title: Dmau_testis_RNAseq_replicate2

city: New Yor

first: Jeffrey

last: Vedanayagam

address: 1275 York Avenue

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

description: Dmau testis RNA replicate 2

data_processing:
RNA-seq data: Paired-end RNA-seq reads was mapped to both PacBio genome assemblies for Dsim, Dmau, and Dsech using hisat2 aligner with the following command hisat2 -x indexed_genome_assembly -1 $ read1.fastq.gz -2 read2.fastq.gz -S file.sam. The alignment file in SAM format was then converted to a compressed BAM file using SAMTOOLS1 with the following commands: (1) samtools view -bS file.sam > file.bam (2) samtools sort file.bam > file_sorted.bam (3) samtools index file_sorted.bam. Mapping statistics for the BAM alignment files were obtained using bam_stat.py script from the RSeqQC package2.
small RNA data: sRNA reads were processed as follows: Raw sequence reads were adapter trimmed using Cutadapt software (https://cutadapt.readthedocs.io/en/stable/). After clipping the adapter sequence, we removed the 4bp random-linker sequence inserted at 5’ and 3’ of the sRNA sequence (total 8bp). After filtering <=15 nt reads, we mapped the small RNA data to PacBio genome assemblies using Bowtie (with –v0 –best –strata options.) The resulting small RNA alignments in SAM format were converted to BED for downstream processing using the BEDops software and visualized on IGV.
Genome_build: Data was mapped to PacBio genome assemblies for D. simulans, D. mauritiana, and D. sechellia from Chakraborty et al. 2021 (Genome Research)
Supplementary_files_format_and_content: The processed data files are in bigWig format for viewing in the IGV browser

organism: Drosophila mauritiana

source_name: testis

growth_protocol: All flies were raised in 25C for testis extraction

extract_protocol:
For small RNA analysis, we extracted RNA from testes and accessory glands of 7-day-old Dsim w[XD1], Dmau w[1] 14021-0241.60, and Dsech 14021-0248.25 strains using Trizol (Invitrogen). 1 μg of total RNA was used to prepare small RNA libraries as described3, with the addition of QIAseq miRNA Library QC Spike-ins for normalization (Qiagen). Adenylation of 3' linker was performed in a 40 µL reaction at 65°C for 1 hr containing 200 pmol 3' linker, 1X 5' DNA adenylation reaction buffer, 100 nM ATP and 200 pmol Mth RNA ligase and the reaction is terminated by heated to 85°C for 5 min. Adenylated 3' linker was then precipitated using ethanol and was used for 3' ligation reaction containing 10% PEG8000, 1X RNA ligase buffer, 20 µM adenylated 3' linker and 100 U T4 RNA Ligase 2 truncated K227Q. The 3' ligation reaction was performed at 4°C overnight and the products were purified using 15% Urea-PAGE gel. The small RNA-3' linker hybrid was then subjected to 5' ligation reaction at 37°C for 4 hr containing 20% PEG8000, 1X RNA ligase buffer, 1 mM ATP, 10 µM RNA oligo, 20 U RNaseOUT and 5 U T4 RNA ligase 1. cDNA synthesis reaction was then proceeded immediately by adding following components to the ligated product: 2 μl 5x RT buffer, 0.75 μl 100 mM DTT, 1 μl 1 μM Illumina RT Primer, and 0.5 μl 10 mM dNTPs. The RT mix was incubated at 65 C for 5 min and cooled to room temperature and transfer on to ice. 0.5 µL of superscript III RT enzyme and 0.5 µL RNase OUT were added to the RT mix and the reaction was carried out at 50°C for 1 hr. cDNA libraries were amplified using 15 cycles of PCR with forward and illumine index reverse primers and the amplified libraries were purified by 8% non-denaturing acrylamide gel. Purified libraries were sequenced on HiSeq2500 using SR50 at the New York Genome Center.
We used Dsim w[XD1] and Dmau w[1] 14021-0241.60, which were used for PacBio genome sequencing, and Dsech 14021-0248.25 used for the short read genome. We isolated total RNA from ~ 5-day-old flies and for Dsim, Dmau and Dsech samples. We extracted RNA from testes (dissected free of accessory glands) using Trizol (Invitrogen). We made two independent dissections to generate biologically replicate RNA samples, whose quality was assessed by Bioanalyzer. We used the Illumina TruSeq Total RNA library Prep Kit LT to make RNA-seq libraries from 650 ng of total RNA. Manufacturer's protocol was followed except for using 8 cycles of PCR to amplify the final library instead of the recommended 15 cycles, to minimize artifacts caused by PCR amplification. All samples were pooled together, using the barcoded adapters provided by the manufacturer, over 2 flow cells of a HiSeq2500 and sequenced using PE75 at the New York Genome Center.
Single-end sequencing for small RNA sequencing and paired-end sequencing for RNA sequencing data

value: testis

value: wildtype


title: Dmau_testis_RNAseq_replicate1

status: Public on Oct 07 2021

type: SRA

state: NY

country: USA

description: Dmau testis RNA replicate 1

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: Fibroblast_F1_PladB1

city: Shenzhen

first: Lei

last: Li

state: --- Select a state ---

address: China

department: Institute of Systems and Physical Biology

country: China

institute: Shenzhen Bay Laboratory

data_processing:
Sequenced reads from cortex, heart, and kidney were trimmed from 3' end into 76 bp, and all reads are aligned to reference genome mm10 and reference genome of SPRET/EiJ (http://www.sanger.ac.uk/) separately by HISAT2 (version 2.0.1) with parameters -p 12 -k 2 --reorder –no-softclip
Reads were assigned to the genome with less mapping edit distance. The reads with equal mapping distance to both genomes were designated as common reads.
Genomic alignment coordinates of the reads that were assigned to SPRET/EiJ were then converted to the corresponding locations in the C57BL/6J reference genome using the g2gtools software (version 0.1.29)
Alternative splicing detection and differential analysis between alleles were performed by rMATS with unambiguously assigned reads only
Alternative splicing detection and differential analysis between union reads (unambiguously assigned allelic reads plus common reads) and unambigously assigned reads were performed by rMATS
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files generated by rMATS include PSI value of each event for the two alleles in each sample
Supplementary_files_format_and_content: tab-delimited text files generated by rMATS include PSI value of each event for the total in each sample

organism:
Mus musculus
Mus spretus

source_name: Fibroblast

growth_protocol: The embryonic stem cells (ES cells) were cultured in Neuralbasal-DMEM/F12 (Gibco) with N2B27 (Invitrogen), 2i (Selleck), LIF (Millipore). The mouse fibroblast cells were cultured in DMEM containing 10% FBS and 1% P/S.

extract_protocol:
Mice were sacrificed at the age of eight weeks, and tissues were dissected and stored in -80°C before RNA extraction. Total RNA was extracted from all tissues and cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).
mRNA libraries were prepared using standard Illumina protocols for strand-specific sequencing

treatment_protocol: For perturbing splicing machinery in fibroblast, Pladienolide B (#16538, Cayman) was prepared in DMSO at 0.1 mM, and used to treat fibroblast cells at 0.1 µM for 4 hours. Control fibroblast cells were treated with same amount of DMSO for 4 hours.

tag: strain

value: C57BL/6J x SPRET/EiJ

value: Fibroblast

tag: treatment

value: treated with Pladienolide B at 0.1 microM for four hours


title: WT_A_T5

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped
For differential expression analysis of samples at T=0 replicate data sets were grouped and normalized using "quantile normalization"
Genome_build: The reference genome used for the analysis was based on NC_007793 and included annotations for sRNA genes (https://dx.doi.org/10.6084/m9.figshare.2061132.v1)
Supplementary_files_format_and_content: Expression values for each sample are calculated as RPKM values. For differential expression analysis of samples at T=0 the RPKM values were  normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in TSB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free; total RNA, rRNA-depleted
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were snap frozen in liquid nitrogen and stored at -80°C prior to RNA extraction

value: wild-type

tag: growth medium

value: TSB

tag: temperature

tag: exposed to

value: rifampicin

tag: time

value: 0 min


title: NIH 3T3-RheoSwitch-Ier2, DMSO, biological rep1

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Cells harvested after DMSO treatment

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2-type from Affymetrix. A Custom CDF Version 10 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

organism: Mus musculus

source_name: NIH 3T3-RheoSwitch-Ier2 cells treated with corresponding volume of DMSO and harvested after 24hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 7500/cm2 of NIH 3T3 cells were seeded on 14.5 cm petri dish and cultivated overnight in DMEM containing 4.5 g/l glucose (Gibco, Carlsbad, CA, USA) supplemented with 10% foetal bovine serum (Sigma Aldrich, St. Louis, MO, USA), 5% penicillin/streptomycin sulfate (Gibco, Carlsbad, CA, USA), G418 (500 mg/ml; Roche Applied Science, Penzberg, Germany) and hygromycin (500 mg/ml; Merck, Darmstadt, Germany). Cells were kept at 37°C under 5% CO2 atmosphere and 95% humidity.

extract_protocol: Trizol extraction (Thermo Fisher Scientific, Waltham, MA, USA) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NIH 3T3 cells were treated with 200 nM RheoSwitch Ligand (RSL-1) purchased from New England Biolabs (Ipswich, MA, USA). Cells were harvested 24 hours after the RSL-1 treatment.

tag: cell type

value: DSMO


title: NIH 3T3-RheoSwitch-Ier2, DMSO, biological rep3

description: Cells harvested after DMSO treatment


title: NIH 3T3-RheoSwitch-Ier2, DMSO, biological rep2

description: Cells harvested after DMSO treatment


title: siCon-FP1h-30-PAF_rep2

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate

growth_protocol: LNCaP-abl cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300 nM FP for indicated time.

value: prostate cancer cells

tag: passages

tag: cell line

value: LNCaP-abl

value: flavopiridol, 300 nM, 1hr; release 30min

tag: sirna

tag: chip antibody

value: PAF1 (Abcam, ab20662)


title: Fibroblast_F1_Control2

description: DMSO.allelic.SE.MATS.JC.txt

value: treated with DMSO at 0.1 microM for four hours


title: NIH 3T3-RheoSwitch-Ier2, RSL-1, biological rep1

description: Cells harvested after RSL1 treatment

source_name: NIH 3T3-RheoSwitch-Ier2 cells treated with 200 nM RSL-1 and harvested 24 and harvested after 24hrs


title: NIH 3T3-RheoSwitch-Ier2, RSL-1, biological rep2

description: Cells harvested after RSL1 treatment

source_name: NIH 3T3-RheoSwitch-Ier2 cells treated with 200 nM RSL-1 and harvested after 24hrs


title: ESC_F1_rep2

description:
ESC.total.SE.MATS.JC.txt
ESC.allelic.SE.MATS.JC.txt

source_name: ESC

value: Embryonic stem cells


title: HM-555

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36) and cutadapt (ver. 1.16) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.91) using STAR (ver. 2.6.1a).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.1)
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the Magnosphere™ UltraPure mRNA Purification Kit (Clontech). Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control-fed group) or C. acnes (HM-122- or HM-555-fed group).

value: Bristol N2

tag: Sex

value: hermaphrodite

tag: age

value: three-day-old

tag: fed with c. acnes strain


title: siCon-FP1h-20-PAF_rep4

value: flavopiridol, 300 nM, 1hr; release 20min


title: siCon-FP1h-20-PAF_rep5


title: ESC_F1_rep1

value: C57BL/6J x SPRET/EiJ


title: Fibroblast_F1_Control1

description: DMSO.allelic.SE.MATS.JC.txt

value: Fibroblast


title: siCon-FP1h-20-PAF_rep2


title: HM-122

value: wild-type


title: OP50


title: siCon-FP1h-10-PAF_rep5

value: flavopiridol, 300 nM, 1hr; release 10min


title: Spleen_F1_rep1

description:
Spleen.total.SE.MATS.JC.txt
Spleen.allelic.SE.MATS.JC.txt

source_name: Spleen

value: Spleen

value: 8 week


title: Lung_F1_rep2

description:
Lung.total.SE.MATS.JC.txt
Lung.allelic.SE.MATS.JC.txt

source_name: Lung

value: Lung


title: Dmau_testis_sRNA_replicate2

description: Dmau testis sRNA replicate 2

value: testis

value: wildtype


title: siCon-FP1h-10-PAF_rep3

value: prostate cancer cells

value: LNCaP-abl


title: siCon-FP1h-10-PAF_rep2

value: PAF1 (Abcam, ab20662)


title: siCon-FP1h-20-PAF_rep3


title: Lung_F1_rep1


title: Dmau_testis_sRNA_replicate1

description: Dmau testis sRNA replicate 1


title: Liver_F1_rep1

description:
Liver.total.SE.MATS.JC.txt
Liver.allelic.SE.MATS.JC.txt

source_name: Liver

value: C57BL/7J x SPRET/EiJ

value: Liver


title: siCon-FP1h-0-PAF_rep5

value: flavopiridol, 300 nM, 1hr; release 0min


title: siCon-FP1h-0-PAF_rep4


title: Liver_F1_rep2

value: C57BL/8J x SPRET/EiJ


title: Kidney_F1_rep2

description:
Kidney.total.SE.MATS.JC.txt
Kidney.allelic.SE.MATS.JC.txt

source_name: Kidney

value: Kidney


title: Kidney_F1_rep1

value: C57BL/6J x SPRET/EiJ


title: siCon-FP1h-0-PAF_rep2


title: siCon-FP1h-0-PAF_rep3


title: Heart_F1_rep2

description:
Heart.total.SE.MATS.JC.txt
Heart.allelic.SE.MATS.JC.txt

source_name: Heart

value: Heart


title: Heart_F1_rep1


title: siCon-FP1h-10-PAF_rep4


title: UVB-HaCaT-UA-1

city: Piscataway

first: Hsiao-Chen Dina

last: Kuo

address: 160 frelinghuysen road

department: Ernest Mario School of Pharmacy

institute: Rutgers University

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to hs19 using Hisat2 with default parameters
Duplicates removed by Picard
Reads overlapping gene features were counted by featureCounts.
Differential expression by DESeq2 in R
Genome_build: hs19
Supplementary_files_format_and_content: Comma delimited tables with raw counts.

source_name: human skin keratinocytes

growth_protocol: HaCaT cells were cultured in DMEM medium (10% Fetal Bovine Serum and 1% penicillin-streptomycin) and passaged every 2-3 days (typically 1*10^6 cells were seeded per 100mm plate every passage)

extract_protocol:
Qiagen Allprep DNA/RNA extraction
Standard Illumina protocols

treatment_protocol: Treated normal HaCaT cells or UVB exposed cells with/without 10 mM SFN or UA. UVB exposed cells were generated from exposing UVB to HaCaT with 10 mg/cm^2 UVB for 10 times (around one week gap between each exposure)

value: skin

value: keratinocytes (HaCaT)

value: 10 mJ/cm^2 UVB (10 cycles)+UA


title: UVB-HaCaT-UA-2


title: LI_MBELN3

city: LOUISVILLE

first: Mukesh

last: Sriwastva

state: KY

address: 505 S Hancock St

institute: University of Louisville

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Transcriptome analysis console 4.0 was used to analyze the data.
gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish

source_name: B6 Colon tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 90 ng total RNA (IonAmpliseq Trancriptome Mouse gene expression).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 10 x 10E+09 particle/100 µl MBELN (Mulberry, an edible plant, bark derived exosomes-like nanoparticles) per dose were orally given to each mice every day for 7 days. After 7 days mice were sacrificed and organs (colon) tissues were harvested for RNA isolation.

value: colon

value: mice orally gavaged with MBELN for 7 days


title: UVB-HaCaT-SFN-2

value: 10 mJ/cm^2 UVB (10 cycles)+SFN


title: Crypt_MBELN3

source_name: B6 Colon crypt

treatment_protocol: 10 x 10E+09 particle/100 µl MBELN (Mulberry, an edible plant, bark derived exosomes-like nanoparticles) per dose were orally given to each mice every day for 7 days. After 7 days mice were sacrificed and organs (colon) tissues were harvested following which crypt were isolated for RNA isolation.

value: colon crypt


title: LI_PBS1

value: control mice


title: Crypt_PBS3


title: LI_MBELN1


title: LI_MBELN2


title: LI_PBS3


title: LI_PBS2


title: Crypt_MBELN1


title: Crypt_MBELN2


title: Cortex_F1_rep2

description:
Cortex.total.SE.MATS.JC.txt
Cortex.allelic.SE.MATS.JC.txt

source_name: Cerebral cortex

value: Cerebral cortex

value: 8 week


title: UVB-HaCaT-SFN-1


title: UVB-HaCaT-Control-2

value: 10 mJ/cm^2 UVB (10 cycles)+Control


title: Cortex_F1_rep1


title: HaCaT-UA-2

value: UA


title: HaCaT-UA-1


title: UVB-HaCaT-Control-1

value: 10 mJ/cm^2 UVB 10 cycles+Control


title: CD4 sort T cell 3 TCR

city: Suita

first: Daisuke

last: Motooka

address: Yamadaoka

institute: Osaka University

description:
36_S864-882_10days_stim_TCR
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv

data_processing:
bcl2fastq v2.20.0.422
CellRanger software (v4.0.0) (10X Genomics) (default parameters) GRCh38 genome
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata in metadata.tsv
batch12_barcodes.tsv.gz (Cell ID list for batch12)
batch12_genes.tsv.gz (Genes list for batch12)
batch12_matrix.mtx.gz (count matrix for all cells from all samples in matrix.mtx for batch12)
batch12_metadata.tsv.gz (Metadata for batch12)
batch4_barcodes.tsv.gz (Cell ID list for batch4)
batch4_genes.tsv.gz (Genes list for batch4)
batch4_matrix.mtx.gz (count matrix for all cells from all samples in matrix.mtx for batch4)
batch4_metadata.tsv (Metadata for batch4)

molecule: polyA RNA

source_name: PBMC

growth_protocol: Human PBMCs were isolated and cryo-preserved until they were thawed and used in stimulations.

extract_protocol: Chromium Next GEM Single Cell 5′ Library (10x Genomics)

treatment_protocol: Human PBMCs were stimulated with SARS-CoV-2 ligands and sorted before applied to sc-RNA and -TCR analysis.

value: T cells

value: 10 days stimulation


title: Crypt_PBS2


title: CD4 sort T cell 4 TCR

description:
40_S864-882_10days_stim_TCR
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv


title: CD4 sort T cell 5 TCR

description:
44_S864-882_10days_stim_TCR
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv


title: CD4 sort T cell 2 TCR

description:
34_S864-882_10days_stim_TCR
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv


title: HaCaT-SFN-2

value: SFN


title: CTRL_Syrah_rep3 [OX.CARPO]

city: Verona

first: Sara

last: Zenoni

address: Strada Le Grazie 15

country: Italy

institute: Università degli Studi di Verona

hyb_protocol: For microarray analysis on Syrah leaves stably overexpressing VviCARPO, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

scan_protocol: Scanning and Feature Extraction were performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual.

data_processing: A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe. The data were normalized on the 75th percentile and a correlation analysis was then performed to assess the consistency of the biological quadruplicates.

organism: Vitis vinifera

source_name: Control leaves of Vitis vinifera cv. Syrah_rep3

label_protocol: For microarray analysis on Syrah leaves stably overexpressing VviCARPO, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: Grapevine plants (Vitis vinifera cv. Syrah, BVRC12 clone) were grown at the University of Verona greenhouse, starting from calli developed from anthers collected during the 2009 seasons in Coombe Vineyard (University of Adelaide, Urrbrae, South Australia). For the microarray analysis performed on grapevine, three biological replicates of fully expanded leaves were collected from control and transgenic plants.

extract_protocol: Total RNA was isolated from ~100 mg of the ground grapevine leaves tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).

tag: cultivar

value: Syrah

value: control

value: Fully expanded leaves


title: CD4 sort T cell 1 TCR

description:
33_S864-882_10days_stim_TCR
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv


title: OX.CARPO_Syrah_rep2

source_name: OX.CARPO leaves of Vitis vinifera cv. Syrah_rep2

value: CARPO overexpression

tag: tissue


title: OX.CARPO_Syrah_rep3

source_name: OX.CARPO leaves of Vitis vinifera cv. Syrah_rep3

tag: genotype


title: OX.CARPO_Syrah_rep1

source_name: OX.CARPO leaves of Vitis vinifera cv. Syrah_rep1


title: HaCaT-SFN-1

value: skin

value: keratinocytes (HaCaT)


title: HaCaT-control-2

value: Control


title: AIM sort T cell 8 TCR

description:
Patient14_and_15_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

value: 20 hrs stimulation


title: AIM sort T cell 9 TCR

description:
Patient16_and_17_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: OX.CARPO_Sultana_rep3

hyb_protocol: For microarray analysis on Sultana leaves transiently overexpressing VviCARPO, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

source_name: OX.CARPO leaves of Vitis vinifera cv. Sultana_rep3

label_protocol: For microarray analysis on Sultana leaves transiently overexpressing VviCARPO, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: For the transient overexpression of VviCARPO in grapevine, plantlets of Vitis vinifera cv. Sultana were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod.

treatment_protocol: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VviCARPO construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty pK7WG2 containing a non-coding sequence. Seven in vitro six-week-old plants of grapevine cv. Sultana for overexpression and five for the control were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa).

value: Sultana

value: Young leaves


title: Crypt_PBS1

tag: strain

value: colon crypt

value: control mice


title: CTRL_Syrah_rep2 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Syrah_rep2


title: AIM sort T cell 10 TCR

description:
Patient18_and_19_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

tag: treatment


title: UVB-HaCaT

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to hs19 using Bismark with default parameters
Duplicates removed by Picard
Reads overlapping gene features were counted by DMRfinder
Annotation by ChIPseeker
DMR analysis by DSS in R
Genome_build: hs19
Supplementary_files_format_and_content: Tab delimited tables with CpG counts and annotation.

treatment_protocol: Treated normal HaCaT cells with 0.1%DMSO(cont), SFN or UA. UVB exposed cells were generated from exposing UVB to HaCaT with 10 mg/cm^2 UVB for 10 times (around one week gap between each exposure)

value: 10 mJ/cm^2 UVB 10 cycles


title: AIM sort T cell 5 TCR

description:
Patient8_and_9_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: AIM sort T cell 6 TCR

description:
Patient10_and_11_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: AIM sort T cell 7 TCR

description:
Patient12 and_13_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: HaCaT-control-1


title: OX.CARPO_Sultana_rep2

source_name: OX.CARPO leaves of Vitis vinifera cv. Sultana_rep2


title: HaCaT-SFN


title: OX.CARPO_Sultana_rep4

source_name: OX.CARPO leaves of Vitis vinifera cv. Sultana_rep4


title: CTRL_Syrah_rep1 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Syrah_rep1


title: CTRL_Sultana_rep3 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Sultana_rep3


title: HaCaT-UA

value: UA


title: HaCaT-control


title: AIM sort T cell 2 TCR

description:
Patinet2_and_3_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

value: T cells


title: AIM sort T cell 3 TCR

description:
Patient4_and_5_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: OX.CARPO_Sultana_rep1

source_name: OX.CARPO leaves of Vitis vinifera cv. Sultana_rep1


title: AIM sort T cell 4 TCR

description:
Patient6_and_7_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: exosome derived from ectopic endometrial tissue-3

city: Ningbo

first: yichen

last: chen

address: NO.46 Yangshan Road，Ningbo

institute: Ningbo Institute of Medical Science

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.  After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: expression trf.xlsx (counts, cpms)

source_name: exosomes

extract_protocol:
Total RNAs that were extracted from exosomes were pretreated with rtStar tRF & tiRNA Pretreatment Kits to remove RNA modifications that interfere with the construction of small RNA-seq libraries.
The cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, 134–160-bp PCR-amplified fragments (corresponding to small RNAs that were each 14–40 nt in length) were extracted and purified from an agarose gel.

treatment_protocol: [Exosome purification method] We digested the fresh control endometrial tissues and ectopic endometrial tissues used by collagenase IV in 37℃. The supernatant was collected and tissue exosomes were obtained by ultracentrifugation

value: endometrial tissue

tag: disease state

value: endometriosis

tag: sample type

value: exosomes

tag: fraction

value: tRF&tiRNAs


title: exosome derived from ectopic endometrial tissue-1


title: Dsech_testis_RNAseq_replicate2

description: Dsech testis RNA replicate 2

organism: Drosophila sechellia

source_name: testis

value: testis

value: wildtype


title: exosome derived from ectopic endometrial tissue-2


title: Dsech_testis_sRNA_replicate1

description: Dsech testis sRNA replicate 1


title: CTRL_Sultana_rep4 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Sultana_rep4

value: control


title: Dsech_testis_RNAseq_replicate1

description: Dsech testis RNA replicate 1


title: CD4 sort T cell 5 GEX

description:
44_S864-882_10days_stim_GEX
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv

value: 10 days stimulation


title: exosome derived from control endometrial tissue-2

value: Uterine polyps


title: exosome derived from control endometrial tissue-1


title: AIM sort T cell 1 TCR

description:
Healthy_contorol_and_Patient1_TCR
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

value: 20 hrs stimulation


title: ir71_shoot apex

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Illumina Casava1.8 software used for basecalling.
FASTQ file generation and demultiplexing was done by the Functional Genomic Center Zurich.
Adaptors sequence removal using fastx_clipper from fastx-toolkit with parameters -a TGGAATTCTCGGGTG -l 15 -c -Q 33
Small RNA reads were filtered to 17-30nt long reads for analysis. Reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2 (options : -k 100 --score-min L,0,0)
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values.

organism: Arabidopsis thaliana

source_name: shoot apex

growth_protocol: Plants were grown in soil under 12:12 light:dark conditions

extract_protocol:
Total cellular RNA was extracted using TRIzol reagent (Invitrogene)
Extracted RNA was processed into sequencing libraries using Illumina protocols and sequenced at the Functional Genomic Center Zurich (http://www.fgcz.ch) using the Illumina HiSeq sequencer

tag: ecotype

tag: genotype/variation

value: ir71 mutant

tag: development stage

value: 4-5 weeks old rosettes

value: shoot apex (include shoot apical meristem and young emerging leaves)


title: AIM sort T cell 10 GEX

description:
Patient18_and_19_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

tag: cell type


title: IF7

city: La Jolla

first: Nicola

last: Allen

state: CA

address: 10010 North Torrey Pines Rd

institute: Salk Institute

description: from single nucleus barcode

data_processing:
BCL files from sequencer were demultiplexed by cellranger "mkfastq" function (v3.1.0)
Resulting FASTQ files were mapped by cellranger "count" function to mouse mm10 genome with gene annotations that came with cellranger to get the BAM file.
Genome_build: mm10

source_name: visual cortex

growth_protocol: 12 hour light/dark cycle with ad lib access to standard mouse chow

extract_protocol:
mice anesthetized with Ketamine/ Xylazine injection,  then brain microdissection in cold PBS, snap freeze in ethanol+CO2. stored at -80C until use. On day of experiment, tissue digested to release single nucleus suspension, then immunostained against Neun, and FACS sorted to obtain Neun negative nuclei. Immediately proceeded to 10x chromium protocol, barcoding and cDNA preparation. cDNA stored at -30C until all samples collected. Libraries prepared from all samples at the same time.
10X chromium kit following manufacturer's instructions

value: post natal day 14

value: female

value: Ip3r2 wt


title: IF8

description: from single nucleus barcode

value: Ip3r2 ko


title: wild_type_b_cells_rep1&2_HTO

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
wildtype C57BL/6 bone marrow FACS sorted at 1:1 ratio of B220+CD43+ and B220+CD43- cells
WT_1 = rep 1, WT_2 = rep 2

data_processing:
10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Each gel bead in emulsion (GEM) was identified and all gene specific reads were mapped via cellranger count (ver. 3.1.0) using the mouse reference genome (mm10).
Gene level quantification was completed using cellranger count software (ver. 3.1.0).
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

source_name: bone marrow B cells

extract_protocol:
Bilateral femurs and tibias were harvested from two wildtype C57BL/6 mice. Bones were flushed with 1X PBS with 2% fetal bovine serum (FBS), 0.1% sodium azide and 0.5 mM ethylenediaminetetraacetic acids, pH 7.4. The cells were filtered through a 70 µm mesh, centrifuged at 1200 rpm for 5 minutes and then incubated for 5 minutes with 5 mL of ACK lysis buffer for red blood cell lysis. Cells were then washed and centrifuged at 1200 rpm and subsequently resuspended. Cells were stained with two distinct oligo-labeled antibodies that recognize CD45 and MHC class I, which allow identification of cells derived from each individual mouse (referred to as hashtag antibodies).  We further stained cells with a panel of CITE-Seq antibodies (B220, CD19, CD93, CD25, IgM, and CD43) as well as fluorescently labeled B220 and CD43. Cells were sorted at a 1:1 ratio of B220+CD43+ and B220+CD43- cells to enrich for early progenitor B cell subsets.
For 10X Genomics scRNA-seq, we generated three libraries that measure: (1) mRNA transcript expression (RNA), (2) mouse-specific hashtag oligos (HTO), and (3) cell surface marker levels using antibody derived tags (ADT). Cells were harvested and stained as described above. In order to have balanced populations of various B cell development stages, we enriched for earlier progenitor B cells (B220+CD43+) by sorting at a 1:1 ratio of Dump-B220+CD43+ cells and Dump-B220+CD43- cells. A total of 20,000 cells per mouse were sorted into a single microtube containing 1X PBS with 50% FBS and were washed and resuspended in 1X PBS with 10% FBS prior to cell capture. The sample was split into three libraries (RNA, HTO, and ADT). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations. After library prep, quality control was performed using a bioanalyzer (Agilent 2100 Bioanalyzer; Agilent Technologies) and preliminary sequencing of the RNA library on a MiSeq (Illumina) to determine the approximate number of cells and general quality. After passing quality control, the library was sequenced on the NovaSeq 6000 with 2x150 bp paired-end reads (Illumina).

tag: sequenced molecule

value: HTO

tag: replicate

value: non-demultiplexed sample:rep 1 and 2 included

value: bone marrow

value: early progenitor B cells

tag: cell markers

value: FACS sorted 1:1 ratio of B220+CD43+ and B220+CD43-

value: untreated


title: IF6

description: from single nucleus barcode

tag: age

tag: Sex

value: male


title: exosome derived from control endometrial tissue-3

value: endometrial tissue

value: exosomes

value: tRF&tiRNAs


title: AIM sort T cell 8 GEX

description:
Patient14_and_15_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

source_name: PBMC

value: T cells

value: 20 hrs stimulation


title: CTRL_Sultana_rep1 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Sultana_rep1

tag: cultivar

value: Sultana

value: control

value: Young leaves


title: IF5

description: from single nucleus barcode

value: post natal day 14

value: Ip3r2 wt


title: wild_type_b_cells_rep1&2_ADT

value: antibody derived tags (ADT)

tag: tissue


title: AIM sort T cell 9 GEX

description:
Patient16_and_17_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: CD4 sort T cell 1 GEX

description:
33_S864-882_10days_stim_GEX
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv

value: 10 days stimulation


title: WT_shoot apex

value: wild type

value: 4-5 weeks old rosettes

value: shoot apex (include shoot apical meristem and young emerging leaves)


title: siPAF-FP-40-5095

source_name: prostate

value: prostate cancer cells

tag: passages

tag: cell line

value: LNCaP-abl

value: flavopiridol, 300 nM, 40min

tag: sirna

tag: chip antibody

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: wild_type_b_cells_rep1&2_GEX

value: RNA

value: non-demultiplexed sample:rep 1 and 2 included

tag: strain

value: bone marrow

value: early progenitor B cells

value: FACS sorted 1:1 ratio of B220+CD43+ and B220+CD43-

tag: treatment

value: untreated


title: CD4 sort T cell 2 GEX

description:
34_S864-882_10days_stim_GEX
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv

value: T cells


title: siPAF-FP-30-5095

value: flavopiridol, 300 nM, 30min


title: IF4

description: from single nucleus barcode

value: post natal day 14

value: female

tag: genotype

value: VGlut2 f/f;ROR acre


title: NRG1/CXCL1 stimulated Bacs

city: Bronx

middle: E

last: Segall

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: Gene expression data from cells stimulated with NRG1/CXCL1

hyb_protocol: Labeling, hybridization, and scanning were performed by the Einstein Genomics Facility following Affymetrix recommended protocols.

source_name: BAC 1.2F5 macrophage  in medium plus NRG1/CXCL1

growth_protocol: BAC 1.2F5 macrophages were cultured in αMEM with L-glutamine, 10% FBS, 3000 units/ml CSF-1

extract_protocol: RNA was isolated using Qiagen kit

treatment_protocol: cells were treated with medium or medium containing 12 nM NRG1+50ng/ml CXCL1 for 2 hours

tag: strain background

value: BALB/c x A.CA F1

value: BAC 1.2F5 macrophage

value: medium plus NRG1/CXCL1


title: CD4 sort T cell 4 GEX

description:
40_S864-882_10days_stim_GEX
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv

value: 10 days stimulation


title: Spleen_F1_rep2

description:
Spleen.total.SE.MATS.JC.txt
Spleen.allelic.SE.MATS.JC.txt

source_name: Spleen

value: C57BL/6J x SPRET/EiJ

value: Spleen

value: 8 week


title: siPAF-FP-20-5095

value: prostate cancer cells

value: LNCaP-abl

value: flavopiridol, 300 nM, 20min

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: Unstimulated Bacs

description: Gene expression data from cells in medium

scan_protocol: Labeling, hybridization, and scanning were performed by the Einstein Genomics Facility following Affymetrix recommended protocols.

source_name: BAC 1.2F5 macrophage  in plain medium

value: plain medium


title: IF3

description: from single nucleus barcode

value: VGlut2 f/f


title: siPAF-FP1h-40-5095

value: flavopiridol, 300 nM, 1hr; release 40min


title: AIM sort T cell 7 GEX

description:
Patient12 and_13_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

value: T cells

value: 20 hrs stimulation


title: CD4 sort T cell 3 GEX

description:
36_S864-882_10days_stim_GEX
batch4_matrix.mtx.gz
batch4_barcodes.tsv.gz
batch4_genes.tsv.gz
batch4_metadata.tsv


title: AIM sort T cell 5 GEX

description:
Patient8_and_9_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: CTRL_Sultana_rep2 [OX.CARPO]

source_name: Control leaves of Vitis vinifera cv. Sultana_rep2

value: Sultana

value: control

value: Young leaves


title: AIM sort T cell 3 GEX

description:
Patient4_and_5_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: IF2

description: from single nucleus barcode

value: post natal day 14

value: male

value: VGlut2 f/f;ROR acre


title: AIM sort T cell 2 GEX

description:
Patinet2_and_3_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: siPAF-FP1h-30-5095

value: flavopiridol, 300 nM, 1hr; release 30min


title: AIM sort T cell 4 GEX

description:
Patient6_and_7_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: siPAF-FP1h-0-5095

value: flavopiridol, 300 nM, 1hr; release 0min


title: siPAF-FP1h-20-5095

value: prostate cancer cells

value: flavopiridol, 300 nM, 1hr; release 20min


title: siCon-FP1h-40-PAF

value: LNCaP-abl

value: PAF1 (Abcam, ab20662)


title: IF1

description: from single nucleus barcode


title: AIM sort T cell 1 GEX

description:
Healthy_contorol_and_Patient1_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz


title: siPAF-FP1h-10-5095

value: flavopiridol, 300 nM, 1hr; release 10min

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: siPAF-FP-10-5095

value: flavopiridol, 300 nM, 10min


title: AIM sort T cell 6 GEX

description:
Patient10_and_11_GEX
batch12_matrix.mtx.gz
batch12_barcodes.tsv.gz
batch12_genes.tsv.gz
batch12_metadata.tsv.gz

value: T cells


title: HeLaPBS rep 2

city: El Paso

first: Shrikanth

last: Gadad

state: TX

address: 5001 El Paso Drive

department: Department of Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

data_processing:
Reads were aligned to GRCh38.p13 using the hisat2 aligner
Read counts were generated using feature counts with Ensembl version 101 and GENCODE v35 as reference with "-t exon, -g gene_id or -g exon_id, and -a annotation.gtf" as options.
Differential gene expression was determined using the DeSeq2 package in R
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab delimited txt file with raw read counts for each sample

source_name: HeLaPBS

growth_protocol: HeLa cells (CCL-2) were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% FBS in a humid chamber at 37°C and 5% CO2. After confluent growth, cells were washed twice with 1x sterile PBS, trypsinized and counted in an automatic cell counter. After counting, the cells were plated (1.5x106 cells/well) in 6-well culture plate and grown for 24 h before infection.

extract_protocol:
HeLa cells (1.5x106 cells/well) in each well of 6-well culture pate was infected with M. genitalium G37 or M. pneumoniae at an MOI of 1:10 (1 cell: 10 bacteria) or uninfected (control cells) and incubated for 4 h at 37ºC in a CO2 incubator. Thereafter, the cells were collected, washed with PBS and RNA isolated using EZ-10 DNAaway RNA Mini-Preps Kit (Bio Basic, Toronto, Canada). Agilent Technologies 4200 TapeStation was used to analyze RNA integrity of the preparation and RNA quantification was done using Nanodrop.
Only samples with RIN values of >9 in agilent tapestation were included in subsequent analysis. Libraries were prepared by Novogene Corporation.
Strand-Specific (dUTP-based) paired end libraries

treatment_protocol: M. genitalium G37 and M. pneumoniae were grown in 100 ml of SP-4 medium at 37°C in 150 cm2 tissue culture flasks (Corning, NY) for three to four days or until the medium changes color to light orange. The adherent mycoplasmas are scraped from the culture flasks, washed with 1x sterile PBS and suspended in PBS. The bacterial suspension was passed through 23G needle to disperse the clumps and diluted to obtain OD600= 1.00 which is equivalent to 1X 107 CFU/ml. This was further diluted with PBS to the required multiplicity of infection.

value: HeLa

tag: tissue source

value: Uterus;Cervix

value: Epithelial

tag: treatment/infection

value: PBS


title: HeLaMp rep 2

source_name: HeLaMp

tag: cell type

value: M. pneumoniae


title: HeLaMp rep 1


title: siCon-FP1h-30-PAF


title: ALDH1A3-KO, biological rep5

city: Mobile

first: Robert

middle: W.

last: Sobol

state: AL

address: 1660 Springhill Avenue

department: Mitchell Cancer Institute

institute: University of South Alabama

description: Gene expression data from ALDH1A3-KO GSC cells

hyb_protocol: Following cRNA purification, 10 ug of cRNA were hybridized for 16 hr at 45C  on Human Genome U219 Array Strip, then washed and stained using GeneAtlas™ Hybridization, Wash, and Stain Kit for 3' IVT Array Strips by GeneAtlas system.

scan_protocol: The array strip were scanned by the image station of GeneAtlas system.

data_processing: The data were analyzed with Partek Express software using Affymetrix default analysis settings and normalization method.

source_name: GSC-326 ALDH1A3-KO cell, biological rep5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA ( GeneAtlas™ 3' IVT Express Kit, Affymetrix).

growth_protocol: Glioma stem cells (GSCs) derived from high-grade glioma (HGG) samples were cultured in suspension in GSC growth medium [DMEM-F12 (Cat# 10565, Life Technologies) supplemented with B27 (1:50), heparin (5 mg/mL), basic FGF (bFGF) (20 ng/mL), and EGF (20 ng/mL)] in 100x20 mm Petri dishes (Cat# 0875711Z, Fisher Scientific) at 37°C with 5% CO2. Growth medium was changed every 3 or 4 days.

treatment_protocol: Guide RNAs (gRNAs) targeting ALDH1A3 exon 1 or exon 2 were designed using the CRISPR Design Tool (Hsu et al. 2013). Each separate gRNA was cloned into pLentiCRISPRv2. 326-GSC  cells were transduced by lentivirus prepared from the corresponding gRNA plasmids. Cells were then seeded for selection of single cell clones and knockout was confirmed by immunoblotting analysis of whole-cell lysates with an ALDH1A3 antibody (Abcam cat# ab129815). The pLentiCRISPRv2 with a gRNA insert was used as the negative control.

tag: cell

value: GSC cells isolated from glioblastoma tumor


title: HeLaG372 rep 2

value: M. genitalium G37


title: ALDH1A3-KO, biological rep6

source_name: GSC-326 ALDH1A3-KO cell, biological rep6


title: siPAF-FP-0-5095

value: flavopiridol, 300 nM, 0min


title: HeLaG371 rep 1


title: HeLaPBS rep 1


title: ALDH1A3-KO, biological rep4

source_name: GSC-326 ALDH1A3-KO cell, biological rep4


title: siCon-FP1h-20-PAF


title: MH-S_IL-4 rep1

status: Public on Oct 06 2021

city: Guangzhou

first: Qiujie

last: Wang

state: Guangdong

address: No.107 Yan jiang West Road

department: Department of Respiratory Medicine

institute: Sun Yat-sen University Second University Hospital

description: miRNA expression after 48hr in lL-4-induced alveolar macrophages

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: alveolar macrophage

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer's guideline for miRNA labelling.

growth_protocol: The murine alveolar macrophages (MH-S) purchased from ATCC were maintained in RPMI 1640 containing 10% FBS supplemented with 1% penicillin/streptomycin and incubated at 37 °C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: MH-S cells were seeded into plastic 6-well plates at a concentration of 1×105 cells/mL and incubated in serum-deprived medium for 12 h followed by treatment with IL-4 at 20 ng/mL for 48 h.

value: alveolar macrophage


title: MH-S_IL-4 rep2


title: MH-S_control rep3

description: miRNA expression after 48hr in PBS-induced alveolar macrophages

value: PBS, 48h


title: ALDH1A3-KO, biological rep2

source_name: GSC-326 ALDH1A3-KO cell, biological rep2


title: Δgds1 H3

city: Boston

first: Stephen

last: Buratowski

state: MA

address: 240 Longwood Avenue

department: BCMP

institute: Harvard Medical School

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads mapped to sacCer3 whole genome using bowtie v1.1.1 with parameters -S -p 4 -m 1
peaks were called using Macs2 (v2.1.0) with parameters –c  -f BAM -g 12100000 -B -q 0.01 --nomodel --extsize 150 --SPMR
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph file generated by macs2 possessing SPMR value.

organism: Saccharomyces cerevisiae

source_name: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0, gds1∆::KanMX

growth_protocol: Yeast cells were grown in rich media (YPD) and harversted at early exponetial growing stage (OD600 was not over 0.5) after crosslinking with 1% formaldehyde.

extract_protocol:
Sheared chromatin (100 bp ~ 300 bp) was prepared using a Misonix sonicator 300 with cup horns. Crosslinked chromatin was precipitated by standard methods with specific antibodies.
Libraries were prepared according to previous methods (Wong, K.H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7,  unit7.11.–7.11.11.).

tag: growth phase

value: early exponential growing

value: MATa, ura3delta0, leu2delta0, his3delta1, met15delta0, gds1delta::KanMX

tag: chip ab

value: Histone H3 (abcam, ab1791)


title: ALDH1A3-WT, biological rep2

description: Gene expression data from ALDH1A3 WT GSC cells

source_name: GSC-326 WT cell, biological rep2


title: siCon-FP1h-10-PAF

value: prostate cancer cells

value: LNCaP-abl

value: flavopiridol, 300 nM, 1hr; release 10min

value: PAF1 (Abcam, ab20662)


title: ALDH1A3-KO, biological rep3

source_name: GSC-326 ALDH1A3-KO cell, biological rep3


title: ALDH1A3-WT, biological rep1

source_name: GSC-326 WT cell, biological rep1


title: siCon-FP1h-0-PAF

value: flavopiridol, 300 nM, 1hr; release 0min


title: ALDH1A3-KO, biological rep1

source_name: GSC-326 ALDH1A3-KO cell, biological rep1


title: MH-S_control rep2


title: ALDH1A3-WT, biological rep3

source_name: GSC-326 WT cell, biological rep3


title: WT H4ac

source_name: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0

value: MATa, ura3delta0, leu2delta0, his3delta1, met15delta0

value: Acetyl Histone H4 (Millipore, 06-598)


title: WT H3


title: Δgds1 H4ac


title: MH-S_control rep1


title: MH-S_IL-4 rep3


title: IMR90_siGFP_exp3_rep2

city: Palermo

first: Salvatore

last: Feo

address: Viale delle Scienze, ed 16

department: STEBICEF

institute: University of Palermo

hyb_protocol: 1.0 ug of Cy3- or Cy5-labelled cRNA (specific activity >9.0 pmol Cy/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (Agilent-G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channels PMT set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol: GE2-v5_95_Feb07 and Grid: 014850_D_F_20110325) to obtain background subtracted, dye normalized and spatially detrended processed signal intensities

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 labeled cRNA was prepared from 200 ng total RNA using the LowInput QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions (Agilent protocol: G4140-90050_GeneExpression_TwoColor_ver._6.9.1), followed by RNAeasy mini kit column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer

growth_protocol: Cultivated in MEM medium supplemented with 10% foetal calf serum, 100 U/mL Penicillin, 100 μg/mL Streptomycin, 1 mM Sodium Pyruvate and 1% Non-Essential Amino Acids

extract_protocol: Total RNA from siRNA treated cells was extracted using Trizol reagent (Invitrogen) and further purified with RNeasy RNA isolation kit according to manufacturer’s instructions (Qiagen). RNA 6000 Nano LabChip kit (Agilent) was used to determine the concentration, the purity and the integrity of the RNA samples using an Agilent 2100 bioanalyzer. Only samples with a RIN (RNA Integrity Number) > 8.0 were used for analysis.

treatment_protocol: IMR-90 cells were transfected with gene specific siRNA with Lipofectamine 2000 Reagent (Invitrogen), according to manufacturer’s recommendation

value: Fetal lung fibroblast

tag: genotype/variation

value: GFP siRNA


title: IMR90_siGFP_exp2_rep1


title: IMR90_siCENPE_72h_exp3_rep2

value: CENPE siRNA


title: IMR90_siGFP_exp3_rep1


title: IMR90_siGFP_exp1_rep2


title: IMR90_siGFP_exp2_rep2


title: IMR90_siCENPE_72h_exp2_rep1


title: IMR90_siCENPE_72h_exp3_rep1


title: IMR90_siCENPE_72h_exp1_rep2


title: 20_time0_H3K9me3

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

institute: The University of Tokyo

description: ChIP-seq data of human endothelial cells through VEGF-induced angiogenic signaling

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome hg19 with Bowtie2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Human Genome 19 (hg19)
Supplementary_files_format_and_content: bigwig

source_name: HUVEC

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Kanki et al., 2011; Kanki et al., 2017). In brief, 10 million HUVECs were cross-linked with 1% formaldehyde (Wako) for 10 min. For p65 and FLAG ChIP analysis, cells were fixed with 2 mM EGS (ethylene glycol bis [succinimidyl succinate]) (Thermo Fisher Scientific) for 1 hr prior to formaldehyde fixation. After neutralization by using 0.2 M glycine, cells were collected, re-suspended in 2 ml SDS lysis buffer composed of 10 mM Tris-HCl; pH8.0 (Thermo Fisher Scientific), 150 mM NaCl (Thermo Fisher Scientific), 1% SDS (Sigma-Aldrich), 1mM EDTA; pH 8.0 (Thermo Fisher Scientific), cOmplete™ EDTA-free Protease Inhibitor Cocktail (Sigma-Aldrich), and fragmented by the Picoruptor (40 cycles for histones and p65, and 20 cycles for FLAG, 30 sec on/30 sec off; Diagenode, Liege Science Park, Belgium). Sonicated solution was diluted by ChIP dilution buffer (20 mM Tris-HCl; pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 (Sigma-Aldrich)) up to 10.3 ml, which was used for immunoprecipitation (10 ml) and the rest 300 μl as a non-immunoprecipitated chromatin (INPUT). Specific antibody was bound with magnetic Dynabeads M-280 and applied to diluted sonicated solution for immunoprecipitation. Antibodies against H3K4me3, H3K27ac, H3K9me2, H3K27me3 (MAB Institute, Inc. Hokkaido, Japan), p65 (abcam for ChIP-Seq and Santa Cruz Biotechnology Inc for ChIP-PCR), and FLAG (Sigma-Aldrich) were used. Prepared DNA was quantified using NanoDrop 2000 (Thermo Fisher Scientific) and more than 10 ng of DNA was processed for qPCR or sequence.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 50 ng/ml VEGF-a (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

value: HUVEC

tag: antibody used  for chip

value: VEGF-treatment

tag: time


title: 18_time15_H2AK119Ub


title: 23_time0_FAIRE

description: FAIRE-seq data of human endothelial cells through VEGF-induced angiogenic signaling


title: 19_time60_H2AK119Ub


title: 17_time0_H2AK119Ub


title: 25_time60_FAIRE


title: 24_time15_FAIRE


title: 16_time60_2SP-POL2

value: Ser2-p-RNA polymerase II


title: 15_time15_2SP-POL2


title: IMR90_siGFP_exp1_rep1


title: IMR90_siCENPE_72h_exp2_rep2


title: 21_time15_H3K9me3


title: IMR90_siCENPE_2w_exp3_rep1


title: IMR90_siCENPE_2w_exp3_rep2


title: IMR90_siCENPE_2w_exp2_rep1


title: 22_time60_H3K9me3


title: IMR90_siCENPE_72h_exp1_rep1


title: IMR90_siCENPE_2w_exp1_rep1


title: 14_time0_2SP-POL2


title: IMR90_siCENPE_2w_exp2_rep2


title: 12_time15_5SP-POL2

value: Ser5-p-RNA polymerase II


title: 11_time0_5SP-POL2


title: IMR90_siCENPE_2w_exp1_rep2


title: 10_time60_H3K27ac


title: 8_time0_H3K27ac


title: 7_time60_H3K27me3


title: 4_time60_H3K4me3


title: 2_time0_H3K4me3


title: 3_time15_H3K4me3


title: 5_time0_H3K27me3


title: IEL WT CD69+CD103+ rep3 [ATAC-seq]

city: San Antonio

first: Nu

last: Zhang

address: 7703 Floyd Curl Drive

institute: University of Texas Health Science Center at San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 (--very sensitive -X 2000 -x index), then sort and remove duplication using samtools
Then mitochondrial chromatin were filtered (grep -v chrM)
Peaks were called using macs2
The replications in same group were merged
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using deeptools

source_name: WT CD69+CD103+CD8+ Intraepithelial lymphocytes

growth_protocol: WT, Tbet-/-, Tgfbr2-/-, and Tbet-/-Tgfbr2-/- P14 Naive CD8 T cells were adoptively transferred into C57BL/6 recipient mice followed by LCMV-Arm infection. Around 27 days later, all recipient mice were sacrificed and the lymphoctes were isolated from spleen and small intestine.

extract_protocol:
Donor P14 T cells were FACS sorted based on CD8, CD45.1 and CD45.2. After harvesting, cells are lysed with a nonionic detergent to yield pure nuclei.
The resulting chromatin is then fragmented and simultaneously tagmented with sequencing adapters using the Tn5 transposase to generate the ATAC-Seq library

treatment_protocol: All recepients mice were infectied with LCMV-Arm by i.p.

value: wild type

tag: tissue/cell type

value: Small Intestine Intraepithelial lymphocytes

value: day 15 after LCMV-Arm infection


title: IEL WT CD69+CD103+ rep1 [ATAC-seq]


title: IEL WT CD69+CD103+ rep2 [ATAC-seq]


title: 13_time60_5SP-POL2


title: SP WT rep1

data_processing:
Original image data file from Illumina is transformed to sequenced reads (Raw reads) by CASAVA base recognition
Raw reads of FASTQ format were firstly processed through fastp to obtain the clean reads
Paired-end clean reads were aligned to the reference genome (mm10) using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: WT KLRG1-CD8+ Splenic T cells

extract_protocol:
Donor P14 T cells were FACS sorted based on CD8, CD45.1 and CD45.2. RNA was extracted from sorted cells using the Quick-RNA™ MiniPrep, according to manufacturer’s instructions (Zymo Research). RNA-seq analysis was performed by Novogene
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: Spleen

value: day 27 after LCMV-Arm infection


title: 1_input

value: none (input)


title: IEL Tgfbr2-KO CD69-CD103- rep2 [ATAC-seq]

source_name: Tgfbr2-KO CD69-CD103-CD8+ Intraepithelial lymphocytes


title: IEL Tbet-KO CD69+CD103+ rep2 [ATAC-seq]

source_name: Tbet-KO CD69+CD103+CD8+ Intraepithelial lymphocytes

value: Tbet-/-


title: IEL Tbet&Tgfbr2-KO CD69+CD103+ [ATAC-seq]

source_name: Tbet&Tgfbr2-KO CD69+CD103+CD8+ Intraepithelial lymphocytes


title: IEL Tgfbr2-KO CD69-CD103- rep1 [ATAC-seq]


title: 9_time15_H3K27ac


title: IEL Tbet-KO CD69+CD103+ rep1 [ATAC-seq]


title: IEL WT CD69+CD103+ rep1


title: IEL WT CD69+CD103+ rep2


title: IEL Tbet-KO CD69+CD103+ rep1


title: IEL WT CD69+CD103- rep2

source_name: WT CD69+CD103-CD8+ Intraepithelial lymphocytes


title: 6_time15_H3K27me3


title: IEL Tbet-KO CD69+CD103+ rep2


title: IEL Tgfbr2-KO CD69+CD103- rep2

source_name: Tgfbr2-KO CD69+CD103-CD8+ Intraepithelial lymphocytes


title: IEL Tgfbr2-KO CD69-CD103- rep1


title: IEL Tgfbr2-KO CD69-CD103- rep2


title: IEL Tbet&Tgfbr2-KO CD69+CD103+ rep2


title: IEL Tgfbr2-KO CD69+CD103- rep1


title: IEL Tbet&Tgfbr2-KO CD69+CD103+ rep1


title: SP WT rep2


title: Dio2cochlea043

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: Dio2-expression cell in P10 cochlea

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq3000 Sequencer at NIDDK Genomics Facility
single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.3a)
Output bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each gene of all samples

source_name: P10 Cochlea

extract_protocol:
Fresh cochlea from Dio2ERt2 heterozygous mice were disected, and dissassociated into suspension cells after quick Papain  treatment. Fluorescent cells were identified on a Zeiss Axiovert 200M microscope and collected individually using an Eppendorf micromanipulator and suction pipette.
Single-cell RNA-seq libraries were constructed by using SMART-Seq v4 Ultra Low Input RNA Kit and ThruPLEX DNA-Seq Kit.

tag: tissue

value: cochlea

tag: age

value: post natal day 10


title: Dio2cochlea046

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea044

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea029

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea025

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea030

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea041

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea027

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea037

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea031

description: Dio2-expression cell in P10 cochlea


title: IEL WT CD69+CD103- rep1


title: Dio2cochlea036

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea033

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea042

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea023

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea040

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea039

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea035

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea028

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea021

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea020

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea022

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea034

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea038

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea024

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea019

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea045

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea016

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea017

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea015

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea026

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea032

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea012

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea011

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea014

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea007

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea010

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea004

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea002

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea008

description: Dio2-expression cell in P10 cochlea


title: N3

city: Perth

first: Zhenjun

last: Deng

state: Western Australia

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
Real Time Analysis (RTA) v3.4.4 software used for base-calling. Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data
Merge the two files for each sample if needed prior to secondary analyses
Fastp used for trimming
STAR used for aligment and SAMtools used to generate bam files for further analyses
DESeq2 used for differential gene expresson analyses
Genome_build: hg19
Supplementary_files_format_and_content: CSV files with raw abundance counts

source_name: normal skin tissue

growth_protocol: Keratinocytes were grown in keratinocytes growth media (KGM, EpigrowTM, human epidermal keratinocyte complete culture media kit, Merck, Millipore, Massachusetts, USA) with 1% penicillin/streptomycin

extract_protocol:
Keratinocytes were harvested by trypsinization using 0.05% trypsin-EDTA and washed in PBS. RNA was extracted using the RNeasy Mini kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: keratinocyte

tag: diagnosis

value: control donor


title: Dio2cochlea009

description: Dio2-expression cell in P10 cochlea

tag: strain


title: Dio2cochlea013

description: Dio2-expression cell in P10 cochlea


title: Dio2cochlea003

description: Dio2-expression cell in P10 cochlea


title: K8

source_name: keloid tissue

value: keloid


title: Dio2cochlea005

description: Dio2-expression cell in P10 cochlea


title: K9


title: Dio2cochlea001

description: Dio2-expression cell in P10 cochlea


title: N5


title: K7


title: N6


title: N4


title: N7


title: N1


title: K4


title: N8


title: K5


title: K3


title: Dio2cochlea006

description: Dio2-expression cell in P10 cochlea


title: N2


title: K6


title: ADR/AD-MYDGF

city: Jinan, Shandong

first: Ping

last: Zhan

address: School of Basic Medical Sciences, Shandong University  44# Wenhua Xi Road

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRCh38.91 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: podocytes

growth_protocol: human podocyte cell line (HPC) was cultured under growth permissive conditions in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) , and then the human podocytes were transfected with NC-adenovirus or mydgf-adenovirus for 24 hours to construct NC- MYDGF or AD-MYDGF podocyte cell line,  and treated with 0.4 μg/ml Adriamycin (ADR) for 24 hours for this study

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol: Adriamycin (ADR) at a final concentration of 0.4 μg/mL in culture medium

tag: cell line

value: HPC

value: podocyte

tag: treatment

value: MYDGF-adenovirus transfection human podocyte cell for 24 hours and treated with 0.4 μg/mL Adriamycin (ADR)  for 24 hours


title: 5Y_Input_2

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Input genomic DNA replicate 2

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to reference genome of homo sapiens using STAR software (version 2.5.3a) with default parameters.
The RSeQC (version 2.6) was used for reads distribution analysis. The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Read densities were visualized by preparing normalized BigWig files using HOMER.

source_name: SH-SY5Y cells

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Cells were fixed in 1% formaldehyde for 10 min at room temperature, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction.

value: neuroblastoma cell line

tag: passages


title: NSCLC.P029.post.01

city: Beijing

first: Zemin

address: No. 5, Summer Palace Road, Haidian District, Beijing

department: BIOPIC

institute: Peking University

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 3.0.2) against the GRCh38 human reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 3.1) with the manufacturer-supplied human VDJ reference genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger version 3.0.2

extract_protocol:
Fresh tumour biopsies were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 μm SmartStrainer and centrifuged at 400g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS). The concentration of single-cell suspensions was adjusted to 500~1200 cells/ul. 10,000~18,000 cells were used for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), according to the manufacturer’s instructions.
10x Chromium Single cell 5’ + VDJ Library

tag: patient id

tag: disease state

value: non-small-cell lung cancer patients

tag: condition

value: On-treatment

tag: platform

value: 10X Genomics


title: 5Y_Input_1

description: Input genomic DNA replicate 1

tag: cell type


title: NSCLC.P035.pre.01

value: Pre-treatment


title: NSCLC.P033.pre.01


title: NSCLC.P034


title: 5Y_ZRF1

description: Genomic DNA immunoprecipitated by ZRF1 antibody

tag: chip antibody

value: ZRF1 Rabbit mAb, Cell Signaling Technology Inc., Cat  #12844S


title: K1


title: NSCLC.P033.post.01


title: AD-MYDGF

value: MYDGF-adenovirus transfection human podocyte cell for 24 hours


title: NSCLC.P025


title: K2


title: 5Y_BRD4

description: Genomic DNA immunoprecipitated by BRD4 antibody

value: BRD4 Rabbit mAb, Cell Signaling Technology Inc., Cat  #13440


title: NSCLC.P029.pre.01


title: NSCLC.P036.post.01


title: ADR/NC-MYDGF

value: NC-adenovirus transfection human podocyte cell for 24 hours and treated with 0.4 μg/mL Adriamycin (ADR)  for 24 hours


title: NC-MYDGF

value: NC-adenovirus transfection human podocyte cell for 24 hours


title: NSCLC.P038.post.01


title: NSCLC.P030.pre.01


title: NSCLC.P028


title: NSCLC.P037.post.01


title: NSCLC.P027


title: NSCLC.P026


title: NSCLC.P023


title: NSCLC.P035.post.01


title: NSCLC.P030.post.01


title: NSCLC.P024


title: Dio2cochlea018

description: Dio2-expression cell in P10 cochlea

value: cochlea

value: post natal day 10

tag: genotype


title: NSCLC.P022


title: NSCLC.P020


title: NSCLC.P015


title: NSCLC.P017


title: NSCLC.P014


title: NSCLC.P011


title: NSCLC.P013.post.03


title: NSCLC.P009


title: NSCLC.P013.pre.01


title: NSCLC.P004


title: NSCLC.P010.post.01


title: NSCLC.P018


title: NSCLC.P012


title: NSCLC.P008


title: NSCLC.P016


title: NSCLC.P010.pre.01


title: NSCLC.P003


title: NSCLC.P002


title: NSCLC.P006


title: NSCLC.P001.post.02


title: NSCLC.P007


title: NSCLC.P021


title: NSCLC.P001.pre.01


title: NSCLC.P001.post.03


title: NSCLC.P001.post.01


title: NSCLC.P019.pre.01


title: COV19_56

first: zhaoming

last: Zhou

address: 1023-1063 shatai South Road, Baiyun District, Guangzhou

institute: School of Public Health,Southern Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and maskerd for low-complexity or low-quality sequence using Fastp software.
The cleaned reads of each sample were mapped to the Human Genome Hg38 using Histat2 with default parament, and annotated by Ensembl database.
Gene expression measurements were generationed and normalized using StringTie.The normalized standard were conts per million (CPM)
Genome_build: Human Genome Hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized CPM values

source_name: Peripheral blood

growth_protocol: Blood samples were collected and transported with PAXgene Blood RNA Tubes (BD, America). The transportation were completed within 3 days in room-temperature and PAXgene Blood RNA Tubes were stored at -20℃ before use.

extract_protocol:
RNA isolation and purification were performed with the PAXgene Blood RNA Kit (Qiagen, Germany) as the manufacture indicated and purified RNA was stored at -80°C for further analyzing.
Ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit, RNA libraries were prepared for sequencing using  the rRNA-depleted RNA by NeBNext Ultra Directional RNA Library Prep Kit for  Illumina following manufactrurer's recommedndations.

treatment_protocol: Whole blood RNA isolation and purification were performed with the PAXgene Blood RNA Kit (Qiagen, Germany) as the manufacture indicated and purified RNA was stored at -80°C for further analyzing. Quantification of purified RNA was performed with Bioanalyzer 2100 (Agilent, CA, USA).

value: PBMC


title: NSCLC.P013.post.01


title: COV19_57


title: COV19_55


title: NSCLC.P005


title: COV19_49


title: COV19_47


title: COV19_50


title: COV19_51


title: COV19_53


title: COV19_52


title: COV19_43


title: COV19_46


title: COV19_48


title: COV19_44


title: COV19_39


title: COV19_40


title: COV19_41


title: COV19_35


title: COV19_34


title: COV19_37


title: COV19_42


title: COV19_45


title: COV19_27


title: COV19_38


title: COV19_36


title: COV19_31


title: COV19_26


title: COV19_32


title: COV19_30


title: COV19_54


title: COV19_33


title: COV19_29


title: COV19_28


title: COV19_25


title: COV19_24


title: COV19_22


title: COV19_23


title: COV19_21


title: COV19_20


title: COV19_19


title: COV19_18


title: Sample 35, Ulcerative colitis patient 5, 48 h [UC_48h_pUC5_35]

city: Herlev

first: Jakob

middle: Benedict

last: Seidelin

address: Borgmester Ib Juuls Vej 1

department: Department of Gastroenterology D

country: Denmark

institute: Herlev Hospital, University of Copenhagen

data_processing:
Sequenced reads were trimmed with Trimmomatic (v0.32) with command parameter settings:  ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:1:true HEADCROP:12 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed PE reads were aligned to the hg38 genome assembly (canonical chromosomes only) using the STAR (v2.7.3a) aligner with parameter settings: --sjdbGTFfile ncbiRefSeqCurated_hg38.gtf --sjdbOverhang 137  --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 25 --outFilterMismatchNmax 5 --peOverlapNbasesMin 20
Uniquely aligned reads were assigned to RefSeq genes using featureCounts with parameter settings:  featureCounts -p -B -s 0 -J -a ncbiRefSeqCurated_hg38.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing raw counts from running featureCounts on all bam files

source_name: Ulcerative colitis_48 h_Sigmoid colon mucosa

extract_protocol:
Tissue samples were embedded in RNA until lysis with lysis buffer containing 2% mercaptoethanol, homogenization. Total RNA purification was done by Nucleospin columns (Macherey-Nagel, Düren, Germany).
Illumina PE150 system, Illumina, San Diego, CA, USA

tag: subject id/diagnosis

value: Ulcerative colitis patient 5

value: Ulcerative colitis

tag: endoscopic mayo score

tag: gender

value: M

tag: medicine

value: Oral mesalazine

tag: maximal prior disease extend

value: Proctosigmoiditis

value: Sigmoid colon mucosa


title: Sample 36, Ulcerative colitis patient 6, 48 h [UC_48h_pUC6_36]

value: Ulcerative colitis patient 6

tag: diagnosis

tag: age

value: F

tag: tissue


title: Sample 19, Ulcerative colitis patient 4, 24 h [UC_24h_pUC4_19]

source_name: Ulcerative colitis_24 h_Sigmoid colon mucosa

value: Ulcerative colitis patient 4


title: Sample 31, Ulcerative colitis patient 4, 48 h [UC_48h_pUC4_31]


title: Sample 23, Ulcerative colitis patient 5, 24 h [UC_24h_pUC5_23]


title: Sample 30, Ulcerative colitis patient 3, 48 h [UC_48h_pUC3_30]

value: Ulcerative colitis patient 3


title: Sample 18, Ulcerative colitis patient 3, 24 h [UC_24h_pUC3_18]


title: Sample 24, Ulcerative colitis patient 6, 24 h [UC_24h_pUC6_24]


title: Sample 17, Ulcerative colitis patient 2, 24 h [UC_24h_pUC2_17]

value: Ulcerative colitis patient 2

value: Pancolitis


title: Sample 16, Ulcerative colitis patient 1, 24 h [UC_24h_pUC1_16]

value: Ulcerative colitis patient 1


title: MM_M1_2_sample 3045

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted 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: ASM275486v1
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

organism: Callithrix jacchus

extract_protocol:
M1 regions of human/marmoset brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: brain

tag: brain region


title: MM_M1_2_sample 3046


title: Sample 7, Ulcerative colitis patient 4, 0 h [UC_0h_pUC4_7]

source_name: Ulcerative colitis_0 h_Sigmoid colon mucosa


title: MM_M1_2_sample 3044


title: Sample 11, Ulcerative colitis patient 5, 0 h [UC_0h_pUC5_11]


title: Sample 12, Ulcerative colitis patient 6, 0 h [UC_0h_pUC6_12]


title: MM_M1_2_sample 3043


title: MM_M1_2_sample 3041


title: MM_M1_2_sample 3038


title: Sample 6, Ulcerative colitis patient 3, 0 h [UC_0h_pUC3_6]


title: MM_M1_2_sample 3040


title: Sample 5, Ulcerative colitis patient 2, 0 h [UC_0h_pUC2_5]


title: MM_M1_2_sample 3042


title: MM_M1_2_sample 3039


title: Sample 29, Ulcerative colitis patient 2, 48 h [UC_48h_pUC2_29]


title: MM_M1_2_sample 3037


title: Sample 4, Ulcerative colitis patient 1, 0 h [UC_0h_pUC1_4]


title: Sample 33, Control subject 5, 48 h [Control_48h_pC5_33]

source_name: Control subject_48 h_Sigmoid colon mucosa

value: control subject 5

value: Control subject


title: Sample 26, Control subject 2, 48 h [Control_48h_pC2_26]

value: control subject 2


title: Sample 28, Ulcerative colitis patient 1, 48 h [UC_48h_pUC1_28]


title: Sample 34, Control subject 6, 48 h [Control_48h_pC6_34]

value: control subject 6


title: MM_M1_2_sample 3033


title: Sample 32, Control subject 4, 48 h [Control_48h_pC4_32]

value: control subject 4


title: Sample 22, Control subject 6, 24 h [Control_24h_pC6_22]

source_name: Control subject_24 h_Sigmoid colon mucosa


title: MM_M1_2_sample 3036

value: M


title: MM_M1_2_sample 3035


title: MM_M1_2_sample 3032


title: Sample 20, Control subject 4, 24 h [Control_24h_pC4_20]


title: MM_M1_2_sample 3030


title: MM_M1_2_sample 3029


title: Sample 21, Control subject 5, 24 h [Control_24h_pC5_21]


title: MM_M1_2_sample 3034


title: Sample 15, Control subject 3, 24 h [Control_24h_pC3_15]

value: control subject 3


title: Sample 14, Control subject 2, 24 h [Control_24h_pC2_14]


title: Sample 13, Control subject 1, 24 h [Control_24h_pC1_13]

value: control subject 1


title: Sample 9, Control subject 5, 0 h [Control_0h_pC5_9]

source_name: Control subject_0 h_Sigmoid colon mucosa

value: Sigmoid colon mucosa


title: Sample 27, Control subject 3, 48 h [Control_48h_pC3_27]


title: MM_M1_2_sample 3024


title: Sample 25, Control subject 1, 48 h [Control_48h_pC1_25]


title: MM_M1_2_sample 3026


title: MM_M1_2_sample 3023


title: Sample 3, Control subject 3, 0 h [Control_0h_pC3_3]


title: MM_M1_2_sample 3025


title: MM_M1_2_sample 3031


title: MM_M1_2_sample 3028


title: MM_M1_2_sample 3021


title: Sample 1, Control subject 1, 0 h [Control_0h_pC1_1]


title: Sample 2, Control subject 2, 0 h [Control_0h_pC2_2]


title: MM_M1_2_sample 3022


title: MM_M1_2_sample 3019


title: MM_M1_2_sample 3018


title: MM_M1_2_sample 3016


title: MM_M1_2_sample 3017


title: MM_M1_2_sample 3020


title: MM_M1_2_sample 3027


title: HS_M1_2_sample 3049

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 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: hg19
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


title: HS_M1_2_sample 3048


title: HS_M1_2_sample 3047


title: HS_M1_2_sample 3051


title: HS_M1_2_sample 3050


title: Sample 8, Control subject 4, 0 h [Control_0h_pC4_8]


title: MM_M1_2_sample 3015


title: Sample 10, Control subject 6, 0 h [Control_0h_pC6_10]


title: HS_M1_2_sample 3046


title: MM_M1_2_sample 3014


title: MM_M1_2_sample 3013


title: HS_M1_2_sample 3044


title: MM_M1_2_sample 3012


title: HS_M1_2_sample 3045


title: MM_M1_2_sample 3011


title: HS_M1_2_sample 3042


title: MM_M1_2_sample 3010


title: HS_M1_2_sample 3041


title: MM_M1_2_sample 3009


title: HS_M1_2_sample 3043


title: HS_M1_2_sample 3040


title: HS_M1_2_sample 3039


title: MM_M1_2_sample 3006


title: MM_M1_2_sample 3004


title: HS_M1_2_sample 3038


title: MM_M1_2_sample 3005


title: MM_M1_2_sample 3003


title: HS_M1_2_sample 3036


title: HS_M1_2_sample 3035


title: MM_M1_2_sample 3007


title: HS_M1_2_sample 3034


title: MM_M1_2_sample 3001


title: HS_M1_2_sample 3032


title: MM_M1_2_sample 3002


title: MM_M1_2_sample 2998


title: HS_M1_2_sample 3031


title: HS_M1_2_sample 3029


title: HS_M1_2_sample 3030


title: HS_M1_2_sample 3033


title: MM_M1_2_sample 2999


title: HS_M1_2_sample 3037


title: HS_M1_2_sample 3028


title: MM_M1_2_sample 3008


title: HS_M1_2_sample 3027


title: MM_M1_2_sample 2995


title: MM_M1_2_sample 3000


title: MM_M1_2_sample 2993


title: MM_M1_2_sample 2997


title: MM_M1_2_sample 2994


title: HS_M1_2_sample 3025


title: MM_M1_2_sample 2996


title: HS_M1_2_sample 3026


title: HS_M1_2_sample 3023


title: MM_M1_2_sample 2991


title: MM_M1_2_sample 2990


title: MM_M1_2_sample 2989


title: HS_M1_2_sample 3024


title: MM_M1_2_sample 2992


title: HS_M1_2_sample 3022


title: HS_M1_2_sample 3020


title: HS_M1_2_sample 3019


title: MM_M1_2_sample 2987


title: MM_M1_2_sample 2988


title: MM_M1_2_sample 2986


title: MM_M1_2_sample 2985


title: MM_M1_2_sample 2984


title: HS_M1_2_sample 3017


title: HS_M1_2_sample 3015


title: MM_M1_2_sample 2983


title: HS_M1_2_sample 3013


title: MM_M1_2_sample 2982


title: MM_M1_2_sample 2981


title: HS_M1_2_sample 3014


title: MM_M1_2_sample 2978


title: MM_M1_2_sample 2980


title: MM_M1_2_sample 2976


title: MM_M1_2_sample 2977


title: HS_M1_2_sample 3011


title: HS_M1_2_sample 3016


title: HS_M1_2_sample 3018


title: HS_M1_2_sample 3008


title: MM_M1_2_sample 2974


title: HS_M1_2_sample 3012


title: HS_M1_2_sample 3009


title: MM_M1_2_sample 2975


title: HS_M1_2_sample 3007


title: MM_M1_2_sample 2973


title: HS_M1_2_sample 3004


title: HS_M1_2_sample 3006


title: HS_M1_2_sample 3005


title: MM_M1_2_sample 2972


title: HS_M1_2_sample 3002


title: HS_M1_2_sample 3003


title: MM_M1_2_sample 2970


title: MM_M1_2_sample 2971


title: MM_M1_2_sample 2979


title: HS_M1_2_sample 3000


title: HS_M1_2_sample 3010


title: HS_M1_2_sample 3021


title: MM_M1_2_sample 2969


title: HS_M1_2_sample 2999


title: MM_M1_2_sample 2968


title: MM_M1_2_sample 2966


title: MM_M1_2_sample 2963


title: HS_M1_2_sample 2998


title: MM_M1_2_sample 2967


title: HS_M1_2_sample 2996


title: MM_M1_2_sample 2959


title: MM_M1_2_sample 2965


title: MM_M1_2_sample 2957


title: HS_M1_2_sample 3001


title: HS_M1_2_sample 2994


title: MM_M1_2_sample 2964


title: HS_M1_2_sample 2997


title: MM_M1_2_sample 2956


title: MM_M1_2_sample 2960


title: MM_M1_2_sample 2961


title: HS_M1_2_sample 2990


title: HS_M1_2_sample 2992


title: HS_M1_2_sample 2993


title: HS_M1_2_sample 2989


title: MM_M1_2_sample 2958


title: HS_M1_2_sample 2991


title: HS_M1_2_sample 2988


title: MM_M1_2_sample 2955


title: HS_M1_2_sample 2987


title: MM_M1_2_sample 2954


title: HS_M1_2_sample 2986


title: HS_M1_2_sample 2985


title: MM_M1_2_sample 2953


title: HS_M1_2_sample 2995


title: MM_M1_2_sample 2951


title: HS_M1_2_sample 2982


title: MM_M1_2_sample 2962


title: HS_M1_2_sample 2983


title: MM_M1_2_sample 2948


title: MM_M1_2_sample 2946


title: HS_M1_2_sample 2984


title: HS_M1_2_sample 2980


title: MM_M1_2_sample 2947


title: MM_M1_2_sample 2949


title: MM_M1_2_sample 2952


title: HS_M1_2_sample 2981


title: HS_M1_2_sample 2978


title: HS_M1_2_sample 2979


title: MM_M1_2_sample 2942


title: HS_M1_2_sample 2974


title: HS_M1_2_sample 2972


title: MM_M1_2_sample 2943


title: HS_M1_2_sample 2970


title: HS_M1_2_sample 2973


title: MM_M1_2_sample 2941


title: HS_M1_2_sample 2975


title: MM_M1_2_sample 2940


title: HS_M1_2_sample 2969


title: MM_M1_2_sample 2950


title: MM_M1_2_sample 2944


title: HS_M1_2_sample 2971


title: MM_M1_2_sample 2938


title: MM_M1_2_sample 2939


title: HS_M1_2_sample 2968


title: MM_M1_2_sample 2937


title: HS_M1_2_sample 2977


title: MM_M1_2_sample 2945


title: HS_M1_2_sample 2976


title: HS_M1_2_sample 2967


title: HS_M1_2_sample 2966


title: HS_M1_2_sample 2965


title: MM_M1_2_sample 2936


title: MM_M1_2_sample 2933


title: HS_M1_2_sample 2964


title: MM_M1_2_sample 2932


title: HS_M1_2_sample 2963


title: HS_M1_2_sample 2962


title: HS_M1_2_sample 2961


title: HS_M1_2_sample 2960


title: MM_M1_2_sample 2929


title: MM_M1_2_sample 2931


title: MM_M1_2_sample 2930


title: MM_M1_2_sample 2928


title: HS_M1_2_sample 2958


title: MM_M1_2_sample 2927


title: MM_M1_2_sample 2926


title: MM_M1_2_sample 2925


title: MM_M1_2_sample 2924


title: HS_M1_2_sample 2957


title: HS_M1_2_sample 2959


title: HS_M1_2_sample 2955


title: MM_M1_2_sample 2923


title: MM_M1_2_sample 2934


title: MM_M1_2_sample 2935


title: HS_M1_2_sample 2956


title: HS_M1_2_sample 2954


title: MM_M1_2_sample 2922


title: HS_M1_2_sample 2953


title: MM_M1_2_sample 2921


title: MM_M1_2_sample 2920


title: HS_M1_2_sample 2952


title: HS_M1_2_sample 2951


title: HS_M1_2_sample 2950


title: MM_M1_2_sample 2918


title: HS_M1_2_sample 2947


title: HS_M1_2_sample 2946


title: HS_M1_2_sample 2949


title: MM_M1_2_sample 2916


title: MM_M1_2_sample 2914


title: HS_M1_2_sample 2944


title: HS_M1_2_sample 2942


title: HS_M1_2_sample 2948


title: MM_M1_2_sample 2907


title: HS_M1_2_sample 2943


title: MM_M1_2_sample 2912


title: HS_M1_2_sample 2945


title: MM_M1_2_sample 2909


title: MM_M1_2_sample 2908


title: HS_M1_2_sample 2941


title: HS_M1_2_sample 2939


title: HS_M1_2_sample 2937


title: MM_M1_2_sample 2919


title: MM_M1_2_sample 2911


title: MM_M1_2_sample 2906


title: HS_M1_2_sample 2935


title: MM_M1_2_sample 2910


title: MM_M1_2_sample 2917


title: HS_M1_2_sample 2940


title: MM_M1_2_sample 2905


title: MM_M1_2_sample 2903


title: HS_M1_2_sample 2938


title: HS_M1_2_sample 2936


title: MM_M1_2_sample 2902


title: MM_M1_2_sample 2900


title: HS_M1_2_sample 2932


title: MM_M1_2_sample 2913


title: MM_M1_2_sample 2904


title: HS_M1_2_sample 2933


title: MM_M1_2_sample 2915


title: MM_M1_2_sample 2898


title: HS_M1_2_sample 2934


title: HS_M1_2_sample 2930


title: HS_M1_2_sample 2931


title: MM_M1_2_sample 2899


title: HS_M1_2_sample 2927


title: MM_M1_2_sample 2901


title: MM_M1_2_sample 2896


title: MM_M1_2_sample 2897


title: HS_M1_2_sample 2924


title: MM_M1_2_sample 2891


title: HS_M1_2_sample 2925


title: MM_M1_2_sample 2895


title: HS_M1_2_sample 2926


title: MM_M1_2_sample 2894


title: HS_M1_2_sample 2920


title: HS_M1_2_sample 2928


title: HS_M1_2_sample 2929


title: HS_M1_2_sample 2922


title: MM_M1_2_sample 2892


title: MM_M1_2_sample 2887


title: MM_M1_2_sample 2889


title: HS_M1_2_sample 2919


title: HS_M1_2_sample 2918


title: MM_M1_2_sample 2890


title: HS_M1_2_sample 2923


title: MM_M1_2_sample 2886


title: MM_M1_2_sample 2888


title: MM_M1_2_sample 2885


title: HS_M1_2_sample 2916


title: MM_M1_2_sample 2893


title: HS_M1_2_sample 2914


title: HS_M1_2_sample 2913


title: MM_M1_2_sample 2883


title: MM_M1_2_sample 2881