title: Hum d5 batch 3

city: Cambridge

first: Paula

last: Freire Pritchett

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: Medical Research Council

description:
H9_d10_2204
RNA was isolated from ~300 H9 batch 3 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i703 and i504

data_processing:
Fastq files were trimmed using Trim Galore version 0.6.3_dev and Cutadpt version 2.4.
Human and gorilla reads were aligned to GRCh38 and Kamilah_GGO_v0 reference genomes respectively using HISAT2 (version 2.0.0-beta).
GTF gene annotation files for both of the reference genomes were downloaded and filtered for a list of 16,763 genes that are annotated with identical gene names in both species
Read counts were normalized to transcripts per million (TPM). Results can be found in hum_gor_combined_tpms_HISAT2.txt
Genome_build: GRCh38 or Kamilah_GGO_v0s
Supplementary_files_format_and_content: hum_gor_combined_tpms_HISAT2.txt contains TPM results for all samples as well as the mean and standard deviation for each condition.

source_name: H9 human ES cell-derived organoids

growth_protocol: Human (H9) or Gorilla (G1) stem cells were used to generate brain organoids in Aggrewell 800 plates (StemCell Technologies) with 2000 cells per microwell. Organoids were cultured in and followed the timing of the STEMdiff Cerebral Organoid Kit protocol (StemCell Technologies, #08570) .

extract_protocol:
Samples were flash-frozen in LN2 and stored at -80 °C. RNA from all 42 samples was purified in parallel directly from Trizol with the Direct-zol-96 RNA kit (Zymo Research).
cDNA libraries were generated according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760). cDNA was amplified for 12 cycles and barcoded with NEBNext Multiplex Oligos for Illumina (NEB #E7600). Samples were pooled together to 15 nM concentration and sequenced with single-end 50 base mode on 3 lanes of an Illumina HiSeq 4000 instrument.
bulk RNAseq

tag: time point

value: Day 5


title: Hum d10 batch 3

status: Public on Jul 06 2020

type: SRA

description:
H9_d15_2204
RNA was isolated from ~150 H9 batch 3 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i703 and i505

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: Day 10


title: BCL2_KD_3

type: RNA

city: Stockholm

first: Erik

last: Sonnhammer

address: Tomtebodavagen 23A

department: Biochemistry & Biophysics

country: Sweden

institute: SciLifeLab/ Stockholm University

data_processing: Data normalized by first averaging technical replicates and then by dividing by spike-in gene. Fold Change calculated via deltaDeltaCt R package using positive and negative experimental controls

label: FAM

source_name: human squamous carcinoma cell line

label_protocol: For FAM, the filter 465/510 gets excitation absorbance ~0.38 and emission intensity ~0.31

growth_protocol: A diverse set of genes is assembled from different pathways and complexes, each interacting to some degree with the oncogene MYC. Each readout gene is perturbed in the human squamous carcinoma cell line A431 via transfection with short interfering RNAs (siRNAs) using the Ambion RNA-Seq Library Construction Kit. In order to minimizing siRNA off target effects, three to four siRNA are used per RNA interference (RNAi), which are then averaged to highlight the effects of the targeted siRNA perturbation. Cells were collected at 72 hours after siRNA knockdown and washed of Phosphate-Buffer Solution (PBS), and lysed using CelluLyser. Cell counts were calculated using the resazurin fluorescence assay. Since no endogenous gene can be assumed to be free of MYC regulation, which is thought to be a universal transcriptional amplifier, a proprietary RNA transcript was added to each sample to act as a reference gene for the quantitative polymerase chain reaction (qPCR) analysis, spiked-in in proportion to the cell count before RNA isolation. Negative controls are included, which siRNA does not map to human genes, as well as an untreated control absent of any siRNA. The cDNA was prepared from the RNA and preamplified in preparation for the high-throughput qPCR screening. Finally, the transcript profiles with respect to the 40 target genes were determined using TaqMan assays on Fluidigm's Biomark platform using 96x96 Dynamic Array integrated fluidic circuits. Raw qPCR output was then processed as a function of the samples’ initial quantity returning a measure of fold change via the experimental controls. Three experimental replicates were made per targeted perturbation and five outlying replicates were discarded due to clear machine read error, thus the dataset is composed of 40 genes (N) and 115 samples. Including all controls, a total of 18432 qPCRs were performed on 192 samples. Two technical replicates were performed to ensure minimal machine error. They generated very similar values up to 25 qPCR cycles.

treatment_protocol: Wells prepared with transfection reagents and RNAi. Transfection proceeded by adding cells to wells and waiting 4 hours. During this time the RNAi sequences go into the cells, and probably start working. Media changed; at this point you should have constant perturbation until RNAi effect diminishes. RNAi diminished, perturbation ends, happening several days after transfection.

tag: cell line

tag: sample type

value: third targeted knockdown of BCL2 via ASX04ZKL


title: Hum d15 batch 3

description:
H9_d20_2204
RNA was isolated from ~100 H9 batch 3 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i703 and i506

value: Day 15


title: Hum d2 batch 3

description:
H9_d7_2204
RNA was isolated from ~300 H9 batch 3 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i703 and i502

value: Day 2


title: M2D4

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
After demultiplexing, quality of data was examined using FastQC (v 0.11.7). Illumina and MATQ-seq adapters were removed using cutadapt (v 1.9). Trimmed reads were mapped to salmonella enterica SL1344 genome (NCBI RefSeq accession numbers: NC_016810.1, NC_017718.1, NC_017719.1 and NC_017720.1) using STAR aligner (v 2.5.4b) with default settings. Read counts of each gene was determined using the featurecount program. Afterwards, data was normalized using DESeq2 package and the normalized data was used for PCA analysis. The normalized libraries were subjected to a PCA. The differentially expressed genes between different culture conditions were analyzed using DEseq2.
Genome_build: NC_016810.1, NC_017718.1, NC_017719.1 and NC_017720.1
Supplementary_files_format_and_content: csv file:Read count table for each gene was determined using the HTSeq program

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacteria

growth_protocol: Salmonella Typhimurium SL1344 strain (JVS 1574) and Pseudomonas aeruginosa strain PAO1 were grown in 5 ml Lennox broth in a 37°C at 220 rpm, overnight (O/N) and diluted 1:1,000 in a new 250 mL flask, containing 10 mL of LB. The cells were grown at 37°C and 220 rpm until an OD600 of 0.3 was reached indicating mid exponential phase. Stationary phase culture (SPI1) was grown in Lennox broth over night to an OD600 of 2.0.

extract_protocol:
Each well of the 48-well plate was pre-filled with 2.6 µL lysis buffer containing 0.26 µL Lysis buffer (Takara), 0.03 µL RNase Inhibitor (100U/uL, Takara), 0.25 µL DPBS (Gibco) and 0.5 uL Lysozyme (5 Units, Epicentre). The lysis buffer was always prepared freshly and ready plates were kept on ice.
MATQ-seq protocol was performed following the initial report (Sheng, Cao et al. 2017). In brief, RNA was reverse transcribed using Superscript III (Life Technologies). Residual primers were digested with T4 DNA Polymerase (New England Biolabs). In a further step RNase H and RNase If (New England Biolabs) were used for enzymatic RNA digestion. Tdt Terminal Transferase (New England Biolabs) and dCTP were provided for the tailing step. Subsequently second strand was synthesized using GAT21 6N3G MALBAC primer and deepvent exo- DNA polymerase (New England Biolabs). Amplification was performed with a PCR mix including GAT27 PCR primer, and a 24 cycle PCR program. Amplified cDNA was purified using 40 µL of Ampure XP beads (Beckman Coulter) with a 1:1 v/v beads: amplicons. cDNA concentration was measured using Qubit HS Assay (Life Technologies) and fragment size distribution was observed using a high sensitivity DNA kit Bioanalyzer (Agilent). Libraries were prepared using Nextera XT (Illumina) with the minor modifications as described in (Patel, Tirosh et al. 2014). Briefly, an input of 1 ng of cDNA was tagmented using one-quarter of the recommended volumes and a longer fragmentation time (10 min) and resuspended in 15 µL EB (Qiagen).

treatment_protocol: NaCl shock and Anaerobic shock conditions were generated as described in (Kroger, Colgan et al. 2013). For NaCl shock generation, NaCl was added to MEP-bacteria cultures to a final concentration of 0.3 M, followed by 10 minutes continued incubation at 37°C shaking. For anaerobic shock generation, 5 ml of MEP-bacteria cultures were filled in a test-tube, covered with 2 ml of mineral oil and subsequently incubated at 37°C for 30 min without agitation. 2 mL of culture (stationary or stimulated cells) were pelleted, washed twice with 1 mL of Dulbecco's phosphate-buffered saline (DPBS, Gibco) and subjected to a mild-fixation to prevent advert transcriptome changes by replacing DPBS with 1 mL of a 1:1 v/v RNAlater (Thermo Fischer) – DPBS solution.

tag: condition

value: NaCl Shock

tag: number of cells


title: Hum d3 batch 3

description:
H9_d8_2204
RNA was isolated from ~300 H9 batch 3 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i703 and i503

value: Day 3


title: Hum d25 batch 3

description:
H9_d30_2204
RNA was isolated from ~50 H9 batch 3 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i703 and i507

value: Day 25


title: BCL2_KD_2

value: second targeted knockdown of BCL2 via ASX04ZKL


title: BCL2_KD_1

value: first targeted knockdown of BCL2 via ASX04ZKL


title: Hum d0 batch 3

description:
H9_d5_2204
RNA was isolated from ~300 H9 batch 3 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i703 and i501

value: Day 0


title: Hum d25 batch 2

description:
H9_d30_1704
RNA was isolated from ~50 H9 batch 2 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i702 and i507


title: WM with bone lesion-2

city: Tachikawa

first: NAOHIRO

last: SEKIGUCHI

state: Tokyo

address: 3256, Midori

department: Hematology

country: Japan

institute: Disaster Medical Center

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with MBEI (Li and Wong, 2001 PNAS, 98, 31-36) using GeneSpring software (Agilent technologies).

label: biotin

source_name: WM with bone lesion-2

label_protocol: Biotinylated cRNA were prepared using Ovation FFPE WTA System and Encore Biotin Module (NuGEN Technologies, Inc) according to the manufacturer's protocol from 100 ng total RNA.

extract_protocol: Total RNA were extracted from FFPE-embedded bone marrow samples using RNeasy FFPE kit (Qiagen) according to manufacturer’s manual.

treatment_protocol: formalin-fixed parrafin-embedded bone marrow biopsied specimen

tag: tissue

value: bone marrow

tag: disease

value: waldenstrom macroglobulinemia


title: MM with bone lesion-1

source_name: MM with bone lesion-1

value: myeloma


title: MM with bone lesion-2

source_name: MM with bone lesion-2


title: M2C11

value: Anaerobic Shock


title: MM with bone lesion-3

source_name: MM with bone lesion-3


title: WM with bone lesion-4

source_name: WM with bone lesion-4


title: M2D3


title: Hum d15 batch 2

description:
H9_d20_1704
RNA was isolated from ~100 H9 batch 2 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i702 and i506


title: AKT1_YY1_doubleKD

value: AKT1_YY1 double knock down


title: WM with bone lesion-3

source_name: WM with bone lesion-3


title: AKT1_NMYC_doubleKD

value: AKT1_NMYC double knock down


title: M2D6


title: M2C9


title: Hum d3 batch 2

description:
H9_d8_1704
RNA was isolated from ~300 H9 batch 2 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i702 and i503


title: Hum d5 batch 2

description:
H9_d10_1704
RNA was isolated from ~300 H9 batch 2 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i702 and i504

value: Day 5


title: Hum d2 batch 2

description:
H9_d7_1704
RNA was isolated from ~300 H9 batch 2 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i702 and i502


title: AKT1_KD_3

value: third targeted knockdown of AKT1 via ASX04WP6


title: Hum d25 batch 1

description:
H9_d30_0103
RNA was isolated from ~50 H9 batch 1 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i701 and i507


title: Hum d15 batch 1

description:
H9_d20_0103
RNA was isolated from ~100 H9 batch 1 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i701 and i506


title: Hum d0 batch 2

description:
H9_d5_1704
RNA was isolated from ~300 H9 batch 2 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i702 and i501


title: AKT1_KD_2

value: second targeted knockdown of AKT1 via ASX04WP6


title: M2C10


title: AKT1_KD_1

value: first targeted knockdown of AKT1 via ASX04WP6


title: M2C7


title: WM with bone lesion-1

source_name: WM with bone lesion-1


title: Hum d3 batch 1

description:
H9_d8_0103
RNA was isolated from ~300 H9 batch 1 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i701 and i503


title: AIB1_KD_2

value: second targeted knockdown of AIB1 via ASX04YYH


title: Hum d2 batch 1

description:
H9_d7_0103
RNA was isolated from ~300 H9 batch 1 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i701 and i502

value: Day 2


title: M2C6


title: AIB1_KD_1

value: first targeted knockdown of AIB1 via ASX04YYH


title: M2C3

value: NaCl Shock


title: M2C4


title: Hum d5 batch 1

description:
H9_d10_0103
RNA was isolated from ~300 H9 batch 1 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i701 and i504


title: AES_TBP_doubleKD

value: AES_TBP double knock down


title: M2B12


title: M2C8


title: hiPS_s4d4_s3m_R3

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

institute: Kyoto University

description: replicate 3

data_processing:
fastq: bcl2fastq conversion software 1.8.4 in the CASAVA 1.8.2 pipeline
Sequences were trimmed with Cutadapt v1.8.1 (Martin, 2011) with parameters -q 20 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA.
Processed reads were mapped to hg38 whole genome using TopHat v2.1.0 (Trapnell et al., 2009) with parameters -p 4 --library-type fr-firststrand --b2-very-sensitive.
Transcript abundance was quantified by HTSeq v0.6.1 (Anders et al., 2015) with parameters -a 20 -i gene_name (gencode.v24.annotation.gtf provided by iGenome).
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file contains gene name and raw count columns.

source_name: Human iPSC

growth_protocol: 585A1 hiPS cell line was grown on Synthemax (Corning)-coated wells in Essential 8 medium (Thermo Fisher Scientific).

extract_protocol:
RNA was isolated with RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA integrity number was analyzed using RNA 6000 Nano Kit (Agilent Technologies) on Bioanalyzer (Agilent Technologies), and RNA was quantified using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).
Sequencing libraries were prepared from 4 µg of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina). The libraries were quantified by Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific), and analyzed using DNA 1000 Analysis Kit (Agilent Technologies). Each library was diluted to 4 nM and pooled together.

treatment_protocol: Differentiation into pancreatic progenitor cells was performed as previously described (Toyoda et al., 2017; Kimura et al., 2017).

tag: gender

value: Male

tag: cell type

value: AT7867-treated pancreatic progenitor (s3m)


title: hiPS_s4d4_s4m_R3

description: replicate 3

value: AT7867-treated pancreatic progenitor (s4m)


title: hiPS_s3d3_R3

description: replicate 3

value: hiPSC derived pancreatic progenitor


title: Hum d0 batch 1

description:
H9_d5_0103
RNA was isolated from ~300 H9 batch 1 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i701 and i501

value: Day 0


title: hiPS_s2d4_R3

description: replicate 3

value: hiPSC derived primitive gut tube


title: M2B11

value: Anaerobic Shock


title: Osteoarthritic cartilage-MT-3

city: Durham

first: Virginia

middle: Byers

last: Kraus

state: United States

address: 300 N Duke St

department: Duke Molecular Physiology Institute

country: USA

institute: Duke University

description:
Single cell RNA sequencing
OA-MT-118

data_processing:
Basecalling and fastq files generated using 10X Cellranger v2.0.0 with default parameters
Alignment, counting, filtering, of all  SY,OLT & IMT single cell RNA-Seq samples , using 10X Cellranger v2.0.0 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Homo Sapiens SY,OLT & IMT samples. Columns correspond to individual cells(barcodes), while rows correspond to genes.
genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: Osteoarthritic cartilage

extract_protocol:
Single cell RNA were extracted using Chromium Single Cell 5' Gel Bead Kit according to the manufacturers’ recommendations (10x Genomics, CA)
Libraries were prepared using Chromium single-cell RNA-Seq library kit v2 according to the manufacturers’ recommendations (10x Genomics, CA)

value: Damaged medial tibial (MT) plateau cartilage

tag: cells

value: Chondrocytes

value: Female


title: AIB1_KD_3

value: third targeted knockdown of AIB1 via ASX04YYH


title: Hum d10 batch 1

description:
H9_d15_0103
RNA was isolated from ~150 H9 batch 1 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i701 and i505

value: Day 10


title: AES_RPL11_doubleKD

value: AES_RPL11 double knock down


title: AES_KD_3

value: third targeted knockdown of AES via ASX053MJ


title: M2B10


title: Osteoarthritic cartilage-MT-2

description:
Single cell RNA sequencing
OA-MT-116


title: M2B9


title: hiPS_s1d0_R3

description: replicate 3

value: Undifferentiated hiPSCs


title: hiPS_s1d4_R3

description: replicate 3

value: hiPSC derived definitive endoderm


title: Osteoarthritic cartilage-MT-1

description:
Single cell RNA sequencing
OA-MT-113


title: AES_KD_2

value: second targeted knockdown of AES via ASX053MJ


title: hiPS_s4d4_s4m_R2

description: replicate 2

value: Male


title: AES_KD_1

value: first targeted knockdown of AES via ASX053MJ


title: M2B8

value: NaCl Shock


title: Osteoarthritic cartilage-oLT-3

description:
Single cell RNA sequencing
OA-oLT-118

value: Minimally damaged outer lateral tibial (oLT) plateau cartilage


title: hiPS_s4d4_s3m_R2

description: replicate 2

value: AT7867-treated pancreatic progenitor (s3m)


title: Osteoarthritic cartilage-oLT-2

description:
Single cell RNA sequencing
OA-oLT-116


title: M2B7


title: hiPS_s3d3_R2

description: replicate 2

value: hiPSC derived pancreatic progenitor


title: Osteoarthritic cartilage-oLT-1

description:
Single cell RNA sequencing
OA-oLT-113


title: M2B5


title: YY1_KD_3

value: third targeted knockdown of YY1 via ASX053W2


title: M2B6

value: Anaerobic Shock


title: YY1_MIZ1_doubleKD

value: YY1_MIZ1 double knock down


title: hiPS_s2d4_R2

description: replicate 2

value: hiPSC derived primitive gut tube


title: YY1_KD_2

value: second targeted knockdown of YY1 via ASX053W2


title: hiPS_s1d4_R2

description: replicate 2


title: Osteoarthritic synovial membrane-3

description:
Single cell RNA sequencing
SY-118

source_name: Osteoarthritic synovial membrane

value: Synovial membrane

value: Synoviocytes

value: Female


title: Osteoarthritic synovial membrane-2

description:
Single cell RNA sequencing
SY-116


title: M2B3

value: Late Stationary Phase


title: hiPS_s1d0_R2

description: replicate 2

value: Undifferentiated hiPSCs


title: hiPS_s4d4_s4m_R1

description: replicate 1

value: AT7867-treated pancreatic progenitor (s4m)


title: Osteoarthritic synovial membrane-1

description:
Single cell RNA sequencing
SY-113

value: Male


title: M2A11


title: TIF1B_KD_3

value: third targeted knockdown of TIF1B via ASX05101


title: YY1_KD_1

value: first targeted knockdown of YY1 via ASX053W2


title: M2A12


title: TIF1B_KD_2

value: second targeted knockdown of TIF1B via ASX05101


title: hiPS_s4d4_s3m_R1

description: replicate 1

value: AT7867-treated pancreatic progenitor (s3m)


title: shIMPDH2_rep3

city: St. John's

first: Touati

last: Benoukraf

state: Newfoundland

address: Craig L. Dobbin Genetics Research Centre

department: Faculty of Medicine, Discipline of Genetics

country: Canada

institute: Memorial University of Newfoundland

data_processing:
Raw sequence data was trimmed and adaptor sequences were removed from the sequenced reads using Trim Galore coupled with Cutadapt.
High-quality trimmed reads were aligned to the human genome reference hg38 using the Spliced Transcripts Alignment to a Reference (STAR) software.
Raw read counts for each gene were subsequently measured using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: text file containing raw read count for each gene across different samples

source_name: Huh7 cell line

growth_protocol: Huh7 cells were maintained in DMEM with 10% FBS and 1% Pen Strep.

extract_protocol: Integrity and quality of RNA was determined using a 2100 Bioanalyzer system (Agilent). Only samples with RNA integrity number (RIN) values between 9 and 10 were used for RNA sequencing. cDNA libraries were generated from strand-specific mRNA using a TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer instructions, following which the library quality was assessed using a Bioanalyzer and quantified. The libraries were then multiplexed and clustered using a cBot 2 System (Illumina), and sequenced on a HiSeq 4000 (Illumina) at NovogeneAIT Genomics.

treatment_protocol: Knockdown of IMPDH1 or IMPDH2 was achieved by lentiviral infection of cells with shRNA in a pLKO.1 lentiviral vector backbone. Lentiviral supernatant was produced by co-transfection of lentiviral vectors and expression and packaging plasmids into HEK293T cells using the calcium phosphate transfection method, following which the supernatant was collected after 48 hours and filtered through a 0.45 μm filter. To generate stable knockdown cells, Huh7 cells were then incubated with the undiluted supernatant in the presence of 8 μg/ml polybrene, and selected thereafter using 1.5 μg/ml puromycin.

value: liver


title: shIMPDH2_rep2


title: hiPS_s3d3_R1

description: replicate 1

value: hiPSC derived pancreatic progenitor


title: M2A9

value: NaCl Shock


title: TIF1B_KD_1

value: first targeted knockdown of TIF1B via ASX05101


title: shIMPDH2_rep1


title: TCF7L2_KD_3

value: third targeted knockdown of TCF7L2 via ASX04XU9


title: M2A8


title: TCF7L2_KD_2

value: second targeted knockdown of TCF7L2 via ASX04XU9


title: hiPS_s2d4_R1

description: replicate 1

value: hiPSC derived primitive gut tube


title: M2A7

value: Anaerobic Shock


title: hiPS_s1d4_R1

description: replicate 1

value: hiPSC derived definitive endoderm


title: shIMPDH1_rep3


title: TCF7L2_KD_1

value: first targeted knockdown of TCF7L2 via ASX04XU9


title: M2A5


title: TBP_GCN1L1_doubleKD

value: TBP_GCN1L1 double knock down


title: shIMPDH1_rep1


title: shIMPDH1_rep2


title: M2A3

value: Late Stationary Phase


title: M2A10


title: MCF-7_ZNF414 overexpressing_rep2

city: Tampere University

first: Matti

last: Nykter

state: Please select one below:

address: MET / Computational biology

country: Finland

institute: Tampere University

description:
MACE tool consolidates signal from replicates and generates a single output file.
MCF7_overexpressing_ZNF414_binding_sites_MACE_border_pair.bed

library_source: genomic

data_processing:
Library strategy: ChIP-exo
Single-end read alignment using Bowtie2 v2.3.2 (Langmead et al., Nature Methods, 2012) with ``--very-sensitive -U`` parameters.
The bam files were filtered to keep reads with a mapping quality greater than 1 using samtools v1.3 (Handsaker et al., 2009, Bioinformatics).
Signal consolidation over two replicates of each cell line was performed using MACE v.1.2 (Wang et al., 2014, Nucleic Acids Research) tool command ``preprocessor.py``.
Peaks were identified using MACE v.1.2 tool command ``mace.py`` with parameter ``--fold 0.1`` representing the cutoff level as the minimum coverage signal used to build model and consolidated signal generated by MACE ``preprocessor.py`` command.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data in BED format contain border pairs detected by MACE tool from consolidated signal from two replicates of each cell line. Peaks detected by MACE are classified into Single Forward Border (SFB) peaks, Single Reverse Border (SRB) peaks and Gale-Sharpley paired Border (GSB) peaks.

molecule: genomic DNA

source_name: Breast cancer cell line

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. Nuclear extraction was achieved lysing the cells with Schmidt's LB1 buffer and through sonication in the Bioruptor Standard device. Nuclei were then pelleted and lysed with ChIP-lysis buffer. Chromatin was sonicated to 100-400 bp fragments in the Bioruptor. Immunoprecipitation was performed using an antibody against the V5 tag (ab9116, Abcam). Immunoprecipitation was performed using the Active Motif ChIP-exo Kit following the manufacturer's instructions.
Libraries were prepared according to Active Motif ChIP-exo kit instructions, except for one DNA purification step (done with NEB's Monarch PCR & DNA cleanup kit) and the gel extraction for library size selection (done with NEB's Monarch DNA Gel extraction kit). The protocol steps were: end repair, P7 Exo-Adapter ligation, nick repair, exonuclease digestion, reversal of cross-links, DNA purification, P7 primer extension, P5 Exo-Adapter ligation, library amplification and size selection.

treatment_protocol: Approximately 50x10^6 cells per sample were transfected with pcDNA6.2/EmGFP-Bsd/V5-DEST-ZNF414 plasmid using Lipofectamine 3000 regent. Cells were harvested 48 h posttransfection.

value: Breast

tag: chip antibody

value: V5 tag (ab9116, Abcam)

tag: transfection


title: M2A2


title: shControl_rep3


title: MCF-7_ZNF414 overexpressing_rep1


title: TBP_KD_2

value: second targeted knockdown of TBP via ASX04XTS


title: shControl_rep2


title: Hs700T_ZNF414 overexpressing_rep2

description:
MACE tool consolidates signal from replicates and generates a single output file.
Hs700T_overexpressing_ZNF414_binding_sites_MACE_border_pair.bed

source_name: Pancreatic cancer cell line

value: Pancreas


title: M1H11


title: shControl_rep1


title: Hs700T_ZNF414 overexpressing_rep1


title: M1H5


title: TBP_KD_1

value: first targeted knockdown of TBP via ASX04XTS


title: STAT5B_KD_3

value: third targeted knockdown of STAT5B via ASX04Y97


title: K23+FN

city: Hamburg

first: Matthias

last: Rath

address: Am Kaiserkai 1

department: Institute of Molecular Medicine

institute: MSH Medical School Hamburg

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing; grown on 5µg/cm² fibronectin for 48h.
processed data file: Count_FPKM_Differential Expression_FN.xlsx

data_processing:
STAR aligner was used for split-read alignment against the human genome assembly hg19 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count_FPKM_Differential_Expression_FN.xlsx: Excel file includes counts, FPKM values, and differential expression analyses.

source_name: CI-huVEC (InSCREENeX)

extract_protocol:
RNA was harvested using PeqGold TriFast reagent (Peqlab-VWR, Radnor, USA) and extracted with the Direct-zol RNA MiniPrep Plus Kit (Zymo Research, Irvine, USA).
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA protocol.

value: CI-huVEC

tag: clone

value: HKO

tag: passage

tag: genotype/variation

tag: treatment

value: Fibronectin


title: K22+FN


title: hiPS_s1d0_R1

description: replicate 1

value: Male

value: Undifferentiated hiPSCs


title: MCF-7_siZNF414_24h_rep1

description:
poly A capture
mcf7_24h_deseq_siZNF414_vs_siLUC.xlsx

data_processing:
Paired-end read alignment using Tophat2 v2.1.0 (Kim et al., Genome Biology, 2013) with parameters ` --library-type fr-firststrand`.
The bam files were filtered to keep reads with a mapping quality greater than 20 using samtools v1.3 (Handsaker et al., 2009, Bioinformatics).
Gene expression was quantified with HTSeq tool (Anders et al.,  Bioinformatics, 2014) using ` -s reverse -t gene` parameter using protein-coding genes annotated in gencode.v26lift37 reference assembly.
Differential expression analysis of treatment (siZNF414) versus control (siLUC) samples in each of the two cell lines was performed using DESeq2 R package (Love et al., Genome Biology, 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data in excel format contain statistics from DESeq2 tool for comparing gene expression between treatment (siZNF414) and control (siLUC) samples as well as a table of raw gene expression counts across the samples calculated by HTSeq tool.

extract_protocol:
Samples were collected 12 h and 24 h after transfection, and total RNA was extracted using a Nucleospin miRNA kit (Macherey-Nagel, Düren, Germany).
Library preparation and sequencing were done at the Biomedicum Functional Genomics Unit. Total RNA was subjected to poly A capture, and the sequencing libraries were prepared using the SureSelect Strand-specific RNA kit (Agilent, Santa Clara, CA, USA).

treatment_protocol: Transfections were performed on 6-well plates. Twenty-four hours after seeding, the cells were transfected with 10 nM siRNA using Interferin reagent (Polyplus Transfection, San Marcos, CA, USA) as per the manufacturer’s instructions. An siRNA targeting the firefly luciferase (LUC) gene was used as a control in all experiments.

value: ZNF414 siRNA transfection

tag: timepoint


title: STAT5B_KD_2

value: second targeted knockdown of STAT5B via ASX04Y97


title: MCF-7_siZNF414_24h_rep2


title: M1H2


title: STAT5B_KD_1

value: first targeted knockdown of STAT5B via ASX04Y97


title: K21+FN


title: K23

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing.
processed data file: Count_FPKM_Differential Expression_FN.xlsx


title: TBP_KD_3

value: third targeted knockdown of TBP via ASX04XTS


title: M1G6


title: STAT3_BRD4_doubleKD

value: STAT3_BRD4 double knock down


title: MCF-7_siLuc_24h_rep2

value: Luciferase siRNA transfection


title: MCF-7_siLuc_24h_rep1

value: Breast


title: K22


title: STAT3_KD_3

value: third targeted knockdown of STAT3 via ASX04Y94


title: M1G3

value: Late Stationary Phase


title: M1G2


title: K21


title: Hs700T_siZNF414_24h_rep1

description:
poly A capture
hs700t_24h_deseq_siZNF414_vs_siLUC.xlsx

value: Pancreas


title: M1H3


title: M1F11


title: STAT3_KD_1

value: first targeted knockdown of STAT3 via ASX04Y94


title: WT-3

description: processed data file: Count_FPKM_Differential Expression_FN.xlsx

value: Wild-type


title: Hs700T_siLuc_24h_rep2


title: M1F9


title: M1F7


title: Hs700T_siLuc_24h_rep1


title: SP1_DP2_doubleKD

value: SP1_DP2 double knock down


title: MCF-7_siZNF414_12h_rep2

description:
poly A capture
mcf7_12h_deseq_siZNF414_vs_siLUC.xlsx


title: SP1_KD_2

value: second targeted knockdown of SP1 via ASX04Y7O


title: SP1_KD_3

value: third targeted knockdown of SP1 via ASX04Y7O


title: WT-1

value: CI-huVEC

value: HKO


title: M1F6


title: K19

description:
CCM3 Exon 3 targeted CRISPR/Cas9 editing.
processed data file: Count_FPKM_Differential_Expression.xlsx

data_processing:
STAR aligner was used for split-read alignment against the human genome assembly hg19 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count_FPKM_Differential_Expression.xlsx: Excel file includes counts, FPKM values, and differential expression analyses.


title: Hs700T_siZNF414_24h_rep2

value: ZNF414 siRNA transfection


title: M1F5


title: K18


title: STAT3_KD_2

value: second targeted knockdown of STAT3 via ASX04Y94


title: SP1_KD_1

value: first targeted knockdown of SP1 via ASX04Y7O


title: M1F4


title: RPL11_TCF7L2_doubleKD

value: RPL11_TCF7L2 double knock down


title: K17


title: MCF-7_siZNF414_12h_rep1


title: MCF-7_siLuc_12h_rep2


title: M1F3


title: MCF-7_siLuc_12h_rep1


title: Hs700T_siZNF414_12h_rep2

description:
poly A capture
hs700t_12h_deseq_siZNF414_vs_siLUC.xlsx


title: WT 4

description: processed data file: Count_FPKM_Differential_Expression.xlsx


title: M1F2


title: WT 2


title: RPL11_KD_3

value: third targeted knockdown of RPL11 via ASX0571N


title: RPL11_KD_2

value: second targeted knockdown of RPL11 via ASX0571N


title: Hs700T_siZNF414_12h_rep1


title: M1E11


title: Hum d10 batch 2

description:
H9_d15_1704
RNA was isolated from ~150 H9 batch 2 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i702 and i505

source_name: H9 human ES cell-derived organoids

tag: time point

value: Day 10


title: RPL11_KD_1

source_name: human squamous carcinoma cell line

tag: cell line

value: first targeted knockdown of RPL11 via ASX0571N


title: WT 1


title: Hs700T_siLuc_12h_rep2

value: Luciferase siRNA transfection


title: RELA_LKB1_doubleKD

tag: sample type

value: RELA_LKB1 double knock down


title: M1E5

source_name: bacteria

tag: condition

value: Late Stationary Phase


title: 2CBS_downstream_PLAC-seq_rep2

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
Library strategy: PLAC-seq
For PLAC-seq, paired-end reads were first mapped to mm10 reference genome. We modified the original WAPS mapping procedure by replacing the bowtie2 alignment tool with bwa-mem and integrated MAPS feather post-filtering pipeline to resolve the chimeric reads
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Genome_build: mm10
Supplementary_files_format_and_content: juicer hic files that can be visualized in Juicebox and cis-contacts of chr3 of the PLAC-seq data.

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

extract_protocol: PLAC-seq experiments were performed in biological replicates using MboI, following the protocol described by Fang, R., Yu, M., et al., Cell research 2016(PMID: 27886167). Hi-C experiments were performed in biological replicates using MboI, following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)

value: F123 ESC

tag: strain

value: F1 hybrid (castaneus x S129/SvJae)

value: Millipore, 04-745

tag: genotype


title: M1E3

tag: number of cells


title: WT_PLAC-seq_rep2

value: Wild-type


title: RELA_KD_3

value: third targeted knockdown of RELA via ASX04XXT


title: RELA_KD_2

value: second targeted knockdown of RELA via ASX04XXT


title: MCF-7_ZNF414 overexpressing

data_processing:
Paired-end read were trimmed with TrimGalore tool (https://github.com/FelixKrueger/TrimGalore) using parameters `--fastqc --paired --nextera --length 20 -q 20`.
Read alignment was performed using Bowtie2 v2.3.2 (Langmead et al., Nature Methods, 2012) with ``--very-sensitive`` parameters.
Reads with mapping quality lower than 20 were filtered using samtools v1.3 (Handsaker et al., 2009, Bioinformatics).
qPCR duplicates were filtered from the bam files using samtools v1.3 ``rmdup``.
Detection of open chromatin areas was performed with MACS2 peak detection tool (Zhang et al., Genome Biology, 2008) using `callpeak --format BAMPE` command.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data in NARROWPEAK format contain locations of statistically significantly enriched genomic regions detected by MACS2 tool.

extract_protocol:
Cells were resuspended in ice cold lysis buffer and centrifuged 10 min at 700g and 4oC. The supernatant was removed.
A transposition mix containing Transposase was added to the nuclear pellet and this was incubated at 37oC for 45 minutes with shaking. DNA was then purified using Qiagen MinElute PCR purification kit and libraries were PCR amplified. The libraries were purified using Qiagen MinElute PCR Purification Kit and further cleaned with Agencourt AMPure XP magnetic beads.

treatment_protocol: 70,000 cells were plated per sample. Cells were transfected with pcDNA6.2/EmGFP-Bsd/V5-DEST-ZNF414 plasmid using Lipofectamine 3000 regent. Cells were harvested 48 h posttransfection and 50,000 cells were subsequently used in the experiments.

tag: tissue

value: Breast

value: transfection with pcDNA6.2/EmGFP-Bsd/V5-DEST-ZNF414 plasmid


title: M1D6


title: 2CBS_PLAC-seq_rep2


title: RELA_KD_1

value: first targeted knockdown of RELA via ASX04XXT


title: M1C5


title: 4CBS_downstream_PLAC-seq_rep2


title: M1E2


title: M1D2


title: RB1_RELA_doubleKD

value: RB1_RELA double knock down


title: M1C4


title: RB1_KD_2

value: second targeted knockdown of RB1 via ASX04XXA


title: M1C2


title: RB1_KD_3

value: third targeted knockdown of RB1 via ASX04XXA


title: 4CBS_PLAC-seq_rep1


title: P53_MYCBP_doubleKD

value: P53_MYCBP double knock down


title: RB1_KD_1

value: first targeted knockdown of RB1 via ASX04XXA


title: 4CBS_downstream_PLAC-seq_rep1


title: 2CBS_downstream_PLAC-seq_rep1


title: Hs700T_siLuc_12h_rep1

value: Pancreas

value: Luciferase siRNA transfection


title: M1B7

value: Late Stationary Phase


title: M1B4


title: 4CBS_PLAC-seq_rep2

value: F123 ESC


title: WT_PLAC-seq_rep1

value: F1 hybrid (castaneus x S129/SvJae)


title: Hs700T_ZNF414 overexpressing

description: Processed data in NARROWPEAK format contain locations of statistically significantly enriched genomic regions detected by MACS2 tool.


title: P53_KD_3

value: third targeted knockdown of P53 via ASX053MH


title: M1B2


title: M1B3


title: P53_KD_2

value: second targeted knockdown of P53 via ASX053MH


title: P53_KD_1

value: first targeted knockdown of P53 via ASX053MH


title: M1A12


title: M1B1


title: M1A7


title: 2CBS_PLAC-seq_rep1

value: Millipore, 04-745


title: P300_LMYC_doubleKD

value: P300_LMYC double knock down


title: P300_KD_2

value: second targeted knockdown of P300 via ASX04ZYU


title: P300_KD_1

value: first targeted knockdown of P300 via ASX04ZYU


title: M1A3


title: PV-Cre/tdTomato/Dnmt1loxp_WT_6month_rna/rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina's CASAVA-1.8.2 was used to convert the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Along with base calling, adapter trimming and demultiplexing were performed.
Samples aligned to mm10 using STAR 2.5.2a
Reads quantified to mouse genes in gene version mm10 version 97 using featureCounts 1.5.0-p1
Supplementary_files_format_and_content: mm10

source_name: PV-positive cortical interneurons isolated from 6month old mice

growth_protocol: transgenic mice on the C57BL/6 background including PV-Cre/tdTomato/Dnmt1 wild-type as well as PV-Cre/tdTomato/Dnmt1 loxP2 mice. The transgenic mice were established by crossing the PV-Cre line (obtained from Christian Huebner, University Hospital Jena, Germany and described in Hippenmeyer et al., 2005(1)) with the tdTomato transgenic reporter mice (obtained from Christian Huebner, University Hospital Jena, Germany and described in Madisen et al., 2010(2)) and Dnmt1 floxP2 mice, (B6;129Sv-Dnmt1tm4Jae/J, Jaenisch laboratory, Whitehead Institute; USA). The Dnmt1 floxP2 mice have LoxP-sites flanking exons 4 and 5 of the Dnmt1 gene. Cre-mediated deletion leads to out-of-frame splicing from exon 3 to exon 6, resulting in a null Dnmt1 allele(3).

extract_protocol:
Mice were deeply anesthetized intraperitoneally with 50% chloral hydrate in phosphate buffered saline (PBS; pH7.4, 2.5 μg chloral hydrate per g body weight). Adult brains were dissected in GBSS (1.53 mM CaCl2, 3.66mM KCl, 0.22 mM KH2PO4, 1.03 mM MgCl2 * 6H2O, 0.28 mM MgSO4 + 7H2O, 137.93 mM NaCl, 2.7 mM NaHCO3, 0.84 mM Na2HPO4, 5.56 mM Glucose, pH7.4) supplemented with 0.65% glucose. Cortical hemispheres were dissected and subsequently handled separately. All following volumes are calculated per cortical hemisphere, which were cut into small pieces and transferred to 5 ml HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin and 0.65% glucose and washed twice. The tissue was then transferred to 5 ml pre-warmed (20 min at 37°C) Trypsin/EDTA (Life technologies, U.S.A.) supplemented with 132 mM trehalose (Sigma-Aldrich, Germany), 100 U/mL penicillin, 100 g/mL streptomycin, 10 mM HEPES and 600 U DNase (Applichem, Germany) and incubated for 30 min at 37°C, rotating the samples every 5 min. Samples were washed with 2.1 ml pre-warmed DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose. After adding 0.9 ml pre-warmed HBSS containing 10 mg/ml Collagenase Type 2 (Worthington, Great Britain) samples were incubated for 25 min at 37°C rotating every 5 min and then washed with 2 ml pre-warmed DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin, 3.3 mM EDTA and 132 mM trehalose prior to cool down on ice for 2 min. Dissolving of samples occurred in 1.5 ml DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose. Trituration was performed using fire-polished and heat-treated (180°C for 8 h) glass capillaries of three different diameters (about 500 μM; 250 μM and 100 μm), which were coated with DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin prior to use. Mechanical dissociation was performed by pipetting up and down gently 3-5 times for each diameter starting with the largest diameter, avoiding air bubbles. After each step, the supernatant was collected in 1 ml DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose was added to the original sample. After trituration with the smallest glass capillary, suspension was filtered through nylon gauze (80-100 μm) and centrifuged for 5 min at 160 g, 4°C. After supernatant removal, the pellet was dissolved in 4 ml HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose. After centrifugation (5 min, 160 g, 4°C), the pellet was dissolved in 1xPBS (pH7.4) with 30% Percoll (Sigma-Aldrich) and 132 mM trehalose to perform a density gradient centrifuged for 10 min at 500 g and 4°C. The supernatant was removed and the pellet was dissolved in 250 μl HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose for FACS. Following the addition of DAPI, cells were sorted using an ARIA III FACS sorter (BD Biosciences, U.S.A.) with the maximal flow rate of 6. The tdTomato reporter was excited by a 561 nm yellow/green solid state laser and emission signal was detected in a range of 579 nm to 593 nm. According to their FCS/SSC criteria followed by cell doublet exclusion via a FSC-H vs. FSC-W criterium, DAPI-negative living cells were sorted based on a distinctive tdTomato signal. Cells of interest were collected in HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose at 4°C and pelleted by centrifugation (10 min at 10.000 g, 4°C). Enriched tdTomato cells of one hemisphere were prepared for RNA-sequencing, while cells of the contralateral hemisphere were subjected to DNA-isolation for MeDIP-sequencing for each brain used. For RNA isolation, pellets were dissolved in 500 μl Trizol®Reagent (Life Technologies, U.S.A.) and subsequential frozen on dry ice. For MeDIP-Seq analysis cell pellets were frozen at -80°C until further use. Only male mice were used for RNA and MeDIP sequencing.          For RNA isolation the samples were then subjected to standard RNA isolation procedure using  Trizol Reagent (Life Technologies) with  additional application of GlycoBlue (Thermo Fisher Scientific) to  a final concentration of 0.2% during RNA precipitation for better  visualization of the pellet., digested with RNase-free  DNase (Qiagen) and checked for integrity by capillary gel  electrophoresis (Bioanalyzer, Agilent Technologies, Inc.).  DNA isolation of FACS-enriched tdTomato cells was performed using QIAamp DNA Micro Kit  (Qiagen) according to manufacturer’s instruction.
RNA was isolated using the Trizol protocol according to manufacturer’s instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using the fragment analyzer from Advanced Analytical (U.S.A.). Library preparation for RNA-Seq was performed using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Cat. N°RS-122-2002, U.S.A.) starting from 50 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega, U.S.A.). The size range of final cDNA libraries was determined applying the DNA chip on the fragment analyzer (average 350 bp; Advanced Analytical). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; ~30-40 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics, G.B.). Read alignment was performed using STAR (v2.3.0; 25) to the mm10 reference genome. Data were converted and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12; 26) loading DESeq2 (27).

tag: strain background

value: PV-Cre/tdTomato/Dnmt1 wild-type

tag: age

value: 6 month

value: brain

tag: region

value: cortex

tag: cell type

value: mature Pvergic cortical interneurons

value: wild type


title: M1A1


title: P107_GCN1L1_doubleKD

value: P107_GCN1L1 double knock down


title: M1A2

value: Late Stationary Phase


title: PV-Cre/tdTomato/Dnmt1loxp_WT_6month_rna/rep1


title: PV-Cre/tdTomato/Dnmt1loxp_WT_18month_rna/rep2

source_name: PV-positive cortical interneurons isolated from 18month old mice

value: 18 months


title: P107_CCNB1_doubleKD

value: P107_CCNB1 double knock down


title: P107_KD_3

value: third targeted knockdown of P107 via ASX04XXC


title: PV-Cre/tdTomato/Dnmt1loxp_KO_6month_rna/rep2

source_name: PV-positive cortical interneurons isolated from 6month old mice after DNMT1 knockout

value: PV-Cre/tdTomato/Dnmt1 loxP2

value: Dnmt1 knockout


title: M1A6


title: H37Ra Control Day0

city: Wuhan

first: Habib

last: Zeshan

state: Hubei

address: shizishan street No.1

department: College of veterinary medicine

country: China

institute: Huazhong Agricultural University

data_processing:
Alignment reads to reference use TopHat2 (parameters: --library-type fr-unstranded, TopHat2  v2.1.0)
Sort alignment result bam file using samtools(parameters: samtools sort -n, samtools version:1.2)
Count expression using htseq-count (parameters: -f bam -r name -s yes -i gene_id, htseq version 0.7.2)
Normalize count table by house keeping gene’s expression level.
Clustering gene’s by it’s expression pattern.
Genome_build: ASM1614v1 assembly for Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: tab delimited file include expression counts of each gene.

organism: Mycobacterium tuberculosis H37Ra

source_name: H37Ra Control Day0

growth_protocol: H37Ra growth OD of kanamycin treated and control samples were detected at each step

extract_protocol:
RNA isolation through standard protocol
RNA library was constructed by using RNA-Seq library preparation kit (Vazyme Biotech Co. Ltd) following standard protocol

treatment_protocol: H37Ra were treated with sub-lethal kanamycin exposure for 72 hours alongwith untreated sample as control.Half of them were sub-cultured every three days and remaining were subjected for RNA seq.

value: untreated control


title: H37Ra Control Day45

source_name: H37Ra Control Day45


title: P107_KD_2

value: second targeted knockdown of P107 via ASX04XXC


title: P300_NFKB1_doubleKD

value: P300_NFKB1 double knock down


title: PV-Cre/tdTomato/Dnmt1loxp_WT_18month_rna/rep1


title: H37Ra treated Day45

source_name: H37Ra treated Day45

value: kanamycin


title: P107_KD_1

value: first targeted knockdown of P107 via ASX04XXC


title: negative control replicate 7


title: PV-Cre/tdTomato/Dnmt1loxp_KO_18month_rna/rep2

source_name: PV-positive cortical interneurons isolated from 18month old mice after DNMT1 knockout


title: PV-Cre/tdTomato/Dnmt1loxp_KO_6month_rna/rep1

value: 6 month


title: H37Ra treated Day27

source_name: H37Ra treated Day27


title: PV-Cre/tdTomato/Dnmt1loxp_KO_18month_rna/rep1

value: brain


title: H37Ra treated Day15

source_name: H37Ra treated Day15


title: P300_KD_3

value: third targeted knockdown of P300 via ASX04ZYU


title: H37Ra treated Day3

source_name: H37Ra treated Day3


title: PV-Cre/tdTomato/Dnmt1loxp_WT_6month_MeDIP-Seq

data_processing:
Illumina's CASAVA-1.8.2  was used to convert the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images. Along with base calling, adapter trimming and demultiplexing were performed.
Samples aligned to mm10 using Bowtie2 2.3.4
Alignments were filtered for high-quality to keep those with MAPQ=1 or MAPQ>4
Coverage files bigWig were created from the high-quality BAM files using bamCoverage 3.2.1
Supplementary_files_format_and_content: mm10

extract_protocol:
Mice were deeply anesthetized intraperitoneally with 50% chloral hydrate in phosphate buffered saline (PBS; pH7.4, 2.5 μg chloral hydrate per g body weight). Adult brains were dissected in GBSS (1.53 mM CaCl2, 3.66mM KCl, 0.22 mM KH2PO4, 1.03 mM MgCl2 * 6H2O, 0.28 mM MgSO4 + 7H2O, 137.93 mM NaCl, 2.7 mM NaHCO3, 0.84 mM Na2HPO4, 5.56 mM Glucose, pH7.4) supplemented with 0.65% glucose. Cortical hemispheres were dissected and subsequently handled separately. All following volumes are calculated per cortical hemisphere, which were cut into small pieces and transferred to 5 ml HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin and 0.65% glucose and washed twice. The tissue was then transferred to 5 ml pre-warmed (20 min at 37°C) Trypsin/EDTA (Life technologies, U.S.A.) supplemented with 132 mM trehalose (Sigma-Aldrich, Germany), 100 U/mL penicillin, 100 g/mL streptomycin, 10 mM HEPES and 600 U DNase (Applichem, Germany) and incubated for 30 min at 37°C, rotating the samples every 5 min. Samples were washed with 2.1 ml pre-warmed DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose. After adding 0.9 ml pre-warmed HBSS containing 10 mg/ml Collagenase Type 2 (Worthington, Great Britain) samples were incubated for 25 min at 37°C rotating every 5 min and then washed with 2 ml pre-warmed DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin, 3.3 mM EDTA and 132 mM trehalose prior to cool down on ice for 2 min. Dissolving of samples occurred in 1.5 ml DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose. Trituration was performed using fire-polished and heat-treated (180°C for 8 h) glass capillaries of three different diameters (about 500 μM; 250 μM and 100 μm), which were coated with DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin prior to use. Mechanical dissociation was performed by pipetting up and down gently 3-5 times for each diameter starting with the largest diameter, avoiding air bubbles. After each step, the supernatant was collected in 1 ml DMEM/F12 supplemented with 10% FBS, 100 U/mL penicillin, 100 g/mL streptomycin and 132 mM trehalose was added to the original sample. After trituration with the smallest glass capillary, suspension was filtered through nylon gauze (80-100 μm) and centrifuged for 5 min at 160 g, 4°C. After supernatant removal, the pellet was dissolved in 4 ml HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose. After centrifugation (5 min, 160 g, 4°C), the pellet was dissolved in 1xPBS (pH7.4) with 30% Percoll (Sigma-Aldrich) and 132 mM trehalose to perform a density gradient centrifuged for 10 min at 500 g and 4°C. The supernatant was removed and the pellet was dissolved in 250 μl HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose for FACS. Following the addition of DAPI, cells were sorted using an ARIA III FACS sorter (BD Biosciences, U.S.A.) with the maximal flow rate of 6. The tdTomato reporter was excited by a 561 nm yellow/green solid state laser and emission signal was detected in a range of 579 nm to 593 nm. According to their FCS/SSC criteria followed by cell doublet exclusion via a FSC-H vs. FSC-W criterium, DAPI-negative living cells were sorted based on a distinctive tdTomato signal. Cells of interest were collected in HBSS w/o Ca2+ and Mg2+ supplemented with 7 mM HEPES, 100 U/mL penicillin, 100 g/mL streptomycin, 0.65% glucose and 132 mM trehalose at 4°C and pelleted by centrifugation (10 min at 10.000 g, 4°C). Enriched tdTomato cells of one hemisphere were prepared for RNA-sequencing, while cells of the contralateral hemisphere were subjected to DNA-isolation for MeDIP-sequencing for each brain used. For RNA isolation, pellets were dissolved in 500 μl Trizol®Reagent (Life Technologies, U.S.A.) and subsequential frozen on dry ice. For MeDIP-Seq analysis cell pellets were frozen at -80°C until further use. Only male mice were used for RNA and MeDIP sequencing.
For genome-wide methylation analysis we applied immunoprecipitation methods for the enrichment of 5-methylcytosines. Specifically, 100 ng of genomic DNA were used as starting material. The Methylated-DNA IP Kit from Zymo (Cat. N° D5101) was applied according to manufacturer’s instructions. The product of the IP and control reaction were then used for  preparation of Illumina compatible libraries according to the TruSeq Nano DNA Library Prep Kit  (Cat. N° FC-121-4001). Libraries were sequenced on a HiSeq 2000 yielding 50 bp single end  reads. The sequencing reads were demultiplexed using the Illumina CASAVA tool and sequence  quality was checked using FASTQC  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were then aligned to the  genome of Mus musculus (mm10) using Bowtie 2 (versions 2.0.2) with standard parameters.  Differentially methylated regions were identified using the MEDIPS package for R (version  1.16.0; 28) with a window size of 700bp and a minimum coverage of 5% of the window length. A  detailed description of the analysis pipeline can be found in Halder et al., 2016(29).

value: PV-Cre/tdTomato/Dnmt1 wild-type

value: 6 months

value: cortex

value: mature Pvergic cortical interneurons

tag: enrichtment

value: MeDIP


title: negative control replicate 5


title: negative control replicate 4


title: negative control replicate 3


title: DU16-02S0004892_L1

first: Sunil

last: Suchindran

state: NC

address: 101 Science Drive

department: Center for Applied Genomics and Precision Medicine

data_processing:
For Batch 1 the HiSeq 2500 system was used for basecalling. For Batch 2 NovaSeq 6000 RTA version 3.4.4 was used for basecalling.
Adapters were removed using Trimmomatic v0.38 in batch 2. Batch 1 fastq files are already trimmed.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used and for batch 2 "strand fr-stranded" was used.
Data was normalized using the TMM function from the Bioconductor package edgeR.
The ComBat method was used to account for a sequencing batch effect.

extract_protocol:
Total RNA was extracted from human blood using the Qiagen PAXgene Blood RNA Kit according to the manufacturer’s protocol.
In the first batch, stranded mRNA sequencing libraries were prepared using the GLOBINclear Human Kit (Invitrogen) with a TruSeq Stranded mRNA Kit library Prep. In the second batch, stranded RNA-seq libraries were prepared using the commercially available Nugen Universal Plus mRNA-seq kit. Nugen’s AnyDeplete mediated transcript depletion was used to eliminate globin mRNA transcripts from the final libraries.
In the first batch libraries were sequenced at 50 bp paired-end on an Illumina HiSeq instrument. In the second batch libraries were sequenced at 50 bp paired-end on an Illumina NovaSeq instrument.

tag: diagnosis

value: VIRAL


title: WT-2

value: CI-huVEC

tag: clone

value: HKO

tag: passage

tag: genotype/variation

value: Wild-type


title: H37Ra treated Day39

source_name: H37Ra treated Day39

tag: treatment


title: negative control replicate 8

tag: cell line


title: polyA_miR106b_4

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the mRNA transcriptome, defined by a gtf for the GRCm38 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the gtf file.
The data have not been further normalized or manipulated, so that each user can perform sample (library) depth and other normalization using software such as DESeq or edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each mRNA.

source_name: Engineered juxtaglomerular (JG) cells

extract_protocol:
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
RISC RNA was isolated from immunoprecipitated Ago2 via direct incubation of immunoprecipitates with Trizol reagent (Invitrogen).  Chemical fragmentation and preparation of single-end RNA-Seq libraries proceeded as for polyadenylated RNA.
non-strand-specific, single-end RNA-Seq

treatment_protocol: 48 h after transfection, JG cells growing as monolayer cultures were harvested directly into Trizol reagent (for polyadenylated RNA isolation) or trypsinized and lysed for Ago2 immunoprecipitation.

tag: transfection

tag: molecule subtype

value: Total cytoplasmic + nuclear RNA


title: DU16-02S0004883_L7


title: DU16-02S0004882_L6


title: negative control replicate 2

data_processing: Data normalized by first averaging technical replicates and then by dividing by spike-in gene. Fold Change calculated via deltaDeltaCt R package using positive and negative experimental controls


title: DU16-02S0004880_L4

value: BACTERIAL


title: polyA_miR106b_3


title: polyA_miR106b_2


title: DU16-02S0004876_L4


title: negative control replicate 1


title: NMYC_GNL3_doubleKD

tag: sample type

value: NMYC_GNL3 double knock down


title: DU16-02S0004867_L1


title: polyA_miR106b_1


title: DU16-02S0004898_L1


title: polyA_control_4

value: control


title: negative control replicate 6


title: PV-Cre/tdTomato/Dnmt1loxp_WT_18month_MeDIP-Seq

value: 18 months


title: NMYC_KD_3

value: third targeted knockdown of NMYC via ASX050M7


title: NMYC_KD_2

value: second targeted knockdown of NMYC via ASX050M7


title: NMYC_KD_1

value: first targeted knockdown of NMYC via ASX050M7


title: polyA_control_3


title: NFKB1_KD_3

value: third targeted knockdown of NFKB1 via ASX053S7


title: DU16-02S0004857_L1_1


title: polyA_control_2


title: DU16-02S0004859_L8


title: polyA_control_1


title: NFKB1_KD_1

value: first targeted knockdown of NFKB1 via ASX053S7


title: Ago2_miR106b_4

description:
Ago2-bound RNA
Ago2_miR106b_4

tag: antibody


title: PV-Cre/tdTomato/Dnmt1loxp_KO_6month_MeDIP-Seq

value: PV-Cre/tdTomato/Dnmt1 loxP2

value: 6 months

value: brain

value: cortex


title: PV-Cre/tdTomato/Dnmt1loxp_KO_18month_MeDIP-Seq

value: mature Pvergic cortical interneurons

value: MeDIP


title: MYCBP_KD_3

value: third targeted knockdown of MYCBP via s25391


title: Ago2_miR106b_3

description:
Ago2-bound RNA
Ago2_miR106b_3


title: DU16-02S0004852_L1


title: DU16-02S0004853_L6


title: Ago2_miR106b_2

description:
Ago2-bound RNA
Ago2_miR106b_2


title: DU16-02S0004846_L5

value: VIRAL


title: MYCBP_KD_2

value: second targeted knockdown of MYCBP via s25391


title: DU16-02S0004847_L5


title: DU16-02S0004843_L3

value: BACTERIAL


title: Ago2_miR106b_1

description:
Ago2-bound RNA
Ago2_miR106b_1


title: NFKB1_KD_2

value: second targeted knockdown of NFKB1 via ASX053S7


title: DU16-02S0004856_L7


title: MYC_STAT5B_doubleKD

value: MYC_STAT5B double knock down


title: MYCBP_KD_1

value: first targeted knockdown of MYCBP via s25391


title: Ago2_control_4

description:
Ago2-bound RNA
Ago2_control_4

value: control


title: Control rep3

city: Singapore

first: Takayoshi

last: Matsumura

address: 14 Medical Drive #12-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

data_processing:
Reads that passed the quality filter step with trimmomatic-0.38 were mapped to the reference mouse genome sequence (mm10) using Tophat
CuffDiff was used for differential expression analyses
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files generated by CuffDiff

source_name: bone marrow

extract_protocol:
CD34-Flt3-Lin-Sca1+cKit+ long-term hematopoietic stem cells (LT-HSCs) were sorted directly into TRIzol Reagent (Thermo Fisher), and RNA was extracted. RNA quality and concentration were assessed using an RNA 6000 bioanalyzer pico kit (Agilent Technologies), and samples with an RNA integrity number more than 8 were used.
Complementary DNA was amplied by the SMARTer Ultra Low RNA Kit (Clontech), and sequencing was performed on an Illumina HiSeq with 150 bp paired-end reads

tag: strain

tag: cells

value: LT-HSCs

value: Control


title: Homo rep3

value: RUNX1 methylation-deficient


title: DU16-02S0004842_L3


title: MYC_P53_doubleKD

value: MYC_P53 double knock down


title: ATAC-seq_Homo rep1

data_processing:
Reads that passed the quality filter step were mapped to the reference mouse genome sequence (mm10) using Bowtie2,11.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bamCoverage

extract_protocol:
LT-HSCs were sorted and lysed in lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630).
Chromatin was extracted and processed for Tn5 transposase-mediated tagmentation and adapter incorporation for 30 min at 37 °C using the Nextera DNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. Transposed DNA was amplified using NEBNext High-Fidelity 2× Master Mix (New England Biolabs). Samples were pooled and run on an Illumina HiSeq.

value: long-term hematopoietic stem cells (LT-HSCs)

tag: genotype


title: ATAC-seq_Control rep2


title: Ago2_control_3

description:
Ago2-bound RNA
Ago2_control_3


title: ATAC-seq_Homo rep2


title: ATAC-seq_Control rep1


title: MYC_KD_3

value: third targeted knockdown of MYC via ASX050M5


title: Homo rep2


title: DU16-02S0004840_L2


title: Ago2_control_2

description:
Ago2-bound RNA
Ago2_control_2


title: DU16-02S0004834_L8


title: Homo rep1


title: Ago2_control_1

description:
Ago2-bound RNA
Ago2_control_1


title: Control rep2


title: MYC_KD_2

value: second targeted knockdown of MYC via ASX050M5


title: MYC_KD_1

value: first targeted knockdown of MYC via ASX050M5


title: Control rep1


title: Gastrocnemius, mKO rep 3

city: Boston

first: Ronald

middle: L

last: Neppl

state: MA

address: 60 Fenwood Rd.

department: Orthopedic Surgery

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v.0.36.
Trimmed reads were mapped to Mus musculus GRCm38/mm10 using STAR aligner v.2.5.2b
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: gene hit counts

source_name: Gastrocnemius

extract_protocol:
Gastrocnemius muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The NEBNext Ultra RNA Library Prep Kit for Illumina  was used for the construction of sequencing libraries.
Libraries were constructed using standard protocols.

value: mixed C57BL/6 129

tag: tissue

value: gastrocnemius

tag: age

value: 3 months

value: Hnrnpu muscle specifc knockout


title: MYB_NFKB1_doubleKD

source_name: human squamous carcinoma cell line

value: MYB_NFKB1 double knock down


title: MYB_KD_3

value: third targeted knockdown of MYB via ASX050LY


title: DU16-02S0004828_L6

value: VIRAL


title: DU16-02S0004822_L5


title: MYB_KD_2

value: second targeted knockdown of MYB via ASX050LY


title: DU16-02S0004826_L5


title: Gastrocnemius, mKO rep 2


title: DU16-02S0004819_L4


title: DU16-02S0004818_L4


title: Gastrocnemius, mKO rep 1


title: MIZ1_KD_3

value: third targeted knockdown of MIZ1 via s15211


title: Gastrocnemius, WT rep 3

value: WT


title: MIZ1_KD_2

value: second targeted knockdown of MIZ1 via s15211


title: DU16-02S0004831_L7


title: Gastrocnemius, WT rep 2


title: DU16-02S0004814_L2

value: BACTERIAL


title: Gastrocnemius, WT rep 1


title: DU16-02S0004813_L2


title: MIZ1_KD_1

value: first targeted knockdown of MIZ1 via s15211


title: DU16-02S0004810_L1


title: DU16-02S0004808_L1


title: UT_8

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: MBD-protein captured; the processed files are in logRPKM

data_processing:
FASTQ files were first inspected with the FastQC tool (v.0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and all files passed the initial quality checks.
Alignment was then done to the mouse reference genome (mm10/GRCm38) using the Bowtie2 aligner (v.2.3.4.3) (Langmead and Salzberg, 2012), and alignment quality was evaluated with SAMtools (v.1.9) (Li et al., 2009), and SAMstat v.1.5.1 (Lassmann et al., 2011).
Potential PCR duplicates and reads with mapping quality of less than 10 were filtered out, and sorted Bam files were created. Then provided bam files are sorted
The sorted Bam files were then analyzed using the MEDIPS R package (Chavez et al., 2010). Sequenced reads were counted for every 150 bp non-overlapping window with normalization to the local CpG density (i.e., coupling factor CF). This process was done according to the following MEDIPS parameters: ws =150, extend = 150, uniq = 1, shift=0. The read counts generated on the MEDIPS package were loaded to the EdgeR R package (Robinson et al., 2010). First, bins with no CpGs (CF = 0) and mean read counts ≤ 1 were excluded, resulting in 4,286,826 bins. The Y chromosome was also excluded, and only reads with more than 1 count per million in 2 or more libraries were retained using the EdgeR R package (Robinson et al., 2010). This resulted in 368300 CpG regions, and logRPKM values for these are provided.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: csv file; contains columns with index, bin name, chromosome (chr), start, end,  CF (CouplingFactor or CpG density), CpG%, GC%, VariantCount (number of sequence variants in the 150 bp bin), followed by methylation data as logRPKM for 70 samples.

source_name: Liver

extract_protocol:
DNA from liver tissue was extracted using Qiagen DNeasy Blood & Tissue Kit (http://www.qiagen.com); methylated-CpG enrichment done using MethylMiner DNA enrichment kit (https://www.thermofisher.com) according to the manufacturer’s standard protocol
Library construction and sequencing were carried out at Novogene (https://en.novogene.com). Sequencing was done at approximately 50 million reads per sample (150 bp paired-end) on Illumina HiSeq 4000 platform

tag: age in days

tag: Sex

value: F

tag: diet

value: standard chow

value: liver


title: MYB_KD_1

value: first targeted knockdown of MYB via ASX050LY


title: UT_88


title: MAX_KD_3

value: third targeted knockdown of MAX via ASX050J3


title: MAX_KD_2

value: second targeted knockdown of MAX via ASX050J3


title: UT_82


title: RNA-seq OD 0.2 rep 1

city: Odense M

first: Thøger

middle: Jensen

last: Krogh

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description:
RNA-seq OD 0.2 rep 1
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12377

data_processing:
Raw data was mapped to Escherichia coli BW25113 gene using GCF_004355105.1_ASM435510v1_genomic.fna with bowtie2 v2.3.5 with --local
Mapped data was converted and sorted using Samtools v1.2
Peaks were called using MACS v2.1.4 with -g 4640000 --nomodel --extsize 147
Features were created in 1000bp windows, sliding at 500bp clockwise on the genome. These were used to count reads per feature using R-package Rsubread.
Genome_build: NZ_CP037857.1 Escherichia coli BW25113
Supplementary_files_format_and_content: ChIP-seq:  bed files with ChIP peaks
Supplementary_files_format_and_content: RNA-seq:  txt with FPKM normalized cov for 1000bp intervals of genome with a 500bp sliding window

organism: Escherichia coli

source_name: Cell culture

growth_protocol: Fresh pre-heated LB was inoculated with Escherichia coli BW25113 culture grown ON at 37C on a LA plate and grown to the desired OD600 in a waterbath with aeration at 37 degrees Celsius.

extract_protocol:
RNA was purified using hot-phenol-chloroform extraction; rRNA depleted total RNA. ChIP-dna was purified using antibodies from biolegend.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At desired OD600, culture were split in two. One part for RNA-seq was flash freezed in liquid nitrogen, spun down at >10.000g for 10 minutes, supernatant removed and pellet stored at -80C till extraction. Second part for ChIP-seq were crosslinked with formaldehyde to a final concentration of XX for YY minutes before crosslinking was stopped using ZZZ at a final concentration of ÆÆ, culture was spun down at >10.000g for 10 minutes, supernatant removed and pellets stored at -80C till extraction.


title: RNA-seq OD 1.2 rep 2

description:
RNA-seq OD 1.2 rep 2
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12383


title: RNA-seq OD 0.2 rep 2

description:
RNA-seq OD 0.2 rep 2
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12382


title: RNA-seq OD 1.2 rep 1

description:
RNA-seq OD 1.2 rep 1
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12379


title: RNA-seq OD 5 rep 2

description:
RNA-seq OD 5 rep 2
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12381


title: RNA-seq OD 0.5 rep 2

description:
RNA-seq OD 0.5 rep 2
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12378


title: RNA-seq OD 2 rep 2

description:
RNA-seq OD 2 rep 2
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12380


title: RNA-seq OD 5 rep 1

description:
RNA-seq OD 5 rep 1
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12376


title: MAX_GNL3_doubleKD

first: Erik

last: Sonnhammer

address: Tomtebodavagen 23A

value: MAX_GNL3 double knock down


title: RNA-seq OD 0.5 rep 1

description:
RNA-seq OD 0.5 rep 1
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12375


title: LMYC_KD_3

value: third targeted knockdown of LMYC via ASX050M6


title: RNA-seq OD 2 rep 1

description:
RNA-seq OD 2 rep 1
FC_FPKM_Escherichia coli BW25113_PAIRED_window_1000_Int_500_GenoCov.txt
F12374


title: LMYC_KD_2

value: second targeted knockdown of LMYC via ASX050M6


title: MAX_KD_1

value: first targeted knockdown of MAX via ASX050J3


title: LMYC_KD_1

value: first targeted knockdown of LMYC via ASX050M6


title: DU16-02S0004794_L5

tag: diagnosis

value: VIRAL


title: DU16-02S0004803_L6


title: DU16-02S0004805_L7


title: DU16-02S0004801_L6


title: DU16-02S0004795_L5


title: UT_59


title: ChIP Input OD 1.2 rep 2

description: ChIP Input OD 1.2 rep 2

tag: chip antibody


title: UT_77


title: UT_72

value: high fat diet


title: UT_60


title: LKB1_KD_3

value: third targeted knockdown of LKB1 via ASX04WWS


title: DU16-02S0004787_L1


title: ChIP Input OD 5 rep 2

description: ChIP Input OD 5 rep 2


title: LKB1_KD_2

value: second targeted knockdown of LKB1 via ASX04WWS


title: DU16-02S0004792_L1


title: ChIP Input OD 0.2 rep 2

description: ChIP Input OD 0.2 rep 2


title: DU16-02S0004784_L1


title: LKB1_KD_1

value: first targeted knockdown of LKB1 via ASX04WWS


title: JUND_KD_3

value: third targeted knockdown of JUND via ASX050EM


title: ChIP Input OD 2 rep 2

description: ChIP Input OD 2 rep 2


title: DU16-02S0004783_L8


title: ChIP Input OD 0.5 rep 2

description: ChIP Input OD 0.5 rep 2


title: UT_563

value: F


title: UT_570

value: standard chow


title: UT_564

value: liver


title: UT_57


title: ChIP Input OD 1.2 rep 1

description: ChIP Input OD 1.2 rep 1


title: ChIP Input OD 0.2 rep 1

description: ChIP Input OD 0.2 rep 1


title: DU16-02S0004776_L5


title: DU16-02S0004782_L8


title: JUND_KD_2

value: second targeted knockdown of JUND via ASX050EM


title: JUND_KD_1

value: first targeted knockdown of JUND via ASX050EM


title: DU16-02S0004772_L4

value: BACTERIAL


title: DU16-02S0004774_L5


title: ChIP Input OD 0.5 rep 1

description: ChIP Input OD 0.5 rep 1


title: ChIP Input OD 5 rep 1

description: ChIP Input OD 5 rep 1


title: DU16-02S0004770_L4


title: JUN_AIB1_doubleKD

value: JUN_AIB1 double knock down


title: JUN_TIF1B_doubleKD

value: JUN_TIF1B double knock down


title: JUN_KD_3

value: third targeted knockdown of JUN via ASX050EK


title: UT_529

value: M


title: UT_509


title: UT_543


title: UT_549


title: UT_548


title: ChIP Input OD 2 rep 1

description: ChIP Input OD 2 rep 1


title: JUN_KD_2

value: second targeted knockdown of JUN via ASX050EK


title: DU16-02S0004767_L3

value: VIRAL


title: ChIP Beta OD 1.2 rep 2

description: ChIP Beta OD 1.2 rep 2

value: Biolegend RNAP subunit beta Mouse IgG1 clone   8RB13


title: DU16-02S0004765_L3


title: UT_505


title: 40d_PTc _Testosterone_Treated 2

city: New Delhi

first: Subeer

middle: S

last: Majumdar

state: Delhi

address: Aruna Asaf Ali Marg, JNU Complex

country: India

institute: National Institute of Immunology

description: Gene expression on Peritubular myoid cells after testosterone treatment

hyb_protocol: The labeled cRNA samples were hybridized on to Agilent's Whole Genome Rat 4x44k (AMADID No: 014879). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software Version 10.5 and Normalization of the data was done in GeneSpring GX V 11.0

organism: Rattus norvegicus

source_name: Peritubular myoid cells_testosterone

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was extracted using Qiagen RNAEasy Mini kit (Qiagen, Valencia, CA USA) following manufactureres instructions. The protocol included lysis of cells in lysis buffer and loading of the lysate onto RNAEasy Silica membrane columns. The RNA binds to the column which is eluted after washing the membrane.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Testicular myoid peritubular cells were isolated from 40 day old rat testis and cultured in DMEM HAM F-12 medium with defined growth factors for 4 days. Peritubular cells were treated with 10-7 M testosterone in a pulsatile manner.

value: Testis

tag: cell type

value: Peritubular myoid cells

tag: gender

value: male

value: 40 days


title: 40d PTc Control 1

description: Gene expression on control Peritubular myoid cells

source_name: Peritubular myoid cells_control


title: ChIP Beta OD 0.2 rep 2

description: ChIP Beta OD 0.2 rep 2


title: 40d_PTc_Testosterone_ Treated 1


title: JUN_KD_1

city: Stockholm

institute: SciLifeLab/ Stockholm University

tag: cell line

value: first targeted knockdown of JUN via ASX050EK


title: UT_490

value: F

value: high fat diet


title: DU16-02S0003206_S10


title: 40d PTc Control 2


title: ChIP Beta OD 5 rep 2

description: ChIP Beta OD 5 rep 2


title: GNL3_KD_3

value: third targeted knockdown of GNL3 via ASX051NW


title: UT_480

value: standard chow

value: liver


title: UT_44


title: DU16-02S0003200_S51


title: UT_427


title: DU16-02S0003193_S27


title: DU16-02S0003199_S50

value: BACTERIAL


title: UT_414


title: ChIP Beta OD 0.5 rep 2

description: ChIP Beta OD 0.5 rep 2


title: UT_502


title: ChIP Beta OD 1.2 rep 1

description: ChIP Beta OD 1.2 rep 1


title: GCN1L1_KD_2

value: second targeted knockdown of GCN1L1 via ASX0518S


title: ChIP Beta OD 0.2 rep 1

description: ChIP Beta OD 0.2 rep 1


title: GCN1L1_KD_3

value: third targeted knockdown of GCN1L1 via ASX0518S


title: DU16-02S0003204_S2


title: UT_404


title: DU16-02S0003185_S11


title: ChIP Beta OD 2 rep 2

description: ChIP Beta OD 2 rep 2


title: ChIP Beta OD 0.5 rep 1

description: ChIP Beta OD 0.5 rep 1


title: DU16-02S0003184_S10


title: UT_380


title: DU16-02S0003186_S12


title: ChIP Beta OD 5 rep 1

description: ChIP Beta OD 5 rep 1


title: UT_386


title: GCN1L1_KD_1

value: first targeted knockdown of GCN1L1 via ASX0518S


title: DU16-02S0003180_S50


title: FOXO3A_KD_3

value: third targeted knockdown of FOXO3A via ASX0501W


title: FOXO3A_KD_2

value: second targeted knockdown of FOXO3A via ASX0501W


title: UT_37


title: ChIP SigmaD OD 1.2 rep 2

description: ChIP SigmaD OD 1.2 rep 2

value: Biolegend SigmaD Mouse IgG2b clone 2G10


title: FOXO3A_MYCBP_doubleKD

value: FOXO3A_MYCBP double knock down


title: DU16-02S0003179_S49


title: DU16-02S0003178_S48

value: VIRAL


title: FOXO3A_KD_1

value: first targeted knockdown of FOXO3A via ASX0501W


title: ChIP SigmaD OD 0.2 rep 2

description: ChIP SigmaD OD 0.2 rep 2


title: UT_376


title: FOXM1C_TCF7L2_doubleKD

value: FOXM1C_TCF7L2 double knock down


title: UT_36


title: ChIP SigmaD OD 5 rep 2

description: ChIP SigmaD OD 5 rep 2


title: ChIP Beta OD 2 rep 1

description: ChIP Beta OD 2 rep 1

value: Biolegend RNAP subunit beta Mouse IgG1 clone   8RB13


title: ChIP SigmaD OD 2 rep 2

description: ChIP SigmaD OD 2 rep 2


title: UT_347

value: F


title: ChIP SigmaD OD 1.2 rep 1

description: ChIP SigmaD OD 1.2 rep 1


title: ChIP SigmaD OD 0.5 rep 2

description: ChIP SigmaD OD 0.5 rep 2


title: FOXM1C_KD_2

value: second targeted knockdown of FOXM1C via ASX04ZYQ


title: UT_33

value: high fat diet


title: FOXM1C_KD_3

value: third targeted knockdown of FOXM1C via ASX04ZYQ


title: ChIP SigmaD OD 0.2 rep 1

description: ChIP SigmaD OD 0.2 rep 1


title: ENO1_DP1_doubleKD

value: ENO1_DP1 double knock down


title: FOXM1C_KD_1

value: first targeted knockdown of FOXM1C via ASX04ZYQ


title: UT_320

value: liver


title: ChIP SigmaD OD 5 rep 1

description: ChIP SigmaD OD 5 rep 1


title: ENO1_KD_3

value: third targeted knockdown of ENO1 via ASX04ZYQ


title: DU16-02S0003164_S12


title: DU16-02S0003171_S27


title: DU16-02S0003163_S11


title: DU16-02S0003173_S29


title: DU16-02S0003172_S28


title: DU16-02S0003177_S47


title: ChIP SigmaD OD 0.5 rep 1

description: ChIP SigmaD OD 0.5 rep 1


title: DU16-02S0003158_S46


title: UT_319

value: standard chow


title: UT_32


title: ENO1_KD_1

value: first targeted knockdown of ENO1 via ASX04ZYQ


title: ChIP SigmaD OD 2 rep 1

description: ChIP SigmaD OD 2 rep 1


title: DU16-02S0003157_S45


title: E2F4_FOXO3A_doubleKD

value: E2F4_FOXO3A double knock down


title: UT_324


title: DU16-02S0003156_S44


title: Gor d25 batch 3

city: Cambridge

first: Paula

last: Freire Pritchett

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus

institute: Medical Research Council

description:
GC_d30_2503
RNA was isolated from ~50 G1 batch 3 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i706 and i507

data_processing:
Fastq files were trimmed using Trim Galore version 0.6.3_dev and Cutadpt version 2.4.
Human and gorilla reads were aligned to GRCh38 and Kamilah_GGO_v0 reference genomes respectively using HISAT2 (version 2.0.0-beta).
GTF gene annotation files for both of the reference genomes were downloaded and filtered for a list of 16,763 genes that are annotated with identical gene names in both species
Read counts were normalized to transcripts per million (TPM). Results can be found in hum_gor_combined_tpms_HISAT2.txt
Genome_build: GRCh38 or Kamilah_GGO_v0s
Supplementary_files_format_and_content: hum_gor_combined_tpms_HISAT2.txt contains TPM results for all samples as well as the mean and standard deviation for each condition.

organism: Gorilla gorilla

source_name: G1 gorilla iPS cell-derived organoids

extract_protocol:
Samples were flash-frozen in LN2 and stored at -80 °C. RNA from all 42 samples was purified in parallel directly from Trizol with the Direct-zol-96 RNA kit (Zymo Research).
cDNA libraries were generated according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760). cDNA was amplified for 12 cycles and barcoded with NEBNext Multiplex Oligos for Illumina (NEB #E7600). Samples were pooled together to 15 nM concentration and sequenced with single-end 50 base mode on 3 lanes of an Illumina HiSeq 4000 instrument.
bulk RNAseq

tag: time point

value: Day 25


title: UT_308

value: M


title: Gor d15 batch 3

description:
GC_d20_2503
RNA was isolated from ~100 G1 batch 3 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i706 and i506

value: Day 15


title: ENO1_KD_2

value: second targeted knockdown of ENO1 via ASX04ZYQ


title: UT_291


title: E2F4_KD_2

value: second targeted knockdown of E2F4 via ASX04ZWZ


title: E2F4_KD_3

value: third targeted knockdown of E2F4 via ASX04ZWZ


title: Gor d10 batch 3

description:
GC_d15_2503
RNA was isolated from ~150 G1 batch 3 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i706 and i505

value: Day 10


title: UT_317

value: F


title: E2F4_KD_1

value: first targeted knockdown of E2F4 via ASX04ZWZ


title: UT_310


title: DU16-02S0003144_S19

value: VIRAL


title: UT_28


title: Gor d3 batch 3

description:
GC_d8_2503
RNA was isolated from ~300 G1 batch 3 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i706 and i503

value: Day 3


title: Gor d5 batch 3

description:
GC_d10_2503
RNA was isolated from ~300 G1 batch 3 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i706 and i504

value: Day 5


title: UT_280

description: MBD-protein captured; the processed files are in logRPKM

value: high fat diet

value: liver


title: DU16-02S0003143_S18


title: DU16-02S0003149_S14_L001


title: UT_275


title: DVL3_STAT3_doubleKD

value: DVL3_STAT3 double knock down


title: DVL3_KD_3

value: third targeted knockdown of DVL3 via ASX04X6U


title: DVL3_LKB1_doubleKD

value: DVL3_LKB1 double knock down


title: Gor d2 batch 3

description:
GC_d7_2503
RNA was isolated from ~300 G1 batch 3 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i706 and i502

value: Day 2


title: DU16-02S0003150_S15_L001


title: DU16-02S0003142_S9

value: BACTERIAL


title: UT_274


title: DVL3_KD_2

value: second targeted knockdown of DVL3 via ASX04X6U


title: DU16-02S0003141_S8


title: Gor d0 batch 3

description:
GC_d5_2503
RNA was isolated from ~300 G1 batch 3 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i706 and i501

value: Day 0


title: UT_272

value: standard chow


title: Gor d25 batch 2

description:
GC_d30_2103
RNA was isolated from ~50 G1 batch 2 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i705 and i507

value: Day 25


title: DVL3_KD_1

value: first targeted knockdown of DVL3 via ASX04X6U


title: DU16-02S0003136_S56


title: UT_261

value: F


title: Gor d15 batch 2

description:
GC_d20_2103
RNA was isolated from ~100 G1 batch 2 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i705 and i506

value: Day 15


title: DU16-02S0003134_S54

value: VIRAL


title: UT_25


title: Gor d10 batch 2

description:
GC_d15_2103
RNA was isolated from ~150 G1 batch 2 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i705 and i505

value: Day 10


title: UT_252


title: DU16-02S0003129


title: DP2_KD_3

value: third targeted knockdown of DP2 via ASX04XZ2


title: DP2_KD_2

value: second targeted knockdown of DP2 via ASX04XZ2


title: UT_23

value: liver


title: UT_237


title: Gor d3 batch 2

description:
GC_d8_2103
RNA was isolated from ~300 G1 batch 2 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i705 and i503

value: Day 3


title: UT_235

value: high fat diet


title: Gor d2 batch 2

description:
GC_d7_2103
RNA was isolated from ~300 G1 batch 2 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i705 and i502


title: DP2_KD_1

value: first targeted knockdown of DP2 via ASX04XZ2


title: DU16-02S0003120_S17


title: DP1_TIF1B_doubleKD

value: DP1_TIF1B double knock down


title: DU16-02S0003122

value: BACTERIAL


title: Gor d0 batch 2

description:
GC_d5_2103
RNA was isolated from ~300 G1 batch 2 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i705 and i501


title: UT_230


title: DP1_KD_2

value: second targeted knockdown of DP1 via ASX04XZ1


title: Gor d25 batch 1

description:
GC_d30_1903
RNA was isolated from ~50 G1 batch 1 organoids on day 25, cDNA libraries were barcoded with NEBNext indexing primers i704 and i507


title: DU16-02S0003113_S2


title: DU16-02S0003128_S40


title: DP1_KD_1

value: first targeted knockdown of DP1 via ASX04XZ1


title: DU16-02S0003112_S1


title: Gor d15 batch 1

description:
GC_d20_1903
RNA was isolated from ~100 G1 batch 1 organoids on day 15, cDNA libraries were barcoded with NEBNext indexing primers i704 and i506


title: Gor d5 batch 2

description:
GC_d10_2103
RNA was isolated from ~300 G1 batch 2 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i705 and i504

value: Day 5


title: Gor d10 batch 1

description:
GC_d15_1903
RNA was isolated from ~150 G1 batch 1 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i704 and i505


title: UT_226


title: Gor d5 batch 1

description:
GC_d10_1903
RNA was isolated from ~300 G1 batch 1 organoids on day 5, cDNA libraries were barcoded with NEBNext indexing primers i704 and i504


title: DU16-02S0003114_S3


title: DP1_KD_3

value: third targeted knockdown of DP1 via ASX04XZ1


title: Gor d3 batch 1

description:
GC_d8_1903
RNA was isolated from ~300 G1 batch 1 organoids on day 3, cDNA libraries were barcoded with NEBNext indexing primers i704 and i503


title: UT_204

value: standard chow


title: positive control replicate 2


title: Gor d2 batch 1

description:
GC_d7_1903
RNA was isolated from ~300 G1 batch 1 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i704 and i502

value: Day 2


title: positive control replicate 1


title: UT_22

value: F


title: UT_1


title: UT_207


title: UT_214


title: w1118_Male_4hr_3

city: Detroit

first: Ekta

last: Shah

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

data_processing:
After de-multiplexing with Illumina’s CASAVA 1.8.2 software, the 50 bp reads were aligned to the Drosophila genome (Build dm3) with STAR_2.4 and tabulated for each gene region.
Differential gene expression analysis was used to compare transcriptome changes between conditions using edgeR v.3.22.3 and transcripts were defined  as significantly differentially expressed at absolute Log2 fold change >1, FDR <0.05
Genome_build: Dm3
Supplementary_files_format_and_content: Differential gene expression and counts data.xlsx

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Direct-zolä RNA MicroPrep kit
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (low-input protocol and 15 ng RNA input)

value: male

tag: treatment

value: traumatic brain injury


title: CTNNB1_FOXM1C_doubleKD

tag: sample type

value: CTNNB1_FOXM1C double knock down


title: CTNNB1_AIB1_doubleKD

value: CTNNB1_AIB1 double knock down


title: UT_223

value: liver


title: positive control replicate 4


title: CTNNB1_KD_3

value: third targeted knockdown of CTNNB1 via ASX04X6P


title: Gor d0 batch 1

description:
GC_d5_1903
RNA was isolated from ~300 G1 batch 1 organoids on day 0, cDNA libraries were barcoded with NEBNext indexing primers i704 and i501

value: Day 0


title: CTNNB1_KD_2

value: second targeted knockdown of CTNNB1 via ASX04X6P


title: positive control replicate 3


title: UT_188

description: MBD-protein captured; the processed files are in logRPKM


title: GNL3_KD_2

value: second targeted knockdown of GNL3 via ASX051NW


title: GNL3_KD_1

value: first targeted knockdown of GNL3 via ASX051NW


title: UT_153


title: UT_201


title: w1118_Male_4hr_2


title: w1118_Male_2hr_2


title: UT_124


title: w1118_Male_2hr_1


title: w1118_Male_4hr_1


title: w1118_Male_1hr_3


title: UT_120


title: w1118_Male_1hr_2


title: CHUK_MIZ1_doubleKD

value: CHUK_MIZ1 double knock down


title: UT_113


title: w1118_Male_1hr_1


title: CHUK_KD_2

value: second targeted knockdown of CHUK via ASX04WNH


title: CHUK_KD_3

value: third targeted knockdown of CHUK via ASX04WNH


title: UT_111


title: w1118_Male_2hr_3


title: CHUK_KD_1

value: first targeted knockdown of CHUK via ASX04WNH


title: w1118_Male_Ctrl_3


title: UT_109

value: high fat diet


title: w1118_Male_Ctrl_2


title: CHUK_SP1_doubleKD

value: CHUK_SP1 double knock down


title: CEBPB_LMYC_doubleKD

value: CEBPB_LMYC double knock down


title: UT_104

value: F

value: standard chow


title: CEBPB_E2F4_doubleKD

value: CEBPB_E2F4 double knock down


title: w1118_Male_Ctrl_1

value: male


title: CEBPB_KD_2

value: second targeted knockdown of CEBPB via ASX04ZP9


title: UT_103

value: liver


title: CEBPB_KD_3

value: third targeted knockdown of CEBPB via ASX04ZP9


title: w1118_Female_4hr_3

value: Female

value: traumatic brain injury


title: CEBPB_KD_1

value: first targeted knockdown of CEBPB via ASX04ZP9


title: CTNNB1_KD_1

value: first targeted knockdown of CTNNB1 via ASX04X6P


title: w1118_Female_4hr_2


title: CCNB1_JUND_doubleKD

value: CCNB1_JUND double knock down


title: clf0Sh3

city: Amherst

first: Jeeyon

last: Jeong

address: 25 East Drive

department: Biology

institute: Amherst College

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were filgered to remove reads containing adapters or reads of low quality, then mapped to Arabidopsis TAIR10 reference genome using TopHat2 (TMR>70%; MMR<10%)
RPKM (Reads Per Kilo bases per Million reads) method (Mortazavi et al 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: Germinated and grown for 12 days on B5, followed by 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media; 16/8 light/dark cycle at 22°C

extract_protocol:
Total RNA was extracted from fresh Arabidopsis root tissue using Plant RNA Isolation Kit (Agilent) per manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Grown for 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media

value: clf

value: root

value: iron deficient


title: w1118_Female_4hr_1


title: clf0Sh2


title: clf0Sh1


title: w1118_Female_2hr_3


title: CCNB1_KD_3

value: third targeted knockdown of CCNB1 via ASX04ZMX


title: RTX-REC

city: Aarhus

first: Jacob

middle: GIehm

last: Mikkelsen

address: Høegh-Guldbergs Gade 10

department: Biomedicin

institute: Aarhus University

data_processing:
Library strategy: Targeted deep sequencing of DNA amplicons
MAGeCK v0.5.8 -count, with default parameters
MAGeCK v0.5.8 -test, with default parameters
Genome_build: Mapped to the genome-wide library GeCKO v2 (A+B) from Feng Zhang. (Addgene#1000000049)

growth_protocol: Cells were kept at 0.3-1x106 cells/mL, cultured in RPMI 10% FBS and 1% P/S

extract_protocol:
Cells were lysed and gDNA was extracted by precipitation  of proteins by NaCl (6M) and subsequent precipitation  of gDNA with isopropanol
A nested PCR approach was used to generate PCR amplicons with sufficient coverage of the lirary. PCR amplicons were processed by end repair, ligated to BGISEQ sequencer compatible adapters, generating DNB-based sequencing libraries without PCR amplification

treatment_protocol: Mock; medium containing human serum, RTX-SEC; medium containing 10 µg/mL rituximab and human serum (14 days), and RTX-REC; medium with 10 µg/mL rituximab increased to 25 µg/mL at day 16 and with repeated re-administration of human serum (21 days)

value: Diffuse Large B-cell Lymphoma (GCB-subtype) cell line


title: RTX-SEC


title: clf50Sh3

value: iron sufficient


title: w1118_Female_2hr_2


title: clf50Sh2


title: 8_D492M_KD_MGE3

city: Reykjavik

first: Zuzana

last: Budkova

address: Vatnsmyrarvegi 14

department: BioMedical Center, School of Health Sciences

country: Iceland

institute: University of Iceland

description: CRISPRi pLenti-dCas9-KRAB-mCherry

data_processing:
Illumina
STAR version 2.6.1
htseq-count
DESeq2
Genome_build: Ensembl primary assembly, version GRCh38
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each Sample

source_name: Breast epithelial cell line D492M

growth_protocol: D492M was cultured in H14 medium (DMEM:F12 supplemented with 50 IU/ml penicillin, 50 ug/ml streptomycin, 250 ng/ml insulin, 10 ug/ml transferrin, 2.6 ng/ml sodium selenite, 0.1 nM estradiol, 0.5 ug/ml hydrocortisone, 5 ug/ml prolactin and 10 ng/ml EGF), in flasks coated with collagen I. Media was changed three times a week.

extract_protocol:
RNA was extracted using a Tri-Reagent standard protocol
Libraries were prepared according to Illumina's instructions

tag: passages

value: Breast epithelial cell line (D492) mesenchymal derivative (D492M)

value: MEG3 knockdown


title: w1118_Female_2hr_1

tag: strain


title: 10_D492M_KD_MGE3

description: CRISPRi pLenti-dCas9-KRAB-mCherry


title: Mock


title: Baseline


title: w1118_Female_1hr_3


title: 7_D492M_KD_MGE3

description: CRISPRi pLenti-dCas9-KRAB-mCherry