title: Lumbar from GW18 Embryo

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

description: Gene expression data from GW 18 human cervical embryonic tissue

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Signal values were computed using the Affymetrix® GeneChip™ Command Console software. . Obtained raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).
After importing CEL files, the data were summarized and normalized with the robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis

label: biotin

source_name: G.W. 18 human embryo

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal Labeling kit

extract_protocol: The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit).  cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer

value: Tissue derived from human embryonic CNS


title: Liver_Ionic_3d rep1

status: Public on May 31 2019

type: RNA

city: Leioa

first: José María

last: Lacave

state: Bizkaia

address: Sarriena s/n

department: Zoology and Animal Cell Biology

country: Spain

institute: University of the Basque Country

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 1.65 ƒÝg. Volume: 100 uL. Temperature (oC): 65. Duration: 17 hours at 10 rpm in the hybridization oven.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent Technologies), with ozone-barrier slide covers (Agilent P/N G2505-60550) SCAN C SETTINGS Dye Channel Scan RegionGreen 61 x 21,6 mm Scan resolution (um) 6 Tiff 20 bit

data_processing: Images (.tiff images) were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies). The Feature Extraction software (FE) extracts the raw data from Cy3 (Green(g) channel) fluorescence signal (mean signal) from the spot which contains the probes (control features and biological or non control features) and from background. After processing of the raw signal it applies several algorithms for the calculation of the processed signal, which will be used in the analysis, and other useful data for the assessment of the quality of the processed data. The processed signal is corrected for background and microarray processing artifacts (Spatial detrending). For background correction it uses the negative control feature data, which corresponds to sequences with no expected hybridization, and it is an indication of unspecific binding or hybridization. More detailed data processing description is available on the series record.

molecule: total RNA

organism: Danio rerio

source_name: Liver, Ionic silver, 3d

label_protocol: Amount of nucleic acid labeled: 100 ng. Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) Version 6.5 May 2010. Samples are retrotranscribed (first strand synthesis) and labeled using Low imput Quick Amp Labeling kit, One color (Agilent Technologies, Cat. Nº 5190-2305) following manufacturer instructions. First, total RNA is retrotranscribed with AffinityScript Reverse Transcriptase (AffinityScript RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT is in vitro transcribed by T7 RNA pol in the presence of either Cy3-CTP or Cy5-CTP fluorophores to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen). After labeling and purification, cRNA is quantify with NanoDrop ND-1000 spectrophotometer in order to determine the yield and specific activity of each reaction. Yield: µg of cRNA. Should be > 1.65 µg. Specific activity: pmol Cy3 per µg of cRNA. Should be >6. All the labeled samples where above those limits.

extract_protocol: Total RNA was extracted following the TRizol® extraction method (ThermoFisher Scientific). Concentration of RNA was measured in a Biophotometer (Eppendorf, Hamburg, Germany). RNA was purified with RNeasy mini kit (Qiagen, Venlo, The Netherlands). In addition, RNA quality was assessed in an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with a RIN value above 8.1 were used for microarray and qPCR analysis.

treatment_protocol: Samples were waterborne exposed to 0.01 mg/L of maltose-coated Ag NPs of 20 nm or ionic silver for 3 and 21 days

tag: tissue

value: Liver

tag: gender

value: Male


title: Liver_Nano_3d rep2

source_name: Liver, Ag NPs, 3d


title: Cervical from GW18 Embryo

description: Gene expression data from GW 18 human lumbar embryonic tissue

organism: Homo sapiens


title: WT_UNINJ WT_un3_R_R1

type: SRA

city: Rochester

first: Hani

middle: A

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

country: USA

institute: University of Rochester

library_source: transcriptomic

data_processing:
demultiplexed using bcltofastq-2.19.0
Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
STAR_2.5.2b "--twopassMode Basic --runMode alignReads  --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
subread-1.5.0p3, featurecounts "-s 0 -t exon -g gene_name"
Differential expression was perfromed using R 3.3.2 and DeSeq2 v1.14.1
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: text file of raw read counts across all genes for each sample

organism: Mus musculus

source_name: deep digital flexor tendon tissue

extract_protocol:
RNeasy Plus Micro Kit (Qiagen, Valencia, CA) or Arcturus Pico Pure kit (Life Technnologies, Carlsbad, CA)
NexteraXT library preparation kit

tag: genotype

value: C57Bl/6J (WT)

tag: treatment

value: Normal, Uninjured


title: PAI-1_UNINJ PAI-un7_R1

value: B6.129S2-Serpine1tm1Mlg/J (PAI-1 KO)


title: WT_UNINJ WT_un4_R_R1


title: PAI-1_UNINJ PAI-un3_R_R1


title: PAI-1_UNINJ PAI-un3_L_R1


title: TOX_WT2

city: La Jolla

first: Anjana

last: Rao

state: CA

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

description:
TPM_counts_mesenteric.csv.gz
Raw_counts_mesenteric.csv.gz

data_processing:
Through the use of Illumina Basespase FASTQ format single-end sequencing files were generated.
RNA-seq reads were mapped against the mm10 using STAR (STAR_2.5.3) with the following parameters “--genomeLoad LoadAndRemove --outFilterMultimapNmax 1 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --outFilterMismatchNmax 0” and the RefSeq gene annotation was obtained from the UCSC genome Bioinformatics database.
The number of reads mapping to each gene was counted using featureCounts (subread-1.4.3-p1) with the following parameters “-g gene_name -s 0”.
Transcripts per million counts were calculated by normalizing the size of the meta-transcript (in kilobases),by 1,000,000 ("per million" scaling factor) and by the library size.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values delimited file that include TPM values for each sample (columns) or the raw counts per gene per sample (column)

source_name: Tumor infiltrating lymphocyte

extract_protocol:
GFP+CD8+Thy1.1+ CAR T cells were sorted from B16-OVA-huCD19 tumors. And  total RNA were extracted using Qiagen RNeasy plus micro kit
Libraries were constructed by Smart2seq protocol

tag: strain

tag: age

value: 12 weeks old


title: TOX_WT1


title: WT_2wPL m474_R_R1

value: Partially lacerated

tag: time

value: 2-weeks Post Injury


title: TOX_DKO4


title: TOX_DKO2


title: TOX and TOX2 DKO CAR TILs 1_1

description:
Condition Biological Replicate 1
DKO.1

library_source: genomic

data_processing:
Through the use of Illumina Basespase FASTQ format Paired-end sequencing files were generated.
Reads were mapped to mouse (mm10) genome using a two-step mapping strategy. bowtie (v1.0.0) was used to map the untrimmed reads with parameters """-p 4 -m 1 --best --strata -X 2000 --tryhard -S --fr --chunkmbs 2048".
The unmapped reads were collected and processed with Trim_galore! using parameters "--paired --nextera --length 37 --stringency 3 --three_prime_clip_R1 1 --three_prime_clip_R2 1". These filtered reads were mapped again with same parameters plus "-X 2500 -v 3 -e 100".
Both final bam files were merged and processed to remove duplicated reads (Picard "MarkDuplicates") and reads aligning to either mitochondrial genome (custom perl script) or ENCODE blacklisted regions.
To identify peaks of accessibility, first the filtered mapping results were processed to identify nucleosome-free DNA fragments less than 100nt in length with samtools and awk '{if(sqrt($9*$9)<100){print $0}}'.
These subnucleosomal fragments were used to call peaks summits for each sequenced sample using MACS2 with parameters "callpeak -g mm -q 0.001 --keep-dup all --nomodel --call-summits".
Resulting summits were further expanded to uniform 200 bp sized regions and merged into a global set of peaks and filtered to remove the Y chromosome.
For the differential enrichment of accessibility signal analysis between sample groups we first collected the number of transposase insertions overlapping each peak from the global set using "summarizeOverlaps" function from the GenomicAlignments Package.
These insertion counts were further normalized between replicates using "voom" from Limma package.
Finally, pairwise contrast were performed with limma and differentially accessible regions were filtered based on a FDR adjusted p-value of less than 0.05 and an estimated fold change of at least 2.
For DeNovo Motifs analysis we used findMotifsGenome.pl from HOMER
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited values that include normalized Tn5 insertion counts on the log2 scale for each sample (columns) on all and each of the peaks called as described above.

molecule: genomic DNA

extract_protocol:
GFP+CD8+Thy1.1+ CAR T cells were sorted and lyzed from B16-OVA-huCD19 tumors.
The transposition reaction was performed using Nextera enzyme (Illumina) and purified using the MinElute kit (Quagen) prior to PCR amplification (KAPA Biosystems) with 12 cycles using barcoded primers

value: TOX and TOX2 DKO


title: TOX_DKO3


title: TOX and TOX2 WT CAR TILs 2_1

description:
Control Biological Replicate 1
WT.1

value: TOX and TOX2 WT


title: TOX and TOX2 WT CAR TILs 2_2

description:
Control Biological Replicate 2
WT.2


title: TOX and TOX2 DKO CAR TILs 1_2

description:
Condition Biological Replicate 2
DKO.2


title: TOX_WT3


title: WT_1

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

description:
Gene expression in wild-type gastrocnemius muscle tissues. [rep1]
fpkm_quntification_jihwanpark.txt

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
The adaptor sequences were trimmed by the cutadapt (v1.4.2) and then aligned to the reference mouse genome (GRCm38.p6) using the STAR aligner(ver 2.6.1).
The align data were quantified to the gene features (GRCm38.95.gtf) in fragments per kilobase of transcript per million fragments mapped values (FPKM) using Cufflinks (ver 2.2.1).
We defined “expressed gene” with FPKM ≥ 1 for at least one of the six samples. For these expressed genes, the normalized log2(FPKM) values were obtained by using the quantile normalization method (MATLAB R2018a).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files including FPKM and normalized FPKM for each sample

molecule: polyA RNA

source_name: gastrocnemius muscle tissues, wild-type, replicate 1

growth_protocol: The Nogo KO mice were generously provided by Binhai Zheng (University of California, San Diego, CA, USA). Mice (WT and Kogo KO) were housed under appropriates conditions with 12 h light-dark cycles and access to water ad libitum in accordance with the Kyungpook National University animal facility regulations.

extract_protocol:
Total RNA was isolated from the gastrocnemius muscle tissues of WT and Nogo KO mice (3 biological replicates per each group) using Qiagen RNeasy mini Kit. mRNA was then isolated from the total RNA and fragmented using Illumina Truseq™ Stranded mRNA LT Sample Prep Kit with poly-T oligo magnetic beads, and reverse transcription of the mRNA fragments was conducted using Superscript III reverse transcriptase (Life Technologies).
Adaptor ligated libraries were generated according to the manufacture’s standard protocol and sequenced using HiSeq 2500 system.

value: gastrocnemius muscle tissues

value: wild-type


title: TOX_WT4


title: TOX_DKO1


title: WT_2wPL m471_R_R1


title: WT_UNINJ WT_un4_L_R1


title: WT_4wPL m463R_R1

value: 4-weeks Post Injury


title: WT_2wPL m470_R_R1


title: WT_4wPL m465R_R1


title: PAI-1_4wPL 457R_R1


title: WT_4wPL m467R_R1


title: PAI-1_4wPL 455R_R1


title: PAI-1_4wPL 456R_R1


title: 82Qm120a_8wk_rep4

city: Minneapolis

first: Harry

middle: T

last: Orr

state: MN

address: 2101 6th Strreet SE

department: Laboratory Medicine and Pathology

institute: University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to mm10 with hisat2 2.0.1-beta using all default parameters, a hisat2 index created from the UCSC mm10 reference genome, and the igenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html) UCSC mm10 annotation from igenomes (version 2015-07-17-14-33-26, downloaded from https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were assigned to genes and summed using featureCounts from the Subread package (http://subread.sourceforge.net/) with all default parameters, except the addiion of -p.
Differential expression on count data was carried out in R v.3.3.3 using DESeq2 v.1.14.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with read counts for all genes (rows) and all samples (columns)

source_name: cerebellum

extract_protocol:
Total RNA was isolated from dissected mouse cerebella using TRIzol Reagent and purified for sequencing using the RNeasy MiniKit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA libraries)

tag: age (weeks)


title: PAI-1_2wPL 094_R_R1


title: PAI-1_2wPL 093_R_R1


title: 82Qm120a_8wk_rep1


title: FVB_9wk_rep5

value: FVB/nJ

value: wild type


title: 82Q_9wk_rep3


title: FVB_9wk_rep1


title: FVB_9wk_rep4


title: 82Q_9wk_rep4


title: WT_Vehicle_Pons_week28_rep4

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to GRCm38 with hisat2 v.2.0.2 using all default parameters except --rna-strandness RF, the hisat2 grcm38_snp_tran index (ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grcm38_snp_tran.tar.gz) and release 87 of the ENSEMBL GRCm38 gtf (http://ftp.ensembl.org/pub/release-87/gtf/mus_musculus/Mus_musculus.GRCm38.87.gtf.gz)
Aligned reads were assigned to genes and summed using featureCounts from the Subread package (http://subread.sourceforge.net/) with all default parameters except the addition of -s 2.
Differential expression on count data was carried out in R v.3.3.3 using DESeq2 v.1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with read counts for all genes (rows) and all samples (columns)

source_name: pons

extract_protocol:
Total RNA was isolated from dissected mouse cerebella, pons and medulla using TRIzol Reagent and purified for sequencing using the RNeasy MiniKit (Qiagen).
Stranded RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded RNA libraries)

value: pons

value: treated with vehicle (no anti-sense oligonucleotide)


title: 82Qm120a_8wk_rep3


title: 82Qm120a_8wk_rep2


title: 82Qm120a_8wk_rep5


title: 82Q_9wk_rep1


title: 82Q_9wk_rep5


title: WT_Vehicle_Pons_week28_rep1


title: FVB_9wk_rep3


title: 82Q_9wk_rep2


title: WT_Vehicle_Pons_week28_rep3


title: SCA_Vehicle_Pons_week28_rep4


title: WT_Vehicle_Pons_week28_rep2


title: SCA_Vehicle_Pons_week28_rep3


title: SCA_Vehicle_Pons_week28_rep1


title: SCA_Vehicle_Pons_week28_rep2


title: SCA_ASO_Pons_week28_rep4

value: treated with an anti-sense oligonucleotide against Atxn1


title: FVB_9wk_rep2


title: SCA_ASO_Pons_week28_rep3


title: SCA_ASO_Pons_week28_rep1


title: SCA_ASO_Pons_week28_rep2


title: WT_Vehicle_Medulla_week28_rep8_batch2

source_name: medulla

value: medulla

value: treated with vehicle (no anti-sense oligonucleotide); batch 2


title: WT_Vehicle_Medulla_week28_rep7_batch2


title: WT_Vehicle_Medulla_week28_rep6_batch2


title: WT_Vehicle_Medulla_week28_rep5_batch2


title: SCA_Vehicle_Medulla_week28_rep6_batch2


title: WT_Vehicle_Medulla_week28_rep2_batch1

value: treated with vehicle (no anti-sense oligonucleotide); batch 1


title: WT_Vehicle_Medulla_week28_rep3_batch1


title: SCA_Vehicle_Medulla_week28_rep7_batch2


title: SCA_Vehicle_Medulla_week28_rep4_batch1


title: SCA_Vehicle_Medulla_week28_rep8_batch2


title: WT_Vehicle_Medulla_week28_rep1_batch1


title: SCA_ASO_Medulla_week28_rep6_batch2

value: treated with an anti-sense oligonucleotide against Atxn1; batch 2


title: SCA_Vehicle_Medulla_week28_rep2_batch1


title: SCA_Vehicle_Medulla_week28_rep1_batch1


title: SCA_ASO_Medulla_week28_rep5_batch2


title: SCA_ASO_Medulla_week28_rep7_batch2


title: SCA_Vehicle_Medulla_week28_rep5_batch2


title: SCA_ASO_Medulla_week28_rep1_batch1

value: treated with an anti-sense oligonucleotide against Atxn1; batch 1


title: SCA_Vehicle_Pons_week18_rep1


title: SCA_ASO_Medulla_week28_rep3_batch1


title: WT_Vehicle_Pons_week18_rep2


title: WT_Vehicle_Pons_week18_rep1


title: WT_Vehicle_Pons_week18_rep3


title: SCA_ASO_Medulla_week28_rep4_batch1


title: SCA_ASO_Medulla_week28_rep2_batch1


title: SCA_Vehicle_Pons_week18_rep2


title: PAI-1_2wPL 092_R_R1

value: B6.129S2-Serpine1tm1Mlg/J (PAI-1 KO)

value: Partially lacerated


title: SCA_ASO_Pons_week18_rep1


title: SCA_ASO_Pons_week18_rep2


title: SCA_ASO_Pons_week18_rep3


title: WT_Vehicle_Medulla_week28_rep4_batch1


title: WT_Vehicle_Medulla_week18_rep1


title: SCA_Vehicle_Medulla_week18_rep2


title: WT_Vehicle_Medulla_week18_rep2


title: SCA_Vehicle_Medulla_week18_rep1


title: SCA_ASO_Medulla_week18_rep3


title: SCA_Vehicle_Cerebellum_week18_rep4

value: cerebellum


title: WT_Vehicle_Cerebellum_week18_rep4


title: SCA_Vehicle_Medulla_week18_rep3


title: SCA_Vehicle_Medulla_week28_rep3_batch1


title: WT_Vehicle_Cerebellum_week18_rep3


title: WT_Vehicle_Cerebellum_week18_rep2


title: SCA_ASO_Medulla_week18_rep1


title: SCA_Vehicle_Cerebellum_week18_rep2


title: SCA_Vehicle_Cerebellum_week18_rep1


title: WT_Vehicle_Medulla_week18_rep3


title: SCA_ASO_Cerebellum_week18_rep1


title: SCA_ASO_Cerebellum_week18_rep3


title: SCA_ASO_Cerebellum_week18_rep2


title: SCA_Vehicle_Pons_week18_rep3


title: SCA_Vehicle_Cerebellum_week18_rep3


title: SCA_ASO_Cerebellum_week18_rep4


title: SCA_ASO_Medulla_week18_rep2


title: WT_Vehicle_Cerebellum_week18_rep1


title: 78_Vehicle_microglia (MG)

city: Philadelphia

first: Robert

middle: L

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to the mouse genome mm10 using the STAR aligner v2.5.0e with default parameters.
Reads were mapped to genes using the default parameters provided b STAR (based on HT-Seq counts).
Gene counts were normalized and analyzed for differential exprssion with DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content:  txt file of raw counts from STAR

source_name: Tumor-associated macrophages

growth_protocol: Tumor bearing mice were anesthetized with 1.25% Avertin, and transcardially perfused with PBS. Tumors were macrodissected and dissociated using the Mouse Tumor Dissociation Kit (mTDK, Miltenyi) using the OctoMACS disocciator. Tumors were filtered through a 40 μM mesh filter and underwent RBC lysis (PharmLyse BD). Tissue underwent myelin removal using the Myelin Removal Beads (Miltenyi). Single cell suspensions were FC blocked (BD cat #553141) for 15 minutes at 4 degrees Celsius. Cells were then incubated with directly conjugated antibody panels for 15 minutes at 4 degrees Celsius. Cell suspensions were washed (PBS +2% fetal bovine serum) and resuspended in a DAPI solution. All flow cytometry analysis was completed on a BD Fortessa device at the Flow Cytometry Core Facility (FCCF) at MSKCC. All cell sorting was completed on an Aria III device at the FCCF at MSKCC. Tumor assocaited microglia (MG) were isoalted as Cd45+Cd11b+Ly6c-Ly6g-Cd49d- cells while tumor associated bone marrow derived macrophages (BMDM) were isolated as Cd45+Cd11b+Ly6c-Ly6g-Cd49d+ cells. Samples were sorted directly into TriZOL LS.

extract_protocol:
RNA was isolated from TriZOL with a chloroform extraction, following by isopropanol precipitation with glycogen carrier.
Libraries were generated using the Smart-Seq kit (Clonetech).

treatment_protocol: For the glioma generation intracranial injections were performed on 5-6 week old mice as previously described (Pyonteck et al., 2013). Briefly, mice were fully anesthetized with ketamine/xylazine and bupivacaine was applied as a local anesthetic. Using a stereotactic apparatus, cells were injected into the right frontal cortex (1 mm caudal, 1.5 mm lateral from bregma, 2-3 mm deep). 3x10^5 DF1 cells RCAS-PDGFB-HA cells were injected at week 6 of age into nTVA Ink4a/Arf KO/KO mice.

tag: cell type

value: microglia (MG)

tag: Stage

value: Vehicle

tag: mouse


title: 78_Vehicle_bone marrow-derived macrophages (BMDM)

value: bone marrow-derived macrophages (BMDM)


title: 70696_BLZ945_Recurrent_microglia (MG)


title: 68346_IR_Recurrent_microglia (MG)


title: 68344_IR_Recurrent_bone marrow-derived macrophages (BMDM)


title: 68362_IR-BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 68362_IR-BLZ945_Recurrent_microglia (MG)


title: 68346_IR_Recurrent_bone marrow-derived macrophages (BMDM)


title: 68345_IR_Recurrent_microglia (MG)


title: 68345_IR_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67947_IR-BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67947_IR-BLZ945_Recurrent_microglia (MG)


title: 67668_BLZ945_Recurrent_microglia (MG)


title: 68344_IR_Recurrent_microglia (MG)


title: 70696_BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67668_BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67543_IR-BLZ945_Recurrent_microglia (MG)


title: 68343_IR_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67537_IR-BLZ945_5day_microglia (MG)


title: 67543_IR-BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 67169_IR-BLZ945_Recurrent_microglia (MG)


title: 67537_IR-BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 65975_BLZ945_5day_microglia (MG)


title: 67169_IR-BLZ945_Recurrent_bone marrow-derived macrophages (BMDM)


title: 65972_IR_5day_microglia (MG)


title: 65975_BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 65972_IR_5day_bone marrow-derived macrophages (BMDM)


title: 65971_IR-BLZ945_5day_microglia (MG)


title: 68343_IR_Recurrent_microglia (MG)


title: 65971_IR-BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 65967_Vehicle_microglia (MG)


title: 65966_Vehicle_bone marrow-derived macrophages (BMDM)


title: 65696_IR-BLZ945_5day_microglia (MG)


title: 65698_IR_5day_bone marrow-derived macrophages (BMDM)


title: 65696_IR-BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 124_BLZ945_5day_microglia (MG)


title: 41_Vehicle_microglia (MG)


title: 124_BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 123_BLZ945_5day_microglia (MG)


title: 122_BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: 122_BLZ945_5day_microglia (MG)


title: 65967_Vehicle_bone marrow-derived macrophages (BMDM)


title: 41_Vehicle_bone marrow-derived macrophages (BMDM)


title: 123_BLZ945_5day_bone marrow-derived macrophages (BMDM)


title: RAW 264.7 cells treated with Bacillus clausii for 6 hours  vs untreated cells 1

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

country: India

institute: National Institute of Science Education and Research Bhubaneswar

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BC_6h_Replicate1

hyb_protocol: 825 ng each of test and reference Cy dye  labeled RNA was mixed together and was fragmented using Agilent fragmentation kit in the presence of blocking reagent for 30 minutes in 60 degree celsius. Equal volume of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture to stop the reaction. 100 μl of the mixture was added to each of the chamber of the hybridization gasket and the array slide was sandwitched over it. The hybridization reaction was done for 17 hours in 65 degree celsius with moist condition in a hybridization oven.

scan_protocol: Scanned on an Agilent G2505C scanner using Agilent Scan control (version 8.3.1.1). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: RAW 264.7_Bacillus clausii for 6 hrs

label_protocol: 500 ng of total RNA were primed with 1.2 µl (3rd dilution) of  T7 promoter primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of MMLV Rtase. The c-DNA was then transcribed by T7 RNA Polymerase in the presence of NTPs and labeled with Cy3-CTP (For Rererence) and Cy5-CTP (For test).

growth_protocol: Cells were grown in DMEM medium (Himedia, India) supplemented with 10% heat inactivated fetal bovine serum (Himedia, India) (without any antibiotic) in 75 cm2 tissue culture flasks (BD Biosciences, USA) at 37 degree Celcius in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Qiagen RNEasy mini kit following manufacturer's instructions

tag: cell line

tag: strain source

value: BALB/c mice

tag: treated with

value: Bacillus clausii for 6 hrs

source_name: RAW 264.7_time-matched untreated control

value: none (untreated control)


title: THP-1 cells treated with Bacillus clausii for 6 hours  vs untreated cells 3

source_name: THP-1_Bacillus clausii for 6 hrs

growth_protocol: Cells were grown in RPMI-1640 medium (Himedia, India) supplemented with 10% heat inactivated fetal bovine serum (Himedia, India) (without any antibiotic) in 75 cm2 tissue culture flasks (BD Biosciences, USA) at 37 degree Celcius in a humidified atmosphere containing 5% CO2.

tag: cell line source

value: peripheral blood monocyte of an 1 year old human infant

source_name: THP-1_time-matched untreated control


title: RAW 264.7 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 3

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BF_6h_Replicate3

source_name: RAW 264.7_Bifidobacterium bifidum for 6 hrs

value: Bifidobacterium bifidum for 6 hrs


title: THP-1 cells treated with Lactobacillus acidophilus for 6 hours  vs untreated cells 2

source_name: THP-1_Lactobacillus acidophilus for 6 hrs

value: Lactobacillus acidophilus for 6 hrs


title: THP-1 cells treated with Bacillus clausii for 6 hours  vs untreated cells 1


title: RAW 264.7 cells treated with Bacillus clausii for 6 hours  vs untreated cells 2

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BC_6h_Replicate2


title: THP-1 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 3

source_name: THP-1_Bifidobacterium bifidum for 6 hrs


title: RAW 264.7 cells treated with Bacillus clausii for 6 hours  vs untreated cells 3

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BC_6h_Replicate3


title: THP-1 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 1


title: RAW 264.7 cells treated with Lactobacillus acidophilus for 6 hours  vs untreated cells 1

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_LA_6h_Replicate1

source_name: RAW 264.7_Lactobacillus acidophilus for 6 hrs


title: THP-1 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 2


title: THP-1 cells treated with Bacillus clausii for 6 hours  vs untreated cells 2


title: RAW 264.7 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 2

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BF_6h_Replicate2


title: RAW 264.7 cells treated with Bifidobacterium bifidum for 6 hours  vs untreated cells 1

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_BF_6h_Replicate1


title: THP-1 cells treated with a mixture of CNT, GNP, and Indolicidin (Spiked) for 6 hours  vs reference

description: Common reference for all groups

source_name: THP-1 cells, originated from peripheral blood monocyte of an 1 year old human infant, purchased from NCCS, India

source_name: pooled whole RNA from all the test groups and untreated group (Reference)


title: THP-1 cells treated with Indolicidin (20 μg/ml) for 6 hours  vs reference

description: Common reference for all groups

value: THP-1 cells, originated from peripheral blood monocyte of an 1 year old human infant, purchased from NCCS, India


title: THP-1 cells treated with a mixture of CNT and Indolicidin (Spiked) for 6 hours  vs reference

description: Common reference for all groups


title: THP-1 cells treated with free GNP (equivalent amount present in GNP-Indolicidin conjugate) for 6 hours vs reference

description: Common reference for all groups


title: RAW 264.7 cells treated with Lactobacillus acidophilus for 6 hours  vs untreated cells 2

description:
RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India
Raw264.7_LA_6h_Replicate2


title: THP-1 cells treated with free CNT (equivalent amount present in CNT-Indolicidin conjugate) for 6 hours vs reference

description: Common reference for all groups


title: THP-1 cells treated with a mixture of free CNT and GNP (equivalent amount present in conjugate) for 6 hours vs reference

description: Common reference for all groups


title: THP-1 cells treated with Indolicidin (0.02 μg/ml) for 6 hours  vs reference

description: Common reference for all groups


title: THP-1 cells treated with a mixture of GNP and Indolicidin (Spiked) for 6 hours  vs reference

description: Common reference for all groups


title: THP-1 cells treated with a mixture of CNT-Indolicidin and GNP-Indolicidin conjugate for 6 hours vs reference

description: Common reference for all groups


title: THP-1 cells treated with CNT-Indolicidin conjugate for 6 hours  vs reference

description: Common reference for all groups


title: THP-1 cells treated with GNP-Indolicidin conjugate for 6 hours  vs reference

description: Common reference for all groups


title: ECFC_3

city: Novosibirsk

first: Marsel

last: Kabilov

address: Lavrentyev av. 8

country: Russia

institute: ICBFM SB RAS

data_processing:
bcl2fastq v2.20.0.422 software used for basecalling
Removing of the first nine nucleotides from Read 1 and the first six nucleotides from Read 2 by cutadapt v.1.18.
Adapter and low-quality sequences were removed using TrimGalore v.0.5.0
RNA-seq analysis was performed against the Ensembl annotated human genome (GRCh38.93) with CLC GW 12.0 (Qiagen)
Analysis of differential expression of genes, principal component analysis, Venn diagrams, heatmap were conducted by CLC GW 12.0 (Qiagen)
Genome_build: Ensembl annotated human genome (GRCh38.93)
Supplementary_files_format_and_content: xlsx file with DEG and GO analysis

source_name: Cell culture

extract_protocol:
Cells were lysed with TRIzol (Invitrogen) with the following total RNA isolation (Purelink RNA Micro Scale Kit, Invitrogen) and DNAse treatment (Sigma).
For the 1 µg of isolated RNA, we performed rRNA depletion (RiboCop rRNA Depletion Kit V1.2, 037.96, Lexogen) followed by DNA library preparation (SENSE Total RNA-Seq Library Prep Kit, 042.96, Lexogen). DNA libraries were sequenced on HiSeq 2000 (Illumina) using 2 × 125 bp chemistry.

value: endothelial progenitor cell

value: endothelial colony-forming cells


title: HCAEC_1

value: endothelium

value: human coronary artery endothelial cells


title: HCAEC_2


title: ECFC_1


title: SAT-SVF_4

value: stromal vascular fraction

value: subcutaneous adipose tissue-derived stromal vascular fraction


title: SAT-SVF_3


title: SAT-SVF_1


title: HCAEC_3


title: ECFC_2


title: ECFC_4


title: RAW 264.7 cells treated with Lactobacillus bulgaricus for 4 hour  vs reference

description: Common reference for all groups

source_name: RAW 264.7 cells, origin BALB/c mice purchased from NCCS, India

value: BALB/c


title: Time matched Untreated THP-1 cells  vs reference

description: Common reference for all groups


title: RAW 264.7 cells treated with Lactobacillus bulgaricus for 6 hour  vs reference

description: Common reference for all groups


title: Untreated RAW 264.7 cells  vs reference

description: Common reference for all groups

value: untreated


title: HCAEC_4


title: RAW 264.7 cells treated with Lactobacillus bulgaricus for 1 hour  vs reference

description: Common reference for all groups


title: HUVEC_4

value: human umbilical vein endothelial cells


title: HUVEC_2


title: SAT-SVF_2


title: THP-1 cells treated with Lactobacillus acidophilus for 6 hours  vs untreated cells 1


title: FaDu-exosome

city: Taipei

first: Hsieh

last: Chia-Hsin

address: No.155, Sec.2, Linong Stree

country: Taiwan

institute: National Yang-Ming University

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 18 nucleotides, before aligning reads to the ____Human&Mouse___ genome from UCSC
Genome_build: GRCh38
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

source_name: FaDu cell secreted exosome

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
TruSeq Small RNA Library Preperation Kit

value: human pharynx squamous cell carcinoma


title: PP_CD4_3

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: Peyer's Patch CD4 T-cells

data_processing:
Reads were mapped to the mm10 transcriptome using Salmon (0.8.2) with default flags.
Transcript-level quantifications were transformed to gene-level quantifications in R using the tximport (1.10.1) package.
Genes that had less than 10 reads in total across all samples were filtered out.
DESeq2 (1.22.2) was used to perform differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CSV of log2 normalized counts for each gene (one file per sample)

source_name: Peyer's Patch CD4 T-cells

extract_protocol:
Peyer’s patch cells and spleen cells were prepared from 3 littermate Va14 female mice. Cell preparations were stained with CD1d-PBS57 tetramer and antibodies to CD4, CD45, and CD3. iNKT cells were sorted by FACS from both tissues and CD4+CD1dtet- cells were sorted from Peyer’s patches into collection tubes containing RNA isolation buffer (Qiagen RNA mini plus).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tag

value: CD4 T-cells


title: SP_NKT_3

description: Spleen iNKTs

source_name: Spleen iNKTs

value: Invariant natural killer T cells


title: PP_CD4_2

description: Peyer's Patch CD4 T-cells


title: PP_CD4_1

description: Peyer's Patch CD4 T-cells


title: HUVEC_1


title: e17-246

city: New York

first: Nicholas

last: Gomez

state: New York

address: 1230 York Ave

department: Laboratory of Mammalian Cell Biology and Development

institute: Rockefeller Univeristy

data_processing:
FASTQ files were pseudo-aligned to the mouse transcriptome (Gencode M18) using Salmon
Transcripts were collapsed into gene quantifications using tximport
Cells with < 3000 genes or genes detected in < 5 cells were discarded
We combined all single cell data sets (E12.5 , E12.5 LV, E17.5, ANNpos, ANNneg, E12.5 Myc +/-) to create a union set for identifying highly variable genes (HVG).  We utilized a statistical model (Brennecke et al 2013) incorporating ERCC spike-ins to identify biological variability from technical noise in our experiments.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered (Passing the parameters above) or Unfiltered Gene counts and TPM tables

extract_protocol:
Tissue was treated overnight at 4C in dispase. Epidermis was separated from dermis and dermis was discarded. Epidermis was then treated 20 min at 37C in 1:1 mix of trypsin/versene. Tissue was then homogenized and filtered to obtain a single cell suspension using 70um cell strainers. Single cell suspensions were stained with AnnexinV (Alexa Fluor 568 conjugated, Thermofisher, 1:200) and sorted into 96-well plates using a BD FACSAriaII. CD45 (biotinylated rat anti CD45, BD Biolegend, 1:200), CD117 (biotinylated rat anti CD117/c-kit, Biolegend, 1:200), CD31 (biotinylated rat anti-CD31/PECAM, Bioscience, 1:200), and CD140a (biotinylated rat anti-CD140a, Biolegend, 1:200) were used as lineage negative markers (to exclude immune cells, melanoblasts, endothelium, and fibroblasts, respectively). All lin- were detected with a strepdavidin-conjugated FITC or APCCy7 secondary (Biolegend, 1:500).
Single cell RNA-seq libraries were prepared using the Smart-seq2 protocol (see reference 40) with a few modifications as follows: plates were thawed on ice and incubated for 3 min at 72C to lyse cells. Reverse transcription (4U/ml Maxima H- transcriptase), template switching reaction and PCR pre-amplification (15 cycles) were performed according to the manufacturers’ protocol. PCR products were cleaned up using 0.8X AMPure XP beads (Beckman Coulter). The cDNA library quality was assessed by qPCR for primer pairs targeting the housekeeping gene, Gapdh. Samples showing high Ct value (>35 cycles) or having no PCR amplification were excluded from downstream analysis. 50-100pg of each cDNA library was used for generating Illumina sequencing libraries using a Nextera XT DNA library preparation kit (Illumina). After the final PCR amplification step, samples were pooled and cleaned by 0.9X AMPure XP beads. The pooled sequencing libraries were sequenced in the RU genomics facility on an Illumina Nextseq500 instrument using the High Output 75 PE kit.

tag: embryo stage

tag: sorted population

value: GFP+lin-


title: e17-247


title: PP_NKT_2

description: Peyer's Patch iNKTs

source_name: Peyer's Patch iNKTs


title: e17-248


title: SP_NKT_2

description: Spleen iNKTs


title: PP_NKT_1

description: Peyer's Patch iNKTs


title: e17-245


title: e17-240


title: e17-239


title: HUVEC_3


title: e17-241


title: SP_NKT_1

description: Spleen iNKTs


title: e17-243


title: e17-237


title: e17-238


title: e17-236


title: e17-234


title: e17-235


title: e17-244


title: e17-231


title: e17-232


title: e17-228


title: e17-227


title: e17-225


title: e17-226


title: e17-221


title: e17-215


title: e17-218


title: 65966_Vehicle_microglia (MG)

source_name: Tumor-associated macrophages

value: microglia (MG)

value: Vehicle


title: e17-216


title: e17-224


title: e17-223


title: e17-213


title: e17-214


title: e17-249


title: e17-217


title: PP_NKT_3

description: Peyer's Patch iNKTs


title: e17-222


title: e17-233


title: e17-212


title: e17-211


title: e17-229


title: e17-230


title: e17-209


title: e17-208


title: e17-207


title: e17-220


title: e17-219


title: e17-242


title: e17-204


title: e17-206


title: e17-203


title: e17-205


title: e17-202


title: e17-197


title: e17-196


title: e17-192


title: e17-194


title: e17-190


title: e17-189


title: e17-200


title: e17-201


title: e17-188


title: e17-195


title: e17-199


title: e17-193


title: e17-191


title: e17-210


title: e17-187


title: e17-186


title: e17-185


title: e17-184


title: e17-183


title: e17-182


title: e17-180


title: e17-181


title: e17-179


title: e17-177


title: e17-198


title: e17-174


title: e17-175


title: e17-173


title: e17-166


title: e17-171


title: e17-170


title: e17-167


title: e17-157


title: e17-163


title: e17-165


title: e17-162


title: e17-172


title: e17-169


title: e17-168


title: e17-159


title: e17-160


title: e17-155


title: e17-158


title: e17-161


title: e17-156


title: 65698_IR_5day_microglia (MG)


title: e17-164


title: e17-152


title: e17-153


title: e17-178


title: e17-151


title: e17-176


title: e17-149


title: e17-150


title: e17-148


title: e17-147


title: e17-143


title: e17-145


title: e17-144


title: e17-141


title: e17-154


title: e17-133


title: e17-138


title: e17-135


title: e17-131


title: e17-139


title: e17-142


title: e17-140


title: e17-136


title: e17-134


title: e17-125


title: e17-127


title: e17-126


title: e17-128


title: e17-132


title: e17-137


title: e17-129


title: e17-122


title: e17-124


title: e17-123


title: e17-121


title: e17-120


title: e17-146


title: e17-118


title: e17-119


title: e17-130


title: e17-116


title: e17-117


title: e17-115


title: e17-113


title: e17-114


title: e17-103


title: e17-110


title: e17-102


title: e17-107


title: e17-109


title: e17-111


title: e17-105


title: e17-104


title: e17-106


title: e17-112


title: e17-94


title: e17-95


title: e17-96


title: e17-98


title: e17-92


title: e17-101


title: e17-99


title: e17-91


title: e17-93


title: e17-97


title: e17-108


title: e17-100


title: e17-90


title: e17-89


title: e17-88


title: e17-87


title: e17-85


title: e17-83


title: e17-82


title: e17-80


title: e17-79


title: e17-78


title: e17-84


title: e17-81


title: e17-74


title: e17-72


title: e17-73


title: e17-76


title: e17-69


title: e17-66


title: e17-75


title: e17-71


title: e17-70


title: e17-65


title: e17-77


title: e17-64


title: e17-68


title: e17-63


title: e17-62


title: e17-60


title: e17-86


title: e17-58


title: e17-67


title: e17-51


title: e17-52


title: e17-53


title: e17-50


title: e17-54


title: e17-49


title: e17-61


title: e17-55


title: e17-46


title: e17-44


title: e17-43


title: e17-57


title: e17-45


title: e17-59


title: e17-39


title: e17-41


title: e17-48


title: e17-40


title: e17-36


title: e17-37


title: e17-38


title: e17-31


title: e17-35


title: e17-34


title: e17-56


title: e17-32


title: e17-33


title: e17-30


title: e17-28


title: e17-29


title: e17-26


title: e17-42


title: e17-25


title: e17-27


title: e17-24


title: e17-21


title: e17-23


title: e17-20


title: e17-22


title: e17-18


title: e17-11


title: e17-15


title: e17-12


title: e17-13


title: e17-10


title: e17-16


title: e17-14


title: e17-6


title: e17-7


title: e17-8


title: e17-5


title: e17-2


title: e17-4


title: e17-19


title: e17-1


title: e12LV-128

source_name: K14H2B::GFP; +/+; LV-CreH2BmRFP

value: GFP+RFP+lin-


title: e12LV-132


title: e12LV-127


title: e12LV-130


title: e17-17


title: e12LV-129


title: e17-9


title: e12LV-122


title: e12LV-123


title: e12LV-125


title: e12LV-126


title: e12LV-119


title: e12LV-120


title: e12LV-121


title: e12LV-131


title: e12LV-118


title: e12LV-117


title: e17-3


title: e12LV-116


title: e12LV-113


title: e12LV-115


title: e12LV-111


title: e12LV-112


title: e12LV-110


title: e12LV-124


title: e12LV-108


title: e12LV-107


title: e12LV-109


title: e12LV-99


title: e12LV-104


title: e12LV-102


title: e12LV-100


title: e12LV-98


title: e12LV-97


title: e12LV-101


title: e12LV-105


title: e12LV-94


title: e12LV-92


title: e12LV-114


title: e12LV-90


title: e12LV-95


title: e12LV-96


title: e12LV-89


title: e12LV-103


title: e12LV-88


title: e12LV-87


title: e12LV-86


title: e12LV-84


title: e12LV-85


title: e12LV-106


title: e12LV-83


title: e12LV-82


title: e12LV-81


title: e12LV-79


title: e12LV-93


title: e12LV-91


title: e12LV-78


title: e12LV-75


title: e12LV-73


title: e12LV-77


title: e12LV-74


title: e12LV-70


title: e12LV-76


title: e12LV-71


title: e12LV-72


title: e12LV-64


title: e12LV-69


title: e12LV-68


title: e12LV-66


title: e12LV-63


title: e12LV-67


title: e12LV-65


title: e12LV-62


title: e12LV-59


title: e12LV-58


title: e12LV-80


title: e12LV-56


title: e12LV-60


title: e12LV-57


title: e12LV-51


title: e12LV-53


title: e12LV-54


title: e12LV-52


title: e12LV-45


title: e12LV-48


title: e12LV-50


title: e12LV-55


title: e12LV-44


title: e12LV-41


title: e12LV-49


title: e12LV-40


title: e12LV-38


title: e12LV-61


title: e12LV-37


title: e12LV-36


title: e12LV-35


title: e12LV-39


title: e12LV-32


title: e12LV-34


title: e12LV-28


title: e12LV-29


title: e12LV-33


title: e12LV-31


title: e12LV-47


title: e12LV-46


title: e12LV-43


title: e12LV-25


title: e12LV-23


title: e12LV-24


title: e12LV-42


title: e12LV-20


title: e12LV-27


title: e12LV-22


title: e12LV-26


title: e12LV-17


title: e12LV-16


title: e12LV-15


title: e12LV-13


title: e12LV-18


title: e17-47


title: e12LV-21


title: e12LV-19


title: e12LV-30


title: e12LV-14


title: e12LV-4


title: e12LV-7


title: e12LV-5


title: e12LV-9


title: e12LV-8


title: e12LV-10


title: e12LV-6


title: e12LV-2


title: e12LV-3


title: e12MYC-137

source_name: K14H2B::GFP; Mycn fl/+; LV-CreH2BmRFP


title: e12LV-1


title: e12MYC-136


title: e12LV-12


title: e12MYC-134


title: e12MYC-135


title: e12MYC-132


title: e12MYC-130


title: e12MYC-133


title: e12MYC-131


title: e12MYC-129


title: e12LV-11


title: e12MYC-128


title: e12MYC-124


title: e12MYC-125


title: e12MYC-126


title: e12MYC-122


title: e12MYC-123


title: e12MYC-121


title: e12MYC-120


title: e12MYC-119


title: e12MYC-118


title: e12MYC-112


title: e12MYC-117


title: e12MYC-111


title: e12MYC-116


title: e12MYC-109


title: e12MYC-110


title: e12MYC-104


title: e12MYC-100


title: e12MYC-102


title: e12MYC-99


title: e12MYC-101


title: e12MYC-107


title: e12MYC-127


title: e12MYC-103


title: e12MYC-95


title: e12MYC-97


title: e12MYC-115


title: e12MYC-96


title: e12MYC-93


title: e12MYC-113


title: e12MYC-94


title: e12MYC-92


title: e12MYC-91


title: e12MYC-89


title: e12MYC-86


title: e12MYC-90


title: e12MYC-108


title: e12MYC-85


title: e12MYC-98


title: e12MYC-84


title: e12MYC-88


title: e12MYC-83


title: e12MYC-82


title: e12MYC-79


title: e12MYC-80


title: e12MYC-78


title: e12MYC-81


title: e12MYC-77


title: e12MYC-76


title: e12MYC-87


title: e12MYC-105


title: e12MYC-72


title: e12MYC-70


title: e12MYC-75


title: e12MYC-71


title: e12MYC-114


title: e12MYC-68


title: e12MYC-74


title: e12MYC-69


title: e12MYC-67


title: e12MYC-65


title: e12MYC-64


title: e12MYC-66


title: e12MYC-63


title: e12MYC-62


title: e12MYC-61


title: e12MYC-59


title: e12MYC-60


title: e12MYC-58


title: e12MYC-57


title: e12MYC-56


title: e12MYC-73


title: e12MYC-55


title: e12MYC-53


title: e12MYC-54


title: e12MYC-49


title: e12MYC-52


title: e12MYC-51


title: e12MYC-48


title: e12MYC-47


title: e12MYC-50


title: e12MYC-46


title: e12MYC-41


title: e12MYC-39


title: e12MYC-42


title: e12MYC-44


title: e12MYC-40


title: e12MYC-37


title: e12MYC-43


title: e12MYC-38


title: e12MYC-35


title: e12MYC-36


title: e12MYC-45


title: e12MYC-34


title: e12MYC-31


title: e12MYC-32


title: e12MYC-33


title: e12MYC-29


title: e12MYC-28


title: e12MYC-26


title: e12MYC-27


title: e12MYC-30


title: e12MYC-24


title: e12MYC-22


title: e12MYC-23


title: e12MYC-20


title: e12MYC-19


title: e12MYC-21


title: e12MYC-18


title: e12MYC-10


title: e12MYC-14


title: e12MYC-9


title: e12MYC-11


title: e12MYC-12


title: e12MYC-13


title: e12MYC-15


title: e12MYC-8


title: e12MYC-7


title: e12MYC-16


title: e12MYC-5


title: e12MYC-3


title: e12MYC-25


title: e12MYC-4


title: e12ANNpos-180

value: GFP+AnnexinV+lin-


title: e12MYC-1


title: e12ANNpos-179


title: e12ANNpos-178


title: e12ANNpos-177


title: e12ANNpos-176


title: e12MYC-17


title: e12ANNpos-174


title: e12ANNpos-173


title: e12ANNpos-175


title: e12ANNpos-171


title: e12MYC-6


title: e12ANNpos-170


title: e12ANNpos-168


title: e12ANNpos-166


title: e12ANNpos-165


title: e12ANNpos-167


title: e12ANNpos-163


title: e12ANNpos-164


title: e12ANNpos-162


title: e12ANNpos-161


title: e12MYC-2


title: e12ANNpos-156


title: e12ANNpos-157


title: e12ANNpos-158


title: e12ANNpos-159


title: e12ANNpos-152


title: e12ANNpos-150


title: e12ANNpos-151


title: e12ANNpos-172


title: e12ANNpos-155


title: e12ANNpos-149


title: e12ANNpos-148


title: e12ANNpos-153


title: e12ANNpos-147


title: e12ANNpos-160


title: e12ANNpos-145


title: e12ANNpos-143


title: e12ANNpos-144


title: e12ANNpos-141


title: e12ANNpos-139


title: e12ANNpos-140


title: e12ANNpos-136


title: e12ANNpos-135


title: e12ANNpos-138


title: e12ANNpos-134


title: e12ANNpos-133


title: e12ANNpos-154


title: e12ANNpos-131


title: e12ANNpos-130


title: e12ANNpos-132


title: e12ANNpos-129


title: e12ANNpos-127


title: e12ANNpos-169


title: e12ANNpos-126


title: e12ANNpos-125


title: e12ANNpos-146


title: e12ANNpos-124


title: e12ANNpos-142


title: e12ANNpos-119


title: e12ANNpos-123


title: e12ANNpos-137


title: e12ANNpos-120


title: e12ANNpos-122


title: e12ANNpos-121


title: e12ANNpos-117


title: e12ANNpos-113


title: e12ANNpos-112


title: e12ANNpos-111


title: e12ANNpos-110


title: e12ANNpos-114


title: e12ANNpos-116


title: e12ANNpos-107


title: e12ANNpos-105


title: e12ANNpos-106


title: e12ANNpos-118


title: e12ANNpos-128


title: e12ANNpos-104


title: e12ANNpos-109


title: e12ANNpos-108


title: e12ANNpos-102


title: e12ANNpos-99


title: e12ANNpos-101


title: e12ANNpos-97


title: e12ANNpos-103


title: e12ANNpos-96


title: e12ANNpos-94


title: e12ANNpos-98


title: e12ANNpos-92


title: e12ANNpos-93


title: e12ANNpos-95


title: e12ANNpos-91


title: e12ANNpos-90


title: e12ANNpos-115


title: e12ANNpos-87


title: e12ANNpos-88


title: e12ANNpos-86


title: e12ANNpos-85


title: e12ANNpos-84


title: e12ANNpos-81


title: e12ANNpos-78


title: e12ANNpos-79


title: e12ANNpos-80


title: e12ANNpos-77


title: e12ANNpos-82


title: e12ANNpos-83


title: e12ANNpos-100


title: e12ANNpos-75


title: e12ANNpos-74


title: e12ANNpos-73


title: e12ANNpos-76


title: e12ANNpos-72


title: e12ANNpos-71


title: e12ANNpos-70


title: e12ANNpos-68


title: e12ANNpos-69


title: e12ANNpos-89


title: e12ANNpos-67


title: e12ANNpos-66


title: e12ANNpos-63


title: e12ANNpos-65


title: e12ANNpos-62


title: e12ANNpos-59


title: e12ANNpos-58


title: e12ANNpos-61


title: e12ANNpos-56


title: e12ANNpos-55


title: e12ANNpos-51


title: e12ANNpos-53


title: e12ANNpos-52


title: e12ANNpos-54


title: e12ANNpos-49


title: e12ANNpos-48


title: e12ANNpos-45


title: e12ANNpos-47


title: e12ANNpos-46


title: e12ANNpos-44


title: e12ANNpos-42


title: e12ANNpos-38


title: e12ANNpos-40


title: e12ANNpos-60


title: e12ANNpos-37


title: e12ANNpos-36


title: e12ANNpos-57


title: e12ANNpos-34


title: e12ANNpos-39


title: e12ANNpos-32


title: e12ANNpos-50


title: e12ANNpos-64


title: e12ANNpos-33


title: e12ANNpos-30


title: e12ANNpos-41


title: e12ANNpos-28


title: e12ANNpos-27


title: e12ANNpos-25


title: e12ANNpos-29


title: e12ANNpos-26


title: e12ANNpos-24


title: e12ANNpos-35


title: e12ANNpos-43


title: e12ANNpos-21


title: e12ANNpos-22


title: e12ANNpos-20


title: e12ANNpos-19


title: e12MYC-106


title: e12ANNpos-15


title: e12ANNpos-16


title: e12ANNpos-14


title: e12ANNpos-31


title: e12ANNpos-9


title: e12ANNpos-11


title: e12ANNpos-13


title: e12ANNpos-12


title: e12ANNpos-23


title: e12ANNpos-1


title: e12ANNpos-7


title: e12ANNpos-8


title: e12ANNpos-4


title: e12ANNpos-5


title: e12ANNneg-152

value: GFP+AnnexinV-lin-


title: e12ANNpos-2


title: e12ANNneg-153


title: e12ANNpos-18


title: e12ANNneg-147


title: e12ANNneg-149


title: e12ANNneg-151


title: e12ANNneg-150


title: e12ANNpos-17


title: e12ANNpos-6


title: e12ANNneg-146


title: e12ANNpos-10


title: e12ANNneg-145


title: e12ANNneg-143


title: e12ANNneg-148


title: e12ANNneg-141


title: e12ANNneg-144


title: e12ANNpos-3


title: e12ANNneg-137


title: e12ANNneg-138


title: e12ANNneg-140


title: e12ANNneg-136


title: e12ANNneg-135


title: e12ANNneg-142


title: e12ANNneg-134


title: e12ANNneg-131


title: e12ANNneg-132


title: e12ANNneg-127


title: e12ANNneg-125


title: e12ANNneg-126


title: e12ANNneg-133


title: e12ANNneg-123


title: e12ANNneg-122


title: e12ANNneg-121


title: e12ANNneg-119


title: e12ANNneg-115


title: e12ANNneg-120


title: e12ANNneg-139


title: e12ANNneg-118


title: e12ANNneg-117


title: e12ANNneg-112


title: e12ANNneg-113


title: e12ANNneg-114


title: e12ANNneg-116


title: e12ANNneg-110


title: e12ANNneg-109


title: e12ANNneg-111


title: e12ANNneg-108


title: e12ANNneg-107


title: e12ANNneg-106


title: e12ANNneg-128


title: e12ANNneg-129


title: e12ANNneg-105


title: e12ANNneg-104


title: e12ANNneg-130


title: e12ANNneg-103


title: e12ANNneg-101


title: e12ANNneg-99


title: e12ANNneg-98


title: e12ANNneg-100


title: e12ANNneg-96


title: e12ANNneg-95


title: e12ANNneg-94


title: e12ANNneg-93


title: e12ANNneg-87


title: e12ANNneg-91


title: e12ANNneg-90


title: e12ANNneg-88


title: e12ANNneg-89


title: e12ANNneg-86


title: e12ANNneg-92


title: e12ANNneg-85


title: e12ANNneg-82


title: e12ANNneg-84


title: e12ANNneg-83


title: e12ANNneg-81


title: e12ANNneg-80


title: e12ANNneg-79


title: e12ANNneg-102


title: e12ANNneg-78


title: e12ANNneg-75


title: e12ANNneg-74


title: e12ANNneg-76


title: e12ANNneg-73


title: e12ANNneg-97


title: e12ANNneg-72


title: e12ANNneg-70


title: e12ANNneg-68


title: e12ANNneg-71


title: e12ANNneg-69


title: e12ANNneg-67


title: e12ANNneg-64


title: e12ANNneg-63


title: e12ANNneg-66


title: e12ANNneg-65


title: e12ANNneg-61


title: e12ANNneg-59


title: e12ANNneg-58


title: e12ANNneg-60


title: e12ANNneg-56


title: e12ANNneg-55


title: e12ANNneg-62


title: e12ANNneg-124


title: e12ANNneg-54


title: e12ANNneg-52


title: e12ANNneg-53


title: e12ANNneg-51


title: e12ANNneg-47


title: e12ANNneg-46


title: e12ANNneg-48


title: e12ANNneg-45


title: e12ANNneg-43


title: e12ANNneg-77


title: e12ANNneg-42


title: e12ANNneg-41


title: e12ANNneg-39


title: e12ANNneg-38


title: e12ANNneg-40


title: e12ANNneg-50


title: e12ANNneg-37


title: e12ANNneg-36


title: e12ANNneg-35


title: e12ANNneg-33


title: e12ANNneg-32


title: e12ANNneg-31


title: e12ANNneg-30


title: e12ANNneg-57


title: e12ANNneg-26


title: e12ANNneg-25


title: e12ANNneg-28


title: e12ANNneg-24


title: e12ANNneg-23


title: e12ANNneg-44


title: e12ANNneg-20


title: e12ANNneg-19


title: e12ANNneg-17


title: e12ANNneg-18


title: e12ANNneg-49


title: e12ANNneg-27


title: e12ANNneg-21


title: e12ANNneg-34


title: e12ANNneg-15


title: e12ANNneg-14


title: e12ANNneg-12


title: e12ANNneg-11


title: e12ANNneg-29


title: e12ANNneg-10


title: e12ANNneg-7


title: e12ANNneg-1


title: e12ANNneg-3


title: e12ANNneg-2


title: e12-123


title: e12ANNneg-5


title: e12-124


title: e12-122


title: e12ANNneg-6


title: e12ANNneg-4


title: e12-120


title: e12-119


title: e12ANNneg-16


title: e12-118


title: e12-117


title: e12-121


title: e12-113


title: e12-115


title: e12-110


title: e12-108


title: e12-109


title: e12ANNneg-9


title: e12ANNneg-13


title: e12ANNneg-8


title: e12-116


title: e12ANNneg-22


title: e12-112


title: e12-104


title: e12-105


title: e12-101


title: e12-103


title: e12-99


title: Col

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

data_processing:
ChIP-seq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files converted to bedgraph via bedtools, bedgraph files were converted to bigwig files via the UCSC "bedGraphToBigWig" executable script

organism: Arabidopsis thaliana

source_name: Aerial tissue

growth_protocol: Arabidopsis plants were grown in soil at 22 degree under long day (16 hrs light) or short day (8 hrs light) conditions .

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850. FLAG antibody is from Sigma company (A8592).
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330).

value: Columbia-0 background

tag: antibody

value: immnuoprecipitated chromatin using FLAG antibody (Sigma)


title: e12-100


title: SHL-FLAG


title: e12-98


title: e12-114


title: e12-106


title: e12-111


title: e12-97


title: e12-96


title: mamgland_rep2

first: Sundari

last: Chetty

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

description:
in vivo mammary epithelium
tagAlign.counts.for.naive.overlap.merged.peaks.txt
atac_mamgland_ppr.IDR0.1.filt.narrowPeak.gz
atac_mamgland_ppr.naive_overlap.filt.narrowPeak.gz
mamgland_1_ENCFF488ELU.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
mamgland_1_ENCFF488ELU.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig

data_processing:
FASTQ files for each sample were processed through the ENCODE DCC ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline/) version 1.3.0
A merged peak set was generated by concatenating the optimal naive overlap peaks for all samples, truncating the concatenated peak set to 200 bp around the summit, sorting and merging the resulting peaks. This yielded a merged peak set of 221,510 peaks.
Read counts for each replicate for each peak were obtained by running bedtools coverage on the the filtered tagAlign file generated by the ENCODE DCC pipeline over the set of 221,510 merged peaks.
Differential accessibility across each pair of samples was obtained via DESeq2 on the count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: fold change bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: pval bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: Tab-delimited text file including un-normalized read counts from each replicate for each peak in the merged naive overlap peak set.
Supplementary_files_format_and_content: Naive overlap optimal narrowPeak calls

source_name: MCF10A mammary epithelial cells

growth_protocol: MCF10A cells were grown in alginate-recombinant basement membrane hydrogels of 100 Pa or 2000 Pa elastic modulus, or on 2D polyacrylamide (100 Pa) or on tissue culture plastic. Standard MCF10A growth media was used.

extract_protocol:
Cells were extracted from matrices by incubating gels in ice cold 50 mM EDTA in PBS for 10 minutes with pipette mixing. The suspensions were centrifuged at 500 g at 4oC for 10 mins to pellet cells. The pellets were incubated in 1 ml of 0.25% trypsin/2.21 mM EDTA at 37oC for 5 minutes to digest any remaining rBM, then centrifuged at 500 g for 10 mins again.
Libraries were prepared using Illumina Nextera Tn5 Transposase (FC-121-1030)

treatment_protocol: Some groups were treated with 1 uM suberoylanilide hydroxamic acid

tag: stiffness

tag: tissue culture substrate


title: e12-95


title: 2D_TCPS_rep2

description:
MCF10A cells cultured on tissue culture polystyrene
tagAlign.counts.for.naive.overlap.merged.peaks.txt
2D_TCPS_ppr.IDR0.1.filt.narrowPeak.gz
2D_TCPS_ppr.naive_overlap.filt.narrowPeak.gz
2D_TCPS_1_CAGAGAGG_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
2D_TCPS_1_CAGAGAGG_R1.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig

tag: treatment

value: 2D Tissue culture polystyrene


title: 2D_TCPS_rep3


title: mamgland_rep1


title: 2D_TCPS_rep1


title: 2000Pa_SAHA_rep3

description:
MCF10A cells cultured in soft 3D matrices, treated with SAHA
tagAlign.counts.for.naive.overlap.merged.peaks.txt
saha_2000Pa_ppr.IDR0.1.filt.narrowPeak.gz
saha_2000Pa_ppr.naive_overlap.filt.narrowPeak.gz
2000Pa_saha_1_TCCTGAGC_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
2000Pa_saha_1_TCCTGAGC_R1.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig

value: SAHA

value: 3D matrix


title: 2000Pa_SAHA_rep2


title: e12-92


title: e12-93


title: e12-102


title: e12-94


title: 2000Pa_SAHA_rep1


title: e12-91


title: e12-107


title: 2000Pa_rep3

description:
MCF10A cells cultured in soft 3D matrices
tagAlign.counts.for.naive.overlap.merged.peaks.txt
2000Pa_3D_ppr.IDR0.1.filt.narrowPeak.gz
2000Pa_3D_ppr.naive_overlap.filt.narrowPeak.gz
2000Pa_1_TCCTGAGC_1_pf.nodup.tn5_pooled.pf.fc.signal.bigwig
2000Pa_1_TCCTGAGC_1_pf.nodup.tn5_pooled.pf.pval.signal.bigwig


title: e12-89


title: 2000Pa_rep2


title: e12-90


title: e12-87


title: 100Pa_SAHA_rep2

description:
MCF10A cells cultured in soft 3D matrices, treated with SAHA
tagAlign.counts.for.naive.overlap.merged.peaks.txt
saha_100Pa_ppr.IDR0.1.filt.narrowPeak.gz
saha_100Pa_ppr.naive_overlap.filt.narrowPeak.gz
100Pa_saha_1_TAAGGCGA_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
100Pa_saha_1_TAAGGCGA_R1.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig


title: 100Pa_SAHA_rep1


title: e12-86


title: e12-85


title: 100Pa_rep3

description:
MCF10A cells cultured in soft 3D matrices
tagAlign.counts.for.naive.overlap.merged.peaks.txt
100Pa_3D_ppr.IDR0.1.filt.narrowPeak.gz
100Pa_3D_ppr.naive_overlap.filt.narrowPeak.gz
100Pa_1_TAAGGCGA_1_pf.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
100Pa_1_TAAGGCGA_1_pf.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig


title: 2000Pa_rep1

description:
MCF10A cells cultured in stiff 3D matrices
tagAlign.counts.for.naive.overlap.merged.peaks.txt
2000Pa_3D_ppr.IDR0.1.filt.narrowPeak.gz
2000Pa_3D_ppr.naive_overlap.filt.narrowPeak.gz
2000Pa_1_TCCTGAGC_1_pf.nodup.tn5_pooled.pf.fc.signal.bigwig
2000Pa_1_TCCTGAGC_1_pf.nodup.tn5_pooled.pf.pval.signal.bigwig


title: e12-88


title: e12-83


title: 100Pa_rep2


title: e12-79


title: e12-82


title: 100Pa_rep1


title: e12-81


title: e12-80


title: e12-78


title: e12-76


title: e12-73


title: e12-75


title: e12-77


title: 100Pa_SAHA_rep3


title: e12-74


title: e12-72


title: control5

city: Tartu

first: Epp

last: Kaleviste

state: no

address: Ravila 19

department: Institute of biomedicine and translational medicine

country: Estonia

institute: University of Tartu

data_processing:
Large scale data processing steps were carried out in the High Performance Computing Center of the University of Tartu. The quality control of the raw data was done with FastQC version 0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw reads were trimmed with Trim Galore! version 0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the Phred score > 30 to filter out low-quality bases.
The human reference genome GRCh37/hg19 was downloaded from the UCSC Genome Browser data repository (Karolchik et al., n.d.).
The trimmed single-end reads were aligned to the reference genome with bowtie2 version 2.0.2 (Langmead & Salzberg, 2012).
The SAMtools software suite (https://www.htslib.org/) was used to retain only alignments with mapping quality ≥ 30, and the read duplicates were removed with MarkDuplicates from the Picard tools (http://broadinstitute.github.io/picard).
Peaks were called with MACS2 version 2.1.0 (https://github.com/taoliu/MACS/).
The mappable genome size (-g 2627947484) for 50 bp reads was taken from (Derrien et al., 2012). Only the peaks with q-value <0.01 were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files were generated using MACS2 version 2.1.0; narrowpeak is ENCODE-specific formats, it is a BED6+4 format; Scores (the 5th column) represent int(-10*log10qvalue).

source_name: PBMC

growth_protocol: PBMCs were isolated by density gradient centrifugation and fixated immediately.

extract_protocol:
Cells were sonicated using a Bioruptor UCD-200 sonicator (Diagenode). Sheared chromatin was immunoprecipitated with 2 μl of anti-H3K4me3 antibody (#07-473, Millipore) and 2 μl of Dynabeads M-280 magnetic beads (Sheep Anti-Mouse IgG, Sheep Anti-Rabbit IgG, Life Technologies) using the SX-8G IP-Star Automated System (Diagenode). ChIP samples were decrosslinked 65oC for 4 hr. After incubation the samples were treated with 0.2 mg/ml RNaseA (RNase Cocktail Enzyme Mix, Ambion, Life Technologies) and of 0.4 mg/ml ProteinaseK (Thermo Scientific). DNA was purified with DNA Clean kit & Concentrator TM-5 (Zymo Research) according to the manufacturer's protocol.
Libraries were prepared using the supplied Ovation® Ultralow Systems Kit (NuGeneration Limited, England and Wales) according to the manufacturer's protocol. The barcoded libraries were quantified by Qubit 2.0 Fluorometer and validated with Agilent 2200 TapeStation analysis (Agilent Technologies, Inc.). Samples were sequenced with HiSeq 2500 (Illumina, San Diego, USA) producing 50 bp single-end sequences. Sequencing raw data was demultiplexed with CASAVA 1.8.2 software (Illumina, San Diego, USA).

tag: individual

value: control

tag: genotype

value: PBMC

tag: chip antibody

value: H3K4me3 (Millipore, catalog# 07-473, lot# 2930138)


title: control4

tag: cell type


title: control6


title: e12-70


title: control3


title: e12-68


title: e12-67


title: e12-84


title: control1


title: e12-69


title: e12-66


title: patient3

value: patient

value: STAT1 gain-of-function mutation


title: patient4


title: e12-65


title: patient5


title: e12-63


title: e12-64


title: e12-62


title: patient1


title: EM1_lic_scRNA-Seq

city: Erlangen

first: Arif

middle: B

last: Ekici

address: Schwabachanlage 10

country: Germany

institute: Institute of Human Genetics

description: single-cell RNA-seq of licensed mesenchymal stem cells

data_processing:
Demultiplexing of raw reads was performed using the cellranger mkfastq wrapper (10X Genomics) for bcl2fastq 2.17 (Illumina, San Diego, CA).
Read alignment and counting was performed using cellranger count (version 2.0.0).
Both samples were aggregated using cellranger aggr.
Genome_build: hg19
Supplementary_files_format_and_content: Hdf5 object containing the count matrix as well as barcode information and gene identifiers.

source_name: Bone marrow-derived MSCs

growth_protocol: MSCs were isolated from iliac crest aspirates of healthy donors and expanded in StemMACS MSC Medium XF (Milentyi Biotech)

extract_protocol:
RNA extraction, cDNA synthesis, and barcoding were performed using the 10X Chromium Controller (10X Genomics,  Pleasanton, CA) using the 3' v2 chemistry.
Sequencing libraries for Illumina sequencers were prepared according to manufacturer instructions for the Chromium v2 chemistry.
single-cell RNA-Seq (10X system)

value: mesenchymal stem cells (MSCs)

value: 10 ng/ml IFN-γ and 15 ng/ml TNF-α

tag: passage


title: e12-61

value: GFP+lin-


title: e12-71


title: EM1_un_scRNA-Seq

description: single-cell RNA-seq of unlicensed mesenchymal stem cells


title: e12-60


title: e12-59


title: e12-58


title: control2


title: e12-56


title: Retina_Flight_9

city: Loma Linda

first: Xiao

middle: Wen

last: Mao

address: 11175 Campus St

department: Basic Sciences

institute: Loma Linda University

data_processing:
Fastq files generated from the sequence run were demultiplexed (Loma Linda University Center for Genomics), quality checked (quality score > 38),    trimmed from adapters with Trimmomatic and mapped against mouse reference genome (NCBI_build_37.2) with TOPHAT2 (Biogenlink.digicon.com; Digicon’s BioGenLink™).
Expressed transcripts were counted with Multi HTSeq. For counting transcripts with HTSeq gene.gtf  annotation file from Mus_Musculus_NCBI_build_37.2.tar.gz was used to assign reads in a bam file to a gene annotation ( steps performed on Biogenlink.digicon.com; Digicon's BioGenLink).
Differential Expression analysis was carried out using raw counts from input to the R package DEseq2 Version 1.22.2 using R version 3.5.1. A gene was considered differentially expressed (DE) if was below a false discovery rate (FDR) adjusted p-value of 0.1
RefSeq accession numbers
Genome_build: NCBI_build_37.2
Supplementary_files_format_and_content: Text document files include mapped transcript counts for each sample
HTSeq_RR9_Ground Ctrl_vs_Flight_AllCounts.txt : raw total counts of sequencing reads for gene transcripts (HTSeq)
HTSeq_RR9_Ground Ctrl_vs_Flight_SigCounts.txt: raw significant counts of sequencing reads for gene transcripts (HTSeq)
DESeq_RR9_Ground Ctrl_vs_Flight_All.txt: normalized abundance measurement; total (DESeq output)
DESeq2_RR9_Ground Ctrl_vs_Flight_DEGs.txt: normalized abundance measurement; total (DESeq output)

source_name: Retina

extract_protocol:
The right eyes from 2 experimental groups: Ground Control and Flight were dissected to obtain the retina, and the retinas were fresh-frozen.Total RNA and DNA were extracted using the QIAGEN AllPrep DNA/RNA/miRNA Universal Kit
The Ovation® Mouse RNA-Seq System 1-16 (NuGEN Technologies) was used per manufacturer’s instructions to construct stranded RNA-seq libraries. 100 ng of total RNA was used as input.

value: space flight

tag: strain

tag: tissue

value: retina

tag: age

value: 10-week old

value: wild type


title: Retina_Flight_18


title: Retina_Flight_11


title: Retina_Flight_17


title: Retina_Flight_16


title: Retina_Flight_20


title: Retina_Flight_15


title: e12-55


title: e12-54


title: e12-53


title: e12-52


title: Retina_Ground Control_19

value: ground control


title: Retina_Ground Control_18


title: Retina_Ground Control_20


title: Retina_Ground Control_17


title: e12-50


title: Retina_Ground Control_16


title: e12-49


title: e12-47


title: Retina_Ground Control_11


title: e12-48


title: e12-57


title: Retina_Ground Control_9


title: Retina_Ground Control_15


title: e12-46


title: e12-45


title: e12-44


title: F4/80+Epor-eGFP-_2

city: zhengzhou

first: huizhi

last: zhao

address: No.100 Science Avenue

country: China

institute: zhengzhou university

data_processing:
BCL to FASTQ file converter bcl2fastq v2.19.1.403
RNA-seq reads were filtered using trimmomatic-0.35
RNA-seq reads were aligned to the mm10 genome assembly using Tophat V2.1.0
Gene quantification and differiation analysis were estimated by Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: txt files were generated using Cuffquant, FPKM represent normalized gene abundance

source_name: macrophage cells

extract_protocol:
RNA was extracted from FACS-sorted F4/80+Epor-eGFP+ and F4/80+Epor-eGFP- macrophages
Libraries were prepared according to Illumina's instructions according to TruSeq® RNA Sample Prep Kit v2 48

value: bone marrow derived macrophage cells

value: erythroblastic island macrophages

tag: cell population


title: F4/80+Epor-eGFP-_1


title: F4/80+Epor-eGFP+_3


title: F4/80+Epor-eGFP-_3


title: e12-42


title: e12-43


title: High Fat Diet TSP1 Knockout Mice 5

city: Cambridge

first: Ju

last: Wang

address: 610 Main Street

department: Inflammation & Immunology

institute: Pfizer Inc

data_processing:
20 M 2x150 paired end reads were generated from an Illumina HiSeq 4000 Platform
Following raw reads were filtered: reads containing adaptors, reads containinng N>10% (N represents the base connot be determined); reads containing low quality (Qscore<=5) bases which is over 50% of the total reads.
QuickRNASeq pipeline was used in reads mapping and counting: STAR 2.5.2.a was used for mapping; featureCounts subread-1.5.1 was used for counting; RSeQC was used for read QC; VarScan.v2.4.0 was used for SNP calling.
Genome_build: Genome fasta file is GRCh38.primary.genome.fa. Gene annotation file is GRCh38.gencode v25 annotation file. Gtf file is GRCh38.gencode.v25.gtf;  Bed file is GRCh38.gencode.v25.bed
Supplementary_files_format_and_content: Processed data is a tab delimited text file contains gene name as row, and the fpkm for that gene from each sample is the column.

source_name: High Fat Diet TSP1 Knockout mice

extract_protocol:
RNA extraction was performed with Trizol (Thermo Fisher Scientific # 15596026)  after tissue homogenization with Omni TH Tissue Homogenizer.
1 ug of RNA was used for cDNA library construction at Novogene using an NEBNext Ultra Directional RNA library Prep Kit for Illumina (cat# E7420S, New England Biolads, Ipswich, MA, USA) according to the manufacture's protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by two rounds of purification, and fragmented randowmly by adding fragmentation bufffer. The first strand cDNA was synthesized using random hezamers primer, after which as custom second-strand synthesis biffer (Illumina), dNTPs, RNase H and DNA polymnerase I were added to generate the second-strand (ds cDNA). After a series of terminal repair, poly-adenylation, and sequencing adaptor ligation, the double-stranded cDNA library was completed following size selection and PCR enrichment. The resulting 250-350 bo insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Walthan, MA, USA) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Techmologies, Santa Clara, CA, USA). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina, San Diego, CA, USA) using a paired-end 150 run (2x150 bases). 20M raw reads were generated from each library.

tag: strain background

tag: genotype/variation

value: TSP-1 Knockout

tag: diet

value: CDAHFD

value: liver


title: F4/80+Epor-eGFP+_1


title: e12-41

tag: embryo stage

tag: sorted population


title: e12-40


title: e12-51


title: e12-39


title: e12-36


title: High Fat Diet TSP1 Knockout Mice 2


title: e12-34


title: e12-33


title: e12-35


title: High Fat Diet TSP1 Knockout Mice 1


title: e12-32


title: Normal Diet TSP1 Knockout Mice 4

source_name: Normal Diet TSP1 Knockout mice

value: Normal Diet


title: F4/80+Epor-eGFP+_2


title: Normal Diet TSP1 Knockout Mice 3


title: e12-38


title: e12-31


title: Normal Diet TSP1 Knockout Mice 2


title: e12-30


title: Normal Diet TSP1 Knockout Mice 1


title: High Fat Diet Wild type Mice 5

source_name: High Fat Diet Wild type mice

value: Wild Type


title: High Fat Diet Wild type Mice 4


title: e12-26


title: High Fat Diet TSP1 Knockout Mice 4


title: High Fat Diet Wild type Mice 1


title: e12-29


title: e12-25


title: e12-27


title: e12-28


title: Retina_Flight_19


title: e12-37


title: High Fat Diet Wild type Mice 2


title: High Fat Diet TSP1 Knockout Mice 3


title: High Fat Diet Wild type Mice 3


title: Normal Diet TSP1 Knockout Mice 5


title: e12-24


title: Normal Diet Wild type Mice 4

source_name: Normal Diet Wild type mice


title: Normal Diet Wild type Mice 5


title: e12-23


title: e12-22


title: e12-21


title: Normal Diet Wild type Mice 2


title: Normal Diet Wild type Mice 3


title: e12-20


title: Normal Diet Wild type Mice 1


title: e12-19


title: infD6-IFNARfl/fl-CD4cre/+, 3

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
Transcriptome analysis is performed using the Tuxedo suite. Reads are mapped on the mouse reference genome (Mus musculus, Ensembl e87, December 2016) using TopHat2 (v2.0.10).
Cufflinks (v2.2.1) is further used to assemble transcripts from spliced read alignments, using the Ensembl e87 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression is assessed with Cuffdiff (v2.2.1). Transcriptome sets of all replicates for each sample group will be combined with Cuffmerge.
Genome_build: Ensembl version e87 (December 2016) of the Mus musculus genome.
Supplementary_files_format_and_content: tab-delimited text file of normalised cufflinks FPKM

source_name: Inguinal fat pad

extract_protocol:
Fad pads were snap frozen upon collected and then smashed into powder (on dry ice) using BioMasher. After that 1ml Qiazol was added, samples were centrifuged to remove excess oil layer, and standard Qiazol RNA isolated procedure was carried on.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
Libraries will be pooled, diluted and sequenced on Illumina HiSeq 4000 using 50 bp single-read chemistry.

treatment_protocol: Mice were infected with 2x10^6 focal-forming units of  lymphocytic choriomeningitis virus (LCMV) clone 13 intravenously.

value: Inguinal fat pad

tag: agent

value: LCMV clone13 2x10^6PFU


title: infD6-IFNARfl/fl-CD4cre/+, 1


title: infD6-IFNARfl/fl-CD4cre/+, 2


title: Ctrl-IFNARfl/fl-CD4cre/+, 3

value: control


title: e12-16


title: Ctrl-IFNARfl/fl-CD4cre/+, 1


title: e12-15


title: Ctrl-IFNARfl/fl-CD4cre/+, 2


title: infD6-IFNARfl/fl, 2

value: IFNARfl/fl


title: infD6-IFNARfl/fl, 1


title: infD6-IFNARfl/fl, 3


title: e12-14

value: GFP+lin-


title: e12-11


title: e12-13


title: ctrl-IFNARfl/fl, 3


title: ctrl-IFNARfl/fl, 2


title: e12-8


title: e12-7


title: e12-6


title: e12-10


title: CycD_E2F_44h_rna_rep2

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

institute: University of Utah

data_processing:
FAIRE-Seq sequencing reads were aligned to  reference genome using Bowtie2. Merged bam files were generated for each genotype by combining replicates. The  Z-scores were calculated using the mean and standard deviation per chromosome arm
RNA-Seq sequencing reads were aligned to thereference genome using STAR and further counted using HTSeq
Genome_build: dm6
Supplementary_files_format_and_content: bigwig, count

organism: Drosophila melanogaster

source_name: wing

growth_protocol: female fly wings from wildtype or transgenic flies expressing flippase control, E2F1+DP (E2F) and CycD+Cdk4+E2F1+DP (CycD_E2F) were dissected at corresponding timepoints

extract_protocol:
For FAIRE- samples, fly wings were dissected in PBS and brifely fixed before sonication and pheno-chloroform extraction; For RNA collections, fly wings were dissected and harvested in Trizol
FAIRE-Seq libraries were constructed using the Rubicon Thruplex DNA-seq kit; RNA-Seq libraries  were generated using the stranded mRNA sequencing kit from KAPA Biosystems

tag: Sex

value: female

tag: developmental stage

value: 44h APF


title: CycD_E2F_44h_rna_rep1


title: e12-18


title: e12-5


title: E2F_44h_rna_rep2


title: e12-17


title: e12-4


title: E2F_44h_rna_rep1


title: e12-3


title: e12-2


title: Ctr_44h_rna_rep1

value: flp control


title: CycD_E2F_24h_rna_rep2

value: 24h APF


title: e12-12


title: CycD_E2F_24h_rna_rep1


title: e12-1


title: ctrl-IFNARfl/fl, 1


title: E2F_24h_rna_rep1


title: 2C_WT_rep1

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: 23 pooled 2-cell wild-type embryos from the same litter

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina bcl2fastq v.2.19.1 and overall sequence quality was assessed with FastQC v.0.11.5
The reads were aligned to the mouse reference genome NCBIM37 with annotation from Gencode release M1 using STAR v.2.5.2b with default parameters except '--outFilterMismatchNoverLmax 0.04'
Mapped read summarisation on the gene level was performed using Subread featureCounts v.1.5.1 with default parameters
Differential expression analysis was performed using the Bioconductor package DESeq2 v.1.18.1 with Independent Hypothesis Weighting (IHW) multiple testing procedure and 10% FDR cutoff
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from featureCounts

source_name: 2-cell wild-type embryos, replicate 1

extract_protocol:
Each pool of 2-cell embryos was collected in M2 medium (Sigma) supplemented with 0.3 mg/ml hyaluronidase (Sigma), washed twice with PBS and directly transferred into lysis buffer. cDNA was prepared with the Smart Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) according to the manufacturer's recommendations using 11 PCR cycles.
NGS library preparation was performed using Ovation Ultralow System V2 1-96 (NuGEN) with a starting amount of 2,36 ng fragmented cDNA which was amplified in 11 PCR cycles. Libraries were profiled in a High Sensitivity DNA mode on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer (Life Technologies). All 8 samples were pooled in equimolar ratio and sequenced on one NextSeq 500 high-output flow cell, SR for 85 cycles plus 7 cycles for the index read.

value: wild-type


title: e12-9


title: 2C_WT_rep3

description: 25 pooled 2-cell wild-type embryos from the same litter

source_name: 2-cell wild-type embryos, replicate 3


title: 2C_WT_rep2

description: 30 pooled 2-cell wild-type embryos from the same litter

source_name: 2-cell wild-type embryos, replicate 2


title: 2C_DKO_rep4

description: 35 pooled 2-cell DKO embryos from the same litter

source_name: 2-cell DKO embryos, replicate 4

value: Gadd45a/Gadd45b double knockout (DKO)


title: E2F_24h_rna_rep2


title: Ctr_24h_rna_rep2


title: 2C_DKO_rep3

description: 28 pooled 2-cell DKO embryos from the same litter

source_name: 2-cell DKO embryos, replicate 3


title: 2C_DKO_rep2

description: 27 pooled 2-cell DKO embryos from the same litter

source_name: 2-cell DKO embryos, replicate 2


title: 44h_wt_rna_rep2

value: wildtype


title: 2C_DKO_rep1

description: 23 pooled 2-cell DKO embryos from the same litter

source_name: 2-cell DKO embryos, replicate 1


title: Ctr_24h_rna_rep1


title: Mutant_4_S10

city: Pittsburgh

first: Andrew

middle: Scott

last: Clugston

address: 872 Mirror Street

department: Integrative Systems Biology

institute: University of Pittsburgh

data_processing:
Adapter trimming was performed with BBDuk from the BBMap software package version 37.41 with parameter ktrim=l.
Reads were aligned to the mm10 genome using STAR version 2.5.3a.
Reads which aligned to known transcripts were counted using the Bioconductor package GenomicAlignments (version 1.10.1).
Differential expression between VHLNP+/- and VHLNP-/- samples was calculated using the DESeq2 R package (version 1.18.1).
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing known transcript counts.

source_name: mutant_nephron progenitor cells

extract_protocol:
Cells were isolated from kidneys dissected from embryonic day 17.5 embryos. Kidneys were digested with 0.3% collagenase and put into single-cell suspension by forcing through needlepoint. Cells were sorted by GFP fluorescence on a FACsaria II Cell Sorter.
Libraries were barcoded and prepared using the TruSeq Stranded mRNA library preperation kit according to the manufacturer's protocol.

value: VHLNP-/-

tag: embryonic day

value: kidney

value: Sorted nephron progenitor cell suspension


title: Mutant_3_S9


title: Ctr_44h_rna_rep2


title: 44h_wt_rna_rep1


title: 36h_wt_rna_rep1

value: 36h APF


title: 24h_wt_rna_rep2


title: 36h_wt_rna_rep2


title: Mutant_2_S8


title: 24h_wt_rna_rep1


title: 2C_WT_rep4

source_name: 2-cell wild-type embryos, replicate 4

tag: genotype


title: Mutant_1_S7


title: 18h_wt_rna_rep2

value: 18h APF


title: 18h_wt_rna_rep1


title: Control_4_S6

source_name: control_nephron progenitor cells

value: VHLNP+/-


title: Control_3_S5


title: low prolific Erhualian sows 2

city: Nanjing

first: Xiang

last: Ma

state: Jiangsu

address: Weigang No.1

institute: Nanjing Agriculture University

description:
normalizeExp.csv
EL2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa 11.1 whole genome using subjunct of Subread v1.6.
FeatureCounts of Subread package was adopted for counting reads to genomic features such as genes, exons, promoters, and genomic bins.The differential expression analysis between EH and EL was performed by using edgeR package.
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: A csv file include the normalized expression values of all genes for each Sample

organism: Sus scrofa

source_name: Uterus

extract_protocol:
Endometrium were collected, immediately frozen in liquid nitrogen and then stored at −80 °C until RNA was isolated. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: low prolific

value: Endometrium

value: Erhualian

tag: parity

tag: Stage

value: day 12 of gestation


title: low prolific Erhualian sows 3

description:
normalizeExp.csv
EL3

tag: strain


title: 6h_wt_rna_rep2

value: female

value: 6h APF


title: high prolific Erhualian sows 3

description:
normalizeExp.csv
EH3

value: high prolific

tag: tissue


title: low prolific Erhualian sows 1

description:
normalizeExp.csv
EL1


title: Control_2_S4

tag: cell type


title: Control_1_S3


title: high prolific Erhualian sows 2

description:
normalizeExp.csv
EH2


title: high prolific Erhualian sows 1

description:
normalizeExp.csv
EH1


title: mESC_TKO_clone228

description: Gadd45 TKO mESC, replicate 2

data_processing:
Low-quality bases and adapter-containing reads were trimmed using Trim Galore v.0.4.4 with default parameters
Reads were aligned to the reference mouse genome (NCBI38/mm10) using Bismark v.0.18.0 with parameters, ‘-n 1 -I 0 -X 1000 --score_min L,0,-0.6’
Methylation calling was performed using the Bismark script "bismark_methylation_extractor" with parameters ‘-p --ignore 5 --ignore_r2 5 --ample_memory –bedGraph --counts’
Differentially methylated regions (DMRs) were identified using methylKit v.1.3.3
Genome_build: NCBIM38 (mm10)
Supplementary_files_format_and_content: tab-delimited text file with methylation calls for all CpG sites from Bismark (chromosome, position, strand, count_methylated, count_unmethylated, C_context, trinucleotide_context)

source_name: Gadd45 TKO mESC

growth_protocol: ESCs were cultured on gelatinized cell culture vessels in LIF-conditioned DMEM supplemented with 15% ESC-grade FBS, 2 mM L-Glutamine, 50 U/ml Penicillin/Streptomycin, 1x NEAA, 1 mM sodium pyruvate and 100 µM β-mercaptoethanol at 37°C, 5% CO2 and 21% O2, with daily medium changes. Cells were passaged every 2 days once reaching approximately 60% confluency.

extract_protocol:
Genomic DNA from two Gadd45 TKO and two Control mESC clones was extracted and purified using a QIAamp DNA Mini kit (Qiagen) according to the manufacturer´s recommendations. An additional RNaseA treatment (10mg/ml, Qiagen) was done after cell lysis.
WGBS library preparation was carried out using the TruSeq PCR-Free Library Prep Kit (LT)  and the Epitect Kit (Qiagen) for bisulfite conversion.

value: Gadd45 triple knockout (TKO)

value: mouse embryonic stem cells (mESC)


title: l3_wt_rna_rep2


title: mESC_TKO_clone227

description: Gadd45 TKO mESC, replicate 1


title: l3_wt_rna_rep1


title: mESC_Control_clone283

description: Control mESC, replicate 2

source_name: Control mESC

value: wild-type


title: mESC_Control_clone5

description: Control mESC, replicate 1


title: CycD_E2F_FAIRE_44h_rep3

value: 44h APF


title: CycD_E2F_FAIRE_44h_rep2


title: CycD_E2F_FAIRE_44h_rep1


title: MGG4-shMyc_JF3

city: Minneapolis

first: Jianfang

last: Ning

state: Minnesota

address: 530 Masonic Cancer Research Building, 425 East River Parkway

department: Neurosurgery

institute: University of Minnesota

data_processing:
NextSeq control software 2.1.0.31 and RTA 2.4.11
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to the hg19 human genome using STAR (ref: PMID: 23104886).
The number of reads per kilobase of transript per million total reads (RPKM) were calculated as described in the ref, PMID: 24509080.
RPKM = gene_specific_reads * 1,000,000 * 1,000 / (total_sample_reads * gene_length (in bp))
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file includes RPKM values for each Sample.

source_name: GBM MGG4 cells expressing shRNA targeting Myc

growth_protocol: Cells were grown in EF20 medium with doxycycline (Dox, 1 mg/ml) for 6 days before treatment

extract_protocol:
RNA was extracted with Trizol  according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with olaparib (Ola, 10 microM) or DMSO for 24h

tag: cell line

value: GBM MGG4 cells

value: Myc knockdown

tag: treatment

value: DMSO + doxycycline


title: E2F_FAIRE_44h_rep3

tag: genotype/variation


title: MGG4-shMyc_JF4

value: PARPi + doxycycline


title: MGG4-shControl_JF2

source_name: GBM MGG4 cells expressing scramble shRNA

value: control


title: MGG4-shControl_JF1


title: Ctr_FAIRE_44h_rep2

value: flp control


title: E2F_FAIRE_44h_rep1


title: E2F_FAIRE_44h_rep2


title: 6h_wt_rna_rep1

value: wildtype


title: Ctr_FAIRE_44h_rep1


title: 25 μM C10 B

city: St. Louis

first: Gregory

last: Harrison

address: 660 South Euclid Avenue

department: Molecular Microbiology

institute: Washington University School of Medicine

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
Reads were pseudo-aligned and quantified using Salmon
Data was imported into R from Salmon using tximport
Differential expression analysis was performed using DESeq2
Genome_build: NC_000962.3
Supplementary_files_format_and_content: DESeq2 expression profiles for both 5 μM C10 and 25 μM C10 compared to DMSO samples are presented in each excel file. Column A is the gene identification number based on H37Rv genome annotation; Column B is the base mean; Column C is the Log2 fold change in C10-treated vs DMSO-treated samples; Column D is the Linear fold change for C10-treated vs DMSO-treated samples; Column E is the Log2 fold change standard error; Column F is the Wald statistic; Column G is the p value; Column H is the adjusted p value; Column I is the functional annotation as annotated in Mycobrowser; Column J is the gene product as annotated in Mycobrowser; Column L is the predicted function as annotated in Mycobrowser

organism: Mycobacterium tuberculosis

source_name: Bacterial cell extract

extract_protocol:
Bacteria were harvested from 60 mL of the culture by centrifugation, resuspended in 1 mL of Trizol and lysed by bead beating. RNA was extracted by chloroform extraction, followed by isopropanol precipitation, and the extracted RNA was resuspended in 50 μL of water. RNA integrity and concentration was measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: Logarithmically growing Mycobacterium tuberculosis in Sauton's medium was inoculated into fresh Sauton's medium containing DMSO, 5 μM C10, or 25 μM C10 at an OD600 of 0.1 and incubated at 37°C for 48 hours.

value: Erdman


title: 25 μM C10 C


title: CycD_E2F_FAIRE_24h_rep2

source_name: wing

value: 24h APF


title: CycD_E2F_FAIRE_24h_rep1


title: 25 μM C10 A


title: 5 μM C10 B

value: 5 μM C10


title: 5 μM C10 C


title: CycD_E2F_FAIRE_24h_rep3

value: female


title: E2F_FAIRE_24h_rep3


title: 5 μM C10 A


title: E2F_FAIRE_24h_rep2


title: DMSO C

value: DMSO


title: DMSO B


title: E2F_FAIRE_24h_rep1


title: Ctr_FAIRE_24h_rep2


title: GAS_WT_Liquid LC1-3

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

description:
Streptococcus pyogenes grown in chemically defined medium (CDM) replicate 3
sample3_LC-1-3_AGTCAA_L008

data_processing:
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: TopHat v2.0.13
Customized sample merged reference genome for transcripts assembly with featureCounts: cufflinks cuffmerge
Samples gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Genome_build: UCSC mouse genome model: mm10; NCBI bacteria genome model: Streptococcus pyogenes NZ131 Refseq NC_011375.1
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample, and cuffmerge processed reference genome file.

organism: Streptococcus pyogenes

source_name: Bacteria - liquid culture

growth_protocol: Samples grown in liquid medium were grown overnight, diluted and then grown to mid-log phase. In the vaginal tract, samples were inoculated at 10^7 CFU/mouse and bacteria were collected by vaginal lavage at 48 hours post-inoculation

extract_protocol:
RNA was extracted from liquid cultures or vaginal lavage fluid using the Ambion Ribopure Bacterial RNA prep kit (Thermofisher AM1925), for mouse samples, eukaryotic RNA was depleted using MICROBEnrich kit (Thermo Fisher AM1901) rRNA was removed via the MICROBExpress kit (Thermo Fisher AM1905)
cDNA libraries were constructed using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina Platforms (KAPABiosystems, KR0934).

tag: sample type

value: WT GAS samples taken from liquid culture


title: GAS_WT_Mouse LC5

description:
Streptococcus pyogenes colonizing the murine vaginal tract 48 hours post-inoculation Rep 1
sample4_LC5_GTCCGC_L007

source_name: Bacteria - murine vaginal lavage

value: WT GAS samples taken from murine vaginal tract


title: GAS_WT_Mouse LC5-4

description:
Streptococcus pyogenes colonizing the murine vaginal tract 48 hours post-inoculation Rep 3
sample6_LC5-4_GTCCGC_L006


title: GAS_WT_Liquid LC1

description:
Streptococcus pyogenes grown in chemically defined medium (CDM) replicate 1
sample1_LC1_ATGTCA_L007


title: GAS_WT_Mouse LC5-3

description:
Streptococcus pyogenes colonizing the murine vaginal tract 48 hours post-inoculation Rep 2
sample5_LC-5-3_CAACTA_L008


title: Ctr_FAIRE_24h_rep1


title: GAS_WT_Liquid LC1-2

description:
Streptococcus pyogenes grown in chemically defined medium (CDM) replicate 2
sample2_LC1-2_CGATGT_L007


title: PntRNAi RNAseq [112]

city: London

first: Adam

last: Dobson

address: Gower Street

department: GEE

country: United Kingdom

institute: University College London

description:
112
PolyA RNA
processed data file: processedData_FxAxP.xlsx

data_processing:
UMIs clipped with Je.
Aligned with hisat2.
Sorted with SAMTOOLS.
Duplicates removed with Je.
Counted with featurecounts.
Analysed with DESeq2.
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_PntRNAi.xlsx: Excel file containing read counts and variance-stabilised reads for genes analysed in either tissue (i.e., where at least 1 read detected/gene).

source_name: gut

growth_protocol: Flies reared on 10% yeast, 5% sucrose.

extract_protocol:
Trizol-chloroform extraction, polyA enrichment using PerkinElmer NextFlex polyA beads.
PerkinElmer NextFlex qRNAseq v2 kit with 16 PCR cycles.

treatment_protocol: Mated 48h, separated from males, fed 200 µM RU486 for 6 days.

value: Gut

tag: induction


title: PntRNAi RNAseq [106]

description:
106
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: fat body

value: Fat body


title: PntRNAi RNAseq [104]

description:
104
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [110]

description:
110
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [102]

description:
102
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: +RU486 (expression induced)


title: PntRNAi RNAseq [111]

description:
111
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [103]

description:
103
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [108]

description:
108
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [107]

description:
107
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [101]

description:
101
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PntRNAi RNAseq [105]

description:
105
PolyA RNA
processed data file: processedData_FxAxP.xlsx