHAP, control for HSPA8_107 target site


title: eHAP FNLS + sgRNA HSPA8_107, no treatment

value: base editing, control, no treatment


title: 7F_M_891


title: eHAP, control for DHX16_1 target site


title: 7F_M_898


title: 7F_M_893


title: eHAP FNLS + sgRNA DHX16_1, no treatment


title: eHAP FNLS + sgRNA SF1_265, no treatment


title: 7F_M_892


title: eHAP FNLS + sgRNA SF3B3_378, no treatment


title: eHAP, control for CDC40_10 target site


title: genomic DNA from Blood from ShamOldHet3

description:
Old heterochronic sham parabiosis
206604260006_R02C02

source_name: Blood from ShamOldHet3


title: 7F_M_826

source_name: C57BL/6J Male P56 Mouse Brain


title: eHAP FNLS + sgRNA CDC40_10, no treatment


title: 7F_M_825


title: eHAP, control for CDC40_13 target site


title: genomic DNA from Blood from ShamOldHet4

description:
Old heterochronic sham parabiosis
206604260006_R05C01

source_name: Blood from ShamOldHet4


title: eHAP FNLS + sgRNA CDC40_13, no treatment


title: 7F_M_822


title: 7F_M_823


title: eHAP, control for CACTIN_117 target site


title: genomic DNA from Liver from ShamOldHet4

description:
Old heterochronic sham parabiosis
206604260011_R04C02

source_name: Liver from ShamOldHet4


title: eHAP FNLS + sgRNA CACTIN_117, no treatment


title: genomic DNA from Blood from ShamOldHet1

description:
Old heterochronic sham parabiosis
206604260006_R03C01

source_name: Blood from ShamOldHet1


title: 7F_M_821


title: 7F_M_819


title: eHAP FNLS + sgRNA USP39_213, no treatment


title: genomic DNA from Liver from ShamOldHet1

description:
Old heterochronic sham parabiosis
206604260006_R02C01

source_name: Liver from ShamOldHet1


title: eHAP, control for SF3B3_511 target site


title: genomic DNA from Liver from ShamOldHet5

description:
Old heterochronic sham parabiosis
206604260005_R02C01

source_name: Liver from ShamOldHet5


title: 7F_M_820


title: eHAP FNLS + sgRNA SF3B3_511, no treatment


title: genomic DNA from Liver from ShamOldHet2

description:
Old heterochronic sham parabiosis
206604260011_R01C01

source_name: Liver from ShamOldHet2


title: eHAP, control for USP39_213 target site


title: 7F_M_817


title: eHAP, control for SF3B3_55 target site


title: 7F_M_816


title: 7F_M_824


title: 7F_M_815


title: genomic DNA from Blood from ShamOldHet5

description:
Old heterochronic sham parabiosis
206604260003_R06C01

source_name: Blood from ShamOldHet5


title: genomic DNA from Liver from ShamOldHet3

description:
Old heterochronic sham parabiosis
206604260003_R03C02

source_name: Liver from ShamOldHet3


title: eHAP FNLS + sgRNA SF3B3_55, no treatment


title: eHAP FNLS + sgRNA SF3A3_69, no treatment


title: 7F_M_813


title: 7F_M_812


title: eHAP, control for SF3A1_121 target site


title: eHAP FNLS + sgRNA SF3A1_135, no treatment


title: 7F_M_814


title: eHAP, control for SF3A3_69 target site


title: 7F_M_809


title: eHAP FNLS + sgRNA SF3A1_135, DMSO, 8 days

value: base editing, DMSO, 8 days


title: 7F_M_810


title: eHAP FNLS + sgRNA SF3A1_121, no treatment


title: eHAP, control for SF3A1_283 target site


title: 7F_M_806


title: 7F_M_807


title: 7F_M_804


title: 7F_M_805


title: eHAP, control for PUF60_139 target site


title: eHAP FNLS + sgRNA PUF60_139, no treatment


title: 7F_M_803


title: eHAP, control for PUF60_315 target site


title: 7F_M_802


title: eHAP, control for PRPF6_291 target site


title: 7F_M_800


title: 7F_M_801


title: eHAP FNLS + sgRNA PRPF6_291, no treatment


title: 7F_M_818


title: 7F_M_811


title: eHAP, control for SF3A1_135 target site


title: 7F_M_799


title: 7F_M_798


title: eHAP FNLS + sgRNA SF3A1_283, no treatment


title: 7F_M_797


title: eHAP, control for DHX35_31 target site


title: 7F_M_808


title: 7F_M_795


title: eHAP FNLS + sgRNA PUF60_315, no treatment


title: 7F_M_792


title: eHAP FNLS + sgRNA DHX15_228, no treatment


title: eHAP FNLS + sgRNA DDX5_182, no treatment


title: 7F_M_793


title: eHAP, control for DDX5_182 target site


title: 7F_M_791


title: 7F_M_796


title: eHAP, control for DDX46_78 target site


title: 7F_M_794


title: 7F_M_788


title: eHAP, control for DNAJC8_28 target site


title: 7F_M_787


title: eHAP FNLS + sgRNA DNAJC8_28, no treatment


title: eHAP FNLS + sgRNA DDX46_78, no treatment


title: eHAP FNLS + sgRNA DHX35_31, no treatment


title: eHAP, control for CDC40_65 target site


title: eHAP, control for DHX15_228 target site


title: eHAP FNLS + sgRNA CDC40_53, no treatment


title: 7F_M_786


title: eHAP, control for CDC40_139 target site


title: eHAP FNLS + sgRNA CDC40_65, no treatment


title: 7F_M_785


title: eHAP FNLS + sgRNA CDC40_139, no treatment


title: eHAP, control for CDC40_53 target site


title: 7F_M_784


title: eHAP, control for CDC40_47 target site


title: 7F_M_783


title: 7F_M_790


title: eHAP FNLS + sgRNA CDC40_47, no treatment


title: eHAP FNLS + sgRNA U2AF2_239, no treatment


title: 7F_M_781


title: 7F_M_780


title: 7F_M_779


title: 7F_M_782


title: eHAP FNLS + sgRNA SNRPB_48, no treatment


title: eHAP, control for U2AF2_239 target site


title: 7F_M_777


title: eHAP FNLS + sgRNA SF3B1_166, DMSO, 15 days

value: DMSO, 15 days


title: eHAP, control for SF3B1_166 target site


title: 7F_M_776


title: eHAP FNLS + sgRNA SF3B1_166, 2 nM PB, 15 days

value: 2 nM PB, 15 days


title: 7F_M_775


title: eHAP FNLS + sgRNA SF3B1_166, no treatment


title: 7F_M_773


title: 7F_M_789


title: eHAP FNLS + sgRNA PRPF6_488, no treatment


title: 7F_M_774


title: 7F_M_771


title: eHAP FNLS + sgRNA SF3B1_166, 2 nM PB, 8 days

value: base editing, 2 nM PB, 8 days


title: eHAP, control for PRPF6_488 target site


title: eHAP FNLS + sgRNA SF3B1_166, DMSO, 8 days


title: 7F_M_772


title: eHAP, control for PRPF31_384 target site


title: eHAP FNLS + sgRNA PRPF31_384, no treatment


title: 7F_M_770


title: 7F_M_768


title: 7F_M_767


title: eHAP FNLS + sgRNA MTREX_170, no treatment


title: eHAP, control for MTREX_170 target site


title: 7F_M_766


title: eHAP, control for SNRPB_48 target site


title: 7F_M_778


title: 7F_M_765


title: eHAP, control for PRCC_257 target site


title: eHAP FNLS + sgRNA LUC7L3_140, no treatment


title: 7F_M_763


title: eHAP, control for LUC7L3_140 target site


title: 7F_M_762


title: eHAP, control for ISY1_91 target site


title: eHAP FNLS + sgRNA PRCC_257, no treatment


title: 7F_M_761


title: eHAP FNLS + sgRNA CWC25_234, no treatment


title: 7F_M_759


title: eHAP, control for SUGP1_188 target site


title: eHAP, control for CWC25_234 target site


title: 7F_M_758


title: 7F_M_757


title: eHAP FNLS + sgRNA SUGP1_188, 2 nM PB, 15 days


title: eHAP FNLS + sgRNA SUGP1_188, DMSO, 15 days


title: 7F_M_760


title: eHAP FNLS + sgRNA SUGP1_188, 2 nM PB, 8 days


title: 7F_M_755


title: 7F_M_756


title: 7F_M_754


title: eHAP FNLS + sgRNA SUGP1_238, 2 nM PB, 15 days


title: eHAP FNLS + sgRNA SUGP1_188, no treatment


title: eHAP, control for SUGP1_238 target site


title: eHAP FNLS + sgRNA SUGP1_188, DMSO, 8 days


title: 7F_M_753


title: 7F_M_769


title: 7F_M_751


title: 7F_M_748


title: 7F_M_750


title: 7F_M_752


title: 7F_M_749


title: eHAP FNLS + sgRNA SUGP1_238, no treatment


title: eHAP FNLS + sgRNA SUGP1_238, DMSO, 15 days


title: eHAP FNLS + sgRNA ISY1_91, no treatment


title: eHAP FNLS + sgRNA SUGP1_238, 2 nM PB, 8 days


title: 7F_M_747


title: eHAP FNLS + sgRNA SF1_204, no treatment


title: eHAP, control for SF1_204 target site


title: 7F_M_746


title: 7F_M_742


title: 7F_M_743


title: eHAP, control for PHF5A_26 target site


title: 7F_M_739


title: eHAP, control for SF1_508 target site


title: eHAP FNLS + sgRNA PHF5A_26, 2 nM PB, 15 days


title: 7F_M_741


title: eHAP FNLS + sgRNA PHF5A_26, DMSO, 15 days


title: eHAP FNLS + sgRNA PHF5A_26, no treatment


title: eHAP FNLS + sgRNA PHF5A_26, DMSO, 8 days


title: 7F_M_738


title: 7F_M_737


title: eHAP FNLS + sgRNA PHF5A_26, 2 nM PB, 8 days


title: 7F_M_744


title: eHAP, control for PHF5A_21 target site


title: 7F_M_736


title: 7F_M_745


title: 7F_M_735


title: eHAP FNLS + sgRNA PHF5A_21, 2 nM PB, 15 days


title: eHAP FNLS + sgRNA PHF5A_21, DMSO, 15 days


title: 7F_M_732


title: eHAP FNLS + sgRNA PHF5A_21, no treatment


title: eHAP FNLS + sgRNA SF1_508, no treatment


title: eHAP FNLS + sgRNA SUGP1_238, DMSO, 8 days


title: eHAP FNLS + sgRNA PHF5A_21, 2 nM PB, 8 days


title: eHAP FNLS + sgRNA PHF5A_21, DMSO, 8 days


title: 7F_M_730


title: 7F_M_729


title: 7F_M_740


title: eHAP, control for PHF5A_6 target site


title: eHAP FNLS + sgRNA PHF5A_6, no treatment


title: eHAP FNLS + sgRNA PHF5A_6, 2 nM PB, 15 days


title: 7F_M_728


title: 7F_M_727


title: 7F_M_726


title: eHAP FNLS + sgRNA PHF5A_6, DMSO, 15 days


title: 7F_M_724


title: 7F_M_723


title: 7F_M_734


title: eHAP, control for PHF5A_7 target site


title: eHAP FNLS + sgRNA PHF5A_6, 2 nM PB, 8 days


title: 7F_M_722


title: 7F_M_725


title: eHAP FNLS + sgRNA PHF5A_7, 2 nM PB, 15 days


title: eHAP FNLS + sgRNA PHF5A_6, DMSO, 8 days


title: eHAP FNLS + sgRNA PHF5A_7, DMSO, 15 days


title: 7F_M_721


title: 7F_M_720


title: eHAP FNLS + sgRNA PHF5A_7, no treatment


title: 7F_M_719


title: 7F_M_731


title: 7F_M_733


title: eHAP FNLS + sgRNA PHF5A_7, 2 nM PB, 8 days


title: eHAP FNLS + sgRNA PHF5A_7, DMSO, 8 days


title: 7F_M_717


title: 7F_M_718


title: eHAP FNLS + sgRNA PHF5A_47, 2 nM PB, 15 days


title: 7F_M_716


title: 7F_M_715


title: eHAP, control for PHF5A_47 target site


title: 7F_M_714


title: eHAP FNLS + sgRNA PHF5A_47, DMSO, 15 days


title: 7F_M_712


title: HC382HC335, snRNAseq

city: Auckland

first: Andrew

last: Jiang

address: 3 Symonds Street

country: New Zealand

institute: The University of Auckland

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.0.0 pipeline with STAR v2.7.2a (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Sequencing ready libraries were sequenced on HiSeq Xten platform to generate on average 150 bp paired end reads. Alignment of reads was performed using the CellRanger v7.0.0 pipeline with STAR v2.7.2a to the sheep Oar_rambouillet_v1.0 reference genome and annotation (Ensembl release 107).
Assembly: Oar_Rambouilletv1.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Ovis aries

source_name: Striatum

extract_protocol:
Nuclei were extracted from frozen anterior dorsal ventral striatal (Figure 1) tissue utilising an adapted protocol from Krishnaswami et al., 2016 33. Briefly, approximately 50-100 mg of brain tissue was transferred to a dounce homogenizer containing 1mL homogenization buffer, HB (250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris buffer pH 8.0, 1µM DTT, 1X protease inhibitor (Sigma), 0.4 U/µL RNaseIn (ThermoFisher Scientific), 0.2 U/µL Superasein (ThermoFisher Scientific), 0.1 % Triton X-100). Tissue was homogenised using 5 strokes with the loose dounce pestle A, followed by 10-15 strokes of tight dounce pestle B. The homogenate was filtered through a 40 µm strainer into 5 mL Eppendorf tubes and centrifuged at 1000 rcf (4 oC) for 8 minutes. The supernatant was removed, and the pellet was resuspended in 250 µL of HB. A 50% - 29% iodixanol gradient (OptiPrep™ Density Gradient Medium, Sigma) was prepared to allow removal of the myelin layer. 250 µL of 50 % iodixanol was added to the nuclei-HB mixture and slowly layered on top of 500 µL of 29 % iodixanol in a new Eppendorf tube. The resultant gradient was centrifuged at 13,000 rcf (4oC) for 40 minutes. The supernatant and myelin was removed and the purified nuclei pellet was resuspended in 1 mL PBS, 1 % BSA, 0.2 U/µl RNAse inhibitor. 5 µL of resuspended nuclei was stained with 5 µL trypan blue and the quality and number of nuclei was assessed using the Countess II FL Automated Cell Counter (ThermoFisher Scientific).
Single nuclei RNA libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) as per manufacturer’s instructions.

value: Brain

value: Striatum

value: 5 year old


title: 7F_M_710


title: 7F_M_709


title: eHAP FNLS + sgRNA PHF5A_47, 2 nM PB, 8 days


title: HC373HC337, snRNAseq

description: 10x Genomics


title: 7F_M_711


title: HD372HD317, snRNAseq

description: 10x Genomics


title: HD377HD339, snRNAseq

description: 10x Genomics


title: 7F_M_713


title: HC334,snRNAseq

description: 10x Genomics


title: 7F_M_705


title: HD376HD383, snRNAseq

description: 10x Genomics


title: 7F_M_708


title: HC357, snRNAseq

description: 10x Genomics


title: 7F_M_703


title: Sample 4_day6

city: Ann Arbor

first: Yue

last: Liu

address: 2350 Hayward St

institute: University of Michigan

data_processing:
Illumina NovaSeq-6000 for basecalling
10x Genomics Cell Ranger pipeline (version 3.1.0) for barcoding, alignment, filtering
Assembly: GRCh38
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix. RDS file is generated using Seurat, including integrated data of day2, day3, day4, and day6.

source_name: hPSC-based somite formation model

extract_protocol:
somite formation models were dissociated into single cells using accutase. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v2). The libraries were sequenced on Illumina NovaSeq-6000 with paired-end sequencing (One sample per flow cell).

tag: timepoint

tag: batch

value: hPSC-based somite formation model


title: 7F_M_704

tag: brain region

tag: age


title: eHAP FNLS + sgRNA PHF5A_47, no treatment


title: eHAP FNLS + sgRNA PHF5A_47, DMSO, 8 days


title: Sample 3_day4


title: 7F_M_701

tag: strain


title: 7F_M_700


title: Sample 1_day2


title: Control LNCaP, androgen deprived, + R1881, rep 3

city: New York

first: Michael

last: Garabedian

state: NY

address: 500 First Ave

institute: NYU School of Medicine

data_processing:
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt. Quality scores were assessed using FastQC. Reads were aligned to the Homo sapiens genome build hg19 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several databases were referenced for enrichment analysis, including Interpro, NCBI, KEGG, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: text file includes nomalized counts for each sample

source_name: Control  LNCaP

growth_protocol: LNCaP cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Hyclone; Fisher Scientific) and 1% penicillin-streptomycin (Cellgro; Mediatech, Inc.)  For assays under androgen deprivation, cells were cultured in androgen-depleted RPMI: phenol red- and L-glutamine-free RPMI-1640 supplemented with 10% FBS dextran charcoal-stripped of androgens (c-FBS, Hyclone) and 1% L-glutamine (Cellgro Mediatech, Inc.).  Cells were cultured on poly-d-lysine-coated plates.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen).
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina with polyA selection

treatment_protocol: Cells were with 10 nM R1881 or ethanol vehicle for 16 hours

tag: cell line

value: Control  LNCaP

value: prostate


title: Control LNCaP, androgen deprived, + R1881, rep 2

tag: cell type


title: 7F_M_699


title: 7F_M_707


title: 7F_M_698


title: Control LNCaP, androgen deprived, Vehicle, rep 3

value: Vehicle (ETOH)


title: 7F_M_697


title: Control LNCaP, androgen deprived, Vehicle, rep 2


title: Control LNCaP, androgen deprived, Vehicle,  rep 1


title: Control LNCaP, androgen deprived, + R1881,  rep 1


title: 7F_M_693


title: 7F_M_695


title: 7F_M_692


title: canonical MED19 LNCaP, androgen deprived, + R1881, rep 1

source_name: Canonical MED19-LNCaP

value: Canonical MED19-LNCaP


title: 7F_M_696

value: GP


title: 7F_M_691


title: canonical MED19 LNCaP, androgen deprived, vehicle, rep 2


title: 7F_M_694


title: Sample 2_day3


title: canonical MED19 LNCaP, androgen deprived, vehicle ,rep 1


title: 7F_M_690


title: 7F_M_689


title: 7F_M_702


title: 7F_M_688


title: LI7_2

city: shanghai

first: Lilei

last: Lv

address: No.518 Ziyue Road

country: China

institute: Shanghai veterinary research institute

data_processing:
Quality control Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Reads mapping The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Expression analysis: we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Differential expression analysis: Then difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, we used R language Pheatmap (v1.0.12) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Enrichment analysis: we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO (v2.50.0) to perform GO enrichment analysis on the differential genes (all DEGs / up DEGs / down DEGs), calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler(v4.6.0) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05. Gene Set Enrichment Analysis (GSEA) (v4.1.0) tool was used for GSEA enrichment analysis of all genes, and GSEA enrichment analysis pathway map was drawn.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: liver

growth_protocol: Huh7, HepG2, Hep3B217(known as Hep 3B2.1-7),FU97 and Hela were cultured in DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃. Li-7, SNU182, SNU387, and SNU761 were cultured in RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol Reagent(Invitrogen Life Technologies),after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer(Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard illumina protocols. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction.Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina).

tag: tissue

value: liver

value: hepatoma cell


title: 7F_M_687


title: LI7_1


title: SNU182_2


title: 7F_M_686


title: 7F_M_685


title: canonical MED19 LNCaP, androgen deprived, vehicle, rep 3

tag: treatment


title: canonical MED19 LNCaP, androgen deprived, + R1881, rep 2


title: SNU_761_2


title: SNU_761_1


title: Hela_2

source_name: cervix uteri

value: cervix uteri

value: Hela

value: cervical cancer cell


title: 7F_M_684


title: 7F_M_681


title: 7F_M_764


title: 7F_M_683


title: 7F_M_680


title: Hela_1


title: 7F_M_679


title: 7F_M_678


title: SNU_387_2


title: SNU_387_1


title: FU97_2

source_name: stomach

value: stomach

value: gastric carcinoma cell


title: Hep3B_2


title: 7F_M_677


title: Hep3B_1


title: SNU182_1


title: 7F_M_675


title: HepG2_2


title: 7F_M_674


title: HepG2_1


title: 7F_M_676


title: Huh7_2


title: 7F_M_682


title: 7F_M_672


title: Huh7_1


title: 7F_M_673


title: 7F_M_671


title: FU97_1


title: 7F_M_668


title: 7F_M_670


title: MtD3_155

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

description: 10x Genomics

data_processing:
The gene counting and aggregation were made using the  10X Genomics Cell Ranger software( version 7.0.1 )(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct)
Assembly: CellRanger_GRCh38_2020-A (Genome build from 10X Reference Packages- https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mitochondrial Disease Patient

extract_protocol:
10X Chromium instrument from 10X Genomics.
scRNA-Seq libraries were prepared from 16k cells using a 10X Genomics Chromium device and Chromium Single Cell 3’ Reagent Kit v3.1 according to manufacturer’s protocol. Libraries were pooled and sequenced on a NovaSeq 6000 DNA sequencer (Illumina, Inc.) using V1.5 chemistry, generating >270M reads per sample. The raw data were processed using RTA 3.4.4.

value: PBMC

tag: disease state

value: pediatric mitochondrial disease


title: MtD4_132

description: 10x Genomics


title: 7F_M_667

source_name: C57BL/6J Male P56 Mouse Brain


title: MtD1_326

description: 10x Genomics


title: CTRL4_295

description: 10x Genomics

source_name: Control

value: healthy control


title: 7F_M_666


title: CTRL3_165

description: 10x Genomics


title: 7F_M_665


title: CTRL2_301

description: 10x Genomics


title: 7F_M_663


title: 7F_M_664


title: CTRL1_300

description: 10x Genomics


title: 7F_M_662


title: 7F_M_660


title: 7F_M_661


title: mDC, 3mg, rpm, 1

city: Abu Dhabi

first: Mei

last: ElGindi

address: Saadiyat Island

department: Engineering

country: United Arab Emirates

institute: NYUAD

data_processing:
Raw FASTQ sequenced reads were first assessed for quality using FastQC v0.11.5 (available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) . The reads were then passed through Trimmomatic v0.36 for quality trimming and adapter sequence removal with the following parameters (ILLUMINACLIP: trimmo-matic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36). The surviving trimmed read pairs were then processed with Fastp to remove poly-G tails and Novaseq/Nextseq-specific artifacts. Following quality trimming, the reads were assessed again using FastQC. After QC and QT, the reads were aligned to the human reference genome GRCh38.p4 using HISAT2 with the default parameters and by providing the –dta flag. The resulting SAM alignments were then converted to BAM format and coordinate sorted using SAMtools v1.3.1. The sorted alignment files were then passed through HTSeq-count v0.6.1p1 using the following options (-s no -t exon -I gene_id) for raw count generation. Concurrently, the sorted alignments were processed through Stringtie v1.3.0 for transcriptome quantification. Briefly, the process was stringtie -> stringtie merge (to create a merged transcriptome GTF file of all the samples) -> stringtie (this time using the GTF generated by the previous merging step). Finally, Qualimap v2.2.2 was used to generate RNA-Seq-specific QC metrics per sample.
Assembly: human GRCh38.p4
Supplementary files format and content: excel file of merged raw counts for all samples

source_name: blood

extract_protocol:
RNA was extracted using TRIzol (Invitrogen, Thermo Fisher Scientific, Inc., Dreieich, Germany), followed by chloroform extraction (Sigma‒Aldrich, Schnelldorf, Germany) using the manufacturer’s protocol. Afterward, purification using the RNeasy mini kit (Qiagen, Hilden, Germany) was performed according to the manufacturer’s protocol. The obtained RNA concentration and purity (the ratio of absorbance at 260 nm and 280 nm) were quantified using a Nanodrop (Thermo Fisher Scientific, Inc., Dreieich, Germany) and confirmed by a Qi RNA kit using a Qubit 4 fluorometer (Thermo Fisher Scientific, Inc., Dreieich, Germany) prior to performing RNA sequencing.
Purified RNA samples were prepared with an NEB Ultra II RNA kit (New England Biolabs, Ipswich, MA, USA) according to the protocol instructions using the NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs, Ipswich, MA, USA) and uniquely dual indexed. The resulting library concentration, size distribution, and quality were assessed on a Qubit 4 fluorometer (Thermo Fisher Scientific, Inc., Dreieich, Germany) with a dsDNA high sensitivity kit (Invitrogen, Carlsbad, CA, USA) and on a 4200 TapeStation using a High Sensitivity D5000 kit (Agilent, Santa Clara, CA, USA). Based on these results, libraries were normalized according to their molarity and pooled and then quantified with a library quantification kit for Illumina platforms (Roche, Basel, Switzerland) on a StepOnePlus qPCR machine (Thermo Fisher Scientific, Inc., Dreieich, Germany). Finally, pooled libraries were loaded at 350 pM with 1% PhiX on S2 FlowCell and paired end sequenced (2 × 150 bp) on a NovaSeq 6000 next generation sequencer (Illumina, San Diego, CA, USA). RNA-Seq was performed in triplicate.

value: blood

value: monocyte

value: WT

value: mature dendritic cell differentiation


title: mDC, 1mg, rpm, 3


title: MtD2_319

description: 10x Genomics


title: 7F_M_658


title: mDC, 3mg, rpm, 3


title: 7F_M_656


title: 7F_M_657


title: mDC, 3mg, static, 3


title: 7F_M_659


title: mDC, 1mg, rpm, 2


title: 7F_M_654


title: 7F_M_653


title: 7F_M_652


title: mDC, 1mg, static, 3


title: 7F_M_655


title: mDC, 3mg, static, 2


title: mDC, 3mg, static, 1


title: mDC, 1mg, rpm, 1


title: 7F_M_651


title: mDC, 1mg, static, 1


title: iDC, 3mg, rpm, 3

value: immature dendritic cell differentiation


title: iDC, 3mg, rpm, 2


title: mDC, 3mg, rpm, 2


title: iDC, 3mg, rpm, 1


title: 7F_M_648


title: 7F_M_647


title: iDC, 1mg, rpm, 3


title: iDC, 1mg, rpm, 2


title: 7F_M_644


title: 7F_M_645


title: 7F_M_642


title: mDC, 1mg, static, 2


title: iDC, 3mg, static, 1


title: iDC, 3mg, static, 2


title: iDC, 1mg, static, 3


title: 7F_M_641


title: 7F_M_640


title: 7F_M_638


title: 7F_M_639


title: 7F_M_650


title: 7F_M_649


title: 7F_M_637


title: 7F_M_636


title: 7F_M_635


title: SKIN_AGE89_M_GR5_Gt132

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Circular RNAs were identified using CIRCexplorer v1.1.10.
Assembly: hg19
Supplementary files format and content: *geneCOUNT.txt: Tab-delimited text files containing counts.
Supplementary files format and content: *circRNA.txt: Tab-delimited text files containing circRNA annotation.

source_name: primary skin fibroblasts

growth_protocol: Punch skin biopsies were obtained from the inner axilla of 82 healthy GESTALT participants. Skin biopsies were minced into smaller pieces and distributed into 3 wells of 6-well collagen-coated plates to establish the human dermal fibroblast cultures.

extract_protocol:
After expansion, total RNA was isolated using the Direct-zolTM RNA MiniPrep kit (Zymo Research) following the manufacturer’s instruction.
Ribo-RNA depletion with Low Input RiboMinus Eukaryote System v2 (Thermo Fisher Scientific). Ribo-RNA-depleted samples were then used for cDNA synthesis with Ovation® RNA-Seq System V2 (Nugen) following the manufacturer’s protocol. Following cDNA fragmentation and size selection, libraries were prepared using Illumina TruSeq ChIP Library Preparation Kit (Illumina) according to manufacturer’s protocol.

value: primary skin fibroblasts

value: Male


title: iDC, 1mg, static, 2


title: 7F_M_508

value: GP


title: 7F_M_507


title: iDC, 1mg, rpm, 1


title: 7F_M_646


title: SKIN_AGE85_M_GR5_Gt125


title: SKIN_AGE81_M_GR5_Gt110


title: iDC, 3mg, static, 3


title: SKIN_AGE83_M_GR5_Gt026


title: 7F_M_506


title: SKIN_AGE81_M_GR5_Gt108


title: 7F_M_504


title: SKIN_AGE81_M_GR5_Gt029


title: SKIN_AGE80_F_GR5_Gt083

value: Female


title: 7F_M_505


title: iDC, 1mg, static, 1


title: SKIN_AGE80_F_GR5_Gt032


title: 7F_M_502


title: 7F_M_503


title: 7F_M_500


title: 7F_M_501


title: SKIN_AGE77_F_GR4_Gt113


title: 7F_M_498


title: SKIN_AGE76_M_GR4_Gt115


title: 7F_M_496


title: SKIN_AGE73_F_GR4_Gt018


title: SKIN_AGE72_M_GR4_Gt084


title: SKIN_AGE86_M_GR5_Gt111


title: SKIN_AGE72_M_GR4_Gt114


title: SKIN_AGE72_M_GR4_Gt065


title: 7F_M_494


title: 7F_M_495


title: 7F_M_492


title: FR_RNA_T1D_HU_20210520_P2_CD4T-cells-96-single_cell_sorted_cells

type: RNA

description: CD4+ T cell

data_processing: Data was processed using custom R scripts

label: EVAGREEN

source_name: Blood

label_protocol: Per donor: PBMCs were split and stained with either tetramer for 1 hour at 4C in the dark. Washed twice with FACS Wash (2% FCS, 2 mM EDTA, 1x PBS) and then stained with surface antibodies for 30 minutes at 4C in the dark.

extract_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were isolated via Ficoll gradient from blood isolated from all donors


title: SKIN_AGE72_M_GR4_Gt014


title: 7F_M_491


title: SKIN_AGE72_F_GR4_Gt109


title: FZ_RNA_T1D_HU_20200527_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE72_F_GR4_Gt071


title: FR_RNA_T1D_HU_20210520_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE78_F_GR4_Gt035


title: 7F_M_490


title: FR_RNA_T1D_HU_20210517_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20210514_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE71_F_GR4_Gt138


title: 7F_M_497


title: FR_RNA_T1D_HU_20210507_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20210507_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20210427_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_487


title: FR_RNA_T1D_HU_20210427_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_486


title: FR_RNA_T1D_HU_20210324_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FZ_RNA_T1D_HU_20200527_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_483


title: SKIN_AGE70_F_GR4_Gt089


title: SKIN_AGE69_F_GR4_Gt095


title: FR_RNA_T1D_HU_20210122_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_482


title: FR_RNA_T1D_HU_20210122_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20210324_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE67_M_GR4_Gt039


title: 7F_M_481


title: 7F_M_479


title: SKIN_AGE67_M_GR4_Gt002


title: FR_RNA_T1D_HU_20210106_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201230_P4_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20210106_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE67_F_GR4_Gt080


title: 7F_M_478


title: FR_RNA_T1D_HU_20201230_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201230_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE70_M_GR4_Gt061


title: SKIN_AGE66_F_GR3_Gt156


title: FR_RNA_T1D_HU_20201230_P3_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201222_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_477


title: FR_RNA_T1D_HU_20201215_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_475


title: FR_RNA_T1D_HU_20201215_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE65_F_GR4_Gt033


title: SKIN_AGE63_M_GR3_Gt092


title: FR_RNA_T1D_HU_20201119_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201105_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_474


title: SKIN_AGE63_F_GR3_Gt101


title: FR_RNA_T1D_HU_20201105_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201005_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_473


title: 7F_M_472


title: SKIN_AGE62_F_GR3_Gt070


title: FR_RNA_T1D_HU_20200611_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200317_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE61_F_GR3_Gt102


title: FR_RNA_T1D_HU_20200611_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200303_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200317_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_470


title: 7F_M_471


title: SKIN_AGE61_F_GR3_Gt003


title: FR_RNA_T1D_HU_20200228_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE60_M_GR3_Gt013


title: 7F_M_467


title: FR_RNA_T1D_HU_20200303_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200228_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200130_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20200131_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20201119_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE57_M_GR3_Gt004


title: 7F_M_466


title: FR_RNA_T1D_HU_20200129_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_465


title: FR_RNA_T1D_HU_20200109_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_464


title: FR_RNA_T1D_HU_20200109_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE56_F_GR3_Gt120


title: FR_RNA_T1D_HU_20191219_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE55_M_GR3_Gt136


title: 7F_M_463


title: FR_RNA_T1D_HU_20190613_P2_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: FR_RNA_T1D_HU_20190613_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE54_M_GR3_Gt057


title: SKIN_AGE58_F_GR3_Gt011


title: FR_RNA_T1D_HU_20190104_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE53_F_GR3_Gt146


title: 7F_M_462


title: 7F_M_461


title: FR_RNA_T1D_HU_20190103_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: SKIN_AGE52_M_GR3_Gt056


title: SKIN_AGE52_M_GR3_Gt007


title: FR_RNA_T1D_HU_20190227_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_460


title: 7F_M_459


title: SKIN_AGE52_F_GR3_Gt063


title: 7F_M_458


title: SKIN_AGE52_F_GR3_Gt027


title: FR_RNA_T1D_HU_20191219_P1_CD4T-cells-96-single_cell_sorted_cells

description: CD4+ T cell


title: 7F_M_457


title: SKIN_AGE51_M_GR3_Gt015


title: 7F_M_456


title: Macrophages_mono-culture_biological rep4

city: Düsseldorf

first: Stephanie

middle: Daniela

last: Wolf

state: NRW

address: Moorenstrasse 5, Geb. 13.58 Raum 04

department: Gastroenterology, Hepatology and Infectious Disease

country: Germany

institute: Universitätsklinikum Düsseldorf

hyb_protocol: After fragmentation labeled cDNA was hybridized to Applied Biosystems™ Clariom™ S Mouse Gene Expression Microarrays for 16 hr at 45°C and stained by streptavidin/phycoerythrin conjugate, according to the manufacturer's protocol. Fluidics Station 450 was used.

scan_protocol: Using the Affymetrix Calvin Scan Acquisition on the Affymetrix GeneChip Scanner 3000 7G with the Affymetrix GeneChip Command Console Scan Control Version 4.0.0.1567.

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by GeneSprings’ ExonSSTRMAWithoutStabilization algorithm after quantile normalization of probe-level signal intensities across all samples to reduce interarray variability (Bolstad et al., 2003). Input data preprocessing was concluded by baseline transformation to the median of all samples. After grouping of samples (five biological replicates each) according to their respective experimental condition, a given probe set had to be expressed above background (i.e., fluorescence signal of that probe set was detected within the 20th and 100th percentiles of the raw signal distribution of a given array) in 75% of the replicates in at least one of the conditions to be further analyzed in pairwise comparisons.

label: biotin

source_name: primary wt BMDM

label_protocol: According to the manufacturer's protocol: 10 ng of total RNA were converted to cDNA, amplified to complementary RNA (cRNA) followed by in vitro transcription and biotin labeling of cDNA.

growth_protocol: primary hepatocytes were isolated and cultivated in sandwich matrix, bone marrow cells were isolated and differentiated to bone marrow derived macrophages (BMDM) by mCSF for 7 days.

extract_protocol: RNA from hepatocytes and BMDM were isolated with the RNeasy Mini Kit (Qiagen) according manufacturer's instructions. The RNA was quantified and quality measured by capillary electrophoresis Bioanalyzer assay (Eukaryote Total RNA Pico, Agilent)

treatment_protocol: hepatocytes were cultivated in sandwich culture (0.8 Mio per Well in a 6 well plate) alone or together with BMDM which were cultivated in transwells (0.1 Mio per transwell). In comparison, BMDM were cultivated without hepatocytes.

value: Macrophages

tag: cultivation

value: mono-culture


title: SKIN_AGE49_M_GR2_Gt128

tag: Sex


title: 7F_M_455


title: 7F_M_454


title: Macrophages_mono-culture_biological rep5


title: Hepatoyctes_mono-culture_biological rep5

source_name: primary wt Hepatocytes

value: Hepatocytes


title: Macrophages_mono-culture_biological rep1


title: Macrophages_mono-culture_biological rep2


title: 7F_M_453


title: Hepatoyctes_mono-culture_biological rep2


title: SKIN_AGE48_F_GR2_Gt149


title: SKIN_AGE48_F_GR2_Gt133


title: Hepatoyctes_mono-culture_biological rep3


title: SKIN_AGE47_M_GR2_Gt060


title: 7F_M_452


title: SKIN_AGE47_F_GR2_Gt078


title: Macrophages_mono-culture_biological rep3


title: 7F_M_451


title: SKIN_AGE45_M_GR2_Gt030


title: Marcrophages_co-culture_biological rep3

value: co-culture


title: Marcrophages_co-culture_biological rep5


title: Marcrophages_co-culture_biological rep4


title: Marcrophages_co-culture_biological rep1


title: Marcrophages_co-culture_biological rep2


title: Hepatoyctes_mono-culture_biological rep1


title: Hepatoyctes_mono-culture_biological rep4


title: Hepatocytes_co-culture_biological rep3


title: Hepatocytes_co-culture_biological rep4


title: Hepatocytes_co-culture_biological rep5


title: Hepatocytes_co-culture_biological rep2


title: sgILRAP_IR rep 1

city: Houston

first: Citu

state: Texas

address: 7000 Fannin Street

department: McWilliams School of Biomedical Informatics

institute: University of Texas Health Science Centre

data_processing:
Sequence reads were trimmed for adapter content and low quality bases using Cutadapt version 1.15
Trimmed sequence reads were mapped to GRCh38 using STAR version 2.5.3a
Reads count extraction was done using HTseq-count
The raw reads were normalized using DESeq2 for which there are > 5 reads in at least one sample
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include TPM values for each sample

source_name: breast

growth_protocol: MCF10A normal breast epithelial cells were grown in DMEM/F12 medium supplemented with 20 ng/ml epithelial growth factor (EGF; Fisher Scientific), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 μg/ml insulin (Sigma-Aldrich), 0.5 mg/ml hydrocortisone (Sigma-Aldrich), and 5% horse serum (Fisher Scientific).

extract_protocol:
Total RNA was extracted (Qiagen)
An Illumina TruSeq Stranded Total RNA Library Prep Kit was used to prepare the library after rRNA depletion.

treatment_protocol: Cells were seeded in  6-well plates 1 day before RT, which was performed by a Precision X-RAD 320 Biological Irradiator. For a single high dose of RT, cells were irradiated at a single dose of 20 Gy at one time.

value: breast

value: epithelial cell

value: IL1RAP KO

value: 20Gy irradiation


title: Hepatocytes_co-culture_biological rep1


title: SKIN_AGE42_M_GR2_Gt024


title: WY_IR rep 2

value: wild type


title: 7F_M_449


title: SKIN_AGE42_F_GR2_Gt145


title: WY_IR rep 1


title: 7F_M_448


title: sgIL1R1_IR rep 1

value: ILIR1 KO


title: 7F_M_447


title: sgILRAP rep 1

value: no


title: sgILRAP_IR rep 2


title: 7F_M_446


title: sgILRAP rep 2


title: 7F_M_450


title: SKIN_AGE42_F_GR2_Gt059


title: sgIL1R1_IR rep 2


title: sgIL1R1 rep 1


title: SKIN_AGE38_M_GR2_Gt093


title: SKIN_AGE39_M_GR2_Gt126


title: SKIN_AGE45_M_GR2_Gt017


title: WT rep 2


title: 7F_M_381


title: eHAP FNLS, t14, 2 nM PB

description:
t14_2PB
col7

data_processing:
IlluminaHiSeq4000 was PE100 run (requires trimming of R1 and R2), Illumina NextSeq550 was a R1 55 nt and R2 20 nt (only requires trimming of R1).
Sequencing reads werer trimmed (BBMap BBDuk v.38.94). Hard lefttrim for R1 with 5'-cccttggagaaccaccttgttgg-3', retain only 20 nt. For R2 where necessary only retain 20 nt.
Sequencing reads corresponding to the same sample were pooled.
Reads were counted by alignment to a reference file of all sgRNAs present in the pool.
For each individual sgRNA, each barcode was randomly assigned to either of two replicates.
Assembly: hg38
Supplementary files format and content: tab-delimited textfile containing counts per sgRNA for all treatments and time points
Library strategy: sgRNA sequencing

source_name: eHAP

extract_protocol:
At screen end point cells were harvested and gDNA was extracted with QIAamp DNA Blood Maxi Kit (Qiagen #51194). Genome weight was estimated based on measured ploidy of cells.
The sequencing library was prepared using NEBnext® Ultra II Q5 Master Mix (NEB #M0544) and custom primers (forward i5: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT[N]cccttggagaaccaccttgTTG-3' with N=(0-8) nt stagger and reverse primer for multiplexing: 5'-CAAGCAGAAGACGGCATACGAGAT[8N]GTGACTGGAGTTCAGACGTG-3')  to have a balanced read sample. A barcode in the reverse primer was used for identification of the sequencing libraries. Libraries were gel purified and cleaned up. Libraries were balanced and quality was assessed with Bioanalyzer High Sensitivity DNA Kit, Agilent #5067-4626). R1 was used for sgRNA identification, R2 was used to read out barcode associated with each single sgRNA in the pool

treatment_protocol: The screen was performed at 500x sgRNA representation for entire duration. 66 million eHAP FNLS cells were infected with the lentiviral spliceosome library (marked with BFP) at an MOI of ~0.3, such that every sgRNA was represented in approximately 500 cells. Puromycin selection was started at 48 h post transduction. At six days post-transduction, cells were assessed by flow cytometry to only contain sgRNA carrying cells (BFP-positive cells >95%). Cells were then split into treatment arms (DMSO vs. 2 nM PB; with identical DMSO concentration in both treatment arms). Cells were propagated and treatment was renewed every second day.

value: eHAP

value: expressing FNLS

value: 2 nM pladienolide B, 14 days


title: WT rep 1


title: SKIN_AGE38_F_GR2_Gt152

value: primary skin fibroblasts


title: 7F_M_379

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: GP


title: eHAP FNLS, t14, DMSO control

description:
t14_ctrl
col6

value: DMSO, 14 days


title: 7F_M_380


title: eHAP FNLS, t8, 2 nM PB, part 2

description:
t8_2PB_run2
col5

value: 2 nM pladienolide B, 8 days


title: eHAP FNLS, t8, DMSO control, part 2

description:
t8_ctrl_run2
col4

value: DMSO, 8 days


title: SKIN_AGE38_F_GR2_Gt016

value: Female


title: SKIN_AGE37_M_GR2_Gt064

value: Male


title: control, eHAP FNLS, t0, part 2

description:
t0_ctrl_run2
col3

value: no treatment


title: 7F_M_378


title: plasmid control part 2

description:
pla_ctrl_run2
col2

source_name: plasmid control

value: plasmid control


title: sgIL1R1 rep 2

value: breast

value: epithelial cell


title: SKIN_AGE35_M_GR2_Gt129


title: SKIN_AGE35_M_GR2_Gt104


title: 7F_M_376