title: S175.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.C1

status: Public on Feb 07 2019

type: SRA

city: Santa Cruz

first: Christopher

last: Villarreal

state: CA

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

department: Genomics Institute

country: USA

description: PrimaryOrganoidAndPublishedCPM.txt

library_source: transcriptomic

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)

molecule: polyA RNA

organism: Pan troglodytes

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)

tag: tissue

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

tag: datecaptured

tag: Sex

value: Male

tag: organoidid

tag: protocol

value: Kadoshima

tag: captureplate

tag: capturechamber


title: Batch2_IL13_Biological_Replicate_3

city: Iowa City

first: Alejandro

middle: A

last: Pezzulo

state: IA

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

data_processing:
The six fastq files for each sample (Paired read 1 and read 2 for same library across three lanes) were processed with Kallisto v0.44.0 (default parameters except 75 bootstraps) using Homo sapiens GRCh38 Ensembl release 91 cDNA FASTA file as reference for Kallisto index.
Differential expression was analyzed with Sleuth v0.29.0 for transcript level analysis.
Additionally, tximport v1.3.4 was used to summarize the Kallisto output into gene-level estimates for DESeq2 v1.18 analysis in R v3.4.3 and Bioconductor v3.5.
Genome_build: GRCh 38, Ensembl release 91
Supplementary_files_format_and_content: Tab delimited text file containing Kallisto abundance measurement for each transcript

molecule: total RNA

organism: Homo sapiens

source_name: Cultured primary human airway epithelia at air-liquid interface

growth_protocol: Epithelial cells were isolated from the trachea and bronchi by enzymatic digestion, seeded onto collagen-coated, semi-permeable membranes (0.6 cm2 Millicell-PCF; Millipore), and grown at the air–liquid interface as previously described in Karp et al, Methods Mol Biol 2002;188:115. Culture medium, a 1:1 mixture of DMEM/F12, was supplemented with 2% Ultroser G (PALL France SAS). Differentiated epithelia were used at least 14 days after seeding. Media was changed every 2 days. At every media change, 20 µL basolateral media was uniformly added to the apical surface to allow basolateral and apical exposure to treatment conditions.

extract_protocol:
RNA from primary human airway epithelia was isolated with the RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). Two cultures (approximately 600,000 cells total) were used for each extraction. Initial quality control was performed with Nanodrop 2000 (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).
Library prep and sequencing performed at the Iowa Institute of Human Genetics Genomics Division. Sequencing libraries were prepared with the Illumina TruSeq Stranded total RNA ribozero gold sample preparation kit (Illumina, San Diego, CA) starting with 500 ng of input total RNA, and following Illumina's sample preparation guide.  The libraries were analyzed on the Fragment Analyzer (Advanced Analytical, Ankeny, IA) and combined in equimolar concentrations into pools. The pools were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) using the High Sensitivity chip to evaluate size distribution. The concentration of each pool was measured using the KAPA Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Pools were sequenced on the Illumina HiSeq 4000 sequencer with a 150 bp Paired-End SBS chemistry (Illumina) across three lanes.

treatment_protocol: In batch 1 (XAM1), epithelia were exposed to vehicle (DMSO 0.5%),  geldanamycin 25 uM, or the HDAC6 inhibitor ISOX 10 uM for 48 hours. In batch 2 (XAM3), the epithelia were exposed to vehicle (DMSO 0.5%), IL13 (20 ng/mL) or IL13 plus geldanamycin (10 uM) for 48 hours.

tag: cell type

value: Primary human airway epithelia

tag: treatment


title: Batch2_IL13+Geldanamycin_Biological_Replicate_2


title: S175.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.B9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.A7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch2_Vehicle_Biological_Replicate_2

value: Vehicle


title: S175.A5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch2_IL13+Geldanamycin_Biological_Replicate_1


title: Batch2_IL13_Biological_Replicate_2


title: Batch1_Geldanamycin_Biological_Replicate_8

value: Geldanamycin


title: Batch2_Vehicle_Biological_Replicate_3


title: Batch2_Vehicle_Biological_Replicate_1


title: Batch1_ISOX_Biological_Replicate_8

value: ISOX


title: S175.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.H12

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch2_Vehicle_Biological_Replicate_5


title: Batch1_Vehicle_Biological_Replicate_8


title: Batch1_Geldanamycin_Biological_Replicate_7


title: Batch1_ISOX_Biological_Replicate_7


title: Batch1_Vehicle_Biological_Replicate_7


title: S173.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.H4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.G8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_6


title: Batch2_IL13_Biological_Replicate_1


title: S173.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Vehicle_Biological_Replicate_6


title: S173.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.A10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Geldanamycin_Biological_Replicate_6


title: S173.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_4


title: S173.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Geldanamycin_Biological_Replicate_5


title: S173.E10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.D7

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_5


title: Batch1_Geldanamycin_Biological_Replicate_4


title: Batch1_Vehicle_Biological_Replicate_5


title: S173.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.D12

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Geldanamycin_Biological_Replicate_3


title: S173.D11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.C8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.C7

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Vehicle_Biological_Replicate_3


title: S173.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_2


title: S173.D1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Vehicle_Biological_Replicate_4


title: Y537S_E2_24h_3

city: Urbana

first: David

middle: J

last: Shapiro

state: IL

address: 600 South Mathews Avenue

department: Biochemistry

institute: University of Illinois Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Quality control was performed using fastqc 0.11.5. Adapters were trimmed using bcl2fastq v2.17.1.14.
STAR aligner (version 2.5.1b) was employed to generate a genome index using ensembl genome annotation (version GRCh38.p10), and single end reads were aligned to human genome using the genome index as reference.
Raw read counts from BAM files were calculated using featureCounts (subread 1.5.0).
The R package ‘edgeR’ was used to normalize counts using trimmed mean of M-values (TMM) method. Tagwise dispersions were estimated and negative binomial model was used to determine differentially expressed genes between the mutants and parental cell line
Genome_build: Ensembl GRCh38.p10
Supplementary_files_format_and_content: Text files of raw read counts generated by featureCounts

source_name: TYS

growth_protocol: T47D cells were cultured in MEM containing 10% FBS. TYS and TDG cells were cultured in MEM containing 10% charcoal dextran treated FBS (CD-FBS).

extract_protocol:
Total RNA of three biological replicates were extracted using Qiagen RNeasy Plus Mini Kit to eliminate genomic DNA.
cDNA libraries were prepared with TruSeq Stranded mRNAseq Sample Prep kit (Illumina).

treatment_protocol: Cells were transferred to MEM containing 10% CD-FBS for 48 hours and then cultured in MEM containing 10% CD-Calf for 96 hours. After hormone depletion, cells were treated with 10nM estrogen or ethanol for 4 hours or 24 hours.

tag: mutation status

value: ESR1 Y537S

value: 10nM estrogen

tag: treatment time

value: 24 hours


title: S173.A6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Geldanamycin_Biological_Replicate_1


title: Batch1_Vehicle_Biological_Replicate_2


title: Y537S_E2_24h_1


title: S173.A2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Vehicle_Biological_Replicate_1


title: S173.A7

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_Geldanamycin_Biological_Replicate_2


title: Y537S_E2_24h_2


title: S173.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_1


title: T47D_E2_24h_3

value: ESR1 WT


title: D538G_E2_24h_1

source_name: TDG

value: ESR1 D538G


title: D538G_E2_24h_2


title: S173.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.H5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Batch1_ISOX_Biological_Replicate_3


title: T47D_E2_24h_1


title: S173.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S173.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: D538G_E2_24h_3


title: Y537S_E2_4h_3

value: 4 hours


title: S169.H4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Y537S_E2_4h_1


title: Y537S_Veh_2

value: ethonol


title: S169.H12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.H10

description: PrimaryOrganoidAndPublishedCPM.txt


title: D538G_E2_4h_3


title: S169.G6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Y537S_Veh_1


title: S169.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: T47D_E2_24h_2


title: S169.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: D538G_E2_4h_1


title: S169.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: Y537S_E2_4h_2


title: D538G_Veh_2


title: D538G_E2_4h_2


title: S169.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: T47D_E2_4h_3


title: D538G_Veh_3


title: D538G_Veh_1


title: T47D_E2_4h_2


title: S169.F7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: Y537S_Veh_3


title: T47D_E2_4h_1


title: S169.F4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: T47D_Veh_3


title: T47D_Veh_2


title: S169.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.F10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: T47D_Veh_1


title: S169.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: High BiFC sort; Replicate 2

first: Erik

last: Procko

address: 601 S Goodwin Ave

institute: University of Illinois

description: Deep mutational scan of 001428 Env for interactions with MA domain of Gag based on BiFC

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: python Paired_read_fuser.py --path output/ --read1 001428_sample_R1.fastq.bz2 --read2 001428_sample_R2.fastq.bz2 --wtseq AATTGGCTCTGGTATATAAAAATTTTCATAATGATAGTAGGTGGGTTGATTGGTCTTCGCATCATTTTTGCGGTATTGTCTATCGTCAACCGAGTAAGACAGGGGTATTCCCCATTGTCTTTCCAAACATTGACCCCAAACCCGACTGGCCCCGACAGACTCGGGAGAATCGAAGAAGAGGGAGGTGAGCAGGATAGAGATAGGAGCGTGAGGCTTGTGAACGGTTTCCTG --read1_overlap_start 22 --read1_overlap_end 253 --read2_overlap_start 42 --read2_overlap_end 273  --paired_mismatch_threshold 301 --mode B
Aligner script: python Fused_read_aligner.py --path output/ --infile 001428_sample_R1.fast_B_qc1 --referenceDNA AATTGGCTCTGGTATATAAAAATTTTCATAATGATAGTAGGTGGGTTGATTGGTCTTCGCATCATTTTTGCGGTATTGTCTATCGTCAACCGAGTAAGACAGGGGTATTCCCCATTGTCTTTCCAAACATTGACCCCAAACCCGACTGGCCCCGACAGACTCGGGAGAATCGAAGAAGAGGGAGGTGAGCAGGATAGAGATAGGAGCGTGAGGCTTGTGAACGGTTTCCTG --referenceAA NWLWYIKIFIMIVGGLIGLRIIFAVLSIVNRVRQGYSPLSFQTLTPNPTGPDRLGRIEEEGGEQDRDRSVRLVNGFL --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path output/ --infile 001428_sample_R1.fast_R1_qc1_PRO_qc2
MapRatios script: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size 77
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

organism: Human immunodeficiency virus 1

source_name: Synthetic coding sequences

growth_protocol: Expi293F cells with the CXCR4 gene knocked out using genome editing, and stably expressing the MA domain of Gag fused to VN.  Cells were cultured in Expi293 Expression Medium (Life Technologies).

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA was prepared using Accuscript Hi-Fi (Agilent Genomics) primed with EBV reverse primer (GTGGTTTGTCCAAACTCATC).
In a first round of PCR, the 001428 coding sequence was amplified using oligonucleotides with complementary overhangs for annealing to Illumina sequencing primers.
Primer pair for gene-specific amplification: Illumina_001428VC_1996_for (TCTTTCCCTACACGACGCTCTTCCGATCTTTGGTCATGGTTTGATATCTC) and Illumina_001428VC_2277_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTTCTTCTGCTTGTCTCCAG)
In a second round of PCR, Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a MiSeq using a 2x300nt PE v3 paired end protocol.

treatment_protocol: Env sequence variants were cloned into pCEP4 (Invitrogen) containing a chimeric intron in the 5' UTR.  Cells were transfected with the 001428(753)-VC plasmid DNA library under conditions that typically give no more than one sequence variant per cell.  24 hours post-transfection, cells were stained with 2 nM PG16 (secondary: APC-conjugated anti-human IgG Fc) to detect Env expression.  On a BD FACS Aria II, single cells were gated by FSC/SSC properties, and propidium iodide-positive dead cells and autofluorescent cells in the Pacific Blue channel were excluded.  From the PG16-positive population, the 15 % of cells with highest and lowest BiFC signals were collected.

tag: protein

value: Env (gp160)

tag: sort gate

value: Top 15 % of the PG16-positive population for Venus fluorescence

tag: # collected cells


title: High BiFC sort; Replicate 1


title: Low BiFC sort; Replicate 2

value: Bottom 15 % of the PG16-positive population for Venus fluorescence


title: 001428 Env Naive Plasmid DNA Library

description: plasmid DNA, Naive Env SSM library (strain 001428, a.a. N677-L753 )

library_source: genomic

molecule: genomic DNA


title: Low BiFC sort; Replicate 1


title: ChIPseq_noAb_DMS3-ZF_fwa_nrpd1_FigureS6

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description: ChIPseq for no antibody control in DMS3-ZF in fwa x nrpd1 used for FigureS6

data_processing:
For ChIP-seq data analysis, raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie (v1.0.0) (Langmead et al., 2009), allowing only uniquely mapping reads with fewer than two mismatches, and duplicated reads were removed with Samtools 0.1.19 (Li et al., 2009). For all ChIP-seq experiments, peaks were called using MACS2 (v 2.1.1.) (Zhang et al., 2008). To call peaks for DMS3-ZF (Flag) and ZF (HA) ChIP-seq, Flag and HA ChIP-seq in Col-0 was used as controls. Only Flag or HA peaks with more than 2 fold of enrichment were used for following analysis. DMS3-ZF sites without NRPE1 recruitment correspond to ZF off-target sites with greater than 4 fold enrichment and FDR of 0.05 (tested with R package DESeq (Anders and Huber, 2010) of Flag DMS3-ZF ChIP-seq over NRPE1 ChIP-seq normalized readcounts. The rest of the ZF off-targets were considered sites with NRPE1 recruitment. Genomic distribution of ChIP-seq peaks was calculated using HOMER (Heinz et al., 2010).
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:
ChIPs were performed as described previously with minor modifications (Johnson et al., 2014). 2g of inflorescences were used for Flag, HA, NRPE1 and AGO ChIPs. 2g of 12 day-old seedlings were used for Pol II Ser5 ChIP. All samples were ground and crosslinked with 1% formaldehyde. Chromatin was sheared using a Bioruptor Plus (Diagenode) and immunoprecipitated with Anti-Flag M2 (Sigma), Anti-HA 3F10 (Roche), Anti-Pol II phospho Ser5 Ab5131 (Abcam), Anti-NRPE1 and NRPE1 preimmune serum for NRPE1 control (Liu et al., 2018), Anti-AGO4, Anti-AGO6 and Anti-AGO9 (provided by Dr Olivier Voinnet, ETH, Switzerland) antibodies.
Libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN) following the manufacturer’s instructions.

tag: tissue

value: inflorescence

tag: genotype

tag: ecotype

value: Columbia


title: S169.E10

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

value: Male

value: Kadoshima


title: ChIPseq_AGO9_fwa_Figure6

description: ChIPseq for AGO9 in fwa used for Figure6

value: fwa


title: S169.C7

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured

tag: Sex

tag: organoidid


title: S169.E12

description: PrimaryOrganoidAndPublishedCPM.txt

tag: protocol

tag: captureplate

tag: capturechamber


title: S169.F1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.C2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: C60_rep4

type: RNA

city: London

first: Graeme

last: Thorn

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer institute, Queen Mary University of London

description: 60 mins cordycepin incubation, LPS added, 60 mins further incubation replicate 4

hyb_protocol: Labelled RNA was fragmented and diluted (v/v) in hybridization buffer. Hybridization to the Agilent SurePrint G3 Mouse GE 8x60K Microarray slides was performed in a microarray hybridization oven overnight at 65 °C. The location of each sample was randomized over two chips: replicates 3 and 4 on chip serial no. 252800516931; replicates 1 and 2 on chip serial no. 252800516932.

scan_protocol: The slides were rinsed and immediately scanned using a DNA Microarray Scanner (Agilent model G2505C)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (under protocol GE1_1010_Sep10 and Grid: 028005_D_F_20131202). Text files from feature extraction were analyzed using the R/Bioconductor limma package with log intensities quantile-regressed for normalization. Gene expression was quantified and significance assessed using the empirical Bayes method across all samples.

organism: Mus musculus

source_name: Gene expression 60 mins after addition of 1 μg/ml LPS following 60 mins incubation in 20 µM cordycepin

label_protocol: Total RNA samples were labelled with Cy3 dye using the Agilent Low Input Quick Amp 1-colour Labelling Kit. The level of dye incorporation was evaluated by spectrophotometry (Nanodrop ND1000, LabTech, Uckfield, UK).

growth_protocol: RAW 264.7 cells were grown in DMEM (Sigma, cat no 6429) supplemented with 10% foetal bovine serum (Sigma, cat no F9665) in a humidified incubator at 37 °C with 5% CO2. Cells were subcultured when they reached >80% confluence.

extract_protocol: RNA was extracted from cell lysates using the Macherey Nagel Nucleospin RNA kit (Macherey Nagel, cat no 740955).

treatment_protocol: RAW 264.7 cells were seeded at 2.1E5 cells in 3 ml DMEM + 10% FBS per well in four wells of a 6-well plate (TPP, cat no 92006). 24 hours after seeding, the medium was aspirated, cells were washed in 3 ml phosphate-buffered saline (PBS), and then DMEM + 0.5% FBS was added. 24 hours after this, 3µl DMSO was added to D0 and D60 wells; and 3 µl of 20 mM cordycepin (Sigma, C3394) in DMSO was added to C0 and C60 wells (final concentration 20 µM). 60 minutes later, LPS (Sigma, cat no L6761) was added to D60 and C60 wells at a final concentration of 1 μg/ml for 60 minutes. The 6-well plate was subsequently placed on ice, cells washed with ice-cold PBS, and 350 µl of lysis buffer from the Macherey Nagel Nucleospin RNA kit (Macherey Nagel, cat no 740955) was added to all wells. Cells were in a humidified incubator at 37 °C with 5% CO2 until the end of the experiment, except for brief periods at ambient temperature while LPS, DMSO, and cordycepin were being added.

tag: cell type

value: RAW 264.7 macrophage

tag: treatment


title: S169.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: C60_rep3

description: 60 mins cordycepin incubation, LPS added, 60 mins further incubation replicate 3


title: S169.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.D1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_AGO9_DMS3-ZF_fwa_nrpd1_Figure6

description: ChIPseq for AGO9 in DMS3-ZF in fwa x nrpd1 used for Figure6


title: ChIPseq_NRPE1_fwa_Figure6

description: ChIPseq for NRPE1 in fwa used for Figure6


title: ChIPseq_FLAG_fwa_Figure6

description: ChIPseq for Flag in fwa used for Figure6


title: S169.C6

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_AGO6_fwa_Figure6

description: ChIPseq for AGO6 in fwa used for Figure6


title: D60_rep2

description: 60 mins DMSO incubation, LPS added, 60 mins further incubation replicate 2

source_name: Gene expression 60 mins after addition of 1 μg/ml LPS following 60 mins incubation in DMSO


title: S169.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: C60_rep2

description: 60 mins cordycepin incubation, LPS added, 60 mins further incubation replicate 2


title: S169.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_AGO4_fwa_Figure6

description: ChIPseq for AGO4 in fwa used for Figure6


title: ChIPseq_AGO6_DMS3-ZF_fwa_nrpd1_Figure6

description: ChIPseq for AGO6 in DMS3-ZF in fwa x nrpd1 used for Figure6


title: ChIPseq_AGO4_DMS3-ZF_fwa_nrpd1_Figure6

description: ChIPseq for AGO4 in DMS3-ZF in fwa x nrpd1 used for Figure6


title: S165.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: D60_rep4

description: 60 mins DMSO incubation, LPS added, 60 mins further incubation replicate 4


title: S165.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: C60_rep1

description: 60 mins cordycepin incubation, LPS added, 60 mins further incubation replicate 1


title: S165.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.G8

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_DMS3-ZF_fwa_nrpd1_Figure6

description: ChIPseq for NRPE1 in DMS3-ZF in fwa x nrpd1 used for Figure6


title: ChIPseq_AGO9_DMS3-ZF_fwa_Figure6

description: ChIPseq for AGO9 in DMS3-ZF in fwa used for Figure6


title: S165.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_DMS3-ZF_fwa_nrpd1_Figure6

description: ChIPseq for Flag in DMS3-ZF in fwa x nrpd1 used for Figure6


title: D60_rep1

description: 60 mins DMSO incubation, LPS added, 60 mins further incubation replicate 1


title: D60_rep3

description: 60 mins DMSO incubation, LPS added, 60 mins further incubation replicate 3


title: C0_rep3

description: 120 mins cordycepin incubation, replicate 3

source_name: Gene expression after 120 minute incubation in 20 µM cordycepin

value: 120 mins cordycepin incubation


title: C0_rep4

description: 120 mins cordycepin incubation, replicate 4


title: S165.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_AGO6_DMS3-ZF_fwa_Figure6

description: ChIPseq for AGO6 in DMS3-ZF in fwa used for Figure6


title: C0_rep1

description: 120 mins cordycepin incubation, replicate 1


title: S165.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: D0_rep4

description: 120 mins DMSO incubation, replicate 4

source_name: Gene expression after 120 minute incubation in DMSO

value: 120 mins DMSO incubation


title: S165.H5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_AGO4_DMS3-ZF_fwa_Figure6

description: ChIPseq for AGO4 in DMS3-ZF in fwa used for Figure6


title: S165.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S175.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: C0_rep2

description: 120 mins cordycepin incubation, replicate 2


title: S165.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_DMS3-ZF_fwa_Figure6

description: ChIPseq for NRPE1 in DMS3-ZF in fwa used for Figure6


title: S165.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: D0_rep3

description: 120 mins DMSO incubation, replicate 3


title: S165.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_DMS3-ZF_fwa_Figure6

description: ChIPseq for Flag in DMS3-ZF in fwa used for Figure6


title: ChIPsesq_NRPE1_fwa_ago469_FigureS4

description: ChIPseq for NRPE1 in fwa x ago4/6/9 used for FigureS4


title: S165.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPsesq_FLAG_fwa_ago469_FigureS4

description: ChIPseq for Flag in fwa x ago4/6/9 used for FigureS4


title: D0_rep2

description: 120 mins DMSO incubation, replicate 2


title: D0_rep1

description: 120 mins DMSO incubation, replicate 1


title: S165.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPsesq_FLAG_fwa_drm12_FigureS4

description: ChIPseq for Flag in fwa x drm1/2 used for FigureS4


title: S165.F10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.G11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_Col-0_Figure4

description: ChIPseq for NRPE1in Col-0 used for Figure4


title: ChIPseq_NRPE1preimm_in_DMS3-ZF_Col-0_line2_Figure4

description: ChIPseq for NRPE1preimm in DMS3-ZF in Col-0 line2 used for Figure4


title: S165.E10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.D9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1preimm_in_DMS3-ZF_Col-0_line1_Figure4

description: ChIPseq for NRPE1preimm in DMS3-ZF in Col-0 line1 used for Figure4


title: S165.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_DMS3-ZF_Col-0_line2_Figure4

description: ChIPseq for NRPE1 in DMS3-ZF in Col-0 line2 used for Figure4


title: S165.D6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.D3

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_DMS3-ZF_Col-0_line1_Figure4

description: ChIPseq for NRPE1 in DMS3-ZF in Col-0 line1 used for Figure4


title: S165.D4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: WNV 10x3_spinal cord_3

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

institute: University of Mississippi Medical Center

description: Fixed dose: 10x3 WNV  treated spinal cord, replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized to Rat GeneChip 2.0ST Arrays. GeneChips were automatically washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G

data_processing: Analysis of microarray data was performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software) and commercially available GeneSifter™ software platform using RMA

label: biotin

source_name: Fresh spinal cord tissue after light sedation and decapitation.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for Rat GeneChip 2.0ST Arrays

growth_protocol: Adult male and female mice were purchased from Jackson labs. Animals were bred to obtain pups and 7-9 day old pups were used for slice cultures.

extract_protocol: RNA was isolated using TRIzol® and Invitrogen PureLink Kit (Life Technologies) and evaluated for quality and integrity (Bio-Rad Experion™ System)

treatment_protocol: Whole genome transcript analysis was performed using Affymetrix platform on mouse brain(cerebellum) or spinal cord treated with west nile virus.

tag: age

value: 7-9 day old

value: 10x3 WNV


title: WNV 10x3_spinal cord_1

description: Fixed dose: 10x3 WNV  treated spinal cord, replicate 1


title: S165.D1

description: PrimaryOrganoidAndPublishedCPM.txt


title: mock_spinal cord_2

description: Fixed dose: mock/vehicle spinal cord, replicate 2

value: mock/vehicle


title: ChIPseq_FLAG_DMS3-ZF_Col-0_line2_Figure4

description: ChIPseq for Flag in DMS3-ZF in Col-0 line2 used for Figure4


title: WNV 10x5_cerebellum_3

description: Fixed dose: 10x5 WNV  treated cerebellar slice, replicate 3

source_name: Fresh cerebellar tissue after light sedation and decapitation.

value: 10x5 WNV


title: ChIPseq_FLAG_DMS3-ZF_Col-0_line1_Figure4

description: ChIPseq for Flag in DMS3-ZF in Col-0 line1 used for Figure4


title: WNV 10x3_spinal cord_2

description: Fixed dose: 10x3 WNV  treated spinal cord, replicate 2


title: S165.C9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: mock_spinal cord_3

description: Fixed dose: mock/vehicle spinal cord, replicate 3


title: WNV 10x5_cerebellum_1

description: Fixed dose: 10x5 WNV  treated cerebellar slice, replicate 1


title: ChIPseq_FLAG_Col-0_Figure4

description: ChIPseq for Flag in Col-0 used for Figure4


title: mock_spinal cord_1

description: Fixed dose: mock/vehicle spinal cord, replicate 1


title: S165.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.C2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_HA_ZF_Col-0_line2_Figure4

description: ChIPseq for HA in ZF in Col-0 line2 used for Figure4

value: ZF_in _Col-0


title: S165.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_HA_ZF_Col-0_line1_Figure4

description: ChIPseq for HA in ZF in Col-0 line1 used for Figure4


title: S165.B8

description: PrimaryOrganoidAndPublishedCPM.txt


title: mock_cerebellum_3

description: Fixed dose: mock/vehicle cerebellar slice, replicate 3


title: WNV 10x5_cerebellum_2

description: Fixed dose: 10x5 WNV  treated cerebellar slice, replicate 2


title: ChIPseq_HA_Col-0_Figure4

description: ChIPseq for HA in Col-0 used for Figure4


title: S165.B7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: mock_cerebellum_2

description: Fixed dose: mock/vehicle cerebellar slice, replicate 2


title: mock_cerebellum_1

description: Fixed dose: mock/vehicle cerebellar slice, replicate 1


title: S165.B2

description: PrimaryOrganoidAndPublishedCPM.txt


title: 10x7 WNV_1

description: Dose response: 10x7 WNV  treated cerebellar slice

value: 10x7 WNV


title: ChIPseq_noAB_control_in_DMS3-ZF_fwa_nrpe1_rep2_FigureS2

description: ChIPseq for noAb in DMS3-ZF in fwa x nrpe1 replicate 2 used for FigureS2

source_name: seedling

value: seedling


title: ChIPseq_noAB_control_in_DMS3-ZF_fwa_nrpe1_rep1_FigureS2

description: ChIPseq for noAb in DMS3-ZF in fwa x nrpe1 replicate 1 used for FigureS2


title: ChIPseq_noAB_control_in_DMS3-ZF_fwa_drm12_rep2_FigureS2

description: ChIPseq for noAb in DMS3-ZF in fwa x drm1/2 replicate 2 used for FigureS2


title: S165.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: 10x5 WNV_1

description: Dose response: 10x5 WNV  treated cerebellar slice


title: S165.B5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Suv39h1mut (Mut.2)

city: Munich

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

country: Germany

institute: Helmholtz Munchen

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Reads were mapped onto the mm9 assembly of the Mus musculus genome by using Tophat v2.0.14 and the bowtie v2-2.1.0.  Quantification of gene expression has been performed using HTSeq v0.6.1. Normalization was performed according to the following reference: Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol 11, R106 (2010).
Genome_build: mm9
Supplementary_files_format_and_content: Table S5: Analysis of gene expression in Non-injected (NI.1 NI.2), Suv39h1-injected (H1.1 H1.2) and Suv39h1mut injected (Mut.1, Mut.2) and differential gene expression analysis (H1 vs Mut)
Supplementary_files_format_and_content: Table S6: Analysis of repetitive element (RE) expression in Non-injected (NI.1 NI.2), Suv39h1-injected (H1.1 H1.2) and Suv39h1mut injected (Mut.1, Mut.2) and differential RE expression analysis (H1 vs Mut)

source_name: Total RNA (non-purified).

growth_protocol: incubation in KSOM

extract_protocol: Amplified cDNA was prepared from 2 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, first-strand cDNA was prepared from total RNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers and reverse transcriptase, resulting in a cDNA/mRNA hybrid molecule. Priming sites created by a heating fragmentation of the mRNA within the cDNA/mRNA complex were used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.). The purified product was then used as the substrate of a linear amplification process, SPIA (single primer isothermal amplification). During the amplification step, RNase H degrades RNA in DNA/RNA heteroduplex at the 5'end of the first cDNA strand, creating a binding site for the DNA/RNA SPIA chimeric primer, then DNA polymerase starts replication at the 3'end of the primer displacing the existing forward strand. The process including SPIA DNA/RNA primer binding, DNA replication, strand displacement and RNA degradation is repeated and results in rapid generation of microgram quantities of amplified cDNA. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds).  The next steps of RNA-Seq Library preparation were performed using Ovation Ultralow Library System kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, in this system 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 6 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit  (Kapa Biosystems) following manufacturer's instructions. The libraries were loaded in the flow cell at 14pM concentration and sequenced in the Illumina Hiseq 2500.

treatment_protocol: microinjection at zygote fertilisation cone stage with mRNA

value: 2-cell stage embryo

tag: injected with

value: microinjected with Suv39h1mut mRNA


title: S165.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S165.A7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.H9

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_noAB_control_in_DMS3-ZF_fwa_drm12_rep1_FigureS2

description: ChIPseq for noAb in DMS3-ZF in fwa x drm1/2 replicate 1 used for FigureS2

value: Columbia


title: S159.H7

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid


title: CRISPRscreenTend

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

description: Tend

data_processing:
The sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
The resulting reads were aligned and statistical significance calculated with Mageck (v0.5.7)
Supplementary_files_format_and_content: normalized count file representing number of reads per guide scored in T0, T24 and T42 samples

source_name: BcorΔE9-10KrasG12D cell line

growth_protocol: Cas9+ BcorΔE9-10KrasG12D  tumor cells were cultured in Anne Kelso media supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 20% foetal calf serum, 0.1mM L-asparagine, 2 ng/mL IL-3, 2 ng/mL IL-6, 10 ng/mL SCF at 37°C and 10% CO2.

extract_protocol:
Genomic DNA was extracted from cells using DNeasy Blood & Tissue Kit (Qiagen)
Sequencing libraries were prepared by nested PCR method to amplify integrated CRISPR guides.

tag: cell line

value: Cas9+ cell line derived from Bcor{delta}E9-10KrasG12D mice

tag: timepoint

value: Day 42


title: ChIPseq_PolIISer5_in_DMS3-ZF_fwa_nrpe1_rep2_FigureS2

description: ChIPseq for PolIIser5 in DMS3-ZF in fwa x nrpe1 replicate 2 used for FigureS2

tag: tissue

tag: genotype


title: 10x3 WNV_1

description: Dose response: 10x3 WNV  treated cerebellar slice

source_name: Fresh cerebellar after light sedation and decapitation.


title: Mock_1

description: Dose response: mock/vehicle cerebellar slice


title: Non-injected (NI.2)

value: non-injected


title: ChIPseq_PolIISer5_in_DMS3-ZF_fwa_drm12_rep2_FigureS2

description: ChIPseq for PolIIser5 in DMS3-ZF in fwa x drm1/2 replicate 2 used for FigureS2

tag: ecotype


title: S159.H3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid

tag: cloneid

value: Male

value: Kadoshima


title: Non-injected (NI.1)


title: ChIPseq_PolIISer5_in_DMS3-ZF_fwa_nrpe1_rep1_FigureS2

description: ChIPseq for PolIIser5 in DMS3-ZF in fwa x nrpe1 replicate 1 used for FigureS2


title: Suv39h1mut (Mut.1)


title: S159.G5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: age (weeks)

tag: datecaptured


title: S159.H5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: Sex

tag: organoidid


title: Suv39h1wt (H1.2)

value: microinjected with Suv39h1wt mRNA


title: S159.G4

description: PrimaryOrganoidAndPublishedCPM.txt

tag: protocol

tag: captureplate


title: S159.H1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: capturechamber


title: Suv39h1wt (H1.1)


title: ChIPseq_NRPE1_in_MORC6-ZF_fwa_drm12_Figure2

description: ChIPseq for NRPE1 in MORC6-ZF in fwa x drm1/2 used for Figure2

value: inflorescence


title: S159.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_PolIISer5_in_DMS3-ZF_fwa_drm12_rep1_FigureS2

description: ChIPseq for PolIIser5 in DMS3-ZF in fwa x drm1/2 replicate 1 used for FigureS2


title: S159.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S169.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIP-seq_kmt2d_wt

city: Baltimore

first: Giovanni

last: Carosso

state: MD

address: 733 N Broadway, MRB 426

institute: Johns Hopkins School of Medicine

data_processing:
Sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2(Langmead and Salzberg, 2012). Then, duplicate reads were removed with the function MarkDuplicates from Picard (http://broadinstitute.github.io/picard/)
Peaks were subsequently called using MACS2(Zhang et al., 2008), with the “keep-dup” parameter equal to “all”. After peak calling, we excluded all peaks that overlapped with blacklisted regions provided by ENCODE (https://sites.google.com/site/anshulkundaje/projects/blacklists).
To identify genes whose promoters were bound by KMT2D, we defined promoters as 10kb regions centered around the TSS. We obtained TSS coordinates using the “exonsBy” function from the “TxDb.Mmusculus.UCSC.mm10.knownGene” R package (Team BC, Maintainer BP (2018). TxDb.Mmusculus.UCSC.mm10.knownGene: Annotation package for TxDb object(s). R package version 3.4.4.), with the “by” parameter equal to “gene”.
Genome_build: mm10
Supplementary_files_format_and_content: called peaks in narrowpeak format

source_name: HT22 hippocampal cell line

growth_protocol: HT22 cells were plated at equal density and sampled at 70% confluency

extract_protocol:
Sonicated nuclear lysates were pre-cleared and histone-DNA complexes were isolated with anti-KMT2D antibody (Millipore ABE1867) and purified by DNA Clean and Concentrator (Zymo Research)
NEBNext UltraII DNA Library Prep Kit for Illumina

tag: sample type

value: wild-type clone

value: wild-type

value: hippocampal cell line

tag: chip antibody

value: KMT2D (Millipore ABE1867)


title: input_wt

value: none (input control)


title: ChIPseq_NRPE1_in_MORC6-ZF_fwa_Figure2

description: ChIPseq for NRPE1 in MORC6-ZF in fwa used for Figure2


title: S159.H6

description: PrimaryOrganoidAndPublishedCPM.txt

source_name: iPS-derived cerebral organoid


title: S159.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_in_ZF-SUVH9_fwa_drm12_Figure2

description: ChIPseq for NRPE1 in ZF-SUVH9 in fwa x drm1/2 used for Figure2


title: RNA-seq_set_hom_3_3

description: bulk RNA-seq

data_processing:
reads were pseudoaligned to the mouse reference transcriptome (GRCm38)
Transcript abundances were subsequently quantified using Salmon (Patro et al., 2017). We then used the tximport R package(Soneson et al., 2015) to convert the transcript abundances into normalized gene-level counts, by setting the “countsFromAbundance” parameter equal to “lengthScaledTPM”. Next, we used the edgeR(Robinson et al., 2010) and limma(Ritchie et al., 2015) R packages to log2 transform these gene-level counts, estimate the mean-variance relationship, and calculate weights for each observation. In order to account for the correlation between technical replicates of the same clone when performing the differential analysis, we fit a mixed linear model, using the function “duplicateCorrelation” from the statmod R package(Giner and Smyth, 2016) to block on clone.
Differential analysis: limma R package, using FDR=0.05 cutoff
Principal component analysis, transcript abundances were first converted into gene-level counts using the tximport R package, with the “countsFromAbundance” parameter equal to “no”. Then, we applied a variance stabilizing transformation to these gene-level counts using the “vst” function from the DESeq2 R package(Love et al., 2014) with the parameter “blind” set to “TRUE”, and subsequently estimated the principal components using the 1000 most variable genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: expr_mat_ht22 (both in rda and csv format) is a gene expression matrix where the rows correspond to genes, the columns correspond to samples, and the entries correspond to the quantified expression level of a given gene in a given sample, after using tximport (see methods in the paper) and summing up the expression of a given technical replicate in the different flowcells and lanes. The column names provide information about the sample. For instance, "hom.clone3.rep3" indicates the third technical replicate of the third biological replicate of homozygous mutant clone number 3.

growth_protocol: HT22 cells were plated at equal density and sampled at 60% confluency

extract_protocol:
Poly(A) RNA was isolated using Direct-Zol RNA MicroPrep followed by NEBNext Poly(A) Magnetic Isolation Module
NEBNext UltraII RNA Library Prep Kit for Illumina

value: mutant clone 4 (technical replicate 3)

value: Kmt2d mut/mut


title: ChIPseq_NRPE1_in_ZF-SUVH9_fwa_Figure2

description: ChIPseq for NRPE1 in ZF-SUVH9 in fwa used for Figure2


title: S159.G6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_set_hom_3_2

description: bulk RNA-seq

value: mutant clone 4 (technical replicate 2)


title: ChIPseq_NRPE1_in_DMS3-ZF_fwa_ago469_Figure2

description: ChIPseq for NRPE1 in DMS3-ZF in fwa x ago4/6/9 used for Figure2

value: Columbia


title: RNA-seq_set_hom_3_1

description: bulk RNA-seq

value: mutant clone 4 (technical replicate 1)


title: S159.G2

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid


title: S159.F7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_in_DMS3-ZF_fwa_Figure2

description: ChIPseq for NRPE1 in DMS3-ZF in fwa used for Figure2


title: S159.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_set_hom_2_3

description: bulk RNA-seq

value: mutant clone 3 (technical replicate 3)


title: ChIPseq_NRPE1_in_DMS3-ZF_fwa_drm12_Figure2

description: ChIPseq for NRPE1 in DMS3-ZF in fwa x drm1/2 used for Figure2


title: ChIPseq_NRPE1_in_fwa_drm12_Figure2

description: ChIPseq for NRPE1 in fwa x drm1/2 used for Figure2


title: S159.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.D10

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_NRPE1_in_fwa_Figure2

description: ChIPseq for NRPE1 in fwa used for Figure2

value: fwa


title: ChIPseq_HA_in_MORC6-ZF_fwa_drm12_Figure2

description: ChIPseq for HA in MORC6-ZF in fwa x drm1/2 used for Figure2


title: S159.C8

description: PrimaryOrganoidAndPublishedCPM.txt

value: Male


title: RNA-seq_set_hom_1_3

description: bulk RNA-seq

value: mutant clone 2 (technical replicate 3)


title: RNA-seq_set_hom_2_2

description: bulk RNA-seq

value: mutant clone 3 (technical replicate 2)


title: RNA-seq_set_hom_2_1

description: bulk RNA-seq

value: mutant clone 3 (technical replicate 1)


title: S159.E12

description: PrimaryOrganoidAndPublishedCPM.txt

value: Kadoshima


title: S159.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_HA_in_MORC6-ZF_fwa_Figure2

description: ChIPseq for HA in MORC6-ZF in fwa used for Figure2

value: inflorescence


title: S159.C7

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_set_hom_1_2

description: bulk RNA-seq

value: mutant clone 2 (technical replicate 2)

value: hippocampal cell line


title: S159.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_set_hom_1_1

description: bulk RNA-seq

value: mutant clone 2 (technical replicate 1)


title: S159.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_HA_in_ZF-SUVH9_fwa_drm12_Figure2

description: ChIPseq for HA in ZF-SUVH9 in fwa x drm1/2 used for Figure2


title: S159.C3

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_wt_3

description: bulk RNA-seq

value: wild-type clone (technical replicate 3)

value: wild-type


title: ChIPseq_HA_in_ZF-SUVH9_fwa_Figure2

description: ChIPseq for HA in ZF-SUVH9 in fwa used for Figure2


title: S159.C2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S159.B9

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNA-seq_wt_1

description: bulk RNA-seq

value: wild-type clone (technical replicate 1)


title: RNA-seq_wt_2

description: bulk RNA-seq

value: wild-type clone (technical replicate 2)


title: S159.B7

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_in_DMS3-ZF_fwa_ago469_Figure2

description: ChIPseq for Flag in DMS3-ZF in fwa x ago4/6/9 used for Figure2

value: Columbia


title: ChIPseq_HA_in_fwa_Figure2

description: ChIPseq for HA in fwa used for Figure2


title: S159.B6

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid


title: Kmt2d_mutant_DG_EdU_nuclei

description: 500 nuclei pooled from 3 mice

data_processing:
Paired-end reads were aligned to the mouse reference genome (mm10) using HISAT2(Kim et al., 2015) with default parameters except: -p 8.
Aligned reads from individual samples were quantified against a reference genome (GENCODE vM8)(Mudge and Harrow, 2015).
Quantification was performed using cuffquant with default parameters and the following additional arguments: --no-update-check –p 8. Normalized expression estimates across all samples were obtained using cuffnorm with default parameters(Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with Cuffdiff output

source_name: EdU+ dentate gyrus nuclei (adult)

growth_protocol: 8-week old mice: wild-type (n=3) and Kmt2d +/mut (n=3)

extract_protocol:
Total nuclei (500 per genotype) were purified as described (Rizzardi et al., 2017) with addition of RNase inhibitor to all buffers, and EdU+ nuclei labeled by Click-it (Invitrogen) and isolated using Beckman Coulter MoFlo Cell Sorter
Smart-seq2 protocol (Picelli et al., 2013) was modified using 22 cycles fo cDNA amplification and 20 enrichment cycles of tagmented fragments

treatment_protocol: Mice were given 150 mg/kg EdU by intraperitoneal injection and sampled after 16 hours fordentate gyrus (DG) microdissection

value: dentate gyrus nuclei

value: Kmt2d +/mut

tag: developmental stage

value: adult


title: S159.B3

description: PrimaryOrganoidAndPublishedCPM.txt

value: Male


title: S159.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_in_DMS3-ZF_fwa_Figure2

description: ChIPseq for Flag in DMS3-ZF in fwa used for Figure2


title: S159.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: Kmt2d_wild-type_DG_EdU_nuclei

description: 500 nuclei pooled from 3 mice


title: S159.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_in_fwa_Figure2

description: ChIPseq for Flag in fwa used for Figure2

value: fwa


title: S159.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Eos-RNA-seq-1

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

description: BioWardrobe ID: 2773

data_processing:
Data analysis was performed in BioWardrobe [PMID:26248465]
RNA-Seq data: Fastq files from Illumina pipeline were aligned by STAR (version STAR_2.4.0c PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 --outFilterMismatchNmax 2”. RefSeq annotation from UCSC genome browser (11/2012 PMID: 23155063) for mm10 genome was used. The --outFilterMultimapNmax parameter is used to allow uniq alignment only and --outFilterMismatchNmax parameter is used to allow at max 2 errors.
RPKM values were calculated by BioWardrobe
Genome_build: mm10
Supplementary_files_format_and_content: The columns are RefSeqIDs, Read numbers, RPKM values

source_name: pooled bone marrow at homeostasis

extract_protocol:
Eosinophils (CCR3+, SiglecF+) were sorted from pooled bone marrow. RNA was harvested from Trizol lysates.
Libraries were prepared for sequencing using standard Illumina stranded polyA RNA-Seq protocols
polyA RNA-Seq dUTP

treatment_protocol: No treatment - naïve animals

tag: strain

value: bone marrow

tag: cell type

value: Eosinophils (CCR3+, SiglecF+)


title: S159.A5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: tissue

value: Kadoshima


title: Eos-RNA-seq-2

description: BioWardrobe ID: 2774


title: S159.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_NRPD1-ZF_T1-3_Figure7

description: RNAseq of NRPD1-ZF T1-3 used for Figure7

data_processing:
For RNA-seq data analysis, raw reads were first aligned to TAIR10 gene annotation using Tophat (v 2.0.13) (Trapnell et al., 2009) by allowing up to two mismatches and only allowing one multiple hits. When reads did not map to the annotated genes, the reads were mapped to the TAIR10 genome. Number of reads mapping to genes were calculated by HTseq (Anders et al., 2015) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads). Differentially expressed genes were defined with R package DESeq (Anders and Huber, 2010) using a 2 fold change and FDR less than 0.05 as cut off.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig

source_name: leaf

extract_protocol:
For FWA expression in DMS3-ZF T2 lines, RNA from 12 day-old seedlings was extracted using Direct- zol kit (ZYMO research). For the rest of experiments, RNA from 4-5 week-old leaves was extracted using Direct-zol kit (ZYMO research).
75ng of total RNA was used to prepare libraries using the Neoprep stranded mRNA-seq kit (Illumina). Alternatively, 1μg of total RNA was used to prepare libraries using the TruSeq Stranded mRNA kit (Illumina).

value: leaf

tag: genotype


title: S159.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_NRPD1-ZF_T1-1_Figure7

description: RNAseq of NRPD1-ZF T1-1 used for Figure7

tag: ecotype


title: S159.B5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid


title: S159.A11

description: PrimaryOrganoidAndPublishedCPM.txt

tag: cloneid


title: S159.A10

description: PrimaryOrganoidAndPublishedCPM.txt

tag: age (weeks)


title: mESC shβcat #1, replicate 1

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: C/ Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

data_processing:
Basecalls and adaptor trimming was performed using Illumina Pipeline Casava (v1.8.2).
Data was filtered for low quality reads Trim Galore (v0.2.8).
Reads were aligned to the NCBI37/mm9 genome assembly using Bismark (v0.7.9).
CpG methylation calls were extracted using the Bismark methylation extractor (v0.7.9).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Bismark software's report of methylation level of symmetric CpGs at least 10x covered.

source_name: mESC shβcat #1, replicate 1

growth_protocol: E14 (129/Ola) mouse embryonic stem cells (mESCs) were maintained in gelatine (Millipore ES-006-B)-coated plates with DMEM supplemented with 15% fetal bovine serum (FBS), L– glutamine (2mM), penicillin (100U/ml), streptomycin (100µg/ ml), sodium pyruvate (1mM), non-essential amino acid (NEAA) (0,1mM), 2-mercaptoethanol (0,5mM) and ESGRO mLif (1000U/ml). at 37 °C under an atmosphere of 5% CO2.

extract_protocol:
For library preparation 100-200 ng of genomic DNA was used with the NuGEN Ovation Ultralow Methyl-Seq Library System.
NuGen Ovation RRBS Methyl-seq system

treatment_protocol: Methylation analysis was performed in E14 mESCs Young, Old, Old mutant clones, in shCtrl- and shBcat-transduced mESCs and EBs.

value: Embryonic stem cells

tag: shRNA

value: shbetaca


title: S159.A2

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured

tag: Sex


title: S159.A1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: organoidid

tag: protocol


title: mESC shβcat #1, replicate 2

source_name: mESC shβcat #1, replicate 2


title: EB shCtrl, replicate 2

source_name: EB shCtrl, replicate 2

value: Embryoid bodies

value: shCtr


title: S150.H3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: captureplate

tag: capturechamber


title: S150.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: ChIPseq_FLAG_in_DMS3-ZF_fwa_drm12_Figure2

description: ChIPseq for Flag in DMS3-ZF in fwa x drm1/2 used for Figure2

source_name: inflorescence

value: inflorescence


title: RNAseq_ZF_line3_rep3_Figure7

description: RNAseq of ZF line2 replicate 3 used for Figure7


title: EB shCtrl, replicate 1

source_name: EB shCtrl, replicate 1


title: S150.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_NRPD1-ZF_T1-2_Figure7

description: RNAseq of NRPD1-ZF T1-2 used for Figure7


title: S150.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_ZF_line2_rep2_Figure7

description: RNAseq of ZF line2 replicate 2 used for Figure7


title: RNAseq_ZF_line2_rep1_Figure7

description: RNAseq of ZF line2 replicate 1 used for Figure7


title: S150.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.G6

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_ZF_line1_rep3_Figure7

description: RNAseq of ZF line1 replicate 3 used for Figure7


title: S150.F9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_ZF_line1_rep2_Figure7

description: RNAseq of ZF line1 replicate 2 used for Figure7


title: S150.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_ZF_line1_rep1_Figure7

description: RNAseq of ZF line1 replicate 1 used for Figure7


title: S150.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: E14 mESCs Young, replicate 1

source_name: E14 mESCs Young, replicate 1


title: E14 mESCs Old, replicate 2

source_name: E14 mESCs Old, replicate 2


title: RNAseq_DMS3-ZF_x_NRPD1-ZF_T1-4_Figure7

description: RNAseq of DMS3-ZF x NRPD1-ZF (T1-4) used for Figure7


title: S150.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.F1

description: PrimaryOrganoidAndPublishedCPM.txt


title: E14 mESCs Young, replicate 2

source_name: E14 mESCs Young, replicate 2


title: E14 mESCs Old, replicate 1

source_name: E14 mESCs Old, replicate 1


title: EB shβcat #1, replicate 2

source_name: EB shβcat #1, replicate 2


title: RNAseq_DMS3-ZF_x_NRPD1-ZF_T1-1_Figure7

description: RNAseq of DMS3-ZF x NRPD1-ZF (T1-1) used for Figure7


title: S150.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: mESC shCtrl, replicate 1

source_name: mESC shCtrl, replicate 1


title: mESC shCtrl, replicate 2

source_name: mESC shCtrl, replicate 2


title: EB shβcat #1, replicate 1

source_name: EB shβcat #1, replicate 1


title: O-S33Y # 2, replicate 2

source_name: O-S33Y # 2, replicate 2


title: S150.E3

description: PrimaryOrganoidAndPublishedCPM.txt

source_name: iPS-derived cerebral organoid


title: S150.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: O-S33Y # 2, replicate 1

source_name: O-S33Y # 2, replicate 1


title: RNAseq_T3_ZF_line3_rep3_Figure5

description: RNAseq for T3 ZF line3 replicate 3 used for Figure5

source_name: leaf


title: S150.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_ZF_line3_rep2_Figure5

description: RNAseq for T3 ZF line3 replicate 2 used for Figure5


title: S150.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: O-S33Y # 1, replicate 2

source_name: O-S33Y # 1, replicate 2


title: S150.E10

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_ZF_line3_rep1_Figure5

description: RNAseq for T3 ZF line3 replicate 1 used for Figure5


title: S150.D9

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_ZF_line2_rep3_Figure5

description: RNAseq for T3 ZF line2 replicate 3 used for Figure5


title: S150.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_DMS3-ZF_x_NRPD1-ZF_T1-2_Figure7

description: RNAseq of DMS3-ZF x NRPD1-ZF (T1-2) used for Figure7


title: O-S33Y # 1, replicate 1

source_name: O-S33Y # 1, replicate 1


title: S150.E12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.E5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_DMS3-ZF_x_NRPD1-ZF_T1-3_Figure7

description: RNAseq of DMS3-ZF x NRPD1-ZF (T1-3) used for Figure7


title: RNAseq_T3_ZF_line2_rep1_Figure5

description: RNAseq for T3 ZF line2 replicate 1 used for Figure5


title: S150.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_ZF_line2_rep2_Figure5

description: RNAseq for T3 ZF line2 replicate 2 used for Figure5


title: S150.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D11

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_ZF_line1_rep2_Figure5

description: RNAseq for T3 ZF line1 replicate 2 used for Figure5


title: RNAseq_T3_ZF_line1_rep3_Figure5

description: RNAseq for T3 ZF line1 replicate 3 used for Figure5


title: RNAseq_T3_ZF_line1_rep1_Figure5

description: RNAseq for T3 ZF line1 replicate 1 used for Figure5


title: S150.C9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.C8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.C7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_DMS3-ZF_line2_rep2_Figure5

description: RNAseq for T3 DMS3-ZF line2 replicate 2 used for Figure5


title: S150.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_DMS3-ZF_line2_rep3_Figure5

description: RNAseq for T3 DMS3-ZF line2 replicate 3 used for Figure5


title: Lyl1-/-, biological replicate 3

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

description: Gene expression data from Lyl1-/- CD135+ LSK

hyb_protocol: GeneChip Hybridization, Wash and stain Kit Affymetrix

scan_protocol: GeneChip Scanner 3000  Affymetrix

data_processing: CEL files were normalized using the rma function in the R Bioconductor package oligo.

source_name: Lyl1-/- mouse Lineage-CD117+SCA-1+CD135+ bone marrow

label_protocol: GeneChip 3 ÍVT Express kit Affymetrix

extract_protocol: RNA Easy  micro kit Qiagen

value: Lineage-CD117+SCA-1+CD135+ cells


title: RNAseq_T3_DMS3-ZF_line2_rep1_Figure5

description: RNAseq for T3 DMS3-ZF line2 replicate 1 used for Figure5

value: Columbia


title: Lyl1-/-, biological replicate 2


title: S150.C2

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid


title: S150.C10

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_DMS3-ZF_line1_rep3_Figure5

description: RNAseq for T3 DMS3-ZF line1 replicate 3 used for Figure5


title: Lyl1-/-, biological replicate 1


title: S150.B8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.D10

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_DMS3-ZF_line1_rep2_Figure5

description: RNAseq for T3 DMS3-ZF line1 replicate 2 used for Figure5


title: E2A-/-, biological replicate 2

description: Gene expression data from E2A-/- CD135+ LSK

source_name: E2A-/- mouse Lineage-CD117+SCA-1+CD135+ bone marrow


title: E2A-/-, biological replicate 1


title: S150.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_T3_DMS3-ZF_line1_rep1_Figure5

description: RNAseq for T3 DMS3-ZF line1 replicate 1 used for Figure5


title: WT control, biological replicate 2

description: Gene expression data from control CD135+ LSK

source_name: WT mouse Lineage-CD117+SCA-1+CD135+ bone marrow

value: wild-type


title: S150.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.B7

description: PrimaryOrganoidAndPublishedCPM.txt


title: Sample_circCSNK1G3-sh2

city: Toronto

first: Housheng

middle: Hansen

last: He

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto

description: Sample 7

data_processing:
RNA-Seq reads were mapped to GRCh37 with Gencode v24lift37 annotation using STAR (v2.5.3a), the GeneCounts parameter was set to quantMode to get raw counts on genes
edgeR(v3.12.1) was used for differential expression analysis
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for gene raw counts

growth_protocol: PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Samples were cleaned-up by phenol-chloroform before resuspension in a small volume of RNase-free H2O.
RNA-Seq library for circCSNK1G3 was constructed with the kit from Illumina (TruSeq Stranded mRNA Library Prep Kit) according to the manufacturer’s protocol. RNA-Seq libraries were sequenced as single-end reads in duplicates at ~30 million reads per library using HiSeq 2000 platforms.

treatment_protocol: For knockdown, The shRNA expressing lentiviral transfer vector was transfected together with the packaging (psPAX2) and envelope plasmid (pMD2.G) by lipo3000. The medium was harvested at 24 and 48 hours after transfection before storing at -80 °C. For infection, 5 x 104 cells were seeded per well in six-well plates and infected with lentivirus on the next day. Infected cells were selected with 3 μg/mL puromycin. For overexpression, PCa cells were transfected with 1.2 μg circRNA overexpressing plasmids or empty vector by lipo3000 transfection reagent (Invitrogen, USA) as per the manufacturer’s protocol. The transfected cells were harvested 24 hours after transfection for RNA extraction or other assays.

tag: treatment

value: knockdown of circCSNK1G3

tag: cell line

value: prostate cancer cell line


title: WT control, biological replicate 3


title: S150.B9

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)

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

value: Male


title: E2A-/-, biological replicate 3


title: S150.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: Sample_OEcircCSNK1G3

description: Sample 5

value: overexpression of circCSNK1G3


title: S150.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.A5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: WT control, biological replicate 1


title: RNAseq_DMS3-ZF_fwa_drm1/2_line3_FigureS2

description: RNAseq for DMS3-ZF fwa x drm1/2 line 3 used for FigureS2

source_name: seedling

value: seedling


title: RNAseq_DMS3-ZF_fwa_line3_FigureS2

description: RNAseq for DMS3-ZF fwa line 3 used for FigureS2


title: Sample_circCSNK1G3_sh1

description: Sample 6


title: S150.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_DMS3-ZF_fwa_drm1/2_line2_FigureS2

description: RNAseq for DMS3-ZF fwa x drm1/2 line 2 used for FigureS2


title: Sample_shGFP2

description: Sample 4

value: shGFP


title: S150.A2

description: PrimaryOrganoidAndPublishedCPM.txt

value: Kadoshima


title: RNAseq_DMS3-ZF_fwa_line2_FigureS2

description: RNAseq for DMS3-ZF fwa line 2 used for FigureS2


title: S150.A3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.A12

description: PrimaryOrganoidAndPublishedCPM.txt


title: Sample_shGFP1

description: Sample 3


title: RNAseq_DMS3-ZF_fwa_line1_FigureS2

description: RNAseq for DMS3-ZF fwa line 1 used for FigureS2


title: S150.B3

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_DMS3-ZF_fwa_drm1/2_line1_FigureS2

description: RNAseq for DMS3-ZF fwa x drm1/2 line 1 used for FigureS2


title: S149.H9

description: PrimaryOrganoidAndPublishedCPM.txt


title: Sample_OEvehicle2

description: Sample 2

value: overexpression vehicle


title: RNAseq_fwa_rep3_FigureS2

description: RNAseq for fwa replicate 3 used for FigureS2

value: fwa


title: Sample_OEvehicle1

description: Sample 1


title: S149.H3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_fwa_rep1_FigureS2

description: RNAseq for fwa replicate 1 used for FigureS2


title: RNAseq_fwa_rep2_FigureS2

description: RNAseq for fwa replicate 2 used for FigureS2


title: S149.H5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.H1

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_Col-0_rep2_FigureS2

description: RNAseq for Col-0 replicate 2 used for FigureS2


title: S150.A11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_Col-0_rep1_FigureS2

description: RNAseq for Col-0 replicate 1 used for FigureS2


title: WGBS_ZF_line2_x_NRPD1-ZF_T1-3_Figure7

description: WGBS for ZF line 2 x NRPD1-ZF (T1-3) used for Figure7

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

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: S149.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S150.A1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G12

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_ZF_line2_x_NRPD1-ZF_T1-1_Figure7

description: WGBS for ZF line 2 x NRPD1-ZF (T1-1) used for Figure7


title: S149.G4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_ZF_line1_x_NRPD1-ZF_T1-3_Figure7

description: WGBS for ZF line 1 x NRPD1-ZF (T1-3) used for Figure7


title: S149.H8

description: PrimaryOrganoidAndPublishedCPM.txt


title: RNAseq_Col-0_rep3_FigureS2

description: RNAseq for Col-0 replicate 3 used for FigureS2


title: WGBS_ZF_line1_x_NRPD1-ZF_T1-2_Figure7

description: WGBS for ZF line 1 x NRPD1-ZF (T1-2) used for Figure7


title: S149.F8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.G6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_ZF_line1_x_NRPD1-ZF_T1-1_Figure7

description: WGBS for ZF line 1 x NRPD1-ZF (T1-1) used for Figure7


title: S149.F11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.F12

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_NRPD1-ZF_T1-3_Figure7

description: WGBS for NRPD1-ZF (T1-3) used for Figure7

value: NRPD1_ZF_in _Col-0


title: S149.E8

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_DMS3-ZF_line2_x_NRPD1-ZF_T1-2_Figure7

description: WGBS for DMS3-ZF line 2 x NRPD1-ZF (T1-2) used for Figure7


title: WGBS_DMS3-ZF_line2_x_NRPD1-ZF_T1-1_Figure7

description: WGBS for DMS3-ZF line 2 x NRPD1-ZF (T1-1) used for Figure7


title: S149.E9

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_DMS3-ZF_line2_x_NRPD1-ZF_T1-3_Figure7

description: WGBS for DMS3-ZF line 2 x NRPD1-ZF (T1-3) used for Figure7


title: S149.E2

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_ZF_line2_x_NRPD1-ZF_T1-2_Figure7

description: WGBS for ZF line 2 x NRPD1-ZF (T1-2) used for Figure7


title: WGBS_DMS3-ZF_line1_x_NRPD1-ZF_T1-3_Figure7

description: WGBS for DMS3-ZF line 1 x NRPD1-ZF (T1-3) used for Figure7


title: S149.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.E7

description: PrimaryOrganoidAndPublishedCPM.txt


title: V_T16_rep2

description: Sample 24

data_processing:
Sequencing FASTQ files were first trimmed so that shRNA sequence starts at the first base.
Essential circRNAs were identified from shRNA screen sequencing results with MAGeCK (v0.5.4) software
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for shRNA count

growth_protocol: The four PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Genomic DNA was extracted for replicate samples (QIAamp Blood Midi kit)
shRNA inserts were amplified by PCR using standard Illumina library sequencing. 250x genomic DNA was used as input for each sample and resulting libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: Cell lines were infected with the library at an MOI of ~ 0.3 such that every shRNA was represented in 300 cells. 24 hrs after infection, cells were selected with puromycin for 48-72 hrs (PC-3, 3.5 µg/mL, 22Rv1, V16A, 3 µg/mL, LNCaP, 2.5 µg/mL). Following selection, cells were split into triplicates, passaged every 3-4 days, and maintained at 300x coverage for the duration of the screen. Cells were sampled in replicates on Day 0, Day 8 and Day 16 post- selection for genomic DNA analysis.

tag: days post-selection


title: S149.F9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.E11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_DMS3-ZF_line1_x_NRPD1-ZF_T1-2_Figure7

description: WGBS for DMS3-ZF line 1 x NRPD1-ZF (T1-2) used for Figure7


title: V_T16_rep1

description: Sample 23

tag: cell type


title: S149.D7

description: PrimaryOrganoidAndPublishedCPM.txt

tag: tissue


title: S149.D8

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_NRPD1-ZF_T1-2_Figure7

description: WGBS for NRPD1-ZF (T1-2) used for Figure7

tag: genotype


title: WGBS_DMS3-ZF_line1_x_NRPD1-ZF_T1-1_Figure7

description: WGBS for DMS3-ZF line 1 x NRPD1-ZF (T1-1) used for Figure7

tag: ecotype


title: WGBS_DMS3-ZF_fwa_nrpd1_line2_Figure6

description: WGBS for DMS3-ZF fwa x nrpd1 replicate 2 used for Figure6


title: V_T8_rep2

description: Sample 22


title: S149.C8

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid


title: S149.C7

description: PrimaryOrganoidAndPublishedCPM.txt

tag: cloneid


title: S149.D3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: age (weeks)


title: V_T8_rep1

description: Sample 21


title: S149.D6

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_DMS3-ZF_fwa_nrpd1_line1_Figure6

description: WGBS for DMS3-ZF fwa x nrpd1 replicate 1 used for Figure6


title: S149.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: WGBS_fwa_nrpd1_rep2_Figure6

description: WGBS for fwa x nrpd1 replicate 2 used for Figure6


title: S149.E12

description: PrimaryOrganoidAndPublishedCPM.txt


title: V_T0_rep1

description: Sample 19


title: WGBS_fwa_nrpd1_rep1_Figure6

description: WGBS for fwa x nrpd1 replicate 1 used for Figure6


title: S149.C11

description: PrimaryOrganoidAndPublishedCPM.txt


title: V_T0_rep2

description: Sample 20


title: S149.C12

description: PrimaryOrganoidAndPublishedCPM.txt


title: M. pachydermatis KCTC 27587

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Malassezia pachydermatis KCTC 27587 whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and normalized as TMM value by using edgeR.
Genome_build: M. pachydermatis KCTC 27587
Supplementary_files_format_and_content: Excel file including TMM values and locus_tags for genes of M. pachydermatis KCTC 27587
Supplementary_files_format_and_content: GTF file including genome information

organism: Malassezia pachydermatis

source_name: Clinical isolate

growth_protocol: M. pachydermatis cells were cultured on mDixon agar medium at 34C for 3 days.

extract_protocol:
Total RNA was extracted using TransZolUp (Trans, Cat#ET111-01)
Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: M. pachydermatis cells were incubated in mDixon broth at 34C for 6h.

tag: azole susceptibility

value: resistant to ketoconazole


title: S149.C1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured


title: S149.B9

description: PrimaryOrganoidAndPublishedCPM.txt

tag: Sex


title: S149.B8

description: PrimaryOrganoidAndPublishedCPM.txt

tag: organoidid


title: R_T16_rep1

description: Sample 17


title: M. pachydermatis CBS 1879

source_name: CBS, Netherlands

value: sensitive to ketoconazole


title: R_T8_rep2

description: Sample 16


title: S149.B7

description: PrimaryOrganoidAndPublishedCPM.txt

tag: protocol


title: S149.B6

description: PrimaryOrganoidAndPublishedCPM.txt

tag: captureplate


title: S149.B3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: capturechamber


title: S149.B12

description: PrimaryOrganoidAndPublishedCPM.txt


title: L_T16_rep2

description: Sample 12

source_name: LNCaP

value: LNCaP


title: S149.B1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.B11

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: R_T0_rep1

description: Sample 13


title: S149.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.A7

description: PrimaryOrganoidAndPublishedCPM.txt


title: R_T16_rep2

description: Sample 18


title: S149.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S149.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: L_T16_rep1

description: Sample 11


title: Immuno DTCC-12

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

institute: City University of Hong Kong

data_processing:
Raw Crt, “relative threshold”, values were generated by OpenArray system, the undetected Crt values were replaced by 40 (Matrix non-normalized); the Crt values were normalized to 18S using the -△Crt method (Matrix normalized); fold change was calculated by 2^-△Crt.
Fold Change worksheet reports relative single cell gene expression level.

label: TaqMan

label_protocol: The single-cell reverse transcription and pre-amplification procedures were provided by the same kit. Single-cell RT-PCR was performed in OpenArray chips, using QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems).

extract_protocol: The single cells were lysed directly using Single cell-to-CT qRT-PCR Kit (Ambion).

treatment_protocol: The cell clusters were picked up then dissociated into single cells. Both the cell clusters and single cells were picked up manually under a microscope using Kuiqpick through a glass capillary.

tag: subgroup

value: DTCC-E

value: Epithelial ovarian cancer ascites


title: Immuno DTCC-11


title: Immuno DTCC-13


title: S149.A3

description: PrimaryOrganoidAndPublishedCPM.txt

value: iPS-derived cerebral organoid


title: R_T0_rep2

description: Sample 14

tag: cell line


title: S149.A2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-10


title: L_T8_rep1

description: Sample 9

tag: days post-selection


title: S14.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-9

tag: cell type


title: S14.H5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: tissue


title: S14.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-8


title: S149.A6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-14


title: L_T0_rep2

description: Sample 8


title: S14.H3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: L_T0_rep1

description: Sample 7


title: S14.H10

description: PrimaryOrganoidAndPublishedCPM.txt


title: P_T16_rep2

description: Sample 6


title: S14.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: L_T8_rep2

description: Sample 10


title: S14.F9

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-6


title: P_T16_rep1

description: Sample 5


title: Immuno DTCC-4


title: R_T8_rep1

description: Sample 15


title: Immuno DTCC-5


title: Immuno DTCC-3


title: S14.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: P_T8_rep1

description: Sample 3


title: S14.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: P_T0_rep2

description: Sample 2


title: S14.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-7


title: S14.D7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.E10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Immuno DTCC-1


title: Immuno DTCC-2


title: Random DTCC-128

value: DTCC-R


title: S14.F7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.C9

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.C8

description: PrimaryOrganoidAndPublishedCPM.txt


title: P_T0_rep1

description: Sample 1

value: prostate cancer cell line


title: S14.D4

description: PrimaryOrganoidAndPublishedCPM.txt

value: Male


title: Random DTCC-126


title: 143B rhoZero 20mM H3K27ac rep2 control

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
The reads passing the initial processing were aligned to the human reference genome (hg19; Genome Reference Consortium GRCh37 from February 2009) with with Bowtie2 –sensitive-local settings and 1,000-bp maximum fragment length (−D 15 −R 2 −N 0 −L 20 −i S,1,0.75 −X 1000) .
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bedgraph files using bedGraphToBigWig; Scores represent mapped read coverage

source_name: 143B rho-aKG H3K27ac control, input DNA

growth_protocol: cells were grown in medium supplemented with high glucose, pyruvate and uriding

extract_protocol: Genomic DNA was isolated from sonicated formaldehyde-fixed pellets by chromatin immunoprecipitation

treatment_protocol: cells were exposed to 20 mM of DM-α-KG for 4h, after which medium was removed and cells crosslinked with formaldehyde for ChIP-seq

tag: chip antibody

value: H3K27ac (Active Motif)


title: S14.B9

first: Christopher

last: Villarreal

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

description: PrimaryOrganoidAndPublishedCPM.txt

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


title: S14.C6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-125


title: Random DTCC-127


title: 143B rhoZero 20mM H3K27ac rep2 treat

source_name: 143B rho treat with aKG H3K27ac


title: S14.C3

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero 20mM H3K27ac rep1 treat


title: S14.B6

description: PrimaryOrganoidAndPublishedCPM.txt


title: P_T8_rep2

description: Sample 4


title: 143B rhoZero 20mM H3K27ac rep1 control


title: S14.B5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-123


title: S14.B4

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero CTL H3K27ac rep2 treat

source_name: 143B rhoZero H3K27ac


title: S14.A4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.A8

description: PrimaryOrganoidAndPublishedCPM.txt


title: S14.A9

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-122


title: S13.H7

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero CTL H3K27ac rep2 control

source_name: 143B rhoZero H3K27ac control, input DNA


title: Random DTCC-121


title: 143B rhoZero CTL H3K27ac rep1 treat


title: S14.C5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.H2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.G5

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-120


title: 143B rhoZero CTL H3K27ac rep1 control


title: 143B rho-aKG H3K9ac rep2 treat

source_name: 143B rho treat with aKG H3K9ac

value: H3K9ac (Active Motif)


title: S13.F8

description: PrimaryOrganoidAndPublishedCPM.txt

source_name: iPS-derived cerebral organoid


title: S13.F6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-124


title: S13.G1

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rho-aKG H3K9ac rep1 treat


title: S13.F5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.F4

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.F3

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rho-aKG H3K9ac rep2 control

source_name: 143B rho-aKG H3K9ac control, input DNA


title: S13.F2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-118


title: Random DTCC-119


title: 143B rho-aKG H3K9ac rep1 control


title: Random DTCC-117


title: Random DTCC-116


title: S13.E4

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero H3K9ac rep2 treat

source_name: 143B rhoZero H3K9ac


title: S13.E6

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-115


title: 143B rhoZero H3K9ac rep1 treat


title: S13.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.F1

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.E3

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.D6

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.E1

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero H3K9ac rep2 control

source_name: 143B rhoZero H3K9ac control, input DNA


title: S13.D5

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.D2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-114


title: S13.C6

description: PrimaryOrganoidAndPublishedCPM.txt


title: 143B rhoZero H3K9ac rep1 control


title: S13.C4

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_Vehicle_NHS_RPB1_ChIP_Rep2

city: Freiburg

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed. Peak calling was done with MACS2 using "--keep-dup all", "--nomodel", "--extsize" and "--broad". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Cutadapt was used to cut adapter from sequenced reads. Filtered reads were first mapped to a single copy of ribosomal DNA to remove the contribution of nascent RNAs from ribosomal genes. The remaining reads were mapped to human genome build hg38 using Bowtie2 using default parameters. PRO-seq libraries were normalized using 3’-end of long genes as described by Mahat et al., 2016
DESeq2 was used to identify differentially express.ed genes upon heat shock. Differential gene expression was done using DESeq2
Genome_build: hg38

source_name: Flp-In T-REx 293 Cell Line

growth_protocol: Flp-In T-REx 293 were cultured in DMEM High Glucose supplemented with 10% FBS. K562 cells were cultured in IMDM supplemented with 10% FBS.

extract_protocol: Cells were fixed using 1% methanol-free formaldehyde (CAT no) in DMEM (HEK293) or IMDM (K562) at room temperature for 10 minutes, followed by 5 minutes blocking in 0.125M glycine. Cells were washed twice with ice-cold PBS. Cell pellet was resuspended in Farnham Buffer (5 mM PIPES pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated in 1ml Covaris tubes using Covaris S220 with the following settings: Peak Power=75; Duty Factor=2; Cycles/Burst=200. Sonication time varied from cell type to cell type; K562=~2.5minutes and HEK293=~3minutes. Isolated nuclei were washed with Farnham Buffer and suspended in shearing buffer (10 mM Tris-HCl pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication in 1ml Covaris tubes using the following settings: Peak Power=140; Duty Factor=5; Cycles/Burst=200, Time=25-30 minutes. Debris was removed by centrifugation. A DNA fragment-size distribution of 200-600bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer to achieve a final 0.05% SDS concentration. 200 μg of good quality chromatin was used for immunoprecipitation. Protein A or G magnetic beads (CAT) were incubated (rotated) with 5-10μg of antibody for 6h at 4ºC. This bead-antibody complex was then incubated overnight at 4ºC with chromatin.

treatment_protocol: Cycloheximide and NSC624206 (Ub-E1 inhibitor) were used as pretreatments prior to Heat shock, always using an appropriate solvent control. To inhibit translation, 30ug/ml Cycloheximide were used for 1.5h. To inhibit ubiquitin-activating enzyme E1 (Ub-E1 inhibitor), 2uM NSC624206 was used for 0.5h.

value: RNA PolII (RPB1) Cell Signaling 14958

tag: treatment

value: Vehicle

tag: condition

value: Non Heat-Shock


title: Random DTCC-113


title: Random DTCC-112


title: S13.D3

city: Santa Cruz

description: PrimaryOrganoidAndPublishedCPM.txt

tag: donorid

tag: cloneid

value: Kadoshima


title: HEK_Vehicle_HS_RPB1_ChIP_Rep2

value: Heat-Shock


title: Random DTCC-110


title: S13.B5

description: PrimaryOrganoidAndPublishedCPM.txt

tag: age (weeks)


title: S13.B6

description: PrimaryOrganoidAndPublishedCPM.txt

tag: datecaptured


title: S13.B3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: Sex


title: Random DTCC-109


title: HEK_Ub-E1_NHS_RPB1_ChIP_Rep2

value: NSC624206 (Ub-E1 inhibitor)


title: S13.A4

description: PrimaryOrganoidAndPublishedCPM.txt

tag: organoidid


title: Random DTCC-108


title: HEK_siNELFE_NHS_RPB1_ChIP_Rep2

value: siRNA NELFE


title: HEK_Ub-E1_HS_RPB1_ChIP_Rep2


title: S13.A3

description: PrimaryOrganoidAndPublishedCPM.txt

tag: protocol


title: Random DTCC-106


title: S13.A1

description: PrimaryOrganoidAndPublishedCPM.txt

tag: captureplate


title: Random DTCC-107


title: S12.H8

description: PrimaryOrganoidAndPublishedCPM.txt

tag: capturechamber


title: S13.C1

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_Scramble_NHS_RPB1_ChIP_Rep2

value: siRNA Scramble


title: HEK_siNELFE_HS_RPB1_ChIP_Rep2


title: S12.H12

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.H9

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-111

tag: subgroup


title: S12.H6

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_Scramble_HS_RPB1_ChIP_Rep2


title: S12.H11

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_NHS_Input


title: S12.H10

description: PrimaryOrganoidAndPublishedCPM.txt


title: S13.B10

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-105


title: Random DTCC-104


title: S13.A2

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.G7

description: PrimaryOrganoidAndPublishedCPM.txt


title: S12.G8

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_HS_Input


title: S12.G3

description: PrimaryOrganoidAndPublishedCPM.txt


title: HEK_CHX_NHS_RPB1_ChIP_Rep2

value: Cycloheximide


title: S12.G2

description: PrimaryOrganoidAndPublishedCPM.txt


title: Random DTCC-101


title: S12.H4

description: PrimaryOrganoidAndPublishedCPM.txt