title: 100994770046_R01C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholinebl

tag: logdmgbl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: control rep1 [dvqmR_pCtrl]

status: Public on Jun 25 2018

type: SRA

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

country: Germany

institute: Friedrich-Schiller-Universität Jena

description:
dvqmR_pCtrl_1_AGTCAA
ΔvqmR + pBAD-ctr
processed data file: VqmR_pulse_read_counts.xlsx

library_source: transcriptomic

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3' adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4.
The trimmed reads were checked for quality and mapped to the V. cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1.
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.5 and a Bonerroni adjusted p-value < 1E-10 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: VqmR_pulse_read_counts.xlsx: Read count table and edgeR (exact mode) analysis.

molecule: total RNA

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: Vibrio cholerae C6706 ΔvqmR strains carrying pBAD-ctr or pBAD-vqmR plasmids were grown to exponential phase (OD600=0.5) in 100ml LB media containing 50µg/ml kanamycin. At this point, 0.2% L-arabinose was added to induce vqmR expression and cells were harvested 15minutes after induction.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) according to the manufacturer's instructions, and tested using a Bioanalyzer.

treatment_protocol: The cells were treated with 0.2% L-arabinose in mid-exponential growth phase (OD600=0.5). After 15 minutes of treatment 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethanol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

tag: strain/background

tag: genotype/variation

value: <delta>vqmR + pBAD-ctr

tag: growth phase

value: exponential

tag: treatment

value: 0.2% L-arabinose


title: lgs000379_RNA-seq

city: Oklahoma City

first: Patrick

middle: M

last: Gaffney

state: OK

address: 825 NE 13th Street

department: Genes and Human Disease

country: USA

institute: Oklahoma Medical Research Foundation

description: processed data: Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt.gz

data_processing:
For ChIP-seq, raw FASTQ reads were quality filtered and trimmed for Illumina adapters using Trimmomatic v0.35
To assess the quality of the ChIP-seq data, we calculated the fraction of reads in peaks (FRiP) for acCBP/p300 and RNAPII enrichment peaks and scrutinized experiments with FRiP scores <1%. We also used strand cross-correlation to calculate the normalized strand coefficient (NSC) and relative strand coefficient (RSC), and repeated experiments with NSC < 1.05 and RSC < 0.8.
Reads aligning to Poly-A, Poly-C, ribosomal, mitochondrial, or Phi-X sequences were excluded using Bowtie v2.2.4 with option -L 10.
Filtered reads were aligned using the Burrows Wheeler Aligner (BWA) to the human hg19 genome with the following options: -n 2 –o 0 –l 20.
To reduce reference genome bias on read mappability, we used the WASP pipeline to relocate reads potentially biased by genetic variation.  Only reads overlapping single nucleotide polymorphisms (SNPs) which were segregating in the genotyping data (≥2 minor alleles across population) were targeted by the realignment procedure.
For RNA-seq, post-sequence reads were quality filtered and trimmed for Illumina adapters using Trimmomatic v0.35
Resulting reads were aligned to the hg38 genome using Kallisto v0.43.0 with the following options: --bias enabled, 50 bootstraps.
Transcript expression values were summarized at the gene level to transcript-length adjusted, library-size scaled counts per million (CPM) with the R package tximport (PMID:26925227)
RNA-seq expression data were normalized with PEER using K=10 latent factors on genes with positive expression in >50% of individuals. The PEER-derived weights were then scaled by the mean of each gene.
For HiChIP-seq, sequenced reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Loop calling was performed with hichipper (PMID: 29489746) for each sample
Alignment was performed on the entire hg19 genome, and also to custom genomes of the hg19 COX and hg19 PGF Major Histocompatibility Complex loci.
Genome_build: hg19 (ChIP-seq, HiChIP-seq), hg38 (RNA-seq)
Supplementary_files_format_and_content: Adjusted.hetp.txt (Output of the Combined Haplotype Test software after WASP alignment bias correction),
Supplementary_files_format_and_content: connectome.txt (High-confidence loop calls  and paired-end tag counts from genome-wide alignment of HiChIP-seq data to the hg19 genome)
Supplementary_files_format_and_content: interactions.all.mango (High-confidence loop calls from custom haplotype alignment of HiChIP-seq data to the COX and PGF sequences)
Supplementary_files_format_and_content: Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt (Matrix of normalized gene-level abundances from RNA-seq data)

organism: Homo sapiens

source_name: RNA-seq

growth_protocol: LCLs were maintained in RPMI 1640 medium supplemented with 10% FBS, penicillin, streptomycin, and L-glutamine.

extract_protocol:
For ChIP-seq, we crosslinked 10 million Epstein-Barr Virus (EBV)-transformed B cells with 1% formaldehyde for 5 minutes followed by careful cell lysis using the truChIP Chromatin Shearing Kit (Covaris).  Nuclei were isolated and fragmented using a Covaris E220e sonicator   with the following operating conditions: Peak Incident Power: 140 Watts; duty cycle: 5%; cycles per burst: 200; treatment time: 15 minutes; setpoint temperature: 6°C).  Crosslinked protein/DNA was immunoprecipitated using H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml)  or H3K4me1 (rabbit polyclonal, Abcam #ab8895, 20ug/ml) antibodies on Protein A + G immunomagnetic beads.  Anti-acetyl histone H3 antibodies and isotype matched IgG antibodies were included as positive and negative controls, respectively.  An aliquot of the fragmented chromatin, not subjected to immunoprecipitation, was also used as an input control.  Chromatin crosslinks were reversed, then protein was digested with proteinase K and DNA fragments were purified using Ampure XP beads (Beckman Coulter).  For HiChIP-sequencing, We crosslinked 10 million EBV-transformed B cells using 1% formaldehyde for 10 minutes at room temperature.  Intact nuclei were isolated and digested using the MboI restriction enzyme for 4 hours at 37C.  DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature overnight.  Following the in situ ligation, we fragmented the ligated chromatin as previously described64.  Crosslinked protein/DNA was immunoprecipitated using antibodies to H3K27ac (rabbit polyclonal, Abcam #ab4729, 20ug/ml) and CTCF (rabbit mAb, clone D31H2, Cell Signaling #3418, 20ug/ml) and then purified by Protein A+G immunomagnetic beads.  The amount of MboI enzyme, antibody, and beads are determined by the number of cells in each sample64. After immunoprecipitation, DNA was eluted from the beads by incubating at 65C for 4 hours with 5% Proteinase K. DNA was purified by Zymo DNA Clean & Concentrator Column and quantified by Qubit High Sensitivity Assay Kit.  RNA was isolated from each LCL using TRIzol.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols. DNA libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads.  RNA libraries were sequenced on the Illumina HiSeq 3000 using 75bp paired-end reads with 10 samples per lane, yielding 30 million reads per sample.

tag: cell line

value: lymphoblastoid cell lines (LCLs)

tag: disease

value: Systemic lupus erythematosus

value: European-American

tag: gender

value: Female

tag: chip antibody


title: 101103430068_R04C02

type: genomic

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University

description: HumanMethylation450 BeadChip - standard protocol

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted. CpGAssoc package was used to filter out CpG sites that have a Detection P-Value greater than 0.001 in more than 10% of the samples and samples that have a Detection P-Value greater than 0.001 in more than 5% of the CpG sites. After this, cross-reactive probes were removed and normalization was performed using BMIQ and combat

label: biotin

molecule: genomic DNA

source_name: Whole Blood

extract_protocol: Invitrogen Puregene Genomic DNA kit

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

value: Not disclosed

tag: ga

value: TC

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logmethioninebl

tag: loghomocysteinebl


title: AI-2+CAI-1+DPO rep2

description:
AI2+CAI1+DPO_2_ACTGAT
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3' adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4.
The trimmed reads were checked for quality and mapped to the V. cholerae reference genome: NCBI Acc.number: NC_002505.1, NC_002506.1 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1.
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 2.0 and a FDR adjusted p-value < 0.01 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: AI_RNAseq_read_counts.xlsx: Excel file containing read counts and edgeR (exact mode) analysis.

growth_protocol: Vibrio cholerae C6706 ΔluxS ΔcqsA Δtdh strains were grown overnight in M9 minimal media, supplemented with 0.4% glucose and in the presence of 5µM final concentration of the autoinducers: autoinducer 2 (AI-2), cholera-autoinducer-1 (CAI-1), or 3,5-dimethylpyrazin-2-ol (DPO), or water (control) or combinations. The following day, bacteria were diluted 1:500 in fresh media with the same compositions and RNA samples were collected at OD600 = 0.2.

treatment_protocol: The bacteria were treated with 5µM final concentration of the autoinducers: autoinducer 2 (AI-2), cholera-autoinducer-1 (CAI-1), 3,5-dimethylpyrazin-2-ol (DPO), water (control), or combinations. In early exponential phase (OD600=0.2) 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethanol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

tag: strain/background

tag: genotype/variation

value: <delta>luxS<delta>cqsA<delta>tdh

tag: growth phase

value: early exponential

tag: treatment

value: 5uM AI-2, 5uM CAI-1, 5uM DPO


title: lgs102943_RNA-seq

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: B.theta22

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho. Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Type of Sequencer:Illumina MiSeq, paired end
USEARCH algorithm was used to filter the high quality reads, cluster into operational taxonomic units (OTUs) and remove chimeras based on the database in RDP classifier.
Minimum identity of 97% was set to identify OTUs. The QIIME scripts (version 1.9.1) were then used to assign taxonomy, align sequences to the greengenes reference database, perform alpha and beta diversity analysis and summarize taxonomy.
16Sana1,2,4: taxa summary data at the family level
16Sana3: OUT table for sequence counts

organism: Bacteria

source_name: mouse feces

extract_protocol:
Genomic DNA was isolated from fecal samples using the PowerSoil bacterial DNA extraction kit (MoBio). DNA samples were amplified using the following barcoded primers targeting V1–V2 region of the 16SrRNA gene.
The amplicons were purified with AMPure XP beads (Beckman), indices and sequencing adaptors were introduced  using the Nextera XT Index kit (Illumina), quantified by using THUNDERBIRD SYBR qPCR mix (TOYOBO) and pooled according to the Illumina protocol.

value: metronidazole+ciprofloxacin, 4 weeks after colonization

tag: host

tag: sample type

value: fecal content

tag: molecule

value: BT[delta]MAFF


title: 100994770067_R01C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: H

tag: ga

value: TT

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logcholinebl

tag: logdmgbl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: AI-2+CAI-1+DPO rep1

description:
AI2+CAI1+DPO_1_GAGTGG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

tag: strain/background

tag: genotype/variation

tag: growth phase

tag: treatment


title: 100994770028_R06C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logserumfolate

tag: logserumfolatebl

tag: logmethioninebl

tag: loghomocysteinebl


title: lgs304761_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

library_source: genomic

source_name: H3K27ac ChIP-seq

tag: cell line

tag: disease

tag: gender

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: 100994770028_R03C01

tag: sample

tag: subjectid

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logcholinebl

tag: logdmgbl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: lgs304761_RNA-seq

tag: cell line

tag: disease

tag: race


title: CAI-1+DPO rep3

description:
CAI1+DPO_3_CGTACG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

tag: strain/background

tag: genotype/variation

tag: growth phase

tag: treatment

value: 5uM CAI-1, 5uM DPO


title: B.theta21

tag: host

tag: sample type

tag: molecule


title: lgs000502_RNA-seq

tag: gender

tag: chip antibody


title: 100994770020_R03C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: AA

tag: ga

value: CC

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl


title: lgs303260_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

tag: cell line

value: lymphoblastoid cell lines (LCLs)

tag: disease

value: Systemic lupus erythematosus

tag: race

tag: gender

value: Male

tag: chip antibody


title: 100994770046_R04C01

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: MIED

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: B.theta20

tag: treatment

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: 100994770020_R06C01

tag: sample

tag: subjectid

tag: tp

tag: race

value: TC

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl


title: B.theta23

tag: treatment

tag: host

tag: sample type

tag: molecule


title: CAI-1+DPO rep2

description:
CAI1+DPO_2_GTTTCG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

tag: strain/background

tag: genotype/variation

value: <delta>luxS<delta>cqsA<delta>tdh

tag: growth phase


title: lgs301315_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

value: European-American

tag: gender

value: Female

tag: chip antibody


title: 100994770020_R04C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: W

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: B.theta34

tag: treatment

value: metronidazole+ciprofloxacin, 4 weeks after colonization

tag: host

tag: sample type

value: fecal content

tag: molecule

tag: genotype/variation


title: 100994770020_R01C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

tag: race

tag: ga

tag: genocord

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logcholinebl

tag: logdmgbl

tag: logmethioninebl

tag: loghomocysteinebl


title: B.theta19

tag: treatment

tag: host

tag: sample type

tag: molecule

value: BT[delta]MAFF


title: AI-2+DPO rep3

description:
AI2+DPO_3_GTGAAA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

tag: strain/background

tag: genotype/variation

tag: growth phase

value: early exponential

value: 5uM AI-2, 5uM DPO


title: lgs303260_RNA-seq

tag: cell line

tag: disease

tag: race

tag: gender

tag: chip antibody


title: CAI-1+DPO rep1

description:
CAI1+DPO_1_GTGGCC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: 5uM CAI-1, 5uM DPO


title: lgs100111_RNA-seq


title: B.theta17


title: lgs100111_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

value: H3K27ac (Abcam, #ab4729)


title: B.theta18


title: lgs301315_RNA-seq


title: AI-2+DPO rep2

description:
AI2+DPO_2_GTCCGC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: lgs303397_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: lgs304082_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: B.theta16

value: BTWT


title: lgs304082_RNA-seq

value: lymphoblastoid cell lines (LCLs)


title: B.theta15


title: lgs303397_RNA-seq

value: Systemic lupus erythematosus


title: lgs101301_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: AI-2+DPO rep1

description:
AI2+DPO_1_CCGTCC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: lgs101301_RNA-seq


title: AI-2+CAI-1 rep2

description:
AI2+CAI1_2_AGTTCC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: 5uM AI-2, 5uM CAI-1


title: AI-2+CAI-1 rep3

description:
AI2+CAI1_3_ATGTCA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: lgs000705_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: B.theta14


title: lgs304654_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: B.theta12


title: lgs304629_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

value: Male


title: lgs304654_RNA-seq


title: lgs100953_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: lgs100953_RNA-seq


title: DPO rep3

description:
DPO3_CTTGTA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: 5uM DPO


title: B.theta13


title: lgs304629_RNA-seq


title: lgs000705_RNA-seq


title: lgs106435_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: DPO rep2

description:
DPO2_GGCTAC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: <delta>luxS<delta>cqsA<delta>tdh


title: 100994770028_R01C02

tag: sample

tag: subjectid

tag: tp

tag: characteristics

tag: maternalage

value: H

tag: ga

value: CC

tag: genocord

value: TC

tag: logfolicacid

tag: logcholine

tag: logdmg

tag: logmethionine

tag: logbetaine

tag: logtmoa

tag: loghomocysteine

tag: logsah

tag: logserumfolate

tag: logserumfolatebl

tag: logsahbl

tag: logbetainebl

tag: logtmaobl

tag: logfolicacidbl


title: B.theta10

tag: treatment

value: metronidazole+ciprofloxacin, 4 weeks after colonization

tag: host

tag: sample type

tag: molecule

tag: genotype/variation


title: AI-2+CAI-1+DPO rep3

description:
AI2+CAI1+DPO_3_ATTCCT
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

tag: strain/background

tag: growth phase

value: 5uM AI-2, 5uM CAI-1, 5uM DPO


title: B.theta9

value: fecal content


title: lgs102580_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

tag: cell line

tag: disease

tag: race

value: European-American

tag: gender

value: Female

tag: chip antibody


title: lgs106435_RNA-seq


title: CAI-1 rep3

description:
CAI1_3_GATCAG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: early exponential

value: 5uM CAI-1


title: lgs102580_RNA-seq


title: CAI-1 rep2

description:
CAI1_2_ACTTGA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: B.theta11

value: BTWT


title: lgs101645_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

value: lymphoblastoid cell lines (LCLs)

value: H3K27ac (Abcam, #ab4729)


title: B.theta8


title: lgs304714_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment

value: Systemic lupus erythematosus


title: AI-2+CAI-1 rep1

description:
AI2+CAI1_1_AGTCAA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: 5uM AI-2, 5uM CAI-1


title: CAI-1 rep1

description:
CAI1_1_CAGATC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: lgs304714_RNA-seq

description: processed data: Kallisto_expression_25cellLines_filtered_PEERnormalized+scaled_lengthScaledTPM.txt.gz

value: Male


title: B.theta7


title: B.theta6


title: lgs302634_RNA-seq


title: lgs304050_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: AI-2 rep3

description:
AI2_3_GCCAAT
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: <delta>luxS<delta>cqsA<delta>tdh

value: 5uM AI-2


title: AI-2 rep2

description:
AI2_2_ACAGTG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: lgs304050_RNA-seq


title: B.theta4


title: DPO rep1

description:
DPO1_TAGCTT
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: 5uM DPO


title: lgs301430_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: lgs000502_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: AI-2 rep1

description:
AI2_1_TGACCA
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: B.theta5


title: lgs302634_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: lgs101645_RNA-seq


title: lgs301430_RNA-seq


title: lgs301283_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: control rep3

description:
control3_TTAGGC
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx

value: water


title: B.theta3

value: metronidazole+ciprofloxacin, 4 weeks after colonization


title: lgs101293_H3K27ac ChIP-seq

description: H3K27ac ChIP-Seq experiment


title: lgs101293_RNA-seq


title: B.theta1


title: B.theta2


title: control rep2

description:
control2_CGATGT
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: control rep1

description:
control1_ATCACG
ΔluxSΔcqsAΔtdh
processed data file: AI_RNAseq_read_counts.xlsx


title: Primary breast cancer 2 CD103-

status: Public on Jun 24 2018

city: Parkville

first: Chengzhong

last: Ye

state: Victoria

address: Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade

department: Bioinformatics Division

country: Australia

description:
185-T2
Raw data (controlled access) at EGAN00001668302

data_processing:
RNASeq data were quantified using kallisto (0.43.0), against the Ensembl transcript reference (release 79, GRCh38)
Count matrix was constructed using tximport (1.4.0) with countsFromAbundance = "lengthScaledTPM"
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts for 6 samples, tsv

source_name: Primary Tumor

extract_protocol:
Single cell suspensions of breast cancer tissue were obtained by enzymatic dissociation on the day of surgery, from one primary TNBC, one primary ER negative HER2 amplified breast cancer, and one TNBC liver metastasis. Viable cells were FACS sorted on BD FACSAria II Cell Sorter (BD Biosciences) by propidium iodide staining and further sorted for CD8+CD69+CD103+ and CD8+CD69+CD103- TIL subsets. Total RNA was extracted using the RNAqueous-4PCR RNA isolation kit (Thermo Fisher) with cell concentrations ranging between 1 x 10^5 - 2 x 10^5 cells for RT PCR. Between 50 and 200ng total RNA were used per sample.
Libraries were prepared using the Illumina Trussed RNA Sample Prep Kit v2 following the vendors protocol. Briefly, poly-A mRNA was purified using poly-T magnetic beads, fragmented using divalent cations under elevated temperature and reverse transcribed to cDNA with random primers. Indexed adaptors were then ligated and the libraries amplified. 15 to 19 cycles of PCR were necessary. Library concentration was measured using Qubit High Sensitivity kit and fluorometer (Thermo Fisher Scientific) and the quality checked using the High Sensitivity D1000 reagents in an Agilent Tape Station.
polyA selected unstranded RNASeq

tag: breast cancer subtype

tag: phenotype

tag: tissue

value: Primary breast cancer 2


title: Liver metastasis CD103+

institute: Walter and Eliza Hall Institute of Medical Research

description:
175-T1
Raw data (controlled access) at EGAN00001668299

source_name: Liver metastasis

value: triple negative

value: Liver metastasis


title: Primary breast cancer 1 CD103+

description:
179-T1
Raw data (controlled access) at EGAN00001668303

value: Primary breast cancer 1


title: TERC_WT_rep2_comb_D2

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

description:
RNA fraction of TERT-IP
icSHAPE_wildtype_rep2.txt

data_processing:
SHAPE data analysis was performed as described in R. C. Spitale et al (2015) and R. A. Flynn et al. (2016). Analysis pipline is available at https://github.com/qczhang/icSHAPE
Genome_build: hg19
Supplementary_files_format_and_content: icSHAPE score pre nucleotide

source_name: HeLa cells TERT-IP

growth_protocol: HeLa S3 and 293T cells were cultured in DMEM containing 10% fetal bovine serum at 37 deg C, 5% CO2

extract_protocol:
Purified telomerase RNP where thawed on ice and equilibrated at 37°C for 30 minutes. NAI-N3 was added to a final concentration of 100 μM and incubated for 12 minutes. An equal volume of DMSO was added to control samples. Reaction was stopped by addition of TRIzol LS reagent.
Total RNA was recovered and libraries constructed according to R. C. Spitale et al (2015) and R. A. Flynn et al. (2016)
RNA-seq single step

treatment_protocol: Nuclear extract was prepared from indicated Hela cells per (2). Affinity purified rabbit polyclonal anti-TERT antibody (T421) used in IPs were described in (3). Typically, 30ug of T421 antibody was incubated with 1ml of nuclear extract prior to addition of protein A-agarose Fast Flow (P3476 Sigma). Immunoprecipitated complex was washed extensively with Lys450 (10 mM HEPES pH 7.9, 10% glycerol, 100 mM NaCl, 1.5 mM MgCl2, 0.05% TritonX-100, and freshly added 1 mM DTT, 200 μM PMSF, and Protease Inhibitor Cocktail [P8340 Sigma]), then equilibrated as a 50% slurry in 1x direct assay buffer (50 mM Tris-HCl pH8.0, 50 mM KCl, 1 mM MgCl2, 1 mM Spermidine, 5 mM β-mercaptoethanol, and 30% Glycerol), lastly aliquoted and snap-froze on dry ice and store in -80 freezer. Fresh aliquots were used in western and northern blottings, telomerase assays, and in vitro SHAPE analysis.

tag: genotype

value: Wild Type


title: TERC_WT_rep2_comb_N1


title: Liver metastasis CD103-

description:
175-T2
Raw data (controlled access) at EGAN00001668300


title: TERC_WT_rep2_comb_D1


title: TERC_KO_rep2_comb_N1

description:
RNA fraction of TERT-IP
icSHAPE_TCAB_KO_rescue_rep2.txt

value: TCAB KO


title: TERC_KO_rep2_comb_D1


title: Primary breast cancer 2 CD103+

description:
185-T1
Raw data (controlled access) at EGAN00001668301


title: TERC_KO-R_rep2_comb_N2

description:
RNA fraction of TERT-IP
icSHAPE_TCAB_KO_rep2.txt


title: TERC_KO_rep2_comb_N2


title: lgs301283_RNA-seq

value: European-American

value: Female


title: TERC_KO_rep2_comb_D2


title: TERC_KO-R_rep2_comb_N1


title: TERC_KO-R_rep2_comb_D2


title: TERC_KO-R_rep2_comb_D1


title: TERC_WTa_N2

description:
RNA fraction of TERT-IP
icSHAPE_wildtype.txt


title: TERC_WTa_D2


title: Primary breast cancer 1 CD103-

description:
179-T2
Raw data (controlled access) at EGAN00001668304


title: TERC_WTa_N1


title: TERC_WT_rep2_comb_N2


title: TERC_WTa_D1


title: PP1_M3

city: Wuhan

first: Lu

last: Zhao

state: Hubei

address: No.1,Shizishan Street ,Hongshan District

department: College of Veterinary Medicine

country: China

institute: Huazhong Agricultural University

description: 21 d.p.i. worm pairs treated with Sj-pp1c dsRNAs were cultured in vitro for 7 d

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 whole genom(WormBase ParaSite,version 7.0) using by Tophat (version v2.0.12) with mismatch=2
Fragments Per Kilobase of transcript sequence per Millions base pairs(FPKM) was calculated using a protocal from Trapnell et al.,Nat Biotechnol,2010.HTSeq v0.6.1 software was used to analyze the gene expression levels using the union mode.
Genome_build: PRJEA34885
Supplementary_files_format_and_content: Excel files include FPKM ,readcount values and gene information for each sample

organism: Schistosoma japonicum

source_name: Sj-pp1c KD_21 dpi_male_worm

growth_protocol: The worm pairs were cultured in 841 medium with or without Sj-pp1c dsRNAs for 7 days in vitro.

extract_protocol:
Pair worms were mechanically separated and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Jiangsu

value: Sj-pp1c KD

tag: Sex

value: male

tag: age

value: 21 days post infection (d.p.i.)

value: whole worm


title: TERC_TCAB-KOa_N2

description:
RNA fraction of TERT-IP
icSHAPE_TCAB_KO.txt


title: PP1_M2


title: PP1_M1


title: PP1_FE3

source_name: Sj-pp1c KD_21 dpi_female_worm

value: female


title: skeletal muscle from subject#9 at day 0, biological replicate 9

type: RNA

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2,0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: Offspring of Type 2 diabetic parent; before the diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

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

value: skeletal muscle


title: skeletal muscle from subject#10 at day 0, biological replicate 10


title: BLA_M3

description: 21 d.p.i. worm pairs were cultured in vitro for 7d

source_name: WT_21 dpi_male_worm

value: wild type


title: TERC_TCAB-KOa_D2


title: PP1_FE2


title: skeletal muscle from subject#8 at day 0, biological replicate 8


title: skeletal muscle from subject#7 at day 0, biological replicate 7


title: skeletal muscle from subject#10 at day 7, biological replicate 10

source_name: Offspring of Type 2 diabetic parent; after the high fructose diet


title: skeletal muscle from subject#2 at day 0, biological replicate 2


title: BLA_M2


title: PP1_FE1


title: skeletal muscle from subject#8 at day 7, biological replicate 8


title: skeletal muscle from subject#7 at day 7, biological replicate 7


title: TERC_TCAB-KOa_D1


title: skeletal muscle from subject#6 at day 0, biological replicate 6


title: BLA_M1


title: TERC_TCAB-KO-invitroR_N2

description:
RNA fraction of TERT-IP
icSHAPE_TCAB_KO_invitroRescue.txt


title: BLA_FE3

source_name: WT_21 dpi_female_worm


title: BLA_FE2


title: TERC_TCAB-KOa_N1


title: BLA_FE1


title: TERC_TCAB-KO-invitroR_N1


title: skeletal muscle from subject#5 at day 0, biological replicate 5


title: TERC_TCAB-KO-invitroR_D2


title: skeletal muscle from subject#5 at day 7, biological replicate 5


title: skeletal muscle from subject#9 at day 7, biological replicate 9


title: skeletal muscle from subject#4 at day 0, biological replicate 4


title: RNA-Seq_OG+PDGFRAlow/-PECAM-

city: Beijing

first: Yifang

last: Liu

address: Haidian District

institute: Peking University

data_processing:
scRNA-Seq: We checked the quality of raw sequencing data by FastQC software. The read2 fastq sequence was trimmed by FASTX-Toolkit. We used 10x genomics cellranger count pipeline 2.0.1 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
WGBS: WGBS analysis was performed using Bismark/Bowtie2 algorithm. The clean fastq format reads were obtained from the sequencer and aligned to mouse mm10 reference with Bismark in directional mode using the default parameters. The deduplication tool from Bismark was used to remove duplicate reads. The methylation calls were extracted from the unique read alignment using bismark_methylation_extractor and bismark2bedGraph command. The methylation calls from both Watson and Crick strand were combined for the following analysis.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations (where rows are genes, and columns are cell barcodes); RNA-Seq: FPKM matrix; WGBS: bedGraph

organism: Mus musculus

source_name: Intermediate cells on stage II day 12 and FACS sorted OG+PDGFRAlow/-PECAM-

growth_protocol: MEFs were cultured in high glucose DMEM (Gibco) supplemented with 15% fetal bovine serum (FBS, Pan-Biotech), 1% GlutaMAX-I (Gibco), 1% nonessential amino acids (NEAA, Gibco), 0.1 mM β-mercaptoethanol (Sigma-Aldrich) and 1% penicillin-streptomycin (Gibco). Mouse ESCs and CiPSCs were maintained on feeder layers (the mitomycin C-treated MEFs) in ESC culture medium containing KnockOut DMEM (Gibco), 10% knockout serum replacement (KSR, Gibco), 10% FBS, 1% GlutaMAX-I, 1% NEAA, 0.1 mM β-mercaptoethanol, 1% penicillin-treptomycin  supplemented with 2iL (3 µM CHIR99021, 1 µM PD0325901 and 10 ng/ml LIF) or with additional 50 μg/ml vitamin C (for scRNA-seq in Figure 6A). MEFs, ESCs and CiPSCs were incubated at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit (Zymo Research). Genomic DNA of sorted pZscan4c-Em+, pZscan4c-Em- cells at stage II D12, XEN-like cell with pZscan4c-Emerald reporter and CiPSCs were extracted using EasyPure Genomic DNA Kit (TransGen, EE101-11).
Total RNA was isolated using Direct-zol RNA MiniPrep Kit (Zymo Research). RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB England BioLabs)..   Genomic DNA of sorted pZscan4c-Em+, pZscan4c-Em- cells at stage II D12 and pZscan4c-Emerald XEN-like cell were extracted using EasyPure Genomic DNA Kit (TransGen, EE101-11). DNA were denatured and bisulfite converted using EZ DNA Methylation-GoldTM Kit (Zymo Research, D5005). In brief, 20 µl DNA (300 ng) was mixed with 130 µl CT Conversion Reagent and performming the following steps: 98°C for 10 minutes, 64°C for 2.5 hours. Samples and 600 µl M-Binding Buffer were added into a Zymo-Spin™ IC Column, followed by inverting the column several times and centrifuging at full speed (>10,000 x g) for 30 seconds. 100 µl M-Wash Buffer was added to the column and centrifuged at full speed for 30 seconds. Add 200 µl M-Desulphonation Buffer to the column, incubate at room temperature (20-30°C) for 15-20 minutes and then centrifuging at full speed for 30 seconds. Wash the column with 200 µl M-Wash Buffer twice and elute the DNA with 10 µl M-Elution Buffer. Recovered bisulfite-converted DNAs were constructed into sequencing libraries using Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions.  Cells at different timepoints throughout chemical reprogramming process were harvested and resuspended at 1 × 106 cells per milliliter in 1 × PBS with 0.04% BSA. Then, cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V2 (10x Genomics, 120237). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq libraries were prepared using Single Cell 3' Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

treatment_protocol: MEFs were seeded at a density of 50,000 cells per well of a 6-well plate or 300,000 cells per 100 mm dish with MEF culture medium. The next day (day 0), change the medium into stage I medium. Change the medium every 4 days. On day 12, for the induction with FBS/KSR-SII condition, re-plate the cells at a density of 50,000-200,000 cells per well of a 6-well plate with stage I medium  reduced concentrations of bFGF and CHIR99021). For the induction with N2B27-SII condition, feeder cells (MEFs treated with mitomycin C and seeded at 150,000 cells per well of 6-well plate) should be  prepared one day before re-plating. Re-plate the cells on feeder cells at a density of 2,000-10,000 cells per well of 6-well plate with stage I medium (reduced concentrations of bFGF and CHIR99021). On day 16, XEN-like epithelial colonies are formed and the culture is changed into stage II medium. On day 28, change the culture into stage III medium.

tag: cell type

value: Intermediate cells

tag: strain

tag: time

value: stage II day 12


title: WGBS_CiPSCs

source_name: CiPS cell line

value: CiPSCs


title: WGBS_pZscan4c-Em+

source_name: Reprogramming pZscan4-Emerald ESC derived XEN-like cells and FACS sorted pZscan4c-eme+ cells at stage II day 12

value: 129S6/SvEvTac x C57BL/6Ncr)


title: WGBS_pZscan4c-Em-

source_name: Reprogramming pZscan4-Emerald ESC derived XEN-like cells and FACS sorted pZscan4c-eme- cells at stage II day 12


title: TERC_TCAB-KO-invitroR_D1


title: RNA-Seq_Control

source_name: Intermediate cells on stage III day 4 without Opt. VPA treatment

value: stage III day 4


title: RNA-Seq_Opt. VPA

source_name: Intermediate cells on stage III day 4 with Opt. VPA treatment


title: skeletal muscle from subject#4 at day 7, biological replicate 4


title: skeletal muscle from subject#3 at day 0, biological replicate 3


title: TERC_TCAB-KO-Ra_N1

description:
RNA fraction of TERT-IP
icSHAPE_TCAB_KO_rescue.txt


title: RNA-Seq_CiPSCs#1

source_name: CiPS cell line #1


title: TERC_TCAB-KO-Ra_D2


title: RNA-Seq_ESCs

source_name: Embryonic stem cells derived from mouse E3.5 embryo

value: ESCs

value: ICR x ICR


title: RNA-Seq_SIII D21

source_name: Intermediate cells on stage III day 21 during chemical reprogramming of MEFs

value: stage III day 21


title: RNA-Seq_SIII D15

source_name: Intermediate cells on stage III day 15 during chemical reprogramming of MEFs

value: stage III day 15


title: RNA-Seq_FBS/KSR-SII condition

source_name: Intermediate cells on stage II day 12 using FBS/KSR-SII condition


title: RNA-Seq_SIII D6

source_name: Intermediate cells on stage III day 6 during chemical reprogramming of MEFs

value: stage III day 6


title: TotalB.rep2

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

description:
raw_counts.txt
CAGRF9188-1283

data_processing:
Sequence reads were alligned using the Subread aligned
Genewise counts were obtained using FeatureCounts
Genes were filtered from downstream analysis if they failed to achieve 0.5 CPM or greater in at least two libraries
Counts were converted to log2 counts per million, quantile normaliszed and precision weighted with the "voom" function of limma
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw_counts file is the counts as given by FeatureCounts
Supplementary_files_format_and_content: norm_Log2RPKM files give the normalized Log2 reads per kilobase of transcript, per million mapped reads

source_name: Total B Cells

growth_protocol: All cells were purified from mice between 7 and 12 weeks of age.

extract_protocol:
RNA was isolated from two biological repliates (RNAeasy plus micro kit, QIagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal cavity was flushed with PBS to harvest the cells, before staining with antibodies and sorting on flurouresence cytometer

value: B Cells

tag: antibodies

value: Peritoneal Cavity Lavage


title: RNA-Seq_SII D12 (N2B27-SII condition)

source_name: Intermediate cells on stage II day 12 during chemical reprogramming of MEFs


title: TERC_TCAB-KO-Ra_N2

source_name: HeLa cells TERT-IP

value: TCAB KO


title: TERC_IVT_N2

description:
RNA fraction of TERT-IP
icSHAPE_IVT.txt

source_name: IVT RNA

value: in vitro transcribed


title: skeletal muscle from subject#2 at day 7, biological replicate 2

source_name: Offspring of Type 2 diabetic parent; after the high fructose diet


title: RNA-Seq_XEN-like cells

source_name: Establishment of purified XEN-like cell lines sing stage 1 medium (with VC6TFAE plus 20 ng/ml bFGF)

value: XEN-like cells


title: skeletal muscle from subject#1 at day 0, biological replicate 1

source_name: Offspring of Type 2 diabetic parent; before the diet

value: skeletal muscle


title: skeletal muscle from subject#3 at day 7, biological replicate 3


title: TERC_IVT_N1

description:
RNA fraction of TERT-IP
icSHAPE_IVT.txt


title: pDC.rep1

description:
raw_counts.txt
CAGRF11700-1543

source_name: pDCs

treatment_protocol: After harvesting spleens they were processed to single cell suspension and put through a seive. Red Cell removal buffer was applied before staining with antibodies and sorting on flurouresence cytometer

value: plasmacytoid dendritic cells

value: CD11c Lo CD45RAHi

value: Spleen


title: pDC.rep2

description:
raw_counts.txt
CAGRF11700-1544


title: RNA-Seq_pZscan4c-Em+

source_name: Reprogramming pZscan4-Emerald ESC derived XEN-like cells and FACS sorted pZscan4c-eme+ cells at stage II day 12

value: Intermediate cells

value: stage II day 12


title: RNA-Seq_MEFs

source_name: Mouse embryonic fibroblast cells from E13.5 embyos

value: MEFs


title: skeletal muscle from subject#6 at day 7, biological replicate 6


title: scRNA-Seq_ESCs

description: ESCs.tar

molecule: polyA RNA

value: ESCs

value: 129S6/SvEvTac x C57BL/6Ncr)


title: TERC_TCAB-KO-Ra_D1


title: RNA-Seq_pZscan4c-Em-

source_name: Reprogramming pZscan4-Emerald ESC derived XEN-like cells and FACS sorted pZscan4c-eme- cells at stage II day 12


title: TERC_IVT_D2

description:
RNA fraction of TERT-IP
icSHAPE_IVT.txt


title: naiveCD8.rep2

description:
raw_counts.txt
CAGRF11700-1533

source_name: Naïve CD8+ T Cells

treatment_protocol: After harvesting spleens and lymph nodes they were processed to single cell suspension and put through a seive. Red Cell removal buffer was applied before staining with antibodies and sorting on flurouresence cytometer

value: naive CD8+ T Cells

value: Spleen and Lymph nodes


title: scRNA-Seq_SIII D21

description: AGG.tar

value: stage III day 21


title: TotalB.rep1

description:
raw_counts.txt
CAGRF9188-1278

value: B Cells


title: TERC_Coilin_KO_N2

description:
RNA fraction of TERT-IP
icSHAPE_Coilin_KO.txt

value: Coilin KO


title: scRNA-Seq_SIII D15

description: AGG.tar

value: stage III day 15


title: skeletal muscle from subject#1 at day 7, biological replicate 1


title: scRNA-Seq_SIII D10

description: AGG.tar

source_name: Intermediate cells on stage III day 10 during chemical reprogramming of MEFs

value: stage III day 10


title: naiveCD4.rep2

description:
raw_counts.txt
CAGRF11700-1520

source_name: Naïve CD4+ T Cells

value: naive CD4+ T Cells


title: scRNA-Seq_SIII D8

description: AGG.tar

source_name: Intermediate cells on stage III day 8 during chemical reprogramming of MEFs

value: stage III day 8


title: TERC_Coilin_KO_N1


title: scRNA-Seq_SIII D6

description: AGG.tar

value: stage III day 6


title: naiveCD4.rep1

description:
raw_counts.txt
CAGRF11700-1519


title: scRNA-Seq_SIII D3

description: AGG.tar

source_name: Intermediate cells on stage III day 3 during chemical reprogramming of MEFs

value: stage III day 3


title: TERC_IVT_D1

description:
RNA fraction of TERT-IP
icSHAPE_IVT.txt

value: in vitro transcribed


title: WGBS_XEN-like cells

value: XEN-like cells

value: C57BL/6J-Tg(GOFGFP)11Imeg/ brcxICR


title: scRNA-Seq_SII D12

description: AGG.tar

value: Intermediate cells

value: stage II day 12


title: Primary TNBC infiltrating T cells case 2

data_processing:
Demultiplexing, read alignment and count summarization were performed using CellRanger v1.3.1 using the Illumina BCL files as input.
Aggregation of libraries and samples were performed using CellRanger v1.3.1
Genome_build: hg38
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: Primary tumour

extract_protocol:
Primary tumour tissues were resected from two patients with triple-negative breast cancer.  Tissues were treated with collagenase and mechanically dissociated. Single cell suspensions were generated and the viable cells were FACS sorted for CD3+ T cells on a BD FACSAria II Cell Sorter (BD Biosciences). Sorted cells were then counted, assessed for viability and resuspended. Cell suspensions were loaded onto a Chromium Single Cell Chip along with the reverse transcription (RT) mastermix and single cell 3’ gel beads, aiming for 2000 – 6000 cells per channel.
Following generation of single cell gel bead-in-emulsions (GEMs), reverse transcription was performed using a C1000 Touch Thermal Cycler with a Deep Well Reaction Module (Bio-Rad Laboratories, Hercules, CA, USA). Amplified cDNA was purified using SPRIselect beads (Beckman Coulter, Lane Cove, NSW, Australia) and sheared to approximately 200bp with a Covaris S2 instrument (Covaris, Woburn, MA, USA) using the manufacturer’s recommended parameters. Sequencing libraries were generated with unique sample indices (SI) for each sample. Libraries were sequenced on an Illumina HiSeq 2500 High Output Mode using V4 clustering and sequencing chemistry to achieve paired-end 100 bp reads..

tag: breast cancer subtypes

value: triple negative

tag: number of cells

tag: number of channels


title: scRNA-Seq_SII D8

description: AGG.tar

source_name: Intermediate cells on stage II day 8 during chemical reprogramming of MEFs

value: stage II day 8


title: scRNA-Seq_SI D12

description: AGG.tar

source_name: Intermediate cells on stage I day 12 during chemical reprogramming of MEFs

value: stage I day 12


title: TERC_Coilin_KO_D1

source_name: HeLa cells TERT-IP


title: scRNA-Seq_SI D5

description: AGG.tar

source_name: Intermediate cells on stage I day 5 during chemical reprogramming of MEFs

value: stage I day 5


title: Primary TNBC infiltrating T cells case 1


title: naiveCD8.rep1

description:
raw_counts.txt
CAGRF11700-1532

value: naive CD8+ T Cells

value: Spleen and Lymph nodes


title: scRNA-Seq_MEF, XEN-like cells and CiPSCs

description: AGG.tar

source_name: MEF, XEN-like cell line and CiPSCs were digested into single cell and mixed in proportion

value: MEF, XEN-like cell line and CiPSCs


title: TERC_Coilin_KO_D2

value: Coilin KO


title: Liver Tumor Tissue 62

status: Public on Jun 23 2018

city: Shantou

first: Jincheng

last: Guo

address: Xinling Road

department: Medical collage

institute: Shantou University

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

data_processing: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

label_protocol: Biotinylated cRNA Labeling Protocol. Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev. 2, Affymetrix).

extract_protocol: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

value: liver tumor


title: Liver Tumor Tissue 61


title: Liver Tumor Tissue 59


title: Liver Tumor Tissue 54


title: Liver Tumor Tissue 60


title: Liver Tumor Tissue 44


title: Liver Tumor Tissue 38


title: Liver Tumor Tissue 51


title: Liver Tumor Tissue 64


title: Liver Tumor Tissue 40


title: Liver Tumor Tissue 49


title: Liver Tumor Tissue 43


title: Liver Tumor Tissue 55


title: Liver Tumor Tissue 37


title: Liver Tumor Tissue 57


title: Liver Tumor Tissue 45


title: Liver Tumor Tissue 50


title: Liver Tumor Tissue 47


title: Liver Tumor Tissue 58


title: Liver Tumor Tissue 46


title: Liver Tumor Tissue 48


title: Liver Tumor Tissue 39


title: Liver Tumor Tissue 56


title: Liver Tumor Tissue 42


title: Liver Tumor Tissue 63


title: Liver Tumor Tissue 52


title: Liver Tumor Tissue 53


title: Liver Tumor Tissue 36


title: Liver Tumor Tissue 41


title: Liver Tumor Tissue 35


title: Liver Tumor Tissue 32


title: Liver Tumor Tissue 34


title: Liver Tumor Tissue 21


title: Liver Tumor Tissue 29


title: Liver Tumor Tissue 19


title: Liver Tumor Tissue 22


title: Liver Tumor Tissue 33


title: Liver Tumor Tissue 23


title: Liver Tumor Tissue 25


title: Liver Tumor Tissue 30


title: Liver Tumor Tissue 28


title: Liver Tumor Tissue 26


title: Liver Tumor Tissue 14


title: Liver Tumor Tissue 27


title: Liver Tumor Tissue 20


title: Liver Tumor Tissue 31


title: Liver Tumor Tissue 18


title: Liver Tumor Tissue 16


title: Liver Tumor Tissue 24


title: Liver Tumor Tissue 17


title: Liver Tumor Tissue 15


title: Liver Tumor Tissue 13


title: Liver Tumor Tissue 9


title: Liver Tumor Tissue 11


title: Liver Tumor Tissue 10


title: Liver Tumor Tissue 12


title: Liver Tumor Tissue 61

hyb_protocol: Samples were hybridized to a GeneChip miRNA 2.0 Array (Affymetrix) at 48°C and 60 rpm for 16 hours, then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003).

scan_protocol: Standard  Affymetrix scanning protocol

data_processing: The data were analyzed with Affymetrix miRNA QC tool and normalized using default parameters, and batch corrected using Partek default, human probes were selected.

label_protocol: MiRNAs were labelled using the FlashTag™ Biotin RNA Labeling Kit.

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

value: Liver tumor


title: Liver Tumor Tissue 57


title: Liver Tumor Tissue 64


title: Liver Tumor Tissue 63


title: Liver Tumor Tissue 62


title: Liver Tumor Tissue 59


title: Liver Tumor Tissue 60


title: Liver Tumor Tissue 58


title: Liver Tumor Tissue 51


title: Liver Tumor Tissue 55


title: Liver Tumor Tissue 56


title: Liver Tumor Tissue 50


title: Liver Tumor Tissue 49


title: Liver Tumor Tissue 54


title: Liver Tumor Tissue 7


title: Liver Tumor Tissue 8


title: Liver Tumor Tissue 5


title: Liver Tumor Tissue 3


title: Liver Tumor Tissue 2


title: Liver Tumor Tissue 6


title: Liver Tumor Tissue 4


title: Liver Tumor Tissue 43


title: Liver Tumor Tissue 1


title: Liver Tumor Tissue 53


title: Liver Tumor Tissue 45


title: Liver Tumor Tissue 52


title: Liver Tumor Tissue 46


title: Liver Tumor Tissue 48


title: Liver Tumor Tissue 41


title: Liver Tumor Tissue 47


title: Liver Tumor Tissue 38


title: Liver Tumor Tissue 40


title: Liver Tumor Tissue 37


title: Liver Tumor Tissue 44


title: Liver Tumor Tissue 35


title: Liver Tumor Tissue 31


title: Liver Tumor Tissue 32


title: Liver Tumor Tissue 34


title: Liver Tumor Tissue 30


title: Liver Tumor Tissue 29


title: Liver Tumor Tissue 33


title: Liver Tumor Tissue 26


title: Liver Tumor Tissue 27


title: Liver Tumor Tissue 25


title: Liver Tumor Tissue 28


title: Liver Tumor Tissue 24


title: Liver Tumor Tissue 22


title: Liver Tumor Tissue 39


title: Liver Tumor Tissue 23


title: Liver Tumor Tissue 36


title: Liver Tumor Tissue 21


title: Liver Tumor Tissue 16


title: Liver Tumor Tissue 18


title: Liver Tumor Tissue 19


title: Liver Tumor Tissue 17


title: Liver Tumor Tissue 10


title: Liver Tumor Tissue 11


title: Liver Tumor Tissue 13


title: Liver Tumor Tissue 12


title: Liver Tumor Tissue 7


title: Liver Tumor Tissue 5


title: Liver Tumor Tissue 9


title: Liver Tumor Tissue 8


title: Liver Tumor Tissue 4


title: Liver Tumor Tissue 3


title: Liver Tumor Tissue 6


title: Liver Tumor Tissue 2


title: Liver Tumor Tissue 1


title: Liver Tumor Tissue 15


title: Liver Tumor Tissue 20


title: Liver Tumor Tissue 14


title: Macrophages infected with virulent strain_8h_rep3

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

description: miRNA profile expression of macrophages infected with Leptospira spp, at 8h.

hyb_protocol: Hybridization of samples to the strips was carried out at 48ºC for 20h in a GeneAtlas™ Hybridization Oven, according to the instructions of the GeneAtlas® Hybridization,  Wash, and Stain Kit for miRNA Array Strips.

scan_protocol: Following hybridization, wash and stain of strips were performed using the GeneAtlas® Hybridization, Wash, and Stain Kit for miRNA Array Strips in the GeneAtlas Robotic Wash Station. Following, strips were and scanned using the GeneAtlas® Imaging System (Affymetrix).

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm.

source_name: J774A.1 macrophages in vitro, infected with L. interrogans serovar Copenhageni

label_protocol: MicroRNA profiles were obtained from 250 ng/sample of total RNA (RIN 10) using the FlashTag™ Biotin HSR RNA Labeling Kit, and the Affymetrix® miRNA 4.1 Array strip (Affymetrix, Santa Clara, Califórnia, EUA), according to the manufacturer’s instructions. A recommended ELOSA quality control assay was run for all samples.

growth_protocol: Murine macrophage cell line J774A.1, provided by the Paul Ehrlich cell bank, Rio de Janeiro, Brazil, was maintained in RPMI-1640 media (Sigma®, USA) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, USA), 100ug/mL streptomycin (Sigma Chemical Co St.Louis, MO), 0.03% L-glutamine solution (Sigma) and 100 UI/mL of penicillin. Cells were incubated at 37º C, 5% CO2 until formation of a confluent monolayer in 6-well plates (3cm wells).

extract_protocol: Total RNA was extracted from macrophages with a miRVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.  RNA samples were immediately stored at -80ºC. Quantification was performed using NanoDrop (ND-2000 spectrophotometer, Thermo Scientific, Wilmington, DE, USA) and quality of samples was assessed using capillary electrophoresis (Bioanalyzer 2100 Agilent, Santa Clara, CA, USA).

treatment_protocol: Cultured cells were washed tree times with sterile phosphate buffer solution (pH 7,2) for removal of antibiotics and non-adherent cells. L. interrogans and L. biflexa were harvested by centrifugation and the pellet was resuspended in RPMI-1640 media (Sigma®, USA), and 100:1 bacteria:cell were added to macrophages at >90% confluency. Treatments, performed in triplicates, were carried as follows: infection of macrophages with a virulent strain (L. interrogans), infection with attenuated strain (L. interrogans), saprophyte strain (L. biflexa) and non-infected macrophages (controls). All treatments were incubated in fresh RPMI medium, without antibiotics, for 8h at 37º C, 5% C02. Following this period, RNA extraction was immediately performed as described below.

tag: cell line

value: J774A.1 murine macrophages

tag: leptospira strain

value: L. interrogans serovar Copenhageni (FIOCRUZ L1-130)


title: Macrophages infected with virulent strain_8h_rep2


title: Macrophages infected with virulent strain_8h_rep1


title: Macrophages infected with attenuated strain_8h_rep3

source_name: J774A.1 macrophages in vitro, infected with L. interrogans serovar Copenhageni M20

value: L. interrogans serovar Copenhageni M22


title: Macrophages infected with attenuated strain_8h_rep2

value: L. interrogans serovar Copenhageni M21


title: Macrophages infected with saprophyte strain_8h_rep1

source_name: J774A.1 macrophages in vitro, infected with L. biflexa serovar Patoc

value: L.biflexa serovar Patoc (FIOCRUZ -Patoc I)


title: Macrophages_non-infected_8h_rep3

description: miRNA profile expression of macrophages non-infected, at 8h

source_name: J774A.1 macrophages in vitro, non-infected


title: TAZI_miRNA_v2_DMSO_D5_NI

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

institute: CNRS

description: Gene expression

hyb_protocol: RNA were  hybridized overnight to the Affymetrix Genechip miRNA Array 2.0 (P/N 901753)

scan_protocol: The arrays were washed and stained using standard Affymetrix protocol FS450-003 and scanned using the Affymetrix GCS 3000 7G Scanner.

data_processing: All miRNA arrays were normalized using the Affymetrix Expression Console with dedicated annotation files downloaded from the Affymetrix web server.

source_name: CD4+ and CD8+ T cells

label_protocol: Total RNA were labeled using FlashTag™ Biotin HSR RNA Labeling Kit (P/N 901911)

growth_protocol: PBMCs, CD4+ and CD8+ T cells were grown at 37°C and 5% CO2 to a density of 1.5×106 cells/ml in RPMI GlutaMAX medium (Life Technologies) supplemented with 10% fetal calf serum (FCS) (Thermo Fisher), 40 U/ml of IL2 (PeproTech) and 5 µg/mL of PHA (Roche) for 2 days

extract_protocol: Cells were resuspended at 1.5×106 cells/ml in RPMI+  supplemented with 40 U/ml IL2 and separated into two parts (infected and uninfected cells)

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll (Axis-Shield PoC AS) gradient centrifugation. CD4+ and CD8+ T cells were purified from PBMCs after Ficoll gradient centrifugation by Human CD4+ beads positive selection and CD8+ beads positive selection, respectively (Miltenyi )

tag: group

value: Not Infected

value: peripheral blood

tag: treatment

value: DMSO

value: adult


title: TAZI_miRNA_v2_DMSO_D5_I

description: Gene expression

value: Infected


title: Macrophages infected with saprophyte strain_8h_rep2


title: Macrophages_non-infected_8h_rep1


title: Macrophages infected with saprophyte strain_8h_rep3


title: Macrophages infected with attenuated strain_8h_rep1

value: L. interrogans serovar Copenhageni M20


title: TAZI_miRNA_v2_DMSO_D6_NI

description: Gene expression


title: TAZI_miRNA_v2_DMSO_D6_I

description: Gene expression


title: TAZI_miRNA_v2_464_D1_NI

description: Gene expression


title: TAZI_miRNA_v2_464_D2_NI

description: Gene expression


title: TAZI_miRNA_v2_464_D6_I

description: Gene expression


title: TAZI_miRNA_v2_DMSO_D1_I

description: Gene expression


title: Macrophages_non-infected_8h_rep2


title: TAZI_miRNA_v2_DMSO_D1_NI

description: Gene expression


title: TAZI_miRNA_v2_464_D5_NI

description: Gene expression


title: TAZI_miRNA_v2_DMSO_D2_NI

description: Gene expression


title: TAZI_miRNA_v2_464_D6_NI

description: Gene expression


title: KCa3.1 silenced Huh7 cells, rep3

city: Hangzhou

first: Yehui

last: Du

state: Zhejiang

address: 79# Qinchun Road

institute: Zhejiang University

description:
KCa3.1 silenced 3
Gene expression data.

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip PrimeView human.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: hepatocellular carcinoma cell line Huh7

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured under an atmosphere containing 5% CO2 at 37°C. Medium was exchanged one day before extraction.

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

treatment_protocol: After washed under the ice, cells were collected for further total RNA extraction.

value: hepatocellular carcinoma cell line

tag: genotype/variation

value: KCa3.1 knockdown

tag: growth phase

value: logarithmic


title: TAZI_miRNA_v2_DMSO_D3_NI

description: Gene expression

tag: tissue


title: TAZI_miRNA_v2_DMSO_D3_I

description: Gene expression


title: KCa3.1 silenced Huh7 cells, rep2

description:
KCa3.1 silenced 2
Gene expression data.


title: TAZI_miRNA_v2_DMSO_D2_I

description: Gene expression


title: TAZI_miRNA_v2_464_D3_NI

description: Gene expression


title: TAZI_miRNA_v2_464_D5_I

description: Gene expression


title: KCa3.1 silenced Huh7 cells, rep1

description:
KCa3.1 silenced 1
Gene expression data.


title: TAZI_miRNA_v2_464_D3_I

description: Gene expression


title: control Huh7 cells, rep3

description:
control 3
Gene expression data.

value: control


title: ESC_HCN4GFPH7

city: Baltimore

first: Chulan

last: Kwon

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

data_processing:
For analysis, raw sequencing reads were trimmed using Trimmomatic(0.36) with a minimum quality threshold of 35 and minimum length of 36 (Bolger, Lohse et al. 2014). Processed reads were mapped to the mm10 reference genome using HISAT2 (2.0.4) (Kim, Langmead et al. 2015). Counts were then assembled using Subread featureCounts (1.5.2) in a custom bash script (Liao, Smyth et al. 2014). Differential gene expression analysis was done using the DESeq2 package in R. Gene ontology analysis was performed using the PANTHER Version 12.0 classification.
Trimming
Trimmomatic 0.36
ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:38 TRAILING:35 SLIDINGWINDOW:4:20 MINLEN:36
Alignment
HISAT2 2.0.4
-q -x
Read summarization
featureCounts 1.5.2
-t exon -g gene_id
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: mESC-derived

growth_protocol: mESCs were maintained on gelatin-coated dishes in maintenance medium (Glasgow minimum essential medium supplemented with 10% fetal bovine serum and 3 μM Chir99021 and 1 μM PD98059 or 1000 U/ml ESGRO (Millipore, Billerica, MA), Glutamax, sodium pyruvate, MEM non-essential amino acids (Thermo Fisher Scientific). For spheroid formation and differentiation, mouse ESCs were plated in IMDM/Ham’s F12 (Cellgro) (3:1) supplemented with N2, B27, penicillin/streptomycin, 2 mM GlutaMAX, 0.05% BSA, 5 ng/ml L-ascorbic acid (Sigma-Aldrich) and α-monothioglycerol (MTG; Sigma-Aldrich) at a final density of 100,000 cells/ml to allow spheroid formation. After 48h spheroids were collected and transferred to ultra-low attachment plastic surface and induced for 40 hours with Activin A, Bmp4, Wnt3A, Wnt5A, Wnt11 (R&D Systems) alone or in combination. Human iPSCs were maintained in Geltrex-coated T25 flasks using Essential 8 medium. For spheroid formation and differentiation, hiPSCs were plated in RPMI plus B27 minus insulin with Bmp4 and CHIR99021 and incubated for 48h. After 48h media was changed to RPMI plus B27 minus insulin

extract_protocol:
Mouse embryos (E7.75¬) were dissected using forceps under a stereomicroscope (Zeiss) and regions of interest were dissociated and harvested using TrypLE. Embryoid bodies (EBs) and cells were dissociated and harvested using TrypLE. Single-cells were analyzed for RFP/GFP expression or sorted using a SH800 Cell sorter (Sony Biotechnologies). GFP+ and RFP+ cells were isolated using a SH800 cell sorter (Sony Biotechnologies) into 96 plates containing water (2.4 mL) with RNase-free DNase I (0.2 mL; NEB) and RNase inhibitor (0.25 mL; NEB). Each sample represents 10 cells. DNase I was inactivated by increasing the temperature (72 C for 3 min), and samples were then stored on ice.
Custom-designed 2A oligo 1-mL primer (12 mM, Integrated DNA Technologies was added and annealed to the polyadenylated RNA by undergoing a temperature increase (72 C for 2 min) and being quenched on ice. A mixture of 1 mL of SMARTscribe reverse transcriptase (Clontech Laboratories), 1 mL of custom-designed TS oligo (12 mM, Integrated DNA Technologies , 0.3 mL of MgCl2 (200 mM, Sigma), 0.5 mL of RNase inhibitor (Neb), 1 mL of dNTP (10 mM each, Thermo), and 0.25 mL DTT (100 mM, Invitrogen) were incubated at 42 C for 90 min, which was followed by enzyme inactivation at 70 C for 10 min. A mixture of 29 mL of water, 5 mL of Advantage2 taq polymerase buffer, 2 mL of dNTP (10 mM each, Thermo), 2 mL of custom-designed PCR primer (12 mM, Integrated DNA Technologies, and 2 mL of Advantage2 taq polymerase was directly added to the reverse transcription product, and the amplification was performed for 19 cycles. The amplification product was purified using Ampure XP beads (Beckman-Coulter). Libraries and transposome assembly were made using a previously published protocol. Briefly, 100 pg of total cDNA was added to a 2x tagment DNA Buffer (TD) (2x TAPS buffer: 20 mM TAPS-NaOH, 10 mM MgCl2 (pH 8.5) at 25 C, and 16% weight volume (w/v) PEG 8000), and then spiked with 0.5 mL of 1:64 diluted Tn5 (Epicenter) and incubated for 8 min at 55 C. Tn5 was stripped off from the tagmented DNA by adding 0.2% SDS for a final concentration of 0.05%. Libraries were enriched used KAPAHiFi, which included 5X Kappa Fidelity Buffer, 10 mM dNTPs, and HIFI polymerase, and 1 uL of index primers was used directly in the enrichment PCR amplification of libraries for the Illumina sequencers for a 50-mL reaction. The PCR program was as follows: 5 min at 72 C and 1 min at 95 C, and then 16 cycles at 30s at 95 C, 30s at 55 C, 30s at 72, and 5 min at 72.

tag: source

value: in vitro

tag: marker


title: ESC_HCN4GFPH9


title: ESC_HCN4GFPH8


title: ESC_HCN4GFPG7


title: ESC_HCN4GFPF9


title: ESC_HCN4GFPG10


title: ESC_HCN4GFPF7


title: AAV_5

city: wuhan

first: Gang

last: Cao

state: hubei

address: Lion Rock One

description:
single cell RNA-Seq( The number represent different group of neuron in different circuit )
single_cell_expression.xls

data_processing:
All the raw sequencing data from different samples were taken for quality check by FastQC and the samples with high-quality reads were collected for downstream analysis.
Library construction adapters in reads were trimmed by Trimmomatic and the clean reads were aligned to the mouse genome GRCm38(mm10) with HISAT2.
The expression level of all genes were counted and normalized to FPKM (Fragments Per Kilobase of transcript per Million) by StringTie
Differential gene expression analysis for RNA-Seq data were performed using edgeR R pakage and KEGG enrichment analysis were performed using clusterProfiler package . And for single cell RNA-Seq ,We designed a differential analysis step.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Brain neuron

growth_protocol: For the tissue mRNA-seq C57BL/6 mice of 8 weeks were injected with 200 nL RV-ΔG-EGFP or rAAV2-retro-YFP and housed for 2 weeks. For the single cell RNA sequenece of neuron labeled by virus 4 weeks Ai9 reporter mice were used for RV-ΔG-EGFP injections, and 3 weeks mice were used for rAAV2-retro-cre-tagBFP injection.

extract_protocol:
Total RNA of the dissected tissue was extracted using TRIzol  Reagent.
The RNA-seq library was constructed in accordance with the manufacturer's protocol using the VAHTSTM Stranded mRNA-seq Library Preparation Kit for Illumina® . For single-cell RNA-seq library construction, cDNA was generated in accordance with the Smart-seq2 method
mRNA-seq and scRNA-seq

treatment_protocol: For the tissue mRNA-seq mice were anesthetized using isoflurane, immediately following which the brains were dissected and sectioned to a thickness of 300 μm in ice-cold ACSF, tissue were micro-dissected under a fluorescence microscope.For the single cell RNA-seq the Fluorescence-labeled neuron were isolated using the papain-based dissociation protocol.

tag: age

value: 5 weeks

tag: injected virus

tag: injection site

value: Different nuclei of mouse brain including hypothalamus, thalamus, hippocampus and amygdala

tag: sequeneced tissue name

value: rAAV-retro-YFP retrograde labeled neurons in different nuclei


title: AAV_6

tag: strain


title: AAV_7


title: AAV_30


title: TAZI_miRNA_v2_464_D2_I

description: Gene expression


title: control Huh7 cells, rep1

description:
control 1
Gene expression data.

tag: cell type


title: ESC_HCN4GFPG8


title: AAV_8


title: AAV_4


title: AAV_29


title: TAZI_miRNA_v2_464_D1_I

description: Gene expression


title: ESC_HCN4GFPG9


title: AAV_9


title: ESC_HCN4GFPF11


title: AAV_28


title: ESC_HCN4GFPF8


title: control Huh7 cells, rep2

description:
control 2
Gene expression data.


title: AAV_2


title: AAV_27


title: AAV_3


title: ESC_HCN4GFPF10


title: ESC_HCN4GFPH10


title: AAV_26


title: AAV_24


title: ESC_HCN4GFPE9


title: AAV_25


title: AAV_23


title: AAV_20


title: AAV_22


title: AAV_21


title: ESC_HCN4GFPD9


title: ESC_HCN4GFPE10


title: ESC_HCN4GFPD8


title: ESC_HCN4GFPE11


title: AAV_17


title: ESC_HCN4GFPD7


title: ESC_HCN4GFPD10


title: ESC_HCN4GFPE7


title: ESC_HCN4GFPC9


title: AAV_19


title: AAV_14


title: ESC_HCN4GFPD11


title: ESC_HCN4GFPC8


title: Liver Tumor Tissue 42

value: Liver tumor


title: AAV_13


title: ESC_HCN4GFPC7


title: ESC_HCN4GFPC11


title: ESC_HCN4GFPE8


title: AAV_18


title: AAV_12


title: AAV_1


title: ESC_HCN4GFPC10


title: AAV_16


title: AAV_11


title: RV_9

value: the recombinant glycoprotein (G)-deleted rabies virus（rRV-deltaG-GFP）

value: RV-deltaG-EGFP retrograde labeled neurons in different nuclei


title: ESC_HCN4GFPB8


title: AAV_10


title: ESC_HCN4GFPB7


title: ESC_HCN4GFPB11


title: RV_7


title: RV_8


title: RV_5


title: ESC_HCN4GFPA9


title: ESC_HCN4GFPA8


title: ESC_HCN4GFPA7


title: ESC_HCN4GFPB10


title: RV_6


title: ESC_Tbx1RFPH6


title: ESC_HCN4GFPA10


title: ESC_HCN4GFPA11


title: RV_4


title: ESC_Tbx1RFPH4


title: RV_3


title: ESC_Tbx1RFPH5


title: ESC_Tbx1RFPH3


title: ESC_HCN4GFPB9


title: AF (Post fever remission ) [3998405173_J]

city: Kolkata

first: Bijurica

last: Chakraborty

state: West  Bengal

address: 35, Ballygunge Circular Road

department: Biochemistry

country: India

institute: University of Calcutta

description: Post fever remission

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using Illumina iscan system

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: patient PBMC_Post fever remission

label_protocol: Biotinylated cRNA were prepared with Illumina Totalprep cRNA amplification kit.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: subject

value: malaria infected human host

tag: pathogen strain

value: Post fever remission

value: PBMC


title: AF (Post fever remission) [3998405173_K]

description: Post fever remission


title: ESC_Tbx1RFPH2


title: ESC_Tbx1RFPH1


title: RV_32


title: ESC_Tbx1RFPG6


title: AF (Post fever remission )  [3998405173_I]

description: Post fever remission


title: RV_31


title: RV_30


title: ESC_Tbx1RFPG2


title: ESC_Tbx1RFPG3


title: ESC_Tbx1RFPG4


title: RV_2


title: PF 13 (P. falciparum infection) [3998405173_H]

description: Falciparum malaria infection

source_name: patient PBMC_P. falciparum

value: P. falciparum


title: RV_29


title: ESC_Tbx1RFPG1


title: ESC_Tbx1RFPF5


title: AF (Post fever remission ) [3998405173_L]

description: Post fever remission


title: PF 112 (P. falciparum infection) [3998405173_E]

description: Falciparum malaria infection


title: PV 05 (P. vivax infection) [3998405173_G]

description: Vivax malaria infection

source_name: patient PBMC_P. vivax

value: P. vivax


title: PF 03 (P. falciparum infection) [3998405173_C]

description: Falciparum malaria infection


title: ESC_Tbx1RFPF4


title: ESC_Tbx1RFPF3


title: ESC_Tbx1RFPG5


title: PF 11 (P. falciparum infection) [3998405173_D]

description: Falciparum malaria infection


title: PV 03 (P. vivax infection) [3998405173_F]

description: Vivax malaria infection


title: RV_28


title: RV_27


title: ESC_Tbx1RFPF6


title: RV_24


title: RV_26


title: PV 08 (P. vivax infection) [3998405173_B]

description: Vivax malaria infection


title: ESC_Tbx1RFPE6


title: ESC_Tbx1RFPF2


title: ESC_Tbx1RFPF1


title: ESC_Tbx1RFPE5


title: PV 06 (P. vivax infection) [3998405173_A]

description: Vivax malaria infection


title: RV_19


title: RV_1


title: ESC_Tbx1RFPD3


title: RV_20


title: ESC_Tbx1RFPD6


title: RV_23


title: ESC_Tbx1RFPC3


title: ESC_Tbx1RFPE3


title: RV_21


title: ESC_Tbx1RFPD1


title: ESC_Tbx1RFPC5


title: ESC_Tbx1RFPD5


title: ESC_Tbx1RFPD4


title: ESC_Tbx1RFPE1


title: ESC_Tbx1RFPC6


title: ESC_Tbx1RFPE2


title: ESC_Tbx1RFPE4


title: PF 18 (P. falciparum infection) [3998386021_H]

description: Falciparum malaria infection


title: PV 04 (P. vivax infection) [3998386021_L]

description: Vivax malaria infection


title: PF 20 (P. falciparum infection) [3998386021_J]

description: Falciparum malaria infection


title: PF 19 (P. falciparum infection) [3998386021_I]

description: Falciparum malaria infection


title: PF 28 (P. falciparum infection) [3998386021_G]

description: Falciparum malaria infection


title: PF 13 (P. falciparum infection) [3998386021_F]

description: Falciparum malaria infection (replicate)


title: PV 01 (P. vivax infection) [3998386021_K]

description: Vivax malaria infection


title: ESC_Tbx1RFPC2


title: ESC_Tbx1RFPC1


title: PF 12 (P. falciparum infection) [3998386021_E]

description: Falciparum malaria infection


title: ESC_Tbx1RFPB5


title: ESC_Tbx1RFPB6


title: RV_14


title: RV_17


title: RV_18


title: RV_15


title: ESC_Tbx1RFPB3


title: RV_16


title: ESC_Tbx1RFPA5


title: RV_13


title: ESC_Tbx1RFPB1


title: ESC_Tbx1RFPB2


title: ESC_Tbx1RFPA4


title: ESC_Tbx1RFPA3


title: ESC_Tbx1RFPA1


title: ESC_Tbx1RFPB4


title: RV_12


title: ESC_Tbx1RFPA2


title: PF 10 (P. falciparum infection) [3998386021_D]

description: Falciparum malaria infection


title: E8_5_Tbx1G12

source_name: mouse embryonic heart

value: in vivo


title: ESC_Tbx1RFPA6


title: PF 05 (P. falciparum infection) [3998386021_A]

description: Falciparum malaria infection


title: PF 09 (P. falciparum infection) [3998386021_C]

description: Falciparum malaria infection


title: PF 08 (P. falciparum infection) [3998386021_B]

description: Falciparum malaria infection


title: Embryo at early neurula, injected with 9.2nL water, biological replicate 3

city: Notre Dame

first: Paul

last: Huber

state: IN

address: University of Notre Dame

institute: University of Notre Dame

description:
EN_ddH2O.03
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 9.2nL water.

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation, per manufacturer's recommendations (http://www.affymetrix.com/support/technical/byproduct.affx?product=X_laevis_2).

scan_protocol: The hybridized probe array is scanned by the GeneChipTM Scanner 3000.

data_processing: The Affymetrix data files were processed using Bioconductor software package (http://www.bioconductor.org/). The mean fluorescence intensity was derived from a log2 transformation of the normalized data.

organism: Xenopus laevis

source_name: Xenopus embryos 16.5 hours post fertilization, injected with 9.2nL water

label_protocol: Total RNA (50-500 ng) was used for cDNA synthesis according to the GeneChip 3’ IVT Express Kit for Affymetrix microarray chips. The cDNA was then converted to double-stranded DNA and used as a template for transcription of amplified RNA (aRNA) which was labeled with a biotin-conjugated nucleotide. aRNA samples (15 ug) were subsequently purified and fragmented to produce probes for hybridization onto Xenopus laevis 2.0 GeneChip 3’expression arrays.

growth_protocol: Female X. laevis were injected with 500 units of human chorionic gonadotropin (HCG) at least 12 hours prior to spawning. Testes were isolated and stored at 4oC in high salt MBS (0.7 mM CaCl2, 108 mM NaCl, 1 mM KCl, 1 mM MgSO4, 5 mM HEPES, pH 7.8, 2.5 mM NaHCO3 ) for up to a week. Minced testis and eggs were mixed together with 3 mL 1/3 MMR (0.1 M NaCl, 2.0 mM KCl, 1 mM MgSO4, 2 mM CaCl2, 5 mM HEPES, pH7.8) and left to fertilize at room temperature. After 10 minutes, eggs were flooded with additional 1/3 MMR and after an additional 30 minutes eggs were washed with 2% cysteine (< 5 minutes) in order to remove the jelly coating, upon which eggs were washed 8 times with 1/3 MMR.

extract_protocol: Twenty embryos from each time point were homogenized in 500 uL proteinase K buffer (100 mM Tris pH 8, 150 mM NaCl, 12.5 mM EDTA pH 8.0, 1% SDS, 200 ug proteinase K) and incubated at 37oC for one hour. Samples were then extracted twice with an equal volume of phenol, pH 4.5, and twice with 24:1 chloroform:isoamylalcohol. RNA was purified using an RNeasy spin column (Qiagen, #74104) and precipitated with 2.5 volumes of ice-cold ethanol.

treatment_protocol: Embryos were injected in the animal hemisphere (volumes ranged between 5 to 30 nl) and allowed to develop at room temperature in 1/3 MMR.

value: Whole embryo

tag: developmental stage

value: Early neurula

value: 16.5 hours post fertilization

value: water


title: RV_10


title: RV_11


title: E8_5_Tbx1H11


title: rAAV2_LHA_L2

description:
RNA-Seq (L2: the injected group)
RNAseq_expression.xls

source_name: Brain tissue

value: 10 weeks

value: lateral hypothalamic area (LHA)

value: medial prefrontal cortex (mPFC)


title: Embryo at early neurula, injected with 9.2nL water, biological replicate 2

description:
EN_ddH2O.02
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 9.2nL water.


title: WS_MSC_QUE_rep2

first: Zunpeng

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description:
WS-MSC under quercetin treatment.
mRNA

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human reference genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.tsv: Tab-separated file includes HTseq reads count.

source_name: Werner syndrome mesenchymal stem cells

growth_protocol: Human MSCs were cultured in MSC culture medium containing 90% alpha-MEM with Glutmax (Gibco), 10% fetal bovine serum (FBS, Gemcell, Lot A77E01F), 1 ng/mL FGF2 (Joint Protein Central) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Cells were harvested in TRIzol reagent (Invitrogen) and RNA was extracted according to the manufacturers’ instruction.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: WS-MSCs were treated with vehicle DMSO (Ctrl) and quercetin (100 nM) from passage 5 to passage 7.

value: ES-mesenchymal stem cells

value: WRN Knockout

tag: passage

tag: condition

value: Quercetin


title: Con2_mPFC_L1

description:
RNA-Seq (L1: the control group)
RNAseq_expression.xls

value: control (no injected)


title: rAAV1_LHA_L2


title: Embryo at early neurula, injected with 9.2nL water, biological replicate 1

description:
EN_ddH2O.01
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 9.2nL water.

tag: treatment


title: WS_MSC_QUE_rep1

description:
WS-MSC under quercetin treatment.
mRNA

tag: genotype/variation


title: E8_5_HCN4A12


title: E8_5_Tbx1G11


title: E8_5_HCN4D12


title: E8_5_HCN4C12


title: E8_5_HCN4B12


title: Con1_mPFC_L1


title: E8_5_Tbx1F12


title: Con2_NAC_L1

value: accumbens (NAC)


title: WS_MSC_CTRL_rep2

description:
WS-MSC under basal condition.
mRNA

value: Basal


title: E8_5_HCN4E12


title: WS_MSC_CTRL_rep1

description:
WS-MSC under basal condition.
mRNA


title: Con1_NAC_L2


title: SH-SY5Y-shKIT day 30

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: The data were normalised using quantile normalisation in R (package preprocessCore).

source_name: SH-SY5Y cell line

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturer's protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

growth_protocol: Human neuroblastoma cells SH-SY5Y and SN-N-AS were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS) 100 units/ml penicillin, 100ug/ml streptomycin and 1 mM sodium pyruvate at 370C and 5% CO2.

extract_protocol: Attached cells were treated with trypsin and collected by centrifugation. Cell pellets (approximately 10^6 cells per sample) were resuspended with  500 ul of  TRI Reagent (MRC). RNA extraction was performed using Direct-zol™ RNA MiniPrep (Zymo Research) kit. RNA was quantified with Nanodrop (Thermo Fisher Scientific).

treatment_protocol: Lentiviral stocks were initially titrated on HEK293T to evaluate titer. For that HEK293T cells were seeded in 24-well plate, 3*104 cells per well in 0.5 ml final volume. On the next day different volumes of lentiviral stocks (1-10 μl) were to the cells and cells were centrifuged for 1 hour at 1000 g. 72 hours after transduction rates were measured by LSRFortessa flow cytometer. Cells positive for fluorescent protein mCherry (LeGO shRNA lentiviral vectors) and for mClover (pLentiCMV Puro DEST ERKKTRClover) were determined as transduced. Titer (lentiviral particles per ml of supernatant) was calculated for each lentiviral stock using volumes of stock where transduction was still linear (10-30%). For transduction of neuroblastoma cells the same amount of each shRNA lentiviral vector was used. To determine working amounts of lentiviral particles we performed titration on SH-SY5Y and SK-N-AS cells in the same manner as for HEK293T cells. The amount of shRNA lentiviral particles per cell that resulted in at least 90% transduction was used for further experiments (Supplementary figure 2a). 72 hours after transduction 1 μg/ml puromycin (Sigma) was added. After one week the selection was confirmed on epifluorescence microscope. Transduction rates were verified for each time point used in the experiments.

tag: cell line

tag: transduction with lentivirus harbouring shrna sequences

value: anti-KIT shRNA

tag: days after transduction


title: SH-SY5Y-shSCR day 30

value: non-specific control SCR shRNA


title: Con1_LHA_L1


title: RV1_NAC_L2

value: the recombinant glycoprotein (G)-deleted rabies virus（rRV-∆G）


title: SH-SY5Y-shKIT day 6


title: RV2_NAC_L2


title: Embryo at early neurula, injected with 0.5ng Gam1 mRNA, biological replicate 3

description:
EN_Gam1.03
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

source_name: Xenopus embryos 16.5 hours post fertilization, injected with 0.5ng Gam1 mRNA

tag: tissue

value: Gam1 mRNA


title: SK-N-AS-shKIT day 6

source_name: SN-N-AS cell line

value: SN-N-AS


title: RV2_LHA_L2

tag: age


title: SH-SY5Y-shSCR day 6


title: SH-SY5Y-shKIT day 3


title: Embryo at early neurula, injected with 0.5ng Gam1 mRNA, biological replicate 2

description:
EN_Gam1.02
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

value: Whole embryo

value: Early neurula


title: SK-N-AS-shSCR day 6


title: Con2_LHA_L1

tag: injected virus


title: Embryo at late gastrula, injected with 9.2nL water, biological replicate 1

description:
LG_ddH2O.01
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 9.2nL water.

source_name: Xenopus embryos 13.5 hours post fertilization, injected with 9.2nL water

value: Late gastrula

value: 13.5 hours post fertilization

value: water


title: Embryo at early neurula, injected with 0.5ng Gam1 mRNA, biological replicate 1

description:
EN_Gam1.01
Gene expression data from Xenopus laevis embryos at the early neurula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

value: 16.5 hours post fertilization


title: rAAV1_mPFC_L2

value: 10 weeks

tag: injection site

value: lateral hypothalamic area (LHA)

value: medial prefrontal cortex (mPFC)


title: A549_CPP_AGO1_SCRAMBLE_48hr_rep1

city: Bangkok

first: Piyapat

last: Pin-on

address: ChalongKrung

country: Thailand

institute: KMITL

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: All microarray experiment were classified as down-regulated (Dn), neutral (Nu), or up-regulated (Up) genes using our software, namely CU-DREAM.

source_name: Epithelial cell, A549, CPP-AGO1-SCRAMBLE, 48hr, replicate 1

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: A549 cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Scientific) with 2mM L-glutamine (Sigma-Aldrich), 10% (v/v) heat-inactivated fetal bovine serum (Thermo Scientific), 10 mg/ml antibiotic/antimycotic (Thermo Scientific), at 37oC and 5% (v/v) CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA). Purity and integrity were evaluated by the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: The purified CPP-AGOs were conjugated to U21. Briefly, desired amount 600 ng of each CPP-AGOs protein were mixed with 200 nM of each PolyUs in conjugation buffer [1.5 mM MgCl2, 5% glycerol, 50 mM KCl and 20 mM Tris HCl pH 7.0] and incubated at 37 oC water-bath for 30 minutes. The conjugated complexes of CPP-AGOs-PolyUs and scramble were added to 500 µl DMEM cultured of A549 cell lines. 7.5x104 cells in 24 well-plate to let the complexes penetrate into cells. After transfection for 2 days, cells were collected to observe  gene expression changes.

tag: transfection

value: scramble

tag: gender

value: male


title: rAAV2_mPFC_L2

tag: strain

tag: sequeneced tissue name


title: SH-SY5Y-shSCR day 3


title: Embryo at late gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 3

description:
LG_Gam1.03
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.

source_name: Xenopus embryos 13.5 hours post fertilization, injected with 0.5ng Gam1 mRNA


title: A549_CPP_AGO1_U21_48hr_rep3

source_name: Epithelial cell, A549, CPP-AGO1-U21, 48hr, replicate 3


title: SK-N-AS-shSCR day 3


title: A549_CPP_AGO1_U21_48hr_rep2

source_name: Epithelial cell, A549, CPP-AGO1-U21, 48hr, replicate 2


title: RV1_LHA_L2


title: Embryo at early gastrula, injected with 9.2nL water, biological replicate 3

description:
EG_ddH2O.03
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 9.2nL water.

source_name: Xenopus embryos 9 hours post fertilization, injected with 9.2nL water

value: Early gastrula

value: 9 hours post fertilization


title: Embryo at late gastrula, injected with 9.2nL water, biological replicate 3

description:
LG_ddH2O.03
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 9.2nL water.


title: Embryo at early gastrula, injected with 9.2nL water, biological replicate 2

description:
EG_ddH2O.02
Gene expression data from Xenopus laevis embryos at the early gastrula developmental stage which were injected at one cell with 9.2nL water.


title: Embryo at late gastrula, injected with 0.5ng Gam1 mRNA, biological replicate 2

description:
LG_Gam1.02
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 0.5ng Gam1 mRNA.


title: A549_CPP_AGO1_U21_48hr_rep1

source_name: Epithelial cell, A549, CPP-AGO1-U21, 48hr, replicate 1


title: SK-N-AS-shKIT day 3

value: anti-KIT shRNA


title: Embryo at late gastrula, injected with 9.2nL water, biological replicate 2

description:
LG_ddH2O.02
Gene expression data from Xenopus laevis embryos at the late gastrula developmental stage which were injected at one cell with 9.2nL water.


title: A549_CPP_AGO1_SCRAMBLE_48hr_rep3

source_name: Epithelial cell, A549, CPP-AGO1-SCRAMBLE, 48hr, replicate 3