title: siLSD1_48hours_rep2

city: Kyoto

first: Kohei

last: Doi

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

country: Japan

institute: Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped against the reference genome hg38 using HISAT2 (v2.1.0) and counted using feature Counts (v1.6.3) with Galaxy (Goecks et al. 2010).
Reads were normalized using DESeq2 (v1.18.1) with Galaxy.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD14-positive monocytes

growth_protocol: Human CD14-positive monocytes were nucleofected with scrambled control or LSD1-specific siRNAs

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit.
Libraries were created using NEBNext Ultra RNA LP Kit

treatment_protocol: Monocytes were cultured with M-CSF (20 ng/ml) and RANKL (40 ng/ml) stimulation for 0, 24, or 48 hours.

tag: sirna

tag: treatment

value: treated with RANKL for 48 hours

tag: donor


title: siLSD1_24hours_rep2

status: Public on Feb 01 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: treated with RANKL for 24 hours


title: M1-3

city: New Haven

first: Gianfilippo

last: Coppola

state: CT

address: 333 Cedar st

department: Pathology

country: USA

institute: Yale University

description:
30M1-3
Cerebral Cortex
Cortical Astroglial RNA

data_processing:
Library strategy: TRAP-Seq
Illumina Casava software used for basecalling.
Sequencing reads were mapped to the mouse genome (GRCm38.p5) and the Ensembl (release-84) transcriptome annotation, using HISAT2 (Pertea et al., 2016). The resulting SAM files were converted to BAM formant using SAMtools (Li et al., 2009). The gene expression levels as counts were estimated using featureCounts (Liao et al., 2014) with the following options: -t exon; -g gene_id; -F “GTF”; -B; -s 0; -p; -a. Counts from technical replicates were added.
Raw read counts were then filtered requiring more than 1 CPM (counts per million) in at least 25% of the samples and 16208 survived the filter and were considered for further analysis.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: data_Counts.tsv: Matrix table with raw counts for every gene and every sample.

organism: Mus musculus

source_name: P1 Male 3

growth_protocol: Mice raised in conventional housing (ad lib food and water) with enrichment (house and chew block) and group housed with littermates until tissue collection.

extract_protocol:
Whole cortex of Aldh1l1-L10-GFP+ mice were used; mice underwent rapid decapitation and cortex was dissected and fixed in cyclohexamide to fix the polysomes (mRNA with ribosomal subunits). Cortical tissues were homogenized and then incubated with biotinylated magnetic beads coated with protein L + anti-GFP to immunoprecipitate astroglial-specific polysomes. Polysomes were lysed and mRNA was extracted (see previous work for detailed methods: Simard et al., (2018) Neuropsychopharmacol.)
RNA samples were sent to the Yale K.E.C.K facility for sample QC as per Simard et al. 2018: RNA quality was determined using a nanodrop and RNA integrity was determined by running an Agilent Bioanalyzer gel (RINs >8). mRNA was purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C. Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries. The cDNA library was then end-repaired and A-tailed, adapters were ligated and second-strand digestion was performed by Uricil-DNA-Glycosylase. Indexed libraries that met appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit: Kapa Library Quant Kit (Illumina) (KAPA Biosystems # KK4854-07960298001) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Only samples with a yield of ≥0.5 ng/ul were used for sequencing.

tag: age

value: postnatal day 1

tag: Sex

value: male

tag: genotype

tag: background strain

tag: cell type

value: Astroglial Cells


title: siLSD1_00hours_rep2

value: untreated


title: Male_Day6 Nons1

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using hisat2 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

source_name: mESC

growth_protocol: Male C57/Bl6 mESC lines were established as described in the associated manuscript.  Cells were expanded in 2i, then induced to differentiate by weaning into DME HiHi media.

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo Quick RNA kit
Libraries were prepared according to standard Illumina RNA-seq protocols

treatment_protocol: Cells were virally transduced with shRNA on day 2 of differentiation, then selected with puromycin on day3 and harvested on the indicated days.

tag: strain

value: Male

value: mESC line

tag: genotype/variation

value: Nonsilencing control


title: F7-30

description:
28M7-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 30

value: postnatal day 7

value: female


title: M4-3

description:
29M4-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Male 3

value: postnatal day 4


title: stimulated B cells, DKO, 2C

city: New York

first: Ryan

last: Smolkin

state: NY

address: 408 E 69th St

institute: MSKCC

data_processing:
Illumina Casava software was used for base calling
Sequencing files were put through a GATK-based pipeline to remove illumina adapters and low quality reads, prior to alignment to mm10 with STAR 2.7.7a and removal of duplicates
Aligned samples were combined into a single count matrix according to gencode vM25 using featureCounts v2.0.1 (parameters -p -t exon -g gene_id)
Featurecounts txt file had columns renamed to sample names for consistency and rows renamed to gene names for ease of future analysis
Genome_build: mm10
Supplementary_files_format_and_content: CSV containing raw gene count for each sample

molecule: polyA RNA

source_name: Primary murine B cells activated with LPS and IL4

extract_protocol:
Naive B cells were purified from spleens of 12-week old mice by negative selection using anti-CD43 microbeads. Cells were then stimulated in serum-containing RPMI media with lipopolysaccharide and interleukin-4 for 48 hours. Cells were harvested and their total RNA extracted using Quick-RNA™ Microprep Kit (ZymoResearch). mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation (New England BioLabs).
Stranded Illumina libraries were prepared with Swift Rapid RNA Library Kit according to the manufacturer’s instructions (Swift Biosciences). Indexed libraries were sequenced on a HiSeq X Ten platform, and an average of 30 million 150-bp paired-end reads were generated for each sample (Novogene, Beijing, China).

value: Female

tag: tissue

value: Spleen

value: B cells

value: Gen1-Mus81-double knockout

value: LPS and IL4

tag: biological replicate


title: Male_Day5 Smarcc1.7

value: Smarcc knockdown


title: stimulated B cells, DKO, 2B


title: Male_Day5 Smarcc1.6


title: siControl_48hours_rep2

value: siControl

value: treated with RANKL for 48 hours


title: Male_Day5 Smarca4.6


title: siControl_00hours_rep2


title: siControl_24hours_rep2

value: treated with RANKL for 24 hours


title: M35-3

description:
26M35-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Male 3

value: postnatal day 35

value: male

value: Astroglial Cells


title: stimulated B cells, DKO, 2A


title: Water treatment (control) before [AW]

city: Ames

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description:
RNA samples were collected before exposure to water (AW-bef/BW-bef/CW-bef)
AW-bef

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qulaity checked with fastqc, mapped to GCF_000005845.2_ASM584v2  using BWA
FeatureCounts from subread was used to estimate read counts for genes
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.39
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample.

organism: Escherichia coli

source_name: E. coli cultures

growth_protocol: E. coli cultures were grown in sterilized lake water supplemented with 100 mg/L yeast extract and 1 mM sodium phosphate buffer to a final pH of approximately 8.4 for 48 hours.

extract_protocol:
Cells were lysed using 5 mg/mL lysozyme in TE buffer. Following lysis, RNA was extracted using RNeasy Mini Kit (Qiagen Inc.) and following manufacturers recommended instructions. To ensure the elimination of contaminating DNA, RNA samples were also treated with DNAse 1 (Qiagen Inc.). Ribosomal RNA depletion was carried out to remove rRNA using Ribo-zero rRNA removal kit (Bacteria) from Illumina
RNA libraries of purified RNA were constructed with TruSeq Stranded mRNA library preparation kit following manufacturer’s instructions

treatment_protocol: Cultures were treated with either 35 µM hypochlorite, 400 µM ferrate, or water (control) for 15 minutes. Cultures were harvested through centrifugation, washed in 10 mM phosphate buffer and then suspended in RNAlater (Invitrogen). Samples were kept at 4°C for 48 hours before being centrifuged and stored at -20°C.

tag: replicate number


title: stimulated B cells, DKO, 1B

value: Male


title: stimulated B cells, DKO, 1C


title: M14-3

description:
27M14-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Male 3

value: postnatal day 14


title: Male_Day4 Nons1

value: mESC line

value: Nonsilencing control


title: siLSD1_48hours_rep1


title: MA-3

description:
25MA-3
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Male 3

value: adult


title: stimulated B cells, DKO, 1A


title: stimulated B cells, MKO, 2C

value: Female


title: F4-2

description:
23F4-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Female 2

value: postnatal day 4

value: female


title: siLSD1_24hours_rep1


title: Day7 Smarcc1.7

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using TopHat v2.0.12 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

growth_protocol: Female FVB/CAST F1 mESC lines were established as described in the associated manuscript.  Cells were expanded in 2i, then induced to differentiate by weaning into DME HiHi media.

value: FVB/CAST F1


title: F14-2

description:
21F14-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Female 2


title: siLSD1_00hours_rep1

value: untreated


title: stimulated B cells, MKO, 2B

value: Spleen

value: B cells

value: LPS and IL4


title: Day7 Smarcc1.6

value: Smarcc knockdown


title: stimulated B cells, MKO, 2A


title: M1-2

description:
18M1-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Male 2

value: postnatal day 1


title: Pubis57C

city: Cambridge

first: Mariel

last: Young

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

data_processing:
Ribosomal RNA removal: SortMeRNA version 2.1b
Align and blacklist reads to multiple rRNA databases
Alignment to hg19 genome: STAR version 2.6.0
Default alignment parameters
Read counting: RSEM version 1.2.29
Default read counting parameters
Genome_build: hg19
Supplementary_files_format_and_content: RSEM output tab-delimited file with gene expression data, TPM, and FPKM

source_name: Human Pubis E57

growth_protocol: in vivo collected E50s human pelvis chondrocytes

extract_protocol:
Upon arrival the sample was dissected under a light dissection microscope. Pelvis elements were complete but then manually separated from one another for RNA collection, extraction, and QC. Element samples were then went throuch cDNA library prep and RNA sequencing.
Kapa mRNA Directional Library Preparation

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: chondrocytes

value: Pubis


title: Day4 Smarcc1.7


title: FA-2

description:
19FA-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Female 2

value: Astroglial Cells


title: stimulated B cells, GKO, 2C


title: M14-2

description:
15M14-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Male 2

value: postnatal day 14

value: male


title: stimulated B cells, MKO, 1A

value: Male


title: Day7 Nons

value: mESC line

value: Nonsilencing control


title: siControl_48hours_rep1

value: siControl

value: treated with RANKL for 48 hours


title: Day6 Smarcc1.6

value: FVB/CAST F1

value: Female


title: siControl_00hours_rep1

value: untreated


title: siControl_24hours_rep1

value: treated with RANKL for 24 hours


title: stimulated B cells, MKO, 1B

value: Spleen

value: B cells

value: LPS and IL4


title: Day5 Smarcc1.7

value: Smarcc knockdown


title: Pubis57B

value: chondrocytes

value: Pubis


title: Day5 Smarcc1.6


title: Day6 Smarcc1.7


title: M4-2

description:
17M4-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Male 2

value: postnatal day 4

value: Astroglial Cells


title: F1-1

description:
12F1-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Female 1

value: postnatal day 1

value: female


title: Pubis59

source_name: Human Pubis E59


title: MA-2

description:
13MA-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Male 2

value: adult

value: male


title: stimulated B cells, GKO, 2B


title: Day6 Nons

source_name: mESC

value: mESC line

value: Nonsilencing control


title: Pubis54B

source_name: Human Pubis E54


title: Day4 Smarcc1.6

value: FVB/CAST F1

value: Female


title: stimulated B cells, GKO, 2A

source_name: Primary murine B cells activated with LPS and IL4


title: Pubis57A


title: stimulated B cells, MKO, 1C

value: Male


title: M7-2

description:
16M7-2
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Male 2

value: postnatal day 7


title: F14-1

description:
9F14-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Female 1

value: postnatal day 14


title: stimulated B cells, GKO, 1C

value: Spleen

value: B cells

value: LPS and IL4


title: Day5 Nons


title: Pubis54A

value: chondrocytes

value: Pubis


title: M35-10

description:
8F35-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Male 10

value: postnatal day 35

value: Astroglial Cells


title: stimulated B cells, GKO, 1B


title: Day4 Nons


title: stimulated B cells, GKO, 1A


title: Pubis53A

source_name: Human Pubis E53


title: Day0


title: M1-1

description:
6M1-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P1 Male 1

value: postnatal day 1


title: Ischium59

source_name: Human Ischium E59

value: Ischium


title: M4-1

description:
5M4-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P4 Male 1

value: postnatal day 4

value: male


title: NomeSeq-Smarcc16-day7_S9

library_source: genomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to a bisulfite converted mm10 with FVB and CAST SNP positions N-masked using Bismark
The percentage methylation at individual GpC sites was calculated and averaged across 200 positions using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file showing percentage methylation at individual GpC sites averaged across 200 positions

molecule: genomic DNA

extract_protocol:
Cells were split off the plate fixed and processed with NOMe-seq protocol
Libraries were prepared with Accel-NGS Methyl-Seq DNA Library kit

value: mESC line

value: Smarcc knockdown

tag: molecule subtype

value: Bisulfite converted DNA


title: Ischium57C

source_name: Human Ischium E57


title: stimulated B cells, WT, 2A

value: Female

value: WT


title: NomeSeq-Smarcc16-day5_S7

value: FVB/CAST F1


title: Ischium57B


title: stimulated B cells, WT, 2B

value: Spleen


title: Ischium57A


title: NomeSeq-Smarcc16-day4_S6


title: M14-1

description:
3M14-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P14 Male 1

value: postnatal day 14


title: NomeSeq-Smarcc16-day6_S8


title: stimulated B cells, WT, 1C

value: Male

value: B cells

value: LPS and IL4


title: stimulated B cells, WT, 1B


title: Ischium54B

source_name: Human Ischium E54

value: chondrocytes


title: M35-1

description:
2M35-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P35 Male 1

value: postnatal day 35

value: Astroglial Cells


title: NomeSeq-Nons-day5_S3

value: Nonsilencing control


title: Ischium54A

value: Ischium


title: FA-1

description:
7FA-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Female 1

value: adult

value: female


title: stimulated B cells, WT, 1A


title: MA-1

description:
1MA-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: Adult Male 1

value: male


title: NomeSeq-Nons-day7_S5

value: mESC line

value: Bisulfite converted DNA


title: F7-10

description:
4M7-1
Cerebral Cortex
Cortical Astroglial RNA

source_name: P7 Female 10

value: postnatal day 7


title: Ischium53A

source_name: Human Ischium E53


title: stimulated B cells, WT, 2C

value: Female

value: WT


title: NomeSeq-Nons-day4_S2

source_name: mESC

value: FVB/CAST F1


title: CanZ_GV_ATAC_KO_C

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
All quality assessed ATAC-seq reads were aligned to the mouse reference genome (mm10) using Bowtie 2.3 with following options: --very-sensitive -X 2000 --no-mixed --no-discordant. Alignments resulted from PCR duplicates or locating in mitochondria were excluded. Only unique alignments within each sample were retained in subsequent analysis. ATAC-seq peaks were called separately for each sample by MACS2 with following options: --keep-dup all –nolambda --nomodel. Peaks in individual samples from the same development stage were subsequently merged using bedtools (https://bedtools.readthedocs.io/en/latest/). We normalized the read counts by computing the number of reads per kilobase of bin per million of reads (RPKM). To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250bp and counted the coverage for each base. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/).
Supplementary_files_format_and_content: peaks.narrowPeak, bigwig

source_name: oocytes

extract_protocol:
Oocytes were lysed in ice-cold lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2 and NP-40 (0.5%) for 15 minutes on ice to prepare the nuclei.
For ATAC-seq library preparation, immediately after lysis, Nuclei were then incubated with the Tn5 transposase (TDE1) and tagmentation buffer at 37°C for 30 minutes with shaking on a thermomixer at 500g. After the tagmentation, 0.5 ul of 10% SDS was added directly into the reaction to end the tagmentation and tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen). PCR was performed to amplify the ATAC-seq libraries using Illumina TrueSeq primers and multiplex by indexes primers with the following PCR conditions: 72°C for 3min; 98°C for 30s; and 15 thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; following by 72°C 5 min. After the PCR reaction, libraries were purified with the 1.1X AMPure beads (Beckman). All sequencing libraries were pooled and then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

value: GV oocytes

value: KO


title: Yolk Sac Cdx-DKO rep3

city: Ottawa

first: Tanya

middle: Elizabeth

last: Foley

state: ON

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
Sequencing files were converted to BAM files using R SAMtools and aligned to the mm10 reference genome using the R function GenomicFeatures and a transcript database generated from an Ensembl GTF file (mm10.refGene.gtf)
The summarizeOverlaps function from the GenomicAlignments package was used to generate a SummarizedExperiment object, which could then be used for differential expression analysis.
Differential expression was assessed using the Bioconductor package DESeq2, comparing wild type samples to Cdx-mutant (DKO) with Log2FC > 1 and padj < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: excel sheet with differentially expressed genes (baseMean values, log2FC, SE, p-values, pajd, and fold change)
Supplementary_files_format_and_content: BAM files

source_name: E9.5 yolk sac

extract_protocol:
RNA was collected from E9.5 yolk sacs using the RNeasy Mini Kit (50) (Qiagen) according to the manufacturer’s instructions.
Library preparation and sequencing was conducted by the Genome Quebec Innovation Centre. mRNA libraries were generated using NEB Next dual adapters. Quality control was performed using a bioanalyzer, and samples were multiplexed and sequenced to an average of 25M reads per library using the Illumina HiSeq 4000 SR50 platform.

value: mixed background

value: embryonic yolk sac, E9.5

value: Cdx-DKO

value: tamoxifen, E5.5


title: Iium59

source_name: Human Ilium E59

value: chondrocytes

value: Ilium


title: Yolk Sac Cdx-DKO rep2


title: CanZ_GV_ATAC_KO_B


title: Yolk Sac Cdx-DKO rep1


title: Ilium57C

source_name: Human Ilium E57


title: Ilium57B


title: CanZ_GV_ATAC_KO_A


title: NomeSeq-Nons-day6_S4

value: Nonsilencing control


title: Yolk Sac WT rep3


title: Yolk Sac WT rep2


title: CanZ_GV_ATAC_Het_B

value: Cabin1 Het


title: NomeSeq-day0_S1


title: CanZ_GV_ATAC_Het_C


title: Day3 rep2 [X14_d3_single]

growth_protocol: Female Xmas mESC lines were established as described in the associated manuscript.  Cells were expanded in 2i, then induced to differentiate by weaning into DME HiHi media.

treatment_protocol: Cells were harvested on the indicated days.

value: Xmas mESC line

tag: time point


title: Ilium54B

source_name: Human Ilium E54


title: CanZ_GV_ATAC_Het_A


title: Day4 rep1 [X14_d4_double]


title: Yolk Sac WT rep1


title: Ilium57A


title: Ilium54A


title: 4CBA_3

city: Berkeley

first: Greg

last: Timblin

state: CA

department: MCB

institute: UC Berkeley

data_processing:
Unmanipulated reads were aligned to the mouse geneome (mm10) using STAR, producing SAM files.
SAM files were converted to tag directories using HOMER.
For reporting, HOMER was used to calculate nomalized reads per gene (reads per kilobase per million mapped reads, or RPKM).
For differential expression analysis, HOMER was used to count raw reads per gene. Thes raw read counts were using as input to DESeq2 to call differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing either RPKM values for each gene, or DEseq2 differential expression analysis output.

source_name: brown adipocytes

growth_protocol: Immortalized brown preadipocytes were differentiated to mature adipocytes in DMEM containing 10%FBS, 1%P/S and differentiation cocktail for 6 days

extract_protocol:
Total RNA was isolated using trizol following DNase I treatment.
Libraries were prepared from 500ng of total mRNA using Stranded mRNA-seq Kit (KAPA) and NEXTFlex barcoded adaptors (Bioo Scientific).

treatment_protocol: Brown adipocytes were treated with vehicle control or 4-chlorobenzoic acid (4CBA, 4mM) at day 4 for 48 hours. Media was refreshed after 24 hr.

value: Cell line


title: Zscan4_2cell_C

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the mouse reference genome (mm10) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference. Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. DAVID (https://david.ncifcrf.gov) and IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively.
All quality assessed ATAC-seq reads were aligned to the mouse reference genome (mm10) using Bowtie 2.3 with following options: --very-sensitive -X 2000 --no-mixed --no-discordant. Alignments resulted from PCR duplicates or locating in mitochondria were excluded. Only unique alignments within each sample were retained in subsequent analysis. ATAC-seq peaks were called separately for each sample by MACS2 with following options: --keep-dup all –nolambda --nomodel. Peaks in individual samples from the same development stage were subsequently merged using bedtools (https://bedtools.readthedocs.io/en/latest/). We normalized the read counts by computing the number of reads per kilobase of bin per million of reads (RPKM). To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250bp and counted the coverage for each base. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/).
Genome_build: mm10
Supplementary_files_format_and_content: txt

extract_protocol:
The RNA-seq libraries were generated from individually cells using Smart-seq2 with minor modification. Briefly, individually cells were lysed and mRNA was captured and amplified by using Smart-seq2 v4 kit (Clontech). After pre-amplification and AMPure XP beads purification, amplified RNAs were quality checked using Agilent High Sensitivity D5000 kit (Agilent Technologies). For ATACseq libraries prepration, oocytes or embryos were lysed in ice-cold lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2 and NP-40 (0.5%) for 15 minutes on ice to prepare the nuclei.
High quality of amplified RNAs were subject to library preparation using Nextera XT DNA Library Preparation Kit (Illumina) and multiplexed by Nextera XT Indexes (Illumina). The quality and quantity of sequencing libraries were determined using Qubit 3.0 assay (Life Technologies) and Agilent High Sensitivity kit at Tapestation 4200 system (Agilent), respectively. For ATAC-seq library preparatio, immediately after lysis, Nuclei were then incubated with the Tn5 transposase (TDE1) and tagmentation buffer at 37°C for 30 minutes with shaking on a thermomixer at 500g. After the tagmentation, 0.5 ul of 10% SDS was added directly into the reaction to end the tagmentation and tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen). PCR was performed to amplify the ATAC-seq libraries using Illumina TrueSeq primers and multiplex by indexes primers with the following PCR conditions: 72°C for 3min; 98°C for 30s; and 15 thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; following by 72°C 5 min. After the PCR reaction, libraries were purified with the 1.1X AMPure beads (Beckman). All sequencing libraries were pooled and then sequenced on the Illumina HiSeq X platform with 150-bp paired-end reads.

tag: strain background

value: Zscan4 overexpression

tag: developmental stage/tissue

value: 2-cell embryos


title: 4CBA_1


title: Ilium53A

source_name: Human Ilium E53


title: Acetabulum59

source_name: Human Acetabulum E59

value: Acetabulum


title: 4CBA_2


title: Day2 rep1 [X14_d2_double]

value: Female


title: Day1 rep2 [X14_d1_single]


title: Zscan4_2cell_A


title: Day2 rep2 [X14_d2_single]


title: CTL_3


title: CTL_2


title: Day3 rep1 [X14_d3_double]


title: Acetabulum57A

source_name: Human Acetabulum E57


title: gfp_2cell_D

value: GFP control


title: Zscan4_2cell_B


title: Acetabulum57B


title: CTL_1


title: Day8 rep4 [X18_d8_single]


title: Day7 rep4 [X18_d7_single]


title: gfp_2cell_C


title: Acetabulum54A

source_name: Human Acetabulum E54


title: single-cell RNA-seq_TAC

city: London

first: Miguel

last: Muñoz-Ruiz

address: 1 Midland Rd, Somers Town

country: United Kingdom

institute: The Francis Crick institute

data_processing:
Cellranger-2.1.1 was used to deconvolve, align and quantify the per-cell transcriptomes.
Reads were aligned to mouse mm10-1.2.0 (obtained from 10x genomics)
Genome_build: mouse mm10 (mm10-1.2.0 from 10x Genomics)
Supplementary_files_format_and_content: tar file containing 10x counts matrix, features and barcode data

source_name: Tissue-resident memory T cells (TRM)

extract_protocol:
To analyze epidermal T cell populations, separate epidermal cell suspensions were prepared as described(Mallick-Wood et al., 1998) from ears or back skin of individual animals.
libraries were prepared with the 10x Chromium 3’ mRNA-Seq kit version 2.  The cells were QC’d with trypan blue viability dye and quantified using the EVE automated cell counter.  Approximately 2000 – 3000 cells were loaded onto the 10x and prepared according to manufacturer’s instructions.

treatment_protocol: To induce allergic contact dermatitis (ACD), mice were sensitized on day 0 by epicutaneous application to razor-shaved abdominal skin of 40 μl of 0.5% DNFB in a mixture of acetone:olive oil (3:1). On day 6, mice were challenged (1st Challenge) by applying 20 μl of 0.25% DNFB in acetone:olive oil at the back skin of ear.

value: Epidermal CD8 cells

value: FVB/NTac (FVB.Tac)

value: Skint1 mutant

value: treated


title: Day7 rep3 [X18_d7_double]


title: single-cell RNA-seq_WT

value: FVB/NJ (FVB.WT)

value: WT


title: Day6 rep4 [X18_d6_single]


title: Cabin1_KO_2cell_4


title: gfp_2cell_B


title: Day8 rep3 [X18_d8_double]


title: Cabin1_KO_2cell_2


title: normal tissue 9

city: shanghai

first: Geng

last: chen

address: 500 Dongchuan Road

country: China

institute: East China Normal University

description: Total RNA (poly A+ and poly A-)

data_processing:
RNA-seq reads were mapped to the reference genome GRCh38 using HISAT2 (version 2.1.0).
Gene expression was quantified using StringTie (version 1.3.6).
Genome_build: GRCh38
Supplementary_files_format_and_content: *tpm.txt: Tab-delimited text files include TPM values for each sample.

source_name: Adjacent normal tissue

extract_protocol:
Total RNA was extracted from the 10 mg synovial sarcoma tissues after grinding by Homogenizer (Scientz) using TRIzol® Reagent (Invitrogen) and RNeasy MinElute spin column (Qiagen) according to the manufacturer's instructions. Then the integrity of the total RNA was determined by 2100 Bioanalyser (Agilent) and quantified using the NanoDrop (Thermo Scientific). About 1 ug high-quality or media-quality RNA sample (OD260/280=1.9~2.0, RIN≥4) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at WuXi NextCODE at Shanghai according to the manufacturer’s instructions (Illumina). The rRNA-depleted sequencing libraries from total RNA were prepared using Illumina TruSeq® Stranded Total RNA Gold preparation Kit. About 1 ug total RNA was used as input material, and then Ribo-Zero Gold kit was used to remove both cytoplasmic and mitochondrial rRNA. After purification of the remaining RNA without rRNA, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis. These cDNA fragments then were subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. The products were purified and enriched with PCR, and the AMPure XP Beads (Beckmen) were used to clean up the amplified target fragments to create the final cDNA library. After library construction, Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent).

tag: patient

tag: diagnosis

value: Synovial sarcoma

value: Adjacent normal tissue


title: Day5 rep4 [X18_d5_single]


title: normal tissue 10

description: Total RNA (poly A+ and poly A-)


title: Cabin1_KO_2cell_3


title: normal tissue 7

description: Total RNA (poly A+ and poly A-)


title: R213G_Male_2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Reads were aligned using STAR (v2.5.1b) to the GENCODE vM15 genome build and annotation. Reads overlapping exons were enumerated using featureCounts (subread v.1.4.4) requiring a minimum mapping quality of 10.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts per gene generated by featureCounts are supplied in the raw_count_matrix TSV file.

source_name: Recruited alveolar macrophages

extract_protocol:
7-days post bleomycin treatment, recruited alveolar macrophages (CD64 Hi , SigF Lo, CD11b Hi) were obtained using flow cytometry assisted cell sorting using a MoFlo XDP-70 flow sorter from WT and R213G mice (n = 2).
RNA was isolated from recruited alveolar macrophages using Qiagen RNeasy Micro kit and assessed for quality on an Agilent 4200 Tapestation. Directional RNA-seq was performed by preparing a library using the Nugen Universal Plus mRNAseq kit

treatment_protocol: Mice received 100ul of intratracheal bleomycin (1U/ml).

value: alveolar macrophages

value: Male

value: 8-10 weeks

value: EC-SOD homozygous R213G


title: WT_Male_2


title: Acetabulum54B

value: chondrocytes


title: WT_Male_1


title: Cabin1_Het_2cell_4

value: 2-cell embryos


title: Cabin1_KO_2cell_1


title: R213G_Male_1


title: Day1 rep1 [X14_d1_double]

value: Xmas mESC line


title: Day5 rep3 [X18_d5_double]

value: Female


title: Rad21_Halo_AID_6h_auxin_16HD_ATACseq

first: Robert

last: Tjian

address: LKS

institute: UC Berkeley/HHMI

description: 6h auxin+1.5hour 1,6Hexanediol

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools.
ATAC-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw)

source_name: 6h auxin+1.5hour 1,6Hexanediol (Rad21 depletion)

growth_protocol: JM8.N4 mouse ESCs from the C57BL/6N strain and their genome edited derivatives were cultured on 0.1% gelatin coated plates without feeders at 37°C and 5% CO2. The ESC medium was composed of the knockout DMEM(1X) optimized for ESCs (Thermo Fisher Scientific 10829-018), 15% ESC qualified Fetal Bovine Serum (ATCC SCRR-30-2020), 1 mM GlutaMAX (Thermo Fisher Scientific 35050-061), 0.1 mM MEM nonessential amino acids (Thermo Fisher Scientific 11140-50), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific 21985-023),1000 units of Leukemia inhibitory factor (LIF) (Millipore) and Antibiotic-Antimycotic (Thermo Fisher Scientific 15240-062).

extract_protocol: we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

treatment_protocol: Auxin treatment results in loss of CTCF or Rad21 through proteasomal degradation.

value: embryonic stem cells

tag: tn5 source

value: purified in house


title: gfp_2cell_A

value: GFP control


title: normal tissue 8

description: Total RNA (poly A+ and poly A-)


title: Day6 rep3 [X18_d6_double]


title: normal tissue 6

description: Total RNA (poly A+ and poly A-)


title: Cabin1_Het_2cell_3


title: Day4 rep4 [X18_d4_single]


title: Day4 rep3 [X18_d4_double]


title: Cabin1_Het_2cell_2


title: normal tissue 4

description: Total RNA (poly A+ and poly A-)


title: Rad21_Halo_AID_noauxin_16HD_ATACseq

description: no auxin+1.5hour 1,6Hexanediol

source_name: no auxin+1.5hour 1,6Hexanediol


title: Cabin1_Het_2cell_1


title: Rad21_Halo_AID_6h_auxin_washoff_ATACseq

description: 6hour auxin+24h wash off

source_name: 6hour auxin+24h wash off (Rad21 depletion followed by Rad21 production)


title: Day3 rep4 [X18_d3_single]


title: Rad21_Halo_AID_6h_auxin_ATACseq

description: 6hour auxin

source_name: 6hour auxin (Rad21 depletion)


title: Cabin1_KO_GV_4

value: GV oocytes


title: normal tissue 3

description: Total RNA (poly A+ and poly A-)


title: Day3 rep3 [X18_d3_double]


title: Rad21_Halo_AID_noauxin_ATACseq

description: no auxin

source_name: no auxin


title: normal tissue 2

description: Total RNA (poly A+ and poly A-)


title: Day2 rep4 [X18_d2_single]


title: normal tissue 1

description: Total RNA (poly A+ and poly A-)


title: FAC-sorted T cells, 85_d63

city: Woking

first: Veonica

last: Martini

state: Scotland

address: Ash Road, Pirbright

institute: The Pirbright Institute

data_processing:
Raw fastq files were used for an initial quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
CogentAP (Cogent NGS Analysis Pipeline v1.0, Takara Bio) was used to trim and add the sample barcodes to the fastq header for each sample.
The reads were then trimmed of Illumina and library prep adapters using cutadapt, and subsequentially aligned to Sus scrofa Sscrofa11.1 assembly (GCA_000003025.6) using STAR with default parameters.
UMI-tools was used to discard duplicated reads and featureCounts extracted the number of reads aligned to each gene feature.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: matrix table with FPKM values for each sample
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Broncho alveolar lavage cells (BAL)

extract_protocol:
BAL cells were stained with NP-specific tetramer, CD3 and CD8. CD3+CD8+Tetramer+ cell were FAC-sorted and total RNA extracted using PicoPure RNA Isolation Kit (Thermo Fisher) according to the manufacturer instructions followed by DNase treatment (TURBO DNA-free™ Kit, Thermo Fisher).
Isolated RNA was used as input for SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio) and PCR amplification performed.
cDNA was pooled and sequenced on NovaSeq using an S1 100 PE flow cell.

value: Inbred Babraham pigs

value: Broncho alveolar lavage cells (BAL)

tag: infection

value: intra nasal H1N1pdm09 challenge

tag: time of collection

value: 63 days post infection


title: Day1 rep4 [X18_d1_single]

tag: Sex


title: Cabin1_KO_GV_2


title: tumor tissue 10

description: Total RNA (poly A+ and poly A-)

source_name: Synovial sarcoma tissue

value: Synovial sarcoma

value: Tumor


title: tumor tissue 9

description: Total RNA (poly A+ and poly A-)


title: FAC-sorted T cells, 82_d63


title: FAC-sorted T cells, 76_d21

value: 21 days post infection


title: Cabin1_KO_GV_1


title: FAC-sorted T cells, 84_d63


title: Day2 rep3 [X18_d2_double]


title: Cabin1_KO_GV_3


title: Day1 rep3 [X18_d1_double]


title: Cabin1_Het_GV_4


title: tumor tissue 8

description: Total RNA (poly A+ and poly A-)


title: normal tissue 5

description: Total RNA (poly A+ and poly A-)

value: Adjacent normal tissue


title: tumor tissue 6

description: Total RNA (poly A+ and poly A-)


title: FAC-sorted T cells, 73_d21


title: FAC-sorted T cells, 74_d21


title: Day0 rep2 [X14_d0_single]


title: FAC-sorted T cells, R140_d7

value: 7 days post infection


title: tumor tissue 7

description: Total RNA (poly A+ and poly A-)


title: FAC-sorted T cells, P345_d7


title: Cabin1_Het_GV_3


title: Hira_GV_KO_4


title: tumor tissue 3

description: Total RNA (poly A+ and poly A-)


title: Day8 rep2 [X14_d8_single]


title: FAC-sorted T cells, G132_d7


title: tumor tissue 5

description: Total RNA (poly A+ and poly A-)


title: Cabin1_Het_GV_2


title: Day8 rep1 [X14_d8_double]


title: Hira_GV_KO_3


title: Acetabulum53A

source_name: Human Acetabulum E53

value: chondrocytes

value: Acetabulum


title: Day7 rep2 [X14_d7_single]

value: Xmas mESC line


title: Day0 rep4 [X18_d0_single]

value: Female


title: Day0 rep3 [X18_d0_double]


title: Cabin1_Het_GV_1


title: Hira_GV_KO_1


title: Hira_GV_Het_4


title: Day6 rep1 [X14_d6_double]


title: Hira_GV_Het_2


title: Serum_exosome_Con

type: RNA

city: Zhengzhou

first: Chenchen

last: Cui

state: Henan

address: Weiwu Road #7

department: Department of Reproductive Medicine Center

institute: Henan Provincial People’s Hospital

description: miRNA

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was  fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of  2x Agilent hybridization buffer was added to the fragmentation mixture and  hybridized to Agilent Human miRNA Expression（8*60K）for 17 hours at 65°C in a  rotating Agilent hybridization oven. After hybridization, microarrays were washed 1  minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray  Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area  61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set  to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3  (Agilent) using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

source_name: exosomes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Exosomes were isolated using Exoquick kit purchased from System Biosciences following the manufacturer’s protocol. Exosomal miRNAs were isolated using the miRNeasy mini Kit purchased from Qiagen.

treatment_protocol: Follicular fluid and blood samples were collected on the  day of oocyte retrieval

value: serum

tag: rna fraction

value: exosomal miRNA

tag: disease state

value: non-polycystic ovary syndrome


title: GL261 miR-21 KO cells 2

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Sequencing was done using an Illumina MiniSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text file with read counts per sample

source_name: mouse glioma cells

extract_protocol:
Total RNA was extracted using the Direct-Zol MacroRNA kit (Zymo-research).
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) . Sequencing was done using an Illumina MiniSeq

tag: genotype

value: miR-21 KO

tag: cell type


title: tumor tissue 1

description: Total RNA (poly A+ and poly A-)

tag: tissue


title: Day5 rep2 [X14_d5_single]

tag: strain


title: Hira_GV_Het_1

tag: genotype/variation

value: GV oocytes


title: GL261 miR-21 KO cells 1


title: GL261 miR-21 WT cells 3

value: miR-21 WT


title: Day5 rep1 [X14_d5_double]


title: GL261 miR-21 KO cells 3


title: Hira_GV_Het_3


title: nuclear fraction_GFP_RIP_IP

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

description: nuclear fraction, GFP-IP

data_processing:
Raw reads where trimmed (first 10 nucleotides) with FASTX-Toolki
Adapters were removed using Trimmomatic
rRNA sequences where removed with Bowtie
Clean reads were aligned to the Arabidopis TAIR10 reference genome using HISAT2
Transcript-level abundance for RNA clean reads where estimated using Salmon. Multifasta file with Arabidopsis thaliana reference transcripts (cdna and ncrna) for quasi-mapping was additionally supplemented with pri-miRNA transcirpts described in mirEX2 database.
Genome_build: TAIR10
Supplementary_files_format_and_content: transcript abundance, output format from Salmon software .sf extension

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: aerial tissue

growth_protocol: Plants were grown in soil under 16 hour light/8 hour dark cycle at 22°C

extract_protocol:
Leaves of 4 weeks old Arabidopsis plants were harvested and crosslinked using ice cold 0.1% formaldehyde solution and then flash frozen in Liquid Nitrogen. Nuclear fraction was isolated from this tissue and RNA-IP was performed using GFP Trap magnetic beads (Chromotek, code gtma-20). RNA was isolated using phenol:chloroform.
Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

value: leaf

tag: ecotype background

value: CFP

tag: rip antibodies

value: anti-GFP  (Chromotek, code gtma-20)


title: Follicuar_exosome_PCOS

description: miRNA

value: ovarian follicular fluid

value: polycystic ovary syndrome


title: GL261 miR-21 WT cells 2


title: Follicuar_exosome_Con

description: miRNA


title: SpG_Hi-C_rep2

city: Moscow

first: Anna

last: Kononkova

address: Nobel st., Building 1

department: Skoltech Center of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Hi-C reads were mapped to the D. melanogaster reference genome using distiler-nf with default settings and an option no MAPQ filter. Cooler package was used for Hi-C maps generation, replicates downsampling, and iterative correction.
Genome build: dm3/R5
Supplementary files format and content: Processed data files are genome-wide Hi-C maps merged by replicates. The file corresponding to the SpC stage was downsampled so that the total number of contacts was nearly the same in merged files for both SpG and SpC stages. These are files with multiple resolutions in mcool format. For each replicate, processed files with resolution 10kb in cool format are also supplied. These are downsampled files with the same total number of contacts.

organism: Drosophila melanogaster

source_name: bam∆86 testes mostly filled with spermatogonia

extract_protocol:
A total of 200-300 testes were fixed in PBS containing 2% formaldehyde for 10 min with occasional mixing. The reaction was quenched by an addition of 2 M glycine to a final concentration of 125 mM. Testes were pelleted by centrifugation at 1,000´g for 10 min at 4°C, resuspended in 50 ml PBS, snap-frozen in liquid nitrogen and stored at -80°C. Testes were lysed in 1.5 ml isotonic buffer [(50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5% (v/v) NP-40 substitute, 1% (v/v) Triton-X100, 1×Halt™ Protease Inhibitor Cocktail (Thermo Scientific)] on ice for 15 min after homogenization in glass tissue grinder. Cells were pelleted by centrifugation at 2,500×g for 5 min, resuspended in 100 ml DpnII buffer (New England Biolabs), and pelleted again. The pellet was resuspended in 200 ml 0.3% SDS in 1.1×DpnII buffer and incubated at 37°C for 1 h. Then, 330 ml 1.1×DpnII buffer and 53 ml 20% Triton X-100 were added, and the suspension was incubated at 37°C for 1 h. Next, 600 U of DpnII were added and the chromatin was digested overnight at 37°C with shaking at 1,400 rpm. Then, 200 U of DpnII was added and the cells were incubated for 2 h. DpnII was inactivated by incubation at 65°C for 20 min. The nuclei were harvested for 10 min at 5,000×g, washed with 100 ml NEBuffer 2 (New England Biolabs), and resuspended in 125 ml 1.2×NEBuffer 2. Cohesive DNA ends were biotinylated by adding 25 ml biotin fill-in mixture [0.025 mM dATP, 0.025 mM dGTP, 0.025 mM dTTP, 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (New England Biolabs)]. The samples were incubated at 37°C for 75 min with shaking at 1,400 rpm. Nuclei were pelleted by centrifugation at 3,000´g for 5 minutes, resuspended in 300 ml T4 DNA ligase buffer, and pelleted again. The pellet was resuspended in 300 ml T4 DNA ligase buffer and 75 U of T4 DNA ligase (Thermo Scientific) was added. Chromatin fragments were ligated at 20°C for 6 h. The cross-links were reversed by overnight incubation at 65°C in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction, followed by ethanol precipitation (glycogen at a concentration of 20 μg/ml was used as co-precipitator). After precipitation, the pellets were dissolved in 100 μl 10 mM Tris-HCl, pH 8.0. To remove residual RNA, samples were treated with 50 mg of RNase A (Thermo Scientific) for 45 min at 37°C. To remove residual salts and DTT, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter).
Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase in NEBuffer 2 supplemented with 0.025 mM dATP and 0.025 mM dGTP, at 20°C for 4 h. Next, DNA was purified using Agencourt AMPure XP beads. DNA was then dissolved in 500 μl sonication buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.1% SDS) and was sheared to a size of approximately 100-1,000 bp using a VirSonic 100 (VerTis). The samples were concentrated and simultaneously purified using AMICON Ultra Centrifugal Filter Units (Merck), to a total volume of approximately 50 μl. The DNA ends were repaired by adding of 62.5 μl MQ water, 14 μl 10×T4 DNA ligase buffer, 3.5 μl 10 mM dNTP mix, 5 μl of T4 DNA polymerase (3 U/μl, New England Biolabs), 5 μl of T4 polynucleotide kinase (10 U/μl, New England Biolabs), and 1 μl of Klenow DNA polymerase (5 U/μl, New England Biolabs) and incubating at 20°C for 30 min. DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, DNA samples were supplemented with 6 μl 10×NEBuffer 2, 1.2 μl 10 mM dATP, 1 μl MQ water and 3.6 μl Klenow (exo-) fragment (5 U/μl, New England Biolabs). The reactions were performed for 30 min at 37°C in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65°C for 20 min. DNA was purified using Agencourt AMPure XP beads and eluted with 200 μl 10 mM Tris-HCl (pH 8.0). Biotin pulldown of the ligation junctions was performed as described previously, with minor modifications. Briefly, 10 μl MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads attached to captured ligation junctions were resuspended in 50 μl adapter ligation mixture, composed of 41.5 μl MQ water, 5 μl 10×T4 DNA ligase buffer, 2.5 μl Illumina TruSeq adapters and 1 μl T4 DNA ligase (5 U/μl, Thermo Scientific). Adapter ligation was performed at 22°C for 2.5 h, and the beads were washed twice with 100 μl buffer (5 mM Tris-HCl, pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 2 M NaCl), and once with 100 μl buffer (10 mM Tris-HCl, pH 8.0 and 50 mM NaCl), and then resuspended in 20 μl MQ water. Test PCR reactions containing 4 μl streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles necessary to generate sufficient PCR products for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (KAPA) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 min at 98°C, followed by 6, 9, 12, 15, and 18 cycles of 20 s at 98°C, 15 s at 65°C, and 20 s at 72°C. The PCR reactions were separated on a 2% agarose gel supplemented with ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 9-12 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined and the products were purified using Agencourt AMPure XP beads.

value: testes

tag: developmental stage

value: imago

value: mainly germline


title: SpG_Hi-C_rep1


title: nuclear fraction_MTA_RIP_IP

description: nuclear fraction, MTA-GFP-IP

value: MTA-GFP


title: nuclear fraction_GFP_RIP_input

description: nuclear fraction


title: tumor tissue 4

description: Total RNA (poly A+ and poly A-)

value: Synovial sarcoma

value: Tumor


title: Day7 rep1 [X14_d7_double]

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo Quick RNA kit
Libraries were prepared according to standard Illumina RNA-seq protocols

value: Female

value: Xmas mESC line

tag: time point


title: Day4 rep2 [X14_d4_single]


title: GL261 miR-21 WT cells 1


title: Day0 rep1 [X14_d0_double]


title: nuclear fraction_MTA_RIP_input

description: nuclear fraction


title: Serum_exosome_PCOS

description: miRNA

value: serum

value: exosomal miRNA


title: WT Hela cells, rep2

status: Public on Jan 31 2022

city: Boston

first: Joseph

last: Orofino

address: 72 E. Concord St.

institute: Boston University

data_processing:
Reads were trimmed using Trimmomatic and analyzed for basic QC via FastQC
Reads were aligned using STAR and transcriptomic coordinates were produced for use in RSEM with default parameters
Differential expression was performed on gene-level counts using DESeq2 with default parameters
DE genes were considered significant at a FDR cutoff of <.15
Genome_build: Grch38
Supplementary_files_format_and_content: RSEM calculated gene expression levels

source_name: Hela cells

growth_protocol: N4 Hela cells were grown in 10% FBS, DMEM, no sodium pyruvate with 2.5ug/ml puromycin and WT cells maintained in 10% FBS, DMEM, no sodium pyruvate

extract_protocol:
Cells were lysed and RNA extracted using the Qiagen RNEasy Extraction kit and protocol
Ribo-depletion Illumina Library Prep Kit

tag: cell line

value: Hela

value: WT


title: CRISPR-Cas9 KO Hela, rep6


title: CRISPR-Cas9 KO Hela, rep5


title: 0h giardia control rep1 (encysting)

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
Illumina HiSeq 2500, Demultiplexing and conversion to FASTQ performed using the bclfastq2
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.5.2b. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample, separated by host and parasite

organism: Giardia duodenalis

source_name: encysting trophozoites

growth_protocol: Trophozoites were grown in TYi-S33 until 80% confluency after that encystation was induced for 7h, following the Uppsala encystation protocol reported by Einarsson et al. 2016. 2. Encysting Giardia cells were resuspended in DMEM (HI-FBS) and incubated with previously grown and differenatiated Caco2 cells for 1.5, 3 and 4.5 h. Prior interaction Encysting cells and Caco-2 cells were collected.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction
Sequencing libraries were prepared from 250 ng total RNA using the TruSeq stranded mRNA library preparation kit (Cat# 20020594/5, Illumina Inc.) including polyA selection.The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: After interaction, media was remove and cells were lysate using 1ml of Triazol. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction

value: WB

tag: growth medium

value: TYDK

tag: time

value: 0h giardia control


title: WT Hela cells, rep3


title: 0h giardia control rep2 (encysting)


title: CRISPR-Cas9 KO Hela, rep3


title: WT Hela cells, rep1


title: SpC_Hi-C_rep3

source_name: 3rd instar larvae testes mostly filled with spermatocytes

value: 3rd instar larvae

value: vas-GFP


title: CRISPR-Cas9 KO Hela, rep1


title: 4.5h infection rep3 (encysting)

organism:
Giardia duodenalis
Homo sapiens

source_name: encysting trophozoites, Caco-2

value: DMEM

value: 4.5h infection


title: 1.5h infection rep3 (encysting)

value: 1.5h infection


title: CRISPR-Cas9 KO Hela, rep4


title: CRISPR-Cas9 KO Hela, rep2


title: 4.5h infection rep1 (encysting)


title: 3h infection rep3 (encysting)

value: 3h infection


title: 3h infection rep2 (encysting)


title: 4.5h infection rep2 (encysting)


title: FalcorKO_1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: cDNAs  were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to  GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

label: biotin

source_name: Whole Lung

label_protocol: After amplified, 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter.  Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

extract_protocol: Tissue was homogenized in Trizol using the Qiagen TissueLyzer II, and then total RNA was extracted with Trizol. Isolated RNA was subsequently purified with columns from the the Qiagen Rneasy Micro kit (Qiagene-74004) with on-column DNase I digestion.

tag: treatment

value: 31D post naphthalene


title: FalcorKO_3

value: 33D post naphthalene


title: WildType_3

value: 30D post naphthalene


title: 0h caco-2 control rep1

data_processing:
Illumina NovaSeq 6000, Demultiplexing and conversion to FASTQ performed using the bclfastq2
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.5.2b. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.26.8 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample, separated by host and parasite
Supplementary_files_format_and_content: Raw read counts per human gene

growth_protocol: Giardia trophozoites were grown in TYI-S33 until 80% confluency after that encystation was induced following the Uppsala encystation protocol reported by Einarsson et al. 2016. 2. Giardia cells were left to complete encystation for 32 hours and then collected and wash 3X in cold PBS and resuspended in sterile dH20 and left there for 3 days, on the third day cyst were collected and resuspended in DMEM (HI-FBS) and incubated with previously grown and differenatiated Caco2 cells for 1.5, 3 and 4.5 h. Prior interaction Caco-2 cells were collected.

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (#1000000040498).

treatment_protocol: After interaction, media and cysts were remove and cells were lysate using 1ml of Triazol. Samples were frozen immediatedly in liquid nitrogen and kept at -80 until RNA extraction


title: WildType_1

value: 28D post naphthalene


title: 0h caco-2 control rep2


title: WildType_2

value: 29D post naphthalene


title: 1.5h infection rep2 (encysting)


title: FalcorKO_2

value: 32D post naphthalene


title: 4.5h co-incubation rep1

source_name: cysts, Caco-2

tag: agent

value: Giardia intestinalis WB


title: 4.5h co-incubation rep2


title: 3h co-incubation rep1


title: 3h co-incubation rep3


title: 3h co-incubation rep2


title: 0h human control rep3 (encysting)

value: 0h human control


title: 1.5h co-incubation rep1


title: 1.5h co-incubation rep3


title: 0h human control rep1 (encysting)


title: 3h infection rep1 (encysting)

value: WB


title: 1.5h co-incubation rep2


title: 4.5h co-incubation rep3


title: 0h caco-2 control rep3


title: WT-1

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: WT

extract_protocol: After isolation of EpCAM+ cells with magnetic bead sorting, RNA was extracted with Trizol and then column purified using the Qiagen RNEasy kit with on-column DNaseI digestion.

value: wild type


title: 1.5h infection rep1 (encysting)


title: Foxa2-13


title: WT-5


title: WT-2


title: WT-3


title: Foxa2-11


title: WT-4


title: Double-17

source_name: Double

value: Double-Het (Falcor+/-;Foxa2+/-)


title: Double-16


title: Foxa2-12


title: Falcor-6

source_name: Falcor

value: Falcor-/-


title: Falcor-10


title: Falcor-9


title: Falcor-7


title: Double-18


title: Foxa2-14


title: Double-15


title: Day6 rep2 [X14_d6_single]

city: Royal Parade

first: Andrew

last: Keniry

institute: The Waler and Eliza Hall Institute of Medical Research

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using TopHat v2.0.12 with default parameters
Data were normalized for read depth and counts per million (log2) values calculated using Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing log2 counts per million transcformed value of reads mapping to that gene for all samples.

tag: Sex

value: Female

value: Xmas mESC line


title: Falcor-8


title: Hira_GV_KO_2

tag: strain background

tag: developmental stage/tissue

value: GV oocytes


title: tumor tissue 2

description: Total RNA (poly A+ and poly A-)

tag: patient

tag: diagnosis

value: Synovial sarcoma

value: Tumor


title: genomic DNA from healthy control 39

status: Public on Jan 30 2022

type: genomic

city: Xi’an

first: Congxia

last: Bai

state: Shanxi

address: 127 Changle West Rd

department: Clinical Laboratory Medicine

institute: xijing hospital

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: BeadStudio software v3.2;

label: Cy5 and Cy3

source_name: healthy control peripheral blood

label_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

growth_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

extract_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

treatment_protocol: Standard Illumina Protocol

tag: subject status

value: healthy control

tag: tissue

value: peripheral blood


title: genomic DNA from healthy control 43


title: genomic DNA from healthy control 42


title: genomic DNA from healthy control 40


title: genomic DNA from healthy control 41


title: genomic DNA from healthy control 44


title: genomic DNA from healthy control 36


title: genomic DNA from healthy control 37


title: genomic DNA from healthy control 25


title: genomic DNA from healthy control 38


title: genomic DNA from healthy control 35


title: genomic DNA from healthy control 22


title: genomic DNA from healthy control 33


title: genomic DNA from healthy control 31


title: genomic DNA from healthy control 23


title: genomic DNA from healthy control 32


title: genomic DNA from healthy control 34


title: genomic DNA from healthy control 27


title: genomic DNA from healthy control 28


title: genomic DNA from healthy control 24


title: genomic DNA from healthy control 30


title: genomic DNA from healthy control 16


title: genomic DNA from healthy control 21


title: genomic DNA from healthy control 15


title: genomic DNA from healthy control 29


title: genomic DNA from healthy control 26


title: genomic DNA from healthy control 19


title: genomic DNA from healthy control 17


title: genomic DNA from healthy control 13


title: genomic DNA from healthy control 20


title: genomic DNA from healthy control 11


title: genomic DNA from healthy control 14


title: genomic DNA from healthy control 6


title: genomic DNA from healthy control 9


title: genomic DNA from healthy control 12


title: genomic DNA from healthy control 8


title: genomic DNA from healthy control 10


title: genomic DNA from healthy control 7


title: genomic DNA from healthy control 1


title: genomic DNA from pre-hypertensive patient 44

source_name: pre-hypertensive peripheral blood

value: pre-hypertensive patient


title: genomic DNA from healthy control 2


title: genomic DNA from pre-hypertensive patient 43


title: genomic DNA from healthy control 3


title: genomic DNA from healthy control 18


title: genomic DNA from pre-hypertensive patient 35


title: genomic DNA from pre-hypertensive patient 33


title: genomic DNA from pre-hypertensive patient 41


title: genomic DNA from pre-hypertensive patient 38


title: genomic DNA from pre-hypertensive patient 37


title: genomic DNA from pre-hypertensive patient 29


title: genomic DNA from healthy control 5


title: genomic DNA from pre-hypertensive patient 39


title: genomic DNA from pre-hypertensive patient 42


title: genomic DNA from pre-hypertensive patient 27


title: genomic DNA from pre-hypertensive patient 32


title: genomic DNA from pre-hypertensive patient 36


title: genomic DNA from pre-hypertensive patient 25


title: genomic DNA from pre-hypertensive patient 30


title: genomic DNA from pre-hypertensive patient 31


title: genomic DNA from pre-hypertensive patient 40


title: genomic DNA from pre-hypertensive patient 34


title: genomic DNA from pre-hypertensive patient 24


title: genomic DNA from pre-hypertensive patient 23


title: genomic DNA from pre-hypertensive patient 28


title: genomic DNA from pre-hypertensive patient 26


title: genomic DNA from pre-hypertensive patient 21


title: genomic DNA from pre-hypertensive patient 18


title: genomic DNA from pre-hypertensive patient 20


title: genomic DNA from pre-hypertensive patient 19


title: genomic DNA from pre-hypertensive patient 22


title: genomic DNA from healthy control 4


title: genomic DNA from pre-hypertensive patient 15


title: genomic DNA from pre-hypertensive patient 14


title: genomic DNA from pre-hypertensive patient 12


title: genomic DNA from pre-hypertensive patient 11


title: genomic DNA from pre-hypertensive patient 16


title: genomic DNA from pre-hypertensive patient 17


title: genomic DNA from pre-hypertensive patient 13


title: genomic DNA from pre-hypertensive patient 6


title: genomic DNA from pre-hypertensive patient 9


title: genomic DNA from pre-hypertensive patient 7


title: genomic DNA from pre-hypertensive patient 8


title: genomic DNA from pre-hypertensive patient 5


title: genomic DNA from hypertensive patient 41

source_name: hypertensive patient peripheral blood

value: hypertensive patient


title: genomic DNA from pre-hypertensive patient 4


title: genomic DNA from pre-hypertensive patient 2


title: genomic DNA from hypertensive patient 44


title: genomic DNA from hypertensive patient 40


title: genomic DNA from hypertensive patient 38


title: genomic DNA from hypertensive patient 36


title: genomic DNA from hypertensive patient 43


title: genomic DNA from hypertensive patient 42


title: genomic DNA from pre-hypertensive patient 10


title: genomic DNA from hypertensive patient 34


title: genomic DNA from hypertensive patient 35


title: genomic DNA from hypertensive patient 37


title: genomic DNA from pre-hypertensive patient 3


title: genomic DNA from hypertensive patient 31


title: genomic DNA from hypertensive patient 26


title: genomic DNA from hypertensive patient 32


title: genomic DNA from hypertensive patient 27


title: genomic DNA from hypertensive patient 30


title: genomic DNA from hypertensive patient 24


title: genomic DNA from hypertensive patient 33


title: genomic DNA from hypertensive patient 25


title: genomic DNA from hypertensive patient 23


title: genomic DNA from hypertensive patient 29


title: genomic DNA from hypertensive patient 28


title: genomic DNA from hypertensive patient 15


title: genomic DNA from hypertensive patient 18


title: genomic DNA from hypertensive patient 16


title: genomic DNA from hypertensive patient 20


title: genomic DNA from pre-hypertensive patient 1


title: genomic DNA from hypertensive patient 19


title: genomic DNA from hypertensive patient 21


title: cochlear duct_day14

status: Public on Jan 29 2022

city: Shanghai

first: Jianyong

last: Chen

state: Yangpu

address: 1665 Kongjiang Rd

department: Otorhinolaryngology Head and Neck Surgery

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

description: Single-cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
Sample demultiplexing, barcode processing and single-cell 3’ gene counting by using the Cell Ranger pipeline
sc-RNA-seq data were aligned to Rattus norvegicus reference genome
The Cell Ranger output was loaded into Seurat(version 3.1.1) be used for dimensional reduction, clustering, and analysis of sc-RNA-sequenceing data.
all genes expressed in less than 1 cell were removed, number of genes expressed per cell > 500 as low and <5000 as high cut-off、UMI counts less than 500、the percent of mitochondrial-DNA derived gene-expression <25%.
Genome_build: Rattus norvegicus UCSC
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: cochlear

extract_protocol:
The cochlear duct tissues were placed in a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice, the tissues were transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I)
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cells according to the manufacturer's instructions of the 10X Genomics Chromium Single-Cell 3' kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou, China) at a minimum depth of 20,000 reads per cell.

tag: strain

value: Sprague-Dawley

value: cochlea

tag: cell type

value: greater epithelial ridge cell

tag: age

value: post natal day 14

value: untreated


title: cochlear duct_day1

description: Single-cell

value: post natal day 1


title: mycelium, treated with HSAF for 60 min, L

status: Public on Jan 28 2022

city: Fuzhou

first: Lina

last: Qin

address: No.8 Xuefu South Road, Shangjie, Minhou

department: College of Life Sciences

institute: Fujian normal university

data_processing:
The qualified library was pooled based on pre-designed target data volume and then sequenced on Illumina sequencing platform.
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. These clean data were further mapped to pre-defined reference genome generating mapped data.
Assessment on insert size and sequencing randomness were processed on mapped data as library quality control. Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization.
Genome_build: GCF_000182925.2
Supplementary_files_format_and_content: all_gene_fpkm.txt (tab-delimited text file includes FPKM values for each sample)
Supplementary_files_format_and_content: all_gene_counts.txt (tab-delimited text file with raw gene counts for every gene and every sample)

organism: Neurospora crassa

source_name: mycelium

growth_protocol: N. crassa cells were grown from freezer stocks on Vogel’s + sucrose + 2% agar slants for 1 d at 28 °C in the dark and 4 to 6 d at 28 °C in constant light.

extract_protocol:
The N. crassa sample was frozen with liquid nitrogen immediately. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Treating mycelium with 40 μM HSAF for 0, 5, 30, 60min

value: mycelium

tag: genotype

value: wild type

value: post innoculate 48h

value: HSAF for 60 min


title: mycelium, treated with HSAF for 60 min, K


title: cochlear duct_day7

description: Single-cell

value: post natal day 7


title: genomic DNA from hypertensive patient 7


title: mycelium, treated with HSAF for 60 min, J


title: genomic DNA from hypertensive patient 8


title: genomic DNA from hypertensive patient 11


title: genomic DNA from hypertensive patient 14


title: genomic DNA from hypertensive patient 4


title: mycelium, treated with HSAF for 30 min, H

value: HSAF for 30 min


title: genomic DNA from hypertensive patient 39


title: mycelium, treated with HSAF for 5 min, E

value: HSAF for 5 min


title: genomic DNA from hypertensive patient 13


title: mycelium, untreated, C


title: mycelium, treated with HSAF for 30 min, I


title: genomic DNA from hypertensive patient 10


title: genomic DNA from hypertensive patient 3


title: mycelium, untreated, A


title: genomic DNA from hypertensive patient 6


title: mycelium, treated with HSAF for 5 min, F


title: siUSP7-GFP(+) rep2

status: Public on Jan 14 2022

first: Fei

last: Ji

address: 185 Cambridge St

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm9 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm9
Supplementary_files_format_and_content: read count

source_name: Embryonic stem cells

growth_protocol: Mouse E14 ES cell lines were cultured in DMEM with GlutaMAX (Invitrogen) containing 15% FCS, LIF, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 (a GSK3b inhibitor) and 1 mM PD0325901 (a MEK inhibitor) on the gelatin-coated plate

extract_protocol:
Total RNA was extracted with PicoPure RNA Isolation Kit, treated with DNase and the quality was checked by the bioanalyzer..
Libraries were prepared with Truseq Stranded Total RNA with Ribo-Zero Gold Prep kit (Illumina).

treatment_protocol: ESCs and 2CLCs were sorted by FACS Aria according to the GFP signal 48h after transfection of siRNA.

tag: knockdown

tag: gfp status

value: positive


title: siUSP7-GFP(+) rep1


title: mycelium, untreated, B


title: genomic DNA from hypertensive patient 9

value: peripheral blood


title: siUSP7-GFP(-) rep2

value: negative


title: genomic DNA from hypertensive patient 12

value: hypertensive patient


title: genomic DNA from hypertensive patient 1


title: genomic DNA from hypertensive patient 5


title: genomic DNA from hypertensive patient 17


title: siControl rep1

value: siControl


title: genomic DNA from hypertensive patient 22


title: CTX_p30_2

status: Public on Dec 31 2021

city: Bethesda

first: Timothy

last: Petros

state: MD

address: 35 Convent Drive Building 35A, Room 3B-1002

department: NICHD

institute: NIH

data_processing:
Basecalls were performed with Illumina RTA version 1.18.64
Read alignment and peak calling was performed with the 10X cellranger-atac version 1.2.0
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Filtered peak-barcode matrix contains peak-by-barcode counts in Market Exchange Format (MEX); rows are peaks in BED format; columns are barcodes in TSV format. Filtered tf-barcode matrix contains transcription factor (TF)-by-barcode counts in Market Exchange Format (MEX); rows are TF names in TSV format; columns are barcodes in TSV format.

source_name: Cortex

extract_protocol:
Nuclei isolation followed the 10X Genomics ATAC nuclei isolation protocol with several modifications. All steps were performed on ice. For each brain region, tissue was transferred to a Dounce homogenizer containing 1mL Lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL, 2% BSA). Samples were dounced with 10 strokes pestle A and 10 strokes pestle B. Lysate was strained through a 40 μm filter pre-wetted with wash buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 2% BSA) and neutralized with 2 mL wash buffer. For snATAC-Seq from adult tissue, DAPI (1:10,000 from 1 mg/ml stock) was added to the nuclei suspensions which were passed through a 30 μm filter. GFP+ nuclei were collected using a SH800 Cell Sorter (Sony Biotechnology) using a 100 μm nozzle. DAPI+/GFP+ nuclei were selected using Sony Cell Sorter Software (v2.1.5) and collected in low-bind 1.5 mL tubes containing 50 μL wash buffer. After sorting, nuclei were centrifuged 1000 x G for 10 min at 4oC in a swinging bucket centrifuge. A diluted aliquot of nuclei solution was mixed with Trypan Blue (1:1) and counted on a hemocytometer. For all samples, we prepared 3,000 nuclei/μL samples for snATACseq reactions, with 5 μL (~15,000 nuclei) used for each snATAC reaction.
snATAC reaction was carried out following 10X Genomics ATAC User Guide (revision C), libraries were prepared following 10X Genomics and Illumina guidelines

value: brain

tag: region

value: CTX


title: siControl rep2


title: HP_p30_2

source_name: Hippocampus

value: HP


title: CTX_p30_1


title: HP_p30_1


title: LGE_E12.5_2

source_name: Lateral ganglionic eminence

extract_protocol:
Nuclei isolation followed the 10X Genomics ATAC nuclei isolation protocol with several modifications. All steps were performed on ice. For each brain region, tissue was transferred to a Dounce homogenizer containing 1mL Lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL, 2% BSA). Samples were dounced with 10 strokes pestle A and 10 strokes pestle B. Lysate was strained through a 40 μm filter pre-wetted with wash buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 2% BSA) and neutralized with 2 mL wash buffer. For snATAC-Seq from embryonic tissue, lysates were centrifuged 500 x G for 5 min at 4oC, supernatant removed, nuclei pellet washed once with 1 mL wash buffer, and centrifuged 500 x G for 5 min. A diluted aliquot of nuclei solution was mixed with Trypan Blue (1:1) and counted on a hemocytometer. For all samples, we prepared 3,000 nuclei/μL samples for snATACseq reactions, with 5 μL (~15,000 nuclei) used for each snATAC reaction.
snATAC reaction was carried out following 10X Genomics ATAC User Guide (revision C), libraries were prepared following 10X Genomics and Illumina guidelines

value: WT

value: LGE


title: CGE_E12.5_2

source_name: Caudal ganglionic eminence

value: CGE


title: MGE_E12.5_2

source_name: Medial ganglionic eminence

value: MGE


title: CTX_E14.5_2


title: LGE_E12.5_1


title: CGE_E12.5_1


title: CTX_E12.5_1


title: CTX_P30

data_processing:
Basecalls were performed with Illumina RTA version 1.18.64
Read alignment and transcript counting was performed with the 10X cellranger version 3.0.0
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Filtered feature-barcode matrix contains gene-by-barcode counts in Market Exchange Format (MEX); rows are gene symbols in TSV format; columns are barcodes in TSV format.

extract_protocol:
Adult tissue from Dlx6a-Cre;CAG-Sun1/sfGFP mice was dissected and nuclei was isolated following a previously reported method (Matson et al., J Vis Exp, 2018). DAPI (1:10,000 from 1 mg/ml stock) was added to the nuclei suspensions which were passed through a 30 μm filter. GFP+ nuclei were collected using a SH800 Cell Sorter (Sony Biotechnology) using a 100 μm nozzle. DAPI+/GFP+ nuclei were selected using Sony Cell Sorter Software (v2.1.5) and collected in low-bind 1.5 mL tubes containing 50 μL wash buffer. After sorting, nuclei were centrifuged 1000 x G for 10 min at 4oC in a swinging bucket centrifuge. A diluted aliquot of nuclei solution was mixed with Trypan Blue (1:1) and counted on a hemocytometer.
cDNA synthesis and library amplification was carried out following 10X Genomics ATAC User Guide (revision C), libraries were prepared following 10X Genomics and Illumina guidelines


title: HP_P30


title: MGE_E12.5_1


title: LGE_E12.5

extract_protocol:
Embryonic MGE, LGE, CGE and cortex tissue was incubated in 1 mg/mL Pronase (Roche #10165921001) in ACSF for 20 minutes at RT. Pronase solution was removed and 2 ml of reconstitution solution (1% fetal bovine serum + DNAse (1:10,000, Roche #47167280001)) in oxygenated ACSF was added. Cells were triturated sequentially with fire-polished large, medium and small bore Pasteur pipettes to mechanically dissociate tissue. For scRNA-Seq, DRAQ5 (20 μM) and DAPI (1:10,000) was added to the single cell suspension, which was passed through a pre-wet 30 μm filter and then processed on an SH800 cell sorter to purify the sample. DRAQ5+/DAPI- live cells were collected in low-bind 1.5 mL tubes containing 100 μL ACSF. Cell solutions were centrifuged at 300 x G for 5 min at 4oC in a swinging bucket centrifuge and then counted on a hemocytometer. 15,000 cells (or highest amount recovered after sorting) was used for 10X Genomics scRNA-Seq experiments.
cDNA synthesis and library amplification was carried out following 10X Genomics ATAC User Guide (revision C), libraries were prepared following 10X Genomics and Illumina guidelines

value: wt


title: CGE_E12.5


title: CTX_E12.5


title: genomic DNA from hypertensive patient 2


title: MGE_E12.5


title: RM 18 D3

status: Public on Dec 25 2021

city: Chapel Hill

first: Kristina

last: De Paris

state: North Carolina

address: Mary Ellen Jones Building , 116 manning Drive

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

description: The extracted RNA was  analyzed with Nanostring Non Human Primate  panel comprising 754 immune related genes

hyb_protocol: NanoString nCounter gene expression assay protocol was followed

scan_protocol: Samples were scanned on the nCounter prep station following ncounter protocol

data_processing: Raw data files (RCC) were uploaded to the Nanostring  software nSolver v3.022 with the advanced analysis module v2.0. nSolver employed multivariate linear regression models and raw p values were adjusted to Benjamin Yekutieli method to minimize false discovery rate. The Differentially expressed genes were defined as having log 2 fold change≥ 1.5 in expression and an adjusted p value ≤0.1.. Pathway score were generated using nSolver to define potential immune pathways

label: Followed the Nanostring Protocol

organism: Macaca mulatta

source_name: WHOLE BLOOD

extract_protocol: The total RNA was extracted from whole blood using PAXgene blood RNA kit following the manufacturing protocol except for incubating the sample for 60min at 55℃ after the addition of BR2 and Proteinase K

treatment_protocol: The infant Rhesus macaques were immunized during the first week of life with either 15ug 1086C HIV Env protein with 10ug of 3M-052 adjuvant stable emulsiom or 15ug 1086C HIV Env protein with 10ug of 3M-052 adjuvant and MVA expressing 1086C Env

value: whole blood

tag: group based on vaccine prime regimen

value: Administered adjuvanted HIV Env  protein+ MVA HIV Env Protein

tag: days after vaccine prime


title: RM 18 D0

label_protocol: NanoString nCounter gene expression assay protocol was followed


title: RM 17 D1


title: RM 16 D0


title: RM 14 D3


title: RM 17 D3


title: RM 15 D1


title: RM 16 D1


title: RM 16 D3


title: RM 13 D3


title: RM 17 D0


title: RM 14 D0


title: RM 15 D0


title: RM 13 D1


title: RM 13 D0


title: RM 12 D3


title: RM 11 D0


title: RM 18 D1


title: RM 11 D1


title: RM 12 D1


title: RM 10 D3

value: Administered adjuvanted HIV Env  protein


title: RM 10 D1


title: RM 9 D0


title: RM 9 D1


title: RM 8 D3


title: RM 11 D3


title: RM 10 D0


title: RM 8 D1


title: RM 6 D0


title: RM 5 D1


title: RM 7 D3


title: RM 6 D3


title: RM 1 D3


title: RM 3 D3


title: RM 5 D0


title: COVID19 patient 3 / COVID19 patient 4 [TCR]

status: Public on Dec 09 2021

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description: 68yo female Caucasian severe COVID-19 patient with cytokine release syndrome / 67yo female Caucasian severe COVID-19 patient with cytokine release syndrome

data_processing:
Raw data bcl files were first demultiplexed
Demultiplexed data was then processed using the Cellranger 5.0.0 multi pipeline
Genome_build: GRCh38 + SARSCoV2
Supplementary_files_format_and_content: h5 files including cDNA and FB5P (sample hashing) counts and contig_annotations.csv files including TCR info (output from Cellranger multi)

source_name: PBMCs

extract_protocol:
After thawing PBMCs were counted, isolated and spun down.  The cell pellet was resuspended and incubated for 30 min on ice with staining mix in PBS containing 0.04% BSA, L/D-DAPI, CD3-FITC (HIT3A), CD14-PerCP-Cy5-5 (HIB19), CCR5-PE (2D7), Human TruStain FcX (BioLegend, Cat. 422302) and TotalSeq-C hashing antibodies (BioLegend).
The sorted single-cell suspensions were resuspended and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM). The scRNA/Feature Barcoding/TCR libraries were prepared using the GemCode Single Cell 5’ Gel Bead and Library kit, version 1.1 (10x Genomics, Cat. 1000165) according to the manufacturer’s instructions.

tag: disease

value: COVID19 patient / COVID19 patient

tag: age tier

value: Adult / Adult

tag: family code

value: UNR / UNR

tag: gender composition

value: F / F


title: RM 4 D3


title: Sibling 1 MIS-C patient 1 / Sibling 1 MIS-C patient 7 [TCR]

description: 12yo female Caucasian sibling, not inflammatory at sampling, SARS-CoV-2 IgG negative / 7yo male Middle Eastern sibling, not inflammatory at time of sampling, SARS-CoV-2 IgG positive

value: Sibling MIS-C patient / Sibling MIS-C patient

value: Pediatric / Pediatric

value: FAM01 / FAM07

value: F / M


title: RM 3 D1


title: Sibling 2 MIS-C patient 7 / Sibling 2 MIS-C patient 1 [TCR]

description: 13yo female Middle Eastern sibling, not inflammatory at sampling, SARS-CoV-2 IgG positive / 18yo male Caucasian sibling, not inflammatory at sampling, SARS-CoV-2 IgG negative

value: FAM07 / FAM01


title: RM 1 D0


title: RM 3 D0


title: RM 2 D0


title: RM 1 D1


title: RM 4 D1


title: RM 6 D1


title: MIS-C patient 3 / MIS-C patient 4 [TCR]

description: 9yo male Caucasian MIS-C patient, moderately affected  / 8yo male African MIS-C patient, severely affected

value: MIS-C patient / MIS-C patient

value: FAM03 / FAM04

value: M / M


title: MIS-C patient 7 / Sibling 1 MIS-C patient 5 [TCR]

description: 14yo female Middle Eastern MIS-C patient, severely affected, steroids prior to sampling / 12yo male African sibling, not inflammatory at time of sampling, SARS-CoV-2 IgG negative

value: MIS-C patient / Sibling MIS-C patient

value: FAM07 / FAM05


title: MIS-C patient 1 / MIS-C patient 2 [TCR]

description: 14yo female Caucasian MIS-C patient, severely affected, steroids prior to sampling  / 9yo female Caucasian MIS-C patient, moderately affected

value: FAM01 / FAM02


title: MIS-C patient 5 / MIS-C patient 6 [TCR]

description: 12yo female African MIS-C patient, moderately affected  / 15yo male Middle Eastern MIS-C patient, severely affected

value: FAM05 / FAM06


title: mycelium, treated with HSAF for 5 min, D

value: mycelium

value: wild type

value: post innoculate 48h

tag: treatment

value: HSAF for 5 min


title: COVID19 patient 3 / COVID19 patient 4

value: COVID19 patient / COVID19 patient

value: Adult / Adult

value: UNR / UNR

value: F / F


title: RM 4 D0

value: whole blood

value: Administered adjuvanted HIV Env  protein


title: COVID19 patient 1 / COVID19 patient 2 [TCR]

description: 60yo male Caucasian severe COVID-19 patient with cytokine release syndrome / 62yo male Caucasian severe COVID-19 patient with cytokine release syndrome


title: Sibling 2 MIS-C patient 7 / Sibling 2 MIS-C patient 1

value: Sibling MIS-C patient / Sibling MIS-C patient

value: Pediatric / Pediatric

value: FAM07 / FAM01

value: F / M


title: MIS-C patient 7 / Sibling 1 MIS-C patient 5

value: MIS-C patient / Sibling MIS-C patient

value: FAM07 / FAM05


title: Sibling 1 MIS-C patient 1 / Sibling 1 MIS-C patient 7

value: FAM01 / FAM07


title: COVID19 patient 1 / COVID19 patient 2

value: M / M


title: mycelium, treated with HSAF for 30 min, G

value: mycelium

value: wild type

value: HSAF for 30 min


title: MIS-C patient 3 / MIS-C patient 4

value: MIS-C patient / MIS-C patient

value: FAM03 / FAM04


title: MIS-C patient 5 / MIS-C patient 6

value: FAM05 / FAM06


title: MIS-C patient 1 / MIS-C patient 2

value: FAM01 / FAM02

tag: osition

value: F / F


title: siUSP7-GFP(-) rep1

value: negative


title: 72hpf_2

status: Public on Nov 22 2021

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

institute: Zhejiang University

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Danio rerio

source_name: embryo

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: Tubingen

value: embryo


title: 72hpf_1


title: SC01172A

status: Public on Nov 30 2021

city: Belfast

first: Philip

middle: D.

last: Dunne

address: 97 Lisburn Road

department: The Patrick G Johnston Centre for Cancer Research

institute: Queen's University Belfast

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw microarray .CEL file data were normalized using Robust Multi-array Average (RMA) in Partek Genomics Suite software and then data was collapsed to the probeset with the highest mean value for each gene using the “collapseRows” function from the WGCNA R package

source_name: Primary Colorectal Cancer

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from two sequential 5µm sections using the Roche High Pure FFPE Extraction Kit (Roche Life Sciences, Penzberg, Germany) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos, California, USA). The amplified product was hybridised to the Almac Diagnostics XCEL array (Almac, Craigavon, UK), a cDNA microarray-based technology optimised for archival FFPE tissue, and analysed using the Affymetrix Genechip 3000 7G scanner (Affymetrix, Santa Clara, California, USA) as previously described (12).

treatment_protocol: All the archival formalin-fixed paraffin-embedded (FFPE) tumour tissue samples were tested at Almac’s Diagnostic CLIA Laboratories. Samples were reviewed and tumour material identified on an adjacent H&E stained slide for microdissection.

tag: disease state

value: colorectal cancer


title: SC01166A


title: SC01162A


title: SC01159A


title: SC01175A


title: SC01178A


title: SC01168A


title: SC01158A


title: SC01160A


title: SC01176A


title: SC01165A


title: SC01161A


title: SC01171A


title: SC01155A


title: SC01174A


title: SC01173A


title: SC01157A


title: SC01185A


title: SC01177A


title: SC01156A


title: SC01184A


title: SC01141A


title: SC01188Anew


title: SC01182A


title: 24hpf_2

tag: tissue


title: SC01153A


title: 24hpf_1

tag: strain


title: SC01151A


title: SC01154A


title: muscle_1

source_name: muscle

value: muscle


title: CaudalFin_5

source_name: caudal fin

value: caudal fin


title: CaudalFin_4


title: CaudalFin_6


title: Blood_2

source_name: blood

value: blood


title: Blood_1


title: CaudalFin_3


title: Testis2

source_name: testis

tag: genotype/variation

value: testis


title: Ovary2

source_name: ovary

value: ovary


title: Liver4

source_name: liver

value: liver


title: Heart3

source_name: heart

value: wild type

value: heart


title: Brain4

source_name: brain

value: brain


title: Heart4


title: Eye1

source_name: eye

value: eye


title: Intestine3

source_name: intestinePancreas

value: intestinePancreas


title: Brain2


title: Intestine4


title: Brain1


title: Brain8


title: Muscle2


title: Brain6


title: Brain5


title: muscle_2