title: Rep8_sc_none_allQ_40

description:
in vitro
plasmid DNA


title: Rep7_sc_Reb1_wt_40

status: Public on Feb 10 2020

type: SRA

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

country: Germany

institute: University Medical Center Göttingen

description:
in vitro
plasmid DNA

library_source: genomic

data_processing:
fastq files were aligned to the SacCer3 (R64), EF2 or E. coli strain B (REL606) genomes using Bowtie (Lengmead et al. 2009). Multiple matches were omited.
BAM files were imported into R Studio (RStudio Team, 2015) using GenomicAlignments (Lawrence et al. 2013). Then, reads were shifted by 73 bp to cover the nucleosome dyad and extended to 50 bp. Genome coverage was caluculated.
Coverage files were either aligned to in vivo +1 nucleosome positions, Reb1 SLIM-ChIP hits (Gutin et al. 2019) or Reb1 PWM hits (Badis et al. 2008), or BamHI cut sites. Signal was normalized per gene in a 2000 bp window around the alignment point.
Genome_build: SacCer3, EF2, Ecoli strain B - REL606
Supplementary_files_format_and_content: bw (big wig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: in vitro reconstituted chromatin

growth_protocol: Salt Gradient Dialysis: For low, medium and high assembly degrees, 10 µg of plasmid library DNA (pGP546, S. pombe or E. coli) was mixed with ~2, 4 or 8 µg of Drosophila embryo histones, respectively, in 100 µl assembly buffer (10 mM Tris-HCl, pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 0.2 µg BSA). Samples were transferred to Slide-A-lyzer mini dialysis devices, which were placed in a 3 L beaker containing 300 ml of high salt buffer (10 mM Tris-HCl pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 14.3 mM β-mercaptoethanol), and dialyzed against a total of 3 L low salt buffer (10 mM Tris-HCl pH 7.6, 50 mM NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 1.4 mM β-mercaptoethanol) added continuously via a peristaltic pump over a time course of 16 h under stirring conditions. β-mercaptoethanol was added freshly to all buffers. After complete transfer of low salt buffer, samples were additionally dialyzed against 1 L low salt buffer for 1 h at room temperature. DNA concentration of the SGD chromatin preparations was estimated with a DS-11+ spektrophotometer (Denovix) and if necessary stored at 4 °C for several weeks. To estimate the extend of the assembly degree, an aliquot of the sample was subjected to MNase digestion (as described below) for MNase-ladder read out.

extract_protocol:
Remodeling was started by adding 10 µl SGD chromatin and terminated by adding 0.8 U apyrase followed by incubation at 30 °C for 30 minutes.
For library preparation, approximately 10 - 50 ng of mononucleosomal DNA was incubated with 1.25 U Taq polymerase (NEB), 3.75 U T4 DNA polymerase (NEB) and 12.5 U T4-PNK (NEB) in 1x ligation buffer (B0202S, NEB) for 15 minutes at 12 °C, 15 minutes at 37 °C and 20 minutes at 72 °C. To ligate NEBNext Adaptors (0.75 µM final concentration, from NEBNext Multiplex Oligos Kit) to the DNA, samples were incubated with T4 DNA ligase (NEB) at 25 °C  for 15 minutes, followed by incubation with 2 U USER enzyme (NEB) for 10 minutes at 37°C. Fragments were purified using 2 volumes AMPure XP beads (Beckman Coulter) and amplified for 8-10 cycles using NEBNext Multiplex Oligos, Phusion High-Fidelity DNA Polymerase (1 U, NEB), deoxynucleotide solution mix (dNTP, 2.5 mM, NEB) and Phusion HF Buffer (1x, NEB). The following protocol was applied for amplification: 98 °C for 30 s, 98°C for 10s, 65 °C for 30s, 72 °C for 30s with a final amplification step at 72 °C for 5 minutes. The Qubit dsDNA HS Assay Kit (Invitrogen) was used to assess the DNA content of 1 µL PCR reaction. DNA was purified from agarose gels via PureLink Quick Gel Extraction Kit, measured again with Qubit dsDNA HS Assay Kit and diluted to final concentration of 10 nM (calculation based on the assumption that the DNA fragment length is 272 bp, i. e., 147 bp nucleosomal DNA and 122 bp sequencing adaptor). Diluted samples were pooled according to sequencing reads (~6 Mio reads/ sample). The final pool was quantified by BioAnalyzer (Agilent) and analyzed on an Illumina HiSeq 1500 in the 50 bp single-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

treatment_protocol: Genome-wide remodeling reaction: All remodeling reactions, except Chd1-containing reactions, were performed at 30 °C in 100 µL with final buffer conditions of 26.6 mM HEPES-NaOH pH 7.5, 1 mM Tris-HCl pH 7.6, 85.5 mM NaCl, 8 mM KCl, 10 mM ammonium sulfate, 10 mM creatine phosphate (Sigma), 3mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µL creatine kinase (Roche Applied Science). Chd1-containing reactions were performed in 26.6 mM HEPES-NaOH pH 7.5, 1 mM Tris-HCl pH 7.6, 50 mM NaCl, 10 mM creatine phosphate (Sigma), 3 mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µL creatine kinase. Usually, 10 nM of remodeling enzyme (50 nM Chd1/FACT), 40 nM Reb1 and 20 U of BamHI was added. Before full-length Chd1 (in high-salt buffer) was added to the reaction, it was diluted together with FACT to low salt buffer. For that, full-length Chd1 and purified FACT was mixed in a 1.2:1 ratio in high salt buffer (300 mM NaCl, 20 mM Na·HEPES pH 7.4, 10% (v/v) glycerol, 1 mM DTT), incubated for 5 minutes on ice and then diluted to 30 mM NaCl final concentration.

tag: remodeler

value: wt

tag: barrier

tag: histone-dna ratio


title: CD31+.d0.Muscle#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description: Uninjured

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

organism: Mus musculus

source_name: Hindlimb skeletal muscle

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cell sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

tag: strain

tag: tissue

value: Hindlimb skeletal muscle

tag: age

value: 8 weeks


title: FAPSLN3

source_name: Inguinal, axillary, brachial and cervical lymph nodes


title: FAPSLN2

value: Inguinal, axillary, brachial and cervical lymph nodes


title: FAPSLN1


title: CD31+.inj.d1.Muscle#2

description: Day 1 post-cardiotoxin injury


title: Muscle#2a


title: Muscle#3


title: Rep7_sc_none_none_80

description:
in vitro
plasmid DNA


title: Rep7_sc_Reb1_wt_80

description:
in vitro
plasmid DNA


title: Rep7_sc_none_none_40

description:
in vitro
plasmid DNA


title: mSC.muscle.PBS.8h#3

description: PBS 8 hours


title: Rep7_sc_none_HQ2_80

description:
in vitro
plasmid DNA


title: mSC.muscle.PBS.8h#2

description: PBS 8 hours


title: Rep7_sc_Reb1_ct_40_refill

description:
in vitro
plasmid DNA

value: ct


title: mSC.muscle.PBS.8h#4

description: PBS 8 hours


title: mSC.muscle.PBS.8h#1

description: PBS 8 hours


title: Rep7_sc_none_HQ1_80

description:
in vitro
plasmid DNA


title: mSC.muscle.PBS.4h#4

description: PBS 4 hours


title: mSC.muscle.PBS.4h#3

description: PBS 4 hours


title: mSC.muscle.PBS.4h#2

description: PBS 4 hours


title: Rep7_sc_none_wt_80

description:
in vitro
plasmid DNA


title: Rep7_sc_none_ct_80_refill

description:
in vitro
plasmid DNA


title: Rep7_sc_none_ct_80

description:
in vitro
plasmid DNA


title: mSC.muscle.PBS.4h#1

description: PBS 4 hours


title: Rep7_sc_none_ct_40

description:
in vitro
plasmid DNA


title: Rep7_sc_Reb1_ct_40

description:
in vitro
plasmid DNA


title: Rep7_sc_Reb1_ct_80_refill

description:
in vitro
plasmid DNA


title: Rep7_sc_Reb1_ct_80

description:
in vitro
plasmid DNA


title: Rep7_sc_none_wt_40

description:
in vitro
plasmid DNA


title: Rep7_sc_none_allQ_80

description:
in vitro
plasmid DNA

value: allQ


title: mSC.muscle.CGRP.8h#1

description: CGRP 8 hours


title: mSC.muscle.CGRP.8h#4

description: CGRP 8 hours


title: Rep7_sc_BamHI_wt_80

description:
in vitro
plasmid DNA

value: BamHI


title: mSC.muscle.CGRP.8h#2

description: CGRP 8 hours


title: mSC.muscle.CGRP.4h#4

description: CGRP 4 hours


title: Rep7_sc_BamHI_HQ2_80

description:
in vitro
plasmid DNA


title: mSC.muscle.CGRP.4h#3

description: CGRP 4 hours


title: Rep7_sc_BamHI_HQ2_40

description:
in vitro
plasmid DNA


title: Rep7_sc_BamHI_ct_80_refill

description:
in vitro
plasmid DNA


title: Chromatin Input - sequenced with Pan RNA Pol sample - Ter119+, APH treated Mouse spleen

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Chromatin input for Pol2 ChIP-seq

data_processing:
All analysis was done using NGseqBasic pipeline, using default parameters   ( http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/ )  Including the following steps :
mapping : bowtie -m 2 --maxIns 350
for un-mapping reads : trim_galore -- length 10, flash -m 9 -x 0.125
combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
removing read pairs overlapping Duke Blacklisted regions
removing duplicates : samtools rmdup
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of Reconstructed sequenced fragments

source_name: Ter119+ splenic erythrocytes

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using MACS LS columns (Miltenyi Biotec). 10 million cells aliquots were prepared and resuspended in 10ml of RPMI growth media with FBS (10%) at room temperature. Cells were fixed by the addition of formaldehyde to a final concentration of 1% and quenced using glycine (0.125M) for 5 minutes. Cells were pelleted (300g, 5 mins, 4°C), washed 1x in ice cold 1x PBS and then stored at -80°C until required.
All stages were performed at 4°C on aliquots of 10 million cells, all buffers had protease inhibitors (Roche, 11 873 580 001) added to a final concentration of 1x; A cell pellet was resuspended in 200ul cell lysis buffer (PIPES pH 8.0 5mM,KCl 85mM, IGEPAL-CA 630 0.5%) and incubated on ice for 20 mins. Sample was spun at 900g for 10 mins and supernatant removed. Pellet was resuspended in nuclei lysis buffer (Tris-HCl (pH 7.5) 50mM, EDTA (pH 8.0) 10mM, SDS 1%) and incubated on ice for 5 mins. 30ul of buffer A (-SDS) (Tris-HCl pH 7.5 10mM, EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM, Triton X-100 1%, Na Deoxycholate 0.1%, NaCl 140mM) was used to the sample and mixed. The total sample (130ul) was transferrred to a clean Covaris microTUBE snap cap AFA fiber and sample was sonicated using a covaris S220 machine using an 8 minute program based on the manufatuters truChIP™ Chromatin Shearing guidelines. Sonicate was transferred to a clean 1.5ml safe lock eppendorf and spun @ 20,000g for 20mins, 4°C to pellet insoluable material. Supernatant was transferred to a clean tube and and diluted to 1.1ml using buffer A. 100ul of the diluted sonicated chromatin was taken and 50 buffer A added before freezing. The remaining chromatin was precleared for 2x 30mins on a rotating platform using 5ul of a 50:50 Protein A and Protein G dynabead slurry and 1ul of the sc899c antibody was separately conjugated to 100ul of dynabead slurry for 1hr. The precleared sonicate and antibody conjugated bead slurry were combined and left on the rotating platform for 24 hours @ 4°C. The immunoprecipitate was cleared using a magnet and supernatant discarded. Beads were washed using 500ul of the following buffers in the following order; 2x buffer A + SDS (Tris-HCl pH 7.5 10mM, EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM, Triton X-100 1%, Na Deoxycholate 0.1%, NaCl 140mM, SDS 0.1%), 2 x high salt RIPA buffer (Tris-HCl pH 7.5 10mM, EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM, Triton X-100 1%, Na Deoxycholate 0.1%, NaCl 500mM, SDS 0.1%),  1x LiCL RIPA buffer (Tris-HCl pH 7.5 10mM, EDTA pH 8.0 1mM, EGTA pH 8.0 0.5mM, Triton X-100 1%, Na Deoxycholate 0.1%, LiCl 250mM, SDS 0.1%) and 1x with 1x T.E (Tris-HCl pH 8.0 2mM, EDTA (pH 8.0) 0.5mM). One final wash in 1 x T.E was performed wihtout protease inhibitors. Beads were resuspended in 150ul elution buffer (Tris-HCl 20mM, EDTA (pH 8.0) 5mM, NaCl 50mM. Input sample was thawed and 20mg RNAse A added (Invitrogen) before mixing and incubating at 37°C on a shaking thermomixer 1000 RPM). 20mg Proteinase K was then added and temperature increased to 65°C and incubation continued overnight. Beads were magnetically separated and the supernantant subjected to phenol chloroform extraction followed by ethanol precipitation to yield 55ul of immunoprecipitate DNA for library prep. For input samples 5ng of DNA was used as an input for library prep.
NEBNext Ultra DNA Library Prep Kit for Illumina was used to prepare libraries which were sequenced on a NextSeq550 (both procedures following manufacturers instructions)

treatment_protocol: C57BL/6 mice were treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days)

tag: treatment

value: Phenylhydrazine

value: spleen

tag: cell type

value: primary erythroid ter119+ cell

tag: chip antibody


title: Rep7_sc_BamHI_HQ1_40

description:
in vitro
plasmid DNA


title: mSC.muscle.CGRP.4h#1

description: CGRP 4 hours


title: Rep7_sc_BamHI_HQ1_80

description:
in vitro
plasmid DNA


title: Chromatin Input 2 - biological replicate of Chromatin Input above - Ter119+, APH treated Mouse spleen

description: Chromatin input


title: Rep7_sc_BamHI_ct_40

description:
in vitro
plasmid DNA


title: ChIP-seq - Pan RNA Pol2 - Ter119+, APH treated Mouse spleen

description: Pol2 ChIP-seq

value: Pol II Antibody (N20 clone), Santa Cruz Biotechnology sc899c, lot #H3115


title: Rep7_sc_BamHI_allQ_80

description:
in vitro
plasmid DNA


title: Rep6_sc_Reb1-BamHI_Fun30_40

description:
in vitro
plasmid DNA


title: mSC.muscle.CGRP.8h#3

description: CGRP 8 hours


title: Rep7_sc_BamHI_allQ_40

description:
in vitro
plasmid DNA


title: Rep7_sc_BamHI_wt_40

description:
in vitro
plasmid DNA


title: Rep6_sc_none_none_40

description:
in vitro
plasmid DNA


title: Rep6_sc_none_Fun30_40

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_none_80

description:
in vitro
plasmid DNA


title: mSC.muscle.CGRP.4h#2

description: CGRP 4 hours


title: Rep5_sc_Reb1-BamHI_none_40

description:
in vitro
plasmid DNA


title: Rep7_sc_BamHI_ct_80

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_none_20

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_ISW2_40

description:
in vitro
plasmid DNA


title: Muscle#2b


title: lncRNA profile of 841N

type: RNA

city: Guangzhou

first: Nuoqing

last: Weng

state: Guangdong

address: 651，Dongfengdong road

country: China

institute: State Key Laboratory of Oncology in South China,Sun Yat-sen University

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels,EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.

organism: Homo sapiens

label_protocol: 2.0 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

value: paired non-cancer specimens


title: Rep5_sc_Reb1-BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_ISW1a_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 850N


title: lncRNA profile of 829N


title: lncRNA profile of 834N


title: lncRNA profile of 831N


title: lncRNA profile of 849N


title: lncRNA profile of 852N


title: Rep5_sc_Reb1-BamHI_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_INO80_80_refill

description:
in vitro
plasmid DNA


title: lncRNA profile of 827N


title: Rep5_sc_Reb1-BamHI_ISW1a_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 826N


title: lncRNA profile of 824N


title: lncRNA profile of 825N


title: lncRNA profile of 817N


title: Rep5_sc_Reb1-BamHI_INO80_80

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 812N


title: Rep5_sc_Reb1-BamHI_ISW2_80_refill

description:
in vitro
plasmid DNA


title: lncRNA profile of 811N


title: Rep5_sc_Reb1-BamHI_ISW1a_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_INO80_20

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_Fun30_80

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_Fun30_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 821N


title: Rep5_sc_Reb1-BamHI_Chd1_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_Chd1_80

description:
in vitro
plasmid DNA


title: Rep5_sc_Reb1-BamHI_Chd1_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 794N


title: lncRNA profile of 807N


title: Rep5_sc_none_ISW2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 788N


title: lncRNA profile of 781N


title: Rep5_sc_none_none_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 787N


title: lncRNA profile of 786N


title: Rep5_sc_Reb1-BamHI_Chd1_20

description:
in vitro
plasmid DNA


title: Rep5_sc_none_none_20

description:
in vitro
plasmid DNA


title: Rep5_sc_none_none_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 791N


title: lncRNA profile of 810N


title: Rep5_sc_none_ISW2_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 777N


title: Rep5_sc_none_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_sc_none_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep5_sc_none_ISW1a_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 772N


title: lncRNA profile of 774N


title: lncRNA profile of 759N


title: lncRNA profile of 768N


title: lncRNA profile of 767N


title: Rep5_sc_none_INO80_80

description:
in vitro
plasmid DNA


title: Rep5_sc_none_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 741N


title: lncRNA profile of 745N


title: Rep5_sc_none_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 750N


title: Rep5_sc_none_Fun30_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 742N


title: lncRNA profile of 778N


title: lncRNA profile of 740N


title: Rep5_sc_none_Fun30_40

description:
in vitro
plasmid DNA


title: Rep5_sc_none_Chd1_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sc_none_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 736N


title: Rep5_sc_none_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_sc_none_Chd1_40

description:
in vitro
plasmid DNA


title: Rep5_sc_none_Chd1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 717N


title: lncRNA profile of 731N


title: lncRNA profile of 723N


title: lncRNA profile of 712N


title: Rep4_sc_Reb1_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_ISW1a_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 709N


title: Rep4_sc_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_Chd1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 697N


title: Rep4_sc_none_none_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 722N


title: Rep4_sc_none_none_20

description:
in vitro
plasmid DNA


title: Rep4_sc_Reb1_ISW2_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 690N


title: lncRNA profile of 693N


title: lncRNA profile of 684N


title: lncRNA profile of 681N


title: Rep4_sc_Reb1_ISW1a_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 685N


title: lncRNA profile of 683N


title: lncRNA profile of 678N


title: Rep4_sc_none_ISW1a_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 672N


title: lncRNA profile of 670N


title: lncRNA profile of 641N


title: lncRNA profile of 635N


title: lncRNA profile of 675N


title: lncRNA profile of 703N


title: Rep4_sc_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: Rep4_sc_none_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep4_sc_none_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 633N


title: Rep4_sc_none_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 627N


title: Rep4_sc_BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 623N


title: Rep4_sc_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep4_sc_none_ISW2_20

description:
in vitro
plasmid DNA


title: Rep4_sc_BamHI_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 602N


title: Rep4_sc_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 618N


title: Rep3_sc_Reb1_ISW2_40

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_ISW2_20

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_ISW1a_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 560N


title: lncRNA profile of 590N


title: lncRNA profile of 579N


title: lncRNA profile of 584N


title: Rep3_sc_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 596N


title: lncRNA profile of 599N


title: Rep3_sc_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 555N


title: lncRNA profile of 551N


title: Rep3_sc_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 550N


title: lncRNA profile of 542N


title: Rep3_sc_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_ISW2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 532N


title: lncRNA profile of 540N


title: Rep3_sc_none_none_40

description:
in vitro
plasmid DNA


title: Rep3_sc_Reb1_Chd1_20

description:
in vitro
plasmid DNA


title: Rep3_sc_none_none_80

description:
in vitro
plasmid DNA


title: Rep3_sc_none_none_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 505N


title: lncRNA profile of 528N


title: lncRNA profile of 501N


title: lncRNA profile of 497N


title: Rep3_sc_none_INO80_80

description:
in vitro
plasmid DNA


title: Rep3_sc_none_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_sc_none_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_sc_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_sc_none_Chd1_40

description:
in vitro
plasmid DNA


title: Rep3_sc_none_Chd1_20

description:
in vitro
plasmid DNA


title: Rep3_sc_BamHI_none_40

description:
in vitro
plasmid DNA


title: Rep3_sc_BamHI_ISW2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 484N


title: lncRNA profile of 493N


title: lncRNA profile of 850T

value: esophageal squamous cell carcinoma


title: lncRNA profile of 492N


title: lncRNA profile of 539N


title: Rep3_sc_BamHI_ISW2_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 841T


title: lncRNA profile of 845T


title: Rep3_sc_BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: Rep3_sc_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 852T


title: lncRNA profile of 835T


title: Rep3_sc_BamHI_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 834T


title: lncRNA profile of 849T


title: lncRNA profile of 832T


title: Rep3_sc_BamHI_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 833T


title: Rep2_sc_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: Rep2_sc_Reb1_ISW2_40

description:
in vitro
plasmid DNA


title: Rep3_sc_BamHI_Chd1_40

description:
in vitro
plasmid DNA


title: Rep2_sc_Reb1_ISW2_80

description:
in vitro
plasmid DNA


title: Rep2_sc_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: Rep2_sc_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep2_sc_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 826T


title: lncRNA profile of 827T


title: Rep2_sc_none_none_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 829T


title: lncRNA profile of 831T


title: lncRNA profile of 825T


title: Rep2_sc_none_none_40

description:
in vitro
plasmid DNA


title: Rep3_sc_BamHI_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 822T


title: Rep2_sc_none_ISW2_40

description:
in vitro
plasmid DNA


title: Rep2_sc_none_ISW2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 820T


title: lncRNA profile of 821T


title: Rep2_sc_none_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 818T


title: lncRNA profile of 813T


title: Rep2_sc_none_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 817T


title: Rep2_sc_BamHI_ISW2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 824T


title: Rep2_sc_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: Rep2_sc_BamHI_ISW2_40

description:
in vitro
plasmid DNA


title: Rep2_sc_BamHI_INO80_40

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_wt_90

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_wt_40

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_wt_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 807T


title: lncRNA profile of 810T


title: Rep10_sc_Reb1-BamHI_wt_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 794T


title: lncRNA profile of 811T


title: Rep10_sc_Reb1-BamHI_none_90

description:
in vitro
plasmid DNA


title: lncRNA profile of 796T


title: lncRNA profile of 808T


title: lncRNA profile of 791T


title: lncRNA profile of 812T


title: Rep10_sc_Reb1-BamHI_none_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_wt_100

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_none_100

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_none_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 788T


title: Rep10_sc_Reb1-BamHI_none_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 787T


title: lncRNA profile of 785T


title: lncRNA profile of 786T


title: lncRNA profile of 797T


title: lncRNA profile of 777T


title: Rep10_sc_Reb1-BamHI_HQ2_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 781T


title: lncRNA profile of 772T


title: Rep10_sc_Reb1-BamHI_HQ2_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 774T


title: Rep10_sc_Reb1-BamHI_HQ2_20

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HQ1_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HQ1_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 768T


title: Rep10_sc_Reb1-BamHI_HMGII-HQ2_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HMGII-HQ2_40

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HQ1_20

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HMGII-HQ2_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 767T


title: lncRNA profile of 778T


title: lncRNA profile of 757T


title: lncRNA profile of 759T


title: Rep10_sc_Reb1-BamHI_HMGII-HQ1_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 765T


title: Rep10_sc_Reb1-BamHI_HMGII-HQ1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 745T


title: lncRNA profile of 750T


title: lncRNA profile of 753T


title: lncRNA profile of 747T


title: lncRNA profile of 740T


title: Rep10_sc_Reb1-BamHI_HMGII_20

description:
in vitro
plasmid DNA

value: HMGII


title: Rep10_sc_Reb1-BamHI_DN-Ino80_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HMGII_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_HMGII_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 736T


title: lncRNA profile of 742T


title: lncRNA profile of 731T


title: lncRNA profile of 741T


title: lncRNA profile of 732T


title: Rep10_sc_Reb1-BamHI_HMGII-HQ1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 723T


title: Rep10_sc_Reb1-BamHI_DNhp10_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_DNhp10_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 725T


title: lncRNA profile of 722T


title: Rep10_sc_Reb1-BamHI_ct_80

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_ct_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 712T


title: lncRNA profile of 717T


title: lncRNA profile of 709T


title: METTL3_KD_60m_r2 [HEC-1-A]

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to human genome and transcriptome (hg38, version 29, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness R’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse; or version 29, 2018-08-30, in gtf format for human) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Read counts for each gene and each sample.

molecule: polyA RNA

growth_protocol: Cell were grown in McCoy’s 5A medium (Invitrogen) supplemented with 10% FBS (Gibco), and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Total RNA was purified by Trizol and nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen). Before constructing libraries ERCC RNA spike-in control (Ambion) was added to each sample (0.01 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: Eight 6-cm plates of HEC-1-A cells were seeded and controlled to afford the same amount of cells. After 48 h, 5-ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, 20 min and 10 min before trypsinization collection.

tag: genotype

tag: eu treatment time(min)

tag: eu treatment time (min)


title: Rep10_sc_Reb1-BamHI_DN-Ino80_40

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_ct_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 703T


title: Rep10_sc_Reb1-BamHI_ct_100

description:
in vitro
plasmid DNA


title: METTL3_KD_60m_r1 [HEC-1-A]


title: METTL3_KD_30m_r2 [HEC-1-A]


title: Rep10_sc_Reb1-BamHI_DN-Ino80_20

description:
in vitro
plasmid DNA


title: Rep10_sc_Reb1-BamHI_allQ_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 697T


title: Rep10_sc_Reb1-BamHI_allQ_20

description:
in vitro
plasmid DNA


title: Rep10_sc_none_wt_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_wt_40

description:
in vitro
plasmid DNA


title: METTL3_KD_30m_r1 [HEC-1-A]


title: Rep10_sc_Reb1-BamHI_DNhp10_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 687T


title: Rep10_sc_Reb1-BamHI_ct_90

description:
in vitro
plasmid DNA


title: lncRNA profile of 690T


title: Rep10_sc_none_wt_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 693T


title: Rep10_sc_none_none_90

description:
in vitro
plasmid DNA


title: METTL3_KD_20m_r2 [HEC-1-A]


title: Rep10_sc_none_none_40

description:
in vitro
plasmid DNA


title: Rep10_sc_none_none_20

description:
in vitro
plasmid DNA


title: METTL3_KD_20m_r1 [HEC-1-A]


title: Rep10_sc_Reb1-BamHI_allQ_40

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HQ2_40

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HQ2_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HQ2_20

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HQ1_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HQ1_40

description:
in vitro
plasmid DNA


title: METTL3_KD_10m_r2 [HEC-1-A]


title: Rep10_sc_none_HQ1_20

description:
in vitro
plasmid DNA


title: METTL3_Control_60m_r2 [HEC-1-A]

value: METTL3 Control


title: lncRNA profile of 683T


title: lncRNA profile of 684T


title: Rep10_sc_none_HMGII-HQ2_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HMGII-HQ2_40

description:
in vitro
plasmid DNA


title: METTL3_Control_60m_r1 [HEC-1-A]


title: METTL3_Control_30m_r2 [HEC-1-A]


title: lncRNA profile of 682T


title: lncRNA profile of 681T


title: Rep10_sc_none_HMGII-HQ1_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HMGII-HQ2_20

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HMGII-HQ1_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 685T


title: METTL3_Control_30m_r1 [HEC-1-A]


title: Rep10_sc_none_none_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HMGII-HQ1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 678T


title: lncRNA profile of 680T


title: lncRNA profile of 679T


title: METTL3_Control_20m_r2 [HEC-1-A]


title: Rep10_sc_none_HMGII_80

description:
in vitro
plasmid DNA


title: METTL3_KD_10m_r1 [HEC-1-A]


title: Rep10_sc_none_HMGII_40

description:
in vitro
plasmid DNA


title: METTL3_Control_20m_r1 [HEC-1-A]


title: Rep10_sc_none_DN-Ino80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 675T


title: Rep10_sc_none_DN-Ino80_20

description:
in vitro
plasmid DNA


title: METTL3_Control_10m_r2 [HEC-1-A]


title: lncRNA profile of 674T


title: Rep10_sc_none_DNhp10_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 672T


title: METTL3_Control_10m_r1 [HEC-1-A]


title: Rep10_sc_none_DNhp10_20

description:
in vitro
plasmid DNA


title: Rep10_sc_none_ct_40

description:
in vitro
plasmid DNA


title: METTL3_KD_H3K27ac_r2 [HEC-1-A]

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, and then uniquely mapped to  human genome (hg38, version 29, 2018-08-30) and Drosophila melanogaster chromatin (Spike-in Chromatin) using bowtie (version 1.2.2) allowing one mismatch.
Peaks were called using HOMER with '-size 1000 -minDist 1000 -L 0 -F 2' parameters
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited peak locations reported by HOMER for each sample.

extract_protocol:
Chromatin immunoprecipitation was performed using Auto iDeal ChIP-seq kit for Histone (diagenode) with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.

treatment_protocol: HEC-1-A cells were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 10 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS.

tag: chip-seq

value: rabbit anti-H3K27ac (ab4729, Abcam)


title: lncRNA profile of 665T


title: Rep10_sc_none_ct_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 661T


title: lncRNA profile of 670T


title: Rep10_sc_none_allQ_80

description:
in vitro
plasmid DNA


title: METTL3_KD_H3K27ac_r1 [HEC-1-A]


title: METTL3_Control_H3K27ac_r2 [HEC-1-A]


title: Rep10_sc_none_allQ_40

description:
in vitro
plasmid DNA


title: METTL3_Control_H3K27ac_r1 [HEC-1-A]


title: Rep10_sc_none_allQ_20

description:
in vitro
plasmid DNA


title: Rep10_sc_none_HMGII_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 660T


title: Rep1_sc_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 657T


title: Rep1_sc_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: Rep1_sc_none_none_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_DNhp10_80

description:
in vitro
plasmid DNA


title: Rep10_sc_none_DN-Ino80_40

description:
in vitro
plasmid DNA


title: Rep1_sc_none_none_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 655T


title: Rep1_sc_none_INO80_80

description:
in vitro
plasmid DNA


title: METTL3_KD_H3K4me3_r1 [HEC-1-A]

value: rabbit anti-H3K4me3 (ab8580, Abcam)


title: METTL3_Control_H3K4me3_r2 [HEC-1-A]


title: Rep1_sc_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep10_sc_none_ct_80

description:
in vitro
plasmid DNA


title: Rep1_sc_MNase_in vivo_BY4741

description:
in vivo
genomic DNA
BY4741 strain

source_name: in vivo MNase-seq

value: in vivo


title: METTL3_Control_H3K4me3_r1 [HEC-1-A]


title: LMH-ILTV-3

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads, remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Genome_build: The reference genome and annnotation is download form http://ftp.ensembl.org/pub/release-73/fasta/gallus_gallus/dna/.
Supplementary_files_format_and_content: text file with FPKM

organism: Gallus gallus

source_name: LMH

growth_protocol: DF-1 cells and LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Separated single-cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DF-1 cells and LMH cells were infected with ILTV at MOI 1

value: Chick embryo liver

tag: cell line

value: LMH

tag: infected with

value: ILTV


title: LMH-ILTV-2


title: METTL3_KD_Input_r2 [HEC-1-A]


title: LMH-ILTV-1


title: lncRNA profile of 641T


title: lncRNA profile of 649T


title: LMH-ILTV-4


title: lncRNA profile of 639T


title: METTL3_KD_H3K4me3_r2 [HEC-1-A]


title: METTL3_KD_Input_r1 [HEC-1-A]


title: LMH-Control-3

value: not infected


title: LMH-Control-4


title: METTL3_Control_Input_r2 [HEC-1-A]


title: LMH-Control-2


title: LMH-Control-1


title: METTL3_Control_Input_r1 [HEC-1-A]


title: lncRNA profile of 635T


title: DF1-ILTV-4

value: Chick embryo fibroblast


title: lncRNA profile of 633T


title: lncRNA profile of 631T


title: DF1-ILTV-3


title: 23postNegSel

city: La Jolla

first: Emanuela

middle: Maria

last: Ghia

state: CA

address: 9310 Athena Circle

department: Center For Novel Therapeutics

institute: University of California San Diego

data_processing:
Data were analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build hg19 using STAR
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. DEseq2 was also used to calculate fold changes and p-values.
Genome_build: Homo sapiens genome build hg19
Supplementary_files_format_and_content: tab-delimited text file including normalized values for each sample

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) of 3 CLL samples were collected at day 0 (Pre) and at day 28 of cirmtuzumab treatment (Post). Negative  isolation of CLL cells to ≥95% purity was performed prior to RNA isolation. RNA was harvested using Trizol reagent.
TruSeq Stranded mRNA library prep kit high throughput

value: Peripheral Blood Mononuclear Cells

value: cirmtuzumab

tag: time

value: Post (day 28)


title: DF1-ILTV-2


title: DF1-Control-4


title: lncRNA profile of 654T


title: 22postNegSel


title: DF1-Control-2


title: 21postNegSel


title: lncRNA profile of 627T


title: DF1-Control-1


title: lncRNA profile of 628T


title: Rep5_sp_Reb1-BamHI_none_80

description:
in vitro
plasmid DNA

organism: Schizosaccharomyces pombe


title: 23preNegSel

value: untreated

value: Pre


title: Rep5_sp_Reb1-BamHI_none_20

description:
in vitro
plasmid DNA


title: 22preNegSel


title: lncRNA profile of 623T


title: Rep5_sp_Reb1-BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_sp_Reb1-BamHI_ISW2_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sp_Reb1-BamHI_ISW2_40

description:
in vitro
plasmid DNA


title: DF1-ILTV-1


title: Rep5_sp_Reb1-BamHI_ISW1a_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sp_Reb1-BamHI_none_40

description:
in vitro
plasmid DNA


title: DF1-Control-3


title: Rep5_sp_Reb1-BamHI_ISW1a_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 618T


title: Rep5_sp_Reb1-BamHI_INO80_80_refill

description:
in vitro
plasmid DNA


title: KO3

city: Oslo

first: Xiang Yi

last: Kong

address: Sognsvannsveien 20

country: Norway

institute: Oslo University Hospital

data_processing:
Contaminated adapter and low quality reads were trimmed with Trim Galore (v0.4.1).
Reads were mapped to the mm9 genome assembly using TopHat2 (v2.1.0).
Partek® Genomics Suite® software, version 6.6 Copyright ©;  2018 (Partek Inc., St. Louis, MO, USA) was used to align the reads to the transcriptome  (RefSeq transcript: 01.11.2016) and perform differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM for each file presented as bigwig-files

source_name: Liver

extract_protocol:
Livers were powderized and RNA extracted according to manufacturer's protocol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: EndoV knockout

tag: background strain

value: 12 months


title: KO2


title: KO1


title: Rep5_sp_Reb1-BamHI_INO80_80

description:
in vitro
plasmid DNA

tag: remodeler


title: lncRNA profile of 615T

value: esophageal squamous cell carcinoma


title: Rep5_sp_Reb1-BamHI_INO80_40

description:
in vitro
plasmid DNA

tag: barrier


title: WT3

value: Wildtype


title: 21preNegSel


title: lncRNA profile of 611T


title: lncRNA profile of 619T


title: Rep5_sp_Reb1-BamHI_INO80_20

description:
in vitro
plasmid DNA

tag: histone-dna ratio


title: Rep5_sp_Reb1-BamHI_Chd1_80_refill

description:
in vitro
plasmid DNA


title: lncRNA profile of 602T


title: WT2


title: lncRNA profile of 607T


title: Rep5_sp_Reb1-BamHI_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 599T


title: Rep5_sp_Reb1-BamHI_Chd1_40

description:
in vitro
plasmid DNA


title: WT1


title: Rep5_sp_Reb1-BamHI_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_sp_Reb1-BamHI_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep5_sp_Reb1-BamHI_Chd1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 596T


title: lncRNA profile of 609T


title: Rep5_sp_none_none_40

description:
in vitro
plasmid DNA


title: 697+ H2 dox set4

city: Hershey

first: Irina

last: Elcheva

state: PA

address: 500 Univeristy Drive

department: Pediatrics

institute: PennState College of Medicine

description:
gene expression
Project name: G233

data_processing:
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used for library preparation, and 3’Fwd-mRNAseq was performed on an Illumina sequencer.
The compressed fastq files from RNA sequencing were preprocessed for quality control with FastQC, trimmed and filtered with bbmap.
The sequences were aligned with STAR software.
The SAM tools program was used for indexing the bam file. We then generated gene expression counts with HTSeq-count and detected differential gene expression with DESeq2 in the R program.
These software tools provided a list of differentially expressed genes, P-values, false discovery rate (FDR), q-value, and normalized expressions values.
Genome_build: hg38 (Ensembl GRCh38)
Supplementary_files_format_and_content: text file with Htseq read counts

source_name: ALDH+ subpopulation of  B-cell leukemia cell lines 697(EU3)

growth_protocol: Leukemia 697(EU3) cells were grown in RPMI 1640 (Corning, Pittston, PA) supplemented with 10% heat-inactivated (HI) FBS (Gibco, Gaithersburg, MD).

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD), followed by DNase I treatment with DNA-free DNA Removal Kit (Invitrogen, Carlsbad, CA).
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment closed to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The prfocessed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).

treatment_protocol: 697(EU3) cells were first stained with  ALDEFLUOR Kit (Stem Cell Technologies (green) or Sigma (red)) and ALDH+ cells were sorted. ALDH+ were transduced with the doxycycline-inducible shIGF2BP1(SH2) and scrambled shControl,obtained from GE Dharmacon (Lafayette, CO), with eGFP reporter active upon the doxycycline treatment. After Dox treatment, cells were sorted again for GFP+ cells that expressed SH2. Cells were then used for mice experiments, Ki67-PE staining and RNA isolation.

value: Doxycycline induced shRNA against IGF2BP1 that decreases its mRNA levels

value: B-cell leukemia

tag: cell population

value: ALDH+ subpopulation


title: lncRNA profile of 594T

tag: tissue


title: 697+ H2 NT set4

description:
gene expression
Project name: G233

value: Untreated shRNA SH2 IGF2BP1 control


title: Rep5_sp_none_none_20

description:
in vitro
plasmid DNA


title: Rep5_sp_none_ISW2_80

description:
in vitro
plasmid DNA


title: Rep5_sp_none_ISW2_40

description:
in vitro
plasmid DNA


title: 697+ dox set4

description:
gene expression
Project name: G233

value: Control for doxycycline treatment, cell were treated with dox


title: Rep5_sp_none_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_sp_none_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_sp_none_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep5_sp_none_INO80_80

description:
in vitro
plasmid DNA


title: 697+ H2 dox set3

description:
gene expression
Project name: G233


title: lncRNA profile of 593T


title: Rep5_sp_none_ISW1a_40

description:
in vitro
plasmid DNA


title: 697+ NT set4

description:
gene expression
Project name: G233

value: Control for doxycycline treatment, untreated


title: lncRNA profile of 590T


title: Rep5_sp_none_none_80

description:
in vitro
plasmid DNA


title: Rep5_sp_none_Chd1_80_refill

description:
in vitro
plasmid DNA


title: Rep5_sp_none_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 587T


title: Rep5_sp_none_INO80_40

description:
in vitro
plasmid DNA


title: 697+ H2 dox set2

description:
gene expression
Project name: G233


title: lncRNA profile of 585T


title: Rep5_sp_none_INO80_20

description:
in vitro
plasmid DNA


title: Rep5_sp_none_Chd1_40

description:
in vitro
plasmid DNA


title: 697+ H2 NT set2

description:
gene expression
Project name: G233


title: Rep5_sp_none_Chd1_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 584T


title: lncRNA profile of 582T


title: Rep4_sp_Reb1_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep4_sp_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: Rep4_sp_Reb1_ISW1a_80

description:
in vitro
plasmid DNA


title: 697+ NT set2

description:
gene expression
Project name: G233


title: lncRNA profile of 574T


title: lncRNA profile of 575T


title: Rep4_sp_none_none_80

description:
in vitro
plasmid DNA


title: 697+ H2 NT set3

description:
gene expression
Project name: G233


title: Rep4_sp_none_none_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 579T


title: Rep4_sp_none_ISW1a_40

description:
in vitro
plasmid DNA


title: 697+ H2 dox set1

description:
gene expression
Project name: G233


title: Rep4_sp_none_none_20

description:
in vitro
plasmid DNA


title: Rep4_sp_none_INO80_20

description:
in vitro
plasmid DNA


title: YS2

first: Chunsik

last: Lee

address: NO.7 Jinsui Rd.

institute: Sun Yat-Sen University

description: Experimental library 2 of two replicates

data_processing:
Standard Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, filtered for low-complexity or low-quality sequence, and then mapped to hg19 whole genome using Tophat2 and to reference genes using bowtie2
FPKM (fragments per kilobase of transcript per million mapped fragments) values were calculated using RSEM (v1.2.15).
Differentially expressed genes between control and UHRF1-knockdown cells were detected by EdgeR package for the genes represented by at least > 1 FPKM with ≥ 2-fold difference and a FDR threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text files showing gene names, transcript ids, row count/fpkm for all samples

source_name: Y79 retinoblastoma cell line

extract_protocol:
After lentiviral gene knockdown, total RNA from each sample was isolated using RNeasy Plus Mini kit (Qiagen, #74134), and processed for adapter ligation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Y79 retinoblastoma cell line (ATCC HTB18)

tag: shRNA clone


title: Rep4_sp_BamHI_ISW1a_80

description:
in vitro
plasmid DNA

value: BamHI


title: lncRNA profile of 573T


title: Rep4_sp_BamHI_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_sp_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: YS1

description: Experimental library 1 of two replicates


title: lncRNA profile of 568T


title: Rep3_sp_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: 697+ dox set2

description:
gene expression
Project name: G233

tag: treatment


title: Rep3_sp_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 572T


title: lncRNA profile of 570T


title: YT2

description: Control library 2 of two replicates

value: pLKO.1-TRC control


title: Rep3_sp_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: YT1

description: Control library 1 of two replicates


title: Rep3_sp_none_none_80

description:
in vitro
plasmid DNA


title: Rep3_sp_none_none_40

description:
in vitro
plasmid DNA


title: Rep3_sp_none_INO80_80

description:
in vitro
plasmid DNA


title: 697+ H2 NT set1

description:
gene expression
Project name: G233

tag: cell type


title: LACV infected cells

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
reads demultiplexed and bcl to fastq conversion using cellranger mkfastq v2.1.0
reads aligned and counted using cellranger count v2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes.tsv, Barcodes.tsv, and Matrix.mtx (set of 3 files)

source_name: cerebral organoids

growth_protocol: COs were generated using the protocol and media formulations described in Lancaster and Knoblich (18), with the following minor variations. Source tissue was KYOU-DXR0109B human induced pluripotent stem cells (iPSC; ATCC). Embryoid bodies (EBs) were generated using one 25 cm2 flask of cells to seed a 96-well low-adhesion U-well plate. EBs were transferred into neural induction medium between days 4 and 6 depending upon morphology. Organoids were Matrigel embedded on day 3 or 4 post neural induction.  Four days after embedding, organoids were transferred into agitated culture in upright 25 cm2 low-adhesion flasks on an orbital shaker (Heathrow Scientific) at 85 rpm.  Media was changed 2-3 times per week until 21 days post neural induction when COs were plated individually into low-adhesion 24 well plates for infection. Agitated culture was maintained, and media completely changed/collected daily.

extract_protocol:
Mock and infected COs were dissociated as described above with the exception washes and collection were done in 1X PBS with 1% bovine serum albumin. Cells were counted and diluted to 106/mL prior to loading onto the 10X Genomics Chromium Controller instrument to be individually partitioned into nanoliter scale droplets within an oil emulsion.
RNA sequencing libraries were constructed using the Chromium Single cell 3? Reagent kit V2 (10X Genomics PN-120237) and assayed using a Bioanalyzer 2100 (Agilent) according to the respective manufacturer?s instructions.

treatment_protocol: Virus for CO infection was diluted to either 10e3 or 10e1 plaque forming units (PFU) in 500ul of medium. Medium from wells containing COs was removed and replaced with virus-containing medium for 2hrs in the incubator while shaking. After infection, wells containing COs were washed and refilled with 1mL fresh medium.

value: cerebral organoids

tag: infection

value: La Crosse Virus infected


title: Rep3_sp_none_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 559T


title: lncRNA profile of 555T


title: Rep3_sp_none_INO80_20

description:
in vitro
plasmid DNA


title: lncRNA profile of 560T


title: Pith-S35

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

data_processing:
Araport11 gene annotation file was taken (Araport11_GFF3_genes_transposons.201606.gtf).
FASTQ files were mapped to the genome by STAR (v2.5.0a) using --outFilterMultimapNmax 1 --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterScoreMinOverLread 0.9 options.
Further analysis was carried out in R (v3.5.0). GTF file was imported using makeTxDbFromGRanges in GenomicFeatures library (v1.32.3) with drop.stop.codons option. Position of each gene was extracted by genes function, which also includes the intron region. Reads counts per gene were obtained using summarizeOverlaps in GenomicAlignments library (v1.16.0) with mode = "Union", ignore.strand = TRUE options. Only genes of Arabidopsis was kept in rawCounts table. bigWig files were generated by bamCoverage in deepTools from bam files.
Genome_build: Arabidopsis Tair 10
Supplementary_files_format_and_content: Csv files include raw counts values for each Sample. bigWig files are generated from bam files for coverage tracks.

organism: Arabidopsis thaliana

source_name: Inflorescence stem pith

growth_protocol: Arabidopsis were grown on soil for three weeks in short days (8h light 16h dark, constant 21°C) and then transfered to long days (16h light 8h dark) to stimulate flowering.

extract_protocol:
2nd internode of Arabidopsis inflorescence stem were collected in OCT embedding medium and were snap-frozen. LCM were carried out as previously described (Agusti et al., Plos Genetics, 2011). Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN). Two RNA amplification rounds were performed using the TargetAm 2-Round Aminoallyl-aRNA Amplification Kit (EPICENTRE Biotechnologies, Madison, USA).
The total RNA samples were first treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the RNA was fragmented into short fragments (about 200 bp). Then the first strand of cDNA was synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification and then sequenced using Illumina HiSeq 2000 technology by BGI Tech Solutions (Hong Kong) Co., Limited.

tag: strain

value: pith


title: Rep3_sp_none_Chd1_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 551T


title: Rep3_sp_none_Chd1_40

description:
in vitro
plasmid DNA


title: Mock infected cells

value: Mock infected


title: Rep3_sp_none_none_20

description:
in vitro
plasmid DNA


title: Rep3_sp_BamHI_none_40

description:
in vitro
plasmid DNA


title: Pith-S34


title: Pcap-S33

source_name: Inflorescence stem phloem cap

value: phloem cap


title: Rep3_sp_BamHI_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_sp_BamHI_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_sp_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 550T


title: Pcap-S32


title: Rep3_sp_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep2_sp_Reb1_ISW2_80

description:
in vitro
plasmid DNA


title: LCMCtl-S31

source_name: Inflorescence stem vascular bundle

value: vascular bundle without phloem cap


title: Rep2_sp_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: lncRNA profile of 546T

value: esophageal squamous cell carcinoma


title: lncRNA profile of 542T


title: Rep2_sp_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 539


title: LCMCtl-S30


title: lncRNA profile of 540T


title: Rep2_sp_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: Rep2_sp_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: 32S-3

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

description: Amplified with SMART-Seq Ultra Low Input RNA Kit

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genome TAIR10 using tophat2(v2.1.1) with parameters tophat2 -G ref.gff --library-type fr-unstranded -i 20 -I 500000 -o outdir genome_index fq1 fq2
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
Genome_build: Arabidopsis thaliana genome TAIR10
Supplementary_files_format_and_content: FPKM

source_name: Suspensor of  proembryos at 37-celled embryo stage

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMART-Seq  Ultra Low Input RNA Kit was used to generate cDNA library for sequencing
Libraries were constructed using Nextera XT Library Prep Kit or NEBNext Ultra DNA Library Prep Kit

value: Suspensor

tag: developmental stage

value: 32-celled embryo

tag: corss type

value: Col


title: lncRNA profile of 538T


title: 32S-2

source_name: Suspensor of  proembryos at 36-celled embryo stage


title: Rep2_sp_none_INO80_40

description:
in vitro
plasmid DNA


title: lncRNA profile of 534T


title: METTL3_Control_nuclearRNA_r1 [HEC-1-A]

description: non-ribosome RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to human genome and transcriptome (hg38, version 29, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness RF’  parameters. Annotation files (version 29, 2018-08-30, in gtf format for human) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Read counts for each gene and each sample.

extract_protocol:
The nuclear fraction was separated and total RNA was purified by Trizol. Before purified non-ribosome RNA with RiboMinus transcriptome isolation kit, ERCC RNA spike-in control (Ambion) was added to each sample (0.1 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: 6-cm plates of HEC-1-A cells were seeded and controlled to afford the same amount of cells.

tag: genotype


title: METTL3_Control_nuclearRNA_r2 [HEC-1-A]

description: non-ribosome RNA


title: METTL3_KD_MeRIP_r2 [HEC-1-A: MeRIP]

data_processing:
Library strategy: MeRIP-seq
Illumina Casava software used for basecalling
Raw reads were trimmed with Trimmomatic-0.38, then aligned to human genome and transcriptome (hg38, version 29, 2018-08-30) together with spike-in genomes including unmodified control RNA (Cypridina Luciferase) and  m6A methylated control RNA (Gaussia Luciferase) (New England Biolabs) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters.
Mapped reads were separated by strands with samtools (version 1.9) (http://www.htslib.org/) and m6A peaks on each strand were called using MACS (version 2) with parameter ‘--nomodel’ and ‘--keep-dup 5’ separately.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 for each sample.

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of HEC-1-A cells. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.

tag: m6a antibody


title: lncRNA profile of 529T


title: lncRNA profile of 532T


title: 32S-1

source_name: Suspensor of  proembryos at 35-celled embryo stage


title: 32E-3

source_name: Embro proper of  proembryos at 34-celled embryo stage

value: Embryo proper


title: Rep2_sp_Reb1_ISW2_40

description:
in vitro
plasmid DNA

source_name: in vitro reconstituted chromatin


title: 32E-2

source_name: Embro proper of  proembryos at 33-celled embryo stage


title: lncRNA profile of 528T


title: METTL3_KD_MeRIP_r1 [HEC-1-A: MeRIP]

value: EpiMark N6-Methyladenosine Enrichment Kit


title: METTL3_Control_MeRIP_r2 [HEC-1-A: MeRIP]

value: METTL3 Control


title: lncRNA profile of 514T


title: METTL3_Control_MeRIP_r1 [HEC-1-A: MeRIP]


title: IGF2BP3_2

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

description: IGF2BP3 - replicate 2

data_processing:
Base-calling was performed with bcl2fastq v2.17
The PAR-CLIP sequencing data were processed by PARpipe, which handles the library pre-processing, alignment, clustering, annotation and meta-analysis. (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/).
Adapters were trimmed using Cutadapt 1.8.3 and reads were aligned to the hg38 (GRCh38.p5) genome using Bowtie v1.1.2, allowing for up to one mismatch.
Aligned reads were sorted, converted to BAM files, and indexed with Samtools v0.1.19. PARalyzer v1.5 was used to process reads into groups and clusters via filters for (1) minimum read length, (2) minimum read count, (3) minimum unique T-to-C locations, and (4) minimum T-to-C conversions.
Reads, groups and clusters were annotated to the features in the Gencode v24 annotation file for reference chromosomes, scaffolds, assembly patches and alternative loci.
Genome_build: hg38 (GRCh38.p5)
Supplementary_files_format_and_content: BED : clusters called by PARalyzer for each respective PAR-CLIP replicate. BW : normalized (RPM) coverage of mapped PAR-CLIP reads

source_name: K562 CML-derived cell line

growth_protocol: K562 cells were purchased from ATCC (American Type Culture Collection, Manassas, VA) and cultured in RPMI Medium 1640 (Life Technologies, Grand Island, NY) with 10% FBS (Life Technologies, Grand Island, NY).

extract_protocol:
PAR-CLIP was performed with the off-beads ligation protocol as described by Benhalevy et al, 2017 (https://doi.org/10.1016/j.ymeth.2016.11.009).
The radiolabeled, ligated, and reversed transcribed samples were PCR amplified by a pilot PCR with 10 cycles and another 17 cycles (IGF2BP1) or 15 cycles (IGF2BP3). The amplified samples were concentrated and size selected with BluePippin 3% agarose gel cassette (Sage Science). Library concentrations were measured using Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and D1000 Screen Tape TapeStation System (Agilent).

treatment_protocol: anti-IGF2BP1 antibody (MBL, Woburn, MA) and anti-IGF2BP3 (Milipore) were used on 300 x 10^6 4-SU treated and fixed K562 cells

tag: cell line

value: K562 CML-derived cell line

tag: par-clip target


title: METTL3_KD_nuclearRNA_r2 [HEC-1-A]

description: non-ribosome RNA


title: Rep2_sp_none_INO80_80

description:
in vitro
plasmid DNA

data_processing:
fastq files were aligned to the SacCer3 (R64), EF2 or E. coli strain B (REL606) genomes using Bowtie (Lengmead et al. 2009). Multiple matches were omited.
BAM files were imported into R Studio (RStudio Team, 2015) using GenomicAlignments (Lawrence et al. 2013). Then, reads were shifted by 73 bp to cover the nucleosome dyad and extended to 50 bp. Genome coverage was caluculated.
Coverage files were either aligned to in vivo +1 nucleosome positions, Reb1 SLIM-ChIP hits (Gutin et al. 2019) or Reb1 PWM hits (Badis et al. 2008), or BamHI cut sites. Signal was normalized per gene in a 2000 bp window around the alignment point.
Genome_build: SacCer3, EF2, Ecoli strain B - REL606
Supplementary_files_format_and_content: bw (big wig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

extract_protocol:
Remodeling was started by adding 10 µl SGD chromatin and terminated by adding 0.8 U apyrase followed by incubation at 30 °C for 30 minutes.
For library preparation, approximately 10 - 50 ng of mononucleosomal DNA was incubated with 1.25 U Taq polymerase (NEB), 3.75 U T4 DNA polymerase (NEB) and 12.5 U T4-PNK (NEB) in 1x ligation buffer (B0202S, NEB) for 15 minutes at 12 °C, 15 minutes at 37 °C and 20 minutes at 72 °C. To ligate NEBNext Adaptors (0.75 µM final concentration, from NEBNext Multiplex Oligos Kit) to the DNA, samples were incubated with T4 DNA ligase (NEB) at 25 °C  for 15 minutes, followed by incubation with 2 U USER enzyme (NEB) for 10 minutes at 37°C. Fragments were purified using 2 volumes AMPure XP beads (Beckman Coulter) and amplified for 8-10 cycles using NEBNext Multiplex Oligos, Phusion High-Fidelity DNA Polymerase (1 U, NEB), deoxynucleotide solution mix (dNTP, 2.5 mM, NEB) and Phusion HF Buffer (1x, NEB). The following protocol was applied for amplification: 98 °C for 30 s, 98°C for 10s, 65 °C for 30s, 72 °C for 30s with a final amplification step at 72 °C for 5 minutes. The Qubit dsDNA HS Assay Kit (Invitrogen) was used to assess the DNA content of 1 µL PCR reaction. DNA was purified from agarose gels via PureLink Quick Gel Extraction Kit, measured again with Qubit dsDNA HS Assay Kit and diluted to final concentration of 10 nM (calculation based on the assumption that the DNA fragment length is 272 bp, i. e., 147 bp nucleosomal DNA and 122 bp sequencing adaptor). Diluted samples were pooled according to sequencing reads (~6 Mio reads/ sample). The final pool was quantified by BioAnalyzer (Agilent) and analyzed on an Illumina HiSeq 1500 in the 50 bp single-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).


title: METTL3_KD_Input_r2 [HEC-1-A: MeRIP]


title: 32E-1

source_name: Embro proper of  proembryos at 32-celled embryo stage


title: BC-3

source_name: Basal cell

value: Basal cell

value: 2-celled embryo


title: lncRNA profile of 507T


title: lncRNA profile of 513T


title: METTL3_KD_Input_r1 [HEC-1-A: MeRIP]


title: BC-2


title: IGF2BP1_2

description: IGF2BP1 - replicate 2


title: METTL3_Control_Input_r2 [HEC-1-A: MeRIP]


title: METTL3_KD_nuclearRNA_r1 [HEC-1-A]

description: non-ribosome RNA


title: BC-1


title: IGF2BP1_1

description: IGF2BP1 - replicate 1


title: lncRNA profile of 505T


title: CEPDL2ox rep3

city: Nagoya

first: Yoshikatsu

last: Matsubayashi

state: Aichi

address: Chikusa

department: Graduate School of Science

country: Japan

institute: Nagoya University

data_processing:
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of illumina Base Space Sequence Hub.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was prepared from roots of the plants grown under 10 mM nitrate condition using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (illumina) according to the manufacturer’s instructions.

tag: genotype/variation

value: 10 days

value: Root

value: grown under 10 mM nitrate condition


title: METTL3_Control_Input_r1 [HEC-1-A: MeRIP]


title: AC-3

source_name: Apical cell

value: Apical cell


title: lncRNA profile of 501T


title: HC-3

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

data_processing:
Alignment (TopHat2)
Counts (RSEM, repeatmasker)
Genome_build: hg19
Supplementary_files_format_and_content: txt (counts table by RSEM)

source_name: healthy donor

extract_protocol:
Whole blood samples (~2.5 ml) were collected in PAXGENE tubes to immediately stabilize endogenous RNA from the following patient groups: 1) patients at the indicated times after their first clinical event suggestive of presence of RRMS commonly referred to as a clinically isolated event or CIS (MS-C) who later went on to receive a diagnosis of RRMS, files labeled as sample 1, sample 2, sample 3 or MS-C 1, MS-C 2, MS-C 3, and healthy controls, sample 4, sample 5, sample 6 or HC 1, HC 2, HC 3.
Illumina Tru-Seq Stranded Total RNA kit

tag: disease state

value: healthy control

value: whole blood


title: CEPDL2ox rep2


title: AC-2


title: lncRNA profile of 493T

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels,EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.


title: AC-1


title: IGF2BP3_1

description: IGF2BP3 - replicate 1


title: HC-2


title: lncRNA profile of 497T


title: CEPDL2ox rep1


title: lncRNA profile of 492T


title: WT rep3

value: Wild type


title: WT rep2


title: HC-1


title: WT rep1


title: MS-C2

source_name: patient

value: multiple sclerosis


title: lncRNA profile of 491T

value: esophageal squamous cell carcinoma


title: MS-C3


title: lncRNA profile of 477T


title: lncRNA profile of 484T


title: MS-C1


title: lncRNA profile of 489T


title: TB9033_EPI145

status: Public on Feb 09 2020

type: genomic

city: New York

first: Seonjoo

state: NY

address: 1051 Riverside Drive Unit 48

department: Psychiatry and Biostatistics

institute: NYSPI/Columbia University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation 450K BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio software

label: Cy3, Cy5

source_name: genomic DNA from Placenta, Fetal side

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: tbid

value: Placenta

tag: avgtotsug

tag: avgaddsug

tag: avgcal

tag: birthweight

tag: pcomplication

tag: Sex


title: TB8916

tag: tissue


title: TB9058


title: TB9000_EPI137


title: TB8898


title: TB9044


title: TB9068


title: TB8871


title: TB9063


title: 8678


title: TB9047


title: TB8838


title: TB8723


title: TB8993_EPI143


title: TB9061


title: TB9026_EPI135


title: TB9101_EPI144


title: 8624


title: TB8730


title: TB8788


title: 8634


title: TB8807


title: TB9023_EPI141


title: 8631


title: TB8782


title: 8638


title: TB8686


title: TB8778


title: 8513


title: TB8726


title: 8134


title: 8199


title: 8169


title: 8230


title: 7908


title: 7872


title: 8234


title: 7877


title: 8232


title: 8235


title: 8069


title: 8229


title: 7881


title: 7954


title: 8228


title: 7888


title: 7562


title: 7647


title: 7542


title: 7811


title: 7819


title: 8225


title: 7734


title: 7625


title: 8231


title: 8227


title: 7641


title: 7569


title: 7729


title: 7511


title: 7670


title: 7636


title: 7599


title: 7723


title: Mut43-H3K9ac-rep1

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
ATAC-seq/ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC mm10 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
Genome_build: mm10
Supplementary_files_format_and_content: Wig files of ChIP-seq data were generated using deepTools v3.3.0 with library size normalized to 10 million read pairs.
Supplementary_files_format_and_content: Peaks of ATAC-seq were called by MACS2 software and stored in narrowPeaks text format.

extract_protocol:
ATAC-seq was performed as the following decription. Briefly, 50,000 cells were washed once with 50 μl of ice-cold PBS, then lysed with 50 μl of ice-cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) by incubating on ice for 10 min. The pellet was washed once with 1 ml of washing buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Tansposition reaction was performed in 50 μl of reaction mix containing 10 μl of 5× TTBL (Vazyme, TD501), 5 μl of TTE Mix V50 (Vazyme, TD501), 16.5 μl of PBS, 0.5 μl of 10% Tween-20, 0.5 μl of 1% digitonin, and 17.5 μl of PCR-grade water. The mixture was incubated at 37 ˚C for 30 min on a thermomixer with shaking at 1,000 rpm. Then, DNA was extracted by phenol-chloroform and amplified by KAPA HiFi HotStart ReadyMix (KAPA Biosystems, KK2611) with barcoded primers (Vazyme, TD202). DNA fragments ranging from 200 bp to 1,000 bp were selected for deep sequencing.
For ChIP-seq, Cells were harvested in PBS and cross-linked with 1% formaldehyde for 9 min at room temperature, cells prepared for RNA pol II were pre-cross-linked with 0.2 mM disuccinimidyl glutarate (DSG, ProtecoChem, c1104) for 30 min at room temperature. Reaction was terminated by adding glycine to a final concentration of 125 mM, incubated at room temperature for 5 min. After washing with PBS twice, cells were resuspended in 5 mL of Lysis Buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25%Triton X-100), incubated on ice for 10 min. After centrifuge at 2,000 rpm at 4 ˚C for 5 min, cells were then resuspended in 5 mL of Lysis Buffer 2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA), incubated at room temperature for 10 min. The lysate was centrifuged at 4,000 rpm for 5 min at 4 ˚C. The chromatin fraction was resuspended in 1 mL of Lysis Buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroylsarcosine, 1x proteinase inhibitor (Merck, 5892970001)). Chromatin was then sonicated into 200-400 bp fragments (Covaris M220), in assistance with 0.1% sodium dodecyl sulfate (SDS) or 0.5% SDS (for double cross-linked sample). Supernatant after centrifuging at 12,000 rpm for 10 min at 4 ˚C were flash freezed and kept in -80 ˚C refrigerator.    Keep 10% of chromatin as input, the fragments were immunoprecipitated overnight with antibodies against histone modifications or RNA pol II. Pre-washed Dynabeads protein A or G (ThermoFisher 10002D, or 10004D) was added to the Protein-antibody complexes, and incubated at 4 ˚C for 1 hour. The beads were sequentially washed with buffers as follows: FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5 mM sodium deoxycholate), FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate) for twice, LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0), TE buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA) for twice. Each washing step was incubated for 5 min at 4 ˚C with rotation. Protein-DNA complexes were eluted by incubation with 250 µl of elution buffer (1% SDS, 100 mM NaHCO3, freshly made) for 15 min at 55 ˚C with periodic gentle vortex. This step was repeated once and eluted sample was combined.    Eluted DNA, as well as input, was reverse cross-linked from protein by adding 20 µl of 5M NaCl to the 500 µl of elution, incubated at 65 ˚C over 8 hours. After digested with RNase at 37 ˚C, proteinase K at 55 ˚C, DNA was extracted by phenol-chloroform method.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).

tag: strain background

value: J3 mouse ES cell

tag: cell type

value: embryonic stem cell

value: inner cell mass

value: embryo, blastocyst

tag: antibody

value: Abcam, ab4441


title: 7666


title: 7697


title: 7374


title: WT-H3K9ac-rep1

value: J1 mouse ES cell

value: wild type

tag: developmental stage


title: 7632


title: 7479


title: Mut43-H3K9ac-rep2

value: J4 mouse ES cell


title: Mut18-H4K8ac-rep2

value: Active Motif, 61103


title: Mut18-H3K9ac-rep2


title: Mut18-H3K9ac-rep1


title: 7011


title: 7484


title: WT-H4K8ac-rep1


title: WT-H3K9ac-rep2


title: 7351


title: 7516


title: 7581


title: 7360


title: 7404


title: Mut43-H4K8ac-rep2


title: Mut43-H4K8ac-rep1


title: WT-H4K8ac-rep2


title: Mut18-H4K8ac-rep1


title: Mut43-H4K5ac-rep2

value: Active Motif, 39699


title: 7239


title: 7083


title: 7356


title: Mut18-H4K5ac-rep2


title: 7095


title: 7407


title: 7176


title: WT-H4K5ac-rep2


title: Mut18-H4K5ac-rep1


title: WT-H4K5ac-rep1


title: 7101


title: Mut18-H3K18ac-rep1

value: Active Motif, 39755


title: 7089


title: Mut18-H3K18ac-rep2


title: Mut43-H3K18ac-rep1


title: WT-H3K18ac-rep2


title: Mut43-H3K4me3-rep2

value: Millipore, 07-473


title: 7282


title: Mut43-H3K4me3-rep1


title: Crh_Pet1_rDR_5

first: Benjamin

last: Okaty

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: Sample 67

data_processing:
Illumina 2.2.0.4 - RTA 2.4.11 software for base calling (except for samples 34-38, which used 2.2.68 - RTA 1.18.66.3)
For samples 1-70, transcript mapping to the mm10 genome assembly and feature counts were performed using STAR (version 2.5.4) (Dobin and Gingeras, 2016). For samples 71-72, transcriptome mapping and demultiplexing were performed using the 10X Genomics Cell Ranger software (version  3.0.2). Several data-filtering steps were performed on the matrix of transcript counts   (using R version 3.5.3) prior to further analysis, as described in Okaty, Sturrock, et al. 2020 BioRxiv doi: https://doi.org/10.1101/2020.01.28.923375.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files containing transcript counts

source_name: Acutely dissociated dorsal raphe (DR) single neuron

extract_protocol:
Brain tissue was harvested from  transgenic animals and fluorescently labeled cells were sorted as described in (Okaty, Sturrock, et al. 2020). Samples 1-70 were manually sorted and samples 71-72 were sorted using the On-Chip Sorter.
Samples 1-70 were constructed using the SMART-Seq v4 Ultra Low Input RNA kit, followed by Nextera XT  1212 DNA Library Preparation Kit. Samples 71 and 72 were constructed using 10X Genomics Chromium Single Cell 3’ v3 kit.

tag: genotype

tag: dr subdomain

value: rostral

tag: age

value: postnatal day 119


title: 10X_DR_Pet1_run_2

description: Sample 72

source_name: Acutely dissociated dorsal raphe (DR) neurons

value: full DR

value: postnatal day 59 (mean)


title: Crh_Pet1_rDR_7

description: Sample 69

value: Acutely dissociated dorsal raphe (DR) single neuron

value: postnatal day 83


title: Crh_Pet1_rDR_6

description: Sample 68


title: 10X_DR_Pet1_run_1

description: Sample 71

value: Acutely dissociated dorsal raphe (DR) neurons

value: Pet1::Flpe+/-; hM3Dq+/+

value: postnatal day 65.5 (mean)


title: 7075

value: Placenta


title: 7434


title: 7283


title: Mut18-H3K4me3-rep2

tag: cell line

value: J1 mouse ES cell

value: embryonic stem cell

tag: genotype/variation

value: inner cell mass

value: embryo, blastocyst


title: WT-H3K18ac-rep1

value: wild type


title: 7060

tag: tbid


title: Mut18-H3K4me3-rep1


title: WT-H3K4me3-rep2


title: Crh_Pet1_rDR_3

description: Sample 65


title: Crh_Pet1_rDR_2

description: Sample 64


title: WT-H3K4me3-rep1


title: Crh_Pet1_rDR_1

description: Sample 63


title: Mut43-H3K122ac-rep2

value: J4 mouse ES cell

value: Abcam, ab33309


title: Npy2r_Pet1_rDR_9

description: Sample 62

value: rostral

value: postnatal day 87


title: Mut18-H3K122ac-rep2


title: Mut43-H3K122ac-rep1

value: J3 mouse ES cell


title: Npy2r_Pet1_rDR_8

description: Sample 61


title: Mut18-H3K122ac-rep1


title: WT-H3K122ac-rep2


title: Npy2r_Pet1_cDR_10

description: Sample 53

value: caudal


title: Mut18-H3K4me1-rep2

value: Active Motif, 39297


title: Mut43-H3K4me1-rep1


title: Npy2r_Pet1_rDR_1

description: Sample 54

value: Acutely dissociated dorsal raphe (DR) single neuron

value: postnatal day 77


title: WT-H3K122ac-rep1


title: Npy2r_Pet1_rDR_7

description: Sample 60


title: Mut43-H3K18ac-rep2

value: Active Motif, 39755


title: Mut18-H3K4me1-rep1


title: Npy2r_Pet1_rDR_3

description: Sample 56


title: Mut43-H3K4me1-rep2


title: Npy2r_Pet1_cDR_9

description: Sample 52


title: Npy2r_Pet1_rDR_2

description: Sample 55


title: WT-H3K4me1-rep1


title: WT-H3K4me1-rep2


title: Npy2r_Pet1_cDR_8

description: Sample 51


title: Mut43-H3K27me3-rep2

value: Cell Signaling, 9733S


title: Mut43-H4K5ac-rep1

value: Active Motif, 39699


title: Npy2r_Pet1_cDR_7

description: Sample 50


title: Npy2r_Pet1_cDR_6

description: Sample 49


title: Npy2r_Pet1_cDR_5

description: Sample 48


title: Npy2r_Pet1_rDR_5

description: Sample 58


title: Npy2r_Pet1_rDR_6

description: Sample 59


title: Npy2r_Pet1_rDR_4

description: Sample 57


title: Npy2r_Pet1_cDR_4

description: Sample 47


title: Npy2r_Pet1_cDR_3

description: Sample 46


title: Npy2r_Pet1_cDR_2

description: Sample 45


title: Mut43-ATACseq-rep2

value: J1 mouse ES cell


title: Npy2r_Pet1_cDR_1

description: Sample 44


title: P2ry1_Pet1_cDR_9

description: Sample 42

value: postnatal day 66


title: WT-H3K27me3-rep2

value: embryonic stem cell

value: inner cell mass


title: Crh_Pet1_rDR_8

description: Sample 70

value: postnatal day 119


title: P2ry1_Pet1_cDR_10

description: Sample 43


title: PTBP1 seCLIP

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN IMS

description: mapped to hg38+pCS2.PTBP1.fa

data_processing:
library strategy: eCLIP-seq
Illumina RTA v1.18.54.0 software used for basecalling.
Raw sequencing reads were first trimmed for adaptor sequences, demultiplexed based on barcode sequences (demultiplexed fastq files are provided as raw data), then mapped to a custom genome (hg38 + SINEUP plasmid sequence, fasta files linked to the Series records) using STAR_2.5.0a with default parameters
Replicate BAM files (in the case of HNRNPK) were first merged into a single file using bamtools merge. Data were filtered to remove unmapped reads and any secondary alignments. For SINEUP mapping reads, anything mapping to the reverse strand was also removed.
Peaks were called using a simple thresholding script, whereby all bases that had coverage of at least one third of the maximum coverage for the gene were retained. Any bases within 2% of the total gene length from each other were merged into a single peak region.
Any peaks falling outside of the shared sequence of the two vectors were removed. For peaks which partially overlapped only the portion that fell in the shared sequence was retained.
Genome_build: hg38+custom contig
Supplementary_files_format_and_content: signal tracks (bigwig) generated with bamCoverage (-bs 25) and peak bed file for SINEUP plasmid sequence

source_name: PTBP1 seCLIP

growth_protocol: HEK 293T/17 cells were maintained in DMEM, high glucose, GlutaMAX supplement, pyruvate (Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% penicillin-streptomycin (Wako) at 37oC, 5% CO2

extract_protocol:
HEK293T/17 cells were lysed after irradiation with 300 mJ/cm2 of 254 nm UV light. The cells were treated with anti-hnRNPK or anti-PTBP1 antibodies to capture SINEUP RBP-RNA complexes. The immunoprecipitated (IP) samples were dephosphorylated and end treated with Poly Nucleotide Kinase followed by on-beads 3ʹ RNA linker (with sample barcodes) ligation. After this, RBP-RNA complexes were detected by Western blotting and cut out from the nitrocellulose membrane blot. In order to isolate the RNA, membrane slices were treated with Proteinase K and Urea followed by acid phenol-chloroform extraction and cleanup by Zymo RNA kit (R1013).
The library preparation steps were following seCLIP protocol described by Van Nostrand E.L. et al. 2017

treatment_protocol: pEGFP-C2 and SINEUP vectors were co-transfected into HEK 293T/17 cells using Lipofectamine 2000 (Invitrogen) with OptiMEM (1x) Reduced Serum Medium (Gibco).

value: Human embryonic kidney cells

tag: passages

tag: transfection

value: Transiently cotransfected with SINEUP-GFP and EGFP plasmids for 24 hours

tag: ip antibody

value: anti-PTBP1 mouse monoclonal antibody (Thermofisher, 32-4800)


title: HNRNPK input replicate 1

description: mapped to hg38+pcDNA.HNRNPK.fa

source_name: HNRNPK input

value: anti-hnRNPK mouse monoclonal antibody [3C2]-ChIP Grade (Abcam, ab39975)


title: Mut43-ATACseq-rep1

value: embryo, blastocyst


title: P2ry1_Pet1_cDR_8

city: Boston

description: Sample 41

value: caudal

value: postnatal day 63


title: Mut18-ATACseq-rep2


title: HNRNPK input replicate 2

description: mapped to hg38+pcDNA.HNRNPK.fa


title: Mut43-H3K27me3-rep1

value: J3 mouse ES cell


title: P2ry1_Pet1_cDR_6

description: Sample 39

value: Acutely dissociated dorsal raphe (DR) single neuron

value: postnatal day 64


title: Sert_Pet1_cDR_6

description: Sample 33


title: P2ry1_Pet1_cDR_7

description: Sample 40


title: Mut18-H3K27me3-rep1

value: Cell Signaling, 9733S


title: Sert_Pet1_cDR_4

description: Sample 31


title: Mut18-ATACseq-rep1


title: HNRNPK seCLIP replicate 2

description: mapped to hg38+pcDNA.HNRNPK.fa

source_name: HNRNPK seCLIP


title: Mut18-H3K27me3-rep2


title: PTBP1 input

description: mapped to hg38+pCS2.PTBP1.fa

source_name: PTBP1 input


title: HNRNPK seCLIP replicate 1

description: mapped to hg38+pcDNA.HNRNPK.fa


title: Sert_Pet1_cDR_3

description: Sample 30


title: WT-ATACseq-rep2

source_name: WT-ATAC

value: wild type


title: WT-ATACseq-rep1

value: J1 mouse ES cell


title: Mut43-H3K27ac-rep2

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC mm10 genome by Bowtie2 (2.3.4.2)
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates
RNA-Seq data were mapped to UCSC mm10 by STAR aligner and quantitified by DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files of ChIP-seq data were generated using deepTools v3.3.0 with library size normalized to 10 million read pairs.
Supplementary_files_format_and_content: Raw read counts of RNA-seq for each gene were calculated by summarizeOverlaps method from GenomicAlignments v1.8.4 and stored as tab separated texts.

extract_protocol:
For mRNA-seq, total RNA was directly extracted from cells cultured in 3.5 cm dishes by TRIzol reagent with two biological replicates for each cell line.
For ChIP-seq, Cells were harvested in PBS and cross-linked with 1% formaldehyde for 9 min at room temperature, cells prepared for RNA pol II were pre-cross-linked with 0.2 mM disuccinimidyl glutarate (DSG, ProtecoChem, c1104) for 30 min at room temperature. Reaction was terminated by adding glycine to a final concentration of 125 mM, incubated at room temperature for 5 min. After washing with PBS twice, cells were resuspended in 5 mL of Lysis Buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25%Triton X-100), incubated on ice for 10 min. After centrifuge at 2,000 rpm at 4 ˚C for 5 min, cells were then resuspended in 5 mL of Lysis Buffer 2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA), incubated at room temperature for 10 min. The lysate was centrifuged at 4,000 rpm for 5 min at 4 ˚C. The chromatin fraction was resuspended in 1 mL of Lysis Buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroylsarcosine, 1x proteinase inhibitor (Merck, 5892970001)). Chromatin was then sonicated into 200-400 bp fragments (Covaris M220), in assistance with 0.1% sodium dodecyl sulfate (SDS) or 0.5% SDS (for double cross-linked sample). Supernatant after centrifuging at 12,000 rpm for 10 min at 4 ˚C were flash freezed and kept in -80 ˚C refrigerator.    Keep 10% of chromatin as input, the fragments were immunoprecipitated overnight with antibodies against histone modifications or RNA pol II. Pre-washed Dynabeads protein A or G (ThermoFisher 10002D, or 10004D) was added to the Protein-antibody complexes, and incubated at 4 ˚C for 1 hour. The beads were sequentially washed with buffers as follows: FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5 mM sodium deoxycholate), FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate) for twice, LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0), TE buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA) for twice. Each washing step was incubated for 5 min at 4 ˚C with rotation. Protein-DNA complexes were eluted by incubation with 250 µl of elution buffer (1% SDS, 100 mM NaHCO3, freshly made) for 15 min at 55 ˚C with periodic gentle vortex. This step was repeated once and eluted sample was combined.    Eluted DNA, as well as input, was reverse cross-linked from protein by adding 20 µl of 5M NaCl to the 500 µl of elution, incubated at 65 ˚C over 8 hours. After digested with RNase at 37 ˚C, proteinase K at 55 ˚C, DNA was extracted by phenol-chloroform method.
RNA-seq library construction: Poly-A tailed mRNA molecules were captured using attached oligo-dT and subjected to library construction according to the manufacturer’s recommendations.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).

tag: source tissue

value: embryonic stem (ES) cell

tag: chip antibody

value: Active Motif #39133


title: Sert_Pet1_cDR_2

description: Sample 29


title: Mut43-H3K27ac-rep1

value: inner cell mass


title: Sert_Pet1_cDR_1

description: Sample 28


title: Sert_Pet1_vmDR_7

description: Sample 26

value: ventromedial

value: postnatal day 90


title: Sert_Pet1_vmDR_8

description: Sample 27


title: Sert_Pet1_vmDR_4

description: Sample 23


title: Sert_Pet1_vmDR_5

description: Sample 24


title: Mut18-H3K27ac-rep2


title: Mut43-input


title: Sert_Pet1_vmDR_6

description: Sample 25


title: Sert_Pet1_cDR_5

description: Sample 32


title: Sert_Pet1_vmDR_2

description: Sample 21


title: Sert_Pet1_vmDR_3

description: Sample 22


title: Sert_Pet1_dmDR_8

description: Sample 18

value: dorsomedial


title: Sert_Pet1_dmDR_9

description: Sample 19


title: Sample_7thday-rep2

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

data_processing:
Illumina adapter sequences were removed and low quality sequencing reads removed using Trimmomatic software
Ribosomal contaminant sequences were removed using sortMeRNA software
Reads were aligned to reference genome using Bowtie2 software
Transcript expression was estimated using RSEM software and reported as TPMs
Genome_build: Spodoptera frugiperda mitochondrion genome: NCBI accesssion KM362176; Spodoptera frugiperda chromosomal genome assembly reported by  Gouin et al. (2017) doi:10.1038/s41598-017-10461-4
Supplementary_files_format_and_content: Transcript expression values are reported as TPM values in Microsoft Excel spreadsheet format

organism: Spodoptera frugiperda

source_name: SfAV-1a 7 days infected 3rd instar caterpillar

extract_protocol:
Total RNA was isolated from the entire body of each healthy or SfAV-1a infected Spodoptera frugiperda larva and homogenized separately by mechanical trituration in TRIzol (Invitrogen), followed by DNase-treatment using the RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH) and eluted in ultra pure distilled water (Invitrogen).
The NEBNextPoly(A) mRNA magnetic isolation module kit (New England Biolabs) was used to enrich the mRNA first from the DNase-treated total RNA samples.The libraries were then prepared following the manufacturer’s instructions of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

tag: infection

value: Wild type SfAv-1a

tag: time point

value: 7 days

value: whole insect body


title: Sample_7thday-rep1

tag: tissue


title: amiR-bpm_vs_Col-0_Cor_repl2

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 and Hy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation

scan_protocol: Images were scanned at 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were  normalized by LOWESS algorithm followed by quantile normalization

source_name: Arabidopsis thaliana Col-0

label_protocol: 200 ng of total RNA were reverse transcribed used T7 primer and the cDNA converted to aRNA using T7 RNA polymerase, incorporating cyanine 3- or cyanine 5-labeled CTP, according to 'Two color Microarray-Based Gene Expression Analysis Protocol' (Agilent)

growth_protocol: Seedlings were grown 3 weeks under a 16-h light/8-h dark cycle at 21ºC in 0,5xMS1 solid

extract_protocol: Plant tissue (~100 mg) was ground in liquid nitrogen and total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with RNeasy mini kit (Qiagen, 74104).

value: wild-type

tag: treatment

value: 0,5 uM Coronatine

source_name: Arabidopsis thaliana amiR-bpm

value: amiR-bpm


title: Mut18-H3K27ac-rep1

tag: strain background

value: embryo, blastocyst

tag: cell type


title: Sample_4thday-rep2

source_name: SfAV-1a 4 days infected 3rd instar caterpillar

value: 4 days

tag: developmental stage


title: amiR-bpm_vs_Col-0_Cor_repl3

tag: genotype


title: Sert_Pet1_vmDR_1

description: Sample 20

value: Acutely dissociated dorsal raphe (DR) single neuron

tag: dr subdomain

tag: age

value: postnatal day 63


title: Mut18-input

tag: cell line

tag: genotype/variation


title: Sert_Pet1_dmDR_6

description: Sample 16


title: Sample_4thday-rep1


title: amiR-bpm_vs_Col-0_Cor_repl1


title: WT-H3K27ac-rep2

value: wild type


title: Sert_Pet1_dmDR_7

description: Sample 17


title: Sert_Pet1_dmDR_2

description: Sample 12


title: Sample_48hr-rep2

source_name: SfAV-1a 48h infected 3rd instar caterpillar


title: WT-input

source_name: WT-input

value: embryonic stem (ES) cell


title: Sample_24hr-rep2

source_name: SfAV-1a 24h infected 3rd instar caterpillar


title: Sert_Pet1_dmDR_5

description: Sample 15


title: Sert_Pet1_dmDR_4

description: Sample 14


title: Sample_48hr-rep1


title: Sert_Pet1_dmDR_3

description: Sample 13


title: WT-H3K27ac-rep1

value: Active Motif #39133


title: Sert_Pet1_dmDR_1

description: Sample 11


title: Sert_Pet1_dlDR_10

description: Sample 10

value: dorsolateral