title: EED KO MEF_H2AK119ub, ChIP DNA, rep1

first: Hongjae

last: Sunwoo

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School, HHMI

data_processing:
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: EED KO MEF

growth_protocol: MEF cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol:
CHART-seq: Sheared chromatin from 2.5x10^7 cells was prepared as described earlier as in Simon et al., Nature 504, 465-469 (2013).  160 μL chromatin was mixed with 320 μL 2X hybridization buffer (50 mM Tris-HCl pH 7.0, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, 1 mM DTT, 200 mM PMSF, 1 cOmplete EDTA-free protease inhibitor cocktail tablet [Roche], and 100 U/mL RNase Inhibitor [Roche]) and pre-cleared with 60 μl MyOne Streptavidin C1 beads blocked with yeast total RNA and bovine serum albumin at room temperature for 1 hr. The pre-cleared chromatin was mixed with 36 pmol of either antisense (Xist-targeting) or sense (control) capture probes. We used a pool of 9 capture probes (biotinylated oligos). Hybridization was carried out at 37°C for 4 hr followed by incubation with 240 μL blocked MyOne Streptavidin C1 beads at 37°C for 1 hr. The beads were washed once with 1X hybridization buffer (1:2 mixture of sonication buffer and 2X hybridization buffer) at 37°C for 10 min, five times with wash buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 2% SDS, 2 mM EDTA, 2 mM EGTA, and 1 mM DTT) at 37°C for 5 min, and twice with elution buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 0.5% NP-40, 3 mM MgCl2, and 10 mM DTT) at 37°C for 5 min. CHART-enriched DNA was eluted by 20 μL RNase H (5 U/μL, New England BioLabs) in 200 μL elution buffer two times at 37°C for 30 min. Eluent was treated with 10 μL RNase A (20 mg/mL) at 37°C for 1 hr and then treated with SDS (final 1%), EDTA (final 10 mM), and 10 μL proteinase K (20 mg/mL) at 55°C for 1 hr. Reversal of crosslinks was performed by supplementing the eluent with NaCl (final 0.3 M) and incubation at 65°C overnight. DNA was extracted by phenol-chloroform and further sheared to below 500-bp fragments.
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.
in situ Hi-C: As described in Rao et al. (2014), 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Mouse embryonic fibroblasts (MEF)

value: EED KO

tag: antibody

value: H2AK119ub (Cell Signaling Technology, 8240, lot 2)


title: EED KO MEF_H2AK119ub, input DNA, rep1

status: Public on Mar 01 2019

type: SRA

city: Boston

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype/variation

value: none (input)


title: BFUEs_Day2_22

city: Cambridge

first: Hojun

last: Li

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

library_source: transcriptomic

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 39
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

molecule: polyA RNA

source_name: burst forming unit-erythroid

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
cell culture protocol: BFU-E cell culture. FACS-isolated BFU-E enriched cells were cultured for the denoted number of days in progenitor culture media (PCM) consisting of serum free expansion media (SFEM2, Stem Cell Technologies) supplemented with 100 ng/mL murine SCF (Peprotech), 40 ng/mL murine insulin-like growth factor 1 (Peprotech), 2 U/mL human erythropoietin (Amgen), 1% penicillin/streptomycin (Gibco), and for indicated cultures 100 nM Dexamethasone (Sigma).
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

tag: strain

value: BFUE

value: erythroid progenitor media

tag: time in culture

value: 48 hrs

tag: treatment

value: No


title: Morula C5E1 RNA-seq

first: Wenhao

last: Zhang

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

data_processing:
RNA-seq reads were were mapped to human reference genome (hg19) using TopHat (version 2.1.1) paired-end alignment mode (parameters: --no-coverage-search --no-mixed --no-discordant). Mapped reads were further processed to calculate gene FPKM using Cufflinks (version 2.2.1) by default parameters. RefSeq database (hg19) from UCSC genome browser was used as annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for RNA-seq including FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: human morula embryo

growth_protocol: Human morula embryos were generated by ICSI from patients who have singed consents for providing their otherwise discarded material for research. Briefly, 2PN zygotes were cultured in global® total® medium supplemented with HAS (LifeGlobal, CT, USA) under 5% O2, 6-7% CO2, and 88-89% N2. Then, embryos did not meet the freezing criteria for clinical purpose but developed to the morula like stage were collected and stored at -80 degree centigrade for ChIP-seq and RNA-seq.

extract_protocol: SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech) was used to perform reverse transcription and cDNA amplification (13 cycles) using whole-embryo lysate. cDNAs (80pg) were then fragmented, adaptor-ligated and amplified (12 cycles) using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Paired-end 100bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

tag: tissue

value: embryo

tag: developmental stage

value: morula

tag: chip-antibody

tag: genotype

value: WT


title: RING1A/B KO MEF_H3K27me3, input DNA, rep1

source_name: RING1A/B KO MEF

value: RING1A/B KO


title: Morula C5E3 RNA-seq


title: BFUEs_Day2_20


title: Empty vector 60min 4-OHT Rep4

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: RNA-Seq of chromatin associated RNA from Empty vector 60min 4-OHT Rep4

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm10
Supplementary_files_format_and_content: reads counts on genes

source_name: Empty vector 60min 4-OHT

growth_protocol: Mouse pre-B cell line B3 was grown in IMDM, 10% FCS and  1% penicillin-streptomycin

extract_protocol:
Cells were fractionated according to the protocol described in Pandya-Jones and Black, RNA 2009. Briefly, cells were lysed in 0.15% NP40 buffer and spun over a sucrose cushion to obtain nuclei. Nuclei were lysed in buffer containing 1% NP40 and 1M urea. RNA from chromatin pellet was purified using Qiagen RNeasy columns according to manufacturer protocol. 10 ug of RNA from each sample was depleted of ribosomal RNA using the Invitrogen Human/Mouse Ribominus kit.
Libraries were constructed from 500 ng of rRNA-depleted RNA using the dUTP method described in Levin et al, Nat Methods 2010

treatment_protocol: Cells containing inducible Ikaros were generated by transducing mouse pre-B cell line B3 with mouse stem cell virus (MSCV) retroviral vectors encoding a fusion protein of haemagglutinin-tagged wild type Ikaros (HA-Ikaros) and the estrogen receptor hormone-binding domain (ERt2), followed by an internal ribosomal entry site (IRES) and GFP. B3 cells containing inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP) were plated at a density of 0.5 million cells/ml in IMDM medium containing 10% FCS and 1% penicillin-streptomycin. 0.5uM 4 hydroxy-tamoxifen was added to the cells 2h before collection. Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin.

tag: cell line background

value: pre-B cell line

tag: cell line reference

value: Brown et al. 1997

value: Empty vector

value: 4-OHT 60min


title: BFUEs_Day2_21


title: Morula C4E2 RNA-seq


title: RING1A/B KO MEF_Tsix CHART, rep1

data_processing:
Library strategy: CHART-seq
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

value: CAST/Ei x 129/Sv/Jae


title: RING1A/B KO MEF_CHART, input DNA

value: Mouse embryonic fibroblasts (MEF)


title: RING1A/B KO MEF_Xist CHART, rep1


title: Morula C4E3 RNA-seq


title: BFUEs_Day2_19


title: EED KO MEF_Tsix CHART, rep1

value: EED KO


title: Empty vector 180min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from Empty vector 180min 4-OHT Rep1

source_name: Empty vector 180min 4-OHT

value: 4-OHT 180min


title: Morula C3E3 RNA-seq


title: Morula C3E2 RNA-seq


title: BFUEs_Day2_16


title: EED KO MEF_Xist CHART, rep1


title: BFUEs_Day2_15


title: Morula C4E1 RNA-seq


title: Morula C2E3 RNA-seq


title: EED KO MEF_CHART, input DNA


title: Adamts17KO3

city: Tokyo

first: Takeshi

last: Oichi

address: 7-3-1, Bunkyo-ku, Hongo

country: Japan

institute: The University of Tokyo

data_processing:
Illumina Casava1.8 software used for basecalling.
trimmed mean of M (TMM) values were calculated using protocol described by M.D. Robinson and A. Oshlack. (Genome Biol. 11 (2010) R25)
Genome_build: RefSeq Genes and Transcripts (2012.12.15)
Supplementary_files_format_and_content: xlsx files include TMM values for each Sample

source_name: hypertrophic zone of tibial growth plate

extract_protocol:
Proximal tibia was removed, flash frozen in liquid nitrogen, cryosectioned and transferred to adhesive membrane. Hypertrophic zones of tibial growth plates were collected by LMD. Total RNA was extracted using Picopure RNA Isolation Kit. Amplified RNA (aRNA) was generated by linear amplification of mRNA using RiboAmp HS PLUS Kit. Illumina TruSeq RNA Sample Prep Kit v2 was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age


title: WT3

value: wild type

value: hypertrophic zone of tibial growth plate


title: Morula C3E1 RNA-seq


title: RING1A/B KO MEF_H3K27me3, ChIP DNA, rep1


title: BFUEs_Day2_14

value: BFUE

value: erythroid progenitor media


title: Morula C2E2 RNA-seq


title: Adamts17KO2


title: WT2


title: BFUEs_Day2_13

value: 48 hrs

value: No


title: Adamts17KO1


title: Morula C2E1 RNA-seq

value: embryo

value: morula


title: BFUEs_Day2_12


title: BFUEs_Day2_17


title: H3K27me3 ChIP-seq MEF

city: New Haven

first: Xiao

last: Hu

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
For RNA-seq data analysis, the RNA-seq reads were mapped to mouse genome (mm10) with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons (whichever gives the higher mapping score) independent of the transcriptome annotation. Differentially expressed genes were identified by DESeq2 (v1.16.0) followed by cutting off with FDR-adjusted P value < 0.05 and fold changes > 2. MA plot of differentially expressed genes was also done with the R software. Gene Set Enrichment Analysis (GSEA) was performed with the GSEA software.  Reference gene sets were obtained from Polo et al. Gene Ontology (GO) analysis of differentially expressed genes was performed with DAVID (https://david.ncifcrf.gov).
ChIP-seq reads were aligned to the mouse genome mm10 using Bowtie2 (v2.2.6) with default settings. The resulting BAM files were filtered to remove the reads that have the same sequence, and converted to reads coverage files using the BamCoverage in DeepTools (v2.5.0). Reads coverage files were normalized as RPKM (Reads Per Kilobase of transcript per Million mapped reads) and visualized in IGV (v2.3). For transcription factors, filtered BAM files were used for peak calling and differential peak analysis using MACS2 (v2.1.1). Differential peaks were annotated with PAVIS (https://manticore.niehs.nih.gov/pavis2/).
For ATAC-seq analysis, sequence reads were trimmed using the trimmomatic software to remove nextera adapters and low quality bases at the beginning and end of the reads in paired end mode. Reads were then aligned to the mouse mm10 genome sequence using the bwa mem mapper (arXiv:1303.3997 [q-bio.GN]). Reads were sorted and duplicates were marked using the Picard software (http://broadinstitute.github.io/picard/).  Sequence reads that aligned with poor mapping quality to problematic black list regions or mitochondrial regions were removed. Peaks were called on reads with reads with insert size smaller than 250 bases using the MACS2 peak caller using the paired end mode -f BAMPE option.  Differentially bound peaks were identified using the DiffBind R package utilizing the Deseq2 method with parameters fragmentSize=300 and bFullLibrarySize = TRUE (http://bioconductor.org/packages/release/bioc/html/DiffBind.html). Peaks were normalized by the total number of reads from all the samples.
Genome_build: mm10
Supplementary_files_format_and_content: csv, BAM, BAM index, bigwig

source_name: MEF

growth_protocol: Reprogramming cells were cultured in standard mouse ES cell medium with 1 ug/mL Dox. ES cells or iPS cells were cultured in standard ES cell medium on feeder layer. caMKL1 blocked iPS-like cells were cultured in standard ES cell medium on feeder layer, with 1 ug/mL Dox.

extract_protocol:
RNA was extracted with Trizol; ChIP DNA was extracted with Qiagen Gel Extraction kit; ATAC-seq DNA was extracted with Qiagen MinElute PCR purification kit
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101); ChIP DNA libraries were constructed with ThruPLEX® DNA-seq Kit (Rubicon Genomics), ATAC-seq libraries were prepared with Illumina Nextera DNA Library Prep Kit (15028212).

treatment_protocol: Overexpression was achived by pMSCV mediated viral delivery

value: MEF

tag: passages

value: Millipore, 07-449


title: BFUEs_Day2_11


title: Morula C1E3 RNA-seq

value: WT


title: Morula C1E1 RNA-seq


title: H3K27ac ChIP-seq MEF

value: Abcam, ab4729


title: Input MEF


title: BFUEs_Day2_8


title: BFUEs_Day2_9


title: H3K4me3 ChIP-seq MEF

value: Millipore, 07-473


title: BFUEs_Day2_10


title: H3K27me3 ChIP-seq caMKL1 blocked cells at day 25

source_name: caMKL1 blocked cells at day 25

value: iPS-like cells

value: Day 25


title: H3K4me3 ChIP-seq caMKL1 blocked cells at day 25


title: WT1


title: H3K27ac ChIP-seq caMKL1 blocked cells at day 25


title: Cumulus C2 whole-genome-seq

data_processing:
Library strategy: whole genome-seq
To ensure the accuracy of SNP calling, Burrows-Wheeler Aligner (BWA, version 0.7.17) was used with parameter ‘aln’ to map the reads to human reference genome (hg19). Reads with mapping quality q < 10 and showing multiple-mapped feature were removed. Then duplicates were further removed by Picard MarkDuplicate. After that, all SNPs were identified using UnifiedGenotyper tools from GATK (version 4.0.7.0) (parameter: -stand_call_conf 0 -stand_emit_conf 0 -U ALLOW_N_CIGAR_READS -out_mode EMIT_VARIANTS_ONLY). SNPs with quality < 20 were removed, and the variants within first six bases of a read were discarded. Then SNP sites showing maternal homozygous genotype (FDR < 0.05) with read coverage over 10 were retained.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including information of solid homozygous SNP sites identified from each exome-seq or whole genome-seq sample

source_name: Cumulus cells

growth_protocol: For collection of cumulus cells, immediately following oocyte retrieval, cumulus masses were trimmed of blood, rinsed and then treated with hyaluronidase (60 IU/mL). The remaining cells were collected for exome-seq and/or whole genome sequencing.

extract_protocol:
Cumulus cell genomic DNA is extracted according to standard manuscript of AllPrep DNA/RNA mini kit (Qiagen, 80204).
Cumulus cell DNA whole genome sequencing library was built according to the standard manuscript of Nextera XT Library Prep Kit (Illumina). Paired-end 150 bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).


title: Cumulus C5 exome-seq

data_processing:
Library strategy: Exome-seq
To ensure the accuracy of SNP calling, Burrows-Wheeler Aligner (BWA, version 0.7.17) was used with parameter ‘aln’ to map the reads to human reference genome (hg19). Reads with mapping quality q < 10 and showing multiple-mapped feature were removed. Then duplicates were further removed by Picard MarkDuplicate. After that, all SNPs were identified using UnifiedGenotyper tools from GATK (version 4.0.7.0) (parameter: -stand_call_conf 0 -stand_emit_conf 0 -U ALLOW_N_CIGAR_READS -out_mode EMIT_VARIANTS_ONLY). SNPs with quality < 20 were removed, and the variants within first six bases of a read were discarded. Then SNP sites showing maternal homozygous genotype (FDR < 0.05) with read coverage over 10 were retained.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including information of solid homozygous SNP sites identified from each exome-seq or whole genome-seq sample

extract_protocol:
Cumulus cell genomic DNA is extracted according to standard manuscript of AllPrep DNA/RNA mini kit (Qiagen, 80204).
Exome-seq libraries were prepared using SureSelectXT2 Enrichment System for Illumina (Agilent Technologies) according to the manufacturer’s instructions.  Specifically, 100ng genomic DNA extracted from the maternal cumulus cells were sheared into 150-200 bp using a Covaris M220 sonicator (Covaris) with microTUBE-50 (Covaris). Following end-repair and ligation, five cumulus cell samples were indexed, pooled, and amplified to prepare DNA-seq libraries. To capture human exon sequences including the untranslated regions (UTRs), SureSelectXT2 Human All Exon V6+UTR (Agilent Technologies) probes were used to hybridize with the library DNA pools.  Following hybridization, the SureSelect-enriched indexed library DNA pools were purified and sequenced on an Illumina HiSeq 2500 (Illumina) with paired-end 100bp reads.


title: BFUEs_Day2_7


title: H3K27me3 ChIP-seq Control iPS cells at day 25

source_name: Control iPS cells at day 25

value: iPSCs


title: H3K4me3 ChIP-seq Control iPS cells at day 25


title: BFUEs_Day2_6


title: H3K27ac ChIP-seq Control iPS cells at day 25


title: Cumulus C4 exome-seq


title: Input 15 Control iPS cells at day 25


title: Morula C1E2 RNA-seq


title: Input 19 caMKL1 blocked cells at day 25


title: Oct4 ChIP-seq caMKL1 mESC

source_name: caMKL1 mESC

value: mESCs

value: Cell Signaling Technology, 5677S


title: Cumulus C3 exome-seq


title: BFUEs_Day2_5


title: Input caMKL1 mESC


title: Oct4 ChIP-seq WT mESC

source_name: WT mESC


title: Cumulus C2 exome-seq


title: Input WT mESC


title: SRF (Active Motif) ChIP-seq caMKL1 blocked cells at day 25

value: Actif Motif, 61385


title: Cumulus C1 exome-seq


title: BFUEs_Day2_3

value: BFUE


title: SRF (Active Motif) ChIP-seq Control iPS cells at day 25


title: Oct4 ChIP-seq caMKL1 blocked cells at day 25


title: Input 4 caMKL1 blocked cells at day 25


title: Input caMKL1 blocked cells at day 25


title: BFUEs_Day2_1

value: erythroid progenitor media


title: SRF (Santa Cruz) ChIP-seq Control iPS cells at day 25

value: Santa Cruz, sc-335


title: SRF (Santa Cruz) ChIP-seq caMKL1 blocked cells at day 25


title: Oct4 ChIP-seq Control iPS cells at day 25


title: RNA-seq caMKL1 blocked cells at day 25-3

description:
DiffExpr Day 25.csv
caMKL1 D25-3


title: Input 1 Control iPS cells at day 25


title: BFUE_Day1_96

value: 24 hrs

value: No


title: BFUE_Day1_95


title: Input Control iPS cells at day 25


title: BFUEs_Day2_2

value: 48 hrs


title: RNA-seq caMKL1 blocked cells at day 25-1

description:
DiffExpr Day 25.csv
caMKL1 D25-1


title: BFUE_Day1_93


title: BFUE_Day1_94


title: RNA-seq caMKL1 blocked cells at day 25-2

description:
DiffExpr Day 25.csv
caMKL1 D25-2


title: RNA-seq Control iPS cells at day 25-2

description:
DiffExpr Day 25.csv
Control D25-2


title: RNA-seq caMKL1 expressing reprogramming cells at day 6-2

description:
DiffExpr Day 6.csv
caMKL1 D6-2

value: Reprogramming cells

value: Day 6


title: BFUEs_Day2_4


title: BFUE_Day1_92


title: RNA-seq caMKL1 expressing reprogramming cells at day 6-1

description:
DiffExpr Day 6.csv
caMKL1 D6-1


title: RNA-seq Control iPS cells at day 25-1

description:
DiffExpr Day 25.csv
Control D25-1


title: BFUE_Day1_91


title: RNA-seq Control reprogramming cells at day 6-2

description:
DiffExpr Day 6.csv
Control D6-2

source_name: Control reprogramming cells at day 6


title: BFUE_Day1_90


title: RNA-seq Control reprogramming cells at day 6-1

description:
DiffExpr Day 6.csv
Control D6-1


title: BFUE_Day1_89


title: BFUE_Day1_88


title: Q1039; Cysteamine; 24 hours

city: Philadelphia

first: Zhe

state: PA

address: Translational Research Lab

institute: University of Pennsylvania

data_processing:
Align RNA-seq reads to reference genome (ws235) and transcriptome (iGenome) using the STAR program (version 2.5.1b)
Reads uniquely mapped to known genes were counted to obtain a read count matrix
Genes were annotated by unique Entrez IDs
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file inclduing an integer matrix of gene-level read counts. Row names are unique official gene symbols. Data is not normalized.

source_name: FCL

growth_protocol: Fibroblast cell lines (FCL) from healthy human controls (Q1269p1, Q1508p1) and three primary RC disease subjects with pediatric-onset Leigh syndrome including (1) Q1007 - FBXL4 (c.1067delG;p.G356AfsX15 and c.1790A>C;p.Q597P) with complex I-III dysfunction ; (2) Q1508 - NDUFS8 (c.160C>T;p.R54W and c.58>C;p.G20R) with complex I dysfunction ; and (3) Q1039 - (MT-ND4, m.11778G>A heteroplasmy + MT-ND6 m.14484T>C homoplasmy) with complex I dysfunction

extract_protocol:
RNA was extracted using Trizol, DNAse treated, and analyzed by Agilent Bioanalyzer to assess RNA quality.
cDNA library preparation was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA).

treatment_protocol: Cells were treated with 0.5 µM cysteamine bitartrate for either 6 hrs or 24 hrs, and compared to untreated RC disease and control cells. Each same 2 healthy controls and 3 patients were included in all treatment groups.

tag: cell line

tag: disease

value: NDUFS8 mutations with complex I dysfunction

value: 0.5 uM cysteamine; 24 hours


title: Q1007; Cysteamine; 24 hours

value: FBXL4 mutations with complex I-III dysfunction


title: RNA-seq Control iPS cells at day 25-3

description:
DiffExpr Day 25.csv
Control D25-3


title: BFUE_Day1_87


title: BFUE_Day1_86


title: BFUE_Day1_84


title: BFUE_Day1_83


title: BFUE_Day1_82


title: BFUE_Day1_81


title: Q1508p1; Cysteamine; 24 hours

value: Healthy human controls


title: BFUE_Day1_85


title: Q1269p1; Cysteamine; 24 hours


title: Q1508; Control; 24 hours

value: MT-ND4 mutations with complex I dysfunction

value: Untreated; 24 hours


title: Q1007; Control; 24 hours


title: Q1269p1; Control; 24 hours


title: BFUE_Day1_80


title: BFUE_Day1_78


title: BFUE_Day1_77


title: Q1039; Cysteamine; 6 hours

value: 0.5 uM cysteamine; 6 hours


title: Q1508; Cysteamine; 6 hours


title: BFUE_Day1_79


title: Q1508; Cysteamine; 24 hours


title: Q1007; Cysteamine; 6 hours


title: Q1508p1; Cysteamine; 6 hours


title: BFUE_Day1_75


title: Q1039; Control; 24 hours


title: Q1508p1; Control; 24 hours


title: BFUE_Day1_74


title: BFUE_Day1_73


title: Q1039; Control; 6 hours

value: Untreated; 6 hours


title: BFUE_Day1_76


title: Q1508; Control; 6 hours


title: BFUE_Day1_71


title: Q1007; Control; 6 hours


title: Q1508p1; Control; 6 hours


title: BFUE_Day1_70


title: BFUE_Day1_69


title: Q1269p1; Cysteamine; 6 hours


title: Q1269p1; Control; 6 hours


title: Erythroid RUNX3 knock-down, replicate 3

city: Charlottesville

first: Adam

last: Goldfarb

state: Virginia

address: 415 Lane Road

department: Pathology

institute: University of Virginia

data_processing:
Trimmomatic: Read trimming (usegalaxy.org; default parameters)
HISAT2: Alignment to hg19 (usegalaxy.org; default parameters)
RmDup: PCR duplicate removal (usegalaxy.org; default parameters)
featureCounts: Read counting (usegalaxy.org; default parameters)
DESeq2: Differential gene expression from read counts (usegalaxy.org; default parameters)
Cufflinks: FPKM estimates (usegalaxy.org; default parameters)
Cuffdiff: Differential gene expression from FPKM estimates (usegalaxy.org; default parameters)
Synergizer: Conversion of gene IDs to gene names (http://llama.mshri.on.ca/synergizer/translate/)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files include Cufflinks and DESeq2 output files in xlsx format. They include all default output paramaters, plus gene names derived from the Synergizer tool (see above link). Cufflinks output describes FPKM estimates, and DESeq2 output describes differential gene expression based on read counts.

source_name: Bone marrow

extract_protocol:
RNA was isolated using the Qiagen Rneasy kit (Cat #74134).
Library contruction was performed by Hudson Alpha Genomic Services Laboratory according to standard Illumina protocols.

value: Bone marrow

tag: starting material

value: Adult CD34+ HSPCs

tag: cell culture condition

value: Erythroid differentiation

tag: lentiviral construct

value: RUNX3 shRNA


title: BFUE_Day1_72

tag: cell type

value: BFUE

value: erythroid progenitor media

value: 24 hrs


title: BFUE_Day1_68

tag: strain

value: No


title: Erythroid empty vector, replicate 3

value: Empty vector


title: BFUEs_Day2_18

tag: time in culture

value: 48 hrs


title: BFUE_Day1_67

tag: treatment


title: CD34 empty vector, replicate 3

tag: tissue

value: HSPC expansion


title: BFUE_Day1_65


title: CEP_STAT6_ZsG

type: RNA

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

label: biotin

source_name: bone marrow-derived macrophages from Ai6 reporter mice

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre Nano Total-Amp kit

growth_protocol: Bone marrow-derived cells were cultured in non-tissue culture treated 10cm dishes in DMEM supplemented with 10% fetal bovine serum, antibiotics and 20% exhausted supernatants from L-929 cells (L-supes).  After 6 days, adherent macrophages were washed, removed from dishes by scraping, and replated in tissue-culture treated, 10cm dishes.

extract_protocol: RNA was extracted from sorted cells populations using the Qiagen Rneasy Plus kit.

treatment_protocol: ZsGreen reporter macrophages generated from bone marrow of Ai6 mice were infected with a 1:1 MOI of Toxoplasma tachyzoites.  Parasites were engineered to express mCherry flourescent protein, and target cre recombinase to the parasite rhoptries, a specialized secretion apparatas whose contents are injected into host cells during initial contact.  18-20 hours post-infection, cells were recovered and three distinct populations were sorted by FACS from each dish: (1) ZsGreen-positive, mCherry-negative macrophages (uninfected, but have been injected with roptery contents resulting in activation of zsGreen reporter);  (2) double positive cells (infected), and (3) double negative cells (uninfected and uninjected).  Cells were sorted into media, pelleted and immediately used for RNA extraction.

tag: strain of mouse

tag: strain of toxoplasma

value: CEP

tag: phenotype

value: uninfected-injected

tag: host cell genotype

tag: batch


title: CEP_WT_DP

value: infected

value: WT


title: Pru_STAT6_DN

value: Pru

value: uninfected


title: Erythroid RUNX3 knock-down, replicate 2

value: Bone marrow


title: BFUE_Day1_64


title: Pru_STAT6_DP


title: CEP_WT_DN


title: CEP_STAT6_DP


title: RH_STAT6_ZsG

value: RH


title: CD34 RUNX3 knock-down, replicate 3

value: Adult CD34+ HSPCs


title: Pru_WT_DN


title: CEP_STAT6_DN


title: Erythroid empty vector, replicate 2

value: Erythroid differentiation


title: RH_STAT6_DP


title: RH_STAT6_DN


title: RH_WT_DN


title: RH_WT_ZsG


title: Pru_WT_DP


title: Pru_WT_ZsG


title: Pru_STAT6_ZsG


title: BFUE_Day1_66

value: BFUE


title: CEP_WT_ZsG


title: RH_WT_DP


title: CD34 RUNX3 knock-down, replicate 2

value: RUNX3 shRNA


title: CD34 empty vector, replicate 2


title: BFUE_Day1_61

value: erythroid progenitor media

value: 24 hrs


title: BFUE_Day1_60

value: No


title: Erythroid empty vector, replicate 1

value: Empty vector


title: Erythroid RUNX3 knock-down, replicate 1


title: BFUE_Day1_63


title: BFUE_Day1_58


title: BFUE_Day1_59


title: CD34 empty vector, replicate 1

value: HSPC expansion


title: BFUE_Day1_62


title: High-fat fed, saline treated mouse 5

city: Calgary

first: Christopher

last: Newell

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

description:
HFS5
Gene expression data from saline-treated C57 mice at 24 weeks of age.

hyb_protocol: Following fragmentation, 5.5 ug of fragmented and labeled ss-cDNA was hybridized for 16 hr at 45C on the GeneChip Mouse 1.0 ST arrays. GeneChips were washed and stained using the Affymetrix Fluidics 450 station.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip scanner.

data_processing: The data was analyzed using the Affymetrix Expression Console software using the default settings and the Robust Multi-array Average algorithm as the normalization method. The raw intensity values are background corrected, log2 transformed and then quantile normalized.

source_name: Flash frozen liver tissue, mouse, saline treated for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were fed a high-fat diet for 20 weeks.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were injected with either MSCs (HFM group) or saline as controls (HFS group) before being sacrificed 24 hours following injection.

tag: strain/background

value: Liver

tag: gender

value: Male

tag: age

value: 24 weeks

tag: diet

value: high fat

value: Saline for 24hr


title: High-fat fed, saline treated mouse 7

description:
HFS7
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: BFUE_Day1_57

source_name: burst forming unit-erythroid


title: High-fat fed, saline treated mouse 6

description:
HFS6
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: High-fat fed, saline treated mouse 3

description:
HFS3
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: single cells from micro-organoid

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
The barcode and UMI are included in the first 26 bp of R1 reads (barcode = first 16 bp, followed by 10 bp UMI).
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices.
Celllranger datasets consist of matrix files (matrix.mtx)containing the UMI count values, barcode files (barcodes.tsv) containing the detected cell barcodes and genes files (genes.tsv)  containing the ENSEMBL ids of the detected genes.
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files, compressed.

source_name: CRL1502.C32 human iPSCs

extract_protocol:
CRL1502.C32 kidney organoid were dissociated at D7+18 using cold active protease (Liberase) for 20 minutes at 4c. Cells were centrifuged at 1500 rpm for 3minutes to form a pellet. Single cells were resuspended in fresh DMEM F12 media filtered through 20 µm cell strainers to remove clumps, and stored on ice until analysis.
Chromium Single Cell Library kit V2; Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: iPSC-derived kidney micro-organoid

tag: day of differentiation


title: High-fat fed, saline treated mouse 4

description:
HFS4
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: High-fat fed, saline treated mouse 1

description:
HFS1
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: High-fat fed, saline treated mouse 2

description:
HFS2
Gene expression data from saline-treated C57 mice at 24 weeks of age.


title: High-fat fed, MSC treated mouse 5

description:
HFM5
Gene expression data from MSC-treated C57 mice at 24 weeks of age.

source_name: Flash frozen liver tissue, mouse, MSC treated for 24 hours

value: MSC for 24hr


title: High-fat fed, MSC treated mouse 4

description:
HFM4
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: BFUE_Day1_56


title: High-fat fed, MSC treated mouse 7

description:
HFM7
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: CD34 RUNX3 knock-down, replicate 1

value: Bone marrow

tag: starting material

tag: cell culture condition


title: BFUE_Day1_55

tag: cell type


title: High-fat fed, MSC treated mouse 6

description:
HFM6
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: High-fat fed, MSC treated mouse 3

description:
HFM3
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: High-fat fed, MSC treated mouse 1

description:
HFM1
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: High-fat fed, MSC treated mouse 2

description:
HFM2
Gene expression data from MSC-treated C57 mice at 24 weeks of age.


title: BM_IL7-YFPneg_Rep1

city: Marseille

first: Stéphane

middle: JC

last: Mancini

address: 27 Boulevard Lei Roure

department: Centre de Recherche en Cancérologie de Marseille

country: France

institute: INSERM

hyb_protocol: cDNAs were hybridized for 16 hours at 45°C on GeneChip Mouse Gene 1.0 ST arrays (Affymetrix). The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing: The data were processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: bone marrow

label_protocol: Biotinylated double strand cDNA targets were prepared starting from total RNA (prepared from 2300 sorted cells), using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit

extract_protocol: mRNA extraction was performed using the RNeasy plus micro kit (Qiagen)

tag: strain

tag: genotype

value: IL7-Cre Transgenic/Rosa-eYFP hetero

value: young adults

value: bone marrow stromal cells


title: C2C12_Ad-caERα

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from differentiated myoblastic C2C12 cells transduced with Ad-caERα

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Mouse Gene 1.0 ST Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: Differentiated myoblastic C2C12 cells transduced with Ad-caERα

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Mouse myoblastic C2C12 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (growth medium). When the cells reached confluence, the medium was switched to DMEM supplemented with 2% horse serum (differentiation medium) to induce myotubes for 7 days.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: Differentiated myoblastic C2C12 cells were infected with Ad-caERα or Ad-DsRed at m.o.i. 30 for 48 h.

tag: cell line

tag: transduction

value: Ad-caER[sigma]


title: BFUE_Day1_54

value: BFUE

value: erythroid progenitor media

tag: time in culture

tag: treatment


title: P493-Y518R

city: Birmingham

first: Kushani

last: Shah

state: AL

address: 1825 University Blvd.

department: Biochemistry & Molecular Genetics

institute: University of Alabbama at Birmingham

data_processing:
Basecalls performed using CASAVA version 1.8.4
For RNA-seq, paired-end sequencing was performed on an HiSeq 2500 sequencer (Illumina), and sequences reported as FASTQ files. All reads were aligned to the human genome (GRCh38/hg19) using TopHat (v2.1.1). Low quality mapped reads (MQ<30) were removed from the analysis. Mappable reads were counted with HTSeq (v.0.6.1). All the read count tables were then normalized based on ____and imported into R Studio software for differential gene expression using DESeq2 (v3.0).  Genes with mean count across all groups >30 were chosen for visualization. For heatmap, genes with a difference expression p value < 0.05 were selected. Venn diagrams were generated using jvenn: an interactive Venn diagram viewer (Bardou, et. al., jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293).
Genome_build: Hg19
Supplementary_files_format_and_content: Count tables (transcript counts for genomic features). Normalized counts are available in the file Normalized_DESeq.xlsx, on the series record.

source_name: P493-6 cells_DPY30-binding peptide

growth_protocol: All cells were cultured in Advanced RPMI medium with 2.5% fetal bovine serum (FBS)

extract_protocol:
total RNAs were isolated using Direct-zol RNA Extraction Kit (Zymo Research).
Library preparation and sequencing for RNA samples were performed at Genewiz (South Plainfield, NJ). Briefly, the quality of the total RNA was assessed using Nanodrop 2000, Qubit RNA Assay, and TapeStation). One round of polyA+ selection was performed for RNA samples, followed by conversion to cDNAs. The mRNA library was generated using NEBNext Ultra RNA Library Prep KitA as per manufacturer’s instructions. The indexed DNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.

value: Burkitt's lymphoma model


title: BFUE_Day1_53

value: 24 hrs

value: No


title: C2C12_Ad-DsRed

description: Gene expression data from differentiated myoblastic C2C12 cells transduced with Ad-DsRed

source_name: Differentiated myoblastic C2C12 cells transduced with Ad-DsRed

value: Ad-DsRed


title: totalBM_Rep1

label_protocol: Biotinylated double strand cDNA targets were prepared starting from total RNA (10 ng for total bone marrow or unknown quantity from 1800 to 10 000 sorted cells), using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit

value: wild type

value: total bone marrow cells


title: JUR-Y518R

source_name: JURKAT cells_DPY30-binding peptide

value: JURKAT

value: Myc dependent T cell Leukemia


title: BFUE_Day1_52


title: RAJ-Y518R

source_name: RAJI cells_DPY30-binding peptide

value: RAJI

value: Burkitt's lymphoma


title: BFUE_Day1_51


title: P493-3R

source_name: P493-6 cells_non-binding peptide


title: BFUE_Day1_50


title: K562-Y518R

source_name: K562 cells_DPY30-binding peptide

value: BCR-ABL Leukemia


title: BM_54+BP1+_Rep3


title: RAJ-3R

source_name: RAJI cells_non-binding peptide


title: BFUE_Day1_49


title: BM_54+BP1+_Rep2


title: K562-3R

source_name: K562 cells_non-binding peptide


title: totalBM_Rep2


title: BFUE_Day1_48


title: BM_IL7-YFP_Rep1

value: IL7-Cre Transgenic/Rosa-eYFP hetero


title: BM_IL7-YFP_Rep3

value: young adults


title: BM_IL7-YFP_Rep2

value: bone marrow stromal cells


title: BM_54+BP1+_Rep1


title: KOP-Y518R

source_name: KOPN8 cells_DPY30-binding peptide

value: MLL-ENL Leukemia


title: FLU-specific CD8+ T cells, rep5

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Labeled cDNA was hybridized to 60-mer oligonucleotide Whole Human Genome Microarrays (Human GE 4x44K v2, Agilent Technologies), following the manufacturer’s protocol.

scan_protocol: Microarray slides were scanned with an Agilent dual-laser DNA microarray scanner.

data_processing: The Agilent Feature Extraction software with default settings (user manual version 7.5) was used to obtain normalized expression values from the raw scans. The software package GeneSpring GX v11.5 (Agilent Technologies) was used for quality control checks, data normalization by the quantile method and microarray data analysis.

source_name: FLU-specific CD8+ T cells from healthy donor 39

label_protocol: Total RNA was amplified with the Transplex Whole Transcriptome Amplification (WTA2) kit (Sigma-Aldrich, St.Louis, Mo) and purified with GenElute™ PCR Clean-Up silica spin-columns (Sigma). cDNA was labeled with the ULS Fluorescent Labeling kit (Agilent Technologies).

extract_protocol: RNA was purified from dextramer-sorted human CD8+ T cells with the Nucleospin RNA XS kit (Macherey Nagel, Duren, Germany) according to the manufacturer's instructions. Total RNA concentration was determined with a Nanodrop spectrophotometer and/or with the Ribogreen RNA quantification kit (Molecular Probes, Life Technologies, Carlsbad, CA). RNA integrity was evaluated with a Bioanalyzer 2100 traces system (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PBMCs were isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation and cryopreserved in liquid nitrogen until the day of analysis. After thawing of PBMCs, CD8+ T cells were isolated with the CD8+ T Cell Isolation Kit (Miltenyi Biotec) and labeled with 7-AAD, anti-CD45, anti-CD3, anti-CD8, and HLA-Class I dextramers in order to identify antigen-specific T cell sub-populations. CD8+ dextramer+ cells were sorted with a FACSAria III Cell Sorter (BD Biosciences).

tag: individual

value: healthy donor 39

value: FLU-specific CD8+ T cells


title: JUR-3R

source_name: JURKAT cells_non-binding peptide


title: BFUE_Day1_47

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 39
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

value: BFUE

value: erythroid progenitor media


title: FLU-specific CD8+ T cells, rep4

source_name: FLU-specific CD8+ T cells from healthy donor 23

value: healthy donor 23


title: FLU-specific CD8+ T cells, rep3

source_name: FLU-specific CD8+ T cells from healthy donor 22

value: healthy donor 22


title: FLU-specific CD8+ T cells, rep2

source_name: FLU-specific CD8+ T cells from healthy donor 20

value: healthy donor 20


title: FLU-specific CD8+ T cells, rep1

source_name: FLU-specific CD8+ T cells from healthy donor 16

value: healthy donor 16


title: HCV-specific CD8+ T cells late resolved phase, rep4

source_name: HCV-specific CD8+ T cells from late resolved patient 52

value: late resolved patient 52

value: HCV-specific CD8+ T cells


title: HCV-specific CD8+ T cells late resolved phase, rep3

source_name: HCV-specific CD8+ T cells from late resolved patient 18

value: late resolved patient 18


title: HCV-specific CD8+ T cells late resolved phase, rep2

source_name: HCV-specific CD8+ T cells from late resolved patient 17

value: late resolved patient 17


title: HCV-specific CD8+ T cells late chronic phase, rep6

source_name: HCV-specific CD8+ T cells from late chronic patient 19

value: late chronic patient 19


title: HCV-specific CD8+ T cells late chronic phase, rep7

source_name: HCV-specific CD8+ T cells from late chronic patient 37

value: late chronic patient 37


title: HCV-specific CD8+ T cells late resolved phase, rep1

source_name: HCV-specific CD8+ T cells from late resolved patient 9

value: late resolved patient 9


title: KOP-3R

source_name: KOPN8 cells_non-binding peptide


title: BFUE_Day1_45

source_name: burst forming unit-erythroid

value: 24 hrs

value: No


title: RS4-Y518R

source_name: RS4-11 cells_DPY30-binding peptide

value: MLL-AF4 Leukemia


title: BFUE_Day1_46


title: THP-3R

source_name: THP1 cells_non-binding peptide

value: MLL-AF9 Leukemia


title: THP-Y518R

source_name: THP1 cells_DPY30-binding peptide


title: BFUE_Day1_42

value: BFUE


title: RS4-3R

source_name: RS4-11 cells_non-binding peptide


title: HCV-specific CD8+ T cells late chronic phase, rep5

source_name: HCV-specific CD8+ T cells from late chronic patient 15

value: late chronic patient 15


title: BFUE_Day1_40

value: erythroid progenitor media


title: BFUE_Day1_41


title: HCV-specific CD8+ T cells late chronic phase, rep3

source_name: HCV-specific CD8+ T cells from late chronic patient 13

value: late chronic patient 13


title: MOM-Y518R

source_name: MOLM13 cells_DPY30-binding peptide


title: HCV-specific CD8+ T cells late chronic phase, rep4

source_name: HCV-specific CD8+ T cells from late chronic patient 14

value: late chronic patient 14


title: BFUE_Day1_44


title: HCV-specific CD8+ T cells late chronic phase, rep1

source_name: HCV-specific CD8+ T cells from late chronic patient 6

value: late chronic patient 6


title: HCV-specific CD8+ T cells late chronic phase, rep2

source_name: HCV-specific CD8+ T cells from late chronic patient 8

value: late chronic patient 8


title: HCV-specific CD8+ T cells early self-limited, rep2

source_name: HCV-specific CD8+ T cells from early self-limited  patient 9

value: early self-limited  patient 9

value: HCV-specific CD8+ T cells


title: HCV-specific CD8+ T cells early self-limited, rep4

source_name: HCV-specific CD8+ T cells from early self-limited  patient 17

value: early self-limited  patient 17


title: HCV-specific CD8+ T cells early self-limited, rep1

source_name: HCV-specific CD8+ T cells from early self-limited  patient 7

value: early self-limited  patient 7


title: BFUE_Day1_39


title: BFUE_Day1_43


title: HCV-specific CD8+ T cells early self-limited, rep3

source_name: HCV-specific CD8+ T cells from early self-limited  patient 12

value: early self-limited  patient 12


title: 14967X18: PDX- Breast

city: Salt Lake City

first: Alana

last: Welm

state: utah

address: 2000 Cir of Hope Dr

institute: Huntsman cancer institute

data_processing:
fastq files to the human genome reference (hg38) using STAR ver 2.5.2b
count reads for each gene using feature counts ver. 1.5.1
The gene annotation is taken from Ensembl Homo Sapiens GRCh38
Genome_build: hg38
Supplementary_files_format_and_content: excel files include counts values for each Sample ...

source_name: PDX- Breast

growth_protocol: Tumor fragments (solid tumors) or cell suspensions (PE or ascites, with matrigel) implanted into cleared mammary fat pads of NOD/SCID or NSG mice. Estrogen was supplemented in ER+ cases. See DeRose and Gligorich et al 2013 for detailed methods

extract_protocol:
PDX tumor was removed, flash frozen on dry ice, and RNA was harvested using Qiagen kit . 1 ug of total RNA for the construction of sequencing libraries.
Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 50 Cycle Single-Read Sequencing v4

tag: tissue

value: patient-derived xenograft (PDX) breast tumor

tag: index taga

value: Index 13 AGTCAA

tag: hci - reference  samplename

value: PDX HCI-030, P1


title: HCV-specific CD8+ T cells early chronic phase, rep7

source_name: HCV-specific CD8+ T cells from early chronic patient 37

value: early chronic patient 37


title: 14967X17: PDX- Breast

value: Index 8 ACTTGA


title: HCV-specific CD8+ T cells early chronic phase, rep5

source_name: HCV-specific CD8+ T cells from early chronic patient 15

value: early chronic patient 15


title: HCV-specific CD8+ T cells early self-limited, rep5

source_name: HCV-specific CD8+ T cells from early self-limited  patient 18

value: early self-limited  patient 18


title: HCV-specific CD8+ T cells early chronic phase, rep6

source_name: HCV-specific CD8+ T cells from early chronic patient 19

value: early chronic patient 19


title: MOM-3R

source_name: MOLM13 cells_non-binding peptide

value: MLL-AF9 Leukemia


title: HCV-specific CD8+ T cells early chronic phase, rep8

source_name: HCV-specific CD8+ T cells from early chronic patient 38

value: early chronic patient 38


title: HCV-specific CD8+ T cells early chronic phase, rep4

source_name: HCV-specific CD8+ T cells from early chronic patient 14

value: early chronic patient 14


title: BFUE_Day1_37

source_name: burst forming unit-erythroid

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
cell culture protocol: BFU-E cell culture. FACS-isolated BFU-E enriched cells were cultured for the denoted number of days in progenitor culture media (PCM) consisting of serum free expansion media (SFEM2, Stem Cell Technologies) supplemented with 100 ng/mL murine SCF (Peprotech), 40 ng/mL murine insulin-like growth factor 1 (Peprotech), 2 U/mL human erythropoietin (Amgen), 1% penicillin/streptomycin (Gibco), and for indicated cultures 100 nM Dexamethasone (Sigma).
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

value: BFUE

value: erythroid progenitor media

value: 24 hrs

value: No


title: 14967X16: Patient- Breast

source_name: Patient- Breast

value: breast tumor

value: Index 6 GCCAAT

value: Patient tumor HCI-030


title: BFUE_Day1_36


title: 14967X14: PDX- Breast

value: patient-derived xenograft (PDX) breast tumor

value: Index 9 GATCAG


title: BFUE_Day1_35


title: 14967X15: PDX- Breast

value: Index 11 GGCTAC


title: BFUE_Day1_34


title: BFUE_Day1_38


title: 14967X13: PDX- Breast

value: Index 2 CGATGT


title: BFUE_Day1_33


title: HCV-specific CD8+ T cells early chronic phase, rep1

source_name: HCV-specific CD8+ T cells from early chronic patient 6

value: early chronic patient 6

value: HCV-specific CD8+ T cells


title: 14967X12: PDX- Breast

value: Index 23 GAGTGG


title: HCV-specific CD8+ T cells early chronic phase, rep3

source_name: HCV-specific CD8+ T cells from early chronic patient 13

value: early chronic patient 13


title: BFUE_Day1_32


title: 14967X11: PDX- Breast

value: Index 13 AGTCAA

value: PDX HCI-013 EI (LDEV clean)


title: BFUE_Day1_31

value: BFUE


title: BFUE_Day1_30

value: erythroid progenitor media


title: POR_i1_CD_04

city: Leuven

first: Sare

last: Verstockt

address: O&N4 Herestraat 49 box 610

country: Belgium

institute: KU Leuven

description: Biopsy from ileal mucosa of a post-operative recurrent CD patient (Rutgeerts score i1)

hyb_protocol: Hybridization to GeneChip Human Gene 1.0ST arrays (Affymetrix) was performed at 45°C for 17 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality assessment and outlier detection was performed before and after normalization using the Bioconductor package arrayQualityMetrics. Data were analyzed using the RMA algorithm with the aroma.affymetrix package (R version 3.2.2)

label_protocol: Total RNA (150 ng) was reverse-transcribed into cDNA, followed by the generation of cRNA and ss DNA using the GeneChip WT Synthesis and Amplification kit (Ambion). Fragmented DNA is labeled with biotin (GeneChip WT terminal Labeling kit).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. RNA quality and quantity were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit.

tag: disease

value: Crohn's disease

value: ileum


title: 14967X10: PDX- Breast

value: Index 1 ATCACG

value: PDX HCI-028, P1


title: POR_i1_CD_01

source_name: Biopsy from ileal mucosa of a post-operative recurrent CD patient (Rutgeerts score i1)


title: POR_i1_CD_06


title: POR_CD_21

description: Biopsy from ileal mucosa of a post-operative recurrent CD patient (Rutgeerts score ≥i2b)


title: POR_CD_22

source_name: Biopsy from ileal mucosa of a post-operative recurrent CD patient (Rutgeerts score ≥i2b)


title: 14967X9: PDX- Breast

value: Index 19 GTGAAA

value: PDX HCI-023, P0


title: POR_CD_20


title: POR_i1_CD_03


title: POR_CD_16


title: 14967X8: PDX- Breast

value: patient-derived xenograft (PDX) breast tumor

value: Index 5 ACAGTG

value: PDX HCI-010, Lucs, cells


title: BFUE_Day1_28

value: 24 hrs

value: No


title: BFUE_Day1_29


title: POR_CD_19


title: POR_CD_18


title: POR_CD_17


title: POR_i1_CD_02


title: POR_CD_23


title: POR_CD_14


title: POR_CD_15


title: POR_CD_24


title: POR_CD_11


title: BFUE_Day1_27


title: BFUE_Day1_26


title: HCV-specific CD8+ T cells early chronic phase, rep2

source_name: HCV-specific CD8+ T cells from early chronic patient 8

value: early chronic patient 8

value: HCV-specific CD8+ T cells


title: 14967X5: PDX- Breast

value: Index 18 GTCCGC


title: 14967X6: PDX- Breast

value: Index 25 ACTGAT

value: PDX HCI-026 P0


title: BFUE_Day1_24

value: BFUE

value: erythroid progenitor media


title: 14967X3: PDX- Breast

value: Index 14 AGTTCC


title: 14967X7: PDX- Breast

value: Index 4 TGACCA


title: BFUE_Day1_23


title: 14967X2: PDX- Breast

value: Index 12 CTTGTA


title: BFUE_Day1_22


title: POR_CD_12

value: Crohn's disease

value: ileum


title: POR_CD_13


title: POR_CD_07


title: POR_CD_08


title: POR_CD_06


title: POR_CD_09


title: POR_CD_03


title: POR_CD_04


title: POR_CD_02


title: new_CD_17

description: Biopsy from ileal mucosa of a newly diagnosed CD patient


title: new_CD_18

source_name: Biopsy from ileal mucosa of a newly diagnosed CD patient


title: 14967X4: PDX- Breast

value: patient-derived xenograft (PDX) breast tumor

value: Index 2 CGATGT


title: POR_CD_01


title: OA10

city: Newcastle upon Tyne

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

data_processing:
Illumina CASAVA (1.7.0) was used for the base calling and quality score calculations
FastQC was used to first check quality of the reads.
Quantified using Salmon (0.9.1), against GENCODE v27 (GRCh38)
imported and summarised using tximport in R
Genome_build: GRCh38
Supplementary_files_format_and_content: OA_LengthScaled_TPM.csv.gz

source_name: osteoarthritic cartilage

extract_protocol:
Cartilage samples were ground into powder and homogenized using Invitrogen TRIzol Reagent after which RNA was isolated by RNeasy Kit
cDNA libraries were prepared for sequencing from 5µg of total RNA using Illumina TrueSeq mRNA kits with the manufacturers’ protocols

tag: Sex

value: Female

value: Cartilage

value: Chondrocyte


title: 14967X1: PDX- Breast

source_name: PDX- Breast

value: Index 6 GCCAAT


title: new_CD_16


title: new_CD_14


title: new_CD_15


title: OA9


title: BFUE_Day1_21

address: 455 Main Street

value: 24 hrs

value: No


title: BFUE_Day1_19


title: OA7


title: OA8


title: BFUE_Day1_16


title: new_CD_11


title: new_CD_12


title: BFUE_Day1_17


title: new_CD_08


title: new_CD_09


title: new_CD_13


title: new_CD_10


title: new_CD_06


title: OA6


title: new_CD_07


title: BFUE_Day1_20


title: BFUE_Day1_15


title: OA5


title: new_CD_03


title: BFUE_Day1_18


title: OA4


title: new_CD_05


title: OA3


title: POR_CD_05


title: new_CD_04


title: BFUE_Day1_14


title: BFUE_Day1_13


title: OA2


title: late_CD_13

description: Biopsy from ileal mucosa of a late stage CD patient


title: BFUE_Day1_12


title: OA1


title: new_CD_01


title: new_CD_02


title: BFUE_Day1_11


title: LFLS_EWD_4

city: Oklahoma City

first: Elizabeth

middle: A

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

institute: University of Oklahoma HSC

data_processing:
Reads were trimmed with cutadapt to remove 3' adaptor sequences and low quality 3' bases (Q<10).
Trimmed reads were aligned to both the human (GRCh37) and mouse (GRCm38) genomes using hisat2.
Reads were assigned to either the human or mouse genome using disambiguate and ambiguous reads were discarded.
Unambiguous human reads were assigned to genes using Rsubread’s featureCounts.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-separated gene-level read count matrix

source_name: Breast tumor xenograft

growth_protocol: Tumors were excised from mice and snap frozen in liquid nitrogen

extract_protocol:
RNA was extracted from pulverized tissue using Trizol followed by Qiagen column clean up and DNAse digestion
RNA-seq libraries were prepared from total RNA by the University of Colorado Core using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Tumors were excised from mice fed high fat/high sucrose (HFHS) or low fat/low sucrose (LFLS) diets with and without estradiol supplementation

value: Breast tumor xenograft

tag: xenograft id

value: estrogen withdrawal

tag: diet

value: low fat/low sucrose


title: late_CD_07

source_name: Biopsy from ileal mucosa of a late stage CD patient


title: late_CD_11


title: LFLS_EWD_3


title: BFUE_Day1_10

first: Hojun

last: Li

institute: Whitehead Institute for Biomedical Research

value: BFUE

value: erythroid progenitor media


title: late_CD_08


title: late_CD_09


title: late_CD_10


title: LFLS_EWD_2


title: BFUE_Day1_9


title: BFUE_Day1_8


title: late_CD_12


title: late_CD_04


title: BFUE_Day1_7


title: LFLS_EWD_1


title: LFLS_E2_4

value: estrogen


title: late_CD_03


title: late_CD_06


title: LFLS_E2_3


title: late_CD_01


title: BFUE_Day1_6


title: late_CD_02


title: LFLS_E2_2


title: late_CD_05


title: BFUE_Day1_5


title: i0_CD_02

description: Biopsy from ileal mucosa of a post-operative CD patient (Rutgeert score i0)


title: i0_CD_03

source_name: Biopsy from ileal mucosa of a post-operative CD patient (Rutgeert score i0)


title: BFUE_Day1_4


title: BFUE_Day1_3


title: control_11

description: Biopsy from normal ileal mucosa of control individual

value: normal


title: i0_CD_01

value: Crohn's disease


title: HFHS_EWD_4

value: high fat/high sucrose


title: control_12

source_name: Biopsy from normal ileal mucosa of control individual

value: ileum


title: control_09


title: BFUE_Day1_2


title: control_10


title: HFHS_EWD_3


title: control_08


title: control_06


title: control_04


title: control_07


title: BFUE_Day1_1


title: late_CD_14


title: HFHS_EWD_2


title: LFLS_E2_1


title: 50_60-H8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_23

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 74.
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

source_name: intermediate stages of erythroid development cell with 50-60% expression of CD71/CD24

extract_protocol:
Erythroid progenitor cell isolation: Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).   Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in 0.2% Triton X-100 (Sigma), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).


title: 50_60-H9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_24


title: HFHS_EWD_1


title: control_03


title: control_02


title: Female_DRG_Veh3

city: Richardson

first: Theodore

middle: J

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

description: rRNA depleted RNA

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Then DESeq was used to identify differentially expressing (DE) genes (Anders & Huber, 2010). We considered gene expressions on the medium-to-strong levels, if the maximum mean value of reads for one of groups was >50 per entire read (i.e. 50x106 bp). Basic DE gene analysis focuses on gene(s) of interest (unique gene reads, total gene reads, total exon reads, etc.) and creating statistical charts (heat-map, volcano plots).
Quality control statistical analysis of outliers, intergroup variability, distribution levels, PCA and hierarchical clustering analysis was performed to statistically validate the experimental data.
Pathway analysis was performed with Ingenuity Pathway Analysis software (IPA, Qiagen, CA).
Genome_build: UCSC mouse genome build mm9
Supplementary_files_format_and_content: HTseq gene read counts

source_name: dorsal root ganglion

extract_protocol:
Fresh tissues were homogenized in Rn-easy solution using Bead Mill Homogenizer (Omni International, Kennesaw, GA).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. No: KR1151, KAPA Biosystems, USA). The first step in the workflow involved the depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides, respectively. Following rRNA removal, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library. RNA-Seq libraries were subjected to quantification process by the combination of Qubit and Bioanalyzer, pooled for cBot amplification and subsequent sequenced with 100 bp paired read sequencing run with Illumina HiSeq 3000 platform. After the sequencing run, demultiplexing with CASAVA will be employed to generate the fastq file for each sample.

treatment_protocol: Injected with 20µl Saline into paw

tag: age

value: 8-14 weeks


title: Female_DRG_Veh2

description: rRNA depleted RNA

value: Female


title: Male_DRG_Veh3

description: rRNA depleted RNA

value: Male


title: control_01


title: Female_DRG_Veh1

description: rRNA depleted RNA


title: HFHS_E2_2


title: Male_DRG_Veh2

description: rRNA depleted RNA


title: HFHS_E2_1


title: control_05


title: 50_60-G7

city: Cambridge

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_19


title: Female_paw_Veh1

description: rRNA depleted RNA

source_name: hindpaw tissue


title: Female_paw_Veh2

description: rRNA depleted RNA


title: Male_paw_Veh2

description: rRNA depleted RNA


title: Male_paw_Veh3

description: rRNA depleted RNA


title: 50_60-G8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_20


title: POR_CD_10


title: 50_60-F9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_18


title: HFHS_E2_3


title: 50_60-F8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_17


title: BRG1_KO-2.gene

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

data_processing:
Raw fastq sequences were treated with Trimmomatic tools(v 0.36) using the following options: : TRAILING:20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used to count the reads numbers mapped to each gene. The whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression.
Genome_build: mm10

source_name: colon epithelial cells

growth_protocol: no treatment

extract_protocol:
Total RNA was extracted from cell/tissues using the Trizol (invitrogen) according to the manufacturer’s protocol.
RNA libraries were prepared according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: 1 weeks prior to isolatation of  the colon epethelial cells BRG1F/F and Villin-CreERT2  BRG1F/Fmice are intraperitoneal injected with Tamoxifen and then colon epithelial cells are isolated by EDTA digestion

tag: genotype/variation

value: KO

value: primary colon epithelial cells


title: BRG1_WT-1.gene

value: wild type

tag: cell type


title: BRG1_WT-2.gene

tag: strain


title: 50_60-F7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_16


title: 50_60-H7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_22


title: 50_60-G9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_21


title: Male_DRG_Veh1

description: rRNA depleted RNA


title: 50_60-E9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_15


title: Female_paw_Veh3

description: rRNA depleted RNA


title: HDL + LNA92a + LNA489 10

city: Nashville

first: Kasey

middle: C

last: Vickers

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v1.16
Reads were aligned to the GENCODE GRCm38.p5 genome using STAR v2.5.3a. GENCODE vM12 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
featureCounts v1.15.29 was used to count the number of mapped reads to each gene.
Significantly differential expressed genes with p-value < 0.05 and absolute fold change > 1.5 were detected by DESeq2 (v1.18.1)
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: normalized DESeq2 counts (vsd) and FPKMs

source_name: HDL + LNA92a + LNA489, aortic endothelium

extract_protocol:
RNA from the aortic endothelium was collected by lysing the cells with qiazol. Total RNA was purified with the miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using Nugen Ovation RNA-Seq for model organism kit.

treatment_protocol: Mice received retro orbital injections of either saline, HDL, HDL + LNA92a, HDL + LNA489, or HDL + LNA92a + LNA489 7 weeks after 5/6 nephrectomy surgery. Individual LNAs were administored at 20mg/kg of body weight with 4mg of HDL. Dual LNA treatment was 20mg/kg of body weight for each LNA giving a total of 40mg/kg of LNA per body weight with 4mg of HDL.

tag: genotype

value: Apoe-/-

value: HDL + LNA92a + LNA489

value: Aortic Endothelium


title: BRG1_KO-1.gene


title: 50_60-E8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_14


title: 50_60-E7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_13


title: HDL + LNA489 14

source_name: HDL + LNA489, aortic endothelium

value: HDL + LNA489


title: HDL + LNA92a + LNA489 8


title: HDL + LNA489 19


title: HDL + LNA489 7


title: 50_60-D9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_12


title: HDL + LNA489 13


title: HDL + LNA92a 18

source_name: HDL + LNA92a, aortic endothelium

value: HDL + LNA92a


title: 50_60-D8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_11


title: Male_paw_Veh1

description: rRNA depleted RNA


title: HDL + LNA92a 12


title: HDL + LNA92a 17


title: 50_60-D7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_10


title: 14967X19: PDX- Breast

value: patient-derived xenograft (PDX) breast tumor

value: Index 27 ATTCCT


title: HDL + LNA92a + LNA489 21


title: HDL 11

source_name: HDL, aortic endothelium

value: HDL


title: 50_60-C9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_9


title: HDL + LNA92a + LNA489 15


title: 50_60-C8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_8


title: HDL 4


title: HDL 23


title: Saline 9

source_name: Saline, aortic endothelium

value: Saline


title: HDL 3


title: 50_60-C7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_7


title: Saline 2


title: 50_60-B9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_6


title: HDL + LNA92a 5


title: Saline 24


title: Saline 1


title: 50_60-B7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_4


title: F103NP_NZn31_98 (RNA-seq)

city: Loughborough

first: Sina

last: Fischer

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

institute: University of Nottingham

data_processing:
Data Filtering: 1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read,  we define the low quality base to be the base whose sequencing quality is no more than 5).
Reads Mapping: Bowtie2 [4] to map clean reads to reference gene and use HISAT [3] to reference  genome;  [4] Langmead B, et al. (2009). Ultrafast and memory-efficient alignment of short DNA sequences  to the human genome. Genome Biology, 10(3): 25-34.;  [3] Kim D, Langmead B and Salzberg SL.(2015). HISAT: a fast spliced aligner with low memory  requirements. Nature Methods,12(4):357-60. doi: 10.1038/nmeth.3317
Gene Quantification: use of RSEM [5] to calculate FPKM values;    [5] Li B and Dewey C N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with  or without a reference genome. BMC bioinformatics, 12(1): 323.
DEG definition:  use of the NOISeq method [16];   [16] Sonia Tarazona, et al. (2011). Differential expression in RNA-seq: A matter of depth.  Genome Research, 21:2213–2223.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-35/fasta/brassica_oleracea/dna/
Supplementary_files_format_and_content: files include FPKM values for each Sample

organism: Brassica oleracea

source_name: Plant root

growth_protocol: Hydroponic experiments were performed as follows: Seeds were germinated on the surface of filter paper moistened with deionized water in Petri dishes placed at 16°C in the dark for five days. Six five-day-old seedlings per accession were transferred to a five-litre bucket holding a solution containing 2 mM Ca(NO3)2, 2 mM NH4NO3, 0.75 mM MgSO4, 0.5 mM KOH, 0.1 mM FeNaEDTA, 30 µM H3BO3, 25 µM CaCl2, 10 µM MnSO4,3µM CuSO4 and 0.5 µM Na2MoO4, and either 0.25 mM KH2PO4 (High P treatment) or 0.025 mM KH2PO4 plus 0.225 mM KCl (Low P treatment). Either 1 µM ZnSO4 (High Zn) or no ZnSO4 (Low Zn) was added to each P treatment. Plants were, therefore, subjected to four treatments (Low P & Low Zn, Low P & High Zn, High P & Low Zn and High P & High Zn). The pH was adjusted to 6 in all treatments by addition of H2SO4. Experiments were performed in a glasshouse at the James Hutton Institute (Invergowrie, Scotland, UK, latitude 56°27'22.7" N, longitude 03°04'09.9" W) and lasted two weeks, with one change of the nutrient solution, which was continuously aerated. Buckets were set in a complete randomized design on a single bench. Daytime and night time temperatures were maintained at 24 °C and 18 °C, respectively. Daily irradiance (> 200 W m-2 for 16 h) was obtained by artificial illumination (MASTER SON-T PIA Green Power lamps, Philips, Guildford, UK).

extract_protocol:
Frozen root samples were ground to powder using a pre-cooled pestle and mortar, after which the powdered material was transferred to a 2 ml Eppendorf tube. One mL of Trizol® was added to each sample, shaken thoroughly and incubated at room temperature for 5 min. Subsequently 200µl chloroform were added to each sample after which they were again shaken and incubated for 5 min at room temperature. The samples were centrifuged at 12000×g for 15 min at 4°C and 600µl supernatant was transferred to a new 2 ml Eppendorf tube to which 600µl of isopropanol was added. The Eppendorf tubes were inverted for mixing after which samples were centrifuged at 12000 × g for 15 min at 4 °C. The supernatant was removed and the pellet was rinsed in 700µl 70 % ethanol and dried at room temperature for 10 min before being resuspended in 100 µl of MiliQ water. The RNA was further purified using the ENZO kit (Zymo Research, Irvine, California, USA) following the manufacturer’s instructions. An “On column DNAse treatment” was included and DNA was eluted twice with 100µl of pre-warmed MilliQ water.
Library preparation, SE50 sequencing, data filtering and cleaning, alignments with the reference database (ftp://ftp.ensemblgenomes.org/pub/plants/release-35/fasta/brassica_oleracea/dna/) and gene expression quantification as well as detection of differential gene expression was performed by BGI (https://www.bgi.com/global/) according to their standard analysis pipeline (Fig. S1).

value: Plant root

tag: developmental stage

value: post germination 2weeks

tag: accession

value: NP_NZ (High P & High Zn)


title: F103NP_NZn31_155 (RNA-seq)


title: 50_60-B8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_5


title: 50_60-A9

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_3


title: F103NP_NZn31_65 (RNA-seq)


title: 50_60-A8

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_2


title: F103NP_LZn26_151 (RNA-seq)

value: NP_LZ (High P & Low Zn)


title: F103NP_LZn26_37 (RNA-seq)


title: F103LP_NZn9_120 (RNA-seq)

value: LP_NZ (Low P & High Zn)


title: F103LP_NZn9_116 (RNA-seq)


title: F103LP_LZn12_156 (RNA-seq)

value: LP_LZ (Low P & Low Zn)


title: 50_60-A7

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_50-60_1


title: F103LP_LZn12_142 (RNA-seq)


title: F103LP_LZn12_138 (RNA-seq)


title: 25_35-H6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_24

source_name: intermediate stages of erythroid development cell with 25-35% expression of CD71/CD24


title: C6NP_NZn29_121 (RNA-seq)


title: Dermo1Cre/Mt1-mmp(fl/fl) mammary gland, biological replicate 2

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

description: Gene expression data from intact mammary epithelium-containing inguinal mammary gland tissue harvested from 4-week mice

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 Arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: Data was analyzed using the oligo and limma Bioconductor packages implemented in the R-statistical environment 3.1.1. RMA was used to normalize the data and fit log2 transformed expression values

source_name: Intact inguinal mammary gland

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Intact mammary epithelium-containing inguinal mammary gland tissue was harvested from 4-week-old mice.

extract_protocol: Mammary tissue was flash frozen in liquid nitrogen and homogenized in 1mL TRIzol (Ambion, Life Technologies). Total RNA was extracted with chloroform according to standard protocols and purified with QIAGEN Rneasy Mini-kit columns.

value: 4 weeks


title: C6NP_NZn29_29 (RNA-seq)

value: wild type


title: 25_35-H5

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_23


title: Mt1-mmp(+/+) mammary gland, biological replicate 3


title: F103NP_LZn26_178 (RNA-seq)


title: F103LP_NZn9_137 (RNA-seq)


title: Mt1-mmp(+/+) mammary gland, biological replicate 2


title: 25_35-G6

description:
BFUE_CFUE_andInterm.counts.txt
Intermediate_25-35_21


title: C6NP_LZn6_115 (RNA-seq)


title: C6NP_LZn6_93 (RNA-seq)