title: NPC_H3K27me3_washout_rep1

status: Public on Aug 19 2021

city: Paris

first: Daniel

last: Holoch

state: Cedex 05

address: 26 rue d'Ulm

department: Genetics and Developmental Biology Unit

institute: Institut Curie, Centre de Recherche

data_processing:
Library strategy: Cut&Run
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Peak calling on combined replicates using MACS2 (2.1.1.20160309) with parameters -f BAMPE --gsize mm --broad --broad-cutoff 0.1 --bdg
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)

source_name: Neural progenitor cells, wild-type after washout of 2 uM UNC1999 + 4 uM A395

growth_protocol: neural progenitor cells were grown in N2B27 medium supplemented with EGF and FGF2 (10ng/ml each), on 0.1% gelatin-coated flasks.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. For CUT&RUN permeabilized cells were incubated with specific antibodies followed by incubation with pA-MNAse. Digested DNA fragments were subsequently recovered in the supernatant.
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

value: ES-derived neural progenitor cells

value: wild-type

value: washout of 2 uM UNC1999 + 4 uM A395

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, clone C36B11), catalog# 9733


title: cMYC-overexpressed NCI-H1963 cells_1 [ATAC-seq]

status: Public on Dec 31 2020

type: SRA

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option and filtered off an ATAC blacklist (Buenrostro et al., 2013) for mitochondrial DNA and homologous sequences.
Both fragment ends were shifted +4 nucleotides for positive strand and -5 for negative strand.
Peak were called with MACS2 with parameters --nomodel --extsize 100 --shift 50 --nolambda --keep-dup all
Peaks were filtered by MYC motif using findMotifsGenome function in Homer using four motif matrices MA0058.2 (MAX), MA0059.1 (MAX::MYC), MA0104.4 (MYCN), and MA0147.3 (MYC
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed

molecule: genomic DNA

organism: Homo sapiens

source_name: small cell lung cancer

growth_protocol: Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Five thousand cells were harvested and pre-treated with DNase I. Nuclei were isolated and resuspended in transposase reaction mixture carried out at 37C for 30 minutes followed by DNA purification with DNA Clean and Concentrator-25 (Zymo Research) according to manufacturer’s recommendation.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000 or Illumina NextSeq500 with paired-end 75bp reads.

tag: cell line

tag: cell type

value: small cell lung cancer cell line

tag: overexpression vector

tag: grna vector

tag: cas9 vector


title: NPC_H3K27me3_mock_rep2

country: France

organism: Mus musculus

source_name: Neural progenitor cells, wild-type

tag: genotype

tag: treatment

value: untreated


title: PBMC from sample ACLF10

status: Public on Nov 03 2021

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

description: PBMC from sample ACLF10

library_source: transcriptomic

data_processing:
enumerated and resuspended in RPMI 1640 medium containing penicillin (100 U/ml),
streptomycin (100 U/ml) and L-glutamine (4 mM) without fetal bovine serum (FBS).
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

molecule: polyA RNA

source_name: PBMC

extract_protocol:
PBMCs and PMNs were isolated from 20 ml of EDTA blood. Blood samples were centrifuged at
200 g for 10 min to collect plasma and sedimented cells were diluted with DPBS -/- up to a volume
of 20 ml. Diluted blood was layered over 13.3 ml of Ficoll-Hypaque and centrifuged at 500 g for
25 min with the break off. PBMCs were obtained from the mononuclear cell layer, washed with
Dulbecco’s PBS -/- and centrifuged again at 400 g for 5 min. Pelleted PMNs were incubated with

value: PBMC

tag: disease state

value: ACLF


title: PBMC from sample ACLF7

description: PBMC from sample ACLF7


title: cMYC-overexpressed NCI-H1963 cells_3 [ATAC-seq]


title: NPC_H3K27me3_inhibitors_rep1

source_name: Neural progenitor cells, wild-type + 2 uM UNC1999 + 4 uM A395


title: LacZ-overexpressed NCI-H1963 cells_3 [ATAC-seq]


title: LacZ-overexpressed NCI-H1963 cells_2 [ATAC-seq]


title: cMYC-overexpressed NCI-H1963 cells_2 [ATAC-seq]


title: ATAC for NCIH82 [ATAC-seq]


title: NPC_H3K27me3_inhibitors_rep2

data_processing:
Library strategy: Cut&Run
Alignment to mouse and Drosophila genomes (CUT&RUN, NPC samples) or to mouse genome (Traditional ChIP, others) (Bowtie 2.2.9)
Removal of PCR duplicates (Picard Tools MarkDuplicates 1.97)
Filtering of reads to exclude common artifact regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) and to retain only autosomal reads with MAPQ>10
Calculation of scale factors from Drosophila reads counted in 10kb bins using the median ration method (CUT&RUN, NPC samples) (DESeq2 estimateSizeFactors 1.22.2)
Calculation of RPKM values per 50bp bin for mouse reads, multiplication by scale factors and conversion to bigWig format (CUT&RUN, NPC samples) (DeepTools bamCoverage)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: .bw files contain alignments (reads per kilobase per million within bins)


title: ATAC for NCIH2171 [ATAC-seq]


title: ATAC for NCIH524 [ATAC-seq]


title: ATAC for NCIH1963 [ATAC-seq]


title: ATAC for CORL88 [ATAC-seq]


title: ATAC for NCIH209 [ATAC-seq]


title: cMYC-overexpressed NCI-H1963 cells_1 [RNA-seq]

description:
NCIH1963_cMyc_rep1
H1963_cMYCrep1_RNA_S31
complementary DNA
H1963_cMYC_kallisto_abundance.txt

data_processing:
Sequencing reads were pseudoaligned to the human reference transcriptome GRCh38.95.
Transcript abundance was estimated using kallisto (v0.45.0).
Genome_build: GRCh38.95
Supplementary_files_format_and_content: *_kallisto_abundance.txt: Tab-delimited text files include transcript abundance.

molecule: total RNA

growth_protocol: NCI-H82 and NCI-H1963 cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit. Poly-adenylated RNA was enriched from 1ug of RNA with the NEBNext PolyA mRNA Magnetic Isolation Module, incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module.
Up to 10 ng of cDNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 38bp reads.


title: LacZ-overexpressed NCI-H1963 cells_3 [RNA-seq]

description:
NCIH1963_LacZ_rep3
H1963_LacZrep3_RNA_S20
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LacZ-overexpressed NCI-H1963 cells_1 [ATAC-seq]


title: cMYC-overexpressed NCI-H1963 cells_3 [RNA-seq]

description:
NCIH1963_cMyc_rep3
H1963_cMYCrep3_RNA_S19
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LacZ-overexpressed NCI-H1963 cells_1 [RNA-seq]

description:
NCIH1963_LacZ_rep1
H1963_LacZrep1_RNA_S29
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: cMYC-overexpressed NCI-H1963 cells_2 [RNA-seq]

description:
NCIH1963_cMyc_rep2
H1963_cMYCrep2_RNA_S32
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 2 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgMYC2
H82_LMYCsgMYC2_RNA_S27
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LacZ-overexpressed NCI-H1963 cells_2 [RNA-seq]

description:
NCIH1963_LacZ_rep2
H1963_LacZrep2_RNA_S30
complementary DNA
H1963_cMYC_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 1 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_Lmyc_sgMYC1
H82_LMYCsgMYC1_RNA_S26
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 3 NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgMYC3
H82_LMYCsgMYC3_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed NCI-H82 cells_1 [RNA-seq]

description:
NCIH82_LMyc
H82_LMYC_RNA_S23
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed with non-target gRNA NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LMyc_sgNT1
H82_LMYCsgNT1_RNA_S24
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_3 [RNA-seq]

description:
NCIH82_LacZ_sgNT2
H82_LacZsgNT2_RNA_S22
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 2 NCI-H82 cells_2 [ATAC-seq]


title: LacZ-overexpressed NCI-H82 cells_1 [RNA-seq]

description:
NCIH82_LacZ
H82_LacZ_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMy-overexpressed with non-target gRNA NCI-H82 cells_3 [RNA-seq]

description:
NCIH82_LMyc_sgNT2
H82_LMYCsgNT2_RNA_S25
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_2 [RNA-seq]

description:
NCIH82_LacZ_sgNT1
H82_LacZsgNT1_RNA_cat
complementary DNA
H82_LMYC_CMYC_2_kallisto_abundance.txt


title: LMyc-overexpressed with MYC gRNA 3 NCI-H82 cells_2 [ATAC-seq]


title: LMyc-overexpressed with MYC gRNA 1 NCI-H82 cells_2 [ATAC-seq]


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_2 [ATAC-seq]


title: LacZ-overexpressed NCI-H82 cells_1 [ATAC-seq]


title: FT237p181aN1

status: Public on Dec 01 2020

type: genomic

city: Ann Arbor

first: Analisa

last: DiFeo

state: Michigan

address: 1600 Huron Parkway

institute: UNIVERSITY OF MICHIGAN-ANN ARBOR

description: FT237 cells stably expressing miR-181a (replicate 1)

hyb_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)

data_processing: For CNV analysis, processed data was analyzed using CNV partition according to the default parameters.

label: Cy3, Cy5

source_name: Fallopian tube immortalized cells

growth_protocol: FTSECs were cultured in a 1:1 ratio of DMEM and Ham’s F12 media (Corning) supplemented with L-glutamine, 15mM HEPES, 10% FBS (v/v) (Denville Scientific), and 0.6% Penicillin/Streptomycin (v/v) (Corning).

extract_protocol: Total genomc DNA was extracted using DNAesay kit (Qiagen)

tag: tissue

value: Fallopian tube immortalized cells

tag: genotype/variation

value: stably expressing miR-181a


title: FT237p181a-hmiRN2

description: FT237 cells stably expressing miR181a & miR181a antigomer (replicate 2)

scan_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)


title: FT237p181aN2

description: FT237 cells stably expressing miR-181a (replicate 2)

label_protocol: Infinium CytoSNP-850K v1.2 BeadChip(Illumina)


title: FT237shRBN1

description: FT237 cells stably expressing shRB1 (replicate 1)

value: stably expressing shRB1


title: FT237p000N2

description: FT237 cells stably expressing empty vector control (replicate 1)

value: stably expressing empty vector control


title: FT237p000N1

description: FT237 cells stably expressing empty vector control (replicate 2)


title: LacZ-overexpressed with non-target gRNA NCI-H82 cells_3 [ATAC-seq]


title: FT237p181a-hmiRN1

description: FT237 cells stably expressing miR181a & miR181a antigomer (replicate 1)


title: FT237shRBN2

description: FT237 cells stably expressing shRB1 (replicate 2)


title: K562_H3K27me3_(20200804_SH_Hs_K9m3_0801)

status: Public on Nov 13 2020

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag for K9me3 in K562 cells at home

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalize_counts.bedgraph.gz).

source_name: CUT&TAG-direct

extract_protocol:
CUTnTag-direct_v2_Protocols.io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: H3K27me3 Cell Signaling Technology cat# 9733

value: K562 human immortalised myelogenous leukemia cell line


title: K562_H3K27me3_rem10_(20200804_SH_Hs_K9m3_10_0801)

description: CUTAC Removal for K9me3 20 min in K562 cells at home


title: PPF WT 2

status: Public on Aug 07 2020

city: Salt Lake City

first: Gabrielle

last: Kardon

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
Fastq files were aligned with STAR and samtools using command ~/STAR-2.4.0a/STAR --genomeDir $genomeDB --readFilesCommand zcat --seedSearchStartLmax 50 --runThreadN 4 --outSAMunmapped Within  --outFilterIntronMotifs RemoveNoncanonical  --readFilesIn $file --outStd SAM --outSAMmode Full --outSJfilterReads Unique --sjdbGTFfile $gtf | ~/samtools-1.3/samtools view -bS -> ${file}.bam
Samtools was then used to sort and index the aligned bam file and featurecounts was used to count reads per feature: path_to_/featureCounts  -s 0 -O -t exon -g gene_name -a $gtf -o ./featureCountsResult/$bam_base.counts.txt.temp $bam tail -n +3 $bam_base.counts.txt.temp | awk '{print $1 "\t" $7}' > $bam_base.counts.txt.temp.body  echo -e "gene\t$bam_base" > $bam_base.counts.txt  cat $bam_base.counts.txt.temp.body >> $bam_base.counts.txt
Transcript counts were then normalized to transcript per million based on total reads and gene lengths in R, these normalized expression values were then used to determine expression of CDH and diaphragm related genes
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are gene coordinates, gene names, gene lenghts in base pairs, the number of gene feature counts and the TPM

source_name: Pleuroperitneal fold

extract_protocol:
Pleuroperitoneal folds (PPFs) were isolated from wild-type E12.5 mouse embryos by cutting embryos just above the hindlimbs and below the forelimbs and removing the heart and lungs cranially, leaving the trunk with attached nascent diaphragm. The PPFs were manually dissected and stored in RNAlater (Thermo Fisher, #AM7020) at -80°c. RNA was isolated using a RNeasy Micro Kit (Qiagen, #74004), RNA quality confirmed with RNA TapeStation ScreenTape Assay (Agilent, # 5067-5576), and sequenced using TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mixed, 129s/SvlmJ-C57/BL6J

value: Pleuroperitneal fold

tag: age

value: Embryonic day 12.5

value: wild type


title: PPF WT 1


title: Brn2 MNase ChIP input for LK2

status: Public on Sep 17 2019

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
Peaks were identified by MACS
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: BED

extract_protocol:
For H3K27ac, Sox2 and p63 ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies. For Brn2 ChIP, cells were cross-linked with disuccinimidyl glutarate and formaldehyde. Nuclei were extracted, digested with micrococcal nuclease and sonicated. Then, histone-DNA complexes were isolated with ant-Brn2 antibody.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75bp reads.

value: lung squamous cell carcinoma (LUSC) cell lines


title: Brn2 MNase ChIP input for NCI-H520


title: FT237-181a2

status: Public on Jun 07 2020

type: RNA

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified using the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.  Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.  Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures. Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.

label: biotin

source_name: human fallopian tube cells

label_protocol: Affymetrix

extract_protocol: mRNA was isolated using a total RNA isolation kit (Norgen). Total RNA was extracted from cell lysates of FT237-001, p181a, and p181a inhibitor in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry. In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and unbiased transcriptome coverage. This protocol efficiently generated amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference.

tag: group


title: FT237-181a3


title: FT237-p181a-knockdown-2

value: p181a inhibitor


title: FT237-p181a-knockdown-3


title: ChIP input for LK2_DNp63


title: Brn2 MNase ChIP for NCI-H520

value: Brn2 (Cell Signaling, #12137)


title: FT237-p0013


title: FT237-p0011


title: p63 ChIP for LK2_DNp63

value: p63 (Santa Cruz, sc-8431)


title: H3K27ac ChIP for LK2_GFP

value: acetyl-histone H3K27  (Abcam, ab4729)


title: FT237-p0012


title: Sox2 ChIP for LK2_GFP


title: H3K27ac ChIP for LK2_DNp63


title: Sox2 ChIP for HCC2814


title: Brn2 MNase ChIP for LK2


title: FT237-181a1


title: Sox2 ChIP for KNS62


title: Sox2 ChIP for LK2_DNp63


title: Sox2 ChIP for HCC95


title: FT237-p181a-knockdown-1


title: Sox2 ChIP for LK2


title: Sox2 ChIP for NCI-H520


title: ChIP input for Calu-1

description: ts_hw_calu1_ab4729_input_0414_13c_S13_ALL


title: ChIP input for HCC2279


title: ChIP input for SQ-1


title: ChIP input for HCC2450


title: ChIP input for EBC-1

description: ts_hw_ebc1_ab4729_input_0414_13c_S14_ALL


title: ChIP input for NCI-H2887


title: ChIP input for LK2_replicate1


title: ChIP input for HCC2814


title: ChIP input for HARA

value: HARA


title: ChIP input for KNS62


title: ChIP input for LK2_GFP


title: H3K27ac ChIP for HCC2279


title: H3K27ac ChIP for NCI-H2887


title: H3K27ac ChIP for HCC2450


title: H3K27ac ChIP for EBC-1


title: H3K27ac ChIP for Calu-1


title: ChIP input for LC-1/SQSF


title: H3K27ac ChIP for NCI-H520_replicate1


title: ChIP input for NCI-H520_replicate1

description: ts_hw_h520_ab4729_input_0505_12c_S22_ALL


title: H3K27ac ChIP for LC-1/SQSF


title: H3K27ac ChIP for HCC2814


title: H3K27ac ChIP for LK2_replicate2


title: H3K27ac ChIP for NCI-H520_replicate2


title: H3K27ac ChIP for KNS62


title: H3K27ac ChIP for LK2_replicate1


title: H3K27ac ChIP for SQ-1


title: H3K27ac ChIP for HCC95


title: H3K27ac ChIP for HARA


title: WT rep1

status: Public on Mar 25 2019

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

country: Germany

institute: University of Tuebingen

description:
Single cell RNA-seq libraries were prepared from fresh wild-type root protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. For each replicate, 12,200 cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-‐ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.
The R1 raw data files include the technical reads; the first 16 basepairs are barcode and the last 10 basepairs are UMI. The R2 raw data files include the biological reads.
processed data file: Root_single_cell_wt_datamatrix.csv

data_processing:
Cell Ranger 2.0.2 (10X Genomics) was used to process scRNA-seq data.
Bulk RNA Sequencing reads (pair-end, 75 bp) were trimmed using Trimmomatic (version 0.36), and aligned to the Arabidopsis TAIR10 reference genome with STAR. Gene expression values were calculated on uniquely mapped reads using HTSeq (version 0.7.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: *_datamatrix.csv: Comma-delimited text files include UMI counts values in each cell.
Supplementary_files_format_and_content: Root_bulk_tissue_datamatrix.txt: Tab-delimited text file includes read counts and RPM values for each Sample.

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Seedlings were grown vertically on nylon mesh on ½ Murashige and Skoog 1% agar plates.

extract_protocol:
RNA extraction (for bulk RNA-seq samples) - either protoplasted (reduced to smallest possible volume) or unprotoplasted root tissue was flash-frozen in liquid nitrogen, ground to a powder and RNA extracted using the Spectrum Plant RNA Extraction Kit (Sigma). Quality and quantity were checked using Agilent Bioanalyzer chips and Nanodrop, respectively, prior to library construction.
Bulk RNA libraries were produced using the NEBNext Poly(A) mRNA Magneticb Isolation Module, and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEB Multiplex oligos. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina. Single cell RNA-seq libraries were prepared from fresh protoplasts according to the 10x Genomics Single Cell 3’ Reagent Kit v2 protocol. For each replicate, cells were loaded in the 10x Genomics Chromium single cell microfluidics device with the aim of capturing 7,000 cells. 11 cycles were used for cDNA amplification, as well as for final PCR amplification of the adapter-‐ligated libraries. Final library size and quality were checked on a DNA High Sensitivity Bioanalyzer chip (Agilent), and libraries were quantified using the NEBNext Library Quantification Kit for Illumina.

treatment_protocol: For protoplasting: Roots of 6-day-old seedlings were cut approximately one centimetre from their tip, broadly diced with a scalpel blade, and treated with 7 ml protoplasting solution optimised for scRNA-seq from a protocol in Birnbaum et al., 2003. Immediately before use, 1.5% Cellulase R-10 and 0.1% Pectolyase (Duchefa Biochem.) were added to fresh protoplast buffer (0.1 M KCl, 0.02 M MgCl2, 0.02 M CaCl2, 0.1% BSA (Sigma Aldrich)), 0.08 M MES, and 0.6 M Mannitol adjusted to pH 5.5 with 0.1M Tris HCl) and mixed thoroughly. Root tissues were protoplasted for 2 hours at 20°C on an orbital shaker set at 200 evolutions/minute. The mixture was subsequently filtered through a 100 μm nylon filter and rinsed with 1-5 ml of root protoplast buffer. Protoplasts were then centrifuged for 10 minutes (500 g – 4°C), the supernatant gently removed, and the pellet resuspended in 10 ml root protoplast buffer containing 0.4 M Mannitol and no CaCl2. This wash procedure was repeated once more, the protoplasts centrifuged as before, and resuspended in ~500 μl or less protoplast buffer without CaCl2 and with 0.4 M Mannitol. Protoplasts were validated under a light microscope, and if necessary any excess debris or un-protoplasted tissues removed with an additional washing step. Cells were filtered through a 40 μm cell strainer (Flowmi Bel Art SP Scienceware), quantified using a haemocytometer, and adjusted to a density of approximately 800-‐900 cells per μl.

tag: strain/background

value: Wild type

value: Root

value: 6-day-old seedlings

tag: condition

value: Protoplasted


title: WT rep2

value: Col-0 pMIR166A:erGFP endodermal reporter line


title: Kir4.1cKO_Astrocyte_S8

status: Public on May 01 2018

city: Stanford

first: Kevin

last: Kelley

state: CA

address: 318 Campus Drive, W200

institute: Stanford University

data_processing:
Read quality was assessed using fastqc v0.11.4 and the first 5 bases as well as the last base of each read was trimmed and aligned to the Mus Musculus genome (Ensembl GRCm38) using TopHat2 v2.0.11 with bowtie2 v2.2.3.
TopHat2 was run with the following arguments “--no-coverage-search --segment-mismatches 1” with the genes.gtf file from Ensembl GRCm38.
Gene counts were created from the alignment files using htseq-count v0.6.1p1 with default parameters.
From raw count files, DESeq2 v1.14.1 was used to detect differentially expressed genes
FPKM values were generated using cuffquant and cuffnorm from cufflinks v2.2.1
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample; FPKM values are provided as comma-separated values; DESeq2 output provided as comma-separated values

source_name: spinal cord

extract_protocol:
Spinal cords were dissected. Meninges were removed, then dissociated with papain (20 U ml-1, Worthington) for 80min at 33°C. Aldh1l1-GFP+  cells were FACS sorted.
Total RNA was extracted with Trizol (Invitrogen) and purified using the RNeasy Kit (Qiagen). cDNA was generated from full length RNA using the NuGEN RNA-Seq V2 kit.

value: spinal cord astrocytes

value: mixed swiss-webster

value: spinal cord


title: Kir4.1cKO_Astrocyte_S4


title: Kir4.1cKO_Astrocyte_S5


title: OCI-P5X miR-181a low-n3

status: Public on Jan 21 2019

description: dif-a18006.dif-a1-10.rma-gene-full-Signal

hyb_protocol: Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.

scan_protocol: Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures.

data_processing: Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.

source_name: OCI-P5X miR-181a low

label_protocol: In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and unbiased transcriptome coverage. This protocol efficiently generated amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference.  Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified using the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.

extract_protocol: Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.

value: high-grade serous ovarian carcinoma (HGSOC) cell line

value: OCI-P5X miR-181a low


title: Kir4.1cKO_Astrocyte_S3


title: WT_Astrocyte_S7


title: WT_Astrocyte_S1


title: WT_Astrocyte_S2


title: OCI-P5X miR-181a low-n1

description: dif-a18004.dif-a1-10.rma-gene-full-Signal


title: 5dpf lck:GFPPos_rep2

status: Public on Aug 11 2017

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

description: FACS-sorted

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1
Quality trimmed reads were aligned to the Ensembl zebrafish genome (Zv9) using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9_79 annotation containing few additional genes.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-separated value files include gene counts for each sample

organism: Danio rerio

source_name: 5dpf_lck positive lymphoid cells

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.-Aldrich)

extract_protocol:
Between 200 and 300 larvae per condition were collected at 5 or 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and non-fluorescent cell fraction were subsequently sorted by FACS as described in Rougeot et al., (2014, Methods Mol Biol 1197:41-66). RNA were isolated using the RNAqueous microkit (Ambion) and cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing (Clonetech) according to the manufacturer’s instructions. The integrity of the RNA and cDNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides for the uninfected samples and 1 x 50 nucleotides for the infected samples.

value: zebrafish larvae

tag: developmental stage

value: lck positive lymphoid cells


title: 5dpf lck:GFPNeg_rep2

description: FACS-sorted

source_name: 5dpf_lck negative lymphoid cells

treatment_protocol: For infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.

value: lck negative lymphoid cells


title: OCI-P5X miR-181a high-n1

description: dif-a18001.dif-a1-10.rma-gene-full-Signal

source_name: OCI-P5X miR-181a high

tag: cell line

value: OCI-P5X miR-181a high


title: 5dpf lck:GFPPos_rep1

description: FACS-sorted

tag: cell type


title: 5dpf lck:GFPNeg_rep1

description: FACS-sorted


title: 5dpf mpx:GFPPos_rep2

description: FACS-sorted

source_name: 5dpf_mpx positive neutrophils

value: mpx positive neutrophils


title: 5dpf mpx:GFPNeg_rep1

description: FACS-sorted

source_name: 5dpf_mpx negative neutrophils

value: mpx negative neutrophils


title: 5dpf mpx:GFPNeg_rep2

description: FACS-sorted


title: OCI-P5X miR-181a high-n3

description: dif-a18003.dif-a1-10.rma-gene-full-Signal


title: OCI-P5X miR-181a low-n2

description: dif-a18005.dif-a1-10.rma-gene-full-Signal


title: WT_Astrocyte_S6


title: 5dpf mpx:GFPPos_rep1

description: FACS-sorted


title: 6dpf_mpeg1:mCherryPos_Mm:GFPPos_rep2

description: FACS-sorted

source_name: 6dpf_mpeg1 positive macrophages

tag: caudal vain infection

value: M. marinum M strain, 125cfu

value: mpeg1 positive macrophages


title: 6dpf_mpeg1:mCherryPos_Mm:GFPNeg_rep2

description: FACS-sorted


title: 6dpf_mpeg1:mCherryPos_rep2

description: FACS-sorted


title: OCI-P5X miR-181a high-n2

description: dif-a18002.dif-a1-10.rma-gene-full-Signal


title: 6dpf_mpeg1:mCherryNeg_Mm:GFPNeg_rep2

description: FACS-sorted

source_name: 6dpf_mpeg1 negative macrophages

value: mpeg1 negative macrophages


title: 6dpf_mpeg1:mCherryPos_Mm:GFPPos_rep1

description: FACS-sorted


title: 6dpf_mpeg1:mCherryPos_Mm:GFPNeg_rep1

description: FACS-sorted


title: L-MPP-1

status: Public on Mar 02 2020

city: Baltimore

first: Michael

middle: A

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Genome_build: hg19
Supplementary_files_format_and_content: bed format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME), methylation sensitivity index (MSI), and differential quantities of the above between samples (dMML, dNME, dMSI) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples, as well as tracks of differentially methylated regions (DMR) based on JSD.

source_name: L-MPP

extract_protocol:
Epicentre DNA extraction kit
Whole Genome Bisulfite Sequencing; Illumina TruSeq, NEBNext

tag: tissue type

value: primary

value: L-MPP


title: 6dpf_mpeg1:mCherryNeg_rep1

description: FACS-sorted


title: 6dpf_mpeg1:mCherryPos_rep1

description: FACS-sorted


title: 6dpf_mpeg1:mCherryNeg_Mm:GFPNeg_rep1

description: FACS-sorted


title: 5dpf mpeg1:gal4 ; UAS Kaede Positive_rep2

description: FACS-sorted

source_name: 5dpf_mpeg1 positive macrophages

value: mpeg1:gal4;UAS Kaede Positive


title: 5dpf mpeg1:gal4 ; UAS Kaede Negative_rep2

description: FACS-sorted

source_name: 5dpf_mpeg1 negative macrophages

value: mpeg1:gal4;UAS Kaede Negative


title: 5dpf mpeg1:gal4 ; UAS Kaede Negative_rep1

description: FACS-sorted


title: 6dpf mpeg1:gal4 ; UAS Kaede Positive_rep1

description: FACS-sorted


title: 6dpf mpeg1:gal4 ; UAS Kaede Negative_rep1

description: FACS-sorted


title: 6dpf mpeg1:gal4 ; UAS Kaede Negative_rep2

description: FACS-sorted


title: Non-tumor NMEC17

status: Public on Sep 16 2014

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Laser capture microdissection sample

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

label: Biotin

source_name: Mammary Gland Cell

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

extract_protocol: Total RNA was extracted by Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Mammary grand cells were isolated from frozen tissue sections using laser capture microdissection.

tag: tumor/nontumor

value: Non-tumor

value: Mammary Gland Cell from Non-tumor

tag: scan date (yymmdd)


title: Non-tumor NMEC14

description: Laser capture microdissection sample


title: Non-tumor NMEC11

description: Laser capture microdissection sample


title: 6dpf mpeg1:gal4 ; UAS Kaede Positive_rep2

description: FACS-sorted


title: Tumor 1M029TT1

description: Laser capture microdissection sample

value: Tumor

value: Mammary Gland Cell from Tumor


title: Non-tumor NMEC12

description: Laser capture microdissection sample


title: Non-tumor NMEC15

description: Laser capture microdissection sample


title: Tumor 1M022TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC10

description: Laser capture microdissection sample


title: Tumor 1M026TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC1

description: Laser capture microdissection sample


title: 5dpf mpeg1:gal4 ; UAS Kaede Positive_rep1

description: FACS-sorted

value: zebrafish larvae


title: Tumor 1M015TT1

description: Laser capture microdissection sample


title: Tumor 1M017TT1

description: Laser capture microdissection sample


title: Tumor 1M013TT1

description: Laser capture microdissection sample


title: Tumor 1M010TT1

description: Laser capture microdissection sample


title: Non-tumor NMEC16

description: Laser capture microdissection sample


title: Tumor 1M019TT1

description: Laser capture microdissection sample


title: Tumor 1M021TT1

description: Laser capture microdissection sample


title: Tumor 1M009TT1

description: Laser capture microdissection sample


title: Tumor 1M016TT1

description: Laser capture microdissection sample


title: Tumor 1M018TT1

description: Laser capture microdissection sample


title: Tumor 1M012TT1

description: Laser capture microdissection sample


title: Tumor 1M020TT1

description: Laser capture microdissection sample


title: Tumor 1M004TT1

description: Laser capture microdissection sample


title: Tumor 1M007TT1

description: Laser capture microdissection sample


title: Tumor 1M008TT1

description: Laser capture microdissection sample


title: Whole trachea Scnn1b-T, PND 42, biological replicate 1

status: Public on Sep 11 2014

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3001)

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16 hours at 45 degrees. Washing and staining was performed in the Affymetrix GeneChip Fluidics Station 450, protocol FS450_0007.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets. PND10 samples were further adjusted through Batchremoval by comparing to the rest of the samples.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, trachea

label_protocol: RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit and Ambion WT Expression Kit, according to manufacturer's recommended protocol.

growth_protocol: Mouse whole trachea;  mice grown under specific-pathogen-free conditions in micro-isolator cages

extract_protocol: Whole lungs were dissected and stored in RNALater until extraction using Qiagen RNAeasy columns, followed by ethanol precipitation

treatment_protocol: Not applicable;  no treatment;  mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.

value: C57Bl/6N Tac

tag: genotype

tag: age (postnatal day)


title: Tumor 1M002TT1

description: Laser capture microdissection sample


title: Tumor 1M003TT1

description: Laser capture microdissection sample


title: Whole trachea Scnn1b-T, PND 10, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3618, 3619)


title: Tumor 1M006TT1

description: Laser capture microdissection sample


title: Whole trachea Scnn1b-T, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3589, 3597)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3035, 3057)


title: Whole trachea Scnn1b-T, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3002, 3013)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2376, 2409)

value: PND 0 (<24 hrs)


title: Tumor 1M005TT1

description: Laser capture microdissection sample


title: Whole trachea WT, PND 42, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2999, 3033)

source_name: Wildtype, trachea

value: Wildtype


title: Whole trachea WT, PND 42, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 2997)


title: Whole trachea WT, PND 10, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) from a post natal day 10 wild-type male (animal number 3616)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2419, 2420)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2664, 2665)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-Tg males (animal numbers 22818, 2886, 2887, 2888)


title: Whole trachea WT, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3598, 3601)


title: Whole trachea Scnn1b-T, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784, 2785)


title: Whole trachea Scnn1b-T, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2369, 2377)


title: Whole trachea WT, PND 0, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively); pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)


title: Tumor 1M027TT1

description: Laser capture microdissection sample


title: Whole trachea WT, PND 0, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: Whole trachea Scnn1b-T, PND 10, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 3599, 3600)


title: Whole trachea WT, PND 10, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 10 wild-type males (animal numbers 3588, 3590)


title: Whole trachea WT, PND 3, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2791, 2793)


title: Whole trachea WT, PND 3, biological replicate 2

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2781)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 3013, 3034)

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Scnn1b-Tg, whole lung

growth_protocol: Mouse whole lung (left lobe);  mice grown under specific-pathogen-free conditions in micro-isolator cages


title: Whole trachea WT, PND 3, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 3 wild-type males (animal numbers 2782, 2817)


title: Whole trachea WT, PND 42, biological replicate 3

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from post natal day 42 wild-type males (animal numbers 3036, 3037)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2688, 2746)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2783, 2784)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2752, 2754)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 3

description: whole lung (left lobe) sample from post natal day 42 Scnn1b-transgenic male (animal number 3035)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2420, 2422)


title: Whole lung Scnn1b-Tg, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 Scnn1b-transgenic males (animal numbers 2760, 2761)


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2375, 2376)


title: Whole lung Scnn1b-Tg, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 Scnn1b-transgenic males (animal numbers 2998, 3002)


title: Whole trachea WT, PND 0, biological replicate 1

description: whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2664, 2665)


title: Whole lung Scnn1b-Tg, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 Scnn1b-transgenic males (animal numbers 2662, 2663)


title: Whole lung WT, PND 42, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 2996, 3036)

source_name: Wildtype, whole lung


title: Whole lung Scnn1b-Tg, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) Scnn1b-transgenic males (animal numbers 2409, 2419)


title: Whole lung WT, PND 42, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3037, 3058)


title: Whole lung WT, PND 10, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2745, 2753)


title: Whole lung WT, PND 42, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 42 wild-type males (animal numbers 3067, 3068)


title: Whole lung WT, PND 10, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2683, 2684)


title: Whole lung WT, PND 3, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2781, 2782)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 2

description: purified macrophages

hyb_protocol: Hybridization was performed at 48 degrees using the GeneTitan plate system.

data_processing:
CEL files were imported into Partek Genomics Suite v6.5, and exon-level log2 intensities were obtained through  RMA background correction, GC content and sequence adjustment, quantile normalization, and median polish probeset summarization. Gene-level log2 intensity were summarized as the mean of exon probesets.
MoGene-1_1-st-v1.r4.pgf
MoGene-1_1-st-v1.r4.mps

source_name: Scnn1b-Tg, macrophages, germ-free facility

label_protocol: 12 ng of RNA was used to generate cDNA using Ovation Pico WTA system V2 kig (NuGEN Technologies, CA).

growth_protocol: Mouse lung lavage macrphages purified by negative selection through from a Lys-6G column;  mice grown either under specific-pathogen-free conditions in micro-isolator cages or in a germ-free environment

extract_protocol: Magnetic activated cell sorting uas used to purify macrophages from lung lavage samples using Ant-Ly-6G MicroBeads (Miltenyi Biotec, MA).  Ly-6G negative cells (macrophages) were pelleted, snap-frozen and stored at -80 C.  Frozen macrophage pellets were lysed and homogenized in lysis buffer and QIAshedder (Qiagen).  Genomic DNA was eliminated using gDNA eliminator spin columns;  RNA was isolated using Purelink RNA mini kits (Invitrogen).

treatment_protocol: Mice are either wildtype or Scnn1b-transgenic and were harvested at post natal days 0, 3, 10, and 42.  At PND 42 macrophages were also isolated from wildtype and Scnn1b-transgenic mice grown in a germ-free environment.

tag: animal facility type

value: germ-free


title: Whole lung WT, PND 3, biological replicate 1

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2792, 2793)


title: Whole lung WT, PND 0, biological replicate 1

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2370, 2374)


title: Whole lung WT, PND 3, biological replicate 3

description: whole lung (left lobe) pooled samples from post natal day 3 wild-type males (animal numbers 2817, 2884)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 3

description: purified macrophages


title: Whole lung WT, PND 0, biological replicate 2

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2377, 2410)


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42 germ-free, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 2

description: purified macrophages

source_name: Wildtype, macrophages, germ-free free facility


title: Whole lung WT, PND 0, biological replicate 3

description: whole lung (left lobe) pooled samples from newborn (post natal day 0) wild-type males (animal numbers 2418, 2421)


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 1

description: purified macrophages

source_name: Wildtype, macrophages, germ-free facility


title: Purified lung lavage macrophages WT, PND 42 germ-free, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 3

description: purified macrophages

source_name: Scnn1b-Tg, macrophages, specific pathogene free facility

value: specfic pathogen free


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 42, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 10, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages Scnn1b-Tg, PND 3, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 1

description: purified macrophages

source_name: Wildtype, macrophages, specfic pathogen free facility


title: Purified lung lavage macrophages Scnn1b-Tg, PND 0, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 4

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 10, biological replicate 1

description: purified macrophages


title: A2780-p181a_1

status: Public on Dec 01 2013

data_processing:
Transcriptome raw reads from Illumina HiSeq 2000 were mapped to the human reference genome
The coverage over the length of the gene is variable due to various biases inherent to the sequencing and sample preparation process. To avoid problems arising from this, we generated a density profile using windows of 50 bp sliding over the length of each gene, and the median of this density profile was picked as the representative coverage for the gene using an in-house mRNA-seq expression profile pipeline. The coverage is corrected using log-transformation and quantile normalization. Putative miRNA targets were predicted using TargetScan (http://www.targetscan.org) and miRConnect (http://mirconnect.org).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Ovarian cancer cell line

growth_protocol: A2780 cellswere cultivated  in DMEM media supplemented with 10% FBS and 1% Penicillin-Streptomycin (recommended media). Cells were cultured in a humidified atmosphere (5% CO2) at 37°C. Trypsin (0.25%)/EDTA solution was used to detach the cells from the culture flask for passaging.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen)  from two polyclonal pools of A2780 cells expressing exogenous miR-181a (p181a #1 and p181a #2) and pBABE contro.l
The Illumina RNASeq kit was used to prepare sequencing libraries. The method is as follows: 1 μg of high quality total RNA was incubated with oligo(dT) magnetic beads (SeraMag) in order to enrich for mRNA with poly-A tails. Eluted RNA was randomly cleaved by incubation at 94°C with a magnesium buffer. The RNA is ethanol-precipitated and then reverse transcribed (Invitrogen SuperScript II). DNA polymerase is added to generate a second strand. dsDNA after second strand synthesis contains ends with 5´ and 3´ overhangs, and these are filled in using T4 polymerase and T4 polynucleotide kinase resulting in a blunt-ended DNA molecule. Then a deoxyadenosine (dA) 5´ tail is added to DNA strands using the Klenow fragment (exo-). dsDNA adapters with 3´ thymidine overhangs are ligated to the dA-tailed library using T4 ligase. The library was then size selected on a 2% agarose gel, and amplified with 15 cycles of PCR (NEB Phusion polymerase). This procedure adds the sequences needed for binding to the Illumina flow cell and sequencing primer-binding sites. RNA-Seq libraries were sequenced using the Illumina HiSeq 2000 for a 100nt read length. Transcriptome raw reads from Illumina HiSeq 2000 were mapped to the human reference genome (hg19). The coverage over the length of the gene is variable due to various biases inherent to the sequencing and sample preparation process. To avoid problems arising from this, we generated a density profile using windows of 50 bp sliding over the length of each gene, and the median of this density profile was picked as the representative coverage for the gene using an in-house mRNA-seq expression profile pipeline. The coverage is corrected using log-transformation and quantile normalization.

tag: expression

value: p181a#1( clone 1 expressing miR-181a)

tag: tumor histology

value: ovarian cancer cell line derived from an undifferentiated ovarian tumor


title: Purified lung lavage macrophages WT, PND 3, biological replicate 4

description: purified macrophages

tag: strain


title: A2780-p181a_2

value: p181a#2( clone 2 expressing miR-181a)


title: A2780-pBABE

value: pBABE vector


title: Purified lung lavage macrophages WT, PND 3, biological replicate 1

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 0, biological replicate 2

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 0, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 3, biological replicate 3

description: purified macrophages


title: Purified lung lavage macrophages WT, PND 42, biological replicate 4

description: purified macrophages


title: ytpQ mutant, methylglyoxal (MG) treated, rep3

status: Public on Oct 25 2011

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

description:
ytpQ_3_MG
ytpQ mutant vs. wild type_MG treated_third biological replicate

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing:
We used Cell ranger (6.0, 10x Genomics) to align Raw base call (BCL) sequence files or FASTQ files to the C. elegans genome (WS282, Wormbase), and generated feature-barcode matrices. Doublets were removed based on the recommended ratio provided by the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 user guide (CG000204 Rev D), with a score calculated by Doubletfinder (Github/chris-mcginnis-ucsf). The feature-barcode matrices for each sample were constructed into a Seurat (R package, 4.0.5) object for downstream analysis. Cells were filtered by requiring a minimum of 100 genes to be expressed, and genes were filtered by being expressed in at least 3 cells. Integration of samples was performed with Seurat canonical correlation analysis (CCA) method to remove the batch effects. We tested CCA, reciprocal principal component analysis (PCA) and Harmony (0.1) for integration and chose the method with the best performance. The top 2,000 variable features were used for integration anchor identification. UMAP and tSNE dimension reduction were performed with the first 50 dimensions from PCA. Clustering was performed at multiple Leiden resolutions.
Assembly: WS282
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: cawa_neuronsubclusterlabel.rds (This file contains neuron subcluster identity labels for the Cell Atlas of Worm Aging (CAWA) dataset. Neuron nuclei were subsetted from the integrated Seurat object, re-integrated using Seurat CCA, and clustered at multiple Leiden resolutions to resolve 77 subclusters corresponding to 104 of 118 known adult C. elegans neuron classes. Subcluster annotation was performed using a combination of marker gene identification (via COSG) cross-referenced with known expression profiles, and reference-based mapping(SingleR) with SingleR using the Taylor et al. (2021) C. elegans neuronal transcriptome atlas as the primary reference.)

organism: Bacillus subtilis

source_name: wild type, 2.8 mM MG

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: B. subtilis 168 wild type, delta ytpQ mutant, and delta spx mutant cells were grown under vigorous agitation at 37 °C in a minimal medium described before (Stülke et al., 1993, J Gen Microbiol 139, 2041-2045).

extract_protocol: Total RNA was isolated by the acid phenol method as described (Majumdar et al., 1991, Biotechniques 11: 94-101).

treatment_protocol: At OD500 of 0.4, cells were treated for 10 minutes with 2.8 mM methylglyoxal.

value: wild type

tag: treatment

value: methylglyoxal (MG)

source_name: ytpQ deletion mutant, 2.8 mM MG

value: ytpQ deletion mutant


title: Purified lung lavage macrophages WT, PND 0, biological replicate 1

description: purified macrophages


title: Whole lung WT, PND 10, biological replicate 2

description: whole lung (left lobe) pooled samples from post natal day 10 wild-type males (animal numbers 2685, 2689)


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-K21

status: Public on Dec 17 2025

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of mouse brain were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: age

value: 9 months

tag: brain region

value: CP

tag: gender

value: M


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-N17


title: 6dpf_mpeg1:mCherryNeg_rep2

description: FACS-sorted

source_name: 6dpf_mpeg1 negative macrophages

tag: genotype/variation

tag: tissue

tag: developmental stage

value: mpeg1 negative macrophages