title: T1

city: Clemson

first: Susan

middle: K

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

description: E+/E+ rep1

data_processing:
Basecalls performed by bcl2fastq version 2.20.0
Sequenced reads were trimmed for low quality bases and adaptor sequence using trimmomatic version 0.38 with recommended parameters.
Gsnap was used to align reads to the reference genome.
Subread's featureCounts was used to call features using gff file
BioConductor's edgeR was used to filter and normalize the data and complete the differential gene expression analyses.
Genome_build: Ovis_aries.Oar_v3.1.ensembl93
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ovis aries

source_name: cotyledon

extract_protocol:
Cotyledons were removed, flash frozen in liquid nitrogen, and RNA was extracted using   Trizol reagent and the PureLink Mini RNA purification kit according to manufacturer instructions.
Library preparation was completed using the Illumina Small RNA Sample Preparation Kit

treatment_protocol: Three replicates were fed endophyte-infected tall fescue seed

tag: breed

value: Suffolk

value: cotyledon

value: Ewe 133 +/- 1 gestation

tag: treatment

value: Fed endophyte-infected tall fescue seed


title: C3

status: Public on Sep 08 2020

type: SRA

country: USA

description: E-/E- rep 3

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age

value: untreated (fed endophyte-free tall fescue seed)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B9_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
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
Genome_build: 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

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: CP

tag: Sex

value: male

tag: strain


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B9_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C10_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad002


title: pcDNA3_1_24h_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description: result_origin_basic_expressed_gene_RPKM.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with pvalue < =0.01 and fold change >=2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

molecule: polyA RNA

source_name: N2a cell line

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 5ug of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 oC until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina Next500 system for 150 nt pair-end sequencing by ABlife. Inc (Wuhan, China)。

value: mouse neuroblastoma

tag: cell line

tag: genotype

value: RABV infection

tag: Stage


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C10_ad012


title: pcDNA3_1_24h_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C10_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B8_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B8_ad001


title: T3

description: E+/E+ rep3


title: M_33_1: metPRT_Subject-33_Biopsy-1

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
Total RNA was sequenced on an Illumina HiSeq 4000 system, using a standard paired-end 150 bp dual indexing protocol. The two sets of samples (University of Kentucky and University of Alabama), each containing samples from all timepoints of both placebo and metformin arm as well as young, were sequenced in different batches that were corrected for in the downstream analyses (see batch).
Raw fastq sequence reads were passed through quality control using FastQC (0.11.4) and the QC results were compiled for all samples using MultiQC (1.7).
Raw fastq files were trimmed for adapter sequences, filtered for low quality reads and short reads, using the default parameters in fastp (0.19.4)
After checking for QC, RNA-Sequencing by Expectation Maximization- RSEM (1.3.0) in conjunction with the STAR aligner (2.6.1b) was used to align the raw reads to the hg38 primary assembly build of the reference human genome, with transcript annotations (gencode.v29.annotation.gtf) downloaded from GENCODE
All statistical analysis for the gene expression data were carried out using the R statistical software (R-3.6.0)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample (generated using RSEM)

organism: Homo sapiens

source_name: Vastus lateralis muscle

extract_protocol:
Approximately 35 mg of muscle was subjected to bead homogenization in Qiazol and RNA purified using miRNeasy Mini Kits and stored at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vastus lateralis muscle

tag: study arm

value: metPRT

tag: biopsy

tag: batch


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C1_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B7_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B8_ad012


title: T2

description: E+/E+ rep2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B9_ad007


title: C1

description: E-/E- rep 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B8_ad002


title: M_3_1: metPRT_Subject-3_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B9_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B7_ad002


title: C2

description: E-/E- rep 2


title: cumulus granulosa cells-PCOS_3

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

data_processing:
RNA-seq raw reads with low-quality bases, adapters were trimmed by Trimmomatic to obtain clean reads
clean reads were aligned to the UCSC human hg19 reference genome using the Hisat2 with default settings
Read counts of each gene annotated in RefGene were calculated by featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cumulus granulosa cells

extract_protocol:
oocytes and cumulus granulosa cells were immediately placed in lysis buffer and then performed reverse transcription (RT), template switching and pre-amplification based on the smart-seq2 method
The RNA-Seq libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina® (TD503-02, Vazyme Bio-tech) following the instruction manual.

tag: disease state

value: polycystic ovary syndrome(PCOS)


title: M_30_1: metPRT_Subject-30_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B7_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B7_ad004


title: cumulus granulosa cells-PCOS_4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B6_ad010


title: cumulus granulosa cells-PCOS_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B6_ad001


title: P_29_3: plaPRT_Subject-29_Biopsy-3

value: plaPRT


title: cumulus granulosa cells-PCOS_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B6_ad008


title: P_29_1: plaPRT_Subject-29_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B5_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B5_ad012


title: cumulus granulosa cells-Control_4

value: Control


title: M_30_3: metPRT_Subject-30_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B5_ad010


title: cumulus granulosa cells-Control_3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B4_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B7_ad007


title: cumulus granulosa cells-Control_1


title: cumulus granulosa cells-Control_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B4_ad012


title: oocyte-PCOS_5

source_name: oocyte


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B4_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B3_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B3_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B12_ad007


title: oocyte-PCOS_6


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B2_ad007


title: M_25_3: metPRT_Subject-25_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B2_ad010


title: M_24_1: metPRT_Subject-24_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B2_ad008


title: oocyte-PCOS_3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B2_ad004


title: M_25_1: metPRT_Subject-25_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B2_ad012


title: oocyte-PCOS_4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B12_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B5_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B12_ad012


title: P_23_1: plaPRT_Subject-23_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B12_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B11_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B11_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B11_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B10_ad008


title: oocyte-PCOS_2


title: M_22_1: metPRT_Subject-22_Biopsy-1


title: M_24_3: metPRT_Subject-24_Biopsy-3


title: oocyte-Control_4


title: M_22_3: metPRT_Subject-22_Biopsy-3


title: oocyte-Control_6


title: M_21_1: metPRT_Subject-21_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B1_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad012


title: oocyte-Control_3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad007


title: oocyte-PCOS_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B10_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B1_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B10_ad010


title: oocyte-Control_5


title: M_21_3: metPRT_Subject-21_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A8_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A8_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad010


title: M_20_3: metPRT_Subject-20_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A8_ad008


title: M_2_1: metPRT_Subject-2_Biopsy-1


title: Sample 11_Healthy_donor5 bone marrow cells run3 lane3

city: Helsinki

first: Kaiyang

last: Zhang

state: Finland

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

data_processing:
cellranger-2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with raw UMI counts for every gene and every cell

source_name: Healthy_donor5 bone marrow

growth_protocol: Cells were not cultured

extract_protocol:
Chromium Single Cell A Chip Kit (10x Technologies Cat. PN-120236)
Chromium i7 Multiplex Kit (10X Technologies Cat.PN-120262)

treatment_protocol: Cells did not receive treatment

tag: lane

tag: subject status

value: healthy donor

tag: subject id

value: bone marrow

tag: cell type

value: primary HSPCs


title: Sample 11_Healthy_donor5 bone marrow cells run3 lane4


title: oocyte-Control_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A7_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A9_ad008


title: oocyte-Control_1


title: M_20_1: metPRT_Subject-20_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A7_ad008


title: Sample 11_Healthy_donor5 bone marrow cells run3 lane1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_B10_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A6_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A6_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A7_ad010


title: Sample 11_Healthy_donor5 bone marrow cells run2 lane4


title: M_16_3: metPRT_Subject-16_Biopsy-3


title: P_19_1: plaPRT_Subject-19_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A5_ad012


title: Sample 11_Healthy_donor5 bone marrow cells run3 lane2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A4_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A5_ad008


title: M_14_3: metPRT_Subject-14_Biopsy-3


title: Sample 11_Healthy_donor5 bone marrow cells run2 lane3


title: Sample 11_Healthy_donor5 bone marrow cells run2 lane1


title: Sample 11_Healthy_donor5 bone marrow cells run2 lane2


title: M_14_1: metPRT_Subject-14_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A4_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A4_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A3_ad010


title: P_1_3: plaPRT_Subject-1_Biopsy-3


title: Sample 11_Healthy_donor5 bone marrow cells run1 lane4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A6_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A6_ad004


title: M_13_1: metPRT_Subject-13_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A3_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A6_ad007


title: Sample 11_Healthy_donor5 bone marrow cells run1 lane3


title: P_12_3: plaPRT_Subject-12_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A3_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A2_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A2_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A12_ad012


title: P_12_1: plaPRT_Subject-12_Biopsy-1


title: M_13_3: metPRT_Subject-13_Biopsy-3


title: Sample 10_Healthy_donor4 bone marrow cells lane4

source_name: Healthy_donor4 bone marrow


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A12_ad007


title: Sample 10_Healthy_donor4 bone marrow cells lane3


title: Sample 11_Healthy_donor5 bone marrow cells run1 lane2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A2_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A2_ad012


title: Sample 11_Healthy_donor5 bone marrow cells run1 lane1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A11_ad012


title: P_1_1: plaPRT_Subject-1_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A11_ad007


title: Sample 10_Healthy_donor4 bone marrow cells lane2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A11_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A10_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A2_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A10_ad007


title: Sample 9_Healthy_donor3 bone marrow cells lane4

source_name: Healthy_donor3 bone marrow


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A11_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A1_ad010


title: Sample 9_Healthy_donor3 bone marrow cells lane1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A12_ad010


title: Sample 10_Healthy_donor4 bone marrow cells lane1


title: M_10_3: metPRT_Subject-10_Biopsy-3


title: Sample 9_Healthy_donor3 bone marrow cells lane3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A10_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A1_ad012


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad002


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad008


title: Sample 9_Healthy_donor3 bone marrow cells lane2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A1_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad012


title: M_460_1: metPRT_Subject-460_Biopsy-1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B3_ad008


title: Sample 8_Healthy_donor2 bone marrow cells lane4

source_name: Healthy_donor2 bone marrow


title: M_460_3: metPRT_Subject-460_Biopsy-3


title: Sample 8_Healthy_donor2 bone marrow cells lane1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad001


title: Sample 8_Healthy_donor2 bone marrow cells lane3


title: M_10_1: metPRT_Subject-10_Biopsy-1


title: M_454_3: metPRT_Subject-454_Biopsy-3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B4_ad008


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B3_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B2_ad007


title: M_427_3: metPRT_Subject-427_Biopsy-3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_E8_ad007


title: Sample 7_Healthy_donor1 bone marrow cells lane4

source_name: Healthy_donor1 bone marrow


title: Sample 7_Healthy_donor1 bone marrow cells lane3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B2_ad008


title: Sample 8_Healthy_donor2 bone marrow cells lane2


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B1_ad008


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A9_ad010


title: M_454_1: metPRT_Subject-454_Biopsy-1


title: Sample 7_Healthy_donor1 bone marrow cells lane2


title: CEMBA180904_5J_3_CEMBA180904_5J_4_B1_ad007


title: M_427_1: metPRT_Subject-427_Biopsy-1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A8_ad002


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A8_ad012


title: Sample 6_FA_patient7 bone marrow cells lane4

source_name: FA_patient7 bone marrow

value: Fanconi anemia (FA) patient


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A6_ad012


title: Sample 7_Healthy_donor1 bone marrow cells lane1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A7_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A8_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A5_ad002


title: Sample 6_FA_patient7 bone marrow cells lane2


title: Sample 6_FA_patient7 bone marrow cells lane3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A5_ad012


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A9_ad001


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A5_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A4_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A4_ad012


title: Sample 6_FA_patient7 bone marrow cells lane1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A4_ad008


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A4_ad001


title: Sample 5_FA_patient5 bone marrow cells lane4

source_name: FA_patient5 bone marrow


title: Sample 5_FA_patient5 bone marrow cells lane2


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A3_ad008


title: Sample 5_FA_patient5 bone marrow cells lane3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A4_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A3_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A3_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A3_ad001


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad006


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A6_ad010


title: M_392_3: metPRT_Subject-392_Biopsy-3


title: Sample 4_FA_patient4 bone marrow cells lane3

source_name: FA_patient4 bone marrow


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad008


title: Sample 5_FA_patient5 bone marrow cells lane1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A3_ad002


title: M_392_1: metPRT_Subject-392_Biopsy-1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad007


title: M_367_1: metPRT_Subject-367_Biopsy-1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad012


title: Sample 4_FA_patient4 bone marrow cells lane2


title: Sample 4_FA_patient4 bone marrow cells lane4


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad010


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A11_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad001


title: Sample 3_FA_patient3 bone marrow cells lane4

source_name: FA_patient3 bone marrow


title: Sample 4_FA_patient4 bone marrow cells lane1


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A2_ad002


title: M_334_3: metPRT_Subject-334_Biopsy-3


title: Sample 3_FA_patient3 bone marrow cells lane3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad002


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad007


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad012


title: M_334_1: metPRT_Subject-334_Biopsy-1


title: Sample 3_FA_patient3 bone marrow cells lane1


title: Sample 2_FA_patient2 bone marrow cells lane4

source_name: FA_patient2 bone marrow


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad010


title: M_302_3: metPRT_Subject-302_Biopsy-3


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad004


title: CEMBA180904_5J_1_CEMBA180904_5J_2_H1_ad007


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B8_ad001


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A1_ad008


title: M_302_1: metPRT_Subject-302_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B9_ad002


title: Sample 2_FA_patient2 bone marrow cells lane2


title: CEMBA180904_5J_3_CEMBA180904_5J_4_A11_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B7_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B7_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B6_ad002


title: Sample 2_FA_patient2 bone marrow cells lane3


title: Sample 1_FA_patient1 bone marrow cells lane4

source_name: FA_patient1 bone marrow


title: Sample 3_FA_patient3 bone marrow cells lane2


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B5_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B5_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B9_ad001


title: P_269_3: plaPRT_Subject-269_Biopsy-3


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B6_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B4_ad002


title: M_240_3: metPRT_Subject-240_Biopsy-3


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B8_ad002


title: Sample 1_FA_patient1 bone marrow cells lane3


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B4_ad001


title: M_240_1: metPRT_Subject-240_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B3_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B2_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B2_ad007


title: Sample 1_FA_patient1 bone marrow cells lane1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B2_ad001


title: Sample 2_FA_patient2 bone marrow cells lane1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B12_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B2_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B12_ad002


title: PLC/PRF/5-Cas9NG-mChe, Remdesivir, 24h

city: Boston

first: Richard

middle: I

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

data_processing:
RNA-seq reads were mapped using the Quantseq 3' mRNA mapping pipeline as described by lexogen to GRCh38.p12. Briefly, reads were first trimmed using bbduk from the bbmap suite (v38.79) trimming for low quality tails, poly-A read-through and adapter contamination using the recommended parameters. Then, reads were mapped using the STAR aligner (v2.5.2b) with the recommended modified-Encode settings. Finally, HT-seq (v0.9.1) count was used to obtain per-gene counts
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: raw_counts.csv: matrix table containing raw counts for all samples

source_name: Human liver hepatoma cell line, PLC/PRF/5

growth_protocol: All cell lines were obtained from ATCC and were cultured in: McCoy’s 5A media (Thermo Fisher) + 10% FBS (Thermo Fisher) (HCT-116, HT29); DMEM (Thermo Fisher) + 10% FBS (HepG2, PLC/PRF/5, HEK293-ACE2, Huh7); RPMI (Thermo Fisher) + 10% FBS (OV-90).

extract_protocol:
RNA harvest and purification was performed using the Qiagen RNeasy Plus mini kit
Up to 1000 ng of purified total RNA was prepared for RNA-seq using the Lexogen QuantSeq 3’ mRNA-Seq kit and sequenced using Illumina Nexteq with 75-nt reads at >1.625*10^6 reads per sample

treatment_protocol: Cell lines were plated at 6*10^4/cm2 one day prior to drug treatment. Remdesivir and HCQ were added for 8 or 24 hours at specified doses

value: Liver

value: Human Alexander hepatoma cell line

tag: treatment

value: Remdesivir, 10 uM

tag: duration


title: PLC/PRF/5-Cas9NG-mChe, Remdesivir, 8h

tag: tissue


title: M_159_3: metPRT_Subject-159_Biopsy-3


title: M_159_1: metPRT_Subject-159_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B11_ad002

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

tag: age


title: M_157_3: metPRT_Subject-157_Biopsy-3


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B11_ad001

tag: Sex

tag: strain


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B1_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B10_ad001


title: Sample 1_FA_patient1 bone marrow cells lane2


title: PLC/PRF/5-Cas9NG-mChe, DMSO, 8h

tag: cell line


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B1_ad001


title: PLC/PRF/5-Cas9NG-mChe, HCQ, 8h

value: HCQ, 80 uM


title: PLC/PRF/5-Cas9NG-mChe, DMSO, 24h


title: PLC/PRF/5-Cas9NG-mChe, HCQ, 24h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B1_ad007

value: CP


title: CEMBA180904_5J_1_CEMBA180904_5J_2_B10_ad002

value: male


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad004


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad006


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad010


title: HT29, Remdesivir, 24h

source_name: Human colon colorectal adenocarcinoma cell line, HT29

value: Colon

value: Human colorectal adenocarcinoma cell line

value: Remdesivir, 60 uM


title: P_102_1: plaPRT_Subject-102_Biopsy-1

source_name: Vastus lateralis muscle

value: Vastus lateralis muscle


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad001


title: HT29, DMSO, 24h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad004


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad004


title: HT29, HCQ, 24h

value: HCQ, 100 uM


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad008


title: HT29, DMSO, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad008


title: M_065_3: metPRT_Subject-065_Biopsy-3

value: metPRT


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad006


title: HT29, Remdesivir, 8h


title: M_065_1: metPRT_Subject-065_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad012


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad012


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad001


title: HepG2, Remdesivir, 24h

source_name: Human liver hepatocellular carcinoma cell line, HepG2

value: Human hepatocellular carcinoma cell line


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad007


title: HepG2, Remdesivir, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad004


title: M_157_1: metPRT_Subject-157_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A7_ad002


title: HepG2, HCQ, 24h

value: HCQ, 20 uM


title: HepG2, DMSO, 24h


title: HT29, HCQ, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A8_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad010


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad012


title: M_063_3: metPRT_Subject-063_Biopsy-3


title: HepG2, DMSO, 8h


title: HepG2, HCQ, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad008


title: HCT116, Remdesivir, 8h

source_name: Human colon colorectal carcinoma cell line, HCT116

value: Human colorectal carcinoma cell line

value: Remdesivir, 20 uM


title: M_063_1: metPRT_Subject-063_Biopsy-1


title: P_042_3: plaPRT_Subject-042_Biopsy-3

value: plaPRT


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad007


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A6_ad006


title: HCT116, Remdesivir, 24h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad004


title: M_018_3: metPRT_Subject-018_Biopsy-3


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad006


title: HCT116, HCQ, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad004


title: HCT116, HCQ, 24h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad012


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad007


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad010


title: P_013_1: plaPRT_Subject-013_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad010


title: HCT116, DMSO, 24h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad004


title: M_018_1: metPRT_Subject-018_Biopsy-1


title: HCT116, DMSO, 8h


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad008


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A2_ad012


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A4_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A2_ad004


title: d0__fresh_r2

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Cellranger v3.0.1 count and prefiltering (target cell number 6000)
Seurat 3 QC, exclusion of cells with less genes or UMIs than medians minus 2 standard deviations
Seurat 3 QC, exclusion of cells with more genes or UMIs than the respective medians plus 2 standard deviations (multiplets)
Seurat 3 QC, exclusion of cells with more than 7% mitochondrial gene expression (apoptotic cells)
Seurat 3 metadata extraction
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger count output as filtered_feature_bc_matrix; Seurat 3 metadata as tab-separated-value

source_name: fresh_umbilical cord blood CD34+

growth_protocol: Human CD34+ cells were cultured in HSC expansion media consisting of StemSpan SFEM (StemCell Technologies) supplemented with human 100 ng/ml stem cell factor (SCF, R&D Systems), 100 ng/ml FMS-like trysine kinase 3 ligand (FLT3, R&D Systems), 50 ng/ml thrombopoietin (TPO, R&D Systems), and 10 μg/ml low-density lipoprotein (StemCell Technologies).

extract_protocol:
Single cells were processed using the 10X Chromium controlller.
10X Chromium version 2 3' RNAseq.

treatment_protocol: CD34+ cultures were supplemented with  35 nM UM171 (StemCell Technologies).

value: umbilical cord blood CD34+

tag: cell subtypye

value: fresh


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A12_ad006


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad006


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A3_ad010


title: CRISPRi Library H7 high peak

city: Durham

first: Nikoleta

last: Tsvetanova

state: NC

address: Department of Pharmacology and Cancer Biology Duke University School of Medicine Box 3813, C334 LSRC, 308 Research Drive

department: Pharmacology and Cancer  Biology

institute: Duke University

description: High CRE-DD-GFP

data_processing:
Raw sequencing reads from next-generation sequencing were cropped and aligned to the reference using Bowtie to determine sgRNA counts in each sample.
Supplementary_files_format_and_content: sgRNA counts

source_name: human embryonic kidney 293 cells

growth_protocol: HEK293 and HEK293T cells were obtained from ATCC and grown at 37 C/5% CO2 in Dulbecco’s Modified Eagle Medium (4.5 g/L glucose and L-glutamine, no pyruvate) supplemented with 10% fetal bovine serum. Clonal HEK293 cells stably expressing pCRE-DD-zsGreen1 and dCas9-BFP-KRAB were generated by lentiviral transduction and fluorescence activated cell sorting for GFP and BFP on a BD FACS Aria 2. Individual clones were expanded and tested for high cAMP-induced GFP expression and for efficiency of dCas9-dependent transcriptional repression.

extract_protocol:
Genomic DNA was isolated from FACS-sorter populations using QIAamp DNA Blood Maxi kit.
Genomic DNA was PCR amplified with Q5 Hotstart high-fidelity 2X mastermix and barcoding primers for 27 cycles. PCR reactions were purified on QIAquick PCR purification columns and loaded onto a 20% polyacrylamide/TBE gels. A product band ~270 bp was excised and DNA was extracted, quantified and sequenced on an Illumina HiSeq-4000 using custom primers

treatment_protocol: HEK293 dCas9/reporter-expressing cells were infected with sgRNA libraries at an effective MOI of < 1 sgRNA/cell. Two days after infection, puromycin was added to 0.85 ug/ml final concentration for 72 hr to select infected cells. Then, cells were allowed to recover in medium without puromycin for 3 days. On the day of the experiment, isoproterenol and Shield-1 were added to 1 uM final concentration each for 4 hr. Cells were washed in ice-cold PBS, lifted in ice-cold Trypsin/0.25% EDTA and resuspended in PBS/2% FBS for sorting on a BD FACS Aria2 based on fluorescent reporter expression (GFP). Cells were binned into three fractions (high, medium, low) and used as input for DNA extraction and library preparation.

tag: cell population

value: High cAMP reporter expressing population

tag: library

value: Library H7


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A11_ad007

value: CP


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A2_ad006

value: male


title: CRISPRi Library H6 medium peak

description: Medium CRE-DD-GFP

value: Medium cAMP reporter expressing population

value: Library H6


title: P_013_3: plaPRT_Subject-013_Biopsy-3

tag: study arm

tag: biopsy

tag: batch


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A2_ad010


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A2_ad002


title: P_001_1: plaPRT_Subject-001_Biopsy-1


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad004


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad008


title: d7__UM171_r3

source_name: UM171-expanded_umbilical cord blood CD34+


title: CRISPRi Library H6 low peak

description: Low CRE-DD-GFP

value: Low cAMP reporter expressing population


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A12_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A12_ad002


title: CRISPRi Library H5 medium peak

description: Medium CRE-DD-GFP

value: Library H5


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A9_ad007


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A11_ad004


title: CRISPRi Library H7 low peak

description: Low CRE-DD-GFP


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A11_ad001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad002


title: CRISPRi Library H5 low peak

description: Low CRE-DD-GFP


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A5_ad006


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A11_ad002


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A11_ad006


title: CRISPRi Library H6 high peak

description: High CRE-DD-GFP


title: CRISPRi Library H4 high peak

description: High CRE-DD-GFP

value: Library H4


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad006


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad001


title: Niche_EC

city: Nanjing

first: Shentong

last: Fang

address: Longmian Avenue

institute: China Pharmaceutical University

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package (v2.3.4) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
For further analysis, Seurat R package was used.
Genome_build: mm10

source_name: bone marrow endothelial cells

extract_protocol:
For sample 1-3, red cell-depleted WBM cells were first enriched using lineage depletion kit (Miltenyi Biotec, Germany) and then stained with antibodies against cKit PE-Cy7, Sca1 PE, CD34 Alexa 647 for 90 minutes on ice followed by streptavidin eF450 for 20 minutes on ice. 4’,6-diamidino-2-phenylindole (DAPI) was used to check viability. For sample 3-4, the mice were injected intravenously with VE-Cadherin A647 (BioLegend, CA). WBM plug was obtained by flushing tibias and digestion with Collagenase I (Worthington Biochemical Corporation, NJ), Dispase II (Roche Applied Science, Swizerland) and DNase I (Sigma-Aldrich) in HBSS with calcium and magnesium. The digested marrow was pooled with staining buffer (HBSS +2% FBS +2mM EDTA) to stop the enzymatic reaction. The red cell-depleted WBM cells were stained with antibodies against CD45 eFluor 450, Ter119 eFluor 450, and biotinylated LepR (1:100, R&D Systems, CA) on ice for 30 minutes followed by streptavidin PE-Cy5 on ice for 15 minutes.
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina)

treatment_protocol: For sample 1-3, mice received tamoxifen via gavage.

value: Bone marrow endothelial cells

tag: genotype

value: LepR-Cre;LSL-tdTomato

value: 3-4 months


title: CRISPRi Library H7 medium peak

description: Medium CRE-DD-GFP


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A12_ad012


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A10_ad007


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad004


title: CRISPRi Library H5 high peak

description: High CRE-DD-GFP


title: AML-99-002

type: genomic

city: Houston

first: FENG

last: WANG

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

hyb_protocol: According to the hybridazation protocol in Infinium LCG Assay Reference Guide

scan_protocol: According to the scan protocol in Infinium LCG Assay Reference Guide

data_processing:
The raw log R ratio and B allele frequency were used for ASCAT (allele-specific copy number analysis of tumors) algorithm to identify allele-specific copy-number alterations.
The log R ratio (LRR) and B allele frequency (BAF).

label: Not applicable

source_name: Bone marrow

label_protocol: standard Illumina protocol

growth_protocol: Not Applicable

extract_protocol: Genomic DNA was extracted using an Autopure extractor (QIAGEN/Gentra).

treatment_protocol: Not Applicable

tag: gender

value: Female


title: CRISPRi Library H3 high peak

description: High CRE-DD-GFP

value: Library H3


title: AML-92-001


title: CRISPRi Library H4 medium peak

description: Medium CRE-DD-GFP


title: AML-88-001

source_name: Blood


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad010


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad008


title: AML-83-001


title: CRISPRi Library H2 high peak

description: High CRE-DD-GFP

value: Library H2


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad006


title: CRISPRi Library H3 low peak

description: Low CRE-DD-GFP


title: ATAC_SSCL_V_2

city: Stanford

first: Gerlinde

last: Wernig

address: 265 Campus Drive

department: Pathology

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: ATAC-SEQ

data_processing:
Reads were trimmed for adaptor sequence, then mapped to hg38 using bowtie2, duplicate fragments were then removed using Picard.
MACS2 was used to call all reported ATAC-seq peaks. Peaks were filtered using the consensus excludable ENCODE blacklist.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: primary human SSCL dermal fibroblast with JUN knock-out

growth_protocol: Human fibroblasts were obtained from skin biopsy of SSCL patients (IRB 18891). The tissue was chopped and incubated with Collagenase I (1 mg/ml, Thermo Fisher Scientific) and DNAse I (20 ug/ml, Sigma) for 30 min, centrifuged at 600 g for 5 min and filtered (70 um) to remove non-homogenized pieces of tissue. Tissue homogenate was treated with ACK lysing buffer (Thermo Fisher) for 10-15 min, centrifuged for 600 g, washed twice in DMEM with 10% fetal bovine serum (Gibco) and plated at a density of approximately 500,000 cells/cm2 in DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin (Thermo Fisher Scientific) and Ciproﬂoxacin 10 µg/mL, Corning) and kept in an incubator at 37 °C 95%O2/5%CO2. Media was changed after 24h. For lentiviral-based transduction, primary fibroblasts were washed with PBS prior to transfection. 500 μl Cas9-gRNAJUN-Puromycin (knock out) or IRES-Hygro-TetO-JUN (doxycyclin inducible overexpression) lentivirus,  was added with in fresh medium with 4ug/mL polybrene (Sigma). Medium was replaced after incubation for 24 h at 37 °C 95%O2/5%CO2 and infected cells selected with 1 ug/mL puromycin or 500 ug/mL hygromycin in DMEM 10% FSB for 3 days.

extract_protocol:
FOR ATAC, Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
FOR ATAC, Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

tag: cell type

value: primary dermal fibroblasts

tag: genotype/variation

value: vismodegib treatment


title: ATAC_SSCL_V_1

description: ATAC-SEQ


title: AML-82-001

value: Male


title: AML-81-001


title: AML-80-001


title: Neuroblastoma cell line (SH-SY5Y) with SWT rep1

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

data_processing:
Sequence reads were trimmed for adaptor sequence removal and quality controlled using Trimmomatic (0.36) and reads were trimmed at a length of 73 bases. Sequencing quality was checked using FastQC (0.11.5)
Reads were mapped using STAR aligner (2.5.3a) on human genome version hg38 (UCSC) with RefGene annotation and index with 100bp splice junction overhang. HTSeq was used to quantify gene raw counts.
Relative log expression RLE (normalization) was performed using DESeq2 (filtered for antisense transcripts and genes with missing counts across all samples)
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and RLE for all samples are summarized as two separated tab delimited txt file

source_name: Neuroblastoma cell line (SH-SY5Y)

growth_protocol: Neuroblastoma cell line, SH-SY5Y (ATCC, Mansssas, VA) were cultivated in Dulbecco's Modified Eagle Medium (DMEM) with 4,5 g/l Glucose (PAN Biotech, Aidenbach, Germany) with 10% (vol/vol) fetal calf serum an 1% penicilin-streptomycin solution (both Sigma-Aldrich, St. Louis, MO) and cells were harvested and RNA isolated at 6h upon SWT.

extract_protocol:
Total RNA was isolated using  RNeasy Mini Kit 50 (Qiagen) according to the manufacturer’s protocol.
Library preparation was performed with the TruSeq® Stranded mRNA HT technology, according to the manufacturer´s protocol . Quality was checked by DNA 1000 LabChip kits on the 2100 Bioanalyzer (Agilent Technologies) and quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Invitrogen)

treatment_protocol: Cells were treated  in a specifically designed water bath, which guaranteed avoidance of disturbing reflections and constant temperature at 37°C. Cell culture flasks were filled with culture medium prior to treatment, as SWs would be reflected by air. Culture flasks were subsequently dunked into the water bath and treated at 7 cm distance to the applicator. Thus, 300 impulses at an energy flux density of 0.08 mJ/mm2 and a frequency of 3 Hz were applied.

tag: treatment

value: SWT

value: Nerve tissue (Neurons)


title: CRISPRi Library H4 low peak

description: Low CRE-DD-GFP


title: AML-99-001


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad012

value: CP

value: male


title: AML-95-001


title: ATAC_SSCL_KO_1

description: ATAC-SEQ

value: JUN knockout


title: CEMBA180904_5J_1_CEMBA180904_5J_2_A1_ad007


title: AML-70-001


title: CRISPRi Library H1 high peak

description: High CRE-DD-GFP

value: High cAMP reporter expressing population

value: Library H1


title: AML-91-001


title: CRISPRi Library H3 medium peak

description: Medium CRE-DD-GFP

value: Medium cAMP reporter expressing population


title: CRISPRi Library H1 medium peak

description: Medium CRE-DD-GFP


title: AML-59-001


title: Niche_LepR-tdT

source_name: bone marrow LepR+ cells

tag: tissue

value: LepR-Cre;tdTomato+ cells from bone marrow


title: AML-90-001


title: M. mass-infected macrophages 3

city: Seoul

first: Hailian

last: Quan

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology, and Institute of Endemic Disease

country: South Korea

institute: Seoul, South Korea

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: THP-1 cells

growth_protocol: The human acute monocytic leukemia THP-1 (ATCC TIB-202) cell line was obtained from the ATCC and maintained in RPMI media containing 10% FBS (Gibco) and 1% penicillin-streptomycin (PS; Gibco) at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Differentiation of THP-1 cells into macrophages was performed by incubating the cells with 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) for 2 days, and then, the media was changed to that without 1% PS for 1 day. PMA-differentiated THP-1 cells were infected with HCMV at a multiplicity of infection of 10 (MOI=10) for 3 h, and the media was changed to establish HCMV infection. M. mass was infected at (MOI=2) 24 h post-HCMV infection.

value: peripheral blood

value: Monocyte

tag: passage


title: AML-60-001


title: ATAC_SSCL_1

description: ATAC-SEQ

source_name: primary human SSCL dermal fibroblast

value: wild type


title: AML-58-001


title: Neuroblastoma cell line (SH-SY5Y) with SWT rep2


title: AML-86-001

value: Female


title: ATAC_SSCL_KO_2

description: ATAC-SEQ


title: AML-57-001


title: M. mass-infected macrophages 2


title: AML-54-001


title: CRISPRi Library H2 medium peak

description: Medium CRE-DD-GFP

value: Library H2


title: ATAC_SSCL_2

description: ATAC-SEQ

value: primary dermal fibroblasts


title: AML-53-001


title: AML-63-001


title: M. mass-infected macrophages 1


title: CRISPRi Library H2 low peak

description: Low CRE-DD-GFP

value: Low cAMP reporter expressing population


title: Non-infected macrophages 3


title: Neuroblastoma cell line (SH-SY5Y) control (w/o SWT) rep1

value: Control (no treatment)


title: AML-71-001


title: CRISPRi Library H1 low peak

description: Low CRE-DD-GFP


title: Neuroblastoma cell line (SH-SY5Y) control (w/o SWT) rep2


title: D3_FPKM

city: Changsha

first: hao

last: zhao

state: Hunan

address: 8 Luyun Road

department: School of Basic Medical Science

institute: Central South University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: induced endothelial cells

growth_protocol: For differentiation, hESCs-FLI1 were mechanically isolated and then plated on matrigel (354234, Corning)-coated plates in mTeSR1 (05850, STEMCELL) with 10 μm ROCK inhibitor Y-27632 (688002, Calbiochem). After 24 hours, the medium was changed with mTeSR 1 or EGM-2 (CC-3162, Lonza) supplemented with 1 µM PMA (sc-3576, Santa Cruz) and 1 µg ml-1 DOX (D9891, Sigma-Aldrich). After 3 days, supplements were changed with 50 ng ml-1 VEGF-A (96-100-20-10, PEPROTECH). The medium was replaced every day.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ES-derived endothelial cells

tag: passages


title: AML-44-001

value: Male


title: AML-50-001


title: D2_FPKM


title: AML-37-001


title: Non-infected macrophages 1


title: D0_FPKM

source_name: human embryonic stem cells

value: embryonic stem cells


title: AML-29-001


title: AML-32-001


title: Non-infected macrophages 2


title: HCMV/M. mass co-infected macrophages 3


title: AML-20-001


title: D1_FPKM


title: AML-21-001


title: AML-17-001


title: AML-19-001


title: Fer2 OE_rep3

city: Geneva

first: Federico

last: Miozzo

address: 30 Quai Ernest-Ansermet, CH-1211

country: Switzerland

institute: University of Geneva

data_processing:
Mapping of the sequencing reads and DEG analysis were performed using the HTSstation with default settings (David et al., PLoS One, 2014)
Genome_build: dm3
Supplementary_files_format_and_content: PAM RNA-seq RPKM.xlsx

organism: Drosophila melanogaster

source_name: isolated PAM neurons

growth_protocol: Flies were maintained on standard cornmeal-agar food at 25 °C in a 12 h:12 h light-dark cycle and under controlled humidity.

extract_protocol:
Cells were dissociated from the brains of ~70 14-day-old flies 2 h before lights-on (ZT22). After papain treatment and trituration in SMactive medium containing 50 μm AP5, 20 μm DNQX and 0.1 μm TTX, the cell suspension was filtered through a sterile 70 μm membrane and distributed to three wells of three two-well chamber glass slides (LabTek II, Nunc) kept on ice. RedStinger-positive cells were sorted on a fluorescence microscope equipped with a motorized stage and a needle holder. Cells were selected manually using capillaries with 50 μm tip diameter. Collected cells were released in a clean part of the chamber and immediately picked up again, greatly reducing the amount of debris. Cells were reselected for two rounds and finally transferred using a new capillary with 30-μm tip diameter to 100-μl lysis buffer (Absolutely RNA Nanoprep Kit; Agilent). Cells of multiple collections were pooled if needed to obtain 200 cells per sample, and total RNA was extracted according to the manufacturer's instructions. The RNA was converted to cDNA and amplified using the SMART-Seq4 Kit (Takara Bio).
Libraries were generated using NexteraXT (Illumina) and sequenced on an Illumina HiSeq 2500 at the iGE3 Genomics Platform in Geneva.

tag: age

value: day 14

tag: fer2 levels

value: Fer2 overexpression

value: isolated PAM neurons


title: HCMV/M. mass co-infected macrophages 1


title: HCMV/M. mass co-infected macrophages 2


title: AML-13-001


title: Fer2 OE_rep1


title: AML-08-001


title: HCMV-infected macrophages 3


title: AML-40-001


title: AML-11-001


title: AML-07-002


title: R58-GAL4_rep3

value: R58-GAL4, UAS-RedStinger

value: control


title: Fer2 OE_rep2


title: AML-02-001

label: Cy3 and Cy5


title: AML-03-001


title: R58-GAL4_rep2


title: R58-GAL4_rep1


title: AML-01-001


title: HCMV-infected macrophages 1


title: EPC_FPKM

source_name: endothelial progenitor cells

value: endothelial progenitor cells


title: Pat8_cHCV_P2_8

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Cryopreserved PBMCs, Department of Medicine II of the University Hospital Freiburg, Germany

extract_protocol:
PBMCs from EDTA anticoagulated patient blood were isolated by density gradient centrifugation using Pancoll (Pan-Biotech, Germany). Magnetic bead-based enrichment of antigen-specific CD8 T cells was further performed. For magnetic bead-based enrichment of HCV-specific CD8+ T cells PBMCs were incubated with peptide-loaded HLA- tetramers coupled to phycoerythrin (PE). Subsequent enrichment was performed with anti-PE beads using the MACS technology (Miltenyi Biotec, Germany) according to the manufacturer’s protocol. Enriched HCV-specific CD8+ T cells were used for multiparametric flow cytometry and transcriptome analysis. Epitope-specific HLA tetramers were generated by conjugation of biotinylated peptide-MHC class I monomers with PE-conjugated streptavidin at a HLA:Strepatividin molar ratio of 5:1. The following peptide-loaded HLA tetramers were used: NS31073(CINGVCWTV)/HLA-A*02:01; NS31406(KLVALGINAV/KLSGLGLNAV)/HLA-A*02:01; NS52594(ALYDVVTKL)/HLA-A*02:01; and NS5B2841(ARMILMTHF)/HLA-B*27:05.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: disease state

value: chronic HCV infection

value: Peripheral Blood

value: HCV-specific CD8+ T cells


title: Pat8_cHCV_P2_dup_5


title: HCMV-infected macrophages 2

value: peripheral blood

value: Monocyte


title: Pat8_cHCV_P2_5


title: Pat7_cHCV_P3_9


title: CD LM2 35

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

description: processed data file: tpm_length_scaled_matrix.txt

data_processing:
Basecalls performed using CASAVA version 1.4.
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
Mapping using STAR (v 2.5.2a) to human (GRCh38) and mouse (GRCm38) genomes and assigned to either the human or mouse using disambiguate (v 1.0.0).
Transcript-level expression of transcripts obtained from Ensembl release 89 was quantified using Salmon (v0.11.3, parameters --seqBias and --gcBias) using reads assigned to Human.
Gene-level expression was obtained by aggregating transcript-level abundances using tximport.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.txt.gz are tab-delimited files containing the estimated gene counts as obtained from txImport.
Supplementary_files_format_and_content: tpm_length_scaled_matrix.txt.gz contains length-scaled tpm as obtained from tximport.

extract_protocol:
RNA was captured on beads conjugated with oligo-dT primer according to Macauley et al. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc 11, 2081-2103 (2016).
Libraries were prepared with Smart-Seq2 protocol. Sequencing libraries were generated and indexed from 0.25 ng of cDNA per sample using the Nextera XT DNA Library Preparation Kit (Illumina, Cat# FC-131-2001) according to manufacturer’s instructions.

tag: model

value: Circulating tumor cells (CTCs)

value: Negative

tag: hypoxia


title: Adult ovary dataset2

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

data_processing:
Alignment to Drosophila genome with STAR
Downstream processing with Cell Ranger 2.0.0 (dataset1), 2.1.1 (dataset2) or 3.1.0 (dataset3)
Genome_build: dmel_r6.19
Supplementary_files_format_and_content: Cell Ranger output

source_name: Adult ovary

growth_protocol: 3-5 day old females were fed wet yeast for three consecutive days prior to dissection

extract_protocol:
Flies were dissected within 45 min in ice cold Schneider's Insect Medium with 10% FBS and 167 mg/ml insulin on an ice pack. Tissue was transferred to an eppendorf tube containing ice cold Cell Dissociation Buffer (Thermo Fisher Scientific #13151014) and rinsed once with the buffer. Dissociation was performed at RT in Cell Dissociation Buffer with 4 mg/ml elastase (Worthington Biochemical LS002292) and 2.5 mg/ml collagenase (Invitrogen # 17018-029) with nutation and regular pipetting with a P200 to aid tissue dissociation. After 20 min the solution was passed through a 50 µm filter (Partec #04-0042-2317) and the solution incubated for additional 10 min before passage through a 30 µm filter (Miltenyi Biotec #130-041-407). Enzymes where quenched by adding 500 µl of dissection solution and cells were centrifuged for 5 min at 4°C and 3500 rcf. For the dataset1 dataset cells were subjected to MACS. Cells were washed in dissection solution and centrifuged again before being resuspended in ice cold 200 µl PBS with 0.04 % ultrapure BSA (Thermo Fisher Scientific AM2616). Dissociation was verified and cells were counted using a cell counting chamber and the solution adjusted to 1000 cells per µl.
Single Cell 3' v2, 10X Genomics
Single-cell RNA-sequencing

value: Canton-S

tag: developmental stage adult

value: ovary


title: Pat7_cHCV_P3_10


title: CD LM2 31

value: Positive


title: CD LM2 40


title: Pat6_cured_HCV_9

value: cured HCV infection


title: Pat6_cured_HCV_11


title: Pat8_cHCV_P2_7


title: Pat6_cured_HCV_12


title: AML-07-001

value: Male


title: CD Br16 65


title: Wildtype Repop Thalamus 2 [Tha2Rep]

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Illumina HiSeq4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM)  were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values for all Samples.

source_name: C57BL/6_Irradiation + PLX3397_Thalamus

extract_protocol:
Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice.  RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Irradiation + PLX3397

tag: brain region

value: Thalamus


title: Pat6_cHCV_16


title: Adult ovary dataset3


title: Pat3_cured_HCV_4


title: Wildtype Repop Thalamus 4 [Tha4Rep]


title: Pat3_cured_HCV_2


title: CD Br16 63


title: CD Br16 55


title: CD Br16 57


title: Wildtype Repop Thalamus 3 [Tha3Rep]


title: Wildtype Repop Thalamus 1 [Tha1Rep]


title: Wiltype Repop Hippocampus 4 [Hip4Rep]

value: Hippocampus


title: Pat6_cured_HCV_10


title: Adult ovary dataset1


title: Pat3_cHCV_14


title: CD Br16 53


title: Pat3_cured_HCV_3


title: Pat3_cured_HCV_1


title: Pat3_cHCV_13


title: Wiltype Repop Hippocampus 3 [Hip3Rep]


title: CD LM2 30


title: Pat2_cHCV_P1_3


title: CD Br16 50


title: Pat6_cHCV_15


title: Wiltype Repop Hippocampus 2 [Hip2Rep]


title: Pat2_cHCV_P1_4


title: Pat2_cHCV_P1_2


title: Wiltype Repop Hippocampus 1 [Hip1Rep]


title: Pat2_cHCV_P1_1


title: NMN_kidney_2680mg:kg:d_rep2

city: Shanghai

first: yingnan

last: you

address: 26 Qiuyue Rd., Pudong

institute: Chinese Academy of Sciences

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to rat with STAR by default parameter. The read counts for each genes were calculated by HTSEQ_COUNT. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: mm19
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01)

value: male

value: 2680mg/kg/d NMN-treated

value: kidney


title: Wildtype Repop Cortex 4 [Cor4Rep]

source_name: C57BL/6_Irradiation + PLX3397_Cortex

value: Cortex


title: NMN_kidney_2680mg:kg:d_rep3


title: control_kidney_2680mg:kg:d_rep3

value: control


title: CD 605


title: NMN_kidney_2680mg:kg:d_rep1


title: control_kidney_2680mg:kg:d_rep1


title: CD 609


title: Wildtype Repop Cortex 3 [Cor3Rep]


title: CD 599


title: control_kidney_2680mg:kg:d_rep2


title: CD 601


title: NMN_liver_2680mg:kg:d_rep2

value: liver


title: Wildtype Irradiation Thalamus 3 [Tha9Ir]

value: Irradiation


title: CD 597

value: Circulating tumor cells (CTCs)


title: αKG_Rep1

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
All the sequence reads were aligned to mouse genome (build mm10) using Tophat.
Expression of the transcript was determined using Cufflinks with Refseq mRNAs to guide assembly.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: mBMSCs

growth_protocol: mBMSCs were isolated from the bone marrow of mice at 18-mon-old. The cells were maintained in DMEM, containing 10% fetal bovine serum, 100 U/ml of K-Penicillin G and 100 mg/ml of Streptomycin sulfate at 37°C with a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated after aKG treatment for 48 hours using Trizol reagent according to the manufacturer's instructions. mRNA purification was perfromed using Dynabeads mRNA purification kit (Invitrogen).
libraries were prepared using KAPA Stranded RNA-Seq Kits (Cat No.: KK8400)  for sequencing.

treatment_protocol: aKG was added into the culture medium at the final concentration of 2 mM.

value: bone marrow–derived  cells


title: Wildtype Repop Cortex 1 [Cor1Rep]


title: CD 592

value: Negative


title: Control_Rep2


title: αKG_Rep2


title: Wildtype Repop Cortex 2 [Cor2Rep]


title: NMN_liver_2680mg:kg:d_rep3


title: Wildtype Irradiation Thalamus 2 [Tha6Ir]


title: NMN_liver_2680mg:kg:d_rep1


title: AML-25-001


title: CD 591


title: Wildtype Irradiation Hippocampus 3 [Hip7Ir]


title: Wildtype Irradiation Thalamus 1 [Tha18Ir]


title: CD 585


title: control_liver_2680mg:kg:d_rep3


title: Wildtype Irradiation Hippocampus 4 [Hip9Ir]


title: rde-4; dot-1.1 mut H3K9me2 ChIP-seq repl. 1

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

country: United Kingdom

institute: King’s College London

description: ChIP sample for H3K9me2 ChIP-seq in rde-4; dot-1.1 mutant, replicate 1

data_processing:
Libraries were sequenced on a NextSeq500 Illumina sequencer and FASTQ files were downloaded from Illumina BaseSpace.
Reads were mapped to the C. elegans genome (ce10 assembly) using QuasR (version 1.16.0).
Read counting in regions was performed with BEDtools (MultiCovBed) v2.29.0.. Regions without 0 counts in all samples were not considered for further analyses.
Counts were normalized using the TMM method using the edgeR package (version 1.16.0).
Genome_build: ce10
Supplementary_files_format_and_content: Genome-wide coverage files (bedGraph format) were generated using bamCompare (deepTools suite) v3.3.2.. The log2-transformed ratio between the ChIP sample and the corresponding input sample was calculated for each of 10 bp windows spanning the genome.

organism: Caenorhabditis elegans

source_name: Whole-body organism

growth_protocol: Strains were maintained at 20°C under standard conditions. Hypochlorite-synchronized L1 stage animals were grown for 36 hours post-hatching at 20ºC on standard NGM plates with OP-50 E. coli.

extract_protocol:
Synchronized L3 larvae were washed off the plates using isotonic M9 solution. Fixation was performed for 30 min at 20°C in crosslinking solution (2% paraformaldehyde in M9 buffer), and excess formaldehyde was quenched with 0.1 M Tris-HCl pH 7.5. The pellet was then washed twice with M9 buffer at 4°C. The worm pellet was resuspended in 1 mL ice-cold RIPA buffer (10 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA, 0.15 M NaCl) supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). The suspension was then transferred to a Covaris milliTUBE 1 mL with AFA® fiber and shearing was performed using the following settings in SonoLab7: Peak Incident Power (PIP) = 240W; Duty Factor = 20%; Cycles per burst (cpb) = 200; time = 480 seconds. After shearing, the crude extract was spun for 10 min at 10,000 x g and the supernatant was collected. Protein concentration was determined by the Bradford method. Extract corresponding to 1 mg protein was diluted to 500 μl with ice-cold RIPA buffer supplemented with Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific). Antibody specific for H3K9me2 (Abcam, ab1220, 5 μg) was added and, after incubation at 4°C for 1 h, 50 μl of Dynabeads™ Protein G suspension (Thermo Fisher Scientific) were added and the mixture was incubated at 4°C for 1 h on rotation. Beads were recovered with a Dynal® Magnetic Particle Concentrator (Invitrogen) and washed at 4°C with: 0.5 mL buffer TSE-150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), 2 X 0.5 mL buffer TSE-500 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), 0.5 mL buffer TSE-1M (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 1 M NaCl), 0.5 mL buffer LiCl (250 mM LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), 2 X 0.5 mL buffer TE (10 mM Tris pH 8.0, 1 mM EDTA). Antibody-bound chromatin was recovered in 2 X 0.2 mL elution buffer (1% SDS, 0.1 M NaHCO3) by shaking at room temperature for 15 min. Elution buffer was added to input samples (5%) to a total volume of 0.4 mL. Input and ChIP chromatin samples were subsequently processed in parallel. After 20 μl of 5 M NaCl was added to each sample, cross-links were reversed overnight at 65°C. 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris-HCl pH 6.5 and 0.5 μl of 20 mg/mL Proteinase K (Thermo Fisher Scientific) were added and each sample was incubated for 1 h at 42°C. DNA was recovered using the QIAquick PCR Purification Kit (Qiagen) in accordance with the manufacturer's instructions.
Immunoprecipitated DNA and input libraries were prepared using TruSeq ChIP Library Preparation kit following the manufacturer's instructions (Illumina) and checked for concentration and quality on DNA chips with a Bioanalyzer (Agilent). 75-bp single read sequences were generated on the NextSeq 500 sequencer according to manufacturer’s instructions (Illumina).

tag: developmental stage

value: Third larval (L3) stage

tag: chip antibody

value: H3K9me2 (Abcam, ab1220)


title: control_liver_2680mg:kg:d_rep1

tag: gender


title: CD 583

tag: cell type


title: CD 574

value: Positive


title: Wildtype Irradiation Cortex 4 [Cor9Ir]


title: rde-4; dot-1.1 mut input repl. 1

description: Input sample for H3K9me2 ChIP-seq in rde-4; dot-1.1 mutant, replicate 1


title: NMN_kidney_1340mg:kg:d_rep3

value: 1340mg/kg/d NMN-treated


title: CD 571


title: Wildtype Irradiation Hippocampus 2 [Hip6Ir]


title: NMN_kidney_1340mg:kg:d_rep1


title: rde-1; dot-1.1 mut input repl. 2

description: Input sample for H3K9me2 ChIP-seq in rde-1; dot-1.1 mutant, replicate 2


title: NMN_kidney_1340mg:kg:d_rep2


title: CD 590


title: NMN_kidney_1340mg:kg:d_rep4


title: Control_Rep1


title: CD 264


title: control_liver_2680mg:kg:d_rep2


title: rde-1; dot-1.1 mut H3K9me2 ChIP-seq repl. 1

description: ChIP sample for H3K9me2 ChIP-seq in rde-1; dot-1.1 mutant, replicate 1


title: rde-1; dot-1.1 mut input repl. 1

description: Input sample for H3K9me2 ChIP-seq in rde-1; dot-1.1 mutant, replicate 1


title: CD 580


title: Wildtype Irradiation Hippocampus 1 [Hip18Ir]


title: Wildtype Irradiation Cortex 2 [Cor6Ir]


title: rde-1; dot-1.1 mut H3K9me2 ChIP-seq repl. 2

description: ChIP sample for H3K9me2 ChIP-seq in rde-1; dot-1.1 mutant, replicate 2


title: control_kidney_1340mg:kg:d_rep3


title: CD 224


title: CD 229


title: dot-1.1; ced-3 mut H3K9me2 ChIP-seq repl. 1

description: ChIP sample for H3K9me2 ChIP-seq in dot-1.1; ced-3 mutant, replicate 1


title: Wildtype Irradiation Cortex 3 [Cor7Ir]


title: control_kidney_1340mg:kg:d_rep4


title: CD 222


title: Wildtype Irradiation Cortex 1 [Cor18Ir]


title: CD 208


title: control_kidney_1340mg:kg:d_rep1


title: Wildtype Control Thalamus 3 [Tha35Con]

source_name: C57BL/6_Vehicle _Thalamus

value: Vehicle


title: NMN_liver_1340mg:kg:d_rep4


title: Wildtype Control Thalamus 4 [Tha36Con]

value: Thalamus


title: dot-1.1; ced-3 mut input repl. 2

description: Input sample for H3K9me2 ChIP-seq in dot-1.1; ced-3 mutant, replicate 2


title: dot-1.1; ced-3 mut input repl. 1

description: Input sample for H3K9me2 ChIP-seq in dot-1.1; ced-3 mutant, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_A1_ad008

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
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
Genome_build: 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

source_name: C57BL/6J Male P56 Mouse Brain

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: CP

tag: Sex


title: Wildtype Control Thalamus 2 [Tha34Con]

tag: treatment


title: dot-1.1; ced-3 mut H3K9me2 ChIP-seq repl. 2

description: ChIP sample for H3K9me2 ChIP-seq in dot-1.1; ced-3 mutant, replicate 2


title: NMN_liver_1340mg:kg:d_rep3

value: male

tag: tissue


title: zfp-1 mut H3K9me2 ChIP-seq repl. 2

description: ChIP sample for H3K9me2 ChIP-seq in zfp-1 mutant, replicate 2


title: NMN_liver_1340mg:kg:d_rep2


title: Wildtype Control Thalamus 1 [Tha33Con]


title: zfp-1 mut H3K9me2 ChIP-seq repl. 1

description: ChIP sample for H3K9me2 ChIP-seq in zfp-1 mutant, replicate 1


title: CD 180


title: CD 162


title: control_kidney_1340mg:kg:d_rep2


title: NMN_liver_1340mg:kg:d_rep1


title: zfp-1 mut input repl. 2

description: Input sample for H3K9me2 ChIP-seq in zfp-1 mutant, replicate 2


title: Wildtype Control Hippocampus 4 [Hip36Con]

source_name: C57BL/6_Vehicle _Hippocampus

value: Hippocampus


title: Wildtype Control Hippocampus 3 [Hip35Con]


title: gin2+Glc-3

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis thaliana genome sequence (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/MASKED/ler_0.v7.PR_in_lowercase.fas) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values for 36 Samples.

organism: Arabidopsis thaliana

source_name: 4-day seedlings

growth_protocol: 22-23℃, 12h/12h (Light/Dark), liqiud 1/2MS with 0.5% glucose (for ACC treatments) without glucose(for glucose recovering samples)

extract_protocol: TRIZOL regent

treatment_protocol: For ethylene related samples,Seedlings were treated with 10 μM ACC for 2 and 4 hours and mock-treated seedlings were used as control. For glucose-TOR and glucose-HXK1 related samples,4d glucose depletion seedligns were treated with (+Glc) or without (-Glc) 15 mM glucose for 2 hours and non-treated samples were used as control.

tag: genotype/variation

value: gin2 mutant

value: seedling

value: 4 days


title: CD 190


title: zfp-1 mut input repl. 1

description: Input sample for H3K9me2 ChIP-seq in zfp-1 mutant, replicate 1


title: control_liver_1340mg:kg:d_rep4

value: control

value: liver


title: Wildtype Control Hippocampus 2 [Hip34Con]


title: control_liver_1340mg:kg:d_rep3


title: ced-3 mut H3K9me2 ChIP-seq repl. 2

description: ChIP sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 2


title: ced-3 mut H3K9me2 ChIP-seq repl. 1

description: ChIP sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 1


title: Wildtype Control Cortex 3 [Cor36Con]

source_name: C57BL/6_Vehicle _Cortex

value: Cortex


title: Wildtype Control Hippocampus 1 [Hip33Con]


title: control_liver_1340mg:kg:d_rep1


title: gin2+Glc-1


title: ced-3 mut input repl. 2

description: Input sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 2


title: ced-3 mut input repl. 1

description: Input sample for H3K9me2 ChIP-seq in ced-3 mutant, replicate 1


title: gin2-Glc-2


title: gin2-Glc-3


title: Wildtype Control Cortex 1 [Cor34Con]


title: WT H3K9me2 ChIP-seq repl. 2

description: ChIP sample for H3K9me2 ChIP-seq in wild-type, replicate 2

value: N2 (Bristol)


title: Wildtype Control Cortex 2 [Cor35Con]


title: gin2-Glc-1


title: Ler+Glc-2

value: Wild type


title: WT H3K9me2 ChIP-seq repl. 1

description: ChIP sample for H3K9me2 ChIP-seq in wild-type, replicate 1

value: Third larval (L3) stage


title: CTL.3

city: TianJin

first: Heng

last: Dai

state: TianJin

address: NanKai District NanKai University

institute: NanKai University

data_processing:
RNA-seq raw reads with low-quality bases, adapters were trimmed by Trimmomatic to obtain clean reads
clean reads were aligned to the UCSC mouse mm10 reference genome using the Hisat2 with default settings
Read counts of each gene annotated in RefGene were calculated by featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: rOvary tissue

growth_protocol: The rOvaries were obtained from mice after transplated one month

extract_protocol:
The RNA of rOvaries were extracted by Rneasy Plus Mini Kit(Cat. No. 74134)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For mice，the INK128 was fed at a final concentration of 0.75uM/g in drinking water（based on the weight of mice, weigh the mice once a week）.

value: Control


title: Ler+Glc-3


title: ink128.2


title: gin2+Glc-2


title: ink128.1


title: Ler+Glc-1


title: WT input repl. 1

description: Input sample for H3K9me2 ChIP-seq in wild-type, replicate 1


title: WT input repl. 2

description: Input sample for H3K9me2 ChIP-seq in wild-type, replicate 2


title: CTL.1


title: Anp32eKO_MEF_SMARCA4_CUTTag_Rep3

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

description: Anp32eKO_MEF_SMARCA4_CUTTag.merged.RPKM.bw

data_processing:
Library strategy: CUT&Tag
Sequencing reads were aligned to mm10 genome using Bowtie2, and then PCR duplicates were removed using Picard.
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were cultured in DMEM media (Thermo 11995073) containing 10% FBS and antibiotics. Approximately 200,000 cells were seeded on 10cm plates 1 day prior to RNA isolation or ATAC library preparation. Approximately 100,000 cells were used for CUT&Tag library preparation.

extract_protocol: CUT&Tag libraries were prepared using NEBNext HiFi 2XPCR Master mix with standard protocols, cleaned up using 1.1 volume Ampure XP beads and pooled together for paired-end sequencing.

value: Mouse embryonic fibroblasts (MEFs)

tag: passage

value: below 8

value: Anp32e KO

tag: protein


title: Anp32eKO_MEF_SMARCA4_CUTTag_Rep1


title: Old_Tet1-/-_315_1_TTCCATTG (whs v16)

city: Tianjin

first: wang

middle: hua

last: song

address: Tianjin city, China

institute: nankai university

description: whs v16.txt

data_processing:
we analysed the raw data of fq.gz files by Hisat2,samtools  and featurecounts to get the raw counts.
Genome_build: mm10
Supplementary_files_format_and_content: The reads counts of 133 samples, containg young WT, young Tet2-/-, old WT and old Tet2-/-, and some of Tet1 samples.

source_name: oocyte

extract_protocol:
For oocyte sequence, we obtained 133 ovulated oocytes; for PGC sequence, we purified E13.5 PGC from 4-6 embryos each group
oocyte library were prepared using standard  Illumina protocols; PGC library were prepared according to micro RNA construction

tag: age

tag: genotype

value: Tet1 knock out

value: single MII oocyte


title: Ler-Glc-3


title: control_liver_1340mg:kg:d_rep2

value: male


title: Anp32eKO_MEF_SMARCA4_CUTTag_Rep2


title: Ler-Glc-2


title: CD28_CD3_stim_CITE_ADT

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: antibody oligos

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0 (ATAC) and CellRanger mkfastq v3 (RNA) respectively.
Sequencing reads were aligned using CellRanger-ATAC and CellRanger count for the hg38 reference genome
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

source_name: Peripheral blood mononuclear cells

extract_protocol:
Samples were stained with hashing and surface marker antibodies, fixed with 1% PFA and then extracted using the 10x protocol (Omni-ATAC)
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1.1 protocol while ASAP antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfied using tag-specific handles.GEX libraries were constructed according to the 10x Genomics scRNAseq v3.1 protocol and CITE tags as described in CITE-seq protocols (Stoeckius et al, 2017).
10x Genomics scATAC-seq v1.1 (ASAP-seq) / scRNA-seq v3.1 (CITE-seq)

treatment_protocol: Thawed cryopreserved PBMCs were resuspended to 1M/ml density in either complete medium supplemented with IL2 (unstimulated control) or complete medium supplemented with IL2 and ImmunoCult Human CD3/CD28 T cell Activator (stimulated sample) for 16 hours.

value: Peripheral blood mononuclear cells

value: 16hr incubation with IL2 and anti-CD3/CD28

tag: target molecule

value: Cell Surface Markers

tag: ab tags

value: 15 bases long (227 tags total)

tag: lysis buffer

value: no lysis


title: WT_MEF_SMARCA4_CUTTag_Rep2

value: WT


title: Old_Tet1-/-_209_6_TGTGGTTG (whs v16)

description: whs v16.txt

tag: strain


title: WT_MEF_SMARCA4_CUTTag_Rep3


title: Old_Tet1-/-_209_4_TACAGGAT (whs v16)

description: whs v16.txt


title: WT_MEF_SMARCA4_CUTTag_Rep1


title: tor+Glc-3

value: XVE-TOR RNAi

value: seedling

value: 4 days


title: CD28_CD3_control_CITE_ADT

description: antibody oligos

value: 16hr incubation with IL2


title: Old_Tet1-/-_209_2_TTCCTGCT (whs v16)

description: whs v16.txt


title: CD28_CD3_stim_CITE_GEX

description: cDNA

value: polyA mRNA


title: CD28_CD3_control_CITE_GEX

description: cDNA


title: tor+Glc-2


title: WT_MEF_ANP32E_CUTTag_Rep3

value: Mouse embryonic fibroblasts (MEFs)


title: CD28_CD3_stim_ASAP_ATAC

description: tagmented gDNA

value: Accessible chromatin

value: OMNI


title: CD28_CD3_stim_ASAP_ADT

description: antibody oligos


title: Anp32eKO_MEF_SP1_CUTTag_Rep3

value: below 8

value: Anp32e KO


title: tor-Glc-3


title: tor+Glc-1


title: tor-Glc-2


title: CD28_CD3_control_ASAP_ADT

description: antibody oligos


title: CD28_CD3_control_ASAP_ATAC

description: tagmented gDNA


title: Anp32eKO_MEF_SP1_CUTTag_Rep2


title: Ler-Glc-1

value: Wild type


title: tor-Glc-1


title: Anp32eKO_MEF_SP1_CUTTag_Rep1


title: Old_WT_247_5_TGTATGCG (whs v16)

description: whs v16.txt

value: wild type

value: single MII oocyte


title: d7__UM171_r4

city: Montreal

first: Guy

last: Sauvageau

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Cellranger v3.0.1 count and prefiltering (target cell number 6000)
Seurat 3 QC, exclusion of cells with less genes or UMIs than medians minus 2 standard deviations
Seurat 3 QC, exclusion of cells with more genes or UMIs than the respective medians plus 2 standard deviations (multiplets)
Seurat 3 QC, exclusion of cells with more than 7% mitochondrial gene expression (apoptotic cells)
Seurat 3 metadata extraction
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger count output as filtered_feature_bc_matrix; Seurat 3 metadata as tab-separated-value

source_name: UM171-expanded_umbilical cord blood CD34+

extract_protocol:
Single cells were processed using the 10X Chromium controlller.
10X Chromium version 2 3' RNAseq.

value: umbilical cord blood CD34+

tag: cell subtypye


title: Col-0+Glc-3


title: Old_WT_247_4_TCCAGTCG (whs v16)

description: whs v16.txt


title: d0__fresh_run4

source_name: fresh_umbilical cord blood CD34+

value: fresh


title: WT_MEF_ANP32E_CUTTag_Rep2


title: WT_MEF_SP1_CUTTag_Rep3


title: WT_MEF_ANP32E_CUTTag_Rep1


title: Old_WT_247_7_TGGCTCAG (whs v16)

description: whs v16.txt


title: WT_MEF_SP1_CUTTag_Rep2


title: Old_WT_247_6_TCATTGAG (whs v16)

description: whs v16.txt


title: Col-0+Glc-2


title: WT_MEF_SP1_CUTTag_Rep1


title: X89M_pre

city: Boston

first: James

middle: M.

last: Billingsley

address: Landmark Center, 3rd Floor East, 401 Park Drive

institute: harvard T.H. Chan school of public health

data_processing:
Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the NovaSeq S2 to produce 101bp paired-end reads with eight-base index barcodes. Data was analyzed using the Broad Picard Pipeline, which includes de-multiplexing and data aggregation.
Transcripts were annotated using Ensembl release 94
Counts of reads aligning to known genes were generated by featureCounts
transcripts per million (TPM) measurements per isoform were generated by quasialignment using Salmon.(9) Differential expression at the gene level was called with DESeq2(10) using counts per gene estimated from the Salmon quasialignments by tximport,
Genome_build: UCSC build hg38
Supplementary_files_format_and_content: normalized readcounts

source_name: liver biopsy

extract_protocol:
sample preparation: Participant baseline evaluation included an ultrasound-guided percutaneous liver biopsy yielding two cores, which was completed on all participants except for those with a contraindication (e.g., anticoagulation). The first core was fixed in formalin, and subsequently underwent histopathologic review by a single expert pathologist blinded to treatment (D.E.K., National Institutes of Health). Histological scoring, including NAFLD Activity Score (NAS) and fibrosis stage, was performed according to the Nonalcoholic Steatohepatitis Clinical Research Network scoring system.(4) The second core was placed in an RNA stabilization reagent (RNAlater, Qiagen) and stored at -80o C for gene expression analysis. Both 1H-MRS and liver biopsy were repeated at 12 months following randomization. A total of 19 participants randomized to tesamorelin and 24 participants randomized to placebo had paired liver specimens available for gene sequencing.
Liver cores were placed in an RNA stabilization reagent (RNAlater, Qiagen) and stored at -80 C for gene expression analysis
Following extraction from liver tissue using RNeasy Plus Mini Kit (Qiagen), total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. Following plating, 2 uL of ERCC controls (using a 1:1000 dilution) and a k562 control were spiked into each sample. An 200ng aliquot of each sample was taken for library preparation using the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. oligo dT beads were used to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 400bp cDNA underwent dual-indexed library preparation: ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment the libraries were quantified using Quant-iT PicoGreen (1:200 dilution).

value: liver

tag: patient diagnosis

value: HIV with NAFLD

tag: participant

tag: timepoint

value: TESAMORELIN


title: Col-0-Glc-3

value: seedling


title: Col-0+Glc-1

value: 4 days


title: Col-0-Glc-2


title: Non-epithelial mammary cells - high-fat diet_rep2

city: Baltimore

first: Pang-Kuo

last: Lo

state: Maryland

address: 108 N. Greene St.

department: Biochemistry and Molecular Biology

institute: University of Maryland School of Medicine

description: Sample 4 (HFD_245)

data_processing:
Illumina Casava 1.8.2 software used for basecalling
CellRanger (v3.0.2) was used as a pipeline to wrap Illumina's bcl2fastq for generating Fastq files and sequencing as well as 10x-specific quality control metrics, including barcode quality, accuracy, and diversity.
CellRanger (v3.0.2) was used to generate raw counts (including cell barcodes and gene features) from processing each GEM well from the demultiplexed Fastq.
Genome_build: mm10
Supplementary_files_format_and_content: The R-based Seurat package (v3.1.1) and R scripts (R version 3.6.1) were used to read cell barcodes, gene features and matrix files generated from CellRanger and integrate repeated datasets as a single dataset (RD_236 was integrated with RD_257 to be the RD dataset, and HFD_243 was integrated with HFD_245 to be the HFD dataset) for the subsequent scRNA-seq data analysis such as QC, PCA, t-SNE, and other analyses.
Supplementary_files_format_and_content: The FindMarkers syntax built in the R-based Seurat package (v3.1.1) was used to perform differential gene expression analysis on a specific cell type across two different diet feeding conditions (HFD vs. RD). The differential gene expression results were exported as the csv file format.

source_name: Non-epithelial mammary cells

extract_protocol:
Non-epithelial mammary cells isolated from mammary glands were enriched by removing epithelial cells using the anti-EpCAM antibody and magnetic dynabeads. To isolate viable cells, enriched non-epithelial cells were stained with 7-AAD dye (0.5 µg/ml) and 7-AAD-negative viable cells were sorted using the FACS Aria II cell sorter (BD Biosciences, Franklin Lakes, NJ, USA).
FACS-sorted viable single cells were processed by using the 10X Genomics Chromium device to prepare scRNA-seq libraries (Single Cell 3' v2) according to the manufacturer’s protocol.
Single-cell RNA-seq (scRNA-seq)

treatment_protocol: Four two-month-old female C57BL/6 Brca1-/-;p53+/- mice were randomized and fed with either a lean-fat diet (10% kcal from fat) or a high-fat diet (60% kcal from fat) ad libitum for 10 weeks (n = 2 for each diet group).

value: mammary gland

tag: cell type

value: stromal and immune cells

value: high-fat diets


title: X85M_pre

value: PLACEBO


title: Old_WT_365_5_TACTTCGG (whs v16)

description: whs v16.txt


title: Old_Tet1-/-_209_7_TACTAGTC (whs v16)

description: whs v16.txt

value: Tet1 knock out


title: Old_WT_247_2_TCAGGAGG (whs v16)

description: whs v16.txt


title: Non-epithelial mammary cells - high-fat diet_rep1

description: Sample 3 (HFD_243)


title: Col-0-Glc-1


title: Old_WT_365_4_TGAACTGG (whs v16)

description: whs v16.txt


title: Old_Tet1-/-_209_3_TAGTGACT (whs v16)

description: whs v16.txt


title: X83M_pre


title: Non-epithelial mammary cells - regular diet_rep2

description: Sample 2 (RD_257)

value: regular diets


title: Old_WT_247_3_TAAGTTCG (whs v16)

description: whs v16.txt


title: Col-0-ACC-4-hour-3


title: Non-epithelial mammary cells - regular diet_rep1

description: Sample 1 (RD_236)


title: Old_WT_365_2_TAACGCTG (whs v16)

description: whs v16.txt


title: X83M_post


title: X85M_post


title: Col-0-ACC-4-hour-2


title: Old_WT_365_3_TTGGTATG (whs v16)

description: whs v16.txt


title: Old_WT_365_1_TCGAAGTG (whs v16)

description: whs v16.txt


title: X82M_pre


title: Neu_SP_2

city: Oxford

first: Irina

last: Udalova

state: Oxfordshire

address: The Kennedy Institute of Rheumatology, Roosevelt Drive, Headington

department: NDORMS

institute: Kennedy Institute

data_processing:
Reads were trimmed with Cutadapt prior to mapping with Bowtie2 with the options: "--local --X 2000"
Duplicates were removed with PicardTools markDuplicates, as were reads with MAPQ scores < 10 or insert sizes > 150 bp
Peak calling was conducted using MACS2 with the following settings: "--format BAMPE --nomodel --keep-dup-all --mfold 5,50".
DeepTools was used to generate normalised (FPKM) bigWigs of ATAC signal
Differentially accessible sites were determined by counting reads over a union interval set of all detected peaks and analysis with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig - ATAC signal (FPKM)

source_name: spleen

extract_protocol:
Live cells were sorted as DAPI-negative. For blood/spleen/lung neutrophils were sorted as CD45+CD11b+Ly6G+, for the bone marrow mature neutrophils were sorted as CD11b+Ly6GhighCXCR2high.
Nuclei isolated and accessible DNA tagmented and purified following ATAC-seq protocol. DNA fragments 100 bp - 1 kb were selected with AMPure XP beads and amplified by PCR prior to pooling and sequencing

value: Neutrophil

value: spleen

tag: replicate


title: Old_WT_247_1_TCTCACGG (whs v16)

description: whs v16.txt

value: wild type


title: Col-0-ACC-4-hour-1

value: Wild type


title: X82M_post

tag: treatment


title: X89M_post

tag: tissue


title: Neu_SP_1


title: X78M_pre


title: Young_Tet1-/-_201_8_TTGACTCT (whs v16)

description: whs v16.txt

value: single MII oocyte


title: Col-0-ACC-2-hour-3

tag: genotype/variation


title: Neu_LU_1

source_name: lung

value: lung


title: Young_Tet1-/-_201_6_TGATACGT (whs v16)

description: whs v16.txt


title: Neu_LU_2


title: Young_Tet1-/-_201_4_TTGGAGGT (whs v16)

description: whs v16.txt


title: Young_Tet1-/-_201_7_TGCATAGT (whs v16)

description: whs v16.txt


title: Neu_BM_2

source_name: bone marrow

value: bone marrow


title: Col-0-ACC-2-hour-1


title: Col-0-ACC-2-hour-2


title: Col-0-mock-4-hour-3


title: X78M_post

value: liver

value: HIV with NAFLD


title: Young_Tet1-/-_201_3_TCTGCTGT (whs v16)

description: whs v16.txt


title: X76M_post


title: Col-0-mock-4-hour-1

value: seedling


title: Neu_BL_1

source_name: blood

value: blood


title: X67M_pre

value: TESAMORELIN


title: Col-0-mock-2-hour-3

value: 4 days


title: Col-0-mock-4-hour-2


title: Young_WT__246_15_TAAGCGTT (whs v16)

description: whs v16.txt


title: Neu_BL_2


title: 6M-Exp-Spleen-CD4-Resub

city: Bronx

first: Boris

last: Bartholdy

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter and quality trimming using bbduk.sh from BBTools.
RNA-seq reads were aligned to the mm10 genome assembly using STAR  with default parameters
Aligned bam files were processed in R/Bioconductor using SummarizeOverlaps to summarize the bam for the intervals in TxDb.Mmusculus.UCSC.mm10.knownGene (exons by gene) generating a "summarized experiment".
The "summarized experiment" was analyzed using deseq2 with default parameters. Deseq2 results summary was used to generate a CSV of base mean expression, fold change and p-value comparing wildtype and h1cTKO;vav-iCre expression which was exported as a CSV.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: Results of differential expression between WT and cTKO cells from DESeq2 in comma-separated file format

source_name: CD4+ splenic T cells

extract_protocol:
5x10E5 B, and CD4+ and CD8+ T cells were sorted to Trizol by FACS.
paired-end RNA seq libraries were prepared from polyA-enriched RNA by  GeneWiz (https://www.genewiz.com/)

value: CD4+ splenic T cells

value: cTKO

tag: Sex

value: M


title: Young_Tet1-/-_201_2_TTCTGTGT (whs v16)

description: whs v16.txt

value: Tet1 knock out


title: Col-0-mock-2-hour-2


title: X67M_post


title: X66M_pre

value: PLACEBO


title: X66M_post


title: X65M_pre


title: Young_WT__246_14_TCTCGGTT (whs v16)

description: whs v16.txt


title: X76M_pre


title: Col-0-mock-2-hour-1


title: Young_WT__246_13_TGGTTGTT (whs v16)

description: whs v16.txt


title: Neu_BM_1

value: Neutrophil


title: 5F-Exp-Spleen-B-RNA

source_name: splenic B cells

value: splenic B cells

value: F


title: 5F-Exp-Spleen-CD4--T-RNA


title: X65M_post


title: Young_WT__246_12_CTTGTACT (whs v16)

description: whs v16.txt

value: wild type

value: single MII oocyte