title: RNA_LacZ_rep2

description: cDNA


title: bln1_t0_rep3

status: Public on Feb 08 2019

type: SRA

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

country: USA

institute: USDA/ARS

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 0 HAI

library_source: transcriptomic

data_processing:
The 50 base pair single-end reads obtained from Illumina Hi-Seq 2500 were quality filtered and adapters were trimmed using Trimmomatic version 0.33 (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170).  Reads were compared with the Rfam database using the Infernal program version 1.1.2 (Nawrocki and Eddy, 2013. Bioinformatics 29 (22): 2933-2935. DOI: 10.1093/bioinformatics/btt509) and used to filter tRNAs, rRNAs, snoRNAs and snRNAs from the data. The reads were also filtered using the Triticeae Repeat Sequence Database (Wicker et al., 2008. BMC Genomics 9: 518. DOI: 10.1186/1471-2164-9-518) to remove any known triticeae-specific repeat sequences.
For each of the 90 samples, read count estimation was done using RSEM (Li and Dewey, 2011. BMC Bioinformatics 12: 323. DOI: 10.1186/1471-2105-12-323) with Trimmomatic (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170) trimmed reads as input.
Genome_build: Barley (Mascher et al., 2017. Nature 544: 427–433. DOI: 10.1038/nature22043) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu et al., 2010. Science 330 (6010): 1543-1546. DOI: 10.1126/science.1194573).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew in respective csv files

molecule: total RNA

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: CI 16151 and its derived mutant barley lines were maintained via single seed descent. Genotypes were grown in separate trays (19.5 x 27.5-cm) in a climate-controlled greenhouse using a split plot design. Each tray consisted of six rows of 16 seedlings, with rows randomly assigned to one of six harvest timepoints (0, 16, 20, 24, 32, and 48 HAI).

extract_protocol:
Total RNA was isolated from 0.5 g of each pool using a hot (60˚C) phenol / guanidine thiocyanate method (Caldo et al., 2004. Plant Cell 16: 2514-2528. DOI: 10.1105/tpc.104.023382).
Small RNA-sequencing (small RNA-seq) libraries were prepared by the Iowa State University DNA Facility (Ames, Iowa, USA) using the Illumina TruSeq small RNA library preparation kit and were subjected to single-end sequencing (100-bp reads) using the Illumina Hi-Seq 2500 Sequencing System. A split-split-plot design was used to run the 90 samples on three Hi-Seq 2500 flow cells. Each replication was run on a separate flow cell with each plant genotype randomly assigned to each lane and 6 barcodes randomly assigned to the 6 time points within each genotype (lane).

treatment_protocol: Seven days after sowing, seedling trays were inoculated at 16:00 with a high density of Bgh isolate 5874 (AVRa1, AVRa6, vira8, AVRa12, vira13, AVRLa) and positioned randomly in a controlled growth chamber (18°C, 8 h darkness, 16 h light). Rows of seedlings were harvested at the assigned time points, pooled, and immediately placed into liquid nitrogen. The entire procedure was replicated three times in successive weeks resulting in 90 experimental units (5 genotypes x 6 timepoints x 3 replications).

tag: tissue

value: Barley infected first leaf (PO:0007094)

tag: plant genotype

tag: fungal isolate

value: Bgh isolate 5874

tag: timepoint

value: 0 HAI

tag: replication

value: Rep 3


title: control2

type: RNA

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: no disease

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1,65µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44k using Agilent's recommended hybridization chamber.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9,1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction.

data_processing: the signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median

organism: Homo sapiens

source_name: bone marrow mesenchymal stromal cell from healthy donor

label_protocol: 1µg of total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technologies) following manufacturer's protocol.

growth_protocol: HO explants were seeded in α-MEM supplemented with 10% FCS (foetal calf serum) and 1% antibiotics at 37°C in 5% CO2. Explants were removed after one to two weeks when sprouting adherent cells were in sufficient number.

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer Platform (Agilent Technologies)

treatment_protocol: Adherent cells were trypsinized at sub-confluence and amplified during 2 passages

tag: condition

value: no disease


title: AP2-G-DD 78 hpi

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description: Parental line

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: AP2-G-DD +Shld1

growth_protocol: Parasites were cultured at 37°C in the presence of 6% oxygen and 5% carbon dioxide, in RPMI 1640 media supplemented with hypoxanthine, 0.5% Albumax II (Invitrogen), and 2.5 nM WR99210.

extract_protocol: Starting at 30 hpi, samples were harvested in Trizol for total RNA extraction for the next 66 hours.

treatment_protocol: For all lines, 0.5 μM Shld1 was added starting at 24 hpi to stabilize the AP2-G-DD protein.

tag: strain

tag: hpi

tag: treatment

source_name: 3D7 Mixed Stage Reference Pool + 50% cDNA from samples

value: 3D7 + AP2-G-DD


title: AP2-G-DD 84 hpi

description: Parental line

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: RNA_LacZ_rep1

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

description: cDNA

data_processing:
RNA-seq reads were mapped to the D. melanogaster reference genome (version dm3) using HISAT v2.1.0 with option --max-intronlen 50,000. Reads with low mapping quality were removed using SAMtools with option -q 30.
Gene expression was quantified with StringTie for the reference annotation version r5.12.
Genome_build: dm3
Supplementary_files_format_and_content: RNA-seq processed data files are non-normalized read counts per gene. One processed data file is supplied for each replicate. The files are in a plain text format (tab-delimited).

organism: Drosophila melanogaster

source_name: cultured cells

growth_protocol: Drosophila melanogaster S2 cell line (from the collection of IMG RAS) was grown at 25°C in Schneider’s Drosophila Medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 50 units/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol:
Total RNA was isolated from two biological replicates of Lam-KD or control S2 cells using Trizol reagent (Invitrogen), and contaminating DNA was removed by DNase I treatment. RNA quality was assessed using capillary electrophoresis with a Bioanalyzer 2100 (Agilent). Poly(A)+ RNA was extracted from total RNA using oligo(dT) magnetic beads (Thermo Fisher Scientific).
For library preparation NEBNext Ultra II RNA library preparation kit (New England Biolabs) was used following manufacturer’s instructions.  After preparation, libraries were quantified using a Qubit fluorometer and quantitative PCR.

treatment_protocol: dsRNAs against lacZ or lamin Dm0 for RNAi treatment of S2 cells were prepared as previously described (Shevelyov et al. 2009). dsRNAs against LBR were prepared by the same way using Drosophila genome DNA as a template for PCR amplification and primers provided in the Supplementary Table 1. Treatment of cells with dsRNA was performed during five days using a previously described protocol (Clemens et al. 2000).

tag: cell line

tag: developmental stage

value: late stage embryo

tag: cell type

value: macrophage-like

tag: library strategy

value: RNA-seq


title: rar3_t48_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 48 HAI

value: 48 HAI

value: Rep 2


title: control1

description: no disease


title: AP2-G-DD 72 hpi

description: Parental line


title: control4

description: no disease


title: bln1_t0_rep2


title: rar3_t32_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 32 HAI

value: 32 HAI


title: RNA_Lam_rep1

description: cDNA


title: AP2-G-DD 66 hpi

description: Parental line


title: rar3_t24_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 24 HAI

value: 24 HAI


title: rar3_t48_rep3


title: Input_Lam_rep2

description: ChIP-seq DNA library

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the D. melanogaster reference genome (version dm3) using Bowtie 2 v2.2.1 (with the --very-sensitive option). Reads with low mapping quality were removed using SAMtools with option -q 30. Duplicate reads were removed using SAMtools rmdup.
We calculated ChIP and input signals in 1-kb genomic bins using BEDtools v2.16.2.
Supplementary_files_format_and_content: ChIP-seq processed data files are non-normalized ChiP and input signals in 1-kb genomic bins. One processed data file is supplied for each replicate. The files are in UCSC bedGraph format.

molecule: genomic DNA

extract_protocol:
ChIP-seq from two biological replicates of control and Lam-KD S2 cells with anti-H3-pan acetylated antibodies (Active Motif, #39139) was performed as previously described (Chanas et al., 2014), with some modifications. After rinsing with PBS, ~2×107 cells were fixed with 1.8% formaldehyde in PBS containing 0.5 mM DTT for 20 min at room temperature. Cross-linking was stopped by adding glycine to 225 mM for 5 min and washing in PBS containing 0.5 mM DTT three times for 5 min. Cells were washed once in the A2 buffer (140 mM NaCl, 15 mM HEPES pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.5 mM DTT, complete EDTA-free protease inhibitor cocktail (Roche)). Cells were lysed in the A2 buffer containing 1% SDS for 10 min at room temperature, after that the lysate was 20-fold diluted by the A2 buffer and incubated for 2 min at 4°C. After sonication with VCX 400 Vibra-Cell Processor (Sonics; 30 pulses of 10 sec with 10-sec intervals at 15% max power) and 10-min high-speed centrifugation, the fragmented chromatin (with the average DNA fragment size ~0.5 kb) was recovered in the supernatant. For each immunoprecipitation, ~10 μg of chromatin (~700 µl) was pre-incubated in the presence of 100 μl of Protein A-Sepharose (PAS, 50% w/v, GE Healthcare) for 1 h at 4°C. PAS was removed by centrifugation, 5% of chromatin was isolated as an “Input” material, after that 2 µl anti-H3-pan acetylated antibodies (Active Motif, #39139) were added to the rest chromatin and samples were incubated overnight at 4°C in a rotating wheel. Then, 100 μl of PAS was added and incubation was continued for 4 h at 4°C. Samples were centrifuged at maximum speed for 1 min and the supernatant was discarded. Samples were washed four times in the A2 buffer containing 0.05% SDS and twice in 1 mM EDTA, 10 mM Tris (pH 8), 0.5 mM DTT buffer (each wash for 5 min at 4°C). Chromatin was eluted from PAS in 100 μl of 10 mM EDTA, 1% SDS, 50 mM Tris (pH 8) at 65°C for 10 min, followed by centrifugation and recovery of the supernatant. PAS material was re-extracted in 150 μl of TE, 0.67% SDS. To reverse cross-links, the combined eluate (250 μl) was incubated 6 h at 65°C and treated by Proteinase K for 3 h at 50°C. Samples were phenol-chloroform extracted and isopropanol precipitated in the presence of 20 μg glycogen. DNA was dissolved in 100 μl of water.
ChIP samples containing ~25 ng of precipitated DNA, as well as “Input” samples were prepared for next-generation sequencing using a NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs).

value: ChIP-seq


title: rar3_t24_rep1

value: Rep 1


title: AP2-G-DD 48 hpi

description: Parental line


title: rar3_t32_rep3


title: AP2-G-DD 42 hpi

description: Parental line


title: AP2-G-DD 60 hpi

description: Parental line


title: rar3_t20_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 20 HAI

value: 20 HAI


title: Input_Lam_rep1

description: ChIP-seq DNA library


title: rar3_t20_rep1


title: rar3_t32_rep1


title: Input_LacZ_rep2

description: Input for ChIP-seq DNA library


title: rar3_t24_rep3


title: Chip_Lam_rep1

description: ChIP-seq DNA library


title: Chip_LacZ_rep2

description: ChIP-seq DNA library


title: rar3_t20_rep3


title: AP2-G-DD 30 hpi

description: Parental line


title: AP2-G-DD 36 hpi

description: Parental line


title: Chip_Lam_rep2

description: ChIP-seq DNA library


title: Input_LacZ_rep1

description: Input for ChIP-seq DNA library


title: rar3_t16_rep3

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 16 HAI

value: 16 HAI


title: AP2-G-DD -Shld1 90 hpi

description: AP2-G-DD -Shld1 90 hpi

source_name: AP2-G-DD -Shld1

extract_protocol: Starting at 30 hpi and every six hours up to 90 hpi, samples were harvested in Trizol for total RNA extraction.

treatment_protocol: 0.5 μM Shld1 was added and maintained starting at 24 hpi to stabilize the AP2-G-DD protein. For the negative control, the same volume of ethanol was instead added.

value: Ethanol (vehicle)

source_name: 3D7 Mixed Stage Reference Pool + 63% cDNA from samples


title: input_DNA_rep3

city: Toulouse Cedex 9

first: Luisa

last: Di Stefano

state: France

address: LBCMCP - CNRS UMR5088 -  IFR 109  Bât 4R3-B1 118 route de Narbonne

institute: Université Paul Sabatier - Toulouse III

data_processing:
Reads in fastq files were pre processed with fastx toolkit version 0.0.13.2: fastq_masker fastq_masker -Q33 -q 20 -r N -v -I (mimimum quality threshold : 20, with low quality nucleotides replaced by 'N'
Reads were aligned to the reference Drosophila genome (BDGP6 build based on the  Flybase release 6.13, dm6) using bwa software (version 0.6.2-r126) with standard parameters.
Multimapping reds were removed using samtools version 0.1.18
ChIP-seq narrow peaks were called against the input and pre-immune using MACS2 software with the options --nomodel -p 0.001
Genome_build: dm6

growth_protocol: Approximately 1000 ovary pairs were used in each ChIP-Seq experiment from young w1118 females raised at 25°C, 70% humidity on standard Drosophila medium

extract_protocol:
Dissected ovaries were fixed in 1% formaldehyde, lysed and sonicated. Part of the lysate was kept for the input DNA, the rest was incubated with pre-immune serum or with the anti-dLsd1 antibody. Antibody complexes were recovered with a mixture of protein A- and G-Sepharose. The DNA was recovered by phenol-chloroform extraction and ethanol precipitation.
For the library preparation, ChIP DNA (10 ng) was blunt-ended and phosphorylated, and a single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products was purified and size-selected by agencourt AMPure XP beads. Purified DNA was PCR-amplified to enrich for fragments that have adapters on both ends.

tag: genotype

value: ovary

tag: chip antibody

value: input


title: rar3_t0_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 0 HAI

value: Barley infected first leaf (PO:0007094)

value: Bgh isolate 5874

value: 0 HAI


title: input_DNA_rep2


title: rar3_t16_rep2


title: rar3_t16_rep1


title: rar3_t0_rep1


title: AP2-G-DD -Shld1 72 hpi

description: AP2-G-DD -Shld1 72 hpi

value: 3D7 + AP2-G-DD


title: rar3_t48_rep1


title: mla6_t32_rep1

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 32 HAI


title: rar3_t0_rep3

value: Rep 3


title: mla6_t32_rep2


title: mla6_t32_rep3


title: AP2-G-DD -Shld1 84 hpi

description: AP2-G-DD -Shld1 84 hpi


title: mla6_t24_rep3

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 24 HAI


title: AP2-G-DD -Shld1 66 hpi

description: AP2-G-DD -Shld1 66 hpi


title: Chip_LacZ_rep1

description: ChIP-seq DNA library

value: late stage embryo

value: macrophage-like


title: mla6_t24_rep2

value: Rep 2


title: mla6_t24_rep1


title: mla6_t48_rep3

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 48 HAI

value: 48 HAI


title: mla6_t48_rep2


title: mla6_t48_rep1


title: pre-immune_rep1

value: pre-immune


title: mla6_t20_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 20 HAI


title: mla6_t20_rep1


title: pre-immune_rep2


title: anti-dLsd1_rep3


title: input_DNA_rep1


title: anti-dLsd1_rep2


title: mla6_t16_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 16 HAI


title: AP2-G-DD -Shld1 78 hpi

description: AP2-G-DD -Shld1 78 hpi


title: mla6_t0_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 0 HAI


title: WT_t48_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 48 HAI


title: mla6_t20_rep3


title: AP2-G-DD -Shld1 42 hpi

description: AP2-G-DD -Shld1 42 hpi


title: AP2-G-DD -Shld1 60 hpi

description: AP2-G-DD -Shld1 60 hpi


title: AP2-G-DD -Shld1 30 hpi

description: AP2-G-DD -Shld1 30 hpi


title: mla6_t16_rep3


title: AP2-G-DD -Shld1 54 hpi

description: AP2-G-DD -Shld1 54 hpi


title: AP2-G-DD -Shld1 48 hpi

description: AP2-G-DD -Shld1 48 hpi


title: S2 lamin Dm0 KD_Hi-C_rep1

description:
Hi-C DNA library
processed data file: Lamin-merged_IC-heatmap-20K.txt.gz

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped to the D. melanogaster reference genome (version dm3) using bowtie2 v2.2.1 with --very-sensitive option in a single-end mode.
Hi-C data were processed using ICE pipeline v0.9 with 20 iterations of iterative correction as described previously (Imakaev et al., 2012) at 20-kb resolution.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *_IC-heatmap-20K.txt: Processed data files are genome-wide maps reporting iteratively corrected values for contacts between 20-kb bins. One processed data file is supplied for each replicate plus a merge of the two replicates for each cell line. The files are in a plain text format (tab-delimited) in which rows and columns correspond to 20-kb genomic bins.

extract_protocol:
Hi-C analysis was performed as described previously (Belton et al. 2012), with the minor modifications described below. A total of 3-5 million cells were pelleted and resuspended in 10 ml of 1× PBS (10 mM phosphate buffer, 2.7 mM KCl 137 mM NaCI, pH7.4) and fixed with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 2 M glycine to a final concentration of 125 mM. The cell suspension was incubated on ice for 5 min, and the cells were pelleted (10 min at 1000 x g in a pre-chilled (4oC) centrifuge). The supernatant was removed, and the cell pellet was washed with 500 μl of 1× PBS, frozen and, if necessary, stored in a liquid nitrogen. After thawing, the cells were lysed for 15 min in 1.5 ml of ice-cold lysis buffer (50 mM Tris-HCl (pH8.0), 150 mM NaCl, 0.5% (v/v) NP-40, 1% (v/v) Triton-X100, 1× Protease Inhibitor Cocktail (CALBIOCHEM #539137 of Thermo Scientific #78430)). The nuclei were harvested at 5000 x g for 7 min in a pre-chilled centrifuge, washed twice with 100 μl of 1.2× restriction NEBuffer 2 (NEB) and resuspended in 200 μl of 1.2× NEBuffer 2. Then, 20% SDS was added to a final concentration of 0.3%, and the nuclei were incubated at 37oC for 1 h with constant shaking. After incubation, 330 μl of 1.2× NEBuffer 2 was added, 20% Triton X-100 was added to a final concentration of 1.8%, and the samples were incubated for 1 h under the same conditions. DNA was digested overnight with 600-800 U of 100 U/μl HindIII-HF restriction endonuclease (NEB) at 37oC with shaking. The next morning, 200 U of HindIII-HF was added, and the samples were incubated for 2 h under the same conditions. The nuclei were harvested for 10 min at 5000 x g and 25oC and resuspended in 50 μl of the collected supernatant. Cohesive DNA ends were biotinylated by adding 7.6 μl of the biotin fill-in mixture prepared in 1× NEBuffer 2 (0.025 mM dATP (Thermo Scientific), 0.025 mM dGTP (Thermo Scientific), 0.025 mM dTTP (Thermo Scientific), 0.025 mM biotin-14-dCTP (Invitrogen), 0.8 U/μl Klenow enzyme (NEB)). The samples were incubated at 37oC for 75 min with slow shaking, and 20% SDS was added to a final concentration of 1.8%; the samples were heated at 65oC for 20 min to inactivate the Klenow enzyme and residual HindIII-HF. The samples were transferred into 10-ml tubes with 3 ml of 1× T4 DNA ligase reaction buffer (Thermo Scientific) supplied with 1.8% Triton X-100, incubated at 37oC for 1 h and then cooled on ice. Next, 100 U of T4 DNA ligase (Thermo Scientific) was added, and the DNA was ligated for 6 h at 22oC with slow agitation. The cross-links were reversed by overnight incubation at 65oC in the presence of proteinase K (100 μg/ml). After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation (tRNA (Sigma) at a concentration of 7.5 μg/ml and glycogen (Thermo Scientific) at a concentration of 20 μg/ml were used as co-precipitators due to the low amount of DNA in the samples).
Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries in the presence of 1.5 U of T4 DNA polymerase (NEB) in NEBuffer 2 supplied with 0.025 mM dATP and 0.025 mM dGTP at 20oC for 4 h. Next, the DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The DNA pellets were dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.1% SDS) and treated with 50 μg of RNase A (Thermo Scientific) for 45 min at 37oC; the DNA was then sheared to a size of approximately 100-1000 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units. The fraction of 100-500-bp DNA fragments was captured using Agencourt AMPure XP beads (Beckman Coulter), and the fragments were eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). The DNA ends were repaired by adding 62.5 μl MQ water, 14 μl of 10× T4 DNA ligase reaction buffer, 3.5 μl of 10 mM dNTP mix, 5 μl of 3 U/μl T4 DNA polymerase (NEB), 5 μl of 10 U/μl T4 polynucleotide kinase (NEB), and 1 μl of 5 U/μl Klenow DNA polymerase (NEB) and incubating at 20oC for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 50 μl of 10 mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 6 μl 10× NEBuffer 2, 1.2 μl of 10 mM dATP, 1 μl of MQ water and 3.6 μl of 5 U/μl Klenow (exo-) (NEB). The reactions were carried out for 30 min at 37oC in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65oC for 20 min. The DNA was purified using Agencourt AMPure XP beads and eluted with 100 μl of 10 mM Tris-HCl (pH 8.0). Biotin pull-down of the ligation junctions was performed as described previously, with minor modifications. Briefly, 4 μl of MyOne Dynabeads Streptavidin C1 (Invitrogen) beads were used to capture the biotinylated DNA, and the volumes of all buffers were decreased by 4-fold. The washed beads with captured ligation junctions were resuspended in 50 μl of adapter ligation mixture composed of 41.5 μl MQ water, 5 μl 10× T4 DNA ligase reaction buffer (Thermo Scientific), 2.5 μl of Illumina TruSeq adapters and 1 μl of 5 U/μl T4 DNA ligase (Thermo Scientific). Adapter ligation was performed at 22oC for 2.5 h, and the beads were sequentially washed twice with 100 μl of TWB (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), once with 100 μl of 1× binding buffer (10 mM Tris-HCl (pH8.0), 1 mM EDTA, 2 M NaCl) and once with 100 μl of CWB (10 mM Tris-HCl (pH 8.0) and 50 mM NaCl) and then resuspended in 20 μl of MQ water. Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles needed to generate enough PCR.

treatment_protocol: dsRNAs against lacZ or lamin Dm0 for RNAi treatment of S2 cells were prepared as previously described (Shevelyov et al. 2009). Treatment of cells with dsRNA was performed during five days using a previously described protocol (Clemens et al. 2000).

tag: genotype/variation

value: Lamin Dm0 knockdown


title: WT_t32_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 32 HAI

value: 32 HAI


title: mla6_t16_rep1

value: Rep 1


title: AP2-G-DD +Shld1 84 hpi

description: AP2-G-DD +Shld1 84 hpi


title: WT_t32_rep2


title: pre-immune_rep3


title: bln1_t32_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 32 HAI


title: mla6_t0_rep3


title: anti-dLsd1_rep1


title: mla6_t0_rep1


title: WT_t24_rep2

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 24 HAI

value: 24 HAI


title: ONT_729_Caudate

city: Darlinghurst

first: Simon

middle: Andrew

last: Hardwick

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
ONT reads were base-called using Guppy base-calling software (v1.8.5).
Demultiplexing base-called reads was performed using Porechop (v0.2.3) with the enforced barcode detection parameter.
Reads aligned to hg38 (plus in silico chromosome) using minimap2 (v2.14-r883).
To generate a hybrid transcriptome that leverages both long- and short-read data, we used the FLAIR tool (v1.2). First, we used FLAIR ‘correct’ by inputting spliced ONT read alignments (from minimap2) and correcting misaligned ONT splice junctions using genome annotations (GENCODE v29; with the –f option) and our accompanying Illumina splice junctions (with the –j option). We used the default window size of 10 bp for correcting splice sites. We then collapsed corrected reads into a non-redundant transcriptome using FLAIR ‘collapse’ with default parameters. We then undertook a number of steps in order to produce a high-confidence set of multi-exonic transcripts overlapping GWAS haplotype blocks associated with neuropsychiatric functions.
We quantified transcript expression using Salmon (v0.11.3), providing the chrIS annotation and our hybrid transcriptome as a reference. For ONT samples, we used the following non-default parameters: --fldMean 1000 --fldSD 100 --libtype U.
Genome_build: hg38
Supplementary_files_format_and_content: BED file contains chromosome coordinates of all transcripts in our filtered hybrid transcriptome. The four '*_quant.sf' files provide Salmon expression measurements (TPM) for hybrid transcriptome and RNA sequins.

source_name: Brain tissue

extract_protocol:
RNA was extracted using the QIAGEN miRNeasy kit.
RNA CaptureSeq was performed as per the protocol from Mercer, T.R. et al Nature Protocols 9, 989-1009 (2014), with several modifications for the ONT platform. 1 µg of each of 4 human brain samples was spiked with RNA sequins (Mix A) at 2% fractional abundance. Following reverse transcription, PCA adapters from the ONT ligation sequencing kit 1D (SQK-LSK108) were ligated onto the end-prepped samples. The captured samples were barcoded using ONT 1D native barcoding genomic DNA kit (EXP-NBD103), and library prep was performed using the 1D genomic DNA by ligation kit and protocol for the PromethION sequencer (SQK-LSK109).

tag: brain region

value: Caudate

tag: donor

value: C

tag: age


title: S2 lamin Dm0 KD_Hi-C_rep2


title: AP2-G-DD -Shld1 36 hpi

description: AP2-G-DD -Shld1 36 hpi

value: Ethanol (vehicle)


title: WT_t20_rep2

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 20 HAI

tag: tissue

value: Barley infected first leaf (PO:0007094)

tag: plant genotype

tag: fungal isolate

value: 20 HAI


title: ONT_692_VCx

value: Visual cortex

value: B


title: AP2-G-DD +Shld1 90 hpi

description: AP2-G-DD +Shld1 90 hpi

value: 3D7 + AP2-G-DD


title: S2 control_Hi-C_rep2

description:
Hi-C DNA library
processed data file: LacZ-merged_IC-heatmap-20K.txt.gz

value: late stage embryo

value: Control


title: ONT_692_PFC

value: Prefrontal cortex


title: AP2-G-DD +Shld1 78 hpi

description: AP2-G-DD +Shld1 78 hpi


title: WT_t16_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 16 HAI

value: Bgh isolate 5874

tag: timepoint

value: 16 HAI

tag: replication

value: Rep 3


title: WT_t48_rep1

value: 48 HAI


title: WT_t16_rep2

value: Rep 2


title: WT_t24_rep3

value: 24 HAI


title: WT_t48_rep2


title: WT_t32_rep1

value: 32 HAI

value: Rep 1


title: AP2-G-DD +Shld1 42 hpi

description: AP2-G-DD +Shld1 42 hpi

tag: strain

tag: hpi


title: S2 control_Hi-C_rep1

tag: cell line

value: macrophage-like


title: WT_t20_rep3

value: Barley infected first leaf (PO:0007094)


title: WT_t24_rep1


title: 10304: Wild-type (ACCM-D) 14d

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cb whole genome using bowtie
normalization and comparisons were run using deseq2, matrix_11s.txt is a condensed file of the original with deseq2 normalized reads for each sample listed
Genome_build: GCF_000007765.2  2016/11/10 (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Coxiella_burnetii/latest_assembly_versions/GCF_000007765.2_ASM776v2)

organism: Coxiella burnetii

source_name: ACCM-D axonic media

growth_protocol: C. burnetii strains were inoculated into 20 ml of ACCM-D growth media at 1x105 GE/ml

extract_protocol:
At days 5 and 14, RNA was extracted using a hot trizol extraction
Ribozero gram- --> Truseq mRNA-seq

value: wild type


title: AP2-G-DD +Shld1 72 hpi

description: AP2-G-DD +Shld1 72 hpi

tag: treatment


title: 10331: rpoS KO (ACCM-D) 14d

value: rpoS knock out


title: shWDR43-2_RNA-seq

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

description:
messenger RNA
Spike-in RNA-seq profiling of WDR43-depleted ESCs.txt

data_processing:
alignment: tophat
transcriptome construction and FPKM calculation:cufflinks
genome build: mm9
Supplementary_files_format_and_content: summary of spike-in normalized FPKM

molecule: polyA RNA

organism: Mus musculus

source_name: mES cells

growth_protocol: ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by NEBNEXT  ChIP-seq library preparation kit or  NEBNEXT Ultra RNA-seq library preparation kit  RNA-seq library preparation kit

tag: cell type

value: mES cells

value: shWDR43 knockdown

value: wildtype

tag: antibody


title: AP2-G-DD +Shld1 30 hpi

description: AP2-G-DD +Shld1 30 hpi

value: 3D7 + AP2-G-DD


title: AP2-G-DD +Shld1 54 hpi

description: AP2-G-DD +Shld1 54 hpi


title: WT_t0_rep2

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 0 HAI

value: 0 HAI


title: AP2-G-DD +Shld1 60 hpi

description: AP2-G-DD +Shld1 60 hpi


title: ONT_683_SupCol

value: Superior colliculus

value: A


title: 10330: Wild-type (ACCM-D) 14d

tag: genotype


title: AP2-G-DD 54 hpi

description: Parental line


title: 10318: rpoS KO (ACCM-D) 14d


title: AP2-G-DD +Shld1 48 hpi

description: AP2-G-DD +Shld1 48 hpi


title: WDR43_chrTAP_replicate1

description:
chrTAP-seq RNA
WDR43_chrTAP_replicate1.tag.positive.strand; WDR43_chrTAP_replicate1.tag.negative.strand

data_processing:
Filtering and pre-processing of raw reads:  CIMS: fastq_flter.pl, fasta2collapse.pl and stripBarcode.pl
read mapping and collapsing to obtain unique reads: novoalign
collapsing to obtain unique reads: CIMS: novoalign2bed.pl, tag2collapse.pl,
creation of bedgraph: tag2profle.pl
genome build: mm9
Supplementary_files_format_and_content: positive and negative strand reads of WDR43 chrTAP-seq.bedgraph

value: FLAG affinity gel, sigma A2220; M-280 Streptavidin, Invitrogen  60210


title: 10317: Wild-type (ACCM-D) 14d


title: AP2-G-DD +Shld1 36 hpi

description: AP2-G-DD +Shld1 36 hpi


title: AP2-G-DD +Shld1 66 hpi

description: AP2-G-DD +Shld1 66 hpi


title: 10291: Wild-type (ACCM-D) 5d


title: shCtl-2_RNA-seq

value: shCtl knockdown


title: shCtl-1_RNA-seq


title: WT_t0_rep3

value: Bgh isolate 5874

value: Rep 3


title: Pol II hypoP_shCtl-2_ChIP

description:
ChIP DNA
shCtl-2_Pol II-hypoP-8WG16_peaks.bed

data_processing:
alignment: bowtie2
peak calling: MACS
genome build: mm9
Supplementary_files_format_and_content: bedgraph or bed files for the output by MACS

value: Pol II (8WG16), Covance MMS-126R


title: shWDR43-1_RNA-seq


title: MEF reprogramming intermediate_Day 15 (SSEA1+)

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
The reads quality was initially assesed using FastQC (94% >Q30). For non-allele resolution analyses, reads were aligned to mouse reference genome (mm10; GRCm38.p5) using STAR 2.5.3a supplied with corresponding gencode vM16 annotation file. Mapping was done with default parameters with specified --sjdbOverhang 74 followed by conversion to sorted BAM files. On average, 83.96% of reads were uniquely mapped and only those were passed to next steps. Subsequently, the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) was used to assign mapped reads to genomic features.
For allele resolution analyses, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) supplied with the list of strain specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout entire genome of 20,563,466 SNP positions unique for either strain, of which 634730 on the X chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then splitted into two BAM files containing only strain-specific reads (on average 10,95% for 129 and 10,25% for Cast of total mapped reads) using SNPsplit (details: supplementary table 2). Furthermore, to create count matrices with only reliable allelic information, only SNPs covered by at least 5 reads were selected and genes comprising of at least 8 of such SNPs were retained.
Genome_build: mm10; GRCm38.p5
Supplementary_files_format_and_content: xls file with matrix for all samples with expression values normalized by the library size after log2 transformation

organism: Mus musculus musculus x Mus musculus castaneus

source_name: MEF reprogramming intermediate

growth_protocol: MEFs were cultured in MEF medium [DMEM (Gibco, 41966-554 052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.8% (v/v) beta-mercaptoethanol (Sigma, M7522)].

extract_protocol:
Briefly, sorted SSEA1+ reprogramming intermediates were immediately lysed in the RTL buffer (RNeasy Micro Kit (Qiagen, 74004)) and stored in -80°C until cells from all timepoints were collected. Next, all samples were processed together to extract RNA following manufacturer’s protocol
cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of input RNA, cDNA and individual libraries was assessed using Bioanalyzer (Agilent 2100 Bioanalyzer system).

treatment_protocol: Reprogramming experiments, unless stated otherwise, were performed by conditional induction of lentivirally delivered reprogramming factors. First, P1 MEFs at around 70% confluency were transduced with concentrated lentiviral supernatants. Lentiviruses were generated by transfecting HEK cells separately with two constructs: tetO-FUW-OSKM plasmid, Addgene cat. 20321 (Carey 2009) and FUW-M2rtTA, Addgene cat. 20342 (Hockemeyer 2008) using the calcium precipitation method. Supernatants with lentivirus particles were concentrated using lenti-X-concentrator (Takara, 631231) in ratio 1:100. Infection with the pool of equal volumes of both constructs was carried out overnight, followed by 12 hours culture in MEF medium and 1:5 split. Cells then were sorted using FACS method (described below) in order to isolate homogeneous population in regard to allelic inactivation of X-GFP transgene (either Xi-GFP:Xa or Xi:Xa-GFP). Cells were plated for reprogramming directly after sorting, 50,000 cells per one well of 12 well plate. Reprogramming was induced by doxycycline (final 2 μg/ml) in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1%  GlutaMAX 100X, 1% NEAA 100X, 0.8% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (final 50 μg/ml). Medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with the exception of the dox and AA withdrawal after picking.

tag: Sex

value: Female

value: MEF reprogramming intermediate

tag: time


title: iPSCs (SSEA1+/GFP+)

description: iPSCs

source_name: induced Pluripotent Stem Cells

value: induced Pluripotent Stem Cells


title: 10293: rpoS KO (ACCM-D) 5d


title: ESCs (SSEA1+/GFP+)

source_name: Embryonic Stem Cells

value: Embryonic Stem Cells


title: siCSRP2, replicate 3

city: Luxembourg

first: Joshua

middle: Don

last: Brown-Clay

address: 84 Val Fleuri

department: Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

description: Gene expression data from siCSRP2-transfected cells

hyb_protocol: The cDNA was loaded onto the Affymetrix Human Gene 2.0 array. Target hybridization was performed at 45 °C for 16 hours at 60 rpm by using a GeneChip Hybridization Oven 640. Chip washing and staining were performed with an Affymetrix GeneChip Fluidics Station 400, according to the array type and manufacturer's protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were preprocessed into Partek GS with default partek options.

label: biotin

source_name: Hs578T siCSRP2-transfected cells

label_protocol: 100 ng of total RNA was taken as input material for the GeneChip WT PLUS Reagent Kit (Prod. No. 703174) . The ensuing cDNA was then fragmented with uracil-DNA glycosylase and apurinic/apyrimidinic endonuclease 1 at unnatural dUTP residues. The fragmented cDNA was labeled with terminal deoxynucleotidyl transferase using the proprietary Affymetrix DNA Labeling Reagent, which is covalently linked to biotin. 5.5 ug of cDNA was used for fragmentation and labeling.

growth_protocol: Standard cell culture incubator, media was DMEM + 10% fetal bovine serum + 0.01 mg/ml insulin

extract_protocol: The total RNA was extracted by using the RNeasy mini kit including an on-column DNase treatment according to the manufacturer’s instructions (Qiagen). The RNA concentration and purity were determined using the 2100 Bioanalyser (Agilent).

treatment_protocol: Lipofectamine 2000 was used to transfect cells with non-targeting or CSRP2 siRNA, according to the manufacturer's protocol

tag: sirna

tag: replicate


title: Pol II hypoP_shCtl-1_ChIP

description:
ChIP DNA
shCtl-1_Pol II-hypoP-8WG16_peaks.bed

tag: genotype/variation


title: MEF reprogramming intermediate_Day 13 (SSEA1+)


title: 10279: rpoS KO (ACCM-D) 5d

value: rpoS knock out


title: 10277: Wild-type (ACCM-D) 5d

value: wild type


title: WT_t0_rep1

tag: tissue

value: Barley infected first leaf (PO:0007094)

value: Rep 1


title: MEF reprogramming intermediate_Day 10 (SSEA1+)


title: WT_t16_rep1

tag: plant genotype

value: 16 HAI


title: Pol II Ser5P_shWDR43-2_ChIP

description:
ChIP DNA
Pol II Ser5P ChIP-seq-shWDR43-2_peaks

value: mES cells

value: shWDR43 knockdown

value: wildtype

value: Pol II Ser5P, Cell Signaling Technology 13523


title: siCSRP2, replicate 2


title: siCSRP2, replicate 1


title: siControl, replicate 3

description: Gene expression data from control-transfected cells

source_name: Hs578T control-transfected cells

value: CTRL


title: siControl, replicate 2


title: siControl, replicate 1


title: MEF reprogramming intermediate_Day 8 (SSEA1+)


title: 10305: rpoS KO (ACCM-D) 14d


title: 10265: rpoS KO (ACCM-D) 5d


title: Pol II Ser5P_shCtl-1_ChIP

description:
ChIP DNA
Pol II Ser5P ChIP-seq-shCtl-1_peaks

value: shCtl knockdown


title: Pol II Ser5P_shCtl-2_ChIP

description:
ChIP DNA
Pol II Ser5P ChIP-seq-shCtl-2_peaks


title: Pol II Ser5P_shWDR43-1_ChIP

description:
ChIP DNA
Pol II Ser5P ChIP-seq-shWDR43-1_peaks


title: 6_RNA-seq with atrR null

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

data_processing:
Paired end reads were mapped to the Af293 A. fumigatus genome using HISAT2.  Transcript assembly, quantification of expression levels and analysis of differential expression were done using Stringtie and Ballgown.
Wig files contain graphical representation of FPKM values across the genome. Can be displayed in IGV
Quantitative data for FPKM values are provided in t_data.ctab files from Stringtie.
Genome_build: Aspergillus fumigatus (Af293) genome, s03-m05-r06 (Apr, 2016) from aspgd.org
Supplementary_files_format_and_content: Wig files contain graphical representation of FPKM values across the genome. Can be displayed in IGV
Supplementary_files_format_and_content: ctab.txt files contain Ballgown-compatible transcript-level expression measurements from Stringtie

organism: Aspergillus fumigatus Af293

source_name: with atrR null

growth_protocol: Cell lysates were prepared from mycelial biofilm cultures formed upon inoculating 1X10^6 spores in a petri dish containing 20 ml of Sabouraud dextrose broth and grown for 24 hours at 37°C under non-shaking conditions.

extract_protocol:
Mycelia that formed as a biofilm on the top were collected (∼100 mg) and  ground into a fine powder in liquid nitrogen using a mortar and pestle. Total RNA was then isolated from the ground mycelium using the Trizol reagent (Ambion) according to the manufacturer's instructions. Total RNA was isolated and purified using an RNeasy minikit (Qiagen). Traces of contaminating genomic DNA were eliminated by treating the RNA with turbo DNase followed by a DNase inactivation reagent (both reagents from Ambion).
Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina, Inc., San Diego, CA) and following Illumina's sample preparation guide, started with 500ng of input total RNA.

value: null mutant


title: 5_RNA-seq wild-type strain

source_name: wild-type strain

value: wild-type


title: 8_RNA-seq with hspA-atrR allele present

source_name: with hspA-atrR allele present

value: Overexpressed wild-type factor


title: 7_RNA-seq with atrR-3X HA tag present

source_name: with atrR-3X HA tag present

value: Hyperactive epitope tagged form


title: 3_ChiP-seq with hspA-atrR-3X HA tag present

data_processing:
Reads were mapped using Bowtie software and peaks assigned using MACS.  WIG output from MACS was visualized using IGV software.
Genome_build: Af293 s03-m05-r06 from aspgd.org on 2016-04-17
Supplementary_files_format_and_content: wig output

growth_protocol: 1×10^6 spores/mL of A. fumigatus strains AfS35 (atrR) and SPF89 (atrR-3xHA) were grown in 50 mL of Sabouroud dextrose medium in 250 mL shaking flask cultures for 16 h

extract_protocol:
Cross linked mycelia were harvested and then ground after freezing in liquid nitrogen.  Samples were hydrated in ChIP lysis buffer (CLB: 50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Deoxycholate (Sigma D6750), 0.1% SDS, 1 mM PMSF, 1× fungal proteinase inhibitor cocktail (Sigma)), then sheared using Covaris sonication.  Sheared chromatin was precipitated with anti-HA antibody (Covance) and recovered using magnetic beads.  Cross links were reversed and DNA recovered for library preparation.
Libraries were generated using the Rubicon ThruPlex DNAseq kit as described by the supplier.

value: hspA-atrR-3X HA tag present

tag: chip antibody

value: Purified anti-HA.11 Epitope Tag Monoclonal Antibody (raised in mice)

tag: chip antibody vendor

value: Covance Inc., MA, USA (Now BioLegend)

tag: chip antibody catalog #

tag: chip antibody lot #


title: 5_ChiP-seq with atrR-3X HA tag present

source_name: ChiP-seq with atrR-3X HA tag present

tag: strain

value: atrR-3X HA tag present


title: 4_ChIP-seq with no HA tag present

source_name: ChIP-seq with no HA tag present

value: wild-type copy of atrR with no HA tag present


title: 2_ChiP-seq with atrR-3X HA tag present


title: 4_RNA-seq with hspA-atrR allele present


title: spleen miR-181-HET rep1

city: Munich

first: Natalia

last: Zietara

address: Großhadernerstr. 9

department: Immunology

country: Germany

institute: LMU Munich

description: primary Foxp3+ Treg cells sorted from spleen of miR-181 heterozygous mouse, group 1

hyb_protocol: standard Affymetrix procedures

scan_protocol: Fluorescent images of hybridized microarrays (MOE-430 version 2.0; Affymetrix) were obtained using an Affymetrix Genechip Scanner.

data_processing: Microarray data were analyzed using BioConductor Suite 2.1 software. rma normalized with oligo package on core level in R and annotation pd.mogene.2.0.st

source_name: spleen

label_protocol: standard Affymetrix procedures

growth_protocol: primary cells sorted from thymi and spleens of miR181+/- (control) and miR181-/- (test) mice, carrying GFP reporter expressed from Foxp3 locus

extract_protocol: RNA isolation, cDNA preparation, and DNA microarray analysis of gene expression were performed at the Microarray Genechip Facility of the University of Tübingen (MFT Services)

treatment_protocol: single cell suspensions were prepared from excised thymi and spleens of indicated above mice. Erythocytes were lysed using LCK lysis buffer. All procedures were carried out on ice. Cells were sorted as Foxp3 (GFP)+CD4+CD25+ using Aria II sorter to 98% of purity.

value: primary Foxp3+ Treg cells

value: spleen

value: miR-181 heterozygous

tag: group


title: 3_RNA-seq with atrR-3X HA tag present


title: SEV 2

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

country: China

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GCF_000772875.2_year_151130
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Macaca mulatta

source_name: brain

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rhesus macaque  were exposed to about 2.5%-3% sevoflurane inhalation anesthesia on approximately postnatal day 7 and then again 14 and 28 days later, for four hour each time. We harvested the prefrontal cortex immediately after third times of sevoflurane treatment.

value: brain

tag: agent

value: sevoflurane

value: wild type


title: SEV 3


title: thymus miR-181-HET rep2

description: primary Foxp3+ Treg cells sorted from thymus of miR-181 heterozygous mouse, group 2

source_name: thymus

tag: cell type

value: thymus


title: spleen miR-181-HET rep2

description: primary Foxp3+ Treg cells sorted from spleen of miR-181 heterozygous mouse, group 2


title: spleen miR-181-KO rep1

description: primary Foxp3+ Treg cells sorted from spleen of miR-181 knockout mouse, group 1

value: miR-181 knockout


title: thymus miR-181-KO rep1

description: primary Foxp3+ Treg cells sorted from thymus of miR-181 knockout mouse, group 1


title: CON 3


title: 1_ChIP-seq with no HA tag present


title: CON 2


title: Community-acquired strain

city: Hsinchu

first: Hwan-You

last: Chang

address: No. 101, Section 2, Kuang-Fu Road

country: Taiwan

institute: National Tsing Hua University

data_processing:
Quality Control using CLC Genomics Workbench v9.5
Trim using CLC Genomics Workbench v9.5: 1. Quality trimming based on quality scores. 2. Ambiguity trimming to trim off e.g. stretches of Ns. 3. Adapter trimming. 4. Base trim to remove a specified number of bases at either 3' or 5' end of the reads. 5. Length trimming to remove reads shorter or longer than a specified threshold
RNA-Seq analysis using CLC Genomics Workbench v9.5: alignment and RPKM calculation
Comparison of gene expression of PAO1 and B136-33

organism: Pseudomonas aeruginosa

source_name: Bacterial cell

extract_protocol:
Bacteria were lysed and homogenized using TRIzol reagent (Thermo Fisher Scientific). The homogenates were separated into aqueous, interphase, and organic layers after chloroform was added. RNA was precipitated from the aqueous layer using isopropanol. The precipitated RNA was washed with cold 75% ethanol and then solubilized using RNase-free water. The contaminated DNA was removed after DNase I (Takara) treatment.
RNA samples were reverse-transcribed into cDNA using Ovation Complete Prokaryotic RNA-Seq DR Multiplex System 9-16 (NuGEN), and cDNA fragmented using S220 system (Covaris) then constructed fragment cDNA Library.

value: Wild-type

tag: culture condition


title: Hospital-acquired strain

tag: genotype


title: WT_t20_rep1

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 20 HAI

data_processing:
The 50 base pair single-end reads obtained from Illumina Hi-Seq 2500 were quality filtered and adapters were trimmed using Trimmomatic version 0.33 (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170).  Reads were compared with the Rfam database using the Infernal program version 1.1.2 (Nawrocki and Eddy, 2013. Bioinformatics 29 (22): 2933-2935. DOI: 10.1093/bioinformatics/btt509) and used to filter tRNAs, rRNAs, snoRNAs and snRNAs from the data. The reads were also filtered using the Triticeae Repeat Sequence Database (Wicker et al., 2008. BMC Genomics 9: 518. DOI: 10.1186/1471-2164-9-518) to remove any known triticeae-specific repeat sequences.
For each of the 90 samples, read count estimation was done using RSEM (Li and Dewey, 2011. BMC Bioinformatics 12: 323. DOI: 10.1186/1471-2105-12-323) with Trimmomatic (Bolger et al., 2014. Bioinformatics 30 (15): 2114–2120. DOI: 10.1093/bioinformatics/btu170) trimmed reads as input.
Genome_build: Barley (Mascher et al., 2017. Nature 544: 427–433. DOI: 10.1038/nature22043) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu et al., 2010. Science 330 (6010): 1543-1546. DOI: 10.1126/science.1194573).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew in respective csv files

source_name: Barley infected first leaf (PO:0007094)

extract_protocol:
Total RNA was isolated from 0.5 g of each pool using a hot (60˚C) phenol / guanidine thiocyanate method (Caldo et al., 2004. Plant Cell 16: 2514-2528. DOI: 10.1105/tpc.104.023382).
Small RNA-sequencing (small RNA-seq) libraries were prepared by the Iowa State University DNA Facility (Ames, Iowa, USA) using the Illumina TruSeq small RNA library preparation kit and were subjected to single-end sequencing (100-bp reads) using the Illumina Hi-Seq 2500 Sequencing System. A split-split-plot design was used to run the 90 samples on three Hi-Seq 2500 flow cells. Each replication was run on a separate flow cell with each plant genotype randomly assigned to each lane and 6 barcodes randomly assigned to the 6 time points within each genotype (lane).

value: Barley infected first leaf (PO:0007094)

tag: fungal isolate

value: Bgh isolate 5874

tag: timepoint

value: 20 HAI

tag: replication

value: Rep 1


title: 21NT+TBX3iso2_IGG_2

status: Public on Feb 07 2019

type: genomic

city: London

first: Alan

last: Tuck

address: 339 Windermere Rd

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

description:
GeneChip Human Promoter 1.0R Array (Affymetrix, 900776)
Iso2_vs_EV_enriched.txt
TBX3iso2_vs_EV_IgG_subtracted_processed.xls

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
CEL files were imported into Partek Genomic Suites (PGS) and analyzed using the Chromatin Immunoprecipitation workflow.
Differential probe intensities between TBX3iso1 or TBX3iso2 vs empty vector were determined by ANOVA and enriched regions of significance were determined using the MAT algorithm.
To be further considered, an enriched region had to have a minimum MAT score of 5 at p<0.05.

source_name: Stably transfected breast cancer cell line

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were maintained in αMEM media supplemented with 1mM L-glutamine, 1µg/mL insulin, 12.5ng/mL EGF, 2.8µM hydrocortisone, 10mM HEPES, 1mM sodium pyruvate, 0.1mM non-essential amino acids, 50µg/mL gentamycin sulfate, 500µM G418 (selection agent), and 10% FBS. All reagents were obtained from Wisent Inc.

extract_protocol: Cells were cross-linked with formalin, sonicated, and lysates underwent chromatin immunoprecipitation with either non-specific rabbit IgG antibody or specific rabbit anti-TBX3 antibody.

treatment_protocol: 21NT parental cell lines underwent authentication testing by Idexx Radil (Case No. 20250-2013). Cells were transfected with an empty vector (EV), TBX3iso1, or TBX3iso2 construct within a pcDNA3.1 vector (Invitrogen, V79020) as previously described (Krstic et al. 2016, BMC Cancer).

tag: antibody

value: Rabbit IgG control antibody IP


title: 21NT+TBX3iso2_IGG_1


title: 2_RNA-seq with atrR null

tag: genotype/variation

value: null mutant


title: 21NT+TBX3iso1_TBX3_1

description:
GeneChip Human Promoter 1.0R Array (Affymetrix, 900776)
iso1_vs_EV_enriched.txt
TBX3iso1_vs_EV_IgG_subtracted_processed.xls

value: Rabbit anti-TBX3 antibody IP


title: 21NT+TBX3iso1_TBX3_2


title: 21NT+TBX3iso2_TBX3_2


title: 21NT+TBX3iso1_IGG_2


title: thymus miR-181-KO rep2

description: primary Foxp3+ Treg cells sorted from thymus of miR-181 knockout mouse, group 2

tag: tissue


title: 21NT+TBX3iso1_IGG_1


title: 21NT+TBX3iso2_TBX3_1


title: 21NT+EV_IGG_2

description:
GeneChip Human Promoter 1.0R Array (Affymetrix, 900776)
(used for normalization)
(used for normalization)


title: 21NT+EV_TBX3_1


title: 21NT+EV_IGG_1


title: 21NT+EV_TBX3_2


title: spleen miR-181-KO rep2

description: primary Foxp3+ Treg cells sorted from spleen of miR-181 knockout mouse, group 2


title: 1_RNA-seq wild-type strain

value: wild-type


title: MEF reprogramming intermediate_Day 2

source_name: MEF reprogramming intermediate

tag: Sex

value: Female

value: MEF reprogramming intermediate

tag: time


title: Gefitinib-sensitive lung cancer cell line,biological rep2

city: Taipei

first: Tzu-Hua

address: No. 7, Chung-Shan South Road

department: Department of Internal Medicine

institute: National Taiwan University Hospital

description: Gene expression data from the gefitinib-sensitive lung cancer cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The expression data were analyzed by the SAS JMP Genomics software (Version 4.0; SAS Institute Inc., Cary, NC). Affymetrix CEL files were transformed by RMA algorithm, imported at the probe level and log2 transformed, and each probe set was summarized using the median of the corresponding probes. Each array was normalized by Quantile Normalization.

data_processing: RMA signal intensity

source_name: lung cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: Cells were cultured in RPMI-1640 medium  with 10% fetal bovine serum (FBS), 100 u/ml penicillin and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: HCC827/gef cells were selected from parental HCC827 cells that had been continuously exposed to increasing concentrations of gefitinib.

value: lung adenocacinoma


title: Gefitinib-sensitive lung cancer cell line,biological rep1


title: Acquired gefitinib-resistant lung cancer cell line,biological rep2

description: Gene expression data from the acquired gefitinib-resistant lung cancer cells

source_name: lung cancer cells, long term gefitinib treatment


title: Acquired gefitinib-resistant lung cancer cell line,biological rep3


title: Acquired gefitinib-resistant lung cancer cell line,biological rep1


title: smallRNAseq_NRPD1-ZF_fwa_dcl3_rep2_Figure1

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl3 replicate 2 used for Figure 1

data_processing:
For sRNA-seq data analysis, raw reads were trimmed for Illumina adaptors using Cutadapt (v 1.9.1) and mapped to the TAIR10 reference genome using Bowtie (v1.1.0) (Langmead et al., 2009) allowing only one unique hit (-m 1) and zero mismatch. In order to define off-target sites with 24-nt siRNAs production, flanking 1kb of off-target region with NRPE1 recruitment were first divided into 100bp bins. Then 24-nt siRNAs count were calculated over those 100bp bins and DEseq2 (Love et al., 2014) was applied using 4 fold change and FDR less than 0.05 as cut off for DMS3-ZF vs ZF, NRPD1-ZF vs ZF and DMS3-ZF X NRPD1-ZF vs ZF.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: All plants in this study were grown under long-day conditions (16h light/8h dark). Transgenic plants were obtained by agrobacterium-mediated floral dipping. T1 transgenic plants were selected on 1/2 MS medium + Glufosinate 50 μg/ml (Goldbio) or 1/2 MS medium + Hygromycin B 25 μg/ml (Invitrogen) in growth chambers under long day conditions and subsequently transferred to soil. Successive transgenic generations were germinated directly on soil.

extract_protocol:
RNA from inflorescences was extracted using the Zymo Direct-zol Kit (ZYMO research).
For sRNA-seq libraries, 2ug total RNA was run in 15% UREA gels and small RNAs from 15 to 30bp were cut and precipitated. This RNA was used to prepare libraries using the Truseq small RNA kit (Illumina) following manufacturer’s instructions.

value: inflorescence

tag: ecotype

value: Columbia


title: Pre-NC treated-keratinocytes_48h_rep3

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

institute: hinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression profiles after 48h in Pre-NC treated-keratinocytes

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: keratinocytes,Pre-NC, 48h, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using TRIZOL following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary human keratinocytes were cultured with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were transfected with either miR-146a mimics (Pre-146a) or negative control (Pre-NC) for 48h.

value: keratinocytes

tag: transfection

value: Pre-NC

tag: time point


title: smallRNAseq_Col-0_rep2_Figure1

description: small RNAseq for Col-0 replicate 2 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_dcl2/3/4_rep2_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl2/3/4 replicate 2 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_dcl3_rep1_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl3 replicate 1 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_rep1_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa replicate 1 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_dcl2/4_rep1_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl2/4 replicate 1 used for Figure 1


title: smallRNAseq_fwa_dcl2/3/4_rep2_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for fwa x dcl2/3/4 replicate 2 used for Figure 1


title: Pre-NC treated-keratinocytes_48h_rep1

source_name: keratinocytes,Pre-NC, 48h, replicate 1


title: smallRNAseq_fwa_dcl2/3/4_rep1_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for fwa x dcl2/3/4 replicate 1 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_dcl2/4_rep2_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl2/4 replicate 2 used for Figure 1


title: smallRNAseq_NRPD1-ZF_fwa_rep2_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa replicate 2 used for Figure 1


title: Pre-146a treated-keratinocytes_48h_rep2

description: Gene expression profiles after 48h in Pre-146a treated-keratinocytes

source_name: keratinocytes, Pre-146a,48h, replicate 2


title: smallRNAseq_NRPD1-ZF_fwa_dcl2/3/4_rep1_Figure1

description:
reads for this sample were produced on both Illumina HiSeq 2000 and HiSeq 2500
small RNAseq for NRPD1-ZF in fwa x dcl2/3/4 replicate 1 used for Figure 1


title: thymus miR-181-HET rep1

description: primary Foxp3+ Treg cells sorted from thymus of miR-181 heterozygous mouse, group 1

tag: strain

value: primary Foxp3+ Treg cells

value: thymus

value: miR-181 heterozygous


title: smallRNAseq_fwa_rep1_Figure1

description: small RNAseq for fwa replicate 1 used for Figure 1

value: fwa


title: Gefitinib-sensitive lung cancer cell line,biological rep3


title: Pre-NC treated-keratinocytes_48h_rep2

source_name: keratinocytes,Pre-NC, 48h, replicate 2


title: HUVEC+exo lncRNA-APC1

city: Guangzhou

first: Fengwei

last: Wang

address: No.651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: mRNA expression data from HUVEC cells treated by exosomes derived from colorectal cancer cell line HCT116 transfected with lncRNA-APC1

hyb_protocol: The labeled cRNAs were hybridized onto the Phalanx human OneArray microarrays (HOA 6.1), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505B

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: human umbilical vein endothelial cells, HUVEC

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: HUVEC cell line were cultured in SFM medium with 10%FBS, 0.02ug/ml bFGF, 0.01ug/ml EGF at 37 ℃ in a 5% CO2–95% air incubator (Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: Gene expression profiles of the HUVEC cells incubated with lncRNA-APC1 silenced or control HCT116 cancer cell derived exosomes were determined using Phalanx human OneArray microarrays (HOA 6.1) following the manufacturer's instructions

tag: cell line


title: Pre-146a treated-keratinocytes_48h_rep1

source_name: keratinocytes,Pre-146a, 48h, replicate 1


title: HUVEC+exo control

description: mRNA expression data from HUVEC cells treated by exosomes derived from colorectal cancer cell line HCT116 transfected with control vectorpancreatic ductal adenocarcinoma (PDAC)

value: control vecto


title: smallRNAseq_fwa_rep2_Figure1

description: small RNAseq for fwa replicate 2 used for Figure 1


title: smallRNAseq_Col-0_rep1_Figure1

description: small RNAseq for Col-0 replicate 1 used for Figure 1


title: WGBS_T3_DMS3-ZF_Col-0_line2_minus_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line2 minus (without transgene) replicate 2 for Figure5

data_processing:
For WGBS data analysis, raw reads were aligned using with BSMAP (v 2.74) (Xi and Li, 2009) to the reference TAIR10 genome by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands(-n 1). Methylation levels at each cytosine were then extracted with BSMAP (methratio.py) scripts by allowing only unique mapped reads (-u). Reads with more than 3 consecutive methylated CHH sites were removed. Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between DMS3-ZF and ZF, NRPD1-ZF and ZF, DMS3-ZF X NRPD1-ZF and ZF were calculated as before (Stroud et al., 2013). DMRs were then defined with R package DMRcaller (Catoni et al., 2018) as described before (Stroud et al., 2013) except that the 100bp window tested for DMR are 1kb flanking region over the 10776 ZF binding sites. DMRs within 200bp of each other were merged for further analysis. For analysis of hyperDMRs in DMS3-ZF, NRPD1-ZF or DMS3-ZF X NRPD1-ZF, all three types of hyperDMRs (CG/CHG/CHH) were combined and merged if the distance between two DMRs were less than 200bp. Annotations of hyperDMR to the nearest genes were calculated using HOMER (Heinz et al., 2010). In order to call high confidence CHH hyperDMR in DMS3-ZF fwa nrpd1 (Figure 6B), after calling genome-wide DMR, we filtered out DMRs with pre-existing CHH methylation greater than 0.05 as well as DMRs that overlapped with tRNA regions.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

source_name: leaf

extract_protocol:
Libraries for WGBS were made using 100ng of CTAB-extracted DNA from leaves of adult plants.
DNA was converted using the Epitect Bisulfite Conversion kit (Qiagen) and libraries were prepared using the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions.

value: leaf


title: WGBS_T3_ZF_Col-0_line1_minus_Figure5

description: WGBS for T3 ZF in Col-0 line1 minus (without transgene) replicate 1 for Figure5


title: WGBS_T3_ZF_Col-0_line2_minus_Figure5

description: WGBS for T3 ZF in Col-0 line2 minus (without transgene) replicate 2 for Figure5


title: WGBS_T3_DMS3-ZF_Col-0_line1_minus_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line1 minus (without transgene) replicate 1 for Figure5


title: WGBS_T3_ZF_Col-0_line2_plus_rep2_Figure5

description: WGBS for T3 ZF in Col-0 line2 plus (with transgene) replicate 2 for Figure5


title: WGBS_T3_ZF_Col-0_line1_plus_rep2_Figure5

description: WGBS for T3 ZF in Col-0 line1 plus (with transgene) replicate 2 for Figure5


title: WGBS_T3_Col-0_rep2_Figure5

description: WGBS for Col-0 (control for T3) replicate 2 used for Figure5


title: WGBS_T3_ZF_Col-0_line1_plus_rep1_Figure5

description: WGBS for T3 ZF in Col-0 line1 plus (with transgene) replicate 1 for Figure5


title: WGBS_T3_ZF_Col-0_line2_plus_rep1_Figure5

description: WGBS for T3 ZF in Col-0 line2 plus (with transgene) replicate 1 for Figure5


title: WGBS_T3_DMS3-ZF_Col-0_line2_plus_rep1_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line2 plus (with transgene) replicate 1 for Figure5


title: WGBS_T3_DMS3-ZF_Col-0_line2_plus_rep2_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line2 plus (with transgene) replicate 2 for Figure5


title: WGBS_T2_DMS3-ZF_Col-0_line1_rep1_Figure5

description: WGBS for T2 DMS3-ZF in Col-0 line1 replicate 1 for Figure5


title: WGBS_T2_ZF_Col-0_line2_rep2_Figure5

description: WGBS for T2 ZF in Col-0 line2 replicate 2 for Figure5


title: WGBS_T2_Col-0_rep2_Figure5

description: WGBS for Col-0 (control for T2) replicate 2 used for Figure5


title: WGBS_T2_ZF_Col-0_line1_rep1_Figure5

description: WGBS for T2 ZF in Col-0 line1 replicate 1 for Figure5


title: WGBS_T2_DMS3-ZF_Col-0_line1_rep2_Figure5

description: WGBS for T2 DMS3-ZF in Col-0 line1 replicate 2 for Figure5


title: WGBS_T2_ZF_Col-0_line1_rep2_Figure5

description: WGBS for T2 ZF in Col-0 line1 replicate 2 for Figure5


title: WGBS_DMS3-ZF_fwa_FigureS2

description: WGBS for DMS3-ZF in fwa used for FigureS2


title: WGBS_T2_ZF_Col-0_line2_rep1_Figure5

description: WGBS for T2 ZF in Col-0 line2 replicate 1 for Figure5


title: WGBS_T2_DMS3-ZF_Col-0_line2_rep1_Figure5

description: WGBS for T2 DMS3-ZF in Col-0 line2 replicate 1 for Figure5


title: WGBS_T3_Col-0_rep1_Figure5

description: WGBS for Col-0 (control for T3) replicate 1 used for Figure5


title: WGBS_NRPD1-ZF_fwa_FigureS1

description: WGBS for NRPD1-ZF in fwa used for FigureS1


title: WGBS_fwa_FigureS1

description: WGBS for fwa used for FigureS1


title: WGBS_Col-0_FigureS1

description: WGBS for Col-0 used for FigureS1


title: WGBS_T2_Col-0_rep1_Figure5

description: WGBS for Col-0 (control for T2) replicate 1 used for Figure5


title: Pre-146a treated-keratinocytes_48h_rep3

description: Gene expression profiles after 48h in Pre-146a treated-keratinocytes

source_name: keratinocytes, Pre-146a,48h, replicate 3


title: BSPCR_MORC1-ZF_in_wt_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in MORC1-ZF in fwa_region1to3

data_processing:
Library strategy: BS-PCR-seq
For BS-PCR-seq analysis, raw sequencing reads with designed BS-PCR primers were filtered followed by primer trimming with customized scripts. Trimmed reads were then aligned with BSMAP (v.2.74) (Xi and Li, 2009) to the reference TAIR10 genome by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands (-n 1). The methylation level at each cytosine was then extracted with BSMAP (methratio.py) scripts by allowing only unique mapped reads (-u). Reads with more than 3 consecutive methylated CHH sites were removed. Methylation levels at each cytosine were calculated as #C/(#C+#T). Cytosines with less than 20 reads coverage were discarded. To visualize the BS-PCR- seq data, only cytosines within designated regions were kept and plotted with customized R scripts. For representation of AP1 BS-PCR-seq, the methylation levels present in the three regions analysed were combined.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

extract_protocol:
Leaf tissue from adult plants of representative T2 lines was collected to analyze FWA methylation. Inflorescences of representative T2 lines were collected to analyze AP1 methylation. DNA was extracted following a CTAB-based method and converted using the EZ DNA methylation-lighting kit (ZYMO research) or the Epitect Bisulfite Conversion kit (Qiagen). For FWA, we analyzed methylation over three different regions: Region 1: chr4: 13038143-13038272; Region 2: chr4: 13038356-13038499; Region3: chr4: 13038568-13038695. For AP1, we analyzed methylation over three different regions: Region 1: chr1: 25986270-25986391; Region 2: chr1: 25985976-25986098; Region 3: chr1:25986235-25986108. To amplify the different regions, Pfu Turbo Cx (Agilent) was used together with primers containing the Illumina adaptors. The primers used are listed in Table S1. Different PCR products for the same sample were pooled and purified by AMPure beads (Beckman Coulter).
Libraries were made from purified PCR products by a TruSeq Nano DNA Library Prep kit for Neoprep automated library preparation machine (Illumina), by Kapa DNA hyper kit (Kapa Biosystems) with Illumina TruSeq DNA adapters or by Ovation Ultralow V2 kit (NuGEN).


title: BSPCR_SUVH9-ZF_in_morc6_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in SUVH9-ZF in fwa x morc6_region1to3


title: BSPCR_SUVH9-ZF_in_suvh29_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in SUVH9-ZF in fwa x suvh2/9_region1to3


title: WGBS_T3_DMS3-ZF_Col-0_line1_plus_rep1_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line1 plus (with transgene) replicate 1 for Figure5


title: WGBS_T3_DMS3-ZF_Col-0_line1_plus_rep2_Figure5

description: WGBS for T3 DMS3-ZF in Col-0 line1 plus (with transgene) replicate 2 for Figure5


title: BSPCR_RDM1-ZF_in_rdm1_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in RDM1-ZF in fwa x rdm1_region1to3


title: BSPCR_RDM1-ZF_in_morc6_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in RDM1-ZF in fwa x morc6_region1to3


title: BSPCR_DMS3-ZF_in_dms3_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x dms3_region1to3


title: BSPCR_RDM1-ZF_in_suvh29_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in RDM1-ZF in fwa x suvh2/9_region1to3


title: BSPCR_RDM1-ZF_in_nrpd1_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in RDM1-ZF in fwa x nrpd1_region1to3


title: BSPCR_DMS3-ZF_in_ago4_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x ago4_region1to3


title: BSPCR_DMS3-ZF_in_morc6_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x morc6_region1to3


title: BSPCR_DMS3-ZF_in_rdm1_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x rdm1_region1to3


title: BSPCR_DMS3-ZF_in_wt_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa _region1to3


title: BSPCR_DMS3-ZF_in_drm12_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x drm1/2_region1to3


title: BSPCR_DMS3-ZF_in_such29_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x suvh2/9_region1to3


title: BSPCR_DMS3-ZF_in_nrpd1_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x nrpd1_region1to3


title: BSPCR_DMS3-ZF_in_cmt3_Figure2

description:
PCR amplified DNA
BS-PCR over FWA in DMS3-ZF in fwa x cmt3_region1to3


title: BSPCR_NRPD1-ZF_in_shh1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x shh1_region1to3


title: BSPCR_NRPD1-ZF_in_wt_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa_region1to3


title: BSPCR_NRPD1-ZF_in_dcl24_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x dcl2/4_region1to3


title: BSPCR_NRPD1-ZF_in_clsy1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x clsy1_region1to3


title: BSPCR_NRPD1-ZF_in_dcl3_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x dcl3_region1to3


title: BSPCR_NRPD1-ZF_in_dcl234_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x dcl2/3/4_region1to3


title: BSPCR_NRPD1-ZF_in_ago4_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x ago4_region1to3


title: BSPCR_NRPD1-ZF_in_cmt3_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x cmt3_region1to3


title: BSPCR_RDR2-ZF_in_dcl3_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in RDR2-ZF in fwa x dcl3_region1to3


title: BSPCR_RDR2-ZF_in_wt_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in RDR2-ZF in fwa_region1to3


title: BSPCR_SHH1-ZF_in_clsy1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in SSH-ZF in fwa x clsy1_region1to3


title: BSPCR_NRPD1-ZF_in_nrpd1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in NRPD1-ZF in fwa x nrpd1_region1to3


title: 6_ChiP-seq with hspA-atrR-3X HA tag present

value: hspA-atrR-3X HA tag present

tag: chip antibody

value: Purified anti-HA.11 Epitope Tag Monoclonal Antibody (raised in mice)

tag: chip antibody vendor

value: Covance Inc., MA, USA (Now BioLegend)

tag: chip antibody catalog #

tag: chip antibody lot #


title: BSPCR_RDR2-ZF_in_rdr2_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in RDR2-ZF in fwa x rdr2_region1to3

tag: genotype


title: BSPCR_RDR2-ZF_in_shh1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in RDR2-ZF in fwa x shh1_region1to3


title: BSPCR_RDR2-ZF_in_clsy1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in RDR2-ZF in fwa x clsy1_region1to3


title: BSPCR_SHH1-ZF_in_wt_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in SSH-ZF in fwa_region1to3


title: BSPCR_SHH1-ZF_in_shh1_Figure1

description:
PCR amplified DNA
BS-PCR over FWA in SSH-ZF in fwa x shh1_region1to3


title: BSPCR_SUVH9-ZF_in_wt_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in SUVH9-ZF in fwa_region1to3


title: BSPCR_RDM1-ZF_in_wt_Figure3

description:
PCR amplified DNA
BS-PCR over FWA in RDM1-ZF in fwa_region1to3


title: S7.H10

city: Santa Cruz

first: Christopher

last: Villarreal

state: CA

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

description: PrimaryOrganoidAndPublishedCPM.txt

data_processing:
Trim Galore 3.7
HISAT2
subread-1.5.0 function featureCounts
Human GRCh38.79.gtf
The listed genes in the processed data file are human genes mapped to each respective species using the comparative annotation toolkit (PMID: 29884752). Reads are mapped to each species' native genome and quantified based transcript models from comparative annotation toolkit.
The file GSE124299-metadata on processed samples.xlsx  includes the metadata for all samples in this study-- both the new samples listed in this Series and the re-analyzed samples, including accession IDs, when available.
Genome_build: Human: GRCh38.p2; NCBI:GCA_000001405.17
Genome_build: Chimpanzee: Clint_PTRv2 / UCSC: panTro6
Genome_build: Macaque: RheMac8
Supplementary_files_format_and_content: log(CPM+1)

source_name: iPS-derived cerebral organoid

growth_protocol: Cerebral organoids using Kadoshima et al., 2013 from Sasai lab

extract_protocol:
Fluidigm C1 small IFC (100-5759; 100-6201);  SMARTer® Ultra™ Low RNA Kit (634832)
Nextera XT tagmentation kit (FC-131-096)

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

tag: datecaptured

value: Male

tag: organoidid

tag: protocol

value: Kadoshima

tag: captureplate

tag: capturechamber


title: S7.E8

description: PrimaryOrganoidAndPublishedCPM.txt

tag: tissue

tag: Sex


title: S7.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.A7

description: PrimaryOrganoidAndPublishedCPM.txt

value: Female


title: S73.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.B2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.D12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.D10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S73.B5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.E12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.C7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S7.F10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.D7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.D3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.B2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.H12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.G11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.D9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.H4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.H3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S67.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.D11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.C3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.D3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.B9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.A10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.H10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.H5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S66.B2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.F4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.D12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.D3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.D1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.C3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.C6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H9

description: PrimaryOrganoidAndPublishedCPM.txt

value: WTC


title: S64.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S64.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.D11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.C3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S6.A6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.H10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.F10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.G8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.H12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.D4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S5.D12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S202.H4

description: PrimaryOrganoidAndPublishedCPM.txt