title: 28 days homozygous_2

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (4-26-7-53) and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

organism: Danio rerio

source_name: eyes

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: Eye

tag: time point

value: 28 dpf


title: Ci1.D11

status: Public on Dec 01 2019

type: SRA

city: Yokoham

first: Joachim

middle: Felix

last: Luginbühl

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

molecule: total RNA

organism: Homo sapiens

source_name: Chemically induced fibroblasts

growth_protocol: Human dermal fibroblasts were purchased from Lonza (passages 4-8) and cultured in DMEM containing 10% FBS/L-glutamine/10% Penicilin&Streptomycin at 37°C 5% CO2 until virus infection. For TFi generation, a total of 6 MOI (~0.3 MOI per virus) were pooled into culture medium containing 8 mg*ml-1 Polybrene (SIGMA) to increase infection efficiency. The virus pool was infected and incubated overnight at 37°C 5% CO2. On the following day, virus-containing medium was removed and cells were incubated for an additional day in fresh culture medium at 37°C 5% CO2. For iN generation, infected cells were split onto Poly-d-lysine (100μg*ml-1) / Laminin (50μg*ml-1) (SIGMA)-coated culture plates and incubated overnight in culture medium at 37°C 5% CO2. On the following day, medium was changed to neuronal induction medium containing DMEM/F12 and Neurobasal-A (Thermo Fisher Scientific) mixed at a 1:1 ratio, 2% (vol/vol) B27 supplement and 0.5% N2 Supplement (GIBCO), 1x nonessential amino acids (Thermo Fisher Scientific), 1% GlutaMAX supplement, 10ng*ml-1 BDNF (GIBCO), 10ng*ml-1 NT3 (R&D Systems), 10ng*ml-1 GDNF (Thermo Fisher Scientific), VPA (0.5mM, WAKO), L-Ascorbic acid (200nM, SIGMA), Y-27632 (10μM, WAKO), dcAMP (0.5mM, SIGMA), 10% FBS and 10% Penicilin&Streptomycin (WAKO). The concentrations of small molecules used were as follows: CHIR99021 (2μM, Abcam), SB-431542 (10μM, SIGMA), LDN-193189 (0.5μM, Stemgent), Noggin (100ng*ml-1, SIGMA). Neuronal induction medium was changed every third day, during which the concentration of FBS was gradually reduced from 10% to 1%. After 2 weeks, neuronal induction medium was replaced with neuronal maturation medium without small molecules and 1% FBS and the medium was changed every third day until further analysis.

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: cell type

value: Chemically induced fibroblasts

tag: time

value: 9 days after induction

tag: passages

tag: treatment

value: Chemical cocktail of small molecules

tag: batch


title: 28 days homozygous_3

type: RNA

country: USA

tag: tissue

tag: genotype


title: Ishikawa TH131, input

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

description: Peak file from HOMER: Peaks_Ish_6C_inpTH1TH131.txt

library_source: genomic

data_processing:
Reads were mapped to the human reference genome using bowtie version 1.1.2
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 1.3.1
Peak calling was performed by HOMER 4.7.2
Genome_build: hg19
Supplementary_files_format_and_content: peak files from HOMER, text format

molecule: genomic DNA

source_name: Ishikawa cell line, INPUT

extract_protocol:
Libraries from ChIP samples were made with two different kits. With Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation this modifications were used: ligation with of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA. Supplied by Diagenode) library preparatiopn the manufacturer’s instructions were followed.
ThruPLEX, Rubicon Genomics

tag: cell line

value: Ishikawa

tag: chip antibody


title: Control-K9me3-HiChip-Rep2-plus

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

country: China

institute: Tongji University

data_processing:
Library strategy: HiChIP
Hi-Chip paired-end reads were aligned to mm9 reference genome using the HiC-Pro pipeline (Servant et al., 2015) with default set- tings. We converted .all ValidPairs files to .hic files by the script hicpro2juicebox.sh from HiC-Pro utilities. To detect the differences between experiments, we normalized the interaction matrices for each chromosome separately according to the total contacts in each chromosome. This normalization led to the sum of contacts in each chromosome to 1e8.
Genome_build: mm9

organism: Mus musculus

source_name: AML12 shCtrl

growth_protocol: AML12 cells were cultured in  DMEM/F12 supplemented with 10% fetal bovine serum,  ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.

extract_protocol:
The HiChIP of H3K9me3 was performed as described (Mumbach et al., 2016), started with 2.5 millions of AML12 cells for each sam- ple. Briefly, 2.5 millions of cells were digested by 100U of MboI overnight at 37  C. After biotin filling and DNA ligating, the nuclear were resuspended by sonication buffer (1%SDS, 10mM EDTA, 50mM Tris-HCl, 20mM NaBu, 1 3 Proteinase Inhibitor), and chromatin was sheared into 300-700bp using Bioruptor followed by incubating with antibody overnight at 4 C. 25 mL beads were washed once with cold 0.5% BSA, and added into the sheared chromatin-protein supernatant for 2 hours at 4 C. Washed with high salt wash buffer (50mM HEPEs, 500mM NaCl, 1mM EDTA, 0.1%DOC, 1%Triton X-100) three times; low wash buffer (10mM Tris-HCl, 250mM LiCl, 1mM EDTA, 0.5%NP40, 0.5%DOC) twice; TE once. Chromatin-protein complex were eluted for 15min at 65 C in 50 mL elution buffer (1% SDS in TE). After reverse-crosslinking, DNA was extracted using ultrapure phenol/chloroform. Chromatin fragments con- taining biotin were captured by MyOne Streptatvidin beads (ThermoFished 65601), and libraries were prepared on beads using Tn5 from DNA Library Prep Kit V2 (Vazyme TD503) for 30min at 37 C, followed by amplification.
Illumina sequencing library were prepared according to the standard Illumina protocol.

treatment_protocol: The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.

tag: lentivirus

value: shCtrl

tag: antibody


title: 28 days homozygous_1


title: 28 days heterozygous_3


title: Control-K9me3-HiChip-Rep2


title: Ci1.D10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 28 days heterozygous_2


title: 28 days heterozygous_1


title: Ishikawa TH1, input

extract_protocol:
Libraries from ChIP samples were made with two different kits. With Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation this modifications were used: ligation with of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA. Supplied by Diagenode) library preparatiopn the manufacturer’s instructions were followed.
Illumina TruSeq™ DNA Sample Preparation


title: Ishikawa TH57, FoxA1 ChIP

source_name: Ishikawa cell line, FOXA1-CHIP

value: FoxA1 rabbit ab23738 (lot GR292351-2)


title: Ci1.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: SW1783.TCF4_Wnt

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to hg19 genome using bowtie v1.1.2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS 1.4.2

source_name: SW1783 cells

growth_protocol: SW1783 cell lines were grown in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum (HyClone)

extract_protocol:
The method for chromatin immunoprecipitation was described as ChIP assay kit (Cell Signaling Technology), while the agarose beads were replaced by magnetic beads.
Indexed libraries were prepared from 6ng-20ng of Diagenode Biorupter sheared ChIP DNA using the KAPA Hyper Library Preparation Kit (Kapa Biosystems, Inc).  Libraries were amplified by 6 cycles of PCR then assessed for quality using the Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analyticals) and quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher).

treatment_protocol: SW1783 cells were treated with 50 ng/mL Wnt-3a for 4 hours before collection.

value: Wnt treatment

value: TCF4 antibody (Cell signaling, #2569)


title: Control-K9me3-HiChip-Rep1


title: Control-K9me3-HiChip-Rep1-plus


title: SAFB-K9me3-HiChip-Rep1

source_name: AML12 shSafb

value: shSafb


title: SW1783.IgG

value: IgG control (Cell signaling,  #2729)

value: Rabbit IgG


title: Ci1.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: RBMXOverexpr_POL_Rep3

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then mapped to hg19 transcriptome using TopHat v2.0.13 with default parameters
FPKMs were computed on a per-gene basis with the Cuffnorm program of the Cufflinks suite v2.2.1, providing the UCSC transcripts annotations
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HEK293 cells

growth_protocol: HEK-293 cells were cultured in DMEM with 10% FBS, 100 U/ml penicillin–streptomycin and 0.01 mM l-glutamine (all media ingredients were obtained from Gibco® Thermo Fisher scientific, Waltham, MA USA). Cultures were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Once the 80% confluence was reached, cells were incubated for 3–4 min with 10 µg/ml cycloheximide at 37°C  to block translational elongation. Cells were washed with PBS + 10 µg/ml cycloheximide and scraped directly on the plate with 300 µl lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM Tris-HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor [Fermentas  Burlington, CA], 10 µg/ml cycloheximide, 5 U/mL Dnase I [New England Biolabs, Hitchin, UK] and 1 mM DTT) and transferred to a tube. Nuclei and cellular debris were removed by centrifugation for 5 min at 13,000 g at 4°C. The polysome-containing lysate was stored at -80 °C or directly layered onto a linear sucrose gradient (15–50% sucrose (w/v), in 30 mM Tris–HCl at pH 7.5, 100 mM NaCl, 10 mM MgCl2) and centrifuged in a SW41Ti rotor (Beckman Coulter, Indianapolis, IN) at 4 °C for 100 min at 180,000 g. Ultracentrifugation allows the polysome separation according to the sedimentation coefficient of macromolecules. After ultracentrifugation, gradients can be fractionated and mRNAs in active translation, corresponding to polysome containing fractions, separated from untranslated mRNAs. Fractions of 1 mL volume were collected with continuous monitoring absorbance at 254 nm. Total RNA was obtained by pooling together a fixed amount (20%) of  each collected fraction. To extract RNA,  polysomal and total fractions were  treated directly with 0.1 mg/ml proteinase K (Euroclone,  Italy) for 2 h at 37°C. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of RNAse-free water. Both total RNA and polysome RNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity and quantified using the QBit.
RNA libraries were prepared for sequencing using standard Illumina protocols: Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total or polysomal RNA.

treatment_protocol: 1.5 × 106 HEK cells were seeded into two 10-cm Petri dishes for total and polysomal RNA extractions and were transiently transfected using Lipofectamine2000 (Invitrogen, Thermo Fisher scientific, Waltham, MA USA) with 2µg of pCMV6-HIS-HA-RBMX and with the mock empty vector as control.

tag: genotype/variation

value: RBMX overexpression

tag: extracted molecule type

value: polysomal RNA


title: RBMXOverexpr_POL_Rep2


title: spo11delta Mlh3-Myc8 ChIPseq_5h30_2

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were aligned to the Saccer2 version (SGD June 2008) of the S. cerevisiae S288C genome, using Bowtie, allowing for 2 mismatches. Reads that matched more than once in the genome or matching to mitochondrial or ribosomal DNA were eliminated from further analysis.
Aligned and extended paires-end reads were then normalized using a custom script as follows: for normalization, for the untagged control (or spo11∆ control for Mlh3-Myc samples), the top and bottom outliers of the distribution (Q3+1.5IQR and Q1-1.5IQR, respectively) were removed. The average read number per position (coverage) of the remaining reads of the control was then normalized to 1 (scaled untagged control). Similarly, top and bottom outliers of the distribution were removed from the average read number in the samples. Average coverage for the remaining reads was then calculated for the sample and control at the same positions. This was used to compute the sample/ control ratio. Then all reads of the sample were scaled using this ratio (scaled tagged control).
Both scaled sample and control were converted to big wig format, and the scaled control was substracted from the scaled sample.
Signal smoothing was performed on the normalized and control-subtracted bigwig files using a custom script employing fast Fourier transform convolution with a sliding window of 200 bp. The script is available upon request.
Genome_build: Saccer2
Supplementary_files_format_and_content: bigwile format files (more details in the readme.txt)

organism: Saccharomyces cerevisiae

source_name: SK1 meiotic cells t=5h30 (pCUP1-IME1-synchronized meiosis)

growth_protocol: For synchronous meiosis, cells were either grown in SPS presporulation medium and transferred to 1% potassium acetate with vigorous shaking at 30˚C (for anti-Flag samples) or grown in "semi-YPD" then transferred to sporulation medium and induced to undergo meiosis upon Cu++ addition after two hours (Mlh3-Myc samples).

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq procedure.
Libraries were sequenced on a HiSeq2500 apparatus generating paired-end 50 bp reads.

treatment_protocol: 1. 10^9 cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and chromatin immunoprecipitation was performed as described (De Muyt et al (2018) Genes and Development 32, 283-296)

tag: strain

value: c-Myc monoclonal antibody (9E10, Santa Cruz)


title: SW1783.KDM4C_Wnt

value: KDM4C antibody (Bethyl Laboratories, A300-885A)


title: ChIP-seq AML12 shCtrl-1

data_processing:
We aligned paired-end reads to the mm9 reference using Bowtie2.
We called broad domains using RSEG (Song and Smith, 2011), and retained regions that were more than 100 kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ChIP-seq signal for each replicate.

extract_protocol:
The H3K9me3 ChIP-seq was performed as described (PMID: 19151716 ).
Illumina sequencing library were prepared according to the standard Illumina protocol.

treatment_protocol: Aml12 cells were collected after infected with shCtrl or shSAFB lentivirus 5 days


title: ChIP-seq AML12 shCtrl-2


title: ChIP-seq AML12 shSafb-1

source_name: AML12 Safb KD (shSafb)


title: Ci1.D04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.D01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: RBMXOverexpr_TOT_Rep1

value: total RNA


title: WT_POL_Rep3

value: wild type


title: RBMXOverexpr_TOT_Rep2


title: RBMXOverexpr_POL_Rep1


title: RBMXOverexpr_TOT_Rep3


title: spo11delta Mlh3-Myc8 ChIPseq_5h30_1


title: spo11delta Mlh3-Myc8 ChIPseq_5h

source_name: SK1 meiotic cells t=5h (pCUP1-IME1-synchronized meiosis)


title: Mlh3-Myc8 ChIPseq_5h


title: exo1-nd Mlh3-Myc8 ChIPseq_5h30


title: ChIP-seq AML12 shSafb-2


title: Mlh3-Myc8 ChIPseq_5h30


title: untagged_antiFlag ChIPseq

source_name: SK1 meiotic cells t=4h

value: FLAG monoclonal antibody M2 (Sigma)


title: Ci1.C12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction


title: Mer3-Flag ChIPseq_2


title: Ci1.C10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: Hi-C AML12 shSafb-1 AML12

data_processing:
Raw HiC data were processed through the HiC-Pro pipeline (PMID: 26619908) (including read mapping/binning/ICE correction).
hic files were generated using HiC-Pro script: hicpro2juicebox.sh
Genome_build: mm9
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution.

source_name: Safb KD (shSafb)

extract_protocol:
Hi-C was carried out according to the protocol (PMID: 25497547). Briefly, Five million cells were crosslinked with 1% formaldehyde for 10min at room temperature, and then the cells were divided into two tubes, taking one tube for the subsequent experiments, the cells were permeabilized with 0.2% Igepal CA630, and then the pelleted nuclei were treated with 0.5% SDS. The chromatin was digested with 100 units of MboI overnight, the DNA ends were marked by biotinylated nucleotides, After reversal of crosslinks, the DNA was sheared to a size of 300-500bp, and then the ligated DNA was pull-down by streptavidin magnetic beads.
Illumina sequencing library were prepared according to the standard Illumina protocol.


title: Validation_miseq_Undetermined

city: Stanford

first: Christina

last: Smolke

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

description:
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
final_means_ids_added.csv

data_processing:
Library strategy: FACS-seq
Base-calling: default FASTQ output from Illumina bcl2fastq
Paired-end alignment (Miseq data only): PEAR 0.9.6 with flags -j 8 -v 1 -g 2 -n 20
Consensus sequence extraction (Miseq only): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_align.py)
Read table construction (Nextseqs and validation Miseq): scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/build_table_exact.py)
Mean extraction: scripts to be deposited at github.com/smolkelab/promoter_design (mean_extraction/mean_fitting_likelihood_cuda.py)
Genome_build: not applicable – artificial sequence
Supplementary_files_format_and_content: means_nextseq_*.csv: comma-delimited table. No header – first column sequence, second column promoter activity in replicate A (GPD) or uninduced condition (others), third column activity in replicate B (GPD) or induced condition (others).
Supplementary_files_format_and_content: filtered_read_table_miseq_*.txt: comma-delimited table. No header – first column sequence, second column group identifier (from intermediate processing steps), following columns read counts in each bin, as assigned by ‘barcode_miseq_*.csv’ key tables in deposited code
Supplementary_files_format_and_content: final_means_ids_added.csv: comma-delimited table. “Seqs”: sequence.  “Means_A”: promoter activity, uninduced. “Means_B”: promoter activity, induced. “Experiment”: numerical ID of artificial promoter set this sequence is part of (cf. text Supplementary Tables 1 and 2), “None” if a mutant/mis-assembled sequence. “Design”: numerical ID of sequence within its “Experiment”, -1 if “Experiment” is None.

organism: synthetic construct

source_name: Synthetic promoter reporter gene assay

growth_protocol: Cells were grown in yeast nitrogen base media with 2 percent dextrose, lacking uracil, for three passages after library transformation. Passages were always at least 10 OD600*mL units.

extract_protocol:
Model-derived artificial promoters ordered from Twist Bioscience as an oligo pool; to join two Twist oligos to form each designed sequence, subpools were selectively amplified with designed primers, and sequences were specifically joined using complementary Golden Gate assembly sites.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.

treatment_protocol: 1 micromolar beta-estradiol was added to culture media in the “induced” condition 18 hours presort.

tag: plasmid type

value: Synthetic promoter driving reporter gene


title: Hi-C AML12 shSafb-2 AML12


title: Hi-C AML12 shCtrl-2

source_name: shCtrl AML12

value: shCtrl


title: Mer3-Flag ChIPseq_1


title: Ci1.C09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Hi-C AML12 shCtrl-1


title: Ci1.C08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.C07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_induced_R


title: WT_TOT_Rep1


title: WT_POL_Rep1


title: WT_TOT_Rep2


title: WT_TOT_Rep3


title: 7 days homozygous_3

value: Eye

value: 7 dpf


title: WT_POL_Rep2


title: Validation_miseq_induced_12


title: SAFB_RIPseq_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads from RIP-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
To define enriched RNA, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union. Fold-change and p values were calculated by the R package DESeq2.
To quantify the abundance of RNA, we acquired the transcripts per million (TPM) using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including TPM values for each replicate.

source_name: AML12 SAFB

extract_protocol:
Collect the IP product and extract the RNA, and then digesting the RNA with DNase I for 30 min in 37℃ (Thermo, EN0523). Extract the RNA again and reverse transcript RNA using PrimeScript RT Master Mix (Takara RR036A).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).

treatment_protocol: AML12 cells were cultured in 15cm dish per sample and UV-cross using 4000J. Then collect the cells from dish, extract nucleus, lysate nucleus and sonication. Take out 50ul supernatant as input and divide the rest of the supernatant into two parts incubating with anti-IgG (CST 2729) and anti-SAFB(Bethly A300-812A), respectively in 4℃, overnight.

value: anti-SAFB(Bethly A300-812A)

tag: molecule

value: nuclear RNA


title: SAFB_RIPseq_rep1


title: IgG_RIPseq_rep1

source_name: AML12 IgG

value: anti-IgG (CST 2729)


title: IgG_RIPseq_rep2


title: Ci1.C11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 7 days homozygous_1

source_name: eyes

tag: time point


title: 7 days heterozygous_3


title: 7 days heterozygous_2


title: 7 days homozygous_2


title: 7 days heterozygous_1


title: Validation_miseq_induced_11


title: Validation_miseq_induced_10


title: Ci1.C06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts

tag: cell type


title: Ci1.C04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: time


title: Validation_miseq_induced_9


title: Ci1.C03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: passages


title: Validation_miseq_induced_8


title: Validation_miseq_induced_7


title: Ci1.C02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: treatment


title: Validation_miseq_induced_6


title: Validation_miseq_induced_5


title: Ci1.C05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: batch


title: Ci1.B12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_induced_4


title: Ci1.B11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Brown adipocyte, Z16078526 3

city: Los Angeles

first: laurent

last: vergnes

address: 695 Charles E Young Dr south

department: Human Genetics

institute: University of california, Los Angeles

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: The data were normalized using quantile normalization with GenomeStudio

label: biotin

source_name: brown adipocyte

label_protocol: Standard Agilent protocol

growth_protocol: Cells were differentiated for 8 days.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated for 18 h with DMSO vehicle or 10 µM Z16078526

value: brown adipocyte


title: Colon_C57_Cow milk_High [US81303224_251486832016_S01_GE2-v5_95_Feb07_1_3]

city: Palmerston North

first: Anna

last: Moore

address: Tennent Drive

country: New Zealand

institute: AgResearch Ltd

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed. All steps were performed according to the manufacturer instructions - protocol G4140-90050_Two-Color_GE_5.7.

scan_protocol: Scanned on an Agilent G2565AA scanner and images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Cy5 and Cy3 intensity ratios for all microarray spots were normalized using a global loess algorithm using the limma package in R 2.14.1.  No background correction was applied. Spots that did not pass quality control metrics were flagged and removed from the normalisation calculations.

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

label_protocol: 500 ng total RNA was amplified according to the Agilent protocol protocol G4140-90050_Two-Color_GE_5.7.

growth_protocol: Male mice of C57BL/6J background with or without IL10 gene knockout were kept in conventional conditions (not germ-free or specific-pathogen-free) from approximately 5 weeks of age and inoculated with a mixture of Enteroccocus strains and complex intestinal flora harvested from C57BL/6J mice kept in conventional conditions. Mice were fed AIN76A diet and euthanased by CO2 followed by cervical dislocation.

extract_protocol: Total RNA was extracted from frozen colon samples using the Qiagen Allprep kit according to the manufacturer instructions.

value: Swiss

tag: tissue

source_name: Colon C57 mouse, Cow milk diet, High histology score

tag: background strain

value: wildtype

tag: diet

value: Cow milk

value: Colon

tag: colon histology score level within group

value: High


title: Ci1.C01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.B10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Brown adipocyte, Z16078526 2


title: Colon_IL10_Cow milk_Low [US81303224_251486832015_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon IL10 mouse, Cow milk diet, Low histology score

value: IL10 knockout

value: Low


title: Colon_C57_Sheep milk_High [US81303224_251486832016_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, Sheep milk diet, High histology score

value: Sheep milk


title: Brown adipocyte, DMSO vehicle 4

value: control


title: Colon_IL10_AIN76A_Low [US81303224_251486832016_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon IL10 mouse, AIN76A diet, Low histology score


title: Brown adipocyte, Z16078526 4


title: Colon_IL10_ModifiedAIN76A_High [US81303224_251486832016_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon IL10 mouse, ModifiedAIN76A diet, High histology score


title: Brown adipocyte, Z16078526 1


title: Brown adipocyte, DMSO vehicle 2


title: Validation_miseq_induced_2

value: Synthetic promoter driving reporter gene


title: Ci1.B09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction

value: Chemical cocktail of small molecules


title: Brown adipocyte, DMSO vehicle 1


title: Brown adipocyte, DMSO vehicle 3


title: Arabidopsis leaves_ago1-27_Dark 12h_Replicate 3

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

institute: Sant'Anna School of Advanced Studies

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Microarray Suite 5.0

organism: Arabidopsis thaliana

label_protocol: GeneChip  3' IVT PLUS Reagent Kit

growth_protocol: Arabidopsis plants grown in pots with soil

extract_protocol: Total RNA was extracted as previously described (Perata et al., Plant Cell, 1997) with a minor modiﬁcation (omission of aurintricarboxylic acid)

treatment_protocol: Plants were submerged in tanks with a water level of 10 cm above leaf level. The submergence treatment (12h) was carried out in the dark.

tag: organ

value: Leaves

tag: age

value: 4 weeks old

tag: ecotype

value: ago1-27 mutant

value: Dark


title: Colon_IL10_Sheep milk_High [US81303224_251486832015_S01_GE2-v5_95_Feb07_1_2]

value: Swiss

source_name: Colon IL10 mouse, Sheep milk diet, High histology score

tag: genotype/variation


title: Ci1.B08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_induced_1


title: Arabidopsis leaves_ago1-27_Dark 12h_Replicate 2


title: Colon_C57_Soy_Low [US81303224_251486832015_S01_GE2-v5_95_Feb07_1_3]

tag: strain

source_name: Colon C57 mouse, Soy diet, Low histology score

value: wildtype

value: Soy


title: Ci1.B07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_uninduced_R

tag: plasmid type


title: Colon_C57_Goat milk_Low [US81303224_251486832015_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon C57 mouse, Goat milk diet, Low histology score

value: Goat milk

value: Colon


title: Colon_C57_ModifiedAIN76A_High [US81303224_251486832014_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, ModifiedAIN76A diet, High histology score

value: High


title: Arabidopsis leaves_ago1-27_Submerged 12h_Replicate 3

value: Submergence in the dark


title: Validation_miseq_uninduced_12

source_name: Synthetic promoter reporter gene assay


title: Validation_miseq_induced_3


title: Arabidopsis leaves_ago1-27_Dark 12h_Replicate 1


title: Colon_IL10_Soy_High [US81303224_251486832014_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon IL10 mouse, Soy diet, High histology score

value: IL10 knockout


title: Colon_C57_AIN76A_Low [US81303224_251486832014_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, AIN76A diet, Low histology score

value: Low


title: Colon_IL10_Goat milk_Low [US81303224_251486832014_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon IL10 mouse, Goat milk diet, Low histology score


title: Ci1.B05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts


title: Validation_miseq_uninduced_10

value: Synthetic promoter driving reporter gene


title: Validation_miseq_uninduced_9


title: Ci1.B03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction

value: Chemical cocktail of small molecules


title: Ci1.B02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Ci1.B06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_uninduced_11


title: Validation_miseq_uninduced_8


title: Ci1.B01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Validation_miseq_uninduced_7


title: Ci1.A12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Sheep milk_Low [US81303224_251486822453_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon IL10 mouse, Sheep milk diet, Low histology score

value: Sheep milk


title: Colon_IL10_ModifiedAIN76A_Low [US81303224_251486822453_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon IL10 mouse, ModifiedAIN76A diet, Low histology score


title: Ci1.A11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts


title: 30_P_5

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: Canis_familiaris/Ensembl/CanFam3.1/Annotation/Version-2015-05-20
Supplementary_files_format_and_content: text files holding match counts per gene

organism: Canis lupus familiaris

source_name: Corpus luteum

extract_protocol:
Following surgical ovariectomy, corpora lutea were trimmed from surrounding tissue. Rinsed with phosphate-buffered saline (PBS) solution and immersed in RNA®later for 24h at 4oC. After 24h, tissue material was divided and stored in -80oC until further usage. RNA was isolated using Trizol reagent, following the manufacturer’s recommendations.
Illumina TruSeq RNA Sample Prep Kit v2 was used with 100-1000ng/per sample of total RNA for the construction of sequencing libraries.
RNA-seq polyA-selection

treatment_protocol: Starting at the day of ovulation (day 0), dogs were treated orally with 10mg/kg daily with firocoxib. Treatment was maintained for 5, 10, 20 and 30 days after ovulation. Control groups received for similar periods a placebo.

value: Corpus luteum

tag: day after ovulation

value: Day 30

value: firocoxib-treated


title: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 2

value: Leaves

value: 4 weeks old

value: wild type

value: Dark


title: Colon_C57_AIN76A_High [US81303224_251486822453_S01_GE2-v5_95_Feb07_1_1]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

value: Swiss

source_name: Colon C57 mouse, AIN76A diet, High histology score

value: wildtype

value: Colon


title: Arabidopsis leaves_ago1-27_Submerged 12h_Replicate 1

value: ago1-27 mutant

value: Submergence in the dark


title: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 1


title: Arabidopsis leaves_Wild-Type_Dark 12h_Replicate 3


title: Colon_C57_Sheep milk_Low [US81303224_251486822452_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Sheep milk diet, Low histology score

value: Low


title: Arabidopsis leaves_Wild-type_Submerged 12h_Replicate 3


title: Validation_miseq_uninduced_5

value: Synthetic promoter driving reporter gene


title: 30_P_4


title: Validation_miseq_uninduced_6


title: Colon_IL10_Goat milk_High [US81303224_251486822453_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon IL10 mouse, Goat milk diet, High histology score

value: IL10 knockout

value: Goat milk

value: High


title: Validation_miseq_uninduced_4


title: Colon_C57_ModifiedAIN76A_Low [US81303224_251486822452_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, ModifiedAIN76A diet, Low histology score


title: Colon_IL10_Cow milk_High [US81303224_251486822452_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon IL10 mouse, Cow milk diet, High histology score

value: Cow milk


title: 30_P_2

value: Corpus luteum

value: Day 30

value: firocoxib-treated


title: Colon_C57_Goat milk_High [US81303224_251486822452_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon C57 mouse, Goat milk diet, High histology score


title: Validation_miseq_uninduced_3


title: Colon_C57_Soy_High [US81303224_251486822451_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon C57 mouse, Soy diet, High histology score

value: Soy


title: Ci1.A09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts

value: 9 days after induction

value: Chemical cocktail of small molecules


title: Arabidopsis leaves_Wild-type_Submerged 12h_Replicate 2

value: Leaves

value: 4 weeks old

value: wild type


title: Ci1.A08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Arabidopsis leaves_Wild-type_Submerged 12h_Replicate 1

value: Submergence in the dark


title: Validation_miseq_uninduced_1


title: 30_K_2

value: Control


title: Ci1.A07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 30_K_3


title: Ci1.A06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_Undetermined

description:
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
filtered_read_table_miseq_ZEV.txt

extract_protocol:
PCR amplicons from random oligonucleotide pools, joined by Golden Gate assembly at constant regions encoding transcription factor binding sites based on the PZEV artificial promoter system.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.

value: Synthetic promoter driving reporter gene


title: ZEV_miseq_induced_X


title: Ci1.A05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 20_P_3

value: Day 20


title: ZEV_miseq_induced_R


title: Colon_IL10_AIN76A_High [US81303224_251486822451_S01_GE2-v5_95_Feb07_1_3]

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon IL10 mouse, AIN76A diet, High histology score

value: IL10 knockout

value: Colon


title: Ci1.A04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 30_K_4

value: Corpus luteum

value: Day 30


title: 20_P_2

value: firocoxib-treated


title: Ci1.A03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemically induced fibroblasts


title: Validation_miseq_uninduced_2

source_name: Synthetic promoter reporter gene assay


title: 20_K_3


title: ZEV_miseq_induced_12


title: Ci1.A02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: 9 days after induction


title: Colon_C57_ModifiedAIN76A_High [US81303224_251486822450_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon C57 mouse, ModifiedAIN76A diet, High histology score

value: wildtype

value: High


title: Ci1.A01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Chemical cocktail of small molecules


title: Colon_IL10_Sheep milk_Low [US81303224_251486822450_S01_GE2-v5_95_Feb07_1_2]

value: Sheep milk

value: Low


title: Colon_IL10_Soy_Low [US81303224_251486822451_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon IL10 mouse, Soy diet, Low histology score

value: Soy


title: 20_K_2

value: Control


title: 20_K_1

value: Day 20


title: Colon_C57_Goat milk_Low [US81303224_251486822450_S01_GE2-v5_95_Feb07_1_3]

value: Swiss

source_name: Colon C57 mouse, Goat milk diet, Low histology score

value: Goat milk


title: FIB.H12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts

value: Fibroblasts

value: before induction

value: No treatment


title: ZEV_miseq_induced_9

value: Synthetic promoter driving reporter gene


title: Ci1.A10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Cow milk_High [US81303224_251486822450_S01_GE2-v5_95_Feb07_1_1]

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: IL10 knockout

value: Cow milk

value: Colon


title: FIB.H11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_C57_Cow milk_Low [US81303224_251486822451_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon C57 mouse, Cow milk diet, Low histology score

value: wildtype


title: 10_P_5

value: Corpus luteum

value: Day 10

value: firocoxib-treated


title: Colon_C57_Sheep milk_Low [US81303224_251486822449_S01_GE2-v5_95_Feb07_1_3]

value: Sheep milk

value: Low


title: Colon_C57_AIN76A_Low [US81303224_251486822449_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, AIN76A diet, Low histology score


title: 10_P_4

source_name: Corpus luteum


title: FIB.H10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_induced_11


title: ZEV_miseq_induced_8-2


title: ZEV_miseq_induced_10


title: 10_P_1


title: FIB.H09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_induced_7


title: 10_K_4

value: Control


title: FIB.H08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_induced_6


title: 10_K_3


title: FIB.H07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 10_K_2


title: FIB.H06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_induced_8-1


title: ZEV_miseq_induced_4


title: ZEV_miseq_induced_5


title: FIB.H05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_induced_3


title: Colon_IL10_AIN76A_High [US81303224_251486822415_S01_GE2-v5_95_Feb07_1_3]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

value: Swiss

value: High


title: Colon_C57_Cow milk_Low [US81303224_251486822415_S01_GE2-v5_95_Feb07_1_1]


title: FIB.H04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts


title: ZEV_miseq_induced_2


title: FIB.H03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: before induction


title: 5_P_2

value: Day 5


title: Colon_IL10_ModifiedAIN76A_Low [US81303224_251486822449_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon IL10 mouse, ModifiedAIN76A diet, Low histology score


title: Colon_C57_Soy_High [US81303224_251486822415_S01_GE2-v5_95_Feb07_1_2]

value: Soy


title: Colon_IL10_Goat milk_High [US81303224_251486822415_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

value: Goat milk


title: ZEV_miseq_induced_1

value: Synthetic promoter driving reporter gene


title: Colon_IL10_Soy_High [US81303224_251486822449_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon IL10 mouse, Soy diet, High histology score

value: IL10 knockout

value: Colon


title: 5_P_5

value: Corpus luteum


title: ZEV_miseq_uninduced_R


title: 5_P_4


title: ZEV_miseq_uninduced_12


title: Colon_IL10_Sheep milk_High [US81303224_251486822414_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon IL10 mouse, Sheep milk diet, High histology score


title: 5_K_4


title: FIB.H02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: No treatment


title: Colon_C57_ModifiedAIN76A_Low [US81303224_251486822414_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, ModifiedAIN76A diet, Low histology score

value: wildtype


title: ZEV_miseq_uninduced_11


title: Ci1.B04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Chemically induced fibroblasts

value: Chemically induced fibroblasts

value: 9 days after induction

value: Chemical cocktail of small molecules


title: Colon_IL10_Goat milk_Low [US81303224_251486822414_S01_GE2-v5_95_Feb07_1_1]

value: Swiss

source_name: Colon IL10 mouse, Goat milk diet, Low histology score

value: Low


title: 5_K_3

value: Control


title: FIB.G11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction


title: Colon_IL10_Soy_Low [US81303224_251486822413_S01_GE2-v5_95_Feb07_1_3]

value: Soy


title: 5_P_1

value: Day 5

value: firocoxib-treated


title: 5_K_1


title: ZEV_miseq_uninduced_10

value: Synthetic promoter driving reporter gene


title: Colon_C57_Goat milk_High [US81303224_251486822413_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Goat milk diet, High histology score

value: Goat milk

value: High


title: FIB.G10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: No treatment


title: ZEV_miseq_uninduced_9


title: FIB.G09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: F1, FnyCMV-D

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum lycopersicum x Solanum habrochaites

source_name: shoot apex

growth_protocol: the plants were grown in Conviron Chambers set at 28 and 22°C ( day and ngiht, respectively) with 16 hours of light

extract_protocol:
total RNA was extracted using Tri-reagent and 1.5 ug of total RNA was used for small RNA library construction using Illumina sRNA construction kit version 1.5
Illumina compatible method using standard Illumina adapters

treatment_protocol: the seedlings at 2-3 leaf stage were inoculated with viral RNA. The apical part of the plants were harvested at 9-10dpi.

tag: infection status

value: infected with Cucumber mosaic virus and D satellite RNA

value: shoot apex


title: FIB.G12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

extract_protocol: Single cell RNA-seq analysis was performed using the Fluidigm C1 platform following the manufacturer’s protocol (P100-7168L1, Fluidigm). Briefly, cell number and cell viability were assessed using the Countess II Automated Cell Counter (ThermoFisher). After priming medium size C1 Single-cell Open App IFCs, 250 cells/μL were loaded and capture efficiency and cell morphology was assessed using the IN Cell Analyzer 6000 (GE Healthcare). To exclude chambers loaded with no cells, more than one cell (cell doublets) or dead cells for downstream analysis, we took 11 z-stacking images per chamber. Next, cells were lysed with 20,000-fold diluted ERCC RNA Spike-In Mix1 (L/N 00329960 Life Technologies) and reverse transcription (RT) and cDNA amplification were performed using the SMARTer Ultra Low RNA Kit for the Fluidigm C1TM System (Clontech). The amplified cDNAs were harvested into 96 well plates and quantified with Quant-iT TM  PicoGreen dsDNA Assay kit. Library preparation was performed with the Nextera XT DNA Library Preparation kit (Illumina), Nextera XT Index Kit v2 (Illumina) and AMpure XP beads (Beckman Coulter). Libraries were quantified by High Sensitivity DNA Reagents (Agilent Technologies) and KAPA Library Quantification kit (KAPA BIOSYSTEMS).

tag: cell type


title: ZEV_miseq_uninduced_8-2

source_name: Synthetic promoter reporter gene assay


title: ZEV_miseq_uninduced_8-1


title: FIB.G08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: time


title: FIB.G07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: passages


title: Colon_IL10_Cow milk_Low [US81303224_251486822412_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon IL10 mouse, Cow milk diet, Low histology score

value: IL10 knockout

value: Cow milk

value: Colon


title: ZEV_miseq_uninduced_7


title: FIB.G06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: treatment


title: Colon_C57_Soy_Low [US81303224_251486822413_S01_GE2-v5_95_Feb07_1_1]

value: Swiss

source_name: Colon C57 mouse, Soy diet, Low histology score

value: wildtype

value: Low


title: Colon_IL10_ModifiedAIN76A_High [US81303224_251486822413_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon IL10 mouse, ModifiedAIN76A diet, High histology score


title: ZEV_miseq_uninduced_6


title: FIB.G05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts

value: Fibroblasts

value: before induction

tag: batch


title: ZEV_miseq_uninduced_5


title: Arabidopsis leaves_ago1-27_Submerged 12h_Replicate 2

value: Leaves

value: 4 weeks old

value: ago1-27 mutant

value: Submergence in the dark


title: Colon_C57_Cow milk_High [US81303224_251486822412_S01_GE2-v5_95_Feb07_1_3]

tag: tissue

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Cow milk diet, High histology score


title: S126 F1 OVER BIRTH

city: Storrs

first: Kriste

middle: E

last: Govoni

state: CT

address: 3636 Horsebarn Road Ext., Unit 4040

department: Animal Science

institute: University of Connecticut

description:
S126-F1-OD1_S9
126F1_OVER_birth

data_processing:
Quality control (QC) was performed using Sickle to eliminate sequences that were ≤ 35 bp in length and had a Phred score ≤ 35. Paired ends reads of 150 base pairs and a Q score of ³ 30 were used for analysis.
Genome_build: Ovis Aries V.4.0
Supplementary_files_format_and_content: Excel file with raw counts by sample and gene

organism: Ovis aries

source_name: F1 OVER BIRTH

extract_protocol:
Longissimus dorsi tissue samples were collected from a subset of male fetuses at day 90 (n = 11, CON = 4, OVER = 3, RES = 4), day 135 (n =10, CON = 3, OVER = 3, RES = 4) and lambs at birth (n = 11, CON = 4, OVER = 4, RES = 3) and stored at -80°C until RNA-seq analyses. RNA was isolated as described in Reed et al. (2014). Briefly, tissue was homogenized in 1 mL Qiazol using a Qiagen Tissuelyser (Qiagen, Valencia, CA) and RNA was extracted using a Qiagen Mini Kit according to the manufacturer protocol (Qiagen). A Turbo DNA Free kit (Ambion, Foster City, CA) was used to remove genomic DNA. RNA quality was determined using a Bioanalyzer analysis system (Agilent Technologies, Santa Clara, CA).
A total of 50 ng of RNA (RNA integrity number of 8 or above) from each animal was used to prepare sequencing libraries following Illumina’s TruSeq stranded mRNA Sample Preparation Guide for library preparation protocol.

tag: breed

value: Western White-faced

tag: maternal nutrition

value: over

value: BIRTH

value: longissimus dorsi


title: S118 F2 RESTRICTED DAY 135

description:
S118-F2-R135_S6
118F2_RES_day135

source_name: F2 RESTRICTED DAY 135

value: restricted

value: DAY 135


title: S119 F1 CONTROL DAY 90

description:
S119-F1-C90_S4
119F1_CON_day90

source_name: F1 CONTROL DAY 90

value: control

value: DAY 90


title: Colon_IL10_AIN76A_Low [US81303224_251486822412_S01_GE2-v5_95_Feb07_1_2]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

value: Swiss

source_name: Colon IL10 mouse, AIN76A diet, Low histology score

tag: background strain

value: IL10 knockout

tag: diet

value: Colon

tag: colon histology score level within group


title: S235 F1 OVER BIRTH

description:
S235-F1-OD1_S8
235F1_OVER_birth


title: FIB.G04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction

value: No treatment


title: Colon_C57_Sheep milk_High [US81303224_251486822411_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon C57 mouse, Sheep milk diet, High histology score

value: wildtype

value: Sheep milk

value: High


title: S112 F2 CONTROL BIRTH

description:
S112-F2-CD1_S10
112F2_CON_birth

source_name: F2 CONTROL BIRTH

value: Western White-faced


title: ZEV_miseq_uninduced_4

value: Synthetic promoter driving reporter gene


title: Colon_C57_Sheep milk_High [US81303224_251486822412_S01_GE2-v5_95_Feb07_1_1]

value: adult mouse intestine, kidney, and liver plus fetus tissue


title: S107 F1 CONTROL DAY 135

description:
S107-F1-C135_S1
107F1_CON_day135

source_name: F1 CONTROL DAY 135

value: longissimus dorsi


title: FIB.G03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ZEV_miseq_uninduced_3


title: ZEV_miseq_uninduced_2


title: FIB.G02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Cow milk_Low [US81303224_251486822411_S01_GE2-v5_95_Feb07_1_3]

value: Cow milk

value: Low


title: Colon_IL10_Goat milk_Low [US81303224_251486822411_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon IL10 mouse, Goat milk diet, Low histology score

value: Goat milk


title: S76 F2 RESTRICTED BIRTH

description:
S76-F2-RD1_S5
76F2_RES_birth

source_name: F2 RESTRICTED BIRTH

value: restricted

value: BIRTH


title: FIB.G01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: S12 F2 OVER DAY 90

description:
S12-F2-O90_S3
12F2_OVER_day90

source_name: F2 OVER DAY 90

value: over

value: DAY 90


title: GPD_miseq_BK729

description:
Plasmid DNA and barcodes to assign an artificial promoter to an expression bin
filtered_read_table_miseq_GPD.txt

source_name: Synthetic promoter reporter gene assay

extract_protocol:
PCR amplicons from random oligonucleotide pools, joined by Golden Gate assembly at constant regions encoding transcription factor binding sites based on the PGPD promoter.
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.


title: Colon_IL10_Sheep milk_High [US81303224_251486828634_S01_GE2-v5_95_Feb07_1_4]

value: Swiss

source_name: Colon IL10 mouse, Sheep milk diet, High histology score

value: IL10 knockout

value: Colon


title: ZEV_miseq_uninduced_1


title: S1 F1 RESTRICTED DAY 90

description:
S1-F1-R90_S2
1F1_RES_day90

source_name: F1 RESTRICTED DAY 90


title: S120 F1 OVER DAY 90

description:
S120-F1-O90_S5
120F1_OVER_day90

source_name: F1 OVER DAY 90


title: FIB.F11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts

value: Fibroblasts

value: before induction

value: No treatment


title: FIB.F12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_C57_AIN76A_High [US81303224_251486822411_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon C57 mouse, AIN76A diet, High histology score

value: wildtype

value: High


title: FIB.F10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: S93 F2 OVER DAY 135

description:
S93-F2-O135_S11
93F2_OVER_day135

source_name: F2 OVER DAY 135

value: Western White-faced

value: DAY 135


title: FIB.F09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: GPD_miseq_BK728

value: Synthetic promoter driving reporter gene


title: S108 F1 OVER BIRTH

description:
S108-F1-OD1_S7
108F1_OVER_birth

source_name: F1 OVER BIRTH

value: longissimus dorsi


title: GPD_miseq_BK727


title: Colon_C57_ModifiedAIN76A_Low [US81303224_251486828634_S01_GE2-v5_95_Feb07_1_3]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, ModifiedAIN76A diet, Low histology score

value: Low


title: S94 F2 RESTRICTED DAY 135

description:
S94-F2-R135_S1
94F2_RES_day135

source_name: F2 RESTRICTED DAY 135

value: restricted


title: Colon_C57_Cow milk_High [US81303224_251486828634_S01_GE2-v5_95_Feb07_1_2]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Cow milk diet, High histology score

value: Cow milk


title: GPD_miseq_Undetermined


title: Colon_IL10_ModifiedAIN76A_High [US81303224_251486828632_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon IL10 mouse, ModifiedAIN76A diet, High histology score


title: GPD_miseq_BK726


title: FIB.F08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_C57_Soy_Low [US81303224_251486828632_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon C57 mouse, Soy diet, Low histology score

value: Soy


title: S87 F1 CONTROL DAY 90

description:
S87-F1-C90_S2
87F1_CON_day90

source_name: F1 CONTROL DAY 90

value: control

value: DAY 90


title: S81 F2 CONTROL DAY 135

description:
S81-F2-C135_S3
81F2_CON_day135

source_name: F2 CONTROL DAY 135


title: FIB.F07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Soy_Low [US81303224_251486828634_S01_GE2-v5_95_Feb07_1_1]

value: Swiss

source_name: Colon IL10 mouse, Soy diet, Low histology score

value: IL10 knockout

value: Colon


title: GPD_miseq_BK724

source_name: Synthetic promoter reporter gene assay


title: GPD_miseq_BK725


title: S76 F1 RESTRICTED BIRTH

description:
S76-F1-RD1_S10
76F1_RES_birth

source_name: F1 RESTRICTED BIRTH

value: BIRTH


title: Colon_C57_Goat milk_Low [US81303224_251486828632_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, Goat milk diet, Low histology score

value: wildtype

value: Goat milk


title: FIB.F06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction

value: No treatment


title: FIB.F05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.F04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: S68 F2 OVER DAY 135

description:
S68-F2-CD1_S11
68F2_CON_birth

value: Western White-faced

value: over

value: DAY 135

value: longissimus dorsi


title: high glucose/palmitate-treated 3

city: WUhu

first: Xiang

last: Kong

address: zheshanxi road NO 2

department: Central Laboratory of Yijishan Hospital

institute: The First Aflliated Hospital of Wannan Medical College

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads using Seqtk
Hisat2（version:2.0.4）was used to map the cleaned reads to the mouse Rnor_6.0 reference genome with two mismatches.
Stringtie（version:1.3.0）was run with a reference annotation to generate FPKM values （Fragments Per Kilobase of exon model per Million mapped reads）for known gene models.
Stringtie（version:1.3.0 was used to assemble reads into transcripts. Putative lncRNAs were defined as novel transcripts set through the following filters: length ≥200 bp; number of exons ≥2; ORF≤300 bp; have no or weak protein coding ability (CPC score <0 & CNCI score <0  & no significant similarity with Pfam database
RNA-seq derived lncRNAs with the known lncRNAs previously annotated by NONCODE v4.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values

organism: Rattus norvegicus

source_name: INS-1 beta cell

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), and RNA integrity was determined using an Agilent 2100 system and an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Paired-end strand-specific libraries were prepared using the VAHTS Total RNA-Seq Library PrepKit for Illumina (Vazyme, China) following the manufacturer’s instructions.

value: rat insulinoma cell line

value: pancreatic islet

value: Wistar


title: high glucose/palmitate-treated 2


title: S66 F1 OVER DAY 135

description:
S66-F1-O135_S6
66F1_OVER_day135

source_name: F1 OVER DAY 135


title: Colon_IL10_AIN76A_High [US81303224_251486828632_S01_GE2-v5_95_Feb07_1_1]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon IL10 mouse, AIN76A diet, High histology score

value: High


title: Colon_IL10_AIN76A_Low [US81303224_251486828631_S01_GE2-v5_95_Feb07_1_4]

value: Swiss

source_name: Colon IL10 mouse, AIN76A diet, Low histology score

value: IL10 knockout

value: Low


title: FIB.F02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

data_processing:
Basecalls performed using CASAVA version 1.7
Single-cell RNAseq reads were aligned to the human transcriptome build hg19 using Kallisto v0.42.4 with the default parameter settings for paired-end reads.
We excluded chambers containing no cells, multiple cells or cells exhibiting morphological features of cell death based on visual inspection using the IN Cell Analyzer 6000 (GE Healthcare).
Additionally, cells not expressing either of the two housekeeping genes ACTB and GAPDH (encoding β-actin and glyceraldehyde-3-phosphate dehydrogenase, respectively), or expressing them at less than three standard deviations below the mean, were scored as unhealthy and removed.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values files contain counts and TPM/CPM values for each sample after quality control

source_name: Fibroblasts


title: high glucose/palmitate-treated 1


title: FIB.F03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Goat milk_High [US81303224_251486828631_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon IL10 mouse, Goat milk diet, High histology score

value: Colon


title: S49 F2 CONTROL BIRTH

description:
S49-F2-CD1_S8
49F2_CON_birth

source_name: F2 CONTROL BIRTH

value: control

value: BIRTH


title: S43 F1 RESTRICTED DAY 90

description:
S43-F1-R90_S9
43F1_RES_day90

source_name: F1 RESTRICTED DAY 90

value: restricted

value: DAY 90


title: S19 F2 RESTRICTED DAY 90

description:
S19-F2-R90_S4
19F2_RES_day90

source_name: F2 RESTRICTED DAY 90

value: Western White-faced


title: FIB.F01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction

value: No treatment


title: Colon_C57_ModifiedAIN76A_High [US81303224_251486828631_S01_GE2-v5_95_Feb07_1_1]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, ModifiedAIN76A diet, High histology score

value: wildtype


title: FIB.E12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Control 2

value: rat insulinoma cell line

value: pancreatic islet


title: Colon_C57_Soy_High [US81303224_251486828630_S01_GE2-v5_95_Feb07_1_4]

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Soy diet, High histology score

value: Soy


title: S124 F2 CONTROL DAY 90

description:
S124-F2-C90_S11
124F2_CON_day90

source_name: F2 CONTROL DAY 90

value: longissimus dorsi


title: FIB.E11

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_IL10_Cow milk_High [US81303224_251486828630_S01_GE2-v5_95_Feb07_1_2]

value: Swiss

source_name: Colon IL10 mouse, Cow milk diet, High histology score

value: IL10 knockout

value: Cow milk

value: High


title: Colon_C57_AIN76A_Low [US81303224_251486828630_S01_GE2-v5_95_Feb07_1_3]

source_name: Colon C57 mouse, AIN76A diet, Low histology score

value: Colon

value: Low


title: S105 F1 OVER BIRTH

description:
S105-F1-OD1_S4
105F1_OVER_birth

source_name: F1 OVER BIRTH

value: over

value: BIRTH


title: FIB.E10

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts


title: Colon_C57_Sheep milk_Low [US81303224_251486828631_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon C57 mouse, Sheep milk diet, Low histology score

value: Sheep milk


title: FIB.E09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: before induction

value: No treatment


title: Control 3

source_name: INS-1 beta cell

value: rat insulinoma cell line

value: Wistar


title: S79 F1 CONTROL DAY 135

description:
S79-F1-C135_S2
79F1_CON_day135

source_name: F1 CONTROL DAY 135

value: Western White-faced

value: control

value: DAY 135


title: Control 1

value: pancreatic islet


title: FIB.E08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 252162310328_b4 - 21_100Gy_24h_3 vs 16_0Gy_24h_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Why radiation exposure on seeds at low doses causes stimulation of plant growth after germination?

hyb_protocol: 16_0Gy_24h_3 Cy5 / 21_100Gy_24h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Hordeum vulgare

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: embryo - Media: ddWater Temperature: 20°C Light: dark

treatment_protocol: no treatment

tag: tissue = seeds

tag: barley (barley, nur variety)  - harvest date

treatment_protocol: Name:100 Gy (Gamma-irradiation) - gamma-irradiation - gamma-irradiation,gamma-irradiation:quantity 100 time 100min . Dry seeds of barley were placed in thin plastic bags and irradiated by gamma-rays source (cobalt-60) using dose rate 60 Gy/h.


title: S69 F1 RESTRICTED DAY 135

description:
S69-F1-R135_S1
69F1_RES_day135

source_name: F1 RESTRICTED DAY 135

value: restricted

value: longissimus dorsi


title: FIB.H01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: FIB.E07

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: Colon_C57_Cow milk_Low [US81303224_251486828629_S01_GE2-v5_95_Feb07_1_4]

tag: strain

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Cow milk diet, Low histology score

tag: genotype/variation

value: wildtype

value: Cow milk


title: FIB.E06

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts


title: FIB.E05

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: S38 F1 CONTROL DAY 90

description:
S38-F1-C90_S3
38F1_CON_day90

source_name: F1 CONTROL DAY 90

value: DAY 90


title: S28 F1 CONTROL BIRTH

description:
S28-F1-CD1_S9
28F1_CON_birth

source_name: F1 CONTROL BIRTH

value: BIRTH


title: S101 F1 RESTRICTED DAY 135

description:
S101-F1-R135_S8
101F1_RES_day135


title: S26 F1 OVER DAY 90

description:
S26-F1-O90_S5
26F1_OVER_day90

source_name: F1 OVER DAY 90

value: over


title: FIB.E04

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction


title: 5_K_5

source_name: Corpus luteum

value: Corpus luteum

tag: day after ovulation

value: Day 5

value: Control


title: 252162310328_b2 - 14_100Gy_24h_2 vs 9_0Gy_24h_2

hyb_protocol: 9_0Gy_24h_2 Cy5 / 14_100Gy_24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 9_0Gy_24h_2:10mg. (Qiagenv1_RNeasy.pdf)


title: Colon_C57_Goat milk_High [US81303224_251486828629_S01_GE2-v5_95_Feb07_1_1]

source_name: pooled adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon C57 mouse, Goat milk diet, High histology score

value: Goat milk

value: Colon

value: High


title: 252162310328_b1 - 9_0Gy_24h_2 vs 14_100Gy_24h_2

hyb_protocol: 14_100Gy_24h_2 Cy5 / 9_0Gy_24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Colon_IL10_Sheep milk_Low [US81303224_251486828630_S01_GE2-v5_95_Feb07_1_1]

source_name: Colon IL10 mouse, Sheep milk diet, Low histology score

value: IL10 knockout

value: Sheep milk

value: Low


title: S21 F1 OVER DAY 135

description:
S21-F1-O135_S7
21F1_OVER_day135

source_name: F1 OVER DAY 135

value: Western White-faced

value: DAY 135

value: longissimus dorsi


title: FIB.E03

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: No treatment


title: 252162310327_b4 - 7_100Gy_24h_1 vs 2_0Gy_24h_1

hyb_protocol: 2_0Gy_24h_1 Cy5 / 7_100Gy_24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2_0Gy_24h_1:10mg. (Qiagenv1_RNeasy.pdf)


title: cultured PC, E1

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: plasma cells isolated and cultured for 3 days with ST2 stromal cells in the presence of APRIL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: For quality control data were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Quality checks were performed according to the manufacturer's recommendations. Gene expression was quantified by RMA using affy R package.

source_name: Isolated PC from immunized C57Bl6 mice cultured for 3 days

label_protocol: Labeling and hybridization of total RNA to MG 430 2 GeneChips was performed using the whole-transcriptome pico KIT from Affymetrix according tot he manufactures instruction. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix).

growth_protocol: C57BL/6J were obtained from Charles River laboratories. C57BL/6J mice were primed with NP-CCG in incomplete Freud`s Adjuvants intraperitoneally. Mice were challenged twice after the prime with the same injection in cycles of 21 days. After more than 30 days after the last boost, longlived plasma cells were magnetically isolated (Miltenyi Biotec, Germany) with a 2 step-protocol including depletion of B220 and CD49b expressing cells and subsequent positive enrichment of CD138high plasma cells. Plasma cells were directly processed for RNA preparation or cultured for 3 days in co-culture with murine ST2 stromal cells in the presence of the cytokine APRIL under physiological oxygen conditions. After culture, plasma cells were FACSorted using a FACSAria II.

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

value: plasma cells

tag: mouse origin

value: bone marrow


title: Colon_IL10_ModifiedAIN76A_Low [US81303224_251486828629_S01_GE2-v5_95_Feb07_1_3]

value: Swiss

value: adult mouse intestine, kidney, and liver plus fetus tissue

source_name: Colon IL10 mouse, ModifiedAIN76A diet, Low histology score


title: Colon_IL10_Soy_High [US81303224_251486828629_S01_GE2-v5_95_Feb07_1_2]

source_name: Colon IL10 mouse, Soy diet, High histology score

value: Soy


title: 252162310328_b3 - 16_0Gy_24h_3 vs 21_100Gy_24h_3

hyb_protocol: 21_100Gy_24h_3 Cy5 / 16_0Gy_24h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 252162310327_b3 - 2_0Gy_24h_1 vs 7_100Gy_24h_1

hyb_protocol: 7_100Gy_24h_1 Cy5 / 2_0Gy_24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Colon_C57_AIN76A_High [US81303224_251486822414_S01_GE2-v5_95_Feb07_1_4]

source_name: Colon C57 mouse, AIN76A diet, High histology score

value: wildtype


title: cultured PC, E2, rep 2

tag: cell type

value: cultured for 3 days with ST2 stromal cells in the presence of APRIL


title: S20 F1 RES DAY90

description:
S20-F1-R90_S10
20F1_RES_day90

source_name: F1 RES DAY90

value: restricted

tag: time

value: DAY 90


title: FIB.E02

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

value: Fibroblasts

value: before induction

tag: passages


title: S14 F1 RES BIRTH

description:
S14-F1-RD1_S6
14F1_RES_birth

source_name: F1 RES BIRTH

value: BIRTH


title: FIB.E01

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

tag: treatment


title: GSTS_081: JRy12384_input_arrested_dox_released_90m

city: Berkeley

first: Gavin

middle: Schwebs

last: Schlissel

address: 440 Barker Hall

department: Molecular Cell Biology

institute: UC Berkeley

description:
fig panel: 3c,e
GSTS_081

data_processing:
Raw reads were mapped to SacCer3 reference genome, modified to include the gal10::TetO sequence. Sequences were aligned using Bowtie2 with parameters -p 16 -N 1 -L 17, and raw reads were trimmed to 38bp for all experiments.
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, each base in the genome was counted for how often it appeared in the sequencing library (NOT how often the base was sequenced, but rather how often each base fell between the ends of a concordantly-aligned paired ned read).
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, read midpoints were extracted and stored as a bedGraph, corresponding to a histogram of read midpoints
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All proccessed data is a BedGraph

source_name: input sample used for precipitation

extract_protocol:
Cells were mechanically disrupted, and chromatin was solubilized with Mnase. Chromatin was precipitated using either streptavidin-coupled magnetic beads or a V5 antibody agarose matrix.
NEBNext Ultra II library kit was used with dual index primers to prepare DNA for sequencing

tag: growth conditions

value: arrested with alpha factor, treated with doxycycline, synchronously released from arrest

tag: genotype

value: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) mcm2-3A dpb3<delta>::HIS3 gal10::TetO

tag: preciptation conditions

value: V5 (millipore #A7345)


title: GSTS_080: JRy12384_v5-ChIP-seq_arrested_dox_released_90m

description:
fig panel: 3c,e
GSTS_080

source_name: v5-precipitated chromatin from arrested cells treated with doxycycline, released for 1cc

value: streptavidin (invitrogen #65001)


title: GSTS_079: JRy12384_strepSeq_arrested_dox_released_90m

description:
fig panel: 3c,e
GSTS_079

source_name: streptavidin precipitated chromatin from arrested cells treated with doxycycline, released for 1 cc


title: FIB.D10

city: Yokoham

first: Joachim

last: Luginbühl

address: 1-7-22 Suehiro-cho

institute: RIKEN

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv

source_name: Fibroblasts

value: No treatment

tag: batch


title: 252162310326_b4 - 13_20Gy_48h_2 vs 10_0Gy_48h_2

hyb_protocol: 10_0Gy_48h_2 Cy5 / 13_20Gy_48h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:20 Gy (Gamma-irradiation) - gamma-irradiation - gamma-irradiation,gamma-irradiation:quantity 20 time 20min . Dry seeds of barley were placed in thin plastic bags and irradiated by gamma-rays source (cobalt-60) using dose rate 60 Gy/h.


title: GSTS_078: JRy12384_input_arrested_dox_maintained_90m

description:
fig panel: 3c,e
GSTS_078

value: arrested with alpha factor, treated with doxycycline


title: FIB.D12

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ex vivo PC, E2

description: plasma cells isolated from C57BL6

source_name: Isolated PC ex vivo from immunized C57Bl6 mice

value: plasma cells

tag: tissue

value: bone marrow

value: control


title: 252162310327_b1 - 17_0Gy_48h_3 vs 20_20Gy_48h_3

hyb_protocol: 20_20Gy_48h_3 Cy5 / 17_0Gy_48h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: FIB.D09

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: ex vivo PC, E1

description: plasma cells isolated from C57BL6


title: cultured PC, E2, rep 1


title: 252162310327_b2 - 20_20Gy_48h_3 vs 17_0Gy_48h_3

hyb_protocol: 17_0Gy_48h_3 Cy5 / 20_20Gy_48h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NKG2A+CD8a+CD27loCD11b+ NK subset_sample5

city: Singapore

first: Sarah

last: Daud

address: 1E Kent Ridge Road,NUHS Tower Blk,Lvl 12,

country: Singapore

institute: National University of Singapore

description: Cynomolgus macaque splenic CD27loCD11b+ NK subset

hyb_protocol: The hybridization cocktails containing 1µg of Cy3-labeled cDNA targets were heated at 95ºC for 3 minutes before hybridization. Equal volume of aliquots from each sample were hybridized onto Agilent SurePrint G3 custom-unrestricted GE microarray (8x60K format) at 65ºC for 17 hours at 20 rpm in a rotating hybridization oven. The slide was washed according to the gene expression was buffer pack protocol (Agilent Technologies) in the presence of 0.005% Triton X-102.

scan_protocol: The scanning of microarray slide was performed using Agilent DNA Microarray Scanner (Agilent Technologies) according to manufacturer’s instruction for AgilentG3_GX_1Color protocol. Assignment of grid template was performed based on AMADID 075606.

data_processing: Raw signal data extraction, spot intensities, grid measurements and removal of outlier pixels were performed using Feature Extraction Software v10.7.1.1 (Agilent Technologies). The Feature Extraction output file containing intensity and annotation information for each hybridized samples were transferred into Partek® Genomics Suite® software, version 7.0 (Partek Inc.) for data normalization.

organism: Macaca fascicularis

source_name: Singapore

label_protocol: Purified total RNA of 50ng as input (4-5 biological replicates for each NK subset) was amplified using the Ovation® Pico WTA System V2 kit (NuGEN Technologies Inc.) that includes first-strand cDNA synthesis, second-strand cDNA synthesis and SPIA isothermal linear amplification. The purification of the final SPIA cDNA product was performed using MinElute® Reaction Cleanup Kit (Qiagen). For each sample, 400ng of amplified product was Cy3-labeled using the SureTag DNA Labeling kit (Agilent Technologies) with restriction digestion step based on Agilent’s recommended protocol for 8-pack microarrays. Dye incorporation, specific activity and cDNA yield were analyzed using MicroArray Measurement DNA-50 menu, NanoDrop ND-1000.

growth_protocol: Unstimulated NK cell subpopulations

extract_protocol: Total RNA was extracted from flow-sorted cells using TRIzol reagent (Invitrogen) method combined with RNeasy MinElute kit (Qiagen) purification steps.

treatment_protocol: Cryopreserved samples were thawed in a 37°C water bath, re-suspended in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum to wash away the freezing media. Macaque cells were stained for NK surface markers NKG2A/CD159a, CD8a, CD27, CD11b, NKp80 and lymphocyte lineage markers CD45, CD3, CD14, CD20, HLA-DR. After the addition of DAPI stain to distinguish dead cells, NK subsets were subjected to fluorescence-activated cell sorting using a four laser MoFlo® Astrios™ cell sorter(Beckman Coulter) and cells were flow sorted directly into TriZol solution. All NK subsets were derived from CD45+CD3-CD14-CD20-HLA-DR- live gate.

value: Spleen

tag: gender

value: Female

tag: age

value: 18 years old


title: 252162310326_b3 - 10_0Gy_48h_2 vs 13_20Gy_48h_2

hyb_protocol: 13_20Gy_48h_2 Cy5 / 10_0Gy_48h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue = seeds


title: FIB.D08

description:
tc.mat.count.qc.csv
tc.mat.tpm.qc.csv


title: 252162310326_b2 - 6_20Gy_48h_1 vs 3_0Gy_48h_1

hyb_protocol: 3_0Gy_48h_1 Cy5 / 6_20Gy_48h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 3_0Gy_48h_1:10mg. (Qiagenv1_RNeasy.pdf)

tag: barley (barley, nur variety)  - harvest date


title: 252162310326_b1 - 3_0Gy_48h_1 vs 6_20Gy_48h_1

hyb_protocol: 6_20Gy_48h_1 Cy5 / 3_0Gy_48h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 252162310325_b4 - 19_20Gy_24h_3 vs 16_0Gy_24h_3

hyb_protocol: 16_0Gy_24h_3 Cy5 / 19_20Gy_24h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.