title: OPC protrusion_2

city: Porto

first: Helena

middle: Sofia

last: Domingues

address: Rua Alfredo Allen, 208

department: Neurobiology and Neurologic Disorders

country: Portugal

institute: Instituto de Investigação e Inovação em Saúde

data_processing:
Reads were mapped to the rat genome assembly for Rattus_norvegicus assembly Rnor_5.0 with TopHat using the transcript set from Ensembl v69 to provide splicing information.
Data was quantitated in the SeqMonk program using the transcripts from Ensembl v69.  All read overlaps were counted against the merged set of exons for each gene.  Raw counts were corrected for the total library size and the length of the transcript to produce RPKM values
Genome_build: Annotations were the Ensembl gene build from Jan 2013
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: oligodendrocyte precursor cells (OPC)

growth_protocol: OPCs were isolated from mixed glial cells (MGCs) of postnatal day 0-2 (P0-P2) rat brains (McCarthy and de Vellis, 1980; Chen et al., 2007).  For MGCs, 10-12 brain cortices were dissected, freed of meninges and mechanically homogenized.  The tissue suspension was enzymatically treated with DNase I (0.1mg/mL, Sigma) and 0.25% Trypsin-EDTA (Gibco) for 15 minutes at 37°C.  After centrifugation, the cell pellet was resuspended in C-DMEM, filtered through a 100 μm nylon cell strainer (BD Falcon), plated on poly-D-lysine (PDL)-coated (Sigma) T75 flasks (Sarstedt) at a cell density of ~2 brains/flask and grown at 37°C in 5% CO2 for approximately 10 days with fresh medium feeding every 2-3 days.  To prepare pure OPCs, MGCs were pre-shaken at 220 rpm for 2h in a INFORS HT Minitron incubator with a radius of 2.5 cm at 37ºC.  After addition of fresh C-DMEM, a shake at 240 rpm was performed overnight.  The cell suspension obtained after differential adhesion was passed through a 40 μm nylon cell strainer (BD Falcon). Approximately 2.5x10^5 OPCs were plated in the upper compartment of a Boyden chamber insert, consisting of a permeable PET membrane with 1-um pore size (BD Falcon) that had been previously coated with 10 ug/ml of PDL and human placental laminin-2 (Milipore) on the bottom side to create an haptotactic gradient.  Coating was performed first with PDL for 1h at room temperature (RT) in deionized water, followed by laminin-2 in phosphate-buffered saline (PBS) for 4h at 37°C. To promote extension of OPC membrane protrusions across the pores, a chemotactic gradient was established by adding human PDGFaa and FGF1-basic (Peprotech) (both at 10 ng/ml) to the lower chamber, and the chemorepulsive netrin-1 (R&D Systems) (25 ng/ml) to the upper chamber. OPCs were cultured for 24h in Sato proliferating medium.

extract_protocol:
Total RNA from OPC soma and membrane protrusions was isolated using the Quick-RNA MicroPrep kit (Zymo Research) according with manufacturer’s instructions.  The OPC soma fraction was isolated by scrapping the upper side of the insert with a cotton swab.  Total RNA was further isolated from the cotton swab by dipping it in ZR RNA lysis buffer.  RNA from membrane protrusions was collected from the bottom side of the insert, which was pushed down into a well containing lysis buffer.  RNA from different experiments was pooled and concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research). Total RNA quantity and integrity were assessed using Quant-IT RiboGreen RNA Assay Kit (Invitrogen, Carlsbad, CA, USA) and Agilent Tapestation 2200 R6K. mRNA enrichment was achieved by processing 5 μg of total RNA using the Magnetic mRNA Isolation Kit from NEB (S1550S) with minor modifications.
Generation of double stranded cDNA and library construction were performed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420L) according to manufacturer specifications. Upon ligation of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit), each library was size selected with two Ampure Bead bindings (firstly, 1:0.7x volume and secondly, the supernatant from the first bind was taken for a 1:1.7x volume clean-up). The following custom primers (25 µM each) were used for the PCR enrichment step: Multiplex PCR primer 1.0: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3', Index primer: 5'-CAAGCAGAAGACGGCATACGAGAT(INDEX)CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'. Indices were according to the eight bases tags developed by WTCHG (Lamble et al., 2013). Amplified libraries were analysed for size distribution using the Agilent Tapestation 2200 D1K. Libraries were quantified by quantitative RT-PCR using Agilent qPCR Library Quantification Kit and a MX3005P instrument (Agilent) and relative volumes were pooled accordingly. Finally, a second quantitative RT-PCR was performed to measure the relative concentration of the pool compared to a previously sequenced mRNA library in order to determine the volume to use for sequencing.

tag: background

value: Wistar

value: oligodendrocyte precursor cells (OPC)

tag: origin

value: primary cultures derived from brain cortices

tag: developmental stage


title: LF2

status: Public on May 07 2018

type: SRA

city: Xi'an

first: Jing

last: Yang

address: 620 district of west chang'an avenue

department: College of life sciences

country: China

institute: Anas platyrhynchos

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
TopHat2 mapping to reference genome
HTseq was used for count calculation.
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

organism: Anas platyrhynchos

source_name: late growth flight feathers 2

growth_protocol: Male ducks at three different physiological stages (3-day-old, 27-day-old and 6-month-old) were selected and divided into early growth phase (E), middle growth phase (M) and late growth phase (L) groups.

extract_protocol:
RNAlysis was performed using TRIzol Reagent (Invitrogen, USA) followed by isolation and purification with the RNeasy kit (Qiagen, Germany). RNA purity and integrity were evaluated using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.
Illumina HiSeq sequencing protocol

treatment_protocol: First, the feathers born in the abdomen and inner side of the wing at each stage were sheared and further shaved. Then the ducks were locally anaesthetized with pentobarbital sodium (3%, 1ml/kg) through intraperitoneal injection to minimize the animal suffering. A piece of skin (1 cm in diameter) from the abdominal and wing side were collected with scissors and forceps and immediately washed with 10 mL PBS (PH7.2) and 0.5mM EDTA.

tag: tissue

value: skin tissue of inner side of the wing

tag: age

tag: Sex

value: male

tag: breed

value: Cherry Valley


title: OPC protrusion_1

organism: Rattus norvegicus


title: OPC soma_2


title: OPC soma_1


title: EF1

source_name: early growth flight feathers 1


title: EF2

source_name: early growth flight feathers 2


title: 5448 TEpi MOI 5 infected 6 h rep4

status: Public on May 08 2018

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2_batch_adjusted.txt
5448_4_S12

data_processing:
Base calls performed using RTA v2.
Reads were pooled into a single fastq file representative of one individual biological sample (originally the reads for a single sample were split across 4 lanes of the sequencer).
Two trailing nucleotides were trimmed from all reads with fastx_trimmer version 0.0.14.
Trimmed reads were mapped to hg19 (ENSEMBL 69) whole genome using R version 3.2.1 with package Rsubread version 1.18.0 with default parameters.
Batch correction applied to TMM-adjusted RPKM log2 data using R version 3.2.2 with package limma version 3.26.8 with [5448_1_S9, JRS4_1_S5, Mock_1_S1] [5448_2_S10, JRS4_2_S6, Mock_2_S2] [5448_3_S11, JRS4_3_S7, Mock_3_S3] [5448_4_S12, JRS4_4_S8, Mock_4_S4] as batch groups specified.
Genome_build: hg19, ENSEMBL version 69.
Supplementary_files_format_and_content: tab delimited text file containing raw counts, tab delimited text file containing TMM-RPKM log2 abundance measurements which were subsequently batch adjusted with limma's removeBatchEffect() function.

organism: Homo sapiens

source_name: tonsil

growth_protocol: TEpi cells were seeded at a density of approximately 120,000 viable cells per well in 6 well plates were coated with poly-L-lysine. Cells were grown at 37°C under a 5% CO2/20% O2 until they formed a confluent monolayer. Immediately prior to infection, the TEpi medium was removed, and replaced with fresh TEpi medium.

extract_protocol:
Medium was aspirated and RNA lysis buffer (Buffer RLT (Qiagen) plus 0.1 M -mercaptoethanol) added to each well. Cells were scraped into the buffer using a cell-scraper. Cell lysate was then loaded onto a QIAshredder homogenizer column (Qiagen, Cat. #79654) and homogenized by centrifugation. RNA was then isolated using the RNeasy Mini Kit (Qiagen, Cat. #74104), according to the manufacturer’s instructions. Absorbance of RNA samples was measured at 260 nm using a ND1000 Nanodrop (Biolab), and RNA concentration (µg/ml) was determined by the A260 reading: A260 = 1.0 is equivalent to 40 µg/ml RNA. A260/A280 ratios were measured to determine RNA purity, and an A260/280 ratio of 2.0 – 2.2 was deemed acceptable for subsequent use.
Confluent 6-well plates of TEpi cells were infected with JRS4 or 5448 as described above, at an MOI of 5 for 6 h. Mock cells were included as a control. RNA from four biological replicates was extracted as described above. RNA sequencing was performed by The University of Queensland, Institute of Molecular Biosciences (IMB) sequencing facility. Total RNA was deemed as passing quality control tests (2100 bioanalyzer), with a RIN score of >7.0.  For each sample, the mRNA library was prepared using TruSeq stranded mRNA library prep kit (Illumina) and sequenced using 1 x NextSeq 500, 75 cycle (1 x 75bp) Illumina High Output single-end run.

treatment_protocol: GAS strains were grown to early stationary phase (OD600 = 1.2 for 5448 and OD600 = 1.6 for JRS4), re-suspended in cell culture medium, and then added to cell monolayers at the multiplicity of infection (MOI) of 5. The control included for each experiment were cells not exposed to bacteria (Mock). At 2 h post-infection, the media was aspirated and cells were washed twice with fresh media, before TEpi media containing 100µg/ml of gentamicin was added to each well for the duration of the experiment.

tag: cell type

value: TEpi

tag: infection

tag: treatment length

value: 6 hours

value: 12 years


title: EP2

source_name: early growth plumulaceous feathers 2

value: abdomen skin tissue


title: MF1

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
TopHat2 mapping to reference genome
HTseq was used for count calculation.HTseq was used for count calculation.
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: middle growth flight feathers 1


title: EP1

source_name: early growth plumulaceous feathers 1


title: DND-41

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets of T-ALL cell lines were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1 and Ensembl database for annotated splice junctions
Alignment files from STAR were used for ab initio transcriptome assembly with Cufflinks v2.2.1. A RefSeq GTF file was applied for Cufflinks to guide the assembly
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: DND-41 cells

growth_protocol: All T-ALL cell lines were cultured in RPMI-1640 medium (BioWest) supplemented with 10% fetal bovine serum (FBS; BioWest) in a CO2 incubator.

extract_protocol:
RNA was extracted using an miRNeasy kit (Qiagen) with some modifications.  The cell numbers for each sample were counted before cell pellet was collected. ERCC RNA Spike-in mix (1:10 dilution) was then added to each sample according to the cell numbers (Example: 1ul was added for 1 million cells)  after the addition of Qiazol.  After the addition of chloroform, the samples were transferred to a Maxtract high-density column (Qiagen) to be spun down.  The aqueous layer was then retained for downstream RNA extraction following the manufacturer’s instructions.  The extracted RNA was subjected to DNase treatment (Turbo DNA-freeTM kit, Ambion) according to the manufacturer’s instructions to eliminate any genomic DNA present in the samples and then cleaned up using an RNeasy kit (Qiagen).  Ribosomal RNAs were depleted before library construction.
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

tag: cell line


title: LP2

source_name: late growth plumulaceous feathers 2


title: MP2

source_name: middle growth plumulaceous feathers 2


title: HPB-ALL

source_name: HPB-ALL cells

value: HPB-ALL


title: LF1

source_name: late growth flight feathers 1


title: RPMI-8402

source_name: RPMI-8402  cells


title: TALL-1

source_name: TALL-1 cells


title: Loucy

source_name: Loucy cells

value: Loucy


title: MP1

source_name: middle growth plumulaceous feathers 1


title: MI_3dMI_1

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

country: USA

institute: University of Hawaii

data_processing:
FASTQ files were explored using FastQC and cleaned by filtering out reads having mean Phred quality score less than 20 using Prinseq.
Mus musculus UCSC mm10 reference genome was indexed by Bowtie2 v2.2.5 and filtered high quality reads were mapped against the reference genome using Tophat v2.0.14.
Mapped BAM files for Sham and MI samples were sorted and converted to SAM files using SAMtools v0.1.2, and then used to generate count reads mapped to mouse gene models using htseq-count script on HTSeq package.
Differential gene expression from the count data was identified using DESeq2 bioconductor package.
CLC Genomic Workbench v9 software (CLC Bio) along with empirical analysis of DGE algorithm implemented in it was used for the transcript-level expression analysis. The genes and transcripts with Benjamini and Hochberg q-value <0.05 were called differentially expressed between sham and MI.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files

organism: Mus musculus

source_name: heart tissue

extract_protocol:
RNA was extracted using a Qiagen miRNeasy mini kit according to manufacturer’s instructions.
Total RNA samples were sent to Genewiz (South Plainfield, NJ) for rRNA depletion and paired-end sequencing on an Illumina HiSeq2500.

value: heart left ventricle (free wall)

tag: strain

tag: gender

value: 8-12 weeks

tag: surgery

value: LAD ligation


title: MOLT-4

source_name: MOLT-4 cells


title: LP1

source_name: late growth plumulaceous feathers 1


title: CCRF-CEM

source_name: CCRF-CEM cells

value: CCRF-CEM


title: 2_lacZ_2

status: Public on May 05 2018

city: Philadelphia

first: David

last: Manning

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 (ensemblv67) by STAR-2.5.1b.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.1-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

growth_protocol: C3H10T1/2 cells (ATCC) were maintained in Basal Medium Eagle (BME) supplemented with 2 M L-gluamine and 10% fetal bovine serum at 37°C ant 5% CO2; cells were not used beyond 12 passages from purchase.

extract_protocol:
RNA was extracted with Rneasy Minikit (QIAGEN). RNA quality (RNA  integrity number > 8)was assured by analysis with an Agilent Bioanalyzer and an Invitrgen Qubit fluorometric assay.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transformed with recombinant adenoviruses encoding LacZ, SmoA1, and Galpha13QL at 60-90% confluency by exposure to the viruses at MOIs of 8, 10, and 14, respectively, for 6 h. The cells were cultured for an additional 48 h before extraction of RNA. Each sample for each recombinant adenovirus represents a biological replicate, processed on a different day with a different passage of cell.


title: 5_SmoA1_2

source_name: Cells were transformed with recombinant adenoviruses encoding SmoA1


title: 8_Galpha13QL_2

source_name: Cells were transformed with recombinant adenoviruses encoding Galpha13QL


title: 4_SmoA1_1


title: MF2

source_name: middle growth flight feathers 2


title: 9_Galpha13QL_3


title: Jurkat

source_name: Jurkat cells

value: Jurkat


title: 7_Galpha13QL_1


title: Kieffer-Kwon-2017-HIC093

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

library_source: genomic

data_processing:
The paired end reads were aligned separately using BWA against the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

molecule: genomic DNA

source_name: B cells

growth_protocol: specificed in the SAMPLES section

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, or HiSeq 2500 following the manufacturer's protocols

treatment_protocol: treatment protocol for specific samples are specified in the SAMPLES section

tag: genotype

value: WT

value: spleen

tag: activation time

value: splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection

tag: protocol

value: in situ Hi-C

tag: treatment

value: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen); for acute ATP depletion, 20h-activated cells were shifted to glucose deficient media for 2h then, 2-Deoxy-D-glucose (5mM, Sigma) and Oligomycin (126nM, Sigma) were added to the culture for another 1.5-2h before the harvest.


title: 1_lacZ_1

source_name: Cells were transformed with recombinant adenoviruses encoding LacZ


title: 3_lacZ_3


title: Kieffer-Kwon-2017-HIC078

source_name: mouse ES cells

value: blastocyst


title: Kieffer-Kwon-2017-HIC068


title: Kieffer-Kwon-2017-HIC070


title: Kieffer-Kwon-2017-HIC079


title: Kieffer-Kwon-2017-HIC073


title: Kieffer-Kwon-2017-HIC071


title: 6_SmoA1_3


title: Kieffer-Kwon-2017-HIC069


title: Kieffer-Kwon-2017-HIC075


title: Kieffer-Kwon-2017-HIC074


title: Kieffer-Kwon-2017-HIC077


title: Kieffer-Kwon-2017-HIC058

value: Mycflox/flox-CRE

value: splenic B cells isolated from 6-8 weeks old RosaCreERTam/Myc flox/flox mouse spleen by negative selection

value: mice were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice); B cells were activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen)


title: Kieffer-Kwon-2017-HIC060


title: Kieffer-Kwon-2017-HIC059


title: Kieffer-Kwon-2017-HIC034


title: Kieffer-Kwon-2017-HIC032


title: Kieffer-Kwon-2017-HIC030


title: Kieffer-Kwon-2017-HIC031


title: Kieffer-Kwon-2017-HIC027


title: Kieffer-Kwon-2017-HIC029


title: Kieffer-Kwon-2017-HIC028


title: Kieffer-Kwon-2017-HIC033


title: Kieffer-Kwon-2017-HIC076


title: Kieffer-Kwon-2017-HIC072


title: Kieffer-Kwon-2017-HIC026

value: activated for 72 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen)


title: Kieffer-Kwon-2017-HIC067


title: Kieffer-Kwon-2017-HIC025


title: Kieffer-Kwon-2017-HIC024


title: Kieffer-Kwon-2017-HIC022


title: Kieffer-Kwon-2017-HIC020


title: Kieffer-Kwon-2017-HIC016


title: Kieffer-Kwon-2017-HIC015


title: Kieffer-Kwon-2017-HIC018


title: Kieffer-Kwon-2017-HIC021


title: Kieffer-Kwon-2017-HIC013


title: Kieffer-Kwon-2017-HIC012


title: Kieffer-Kwon-2017-HIC014


title: Kieffer-Kwon-2017-HIC019


title: Kieffer-Kwon-2017-HIC009


title: Kieffer-Kwon-2017-HIC010


title: Kieffer-Kwon-2017-HIC008


title: Kieffer-Kwon-2017-HIC007


title: Kieffer-Kwon-2017-HIC005


title: Kieffer-Kwon-2017-HIC011


title: Kieffer-Kwon-2017-HIC006


title: Kieffer-Kwon-2017-HIC023


title: Kieffer-Kwon-2017-HIC003


title: Kieffer-Kwon-2017-HIC002


title: E13.5_TFAM Ctrl_3

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC (mm9) genome assembly using tophat version 2.0.7, reads were count using htseq-count version 0.5.3
Genome_build: mm9
Supplementary_files_format_and_content: FPKM txt file

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.

extract_protocol:
RNA were purified by Qiagen RNeasy Mini Kit.
Polyadenylated RNA was isolated by Dynabeads®Oligo(dT).

treatment_protocol: E13.5 hearts were flash frozen in liquid nitrogen. 5 hearts were pooled for each replicate, and 3 replicates were performed for mutant (Tfamfl/fl; Nkx2.5IRES-Cre/+) and control (Tfamfl/+; Nkx2.5IRES-Cre/+) groups.

value: Primary tissue

tag: genotype/variation

value: Control


title: E13.5_TFAM Ctrl_2


title: HC19-CD4

city: Bethesda

first: Valentina

last: Giudice

address: 10 Center Drive

department: Hematology Branch

institute: NHLBI

data_processing:
Library strategy: Immune Repertoire Sequencing
Before alignment, raw reads were filtered to remove reads containing adaptor sequences, false positive, and low-quality reads.
For merging two paired-reads into one complete sequence, COPE software v1.1.3 (BGI, Cambridge, MA) was used for an overlap of >90% base matching (10 to 99 nucleotides [nt] for overlapped region).
For other reads, FqMerger software (BGI) was used for 90% identity (matched bases) with overlap length of 50 to 150 nt.
The alignment was performed by MiTCR software (milaboratory) using -pset flex -cysphe 1 -t 6 as parameters and by The International Immunogenetics Information System® (IMGT) as database (http://www.imgt.org).
The number of in-frame reads during analysis was counted as productive reads. The sequence included between the second conserved cysteine encoded by the 3’ region of Vβ gene segment and the conserved phenylalanine encoded by the 5’ portion of Jβ gene segment was considered as CDR3 β sequence
Supplementary_files_format_and_content: excel files containing frequences of reads, nucleotide and amino acid sequences of CDR3 region, and TCR VDJ genes rearrangements

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: PBMCs were isolated by Ficoll-Paque density gradient centrifugation from heparinized fresh whole PB

extract_protocol:
DNA was extracted using Qiagen DNA Mini Kit
TCR repertoire sequencing was performed with Illumina HiSeq 2000 sequencer (Illumina, Inc., San Diego, CA).

treatment_protocol: For VDJ combination and CDR3 sequence profiling, DNA was isolated from FACS-sorted CD4+ and CD8+ T cells from eight SAA patients with CD8+CD57+ cell expansion and three healthy subjects (mean, 2.4 μg of DNA; range, 1.2 – 3.4 μg). DNA was also isolated from beads-sorted (Miltenyi Biotec Inc., San Diego, CA) CD8+CD57+ cells from two of the eight SAA patients with enough cells for further analysis (mean, 1.6 μg of DNA; range, 1.0 – 2.3 μg).

tag: disease state

value: healthy control

value: Peripheral Blood

tag: population

value: CD4+ T cells

tag: sorting

value: Beads


title: HC18-CD4

tag: tissue


title: HC18-CD8

value: CD8+ T cells


title: HC19-CD8


title: HC17-CD4


title: E13.5_TFAM KO_3

tag: age

value: TFAM KO


title: E13.5_TFAM Ctrl_1

tag: cell type


title: E13.5_TFAM KO_2


title: E13.5_TFAM KO_1


title: HC16-CD8


title: HC17-CD8


title: HC15-CD4


title: HC14-CD4


title: HC15-CD8


title: HC14-CD8


title: AA11-CD4

value: acquired aplastic anemia


title: AA12-CD8


title: Kieffer-Kwon-2017-HIC004

value: WT

value: spleen

value: splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection


title: AA11-CD8


title: AA9-CD4


title: AA10-CD8


title: AA9-CD8


title: Kieffer-Kwon-2017-HIC017

value: in situ Hi-C


title: HC3-8

data_processing:
Library strategy: Immune Repertoire Sequencing
Before alignment, raw reads were filtered to remove reads containing adaptor sequences, false positive, and low-quality reads.
For merging two paired-reads into one complete sequence, COPE software v1.1.3 (BGI, Cambridge, MA) was used for an overlap of >90% base matching (10 to 99 nucleotides [nt] for overlapped region).
For other reads, FqMerger software (BGI) was used for 90% identity (matched bases) with overlap length of 50 to 150 nt.
The alignment was performed by MiTCR software (milaboratory) using -pset flex -cysphe 1 -t 6 as parameters and by The International Immunogenetics Information System® (IMGT) as database (http://www.imgt.org).
The number of in-frame reads during analysis was counted as productive reads. The sequence included between the second conserved cysteine encoded by the 3’ region of Vβ gene segment and the conserved phenylalanine encoded by the 5’ portion of Jβ gene segment was considered as CDR3 β sequence
Supplementary_files_format_and_content: files containing frequences of reads, nucleotide and amino acid sequences of CDR3 region, and TCR VDJ genes rearrangements

value: FACS


title: HC16-CD4


title: AA3-CD57

value: CD8+CD57+ T cells


title: AA4-CD57


title: HC2-4


title: AA8-8


title: HC2-8


title: AA12-CD4


title: HC1-4


title: AA6-8


title: AA8-4


title: AA5-8


title: AA4-8


title: AA7-8


title: AA5-4


title: AA7-4


title: AA3-4


title: AA3-8


title: AA4-4


title: AA2-8


title: AA10-CD4


title: Kieffer-Kwon-2017-HIC091

value: activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen); for acute ATP depletion, 20h-activated cells were shifted to glucose deficient media for 2h then, 2-Deoxy-D-glucose (5mM, Sigma) and Oligomycin (126nM, Sigma) were added to the culture for another 1.5-2h before the harvest.


title: AA2-4


title: AA1-8


title: Kieffer-Kwon-2017-HIC092


title: Kieffer-Kwon-2017-HIC089


title: HC1-8


title: HC3-4


title: Kieffer-Kwon-2017-HIC088


title: Kieffer-Kwon-2017-HIC086


title: Kieffer-Kwon-2017-HIC087


title: Kieffer-Kwon-2017-HIC084


title: Kieffer-Kwon-2017-HIC085


title: Kieffer-Kwon-2017-HIC066

value: 0h, TSA

value: treated with trichostatin A


title: Kieffer-Kwon-2017-HIC083


title: Kieffer-Kwon-2017-HIC081


title: Kieffer-Kwon-2017-HIC080


title: Kieffer-Kwon-2017-HIC064


title: Kieffer-Kwon-2017-HIC063


title: Kieffer-Kwon-2017-HIC056

value: Mycflox/flox-CRE

value: splenic B cells isolated from 6-8 weeks old RosaCreERTam/Myc flox/flox mouse spleen by negative selection

value: mice were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice); B cells were activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen)


title: Kieffer-Kwon-2017-HIC054


title: Kieffer-Kwon-2017-HIC053


title: Kieffer-Kwon-2017-HIC061


title: Kieffer-Kwon-2017-HIC057


title: Kieffer-Kwon-2017-HIC065


title: Kieffer-Kwon-2017-HIC052


title: Kieffer-Kwon-2017-HIC051


title: Kieffer-Kwon-2017-HIC050


title: Kieffer-Kwon-2017-HIC090


title: Kieffer-Kwon-2017-HIC049


title: Kieffer-Kwon-2017-HIC047


title: Kieffer-Kwon-2017-HIC048


title: Kieffer-Kwon-2017-HIC046


title: Kieffer-Kwon-2017-HIC044


title: Kieffer-Kwon-2017-HIC045


title: Kieffer-Kwon-2017-HIC043


title: Kieffer-Kwon-2017-HIC082


title: Kieffer-Kwon-2017-HIC062


title: Kieffer-Kwon-2017-HIC041


title: Kieffer-Kwon-2017-HIC036


title: Kieffer-Kwon-2017-HIC055


title: Kieffer-Kwon-2017-HIC042


title: Kieffer-Kwon-2017-HIC038


title: Kieffer-Kwon-2017-HIC037


title: Kieffer-Kwon-2017-HIC035


title: F12/gdv1-asKO 40-48 hpi

status: Public on May 04 2018

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

description: directional RNA-seq

data_processing:
RTA v2 software for base calling and bcl2fastq v2.16.0.10 conversion software for fastq conversion
Data were mapped with BWA samse (Version: 0.7.12-r1039) against the P.falciparum 3D7 transcriptome and reference genome (PlasmoDB version 26)
Sam files were converted to bam files and mapped reads were filtered to mapping quality ≥15 (SAM tools v1.2). Only uniquely mapped reads were used for further analysis.
Bam files were split into reads mapping to the sense strand (PlusStrand; FLAG16) and antisense strand (MinusStrand;FLAG0) respectively.
BedGraph files were generated to visualize directional RNA-seq data in the UCSC Genome Browser using bedtools genomecov with the option -bga and normalized using -scale and the scaling factor ‘1000000/amount of unique reads’.
Genome_build: P.falciparum 3D7 transcriptome and reference genome from PlasmoDB (version 26)
Supplementary_files_format_and_content: Bedgraph files - Purpose: Visualization of directional RNA-seq data in the UCSC Genome browser

molecule: polyA RNA

organism: Plasmodium falciparum

source_name: red blood cell stage, schizont

growth_protocol: P. falciparum F12 and F12/gdv1-asKO parasites were cultured as described (Trager et al. 1978). Growth synchronization was achieved by repeated sorbitol treatments (Lambros et al. 1979). F12/gdv1-asKO parasites were selected and cultured with 4 nM WR99210 (WR).

extract_protocol:
Total RNA was isolated using Ribozol (Amresco) according to the manufacturer’s manual and further purified using the RNeasy Plus Mini Kit (Qiagen) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
Isolated total RNA was PolyA-selected using the Oligotex mRNA Mini Kit (Qiagen, #70022) according to manufacturer’s instructions. Subsequently, 2µ of PolyA-selected total RNA equivalent were fragmented by alkaline hydrolysis (5x fragmentation buffer: 200mM Tris acetate pH 8.2, 500mM potassium acetate, 150mM magnesium acetate) for 1min 45sec at 85°C in a 150µl volume and precipitated as previously described in (Hoeijmakers, Bártfai and Stunnenberg 2013), followed by two TURBO DNase treatments (Ambion, #AM2238) to remove remnants of genomic DNA . Further library preparation for strand-specific RNA-seq was carried out as in (Kensche et al. 2015). In short, first strand cDNA synthesis was performed with AT-corrected Random N9 primers (76% AT) and in presence of 0.2µg Actinomycin D (Thermo 446 Fisher Scientific) to prevent unwanted DNA-dependent second strand cDNA synthesis. To maintain the strand-specific information during second strand synthesis dTTPs were replaced with dUTPs. Resulting double stranded cDNAs (1.9-3.2ng) were end repaired and extended with 3’ A-overhangs. After ligation of NextFlex adapters (Bio Scientific, #514122), libraries were treated with USER enzyme (NEB, #M5505L) to specifically degrade the dUTP-containing second strand and subsequently amplified by PCR (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems, #KM2602) and NEXTflex primer mix (Bio Scientific, #514122). Next, libraries were size-selected for 300-400 bp fragments using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02) and amplified for another 12 cycles using the same PCR protocol as above. Subsequent depletion of adapter dimers and library purification was performed using Agencourt AMPure XP beads (Beckman Coulter, #A63880) in a 1:1 library beads ratio.

treatment_protocol: F12 and F12/gdv1-asKO parasites were synchronized twice 16 hrs apart to obtain an eight hour growth window. Parasites were harvested at 32-40 hpi and 40-48 hpi.

tag: developmental stage

value: red blood cell stage, schizont

tag: genomic modification

value: wildtype


title: F12 32-40 hpi

description: directional RNA-seq

value: gdv1-asRNA loss-of-function mutant line generated using CRISPR/Cas9-based genome editing


title: F12/gdv1-asKO 32-40 hpi

description: directional RNA-seq


title: GDVDD_6h_ON_GFP

description:
chip antibody: anti-mouse GFP antibody (Roche Diagnostics, #11814460001)
anti-GFP ChIP

data_processing:
RTA v2 software for base calling and bcl2fastq v2.16.0.10 conversion software for fastq conversion
Data were mapped with BWA samse (Version: 0.7.12-r1039) to the P. falciparum 3D7 reference genome from PlasmoDB version 26 (http://www.plasmodb.org).
Sam files were converted to bam files, q15 filtered and filtered for unique reads
Bedgraph files were generated using bedtools genomecov with the option –bga (regions with zero coverage are also reported) and normalized using the option -scale and the scaling factor ‘1000000/amount of unique reads’.
Begraph log2 ratio or substraction files were genereated using bedtools unionbedg
Genome_build: PlasmoDB Plasmodium falciparum 3D7 release 26
Supplementary_files_format_and_content: Bedgraph log2 ratio files show the coverage as log2 ratio of ChIP over Input calculated using normalized Bedgraph files
Supplementary_files_format_and_content: Bedgraph substraction files show the coverage as substraction of GDVDD ON ChIP minus GDVDD OFF ChIP calculated using the normalized Begraph files

growth_protocol: Parasite-infected red blood cells were cultured in petri dishes at 5% hematocrit in the presence of  3% O2 and  4% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax and 50mg/l Neomycin sulphate. The  3D7/GDV1-GFP-DD parasite line was cultured in presence of 4nM WR99210 (WR).

extract_protocol:
Synchronized 3D7/GDV1-GFP-DD schizonts on and off Shield1 at 5% parasitemia were cross-linked by incubation with a final concentration of 1% formaldehyde for 15 min at 37ºC. The cross-linking reaction was quenched by addition of 0.125M glycine (final concentration). Nuclei were isolated by releasing parasites from iRBCs using 0.05% saponin followed by lysis in CLB (20 mM Hepes, 10mM KCl, 1mM EDTA, 1mM EGTA, 0.65% NP-40, 1mM DTT supplemented with protease inhibitor). Nuclei were washed and snap-frozen in CLB supplemented with 50% glycerol. To obtain fragmented chromatin for ChIP, nuclei were resuspended in sonication buffer (50 mM Tris pH:8.0, 1% SDS, 10mM EDTA, supplemented with protease inhibitor) and sonicated for 20 cycles of 30 sec ON/30 sec OFF (setting high, BioruptorTM, Diagenode). Fragment sizes ranged from 200-600 bp as determined by decrosslinking a 50μl aliquot and running the purified DNA on a 1.5% agarose gel.    ChIPs were performed by incubating ~500 ng (DNA-content) sonicated chromatin from 3D7/GDV1-GFP-DD on and off Shield1 overnight while rotating at 4°C with 1 μg mouse anti-GFP (Roche Diagnostics, #11814460001) or 1 μg rabbit anti-PfHP1 (Brancucci et al. 2014), respectively, in incubation buffer (5% Triton-X-100, 750mM NaCl, 5mM EDTA, 2.5mM EGTA, 100mM Hepes pH 7.6) with 10 μl protA and 10 μl protG Dynabeads (Life Technologies, 10008D and 10009D). Beads were washed for 5 min at 4°C while rotating with 400 μl of the following wash buffers: 2x wash buffer 1 (0.1% SDS, 0.1% DOC, 1.0% Triton-X100, 1mM EDTA, 0.5mM EGTA, 20mM Hepes pH 7.6), 1x wash buffer 2 (0.1% SDS, 0.1% DOC, 1.0% Triton-X100, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 20 mM Hepes pH 7.6), 1x wash buffer 3 (250mM LiCl, 0.5% DOC, 0.5% NP-40, 1mM EDTA, 0.5mM EGTA, 20mM Hepes pH7.6), 2x wash buffer 4 (1mM EDTA, 0.5mM EGTA, 20 mM Hepes pH7.6). The immunoprecipitated chromatin was eluted in 200 μl elution buffer (1% SDS, 0.1M NaHCO3) while rotating for 20 min at RT and decrosslinked in decrosslinking buffer (1%SDS, 0.1M NaHCO3, 1M NaCl) in a 45°C shaking heat-block overnight. In parallel, 30 μl of sonicated input chromatin was decrosslinked under the same conditions. The DNA was purified over QIAquick MinElute PCR columns (Qiagen) and eight separate anti-GFP or two anti PfHP1ChIPs were pooled over one column.
For each sequencing library generated from 3D7/GDV1-GFP-DD parasites 1ng (anti-mouse GFP antibody) , 5ng (anti-HP1 antibody) of ChIP DNA or 1 ng of the input DNA were end repaired, extended with 3′ A-overhangs, and ligated to barcoded NextFlex adapters (Bio Scientific,  #514122). Libraries were amplified using the KAPA HiFi HotStart ready mix (KAPA Biosystems) and NextFlex primer mix (Bio Scientific, #514122) as follows: 98 °C for 2 min; 4 cycles of 98 °C for 20 sec, 62 °C for 3 min; 62 °C for 5 min. Amplified libraries were gel size-selected for 225-325 bp (mono-nucleosomes + ~125 bp NextFlex adapter) using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02) and again amplified as described above for 10 cycles. Libraries were purified and adapter dimers removed by Agencourt AMPure XP beads purification using a1:1 library beads ratio (Beckman Coulter, #A63880).

treatment_protocol: Parasite cultures were synchronized by repeated sorbitol treatments (Lambros and Vanderberg, 1979).

value: episomal GDV1-GFP-DD construct, driven by calmodulin promoter


title: GDVDD_10h_ON_Input


title: GDVDD_10h_ON_HP1

description:
chip antibody: anti-rabbit PfHP1 antibody (Brancucci et al. 2014)
anti-PfHP1 ChIP


title: GDVDD_2h_OFF_GFP


title: GDVDD_6h_OFF_GFP


title: GDVDD_10h_OFF_GFP


title: GDVDD_10h_OFF_HP1


title: GDVDD_2h_ON_GFP


title: GDVDD_10h_OFF_Input


title: HP1_T2 - replicate3

city: Sao Paulo

first: Erika

middle: Maria

last: de Jesus

state: SP

address: Rua do Matao, 277, sala 153

department: Botany

country: Brazil

institute: University of Sao Paulo

description: transformed with a vector that expresses a hairpin of a Tnt1 retrotransposon reverse transcriptase fragment

data_processing:
Raw sequences were analysed through CLC Genomics Workbench program
Sequences were mapped against the tobacco unigenes present in Genbank, since tobacco´s genome is not completely sequenced up to now
Expression values were calculed as RPKM (Mortazavi et al. 2008), square rooted and Bonferroni’s correction was applied
Statistical analysis was performed using multiple t-test in CLC Genomics Workbench program

organism: Nicotiana tabacum

source_name: leaf

growth_protocol: in vitro transgenic plants were cultivated in MS20 media with the proper antibiotic, under a 14-hour photoperiod at 24oC

extract_protocol:
LiCl method according to Sambrook 1989
SOLID Total RNA-seq Kit (Ambion), according to Whole Transcriptome Library Preparation for SOLID Sequencing Protocol (Applied Biosystems)

tag: transgene

value: 35S-sense fragment-intron-antisense fragment-terminator OCS (hairpin) + hygromycin resistance + reporter gene GUS

tag: age of the plant

tag: origin of the plant

value: HP1(T2) is originated from the auto-pollination of HP1(T1)


title: HP1_T2 - replicate4


title: HP1_T2 - replicate2


title: Kieffer-Kwon-2017-HIC040

tag: strain

value: spleen


title: Kieffer-Kwon-2017-HIC039

tag: genotype


title: HP1_T1 - replicate3

value: regenerant from transformation


title: HP1_T2 - replicate1


title: HP1_T1 - replicate2


title: HP1_T1 - replicate1


title: F12 40-48 hpi

description: directional RNA-seq


title: HP8_T1 - replicate2


title: C - replicate4

description: transformed with the empty vector

value: 35S-intron-terminator OCS (hairpin) + hygromycin resistance


title: HP8_T1 - replicate1


title: HP8_T1 - replicate3


title: GDVDD_10h_ON_GFP


title: HP8_T1 - replicate4


title: C - replicate3

description: transformed with the empty vector


title: C - replicate2

description: transformed with the empty vector


title: C - replicate1

description: transformed with the empty vector


title: WT - replicate4

description: wild-type tobacco plant

value: wild-type


title: WT - replicate1

description: wild-type tobacco plant


title: 1ypf_rep2

city: Dresden

first: Nikolay

last: Ninov

address: Fetscherstrasse 105

country: Germany

institute: CRTD

data_processing:
Trimming using trim_galore using default parameters
Mapping using HISAT2 with default parameters
Counts per gene generated using htseq-count with default parameters
sam files converted to bam using samtools
Genome_build: Zebrafish GRCz10
Supplementary_files_format_and_content: read counts were generated using htseq-count

organism: Danio rerio

source_name: beta-cells

extract_protocol:
FACS
llumina HiSeq2500 in 2x75bp paired-end mode

value: 1 year


title: WT - replicate2

description: wild-type tobacco plant


title: 3mpf_rep1

value: 3 month


title: MT-2

city: Hangzhou

first: Lin

last: Lin

state: Zhejiang

address: No.268, Kaixuan Road

department: Institute of Nuclear-Agricultural Sciences

institute: Zhejiang University

description: with 100 mM H2O2 treatment for 30 minutes

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R1 whole genome using soap maximum number of mismatches allowed = 2bp，  number of valid alignments per read pair (-k) = 40
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans_R1_uid57665
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

source_name: DqsR knockout strain

growth_protocol: D. radiodurans R1 and its derivatives were grown at 30°C in TGY broth (0.5% tryptone, 0.1% glucose, and 0.3% yeast extract).

extract_protocol:
RNA was harvested using Trizol reagent. 4 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For treated group, Cells were incubated to an OD600 of approximately 0.8, centrifuged and resuspended in phosphate buffer, then treated with 100 mM H2O2 for 30 minutes.

value: DqsR knockout strain


title: MT-1

value: with 100 mM H2O2 treatment for 30 minutes


title: MU-1

description: under normal conditions

value: under normal conditions


title: WT-1

source_name: wild type

value: wild type


title: WT-2


title: MU-2

description: under normal conditions


title: HP1_T1 - replicate4


title: WU-1

description: under normal conditions


title: WU-2

description: under normal conditions


title: mRNAseq_Ebr_polyA__het.rep1

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 1

data_processing:
Basecalls performed using CASAVA version CASAVA-1.8.2
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d
Genome_build: mm9
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script.  We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.

extract_protocol:
Total RNA from cerebral cortical regions of control, Sfpq+/-,and Sfpq+/- brains were extracted using Rneasy Plus Micro (Qiagen) according to the manufacturer’s instructions.
Illumina Stranded-RNA-Seq protocol

value: Sfpq+/-

value: mouse embryonic cerebral cortex

value: neuronal stem cell + neuron


title: mRNAseq_Ebr_polyA__homo.rep1

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 1

value: Sfpq-/-


title: mRNAseq_Ebr_polyA__homo.rep3

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 3


title: mRNAseq_Ebr_polyA__het.rep3

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 3


title: mRNAseq_Ebr_polyA__homo.rep2

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 2


title: mRNAseq_Ebr_polyA__het.rep2

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 2


title: mRNAseq_Ebr_polyA__cont.rep1

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 1

value: control


title: WT - replicate3

description: wild-type tobacco plant


title: sfpq_hetero_KO.rep2

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 2

data_processing:
Basecalls performed using CASAVA version CASAVA-1.8.2
The seuqence data was mapped to the genome sequence with Tophat ver. 1.4.1.
Genome_build: mm9
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script.  We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.

source_name: E13.5 mouse embryonic cerebral cortex

extract_protocol:
Total RNA from cerebral cortical regions of control, Sfpq+/-,and Sfpq+/- brains were extracted using Rneasy Plus Micro (Qiagen) according to the manufacturer’s instructions.
Briefly, total RNA was treated with Ribo-Zero™ rRNA removal Kit (Epicentre, illumina) and libraries were constructed with a protocol modified from illumina immature staranded-RNA-seq protocol by GeNAS sequencing facility, RIKEN JAPAN (http://www.osc.riken.jp/english/technicalservice/about/).

value: embryonic cerebral cortex

tag: rna type

value: polyA(+/-) RNA


title: sfpq_hetero_KO.rep3

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 3


title: sfpq_homo_KO.rep1

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 1


title: sfpq_homo_KO.rep2

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 2


title: 1ypf_rep1


title: control.rep1

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 1


title: control.rep3

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 3


title: sfpq_homo_KO.rep3

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF homo kockout), replicate 3


title: SFPQ_CLIP_E13CTX__SMinput

data_processing:
library strategy: CLIP-seq
Basecalls performed using Torrent Suite version 5.0.4
Reads which lengths were >= 50 and average sequencing quality scores were >= 17, were used for the study.
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d
Genome_build: mm9
Supplementary_files_format_and_content: Peak call was performed with Clipper ver. 1.1

extract_protocol:
Extraction of RNAs from transferred membrane was performed according to the eCLIP protocol (Van Nostrand et al. 2016  Nat Methods.) .
Ion Total RNA-Seq Kit (Life Technology)

tag: molecule subtype

value: Size matched input


title: SFPQ_CLIP_E13CTX__IP2

tag: antibody

value: anti-Sfpq antibody

value: IP-ed RNA using Sfpq antibody


title: Kieffer-Kwon-2017-HIC001

value: WT

value: spleen

tag: activation time

value: splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection

tag: protocol

value: in situ Hi-C

tag: treatment

value: activated for 72 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen)


title: control.rep2

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 2

tag: genotype/variation


title: SFPQ_CLIP_N2A__SMinput

growth_protocol: Neuro-2A cell was expanded in D-MEM with 10% FCS, glutamine, and antibiotics (Penicillin/Streptomycin)

treatment_protocol: Induced differentiation in D-MEM with 2% FCS, glutamine, and antibiotics (Penicillin/Streptomycin) and subjected to sample preparation after 24 hrs

value: neronal differentiated condition


title: SFPQ_CLIP_E13CTX__IP1

tag: tissue


title: (III) polII_ChIP__N2A__Spq_KD

description: pol II ChIP-Seq data for Sfpq-knockdown Neuro-2a cells

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
Reads which lengths were >= 50 and average sequencing quality scores were >= 17, were used for the study.
The seuqence data was mapped to the genome sequence with bowtie2 ver. 2.1.0.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated with bedtools.

growth_protocol: Neuro-2A cell was expanded in D-MEM with 10% FCS, glutamine, and antibiotics (Penicillin/Streptomycin) .

extract_protocol:
Lysates were clarified after micrococcal nuclease treatment and RNA-Poymerase II-DNA complexes were isolated with antibody.
Libraries were prepared according to Life Techonology's instructions accompanying the Ion XpressTM Plus gDNA Fragment Library Preparation Kit. Briefly, DNA fragment was treated with the mixture of T4 DNA Polymerase, DNA Polymerase I, Large (Klenow) Fragment, T4 Polynucleotide Kinase using T4 DNA Ligase Buffer (New England Biolabs, Ipswich, MA, UK). ChIP-seq Libraries were prepared from the pretreated ChIP DNA using the Life Techonology Ion XpressTM Plus gDNA Fragment Library Preparation Kit. Ligation products were size-selected by LabChip XT and LabChip XT DNA 750 Assay Kit (PerkinElmer, Waltham, MA, USA). After purifying constructed libraries with Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA), high-throughput sequencing was performed using the Ion Proton System.

treatment_protocol: Knockdown of Sfpq was conducted with reveres transfection using Stealth siRNA and RNAiMAX in differentiation media of D-MEM with 2% FCS, glutamine, and antibiotics (Penicillin/Streptomycin).

value: siRNA for mSfpq using, RNAiMAX

tag: growth condition

value: differentiated condition

tag: chip antibody

value: Anti-RNA polymerase II Antibody, clone CTD4H8 (Millipore, catalog#:05-623, lot#:2378012)


title: SFPQ_CLIP_N2A__IP2

tag: cell type


title: SFPQ_CLIP_N2A__IP1


title: mRNAseq_Ebr_polyA__cont.rep3

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 3

tag: developmental stage

value: mouse embryonic cerebral cortex

value: neuronal stem cell + neuron


title: (II) N2A__rRNA_dep__Sfpq_KD

description: RNA-seq (polyA+/-) data for Sfpq-knockdown Neuro-2a cells

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
Reads which lengths were >= 50 and average sequencing quality scores were >= 17, were used for the study.
Reads mapped to rRNA or tRNA sequences were removed from the following analysis.
The seuqence data was mapped to the genome sequence with Tophat ver. 2.0.10.
Genome_build: mm9
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script.  We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.

extract_protocol:
Libraries were prepared according to Life Techonology's instructions accompanying the Ion AB Library Builder™ System and Library Builder. Briefly, total RNA was treated with RiboMinus™ Eukaryote System v2 (Life technologies, Carlsbad, CA, USA) to ribosomal RNA-depleted RNA. RNA libraries were then prepared using the Life Techonology Ion Total RNA-Seq Kit for the AB Library Builder™ System and Library Builder. High-throughput sequencing was performed using the Ion Proton System. Sfpq mRNA level was down-regulated less than 10% in Neuro-2a treated with Sfpq-siRNA comparing those of Luc-siRNA.
Total RNA from Neuro-2a cells were extracted using RneasyMidi (Qiagen) according to the manufacturer’s instructions.

value: siRNA for mSfpq, using RNAiMAX


title: mRNAseq_Ebr_polyA__cont.rep2

description: mRNA-seq (polyA+) data from neuronal stem cell + neurons of  E13.5 mouse (control), replicate 2

value: control


title: (III) polII_ChIP__N2A__Luc_KD

description: pol II ChIP-Seq data for Luc-knockdown Neuro-2a cells

value: siRNA for Luciferase, using RNAiMAX


title: (I) N2A__mRNA_seq__Sfpq_KD.rep3

description: RNA-seq (polyA+) data for Sfpq-knockdown Neuro-2a cells, replicate 3

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
Reads which lengths were >= 50 and average sequencing quality scores were >= 17, were used for the study.
The seuqence data was mapped to the genome sequence with Tophat ver. 2.0.10.
Genome_build: mm9
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with an in-house perl script.  We counted read counts mapped on exons, then normalized them with library sizes and sum of exon lengths (RPKM; Reads Per Kilobase of exon Model per million mapped reads). In the processed data files, gene ID and RPKM values were described column 1 and 2, respectively.

extract_protocol:
Libraries were prepared according to Life Techonology's instructions accompanying the Ion AB Library Builder™ System and Library Builder. Briefly, total RNA was treated with Dynabeads® mRNA DIRECT™ Microkit to prepare PolyA-selected messenger RNA. RNA libraries were then prepared using the Life Techonology Ion Total RNA-Seq Kit for the AB Library Builder™ System and Library Builder. High-throughput sequencing was performed using the Ion Proton System. Sfpq mRNA level was down-regulated less than 10% in Neuro-2a treated with Sfpq-siRNA comparing those of Luc-siRNA.
Total RNA from Neuro-2a cells were extracted using RneasyMidi (Qiagen) according to the manufacturer’s instructions.

value: polyA(+) RNA


title: (I) N2A__mRNA_seq__Sfpq_KD.rep2

description: RNA-seq (polyA+) data for Sfpq-knockdown Neuro-2a cells, replicate 1


title: (I) N2A__mRNA_seq__Sfpq_KD.rep1


title: (I) N2A__mRNA_seq__Luc_KD.rep2

description: RNA-seq (polyA+) data for Luc-knockdown Neuro-2a cells, replicate 2


title: (I) N2A__mRNA_seq__Luc_KD.rep3

description: RNA-seq (polyA+) data for Luc-knockdown Neuro-2a cells, replicate 3


title: (II) N2A__rRNA_dep__Luc_KD

description: RNA-seq (polyA+/-) data for Luc-knockdown Neuro-2a cells

value: polyA(+/-) RNA


title: sfpq_hetero_KO.rep1

description: RNA-seq (polyA+/-) data from neuronal stem cell + neurons of  E13.5 mouse (PSF hetelo kockout), replicate 1

tag: age

value: embryonic cerebral cortex


title: (I) N2A__mRNA_seq__Luc_KD.rep1

description: RNA-seq (polyA+) data for Luc-knockdown Neuro-2a cells, replicate 1


title: WT5

city: London

first: Rita

last: Monteiro

address: 1 Midland Road

department: Developmental Biology Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description: Untreated embryos, replicate 5

data_processing:
Bases were called using Casava version 1.8.2
Paired-end reads were aligned to a revised version of X. tropicalis gene models 7.2 using Tophat2 (version 2.1.1) with the following parameters: -p 12 --transcriptome-index= xenTro7 --no-novel-juncs --no-coverage-search.
Only read pairs that uniquely align to one gene were counted using HTSeq-count (Anders, Pyl, and Huber, 2015). Differential expression analysis was performed with raw fragment counts using DESeq2 (Love et al., 2014)
For genome browser visualisation, paired-end reads were mapped to the X. tropicalis genome assembly 7.1 and known off-genome EST assemblies using Tophat (version 2.0.10) with the following parameters: -r 77 --mate-std-dev 110 -G v7.2 (gene models of version 7.2 as used above) -g 200 --report-secondary-alignments.
Genome_build: X. tropicalis v7.1  available at ftp://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1/xenopus_tropicalis_v7.1.tar.gz
Supplementary_files_format_and_content: text file with raw counts.  The GTF with gene IDs and chromosomal locations is available on the series record.

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: Embryos were grown to the indicated developmental stage in 5% MMR at 25ºC.

extract_protocol:
10 embryos were homogenised in 400 µl TRIzol (Thermo Fisher Scientific) by vortexing. For phase separation, 80 µl of chloroform was added to the homogenate, shaken vigorously for 15 secs before spinning for 5 mins at 16,000 g at 4ºC. The aqueous phase containing total RNA which was precipitated with one volume of 100% ethanol and cleaned using the RNA Clean and Concentrator 5 or 25 (Zymo Research) with in-column 3 U Turbo DNase (Thermo Fisher Scientific) treatment according to the manufacturer’s instructions.
Libraries were made from ~2 µg total RNA by following version 2 of the TruSeq RNA low sample protocol (Illumina) following the manufacturer's instructions.

treatment_protocol: Embryos were exposed to 0.3M LiCl at 32-cell stage or irradiated with UV for 2 minutes within the first 30 minutes after fertilisation.

value: wild-type (out-bred Nigerian)

value: embryo

value: gastrula (stage NF11-11.5)

value: untreated


title: WT2

description: Untreated embryos, replicate 2


title: WT3

description: Untreated embryos, replicate 3


title: UV5

description: Embryos treated with UV, replicate 5

value: UV


title: UV2

description: Embryos treated with UV, replicate 2


title: UV4

description: Embryos treated with UV, replicate 4


title: UV3

description: Embryos treated with UV, replicate 3


title: LiCl5

description: Embryos treated with LiCl, replicate 5

value: LiCl


title: LiCl3

description: Embryos treated with LiCl, replicate 3


title: LiCl4

description: Embryos treated with LiCl, replicate 4


title: LiCl2

description: Embryos treated with LiCl, replicate 2


title: LiCl1

description: Embryos treated with LiCl, replicate 1


title: MCF7_siEPIC1#2

status: Public on May 03 2018

city: Pittsburgh

first: Da

address: 308 Salk Pavilion

institute: University of Pittsburgh

data_processing:
Sequenced reads were mapped to whole genome using STAR
Read counts were calculated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% FBS, and cells were cultured at 37 degree Centigrade and 5% CO2.

extract_protocol:
After transfection for 72 hours, total RNA was isolated using Rneasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 40 nM siRNAs targeting EPIC1 or a control gene luciferase using the Lipofectamine RNAiMAX (Life Technologies).

tag: cell line

value: human breast adenocarcinoma cell line

tag: transfection

value: EPIC1 siRNA


title: MCF7_siEPIC1#1


title: MCF7_siLuc_1

value: Control siRNA


title: Infect, 6.25 h, mRNA, rep2

city: Tianjin

first: Yongquan

address: No. 94, Weijin Road

institute: Nankai University

data_processing:
Illumina Casava1.8 software used for basecalling.
adaptors of RNA-seq and ribosome profiling reads were trimmed using FASTX Toolkit (v0.0.13.2). The tRNA and rRNA reads were removed by Bowtie (v1.0.1, -l 20). The reads were mapped to both the human genome (Ensembl, GRCh37) and the EV71 genome (GenBank, AB469182.1) using Tophat (v2.0.11).
Raw counts of protein-coding genes were quantified by HTSeq (v0.6.1p2). Raw counts of the host genes and the EV71 genes were combined and RPKMs (reads per kilobase of transcript per million reads) were calculated by edgeR.
Genome_build: Ensembl GRCh37; AB469182.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: muscle and virus

growth_protocol: High glucose DMEM with 10% FBS and 4mM L-Gln

extract_protocol:
Cell were harvest and RNA was extracted as TruSeq Ribo Profile (Mammalian) Kit (Illumina) manual.
RNA libraries were prepared for sequencing using TruSeq Ribo Profile (Mammalian) Kit (Illumina)

treatment_protocol: 100 μg/mL cycloheximaide for 9 minutes

value: RD

tag: infection

value: Enterovirus 71

tag: virus strain

tag: time


title: Infect, 6.25 h, RPF, rep2

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.8 software used for basecalling.
adaptors of RNA-seq and ribosome profiling reads were trimmed using FASTX Toolkit (v0.0.13.2). The tRNA and rRNA reads were removed by Bowtie (v1.0.1, -l 20). The reads were mapped to both the human genome (Ensembl, GRCh37) and the EV71 genome (GenBank, AB469182.1) using Tophat (v2.0.11).
Raw counts of protein-coding genes were quantified by HTSeq (v0.6.1p2). Raw counts of the host genes and the EV71 genes were combined and RPKMs (reads per kilobase of transcript per million reads) were calculated by edgeR.
Genome_build: Ensembl GRCh37; AB469182.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample


title: Mock,6.25 h, mRNA, rep2

source_name: muscle

value: mock

value: not applicable


title: Mock,6.25 h, RPF, rep2


title: Infect, 3.5 h, RPF, rep2


title: Mock,6.25 h, mRNA, rep1


title: Mock,3.5 h, mRNA, rep2


title: Infect, 3.5 h, mRNA, rep2


title: Infect, 6.25 h, mRNA, rep1


title: WT4

description: Untreated embryos, replicate 4

tag: strain


title: Mock,6.25 h, RPF, rep1


title: Infect, 6.25 h, RPF, rep1


title: WT1

description: Untreated embryos, replicate 1


title: Mock,3.5 h, mRNA, rep1


title: UV1

description: Embryos treated with UV, replicate 1


title: Mock,3.5 h, RPF, rep1


title: Infect,1.75 h, RPF


title: Mock,3.5 h, RPF, rep2


title: Mock,1.75 h, RPF


title: Infect, 3.5 h, mRNA, rep1


title: Infect, 3.5 h, RPF, rep1


title: Mock,1.75 h, mRNA


title: Human_8-cell_RNA-seq_amanitin_re2

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

description: amanitin.txt

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the hg19 genome assembly using tophat 2.1.1, transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: hg19

source_name: Preimplantation embryo

growth_protocol: After the control and alpha-amanitin treated embryos reaching the expected developmental stage (2-cell and 8cell stage), embryos were collected and zona pellucida gently removed by treatment of 10 IU/ml Pronase (Sigma P8811)

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

treatment_protocol: After ICSI 18h, transferred the zygotes to G1 media with alpha-amanitin (25ng/ul, Sigma-Aldrich) when embryos development to the pronuclear stage. The control pronuclear stage embryos were transferred to G1 media.


title: Infect,1.75 h ,mRNA


title: Human_8-cell_RNA-seq_control_re2

description: amanitin.txt


title: Human_8-cell_RNA-seq_control_re1

description: amanitin.txt


title: Human_8-cell_RNA-seq_amanitin_re1

description: amanitin.txt


title: Human_2-cell_RNA-seq_amanitin_re1

description: amanitin.txt


title: Human_naive_hESC2_ATAC-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: hg19
Supplementary_files_format_and_content: *peaks.bed: Bed files include ATAC-seq peaks.

source_name: Embryonic stem cell

growth_protocol: The medium for 5iL/A-hESC culture (abbreviated as 5iL/A medium) contains DMEM/DF12 and Neurobasal medium mixed at 1:1 ratio, 0.5 × N2 supplement, 0.5 × B27 supplement, 1 mM GlutaMax, 1% NEAA, 0.1 mM β-mercaptoethanol, 50 ug/ml BSA, 1 μM PD0325901, 20 ng/ml human LIF, 1 μM IM-12 (Enzo), 0.5 μM SB590885 (R&D), 1 μM WH-4-023 (A Chemtek), 10 μM Y27632, 20 ng/ml Activin A (Peprotech).

extract_protocol: ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification

treatment_protocol: ES is incubated in lysis buffe for further ATAC-seq experiment

value: Embryonic stem cell


title: Human_naive_hESC1_ATAC-Seq

data_processing:
Basecalls performed using CASAVA version 1.9
ATAC-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: hg19
Supplementary_files_format_and_content: *peaks.bed: Bed files include ATAC-seq peaks.

growth_protocol: The medium for t2iL/Gö-hESCs culture (abbreviated t2iL/Gö medium) contains DMEM/DF12 and Neurobasal medium mixed at 1:1 ratio, 0.5 × N2 supplement, 0.5 × B27 supplement, 2 mM GlutaMax, 1% NEAA, 0.1 mM β-mercaptoethanol, 50 ug/ml BSA, 10 ug/ml insulin, 1 μM PD0325901, 1 μM CHIR99021, 50 ug/ml L-ascorbic acid (Sigma-Aldrich), 10 ng/ml human LIF, 2.5 μM Gö6983 (Sigma-Aldrich) and 10 μM Y27632 (Selleck).


title: Human_ICM_RNA-Seq_re2

description: expression.txt

growth_protocol: All the 2PN zygotes were cultured to 8-cell using G-1 (Vitrolife) human embryos culture medium,and G-2 (Vitrolife) was used from  8-cell to blastocyst stage in incubater 37℃，6% CO2

treatment_protocol: ICM and TE were separated by laser

value: ICM


title: Human_ICM_RNA-Seq_re1

description: expression.txt


title: Human_2-cell_RNA-seq_control_re2

description: amanitin.txt


title: Human_2-cell_RNA-seq_amanitin_re2

description: amanitin.txt


title: Human_8-cell_RNA-Seq_re1

description: expression.txt

growth_protocol: All the 2PN zygotes were cultured to 8-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.

treatment_protocol: Intra Cytoplasmic Sperm Injection (ICSI) was used in this investigation rather than classical IVF to prevent contamination of sperm and cumulus cell’s DNA. Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 8-cell stages embryos were frozen for ATAC-seq,and zona-pelucida was removed using laser Firstly.


title: Human_2-cell_RNA-seq_control_re1

description: amanitin.txt


title: Human_8-cell_RNA-Seq_re2

description: expression.txt


title: Human_2-cell_RNA-Seq_re2

description: expression.txt

growth_protocol: All the 2PN zygotes were cultured to 2-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2

treatment_protocol: Intra Cytoplasmic Sperm Injection (ICSI) was used in this investigation rather than classical IVF to prevent contamination of sperm and cumulus cell’s DNA. Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 2-cell stages embryos were frozen for RNA-seq,and zona-pelucida was removed using laser Firstly.


title: Human_2-cell_3PN_RNA-Seq_re1

description: expression.txt

growth_protocol: All the 3PN zygotes were cultured to 2-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2

treatment_protocol: Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 3PN zygote were and cultured to 2Cell stag,and zona-pelucida was removed using laser. 2Cell stages embryos were frozen for RNA-seq.


title: Human_4-cell_3PN_RNA-Seq_re1

description: expression.txt

treatment_protocol: Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 3PN zygote were and cultured to 4Cell stag,and zona-pelucida was removed using laser. 2Cell stages embryos were frozen for RNA-seq.


title: Human_MII_RNA-Seq_re2

description: expression.txt

growth_protocol: MII  oocyte were collected in G-mops(Vitrolife) at 37℃

value: MII oocyte


title: Human_2-cell_RNA-Seq_re1

description: expression.txt


title: Human_4-cell_3PN_RNA-Seq_re2

description: expression.txt

growth_protocol: All the 3PN zygotes were cultured to 4-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2


title: Human_GV_RNA-Seq_re2

description: expression.txt

growth_protocol: GV oocyte were collected in G-mops(Vitrolife) at 37℃

value: GV oocyte


title: Human_MII_RNA-Seq_re1

description: expression.txt

growth_protocol: MII oocyte were collected in G-mops(Vitrolife) at 37℃


title: Human_ICM_ATAC-Seq_re2

description:
icm_2pn_100bp_rpkm.wig
icm_2pn_peaks.bed

growth_protocol: All the 2PN zygotes were cultured to 8-cell using G-1 (Vitrolife) human embryos culture medium,and G-2 (Vitrolife) was used from  8-cell to blastocyst stage in incubater 37℃，6% CO2.

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification


title: Human_hESC_ATAC-Seq_re2

description:
primed_hESC_100bp_rpkm.wig
primed_hESC_peaks.bed

growth_protocol: hESCs were cultured in matrigel coated plate with DMEM/F-12   N2, B27, 1 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM -mercaptoethanol and 20 ng/ml recombinant human bFGF

extract_protocol:
ES is incubated in lysis buffe for further ATAC-seq experiment
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification


title: Human_8-cell_3PN_ATAC-Seq_re2

description:
8cell_3pn_100bp_rpkm.wig
8cell_3pn_peaks.bed

growth_protocol: All the 3PN zygotes were cultured to 8-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.

treatment_protocol: Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 3PN zygote were and cultured to 2Cell stag,and zona-pelucida was removed using laser. 8Cell stages embryos were frozen for ATAC-seq.


title: Human_hESC_ATAC-Seq_re1

growth_protocol: hESCs were maintained on Matrigel (BD Biosciences)-coated plates (Corning) in E8 medium (STEMCELL Technologies)


title: Human_ICM_ATAC-Seq_re1


title: Human_8-cell_3PN_ATAC-Seq_re1


title: Human_8-cell_ATAC-Seq_re2

description:
8cell_2pn_100bp_rpkm.wig
8cell_2pn_peaks.bed

growth_protocol: All the 2PN zygotes were cultured to 2-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.


title: Human_4-cell_3PN_ATAC-Seq_re2

description:
4cell_3pn_100bp_rpkm.wig
4cell_3pn_peaks.bed

growth_protocol: All the 3PN zygotes were cultured to 4-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.

treatment_protocol: Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 3PN zygote were and cultured to 2Cell stag,and zona-pelucida was removed using laser. 2Cell stages embryos were frozen for ATAC-seq.


title: Human_4-cell_3PN_ATAC-Seq_re1


title: Human_2-cell_3PN_ATAC-Seq_re2

description:
2cell_3pn_100bp_rpkm.wig
2cell_3pn_peaks.bed

growth_protocol: All the 3PN zygotes were cultured to 2-cell using G-1 (Vitrolife) human embryos culture medium in incubater 37℃，6% CO2.


title: Human_2-cell_3PN_ATAC-Seq_re1


title: Human_2-cell_ATAC-Seq_re2

description:
2cell_2pn_100bp_rpkm.wig
2cell_2pn_peaks.bed

treatment_protocol: Intra Cytoplasmic Sperm Injection (ICSI) was used in this investigation rather than classical IVF to prevent contamination of sperm and cumulus cell’s DNA. Fertilization was assessed 17–20 h after ICSI and embryo cleavage was recorded every 24 h. 2-cell stages embryos were frozen for ATAC-seq,and zona-pelucida was removed using laser Firstly.


title: sample57

city: Houston

first: Jeremy

last: Schraw

state: TX

address: 1 Baylor Plaza MS:305

department: Medicine

institute: Baylor College of Medicine

description:
B12739
Processed data file: Differentially_methylated_sites.txt

data_processing:
Library strategy: MCA-Seq
Adaptor sequences were removed using cutadapt and aligned to reference genome hg19 using bowtie.
Quantifications for each sample and sma interval were extracted using coverageBed.
The top 1000 autosomal differentially methylated sites within CpG island and non-repeat regions were selected on the basis of greatest variation in log-transformed methylation density values between cases and controls and FDR < 0.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Differentially_methylated_sites.txt: Tab-delimited text file includes the log2-transformed methylation density values for the top 1000 autosomal differentially methylated sites within CpG island and non-repeat regions.
Supplementary_files_format_and_content: All_methylated_sites.txt: Tab-delimited text file includes the log2-transformed methylation density values for all methylated sites.

source_name: Bone marrow plasma

extract_protocol:
Ficoll density centrifugation.
We constructed a reference library of human genome hg19 with 62,245 SmaI/XmaI sites ≤ 2kb in length annotated in terms of 1) chromosome, 2) chromosome location of SmaI/XmaI interval start point, 3) end point, 4) interval length, 5) overlap with CpG island, 6) overlap with repeats, 7) closest RefSeq gene, 8) distance to promoter, and 9) genomic location with respect to the closest RefSeq gene. We defined a site as a "promoter" if residing within -1kb to +0.5kb from the transcription start site (TSS); "exon1" if within the first exon; "other exon" if between the second exon and the last exon; "3’ UTR" if within -0.5kb to +1kb from the transcription end site (TES); "intragenic" if within a gene and not inside exons; and "intergenic" if outside of a gene.

value: Bone marrow plasma

tag: leukemia immunophenotype

value: B-cell

tag: age (yr)

tag: maternal rs1050996_dominant; 0 = wild type

tag: maternal rs10733117_dominant, 0 = wild type

tag: maternal rs10754584_dominant, 0 = wild type

tag: maternal rs10802564_dominant, 0 = wild type

tag: maternal rs12759827_dominant, 0 = wild type

tag: maternal rs2282369_dominant, 0 = wild type

tag: maternal rs2297965_dominant, 0 = wild type

tag: maternal rs2385511_dominant, 0 = wild type

tag: maternal rs3768142_dominant, 0 = wild type

tag: maternal rs3768150_dominant, 0 = wild type

tag: maternal rs4659745_dominant, 0 = wild type


title: sample55

description:
B13108
Processed data file: Differentially_methylated_sites.txt

tag: tissue


title: sample56

description:
B1533
Processed data file: Differentially_methylated_sites.txt


title: sample52

description:
B6176
Processed data file: Differentially_methylated_sites.txt


title: sample50

description:
B6861
Processed data file: Differentially_methylated_sites.txt

value: T-cell


title: sample53

description:
B11672
Processed data file: Differentially_methylated_sites.txt


title: sample54

description:
B4287
Processed data file: Differentially_methylated_sites.txt


title: sample49

description:
B3409
Processed data file: Differentially_methylated_sites.txt


title: sample51

description:
B3259
Processed data file: Differentially_methylated_sites.txt


title: Human_GV_RNA-Seq_re1

description: expression.txt

tag: developmental stage


title: sample47

description:
B6829
Processed data file: Differentially_methylated_sites.txt


title: sample46

description:
A1361
Processed data file: Differentially_methylated_sites.txt


title: sample45

description:
A4172
Processed data file: Differentially_methylated_sites.txt


title: sample48

description:
B3471
Processed data file: Differentially_methylated_sites.txt


title: sample43

description:
A1116
Processed data file: Differentially_methylated_sites.txt


title: sample44

description:
A1181
Processed data file: Differentially_methylated_sites.txt


title: Human_8-cell_ATAC-Seq_re1

description:
8cell_2pn_100bp_rpkm.wig
8cell_2pn_peaks.bed


title: B6_old_mtAKR_rep4

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description: Animal tissue

data_processing:
Raw sequence reads were pseudo aligned to the mouse transcriptome mm10 (Ensembl Build 84) using Kallisto (Version 0.43.0, Bray et al. Nat. Biotechnology 2016) runing 30 bootstrap rounds.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

source_name: Liver obtained from C57BL/6J-mtAKR/J mouse

extract_protocol:
Total RNAs were extracted from liver samples obtained from conplastic mouse strains (C57BL/6J and C57BL/6J-mtAKR/J), using innuPREP RNA Mini Kit (Analytik Jena) according to the manufacturer’s protocol. RNAs quality was checked using a Bioanalyzer system (Agilent Genomics).
RNA sequencing of primary samples was carried out employing the TruSeq  stranded Total RNA kit (Illumina Inc.), starting from 0.6µg total RNA of  each sample and sequenced on an Illumina HiSeq4000 (75-nucleotide  paired-end  reads). Aiming for high transcriptome coverage, sequencing runs were  performed out combining 4 samples per lane (corresponding to approximately  50 million reads per sample).

value: Liver

tag: knockdown

value: higher 12A heteroplasmy in OriL

tag: age

value: 19 months

tag: replicate


title: B6_old_mtAKR_rep5

description: Animal tissue

tag: strain


title: sample40

description:
B6691
Processed data file: Differentially_methylated_sites.txt

tag: leukemia immunophenotype

tag: age (yr)

tag: maternal rs1050996_dominant; 0 = wild type


title: sample41

description:
B12860
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs10733117_dominant, 0 = wild type

tag: maternal rs10754584_dominant, 0 = wild type

tag: maternal rs10802564_dominant, 0 = wild type


title: sample42

description:
A2202
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs12759827_dominant, 0 = wild type

tag: maternal rs2282369_dominant, 0 = wild type

tag: maternal rs2297965_dominant, 0 = wild type


title: sample39

description:
A3954
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs2385511_dominant, 0 = wild type

tag: maternal rs3768142_dominant, 0 = wild type

tag: maternal rs3768150_dominant, 0 = wild type


title: Human_2-cell_ATAC-Seq_re1

description:
2cell_2pn_100bp_rpkm.wig
2cell_2pn_peaks.bed

tag: developmental stage


title: B6_old_mtAKR_rep1

description: Animal tissue

tag: tissue

tag: knockdown


title: B6_old_rep5

description: Animal tissue

source_name: Liver obtained from C57BL/6J mouse

value: lower 12A heteroplasmy in OriL

tag: age

value: 20 months

tag: replicate


title: sample38

description:
A1721
Processed data file: Differentially_methylated_sites.txt

tag: leukemia immunophenotype

tag: maternal rs4659745_dominant, 0 = wild type


title: B6_old_rep4

description: Animal tissue

tag: strain


title: B6_old_rep3

description: Animal tissue


title: sample36

description:
B5080
Processed data file: Differentially_methylated_sites.txt

tag: age (yr)

tag: maternal rs1050996_dominant; 0 = wild type

tag: maternal rs10733117_dominant, 0 = wild type


title: B6_young_mtAKR_rep5

description: Animal tissue

value: 4 months


title: sample33

description:
B4255
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs10754584_dominant, 0 = wild type

tag: maternal rs10802564_dominant, 0 = wild type

tag: maternal rs12759827_dominant, 0 = wild type


title: B6_old_rep2

description: Animal tissue


title: sample32

description:
B2707
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs2282369_dominant, 0 = wild type

tag: maternal rs2297965_dominant, 0 = wild type

tag: maternal rs2385511_dominant, 0 = wild type


title: B6_young_mtAKR_rep4

description: Animal tissue

value: 3 months


title: B6_old_rep1

description: Animal tissue


title: B6_young_mtAKR_rep3

description: Animal tissue


title: B6_old_mtAKR_rep2

description: Animal tissue


title: B6_old_mtAKR_rep3

description: Animal tissue


title: sample29

description:
B6393
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs3768142_dominant, 0 = wild type

tag: maternal rs3768150_dominant, 0 = wild type


title: B6_young_mtAKR_rep2

description: Animal tissue

tag: tissue

tag: knockdown


title: sample30

description:
B5077
Processed data file: Differentially_methylated_sites.txt


title: sample28

description:
B2803
Processed data file: Differentially_methylated_sites.txt


title: sample37

description:
A4152
Processed data file: Differentially_methylated_sites.txt


title: sample34

description:
B5186
Processed data file: Differentially_methylated_sites.txt


title: B6_young_mtAKR_rep1

description: Animal tissue

tag: age

tag: replicate


title: sample35

description:
B6160
Processed data file: Differentially_methylated_sites.txt

tag: leukemia immunophenotype

tag: maternal rs4659745_dominant, 0 = wild type


title: sample31

description:
B5215
Processed data file: Differentially_methylated_sites.txt

tag: age (yr)


title: B6_young_rep3

description: Animal tissue

tag: strain


title: sample26

description:
A2586
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs1050996_dominant; 0 = wild type

tag: maternal rs10733117_dominant, 0 = wild type


title: B6_young_rep4

description: Animal tissue


title: sample27

description:
A1359
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs10754584_dominant, 0 = wild type

tag: maternal rs10802564_dominant, 0 = wild type


title: B6_young_rep2

description: Animal tissue


title: sample24

description:
B3435
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs12759827_dominant, 0 = wild type

tag: maternal rs2282369_dominant, 0 = wild type


title: sample23

description:
B2668
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs2297965_dominant, 0 = wild type

tag: maternal rs2385511_dominant, 0 = wild type


title: sample22

description:
B12612
Processed data file: Differentially_methylated_sites.txt

tag: maternal rs3768142_dominant, 0 = wild type

tag: maternal rs3768150_dominant, 0 = wild type


title: monocyte sample replicate 2

city: Jouy en Josas Cedex

first: Helene

last: Kiefer

address: Domaine de Vilvert, Bat 230

country: France

institute: INRA

data_processing:
RRBS sequences were analysed using an integrated pipeline combining homemade scripts developed in Python, R and Shell, together with external tools (https://github.com/FAANG/faang-methylation/tree/master/RRBS-toolkit/).
The sequences were first subjected to FastQC quality control (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Subsequent quality checks and trimming were carried out using Trim Galore v0.3.7 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) that removed adapter sequences, poor quality bases and reads (Phred score below 20) and reads shorter than 20 nucleotides.
High quality reads were aligned on the bovine reference genome (UMD 3.1 assembly) using Bismark v0.14.3 in the default mode with Bowtie 1 (Krueger F. & Andrews S.R. (2011) Bioinformatics 27, 1571-2; Langmead B., Trapnell C., Pop M. & Salzberg S.L. (2009) Genome Biol 10, R25).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Text files (.txt, one file per sample) containing one heading and one line per CpG, that can be used as input for methylKit analysis. There are seven columns: genomic coordinates (3 columns: chrBase, chr, base), strand (F for forward DNA strand), coverage (number of reads aligned to this CpG), freqC (% reads carrying a C) and fredT (% reads carrying a T).

organism: Bos taurus

source_name: Blood monocytes purified from Holstein cow #1103

extract_protocol:
One straw of Holstein bull semen was used for DNA extraction. After thawing at 37°C, the semen was washed with PBS to remove the extender, and incubated overnight at 55°C in 200 µl of lysis buffer (10 mM Tris-HCl pH 7.5, 25 mM EDTA, 1% SDS, 75 mM NaCl, 50 mM DTT and 0.5 µg glycogen) in the presence of 0.2 mg/ml proteinase K. After incubation with 25 µg/ml RNAse A 1h at 37°C, genomic DNA was twice extracted using phenol and phenol:chloroform (1:1), ethanol precipitated and washed. The dried pellet was resuspended in TE buffer (10 mM Tris HCl pH7.5, 2 mM EDTA). DNA extraction from fibroblasts and monocytes was performed as described (Kiefer H. (2015) Methods Mol Biol 1222, 267-80), except that cells were lysed by the direct addition of lysis buffer and proteinase K to the cell pellet.
RRBS libraries were prepared as described ( Gu H., Smith Z.D., Bock C., Boyle P., Gnirke A. & Meissner A. (2011). Nat Protoc 6, 468-81; Auclair G., Guibert S., Bender A. & Weber M. (2014). Genome Biol 15, 545) from two Holstein sperm samples, two monocyte samples and two fibroblast samples. Briefly, 200 ng of genomic DNA were digested by MspI (Thermo Scientific), end-repaired and ligated to 55 bp Illumina adapters for paired-end sequencing. Size selection by gel excision was performed in order to select the fragments ranging from 150 to 400 bp (genomic fragments of 40-290 bp + adapters). The DNA was then purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice consecutively with the EpiTect bisulphite kit (Qiagen), following the manufacturer’s instructions for DNA extracted from FFPE tissues. Converted DNA was amplified with the Pfu Turbo Cx hotstart DNA polymerase (Agilent) using 14 PCR cycles for sperm and fibroblasts and 12 cycles for the monocytes. The libraries were then purified using Agencourt Ampure beads (Beckman-Coulter) and sequenced on an Illumina HiSeq2500 sequencer to produce 75 bp paired-end reads (Integragen SA, France).

tag: cell type

value: monocytes


title: sample21

description:
B11004
Processed data file: Differentially_methylated_sites.txt

tag: tissue


title: monocyte sample replicate 1

source_name: Blood monocytes purified from Holstein cow #1130


title: sample25

description:
B4725
Processed data file: Differentially_methylated_sites.txt


title: fibroblast sample replicate 1

source_name: Ear skin fibroblasts derived from Holstein cow #5538

value: fibroblasts


title: sample19

description:
B1789
Processed data file: Differentially_methylated_sites.txt


title: sample20

description:
B4644
Processed data file: Differentially_methylated_sites.txt


title: sperm sample replicate 2

source_name: Commercial Holstein semen straw (bull #34)

value: sperm


title: sample18

description:
B1785
Processed data file: Differentially_methylated_sites.txt


title: sample17

description:
A4283
Processed data file: Differentially_methylated_sites.txt


title: sample16

description:
A1214
Processed data file: Differentially_methylated_sites.txt


title: sample14

description:
B6689
Processed data file: Differentially_methylated_sites.txt


title: sperm sample replicate 1

source_name: Commercial Holstein semen straw (bull #32)


title: sample13

description:
B5109
Processed data file: Differentially_methylated_sites.txt


title: sample15

description:
A2892
Processed data file: Differentially_methylated_sites.txt


title: sample12

description:
B5326
Processed data file: Differentially_methylated_sites.txt


title: sample8

description:
A3576
Processed data file: Differentially_methylated_sites.txt


title: sample9

description:
B2351
Processed data file: Differentially_methylated_sites.txt


title: sample10

description:
B13303
Processed data file: Differentially_methylated_sites.txt


title: B6_young_rep1

description: Animal tissue

tag: knockdown

tag: age

tag: replicate


title: sample11

description:
B5082
Processed data file: Differentially_methylated_sites.txt

tag: leukemia immunophenotype

tag: age (yr)

tag: maternal rs4659745_dominant, 0 = wild type


title: sample6

description:
HDBM2
Processed data file: Differentially_methylated_sites.txt

value: Control


title: fibroblast sample replicate 2

source_name: Ear skin fibroblasts derived from Holstein cow #029


title: sample5

description:
HDBM3
Processed data file: Differentially_methylated_sites.txt


title: sample3

description:
HDBM1
Processed data file: Differentially_methylated_sites.txt


title: sample4

description:
HDBM6
Processed data file: Differentially_methylated_sites.txt


title: sample2

description:
HDBM4
Processed data file: Differentially_methylated_sites.txt


title: sample1

description:
HDBM5
Processed data file: Differentially_methylated_sites.txt


title: 72-111_3

city: Saint Louis

first: Christina

middle: L

last: Stallings

state: Missouri

address: 660 S. Euclid Avenue

institute: Washington University in St Louis

description: run_2000_s_4_withindex_sequence.txt_CTGGTGG

data_processing:
cDNA libraries were pooled and sequenced in a single Illumina HiSeq2000 Rapid Run flow cell lane.
Sequencing reads were de-multiplexed and converted to FASTQ format by Illumina bcl2fastq script.
STAR aligner was used to trim the adapter sequences from the raw reads and align to M. smegmatis mc2155 reference genome.
SAM files generated from the alignment were converted to BAM files using SAMTools and aligned reads were counted per genome feature using R BioConductor package Subread featureCounts function.
R BioConductor DESeq2 was used to analyze differential expression between the strains.
Genome_build: NC_008596
Supplementary_files_format_and_content: DESeq2 differential expression analysis comparing R79A, R88A and 72-111 against WT is shown in separate tabs labeled a. R79A, b. R88A, and c. 72-111. For each tab, column 1 includes the name of each genomic feature, column 2 is the base mean value of the six samples including 3 replicates of the mutant and 3 replicates of the WT, column 3 is the log2 fold change of mutant relative to WT, column 4 is the log fold change standard error (lfcse), column 5 is the Wald statistic, column  6 is the p-value and column 7 is the adjusted p-value.

organism: Mycolicibacterium smegmatis

source_name: RbpA delta 1-71_cell extract

growth_protocol: Each strain was grown to OD600 = 0.4 - 0.6 by inoculating LB media supplemented with 0.5% dextrose,  0.5% glycerol, 0.05% Tween-80 and 40μg/ml kanamycin from a glycerol stock.

extract_protocol:
Thirty milliliters of culture from each strain was pelleted by centrifugation, resuspended in Trizol and lysed by bead beating. RNA was choloform extracted, isoproponal precipitated and resuspended in water. RNA integrity and concentration were measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols

tag: strain

tag: genotype/variation

value: RbpA delta 1-71

tag: growth phase

value: log phase growth


title: siSUV3_J2_IP (rep2)

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

data_processing:
RNA-sequencing reads were trimmed using Cutadapt and then mapped to the human reference genome with Bowtie2.
Aligned reads were processed to only include properly paired, uniquely mapped reads with no more than 2 mismatches using SAMtools.
Data were scaled to library size (genomeCoverageBed) using Bedtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files containing read densities from RNA-seq experiments.

source_name: HeLa cells, siSUV3, dsRNA IP

growth_protocol: HeLa cells were grown as a monolayer at 37ºC, under 5% CO2 in high glucose DMEM medium supplemented with 10% FBS.

extract_protocol:
HeLa cell lysate was prepared with NP-40 lysis buffer and cellular dsRNA were pulled down with J2 antibody (anti-dsRNA mAb J2, Prod. Nr. 10010500 from Scicons). RNA was extracted using Trizol reagent for library preparation.
Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina, v1.0 (cat. no. E7420) according to the manufacturer's guidelines.

treatment_protocol: HeLa cells treated with siLuc (control), siSUV3 or siPNPase.

tag: cell line

value: HeLa

tag: treatment

tag: antibody

value: anti-dsRNA (J2)


title: siSUV3_J2_IP (rep1)


title: siSUV3_INPUT

source_name: HeLa cells, siSUV3, input


title: siPNPase_J2_IP (rep1)

source_name: HeLa cells, siPNPase, dsRNA IP

value: siPNPase


title: siCntrl_J2_IP

source_name: HeLa cells, siLuc, dsRNA IP

value: siLuc


title: siPNPase_J2_IP (rep2)


title: 72-111_1

description: run_2000_s_4_withindex_sequence.txt_TCGAGAT


title: siPNPase_INPUT

source_name: HeLa cells, siPNPase, input


title: Untreated_J2_IP


title: siCntrl_INPUT

source_name: HeLa cells, siLuc, input


title: sample7

description:
A1400
Processed data file: Differentially_methylated_sites.txt

value: Bone marrow plasma

value: B-cell

tag: maternal rs1050996_dominant; 0 = wild type

tag: maternal rs10733117_dominant, 0 = wild type

tag: maternal rs10754584_dominant, 0 = wild type

tag: maternal rs10802564_dominant, 0 = wild type

tag: maternal rs12759827_dominant, 0 = wild type

tag: maternal rs2282369_dominant, 0 = wild type

tag: maternal rs2297965_dominant, 0 = wild type

tag: maternal rs2385511_dominant, 0 = wild type


title: Mouse_100_mESC_ATAC-seq

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9

source_name: Embryonic stem cell

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

tag: developmental stage

value: Embryonic stem cell


title: R88A_2

description: run_2000_s_4_withindex_sequence.txt_GTTCTCA

source_name: RbpA R88A_cell extract

value: RbpA R88A


title: Mouse_30_mESC_ATAC-seq


title: Mouse_20_mESC_ATAC-seq


title: Mouse_50_mESC_ATAC-seq


title: R88A_1

description: run_2000_s_4_withindex_sequence.txt_TTGCCCC


title: R79A_3

description: run_2000_s_4_withindex_sequence.txt_TAGGTAA

source_name: RbpA R79A_cell extract

value: RbpA R79A


title: Mouse_in_vitro_45h_ctrl_ATAC-seq_re2

source_name: Preimplantation embryo

growth_protocol: Cultured in CZB medium


title: R79A_2

description: run_2000_s_4_withindex_sequence.txt_GACACAG


title: R79A_1

description: run_2000_s_4_withindex_sequence.txt_TGCTGGG


title: Mouse_TBE_45h_ATAC-seq_re1

treatment_protocol: PN3 zygotes 22h after hCG were treated with 250 ng/ul alpha amanitin (Sigma) for 45h

value: Arrest 2-cell


title: WT_3

description: run_2000_s_4_withindex_sequence.txt_TCAAACA

source_name: WT RbpA_cell extract

value: WT RbpA


title: WT_2

description: run_2000_s_4_withindex_sequence.txt_AGCGCCG


title: 72-111_2

description: run_2000_s_4_withindex_sequence.txt_ACTCCAA


title: WT_1

description: run_2000_s_4_withindex_sequence.txt_ATCGAGC


title: R88A_3

description: run_2000_s_4_withindex_sequence.txt_ACTGTCG


title: RNA-seq DMSO rep3

status: Public on May 02 2018

city: Worcester

first: Lucio

last: Castilla

address: 364 Plantation Street

department: MCCB

institute: University of Massachusetts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using topht v2.0.9 with bowtie v2.1.0 with parameters --library-type fr-unstranded --b2-very-sensitive --mate-inner-dist 100 --mate-std-dev 80 --no-coverage-search
Gene expression was quantified using cufflinks v2.2.0 cuffdiff with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, and the log2FC, p-value, FDR adjusted q-value calculated by cuffdiff

extract_protocol:
RNA was harvested using PureLink RNA Mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ME-1 cells were treated with DMSO/ AI-10-49 (1uM) for six hours.

tag: cell type

value: Human inv(16) leukemia cell line

tag: treated with

value: DMSO


title: RNA-seq AI-10-49 rep1


title: RNA-seq AI-10-49 rep3