title: RLM048h_153

value: Diphtheria toxin 48h


title: BI_Mor_R6_C18

status: Public on Oct 08 2019

type: SRA

city: Changsha

first: leng

last: lizhi

address: xiangya road

country: China

institute: Central South University

library_source: transcriptomic

data_processing:
quality control using Trimmomatic version 0.35
clean reads were mapped to the human reference genome of GRCh38 using STAR version v 2.5.2b aligne
uniquely mapped read counts of each annotated Ensemble gene were calculated by HTSeq (v0.9.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Embryo

extract_protocol:
Single-cell poly-A(+) RNA was reverse transcribed and amplified by Smart-seq2 protocol
Single-cell libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina Cat#FC-131-1096)

tag: embryo type

value: BI embryo

tag: developmental stage

value: morula


title: RLM048h_159

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

country: USA

institute: University of California, San Diego

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of TPM values, the parameters -condenseGenes -count exons  -tpm were used which extract only one transcript (most aboundace) for a gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: Table of TPM values for RNA-Seq

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research). FACS purified cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer (100mM Tris-HCl pH7.5, 500mM LiCl, 10mM EDTA pH8.0, 1% LiDS, 5mM DTT) and stored at –80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S).
Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Thermo Fisher Scientific), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primers (3 µg/µL) (Thermo Fisher Scientific), 0.5 µL of Oligo dT primer (50 µM) (Thermo Fisher Scientific), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.5 µL of Superscript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer's instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 2.5 hours. The resulting dUTP-marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 16 cycles, size selected by gel extraction.

tag: strain


title: BI_Mor_R6_C17


title: RLM024h_151

value: Diphtheria toxin 24h


title: BI_Mor_R6_C16


title: MJ_12202017_MIL_54: CD19_60Gy_#_4

type: RNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix  Human Gene 2.1ST array plates  were hybridized, washed, stained and scanned according to the protocol described in GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933) User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneTitan (Single Channel ), software AGCC 3.2.4.1515W

data_processing: The data were analyzed with GeneSpring (V_15) using  default analysis settings. Row data were log2-transformed and normalized by quintile normalisation.

label: biotin

label_protocol: 50ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

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

treatment_protocol: In total 72 samples obtained from four healthy donors were analysed (0h= cells immediately after purification, 24h_0Gy = cells cultivated for 24 hours without prior radiation; 24h_60Gy = cell cultivated for 24 hours after irradiation with 60Gy). At each time point six different cell populations were analysed (unseparated PBMC, and separated PBMC subsets: CD4, CD8, CD14; CD19; CD56).

tag: tissue

value: peripheral blood mononuclear cells

tag: cell population

tag: treatment


title: MJ_12202017_MIL_50: CD56_60Gy_#_4


title: RLM024h_106


title: MJ_12202017_MIL_46: CD4_0Gy_#_4


title: MJ_12202017_MIL_53: CD8_60Gy_#_4


title: MJ_12202017_MIL_49: origin_60Gy_#_4

value: PBMC


title: MJ_12202017_MIL_48: CD19_0Gy_#_4


title: MJ_12202017_MIL_43: origin_0Gy_#_4


title: MJ_12202017_MIL_47: CD8_0Gy_#_4


title: MJ_12202017_MIL_42: CD19_0h_#_4


title: MJ_12202017_MIL_51: CD14_60Gy_#_4


title: MJ_12202017_MIL_41: CD8_0h_#_4


title: RLM024h_161


title: BI_Mor_R6_C14


title: MJ_12202017_MIL_40: CD4_0h_#_4


title: BI_Mor_R6_C15


title: MJ_12202017_MIL_45: CD14_0Gy_#_4


title: MJ_12202017_MIL_52: CD4_60Gy_#_4


title: MJ_12202017_MIL_44: CD56_0Gy_#_4


title: BI_Mor_R6_C13


title: MJ_12202017_MIL_39: CD14_0h_#_4


title: BI_Mor_R6_C12


title: RLM012h_1035

value: Diphtheria toxin 12h


title: MJ_12202017_MIL_38: CD56_0h_#_4


title: MJ_12202017_MIL_34: CD4_60Gy_#_3


title: MJ_12202017_MIL_36: CD19_60Gy_#_3


title: BI_Mor_R6_C11


title: MJ_12202017_MIL_37: origin_0h_#_4


title: MONOctr_6a10

value: No treatment


title: MONOctr_3


title: MJ_12202017_MIL_35: CD8_60Gy_#_3


title: BI_Mor_R6_C10


title: BI_Mor_R6_C1


title: MJ_12202017_MIL_32: CD56_60Gy_#_3


title: RLM012h_481


title: BI_8C_R7_C8


title: shScr_Rep2

city: New York

first: Nicholas

last: Gomez

state: New York

address: 1230 York Ave

department: Laboratory of Mammalian Cell Biology and Development

institute: Rockefeller Univeristy

data_processing:
Sequencing reads were aligned to mouse transcriptome (Gencode M18) using Salmon v0.11.3 with the parameter -l A --seqbias
TPM's were produced from the Salmon quant.sf files
Transcripts for each sample were merged to gene level using tximport within R.
Differential gene expression was identified using DESeq2 and the table prodcued from tximport
Genome_build: mm10
Supplementary_files_format_and_content: Tab delminited files containing TPMs and counts as well as differential expression tables produced by DESeq2.

source_name: Skin

extract_protocol:
Embryonic mouse skin was dissected and single cell preparation achieved, described populations were sorted using flow cytometry and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
Poly-A Enriched RNA libraries were prepared for sequencing using standard Illumina protocols

value: shScramble (control)

value: skin

value: E14.5 Embryo


title: shScr_Rep3


title: MJ_12202017_MIL_30: CD19_0Gy_#_3


title: MJ_12202017_MIL_33: CD14_60Gy_#_3


title: MJ_12202017_MIL_29: CD8_0Gy_#_3


title: BI_8C_R7_C6


title: MJ_12202017_MIL_24: CD19_0h_#_3


title: shScr_Rep1


title: MJ_12202017_MIL_26: CD56_0Gy_#_3


title: MJ_12202017_MIL_25: origin_0Gy_#_3


title: MJ_12202017_MIL_22: CD4_0h_#_3


title: MJ_12202017_MIL_31: origin_60Gy_#_3


title: MJ_12202017_MIL_27: CD14_0Gy_#_3


title: MJ_12202017_MIL_21: CD14_0h_#_3


title: BI_8C_R7_C5


title: BI_8C_R7_C4


title: BI_8C_R7_C7


title: shRhou_Rep2


title: MJ_12202017_MIL_28: CD4_0Gy_#_3


title: iPSC-microglia 4 rep 3

city: Kuopio

first: Tarja

last: Malm

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Read alignment and transcript quantification were performed on fastq files using RSEM 1.3.1 (Li, Dewey, 2011) with “--strandness reverse” and “--estimate-rspd” parameters. Hg38 was used as reference genome.
Genome_build: Hg38
Supplementary_files_format_and_content: RSEM genes.results files with information about gene_id, transcript_id (s), length, effective_length, expected_count,  transcripts per million mapped reads (TPM) and fragments per kilo base per million mapped reads (FPKM)

growth_protocol: iPSC-derived microglia were differentiated as stated in manuscript.

extract_protocol:
iPSC-microglia were cultured at density of 2 mln cells per PDL-coated 6 cm dish and total RNA was extracted using mirVana™ miRNA Isolation Kit (Invitrogen) following manufacturer’s guidelines. RNA integrity (RIN) was measured for all samples using the Bioanalyzer Agilent 2100 series.
Total of 300 ng of RIN score > 9.1 was used to generate sequencing libraries with Illumina TruSeq® Stranded mRNA to obtain poly-A mRNA. The high quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies). The samples were sequenced as single-end 50 bp reads on the Illumina HiSeq 3000 instrument.

treatment_protocol: 24-hour FBS withdrawal

tag: genotype

value: isogenic PSEN1{delta}E9 corrected

tag: cell type

value: iPSC-derived microglia-like cells

tag: differentiation day


title: BI_8C_R7_C3


title: MJ_12202017_MIL_20: CD56_0h_#_3


title: shRhou_Rep1


title: BI_8C_R7_C2


title: MJ_12202017_MIL_23: CD8_0h_#_3


title: iPSC-microglia 3 rep 3


title: fry1rdr1_mRNA_2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Base-caling was performed by the sequncing company, using Illumina Casava.
Raw reads were mapped to the Araport11 genome using STAR v2.6 with the parameters "--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Mapped reads were counted by featureCounts v1.6.4.
All above processing procedures were integrated into a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools)
Genome_build: Araport11
Supplementary_files_format_and_content: Tab-delimited text files containing the gene accession, number of raw read counts, and transcript length.

organism: Arabidopsis thaliana

source_name: seedings

growth_protocol: Arabidopsis seedlings were grown in a growth chamber (Percival) at 23℃ with 16h light

extract_protocol:
Total RNA was extracted from 12-day-old WT and mutant seedlings using TRI reagent (MRC, TR118) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001 and RS-122-2002)

value: two-week

tag: ecotype


title: MJ_12202017_MIL_18: CD19_60Gy_#_2


title: MJ_12202017_MIL_17: CD8_60Gy_#_2


title: MJ_12202017_MIL_16: CD4_60Gy_#_2


title: BI_8C_R6_C8


title: fry1rdr1_mRNA_1


title: MONOctr_pool


title: iPSC-microglia 1 rep 3


title: MJ_12202017_MIL_15: CD14_60Gy_#_2


title: shRhou_Rep3


title: iPSC-microglia 4 rep 2


title: BI_8C_R6_C6


title: MJ_12202017_MIL_19: origin_0h_#_3


title: MJ_12202017_MIL_14: CD56_60Gy_#_2


title: MJ_12202017_MIL_13: origin_60Gy_#_2


title: iPSC-microglia 3 rep 2


title: BI_8C_R6_C5


title: fry1rdr6_mRNA_1


title: MJ_12202017_MIL_12: CD19_0Gy_#_2


title: fry1_mRNA_2


title: iPSC-microglia 2 rep 3


title: BI_8C_R6_C7


title: BI_8C_R6_C4


title: iPSC-microglia 1 rep 2


title: fry1rdr6_mRNA_2


title: MJ_12202017_MIL_10: CD4_0Gy_#_2


title: BI_8C_R6_C3


title: BI_8C_R6_C2


title: iPSC-microglia 2 rep 2


title: WT_mRNA_1

value: WT


title: iPSC-microglia 3 rep 1


title: MJ_12202017_MIL_11: CD8_0Gy_#_2


title: WT_mRNA_2


title: iPSC-microglia 2 rep 1


title: BI_4C_R7_C4


title: iPSC-microglia 1 rep 1


title: BI_4C_R7_C3


title: BI_8C_R6_C1


title: MJ_12202017_MIL_08: CD56_0Gy_#_2


title: Ecoli_gDNA2

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

country: United Kingdom

institute: Imperial College

description:
Mnase digested genomic DNA
Zscore_Merged_replicates_Ecoli_gDNA_40_65bp.bw
Zscore_Merged_replicates_Ecoli_gDNA_70_100bp.bw
Zscore_Merged_replicates_Ecoli_gDNA_total.bw

library_source: genomic

data_processing:
Basecalls performed using CASAVA 1.8.4
Reads were aligned to NC_002578.1  T.acidophilum genome assembly or to E.Coli C600 genome (CP031214) obtained from ncbi, using Bowtie2
Paired-end 100bp reads were first trimmed using BBDuk v37.64 (parameters: ktrim=r, k=21, hdist=1, edist=0, mink=11, qtrim=rl, trimq=30, minlength=10, ordered=t, qin=33) and then merged using BBmerge v37.64 (parameters: mininsert=10, mininsert0=10).
The merged reads were mapped to the T. acidophilum DSM1728 genome (GCA_000195915.1) or to E.Coli C600 genome (CP031214) using Bowtie2 (-U).
Coverage tracks were computed using deeptools bamCoverage (RPGC normalization, effective genome size: 1564906bp), measuring coverage for reads of sizes 40-65bp and 70-100bp separately. Reads from the sonicated DNA control samples were mapped in paired-end mode. Coverage was computed independently of read size and smoothed over 10kbp to avoid introducing noise from the input into the MNase signal. Genome-wide coverage of MNase-digested samples was then divided by its corresponding undigested DNA sample to remove bias in coverage associated with replication. Lastly, coverage was converted into a Z-score using the scale function in R.
Genome_build: T.acidophilum : NC_002578.1 ;  E.coli : CP031214
Supplementary_files_format_and_content: Bigwig

molecule: genomic DNA

organism: Escherichia coli

source_name: E.coli genomic DNA

growth_protocol: T. acidophilum strain 122-1B2 was obtained from DSMZ (https://www.dsmz.de/) and cultured using the medium described in (Searcy and Stein 1980), supplemented to a final concentration of 2g/L yeast extract (BD Biosciences). The medium was boiled for five minutes and allowed to cool to 58°C before inoculation. Cultures were incubated at 59°C with shaking (90rpm) in an INFORS Thermotron incubator.

extract_protocol:
DNA was extracted by phenol chloroform extraction and precipitated with ethanol.
For MNase digestion experiments paired-end reads were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: T. acidophilum cells self-lyse at pH>6 (Robb et al. 1995). Pellets were therefore directly re-suspended in ice-cold MNase digestion buffer (10mM Tris, 5mM Ca2+, pH8) and homogenized by 20 passages through a Dounce homogenizer, on ice. Unfixed crude lysates were digested in the presence of 4U/mL of MNase (Thermo Fisher) at 37°C. Digestion was stopped by addition of EDTA to a final concentration of 20mM. Samples were incubated for an additional 30min at 37°C in the presence of RNAse A to a final concentration of 0.5mg/mL and then overnight at 65°C in the presence of SDS (1%) and proteinase K (125µg/mL). Undigested lysate was incubated as above but without addition of enzyme. Undigested DNA was then sonicated using a Covaris S220 sonicator with the following settings: peak power: 175, duty: 10, cycle/burst: 200 for 430s (target size: 150bp).

value: expressing Hta


title: MJ_12202017_MIL_07: origin_0Gy_#_2


title: MJ_12202017_MIL_09: CD14_0Gy_#_2


title: iPSC-microglia 4 rep 1


title: BI_4C_R7_C2


title: Ecoli_gDNA1


title: BI_4C_R7_C1


title: BI_4C_R6_C4


title: Ecoli_Chr2

description:
Mnase digested chromatin DNA
Zscore_Merged_replicates_Ecoli_ChrDig_40_65bp.bw
Zscore_Merged_replicates_Ecoli_ChrDig_70_100bp.bw
Zscore_Merged_replicates_Ecoli_ChrDig_total.bw

source_name: E.coli cells


title: MJ_12202017_MIL_05: CD8_0h_#_2


title: BI_4C_R6_C3


title: T Cells, Pevonedistat - 24hrs - Patient 1

city: Portland

first: Alexey

last: Danilov

state: Oregon

address: 3681 SW Sam Jackson Rd

department: Knight Cancer Institute

institute: Oregon Health and Science University

description:
CLL Patient T Cells - treated with pevonedistat 24 hours
PEVO_24h_T1

hyb_protocol: Labelled hybridization targets were mixed with hybridization solution containing hybridization controls (Applied Biosystems) according to NuGEN Technologies protocol and hybridized with the GeneChip® Clariom S Human Array (Applied Biosystems)

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and image quality was determined immediately following each scan

data_processing: Image processing was performed with GeneChip Command Console v. 3.1.1 and probe set summarization and CHP file generation was performed using Transcriptome Analysis Console v. 4.0 software.

source_name: Primary patient sample

label_protocol: Three nanograms of total RNA from each sample were amplified and biotin-labelled using the Ovation® RNA Amplification System V.2, and Encore™ Biotin Module (NuGEN Technologies) as per manufacturer recommendations.

growth_protocol: Primary blood samples were collected from patients, PBMCs were separate using a Ficoll Plaque column, T cells were FACS sorted from PBMCs by gating for viable CD4+CD45RA+CD45RO- lymphocytes. Cells were used on the same day as collection.

extract_protocol: Total RNA was isolated using the total RNA Kit I and Homogenizer Mini Columns (Omega Bio-Tek)

treatment_protocol: Cells were treated with either DMSO (control) or 1µM Pevonedistat and .5 µg/ml αCD3/CD28. Cells were harvested for RNA at 3 hours or 24 hours respectively.

tag: disease state

value: chronic lymphocytic leukemia (CLL)

tag: individual

value: Patient 1

value: T Cell

tag: agent

value: pevonedistat

tag: time

value: 24 hours


title: MJ_12202017_MIL_03: CD14_0h_#_2

value: peripheral blood mononuclear cells


title: BI_4C_R6_C2

value: BI embryo


title: total rep-3

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

description:
count_c_total rep-3
processed data file: microRNA_neutrophil_read.counts.txt

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 2500 for Samples 1-5 in Illumina HiSeq 4000 for Samples 6-11.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the zebrafish genome using STAR (v2.5) RNA-seq aligner with the following parameter:  for Samples 1-5:  “--alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000”, for Samples 6-11: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to genes using featureCounts (from subread v1.5.1) with the following parameters: for Samples 1-5:  “-s 1 –Q 10”, for Samples 6-11, "-p -Q 10".
The data was filtered: for Samples 1-5 using read count > 10 in more than 1 of the samples;  for Samples 6-11, using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw counts

organism: Danio rerio

source_name: whole embryo

growth_protocol: zebrafish embryos were grown to 3 day post fertilization in embryonic media

extract_protocol:
tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing.
miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145-160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.).

treatment_protocol: transgenic zebrafish lines were used to produce embryos. For miRNA profiling, transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR-199 target discovery, transgenic lines expressing miR-199 or a vector control together with a GFP reporter were used.

tag: strain background

value: AB

tag: gentoype/variation

value: wild type

value: whole embryo


title: T Cells, Pevonedistat - 24hrs - Patient 2

description:
CLL Patient T Cells - treated with pevonedistat 24 hours
PEVO_24h_T2

value: Patient 2


title: T Cells, Pevonedistat - 24hrs - Patient 4

description:
CLL Patient T Cells - treated with pevonedistat 24 hours
PEVO_24h_T4

value: Patient 4


title: total rep-2

description:
count_c_total rep-2
processed data file: microRNA_neutrophil_read.counts.txt


title: T Cells, Pevonedistat - 24hrs - Patient 3

description:
CLL Patient T Cells - treated with pevonedistat 24 hours
PEVO_24h_T3

value: Patient 3


title: MJ_12202017_MIL_06: CD19_0h_#_2


title: T Cells, Pevonedistat - 3hrs - Patient 4

description:
CLL Patient T Cells - treated with pevonedistat 3 hours
PEVO_3h_T4

value: 3 hours


title: T Cells, Pevonedistat - 3hrs - Patient 3

description:
CLL Patient T Cells - treated with pevonedistat 3 hours
PEVO_3h_T3


title: MJ_12202017_MIL_04: CD4_0h_#_2


title: MJ_09082017_SIM_18: CD19_60Gy_#_1


title: total rep-1

description:
count_total rep-1
processed data file: microRNA_neutrophil_read.counts.txt


title: BI_4C_R6_C1


title: Ecoli_Chr1


title: MJ_12202017_MIL_02: CD56_0h_#_2


title: MJ_09082017_SIM_17: CD8_60Gy_#_1


title: BI_4C_R5_C2


title: T Cells, Control - 24hrs - Patient 4

description:
CLL Patient T Cells - treated with control 24 hours
DMSO_24h_T4

value: control


title: T Cells, Pevonedistat - 3hrs - Patient 2

description:
CLL Patient T Cells - treated with pevonedistat 3 hours
PEVO_3h_T2


title: MJ_09082017_SIM_16: CD4_60Gy_#_1


title: T Cells, Control - 24hrs - Patient 3

description:
CLL Patient T Cells - treated with control 24 hours
DMSO_24h_T3


title: BI_4C_R4_C3


title: T Cells, Pevonedistat - 3hrs - Patient 1

description:
CLL Patient T Cells - treated with pevonedistat 3 hours
PEVO_3h_T1


title: lyzC+

description:
count_lyzc+
processed data file: microRNA_neutrophil_read.counts.txt

source_name: neutrophils

value: neutrophils


title: MJ_12202017_MIL_01: origin_0h_#_2

value: PBMC


title: T Cells, Control - 24hrs - Patient 2

description:
CLL Patient T Cells - treated with control 24 hours
DMSO_24h_T2

value: chronic lymphocytic leukemia (CLL)


title: BI_4C_R4_C1


title: BI_2C_R8_C2


title: BI_4C_R5_C3


title: MJ_09082017_SIM_14: CD56_60Gy_#_1


title: Krt4+

description:
count_krt4+
processed data file: microRNA_neutrophil_read.counts.txt

source_name: keratinocytes

value: keratinocytes


title: SC_IL33_CGRP_1

city: Cambridge

first: Samantha

last: Riesenfeld

state: MA

address: 415 Main St

institute: Broad Institute

description: IL33_CGRP_1.filtered_feature_bc_matrix.h5

data_processing:
For bulk RNA-seq (in vitro samples) data, the raw data was converted to fastq files using bcl2fastq 2.17.1.14 with options “--minimum-trimmed-read-length 10 --mask-short-adapter-reads 10”. Transcript quantification was done using Kallisto 0.42.3 (Bray et al., 2016) with the mm10 mouse genome annotation, and transcript counts were then converted to gene counts and normalized TPM values using the R package tximport (Soneson et al., 2015).
For scRNA-seq data data, gene counts were obtained by aligning reads to the mm10 genome using CellRanger software (v1.3) (10x Genomics). To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in their sample or condition of origin in terms of number of genes or number of unique molecular identifiers (UMIs), which left 83.1% and 84.2% of cells from CGRP and PBS, respectively, and 90.3% and 93% of cells from IL-33 and IL-33+CGRP conditions. Sample-specific minimum and maxium cut-offs per cell were 900–5,000 genes for IL-33 and IL-33+CGRP conditions and 900–3,900 genes for CGRP and PBS. Another 2.1% of the remaining cells were excluded for having greather than 10% of mitochondrial gene counts.
For scRNA-seq data, normalization of gene counts was performed using regularized negative binomial regression via the SCTransform() function from Seurat v3, with the “batch_var” parameter set to the replicate indicator variable and the “vars_to_regress” parameter set to the variable capturing the percentage of mitochondrial gene counts in each cell (Butler et al., 2018; Hafemeister and Satija, 2019). This step takes the place of the typical steps of log-normalization, variable gene selection, and scaling. We used log1p of the corrected counts to compute principle components analysis (PCA).
ATAC-seq: Read alignment, filtering, visualization of signal tracks, and measurement of quality control metrics was performed using a publicly available ATAC-seq pipeline (Lee et al., 2016). Briefly, reads were aligned to the mm10 genome using Bowtie2 and filtered to remove duplicates and mitochondrial reads. Alignment files were merged for biological replicates for peak-calling using MACS2 (Zhang et al., 2008). Read counts per peak were compiled using the bedtools multicov tool. Counts were normalized and processed for differential peak accessibility between conditions using DESeq2 (Love et al., 2014). Gene annotation with putative regulatory elements was performed using GREAT with default parameters (McLean et al., 2010).
Genome_build: mm10

source_name: Lung Innate lymphoid cells

extract_protocol:
Lungs were digested with the lung dissociation kit (Miltenyi Biotec) and subsequently enriched for CD90.2+ cells using CD90.2 MicroBeads (Miltenyi Biotec). Lung ILCs were isolated by fluorescence-activated cell sorting as 7AAD- CD45+ CD90.2+ CD127+ Lineage (CD3, CD4, CD8, CD11b, CD11c, CD19, NK1.1, TCRβ, TCRγδ)- cells.
Sorted ILCs were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v3 (1000075) according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a HiSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 96 bp for Read 2.

treatment_protocol: Nasal administration of PBS, CGRP, IL-33 or IL-33+CGRP daily for three consecutive days. One day after the last treatment, lung ILCs were isolated by fluorescence-activated cell sorting.

value: lung

value: Innate lymphoid cells

tag: batch

value: C

tag: cgrp-treated

value: Yes

tag: timepoint

value: 3 days

tag: in vitro vs. in vivo

value: In vivo

tag: protocol

value: ScRNA-seq (10x)


title: MJ_09082017_SIM_12: CD19_0Gy_#_1

tag: tissue

value: peripheral blood mononuclear cells

tag: cell population


title: MJ_09082017_SIM_13: origin_60Gy_#_1

tag: treatment


title: T Cells, Control - 24hrs - Patient 1

description:
CLL Patient T Cells - treated with control 24 hours
DMSO_24h_T1

value: Patient 1

tag: cell type

value: T Cell

value: 24 hours


title: BI_2C_R8_C1

tag: embryo type

value: BI embryo

tag: developmental stage


title: SC_IL33_2

tag: strain

value: D

value: No


title: MONOctr_8

value: No treatment


title: SC_IL33_1


title: BI_2C_R7_C2


title: BE(2)-C lncNB siRNA-2 transfected replicate 4

city: Kensington

first: Pei

last: Liu

address: C25 Lowy Cancer Research Centre

country: Australia

institute: CCIA

description: MYCN-amplified neuroblastoma cells

hyb_protocol: 2.3 ug of fragmented, labeled cDNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_0007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing: Results from the microarray experiment were analyzed in R (http://www.r-project.org/) and normalized independently with the RMA method for the HuGene-2_st and Clariom_S platforms. The probes with the same gene annotations were extracted from the two platforms. Then, the extracted and normalized data were combined, and adopted as the input of the package 'RankProd' for multiply origins data analysis (meta-analysis). The output p-values were adjusted with the 'BH' method to obtain the adjust p-values.

source_name: BE(2)-C cells

label_protocol: We used the Affymerix GeneChip WT Plus Reagent Kit: Manual Target Preparation for GeneChip Whole Transcript Expression Arrays (Affymetrix_WT_Plus_User_Guide). 100 ng of total RNA was used for input.

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: BE(2)-C neuroblastoma cells were transfected with control siRNA, lncNB1 siRNA-1 or lncNB1 siRNA-2 for 40 hours.

value: BE(2)-C cells

tag: genotype/variation

value: lncNB1 siRNA-2


title: SC_CGRP_2

value: lung


title: MJ_09082017_SIM_11: CD8_0Gy_#_1


title: SC_IL33_CGRP_2

description: IL33_CGRP_2.filtered_feature_bc_matrix.h5

value: Innate lymphoid cells


title: BI_2C_R7_C1


title: SC_CGRP_1

value: C


title: BI_2C_R6_C2


title: T Cells, Control - 3hrs - Patient 2

description:
CLL Patient T Cells - treated with control 3 hours
DMSO_3h_T2

tag: disease state

value: chronic lymphocytic leukemia (CLL)

tag: individual

value: Patient 2

tag: agent

value: control

value: 3 hours


title: BE(2)-C lncNB siRNA-1 transfected replicate 4

description: MYCN-amplified neuroblastoma cells

value: lncNB1 siRNA-1


title: T Cells, Control - 3hrs - Patient 3

description:
CLL Patient T Cells - treated with control 3 hours
DMSO_3h_T3

value: Patient 3

tag: time


title: SC_PBS_2

tag: batch

value: 3 days

value: In vivo

value: ScRNA-seq (10x)


title: T Cells, Control - 3hrs - Patient 1

description:
CLL Patient T Cells - treated with control 3 hours
DMSO_3h_T1

value: Patient 1

value: T Cell


title: BI_2C_R6_C1

value: BI embryo


title: MJ_09082017_SIM_9: CD14_0Gy_#_1

value: peripheral blood mononuclear cells


title: MJ_09082017_SIM_8: CD56_0Gy_#_1


title: T Cells, Control - 3hrs - Patient 4

description:
CLL Patient T Cells - treated with control 3 hours
DMSO_3h_T4

value: Patient 4


title: BE(2)-C control siRNA transfected replicate 4

description: MYCN-amplified neuroblastoma cells

value: BE(2)-C cells

value: Control siRNA


title: MJ_09082017_SIM_10: CD4_0Gy_#_1


title: SC_PBS_1

value: lung

value: Innate lymphoid cells

value: C

tag: cgrp-treated

value: No


title: BI_1C_R7


title: BI_1C_R6


title: MJ_09082017_SIM_7: origin_0Gy_#_1

value: PBMC


title: miR-199-3

source_name: neutrophils_overexpressing miR199

tag: strain background

value: AB

tag: gentoype/variation

value: overexpressing miR199

value: neutrophils


title: miR-199-1


title: miR-199-2


title: AH_RC2_1x

description:
Mnase digested reconstituted chromatin
Zscore_Merged_replicates_CR_1X_40_65bp.bw
Zscore_Merged_replicates_CR_1X_70_100.bw
Zscore_Merged_replicates_CR_1X_total.bw
Chromatin was reconstituted in vitro by assembling Hta and T.Acidophilum genomic DNA to a mass ratio of 0.4. Folling Mnase treatment is similar to the one used for native chromatin digestion.

organism: Thermoplasma acidophilum

source_name: Thermoplasma acidophilum reconstituted chromatin


title: MJ_09082017_SIM_15: CD14_60Gy_#_1


title: AH_RC1_1x


title: lncNB siRNA-1 HEAVY  replicate 4

data_processing: Results from the microarray experiment were analyzed in R Version 3.5.3 (http://www.r-project.org/) with bioconductor package version 3.8 (http://www.bioconductor.org/).The required Platform Design Info for Affymetrix Clariom_S_Human array was installed with the package “pd.clariom.s.human” which was built by James W. MacDonald <jmacdon at uw.edu>. The array data were analyzed with the ‘oligo’ package and normalized with the RMA method. Then, the differential expression analysis was implemented with the Limma package (version 3.38.3). The significant differential expression genes were filtered by using the thresholds of FC>1.45 and p-value<0.05. Finally, the differentially expressed genes were annotated with the annotation file downloaded from the support website of the Affymetrix.

source_name: lncNB siRNA-1 HEAVY

treatment_protocol: BE(2)-C neuroblastoma cells were transfected with control siRNA, lncNB1 siRNA-1 or lncNB1-siRNA-2 for 48 hours, followed by polysome profiling.

tag: cell line

value: MYCN-amplified neuroblastoma cells

value: lncNB siRNA-1

tag: molecule subtype

value: heavy polysomal RNAs


title: Tacidophilum_gDNA2

description:
Mnase digested genomic DNA
Zscore_Merged_replicates_Tacidophilum_gDNA_40_65bp.bw
Zscore_Merged_replicates_Tacidophilum_gDNA_70_100bp.bw
Zscore_Merged_replicates_Tacidophilum_gDNA_total.bw

source_name: Thermoplasma acidophilum genomic DNA


title: Tacidophilum_gDNA1


title: DK_YL

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
small RNAs matching rRNA and tRNA are filtered out
20-21nt small RNA reads were size selected
Supplementary_files_format_and_content: Text files including read sequence and its count for each sample.

organism: Vitis vinifera

source_name: Young leaves

extract_protocol:
Total RNA from young leaves and fruits peels were extracted using the RNeasy Plant Mini Kit according to manufacters’ instructions with slight modifications
Degradome cDNA libraries were construction according to J. Zhai et al., 2014, Methods, 67 (84–90) protocol with slight modifications.

tag: cultivar

value: Dilkhush

tag: tissue

value: Young leaves


title: DK_FP

source_name: Fruit peels

value: Fruit peels


title: MJ_09082017_SIM_6: CD19_0h_#_1

value: peripheral blood mononuclear cells

tag: cell population

tag: treatment


title: IMX1939_Mtt2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. eubayanus IMX1939 was grown in SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

data_processing:
RNA-Seq reads were aligned to CDFM21L.1  or to a hybrid CDFM21L21.1-CBC-1 reference using STAR version 2.5.3a in 2Pass mode
resulted sequence alignment map file (SAM) were filtered on ambigious alignments and sorted with samtools to sorted binary alignement file (BAM)
The sorted BAM file was processed with featureCounts from the SubRead package version1.6.3 with -M and -s 1 for stranded reverse to calculate the transcript counts
The raw transcript counts were normalized on fragments per kilobase million (FPKM) by applying rpkm module from edgeR package
Genome_build: CDFML21L.1 and CBC-1 this study,
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

organism: Saccharomyces eubayanus

source_name: Shake flask mid exponential phase

growth_protocol: S. eubayanus and S. cerevisiae X S. eubayanus batch cultures were grown on synthetic medium (SM) containing 3.0 g L-1 KH2PO4, 5.0 g L-1 (NH4)2SO4, 0.5 g L-1 MgSO4, 7 H2O, 1 mL L-1 trace element solution, and 1 mL L-1 vitamin solution. The pH was set to 6 with 2 M KOH prior to autoclaving at 120 °C for 20 min. Vitamin solutions (Verduyn et al. 1992) were sterilized by filtration and added to the sterile medium. Concentrated sugar solutions were autoclaved at 110 °C for 20 min and added to the sterile flasks to give a final concentration of 20 g L-1 carbon source (glucose (SMG), maltose (SMM)

extract_protocol:
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNAse-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina)and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

treatment_protocol: S. eubayanus CDFM21L.1, IMX1765, IMX1939 and S. cerevisiae X S. eubayanus HTS020 were grown in either SMG or SMMal or SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

tag: carbon source

value: Maltotriose

tag: genotype phenotype

value: MATa/MATα Semalt1Δ/Semalt1Δ Sesga1Δ::ScMAL13/ Sesga1Δ::ScMAL13


title: IMX1939_Mtt1

tag: strain


title: MJ_09082017_SIM_3: CD14_0h_#_1


title: lncNB siRNA-1 LIGHT  replicate 4

source_name: lncNB siRNA-1 LIGHT

tag: cell type

tag: genotype/variation

value: light polysomal RNAs


title: control siRNA HEAVY  replicate 4

source_name: control siRNA HEAVY

value: control siRNA


title: BB_FP

value: Bangalore blue


title: MJ_09082017_SIM_5: CD8_0h_#_1


title: MJ_09082017_SIM_2: CD56_0h_#_1


title: IMX1939_Mal1

description: S. eubayanus IMX1939 was grown in SMMal until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: Maltose


title: IMX1939_Mal2


title: IMX1939_Glu2

description: S. eubayanus IMX1939 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: Glucose


title: BB_YL


title: MJ_09082017_SIM_4: CD4_0h_#_1


title: MJ_09082017_SIM_1: origin_0h_#_1

value: PBMC


title: IMX1939_Glu1


title: IMX1765_Mtt2

description: S. eubayanus IMX1765 was grown in SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: MATa/MATα Sesga1Δ::ScMAL13 / Sesga1Δ::ScMAL13


title: Osteogenic medium and perivascular stem cell-derived exosome (2.5 μg/mL), Rep3

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted with the Partek GS 7.0 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.probeset.csv

source_name: Osteogenic medium and perivascular stem cell-derived exosome (2.5 μg/mL), BMSCs

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: Mesenchymal stem cells (MSCs) were isolated from human bone marrow and cultured in DMEM medium plus 15% FBS, 1% pen/strep

extract_protocol: Cell monolayers were lysed with  Invitrogen Life Technologies TRIzol Reagent (Total RNA Isolation Reagent) and precipitated using the manufacturer's protocol.

treatment_protocol: Human bone marrow MSCs were treated with osteogenic medium and PBS (Control)/perivascular stem cell-derived extracellular vesicles (2.5 μg/mL) for 48 hours

value: Mesenchymal stem cells

tag: culture

value: Osteogenic medium

tag: stimulation

value: Perivascular stem cell-derived extracellular vesicle (2.5 μg/mL)


title: control siRNA LIGHT  replicate 3

source_name: control siRNA LIGHT

value: MYCN-amplified neuroblastoma cells


title: control siRNA LIGHT  replicate 4


title: lncNB siRNA-2 HEAVY  replicate 3

source_name: lncNB siRNA-2 HEAVY

value: lncNB siRNA-2

value: heavy polysomal RNAs


title: Osteogenic medium and perivascular stem cell-derived exosome (2.5 μg/mL), Rep1


title: lncNB siRNA-2 LIGHT  replicate 2

source_name: lncNB siRNA-2 LIGHT


title: lncNB siRNA-2 HEAVY  replicate 2


title: lncNB siRNA-1 LIGHT  replicate 2

value: lncNB siRNA-1


title: lncNB siRNA-1 HEAVY  replicate 2


title: Osteogenic medium and PBS, Rep4

source_name: Osteogenic medium and PBS, BMSCs

value: PBS


title: HTS020_Mtt2

description: Saccharomyces cerevisiae X Saccaharomyces eubayanus HTS020 was grown in SMMal until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass

organism: Saccharomyces cerevisiae x Saccharomyces eubayanus

value: Maltotriose

value: MATa/MATα Mal+ Mtt+


title: 824-C_48-2

city: shanghai

first: Yunpeng

last: Yang

address: 300， Fenglin Road

institute: Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences

hyb_protocol: Hybridization was performed in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

organism: Clostridium acetobutylicum

source_name: bacteria

label_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) .

growth_protocol: C. acetobutylicum strains was firstly inoculated into CGM medium for inoculum preparation, and then transferred into P2 medium using D-glucose as the sole carbon source for solvent production

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Samples were taken at 24 and 48 h, and then centrifuged to collect the bacteria

tag: time

value: collected bacteria at 48 h

value: control strain


title: lncNB siRNA-2 LIGHT  replicate 3

value: light polysomal RNAs


title: IMX1765_Mal2

description: S. eubayanus IMX1765 was grown in SMMal until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: Maltose


title: control siRNA HEAVY replicate 2

value: control siRNA


title: Osteogenic medium and PBS, Rep3


title: control siRNA HEAVY  replicate 3


title: 824-C_24-2

value: collected bacteria at 24 h


title: IMX1765_Mtt1

value: MATa/MATα Sesga1Δ::ScMAL13 / Sesga1Δ::ScMAL13


title: HTS020_Mtt1


title: IMX1765_Mal1


title: Osteogenic medium and PBS, Rep1

value: Mesenchymal stem cells


title: HTS020_Mal2


title: Osteogenic medium and perivascular stem cell-derived exosome (2.5 μg/mL), Rep4

value: Osteogenic medium


title: Osteogenic medium and perivascular stem cell-derived exosome (2.5 μg/mL), Rep2

value: Perivascular stem cell-derived extracellular vesicle (2.5 μg/mL)


title: IMX1765_Glu2

description: S. eubayanus IMX1765 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: Glucose


title: lncNB siRNA-2 HEAVY  replicate 1

value: MYCN-amplified neuroblastoma cells

value: lncNB siRNA-2


title: 824-C_24-1


title: HTS020_Mal1

description: Saccharomyces cerevisiae X Saccaharomyces eubayanus HTS020 was grown in SMMtt until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass


title: control siRNA LIGHT replicate 2


title: IMX1765_Glu1


title: 824-C_48-1


title: Osteogenic medium and PBS, Rep2


title: HTS020_Glu2

description: Saccharomyces cerevisiae X Saccaharomyces eubayanus HTS020 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass


title: AS2_4948_Glu2

description: S. eubayanus CDFM21L.1 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: Wildtype Mal- Mtt-


title: 824-btrK/R_48-1

value: BtrK/BtrR overexpressing strain


title: 824-btrK/R_48-2


title: lncNB siRNA-1 LIGHT  replicate 1

value: lncNB siRNA-1


title: lncNB siRNA-1 HEAVY  replicate 1

value: heavy polysomal RNAs


title: HTS020_Glu1

value: MATa/MATα Mal+ Mtt+


title: lncNB siRNA-2 LIGHT  replicate 1


title: 824-btrK/R_24-2


title: Inflamed mucosa from UC patient 8

status: Public on Oct 07 2019

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  4

hyb_protocol: On average thirteen micrograms of labeled sample were hybridized for 16 hours at 48°C using the Affymetrix Eukaryotic Target Hybridization Controls protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash, and Stain Kit was used according the manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 3.2).

source_name: Intestinal mucosal biopsies

label_protocol: Starting with 350 ng of total RNA, the Affymetrix FlashTagTMBiotin HSR labeling was used to label RNA according to the manufacturer’s protocol.

extract_protocol: Total RNA for microarrays was obtained using Mirvana microRNA Kit (Life Technologies Carlsbad, CA) according to manufacturer instructions, and RNA integrity was evaluated with the High Sensitivity RNA Analysis Kit (Advanced Analytical Technologies Ankeny, IA).

treatment_protocol: Human biopsies taken from colonoscopy procedures were placed in RNA Later solution and then stored in -80ºC freezer until RNA extraction.

tag: diagnosis

value: Ulcerative Colitis

value: Intestinal mucosal biopsies

tag: inflammation

value: Inflamed

tag: mayo score


title: Non inflamed mucosa from UC patient 7

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  3

value: Non Inflamed


title: 824-btrK/R_24-1

value: collected bacteria at 24 h


title: Non inflamed mucosa from UC patient 5

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  1


title: AS2_4948_Glu1


title: Non inflamed mucosa from UC patient 4

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   4


title: Non inflamed mucosa from UC patient 6

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  2


title: Inflamed mucosa from UC patient 7

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  3


title: Inflamed mucosa from UC patient 6

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  2


title: Inflamed mucosa from UC patient 4

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  4


title: fry1_mRNA_1

source_name: seedings

tag: developmental stage

value: two-week

tag: ecotype

tag: genotype


title: Non inflamed mucosa from UC patient 2

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   2

tag: tissue


title: Inflamed mucosa from UC patient 3

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  3


title: Inflamed mucosa from UC patient 2

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  2


title: Non inflamed mucosa from UC patient 3

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)   3


title: Non inflamed mucosa from UC patient 1

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Otni)  1


title: Inflamed mucosa from UC patient 1

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from other treatment inflamed biopsy (Oti)  1


title: control siRNA LIGHT  replicate 1

tag: cell line

value: control siRNA

tag: molecule subtype

value: light polysomal RNAs


title: control siRNA HEAVY  replicate 1


title: Inflamed mucosa from UC patient 5

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gi)  1


title: Pe_16h_2

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
Base-calls performed using CASAVA version 1.4
Reads were trimmed with Trim Galore version 0.4.1 with the --paired option and default parameters
Sequencing reads were mapped to the Dm3 reference genome sequence.
The Ensemble GTF file from BDGP5.25 was used as a starting file for annotations.
STAR aligner version 2.3.0 was used to map the reads to individualized genomes.
Htseq-count version 0.5.4p3 was for generating the count tables.
Supplementary_files_format_and_content: count

organism: Drosophila melanogaster

source_name: Adult fly gut

growth_protocol: Female adult flies (2-3 days post-eclosion) were reared at 25 degrees C until treatment.

extract_protocol:
For each condition, guts from 30 adult female flies were collected in PBS four hours post treatment and directly homogenized in trizol (Invitrogen) using a bead-beater. A standard protocol for RNA extraction was performed.
Paired-end Illumna stranded Truseq libraries

treatment_protocol: Flies were starved for 2 hours at 29 degrees, then were either fed 1.5X sucrose (control) or Pseudomonas entomophila (OD600nm = 100) or Erwinia carotovora carotovora 15 (OD600nm = 100).

tag: treatment


title: Ecc15_4h_2


title: Control_16h_2


title: Ecc15_16h_2


title: Pe_4h_2


title: Pe_16h_1


title: myo>UASlarkRNAi_Pe_4h_3

growth_protocol: For specific knockdown or overexpression of lark in the adult gut enterocyte, F1 lines carrying a copy of the MyoIA-Gal4 and tub-Gal80ts transgenes, as well as one copy of either the UAS-IR or the UAS-ORF were kept at 18°C for three days post-eclosion, and then moved to 29°C for 8 days to activate the UAS transgenes.

treatment_protocol: Flies were subsequently infected with Pseudomonas entomophila using the standard oral infection protocol (OD600 nm of 100 and 1.5% sucrose)

value: myo>UASlarkRNAi

value: Pe


title: myo>w1118_Control_4h_3

value: Control


title: myo>UASlarkRNAi_Control_4h_3


title: Control_16h_1


title: myo>UASlark_Control_4h_3

value: myo>UASlark


title: myo>w1118_Pe_4h_2


title: myo>w1118_Pe_4h_3


title: myo>UASlark_Pe_4h_2


title: myo>UASlark_Pe_4h_3


title: Control_4h_1


title: Pe_4h_1


title: myo.UASlark_Control_4h_2


title: myo>UASlarkRNAi_Pe_4h_2


title: Ecc15_16h_1


title: myo>w1118_Control_4h_2


title: myo>UASlarkRNAi_Control_4h_2


title: myo>UASlark_Pe_4h_1


title: Ecc15_4h_1


title: myo>w1118_Control_4h_1


title: myo>UASlarkRNAi_Pe_4h_1


title: myo>UASlarkRNAi_Control_4h_1


title: myo>w1118_Pe_4h_1


title: myo>UASlark_Control_4h_1


title: Sample 577_Tconv_HPGD_KO

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: Sample 577

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat with default parameters.
mRNA quantification according to RefSeq Transcripts - 2014-07-30.
raw read counts were normalized by DE-Seq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DE-Seq normailzed expression values for each Sample.

growth_protocol: Cells were isolated from spleens

extract_protocol:
Cells were isolated by cell sorting, lyzed in Qiazol and RNA isolated. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain  background

value: HPGD KO

value: spleen

value: conventional CD4+ T cells


title: Non inflamed mucosa from UC patient 8

description:
miRNA expression data from total intestinal mucosal biopsy
Colon RNA from Glucocorticoid non-inflamed biopsy (Gni)  4


title: Sample 486_Treg_HPGD_WT

description: Sample 486

value: wild-type

value: regulatory CD4+ T cells


title: Sample 483_Tconv_HPGD_WT

description: Sample 483


title: Sample 490_Treg_HPGD_WT

description: Sample 490


title: WT-rep1-D8

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

description: processed data file: Enh9E_KO-merge.dexseq_clean_refseq.gene.txt

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample.

source_name: E14/TG2A mES day8 neural progenitors

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; genomic DNA from embryo samples were separated and extracted by modified microChIPseq; RNA from in vitro culture bulk cells were extracted by using Trizol and precipitated by isopropanol.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of bulk RNA seq were prepared by using NEBNext RNAseq library kit.

treatment_protocol: For Enh9E KO sample, the cells were generated by using CRISPR-Cas9 system to delete the target enhancer region in E14 mouse embryonic stem cells. For mouse neural differentiation assay, we take advantage of the protocol published previously (DOI:10.1016/j.stemcr.2015.09.010).

value: WT


title: WT-rep2-D8


title: WT-rep2-D0

source_name: E14/TG2A mES cell line


title: Sample 485_Tconv_HPGD_WT

description: Sample 485


title: Enh9E KO-rep3-D8

value: KO


title: the proband's fetus (III1)

type: genomic

city: hangzhou

first: yixi

last: sun

state: zhejiang

address: XUESHI ROAD 1

institute: Zhejiang University

hyb_protocol: The SNP array was performed according to the manufacturer’s instructions using the CytoScan™ HD array (Affymetrix, USA)

data_processing: The data was analyzed by the Chromosome Analysis Suite (ChAS) software (Affymetrix, Santa Clara, CA) based on the GRCh37/hg19 assembly

source_name: fetal amniotic fluid

extract_protocol: Genomic DNA samples of the peripheral blood and fetal amniotic fluid were extracted using the GentraPuregene Kit (Qiagen, Germany).

value: fetal amniotic fluid

tag: individual

value: proband's fetus (III1)


title: Enh9E KO-rep2-D8


title: WT-rep1-D0


title: Enh9E KO-rep3-D0


title: Enh9E KO-rep2-D0


title: Sample 579_Tconv_HPGD_KO

description: Sample 579

tag: cell type


title: Sample 575_Tconv_HPGD_KO

description: Sample 575

tag: genotype/variation


title: Sample 578_Treg_HPGD_KO

description: Sample 578


title: Sample 574_Treg_HPGD_KO

description: Sample 574


title: Sample 576_Treg_HPGD_KO

description: Sample 576


title: Sample 487_Tconv_HPGD_WT

description: Sample 487


title: Enh9E KO-rep1-D8


title: Sample 488_Treg_HPGD_WT

description: Sample 488


title: Sample 580_Treg_HPGD_KO

description: Sample 580


title: Beijing You -DW377

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

institute: China Agricultural University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

organism: Gallus gallus

source_name: Beijing You

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: chickens were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Blood


title: Beijing You -DW344


title: Sample 484_Treg_HPGD_WT

description: Sample 484


title: Beijing You -DW365


title: Enh9E KO-rep1-D0


title: Rhode Island Red-DW337

source_name: Rhode Island Red


title: the proband (II2)

scan_protocol: The SNP array was performed according to the manufacturer’s instructions using the CytoScan™ HD array (Affymetrix, USA)

source_name: peripheral blood

value: peripheral blood

value: proband (II2)


title: Hongshan-HSRM8

source_name: Hongshan


title: Hongshan-HSRM6


title: Hongshan-HSRM5


title: Hongshan-HSRM4


title: Hongshan-HSRM3


title: Hongshan-HSRM24


title: Hongshan-HSRM23


title: Hongshan-HSRM22


title: Rhode Island Red-DW343


title: Hongshan-HSRM20


title: Hongshan-HSRM17


title: Hongshan-HSRM18


title: Hongshan-HSRM16


title: the proband's husband  (II1)

label_protocol: The SNP array was performed according to the manufacturer’s instructions using the CytoScan™ HD array (Affymetrix, USA)

value: proband's husband  (II1)


title: Hongshan-HSRM15


title: Hongshan-HSRM19


title: Hongshan-HSRM7


title: Hongshan-HSRM11


title: Hongshan-HSRM2


title: Hongshan-HSRM21


title: Hongshan-HSRM10


title: Rhode Island Red-RIR_W50


title: Hongshan-HSRM1


title: Hongshan-HSRM14


title: Sample 581_Tconv_HPGD_KO

description: Sample 581


title: Hongshan-HSRM13


title: Hongshan-HSRM12


title: Rhode Island Red-RIR_W49


title: Control_4h_2

tag: strain


title: Rhode Island Red-RIR_W47


title: Rhode Island Red-RIR_W48


title: Rhode Island Red-RIR_W46


title: Rhode Island Red-RIR_W44


title: Rhode Island Red-RIR_W43


title: Rhode Island Red-RIR_W42


title: Rhode Island Red-RIR_W40


title: Rhode Island Red-RIR_W39


title: Rhode Island Red-RIR_W38


title: Rhode Island Red-RIR_W37


title: Rhode Island Red-RIR_W36


title: Rhode Island Red-RIR_W32


title: Rhode Island Red-RIR_W35


title: Rhode Island Red-RIR_W30


title: Rhode Island Red-RIR_W34


title: Rhode Island Red-RIR_W33


title: Rhode Island Red-RIR_W27


title: Rhode Island Red-RIR_W28


title: Rhode Island Red-RIR_W29


title: Rhode Island Red-RIR_W25


title: Rhode Island Red-RIR_W23


title: Rhode Island Red-RIR_W22


title: Rhode Island Red-RIR_W19


title: Rhode Island Red-RIR_W20


title: Rhode Island Red-RIR_W45


title: Rhode Island Red-RIR_W24


title: Rhode Island Red-RIR_W26


title: Rhode Island Red-RIR_W16


title: Rhode Island Red-RIR_W17


title: Rhode Island Red-RIR_W15


title: Rhode Island Red-RIR_W21


title: Rhode Island Red-RIR_W14


title: Rhode Island Red-RIR_W13


title: Rhode Island Red-RIR_W41


title: Rhode Island Red-RIR_W31


title: Rhode Island Red-RIR_W12


title: Rhode Island Red-RIR_W11


title: Rhode Island Red-RIR_W9


title: Rhode Island Red-RIR_W7


title: Rhode Island Red-RIR_W5


title: Rhode Island Red-RIR_W4


title: Rhode Island Red-RIR_W6


title: Rhode Island Red-RIR_W3


title: Rhode Island Red-RIR_R45


title: Rhode Island Red-RIR_W1


title: Rhode Island Red-RIR_R46


title: Rhode Island Red-RIR_R47


title: Rhode Island Red-RIR_R41


title: Rhode Island Red-RIR_R36


title: Rhode Island Red-RIR_R39


title: Rhode Island Red-RIR_R35


title: Rhode Island Red-RIR_R44


title: Rhode Island Red-RIR_R43


title: Rhode Island Red-RIR_R40


title: Rhode Island Red-RIR_R38


title: Rhode Island Red-RIR_R32


title: Rhode Island Red-RIR_R33


title: Rhode Island Red-RIR_R34


title: Rhode Island Red-RIR_W10


title: Rhode Island Red-RIR_R31


title: Rhode Island Red-RIR_R30


title: Rhode Island Red-RIR_R29


title: Rhode Island Red-RIR_R27


title: Rhode Island Red-RIR_W2


title: Rhode Island Red-RIR_R28


title: Rhode Island Red-RIR_R26


title: Rhode Island Red-RIR_R48


title: Rhode Island Red-RIR_R25


title: Rhode Island Red-RIR_R24


title: Rhode Island Red-RIR_R23


title: Rhode Island Red-RIR_R37


title: Rhode Island Red-RIR_R21


title: Rhode Island Red-RIR_R42


title: Rhode Island Red-RIR_R22


title: Rhode Island Red-RIR_R10


title: Rhode Island Red-RIR_R13


title: Rhode Island Red-RIR_R18


title: Rhode Island Red-RIR_R17


title: Rhode Island Red-RIR_R8


title: Rhode Island Red-RIR_R16


title: Rhode Island Red-RIR_R15


title: Rhode Island Red-RIR_R11


title: Rhode Island Red-RIR_R20


title: Rhode Island Red-RIR_R12


title: Rhode Island Red-RIR_R5


title: Rhode Island Red-RIR_R6


title: Rhode Island Red-RIR_R7


title: Rhode Island Red-RIR_R4


title: Rhode Island Red-RIR_R19


title: Rhode Island Red-RIR_R3


title: Rhode Island Red-RIR_R2


title: Rhode Island Red-RIR_R1


title: Hongshan-HSRF48


title: Rhode Island Red-RIR_R14


title: Hongshan-HSRF46


title: Hongshan-HSRF47


title: Hongshan-HSRF45


title: Rhode Island Red-RIR_R9


title: Hongshan-HSRF44


title: Hongshan-HSRF43


title: Hongshan-HSRF42


title: Hongshan-HSRF41


title: Hongshan-HSRF40


title: Hongshan-HSRF38


title: Hongshan-HSRF36


title: Hongshan-HSRF39


title: Hongshan-HSRF37


title: Hongshan-HSRF30


title: Hongshan-HSRF34


title: Hongshan-HSRF32


title: Hongshan-HSRF29


title: Hongshan-HSRF27


title: Hongshan-HSRF31


title: Hongshan-HSRF28


title: Hongshan-HSRF26


title: Hongshan-HSRF25


title: White Leghorn-WL_YQ188

source_name: White Leghorn


title: White Leghorn-WL_YQ191


title: White Leghorn-WL_YQ189


title: White Leghorn-WL_YQ190


title: White Leghorn-WL_YQ186


title: Hongshan-HSRM9


title: White Leghorn-WL_YQ192


title: White Leghorn-WL_YQ184


title: White Leghorn-WL_YQ185


title: White Leghorn-WL_YQ181


title: Hongshan-HSRF33


title: White Leghorn-WL_YQ183


title: White Leghorn-WL_YQ182


title: White Leghorn-WL_YQ180


title: Hongshan-HSRF35


title: White Leghorn-WL_YQ178


title: White Leghorn-WL_YQ173


title: White Leghorn-WL_YQ172


title: White Leghorn-WL_YQ174


title: White Leghorn-WL_YQ176


title: White Leghorn-WL_YQ175


title: White Leghorn-WL_YQ179


title: White Leghorn-WL_YQ171


title: White Leghorn-WL_YQ170


title: White Leghorn-WL_YQ168


title: White Leghorn-WL_YQ169


title: White Leghorn-WL_YQ187


title: White Leghorn-WL_YQ166


title: White Leghorn-WL_YQ165


title: White Leghorn-WL_YQ164


title: White Leghorn-WL_YQ162


title: White Leghorn-WL_YQ163


title: White Leghorn-WL_YQ156


title: White Leghorn-WL_YQ161


title: White Leghorn-WL_YQ158


title: White Leghorn-WL_YQ177


title: White Leghorn-WL_YQ159


title: White Leghorn-WL_YQ157


title: White Leghorn-WL_YQ153


title: White Leghorn-WL_YQ154


title: White Leghorn-WL_YQ155


title: White Leghorn-WL_YQ152


title: White Leghorn-WL_YQ151


title: White Leghorn-WL_YQ150


title: White Leghorn-WL_YQ147


title: White Leghorn-WL_YQ145


title: White Leghorn-WL_YQ149


title: White Leghorn-WL_YQ148


title: White Leghorn-WL_YQ144


title: White Leghorn-WL_YQ140


title: White Leghorn-WL_YQ167


title: White Leghorn-WL_YQ139


title: White Leghorn-WL_YQ142


title: White Leghorn-WL_YQ143


title: White Leghorn-WL_YQ138


title: White Leghorn-WL_YQ137


title: White Leghorn-WL_YQ141


title: White Leghorn-WL_YQ136


title: White Leghorn-WL_YQ135


title: White Leghorn-WL_YQ134


title: White Leghorn-WL_YQ133


title: White Leghorn-WL_YQ131


title: White Leghorn-WL_YQ130


title: White Leghorn-WL_YQ124


title: White Leghorn-WL_YQ128


title: White Leghorn-WL_YQ123


title: White Leghorn-WL_YQ129


title: White Leghorn-WL_YQ125


title: White Leghorn-WL_YQ127


title: White Leghorn-WL_YQ132


title: White Leghorn-WL_YQ122


title: White Leghorn-WL_YQ121


title: White Leghorn-WL_YQ119


title: White Leghorn-WL_YQ120


title: White Leghorn-WL_YQ146


title: White Leghorn-WL_YQ117


title: White Leghorn-WL_YQ116


title: White Leghorn-WL_YQ118


title: White Leghorn-WL_YQ114


title: White Leghorn-WL_YQ115


title: White Leghorn-WL_YQ112


title: White Leghorn-WL_YQ108


title: White Leghorn-WL_YQ110


title: White Leghorn-WL_YQ109


title: White Leghorn-WL_YQ107


title: White Leghorn-WL_YQ106


title: White Leghorn-WL_YQ126


title: White Leghorn-WL_YQ103


title: White Leghorn-WL_YQ101


title: White Leghorn-WL_YQ99


title: White Leghorn-WL_YQ98


title: White Leghorn-WL_YQ89


title: White Leghorn-WL_YQ96


title: White Leghorn-WL_YQ94


title: White Leghorn-WL_YQ95


title: White Leghorn-WL_YQ92


title: White Leghorn-WL_YQ97


title: White Leghorn-WL_YQ113


title: White Leghorn-WL_YQ88


title: White Leghorn-WL_YQ87


title: White Leghorn-WL_YQ111


title: White Leghorn-WL_YQ93


title: White Leghorn-WL_YQ84


title: White Leghorn-WL_YQ86


title: White Leghorn-WL_YQ85


title: White Leghorn-WL_YQ81


title: White Leghorn-WL_YQ90


title: White Leghorn-WL_YQ82


title: White Leghorn-WL_YQ83


title: White Leghorn-WL_YQ105


title: White Leghorn-WL_YQ80


title: White Leghorn-WL_YQ104


title: White Leghorn-WL_YQ79


title: White Leghorn-WL_YQ78


title: White Leghorn-WL_YQ102


title: White Leghorn-WL_YQ100


title: White Leghorn-WL_YQ77


title: White Leghorn-WL_YQ91


title: White Leghorn-WL_YQ75


title: White Leghorn-WL_YQ74


title: White Leghorn-WL_YQ72


title: White Leghorn-WL_YQ69


title: White Leghorn-WL_YQ71


title: White Leghorn-WL_YQ70


title: White Leghorn-WL_YQ67


title: White Leghorn-WL_YQ66


title: White Leghorn-WL_YQ64


title: White Leghorn-WL_YQ61


title: White Leghorn-WL_YQ68


title: White Leghorn-WL_YQ62


title: White Leghorn-WL_YQ60


title: White Leghorn-WL_YQ63


title: White Leghorn-WL_YQ57


title: White Leghorn-WL_YQ56


title: White Leghorn-WL_YQ55


title: White Leghorn-WL_YQ54


title: White Leghorn-WL_YQ53


title: White Leghorn-WL_YQ58


title: White Leghorn-WL_YQ52


title: White Leghorn-WL_YQ59


title: White Leghorn-WL_YQ47


title: White Leghorn-WL_YQ49


title: White Leghorn-WL_YQ48


title: White Leghorn-WL_YQ76


title: White Leghorn-WL_YQ50


title: White Leghorn-WL_YQ46


title: White Leghorn-WL_YQ73


title: White Leghorn-WL_YQ45


title: White Leghorn-WL_YQ42


title: White Leghorn-WL_YQ41


title: White Leghorn-WL_YQ44


title: White Leghorn-WL_YQ65


title: White Leghorn-WL_YQ37


title: White Leghorn-WL_YQ38


title: White Leghorn-WL_YQ39


title: White Leghorn-WL_YQ43


title: White Leghorn-WL_YQ35


title: White Leghorn-WL_YQ34


title: White Leghorn-WL_YQ31


title: White Leghorn-WL_YQ36


title: White Leghorn-WL_YQ30


title: White Leghorn-WL_YQ32


title: White Leghorn-WL_YQ27


title: White Leghorn-WL_YQ29


title: White Leghorn-WL_YQ26


title: White Leghorn-WL_YQ25


title: White Leghorn-WL_YQ28


title: White Leghorn-WL_YQ24


title: White Leghorn-WL_YQ22


title: White Leghorn-WL_YQ23


title: White Leghorn-WL_YQ21


title: White Leghorn-WL_YQ20


title: White Leghorn-WL_YQ19


title: White Leghorn-WL_YQ18


title: White Leghorn-WL_YQ17


title: White Leghorn-WL_YQ16


title: White Leghorn-WL_YQ14


title: White Leghorn-WL_YQ12


title: White Leghorn-WL_YQ10


title: White Leghorn-WL_YQ11


title: White Leghorn-WL_YQ13


title: White Leghorn-WL_YQ33


title: White Leghorn-WL_YQ8


title: White Leghorn-WL_YQ9


title: White Leghorn-WL_YQ6


title: White Leghorn-WL_YQ5


title: White Leghorn-WL_YQ4


title: White Leghorn-WL_YQ2


title: Hongshan-HSNM70


title: Hongshan-HSNM71


title: Hongshan-HSNM65


title: Hongshan-HSNM68


title: White Leghorn-WL_YQ3


title: Hongshan-HSNM69


title: Hongshan-HSNM67


title: Hongshan-HSNM66


title: Hongshan-HSNM72


title: Hongshan-HSNM64


title: Hongshan-HSNM62


title: Hongshan-HSNM60


title: Hongshan-HSNM58


title: Hongshan-HSNM59


title: Hongshan-HSNM61


title: Hongshan-HSNM63


title: Hongshan-HSNM57


title: Hongshan-HSNM56


title: Hongshan-HSNM55


title: White Leghorn-WL_YQ7


title: Hongshan-HSNM53


title: Hongshan-HSNM54


title: Hongshan-HSNM51


title: Hongshan-HSNF95


title: Hongshan-HSNF96


title: Hongshan-HSNF94


title: Hongshan-HSNM50


title: Hongshan-HSNF93


title: Hongshan-HSNF89


title: Hongshan-HSNF90


title: Hongshan-HSNF87


title: Hongshan-HSNF86


title: Hongshan-HSNF92


title: Hongshan-HSNF85


title: Hongshan-HSNF88


title: Hongshan-HSNF83


title: Hongshan-HSNF84


title: Hongshan-HSNF81


title: Hongshan-HSNF80


title: Hongshan-HSNF78


title: Hongshan-HSNF79


title: Hongshan-HSNF77


title: Hongshan-HSNF82


title: Hongshan-HSNM52


title: Rhode Island Red-RIR389


title: Hongshan-HSNF73


title: Hongshan-HSNF74


title: Beijing You -RIR387


title: Hongshan-HSNM49


title: Hongshan-HSNF76


title: Rhode Island Red-RIR386


title: Hongshan-HSNF75


title: Rhode Island Red-RIR385


title: Rhode Island Red-RIR384


title: Rhode Island Red-BY6836


title: Hongshan-HSNF91


title: Beijing You -RIR383


title: Rhode Island Red-RIR382


title: Rhode Island Red-BY5702


title: Rhode Island Red-BY6886


title: Rhode Island Red-RIR380


title: Rhode Island Red-BY76294


title: Rhode Island Red-BY6815


title: Rhode Island Red-RIR376


title: Rhode Island Red-RIR377


title: Rhode Island Red-RIR379


title: Rhode Island Red-RIR375


title: Rhode Island Red-RIR367


title: Rhode Island Red-RIR369


title: Beijing You -RIR374


title: Rhode Island Red-RIR371


title: Rhode Island Red-RIR373


title: Rhode Island Red-RIR366


title: Rhode Island Red-RIR370


title: Rhode Island Red-RIR365


title: Rhode Island Red-RIR372


title: Rhode Island Red-RIR361


title: Rhode Island Red-RIR362


title: Rhode Island Red-RIR364


title: Rhode Island Red-RIR360


title: Rhode Island Red-RIR381


title: Rhode Island Red-RIR359


title: Rhode Island Red-RIR358


title: Rhode Island Red-BY37980


title: Rhode Island Red-RIR357


title: Rhode Island Red-RIR378


title: Rhode Island Red-RIR356


title: Beijing You -RIR355


title: Rhode Island Red-RIR352


title: Rhode Island Red-RIR353


title: Rhode Island Red-RIR368


title: Rhode Island Red-RIR363


title: Rhode Island Red-RIR354


title: Rhode Island Red-BY6878


title: Rhode Island Red-BY6890


title: Rhode Island Red-BY4459


title: Beijing You -BY37978


title: Rhode Island Red-RIR342


title: Rhode Island Red-BY76205


title: Rhode Island Red-RIR341


title: Rhode Island Red-RIR347


title: Rhode Island Red-RIR351


title: Rhode Island Red-RIR350


title: Rhode Island Red-RIR343


title: Rhode Island Red-BY5750


title: Rhode Island Red-RIR340


title: Rhode Island Red-RIR344


title: Rhode Island Red-BY37973


title: Rhode Island Red-BY6817


title: Rhode Island Red-RIR345


title: Rhode Island Red-BY5790


title: Rhode Island Red-BY76254


title: Rhode Island Red-RIR348


title: Beijing You -RIR346


title: Beijing You -RIR338


title: Rhode Island Red-RIR337


title: Rhode Island Red-RIR339


title: Beijing You -RIR349


title: Beijing You -RIR336


title: Beijing You -RIR335


title: Rhode Island Red-BY37972


title: Rhode Island Red-RIR334


title: Beijing You -RIR333


title: Rhode Island Red-RIR331


title: Rhode Island Red-RIR332


title: Rhode Island Red-RIR318


title: Beijing You -RIR316


title: Beijing You -RIR321


title: Beijing You -RIR323


title: Rhode Island Red-RIR315


title: Beijing You -RIR319


title: Houdan-HD_5_45

source_name: Houdan


title: Houdan-HD_5_44


title: Rhode Island Red-RIR329


title: Houdan-HD_5_43


title: Beijing You -RIR314


title: Rhode Island Red-RIR330


title: Houdan-HD_5_47


title: Houdan-HD_5_49


title: Rhode Island Red-RIR312


title: Beijing You -RIR325


title: Rhode Island Red-RIR322


title: Rhode Island Red-RIR326


title: Houdan-HD_5_48


title: Rhode Island Red-RIR311


title: Rhode Island Red-RIR317


title: Beijing You -RIR328


title: Rhode Island Red-RIR327


title: Houdan-HD_5_41


title: Houdan-HD_5_42


title: Houdan-HD_5_40


title: Rhode Island Red-RIR313


title: Houdan-HD_5_50


title: Houdan-HD_5_38


title: Houdan-HD_5_35


title: Houdan-HD_5_31


title: Houdan-HD_5_32


title: Houdan-HD_5_37


title: Houdan-HD_5_22


title: Houdan-HD_5_30


title: Houdan-HD_5_29


title: Houdan-HD_5_24


title: Houdan-HD_5_18


title: Houdan-HD_5_17


title: Houdan-HD_5_27


title: Houdan-HD_5_19


title: Houdan-HD_5_26


title: Houdan-HD_5_15


title: Houdan-HD_5_28


title: Houdan-HD_5_20


title: Houdan-HD_5_14


title: Houdan-HD_5_23


title: Houdan-HD_5_9


title: Houdan-HD_5_13


title: Houdan-HD_5_25


title: Houdan-HD_5_10


title: Houdan-HD_5_11


title: Houdan-HD_5_7


title: Houdan-HD_5_21


title: Houdan-HD_5_39


title: Houdan-HD_5_5


title: Houdan-HD_5_36


title: Houdan-HD_5_16


title: Houdan-HD_5_4


title: Houdan-HD_5_2


title: Houdan-HD_4_49


title: Houdan-HD_4_50


title: Houdan-HD_4_45


title: Houdan-HD_4_47


title: Houdan-HD_4_46


title: Houdan-HD_4_43


title: Houdan-HD_4_42


title: Houdan-HD_4_41


title: Houdan-HD_4_44


title: Houdan-HD_4_34


title: Houdan-HD_4_40


title: Houdan-HD_4_38


title: Houdan-HD_4_39


title: Houdan-HD_4_36


title: Houdan-HD_4_37


title: Houdan-HD_5_8


title: Houdan-HD_4_32


title: Houdan-HD_4_33


title: Houdan-HD_4_28


title: Houdan-HD_4_30


title: Houdan-HD_4_29


title: Houdan-HD_4_24


title: Houdan-HD_4_26


title: Houdan-HD_4_23


title: Houdan-HD_4_20


title: Houdan-HD_4_22


title: Houdan-HD_4_19


title: Houdan-HD_4_48


title: Houdan-HD_4_15


title: Houdan-HD_4_17


title: Houdan-HD_4_14


title: Houdan-HD_4_16


title: Houdan-HD_4_13


title: Houdan-HD_4_11


title: Houdan-HD_4_12


title: Houdan-HD_4_10


title: Houdan-HD_4_9


title: Houdan-HD_4_1


title: Shouguang-SG_71122

source_name: Shouguang


title: Houdan-HD_4_5


title: Houdan-HD_4_2


title: Shouguang-SG_70678


title: Shouguang-SG_71268


title: Shouguang-SG_70597


title: Shouguang-SG_70688


title: Shouguang-SG_71540


title: Shouguang-SG_71230


title: Shouguang-SG_71892


title: Shouguang-SG_70687


title: Shouguang-SG_70177


title: Shouguang-SG_71271


title: Houdan-HD_4_18


title: Shouguang-SG_71469


title: Shouguang-SG_70344


title: Shouguang-SG_70663


title: Houdan-HD_4_8


title: Houdan-HD_4_7


title: Houdan-HD_4_3


title: Shouguang-SG_70026


title: Shouguang-SG_70169


title: Shouguang-SG_70375


title: Shouguang-SG_70374


title: Shouguang-SG_70198


title: Shouguang-SG_71131


title: Shouguang-SG_71109


title: Shouguang-SG_71845


title: Shouguang-SG_70764


title: Shouguang-SG_70712


title: Shouguang-SG_70407


title: Shouguang-SG_71149


title: Shouguang-SG_70679


title: Shouguang-SG_71334


title: Shouguang-SG_70566


title: Shouguang-SG_70762


title: Shouguang-SG_71546


title: Shouguang-SG_70479


title: Shouguang-SG_71519


title: Shouguang-SG_70757


title: Shouguang-SG_70661


title: Shouguang-SG_71891


title: Shouguang-SG_70093


title: Shouguang-SG_70532


title: Shouguang-SG_71497


title: Shouguang-SG_70504


title: Shouguang-SG_70551


title: Shouguang-SG_71107


title: Shouguang-SG_71518


title: Shouguang-SG_70175


title: Shouguang-SG_70565


title: Shouguang-SG_70550


title: Shouguang-SG_71448


title: Shouguang-SG_71239


title: Shouguang-SG_71539


title: Shouguang-SG_71805


title: Shouguang-SG_71394


title: Shouguang-SG_71544


title: Shouguang-SG_70406


title: Shouguang-SG_71130


title: Shouguang-SG_70763


title: Shouguang-SG_70741


title: Shouguang-SG_71125


title: Shouguang-SG_71176


title: Shouguang-SG_70552


title: Shouguang-SG_71468


title: Shouguang-SG_70772


title: Shouguang-SG_70739


title: Shouguang-SG_70531


title: Shouguang-SG_70572


title: Shouguang-SG_70376


title: Shouguang-SG_70204


title: Shouguang-SG_70203


title: Shouguang-SG_70664


title: Shouguang-SG_70567


title: Shouguang-SG_70477


title: Shouguang-SG_71325


title: Shouguang-SG_71508


title: Shouguang-SG_71335


title: Shouguang-SG_70176


title: Shouguang-SG_71229


title: Shouguang-SG_71882


title: Shouguang-SG_70362


title: Shouguang-SG_70078


title: Shouguang-SG_70341


title: Shouguang-SG_70743


title: Shouguang-SG_70476


title: Shouguang-SG_71393


title: Shouguang-SG_71336


title: Shouguang-SG_71436


title: Shouguang-SG_70740


title: Shouguang-SG_70205


title: Shouguang-SG_71123


title: Shouguang-SG_70769


title: Shouguang-SG_71361


title: Shouguang-SG_71106


title: Shouguang-SG_70573


title: Shouguang-SG_71462


title: Shouguang-SG_70257


title: Tibetan-T_CAU_Z10

source_name: Tibetan


title: Shouguang-SG_70024


title: Tibetan-T_CAU_Z9


title: Shouguang-SG_70714


title: Tibetan-T_CAU_Z11


title: Tibetan-T_CAU_Z4


title: Tibetan-T_CAU_Z7


title: Tibetan-T_CAU_Z2


title: Shouguang-SG_71517


title: Tibetan-T_CAU_Z3


title: Shouguang-SG_71116


title: Shouguang-SG_70046


title: Shouguang-SG_70047


title: Tibetan-T_CAU_Z1


title: Tibetan-T_CAU_Z5


title: Tibetan-T_CAU_Z6


title: Shouguang-SG_71269


title: Shouguang-SG_71541


title: Shouguang-SG_71553


title: Shouguang-SG_71219


title: Shouguang-SG_71507


title: Shouguang-SG_71806


title: Shouguang-SG_71181


title: Shouguang-SG_70258


title: Shouguang-SG_71150


title: Tibetan-T_CAU_Z15


title: Tibetan-T_CAU_Z8


title: Tibetan-T_CAU_Z13


title: Tibetan-T_CAU_Z14


title: Tibetan-T_LZ_L3


title: Tibetan-T_CAU_Z12


title: Tibetan-T_LZ_L2


title: Tibetan-T_ND_N14


title: Tibetan-T_LZ_L1


title: Tibetan-T_ND_N13


title: Tibetan-T_ND_N12


title: Tibetan-T_ND_N11


title: Tibetan-T_ND_N10


title: Tibetan-T_ND_N7


title: Tibetan-T_ND_N4


title: Tibetan-T_ND_N5


title: Tibetan-T_ND_N8


title: Tibetan-T_ND_N3


title: Tibetan-T_ND_N2


title: White Leghorn-WL_CAU_B39


title: Tibetan-T_NM_M6


title: White Leghorn-WL_CAU_B40


title: Tibetan-T_NM_M4


title: White Leghorn-WL_CAU_B38


title: Tibetan-T_NM_M3


title: Tibetan-T_ND_N9


title: White Leghorn-WL_CAU_B32


title: White Leghorn-WL_CAU_B36


title: Tibetan-T_NM_M9


title: Shouguang-SG_71441


title: Tibetan-T_ND_N1


title: White Leghorn-WL_CAU_B29


title: White Leghorn-WL_CAU_B34


title: Tibetan-T_NM_M8


title: White Leghorn-WL_CAU_B31


title: Tibetan-T_NM_M1


title: White Leghorn-WL_CAU_B35


title: Tibetan-T_NM_M7


title: White Leghorn-WL_CAU_B30


title: Tibetan-T_NM_M5


title: White Leghorn-WL_CAU_B37


title: Tibetan-T_NM_M2


title: White Leghorn-WL_CAU_B33


title: White Leghorn-WL_CAU_B28


title: Tibetan-T_NM_M10


title: WKM8_monocytes

city: Utrecht

first: Aditya

last: Barve

address: Uppsalalaan 8

institute: Hubrecht Institute

description: each plate contains 384 sorted cells

data_processing:
In transcriptome libraries, first read contains UMI (6 first nucleotides) and cell barcode (from 7 to 14 nucleotides) and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell-specific barcode file is added as a part of processed data files.
Genome_build: All transcriptome libraries were mapped to Danio rerio assembly Zv9, ensemble 74, extended with ERCC92
Supplementary_files_format_and_content: Tabular separated files, with transcript count (rows) per cell (columns). Cells in each file are labeled according to barcode ID. The cell-specific barcode file is provided in the celseq2_bc.csv.gz ( 1st column represents index of the cell specific barcode, and the second column is the barcode)

extract_protocol:
After organ isolation, live single cells are sorted into 384 well plates containing mineral oil, uniquely barcoded cell specific primers for mRNA detection, Spike-in controls and and RNAse inhibitor.
cellseq2
Illumina TruSeq adapaters

tag: FISHid

value: whole kidney marrow single cells

tag: cell subtype

value: monocytes


title: White Leghorn-WL_CAU_B26


title: White Leghorn-WL_CAU_B24


title: White Leghorn-WL_CAU_B23


title: White Leghorn-WL_CAU_B25


title: WKM8_unenriched

description: each plate contains 384 sorted cells

value: unenriched


title: WKM9_eosinophils

description: each plate contains 384 sorted cells

value: eosinophils


title: White Leghorn-WL_CAU_B22


title: White Leghorn-WL_CAU_B27


title: WKM8_eosinophils_and_lymphocytes

description: each plate contains 384 sorted cells. Cell specific barcodes 1-192 represent GateID enriched eosinophils cells, while barcodes numbered 193-384 represent GateID enriched lymphocytes

value: lymphocytes


title: WKM7_unenriched

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B21


title: WKM9_unenriched

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B16


title: White Leghorn-WL_CAU_B17


title: WKM9_monocytes

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B15


title: White Leghorn-WL_CAU_B20


title: WKM7_monocytes

description: each plate contains 384 sorted cells


title: WKM4_unenriched

description: each plate contains 384 sorted cells


title: WKM6_unenriched

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B18


title: WKM5_unenriched

description: each plate contains 384 sorted cells


title: WKM5_hspcs

description: each plate contains 384 sorted cells

value: hspcs


title: White Leghorn-WL_CAU_B14


title: White Leghorn-WL_CAU_B13


title: WKM4_eosinophils

description: each plate contains 384 sorted cells


title: WKM3_unenriched

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B11


title: WKM3_eosinophils

description: each plate contains 384 sorted cells


title: WKM3_classicalgate-eosinophils

description: each plate contains 384 sorted cells

value: classicalgate-eosinophils


title: White Leghorn-WL_CAU_B10


title: White Leghorn-WL_CAU_B8


title: White Leghorn-WL_CAU_B9


title: WKM6_lymphocytes

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B19


title: WKM2_classicalgate-eosinophils

description: each plate contains 384 sorted cells


title: WKM2_unenriched

description: each plate contains 384 sorted cells


title: WKM1_unenriched_and_eosinphils

description: each plate contains 384 sorted cells. Cell specific barcodes 1-192 represent unenriched cells, while barcodes numbered 193-384 represent GateID enriched eosinophils.


title: White Leghorn-WL_CAU_B5


title: White Leghorn-WL_CAU_B7


title: White Leghorn-WL_CAU_B6


title: WKM5_lymphocytes

description: each plate contains 384 sorted cells


title: WKM2_eosinophils

description: each plate contains 384 sorted cells


title: WKM10_lymphocytes

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B3


title: WKM10_hspcs

description: each plate contains 384 sorted cells


title: TD2_unenriched6

description: each plate contains 384 sorted cells


title: WKM10_unenriched

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B2


title: White Leghorn-WL_CAU_B1


title: TD2_unenriched5

description: each plate contains 384 sorted cells


title: White Leghorn-WL_CAU_B12


title: TD2_unenriched4

description: each plate contains 384 sorted cells


title: Taihe Silkies-SK_S90

source_name: Taihe Silkies


title: Taihe Silkies-SK_S89


title: TD2_unenriched3

description: each plate contains 384 sorted cells


title: TD2_unenriched2

description: each plate contains 384 sorted cells


title: Taihe Silkies-SK_S88


title: Taihe Silkies-SK_S87


title: Taihe Silkies-SK_S86


title: Taihe Silkies-SK_S85


title: White Leghorn-WL_CAU_B4


title: Taihe Silkies-SK_S84


title: TD1c_unenriched2

description: each plate contains 384 sorted cells


title: Taihe Silkies-SK_S83


title: TD1c_unenriched1

description: each plate contains 384 sorted cells


title: TD1b_unenriched1

description: each plate contains 384 sorted cells


title: TD1a_unenriched1

description: each plate contains 384 sorted cells


title: TD1a_unenriched2

description: each plate contains 384 sorted cells


title: TD1b_unenriched2

description: each plate contains 384 sorted cells


title: Taihe Silkies-SK_S81


title: Taihe Silkies-SK_S80


title: Taihe Silkies-SK_S79


title: Taihe Silkies-SK_S77


title: e136_RNA_m2

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

description:
deseq.norm.count.pitx2endel.csv
sample name
e136m2

data_processing:
Alignment: We used STAR (version 2.5.2b) to align raw reads to mouse genome (Gencode, GRCm38) and annotated transcripts and genes using Gencode mouse genome gtf file (vM10). Read abundance was quantified by STAR quantification mode '--quantMode GeneCounts'
Gene filtering: Raw read counts were loaded in R statistical environment and created a deseq object using DESeq2 package (R version 3.5.1, DESeq2 version 1.20.0). Read counts for individual samples were compiled by genes, low read count genes (total read count ≤ number of biological samples) were removed from downstream analyses. Mitochondrial genes and ribosomal genes were also removed.
Read normalization: Raw read counts were then normalized using DESeq2 command 'counts(deseq.df, normalized = T)'.
Genome_build: mm10
Supplementary_files_format_and_content: readcount in csv format, representing normalized read count

source_name: left ventricle

extract_protocol:
Left atrial tissue was isolated from 3-month-old mice and preserved in RNALater Solution (Ambion, AM7021). Disruption and homogenization of the tissue was performed using a cordless pestle motor (VWR, 47747-370) and 1.5 mL microtube disposable pestles (VWR, 47747-362) and the subsequent RNA isolation was performed using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA concentration was measured using the Qubit RNA HS Assay Kit (Invitrogen, Q32855) with the Qubit 2.0 Fluorometer (ThermoFisher, Q32866).
600 ng of RNA from each sample was used an input for RNA Sequencing library preparation using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) for Illumina Platforms (Roche, KK8483). Multiplexing of the libraries was performed using the KAPA Dual-Indexed Adapter Kit for Illumina Platforms (Roche, KK8722). Concentrations of primers (280 nM), fragmentation protocol (6 minutes at 94 °C), and number of amplification cycles (9 cycles) were all selected following kit recommendations. Following library preparation, library concentration was measured using the AATI Fragment Analyzer with the NGS Fragment Kit (1-6000 bp) (Agilent, DNF-473-0500). Libraries were sequenced on the Illumina NextSeq 500 with the NextSeq 500/550 High Output Reagent Cartridge V2 (Illumina, Illumina, 15057931).

value: FVB

value: left ventricle

value: 3 month old adult

value: Pitx2 Enh20k Deletion

tag: gender

value: male


title: e136_RNA_f2

description:
deseq.norm.count.pitx2endel.csv
sample name
e136f2

value: female


title: e136_RNA_m1

description:
deseq.norm.count.pitx2endel.csv
sample name
e136m1


title: Taihe Silkies-SK_S76

value: Blood


title: Taihe Silkies-SK_S78


title: e136_RNA_f1

description:
deseq.norm.count.pitx2endel.csv
sample name
e136f1


title: Taihe Silkies-SK_S75


title: Taihe Silkies-SK_S74


title: Taihe Silkies-SK_S73


title: e135_RNA_m1

description:
deseq.norm.count.pitx2endel.csv
sample name
e135m1


title: TD2_unenriched1

description: each plate contains 384 sorted cells


title: e135_RNA_f2

description:
deseq.norm.count.pitx2endel.csv
sample name
e135f2


title: e135_RNA_f1

description:
deseq.norm.count.pitx2endel.csv
sample name
e135f1


title: Taihe Silkies-SK_S71


title: e135_RNA_m2

description:
deseq.norm.count.pitx2endel.csv
sample name
e135m2


title: ctrl_RNA_m2

description:
deseq.norm.count.pitx2endel.csv
sample name
ctrlm2

value: control


title: Taihe Silkies-SK_S69


title: ctrl_RNA_f2

description:
deseq.norm.count.pitx2endel.csv
sample name
ctrlf2


title: ctrl_RNA_f1

description:
deseq.norm.count.pitx2endel.csv
sample name
ctrlf1


title: Taihe Silkies-SK_S68


title: Taihe Silkies-SK_S67


title: Pitx2EnhDel2_H3K4me1_CUT&RUN

data_processing:
Library strategy: CUT&RUN
Alignment: CUT&RUN raw sequencing reads were aligned to mouse genome (mm10) using bowtie2 (version 2.3.4.3) under “-q --sensitive” mode.
Read normalization: Two independent methods were utilized to normalize read abundance. Firstly, we normalize CUT&RUN peaks by spike-in yeast DNA control. We aligned sequencing reads to yeast genome (Saccharomyces_cerevisiae_Ensembl_R64-1-1) and use modified script “py_sam_spikenormbg.py” (https://github.com/peteskene) to generate bedgraph files. Secondly, we used Homer (version 4.10.3) to normalize abundance to total uniquely mapped reads. The results were consistent between these normalization methods.
Peak calling: To generate a complete peak profile, we combined all sequencing reads from biological replicates of FVB control and Pitx2ΔE20k mice and performed peak calling using Homer findPeaks function with “-style histone” mode for all histone marks and “-style factor” mode for CTCF.
Quantification: We then quantified total number of normalized reads with peak interval for all samples and identified differential peaks using R (version 3.6.1) limma package (version 3.40.6). Track screen shots were produced in WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) and IGV (version 2.4.14)
Genome_build: mm10
Supplementary_files_format_and_content: peaks: csv format, contain peak calling and annotation of the peaks

extract_protocol:
Adult left ventricle tissues were washed in wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine and complete protease inhibitor (EDTA-free, Roche), captured with Concanavalin A beads (Polysciences, Warrington, PA) and incubated with primary antibodies overnight at 4°C. After washing with Dig-wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.08% Digitonin and protease inhibitors), cells were resuspended in 50 μL Digwash buffer and 2.5 μL of protein A-MNase (1:10 diluted, batch 6 from Steve Henikoff) and incubated at room temperature for 10 minutes. Cell pellets were washed again and placed in a 0°C metal block, and 2 mM of CaCl2 was added and incubated for 45 minutes. MNase reaction was terminated by the addition of 2XSTOP buffer and incubated at 37°C 10 minutes. Samples were then digested by proteinase K at 70°C for 10 minutes and DNA was extracted by ethanol precipitation.
Library were prepared using KAPA Hyper Prep Kit (KAPA) and custom Y-shaped TruSeq adapters according to the manufacturer's instructions. The antibodies used were anti-H3K27ac (Abcam, ab4729), anti-H3K27me3 (Cell Signaling, 9733S), anti H3K4me3 (Diagenode, C15410003), anti-CTCF (Diagenode, C15410210), and anti-H3K4me1 (Diagenode, C15410037).

value: adult

tag: chip antibody


title: Pitx2EnhDel2_H3K27me3_CUT&RUN


title: Pitx2EnhDel2_CTCF_CUT&RUN

value: CTCF


title: Taihe Silkies-SK_S65


title: Pitx2EnhDel2_H3K27ac_CUT&RUN


title: Pitx2EnhDel1_H3K27me3_CUT&RUN


title: Taihe Silkies-SK_S63


title: Taihe Silkies-SK_S64


title: Taihe Silkies-SK_S62


title: Pitx2EnhDel1_H3K4me1_CUT&RUN


title: Taihe Silkies-SK_S61


title: Pitx2EnhDel1_H3K27ac_CUT&RUN


title: Taihe Silkies-SK_S72


title: Taihe Silkies-SK_S59


title: FVB2_H3K27me3_CUT&RUN


title: Taihe Silkies-SK_S58


title: FVB2_H3K4me1_CUT&RUN


title: Taihe Silkies-SK_S70


title: Taihe Silkies-SK_S57


title: FVB2_CTCF_CUT&RUN


title: Taihe Silkies-SK_S56


title: Taihe Silkies-SK_S55


title: Taihe Silkies-SK_S66


title: FVB2_H3K27ac_CUT&RUN


title: FVB1_H3K27me3_CUT&RUN


title: Taihe Silkies-SK_S54


title: FVB1_H3K4me1_CUT&RUN


title: Taihe Silkies-SK_S52


title: Pitx2EnhDel1_CTCF_CUT&RUN


title: FVB1_CTCF_CUT&RUN


title: FVB1_H3K27ac_CUT&RUN


title: Taihe Silkies-SK_S53


title: 5741: Tconv KO 5

data_processing:
Illumina Casava v1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with Kallisto (v0.44) against the mm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.3.1) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

source_name: VAT Tconv

extract_protocol:
Mice were perfused with PBS and cells were isolated by enzymatic digestion with Collagenase and DNAse prior to FACS sorting in medium+FCS and stored in TRIZOL (invitrogen). RNA was isolated by Rneasy Microkits (Quiagen) following the manufacturers’ protocol and quality was assessed.
10ng of total RNA was converted into cDNA libraries using the SmartSeq2 protocol (Picelli et al., 2013). cDNA was subsequently sequenced in the NextSeq 500 system and demultiplexed using bcl2fastq2 v2.20

tag: line

value: Hpgd fl; Foxp3-YFP-Cre; Treg cell specific deletion of Hpgd

value: VAT

tag: age

value: 12 weeks


title: 5740: Tconv KO 4


title: Taihe Silkies-SK_S51


title: Taihe Silkies-SK_S60


title: 5739: Tconv KO 3


title: Taihe Silkies-SK_S49


title: Taihe Silkies-SK_S48


title: 5738: Tconv KO 2


title: 5737: Tconv KO 1


title: Taihe Silkies-SK_S47


title: 5734: Treg KO 3

source_name: VAT Treg


title: 5735: Treg KO 4


title: Taihe Silkies-SK_S46


title: Taihe Silkies-SK_S44


title: Taihe Silkies-SK_S43


title: 5733: Treg KO 2


title: 5732: Treg KO 1


title: Taihe Silkies-SK_S42


title: Taihe Silkies-SK_S40


title: 5730: Tconv WT 3


title: 5731: Tconv WT 4


title: 5729: Tconv WT 2


title: Taihe Silkies-SK_S39


title: 5727: Treg WT 3


title: Taihe Silkies-SK_S37


title: 5728: Tconv WT 1


title: Taihe Silkies-SK_S36


title: Taihe Silkies-SK_S35


title: Taihe Silkies-SK_S34


title: 5725: Treg WT 1


title: 5965: Treg WT 4

source_name: mLN Treg from Rag-/- mice

extract_protocol:
Cells were isolated from mLN of animals by FACS sorting for YFP+ cells in medium+FCS and stored in TRIZOL (invitrogen). RNA was isolated by Rneasy Microkits (Quiagen) following the manufacturers’ protocol and quality was assessed.
10ng of total RNA was converted into cDNA libraries using the SmartSeq2 protocol (Picelli et al., 2013). cDNA was subsequently sequenced in the NextSeq 500 system and demultiplexed using bcl2fastq2 v2.20

treatment_protocol: Rag-/- mice were injected with WT Tnaive, WT Treg and either YFP+ WT or YFP+ Hpgd-deficient Treg cells 8 weeks prior to sacrificing.

value: mLN


title: 5964: Treg KO 3


title: 5963: Treg WT 3


title: Taihe Silkies-SK_S45


title: Taihe Silkies-SK_S31


title: 5962: Treg KO 2


title: 5961: Treg KO 1


title: Taihe Silkies-SK_S29


title: 5960: Treg WT 2


title: Taihe Silkies-SK_S30


title: Taihe Silkies-SK_S41


title: Taihe Silkies-SK_S28


title: 5959: Treg WT 1