title: 100_whole_140_hfb.1

description: nucleic acid


title: 099_whole_140_hfb.1

status: Public on Jan 23 2020

type: SRA

city: Stanford

first: Nasa

last: Sinnott-Armstrong

state: California

address: 318 Campus Drive, Clark Center S240

department: Genetics

country: USA

institute: Stanford University

description: nucleic acid

library_source: genomic

data_processing:
Illumina base calling
SeqPurge trimming: SeqPurge -a1 CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -a2 CTGTCTCTTATACACATCTGACGCTGCCGACGA
bowtie2 alignment: bowtie2 -X 2000 --threads {threads} --rg-id {wildcards.sample_label} --fr --rg 'SM:{wildcards.sample_label}' -x [REFERENCE_FILE] -1 {input.left} -2 {input.right} | samtools view -hb -S - | samtools sort -o bams/unprocessed/{wildcards.sample_label}.bam -
macs2 peaks calling: macs2 callpeak -g 3e9  --treatment <sample BAM> --format BAMPE --nomodel --call-summits --nolambda --keep-dup all -p 0.01 -B –SPMR
bedtools overlap counts with multiBamCov
Genome_build: hg38

molecule: genomic DNA

organism: Homo sapiens

source_name: hfb

growth_protocol: The generation and maintenance of hCS and hSS was performed as previously described (Birey et al., 2017; Paşca et al., 2015; Sloan et al., 2017). In brief, intact hiPS cell colonies were enzymatically lifted using dispase (0.35 mg/mL, Life Technologies, 17105) and transferred into ultralow-attachment plates in hiPS medium supplemented with the SMAD inhibitors dorsomorphin (5 μM, Sigma-Aldrich) and SB-431542 (10 μM, Tocris), and the ROCK inhibitor Y-27632 (10 μM, Selleckchem). The hiPS cell medium was changed and supplemented with dorsomorphin and SB-431542 every day. On the sixth day in suspension, the medium was switched to neural medium containing neurobasal A (Life Technologies, 10888), B-27 supplement without vitamin A (Life Technologies, 12587), GlutaMax (1:100, Life Technologies), penicillin and streptomycin (1:100, Life Technologies) and supplemented with EGF (20 ng/ml, R&D Systems) and FGF-2 (20 ng/ml, R&D Systems). The neural medium was changed every day until day 17 and then every other day until day 24. For the generation of hSS, the medium was additionally supplemented with the WNT pathway inhibitor IWP-2 (5 μM, Selleckchem) on days 4-24, the SHH pathway agonist SAG (100 nM, Selleckchem) on days 12-24, retinoic acid (RA, 100 nM, Sigma-Aldrich) on days 12-15 and allopregnanolone (100 nM, Cayman Chemicals, 16930) on days 15-24. From day 25 to day 43, the neural medium for both hCS and hSS was changed every other day and supplemented with BDNF (20 ng/ml, Peprotech) and NT3 (20 ng/ml, Peprotech). From day 45 onwards, hCS and hSS were maintained in neural medium without growth factors with medium changes every four to six days.

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., Corces et al.) with modifications. Briefly, 10,000-50,000 cells were washed in ice-cold PBS, centrifuged at 4C for 5 min at 500 rcf, washed in ice-cold Resuspension Buffer (RSB, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH=7.4) and centrifuged again. Cells were resuspended in 50 uL Lysis Buffer (RSB plus 0.1 % NP-40 and 0.1% Tween-20) and centrifuged at 4C for 10 min at 500 rcf.
Pelleted nuclei were resuspended gently in 50 uL transposition mix (25 uL 2X Tagment DNA Buffer, 2.5 uL Tn5 Tagment DNA Enzyme 1, 0.1% Tween -20, H20) and incubated for 30 minutes at 37 C. DNA was cleaned using Qiagen MinElute columns, and PCR amplified 5 cycles in a 50 uL reaction with Illumina Nextera adaptors using NEBNext High Fidelity 2x Master Mix. A side qPCR reaction was performed using 10% of the pre-amplified PCR to determine the number of additional cycles to amplify. Final PCR products were cleaned using Qiagen MinElute columns and quantified by qPCR against a PhiX standard curve prior to pooling and sequencing to an average depth of ~10M filtered, deduplicated reads per sample on the Illumina NextSeq platform. Whole tissue samples were processed as previously described (Corces et al., 2017). Briefly, tissue samples were dounce homogenized and nuclei were isolated by gradient centrifugation prior to library preparation.

treatment_protocol: Dissociation of neural spheroids and human tissue into single cells was performed as previously described (Birey et al., 2017; Paşca et al., 2015; Sloan et al., 2017; Zhang et al., 2016). Briefly, tissue was chopped and incubated in 40 U/ml papain enzyme solution at 37 °C for 90 minutes. The number of neural spheroids used per sample ranged from 3 to 15 depending on their age and size. After digestion, samples were washed with a protease inhibitor solution and gently triturated to achieve a single cell suspension.  Single cell suspensions were then either FACS-sorted or immunopanned to achieve astrocyte- or neuron-enriched populations. For FACS-sorting, cells were resuspended in 0.2% BSA and DAPI-negative live cells were separated based on their expression of either GFP (pLV-GFAP-eGFP glia) or mCherry (AAV-DJ-hSYN1::mCherry neurons). Positive cells were sorted into ice-cold PBS. For immunopanning, the single cell suspension was added to a series of plastic petri dishes pre-coated with cell type-specific antibodies and incubated for 10-30 minutes at room temperature. Unbound cells were transferred to the subsequent petri dish, while the dish with bound cells was rinsed with PBS to wash away loosely bound contaminating cell types. An anti-Thy1 antibody (CD90, BD Biosciences, 550402) was used to harvest neurons, and an anti-HepaCAM antibody (R&D, MAB4108) was used to harvest astrocytes. Bound cells were then incubated in a trypsin solution (for glia) or Accutase (for neurons) at 37 °C for 3-5 minutes then gently pipetted off the plates with trypsin or Accutase. Cells were then spun down at 200 x g for 5 minutes, and resuspended in cold 0.2% BSA in PBS prior to RNA-seq and ATAC-seq.

tag: purification

value: whole

tag: differentiation media

tag: individual

tag: day of differentiation

tag: isolation method

value: nuclei

tag: sample source

value: hfb

tag: cell count

tag: assay batch


title: 098_neuronal_140_hfb.1

description: nucleic acid

value: neuronal

value: immunopanning


title: 097_glial_140_hfb.1

description: nucleic acid

value: glial


title: 113_whole_25_8858.1_hCS

description: nucleic acid

source_name: forebrain spheroid

value: hCS

value: forebrain spheroid


title: 096_glial_140_hfb.1

description: nucleic acid


city: Memphis

first: Robert

middle: Joseph

last: Autry

state: TN

address: 262 Danny Thomas Pl, MS 313

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

description:
697_24hr_htseq-count.txt
697-240-1-24-2
697 shCELSR2 24hr prednisolone replicate 2

library_source: transcriptomic

data_processing:
STAR Aligner used to align reads
edgeR TIMM normalization
LIMMA used to generate CPM (counts per million) filtered for at least 10 counts per transcript
p.adjust function used to assign FDR
Genome_build: hg19
Supplementary_files_format_and_content: Each processed file contains Counts for each gene, columns are related to each sample (replicates of three) in each time point 0hr prednislone or 24 hr prednisolone in either NALM6 cell line or 697 cell line.

molecule: total RNA

source_name: 697 shCELSR2 24hr prednisolone

growth_protocol: Leukemia cell lines Nalm-6 or 697 were grown in standard conditions RPMI-1640 10%FBS 200mM glutamine with puromycin to select shRNA vectors

extract_protocol:
RNA was extracted using either TRI-reagent or Qiagen RNAeasy
Libraries were constructed using standard Illumina procedures

treatment_protocol: 0 hr or 24 hr prednisolone treatment

tag: knockdown

value: 697 shCELSR2


title: 110_whole_25_2242.1_hSS

description: nucleic acid

value: hSS


description:
697_24hr_htseq-count.txt
697-NTC-24-3
697 non-target control 24hr prednisolone replicate 3

value: 697 non-target control


title: 095_neuronal_140_hfb.1

description: nucleic acid


title: 093_neuronal_140_hfb.1

description: nucleic acid


description:
697_24hr_htseq-count.txt
697-240-1-24-1
697 shCELSR2 24hr prednisolone replicate 1


title: 107_whole_25_2242.1_hCS

description: nucleic acid


title: 094_whole_140_hfb.1

description: nucleic acid


description:
697_24hr_htseq-count.txt
697-NTC-24-2
697 non-target control 24hr prednisolone replicate 2


description:
697_24hr_htseq-count.txt
697-NTC-24-1
697 non-target control 24hr prednisolone replicate 1


description:
697_0hr_htseq-count.txt
697-240-1-0-3
697 shCELSR2 0hr prednisolone replicate 3

source_name: 697 shCELSR2 0hr prednisolone


title: 088_whole_140_hfb.1

description: nucleic acid

value: dissociated


title: 056_neuronal_79_2242.1_hCS

description: nucleic acid

value: facs


title: 055_neuronal_434_8858.1_hCS

description: nucleic acid


title: GABA_Neuron4

city: Sydney

first: John

middle: William

last: Manion

address: Charles Perkins Centre, John Hopkins Drive

department: SOLES

country: Australia

institute: The University of Sydney

data_processing:
QC: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter,  reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30  and GC content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We  selected TopHat as the mapping tool for that TopHat can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
Quantification of gene expression level  HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Ensembl release 90 Human genome
Supplementary_files_format_and_content: Txt file contains FPKM and Raw Reads

source_name: Stem cell derived

extract_protocol:
Total RNAwas harvested from hiPSC and GABAergic neuron cultures by using the Favorgen Blood/Cultured Cell Total RNA kit (Favorgen Biotech Corp.). RNA was treated with DNase in solution using On-Column DNase I Digestion Set (Sigma) and maintained with Ribosafe RNase inhibitor (Bioline) 40U per sample. Quality and quantity of RNA were assessed by absorbance spectroscopy (Nanodrop, Thermo Fisher Scientific Life Sciences), Agilent Bio-analyser and Agarose gel electrophoresis.
Library preparation was performed using the NEBNext Ultra RNA library prep kit for Illumina. Index coded samples were clustered using the HiSeq PE Cluster Kit cBot-HS (illumina) and the resultant libraries were sequenced on an illumine hiseq platform and 125/150BP paired end reads were generated

tag: tissue

value: stem cell-derived GABA neuron


description:
697_0hr_htseq-count.txt
697-240-1-0-2
697 shCELSR2 0hr prednisolone replicate 2


title: 054_neuronal_434_8858.1_hCS

description: nucleic acid


description:
697_0hr_htseq-count.txt
697-240-1-0-1
697 shCELSR2 0hr prednisolone replicate 1


description:
697_0hr_htseq-count.txt
697-NTC-0-1
697 non-target control 0hr prednisolone replicate 1

source_name: 697 non-target control 0hr prednisolone


description:
697_0hr_htseq-count.txt
697-NTC-0-3
697 non-target control 0hr prednisolone replicate 3


title: 053_neuronal_434_2242.1_hCS

description: nucleic acid


description:
N6_24hr_htseq-count.txt
N6-240-1-24-3
NALM-6 shCELSR2 24hr prednisolone replicate 3

source_name: NALM-6 shCELSR2 24hr prednisolone

value: NALM-6 shCELSR2


title: 052_neuronal_371_2242.1_hCS

description: nucleic acid


title: 046_glial_79_8858.1_hCS

description: nucleic acid


title: 045_glial_79_2242.1_hCS

description: nucleic acid


title: 089_whole_140_hfb.1

description: nucleic acid


description:
N6_24hr_htseq-count.txt
N6-240-1-24-2
NALM-6 shCELSR2 24hr prednisolone replicate 2


title: 043_neuronal_104_8858.1_hSS

description: nucleic acid


description:
N6_24hr_htseq-count.txt
N6-240-1-24-1
NALM-6 shCELSR2 24hr prednisolone replicate 1


description:
N6_24hr_htseq-count.txt
N6-NTC-24-2
NALM-6 non-target control 24hr prednisolone replicate 2

value: NALM-6 non-target control


description:
N6_24hr_htseq-count.txt
N6-NTC-24-1
NALM-6 non-target control 24hr prednisolone replicate 1


title: 041_neuronal_104_8858.1_hCS

description: nucleic acid


title: 040_glial_188_1205.4_hCS

description: nucleic acid


title: 039_glial_104_8858.1_hSS

description: nucleic acid


title: 042_neuronal_104_2242.1_hSS

description: nucleic acid


title: 038_glial_104_2242.1_hSS

description: nucleic acid


description:
N6_0hr_htseq-count.txt
N6-240-1-0-3
NALM-6 shCELSR2 0hr prednisolone replicate 3

source_name: NALM-6 shCELSR2 0hr prednisolone


description:
N6_24hr_htseq-count.txt
N6-NTC-24-3
NALM-6 non-target control 24hr prednisolone replicate 3


description:
N6_0hr_htseq-count.txt
N6-NTC-0-3
NALM-6 non-target control 0hr prednisolone replicate 3


title: 036_neuronal_188_1205.4_hCS

description: nucleic acid


description:
N6_0hr_htseq-count.txt
N6-NTC-0-2
NALM-6 non-target control 0hr prednisolone replicate 2


title: 035_neuronal_104_2242.1_hCS

description: nucleic acid


description:
697_0hr_htseq-count.txt
697-NTC-0-2
697 non-target control 0hr prednisolone replicate 2


title: 034_neuronal_230_8858.1_hSS

description: nucleic acid


description:
N6_0hr_htseq-count.txt
N6-240-1-0-1
NALM-6 shCELSR2 0hr prednisolone replicate 1


title: 031_neuronal_230_2242.1_hCS

description: nucleic acid


title: Mouse_4m_2

city: NEW YORK

first: Bo

last: Xia

state: New York

address: 550 1ST AVE

department: Institute for Computational Medicine

institute: New York University School of Medicine

description: scRNA-seq through inDrop platform

data_processing:
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available at (https://github.com/flo-compbio/singlecell).
Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded.
The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated.
Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the sex bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped to the references genomes (here human GRCh38 and mouse GRCm38) by STAR 2.5.3a with parameter ‘—outSAMmultNmax 1’ and default settings otherwise.
Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes and long non-coding RNA genes, based on genome annotations from Ensembl release 90. For each gene, the number of unique UMIs across all reads assigned to that gene was determined (UMI filtering), corresponding to the number of transcripts expressed and captured.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: tsv file which contains the UMI counts matrix of genes by single cells. The each matrix contains 2000 cells, including the low-quality cells before filtering.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse testicular cells

growth_protocol: Fresh human seminiferous tubules were collected separately from testicular sperm extraction (TESE) surgery from two healthy patients with an obstructive etiology for infertility; there were no drug or hormonal treatments prior to TESE surgery. Mouse testes were collected freshly from 4-months old C57BL/6J mice from Jackson lab.

extract_protocol:
Testicular single cells were encapsulated and barcoded with the inDrop microfluidics platform as instructed by the manufacturer (1CellBio).
barcoded single-cell cDNA was purified with Agencourt RNAClean XP magnetic beads (Beckman Coulter, Cat. A63987) followed by second-strand synthesis reaction with NEBNext mRNA Second Strand Synthesis KIT (New England Biolabs, Cat. E6111S). Then linear amplification of cDNA was carried out through in vitro transcription (IVT) using HiScribe T7 High Yield RNA Synthesis kit (New England Biolabs, Cat. E2040S). IVT-amplified RNA was fragmented and purified again with Agencourt RNAClean XP magnetic beads. The second reverse transcription was done with PrimeScriptTM Reverse Transcriptase (Takara Clonetech, Cat. 2680A) followed with cDNA purification with Agencourt AMPure XP magnetic beads (Beckman Coulter, Cat.A63881). cDNA quantity was determined by qPCR on a fraction (5%) of purified cDNA. Final PCR amplification was done according to qPCR results and purified with Agencourt AMPure XP magnetic beads. Library concentration was determined by Qubit dsDNA HS Assay Kit (Invitrogen, Cat. Q32851). Library size was determined by Bioanalyzer High Sensitivity DNA Kit (Agilent, Cat. 5067-4626).

treatment_protocol: Fresh seminiferous tubules were dissociated with Trypsin along with Collagenase IV and TURBO Dnase for single cell suspension.

tag: age

value: 4 months

tag: health condition

value: Healthy

tag: strain


title: 033_neuronal_230_2242.1_hSS

description: nucleic acid


title: 032_neuronal_230_8858.1_hCS

description: nucleic acid


title: Mouse_4m_1

description: scRNA-seq through inDrop platform


title: 027_glial_230_8858.1_hCS

description: nucleic acid


title: 030_glial_104_2242.1_hCS

description: nucleic acid


description:
N6_0hr_htseq-count.txt
N6-NTC-0-1
NALM-6 non-target control 0hr prednisolone replicate 1


title: S-T3E_S155

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
genome Putnam et al. (2007)
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: streptomycin_T3_oral disc/tentacles

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
RNA was extracted from oral discs and tentacles (flash frozen in liquid nitrogen/stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Animals were exposed to one of three types of trauma (streptomycin, cytochalasin D, or calcium-free KSW) and allowed to recover. Sampling occurred at hourly time points during recovery. For streptomycin, sampling occurred after one hour of recovery following designated exposure times to streptomycin.

tag: developmental stage

value: adult

tag: treatment

value: streptomycin

tag: time point

value: time point 3

value: oral disc/tentacles

tag: replicate

value: replicate E


title: S-T3C_S153

value: replicate C


title: S-T3B_S152

value: replicate B


title: S-T3A_S151

value: replicate A


title: S-T3D_S154

value: replicate D


title: 010_glial_79_2242.1_hSS

description: nucleic acid

tag: purification

value: glial

value: hSS

value: forebrain spheroid


title: 005_neuronal_79_8858.1_hCS

description: nucleic acid

value: neuronal

tag: differentiation media

value: hCS

value: facs


title: 026_glial_230_2242.1_hCS

description: nucleic acid

tag: individual


title: 006_neuronal_79_8858.1_hSS

description: nucleic acid

tag: day of differentiation


title: S-T3F_S156

value: replicate F


title: 011_glial_79_8858.1_hSS

description: nucleic acid

tag: isolation method


title: S-T2E_S149

source_name: streptomycin_T2_oral disc/tentacles

value: time point 2


title: S-T2F_S150

value: adult


title: 037_glial_104_8858.1_hCS

description: nucleic acid

tag: sample source


description:
N6_0hr_htseq-count.txt
N6-240-1-0-2
NALM-6 shCELSR2 0hr prednisolone replicate 2

value: NALM-6 shCELSR2


title: 004_neuronal_79_2242.1_hSS

description: nucleic acid

tag: cell count


title: S-T2D_S148

value: streptomycin


title: S-T2C_S147

value: oral disc/tentacles


title: 003_neuronal_371_8858.1_hSS

description: nucleic acid

tag: assay batch


title: S-T2B_S146


title: 001_neuronal_371_2242.1_hSS

description: nucleic acid


title: 002_neuronal_371_8858.1_hCS

description: nucleic acid


title: human_TESE2_1

description: scRNA-seq through inDrop platform

source_name: human testicular cells

value: 45 years

value: Healthy


title: human_TESE2_2

description: scRNA-seq through inDrop platform


title: S-T1F_S130

source_name: streptomycin_T1_oral disc/tentacles

value: time point 1


title: S-T1E_S122

value: replicate E


title: S-T1D_S114

value: replicate D


title: human_TESE1_1

description: scRNA-seq through inDrop platform

value: 40 years


title: S-T1C_S106

value: replicate C


title: human_TESE1_2

description: scRNA-seq through inDrop platform


title: S-T1B_S98

value: replicate B


title: S-T0F_S82

source_name: streptomycin_T0_oral disc/tentacles

value: time point 0


title: S-T1A_S90

value: replicate A


title: S-T0C_S58


title: S-T0E_S74


title: S-T0D_S66


title: S-T0B_S145


title: S-T2A_S138


title: LEC.LCMV.SLN_1

type: RNA

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Critical threshold (Ct) values were obtained from qPCR profiling with an upper limit of 40. Across sample normalization was performed for each qPCR plate separately as follows: i) the arithmetic mean of all assays for each sample was calculated. ii) the median of sample means was divided by the arithmetic mean for each sample to create a scaling factor. iii) Ct values for each sample were multiplied by their scaling factor. Following normalization, individual assay outliers were identified either by visual inspection or based on a Z-score greater than 4, relative to all other samples. Next, normalization was redone with outlier assays set as missing. Missing values were then imputed using the mice package in R with default settings and 10 iterations.
Batch correction was performed only for a subset of miRNAs (223 total) that were assessed to have a significant association with batch, because batch correcting all miRNAs would have removed signal from cell type specific miRNAs that were only seen in a limited number of batches. Batch associated miRNAs were selected in 2 rounds. The first was a broad round of selection that included all cell types that had at least one replicate in 2 different batches. Variation due to cell type was removed using the removeBatchEffect function from the limma package, then an F-test in limma was performed with respect to batch for each miRNA on the resulting values. miRNAs were selected for batch correction if they had a Bonferroni adjusted p value <0.01 and a mean Ct value <35 across all samples involved. After miRNA selection, batch correction was performed using ComBat only for the selected miRNAs.
Following normalization and batch correction, Ct values were converted to arbitrary units (AU) for easier interpretation. We determined a limit of reliable detection at a Ct value of 28, which was assessed through the standard curves of 10 miRNAs and inter-replicate variability at different Ct thresholds. Our AU scale was designed so that a Ct value of 28 corresponded to a value of 1 AU. Ct values were converted to AU with the formula: 2^(28 - exp[i,j]), where exp is the Ct value matrix for all samples and miRNAs, i is a given miRNA, and j is a given cell type. A pseudocount of 0.1 was added to all assays following conversion.

label: SYBR

source_name: primary

growth_protocol: Primary cells harvested from 6-8 week old mice

extract_protocol: miRNeasy Micro Kit (Qiagen)

tag: organ

value: Lymph nodes

tag: cell type

value: LEC, LCMV activated

tag: cell markers

tag: isolation date

tag: lab

value: ST

tag: cell count (thousands)

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender

value: male


title: S-T0A_S137

tag: developmental stage

value: adult

tag: treatment

tag: time point

tag: tissue

tag: replicate


title: FRC.LCMV.SLN_1

value: FRC, LCMV activated

tag: strain


title: FRC.SLN_2

value: Fibroblastic reticular cells


title: LEC.LCMV.SLN_2


title: CD-T4F_S186

source_name: cytochalasin D_T4_oral disc/tentacles

value: cytochalasin D

value: time point 4

value: oral disc/tentacles

value: replicate F


title: DN.LCMV.SLN_2

value: DN, LCMV activated


title: CD-T4E_S185

value: replicate E


title: FRC.SLN_1


title: DN.LCMV.SLN_1


title: CD-T4D_S184

value: replicate D


title: CD-T4A_S181


title: BEC.LCMV.SLN_2

value: BEC, LCMV activated


title: DN.SLN_2

value: Double-negative


title: BEC.SLN_2

value: Blood endothelial cells


title: DN.SLN_1

value: Lymph nodes


title: LEC.SLN_2

value: Lymphatic endothelial cells


title: FRC.LCMV.SLN_2

value: ST


title: LEC.SLN_1

value: male


title: CD-T3E_S179

source_name: cytochalasin D_T3_oral disc/tentacles

value: adult

value: time point 3


title: BEC.LCMV.SLN_1


title: BEC.SLN_1


title: CD-T3C_S177

value: replicate C


title: CD-T3D_S178

value: cytochalasin D


title: CD-T3B_S176

value: replicate B


title: CD-T3A_S175

value: oral disc/tentacles

value: replicate A


title: CD-T2E_S173

source_name: cytochalasin D_T2_oral disc/tentacles

value: time point 2


title: CD-T3F_S180

value: replicate F


title: NKT.Sp.LPS.d3.165_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: Spleen

value: NKT cells 165 ug LPS, 3d

value: CD1d-tetramer+ (loaded with αGalCer)

value: MB


title: CD-T1F_S168

source_name: cytochalasin D_T1_oral disc/tentacles

value: time point 1


title: NKT.Sp.LPS.d3.165_1

description: CD1d-tetramer+ (loaded with αGalCer)


title: CD-T1E_S167

value: replicate E


title: NKT.Sp.LPS.d1.165_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 165 ug LPS, 1d


title: CD-T2D_S172

value: replicate D


title: NKT.Sp.LPS.h3.50_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 50 ug LPS, 3h

value: male


title: NKT.Sp.LPS.d1.50_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 50 ug LPS, 1d


title: CD-T4C_S183

value: adult

value: cytochalasin D

value: time point 4

value: replicate C


title: NKT.Sp.LPS.d1.165_1

description: CD1d-tetramer+ (loaded with αGalCer)


title: CD-T1B_S164

value: oral disc/tentacles

value: replicate B


title: CD-T2F_S174

value: time point 2

value: replicate F


title: NKT.Sp_3

description: CD8-CD19-Gr-1-Ter119-NK1.1interTCRbinter

value: Spleen

value: NKT cells


title: NKT.Sp_2


title: CD-T2A_S169

value: replicate A


title: CD-T4B_S182


title: NKT.Sp_1


title: NKT.Sp.LPS.h3.165_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 165 ug LPS, 3h

value: CD1d-tetramer+ (loaded with αGalCer)

value: MB


title: NKT.Sp.LPS.h3.165_1

description: CD1d-tetramer+ (loaded with αGalCer)


title: NKT.Sp.LPS.d3.50_2

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 50 ug LPS, 3d


title: CD-T0D_S160

source_name: cytochalasin D_T0_oral disc/tentacles

value: time point 0

value: replicate D


title: NK.49b-.MCMV.Lv_1

value: Liver

value: DX5- NK cells, infected (MCMV)

value: LL

value: male


title: CD-T2C_S171

value: adult

value: cytochalasin D

value: oral disc/tentacles

value: replicate C


title: NKT.Sp.LPS.d3.50_1

description: CD1d-tetramer+ (loaded with αGalCer)

value: Spleen


title: NK.49b-.Lv_2

value: DX5- NK cells, steady-state


title: NK.49b-.Lv_1


title: CD-T0A_S157

value: replicate A


title: NKT.Sp.LPS.d1.50_1

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 50 ug LPS, 1d


title: CD-T0C_S159


title: CD-T1D_S166

value: time point 1


title: NKT.Sp.LPS.h3.50_1

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells 50 ug LPS, 3h

value: CD1d-tetramer+ (loaded with αGalCer)

value: MB


title: CA-T4F_S129

source_name: calcium-free KSW_T4_oral disc/tentacles

value: calcium-free KSW

value: time point 4

value: replicate F


title: NKT.Sp_5

description: CD1d-tetramer+ (loaded with αGalCer)

value: NKT cells


title: NK.49b+.Lv_1

value: Liver

value: DX5+ NK cells, steady-state

value: LL

value: male


title: CA-T4D_S113

value: adult

value: oral disc/tentacles

value: replicate D


title: CD-T0E_S161

value: cytochalasin D

value: time point 0

value: replicate E


title: CD-T1C_S165

value: time point 1

value: replicate C


title: NKT.Sp_4

description: CD1d-tetramer+ (loaded with αGalCer)

value: Spleen

value: CD1d-tetramer+ (loaded with αGalCer)

value: MB


title: CA-T4C_S105

value: calcium-free KSW

value: time point 4


title: NK.MCMV.Sp_1

value: Spleen NK, infected (MCMV)


title: CA-T4B_S97

value: replicate B


title: CD-T1A_S163

value: replicate A


title: CD-T2B_S170

value: time point 2


title: CA-T3F_S81

source_name: calcium-free KSW_T3_oral disc/tentacles

value: adult

value: time point 3

value: replicate F


title: NK.Sp_3

value: Spleen NK

value: male


title: CD-T0F_S162

value: cytochalasin D

value: time point 0

value: oral disc/tentacles


title: CD-T0B_S158


title: NK.Sp_4

value: Spleen

value: LL


title: CA-T4E_S121

value: replicate E


title: CA-T3D_S65

value: calcium-free KSW

value: replicate D


title: NK.Sp_2


title: NK.49b+.Lv_2

value: Liver

value: DX5+ NK cells, steady-state


title: NK.49b+.MCMV.Lv_2

value: DX5+ NK cells, infected (MCMV)


title: NK.Sp_1


title: CA-T3C_S57

value: replicate C


title: Tgd.27+.aCD3.LN_1

value: Lymph nodes

value: Activated Tgd CD27+

value: JK


title: CA-T3B_S144

value: adult

value: time point 3

value: replicate B


title: CA-T3A_S136

value: replicate A


title: NK.MCMV.Sp_2

value: Spleen NK, infected (MCMV)

value: male


title: CA-T4A_S89

value: time point 4

value: oral disc/tentacles


title: CA-T3E_S73

value: calcium-free KSW

value: replicate E


title: NK.Sp_5

value: Spleen

value: Spleen NK

value: LL


title: CA-T2E_S120

source_name: calcium-free KSW_T2_oral disc/tentacles

value: time point 2


title: NK.49b+.MCMV.Lv_1

value: Liver

value: DX5+ NK cells, infected (MCMV)


title: CA-T2F_S128

value: replicate F


title: Tgd.CCR6+.aCD3.LN_1

value: Lymph nodes

value: Activated Tgd CCR6+

value: JK


title: CA-T2C_S104

value: adult

value: replicate C


title: Tgd.27+.aCD3.LN_2

value: Activated Tgd CD27+

value: male


title: Tgd.27+.LN_1

value: Tgd CD27+


title: CA-T1E_S72

source_name: calcium-free KSW_T1_oral disc/tentacles

value: calcium-free KSW

value: time point 1

value: oral disc/tentacles


title: Tgd.Sp_3

value: Spleen

value: Naive Tgd


title: Tgd.CCR6+.LN_1

value: Tgd CCR6+


title: CA-T2D_S112

value: time point 2

value: replicate D


title: Tgd.Sp_2


title: Tgd.CCR6+.LN_2


title: Tgd.CCR6+.aCD3.LN_2


title: CA-T2B_S96

value: replicate B


title: CA-T1D_S64


title: CA-T1C_S56


title: T8.mem.LisOVA.d60.Sp_1

description: B220-CD4-MHCII-NK1.1-Gr-1-CD8+CD45.1+KLRG1-CD127+

value: CD8+ memory T cells KLRG1-CD127+ LisOVA, day 60

value: AG


title: CA-T2A_S88

value: replicate A


title: T8.MP.LisOVA.d8.Sp_1

description: B220-CD4-MHCII-NK1.1-Gr-1-CD8+CD45.1+KLRG1+CD127-

value: CD8+ T cells KLRG1-CD127+ +LisOVA, day8


title: CA-T1F_S80

value: adult

value: replicate F


title: CA-T1B_S143


title: Tgd.Sp_1

value: male


title: CA-T1A_S135


title: T8.TE.LisOVA.d8.Sp_2

value: CD8+ T cells KLRG1+CD127- +LisOVA, day8


title: CA-T0E_S119

source_name: calcium-free KSW_T0_oral disc/tentacles

value: calcium-free KSW

value: time point 0

value: replicate E


title: T8.MP.LisOVA.d8.Sp_2

value: Spleen


title: CA-T0D_S111

value: oral disc/tentacles


title: T8.TE.LisOVA.d8.Sp_1


title: T8.OT1.Sp_2

description: B220-CD4-MHCII-NK1.1-Gr-1-CD8+CD44-CD45.1+

value: CD8+ T cells CD44- OT-I


title: T8.mem.LisOVA.d60.Sp_2


title: CA-T0F_S127


title: CA-T0C_S103

value: replicate C


title: CA-T0B_S95


title: CA-T0A_S87


title: oxtr1_male_rep3

city: Sapporo

first: Saori

last: Yokoi

state: Hokkaido

address: Kita 12-jo Nishi 6-chome, Kita-ku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Hokkaido university

data_processing:
Depletion of reads aligned to rRNA sequences with bowtie2.
Filtered reads are aligned to ASM223467v1 using HISAT2.
The numbers of sequence reads uniquely mapped to each exon were counted using featureCounts with the -O option (allowMultiOverlap).
Genome_build: ASM223467v1
Supplementary_files_format_and_content: *.fastq_sorted.bam_exon_count.txt: Tab-delimited text files contain read counts mapped to each gene.

organism: Oryzias latipes

source_name: whole brain

extract_protocol:
Whole brains from two adult females or males for one sample were homogenized in saline and TriZol LS reagent (#10296010, Invitrogen) was used to extract the total RNA.
RNA-seq libraries were made using a Ribo-Zero Gold rRNA Removal Kit (H/M/R) (Illumina), TruSeq Stranded mRNA Library Prep kit (Illumina), and TruSeq RNA Single Indexes Set A and SetB (Illumina), according to the manufacturers’ protocols.

tag: strain/background

value: Cab

tag: genotype/variation

tag: Sex

value: Male

tag: age

value: Adult

value: Whole brain


title: T8.OT1.Sp_1

tag: organ

tag: cell type

tag: cell markers

value: AG


title: oxtr1_male_rep1


title: T8.Nve.Sp_3

value: Naive CD8+ T cells

tag: isolation date

tag: lab

tag: cell count (thousands)


title: T8.Nve.Sp_2

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender


title: Treg.4.FP3+.Co_2

value: Large intestine

value: Regulatory T cells

value: AR


title: T8.Nve.Sp_1

value: male


title: T4.Vb8+.SEB.Sp_2

value: Activated CD4+ T


title: T4.Vb8+.SEB.Sp_1


title: oxtr1_male_rep2


title: Treg.4.FP3+.Co_1


title: oxt_male_rep1

value: oxt I22F/I22F


title: Treg.4.25hi.Sp_3


title: Treg.4.25hi.Sp_2


title: T4.Vb8-.SEB.Sp_2


title: oxt_female_rep2

value: Female


title: oxtr1_female_rep3


title: No_DSG_Input

city: Los Angeles

first: Zhifei

last: Luo

state: CA

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

data_processing:
For RNA_seq, quality control of the sequenced datasets was performed using FastQC and reads were trimmed using Trimmomatic (Bolger, Lohse et al. 2014) ; reads were mapped to the human genome GRCh38 reference using Gencode V29 annotation and STAR (Dobin, Davis et al. 2013) . Differentially expressed genes were determined using DESeq2 (Liao, Smyth et al. 2014) . Transcripts per million (TPM) for each gene were calculated with R script. Genes with an average TPM less than 1 in both control and deletion groups were excluded from downstream analysis.
All ChIP_seq data were quality checked using FASTQC and MultiQC (Ewels,Magnusson et al. 2016) and mapped to GRCh38 using BWA. Low quality, duplicated, not primary aligned, and not properly paired reads were filtered out using SAMtools, Sambamb and Samblaster (Li, Handsaker et al. 2009, Faust and Hall 2014, Tarasov, Vilella et al. 2015) . Peaks were called using MACS2 (Zhang, Liu et al. 2008) on each ChIP_seq replicate and common peaks were identified using IDR (for transcription factors) or the overlap method (for histones).
Genome_build: GRCh38

source_name: Human prostate cell line 22Rv1

growth_protocol: The human prostate cell line 22Rv1 was grown in RPMI 1640 medium (Corning Cellgro) with 10% fetal bovine serum (Gibco Life Technologies) without antibiotics. Cells were grown at 37 °C with 5% CO2 for under 20 passages. The cell line identity was confirmed using the STR cell line authentication method at the Norris Comprehensive Cancer Center Media Core and was shown to be free of mycoplasma using the universal mycoplasma detection kit (ATCC 30_1012K).

extract_protocol:
RNA was extracted using the DirectZol RNA kit (Zymo, R2062).
The RNA_seq libraries were made using Kapa mRNA HyperPrep Kit (KAPA, KKK8581) according to manufacturer’s instructions. ChIP_seq libraries were prepared using the Kapa Hyper prep kit (Kapa, KK8503) according to the manufacturer’s protocol.

treatment_protocol: 22RV1 cells were transfected with DharmaFECT1 reagent (Dharmacon, #T_2001_01) plus siRNAs against human HOXC4 (ON_TARGETplus Human HOXC4 (3221) siRNA_SMARTpool, L_013462_00_0005), human HOXC6 (ON_TARGETplus Human HOXC6 (3223)siRNA_SMARTpool, L_011871_00_0005), or a non_targeting control (ON_TARGETplus Non_targeting Pool). The final concentration of siRNAs in the cell culture media was 50nmol. Cell were incubated for 24 hours and then transfected again using same amount of the same siRNAs and incubated for another 24 hours.

value: human prostate cancer

tag: treatment

tag: genotype

value: wild type

tag: cell line


title: T4.Vb8-.SEB.Sp_1

value: Spleen

tag: strain


title: oxt_female_rep1

tag: strain/background

tag: tissue


title: FOXA1_CST


title: T4.Nve.Sp_3

value: Naive CD4 T cells


title: oxtr1_female_rep2

value: Cab

tag: genotype/variation

tag: Sex


title: oxtr1_female_rep1

tag: age


title: Treg.4.25hi.Sp_1

tag: organ

tag: cell type


title: oxt_male_rep3

value: Male


title: FOXA1_AB


title: oxt_male_rep2

value: Adult


title: T4.Nve.Sp_1

tag: cell markers

tag: isolation date


title: WT_male_rep3

value: Wild-type

value: Whole brain


title: oxt_female_rep3


title: T4.Nve.Sp_4

tag: lab

tag: cell count (thousands)


title: HOXB13


title: T.DP.Th_2

value: Thymus

value: Thymic CD4+CD8+CD3lo DP

tag: rna concentration (ng/ul)

tag: processing batch


title: T4.Nve.Sp_2

tag: gender


title: HOXC4_rep1

tag: treatment

value: HOXC4 expression

tag: genotype


title: WT_male_rep2


title: MAL2_OE

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

description: CD3+ T cell in the breast cancer microenvironment while cancer cell has MAL2 overexpression.

data_processing:
RAW sequencing data were processed by Cell Ranger for making fastq file, alignment to mm10 genome, and generation of normalized gene expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized expression file

source_name: CD3+ T cell

growth_protocol: Human triple-negative breast cancer cell line (MDA-MB-468) and murine triple-negative breast cancer cell lines (EO771 and 4T1) were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. For lentivirus packaging, HEK293T cells were grown in DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol: Libraries were prepared for sequencing using standard 10X genomics protocols

value: CD3+ T cell

value: over expressed


title: WT_male_rep1


title: B4CD200_SingleCell_Bleo

city: San Francisco

first: Jaymin

middle: J

last: Kathiriya

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

data_processing:
Reads were aligned to mm10 mouse genome and quantified using Cell Ranger Single-Cell Software.The matrix outputs were generated with barcodes (cell IDs), genes (gene names).
Genome_build: mm10
Supplementary_files_format_and_content: 10X genomics cellranger output

source_name: Distal lung epithelium

extract_protocol:
Single cells were isolated via flow cytometry based on Itgb4 and Cd200 expression from mouse lungs 9 days after bleomycin injury
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)

tag: strain


title: WT30_2

city: Birmingham

first: Rhea

middle: M

last: Derke

state: Alabama

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Illumina software used for base calling.
Reads mapped to reference genome using Bowtie2.
Differentially expressed transcripts from read alignments determined using Deseq.
Annotation done with the GenomicFeatures package from Bioconductor.
Genome_build: NCBI/RefSeq:CP007799

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: E. coli Nissle 1917 was grown anaerobically (90% N2, 5% CO2, 5% H2, maintained with a Coy Laboratory Products anaerobic chamber) at 37°C in MOPS minimal media (Teknova) in sealed Hungate tubes to an A600 = 0.25.

extract_protocol:
RNA was purified using the RiboPure™-Bacteria Kit (Ambion), according to the manufacturer’s instructions.
mRNA-sequencing was performed at the UAB Heflin Center for Genomic Sciences, using an Illumina NextSeq 500 as described by the manufacturer (Illumina, Inc). The Agilent SureSelect Strand Specific mRNA library kit (Agilent) and ribosome reduction with the RiboMinus protocol for Gram-negative and Gram-positive bacteria (Life Technologies) were used as described by the manufacturer. The resulting mRNA was randomly fragmented with cations and heat, followed by first strand synthesis using random primers. Second strand cDNA production was done with standard techniques, and cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems) prior to cluster generation, which was performed according to the manufacturers recommendations for onboard clustering (Illumina).

treatment_protocol: At A600 = 0.25, the cells were treated anaerobically with 0.4 mM HOCl. Samples (7 ml) were harvested into 7 ml ice-cold isopropanol immediately before and 15 or 30 minutes after HOCl addition, harvested by centrifugation, and stored at -80°C until use.

value: Nissle 1917

tag: time after hocl stress


title: T.DP.Th_1

value: AR

value: male


title: MAL2_WT

description: CD3+ T cell in the microenvironment of wildtype cancer cells


title: B1b.aIgM.PC_2

value: Peritoneal cavity

value: Activated B1a B cells

value: RH


title: WT_female_rep3

tag: strain/background

value: Female

tag: tissue


title: WT30_1


title: WT15_3


title: WT_female_rep1

value: Cab

tag: genotype/variation

tag: Sex


title: 770

city: Bandar Baru Bangi

first: Norashikin

last: Sarpan

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

data_processing:
Raw reads were checked using FastQC v0.11.3 software.
Quality trimming was done using Trim Galore! v0.4.0 at a Phred score of Q20.
Trimmed reads were mapped to Pisifera P5 reference genome using TopHat v2.0.13 (Kim et al., 2013) with the following parameters: --b2-very-sensitive --min-intron-length 30 --max-intron-length 50000 -p 10
Read counts tabulated with HTSeq-Count ver 0.6.1p1 (Anders et al., 2015) with options -s no -t CDS
Genome_build: Elaeis guineensis P5-build of an AVROS pisifera palm (Singh et al., 2015).
Supplementary_files_format_and_content: Text files of raw counts for CDS feature in P5 gene models (Chan et al., 2017, Biology Direct; http://palmxplore.mpob.gov.my).

organism: Elaeis guineensis

source_name: leaf

extract_protocol:
Total RNA was isolated using the RNAprep Pure Plant Kit (Tiangen). Genomic DNA was removed through on-column DNA digestion and the isolated RNA was further purified with RNeasy® kit (Qiagen). The quality and quantity of the purified RNA were evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies).
Stranded RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq kit. Libraries were sequenced paired-end with a read length of 125bp (PE125) on a Hiseq2500 Illumina platform.

tag: plant type

value: clonal plant

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled

tag: palm tree id


title: WT15_1


title: B4CD200_SingleCell

extract_protocol:
Single cells were isolated via flow cytometry
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)

tag: cell type


title: WT30_3


title: B1b.aIgM.PC_1

source_name: primary

tag: organ

tag: cell markers

tag: isolation date

tag: lab

tag: cell count (thousands)


title: 765


title: B1b.PC_3

value: B1a B cells

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender


title: B1b.PC_2

tag: strain


title: B1b.PC_5


title: 764

value: normal


title: 0801 c.elegans NC

city: Seoul

first: Miae

last: Oh

address: Anam 145

institute: Korea University

description: Gene expression after 14 days

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s C. elegans Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

organism: Caenorhabditis elegans

source_name: 0 μM soraprazan

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: C. elegans Bristol strain N2 provided by the CGC was used. Worms were maintained and propagated in peptone-free mNGM (modified nematode growth medium) at 25°C using standard techniques. E. coli OP50 suspended in M9 buffer was seeded on mNGM in 90 mm diameter petri dishes to feed the worms. Escherichia coli OP50 was provided by the Caenorhabditis Genetics Centre (CGC) at the University of Minnesota and used as a standard food for C. elegans. E. coli OP50 was grown in Luria-Bertani (LB) broth (Difco, Detroit, MI, USA) at 37°C with shaking overnight, collected by centrifugation, and washed twice with M9 buffer. Then, the bacteria were diluted to a final concentration of 0.1 mg (wet weight) per mL in M9 buffer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: C. elegans was exposed to a sodium hypochlorite-sodium hydroxide solution to obtain viable eggs. The eggs were incubated overnight in M9 buffer at 25°C for hatching, and the suspension of L1-stage worms was centrifuged at 1,200 × g for 2 min. After eliminating the supernatant, the remaining larvae were transferred to fresh mNGM plates seeded with E. coli OP50 and incubated at 25°C. The worms were allowed to grow on E. coli OP50 until the L4 stage. All experiments used 3-day-old worms (1 day adult) to regulate the reproductive system in C. elegans.  About 600 worms were transferred to the plates containing 0, and 200 μM of soraprazan, and seeded with E. coli OP50. The plates were incubated at 25°C during 14 days.

tag: age

value: 14 days


title: 0801 c.elegans 200

description: Gene expression after 14 days grown on 200 μM soraprazan plates

source_name: 200 μM soraprazan


title: B.Fo.aIgM.Sp_1

description: Ly6C-Ter119-Gr1-CD11c-CD19+CD23+AA4-CD5-

value: Spleen

value: Activated Follicular B cells


title: Liver Snd1 KO rep 4

city: Helsinki

first: Juha

middle: Mikael

last: Saarikettu

address: Viikinkari 1

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization

label: biotin

source_name: Liver, left lobe

label_protocol: Standard Illumina protocol

growth_protocol: Samples were collected at around noon. The mice were not fasted.

extract_protocol: Trizol extraction followed by DNA-free DNA removal kit.

tag: tissue

value: Liver, left lobe

tag: genotype

value: Snd1 KO

value: Male

value: 8-12 week-old


title: 0731 c.elegans NC

description: Gene expression after 14 days


title: 758

tag: plant type


title: B1b.PC_4

value: Peritoneal cavity

value: male


title: WT15_2

value: Nissle 1917

tag: time after hocl stress


title: 754

tag: leaf number

tag: fruit phenotype


title: 753

tag: palm tree id


title: MAL2_KD

description: CD3+ T cell in the breast cancer microenvironment while MAL2 expression in cancer cells are knocked down.

tag: cell type

value: CD3+ T cell

tag: genotype/variation

value: knock out


title: WT0_3


title: 768

value: clonal plant


title: 687

value: frond 0


title: WT0_2


title: WT_female_rep2

tag: strain/background

value: Cab

value: Wild-type

tag: Sex

value: Female

value: Adult

value: Whole brain


title: 767

value: normal


title: B1b.PC_1

tag: organ

value: B1a B cells

tag: cell markers

tag: isolation date

tag: lab

tag: cell count (thousands)


title: WT0_1

tag: strain


title: B.Fo.Sp_2

value: Spleen

value: Follicular B cells

value: RH

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender


title: B.93-.Sp_1

description: Ly6C-Ter119-Gr1-CD11c-CD19+CD23-AA4-CD5+

value: CD19+CD93-CD5+ B cells


title: B.93-.Sp_2

value: male


title: B.Fo.aIgM.Sp_2

value: Activated Follicular B cells


title: B.93+.Sp_2

description: Ly6C-Ter119-Gr1-CD11c-CD19+CD23-AA4+CD5+

value: CD19+CD93+CD5+ B cells


title: B.93+.Sp_1


title: B.Fo.Sp_1


title: Liver WT rep 1

tag: tissue

value: Liver, left lobe

tag: genotype

value: wild type

value: Male

tag: age

value: 8-12 week-old


title: Liver WT rep 4


title: Liver Snd1 KO rep 2

value: Snd1 KO


title: B.Sp_4

value: CD19+ B cells

value: AR


title: 0731 c.elegans 200

value: 14 days


title: Liver Snd1 KO rep 1


title: Liver Snd1 KO rep 3


title: Liver WT rep 3


title: Liver WT rep 2


title: 673

tag: plant type

value: clonal plant

tag: leaf number

value: frond 0

tag: fruit phenotype

value: mantled

tag: palm tree id


title: B.Sp_2

value: Spleen

tag: cell type


title: stool at D0, goat's milk, asthma,rep2

type: genomic

city: Tainan

first: Jiu Yao

last: Wang

address: No.138,Sheng Li Road,Tainan

country: Taiwan

institute: Nation Cheng Kung University

description: stool at D0, goat's milk, asthma (1/3)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 10 minutes, then 48° for 3 minutes. • Transfer 105μl of hyb solution to each array. • Hybridize 23 hours 30 minutes at 48°

scan_protocol: Affymetrix Gene ChIP Scanner

data_processing: Data were processed using MiDAS software.

source_name: wild-type

label_protocol: Samples were enzymatically fragmented and biotinylated using the reagent Kit (Affymetrix)

growth_protocol: Stool samples were obtained from groups of offspring after the weaning period and HDM allergen sensitization (day 0), and sacrificed after allergen intra-tracheal challenge for 2 days (Day 16).

extract_protocol: Stool samples were frozen then stored at -80 °C. QIAamp DNA Stool Mini Kit was used to purify DNA from frozen stool samples according to protocol. DNA quality was evaluated using MaestroNano spectrophotometry (Maestrogen, Las Vegas, NV, USA) in the absorbance ratio A260 nm / A280 nm.

tag: asthma

value: asthma


title: cow's milk (mom),rep2

description: cow's milk (mom) (1/2)

value: naïve


title: stool at D0, goat's milk, naïve,rep3

description: stool at D0, goat's milk, naïve (1/3)


title: CAR-1(dSm)

city: La Jolla

first: Ngang Heok

last: Tang

address: 9500 Gilman Drive

institute: UC San Diego

data_processing:
(Using CZ25180_S1_L008_R1_001.fastq.gz as an example starting fastq file): umi_tools extract --stdin CZ25180_S1_L008_R1_001.fastq.gz --bc-pattern NNNNNNNNNN --log CAR1.CZ25180_IP.---.--.metrics CAR1 --stdout CAR1.CZ25180_IP.umi.r1.fq
cutadapt  -O \  1 \  -f \  fastq \  --match-read-wildcards \  --times \  1 \  -e \  0.1 \  --quality-cutoff \  6 \  -m \  18 \  -o \  CAR1.CZ25180_IP.umi.r1Tr.fq \  '-a AGATCGGAAGAGCAC' \  '-a GATCGGAAGAGCACA' \  '-a ATCGGAAGAGCACAC' \  '-a TCGGAAGAGCACACG' \  '-a CGGAAGAGCACACGT' \  '-a GGAAGAGCACACGTC' \  '-a GAAGAGCACACGTCT' \  '-a AAGAGCACACGTCTG' \  '-a AGAGCACACGTCTGA' \  '-a GAGCACACGTCTGAA' \  '-a AGCACACGTCTGAAC' \  '-a GCACACGTCTGAACT' \  '-a CACACGTCTGAACTC' \  '-a ACACGTCTGAACTCC' \  '-a CACGTCTGAACTCCA' \  '-a ACGTCTGAACTCCAG' \  '-a CGTCTGAACTCCAGT' \  '-a GTCTGAACTCCAGTC' \  '-a TCTGAACTCCAGTCA' \  '-a CTGAACTCCAGTCAC' \  CAR1.CZ25180_IP.umi.r1.fq
cutadapt \   -O \   5 \   -f \   fastq \   --match-read-wildcards \   --times \   1 \   -e \   0.1 \   --quality-cutoff \   6 \   -m \   18 \   -o \   CAR1.CZ25180_IP.umi.r1TrTr.fq \   -a AGATCGGAAGAGCAC \   -a GATCGGAAGAGCACA \   -a ATCGGAAGAGCACAC \   -a TCGGAAGAGCACACG \   -a CGGAAGAGCACACGT \   -a GGAAGAGCACACGTC \   -a GAAGAGCACACGTCT \   -a AAGAGCACACGTCTG \   -a AGAGCACACGTCTGA \   -a GAGCACACGTCTGAA \   -a AGCACACGTCTGAAC \   -a GCACACGTCTGAACT \   -a CACACGTCTGAACTC \   -a ACACGTCTGAACTCC \   -a CACGTCTGAACTCCA \   -a ACGTCTGAACTCCAG \   -a CGTCTGAACTCCAGT \   -a GTCTGAACTCCAGTC \   -a TCTGAACTCCAGTCA \   -a CTGAACTCCAGTCAC \   CAR1.CZ25180_IP.umi.r1Tr.fq
fastq-sort --id CAR1.CZ25180_IP.umi.r1TrTr.fq > CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq
STAR \  --alignEndsType \  EndToEnd \  --genomeDir \  RepBase18.05.STAR \  --genomeLoad \  NoSharedMemory \  --outBAMcompression \  10 \  --outFileNamePrefix \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STAR \  --outFilterMultimapNmax \  30 \  --outFilterMultimapScoreRange \  1 \  --outFilterScoreMin \  10 \  --outFilterType \  BySJout \  --outReadsUnmapped \  Fastx \  --outSAMattrRGline \  ID:foo \  --outSAMattributes \  All \  --outSAMmode \  Full \  --outSAMtype \  BAM \  Unsorted \  --outSAMunmapped \  Within \  --outStd \  Log \  --readFilesIn \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq \  --runMode \  alignReads \  --runThreadN \  8
STAR \  --alignEndsType \  EndToEnd \  --genomeDir \  ce10.STAR \  --genomeLoad \  NoSharedMemory \  --outBAMcompression \  10 \  --outFileNamePrefix \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STAR \  --outFilterMultimapNmax \  1 \  --outFilterMultimapScoreRange \  1 \  --outFilterScoreMin \  10 \  --outFilterType \  BySJout \  --outReadsUnmapped \  Fastx \  --outSAMattrRGline \  ID:foo \  --outSAMattributes \  All \  --outSAMmode \  Full \  --outSAMtype \  BAM \  Unsorted \  --outSAMunmapped \  Within \  --outStd \  Log \  --readFilesIn \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.fq \  --runMode \  alignReads \  --runThreadN \  8
umi_tools \  dedup \  -I \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.bam \  --output-stats \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo \  -S \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
sort \  -o \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
samtools \  index \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam
makebigwigfiles \  --bw_pos \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.pos.bw \  --bw_neg \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.norm.neg.bw \  --bam \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  --genome \  ce10.chrom.sizes
clipper \  --bam \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  --species ce10 \  --outfile CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \  --save-pickle
samtools view -c -F 4 CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  > CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum
overlap_peakfi_with_bam_PE.pl \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.bed \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \  CAR1.CZ26430_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.mappedreadnum \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed
peakscompress.pl \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.bed \  CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.peakClusters.normed.compressed.bed
Genome_build: ce10
Supplementary_files_format_and_content: bed format, contains peaks of predicted RBP binding

extract_protocol: none provided by the submitter

tag: antibody

value: GFP-trap

tag: antibody manufacturer

value: antibody manufacturer:Chromotek

tag: catalog number

value: antibody catalog #:gta-10


title: stool at D0, goat's milk, naïve,rep2

description: stool at D0, goat's milk, naïve (1/3)


title: B.Sp_3

tag: organ

tag: cell markers

tag: isolation date

tag: lab

tag: cell count (thousands)

value: male


title: FGF21 KO, WAT, DIO, treated with Rosiglitazone, technical replicate of bio rep 1

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing: The data were normalized using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: Epididymal white adipose tissue

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: FGF21 KO c57b6/sv129 mixed bkg

value: 4-5 months old

tag: treatment

value: High Fat diet for 10 weeks, last 2 weeks + 10mg/kg rosiglitazone

tag: genetic background

value: mixed c57b6/sv129

tag: tissue

value: Epididymal white adipose tissue

tag: disease state

value: Diet-induced Obesity


title: stool at D0, goat's milk, asthma,rep3

description: stool at D0, goat's milk, asthma (1/3)


title: FGF21 KO, WAT, DIO, treated with Rosiglitazone, biological replicate 1

tag: age


title: 2 stool at D0, cow's milk, naïve,rep1

description: stool at D0, cow's milk, naïve (1/3)


title: FGF21 KO, WAT, DIO, treated with Rosiglitazone, technical replicate of bio rep 2


title: FGF21 KO, WAT, DIO, treated with Rosiglitazone, biological replicate 2


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, treated with Rosiglitazone, technical replicate of bio rep 1

value: wild-type c57b6/sv129 mixed bkg


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, treated with Rosiglitazone, technical replicate of bio rep 2


title: FGF21 KO, WAT, DIO, technical replicate of bio rep 1

value: High Fat diet for 10 weeks


title: FGF21 KO, WAT, DIO, technical replicate of bio rep 2


title: FGF21 KO, WAT, DIO, biological replicate 1


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, treated with Rosiglitazone, biological replicate 2


title: FGF21 KO, WAT, DIO, biological replicate 2


title: shRictor rep2

city: Beijing

first: Sun

last: Fangfang

address: Zhongguancun Street

country: China

institute: Tsinghua University

data_processing:
Illumina Casava1.8 software used for basecalling.
Cutadapt and RSeQC were executed for adapter trimming and quality control of paired-end RNA sequencing data then aligned to the UCSC mm10 mouse reference genome with TopHat2.0.
Read-pairs were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts values for each sample.

source_name: Liver

growth_protocol: lean, wild-type mice, 12/12h light on/off, ad libum fed

extract_protocol:
Livers were removed, snap-frozen in liquid nitrogen, and RNA was extracted using Trizol reagent. RNA was treated with DNaseI and cleaned with Ribo-zero magnetic core kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.1OD of adenovirus injection, 1 week afterwards, food withdrawal for 6 hours, sacrifice.

value: liver

tag: genotype/variation

value: Rictor Knockdown


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, biological replicate 2


title: stool at D0, naïve (mom),rep2

description: stool at D0, naïve (mom)(1/2)


title: B.Sp_1

value: Spleen

tag: cell type

value: CD19+ B cells

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, technical replicate of bio rep 2


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, treated with Rosiglitazone, biological replicate 1


title: lacZ2 rep2

description: lacZ2: control for shRictor

value: wild type


title: stool at D0, naïve (mom),rep1

description: stool at D0, naïve (mom)(1/2)

tag: asthma

value: naïve


title: MC.IgE.PC_1

description: CD45+CD11b-CD11c-CD19-CD4-CD8-FcεR1α+CD117+

tag: organ

value: Peritoneal cavity

value: IgE-sensitized peritoneal mast cells

value: DD


title: stool goat's milk (mom),rep1

description: stool goat's milk (mom)(1/2)


title: 2 stool at D0, cow's milk, asthma,rep1

description: stool at D0, cow's milk, asthma (1/3)

value: asthma


title: MC.PC_2

value: Naïve peritoneal mast cells

tag: cell markers

value: AR

value: male


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, biological replicate 1

value: 4-5 months old

value: mixed c57b6/sv129

value: Epididymal white adipose tissue


title: CAR-1(FL)

tag: antibody

value: GFP-trap

tag: antibody manufacturer

value: antibody manufacturer:Chromotek

tag: catalog number

value: antibody catalog #:gta-10


title: shRictor rep1

tag: strain

value: liver

value: Rictor Knockdown


title: B.fem.Sp_1

value: Spleen

value: CD19+ B cells

tag: isolation date

tag: lab

tag: cell count (thousands)

value: female


title: MC.IgEX.PC_2

value: Peritoneal cavity

value: IgE-activated peritoneal mast cells


title: MC.IgEX.PC_1

value: DD


title: shDnajb9 rep1

tag: tissue

value: Dnajb9 Knockdown


title: MC.PC_1

value: Naïve peritoneal mast cells

value: AR


title: wild-type c57b6/sv129 mixed bkg WAT, DIO, technical replicate of bio rep 1

value: wild-type c57b6/sv129 mixed bkg

tag: age

value: 4-5 months old

tag: treatment

value: High Fat diet for 10 weeks

tag: genetic background

tag: disease state

value: Diet-induced Obesity


title: GN.fem.Sp_1

tag: cell type

value: Neutrophils

tag: rna concentration (ng/ul)

tag: processing batch


title: cr-leaf.sRNA.WT.replicate1

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Capsella rubella one month leaves of wt (Cr1GR1)

data_processing:
Bisulfite-seq: For each sample, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were  trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the Capsella reference genome using the Bismark read mapper (Krueger and Andrews, 2011) using the single end mode. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
small-RNA: Adapters were removed from the 50 bp long single sRNA reads in each library. The resulting18-30 bp long reads were mapped to the reference genomes. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
RNA-seq: For each replicate, reads were mapped to the respective eference genomes using TopHat v2.1.0 (Trapnell et al, 2009)in single end mode. Gene and TE expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
WGS and TE insertion analysis: For each accession the 150 bp long reads were mapped to the Capsella reference genome using TEPID (Stuart el al 2016) in paired-end mode with default parameters.
Genome_build: TAIR10, Caprub1_0
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the reference genomes. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes and transposable elements in both genomes for each condition and replicate.
Supplementary_files_format_and_content: WGS and TE insertion analysis: Identified new TE insertions are shown for the six samples. Rows indicate chromosome (scaffold) and insertion position and values indicate TE identity.

organism: Capsella rubella

source_name: CR one month leaves wt

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
Capsella leaves were ground with liquid nitrogen, and 100 mg of fine powder from each sample was used for RNA isolation using the mirVana™ miRNA isolation kit. Short RNAs (< 200 nt) were seperated and followed by size selection on a 15% TBE-Urea polyacrylamide gel.
sRNA seq libraries were generated with the NEBNext® Multiplex Small RNA kit (NEB #E7300S).

treatment_protocol: Material was harvested from plants directly

value: leaf

tag: genotype

value: wt (Cr1GR1)


title: cr-leaf.sRNA.WT.replicate2


title: stool goat's milk (mom),rep2

description: stool goat's milk (mom)(1/2)

tag: asthma

value: naïve


title: GN.Sp_4

tag: organ

value: Spleen

tag: cell markers

tag: gender

value: male


title: naïve (mom),rep1

description: naïve (mom)(1/2)


title: goat-pNK

city: Yangling

first: Xuefeng

last: Qi

state: Shaanxi

address: Taicheng Road

institute: Northwest A&F University

description: pNK, female goat,peripheral blood

data_processing:
The original image data is transferred into sequence data via base calling.
We get rid the contaminant tags and low qualtity tags from the fq file and get the final clean tags.miRNA is normally 21 nt or 22nt.
We use AASRA to map clean reads to reference genome and other sRNA database.
We perform hierarchical clustering for differentially expressed miRNA using pheatmap, a function of R. For clustering more than two groups, we perform the intersection and union DESs between them, respectively.
Genome_build: reference genome
Supplementary_files_format_and_content: Using TPM to calculated the sRNA expressioin and compare the difference of gene expression

organism: Capra hircus

source_name: goat peripheral NK cells

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: uNK and NK cells were separated from uterus and peripheral blood of goat

value: peripheral blood

tag: cell

value: pNK cells  were separated from peripheral blood


title: goat-uNK

description: uNK, female goat, uterus

source_name: goat uterine NK cells

value: uterus

value: uNK cells were separated from uterus


title: shDnajb9 rep2

tag: strain

value: liver

tag: genotype/variation

value: Dnajb9 Knockdown


title: lacZ2 rep1

description: lacZ2: control for shRictor

value: wild type


title: naïve (mom),rep2

description: naïve (mom) (1/2)


title: GN.Sp_3

tag: isolation date

tag: lab

tag: cell count (thousands)


title: cr-leaf.sRNA.pol4.replicate2

description: Capsella rubella one month leaves of nrpd1a (Cr1GR1)

source_name: CR one month leaves nrpd1a

tag: tissue

value: nrpd1a (Cr1GR1)


title: lacZ1 rep1

description: lacZ1: control for shDnajb9

tag: age


title: cr-leaf.sRNA.pol4.replicate1


title: stool at D16, cow's milk, naïve,rep3

description: stool at D16, cow's milk, naïve (1/3)


title: stool at D16, goat's milk, naïve,rep3

description: stool at D16, goat's milk, naïve (1/3)


title: cr-leaf.BSseq.WT.replicate2

extract_protocol:
Leaves of 6-10 plants of Capsella wildtype were pooled as one replicate. Genomic DNA was extracted using the MagJET Plant Genomic DNA Kit (K2761).
Bisulfite libraries were generated using Ovation Ultralow Methyl-Seq Library Systems (NuGEN) following the manufacturer's protocol using 100 ng of starting DNA.


title: GN.Sp_2

extract_protocol: miRNeasy Micro Kit (Qiagen)


title: GN.Sp_1


title: stool at D16, goat's milk, asthma,rep3

description: stool at D16, goat's milk, asthma (1/3)

value: asthma


title: lacZ1 rep2

description: lacZ1: control for shDnajb9


title: cr-leaf.BSseq.WT.replicate1


title: stool at D16, goat's milk, asthma,rep2

description: stool at D16, goat's milk, asthma (1/3)


title: cr-leaf.BSseq.pol4.replicate2

extract_protocol:
Leaves of 6-10 plants of Capsella pol iv mutants were pooled as one replicate. Genomic DNA was extracted using the MagJET Plant Genomic DNA Kit (K2761).
Bisulfite libraries were generated using Ovation Ultralow Methyl-Seq Library Systems (NuGEN) following the manufacturer's protocol using 100 ng of starting DNA.


title: DC.Sp_3

value: Dendritic cells


title: cr-leaf.BSseq.pol4.replicate1


title: stool at D16, goat's milk, naïve,rep1

description: stool at D16, goat's milk, naïve (1/3)


title: DC.Sp_1


title: cr-leaf.WGS_pol4_individual_5

description:
Capsella rubella two months leaves of nrpd1a (Cr1GR1)
cr.leaves.TEs_detected_insertions.txt.gz

data_processing:
Library strategy: WGS
Bisulfite-seq: For each sample, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were  trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the Capsella reference genome using the Bismark read mapper (Krueger and Andrews, 2011) using the single end mode. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
small-RNA: Adapters were removed from the 50 bp long single sRNA reads in each library. The resulting18-30 bp long reads were mapped to the reference genomes. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
RNA-seq: For each replicate, reads were mapped to the respective eference genomes using TopHat v2.1.0 (Trapnell et al, 2009)in single end mode. Gene and TE expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
WGS and TE insertion analysis: For each accession the 150 bp long reads were mapped to the Capsella reference genome using TEPID (Stuart el al 2016) in paired-end mode with default parameters.
Genome_build: TAIR10, Caprub1_0
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the reference genomes. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes and transposable elements in both genomes for each condition and replicate.
Supplementary_files_format_and_content: WGS and TE insertion analysis: Identified new TE insertions are shown for the six samples. Rows indicate chromosome (scaffold) and insertion position and values indicate TE identity.

source_name: CR two months leaves nrpd1a

extract_protocol:
Genomic DNA was isolated from leaves of pol iv mutants using the MagJET Plant Genomic DNA Kit (K2761).
Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®


title: cr-leaf.WGS_pol4_individual_4


title: DC.Sp_2


title: Mo.6C+II-.BM_2

value: Bone marrow

value: Ly6Chigh monocytes


title: stool at D16, asthma,rep3

description: stool at D16, asthma (1/3)


title: stool at D16, goat's milk, asthma,rep1

description: stool at D16, goat's milk, asthma (1/3)


title: Q.WT 12M E: 12-m-o EpSC rep2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from epidermal stem cells

hyb_protocol: Mouse Gene 1.0 ST arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.3.1).

source_name: Epidermal stem cells from 12-m-o mice

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

growth_protocol: This experiment has been done with animals.

extract_protocol: RNeasy Micro Kit (QIAGEN, Catalog No. 74004) was used according to the manufacturer's instructions.

treatment_protocol: No treatment was applied to the animals

value: 12 months

value: epidermal stem cells


title: R.WT 12M D+F: 12-m-o EpSC rep3


title: stool at D16, naïve,rep3

description: stool at D16, naïve (1/3)

value: naïve


title: P.WT 12M A: 12-m-o EpSC rep1


title: cr-leaf.WGS_pol4_individual_2

value: leaf


title: Mo.6C+II-.BM_1

data_processing:
Critical threshold (Ct) values were obtained from qPCR profiling with an upper limit of 40. Across sample normalization was performed for each qPCR plate separately as follows: i) the arithmetic mean of all assays for each sample was calculated. ii) the median of sample means was divided by the arithmetic mean for each sample to create a scaling factor. iii) Ct values for each sample were multiplied by their scaling factor. Following normalization, individual assay outliers were identified either by visual inspection or based on a Z-score greater than 4, relative to all other samples. Next, normalization was redone with outlier assays set as missing. Missing values were then imputed using the mice package in R with default settings and 10 iterations.
Batch correction was performed only for a subset of miRNAs (223 total) that were assessed to have a significant association with batch, because batch correcting all miRNAs would have removed signal from cell type specific miRNAs that were only seen in a limited number of batches. Batch associated miRNAs were selected in 2 rounds. The first was a broad round of selection that included all cell types that had at least one replicate in 2 different batches. Variation due to cell type was removed using the removeBatchEffect function from the limma package, then an F-test in limma was performed with respect to batch for each miRNA on the resulting values. miRNAs were selected for batch correction if they had a Bonferroni adjusted p value <0.01 and a mean Ct value <35 across all samples involved. After miRNA selection, batch correction was performed using ComBat only for the selected miRNAs.
Following normalization and batch correction, Ct values were converted to arbitrary units (AU) for easier interpretation. We determined a limit of reliable detection at a Ct value of 28, which was assessed through the standard curves of 10 miRNAs and inter-replicate variability at different Ct thresholds. Our AU scale was designed so that a Ct value of 28 corresponded to a value of 1 AU. Ct values were converted to AU with the formula: 2^(28 - exp[i,j]), where exp is the Ct value matrix for all samples and miRNAs, i is a given miRNA, and j is a given cell type. A pseudocount of 0.1 was added to all assays following conversion.

value: male


title: stool at D16, asthma,rep2

description: stool at D16, asthma (1/3)


title: cr-leaf.WGS_pol4_individual_1


title: cr-leaf.WGS.WT

description:
Capsella rubella two months leaves of wt (Cr1GR1)
cr.leaves.TEs_detected_insertions.txt.gz

source_name: CR two months leaves wt

extract_protocol:
Genomic DNA was isolated from leaves of one Capsella wild-type plant mutants using the MagJET Plant Genomic DNA Kit (K2761).
Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: wt (Cr1GR1)


title: Mo.6C-II-.Bl_1

value: Blood

value: Ly6Clow monocytes


title: stool at D16, goat's milk, naïve,rep2

description: stool at D16, goat's milk, naïve (1/3)


title: stool at D16, naïve,rep2

description: stool at D16, naïve (1/3)


title: M.WT 6M E+F: 6-m-o EpSC rep1

source_name: Epidermal stem cells from 6-m-o mice

value: 6 months


title: N.WT 6M B+D: 6-m-o EpSC rep2


title: L.WT 4M E+F: 4-m-o EpSC rep3

source_name: Epidermal stem cells from 4-m-o mice

value: 4 months


title: Mo.6C+II-.Bl_2


title: cr-leaf.WGS_pol4_individual_3


title: K.WT 4M B+C: 4-m-o EpSC rep2


title: stool at D16, naïve,rep1

description: stool at D16, naïve (1/3)


title: cr-microspore.RNAseq.WT.replicate2

description:
Capsella rubella microspore of wt (Cr1GR1)
cr.microspore.RNAseq.rpkm.txt.gz

source_name: CR microspore wt

extract_protocol:
Capsella microspores were ground in a pre-cooled mortar with Lysis/Binding Solution of the mirVana™ miRNA isolation kit. Long RNAs ( > 200 nt) were seperated for RNA-seq.
Total RNA was treated with the Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490) . Libraries were prepared from the resulting mRNA with the NEBNext® Ultra™ II kit (NEB #E7770S).

treatment_protocol: Material was generated by Percoll percoll gradient following previously published procedures (Duplakova et al., 2016)

value: microspore


title: O.WT 6M A+C: 6-m-o EpSC rep3


title: cr-microspore.RNAseq.WT.replicate1


title: stool at D16, asthma,rep1

description: stool at D16, asthma (1/3)


title: cr-microspore.RNAseq.pol4.replicate2

description:
Capsella rubella microspore of nrpd1a (Cr1GR1)
cr.microspore.RNAseq.rpkm.txt.gz

source_name: CR microspore nrpd1a


title: Mo.6C+II-.Bl_1

source_name: primary


title: cr-microspore.RNAseq.pol4.replicate1


title: MF.microglia.CNS_1

value: Brain

value: Microglia


title: MF.microglia.CNS_2


title: stool at D16, cow's milk, naïve,rep2

description: stool at D16, cow's milk, naïve (1/3)


title: H.WT_2.5M_B+D: 2.5-m-o EpSC rep2

source_name: Epidermal stem cells from 2.5-m-o mice

value: 2.5 months


title: J.WT 4M A+D: 4-m-o EpSC rep1


title: I.WT_2.5M_C+E: 2.5-m-o EpSC rep3


title: stool at D16, cow's milk, asthma,rep3

description: stool at D16, cow's milk, asthma (1/3)

value: asthma


title: cr-microspore.sRNA.WT.replicate1

description: Capsella rubella microspore of wt (Cr1GR1)

extract_protocol:
Capsella microspores were ground in a pre-cooled mortar with Lysis/Binding Solution of the mirVana™ miRNA isolation kit. Short RNAs (< 200 nt) were seperated and followed by size selection on a 15% TBE-Urea polyacrylamide gel.
sRNA seq libraries were generated with the NEBNext® Multiplex Small RNA kit (NEB #E7300S).


title: MF.SI_1

value: Small intestine

value: SI macrophages


title: stool at D16, cow's milk, asthma,rep2

description: stool at D16, cow's milk, asthma (1/3)


title: MF.LI_2

value: Large intestine

value: LI macrophages


title: G.WT_2.5M_A+F: 2.5-m-o EpSC rep1

value: epidermal stem cells


title: MF.LI_1


title: cr-microspore.sRNA.pol4.replicate1

description: Capsella rubella microspore of nrpd1a (Cr1GR1)

value: nrpd1a (Cr1GR1)


title: cr-microspore.sRNA.pol4.replicate2


title: F.WT 1M C+D: 1-m-o EpSC rep3

source_name: Epidermal stem cells from 1-m-o mice

value: 1 month


title: MF.SI_2

value: male


title: MF.RP.Sp_2

value: Spleen

value: Red pulp macrophage


title: stool at D0, naive,rep3

description: stool at D0, naive (1/3)

source_name: wild-type

value: naïve


title: cow's milk (mom),rep1

description: cow's milk (mom) (1/2)

value: niave


title: MF.RP.Sp_1


title: at-pollen.sRNA.rdr6

description: Arabidopsis thaliana pollen of rdr6 (Columbia-0)

data_processing:
small-RNA: Adapters were removed from the 36 bp long single-end sRNA reads in each library. The resulting18-30 bp long reads were mapped to the reference genomes. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
Genome_build: TAIR10
Supplementary_files_format_and_content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the reference genome. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.

organism: Arabidopsis thaliana

source_name: AT pollen rdr6

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.

extract_protocol:
Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10%) for 3 min, followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Purification of pollen expressing the GFP-miR845b sensor in dcl1-5/+ and dcl1/+,dcl2/dcl4 mutants was performed by vortexing open flowers in 1 mL of PEB and filtering through a 30um mesh before FACS. Pollen population was identified in SSC/FSC scatter plots, and GFP fluorescence was analyzed by excitation with a 488nm laser and detected with a 530/30 bandpass filter. Pollen total RNA was extracted using Trizol LS reagent (Life Technologies) by vortexing with glass beads for 5 minutes, and concentrated with Direct-zol columns (Zymo Research).  Small RNAs were purified by running total RNA on acrylamide gels (15% polyacrylamide, 7M urea) and performing size selection of approximately 18 to 30-nt region using a small RNA ladder (Zymo Research). The small RNA fraction was isolated from acrylamide gel plugs by grinding with a plastic pestle in Trizol LS (Life Technologies), and concentrated using Direct-zol columns (Zymo Research).
Libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina) following manufacturer instructions.

value: pollen


title: stool at D0, asthma,rep2

description: stool at D0, asthma (1/3)


title: at-pollen.sRNA.rdr2

description: Arabidopsis thaliana pollen of rdr2 (Columbia-0)

source_name: AT pollen rdr2


title: stool at D16, cow's milk, asthma,rep1

description: stool at D16, cow's milk, asthma (1/3)


title: stool at D0, naive,rep2

description: stool at D0, naive (1/3)


title: D.WT 1M A+F: 1-m-o EpSC rep1


title: stool at D0, asthma,rep3

description: stool at D0, asthma (1/3)


title: Blood_24 hr_MCAO_rep3

city: Guangzhou

first: Dan

last: Lu

state: Guangdong

address: No.601, West Huangpu Avenue

department: Neurology and Stroke center

institute: Jinan University

description:
[12](normalized)
circRNA expression after 24 hr in MCAO mouse blood

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Two microarray platform definitions, GPL21826 and GPL7173, were used to uncover genes probed by the arrays. Regular probes that were not at least 10% brighter than the control probes in all twelve arrays were removed, resulting in 10324 high quality probes out of 15712 (66%). Bioconductor’s limma package (Ritchie et al., 2015) was used to identify differently expressed circRNAs at four different time points i.e. time 0, 5 minutes, 3 hours, and 24 hours, each with three replicates, resulting in twelve samples in total. Time 0 is the control group (SHAM), resulting in three comparisons: 5 min (MCAO 5m) versus 0 h (SHAM), 3 h (MCAO 3h) versus 0 h (SHAM), and 24 h (MCAO 24h) versus 0 h (SHAM). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Briefly, the single-channel Agilent data collection model was used where only green signal was considered. Intra-array variation was normalized by adaptive background correction recommended by limma. Inter-array background signals were further corrected by quantile method.
Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering (absolute log fold-change 2, adjusted P value < 0.05). Differentially expressed circRNAs between two samples were identified through Fold-change filtering. Hierarchical Clustering was performed to show the distinguishable circRNA expression pattern among samples. Differentially expressed circRNAs were ranked by log fold-change, and were considered significant if the fold-change was 2.

source_name: Peripheral Blood_24 hr_MCAO

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Prior to blood collection, the PAXgene RNA stabilizer solution was removed from the BD Vacutainer style PAXgene blood RNA tubes. Whole blood obtained from the cardiac puncture of mice under anesthesia was collected into heparinized tube (Wang et al., 2004, Krawiec et al., 2009). All tubes were gently inverted for 5 min directly after collection and incubated for 2 h at room temperature and then stored at -80 °C until processing for RNA extraction. Total RNA was extracted from blood samples using PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Focal ischemia was induced by intraluminal middle cerebral artery occlusion (MCAO) for 5 min, 3h and 24 h using a monofilament nylon string coated with silicon (MSMC23B104PK100, RWD Life Science, Shenzhan, China) in male Balb/c mice under isoflurane anesthesia as described earlier (Wang et al., 2004, Krawiec et al., 2009). Physiological parameters (PaO2, PaCO2, blood pressure) were monitored and rectal temperature was controlled at 37.0±0.5 °C. Cortical cerebral blood flow was monitored using a blood perfusion imager (PeriCam PSI System, Perimed AB, Stockholm, Sweden). None of the animals showed any adverse effects before euthanasia. Animal blood was extracted after different time points of surgery. Sham-operated mice underwent the same surgical procedure except MCAO was used for 0 min time point.

value: 8 weeks

tag: Sex

tag: treatment

value: middle cerebral artery occlusion (MCAO)-operated

tag: timepoint

value: whole blood

tag: molecule subtype

value: circRNA


title: stool at D0, naive,rep1

description: stool at D0, naive (1/3)


title: Blood_24 hr_MCAO_rep2

description:
[11](normalized)
circRNA expression after 24 hr in MCAO mouse blood


title: stool at D0, asthma,rep1

description: stool at D0, asthma (1/3)

value: asthma


title: B.WT p20 D+E: 0.6-m-o EpSC rep2

source_name: Epidermal stem cells from 0.6-m-o mice

value: 18 days


title: Patient 10_T5

first: Yonggang

address: South 4th Ring West Road 119, Fengtai District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080211_raw_Data.txt_T5

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Each single sample was at least performed twice in terms of technical or biological replicates under the reproducibility more than 0.975. The signal intensity was loaded into Rosetta Resolver System® (Rosetta Biosoftware, USA) to do data preprocessing and apply to 75 percentile centering normalization. The errors of the sample were estimated by using the error-weighted approach at the same time. Both of fold change and p-value for pair-wise sample comparison were calculated for evaluating differentially expressed genes.

source_name: atypical meningioma

label_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

extract_protocol: otal RNA was extracted using the TRIzol® Reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions. The concentration and purity of the RNA was measured by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). Purity was checked by the ratio of the OD260/OD280 and OD260/OD230. The quality of total RNA was accessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: All patients underwent gross total surgery resection and adjuvant radiotherapy, the external-beam radiation was delivered by conventional fractionation up to a total dose of 50–60 Gy.

tag: recurrence status 3 years after operation

value: yes

tag: histology

value: atypical


title: E.WT 1M B+E: 1-m-o EpSC rep2

value: epidermal stem cells


title: Patient 8_T3

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080209_raw_Data.txt_T3


title: C.WT p20 F+A: 0.6-m-o EpSC rep3


title: A.WT p20 B+C: 0.6-m-o EpSC rep1


title: MF.pIC.PC_2

first: Brian

last: Brown

institute: Icahn School of Medicine at Mount Sinai

tag: organ

value: Peritoneal cavity

tag: cell type

value: Peritoneal macrophages + poly(I:C)

tag: rna concentration (ng/ul)

tag: processing batch


title: MF.Alv.Lu_1

value: Lung

value: Alveolar macrophage

tag: cell markers

tag: strain

tag: gender

value: male


title: Patient 7_T2

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080208_raw_Data.txt_T2

value: female


title: MF.pIC.Alv.Lu_2

value: Alveolar macrophage + poly(I:C)

tag: isolation date

tag: lab


title: Blood_3 hr_MCAO_rep3

description:
[9](normalized)
circRNA expression after 3 hr in MCAO mouse blood

source_name: Peripheral Blood_3 hr_MCAO

tag: tissue


title: MF.pIC.Alv.Lu_1

tag: cell count (thousands)


title: MF.pIC.PC_1


title: MF.Alv.Lu_2


title: stool at D0, cow's milk, naïve,rep3

description: stool at D0, cow's milk, naïve (1/3)

extract_protocol: Stool samples were frozen then stored at -80 °C. QIAamp DNA Stool Mini Kit was used to purify DNA from frozen stool samples according to protocol. DNA quality was evaluated using MaestroNano spectrophotometry (Maestrogen, Las Vegas, NV, USA) in the absorbance ratio A260 nm / A280 nm.

tag: asthma

value: naïve


title: stool at D0, cow's milk, asthma,rep3

description: stool at D0, cow's milk, asthma (1/3)


title: Blood_3 hr_MCAO_rep2

description:
[8](normalized)
circRNA expression after 3 hr in MCAO mouse blood

tag: age

value: 8 weeks

tag: Sex

tag: treatment


title: Blood_24 hr_MCAO_rep1

description:
[10](normalized)
circRNA expression after 24 hr in MCAO mouse blood

value: middle cerebral artery occlusion (MCAO)-operated

tag: timepoint

tag: molecule subtype


title: Blood_5 min_MCAO_rep3

description:
[6](normalized)
circRNA expression after 5 min in MCAO mouse blood

source_name: Peripheral Blood_5 min_MCAO

value: whole blood


title: MF.fem.PC_1

tag: organ

value: Peritoneal macrophages

value: AR


title: Blood_3 hr_MCAO_rep1

description:
[7](normalized)
circRNA expression after 3 hr in MCAO mouse blood

value: circRNA


title: stool at D0, cow's milk, naïve,rep2

description: stool at D0, cow's milk, naïve (1/3)


title: Patient 6_T1

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080207_raw_Data.txt_T1

tag: recurrence status 3 years after operation

value: yes

tag: histology


title: Patient 5_C5

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080206_raw_Data.txt_C5

value: no

value: atypical


title: stool at D0, cow's milk, naïve,rep1

description: stool at D0, cow's milk, naïve (1/3)


title: stool at D0, cow's milk, asthma,rep2

description: stool at D0, cow's milk, asthma (1/3)

value: asthma


title: MF.PC_4

value: Peritoneal cavity

tag: cell type

tag: rna concentration (ng/ul)

tag: processing batch


title: Blood_5 min_MCAO_rep2

description:
[5](normalized)
circRNA expression after 5 min in MCAO mouse blood


title: stool at D0, cow's milk, asthma,rep1

description: stool at D0, cow's milk, asthma (1/3)


title: Patient 3_C3

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080204_raw_Data.txt_C3

tag: gender


title: Patient 4_C4

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080205_raw_Data.txt_C4


title: MF.PC_1

tag: cell markers

tag: strain

tag: isolation date


title: Blood_5 min_MCAO_rep1

description:
[4](normalized)
circRNA expression after 5 min in MCAO mouse blood

tag: tissue


title: P7 unfractionated Rep1

status: Public on Jan 22 2020

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

description:
Whole cell
Cell ranger V3.0 based mapping and filtering

data_processing:
De-multiplexing and FastQ file generation
Cell ranger based mapping and filtering
Seurat R package for QC filtering and normalization
Seurat and monocle for clustering and trajectory
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of genes, counts and cell barcodes

source_name: perinatal testicular cells

extract_protocol:
Testis tissue was dissociated with two step enzymatic digestion with collagenase-IV and trypsin-EDTA. Single cell suspension were diluted for loading on Chromium chip for 10X Genomics library preparation and subsequent sequencing.
Chromium Single Cell Kit [v2 chemistry]
10x single cell RNA sequencing

value: Postnatal day 7

value: Testes