title: 169RS30

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2day at ZT4 by snap-freezing in liquid nitrogen.

tag: genotype

tag: temperature

tag: replicate

value: collected after 2day at ZT4


title: E10.0_Body_EC5

status: Public on Mar 24 2020

type: SRA

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

country: China

institute: Fifth Medical Center of Chinese PLA General Hospital

library_source: transcriptomic

data_processing:
Read 1 is biological.
Read 2 is technical.  The barcode is the first eight bases from the beginning and UMI is the next 8 bases (i.e., barcode is 1-8 bp and UMI is 9-16 bp in read 2 of length 150 bp.).
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryonic cells

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

tag: tissue

value: Body

tag: cell type

value: embryonic cells

tag: development stage


title: 10_IN_stress

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

country: USA

institute: University of California, Los Angeles

description:
10_S25_L00*
2017-9106

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: logCPM values

molecule: total RNA

extract_protocol:
Input and IP samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using Illumina TruSeq RNA sample prep kit following manufacturer's protocol.  After library preparation, amplified double-stranded cDNA was fragmented into 125 bp (Covaris-S2, Woburn, MA) DNA fragments, which were (200 ng) end-repaired to generate blunt ends with 5’- phosphates and 3’- hydroxyls and adapters ligated.

treatment_protocol: Tamoxifen was injected i.p. at 2 months to induce the expression of Ribotag in astrocytes. After 1 month, mice were stressed by putting them in un bucket with water for 20 minutes. Mice rested for 90 minutes in their homecage before RNA extraction. Control mice stayed in their home cage all the time.

tag: strain background

tag: genotype/variation

tag: age

value: 3 m

tag: treatment

value: Stress

value: somatosensory cortex

tag: molecule subtype

value: cleared lysate as the input and control


title: 12_IN_stress

description:
12_S27_L00*
2017-9106


title: Cg_GABA_(NH4)2SO4_vs_GABA_K2SO4_2

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: For precultivation of C. glutamicum, brain heart infusion (BHI) medium (Becton Dickinson and Company, New Jersey, USA) with 90 g L-1 sorbitol were used. The cells of these precultures were harvested by centrifugation (5,000×g, 4°C, 10 min), and washed twice by PBS buffer (pH 7.0). The main cultures were inoculated to an OD of 1 in CGXII minimal medium with GABA and K2SO4 or (NH4)2SO4. At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

treatment_protocol: see growth protocol

tag: agent


title: Cg_GABA_(NH4)2SO4_vs_GABA_K2SO4_3


title: blast cells, bone marrow, 5412

type: genomic

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

hyb_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

data_processing:
To calculate the copy number of altered regions, the data were normalized to baseline reference intensities using NA 32.3 FFPE v.2 reference model (Affymetrix). The hidden Markov model available within the software package was used to determine the copy number states (CN) and their breakpoints. Thresholds of log 2 ratio ≥0.58 and ≤1 were used to categorize altered regions as CN variation (CNV) gains (amplifications) and copy number losses (deletions), respectively. To prevent the detection of false-positive CNVs arising due to microarray unspecific signals, only regions that involved at least 50 consecutive probes were considered in the analysis of gains or losses in this study. Amplificationsand deletions were analyzed separately. To exclude aberrations representing common normal CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). To identify the genes involved in the CNVs further, the UCSC database ( http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org) were used.
Gene annotation and gene overlap were determined using the human genome build 19 and NetAffx (http://www.affymetrix.com).The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukemia-associated region/gene-specific CNAs (leukemia genes_all_20150505; Fullerton Overlap Map_hg19).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blast cells, bone marrow

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

extract_protocol: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

value: blast cells

tag: gender

value: M


title: 11_IP_control

description:
11_S26_L00*
2017-9106

value: Control

tag: ip antibody

value: Anti-HA.11 Epitope Tag Antibody (Biolegend #901514)

value: astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag


title: blast cells, bone marrow, z370_401

scan_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

treatment_protocol: After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

value: F


title: 9_IN_stress

description:
9_S24_L00*
2017-9106


title: 169RS28

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

data_processing:
genome build:  Bd21-v3.1
Adapters were trimmed off using Trimmomatic with "ILLUMINACLIP:$FA_ADAPTER:2:10:5:1"
The trimmed reads were aligned using Tophat with "--max-multihits --library-type fr-firststrand --no-mixed"
Duplicate reads were removed with Picard using default setting
Alignments in SAM file were assembled into transcripts abundances using htseq-count with "-r name -s no -f bam -t exon -i gene_id" against the GTF annotation"
Supplementary_files_format_and_content: _htseq_count.ct.txt: TSV table containing htseq-counted transcript abundances.

organism: Brachypodium distachyon

source_name: fully expanded leaves

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT20 by snap-freezing in liquid nitrogen.

extract_protocol:
Qiagen RNeasy Mini Kit (74104) was used to extract RNA. RNA quality and integrity were assessed on the Agilent 2200 TapeStation system.
Library preparation was performed with 1µg total RNA using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420L). The libraries were sequenced on a NextSeq500 (Illumina) running a final pooled library. Each pool contained 24 to 30 samples and was sequenced using NextSeq® 500/550 High Output Kit v2 (150 cycles) TG-160-2002 on a NextSeq500 (Illumina).

tag: cultivar

value: fully expanded leaves

tag: photoperiod

value: LD (20 h light/4 h dark)

value: single

tag: time

value: collected after 4 weeks at ZT20


title: 169RS27

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT12 by snap-freezing in liquid nitrogen.

tag: genotype

tag: temperature

value: collected after 4 weeks at ZT12


title: 8_IP_control

description:
8_S23_L00*
2017-9106

value: 3 m

tag: tissue


title: blast cells, bone marrow, Y00439

label_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software,  and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

tag: cell type


title: 169RS29

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 0 day at ZT4 by snap-freezing in liquid nitrogen.

tag: replicate

value: collected after 0 day at ZT4


title: 169RS26

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT4


title: 6_IP_stress

description:
6_S21_L00*
2017-9106

tag: strain background

value: Stress

value: somatosensory cortex


title: RaviLabHam.16: Slc12a2-deficient Phagocytes + Apoptotic Cells

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: GCF_000223135.1_CriGri_1.0_genomic
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

organism: Cricetulus griseus

growth_protocol: alpha-MEM + 10% FBS + 1% PSQ

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

treatment_protocol: Jurkat lymphoma cells were UV C treated at 1500mJ then cultured for 4h prior to co-culture with phagocytes

value: in vitro cultured fibroblast

value: Actively engulfing (i.e. CypHer5E+) phagocytes were FACS sorted. Apoptotic Cells from human (Jurkat Lymphoma)

tag: genotype/variation


title: RaviLabHam.12: Slc12a2-deficient Phagocytes + Apoptotic Cells


title: blast cells, bone marrow, YPK

value: acute lymphoblastic leukemia

value: bone marrow

value: blast cells

tag: age

value: M


title: 7_IN_control

description:
7_S22_L00*
2017-9106

tag: treatment

value: Control

value: cleared lysate as the input and control


title: Cg_GABA_(NH4)2SO4_vs_GABA_K2SO4_1


title: blast cells, bone marrow, 1564


title: RaviLabHam.11: Slc12a2-deficient Phagocytes + Apoptotic Cells


title: 169RS24

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at ZT20 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after NA at ZT20


title: RaviLabHam.15: Slc12a2-deficient Phagocytes + Apoptotic Cells


title: 4_IP_stress

description:
4_S19_L00*
2017-9106

value: Anti-HA.11 Epitope Tag Antibody (Biolegend #901514)

tag: molecule subtype

value: astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag


title: RaviLabHam.14: WT Phagocytes + Apoptotic Cells

source_name: WT Phagocytes + Apoptotic Cells

value: Slc12a2-sufficient (aka Wild-Type)


title: blast cells, bone marrow, 194

value: F


title: 5_IP_stress

description:
5_S20_L00*
2017-9106

value: 3 m

value: Stress


title: RaviLabHam.13: WT Phagocytes + Apoptotic Cells

value: in vitro cultured fibroblast


title: 3_IN_control

description:
3_S18_L00*
2017-9106

value: somatosensory cortex


title: blast cells, bone marrow, YWG

value: acute lymphoblastic leukemia


title: 2_IP_control

description:
2_S17_L00*
2017-9106


title: 169RS23

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at ZT12 by snap-freezing in liquid nitrogen.

value: single

value: collected after NA at ZT12


title: 169RS22

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at ZT4 by snap-freezing in liquid nitrogen.

value: collected after NA at ZT4


title: blast cells, bone marrow, 1475

value: bone marrow

value: blast cells

value: M


title: RaviLabHam.10: WT Phagocytes + Apoptotic Cells

value: Actively engulfing (i.e. CypHer5E+) phagocytes were FACS sorted. Apoptotic Cells from human (Jurkat Lymphoma)


title: 169RS25

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 4 weeks at ZT0


title: blast cells, bone marrow, 659


title: 169RS20

value: collected after 4 weeks at ZT20


title: Del11/CC END-seq

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

description: The file deleted nt.txt contains the deleted nucleotides for each BRCA1 allele used in this study.

library_source: genomic

data_processing:
Library strategy: END-seq
mouse reads were aligned to the GRCm38p2/mm10 .Alignment is done using bowtie version 1.1.2, with the parameters: -l 50 -n 3 -k 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made for plus (*.pos.bw) and minus (*.neg.bw) strand separately using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: MEFs

growth_protocol: Cells are grown in DMEM containing 10% FBS and 1% P/S

extract_protocol:
MEFs were harvested and 9 million cells were embedded in agarose plugs, after which END-seq was performed as previously described (Canela et al., 2016).
Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads). Libraries were prepared and sequenced following standard Illumina protocols

treatment_protocol: Exponentially AsiSI-expressing MEFs were treated with 1uM doxocyclin (DOX) for 24 hours and then, for 4 hours with 4-OHT, resulting in the nuclear translocation of AsiSI

value: MEF

tag: strain

value: Mixed background


title: blast cells, bone marrow, 8514

tag: disease state

value: F


title: blast cells, bone marrow, 1476

tag: gender


title: blast cells, bone marrow, Y7W


title: blast cells, bone marrow, z225_401


title: 1_IN_stress

description:
1_S16_L00*
2017-9106

value: 3 m

value: Stress

value: cleared lysate as the input and control


title: blast cells, bone marrow, 1138

value: acute lymphoblastic leukemia


title: RaviLabHam.09: WT Phagocytes + Apoptotic Cells

value: in vitro cultured fibroblast

value: Slc12a2-sufficient (aka Wild-Type)


title: blast cells, bone marrow, 929

value: bone marrow


title: blast cells, bone marrow, Y00_724

value: blast cells


title: ACD4-12162016: Phagocytes + Apoptotic Cells + Cytochalasin D

value: Apoptotic Cells from human (Jurkat Lymphoma)


title: 169RS19

value: single

value: collected after 4 weeks at ZT12


title: blast cells, bone marrow, Y02359


title: ACD1-12162016: Phagocytes + Apoptotic Cells + Cytochalasin D


title: ACD3-12162016: Phagocytes + Apoptotic Cells + Cytochalasin D


title: 169RS18

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 4 weeks at ZT4


title: blast cells, bone marrow, 1725

value: M


title: blast cells, bone marrow, Y00_615


title: 150RS7

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT20


title: AC4-12162016: Phagocytes + Apoptotic Cells

source_name: Phagocytes + Apoptotic Cells


title: blast cells, bone marrow, 1025


title: blast cells, bone marrow, 1117


title: CC END-seq

institute: Center for Excellence in Molecular Cell Science

value: MEF

value: Mixed background

value: CC


title: ACD2-12162016: Phagocytes + Apoptotic Cells + Cytochalasin D


title: 169RS17

value: collected after 4 weeks at ZT0


title: blast cells, bone marrow, 865

value: acute lymphoblastic leukemia

value: F


title: 169RS21

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at ZT0 by snap-freezing in liquid nitrogen.

value: collected after NA at ZT0


title: AC2-12162016: Phagocytes + Apoptotic Cells

value: in vitro cultured fibroblast


title: oef-1(vr25) RNA-seq rep 1

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: RNA-seq was performed on dissected oef-1(vr25) mutant gonads

data_processing:
ChIP-seq:  The raw paired-end ChIP and corresponding input sequencing fastq reads were mapped to ce10 genome by mapping with Bowtie2 (v2.3.2) with default parameters.
ChIP-seq: Wig files were generated by a custom script (https://github.com/guifengwei/glib/blob/master/bam2wig.py),
ChIP-seq:  Peaks were called by MACS2 (v2.1.1)  with the key parameter (-q 0.001 --nomodel --extsize 150).
RNA-seq: The raw paired-end RNA-seq fastq reads were first mapped to rRNA build by bowtie2 (v2.1.0)
RNA-seq:  The remaining unmapped reads were further aligned to ce10 genome by HISAT2 (v2.0.4) with the mode suppressing the unpaired reads
RNA-seq:  The gene annotation was downloaded from UCSC Genome Browser, filtered to remove transcripts <50 nt, then was employed to estimate gene expression and call differential gene expression by Cuffdiff program [20] (v2.2.1) under the default parameters between VC2010 and glp-1(q224) strains.
Genome_build: ce10
Supplementary_files_format_and_content: BigWig files were generated as an output

organism: Caenorhabditis elegans

source_name: Dissected adult gonads

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on NGM plates seeded with OP50, and grown until young adulthood at 20˚C.

extract_protocol:
TRIzol pellets were thawed and flash-frozen three times. Chloroform was added, and then samples were shaken and spun at 4 degrees. Aqeuous layers were precipiated overnight with isopropanol and DNase-treated the next day and cleaned up using the RNeasy Mini Kit.
Ribozero library preparation

treatment_protocol: Young adult worms were dissected to release gonads and cut at the spermatheca in M9 with levamisole and Tween 20. Dissected gonads were transferred and flash frozen in TRIzol.

tag: Stage

value: Young adult

value: Dissected gonads

tag: antibody


title: WT END-seq

value: WT


title: 150RS8

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT22 by snap-freezing in liquid nitrogen.

tag: cultivar

tag: photoperiod

value: single

value: collected after 2 weeks at ZT22


title: blast cells, bone marrow, Y00303

value: bone marrow

value: blast cells


title: oef-1(vr25) RNA-seq rep 3

tag: genotype


title: N2 RNA-seq rep 3

description: RNA-seq was performed on dissected wild-type gonads

value: wild-type


title: N2 RNA-seq rep 2


title: blast cells, bone marrow, Y00_475

value: M


title: Del11 END-seq

value: MEF


title: 150RS3

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

tag: temperature

tag: time

value: collected after 2 weeks at ZT4


title: oef-1(vr25) RNA-seq rep 2

tag: tissue


title: AC3-12162016: Phagocytes + Apoptotic Cells

tag: cell type

value: Apoptotic Cells from human (Jurkat Lymphoma)


title: N2 RNA-seq rep 1


title: 150RS6

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT16 by snap-freezing in liquid nitrogen.

tag: replicate

value: collected after 2 weeks at ZT16


title: blast cells, bone marrow, E00206

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

value: acute lymphoblastic leukemia


title: ChIP-seq glp-4; oef-1 input rep 2

description: A fraction of the input total chromatin that was used for H3K27me3 or H3K36me3 ChIP on glp-4(bn2); oef-1(vr25)

source_name: Staged young adults from glp-4(bn2); oef-1(vr25) strain

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on peptone-enriched NGM plates seeded with OP50. For wild-type and oef-1(vr25) strains, L1s were grown until young adult at 20˚C. For glp-4 and glp-4; oef-1 strains, L1s were grown until young adulthood at 25˚C. Worms were harvested and washed free of bacteria in M9.

extract_protocol:
Isolated germ cell nuclei were sonicated in a Misonix S-4000 water bath sonicator, and immunoprecipated overnight using 5 µg of anti-H3K27me3 or anti-H3K36me3 antibody.
ChIP-seq library preparation for enriched DNA and the genomic DNA input control for two biological replicates per genotype was performed as described in (Zhong et al. 2010). Libraries were multiplexed as described in Lefrancois et al. (2009) in order to sequence four samples in a single flow cell using the Illumina Genome Analyzer II platform.

treatment_protocol: For all ChIP-seq samples, worms were crosslinked in 2% formaldehyde in M9 buffer for 28 minutes rotating at room temperature. Crosslinking was quenched with 1 M Tris pH 7.5, followed by two washes with M9. Germ cell nuclei were isolated by dounce homogenization and filtering as in Han et al (2019).

value: Whole animal


title: CD2-12162016: Phagocytes + Cytochalasin D

source_name: Phagocytes + Cytochalasin D

value: in vitro cultured fibroblast


title: blast cells, bone marrow, 6066


title: 149RS9

data_processing:
genome build:  Bd21-v3.1
NOTE: This sample was processed using spiper with https://github.com/shouldsee/pipeline-rnaseq-hisat2-stringtie/tarball/0.0.2
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15".
Raw reads were aligned with Hisat2 with arguments "--no-mixed --rna-strandness RF --dta --fr" to produce a SAM file.
Duplicate reads were removed with Picard using default setting
Alignments in SAM file were assembled into transcripts abundances with stringtie with argument "--rf".
Supplementary_files_format_and_content: .stringtie.count.txt: TSV table containing abundance of transcripts with bed-formatted coordinates.
Supplementary_files_format_and_content: _bam.bw:  Raw coverage bigwig files
Supplementary_files_format_and_content: .cpm.bw:  CPM(Count-per-million) normalised bigwig files

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in NA with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at NA by snap-freezing in liquid nitrogen.

value: apices

value: collected after NA at NA


title: CD1-12162016: Phagocytes + Cytochalasin D


title: AC1-12162016: Phagocytes + Apoptotic Cells


title: 149RS8

value: single


title: blast cells, bone marrow, 541


title: blast cells, bone marrow, 159


title: 150RS4

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT8 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT8


title: ChIP-seq glp-4(bn2) input rep 1

description: A fraction of the input total chromatin that was used for H3K27me3 or H3K36me3 ChIP on glp-4(bn2)

source_name: Staged young adults from glp-4(bn2) strain

value: Young adult


title: CT-3-12162016: Phagocytes alone

source_name: Phagocytes alone


title: 150RS5

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT12


title: CD4-12162016: Phagocytes + Cytochalasin D

growth_protocol: alpha-MEM + 10% FBS + 1% PSQ


title: 149RS7

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in NA with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at ZT9 by snap-freezing in liquid nitrogen.

value: collected after NA at ZT9


title: blast cells, bone marrow, 6079

value: bone marrow

value: blast cells

value: M


title: 150RS2

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT1 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: LD (20 h light/4 h dark)

value: collected after 2 weeks at ZT1


title: ChIP-seq glp-4; oef-1 H3K36me3 rep 2

description: ChIP was performed with anti-H3K36me3 on glp-4(bn2); oef-1(vr25) adults


title: CD3-12162016: Phagocytes + Cytochalasin D

value: Apoptotic Cells from human (Jurkat Lymphoma)


title: ChIP-seq glp-4; oef-1 input rep 1


title: blast cells, bone marrow, 1553

value: acute lymphoblastic leukemia


title: 149RS5


title: ChIP-seq glp-4(bn2) input rep 2

value: Whole animal


title: ChIP-seq glp-4; oef-1 H3K27me3 rep 2

description: ChIP was performed with anti-H3K27me3 on glp-4(bn2); oef-1(vr25) adults


title: blast cells, bone marrow, Y01701

value: F


title: CT-4-12162016: Phagocytes alone

value: in vitro cultured fibroblast


title: blast cells, bone marrow, 6768


title: blast cells, bone marrow, YQW


title: CT-2-12162016: Phagocytes alone


title: ChIP-seq glp-4; oef-1 H3K36me3 rep 1


title: CT-1-12162016: Phagocytes alone


title: 149RS30

value: phyC

value: collected after 2 weeks at ZT20


title: 149RS4

value: single


title: N20-0002_2020009167040

first: Aaron

last: Burberry

state: Massachusetts

address: 7 Divinity Avenue SF 258

department: HSCRB

institute: Harvard University

description:
16S rDNA
N20-0002 Processed

data_processing:
Library strategy: 16S rDNA-sequencing
Following the sequencing run, the sequence data was separated based on the nucleotide bar code and then compared to the Greengenes database (http://greengenes.lbl.gov)
Relative abundance, alpha diversity, beta diversity and principal coordinate analysis was performed using QIIME analysis software
Genome_build: One Codex Targeted Loci Database (https://app.onecodex.com/references)
Supplementary_files_format_and_content: relative abundances

organism: feces metagenome

source_name: Mouse feces

extract_protocol:
DNA was isolated by Powersoil (QIAGEN, Germantown, MD) per the manufacturer’s protocol and recovery yield and DNA quality was determined by fluorometric analysis.
DNA concentration was standardized and amplified using 16s rRNA primers spanning the V3 and V4 regions (Illumina). Resulting amplified PCR products were analyzed on a Bioanalyzer (Agilent Technologies, Santa Clara, CA) then purified and amplified with primers containing unique sample nucleotide barcodes (Illumina). PCR products were analyzed with the Bioanalyzer for product quality control and also by SYBR green PCR to determine the quantity. All samples were pooled and standardized to a final concentration of 4.0 nM representation for each sample. The 16S PCR product pool was denatured with sodium hydroxide then adjusted to 4.0 pM and combined with 5% PhiX control DNA prior to loading onto a sequencing flow cell (Illumina) with 300 bp paired ends and a unique molecular tag for each sample.

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces

tag: batch id

tag: mouse id

tag: mouse sex


title: 149RS6

value: collected after NA at ZT9


title: blast cells, bone marrow, E01130

tag: disease state

value: bone marrow

tag: age


title: N20-0002_2020009167039

description:
16S rDNA
N20-0002 Processed


title: N20-0002_2020009167037

description:
16S rDNA
N20-0002 Processed


title: ChIP-seq glp-4(bn2) H3K36me3 rep 2

description: ChIP was performed with anti-H3K36me3 on glp-4(bn2) adults

tag: Stage

value: Young adult

tag: strain


title: N20-0002_2020009167038

description:
16S rDNA
N20-0002 Processed

value: M


title: 149RS3

tag: cultivar

value: fully expanded leaves


title: blast cells, bone marrow, 993

value: blast cells

tag: gender


title: 149RS28

tag: genotype

tag: photoperiod

value: LD (20 h light/4 h dark)

value: collected after 2 weeks at ZT12


title: ChIP-seq glp-4(bn2) H3K36me3 rep 1

tag: antibody


title: 149RS29

tag: tissue

tag: temperature

tag: time

value: collected after 2 weeks at ZT16


title: ChIP-seq glp-4(bn2) H3K27me3 rep 2

description: ChIP was performed with anti-H3K27me3 on glp-4(bn2) adults

value: Whole animal


title: N20-0002_2020009167036

description:
16S rDNA
N20-0002 Processed

tag: host organism


title: ChIP-seq glp-4(bn2) H3K27me3 rep 1


title: blast cells, bone marrow, 6745

value: acute lymphoblastic leukemia

tag: cell type

value: F


title: N20-0002_2020009167035

description:
16S rDNA
N20-0002 Processed

tag: bacterial metagenome source

tag: batch id


title: N20-0002_2020009167034

description:
16S rDNA
N20-0002 Processed

tag: mouse id

tag: mouse sex


title: ChIP-seq oef-1(vr25) input rep 2

description: A fraction of the input total chromatin that was used for H3K27me3 or H3K36me3 ChIP on oef-1(vr25)

source_name: Isolated germ nuclei from oef-1(vr25) mutant adults

value: Isolated germ nuclei


title: 149RS27

value: phyC

tag: replicate

value: collected after 2 weeks at ZT8


title: ChIP-seq oef-1(vr25) input rep 1

tag: Stage


title: ChIP-seq glp-4; oef-1 H3K27me3 rep 1

tag: strain


title: N20-0002_2020009167033

description:
16S rDNA
N20-0002 Processed

value: C9orf72 loss of function mouse


title: 149RS25

tag: cultivar

value: single

value: collected after 2 weeks at ZT1


title: N20-0002_2020009167032

description:
16S rDNA
N20-0002 Processed

value: feces


title: 149RS24

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT0


title: N20-0002_2020009167031

description:
16S rDNA
N20-0002 Processed

value: M


title: ChIP-seq wild-type input rep 1

description: A fraction of the input total chromatin that was used for H3K27me3 or H3K36me3 ChIP on wild type

source_name: Isolated germ nuclei from wild-type adults

value: Young adult

value: wild-type


title: ChIP-seq wild-type input rep 2


title: 150RS1

value: fully expanded leaves

value: LD (20 h light/4 h dark)


title: 149RS23

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT22 by snap-freezing in liquid nitrogen.

value: SD (12 h light/12 h dark)

value: collected after 2 weeks at ZT22


title: ChIP-seq oef-1(vr25) H3K36me3 rep 2

description: ChIP was performed with anti-H3K36me3 on oef-1(vr25) isolated germ nuclei


title: N20-0002_2020009167030

description:
16S rDNA
N20-0002 Processed

value: H->H FTx-12


title: 149RS22

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT20


title: ChIP-seq oef-1(vr25) H3K36me3 rep 1

value: Isolated germ nuclei


title: N20-0002_2020009167029

description:
16S rDNA
N20-0002 Processed

value: H->H FTx-11

value: F


title: blast cells, bone marrow, Y01972

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

value: blast cells

tag: age

tag: gender


title: 149RS21

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT16 by snap-freezing in liquid nitrogen.

tag: genotype

tag: photoperiod

value: single

value: collected after 2 weeks at ZT16


title: blast cells, bone marrow, Y01849

tag: tissue


title: blast cells, bone marrow, YED

value: M


title: ChIP-seq oef-1(vr25) H3K27me3 rep 2

description: ChIP was performed with anti-H3K27me3 on wild-type isolated germ nuclei

value: Young adult

tag: antibody


title: blast cells, bone marrow, Y5D


title: ChIP-seq oef-1(vr25) H3K27me3 rep 1


title: N20-0002_2020009167028

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

value: feces

value: H->H FTx-10


title: N20-0002_2020009167027

description:
16S rDNA
N20-0002 Processed

value: H->H FTx-9


title: ChIP-seq wild-type H3K36me3 rep 2

description: ChIP was performed with anti-H3K36me3 on wild-type isolated germ nuclei

value: wild-type


title: 149RS20

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: fully expanded leaves

value: SD (12 h light/12 h dark)

tag: temperature

tag: time

value: collected after 2 weeks at ZT12


title: 149RS19

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT8 by snap-freezing in liquid nitrogen.

value: collected after 2 weeks at ZT8


title: N20-0002_2020009167026

description:
16S rDNA
N20-0002 Processed

tag: bacterial metagenome source

tag: batch id

value: H->H FTx-8

value: F


title: control accumbens 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Each labeled RNA sample was hybridized onto Agilent 8X60K Human miRNA microarray V21 chip and incubated at 55 °C for 20 h.

scan_protocol: The chip was washed after hybridization and immediately scanned by Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies) software was used to analyze the scanned images.

data_processing: Data were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15.

source_name: control accumbens

label_protocol: Agilent Inc. 50 ng of total RNA from tissues were labeled with Cy3 by using “Agilent miRNA Labeling and Hybridisation Kit” following the protocol recommended by the manufacturers.

growth_protocol: The brains were removed in autopsy and tissue samples were immediately collected from the VTA and the NAc then were flash frozen in liquid nitrogen. Frozen tissues are kept individually in eppendorf tubes at -80°C until RNA extraction.

extract_protocol: NAc and VTA brain tissues were homogenized in 1 mL TRIzol reagent (Invitrogen, USA) per 50-100 mg of tissue. Total RNA was extracted per manufacturer’s instructions.

tag: individual

value: control

value: brain

tag: tissue region

value: nucleus accumbens (NAc)


title: MDMA accumbens 1

source_name: MDMA accumbens

value: MDMA user


title: N20-0002_2020009167025

description:
16S rDNA
N20-0002 Processed

tag: mouse id

value: H->H FTx-7

tag: mouse sex


title: ChIP-seq wild-type H3K36me3 rep 1

tag: Stage

value: Young adult

value: Isolated germ nuclei

tag: strain


title: 149RS18

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT4 by snap-freezing in liquid nitrogen.

tag: cultivar

tag: replicate

value: single

value: collected after 2 weeks at ZT4


title: control accumbens 1


title: blast cells, bone marrow, 1056

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender

value: M


title: MDMA ventral 2

source_name: MDMA ventral

tag: tissue

value: ventral tegmental area (VTA)


title: N20-0002_2020009167024

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

value: feces

value: B->H FTx-6


title: 149RS17

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT1 by snap-freezing in liquid nitrogen.

tag: genotype

value: fully expanded leaves

tag: photoperiod

value: SD (12 h light/12 h dark)

tag: temperature

tag: time

value: collected after 2 weeks at ZT1


title: ChIP-seq wild-type H3K27me3 rep 2

tag: antibody

value: wild-type


title: 149RS2

value: collected after NA at ZT9


title: N20-0002_2020009167023

description:
16S rDNA
N20-0002 Processed

tag: bacterial metagenome source

tag: batch id

tag: mouse id

value: B->H FTx-5

value: F


title: ChIP-seq wild-type H3K27me3 rep 1

tag: Stage

value: Young adult

value: Isolated germ nuclei

tag: strain


title: 149RS26

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT4 by snap-freezing in liquid nitrogen.

value: phyC

tag: cultivar

value: LD (20 h light/4 h dark)

tag: replicate

value: single

value: collected after 2 weeks at ZT4


title: Replication_ASD_F_05

city: Davis

first: Charles

middle: E

last: Mordaunt

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

data_processing:
Filtered raw fastq files using Illumina quality flag
Followed CpG_Me workflow v1.0 which included the steps below.
Trimmed to remove adapters and 5' and 3' methylation bias with Trim Galore! v0.4.5
Aligned to hg38 reference genome with Bismark v0.19.1
Removed PCR duplicates with Bismark v0.19.1
Extracted CpG methylation counts at all covered sites to generate genome-wide cytosine methylation reports with Bismark v0.19.1
Genome_build: hg38
Supplementary_files_format_and_content: Bismark genome-wide cytosine methylation report for each sample with columns for chromosome, CpG position, strand, methylated count, unmethylated count, dinucleotide context, and trinucleotide context

source_name: umbilical cord blood

extract_protocol:
DNA was extracted from whole umbilical cord blood using the Gentra Puregene Blood Kit (Qiagen).
DNA was bisulfite converted with the EZ DNA Methylation Lightning kit (Zymo). WGBS libraries were prepared from 100ng of bisulfite-converted DNA using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.

tag: sample set

value: Replication

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex

tag: study

value: MARBLES


title: blast cells, bone marrow, 6982

source_name: blast cells, bone marrow

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

tag: disease state

value: acute lymphoblastic leukemia

tag: tissue

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: 149RS16

source_name: fully expanded leaves

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 2 weeks at ZT0 by snap-freezing in liquid nitrogen.

tag: genotype

value: fully expanded leaves

tag: photoperiod

value: SD (12 h light/12 h dark)

tag: temperature

tag: time

value: collected after 2 weeks at ZT0


title: MDMA ventral 1

tag: individual

value: MDMA user

value: brain

tag: tissue region

value: ventral tegmental area (VTA)


title: blast cells, bone marrow, YSS

value: M


title: N20-0002_2020009167022

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces

tag: batch id

tag: mouse id

value: B->H FTx-4

tag: mouse sex

value: F


title: control ventral 2

source_name: control ventral

value: control


title: 149RS13

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in NA with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after NA at NA by snap-freezing in liquid nitrogen.

value: Doro

tag: cultivar

tag: replicate

value: single

value: collected after NA at NA


title: N20-0002_2020009167021

description:
16S rDNA
N20-0002 Processed

value: B->H FTx-3


title: Replication_ASD_F_04

tag: sample set

value: Replication

tag: tissue

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex

tag: study

value: MARBLES


title: MDMA accumbens 2

value: MDMA user

value: nucleus accumbens (NAc)


title: blast cells, bone marrow, 1545

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: wt 5h rep2

city: Austin

first: Lydia

middle: M

last: Contreras

address: 200 E. Dean Keeton St Stop C0400

department: McKetta Department of Chemical Engineering

institute: University of Texas at Austin

data_processing:
Illumina NextSeq 500 Real-Time Analysis (RTA v2) basecalling
Adapter sequences and low-quality ends (phred quality < 30) were trimmed from the raw fastq files with cutadapt (v1.3) and reads shorter than 22 nt were discarded.
FastQC was used to verify good read quality for the trimmed files.
Reads were aligned to the Z. mobilis ZM4 reference genome (taxonomy ID 264203) with BWA-mem (v0.7.12-r1039).
Aligned reads were filtered for quality (MAPQ ≥ 10) and sorted by chromosomal coordinates using SAMtools (v0.1.19-44428cd).
The number of reads aligned to each gene was calculated using HTSeq (intersection-nonempty mode for overlaps).
Genome_build: NC_006526.2
Supplementary_files_format_and_content: tab-delimited text file of normalized reads for each gene by sample

organism: Zymomonas mobilis

source_name: Bacterium_wt 5h

growth_protocol: Strains were grown in 500 mL of RMG at 33C to an OD600 of 0.4 and then plasmid expression of sRNA was induced with anhydrotetracycline. Cells were collected at OD600 of 0.4 and OD600 of 0.5 for RNA extractions representing before and after induction, respectively.

extract_protocol:
Cell pellets resuspended in 1 mL TRIzol reagent (Invitrogen) and transferred to screw cap tubes containing glass beads (Sigma) and incubated at 25°C for 5 min. Cells were lysed using a mini-beadbeater (BIOSPEC), with 100 s pulses three times. Cells were kept on ice for 10 min between each 100 s treatment. The beads and cellular debris were centrifuged at 4°C for 2 min. The supernatant was transferred to a clean siliconized 2 mL tube. After addition of 300 µL of chloroform:isoamyl alcohol mix (v/v 24:1), the samples were inverted for 15 s, and then incubated at 25°C for 3 min. Then, tubes were centrifuged at 13,000 rpm for 10 min and the aqueous top phase transferred to a clean siliconized 1.5 mL tube.  Following this step, 270 µL of isopropanol and 270 µL of a mixture of 0.8 M sodium citrate and 1.2 M sodium chloride was added. The samples were mixed well, and then incubated on ice for 10 min. The RNA was pelleted by centrifugation at 13,000 rpm for 15 min. The pellet was washed with 1 mL 95% cold ethanol and centrifuged for 5 min. The pelleted RNA was allowed to air-dry for 5 min, and was resuspended in 50 µL RNase-free water (Ambion). RNA was digested with DNase I (RNase-free, ThermoScientific) for 1 h at 37°C to prevent genomic DNA contamination. DNase I was heat-inactivated by adding 0.5 mM EDTA to the reaction mixture and incubating at 75°C for 10 min. Then, RNA was incubated with isopropanol and GlycoBlue™ (ThermoScientific) at -20°C overnight. After centrifugation, pelleted RNA was washed with 95% cold ethanol and centrifuged. RNA was resuspended in 50 µL RNase-free water (Ambion) and stored at -80°C before sequencing.
NEBNext® Multiplex RNA Library Prep Set for Illumina® (New England Biolabs Inc.) was used for generating RNA libraries.

tag: strain

tag: plasmid

tag: growth phase

value: after sRNA induction (OD600=0.5)


title: Replication_ASD_F_03


title: control ventral 1

tag: individual

value: brain

tag: tissue region

value: ventral tegmental area (VTA)


title: N20-0002_2020009167020

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces

tag: batch id

tag: mouse id

value: B->H FTx-2

tag: mouse sex

value: F


title: blast cells, bone marrow, z369_401

tag: tissue

value: M


title: Replication_ASD_F_02

tag: sample set

value: Replication

tag: diagnosis

tag: Sex


title: 149RS11

tag: genotype

value: apices

tag: cultivar

value: fully expanded leaves

tag: photoperiod

tag: temperature

tag: replicate

value: single

tag: time

value: collected after NA at NA


title: wt 5h rep1

tag: strain

tag: plasmid

tag: growth phase


title: blast cells, bone marrow, E01830

tag: disease state

tag: cell type

tag: age

tag: gender


title: N20-0002_2020009167019

description:
16S rDNA
N20-0002 Processed

tag: host organism

tag: bacterial metagenome source

tag: batch id

tag: mouse id

value: B->H FTx-1

tag: mouse sex


title: Replication_ASD_F_01

tag: sample set

tag: tissue

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex

tag: study

value: MARBLES


title: wt 4h rep2

source_name: Bacterium_wt 4h

tag: strain

value: before sRNA induction (OD600=0.4)


title: 149RS10

tag: genotype

tag: cultivar

tag: photoperiod

tag: temperature

tag: replicate

tag: time


title: 149RS1

value: Martin


title: wt 4h rep1

tag: plasmid

tag: growth phase


title: blast cells, bone marrow, 1074

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: 148RS8

tag: tissue

value: SD (12 h light/12 h dark)

value: collected after 2 weeks at ZT22


title: Replication_ASD_M_14

tag: sample set

tag: diagnosis

value: M


title: pZms6 5h rep2

source_name: Bacterium_pZms6 5h

value: after sRNA induction (OD600=0.5)


title: N20-0002_2020009167016

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces

tag: batch id

tag: mouse id

tag: mouse sex


title: N20-0002_2020009167017

description:
16S rDNA
N20-0002 Processed


title: 148RS7

tag: genotype

tag: cultivar

value: fully expanded leaves

tag: photoperiod

tag: temperature

value: single

value: collected after 2 weeks at ZT20


title: 148RS6

tag: replicate

tag: time

value: collected after 2 weeks at ZT16


title: pZms6 5h rep1

tag: strain

tag: plasmid

tag: growth phase


title: pZms6 4h rep2

source_name: Bacterium_pZms6 4h


title: Replication_ASD_M_12

value: Replication

tag: tissue

value: umbilical cord blood

value: ASD

tag: Sex

tag: study


title: N20-0002_2020009167014

description:
16S rDNA
N20-0002 Processed

tag: host organism


title: blast cells, bone marrow, 684

tag: disease state

tag: cell type

tag: age

tag: gender

value: F


title: pZms6 4h rep1

value: before sRNA induction (OD600=0.4)


title: 148RS5

tag: genotype

value: collected after 2 weeks at ZT12


title: N20-0002_2020009167015

description:
16S rDNA
N20-0002 Processed

tag: bacterial metagenome source

tag: batch id

tag: mouse id

tag: mouse sex


title: N20-0002_2020009167013

description:
16S rDNA
N20-0002 Processed


title: blast cells, bone marrow, 1100

value: acute lymphoblastic leukemia

value: bone marrow

value: blast cells


title: blast cells, bone marrow, 5190


title: blast cells, bone marrow, Y01486

value: M


title: Replication_ASD_M_11

tag: sample set

tag: diagnosis

value: MARBLES


title: 148RS4

tag: cultivar

tag: photoperiod

value: SD (12 h light/12 h dark)

tag: temperature

tag: replicate

tag: time

value: collected after 2 weeks at ZT8


title: N20-0002_2020009167018

description:
16S rDNA
N20-0002 Processed

tag: host organism

value: C9orf72 loss of function mouse

value: feces


title: Replication_ASD_M_10

tag: tissue

tag: Sex

tag: study


title: 149RS12

value: apices

value: fully expanded leaves

value: single

value: collected after NA at NA


title: blast cells, bone marrow, Y00_719

tag: disease state

tag: cell type

tag: age

tag: gender


title: N20-0002_2020009167012

description:
16S rDNA
N20-0002 Processed

tag: bacterial metagenome source

tag: batch id

tag: mouse id


title: pZms4 5h rep2

source_name: Bacterium_pZms4 5h

tag: strain

tag: plasmid

tag: growth phase

value: after sRNA induction (OD600=0.5)


title: pZms4 5h rep1


title: N20-0002_2020009167011

description:
16S rDNA
N20-0002 Processed

tag: mouse sex


title: 148RS2

tag: genotype

tag: cultivar

tag: photoperiod

tag: temperature

tag: replicate

value: collected after 2 weeks at ZT1


title: pZms4 4h rep2

source_name: Bacterium_pZms4 4h

value: before sRNA induction (OD600=0.4)


title: 148RS1

tag: tissue

tag: time

value: collected after 2 weeks at ZT0


title: Replication_ASD_M_07

tag: sample set

value: Replication

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex

tag: study


title: B19-0033_2019044582020

description:
16S rDNA
B19-0033 Processed

tag: host organism

tag: bacterial metagenome source

tag: batch id

value: M


title: blast cells, bone marrow, Y02167

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: B19-0033_2019044582019

description:
16S rDNA
B19-0033 Processed

value: C9orf72 loss of function mouse

tag: mouse id

tag: mouse sex


title: 144RS21

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT16 by snap-freezing in liquid nitrogen.

tag: genotype

tag: cultivar

tag: photoperiod

value: SD (12 h light/12 h dark)

tag: temperature

value: collected after 3 weeks at ZT16


title: blast cells, bone marrow, E00621

tag: tissue


title: Replication_ASD_M_09

tag: sample set

tag: diagnosis

value: MARBLES


title: MS2 rep3

data_processing:
Illumina NextSeq 500 Real-Time Analysis (RTA v2) basecalling
Adapter sequences and low-quality ends (phred quality < 30) were trimmed from the raw fastq files with cutadapt (v1.3) and reads shorter than 22 nt were discarded.
FastQC was used to verify good read quality for the trimmed files.
Reads were aligned to the Z. mobilis ZM4 reference genome (taxonomy ID 264203) with BWA-mem (v0.7.12-r1039).
Aligned reads were filtered for quality (MAPQ ≥ 10) and sorted by chromosomal coordinates using SAMtools (v0.1.19-44428cd).
The number of reads aligned to each gene was calculated using HTSeq (intersection-nonempty mode for overlaps).
DESeq2 was used to normalize and identify differentially expressed transcripts between strains.
Genome_build: NC_006526.2
Supplementary_files_format_and_content: tab-delimited text file of normalized reads for each gene by sample

growth_protocol: Strains were grown in 100 mL of RMG to an OD600 of 1.0.

tag: strain

tag: plasmid

tag: growth phase

value: late exponential phase (OD600=1.0)


title: Replication_ASD_M_06

tag: Sex

tag: study


title: Replication_ASD_M_15


title: MS2 rep2


title: blast cells, bone marrow, 1478

tag: disease state

tag: cell type

value: F


title: Replication_ASD_M_08


title: MS2 rep1


title: Replication_ASD_M_05


title: B19-0033_2019044582018

description:
16S rDNA
B19-0033 Processed

tag: host organism

tag: bacterial metagenome source

value: feces

tag: batch id


title: B19-0033_2019044582017

description:
16S rDNA
B19-0033 Processed

tag: mouse id

tag: mouse sex


title: B19-0033_2019044582016

description:
16S rDNA
B19-0033 Processed


title: pZms4 4h rep1


title: 144RS19

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT8 by snap-freezing in liquid nitrogen.

tag: genotype

tag: cultivar

value: fully expanded leaves

tag: photoperiod

tag: replicate

value: single

tag: time

value: collected after 3 weeks at ZT8


title: 144RS18

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT4 by snap-freezing in liquid nitrogen.

tag: tissue

tag: temperature

value: collected after 3 weeks at ZT4


title: B19-0033_2019044582015

description:
16S rDNA
B19-0033 Processed


title: MS2-Zms6 rep3

tag: strain

tag: plasmid

tag: growth phase


title: 144RS20

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT12 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT12


title: 144RS17

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT0


title: MS2-Zms6 rep2


title: B19-0033_2019044582014

description:
16S rDNA
B19-0033 Processed

value: M


title: MS2-Zms6 rep1


title: B19-0033_2019044582013

description:
16S rDNA
B19-0033 Processed


title: Replication_ASD_M_01

tag: sample set

value: Replication

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex

tag: study


title: 144RS16

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in SD (12 h light/12 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 3 weeks at ZT20 by snap-freezing in liquid nitrogen.

value: collected after 3 weeks at ZT20


title: Replication_ASD_M_02


title: blast cells, bone marrow, Y02335

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: B19-0033_2019044582012

description:
16S rDNA
B19-0033 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

tag: batch id

tag: mouse id

tag: mouse sex


title: Replication_TD_F_01

tag: tissue

value: TD

value: F

value: MARBLES


title: 144RS15

tag: genotype

tag: cultivar

value: fully expanded leaves

tag: photoperiod

value: SD (12 h light/12 h dark)

tag: temperature

tag: replicate

value: single

tag: time

value: collected after 3 weeks at ZT16


title: Replication_ASD_M_04

tag: sample set

tag: diagnosis

tag: Sex

tag: study


title: Replication_TD_M_11


title: MS2-Zms4 rep3

tag: strain

tag: plasmid

tag: growth phase

value: late exponential phase (OD600=1.0)


title: Replication_ASD_M_03

value: M


title: B19-0033_2019044582011

description:
16S rDNA
B19-0033 Processed

tag: host organism

tag: bacterial metagenome source

value: feces

tag: batch id


title: 148RS3

tag: tissue

value: collected after 2 weeks at ZT4


title: B19-0033_2019044582010

description:
16S rDNA
B19-0033 Processed

tag: mouse id

value: Jackson Labs-10

tag: mouse sex


title: MS2-Zms4 rep1


title: 144RS14

tag: genotype

tag: cultivar

tag: photoperiod

value: collected after 3 weeks at ZT12


title: MS2-Zms4 rep2


title: 144RS13

tag: temperature

tag: replicate

tag: time

value: collected after 3 weeks at ZT8


title: Replication_ASD_M_13

tag: sample set

value: Replication

value: umbilical cord blood

tag: diagnosis

value: ASD

tag: Sex


title: blast cells, bone marrow, 907

tag: disease state

value: acute lymphoblastic leukemia

value: bone marrow

tag: cell type

value: blast cells

tag: age

tag: gender


title: Replication_TD_M_10

value: TD

tag: study

value: MARBLES


title: 144RS12

tag: tissue

value: fully expanded leaves

value: SD (12 h light/12 h dark)

value: single

value: collected after 3 weeks at ZT4


title: B19-0033_2019044582009

description:
16S rDNA
B19-0033 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces

tag: batch id

tag: mouse id

value: Jackson Labs-16

value: M


title: xrRNA2' ZIKV Rep3

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University Of Queensland

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) vHD 3.4.0.38 and Real Time Analysis (RTA) v2.7.7, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer.
Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data (fastq).
Quality control of row sequencing data was performed using FastQC software v.0.72.
Data was then trimmed to remove PCR primers, adapters and short reads using TRIMMOMATIC v.0.36.4.
Trimmed reads were mapped to mosquito Aedes aegypti genome v.5.1 using HISAT2 v.2.1.0 allowing 2 mismatches.
Feature count was performed using HTSEQ v.0.9.1 with counting mode set to “Union”, feature type was “exone” and ID attribute was GeneBank ID.
Genome_build: AaegL5.1
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

organism: Aedes aegypti

source_name: whole carcases

growth_protocol: Aedes aegypti mosquitos were obtained from a colony housed at Public Health Virology, Forensic and Scientific Services (FSS), Brisbane, Australia.  The colony was established from eggs collected from Innisfail in April 2017 and the F3 generation was used for the experiments.  All mosquito exposures were conducted in the Biological Safety Level (BSL) 3 insectary at Queenslan Forensic Scinces Services. Inoculated mosquitos were housed in 750 mL gauze-covered polypropylene containers and incubated at 28°C, high relative humidity and 12:12 h light:dark within an environmental cabinet. Mosquitos were provided with unrestricted access to 15% honey water.

extract_protocol:
Mosquitos (10 per sample) were homogenised in 1ml TRIreagent for 5min at 30Hz using Tissue Lyser II (Qiagen, USA), then total RNA was isolated according to the manufacturers instructions.
RNA samples from pooled 10 Aedes aegypti mosquitos infected with WT or xrRNA2’ mutant Zika MR766 or mock-infected were subjected to ribosomal RNA depletion using Ribo-Zero Gold rRNA Removal Kit (Illumina, USA) followed by library preparation using TruSeq 2 Library Preparation Kit (Illumine, USA). Three biological replicates (pools of mosquitos) were used in the experiment.

treatment_protocol: Four to five day old female mosquitos were anesthetised with CO2, then placed on a refrigerated table and injected intrathoracically with 200 nL of wild type ZIKV Uganda MR766, or xrRNA2’ mutant viruses respectively at 5x104 FFU/ml. Viral titres were determined by immunofluorescent plaque assay on Vero cells.

value: Adult mosquito

tag: treatment

value: infected with sfRNA2-deficient ZIKV


title: Replication_TD_M_09

value: Replication

value: umbilical cord blood


title: 144RS11

tag: genotype

tag: cultivar

tag: photoperiod

tag: temperature

value: collected after 3 weeks at ZT0


title: Replication_TD_M_08

tag: sample set

tag: diagnosis


title: Replication_TD_M_07

tag: Sex


title: xrRNA2' ZIKV Rep2


title: B19-0033_2019044582008

description:
16S rDNA
B19-0033 Processed

source_name: Mouse feces

value: Jackson Labs-15

tag: mouse sex


title: xrRNA2' ZIKV Rep1

tag: age


title: WT ZIKV Rep3

value: infected with WT ZIKV


title: Replication_TD_M_06

value: TD


title: 143RS5

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT0 by snap-freezing in liquid nitrogen.

value: LD (20 h light/4 h dark)

tag: replicate

tag: time

value: collected after 4 weeks at ZT0


title: B19-0033_2019044582005

description:
16S rDNA
B19-0033 Processed


title: Replication_TD_M_05

tag: tissue

tag: study

value: MARBLES


title: WT ZIKV Rep2


title: WT ZIKV Rep1


title: 143RS6

value: Bdphyc

value: fully expanded leaves

value: single


title: Replication_TD_M_03


title: B19-0033_2019044582004

description:
16S rDNA
B19-0033 Processed

tag: host organism

value: C9orf72 loss of function mouse

tag: bacterial metagenome source

value: feces


title: 143RS4

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT16 by snap-freezing in liquid nitrogen.

value: collected after 4 weeks at ZT16


title: Mock Rep3

value: Adult mosquito

value: uninfected


title: B19-0033_2019044582006

description:
16S rDNA
B19-0033 Processed

tag: batch id

tag: mouse id

value: Jackson Labs-1

value: M


title: 143RS3

tag: genotype


title: B19-0033_2019044582003

description:
16S rDNA
B19-0033 Processed


title: Replication_TD_M_04

value: Replication

value: umbilical cord blood


title: 143RS2

growth_protocol: Seeds were imbibed in distilled water at 4 ºC for two days before sowing. Plants were grown in 5 parts John Innes #2, 3 parts peat, 1 parts silver sand, 3 parts course vermiculite, Osmocote 2.7 g/L. All plants were grown in growth cabinets in LD (20 h light/4 h dark) with constant temperature 20ºC, 65 % humidity and 350 μmol m-2 s-1 PPFD (Photosynthetic Photon Flux Density). Samples were collected after 4 weeks at ZT8 by snap-freezing in liquid nitrogen.

tag: cultivar

value: collected after 4 weeks at ZT8


title: Replication_TD_M_02

value: TD


title: B19-0033_2019044582002

description:
16S rDNA
B19-0033 Processed


title: Mock Rep2

tag: treatment


title: Replication_TD_M_01


title: 143RS1

tag: photoperiod

value: LD (20 h light/4 h dark)

tag: temperature


title: Mock Rep1


title: 144RS10

value: SD (12 h light/12 h dark)

value: collected after 3 weeks at ZT20


title: B19-0033_2019044582001

description:
16S rDNA
B19-0033 Processed


title: Female WT 8 months_Hippocampus_14

status: Public on Mar 23 2020

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).

data_processing: The data were analyzed with R version 3.2.2 using RMA algorithm for preprocessing (affy_1.48.0) and Entrez based alternative CDF version 19.0.0 for probeset annotation

source_name: Hippocampus

label_protocol: All microarray-related steps for target preparation, including the amplification of total RNA and labeling, were carried out as described in the GeneChip® HT 3’ IVT PLUS Reagent Kit User Manual (Affymetrix 902417).

growth_protocol: Mice were provided with standard laboratory rodent food and tap water ad libitum, while every effort was made to minimize pain in animal use and disturbances in animal well-being.  All protocols have been carried out in accordance with guidelines of the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC), and of the European Communities Council Directive of 24 November 1986 (86/609/EEC) and were approved by Janssen Pharmaceutica Ethical Committee.

extract_protocol: Mouse brains were removed immediately following decapitation and dissected on dry ice. Tissue samples were obtained from the prefrontal cortex as well as the hippocampus from each mouse. After dissection all samples were stored at -80°C. Qiazol Lysis Reagent (Qiagen 79306) was added directly to each frozen brain tissue containing a Stainless steel bead with a diameter of 5 mm. Tissues were then disrupted and homogenized using the TissueLyser at maximum speed for 5 min. and chloroform was added. After phase separation by centrifugation and recovery of the aqueous phase, ethanol was added to provide appropriate binding conditions. The sample is then applied to the wells of the RNeasy 96 RNeasy plate and washed according to the RNeasy 96 Universal Tissue procedure.

value: brain

tag: background strain

tag: brain region

value: Hippocampus

tag: gender

value: Female

value: WT

value: 8 months


title: Female TG 8 months_Hippocampus_9

treatment_protocol: TG mice were produced with Thy1-APPKM670/671NL and Thy1-PS1L166P constructs coinjected into male pronuclei of C57BL6J oocytes.

value: TG

tag: age


title: Female TG 8 months_Hippocampus_12


title: Female WT 8 months_Hippocampus_3


title: Female WT 8 months_Hippocampus_2


title: Male TG 8 months_Hippocampus_46

value: Male


title: Female TG 8 months_Hippocampus_7


title: Female TG 8 months_Hippocampus_10


title: Female TG 8 months_Hippocampus_8


title: Male TG 8 months_Hippocampus_43


title: Male WT 8 months_Hippocampus_42


title: Male TG 8 months_Hippocampus_50


title: Female WT 8 months_Hippocampus_5


title: Female TG 8 months_Hippocampus_4


title: Female WT 8 months_Hippocampus_13


title: Female WT 8 months_Hippocampus_1


title: Male TG 8 months_Hippocampus_53


title: Male TG 8 months_Hippocampus_44


title: Female WT 8 months_Hippocampus_6


title: Male TG 8 months_Hippocampus_40


title: Male TG 8 months_Hippocampus_45


title: Male WT 8 months_Hippocampus_47


title: Female TG 8 months_Hippocampus_11


title: Male WT 8 months_Hippocampus_48


title: Male TG 8 months_Hippocampus_41


title: Male WT 8 months_Hippocampus_52


title: B19-0033_2019044582007

description:
16S rDNA
B19-0033 Processed

value: C9orf72 loss of function mouse

value: feces

value: Jackson Labs-9

tag: mouse sex


title: Male WT 8 months_Hippocampus_39


title: Male WT 8 months_Hippocampus_51


title: Male WT 8 months_Hippocampus_49


title: Female TG 8 months_Frontal Cortex_8

source_name: Frontal Cortex

value: Frontal Cortex


title: Female TG 8 months_Frontal Cortex_10


title: Female TG 8 months_Frontal Cortex_9


title: Female TG 8 months_Frontal Cortex_11


title: Male WT 8 months_Hippocampus_38


title: Female TG 8 months_Frontal Cortex_12


title: Female TG 8 months_Frontal Cortex_4


title: Female WT 8 months_Frontal Cortex_14


title: pleg1a rep4

city: Hangzhou

first: Yanna

last: Dang

email: yannadang@126.com, yannadang@zju.edu.cn

state: Zhejiang

address: 866 Yuhangtang Rd

department: College of Animal Sciences

institute: Zhejiang University

description: Overexpressed pleg1a

data_processing:
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normolized by Salmon
Differentially expressed genes between NC and cKD group were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >2 or <0.5
Genome_build: hg38
Supplementary_files_format_and_content: text files include normalized counts by DESeq2 for each sample

source_name: HEK293T cell line

extract_protocol:
Total RNA was isolated using Total RNA Kit I (Omegabiotek)
mRNAs were separated with oligo(dT)25 beads, and mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

value: human embryonic kidneys

tag: transfection

value: pCAG-pleg1a-3×FLAG vector (pleg1a)


title: Female WT 8 months_Frontal Cortex_6

tag: tissue


title: Female WT 8 months_Frontal Cortex_2


title: Male TG 8 months_Frontal Cortex_50


title: Female WT 8 months_Frontal Cortex_5


title: Male TG 8 months_Frontal Cortex_41


title: Male TG 8 months_Frontal Cortex_43


title: Male TG 8 months_Frontal Cortex_45


title: Female WT 8 months_Frontal Cortex_1


title: Female WT 8 months_Frontal Cortex_13


title: Male TG 8 months_Frontal Cortex_53


title: Male WT 8 months_Frontal Cortex_48


title: Male WT 8 months_Frontal Cortex_49


title: Male TG 8 months_Frontal Cortex_40


title: Male WT 8 months_Frontal Cortex_38


title: Male WT 8 months_Frontal Cortex_39


title: Male WT 8 months_Frontal Cortex_42


title: Male WT 8 months_Frontal Cortex_47


title: Male WT 8 months_Frontal Cortex_51


title: pleg1a rep3

description: Overexpressed pleg1a


title: Male TG 8 months_Frontal Cortex_46


title: NC rep4

description: Negative Control

value: empty pCAG-3×FLAG vector


title: Male TG 8 months_Frontal Cortex_44


title: pleg1a rep2

description: Overexpressed pleg1a


title: NC rep3

description: Negative Control


title: NC rep2

description: Negative Control


title: NC rep1

description: Negative Control


title: Male WT 8 months_Frontal Cortex_52


title: d0

first: Liang

address: number 866 of Yuhangtang road, West Lake Dist

department: College of Life Sciences

data_processing:
the raw reads were filtered by removing reads containing adapter, poly-N (reads with a ratio greater than 5%), and low quality reads (Q < 30). The reference genome (GRCh38.p12) was downloaded from the genome website (ftp://ftp.ensembl.org/pub/release-87/) and its index was built using Hisat2-Build(v2.0.5), and paired-end clean reads were aligned to the reference genome using TopHat (v2.1.1).
The quantitative analysis of gene expression was completed by Cufflinks (v2.2.1)21 based on RPKM which was calculated by Cuffdiff (v1.3.0).
Significant DEGs were identified by adjusting to a P value < 0.05 and an absolute value of log (fold change) > 1 using Cuffdiff (v2.2.1).
Cluster analysis was performed on differentially expressed genes using Euclidean Distance and Pheatmap.
GO enrichment analysis of differentially expressed genes was implemented with Perl module (GO: TermFinder) with a threshold for significance set at P < 0.05. R functions (phyper and q value) were used to test for the statistical enrichment of the differentially expressed genes in the KEGG pathways, corrected to P < 0.05.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: osteogenesis for 0 day

growth_protocol: The SM-31 random position machine (RPM) was used to simulate microgravity conditions. It was operated in random modes of speed (1 -10 r/min) inside a CO2 incubator (5% CO2, 37°C and 100% humidity). After the cells of 3rd passage reached 60-70% confluency, the medium was replaced with osteogenic medium18 (L-Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) supplemented with 10% FBS, 50 μg/mL L-ascorbic acid (Sigma, Shanghai, China), 10 mM β-glycerophosphate (Sigma), 0.1 μM dexamethasone (Sigma), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA from cells was extracted using Trizol reagent (Sigma). All RNA samples were detected and analyzed in Vazyme Biotech Co. (Nanjing, China). Briefly, RNA purity was detected by NanoDrop® spectrophotometer (Thermo Fisher, MA, USA), concentration measured using Qubit® RNA Assay Kit in Qubit® 3.0 Fluorometer (Life Technologies, CA, USA), and the integrity assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s instructions and sequenced on an Illumina Hiseq X Ten platform using 150 bp paired-end module.

treatment_protocol: The flasks were fixed on a cell culture vessel for RPM exposure. Cells grown in NG condition were also filled with osteogenic medium and were statically placed in the same CO2 incubator. The medium was changed twice a week. Cells induced for 0, 2, 7, and 14 days were used to study the effects of simulated microgravity

tag: cell type

value: human bone marrow mesenchymal stem cells

tag: passages

tag: differentiation status

value: osteogenic differentiation day 0

tag: gravity status

value: normal ground gravity

value: bone


title: mg14

source_name: osteogenesis for 14 days under microgravity

value: osteogenic differentiation day 14

value: microgravity


title: mg2

source_name: osteogenesis for 2 days under microgravity

value: osteogenic differentiation day 2


title: mg7

source_name: osteogenesis for 7 days under microgravity

value: osteogenic differentiation day 7


title: g2

source_name: osteogenesis for 2 days under normal ground condition


title: Input-DNA-lung-3

city: Bethesda

first: Jae Young

last: So

state: MD

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH

data_processing:
Gene alignment: Bowtie2 v2.10
Peak calling: MACS v1.4 and SICER
Genome_build: mm10
Supplementary_files_format_and_content: Peaks called by MACS v1.4 and SICER

source_name: 4T1 mammary tumor cell

extract_protocol:
Magna ChIP A/G procedure
SPRIwork system

tag: cell line

value: 4T1 mammary tumor cell

tag: tissue source

value: Lung metastases

tag: strain

value: BALB/c

tag: chip antibody


title: Input-DNA-lung-5


title: ChIPseq-DNA-lung-3


title: ChIPseq-DNA-lung-5


title: pleg1a rep1

description: Overexpressed pleg1a


title: g14

source_name: osteogenesis for 14 days under normal ground condition


title: E12.5-Wnt1Cre;Meis2f/f-rep1 [RNA-seq]

city: New Orleans

first: Linyan

last: Wang

state: LA

address: 6400 freret street

institute: Tulane University

data_processing:
Sequencing reads were mapped to a reference mouse genome (GRCm38/mm10) with  HISAT2 (default parameters)
Gene expression was counted using featureCounts
DEGs were further processed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tabular file including DEGs; GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj data columns

extract_protocol:
the anterior palatal  mesenchyme from E12.5 Wnt1Cre;Meis2f/f and wildtype embryos was  collected after the removal of the palatal  epithelium using Dispase II (Sigma). Three  biological replicates from each group and  genotype were collected for analyses. Total RNA  was isolated using RNeasy Micro Plus Kit  (Qiagen).
The reverse transcription and amplification of RNA were done and followed by library preparation with TruSeq RNA Sample Preparation Kit v2 (Illumina).

tag: strain background

tag: development stage

tag: genotype/variation

tag: tissue/cell type

value: anterior palate mesenchyme


title: E12.5-WT-rep3 [RNA-seq]

value: Wildtype


title: E12.5-Wnt1Cre;Meis2f/f-rep2 [RNA-seq]


title: E12.5-Wnt1Cre;Meis2f/f-rep3 [RNA-seq]


title: E13.5_Shox2Cre/+;R26RmTmG

data_processing:
cells were loaded for capture onto 10x genomics Chromium single cell 3' library & gel bead kit v3
construct an Illumina sequencing library and sequenced on NextSeq 500 with 150 cycle sequencing
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger/2.1.0
Using the CellRanger/2.1.0 software pipeline with default parameters, the FASTQ files were then subjected into cellranger count for the alignment, filtering, barcode counting, and UMI counting, resulting in the filtered feature-cell expression matrix in H5 file format.
H5 filtered-gene-barcode-matrix file can be deconvoluted to barcodes.tsv, features.tsv, and matrix.mtx files using "Read10X_h5" in Seurat V3.0 (H5 file includes the barcode and UMI list of each cell).
Genome_build: mm10
Supplementary_files_format_and_content: H5 file filtered-gene-barcode-matrix can be deconvoluted to tsv and mtx files using Seurat V3.0;

source_name: Shox2-positve palatal mesenchyme cells

extract_protocol:
RNA was extracted from SAN (including atrium) single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit V2
Library construction was performed according to 10X v2 kit protocol.
single cell gene expression RNA-seq

tag: Stage

value: Shox2-positive palatal cells


title: E12.5-Wnt1Cre;Meis2f/f-rep2 [ATAC-seq]

data_processing:
After  removal of the adaptor sequences, truncated reads  were mapped to GRCm38/mm10 reference  genomes with bowtie 2
The bamCoverage was used to generate a bigwig file, which is visible on the Integrative Genomics Viewer
Peaks from each group were respectively identified on a pool of triplicates using MACS2 callpeak
DiffBind was used to identify sites that exhibit differential accessibility between control and Meis2 mutant groups
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file including peaks

extract_protocol:
The GFP-positive anterior palatal shelves  were isolated from E12.5  Wnt1Cre;Meis2f/+;R26RmTmG and  Wnt1Cre;Meis2f/f;R26RmTmG embryos. Samples  were subjected to digestion by a cocktail of 0.02%  collagenase I, II and IV in HBSS for 30min,  followed by Accutase solution (Sigma) treatment  for 5 min at 37℃. After stop of the digestion with  culture medium containing 10% fetal bovine  serum (FBS), cells were washed with PBS  containing 3% FBS and then filtered through a 70-  μm filter. Suspended cells were sorted by  Fluorescence-activated Cell Sorting (FACS) on a  BD FACS Aria Fusion cell sorter (Becton-  Dickinson).
Around 50,000 single GFP-positive  cells from each group were obtained and were  subjected promptly to generation of ATAC-seq  library with the Nextera DNA Library Preparation Kit

tag: genotype

value: Palate mesenchyme cells


title: E12.5-WT-rep3 [ATAC-seq]


title: E12.5-Wnt1Cre;Meis2f/f-rep1 [ATAC-seq]


title: E12.5-WT-rep1 [ATAC-seq]