title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D1_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD001_indexed

status: Public on Sep 02 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
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: MOp

tag: Sex

value: male

tag: age

tag: strain


title: H4K20me2_eSPAN_POLA12A_mESC 100k

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Library strategy: eSPAN
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.

source_name: mESC

growth_protocol: Mouse E14 ES cells (a gift from Dr. Tom Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. Yeast cells were synchronized and cultured following the standard protocol (Dunham et al., 2015).

extract_protocol:
eSPAN in yeast was performed exactly as previously described (Yu et al., 2014). Total RNA samples were purified the same as for RT-PCR. OK-seq was performed as previously described with some modifications (Petryk et al., 2016).
RNA-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.
RNA-Seq, ChIP-Seq, CUT&TAG, OK-Seq, eSPAN

tag: condition

value: 100k cell

tag: genotype

tag: experiments


title: day 7 LPS  IL10Rafl_3

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
IL10R_LPS_d7_482_flox_3
Shemer et al  SOURCE file IL10Ra 29082020.xlsx
UTAP_wt IL10Rfl_normalized.txt

library_source: transcriptomic

data_processing:
UTAP analysis (https://doi.org/10.1186/s12859-019-2728-2)
Demultiplexing
Low-quality trimmng
UMI counting
Normalization
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts, for all genes which are expressed in at least one sample

molecule: total RNA

source_name: Mouse brain

extract_protocol:
Brain homogenization and microglia enrichment
Mars-seq (DOI: 10.1126/science.1247651)

treatment_protocol: 2.5mg/kg LPS injection

tag: tissue

value: Brain

tag: cell type

value: Microglia

tag: treatment

value: 7days post LPS i.p


title: H4K20me2_eSPAN_MCM22A_mESC 100k


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD008_indexed


title: H4K12ac_eSPAN_WT_mESC rep2

value: WT


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD004_indexed


title: H4K12ac_eSPAN_MCM22A_mESC


title: H4K12ac_eSPAN_POLA12A_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD007_indexed


title: H4K20me2_eSPAN_POLA12A_mESC


title: H4K12ac_eSPAN_WT_mESC


title: H4K20me2_eSPAN_POLA12A_mESC rep2


title: H4K20me2_eSPAN_POLE4_KO_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD007_indexed


title: H4K12ac_eSPAN_POLE3_KO_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD008_indexed


title: H4K20me2_eSPAN_POLE4_KO_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD002_indexed


title: H4K12ac_eSPAN_MCM22A_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D11_AD001_indexed


title: H4K20me2_eSPAN_POLE3_KO_mESC


title: H4K20me2_eSPAN_MCM22A_mESC rep2


title: H4K20me2_eSPAN_MCM22A_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD002_indexed


title: H4K20me2_eSPAN_POLE3_KO_mESC rep2


title: H4K20me2_eSPAN_WT_mESC


title: H3K36me3_CUT_POLA12A_mESC

data_processing:
Library strategy: CUT&TAG
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D10_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD004_indexed


title: H4K20me2_eSPAN_WT_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD007_indexed


title: H3K36me3_CUT_WT_mESC


title: H4K12ac_CUT_POLA12A_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD002_indexed


title: H4K12ac_CUT_WT_mESC rep2


title: H4K12ac_CUT_POLE3_KO_mESC


title: H4K12ac_CUT_WT_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD010_indexed


title: H4K20me2_CUT_MCM22A_mESC


title: H4K20me2_CUT_POLE4_KO_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD012_indexed


title: H3K36me3_CUT_POLA12A_mESC rep2


title: H4K20me2_CUT_POLE3_KO_mESC


title: H3K36me3_CUT_WT_mESC rep2


title: H4K20me2_CUT_WT_mESC rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD010_indexed


title: H4K12ac_CUT_MCM22A_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD007_indexed


title: d41 S12 CD8 TCM

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to UCSC human genome build mm10
Gene counts were obtained using featureCounts on GENCODE vM10 annotations
Genome_build: mm10
Supplementary_files_format_and_content: genecounts_20191018.txt

source_name: spleen

growth_protocol: mice were fed with Metformin orally for 30 days

extract_protocol:
Total RNA was extracted following the double extraction protocol:  RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). All mouse RNAs were analyzed on Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA) for quality assessment with a median RNA Quality Score of 9.
cDNA libraries were prepared using 500pg of total RNA and 1ul of a 1:200,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol [1] except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip GX system. All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (16 samples/lane).

treatment_protocol: extracted single cells from mouse spleem and sorted CD8 T cells via MACS sorting, followed by antibody surface staining, continued by sorting of memory T cells via FACS

tag: sample group

value: + BCG  - Met, pop3


title: d41 S11 CD8 TCM


title: d41 S9 CD8 TCM

value: - BCG  + Met, pop3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C9_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD012_indexed


title: d41 S8 CD8 TCM


title: d41 S13 CD8 TCM


title: H4K20me2_CUT_WT_mESC


title: OK_seq_WT_mESC rep2

data_processing:
Library strategy: OK_seq
CUT&TAG, OK-Seq and eSPAN reads were mapped using bowtie2. RNA-Seq reads were mapped using STAR.
Read count on gene body or promoters were calculated by FeatureCount.
Differential genes and log fold change were calculated by DEseq2
Read coverage in each bin was calculated using the R package of Rsamtools. Histone bias was computed from trimmed, mapped, unique reads in each bin as Bias=(W-C)/(W+C), where W and C are the number of reads mapped on Crick and Watson strand in each bin, respectively.
Genome_build: For mouse, reads were mapped to mm10. For yeast, reads were mapped to saccer3.
Supplementary_files_format_and_content: bw files, the score represents reads coverage at each genomic position. Read coverage on plus strand, minus strand and total were calculated seperately.


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD004_indexed


title: d41 S7 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD006_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD002_indexed


title: d41 S18 CD8 TCM

value: + BCG  + Met, pop3


title: d41 S6 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C8_AD006_indexed


title: H4K12ac_CUT_POLE4_KO_mESC


title: H4K20me2_CUT_POLA12A_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD001_indexed


title: OK_seq_WT_mESC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD001_indexed


title: d41 S16 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C7_AD010_indexed


title: d41 S3 CD8 TCM

value: - BCG  - Met, pop3


title: d41 S19 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD004_indexed


title: d41 S1 CD8 TCM


title: d41 S2 CD8 TCM


title: d41 S17 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD006_indexed


title: d41 S4 CD8 TCM


title: d41 S14 CD8 TCM


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD006_indexed


title: SSc3_scrambled + TGFβ

type: RNA

city: Schlieren

first: Elena

last: Pachera

address: Wagistrasse 14

country: Switzerland

institute: USZ

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The R-package ‘lumi’ was used to read and process the microarray raw data. For differential expression analysis was performed using ‘limma'. The annotation is based on the R-package ‘illuminaHumanv4.db’.

label: biotin

organism: Homo sapiens

source_name: dermal fibroblasts

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Primary dermal fibroblasts from SSc patients were derived by outgrowth from 3mm punch biopsy or skin resected from donors undergoing surgery. Fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich) containing 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco) and 10% fetal bovine serum (10% FBS, Gibco) and 100 μM 2-mercaptoethanol (Gibco).

extract_protocol: Total RNA from cells was isolated with Zymo Quick-RNA MicroPrep RNA isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SSc fibroblasts were transfected with 25nM ASO targeting lncRNA H19X or scrambled control for 120h and treated with TGFb for the last 72h.

value: dermal fibroblasts

value: scrambled control

tag: disease state

value: systemic sclerosis


title: SSc6_scrambled + TGFβ

description: replicate 6


title: TAMs - 11 weeks - an3

city: San Francicso

first: Allison

last: Drain

address: 513 Parnassus Ave HSE 560

institute: UCSF

data_processing:
Sequencing reads were aligned to the mouse genome and gene annotation (Ensembl GRCm38.78) using STAR (STAR_2.4 2a). Differentially expressed genes between time points were identified by using the uniquely aligned reads overlapping genes to create a counts matrix and input to DESeq2 (v1.6).
No filtering was applied to this data set.
Supplementary_files_format_and_content: Text and Excel files with read counts for each sample. Columns are a) Fold change, b) Log2 fold change, c) raw p value, d) FDR, e) normalized sample values

source_name: Tumor associated macrophages

extract_protocol:
Mammary glands were collected in DMEM on ice then minced. Tissue was digested in two 30 min rounds of collagenase and DNase with agitation at 37C. At the end of each round, digested tissue was washed through a 100um cell strainer on ice. Red blood cells were lysed with ACK buffer and remaining cells washed and counted. Cells were stained with anti-mouse CD45, anti-mouse CD11b, anti-mouse Ly6C, anti-mouse CD14, anti-mouse I-A/I-E, anti-mouse CD11c, anti-mouse CD24, anti-mouse CD29, anti-mouse CD31, and Zombie NIR live/dead. Sorted macrophages were CD45+, MHCII+, CD14+. Detailed antibody information and gating strategy included in manuscript. Sorted cells were pelleted and snap frozen on dry ice. RNA was harvested using Trizol and measured on a spectrophotometer and run out on a Bioanalyzer to confirm quality.
Libraries were prepared according to manufacturer instructions using Nugen Ovation plus Nextera (<100 ng RNA)

value: Mammary gland-derived macrophage

value: FVB/N

value: MMTV-PyMT


title: SSc5_H19X ASO + TGFβ

description: replicate 5

value: antisense oligonucleotide targeting H19X


title: SSc4_H19X ASO + TGFβ

description: replicate 4


title: SSc6_H19X ASO + TGFβ

description: replicate 6


title: SSc2_scrambled + TGFβ

description: replicate 2


title: SSc3_H19X ASO + TGFβ

description: replicate 3


title: TAMs - 8 weeks - an3


title: SSc1_H19X ASO + TGFβ

description: replicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD006_indexed

value: MOp

value: male


title: SSc4_scrambled + TGFβ

description: replicate 4


title: TAMs - 11 weeks - an2


title: SSc5_scrambled + TGFβ

description: replicate 5


title: TAMs - 8 weeks - an2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C4_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C5_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_D4_AD010_indexed


title: TAMs - 8 weeks - an1


title: treatment 3, input

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

country: China

institute: Newcore biotechnology

data_processing:
Library strategy: meRIP-Seq
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3),
Clean reads of all samples were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software (v1.4.2).
Genome_build: mm10
Supplementary_files_format_and_content: bed peak files

source_name: C57 mouse kidney tissue

extract_protocol:
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an Illumina HiSeq 4000 instrument with 150bp paired-end reads.

value: kidney


title: treatment 4, input


title: treatment 2, input


title: TAMs - 11 weeks - an1


title: treatment 1, input


title: treatment 4

tag: antibody


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD004_indexed


title: treatment 3


title: BAT-gal_mdDA domain from the ventral midbrain, technical replicate 1

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation

source_name: mdDA domain from the ventral midbrain at E12.5

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy FFPE kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, the RNA integrity-preserving tissue staining protocol (Brown and Smith 2009) for subsequent LMD and microarray analysis was performed as follows: E12.5 BAT-gal embryo heads were dissected in ice-cold PBS, fixed for 2 h in 4% PFA at 4°C, incubated in 20% sucrose overnight, embedded in Neg-50 (Thermo Fisher Scientific), frozen in 2-methylbutane on dry ice and stored at -80°C. Consecutive coronal cryosections (20 µm) of the caudal forebrain (diencephalon) and midbrain were mounted on POL frame slides (Leica Microsystems) and stored at -80°C. Mounted sections were post-fixed in acetone at -20°C, dried at 40°C for 1 min, washed twice with cold 2 M NaCl PBS, permeabilized with 0.25% Triton X-100 in 2 M NaCl PBS for 2 h, incubated with rabbit anti-PITX3 (1:100) and chicken anti-b-Galactosidase (1:1000) primary antibodies overnight and AlexaFluor 594 donkey anti-rabbit IgG and AlexaFluor 488 donkey anti-chicken IgG secondary antibodies (1:250 each, diluted in permeabilization solution at 4°C) for 2 h, washed three times with 2 M NaCl PBS and stored in this solution at 4°C. Immediately prior to LMD, tissue sections were dehydrated in 70% and 100% ethanol (2 min each), the ROIs outlined under visual inspection, and tissue fragments corresponding to the WNT/b-catenin-responsive mdDA domain or the lateral non-WNT/b-catenin-responsive, non-mdDA domain of five E12.5 BAT-gal embryos were isolated with an LMD6000 system (Leica Microsystems) and stored at -80°C.

value: B6D2F1 (mixed)

value: ventral midbrain

value: mdDA neurons

tag: developmental stage

tag: gender

value: not determined

value: BAT-gal


title: BAT-gal_mdDA domain from the ventral midbrain, technical replicate 2

scan_protocol: According to the Affymetrix expression protocol


title: BAT-gal_Control region from the lateral midbrain, technical replicate 2

source_name: Control region from the lateral midbrain at E12.5

value: lateral midbrain


title: SSc1_scrambled + TGFβ

description: replicate 1


title: treatment 2


title: injury 3, input


title: injury 4, input


title: SSc2_H19X ASO + TGFβ

description: replicate 2


title: treatment 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD001_indexed


title: BAT-gal_Control region from the lateral midbrain, technical replicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD002_indexed


title: injury 2, input


title: injury 1, input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD006_indexed


title: injury 2


title: Pitx3GFP_mdDA neurons isolated from the ventral midbrain at E14.5, technical replicate 2

source_name: Primary embryonic mdDA neurons isolated from the ventral midbrain at E14.5 by FACS-sorting for GFP

value: C57BL/6 x 129/Ola (mixed)


title: injury 3


title: injury 1


title: control 4, input


title: Pitx3GFP_mdDA neurons isolated from the ventral midbrain at E14.5, technical replicate 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD006_indexed


title: Pitx3GFP_mdDA neurons isolated from the ventral midbrain at E13.5, technical replicate 1

source_name: Primary embryonic mdDA neurons isolated from the ventral midbrain at E13.5 by FACS-sorting for GFP


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD012_indexed


title: control 2, input


title: control 3, input


title: injury 4


title: control 1, input


title: control 4

description: WT 4


title: control 3

description: WT 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C3_AD008_indexed


title: control 1

description: WT 1


title: cxcr3_ko_neg_met (R9585)

data_processing:
FASTQ files were mapped using STAR to UCSC human genome build GRCm38
Gene counts were obtained using featureCounts on GENCODE vM20 annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: genecounts_20200826.txt

source_name: mouse spleen

growth_protocol: WT and CXCR3-KO mice were used, No metformin treatment for these samples (neg_met)

extract_protocol:
Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). All mouse RNAs were analyzed on Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA) for quality assessment with a median RNA Quality Score of 9.
cDNA libraries were prepared using 500pg of total RNA and 1ul of a 1:200,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol [1] except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip GX system. All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq (16 samples/lane).

treatment_protocol: extracted single cells from mouse spleem and sorted CD8 T cells via MACS sorting


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD004_indexed


title: cxcr3_ko_neg_met (R9583)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD012_indexed


title: cxcr3_ko_neg_met (R9587)


title: cxcr3_ko_neg_met (R9584)


title: c57bl_6_wt_neg_met (R9577)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD008_indexed


title: cxcr3_ko_neg_met (R9586)


title: control 2

description: WT 2


title: Pitx3GFP_mdDA neurons isolated from the ventral midbrain at E13.5, technical replicate 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD008_indexed


title: c57bl_6_wt_neg_met (R9575)


title: c57bl_6_wt_neg_met (R9574)


title: c57bl_6_wt_neg_met (R9573)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD002_indexed


title: c57bl_6_wt_neg_met (R9576)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C1_AD002_indexed


title: Sample_DKO2-GCB-3_10X_SingleCell

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Cell Ranger
Further processing was done with Seurat 3.0.2 and Slingshot 1.2.0
Genome_build: mm10
Supplementary_files_format_and_content: gzipped matrix mtx files and gzipped tsv barcode and feature files

source_name: GC B cell

extract_protocol: 10x Chromium - single cell gene expression

value: Male Constitutive H1c-/-;H1e-/-

value: GC B cell


title: Sample_WT5-GCB-2_10X_SingleCell

value: Female WT littermate control


title: Sample_DKO6-GCB-4_10X_SingleCell


title: Sample_WT4-GCB-1_10X_SingleCell


title: Donor 2 HC14 non-neuronal nuclei

city: New Haven

first: Le

last: Zhang

state: CT

address: 300 George Street

department: Neurology

institute: Yale University

data_processing:
A custom pre-mRNA human genome reference was generated with GRCh38 that included pre-mRNA sequences by 10x Cell Ranger.
snRNA-seq data were aligned to this GRCh38–pre-mRNA reference to map both unspliced pre-mRNA and mature mRNA using 10x CellRanger version 3.0.2.
Genome_build: GRCh38, GRCh38-premRNA
Supplementary_files_format_and_content: csv files with raw counts

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei were isolated from post-mortem frozen or flash-frozen human brain tissue. Frozen tissue (50 to 100 mg) was homogenized in 15 ml of ice-cold nuclei homogenization buffer [2 M sucrose, 10 mM Hepes (pH 7.9), 25 mM KCl, 1 mM EDTA (pH 8.0), 10% glycerol, and ribonuclease (RNase) inhibitors freshly added (80 U/ml)] with Dounce tissue grinder (10 strokes with loose pestle and 10 strokes with tight pestle). The homogenate was transferred into an ultracentrifuge tube on top of 10 ml of fresh nuclei homogenization buffer and centrifuged at 24,000 rpm for 60 min at 4°C on high-speed centrifuge. The supernatant was removed, and the pellet was resuspended in 1 ml of nuclei resuspension buffer [15 mM Hepes (pH 7.4), 15 mM NaCl, 60 mM KCl, 2 mM MgCl2, 3 mM CaCl2, and RNase inhibitors freshly added (80 U/ml)] and counted on a hemocytometer.
The snRNA-seq libraries were prepared by the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer’s instructions and sequenced using Illumina HiSeq 4000.

tag: subject id

value: Donor 2

tag: sample type

value: non-neuronal (NeuN-negative) nuclei

value: brain

tag: tissue site

value: Middle temporal gyrus

tag: cellection type

value: Post-Mortem


title: Donor 1 B01 non-neuronal nuclei

value: Donor 1

value: Left lateral temporal cortex

value: Surgical resection


title: Donor 3 HC35 non-neuronal nuclei

value: Donor 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C2_AD004_indexed

tag: brain region

value: MOp

tag: Sex

value: male

tag: age


title: Donor 3  HC35 total nuclei

value: total nuclei


title: Donor 2 HC14 total nuclei


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD006_indexed

tag: strain


title: PHF2 shRNA2, replicate 3 [A673_571_3]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Quality trim to a minimum of Q15
Map to the GRCh38 genome using GSNAP version 2014-12-17 using the commandline /vol2/home/analysiscore/bin/gsnap_20141217_250/gsnap -d GRCh38_nonRedundant -v GRCh38_nonRedundant.snp142 --use-splicing=GRCh38_nonRedundant.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t12 --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam ./Illumina_data/${j}_filtered.fastq.gz > ./Illumina_data/$j.sam
sort and index using SAMTOOLS
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values

molecule: polyA RNA

source_name: A673_PHF2 shRNA2

growth_protocol: Cells were grown in DMEM with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), and further purified using the Qiagen MinElute column kit.
Illumina directional mRNA prep

treatment_protocol: Cells were stably transduced with scrambled shRNA control, KDM5A-targeting or PHF2-targeting shRNA, selected in Puromycin, and harvested at 70-80% confluence.

tag: cell line

value: Ewing Sarcoma cell line

tag: genotype/variation

value: PHF2 shRNA2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD004_indexed


title: PHF2 shRNA2, replicate 1 [A673_571_1]

tag: cell type


title: Donor 1 B01 total nuclei

tag: tissue


title: PHF2 shRNA2, replicate 2 [A673_571_2]


title: KDM5A shRNA2, replicate 2 [A673_872_2]

source_name: A673_KDM5A shRNA2

value: KDM5A shRNA2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD007_indexed


title: KDM5A shRNA1, replicate 1 [A673_632_1]

source_name: A673_KDM5A shRNA1

value: KDM5A shRNA1


title: KDM5A shRNA1, replicate 3 [A673_632_3]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: KDM5A shRNA1, replicate 2 [A673_632_2]


title: KDM5A shRNA2, replicate 1 [A673_872_1]


title: KDM5A shRNA2, replicate 3 [A673_872_3]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD007_indexed


title: control shRNA, replicate 1 [A673_scram_1]

source_name: A673_control shRNA

value: control shRNA


title: control shRNA, replicate 3 [A673_scram_3]


title: C50

type: genomic

city: Jeonju-si

first: Young-Chul

last: Chung

address: 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

department: Psychiatry

country: South Korea

institute: Medical School; Research Institute

description:
genomic DNA from PBMC
patient PBMC sample

hyb_protocol: The whole-genome amplification process requires 250ng of input bisulfite-converted DNA , MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, then placed in a humidified container for a minimum of 16 h at 48°C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Background correction, BMIQ normalization, M value, box plot, correlation etc.Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy3 and Cy5

source_name: genomic DNA from PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: QIAamp DNA Mini Kit (QIAGEN, Germany)

value: Male

value: PBMC

value: nomal


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD012_indexed


title: control shRNA, replicate 2 [A673_scram_2]


title: C49

value: Female


title: Epidermal_keratinocytes_Input

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

data_processing:
Sequencing reads were mapped to the human genome hg19 using Bowtie2 with standard parameters only allowing uniquely aligned reads
Peaks were called against input using MACS2  for H3K27ac and Med1 using broadpeak settings, and CTCF using standard peak settings.
BedGraph files were created using HOMER using standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files are in .bed file format, Bedgraph files are in .bedGraph format for visualization in the UCSC genome browser.

source_name: epidermal keratinocytes from foreskin

growth_protocol: Epidermis was separated from neonatal human foreskin and primary keratinocytes were isolated from epidermis and cultured in serum-free keratinocyte growth medium 154CF containing growth supplements (Gibco, Cascade biologics) containing low (0.07 mM) calcium. Second to fourth passages of keratinocytes were cultured with same medium in low calcium to maintain them. Cells were used under pre-confluent conditions in which density dependent epidermal differentiation was avoided.

extract_protocol:
When keratinocytes are under pre-confluency, they were cross-linked by 1% paraformaldehyde for 8 min for H3K27ac and for 15 min for MED1/CTCF and quenched with 0.125M glycine. Whole cell lysates (for H3K27ac) or purified chromatin (MED1/CTCF) were sonicated by Covaris S2200 ultrasonicator (Covaris, Inc.). The shearing condition was optimized to obtain the DNA to an average length of 300±50 bp, in which size of DNA was verified by Agilent 2100 Bioanalyzer (Agilent Technologies). Sheared chromatin was immunoprecipitated with Protein A-coated magnetic beads (Diagenode) preincubated with antibodies: 3 ug of antibody against H3K27ac (ab4729, Abcam), 1 ug CTCF antibody (Diagenode) and 4.5 ug MED1 antibody (Bethyl). Experiments were carried out in replicates (2-3), and a chromatin input sample was used as a reference to subtract background for peak calling. Complexes were washed, eluted from the beads with washing buffer and crosslinks were reversed by incubation at 65C for 4 hr. Immunoprecipitated DNA along with genomic DNA (Input) were purified using IPure v2 kit (Diagenode). IP efficiency was confirmed by qPCR using primers provided in the kits.
DNA Sequencing libraries were generated using the Accel-NGS 2S Plus DNA library kits (Swift Sciences) and amplified by PCR for 11 cycles. To remove high MW smear in the library, right side size selection was conducted by using SPRI beads (Beckman Coulter). The library was  quantified by Agilent 2100 Bioanalyzer with the High sensitivity DNA assay. They were sequenced on an Illumina HiSeq 4000 (UCSF Center of advanced technology) in a single strand 50bp run (combining 8 libraries per lane).

value: epidermal keratinocytes

tag: chip antibody


title: C45

tag: disease state


title: C48


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD001_indexed


title: Epidermal_keratinocytes_MED1_rep2


title: C46


title: Epidermal_keratinocytes_CTCF_rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD006_indexed


title: C44


title: Epidermal_keratinocytes_CTCF_rep1


title: Epidermal_keratinocytes_CTCF_rep3


title: C47


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD002_indexed


title: Epidermal_keratinocytes_MED1_rep1


title: C36


title: JuFiD2

first: Yang-Hui

last: Yeh

address: 295 Congress Ave.

department: Microbial Pathogenesis

description: only used for IGV plot

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, then mapped to hg38 release 91 plus HIV-1 sequence (HXB2 or HIV-1-dsGFP) whole genome using STAR 2.6.1d or 2.7.0f with parameters --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --chimOutType SeparateSAMold --runThreadN 20 --outFilterType BySJout --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --chimSegmentMin 15 --outSAMstrandField intronMotif --outSAMattributes All --quantMode GeneCounts
DEseq2 normalized count: Total gene count and normalization of STAR aligned bam file was obtained using HTseq (htseq-count -r pos -f bam -s reverse) and DESeq2 with human genome assembly hg38 release 91. Genes with the sum of read count smaller than 10 were filtered out.
Intron retention: Quality trimmed fastq files were analyzed with IRFinder 1.2.5 using STAR-built indexes with human genome assembly hg38 release 91.gtf as reference annotation (77). Up to triplicates of treatments were compared. Output files were filtered with following criteria in Rstudio (1.1.463): `A-IRratio` >= 0.1 & `A-IntronCover` >= 0.7 & `A-IntronDepth` >= 6 & `A-SplicesExact` >= 2 & `B-IRratio` < 0.1 & `B-SplicesExact` >=2. Unequal variance t-test of IRratio between two treatment groups were applied and intron-retained regions with significant difference (p < 0.05) were reported.
Genome_build: hg38 release 91 + HIV-1 sequence (HXB2 and HIV-1-dsGFP)
Supplementary_files_format_and_content: DEseq2 normalized counts: tab-delimited txt files; Intron retention: tab-delimited txt files:
DEseq2_8B10_normalized_DM.txt (DEseq2_normalized gene counts_cell line 8B10 for differential expression, IPA, and GSEA)
DEseq2_Pt_normalized_DM.txt (DEseq2_normalized gene counts_clinical samples for differential expression, IPA, and GSEA)
8B10_IR_FivsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_RuvsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_SpvsDM_D.txt (Intron retention analysis_cell line 8B10)
8B10_IR_MAvsDM_D.txt (Intron retention analysis_cell line 8B10)
Pt_IR_FivsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_RuvsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_SpvsDM_D.txt (Intron retention analysis_clinical samples)
Pt_IR_MAvsDM_D.txt (Intron retention analysis_clinical samples)

source_name: T lymphoblastoid

growth_protocol: Jurkat_clones: RPMI1640 high glucose + 10% FBS, passage every 3-4 days. CD4+ T cells ex vivo culture: RPMI1640 high glucose + 10% FBS

extract_protocol:
Cells were solublized in 300µl TRIzol per million cells then extracted with Direct-zol RNA microprep kits.
Approximately 500 ng of total RNA was used to generate cDNA library using TruSeq mRNA Library Prep kit (Illumina) for Illumina HiSeq 4000 2x100 bp sequencing or NEBNext Ultra II directional mRNA library prep kit (NEB) for Novaseq 6000 2x150 bp sequencing

treatment_protocol: Cells were treated with HIV-1-suppressing drugs (filgotinib, ruxolitinib, spironolactone, mycophenolic acid) for 24 hours in culture media incubated at 37oC with 5% CO2

tag: cell state

value: immortal cell line

tag: hiv-1 infection status

tag: drug treatment

value: Filgotinib

value: T lymphoblastoid


title: Epidermal_keratinocytes_H3K27ac_rep1


title: JuDMD3

description: only used for IGV plot

value: DMSO


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD006_indexed

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

value: MOp


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD012_indexed

value: male


title: C38

tag: gender


title: C35

tag: sample type


title: C41


title: JuDMD1

description: only used for IGV plot


title: C43


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD010_indexed


title: 8B10FiD2

description:
DEseq2_8B10_normalized_DM.txt
8B10_IR_FivsDM_D.txt

value: permanent defected HIV-1-infected cell line


title: JuFiD3

description: only used for IGV plot


title: C40


title: 8B10FiD1


title: C37


title: C42


title: 8B10DMD3

description:
DEseq2_8B10_normalized_DM.txt
8B10_IR_FivsDM_D.txt
8B10_IR_RuvsDM_D.txt
8B10_IR_SpvsDM_D.txt
8B10_IR_MAvsDM_D.txt


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD008_indexed


title: C39


title: C34


title: 8B10DMD1


title: 8B10DMD2


title: BM3

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

data_processing:
The clean reads were aligned to human reference genome (hg38 from Ensembl) by Hisat2 (version 2.0.3-beta), followed by calculating uniquely mapped reads through htseq-count (version 0.9.1) based on the genome annotation file from Ensembl (hg38). Finally, the total number of different UMIs for each gene was quantified as the read count of that gene.
Genome_build: hg38
Supplementary_files_format_and_content: .mtx (UMI matrix of cells); .tsv (cell information); .tsv (gene information)

source_name: bone marrow

extract_protocol:
Samples were incubated on ice for 30 mins in the dark and washed with PBS + 2% FBS (Gibco), cell suspension of which were added with DAPI (1 ug/ml, Sigma-Aldrich) to deplete dead cells for FACS.
Smart-seq2
Single cell RNAseq

treatment_protocol: All samples were freshly prepared and immediately stained with human antibodies including Lineage cocktail.

tag: developmental stage

value: adult

value: bone marrow

value: HSPCs


title: BM2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C11_AD002_indexed


title: C31


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD007_indexed


title: BM1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD004_indexed


title: C33


title: aSLE7 [JB19015]

city: Farmington

first: William

middle: F

last: Flynn

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
FASTQ files for each sample (10X chemistry v2) were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all samples, R1 (26bp) contains a 16bp cell barcode + 10bp UMI barcode and R2 (98bp) contains the biological reads.
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics hg19 reference build (version 1.2.0, GRCh37.82) using 10X Genomics CellRanger count version 2.1.0.
Genome_build: GRCh37.82
Supplementary_files_format_and_content: Counts matrices are provided in Matrix Market CSR format.  Rows correspond to genes in the order provided in genes.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.
digital counts matrix for gene expression (matrix market format)
row labels (genes) of gene expression counts matrix
column labels (cell barcodes) of gene expression counts matrix

source_name: Adult SLE 7

extract_protocol:
PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII.
Briefly, 12,000 cells were loaded for capture onto the Chromium System using the v2 single cell reagent kit (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10X Genomics). The amplified cDNA was used to construct an Illumina sequencing library and sequenced on a single lane of a HiSeq 4000.

tag: age group

value: Adult

tag: groups

value: SLE


title: aSLE6 [JB19014]

source_name: Adult SLE 6


title: JuFiD1

description: only used for IGV plot


title: aSLE5 [JB19013]

source_name: Adult SLE 5


title: aHD6 [JB19011]

source_name: Adult Healthy Donor 6

value: HD


title: JuDMD2

description: only used for IGV plot


title: aHD5 [JB19010]

source_name: Adult Healthy Donor 5


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD008_indexed

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

tag: Sex


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD010_indexed

tag: age

tag: strain


title: aHD4 [JB19009]

source_name: Adult Healthy Donor 4


title: C30

value: PBMC


title: 8B10FiD3


title: aSLE4 [JB19008]

source_name: Adult SLE 4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD012_indexed


title: aSLE2 [JB19006]

source_name: Adult SLE 2


title: aSLE1 [JB19004]

source_name: Adult SLE 1


title: aHD3 [JB19003]

source_name: Adult Healthy Donor 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD002_indexed


title: aHD1 [JB19001]

source_name: Adult Healthy Donor 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD001_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD004_indexed


title: C32

value: Male

value: nomal


title: cHD9 [JB18084]

source_name: Child Healthy Donor 9

value: Children


title: cHD11 [JB18086]

source_name: Child Healthy Donor 11


title: cHD10 [JB18085]

source_name: Child Healthy Donor 10


title: cSLE32 [JB18081]

source_name: Child SLE 32


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD006_indexed


title: cSLE33 [JB18082]

source_name: Child SLE 33


title: cSLE31 [JB18080]

source_name: Child SLE 31


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B9_AD001_indexed


title: cHD8 [JB18083]

source_name: Child Healthy Donor 8


title: cSLE30 [JB18079]

source_name: Child SLE 30


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD012_indexed


title: cHD7 [JB18078]

source_name: Child Healthy Donor 7


title: C27

source_name: genomic DNA from PBMC


title: cHD6 [JB18077]

source_name: Child Healthy Donor 6


title: C24


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B8_AD010_indexed


title: cSLE28 [JB18075]

source_name: Child SLE 28


title: aSLE3 [JB19007]

source_name: Adult SLE 3


title: C29


title: C26

value: Female


title: C21


title: cSLE26 [JB18073]

source_name: Child SLE 26


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD008_indexed


title: cSLE25 [JB18072]

source_name: Child SLE 25


title: C23


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_C10_AD008_indexed


title: cHD5 [JB18070]

source_name: Child Healthy Donor 5


title: cSLE24 [JB18071]

source_name: Child SLE 24


title: cHD4 [JB18069]

source_name: Child Healthy Donor 4


title: cSLE23 [JB18068]

source_name: Child SLE 23


title: cSLE22 [JB18067]

source_name: Child SLE 22


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD010_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: C20


title: C16


title: C15


title: C17


title: cSLE21 [JB18066]

source_name: Child SLE 21


title: C19


title: cSLE20 [JB18065]

source_name: Child SLE 20


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD002_indexed


title: cSLE19 [JB18064]

source_name: Child SLE 19


title: cSLE18 [JB18063]

source_name: Child SLE 18


title: cHD3 [JB17018]

source_name: Child Healthy Donor 3


title: C25

source_name: genomic DNA from PBMC


title: C12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD012_indexed


title: C28


title: cHD2 [JB17017]

source_name: Child Healthy Donor 2


title: cSLE29 [JB18076]

source_name: Child SLE 29


title: C11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD007_indexed


title: cSLE16 [JB17023]

source_name: Child SLE 16


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD008_indexed


title: cSLE15 [JB17022]

source_name: Child SLE 15


title: cSLE14 [JB17021]

source_name: Child SLE 14


title: cSLE17 [JB17024]

source_name: Child SLE 17


title: cSLE13 [JB17020]

source_name: Child SLE 13


title: C07


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD002_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD010_indexed


title: cSLE12 [JB17019]

source_name: Child SLE 12


title: cHD1 [JB17010]

source_name: Child Healthy Donor 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD001_indexed


title: C13


title: C08


title: C18


title: C09


title: C05


title: cSLE27 [JB18074]

source_name: Child SLE 27


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: cSLE11 [JB17016]

source_name: Child SLE 11


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD012_indexed


title: cSLE9 [JB17014]

source_name: Child SLE 9


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 8

type: protein

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description:
Column Block = 16 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment

hyb_protocol: Add 100 µl plasma samples to each well. Incubate arrays at room temperature for 1-2 hour. Wash and then Incubate with Biotinylated Antibody Cocktail.

scan_protocol: The array signals can be visualized through use of a laser scanner equipped with a Cy3 wavelength (green channel).

data_processing: Data extraction were done with the microarray analysis software (GenePix, ScanArray Express, ArrayVision, MicroVigene, etc.). Raw data were normalized and log2 transformed. We used student t-test to determine significant differentially expressed probes between metastasis and non-metastasis groups. Differential expressed transcripts were characterized according to the criterion of absolute Fold change ≥ 1.5, t-test P-value <0.05, and raw average signals of either group ≥ 300.

molecule: protein

source_name: primary nasopharyngeal carcinoma

label_protocol: Cy3 equivalent dye-conjugated streptavidin to each well. Cover the device with aluminum foil to avoid exposure to light or incubate in dark room. Incubate at room temperature for 1 hour.

growth_protocol: Nasopharyngeal carcinoma plasma samples obtained before any anti-tumour treatment.

extract_protocol: Plasma were collected and centrifuged under the anticoagulant condition at 2330 g for 10 minutes at 4°C and stored at -80°C until analysis.

tag: plasma

value: Nasopharyngeal carcinoma


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD008_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 7

description:
Column Block = 15 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: C03


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD007_indexed


title: cSLE10 [JB17015]

source_name: Child SLE 10


title: C04


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 6

description:
Column Block = 14 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B6_AD004_indexed


title: cSLE7 [JB17007]

source_name: Child SLE 7


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD004_indexed


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 5

description:
Column Block = 13 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD006_indexed


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 4

description:
Column Block = 12 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: C06

source_name: genomic DNA from PBMC


title: C10


title: cSLE5 [JB17005]

source_name: Child SLE 5


title: cSLE8 [JB17008]

source_name: Child SLE 8


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 3

description:
Column Block = 11 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: C01


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 2

description:
Column Block = 10 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: cSLE6 [JB17006]

source_name: Child SLE 6


title: cSLE3 [JB17003]

source_name: Child SLE 3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD010_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD001_indexed


title: Non-metastatic locoregionally advanced nasopharyngeal carcinoma patients 1

description:
Column Block = 9 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which did not developed diatant metastasis after treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD007_indexed


title: cSLE2 [JB17002]

source_name: Child SLE 2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B7_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD006_indexed


title: cSLE1 [JB17001]

source_name: Child SLE 1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD012_indexed


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 7

description:
Column Block = 7 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 6

description:
Column Block = 6 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD007_indexed


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 5

description:
Column Block = 5 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: siVret_Siwi-piRNA#2

city: Tokyo

first: Mikiko

middle: C

last: Siomi

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 7th column

data_processing:
Adapters were cut with Cutadapt.
The reads were mapped to 121 Bombyx mori transposon consensus sequences (a gift from S. Kawaoka) using Bowtie2, allowing up to one mismatch for Target-L. For others, reads were mapped to the transposons using bowtie, allowing no mismatch.
The reads were also mapped to the B. mori reference genome (downloaded from Silkbase; silkbase.ab.a.u-tokyo.ac.jp) using bowtie2 and bowtie as above.
The reads were normalized to RPM or frequency(%)
Genome_build: FASTA file of TE sequences is available on the series record.

organism: Bombyx mori

source_name: BmN4 cell

extract_protocol:
RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells using Anti-DDDDK-tag mAb (MBL, FLA-1) and anti-Ago3 mAb (Nishida et al. Cell reports 2015).
Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB)

tag: cell type

value: Cultured cell derived from ovary

tag: cell line

tag: rip target

value: Siwi

tag: knockdown

value: siVret


title: siVret_Siwi-piRNA#1

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 6th column


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 8

description:
Column Block = 8 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 4

description:
Column Block = 4 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: siAgo3_Siwi-piRNA#2

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 5th column


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD010_indexed

institute: HHMI-Salk-Institute

value: MOp

value: male


title: P84

description:
genomic DNA from PBMC
patient PBMC sample

tag: disease state

value: Psychotic disorder NOS


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B5_AD002_indexed


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 3

description:
Column Block = 3 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: P86


title: siLuc_Siwi-piRNA#2

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 3rd column

value: siLuc


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD006_indexed


title: P88


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 2

description:
Column Block = 2 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: Metastatic locoregionally advanced nasopharyngeal carcinoma patients 1

description:
Column Block = 1 in QAH-CHE.txt, QAH-CYT-4.txt, QAH-CYT-5.txt, QAH-CYT-6.txt, QAH-CYT-7.txt, QAH-CYT-8.txt, QAH-CYT-9.txt, QAH-CYT-10.txt, QAH-CYT-11.txt, QAH-CYT-12.txt, QAH-CYT-13.txt, QAH-CYT-14.txt, QAH-CYT-15.txt, QAH-CYT-16.txt, QAH-CYT-17.txt, QAH-CYT-18.txt, QAH-CYT-19.txt, QAH-CYT-20.txt, QAH-CYT-21.txt, QAH-CYT-22.txt, QAH-CYT-23.txt, QAH-CYT-24.txt, QAH-GF.txt, QAH-INF.txt, QAH-REC.txt
Plasma protein expression data from LA-NPC which developed diatant metastasis after treatment


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD004_indexed


title: siLuc_Siwi-piRNA#1

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 2nd column


title: Target-S

description:
RNA associating with Ago3
Target S is an RNA of about 16 bases contained in the Ago3 complex.
Target-L-S_abundance.xlsx


title: FL4 [RNA-Seq]

city: Baoding

first: Huiyan

last: HU

address: Lekai South Street No. 2596

institute: Hebei Agricultural University

data_processing:
Clean data from each library were obtained and then mapped to the reference genome (Sscrofa10.2) downloaded from the Ensembl Genomes (http://www.ensemblgenomes.org) using software Hisat2 (v2.0.1).
The mapped reads were assembled using StringTie V1.0.4 (Trapnell et al., 2012)
The assembled transcripts from each individual were merged with Cuffmerge to generate a single transcriptome annotation from Ensembl.
Rsem (V1.2.6) was used to calculate gene expression levels using the FPKM (Fragments per Kilo bases per Million reads) method for genes in each sample.
Differential expression analysis was performed by DESeq2 package (V1.6.3)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Ovary

extract_protocol:
Total RNA was isolated individually from the ovaries samples using TRIzol Reagent (Invitrogen), purified with RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel.
Each sample with RNA Integrity Number (RIN) value > 7.5 was used for following library preparation. Approximately 3μg RNA of each RNA-seq sample was used to remove ribosomal RNA (rRNA) using Epicentre Ribo-Zero™ rRNA removal Kit (Epicentre, USA). Each sample was amplified by PCR to enrich cDNA libraries.

value: Canadian Large White pig

tag: tissue

value: ovary

value: on the 20 day (day 1 = first day of estrus) after estrus as in the follicular phase

tag: genotype

value: low fecundity


title: C22

tag: gender

value: PBMC


title: P79

tag: sample type

value: Drug-induced psychosis


title: siAgo3_Siwi-piRNA#1

description:
RNA associating with Siwi
siL12siA12siV12_rpm.txt: scores are in 4th column


title: P82

value: Male

value: Schizophreniform disorder(295.40)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD001_indexed

city: La Jolla


title: P85

value: Attenuated psychosis syndrome


title: Target-L

description:
RNA associating with Ago3
Target L is an RNA of 30 to 100 bases contained in the Ago3 complex.
Target-L-S_abundance.xlsx


title: FL3 [RNA-Seq]


title: cSLE4 [JB17004]

source_name: Child SLE 4

value: Children

value: SLE


title: P80

value: Female

value: brief psychotic disorder


title: P83


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD002_indexed

value: MOp


title: FL1 [RNA-Seq]


title: FL2 [RNA-Seq]


title: P75

value: Schizophrenia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD006_indexed

value: male


title: ChIP-Seq BEAS-2B Control of As 96h Input

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
ChIP-seq sequence reads were trimmed with trim galore, then aligned to the hg38 genome using bwa.
RNA-seq datasets were processed using Salmon followed with Deseq2.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: peak files, RNA-seq: transcript level quantification from salmon and/or raw read count

source_name: Lung epithial cell

extract_protocol:
For RNA-seq samples, total RNA was extracted using TRIzol and subsequently continue to prepare RNA-Seq library. For ChIP-Seq samples, mono-nucleosomes were isolated by MNase digestion and sucrose gradient purification from stable cell lines. ChIP was performed using anti-FLAG M2 Affinity-gel. DNA fragments were purified by phenol/chloroform extraction and then continue for ChIP-Seq library preparation.
RNA-Seq and ChIP-Seq library preparation were followed by Illumina TruSeq RNA Library Prep Kit or Illumina TruSeq ChIP Library Preparation Kit.
RNA-Seq and ChIP-Seq

treatment_protocol: Immortalized human bronchial epithelial (BEAS-2B) cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA). Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen, Grand Island, NY) supplemented with 1% penicillin/streptomycin (GIBCO, Grand Island, NY) and 10% heat-inactivated fetal bovine serum (FBS, Atlanta Biologicals, Lawrenceville, GA). All cells were cultured in a 37°C incubator containing 5% CO2. For arsenic exposure, cells were treated with or without 1 μM sodium meta-arsenite (NaAsO2, Sigma, St. Louis, MO) for 96 hr. pcDNA-FLAG- H3.1poly(A) , pcDNA-FLAG- H3.1Loop, pcDNA- H3.1poly(A), and pcDNA - H3.1Loop plasmids were purified using a Qiagen QIAprep Spin Midiprep kit prior to transfection. Overexpression transfections were performed using PolyJet Reagent (SignaGen, Rockville, MD) according to the manufacturer’s instructions. pcDNA-FLAG-empty and pcDNA-empty vectors were used as the control separately. Briefly, 150,000 cells were seeded into 6-well dishes 24 hours prior to transfection. The following day, 1 μg of purified plasmid was transfected into each well using 3 μL of PolyJet per transfection. 16 hours post-transfection, the media was removed and replaced with fresh DMEM. After three days, 0.5 μg/ml of hygromycin selection agent was added to the transfected cells.

value: lung, bronchus


title: FH4 [RNA-Seq]

value: Canadian Large White pig

value: high fecundity


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD010_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B4_AD008_indexed


title: ChIP-Seq BEAS-2B Control of As 96h


title: P76


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD008_indexed


title: FH2 [RNA-Seq]

value: ovary

value: on the 20 day (day 1 = first day of estrus) after estrus as in the follicular phase


title: P74

value: PBMC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD006_indexed


title: P77


title: P73


title: P72


title: FH3 [RNA-Seq]


title: P71


title: ChIP-Seq BEAS-2B As 96h


title: ChIP-Seq BEAS-2B As 96h Input


title: FH1 [RNA-Seq]


title: P81


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD007_indexed


title: P69


title: LL4 [RNA-Seq]

value: on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase

value: low fecundity


title: LL3 [RNA-Seq]


title: ChIP-Seq BEAS-2B NT-Empty


title: ChIP-Seq BEAS-2B NT-H3.1Loop Input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD001_indexed


title: ChIP-Seq BEAS-2B NT-Empty Input


title: LL2 [RNA-Seq]


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD004_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD002_indexed


title: ChIP-Seq BEAS-2B NT-H3.1Loop


title: C14

value: nomal


title: LL1 [RNA-Seq]


title: ChIP-Seq BEAS-2B NT-H3.1poly(A) Input


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B3_AD012_indexed


title: LH3 [RNA-Seq]


title: LH4 [RNA-Seq]


title: ChIP-Seq BEAS-2B NT-H3.1poly(A)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD007_indexed


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1Loop Input


title: Ago3-piRNA

description:
RNA associating with Ago3
siLuc_piRNA_TE_mapped_rpm.txt

value: Cultured cell derived from ovary


title: LH2 [RNA-Seq]


title: P70

value: Male

value: Schizophreniform disorder(295.40)


title: P64

value: Attenuated psychosis syndrome


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1Loop


title: P67

value: Female


title: P66


title: LH1 [RNA-Seq]


title: P68

value: Psychotic disorder NOS


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD004_indexed

value: MOp


title: FL4

data_processing:
The clean reads were obtained by masking adapters, poly-A tails and low-quality reads from the raw data with Trimmomatic10 (v0.30)
The clean reads were then aligned to the porcine genome sequence (Sscrofa10.2) by Bowtie2 (v2.1.0)
Unmapped reads were used to predict the novel miRNAs with miRDeep (v2.0.0.7)
Differentially expression analysis used the DEseq2 package, P-value < 0.05 and |log2 (fold change)| ≥ 1 were described as differentially expressed
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include miRNA expression information for each Sample

extract_protocol:
Total RNA was isolated individually from the ovaries samples using TRIzol Reagent (Invitrogen), purified with RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bio-analyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel.
Illumina small RNA-Seq (RNA sequencing) libraries were constructed using NEBNext® Multiplex Small RNA library Prep Set for Illumina® (NEB, USA) following manufacturer’s recommendations.


title: ChIP-Seq BEAS-2B FH3.3 NT-Empty


title: P65


title: P63


title: FL3


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD002_indexed

value: male


title: FL2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD012_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD007_indexed


title: RNA-Seq BEAS-2B H3.1poly(A)-rep2

value: lung, bronchus


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD008_indexed


title: ChIP-Seq BEAS-2B FH3.3 NT-Empty Input


title: FH4

value: Canadian Large White pig


title: RNA-Seq BEAS-2B H3.1Loop-rep2


title: FL1


title: FH3

value: high fecundity


title: RNA-Seq BEAS-2B H3.1poly(A)-rep1


title: RNA-Seq BEAS-2B H3.1 empty-rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD006_indexed


title: FH2

value: ovary


title: C02


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B2_AD012_indexed


title: RNA-Seq BEAS-2B H3.1 empty-rep1


title: FH1

value: on the 20 day (day 1 = first day of estrus) after estrus as in the follicular phase


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD002_indexed


title: P58

value: PBMC

value: Schizophrenia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD010_indexed


title: G576-18-Quiz-Dex-5d-3_S28

city: Hershey

first: Melat

middle: T

last: Gebru

state: PA

address: 95A University Manor East

department: Pediatrics

institute: Penn State University

description: Quiz + Dex- 5d- 1,2,3.xlsx

data_processing:
Reads that passed the Illumina CASAVA pipelinewere aligned to the human reference genome (GRCh38) using STAR (v2.7.3), and gene and transcript quantifications are performed by RSEM against a gene annotation file, which contains by default GENCODE annotations (gencodeV24pri).
Read counts were extracted, and used for differential expression analysis through edgeR2and DESEQ23packages. Geneswere first filtered by edgeR to remove non expressed genes in both DTPs and parental cells, then a significant false discovery rate of adjusted P value (p < 0.05) were used for differential expression analysis from DESEQ2.
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: MV4-11 cell line

growth_protocol: MV4-11 AML cells were cultured in IMDM supplemented with 10% FBS at 37oC and 5% CO2

extract_protocol:
RNA was extractedusing the mirVana™ miRNA Isolation Kit (Thermo FisherScientific, Waltham, MA).
cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit(BioO Scientific, Austin, TX) per the manufacturer’s instructionsand run on an Illumina HiSeq 2500.

treatment_protocol: MV4-11 AML cells were treated with 10nM quizartinib, 100nM dexamethasone or the combination for 48h or 5d.

value: Acute myeloid leukemia cells

tag: treatment

value: Quizartinib + Dexmethasone treated- 5d


title: RNA-Seq BEAS-2B H3.1Loop-rep1


title: P56


title: P60


title: P57


title: LL4

value: on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase

value: low fecundity


title: LL3


title: G576-17-Quiz-Dex-5d-2_S27

description: Quiz + Dex- 5d- 1,2,3.xlsx


title: P52

value: Male

value: delusional disorder


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD001_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD004_indexed


title: G576-16-Quiz-Dex-5d-1_S26

description: Quiz + Dex- 5d- 1,2,3.xlsx


title: LL2


title: G576-15-Quiz5d-3_S25

description: Quiz- 5d- 1,2,3.xlsx

value: Quizartinib Treated- 5d


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD006_indexed


title: P59

value: Female

value: Psychotic disorder NOS


title: LL1


title: P55

value: Schizophreniform disorder(295.40)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD012_indexed

value: MOp

value: male


title: G576-14-Quiz5d-2_S24

description: Quiz- 5d- 1,2,3.xlsx


title: LH4

value: Canadian Large White pig

value: high fecundity


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD008_indexed


title: P50

value: brief psychotic disorder


title: G576-13-Quiz5d-1_S23

description: Quiz- 5d- 1,2,3.xlsx


title: P49

value: PBMC


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD010_indexed


title: P62


title: LH3

value: ovary


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD007_indexed


title: LH1


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B1_AD004_indexed


title: LH2


title: P61

value: Schizophrenia


title: G576-10-Quiz-Dex48h-1_S20

description: Quiz + Dex- 48h- 1,2,3.xlsx

value: Acute myeloid leukemia cells

value: Quizartinib + Dexmethasone treated- 48h


title: G576-11-Quiz-Dex48h-2_S21

description: Quiz + Dex- 48h- 1,2,3.xlsx


title: G576-12-Quiz-Dex48h-3_S22

description: Quiz + Dex- 48h- 1,2,3.xlsx


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD002_indexed


title: P48

value: Attenuated psychosis syndrome


title: P87


title: P46


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B11_AD001_indexed


title: G576-09-Quiz48h-3_S19

description: Quiz- 48h- 1,2,3.xlsx

value: Quizartinib Treated- 48h


title: P53


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD010_indexed


title: G576-08-Quiz48h-2_S18

description: Quiz- 48h- 1,2,3.xlsx


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD008_indexed


title: P47

value: Male


title: P44


title: G576-06-Dex-3_S16

description: Dex- 48h- 1,2,3.xlsx

value: Dexamethasone Treated- 48h


title: P42

value: Female


title: G576-05-Dex-2_S15

description: Dex- 48h- 1,2,3.xlsx


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD007_indexed


title: G576-07-Quiz48h-1_S17

description: Quiz- 48h- 1,2,3.xlsx


title: Put_PD_2

city: Nijmegen

first: Helena

last: Xicoy

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

data_processing:
QUALITY CONTROL: FASTQC v0.11.4
ALIGNMENT AND COUNTING STEP: Salmon v0.12.0
STATISTICAL SOFTWARE: R 3.5.2
Genome Reference: Homo sapiens GRCh38 cDNA and non coding RNA files, release 86
Filtering: keep only genes/transcripts that have at least 10 reads across samples
Differential Expression Analysis: DESeq2 v1.22.2

source_name: Putamen

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat No./ID: 74804).
RNA-seq directionality library preparation and sequencing with Poly(A) selection was performed by HudsonAlpha Genomic Services Laboratory (Huntsville, AL). Samples underwent sequencing on the HiSeq v4 (PE, 50bp, 25M reads), per standard protocols. 16 samples were run over two lanes (3.125M reads/sample).

value: m

value: Parkinson’s disease

value: Putamen


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD006_indexed

value: MOp

value: male


title: Arecoline [methylation]

city: Ishikari-Tobetsu

first: Durga

last: Paudel

state: Hokkaido

address: Kanazawa

institute: Health Sciences University of Hokkaido

hyb_protocol: Agilent ChIP-on-chip/aCGH Hybridization Kit

scan_protocol: Scan using Agilent’s DNA microarray scanner Quantification using Feature Extraction Software (Agilent Technologies)

data_processing: Data import into Agilent GeneSpring Software . 1. Normalization as following Agilent manual (2-color). 2. Significant genes : Hypermethylated probes (2X Hypermethylated genes); Hypomethylated probes (2X hypomethylated genes)

source_name: Methylation level in genes after cell culture for 1 month with arecoline

label_protocol: total labeled DNA amount > 2.5ug; Cy3 labeled incorporation > 2.5 pmole/ul - Cy5 labeled incorporation > 2.0 pmole/ul

growth_protocol: Human gingival epithelial progenitors  were cultured in CnT-Prime epithelial cell culture medium  containing antibiotics (5% penicillin-streptomycin at 37˚C in an incubator supplied with 5% CO2

extract_protocol: Genomic DNA was extracted using DNeasy® Blood and Tissue kit (Qiagen,

treatment_protocol: The cells were  treated with 50 μg/ml arecoline hydrobromide  for 3 days and without arecoline for another 3 days for a total period of 1 month

tag: tag

value: Human Gingival Epithelial Cell

value: arecoline


title: G576-04-Dex-1_S14

description: Dex- 48h- 1,2,3.xlsx


title: P41

value: PBMC


title: Put_PD_3


title: Put_C_3

value: Control


title: Put_PD_1

value: f


title: Put_C_2


title: G576-03-DMSO-3_S13

value: Acute myeloid leukemia cells

value: DMSO Treated- 48h


title: Put_C_1


title: G576-02-DMSO-2_S12


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD008_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD004_indexed


title: Control [methylation]

source_name: Methylation level in genes after cell culture for 1 month

value: control


title: P39

value: delusional disorder


title: SN_PD_5

source_name: Substantia nigra

value: Substantia nigra


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD004_indexed


title: P36

source_name: genomic DNA from PBMC

value: Schizophrenia


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1poly(A)-input-rep2

description: transfected with pcDNA3.1-FLAG-H3.3, and then pcDNA3.1-NT-H3.1poly(A)

data_processing:
ChIP-seq sequence reads were trimmed with trim galore, then aligned to the hg38 genome using bwa.
RNA-seq datasets were processed using Salmon followed with Deseq2.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: promoter (-150bp to +50bp) RPKM, RNA-seq: transcript level quantification from salmon and/or raw read count

source_name: Lung epithelial cell

extract_protocol:
For RNA-seq samples, total RNA was extracted using TRIzol and subsequently continue to prepare RNA-Seq library. For ChIP-Seq samples, mono-nucleosomes were isolated by MNase digestion and sucrose gradient purification from stable cell lines. ChIP was performed using anti-FLAG M2 Affinity-gel. DNA fragments were purified by phenol/chloroform extraction and then continue for ChIP-Seq library preparation.
RNA-Seq and ChIP-Seq library preparation were followed by Illumina TruSeq RNA Library Prep Kit or Illumina TruSeq ChIP Library Preparation Kit.

treatment_protocol: Beas-2B cells were transfected with designed different pcDNA3.1 plasmids separately to construct different stable cell lines.

value: lung, bronchus


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD001_indexed


title: G576-01-DMSO-1_S11


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1poly(A)-input-rep1


title: SN_PD_3

value: m


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD012_indexed


title: P40

value: Male

value: Attenuated psychosis syndrome


title: SN_PD_2

value: Parkinson’s disease


title: P38

value: Female

value: Schizophreniform disorder(295.40)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD006_indexed

value: MOp

value: male


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_B10_AD001_indexed


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1poly(A)-rep2


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD004_indexed


title: P33

value: PBMC


title: SN_C_5

value: Control


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD006_indexed


title: ChIP-Seq BEAS-2B FH3.3 WT-input-rep2


title: SN_PD_1

value: f


title: SN_PD_4


title: SN_C_4


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD012_indexed


title: ChIP-Seq BEAS-2B FH3.3 WT-input-rep1


title: P31

value: Schizophreniform disorder


title: SN_C_3


title: ChIP-Seq BEAS-2B FH3.3 WT-rep2


title: SN_C_2


title: P35


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD010_indexed


title: ChIP-Seq BEAS-2B FH3.3 WT-rep1


title: P32


title: P37

value: brief psychotic disorder


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD007_indexed


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A9_AD002_indexed


title: ChIP-Seq BEAS-2B FH3.3 NT-H3.1poly(A)-rep1


title: RNA-Seq BEAS-2B FH3.3 WT rep2


title: P45


title: P30


title: P28_tumor

city: Singapore

first: Caroline

last: Lee

address: 12 Science Drive 2

institute: National University of Singapore

data_processing:
The original image data was transferred into sequence data via base calling, which was defined as raw reads and saved as FASTQ file.
The raw reads were filtered by removing adaptor sequences, contamination and low-queality reads.
The clean reads were aligned to a combined genome consisting of the hg19 genome and an HBV-B2 strain using the Tophat aligner (Settings used by Tophat: --min-anchor 8 --splice-mismatches 2 --min-intron-length 50 --max-intron-length 500000 --min-isoform-fraction 0.15 --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --mate-inner-dist 50 --mate-std-dev 20 --no-coverage-search).
Reads per kilo-base per million mapped reads (RPKM) were calculated for each transcript and exon using Partek Genomic Suite 6.6 from output BAM files based on HG19, Refseq version 2015.02.02 annotation.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Liver

extract_protocol:
Liver tissues were homogenized in RLT buffer using the gentleMACS dissociator and total RNA was isloated with RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tumor


title: RNA-Seq BEAS-2B FH3.3 WT rep1


title: P28_adjacent non-tumour 2

value: adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD012_indexed


title: P29

value: Schizophrenia


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD004_indexed


title: RNA-Seq BEAS-2B NT-H3.1poly(A) rep1

value: lung, bronchus


title: P25_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A8_AD002_indexed


title: P28_adjacent non-tumour 1


title: P21


title: RNA-Seq BEAS-2B NT-Empty rep2


title: RNA-Seq BEAS-2B NT-H3.1poly(A) rep2


title: P27


title: P24

value: Psychotic disorder NOS


title: P25_adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD012_indexed


title: P24_tumor


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD010_indexed


title: DTPs-30d (MO14) Rep2

description:
Myeloid cells
DTP
mRNA

data_processing:
Reads that passed the Illumina CASAVA pipeline were aligned to the human reference genome (hg38) using Tophat (v2.0.9).
FPKM counting and differential expression analysis were performed using the Cuffdiff tool by normalizing to the median of the geometric means of fragment counts across all samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.xlsx: Excel files include FPKM values.

growth_protocol: MV4-11 AML cells were cultured in IMDM supplemented with 10% FBS at 37oC and 5% CO2.

extract_protocol:
RNA was extracted from DTPs and parental MV4-11 cells using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific).
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) per the manufacturer’s instructions and run on Illumina HiSeq 2500.

treatment_protocol: MV4-11 AML cells were treated with 100nM quizartinib for 48h and surviving cells (DTPs) were isolated 48h post-treatment, 13d and 30d culture in drug-free media.

value: AML cell line

value: Quizartinib for 48h

tag: timepoint

value: 30d culture in drug-free media


title: P24_adjacent non-tumour


title: P23

data_processing: Background correction, BMIQ normalization, M value, box plot, correlation etc.Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

extract_protocol: QIAamp DNA Mini Kit (QIAGEN, Germany)

value: Male

value: Attenuated psychosis syndrome


title: DTPs-30d (MO13) Rep1

description:
Myeloid cells
DTP
mRNA


title: P28

value: Female


title: P23_tumor


title: P18


title: DTPs-13d (MO12) Rep2

description:
Myeloid cells
DTP
mRNA

value: 13d culture in drug-free media


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD008_indexed

tag: brain region

value: MOp

value: male


title: P23_adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD010_indexed

tag: Sex


title: P16

tag: age

value: PBMC


title: DTPs-13d (MO11) Rep1

description:
Myeloid cells
DTP
mRNA


title: DTPs-48h (MO10) Rep2

description:
Myeloid cells
DTP
mRNA

value: 48h post treatment


title: RNA-Seq BEAS-2B NT-Empty rep1


title: P22_adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A7_AD007_indexed

tag: strain


title: DTPs-48h (MO9) Rep1

description:
Myeloid cells
DTP
mRNA


title: SN_C_1

value: f

value: Control

value: Substantia nigra


title: P19

value: Schizophrenia


title: P15

value: delusional disorder


title: P20

value: brief psychotic disorder


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD001_indexed


title: P21_tumor

value: tumor


title: Untreated (MO8) Rep2

description:
Myeloid cells
Parental
mRNA

value: AML cell line

value: Untreated


title: P21_adjacent non-tumour

value: adjacent non-tumour


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A6_AD006_indexed


title: P26

value: Schizophreniform disorder(295.40)


title: 180627_CEMBA_mm_P56_P63_5D_CEMBA180612_5D_1_CEMBA180612_5D_2_A5_AD008_indexed


title: P11

value: Female


title: P20_tumor