title: healthy controls 5

city: Hong Kong

first: Lai-Shan

last: TAM

state: Hong Kong

address: 30-32 Silver City Street, Shatin

department: Department of Medicine and Therapeutics, Prince of wales hospital

country: Hong Kong

institute: The Chinese University of Hongkong

description:
Control
SAMPLE 25

data_processing:
miRNA profiling data was analyzed using the relative quantification application in the online accessible Thermo Fisher Cloud (https://apps.thermofisher.com/apps/dashboard/), using the relative threshold cycle (Crt) and the comparative threshold cycle method (Livak KJ, Schmittgen TD. 2001).
For the normalization it uses the average of one housekeeping control: RNU6B.
Target miRNA signals normalized to housekeeping control: 2^-deltaCt, where deltaCt = (Ct_mean Target − Ct_mean RNU6B)]
Fold Change worksheet reports Test/Control or Test 1/Test 2(i.e.ERA with erosion/healthy control, ERA without erosion/ healthy control or ERA with erosion/ERA without erosion) ratios.

label: FAM

source_name: plasma (EDTA)

label_protocol: miRNA profiling was performed by TaqMan® RT-qPCR (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. This method allows the simultaneous analysis of 377 miRNAs (Human Pools A V2.1) using 384-well Cards. Briefly, 2.5ul of isolated plasma RNA was reverse-transcribed by using the miRNA multiplex RT primers pool (v2.1 for pool A), and the TaqMan® miRNA reverse transcription kit (Life Technologies, Carlsbad, CA, USA). RT products were pre-amplified using the Megaplex PreAmp Primers Pool A in the presence of the TaqMan® PreAmp Master Mix (Life Technologies, Carlsbad, CA, USA), by using the following thermal cycler conditions: 10 min, 95 °C; 2 min, 55 °C; 2 min, 72 °C and 16 cycles of 15 sec, 95 °C and 4 min, 60 °C and one single cycle of 10 min, 96 °C. The miRNA Open Array profiling was performed on the amplified cDNA, diluted to 1:40, with 0.1 × TE buffer pH 8.0 and subsequently 1:2 by using the TaqMan® Open Array Master Mix on the QuantStudio12 K Flex Real-Time PCR System (Life Technologies).

extract_protocol: Peripheral blood samples were collected using Ethylenediaminetetraacetic acid (EDTA) at the day of fasting status of ERA patients as well as HCs and were centrifuged at 3000×g for 10 minutes at room temperature. Then, the plasma samples were aliquoted and centrifuged at 3000×g for an additional 10 minutes at 4oC to remove any remaining cellular debris. The plasma was immediately stored at –80oC until analysis.Total RNA was extracted from the plasma and purified from 150 μL serum using the miRNeasy Serum/Plasma Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: treatment-naïve

tag: disease

value: healthy controls

tag: Sex

value: Female


title: healthy controls 4

status: Public on Jul 10 2019

type: RNA

description:
Control
SAMPLE 24

molecule: total RNA

organism: Homo sapiens

tag: age


title: WTCHG_261086_277: Cen5 Cnp1 after deletion

type: SRA

city: Nottingham

first: William

last: Brown

address: Queens Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

library_source: genomic

data_processing:
The software Burrows-Wheeler Aligner (BWA) (v0.7.15-r1142-dirty) was used for all the alignments using algorithm “mem” with standard parameters.
Samtools (v1.3.1) was used to select the reads mapped in correct orientation and within insert size.
Coverage vectors were created for using the R package Bioconductor (v3.6).
Coverage plots were created in R (http://www.r-project.org) and were smoothed using the default running medians scatter plot smoothing in R.
Supplementary_files_format_and_content: no processed data because tracks are not applicable to the engineered strains

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: fission yeast cells

extract_protocol: Material was quantified using Qubit (Invitrogen) and the size profile analysed on the 2200 or 4200 TapeStation (Agilent, dsDNA HS Assay). Input material was normalised to 5 ng or maximum available prior to library preparation. Automated library preparation was performed using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >8 million reads per sample.

tag: strain

tag: tissue

value: fission yeast cells


title: WTCHG_261086_284: Cen5 Cnp1 before deletion


title: WTCHG_261086_302: Cen5 Cnp1 before deletion


title: healthy controls 3

description:
Control
SAMPLE 23


title: mock.A.sc14

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
single-cell SLAM-Seq (Smart-Seq kit)
96.tsv

library_source: transcriptomic

data_processing:
Data has been processed using GRAND-SLAM 1.1. Briefly, reads were trimmed using Trimmomatic 0.36 (Smart-Seq libraries: CTGTCTCTTATACACATCTCCGAGCCCACGAGA and CTGTCTCTTATACACATCTGACGCTGCCGACGA, TruSeq Libraries: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were mapped to a combined reference of the mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes  and the ERCC spike-in sequences using STAR 2.5.3a in end to end mode and allowing for 20 mismatches. For TruSeq libraries, the first ten bases were ignored by GRAND-SLAM via its -trim5p 10 parameter. For Smart-seq libraries, the first 25 bases were ignored. Identified SNPs from the combined TruSeq libraries were used for the Smart-seq libraries by copying the .snpdata file. Linear regression parameters were learned from the no4sU samples on plate 1 and specified for libraries from plates 2 and 3 via the parameters -errlm 'TA*0.663' -errlm2 'TA*2.802'.
Genome_build: mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes
Supplementary_files_format_and_content: tsv-files; Output of GRAND-SLAM containing read counts, estimated new/total ratios (with credible interval), beta approximation parameters as well as C-to-T mismatch statistics for each gene and library

organism: Mus musculus

source_name: NIH-3T3 fibroblasts

growth_protocol: Murine NIH-3T3 fibroblasts were cultured and passaged in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% newborn calf serum (NCS) and Penicillin Streptomycin. 10?5 cells per well were seeded overnight on a 24-well plate.

extract_protocol:
Single cells were immediately sorted using a FACSaria III (BD Biosciences; device: 48-well plate; precision: single-cell; nozzle: 100 ?m) into different wells from a 48-well plate ?lled with 4 µl of a hypotonic lysis buffer made of 2U/µL RNase inhibitor and 0.2 % Triton-X-100 in Nuclease-free water. Single-sorted cells were spun down, immediately chilled in a 4°C and stored at ?80 °C.
After thawing the plates 3 min at room temperature, 0.4 µL of 10X PBS (pH=7.4, Ambion) was added in every well followed by dispensing 4.4 µL of 2X Iodoacetamide (IAA) (Thermo Scientific) to reach a final concentration of 10mM IAA and 50% DMSO. The reaction mixture was incubated for 5 min at 50°C. IAA reaction was quenched with 1.3 µL of 0.1 M DTT (final concentration of 15 mM) for 5 min at room temperature. ERCC spike-in control (Thermo Fisher, mix 1, dilution 1:2 millions) was added in every well (except the negative control). RNA was isolated before Reverse Transcription and PCR using a 1:1 volume of RNA XP magnetic beads (Beckman Coulter). After 10 min incubation at room temperature, the beads were washed twice with 50 µl 80% freshly-prepared EtOH on the magnetic stand and the dried beads pellets were resuspended in 4 µL elution buffer (RNAse inhibitor 1/200 Takara, CDS primer 0.5 µL in RNAse free water) immediately followed by an incubation at 72°C for 3 min. All the following experimental steps were performed using the Smart-seq v4 low input kit (Takara) with one-quarter of the recommended reagent volumes. The PCR amplification was performed according to the manual using 24 cycles. Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).0.5 ng of every library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended reagent volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR for multiplexing. After PCR, the libraries were purified using AMPure XP beads and resuspended in 15 µl of resuspension buffer.

treatment_protocol: The cells were infected the next day with WT C5X MCMV strain at a MOI =10 followed by spinoculation of the virus at 800xg for 30min. 4sU (initially dissolved in DMSO at a concentration of 50 mM) was added right before the spinoculation in complete medium to reach a final concentration of 500 µM. RNA metabolic labeling was performed for 2hr at 37°C by replacing the medium with the 4sU-complemented medium. Cells were detached using trypsin and washed twice in cold PBS after centrifugation at 1,400 rpm and finally resuspended in 700 µL cold PBS.

tag: condition

value: mock

tag: replicate

value: A


title: 3-NPA 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Transformed E12 rat mescencephalic neuronal stem cells, dopamine producing, used for neurotoxin studies

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent's Rat Gene Expression  8x60k Array (AMADID: 028279). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method.

organism: Rattus norvegicus

source_name: Immortalised Rat mescencephalic dopaminergic neurons

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. 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 using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: N27 cells were grown in RPMI medium and passaged once in two days by trypsinization

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Cells were treated with 150 µM and 250 µM of Mn or MPP+ respectively, for 48 h

tag: cell line

value: N27 Dopaminergic Neural Cell Line

tag: treatment


title: WTCHG_543859_282179: Neocentromere test sequence


title: mock.A.sc13


title: pan1_Mock_2

city: La Jolla

first: Paula

last: Doblas Ibanez

state: California

address: 9500 Gilman Dr

country: USA

institute: UCSD

data_processing:
Raw reads were processed with HTStream (https://ibest.github.io/HTStream/) to remove adapter contamination and low quality sequences. The paired-end reads were also deduplicated with HTStream.On average, 24% of reads were removed.
The trimmed reads were aligned to the B73 AGPv4 genome with Ensembl gene annotation v.37 using the aligner STAR v.2.5.2b to generate raw counts per gene.
Genome_build: Maize B73 AGPv4
Supplementary_files_format_and_content: two matrix tables: (1) raw counts of reads for gene and (2) normalized abundance expressed in counts per million mapped reads (CPM)

organism: Zea mays

source_name: leaf 4 tissue

growth_protocol: Maize plants were grown in individual 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA.

extract_protocol:
Total RNA from each sample was isolated using RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol.
cDNA libraries were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina), and sequenced (100 bp paired-end reads) on a HiSeq 4000 System (Illumina), generating 21-27 million reads per sample.

treatment_protocol: Major veins of leaf 4 from 20 day-old plants were scratch-inoculated with P. stewartii-GFP or inoculation buffer (mock inoculation). Tissue collection was carried out 1 day after inoculation (1 dpi). Half leaves containing mock- or bacteria-inoculated veins were collected, starting at 0.3 cm from the scratch site and taking 1 cm long pieces in basipetal direction, excluding the midrib. Each sample consisted of the pooled tissue of ~30 plants of the same genotype and treatment group. Inoculation and tissue collection were performed at the same time of the day across the different replicates.

tag: genotype

value: pan1-ems/pan1-ems (R1)

tag: agent

value: Mock (inoculated with PBST)


title: pan1_het_Mock_2


title: healthy controls 6

description:
Control
SAMPLE 26

value: male


title: healthy controls 2

description:
Control
SAMPLE 22


title: healthy controls 1

description:
Control
SAMPLE 21


title: B73_Mock_2

value: B73 (wild type)


title: mock.A.sc12


title: WTCHG_543859_281191: Neocentromere test sequence


title: mcmv.A.sc11

value: mcmv-infected


title: WTCHG_543859_284155: A+T rich C. acetobutylicum DNA Cnp1 after deletion

value: Nott817/818 ura- pool -1st time point


title: ERA without bone erosion 10

description:
Test 2
SAMPLE 20

value: Early rheumatoid arthrits


title: pan1_het_Mock_1


title: ERA without bone erosion 8

description:
Test 2
SAMPLE 18


title: pan1_Mock_1


title: WTCHG_543859_283167: A+T rich C. acetobutylicum DNA Cnp1 after deletion


title: mcmv.A.sc10


title: WTCHG_543859_266181: A+T rich C. acetobutylicum DNA Cnp1 before deletion


title: B73_Mock_1


title: ERA without bone erosion 7

description:
Test 2
SAMPLE 17


title: WTCHG_543859_265193: A+T rich C. acetobutylicum DNA Cnp1 before deletion


title: mcmv.B.sc7

value: B


title: mcmv.B.sc8


title: Mi-R4-4: Host-Race-4 (GEN 306), Cotton, Vargme Grande do Sul, Sao Paulo

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Library strategy: DNA-seq
We trimmed and cleaned the reads from each library with cutadapt tool to remove adapter sequences and bases of a quality inferior to 20.
We aligned the clean reads to the M. incognita reference genome (Blanc-Mathieu et al. 2017), using the BWA-MEM software package.
We used SAMtools to filter alignments with MAPQ lower than 20, sort the alignment file by reference position, and remove duplicate alignments.
We used the FreeBayes variant detection tool to call SNPs and small-scale insertions/deletions, incorporating all the library alignment files simultaneously and produced a variant call file (VCF).
We filtered the resulting VCF file with the vcffilter function of vcflib, retaining the positions that had more than 20 Phred-scaled probability (QUAL) and a coverage depth (DP) > 10
Genome_build: Meloidogyne incognita V2, strain Morelos (Blanc-Mathieu et al. 2017)

organism: Meloidogyne incognita

source_name: Pool of whole individuals

growth_protocol: Nematode strains were multiplied on tomato plants for several generation from the offspring of one single female. After dozens of generations pools of individuals were collected.

extract_protocol:
We extracted and purified the genomic DNA from eggs of each nematode isolate with the supplement protocol for nematodes of the QIAGEN Gentra® Puregene® Tissue Kit with the following modifications: incubation at 65 ° C in the cell lysis buffer for 30 min and incubation at 55 ° C with proteinase K for 4h.
Libraries were pooled at 4nM, loaded on Nextseq 500 High Output Flowcells and sequenced on a NextSeq 500 platform (Illumina) with 2 × 150bp paired-end chemistry.

tag: isolate

value: Pool of whole individuals


title: WTCHG_543859_292154: Art cen 5.9kb Cnp1 after deletion - Pool


title: Mi-R4-3: Host-Race-4 (NG), Watermelon, Londrina, Parana


title: WTCHG_543859_291166: Art cen 5.9kb Cnp1 after deletion - Pool


title: ERA without bone erosion 6

description:
Test 2
SAMPLE 16


title: Mi-R4-1: Host-Race-4 (MT4), Cotton, Campo Verde, Mato Grosso


title: mcmv.B.sc6


title: mock.B.sc5


title: ERA without bone erosion 5

description:
Test 2
SAMPLE 15


title: ERA without bone erosion 4

description:
Test 2
SAMPLE 14


title: ERA without bone erosion 3

description:
Test 2
SAMPLE 13


title: Mi-R3-4: Host-Race-3 (PR-3, MTS-R3, BA-R3), Cotton, Pool of geographical locations


title: WTCHG_543859_268157: Art cen 5.9kb Cnp1 before deletion


title: mcmv.A.sc9


title: ERA without bone erosion 2

description:
Test 2
SAMPLE 12


title: Mi-R3-2: Host-Race-3 (ND), Soybean, Londrina, Parana


title: ERA without bone erosion 9

description:
Test 2
SAMPLE 19


title: mock.B.sc4


title: mock.B.sc3


title: ERA without bone erosion 1

description:
Test 2
SAMPLE 11


title: WTCHG_543859_202177: Empty vector Cnp3 after deletion


title: WTCHG_543859_267169: Art cen 5.9kb Cnp1 before deletion


title: Mi-R3-1: Host-Race-3 (PR-3), Cotton, Umarama, Parana


title: ERA with bone erosion 10

description:
Test 1
SAMPLE 10


title: mock.A.sc2


title: Mi-R2-6: Host-Race-2 (22B), Coffee, Sao Jorge do Patrocínio, Parana

value: Host-Race-2 (22B), Coffee, Sao Jorge do Patrocinio, Parana


title: ERA with bone erosion 9

description:
Test 1
SAMPLE 9


title: mock.A.sc1


title: ERA with bone erosion 8

description:
Test 1
SAMPLE 8


title: Mi-R1-6: Host-Race-1 (LGM39), Tobacco, Mercedes, Parana


title: D9

description: Chromium single cell 3´ v2 (10xGenomics)

data_processing:
Supplementary_files_format_and_content: none
For the analysis, custom genomes and genome annotations were used. To the human genome (hg38), the fasta sequences of HSV was added, to the mouse genome (mm10) the fasta sequences of MCMV was added. For the annotation, human and mouse annotations were downloaded from Ensembl (www.ensembl.org, release 90) and the annotations of the corresponding virus was added to the annotations. The genomes were indexed using the Cell Ranger pipeline (10x Genomics, version 2.1.1) and the command “cellranger mkref”. For the alignment, QC, the estimation of valid barcodes and creating the count matrices, the Cell Ranger pipeline was run with the command “cellranger count” with standard parameters, except that the number of expected cells was set to 2000 and the chemistry was set to “SC3Pv2”.
Genome_build: mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes
Supplementary_files_format_and_content: tsv-files; Output of GRAND-SLAM containing read counts, estimated new/total ratios (with credible interval), beta approximation parameters as well as C-to-T mismatch statistics for each gene and library
Supplementary_files_format_and_content: h5; filtered_gene_bc_matrices, molecule_info

organism:
Homo sapiens
Mus musculus

source_name: NIH-3T3 fibroblasts/HFF primary fibroblasts

growth_protocol: Murine NIH-3T3 fibroblasts were cultured and passaged in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% newborn calf serum (NCS) and Penicillin Streptomycin. 10ˆ5 cells per well were seeded overnight on a 24-well plate. Human primary foreskin fibroblasts HFF were cultured and passaged in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS, high glucose, pyruvate with penstrep and non essential amino acids. Human cells were seeded at 35000 cells per cm2.

extract_protocol: Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.

treatment_protocol: The cells were infected the next day with WT C5X MCMV strain or hHSV at a MOI =10 followed by spinoculation of the virus at 800xg for 30min. For mouse cells virus inocculum was removed immediately after spinocculation and for human cells after 15 min and was replaced with fresh, pre-warmed medium. Cells were detached using trypsin and washed twice in cold PBS after centrifugation at 1,400 rpm and finally resuspended in cold PBS with 0.04% BSA at a final concentration of 1000 cells/μl. Cells were mixed before partinioning 1:1.

tag: cell type

value: 2hrs post mCMV infection/2hrs post hHSV infection


title: WTCHG_543859_204153: Cen8 Cnp3 before deletion


title: WTCHG_261086_265: Empty vector Cnp1 after deletion


title: mock.A.sc0


title: Mi-R1-3: Host-Race-1 (ND), Cucumber, Piracaiba, Sao Paulo


title: D8

value: NIH-3T3 fibroblasts/HFF primary fibroblasts

value: mock/mock


title: Curlcake constructs m6A-modified Replicate 2

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

description:
Rep2_Mod
IVT Product

data_processing:
Reads were locally basecalled using Albacore 2.1.7 and the "U" in basecalled reads were replaced with "T"
Reads were then mapped to reference (FASTA_sequences_of_Curlcakes.txt) using minimap2 : minimap2 -ax map-ont ref.fasta sample.fastq > sample.sam
Variants at each single reference site were extracted from the mapping results using in-house script
Supplementary_files_format_and_content: .csv files
column1: squences of 5mers in reference seqeunce
column2: 1-based positions of 5mers in reference seqeunces
column3: -2,-1,0,+1', and +2 are the relative positions of the bases in 5mers
column4: Reference Sequence ID
column5: reference position
column6: reference base at given positoin
column7: number of reads mapped to that position
column8: mean quality of bases mapped to that position
column9: median quality score of bases mapped to the same position
column10: standard deviation of quality scores of all bases mapped to the same position
column11: percentage of mismatches at the give position
column12: percentages of insertions at the given position
column13: percentage of deletions at the given position
column14: mean current intensity of the 5mers from multiple mapped reads
column15: median current intensity of 5mers from mapped reads
column16: standard deviation of current intensity of 5mers from mapped reads

molecule: other

organism: synthetic construct

source_name: In-vitro transcript Capped/PolyA+

extract_protocol:
In-vitro transcription followed by 5'capping and PolyA tailing
RNA libraries were prepared by following the standart ONT direct RNA sequencing (SQK-RNA001) protocol.
Direct RNA sequencing

tag: construct

value: Curlcake construct m6A-modified


title: ERA with bone erosion 6

description:
Test 1
SAMPLE 6

value: Female


title: ERA with bone erosion 7

description:
Test 1
SAMPLE 7


title: Mi-R1-2: Host-Race-1 (INC15), Soybean, Londrina, Parana


title: ERA with bone erosion 5

description:
Test 1
SAMPLE 5


title: WTCHG_261086_280: Cen8 Cnp1 after deletion

value: fission yeast cells


title: WTCHG_543859_203165: Cen8 Cnp3 before deletion


title: viral.C

description:
RNA-Seq (Smart-Seq kit)
virion_count_viral.tsv

data_processing:
Supplementary_files_format_and_content: none
Reads were mapped against a combined index of the MCMV and Mouse genome (mm10) using STAR 2.5.3a. All reads overlapping an annotated CDS of the MCMV genome were counted.
Genome_build: mouse (Ensembl v90) and MCMV (BAC clone C5X) genomes
Supplementary_files_format_and_content: tsv-files; Output of GRAND-SLAM containing read counts, estimated new/total ratios (with credible interval), beta approximation parameters as well as C-to-T mismatch statistics for each gene and library
Supplementary_files_format_and_content: h5; filtered_gene_bc_matrices, molecule_info

organism: Murid betaherpesvirus 1

source_name: mcmv viral stock

extract_protocol:
Viral RNA has been extracted with the Quick-RNA Viral kit (Zymo) by using 10 μl from four viral stocks. The RNA was eluted in 6 μl nuclease-free water.
3 μl were used for the Smart-seq v4 low input reaction (Takara) with one-quarter of the recommended reagent volumes. ERCC spike-in control was added to a dilution of 1:20 millions. One viral stock was processed without ERCC spike-in. Libraries were prepared using Nextera XT (Illumina) using a quarter of the recommended reagent volumes.

value: mcmv viral stock

value: C


title: Curlcake constructs Non-modified Replicate 2

description:
Rep2_Unm
IVT Product

value: Curlcake construct Non-modified


title: WTCHG_543859_201189: Empty vector Cnp3 after deletion


title: WTCHG_261086_279: Cen8 Cnp1 after deletion


title: Curlcake constructs m6A-modified Replicate 1

description:
Rep1_Mod
IVT Product


title: ERA with bone erosion 4

description:
Test 1
SAMPLE 4


title: WTCHG_261086_266: Empty vector Cnp1 after deletion


title: ERA with bone erosion 3

description:
Test 1
SAMPLE 3


title: ERA with bone erosion 2

description:
Test 1
SAMPLE 2


title: Curlcake constructs Non-modified Replicate 1

description:
Rep1_Unm
IVT Product


title: viral.A

value: A


title: Mi-R2-1: Host-Race-2 (LGM09), Tobacco, Sombrio, Santa Catarina


title: viral.D

value: D


title: s8_dep_CD41pos

status: Public on Jul 09 2019

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/). Reads were further subjected adaptor trimming using cutadapt [1]. Alignment of the reads to the Mouse genome was done using STAR Aligner [2] using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate  --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENCODE) was used for the alignment .
Using the parameters: 'htseq-count -f bam -s reverse -m union -a 20', HTSeq-0.6.1p1 was used to count the reads that map to the genes in the aligned sample files.  The GTF file (gencode.vM12.annotation.gtf) used for read quantification was downloaded from Gencode (https://www.gencodegenes.org/mouse/release_M12.html).
Genome_build: mm10
Supplementary_files_format_and_content: Text file with raw read counts per gene

source_name: HSC CD41+

growth_protocol: Cells were isolated from bone marrow, sorted using markers: Lin- c-Kit+ Sca-1+ CD48- CD150+

extract_protocol:
For library preparation 1.5 ng cDNA was desiccated and rehydrated for 5 min at room temperature with 1 µl tagment mix consisting of 0.1 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 5 min. Next, Illumina indices are added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are purified twice with 1x volume Ampure XP Beads and quantified with the Fragment Analyzer, followed by Illumina sequencing on a Nextseq500 with a sample sequencing depth of 10 mio reads on average.  dT-primer: C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGAC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, where N represents a random base and V any base beside thymidine;  TSO-primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, where rG stands for ribo-guanosine;  UP-primer: AAGCAGTGGTATCAACGCAGAGT
Standard Illumina Protocol

treatment_protocol: RNA from 1000 stem cells was isolated with RNeasy Micro Plus kit (Qiagen) and eluted in nuclease free water. Subsequently, the RNA was desiccated to 3 µl in a Eppendorf Concentator Plus for 25 min at room temperature and subjected to a mix finally consisting of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer* and 4 U RNase Inhibitor (NEB). RNA was denatured for 3 minutes at 72 °C. The reverse transcription is performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. After cDNA synthesis, the reverse transcriptase is inactivated at 70 °C for 15 min. The cDNA is subsequently amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 250 nM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 17 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 1x volume of Ampure XP Beads (Beckman Coulter) and DNA is eluted in 12 ul nuclease free water. The cDNA quality and concentration is determined with the Fragment Analyzer (Advanced Analytical).

value: Sorted hematopoietic stem cells

tag: tretment in vivo

value: Platelet depletion


title: s11_dep_CD41neg

source_name: HSC CD41-


title: s9_dep_CD41neg


title: s10_dep_CD41pos


title: s5_ctrl_CD41neg

value: Control rabbit serum


title: s3_ctrl_CD41neg


title: s2_ctrl_CD41pos


title: s4_ctrl_CD41pos


title: s7_dep_CD41neg


title: s1_ctrl_CD41neg


title: viral.B

value: B


title: WTCHG_261086_288: Cen8 Cnp1 before deletion


title: iSpMNday7_S94

city: Boston

first: Matthew

middle: F

last: Rose

state: MA

address: 3 Blackfan Circle

department: Neurology/Pathology

institute: Boston Children's Hospital

description: single cell

data_processing:
Illumina bcl2fastq software was used to demultiplex and generate fastq files for each cell
For each cell, FASTQ files from all 4 lanes were concatenated to generate single R1 and R2 FASTQ files per cell
RSEM (v1.2) with STAR (v2.5.3a) was run to align reads to the reference sequence and generate estimated expression level TPM matrices
Single cell analysis was performed principally with Seurat version 3.0
Genome_build: mouse mm10 (Ensemble GRCh38-1.2.0)
Supplementary_files_format_and_content: Comma-separated text file with TPM values for each single cell

molecule: polyA RNA

source_name: embryonic stem cell-derived spinal motor neurons

extract_protocol:
One cultured motor neuron was placed in each well of 96-well eppendorf plates in buffer TCL, centrifuged for 1 minute and frozen on dry ice. The Smart-Seq2 single cell RNA-seq library protocol was used to extract the RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESC-derived induced spinal motor neurons 7 days after plating


title: iSpMNday7_S93

description: single cell


title: iSpMNday7_S95

description: single cell


title: iSpMNday7_S92

description: single cell


title: iSpMNday7_S96

description: single cell


title: iSpMNday7_S91

description: single cell


title: iSpMNday7_S90

description: single cell


title: rpfs (Vehicle-treated)

city: Oxford

first: Jack

middle: Edward

last: Feltham

state: Oxfordshire

address: South Parks Road

department: Biochemistry

institute: University of Oxford

data_processing:
library strategy: Ribosome profiling
.fastq files corresponding to the same samples were merged and adaptors were trimmed using cutadapt.
Reads were aligned to combined mouse/cerevisiae rDNA loci using bowtie and unaligned reads were retained.
Unaligned reads were aligned to to combined mouse/cerevisiae genome using bowtie2.
Unique reads were extracted using samtools and converted to .bed format.
Offsets were calculated and applied to .bed files using “R” scripts to provide “P-site locations”.
Genome_build: mm10 and SacCer3
Supplementary_files_format_and_content: .bed

source_name: Primary B Cells_vehicle-treated

growth_protocol: Murine splenic B cells were purified using the Pan B Cell Isolation Kit II (130-104-443, Miltenyi). Cells were cultured at a density of 1 million/ml supplemented with 10 µg/ml LPS (Santa Cruz) for stimulation.

extract_protocol:
Harvested cells were lysed and spiked with S. cerevisiae lysate at the ratio of 13 million B cells: 270 million yeast cells (which equals to ~ 20:4 µg miRNA). Lysate was digested with RnaseI and monosomes were extracted using SEC. RNA was extracted rRNA was depleted using RiboZero and small RNAs were isolated using TBU-PAGE gel extraction.
Libraries were constructed according to Ingolia et al., 2012.

treatment_protocol: 10 uM GC7 was added on day 2 of stimulation for 24 h of treatment. Cells were harvested on day 3.

value: primary splenic B cells

value: Vehicle


title: rpfs (GC7-treated)

source_name: Primary B Cells_GC7-treated


title: WTCHG_261086_287: Cen8 Cnp1 before deletion


title: iSpMNday7_S87

description: single cell


title: iSpMNday7_S88

description: single cell


title: s12_dep_CD41pos


title: iSpMNday7_S89

description: single cell


title: iSpMNday7_S86

description: control well with 50 cells


title: iSpMNday7_S83

description: single cell


title: iSpMNday7_S84

description: single cell


title: ERA with bone erosion 1

description:
Test 1
SAMPLE 1

value: Early rheumatoid arthrits


title: iSpMNday7_S85

description: control well with 50 cells


title: iSpMNday7_S79

description: single cell


title: iSpMNday7_S81

description: single cell


title: iSpMNday7_S75

description: single cell


title: iSpMNday7_S78

description: single cell


title: iSpMNday7_S77

description: single cell


title: iSpMNday7_S76

description: single cell


title: iSpMNday7_S74

description: single cell


title: iSpMNday7_S72

description: single cell


title: iSpMNday7_S69

description: single cell


title: iSpMNday7_S71

description: single cell


title: iSpMNday7_S66

description: single cell


title: iSpMNday7_S67

description: single cell


title: iSpMNday7_S65

description: single cell


title: iSpMNday7_S73

description: single cell


title: iSpMNday7_S63

description: single cell


title: iSpMNday7_S68

description: single cell


title: iSpMNday7_S64

description: single cell


title: iSpMNday7_S82

description: single cell


title: iSpMNday7_S80

description: single cell


title: iSpMNday7_S61

description: single cell


title: iSpMNday7_S62

description: single cell


title: iSpMNday7_S59

description: single cell


title: iSpMNday7_S57

description: single cell


title: iSpMNday7_S60

description: single cell


title: iSpMNday7_S54

description: single cell


title: iSpMNday7_S56

description: single cell


title: iSpMNday7_S55

description: single cell


title: iSpMNday7_S53

description: single cell


title: iSpMNday5_S384

description: single cell

value: ESC-derived induced spinal motor neurons 5 days after plating


title: iSpMNday7_S51

description: single cell


title: iSpMNday7_S49

description: single cell


title: iSpMNday7_S70

description: single cell


title: iSpMNday5_S382

description: single cell


title: iSpMNday7_S50

description: single cell


title: iSpMNday5_S383

description: single cell


title: iSpMNday5_S381

description: single cell


title: iSpMNday5_S377

description: single cell


title: iSpMNday5_S379

description: single cell


title: iSpMNday5_S376

description: single cell


title: iSpMNday5_S380

description: single cell


title: iSpMNday5_S375

description: single cell


title: iSpMNday5_S374

description: control well with 50 cells


title: iSpMNday5_S378

description: single cell


title: iSpMNday5_S373

description: control well with 50 cells


title: iSpMNday5_S372

description: single cell


title: iSpMNday5_S371

description: single cell


title: iSpMNday7_S58

description: single cell


title: iSpMNday5_S370

description: single cell


title: iSpMNday7_S52

description: single cell


title: iSpMNday5_S368

description: single cell


title: iSpMNday5_S369

description: single cell


title: iSpMNday5_S364

description: single cell


title: iSpMNday5_S366

description: single cell


title: iSpMNday5_S361

description: single cell


title: iSpMNday5_S358

description: single cell


title: iSpMNday5_S360

description: single cell


title: iSpMNday5_S365

description: single cell


title: iSpMNday5_S367

description: single cell


title: iSpMNday5_S362

description: single cell


title: iSpMNday5_S356

description: single cell


title: iSpMNday5_S357

description: single cell


title: iSpMNday5_S359

description: single cell


title: iSpMNday5_S355

description: single cell


title: iSpMNday5_S354

description: single cell


title: iSpMNday5_S353

description: single cell


title: iSpMNday5_S351

description: single cell


title: iSpMNday5_S350

description: single cell


title: iSpMNday5_S349

description: single cell


title: iSpMNday5_S347

description: single cell


title: iSpMNday5_S348

description: single cell


title: iSpMNday5_S346

description: single cell


title: iSpMNday5_S345

description: single cell


title: iSpMNday5_S344

description: single cell


title: iSpMNday5_S352

description: single cell


title: iSpMNday5_S343

description: single cell


title: iSpMNday5_S339

description: single cell

value: ESC-derived induced spinal motor neurons 2 days after plating


title: iSpMNday5_S338

description: single cell


title: iSpMNday5_S342

description: single cell


title: iSpMNday5_S340

description: single cell


title: iSpMNday2_S287

description: single cell


title: iSpMNday5_S337

description: single cell


title: iSpMNday2_S283

description: single cell


title: iSpMNday2_S284

description: single cell


title: iSpMNday5_S341

description: single cell


title: iSpMNday2_S281

description: single cell


title: iSpMNday2_S280

description: single cell


title: iSpMNday2_S286

description: single cell


title: iSpMNday2_S279

description: single cell


title: iSpMNday2_S278

description: control well with 50 cells


title: iSpMNday2_S282

description: single cell


title: iSpMNday2_S276

description: single cell


title: iSpMNday2_S285

description: single cell


title: iSpMNday2_S275

description: single cell


title: iSpMNday2_S272

description: single cell


title: iSpMNday2_S271

description: single cell


title: iSpMNday2_S274

description: single cell


title: iSpMNday2_S273

description: single cell


title: iSpMNday2_S270

description: single cell


title: iSpMNday2_S277

description: control well with 50 cells


title: iSpMNday2_S269

description: single cell


title: iSpMNday2_S267

description: single cell


title: iSpMNday2_S266

description: single cell


title: iSpMNday2_S288

description: single cell


title: iSpMNday2_S265

description: single cell


title: iSpMNday2_S263

description: single cell


title: iSpMNday2_S261

description: single cell


title: iSpMNday2_S262

description: single cell


title: iSpMNday2_S264

description: single cell


title: iSpMNday2_S260

description: single cell


title: iSpMNday2_S256

description: single cell


title: iSpMNday2_S259

description: single cell


title: iSpMNday2_S255

description: single cell


title: iSpMNday2_S257

description: single cell


title: iSpMNday2_S253

description: single cell


title: iSpMNday2_S252

description: single cell


title: iSpMNday2_S251

description: single cell


title: iSpMNday2_S250

description: single cell


title: iSpMNday2_S248

description: single cell


title: iSpMNday2_S249

description: single cell


title: iSpMNday2_S245

description: single cell

source_name: embryonic stem cell-derived cranial motor neurons

value: ESC-derived induced cranial motor neurons 7 days after plating


title: iSpMNday2_S247

description: single cell


title: iSpMNday2_S246

description: single cell


title: iSpMNday2_S268

description: single cell


title: iSpMNday2_S254

description: single cell


title: iSpMNday2_S243

description: single cell


title: iSpMNday2_S242

description: single cell


title: iSpMNday2_S241

description: single cell


title: iCrMNday7_S48

description: single cell


title: iCrMNday7_S47

description: single cell


title: iCrMNday7_S45

description: single cell


title: iCrMNday7_S46

description: single cell


title: iSpMNday2_S258

description: single cell


title: iCrMNday7_S44

description: single cell


title: iCrMNday7_S42

description: single cell


title: iCrMNday7_S43

description: single cell


title: iCrMNday7_S40

description: single cell


title: iCrMNday7_S39

description: single cell


title: iCrMNday7_S37

description: single cell


title: iCrMNday7_S36

description: single cell


title: iCrMNday7_S38

description: single cell


title: iCrMNday7_S35

description: single cell


title: iCrMNday7_S32

description: single cell


title: iCrMNday7_S33

description: single cell


title: iSpMNday2_S244

description: single cell


title: iCrMNday7_S31

description: single cell


title: iCrMNday7_S29

description: single cell


title: iCrMNday7_S30

description: single cell


title: iCrMNday7_S28

description: single cell


title: iCrMNday7_S27

description: single cell


title: iCrMNday7_S25

description: single cell


title: iCrMNday7_S26

description: single cell


title: iCrMNday7_S24

description: single cell


title: iCrMNday7_S41

description: single cell


title: iCrMNday7_S23

description: single cell


title: iCrMNday7_S21

description: single cell


title: iCrMNday7_S22

description: single cell


title: iCrMNday7_S18

description: single cell


title: iCrMNday7_S19

description: single cell


title: iCrMNday7_S17

description: single cell


title: iCrMNday7_S34

description: single cell


title: iCrMNday7_S14

description: single cell


title: iCrMNday7_S16

description: single cell


title: iCrMNday7_S15

description: single cell


title: iCrMNday7_S13

description: single cell


title: iCrMNday7_S11

description: single cell


title: iCrMNday7_S20

description: single cell


title: iCrMNday7_S9

description: single cell


title: iCrMNday7_S5

description: single cell

value: ESC-derived induced cranial motor neurons 5 days after plating


title: iCrMNday7_S6

description: single cell


title: iCrMNday7_S4

description: single cell


title: iCrMNday7_S7

description: single cell


title: iCrMNday7_S10

description: single cell


title: iCrMNday7_S3

description: single cell


title: iCrMNday7_S2

description: single cell


title: iCrMNday5_S336

description: single cell


title: iCrMNday5_S335

description: single cell


title: iCrMNday5_S332

description: single cell


title: iCrMNday5_S334

description: single cell


title: iSpMNday5_S363

description: single cell


title: iCrMNday5_S327

description: single cell


title: iCrMNday7_S12

description: single cell


title: iCrMNday5_S328

description: single cell


title: iCrMNday5_S326

description: single cell


title: iCrMNday5_S325

description: single cell


title: iCrMNday5_S324

description: single cell


title: iCrMNday7_S8

description: single cell


title: iCrMNday5_S323

description: single cell


title: iCrMNday5_S322

description: single cell


title: iCrMNday5_S320

description: single cell


title: iCrMNday5_S321

description: single cell


title: iCrMNday5_S317

description: single cell


title: iCrMNday5_S319

description: single cell


title: iCrMNday5_S318

description: single cell


title: iCrMNday7_S1

description: single cell


title: iCrMNday5_S314

description: single cell


title: iCrMNday5_S316

description: single cell


title: iCrMNday5_S313

description: single cell


title: iCrMNday5_S312

description: single cell


title: iCrMNday5_S311

description: single cell


title: iCrMNday5_S310

description: single cell


title: iCrMNday5_S333

description: single cell


title: iCrMNday5_S331

description: single cell


title: iCrMNday5_S329

description: single cell


title: iCrMNday5_S315

description: single cell


title: iCrMNday5_S307

description: single cell


title: iCrMNday5_S306

description: single cell


title: iCrMNday5_S305

description: single cell


title: iCrMNday5_S308

description: single cell


title: iCrMNday5_S301

description: single cell


title: iCrMNday5_S302

description: single cell


title: iCrMNday5_S300

description: single cell


title: iCrMNday5_S304

description: single cell


title: iCrMNday5_S299

description: single cell


title: iCrMNday5_S298

description: single cell


title: iCrMNday5_S303

description: single cell


title: iCrMNday5_S297

description: single cell


title: iCrMNday5_S295

description: single cell

value: ESC-derived induced cranial motor neurons 2 days after plating


title: iCrMNday5_S296

description: single cell


title: iCrMNday5_S293

description: single cell


title: iCrMNday5_S292

description: single cell


title: iCrMNday5_S294

description: single cell


title: iCrMNday5_S290

description: single cell


title: iCrMNday5_S291

description: single cell


title: iCrMNday5_S289

description: single cell


title: iCrMNday2_S239

description: single cell


title: iCrMNday5_S309

description: single cell


title: iCrMNday2_S240

description: single cell


title: iCrMNday2_S235

description: single cell


title: iCrMNday2_S237

description: single cell


title: iCrMNday2_S234

description: single cell


title: iCrMNday2_S233

description: single cell


title: iCrMNday2_S231

description: single cell


title: iCrMNday2_S236

description: single cell


title: iCrMNday2_S232

description: single cell


title: iCrMNday2_S229

description: single cell


title: iCrMNday2_S230

description: single cell


title: iCrMNday2_S226

description: single cell


title: iCrMNday2_S224

description: single cell


title: iCrMNday2_S223

description: single cell


title: iCrMNday2_S228

description: single cell


title: iCrMNday2_S221

description: single cell


title: iCrMNday2_S225

description: single cell


title: iCrMNday2_S220

description: single cell


title: iCrMNday2_S227

description: single cell


title: iCrMNday5_S330

description: single cell


title: iCrMNday2_S222

description: single cell


title: iCrMNday2_S219

description: single cell


title: iCrMNday2_S218

description: single cell


title: iCrMNday2_S217

description: single cell


title: iCrMNday2_S216

description: single cell


title: iCrMNday2_S213

description: single cell


title: iCrMNday2_S238

description: single cell


title: iCrMNday2_S215

description: single cell


title: iCrMNday2_S214

description: single cell


title: iCrMNday2_S210

description: single cell


title: iCrMNday2_S211

description: single cell


title: iCrMNday2_S209

description: single cell


title: iCrMNday2_S208

description: single cell


title: iCrMNday2_S207

description: single cell


title: iCrMNday2_S204

description: single cell


title: iCrMNday2_S203

description: single cell


title: iCrMNday2_S202

description: single cell


title: iCrMNday2_S201

description: single cell


title: iCrMNday2_S198

description: single cell


title: iCrMNday2_S197

description: single cell


title: iCrMNday2_S199

description: single cell

source_name: primary embryonic ocular motor neurons

value: primary embryonic ocular motor neurons


title: iCrMNday2_S194

description: single cell


title: iCrMNday2_S193

description: single cell


title: iCrMNday2_S196

description: single cell


title: iCrMNday2_S212

description: single cell


title: SpMN_S283

description: single cell

source_name: primary embryonic spinal motor neurons

value: E11.5 spinal motor neurons cultured for 7 days


title: SpMN_S284

description: single cell


title: iCrMNday2_S195

description: single cell


title: SpMN_S288

description: single cell


title: SpMN_S278

description: single cell


title: SpMN_S272

description: single cell


title: SpMN_S282

description: single cell


title: SpMN_S264

description: single cell


title: iCrMNday2_S206

description: single cell


title: SpMN_S269

description: single cell


title: SpMN_S266

description: single cell


title: SpMN_S281

description: single cell


title: SpMN_S270

description: single cell


title: SpMN_S259

description: single cell


title: SpMN_S258

description: single cell


title: iCrMNday2_S205

description: single cell


title: SpMN_S257

description: single cell


title: SpMN_S254

description: single cell


title: iCrMNday2_S200

description: single cell


title: SpMN_S248

description: single cell


title: SpMN_S246

description: single cell


title: SpMN_S236

description: single cell


title: SpMN_S240

description: single cell


title: SpMN_S247

description: single cell


title: SpMN_S242

description: single cell


title: SpMN_S260

description: single cell


title: SpMN_S230

description: single cell


title: SpMN_S223

description: single cell


title: SpMN_S228

description: single cell


title: SpMN_S233

description: single cell


title: SpMN_S235

description: single cell


title: SpMN_S234

description: single cell


title: SpMN_S221

description: single cell


title: SpMN_S276

description: single cell


title: SpMN_S224

description: single cell


title: SpMN_S222

description: single cell


title: SpMN_S216

description: single cell


title: SpMN_S252

description: single cell


title: SpMN_S211

description: single cell


title: SpMN_S271

description: single cell


title: SpMN_S218

description: single cell


title: SpMN_S210

description: single cell


title: SpMN_S200

description: single cell


title: SpMN_S209

description: single cell


title: SpMN_S206

description: single cell


title: SpMN_S204

description: single cell


title: SpMN_S245

description: single cell


title: SpMN_S199

description: single cell


title: SpMN_S198

description: single cell


title: SpMN_S197

description: single cell


title: SpMN_S191

description: single cell


title: SpMN_S194

description: single cell


title: SpMN_S190

description: single cell


title: SpMN_S189

description: single cell


title: SpMN_S212

description: single cell


title: SpMN_S182

description: single cell


title: SpMN_S188

description: single cell


title: SpMN_S170

description: single cell


title: SpMN_S178

description: single cell


title: SpMN_S167

description: single cell


title: SpMN_S169

description: single cell


title: SpMN_S165

description: single cell


title: SpMN_S176

description: single cell


title: SpMN_S157

description: single cell


title: SpMN_S166

description: single cell


title: SpMN_S158

description: single cell


title: SpMN_S164

description: single cell


title: SpMN_S153

description: single cell


title: SpMN_S154

description: single cell


title: SpMN_S145

description: single cell


title: SpMN_S146

description: single cell


title: SpMN_S143

description: single cell


title: SpMN_S142

description: single cell


title: SpMN_S179

description: single cell


title: SpMN_S140

description: single cell


title: SpMN_S177

description: single cell


title: SpMN_S131

description: single cell


title: SpMN_S129

description: single cell


title: SpMN_S133

description: single cell


title: SpMN_S130

description: single cell


title: SpMN_S155

description: single cell


title: SpMN_S152

description: single cell


title: SpMN_S122

description: single cell


title: SpMN_S181

description: single cell


title: SpMN_S119

description: single cell


title: SpMN_S121

description: single cell


title: SpMN_S117

description: single cell


title: SpMN_S128

description: single cell


title: SpMN_S106

description: single cell


title: SpMN_S116

description: single cell


title: SpMN_S96

description: single cell


title: SpMN_S141

description: single cell


title: SpMN_S134

description: single cell


title: SpMN_S95

description: single cell


title: SpMN_S91

description: single cell


title: SpMN_S118

description: single cell


title: SpMN_S88

description: single cell


title: SpMN_S85

description: single cell


title: SpMN_S92

description: single cell


title: SpMN_S80

description: single cell


title: SpMN_S79

description: single cell


title: SpMN_S84

description: single cell


title: SpMN_S83

description: single cell


title: SpMN_S72

description: single cell


title: SpMN_S76

description: single cell


title: SpMN_S71

description: single cell


title: SpMN_S67

description: single cell


title: SpMN_S68

description: single cell


title: SpMN_S73

description: single cell


title: SpMN_S64

description: single cell


title: SpMN_S109

description: single cell


title: SpMN_S104

description: single cell


title: SpMN_S61

description: single cell


title: SpMN_S98

description: single cell


title: SpMN_S105

description: single cell


title: SpMN_S110

description: single cell


title: SpMN_S59

description: single cell


title: SpMN_S60

description: single cell


title: SpMN_S52

description: single cell


title: SpMN_S49

description: single cell


title: SpMN_S56

description: single cell


title: SpMN_S97

description: single cell


title: SpMN_S107

description: single cell


title: SpMN_S48

description: single cell


title: SpMN_S47

description: single cell


title: SpMN_S44

description: single cell


title: SpMN_S43

description: single cell


title: SpMN_S37

description: single cell


title: SpMN_S40

description: single cell


title: SpMN_S36

description: single cell


title: SpMN_S32

description: single cell


title: SpMN_S25

description: single cell


title: SpMN_S35

description: single cell


title: SpMN_S23

description: single cell


title: SpMN_S31

description: single cell


title: SpMN_S24

description: single cell


title: SpMN_S19

description: single cell


title: SpMN_S20

description: single cell


title: SpMN_S28

description: single cell


title: SpMN_S11

description: single cell


title: SpMN_S12

description: single cell


title: SpMN_S1

description: single cell


title: SpMN_S7

description: single cell


title: OTrMN_S285

description: single cell


title: SpMN_S16

description: single cell


title: SpMN_S13

description: single cell


title: OTrMN_S286

description: single cell


title: OTrMN_S279

description: single cell


title: OTrMN_S277

description: single cell


title: OTrMN_S280

description: single cell


title: SpMN_S55

description: single cell


title: SpMN_S4

description: single cell


title: OTrMN_S287

description: single cell


title: SpMN_S8

description: single cell


title: OTrMN_S274

description: single cell


title: OTrMN_S275

description: single cell


title: OTrMN_S273

description: single cell


title: OTrMN_S268

description: single cell


title: OTrMN_S255

description: single cell


title: OTrMN_S263

description: single cell


title: OTrMN_S267

description: single cell


title: OTrMN_S262

description: single cell


title: OTrMN_S256

description: single cell


title: OTrMN_S253

description: single cell


title: OTrMN_S261

description: single cell


title: OTrMN_S250

description: single cell


title: OTrMN_S251

description: single cell


title: OTrMN_S249

description: single cell


title: OTrMN_S244

description: single cell


title: OTrMN_S232

description: single cell


title: OTrMN_S243

description: single cell


title: OTrMN_S241

description: single cell


title: OTrMN_S237

description: single cell


title: OTrMN_S265

description: single cell


title: OTrMN_S238

description: single cell


title: OTrMN_S231

description: single cell


title: OTrMN_S229

description: single cell


title: OTrMN_S214

description: single cell


title: OTrMN_S225

description: single cell


title: OTrMN_S213

description: single cell


title: OTrMN_S215

description: single cell


title: OTrMN_S217

description: single cell


title: OTrMN_S220

description: single cell


title: OTrMN_S219

description: single cell


title: OTrMN_S208

description: single cell


title: OTrMN_S203

description: single cell


title: OTrMN_S202

description: single cell


title: OTrMN_S205

description: single cell


title: OTrMN_S201

description: single cell


title: OTrMN_S196

description: single cell


title: OTrMN_S207

description: single cell


title: OTrMN_S187

description: single cell


title: OTrMN_S192

description: single cell


title: OTrMN_S193

description: single cell


title: OTrMN_S239

description: single cell


title: OTrMN_S226

description: single cell


title: OTrMN_S227

description: single cell


title: OTrMN_S183

description: single cell


title: OTrMN_S186

description: single cell


title: OTrMN_S174

description: single cell


title: OTrMN_S180

description: single cell


title: OTrMN_S172

description: single cell


title: OTrMN_S175

description: single cell


title: OTrMN_S184

description: single cell


title: OTrMN_S173

description: single cell


title: OTrMN_S171

description: single cell


title: OTrMN_S195

description: single cell


title: OTrMN_S168

description: single cell


title: OTrMN_S161

description: single cell


title: OTrMN_S159

description: single cell


title: OTrMN_S160

description: single cell


title: OTrMN_S163

description: single cell


title: OTrMN_S139

description: single cell


title: OTrMN_S147

description: single cell


title: OTrMN_S144

description: single cell


title: OTrMN_S138

description: single cell


title: OTrMN_S136

description: single cell


title: OTrMN_S150

description: single cell


title: OTrMN_S137

description: single cell


title: OTrMN_S151

description: single cell


title: OTrMN_S149

description: single cell


title: OTrMN_S185

description: single cell


title: OTrMN_S156

description: single cell


title: OTrMN_S135

description: single cell


title: OTrMN_S132

description: single cell


title: OTrMN_S162

description: single cell


title: OTrMN_S123

description: single cell


title: OTrMN_S126

description: single cell


title: OTrMN_S124

description: single cell


title: OTrMN_S115

description: single cell


title: OTrMN_S125

description: single cell


title: OTrMN_S114

description: single cell


title: OTrMN_S113

description: single cell


title: OTrMN_S112

description: single cell


title: OTrMN_S120

description: single cell


title: OTrMN_S111

description: single cell


title: OTrMN_S108

description: single cell


title: OTrMN_S101

description: single cell


title: OTrMN_S148

description: single cell


title: OTrMN_S103

description: single cell


title: OTrMN_S102

description: single cell


title: OTrMN_S100

description: single cell


title: OTrMN_S94

description: single cell


title: OTrMN_S81

description: single cell


title: OTrMN_S78

description: single cell


title: OTrMN_S127

description: single cell


title: OTrMN_S86

description: single cell


title: OTrMN_S77

description: single cell


title: OTrMN_S99

description: single cell


title: OTrMN_S93

description: single cell


title: OTrMN_S90

description: single cell


title: OTrMN_S89

description: single cell


title: OTrMN_S75

description: single cell


title: OTrMN_S74

description: single cell


title: OTrMN_S66

description: single cell


title: OTrMN_S63

description: single cell


title: OTrMN_S57

description: single cell


title: OTrMN_S58

description: single cell


title: OTrMN_S54

description: single cell


title: OTrMN_S65

description: single cell


title: OTrMN_S62

description: single cell


title: OTrMN_S46

description: single cell


title: OTrMN_S51

description: single cell


title: OTrMN_S50

description: single cell


title: OTrMN_S82

description: single cell


title: OTrMN_S53

description: single cell


title: OTrMN_S45

description: single cell


title: OTrMN_S87

description: single cell


title: OTrMN_S70

description: single cell


title: OTrMN_S30

description: single cell


title: OTrMN_S22

description: single cell


title: OTrMN_S26

description: single cell


title: OTrMN_S29

description: single cell


title: OTrMN_S27

description: single cell


title: OTrMN_S41

description: single cell


title: OTrMN_S18

description: single cell


title: OTrMN_S33

description: single cell


title: OTrMN_S34

description: single cell


title: OTrMN_S21

description: single cell


title: OTrMN_S38

description: single cell


title: OTrMN_S39

description: single cell


title: OTrMN_S17

description: single cell


title: OTrMN_S14

description: single cell


title: OTrMN_S6

description: single cell


title: OTrMN_S15

description: single cell


title: OTrMN_S10

description: single cell


title: OTrMN_S42

description: single cell


title: Tabby_2

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCm38.p5 whole genome using STAR aligner with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.vM13.primary_assembly.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of samples-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCm38.p5 from GENCODE Mus musculus Release M13
Supplementary_files_format_and_content: Raw count matrix of sequencing reads as .txt

source_name: adult lacrimal gland

extract_protocol:
RNA was extracted using Precellys hard-tissue beads and TRIzol. The RNA was purified using RNeasy Mini Kit from Qiagen.
NEBNext Ultra Directional RNA Library Prep Kit with Ribo-Zero rRNA Removal Kit

treatment_protocol: Lacrimal gland were extracted, flash frozen on ice and kept at -80C until total RNA extraction

value: lacrimal gland

value: Eda-/-


title: OTrMN_S3

description: single cell


title: Blacky_3

value: wild-type


title: Tabby_3


title: OTrMN_S2

description: single cell


title: Tabby_1


title: Blacky_2


title: Blacky_1


title: HF/HS 4

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

institute: CGFL

data_processing:
Data were processed thanks to galaxy website
Fastq groomer tool was applied
Alignment was performed with TopHat on mm9 reference genome
Cufflink was applied
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking

growth_protocol: 8-week-old mice were randomly assigned standard, HF/HS or HF/HS +AOF diet and were fed ad libitum with the respective diets for 180 days

extract_protocol:
Total RNA was extracted from eWAT with the RNeasy Lipid Tissue Mini kit (Qiagen) according to the manufacturer's instructions and included a DNAse treatment step . Then, 1µg of total RNA was rRNA depleted thanks to Ribominus Eukaryote kit.
Libraries were prepared according to Bioo Scientific's instructions accompanying the Nextflex RNA Seq-Kit for Illumina. Briefly, RNA was heat fragmented and double strand cDNA synthesis was performed in 2 steps. After purification, the double strand cDNA was end repaired and then adenylated. After adapter ligation, DNA was PCR amplified for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were obtained. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

treatment_protocol: epididymal white adipose  tissues (eWAT) were harvested from fasted mice and immediately snap frozen and stored at -80°C until total RNA extraction

value: 8 weeks

tag: genotype/variation

value: Wild-type

tag: diet

value: High-fat/high-sucrose (HF/HS)

value: epididymal white adipose tissue (eWAT)

tag: molecule subtype

value: rRNA depleted RNA


title: OTrMN_S5

description: single cell


title: HF/HS + AOF 1

source_name: HF/HS + AOF_eWAT

value: HF/HS + antioxidant formulation (AOF)


title: HF/HS + AOF 2


title: PTX rep2

city: xi’an

first: fangfang

last: yang

address: No. 127 Changle West Road

country: China

institute: xijing hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.2.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: skin

growth_protocol: Cells were cultured with DMEM/Low Glucose medium

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: Cells were starved for 12h and then treated with pentoxifylline for 24h

value: hypertrophic scar fibroblasts

value: skin

value: pentoxifylline


title: OTrMN_S9

description: single cell


title: Control rep3

value: control


title: HF/HS 1


title: PTX rep3


title: HF/HS + AOF 4


title: Std 1

value: standard (Std)


title: Std 2


title: HF/HS + AOF 3


title: Std 4


title: HF/HS 2


title: Control rep1


title: Control rep2


title: LPS_2

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Read trimming were performed by Trimmomatic
Reads obtained were aligned to rererence genome (hg38) using STAR genome aligner (v 2.5.0a)
Read counting were preformed by featureCounts (v1.5.0-p1)
Genome_build: hg38
Supplementary_files_format_and_content: text files generated by featureCounts: GeneID; count number per gene

source_name: Monocyte cell culture

growth_protocol: The cells were cultured in RPMI-1640 medium containing 10% heat-inactivated FCS, 2 mM L-glutamine, 100 units/ml of penicillin and 100 μg/ml streptomycin at 37°C under 5% CO2. For differentiation, THP-1 cells in culture medium were placed into 24-well flat-bottomed plates or cells were dissipated in 35 mm Petri dishes (samples for Real Time PCR), and 200 nM phorbol-12-myristate-13-acetate was added. The cells were grown for 72 hours at 37°C under 5% CO2, washed with culture medium and used in the experiments.

extract_protocol:
Total RNA extraction was performed from 1.5-2х106 cells (THP1 line) with Extract RNA reagent (Evrogen, Russia). The concentration of isolated total RNA was measured with a Qubit Fluorometer (Invitrogen, USA). The quality of RNA was determined with an Agilent BioAnalyzer 2100 using an RNA 600 nano kit (Agilent, USA)
Libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s guidelines. Seventy-five bp single-end sequencing was conducted on an Illumina NextSeq 500 platform

treatment_protocol: In experiments that investigated the effects of GYY4137 and LPS on SH-SY5Y neuroblastoma cells, cells were harvested using Trypsin-Versen solution, washed in complete culture medium, diluted in DMEM culture medium with 10% FCS to the required concentration, dissipated in 24-well flat-bottomed plates (Sarstedt, Germany) with increased adhesion and incubated for 24 hours at 37°C with 5% CO2 or cells were placed in 35 mm Petri dishes (samples for Real Time PCR). After that, the cells were supplemented with GYY4137 or LPS (for 120 minutes), and then LPS or GYY4137 was added to the corresponding samples and the cells were incubated for 6 or 24 hours

value: Monocyte cell culture

value: LPS


title: LPS_1


title: LPS_3


title: LPS_4


title: LPS+GYY_4

value: LPS+GYY


title: LPS+GYY_1


title: LPS+GYY_2


title: K_4

description: control


title: HF/HS 3


title: LPS+GYY_3


title: Std 3


title: OTrMN_S69

description: single cell

value: primary embryonic ocular motor neurons


title: PTX rep1


title: K_3

description: control


title: GYY+LPS_4

value: GYY+LPS


title: GYY+LPS_3


title: GYY+LPS_2


title: K_2

description: control


title: TT-Fam120a_Untagged_ES_iCLIP

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

description: iCLIP Fam120a IP RNA

data_processing:
iCLIP libraries were analyzed by Illumina HiSeq 2000. Analysis of iCLIP libraries was performed as previously described (Bosson et al. 2014).
Genome_build: mm9
Supplementary_files_format_and_content: Summary txt file includes the information of enriched iCLIP clusters (FHFam120a over Fam120a, or Fam120a over FHFam120a).

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β- mercaptoethanol.

extract_protocol: mESCs were UV-crosslinked and harvested. Crosslinked cell pellets were resuspended in lysis buffer, partially digested with RNase I, and serially immunoprecipitated with FLAG and HA antibodies. Protein-RNA complexes were resolved on SDS-PAGE gels and transferred to nitrocellulose. Regions corresponding to crosslinked Fam120a complexes were extracted from nitrocellulose with proteinase K digestion and RNA isolated by phenol extraction. Dephosphorylated RNA was ligated to a 3’ linker and reverse transcribed. The resulting cDNA was purified on a denaturing polyacrylamide gel, circularized, and PCR amplified using Illumina-compatible barcoded primers. PCR product was gel purified on a denaturing polyacrylamide gel. Samples were pooled and sequenced on the Illumina HiSeq platform.

treatment_protocol: TT-FHFam120a and TT-Fam120a mESCs were generated utilizing pSLIK lentivirus expression system (Shin et al. 2006). FHFam120a and untagged Fam120a proteins were induced with 2.5 μg/mL doxycycline treatment.

value: mouse embryonic stem cells

value: 2.5 ug/mL Dox


title: TT-FHFam120a_Tagged_ES_iCLIP

description: iCLIP FHFam120a IP RNA


title: WCE_Sen1

city: Sherbrooke

first: François

last: Bachand

state: Québec

address: 3201 Jean Mignault

department: Biochimie

country: Canada

institute: Université de Sherbrooke

data_processing:
Briefly, the raw reads were trimmed using Trimmomatic version 0.32 (Bolger et al., 2014) with parameters ILLUMINACLIP:2:30:15 LEADING:30 TRAILING:30 MINLEN:23, and quality inspection was conducted using FastQC version 0.11.4 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The trimmed reads from all data sets were aligned using BWA version 0.7.12-r1039 (Li and Durbin, 2010) with the algorithm mem and the parameter -split onto the sequence of the S. pombe ASM294v2. Note that no filtering on mapQ was performed in order to avoid discarding the signal at regions of the genome that are duplicated (BWA is randomly assigning the reads), but only primary alignments were kept and we generated mappability tracks for various read length to help the interpretation of particular regions.
Signal density files in BedGraph format were then generated using BEDTools genomecov version 2.17 (Quinlan and Hall, 2010) with default parameters, then converted in uniform 10 nt bins WIG files for further normalization steps (inspired by the script bedgraph_to_wig.py [https://gist.github.com/svigneau/8846527]).
Each signal density file was scaled based on sample's sequencing depth, then the signal of the input data set was subtracted from its corresponding IP data set.
The normalized WIG files were then encoded in bigWig format using the Kent utilities (Rhead et al., 2010). Visual inspection of the data was performed using an AssemblyHub on the UCSC Genome Browser (Casper et al., 2018).
Genome_build: ASM294v2
Supplementary_files_format_and_content: IP: bigwig files of the normalized IP signal after substraction of the WCE signal; WCE: bigwig files of the normalized WCE signal

source_name: yeast culture

growth_protocol: Cells were grown at 30°C in complete YES medium.

extract_protocol:
1,5.10^8 cells were cross-linked with 1% formaldehyde (Sigma) at 18°C for 30 minutes. After 3 washes with cold PBS, the cells were frozen in liquid nitrogen. Frozen cells were then lysed in cold lysis buffer (Hepes-KOH 50mM [pH 7.5], NaCl 140mM, EDTA 1mM, Triton 1%, Na-deoxycholate 0.1%, PMSF Phenylmethanesulfonyl fluoride 1 mM) with glass beads using a Precellys 24 mill (Bertin Technology). To fragment the chromatin, the lysates were sonicated at 4°C using a Covaris S220 or Diagenode Bioruptor sonicator. Immuno-precipitation was done overnight at 4°C using Pan Mouse IgG Dynabeads (Life Technologies, 11041) for TAP-tagged proteins. The immunoprecipitated complexes were washed for 5’ successively with: Wash I buffer (20mM Tris pH 8, 150 mM NaCl, 2mM EDTA, 1% Triton-X100, 0.1% SDS), Wash II buffer (20mM Tris pH 8, 500mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS) and Wash III buffer (20mM Tris pH 8, 1mM EDTA, 0.5% Na-deoxycholate, 1% Igepal, 250mM LiCl). After two additional washes in Tris EDTA pH 8, the beads were resuspended in 10% Chelex resin (Biorad) and incubated at 98°C for 10’. After addition of 2 μL of 10 mg/mL proteinase K, the mixture was incubated at 43°C for 1 hour, then for another 10’ at 98°C. After centrifugation, the supernatant was collected and analyzed by qPCR in a thermocycler Rotor Gene (Qiagen).
DNA libraries for ChIP-seq experiments were prepared as described previously (Lemay et al., 2016) using the SPARK DNA Sample Prep Kit Illumina Platform (Enzymatics) according to the manufacturer’s instructions.

tag: ip tag

value: HTP

tag: chip target

tag: chip antibody


title: WCE_Rpc1_sen1

tag: strain

value: TAP


title: HeLaS3FlpIn_BCDIN3Df_Rep2

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

description: RNA from FLAG eluates

data_processing:
For all datasets, sequence quality was verified by FastQC and reads were aligned using STAR.
Reads were aligned against a custom reference composed of miRBase, tRNAdb, mitotRNAdb, piRNAdb, and rRNA from the UCSC Browser track annotations. Alignments were split based on length (over/under 50bp) and counted using samtools idxstats.
Genome_build: Custom
Supplementary_files_format_and_content: Tab-delimited text files contain read counts were each row is a small RNA feature, the first colum is the feature name, and the second column is the read count

source_name: HeLaS3FlpIn cell line

growth_protocol: RPMI+10%FBS+PSQ in Spinner Flasks at 75 rpm

extract_protocol:
Qiagen RNeasy MinElute Cleanup Kit
TGIRT-seq

tag: flag status


title: WCE_Rpc2_WT


title: WCE_Rpc2_sen1


title: HeLaS3FlpIn_Control_Rep2

description: RNA from FLAG eluates


title: WCE_Rpc1_WT


title: GYY_1

value: GYY


title: GYY_4


title: K_1

description: control


title: GYY_3


title: IP_Sen1

value: Pan Mouse IgG Dynabeads (Life Technologies, 11041)


title: IP_Rpc2_sen1


title: IP_Rpc1_sen1


title: IP_Rpc2_WT


title: GYY+LPS_1


title: HeLaS3FlpIn_BCDIN3Df_Rep1

description: RNA from FLAG eluates


title: IP_Rpc1_WT


title: HCC1806_500nM_JQ1_10uM_GSK2801_72hr

first: Bradley

middle: E

last: Bernstein

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR 2.4..2a
reads were translated to transcriptome coordinates using Salmon 0.60
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R
Genome_build: hg38
Supplementary_files_format_and_content: Processed files (.xlsx) contain normalized transcript abundance estimates, organized by official gene symbol.

source_name: HCC1806 breast carcinoma cell line

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
4 µg total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

value: 500nM JQ1 and 10uM GSK2801 72hr

tag: culture media

value: RPMI 1640 supplemented with 10% FBS

tag: library preparation kit

value: Illumina TruSeq RNA library kit v2


title: HCC1806_10uM_GSK2801_72hr

tag: cell line

tag: treatment


title: GYY_2


title: HCC1806_500nM_JQ1_72hr

value: 500nM JQ1 72hr


title: HeLaS3FlpIn_Control_Rep1

description: RNA from FLAG eluates


title: SmoM2 mutant, Rep#2

city: Worcester

first: Julie

last: Zhu

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA method in Affy package from Bioconductor was used to summarize the probe level data and normalize the dataset to remove across array variation.

label: biotin

source_name: embryonic stomach

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

tag: developmental stage

value: E13.5 embryo

tag: tissue

value: stomach

tag: genotype


title: MDAMB231_100nM_JQ1_10uM_GSK2801_72hr

source_name: MDAMB231 breast carcinoma cell line

value: 100nM JQ1 and 10uM GSK2801 72hr

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone


title: MDAMB231_DMSO_72hr

value: DMSO 72hr


title: SUM159_10uM_GSK2801_72hr

source_name: SUM159 breast carcinoma cell line


title: SUM159_300nM_JQ1_72hr

value: 300nM JQ1 72hr


title: SmoM2 mutant, Rep#1


title: SUM159_DMSO_72hr


title: Wild type, Rep#1

value: wild type


title: Wild type, Rep#3


title: HCC1806_DMSO_72hr


title: MDAMB231_BRD9_100nMJQ1_48h

description: MDAMB231_BRD9_drug_treatment_peakclassification.xlsx

data_processing:
Reads were aligned to hg19 or to a single copy of the ribosomal DNA repeat (GenBank: U13369.1) using Bowtie v1.1.2 with parameters -v 2 -m 1.
Genome_build: hg19
Supplementary_files_format_and_content: The following processing steps were performed to generate peakclassification files:  Calculating read density: The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads (rpm).  The read density of the input chromatin was subtracted from the ChIP read density for normalization.  Peak calling: We used a combination of two algorithms, MACS v1.4.2 and HMCan v1.21, to define enriched regions.  We used HMCan to call peaks in regions of high CNV, defined as regions of size > 50 kb where no MACS peaks are called, and have read coverage that is >3 times the average read coverage.   Peaks within 12.5 kb of each other were stitched as described in Loven et al. 2013 Cell 153.  We used default settings for MACS, and HMCan was run with narrow peak calling configuration file with no blacklisted regions.  Peak genic classification:  A peak region was classified on the basis of its location with respect to GRCh37/hg19 gene annotations.  If the region was +/- 5 kb of any transcription start site, it was classified as a promoter peak.   If it was within -5kb to -200kb of any transcriptional start site, it was classified as a 5' enhancer peak.  If the peak overlapped the gene boundary, and was not classified as a promoter or enhancer peak, it was classified as either a genebody_exon or genebody_intron peak.  If the peak resided within 0 to +200kb from the 3'-most exon, and did not fulfill the criteria for the above classifications, it was classified as a 3' enhancer.   All remaining peaks were designated as "other".

extract_protocol:
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies.
All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone

value: KAPA Hyper Prep

value: BRD9 Bethyl Laboratories A303-781A


title: MDAMB231_BRD9_DMSO_48h

value: DMSO 48h rDNA


title: MDAMB231_BRD9_10uMGSK2801_48h


title: MDAMB231_10uM_GSK2801_72hr


title: MDAMB231_100nM_JQ1_72hr

value: 100nM JQ1 72hr


title: MDAMB231_input_DMSO_48h_rDNA

value: no antibody


title: MDAMB231_BRD9_100nMJQ1_10uMGSK2801_48h

value: 100nMJQ1 and 10uMGSK2801 48h


title: SUM159_300nM_JQ1_10uM_GSK2801_72hr

value: 300nM JQ1 and 10uM GSK2801 72hr


title: PPR-103f

city: Bethesda

first: Mario

middle: G

last: Oyola

state: MD

address: 4301 Jones Bridge Rd

institute: Uniformed Services University

data_processing:
Raw paired-end sequencing reads were aligned to the mouse reference genome (mm10) using MapSplice version 2.2.1.
Gene read counts against UCSC mouse gene models (obtained on February 21, 2016) were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s no
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: sample_gene_counts.txt – tab-delimited text file of gene raw counts for all samples
Supplementary_files_format_and_content: sample_gene_normalized_counts.txt – tab-delimited text file of gene normalized counts (DESeq2 size factor normalization) for all samples

extract_protocol:
Mice were euthanized via carbon dioxide inhalation and rapid decapitation during the nadir of the diurnal CORT cycle 18 hours following the end of the sleep deprivation period. To test the effect of overnight sleep deprivation on the neuroendocrine stress response, half of the subjects were restrained for 20 min in flat-bottom, Plexiglas rodent restrainers. Animals were euthanized ten min after the end of restraint. Whole pituitary glands were harvested. Trunk blood was centrifuged at 6,000g at 4C for 10 min, and serum was harvested in a fresh tube. All samples were stored at -80oC until use.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: female

tag: age

value: 8 weeks old

value: pituitary


title: PPR-103m

value: male


title: PPR-102f


title: PPR-102m


title: PPR-104f


title: SmoM2 mutant, Rep#3

value: E13.5 embryo

value: stomach


title: PPR-101m


title: Wild type, Rep#2


title: MDAMB231_BRD4_100nMJQ1_48h_rDNA

value: 100nMJQ1 48h rDNA

value: BRD4 Bethyl Laboratories A301-985A


title: MDAMB231_BRD4_10uMGSK2801_48h_rDNA

value: 10uMGSK2801 48h rDNA


title: PPN-103f


title: PPR-101f


title: MDAMB231_BRD4_100nMJQ1_10uMGSK2801_48h_rDNA

value: 100nMJQ1 and 10uMGSK2801 48h rDNA

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone


title: PPN-104f


title: PPN-103m


title: MDAMB231_BRD4_DMSO_48h_rDNA

value: KAPA Hyper Prep


title: PPN-102f


title: MDAMB231_BRD2_100nMJQ1_10uMGSK2801_48h_rDNA

value: BRD2 Bethyl Laboratories A302-583A


title: MDAMB231_BRD2_10uMGSK2801_48h_rDNA


title: MDAMB231_BRD2_DMSO_48h_rDNA

value: DMSO 48h rDNA


title: PPN-102m


title: PPN-101m


title: PPN-101f


title: HCC1806_BRD2_BAZ2B_500nMJQ1_48h

description: HCC1806_BRD2_BAZ_siRNA_and_JQ1_peakclassification.xlsx

value: BAZ2B and 500nMJQ1 48h

value: RPMI supplemented with 10% FBS


title: PHR-102f


title: PHR-102m


title: HCC1806_BRD2_NTsiRNA_500nMJQ1_48h

value: NTsiRNA and 500nMJQ1 48h


title: PHN-104m


title: PHR-103f

value: female


title: PHR-104f

value: 8 weeks old


title: PHR-101f

value: pituitary


title: MDA-MB-468 Cells TNFɑ+Apigenin Triplicate3

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description: Gene expression data from MDA-MB-468 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific), using  GeneChip Human Gene 2.1 ST Array cartridges.

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing:
The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific)
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

source_name: MDA-MB-468_TNFɑ 40 ng/ml + Apigenin 40 μM

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: MDA-MB-468 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 10% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: Cells were treated ± TNFɑ [40ng/mL] ± Apigenin [40uM] prepared in HBSS with a pH of 7.4 , both at sub-lethal concentrations.  For whole transcriptome microarray studies,  after a 24 hour treatment, cells were rapidly washed in HBSS 3x, spun and frozen at -80C.

value: MDA-MB-468 (ATCC® HTB-132™)

tag: cell type

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: TNFɑ 40 ng/ml + Apigenin 40 μM


title: MDA-MB-468 Cells Apigenin Triplicate2

source_name: MDA-MB-468_apigenin 40 μM

value: apigenin 40 μM


title: MDA-MB-468 Cells TNFɑ Triplicate3

source_name: MDA-MB-468_TNFɑ 40 ng/ml

value: TNFɑ 40 ng/ml


title: PHN-104f


title: HCC1806_BRD2_BAZ2BsiRNA_48h

value: BAZ2BsiRNA 48h


title: PHN-103m

value: male


title: MDA-MB-468 Cells Control  Triplicate2

source_name: MDA-MB-468_no treatment


title: MDA-MB-468 Cells TNFɑ Triplicate1


title: MDA-MB-468 Cells TNFɑ Triplicate2


title: MDA-MB-468 Cells TNFɑ+Apigenin Triplicate1


title: PHN-103f


title: MDA-MB-468 Cells Control  Triplicate1


title: HCC1806_BRD2_NTsiRNA_48h

value: NTsiRNA 48h


title: PHN-102f


title: SUM159_BRD2_100nMJQ1_10uMGSK2801_48h

description: SUM159_BRD2_drug_treatment_peakclassification.xlsx

value: 100nMJQ1 and 10uMGSK2801 48h

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone

value: KAPA Hyper Prep


title: PHN-101m


title: MDA-MB-468 Cells TNFɑ+Apigenin Triplicate2


title: PHN-102m


title: SUM159_BRD2_100nMJQ1_48h

value: BRD2 Bethyl Laboratories A302-583A


title: PHN-101f


title: MDA-MB-468 Cells Apigenin Triplicate1


title: MDA-MB-468 Cells Control  Triplicate3


title: SUM159_BRD2_10uMGSK2801_48h


title: ATAC_Seq_E14_5_Hindlimb

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

description: Genomic DNA after direct Tn5 transposition from forelimb tissue

data_processing:
mouse mm10 genome using bowtie2 v.2.1.0.
Peaks were called using MACS14 v.2.1 using the background genomic DNA as as pseudo input control
Genome_build: GRCm38, also known as mm10
Supplementary_files_format_and_content: bedgraph format

source_name: ATAC-Seq from hindlimb tissue, E14.5

extract_protocol:
ATAC-seq was performed on dissected C57BL/6NJ E14.5 forelimb and hindlimb.  Nuclei preparation and tagmentation were performed as previously described in Buenrostro et al., 2013, doi: 10.1038/nmeth.2688., with the following modifications.  To minimize endogenous protease activity, cells were strictly limited to 5 + 5 minutes of collagenase A treatment at 37 ºC, with frequent pipetting to aid dissociation into single-cell suspensions.
Following wash steps and cell lysis, 50 000 nuclei were tagmented with expressed Tn5 transposase.  Each tagmented sample was then purified by MinElute columns (Qiagen) and amplified with Q5 High-Fidelity DNA Polymerase (New England Biolabs) using a uniquely barcoded i7-index primer (N701-N7XX) and the N501 i5-index primer.  PCR thermocycler programs were 72ºC for 4 min, 98ºC for 30 s, 6 cycles of 98ºC for 10 s, 65ºC for 30 s, 72ºC for 1 min, and final extension at 72ºC for 4 min.  PCR-enriched samples were taken through a double size selection with PEG-based SPRI beads (Beckman Coulter) first with 0.5X ratio of PEG/beads to remove DNA fragments longer than 600 bp, followed by 1.8X PEG/beads ratio in order to select for Fraction A as described in Milani et al., 2016, doi: 10.1038/srep25474.

value: Hindlimb


title: SUM159_BRD2_DMSO_48h

value: DMSO 48h


title: 4C_Seq_Liver_Rep3_N2

description: Cross-linked, proximity-ligated DNA from live tissue, amplified from the specific genomic location called Nkx3-2 enhancer 2

data_processing:
Library strategy: 4C-seq
Sequence data were processed cleaned up using cutadapt v1.10;
Sequence reads were mapped to the reference mm10 genome using bwa v0.7.10-r789 as paired end reads using the mem module.
Base quality recalibration, duplication marking and insertion/deletion realignment was performed using GATK v3.4-0-gf196186 modules BQSR, MarkDuplicates, IndelRealignment;
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247) and those with MAPQ scores below 30 were excluded from analysis.  Filtered alignments were binned into genome-wide BglII fragments, normalized to Reads Per Kilobase of transcript per Million mapped reads (RPKM), and plotted and visualized in R.
Genome_build: GRCm38, also known as mm10
Supplementary_files_format_and_content: bedgraph format with each interval corresponding to a BglII fragment

source_name: 4C-Seq from liver tissue, replicate 3, viewpoint 2, Nkx3-2

extract_protocol:
Chromosome conformation capture (3C) template was prepared from pooled E14.5 liver, forelimb and hindlimb buds (n = 5–6 C57BL/6NJ embryos per replicate), with improvements to the primer extension and library amplification steps following Sexton et al., 2012 (doi: 10.1038/nprot.2012.071).  The template was amplified with Q5 High-Fidelity Polymerase (New England Biolabs GmbH, Frankfurt am Main, Germany) using a 4C adapter-specific primer and a pool of 6 Nkx3-2 enhancer viewpoint primers.
Amplified fragments were prepared for Illumina sequencing by ligation of TruSeq adapters, followed by PCR enrichment.

value: Liver


title: ATAC_Seq_E14_5_Forelimb

source_name: ATAC-Seq from forelimb tissue, E14.5

value: Forelimb


title: 4C_Seq_Liver_Rep1_N2

source_name: 4C-Seq from liver tissue, replicate 1, viewpoint 2, Nkx3-2


title: PCIA_BuCy_3

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

description: busulfan/cyclophosphamide

data_processing:
The sequenced paired-end reads were aligned to the human reference genome (hg38) and fragments per kilobase per million reads (FPKM) for each gene were calculated from aligned reads using RSEM-1.3.0.
Genome_build: hg38
Supplementary_files_format_and_content: The excel files include FPKM values and raw counts for each genes of each sample

source_name: Hair follicle stem cells

extract_protocol:
Using a PALM MicroBeam (Carl Zeiss), a focused laser beam catapulted identified the basal bulge epithelium. Total 300-500 HFSCs were collected for each replicate and stored at −80°C before RNA library preparation.
RNA-seq library was prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian, 634412, Takara Bio)

value: busulfan/cyclophosphamide

value: Hair follicle


title: 4C_Seq_Hindlimb_Rep3_N2

description: Cross-linked, proximity-ligated DNA from hindlimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 2

source_name: 4C-Seq from hindlimb tissue, replicate 1, viewpoint 2, Nkx3-2


title: MDAMB231_BRD2_BAZ2BsiRNA_100nMJQ1_48h

description: MDAMB231_BRD2_BAZ_siRNA_and_JQ1_peakclassification.xlsx

value: BAZ2BsiRNA and 100nMJQ1 48h


title: 4C_Seq_Hindlimb_Rep2_N2

source_name: 4C-Seq from hindlimb tissue, replicate 2, viewpoint 2, Nkx3-2


title: MDAMB231_BRD2_BAZ2AsiRNA_100nMJQ1_48h

value: BAZ2AsiRNA and 100nMJQ1 48h


title: PCIA_BuCy_2

description: busulfan/cyclophosphamide


title: MDAMB231_BRD2_NTsiRNA_100nMJQ1__48h

value: NTsiRNA and 100nMJQ1 48h


title: 4C_Seq_Forelimb_Rep3_N2

description: Cross-linked, proximity-ligated DNA from forelimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 2

source_name: 4C-Seq from forelimb tissue, replicate 3, viewpoint 2, Nkx3-2


title: 4C_Seq_Hindlimb_Rep1_N2


title: PHR-103m

value: 8 weeks old

value: pituitary


title: PCIA_Bu_3

description: busulfan

value: busulfan


title: PCIA_BuCy_1

description: busulfan/cyclophosphamide


title: MDAMB231_BRD2_BAZ2BsiRNA_48h

value: BAZ2BsiRNA 48h


title: 4C_Seq_Liver_Rep2_N3

description: Cross-linked, proximity-ligated DNA from live tissue, amplified from the specific genomic location called Nkx3-2 enhancer 1

source_name: 4C-Seq from liver tissue, replicate 2, viewpoint 3, Nkx3-2


title: 4C_Seq_Liver_Rep3_N3

source_name: 4C-Seq from liver tissue, replicate 3, viewpoint 3, Nkx3-2


title: 4C_Seq_Liver_Rep2_N2

source_name: 4C-Seq from liver tissue, replicate 2, viewpoint 2, Nkx3-2


title: 4C_Seq_Forelimb_Rep1_N2

source_name: 4C-Seq from forelimb tissue, replicate 1, viewpoint 2, Nkx3-2


title: 4C_Seq_Forelimb_Rep2_N2

source_name: 4C-Seq from forelimb tissue, replicate 2, viewpoint 2, Nkx3-2


title: 4C_Seq_Hindlimb_Rep3_N3

description: Cross-linked, proximity-ligated DNA from hindlimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 3

source_name: 4C-Seq from hindlimb tissue, replicate 1, viewpoint 3, Nkx3-2


title: MDAMB231_BRD2_NTsiRNA_48h

source_name: MDAMB231 breast carcinoma cell line

value: NTsiRNA 48h


title: MDAMB231_BRD2_BAZ2AsiRNA_48h

value: BAZ2AsiRNA 48h

value: DMEM/F12 1:1 supplemented with 5% FBS, 5 ug/ml insulin, 1 ug/ml hydrocortisone


title: PCIA_Bu_1

description: busulfan


title: PCIA_Bu_2

description: busulfan


title: 4C_Seq_Liver_Rep1_N3

source_name: 4C-Seq from liver tissue, replicate 1, viewpoint 3, Nkx3-2


title: MDAMB231_input_DMSO_48h

value: KAPA Hyper Prep

value: no antibody


title: 4C_Seq_Hindlimb_Rep1_N3

value: Hindlimb


title: PCIA_Con_3

description: no treatment

value: no treatment


title: 4C_Seq_Forelimb_Rep3_N3

description: Cross-linked, proximity-ligated DNA from forelimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 3

source_name: 4C-Seq from forelimb tissue, replicate 3, viewpoint 3, Nkx3-2

value: Forelimb


title: 4C_Seq_Hindlimb_Rep2_N3

source_name: 4C-Seq from hindlimb tissue, replicate 2, viewpoint 3, Nkx3-2


title: MDAMB231_BRD4_100nMJQ1_10uMGSK2801_48h

description: MDAMB231_BRD4_drug_treatment_peakclassification.xlsx

value: 100nMJQ1 and 10uMGSK2801 48h

value: BRD4 Bethyl Laboratories A301-985A


title: 4C_Seq_Forelimb_Rep2_N3

source_name: 4C-Seq from forelimb tissue, replicate 2, viewpoint 3, Nkx3-2


title: 4C_Seq_Liver_Rep3_N1

source_name: 4C-Seq from liver tissue, replicate 3, viewpoint 1, Nkx3-2

value: Liver


title: PCIA_Con_2

description: no treatment

value: Hair follicle


title: 4C_Seq_Forelimb_Rep1_N3

source_name: 4C-Seq from forelimb tissue, replicate 1, viewpoint 3, Nkx3-2


title: MDAMB231_BRD4_100nMJQ1_48h


title: PCIA_Con_1

description: no treatment

source_name: Hair follicle stem cells


title: 4C_Seq_Liver_Rep2_N1

source_name: 4C-Seq from liver tissue, replicate 2, viewpoint 1, Nkx3-2


title: MDAMB231_BRD4_10uMGSK2801_48h


title: 4C_Seq_Hindlimb_Rep3_N1

description: Cross-linked, proximity-ligated DNA from hindlimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 1

source_name: 4C-Seq from hindlimb tissue, replicate 1, viewpoint 1, Nkx3-2


title: 4C_Seq_Liver_Rep1_N1

source_name: 4C-Seq from liver tissue, replicate 1, viewpoint 1, Nkx3-2


title: 4C_Seq_Hindlimb_Rep2_N1

source_name: 4C-Seq from hindlimb tissue, replicate 2, viewpoint 1, Nkx3-2


title: MDAMB231_BRD4_DMSO_48h

value: DMSO 48h


title: 4C_Seq_Forelimb_Rep3_N1

description: Cross-linked, proximity-ligated DNA from forelimb tissue, amplified from the specific genomic location called Nkx3-2 enhancer 1

source_name: 4C-Seq from forelimb tissue, replicate 3, viewpoint 1, Nkx3-2


title: 4C_Seq_Forelimb_Rep2_N1

source_name: 4C-Seq from forelimb tissue, replicate 2, viewpoint 1, Nkx3-2


title: MDAMB231_BRD2_100nMJQ1_10uMGSK2801_48h

description: MDAMB231_BRD2_drug_treatment_peakclassification.xlsx

value: BRD2 Bethyl Laboratories A302-583A